Psyllid ID: psy1185

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-
Protein Sequence
MSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPDTETMSKVLMLDQQL
Secondary Structure (PSIPRED)
cccccEEEEccccccccHHHHHHHHHccccEEEEEEEccEEEEEEccHHHHHHHHccccEEEEcccccccccccEEEccccccccHHHHHHHHccccEEEEccEEEEEEEcccccccHHHHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
cccEEEEEEEcccccccHHHHHHHHHHcccHHHHHHHccEEEEEEccHHHHEEccccEEEEEEcccccccccccEEEEEEccHHHHHHHHHHHccccEEEcccEEEEEcccccccccHHHHHHcEEEcccc
Coil and Loop (DISEMBL)
MSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIysspddnkknrgfcfleydshksaSLAKKRLATGRLkvwgcdiivdwadpqeepdteTMSKVLMLDQQL
Flexible Loop (DISEMBL)
MSKVKVLYVRNLTQYCTEEKLKEAfeqygrvervKRIKDYAFVHFedrqeaitvtgLSQVIIYsspddnkknRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVdwadpqeepdtetMSKVLMLDQQL
Low Complexity Region (SEG)
MSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPDTETMSKVLMLDQQL
Disordered region (IsUnstruct)
***VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWA*********************
Disordered Region (DISOPRED)
*SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIY****************Y************LATGRLKVWGCDIIVDWADPQE**********LMLDQ**
Disordered Region (DISEMBL)
MSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPDTETMSKVLMLDQQL
Disordered Region (DISPRO)
*SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPDTETMSKVLMLDQ*L
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPDTETMSKVLMLDQQL
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	131	2.2.26 [Sep-21-2011]
O43390	633	Heterogeneous nuclear rib	yes	N/A	0.549	0.113	0.625	8e-23
Q7TMK9	623	Heterogeneous nuclear rib	no	N/A	0.480	0.101	0.597	1e-21
O60506	623	Heterogeneous nuclear rib	no	N/A	0.480	0.101	0.597	1e-21
Q7TP47	533	Heterogeneous nuclear rib	no	N/A	0.480	0.118	0.597	1e-21
Q9NQ94	594	APOBEC1 complementation f	no	N/A	0.526	0.116	0.5	3e-17
Q5R9H4	587	APOBEC1 complementation f	no	N/A	0.526	0.117	0.5	3e-17
P86049	533	Probable RNA-binding prot	no	N/A	0.534	0.131	0.5	6e-17
Q4R2Z0	485	Probable RNA-binding prot	N/A	N/A	0.534	0.144	0.5	6e-17
Q8TBY0	533	Probable RNA-binding prot	no	N/A	0.534	0.131	0.5	6e-17
Q08BH5	510	Probable RNA-binding prot	no	N/A	0.625	0.160	0.481	9e-17

>sp|O43390|HNRPR_HUMAN Heterogeneous nuclear ribonucleoprotein R OS=Homo sapiens GN=HNRNPR PE=1 SV=1

 Score =  105 bits (262), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 45/72 (62%), Positives = 57/72 (79%)

Query: 56  GLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEE 115
           GL  VI+Y  PDD KKNRGFCFLEY+ HKSA+ A++RL +G++KVWG  + V+WADP EE
Sbjct: 272 GLVDVILYHQPDDKKKNRGFCFLEYEDHKSAAQARRRLMSGKVKVWGNVVTVEWADPVEE 331

Query: 116 PDTETMSKVLML 127
           PD E M+KV +L
Sbjct: 332 PDPEVMAKVKVL 343

Component of ribonucleosomes, which are complexes of at least 20 other different heterogenious nuclear ribonucleoproteins (hnRNP). hnRNP play an important role in processing of precursor mRNA in the nucleus.
Homo sapiens (taxid: 9606)

>sp|Q7TMK9|HNRPQ_MOUSE Heterogeneous nuclear ribonucleoprotein Q OS=Mus musculus GN=Syncrip PE=1 SV=2

 Score =  101 bits (252), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 43/72 (59%), Positives = 57/72 (79%)

Query: 56  GLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEE 115
           GL+ VI+Y  PDD KKNRGFCFLEY+ HK+A+ A++RL +G++KVWG    V+WADP E+
Sbjct: 269 GLTDVILYHQPDDKKKNRGFCFLEYEDHKTAAQARRRLMSGKVKVWGNVGTVEWADPIED 328

Query: 116 PDTETMSKVLML 127
           PD E M+KV +L
Sbjct: 329 PDPEVMAKVKVL 340

Heterogeneous nuclear ribonucleoprotein (hnRNP) implicated in mRNA processing mechanisms. Component of the CRD-mediated complex that promotes MYC mRNA stability. Isoform 1 and isoform 2 are associated in vitro with pre-mRNA, splicing intermediates and mature mRNA protein complexes. Isoform 1 binds to apoB mRNA AU-rich sequences (By similarity). Isoform 1 is part of the APOB mRNA editosome complex and may modulate the postranscriptional C to U RNA-editing of the APOB mRNA through either by binding to A1CF (APOBEC1 complementation factor), to APOBEC1 or to RNA itself (By similarity). May be involved in translationally coupled mRNA turnover. Implicated with other RNA-binding proteins in the cytoplasmic deadenylation/translational and decay interplay of the FOS mRNA mediated by the major coding-region determinant of instability (mCRD) domain (By similarity). Interacts in vitro preferentially with poly(A) and poly(U) RNA sequences. Isoform 2 may be involved in cytoplasmic vesicle-based mRNA transport through interaction with synaptotagmins.

Mus musculus (taxid: 10090)

>sp|O60506|HNRPQ_HUMAN Heterogeneous nuclear ribonucleoprotein Q OS=Homo sapiens GN=SYNCRIP PE=1 SV=2

 Score =  101 bits (252), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 43/72 (59%), Positives = 57/72 (79%)

Query: 56  GLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEE 115
           GL+ VI+Y  PDD KKNRGFCFLEY+ HK+A+ A++RL +G++KVWG    V+WADP E+
Sbjct: 269 GLTDVILYHQPDDKKKNRGFCFLEYEDHKTAAQARRRLMSGKVKVWGNVGTVEWADPIED 328

Query: 116 PDTETMSKVLML 127
           PD E M+KV +L
Sbjct: 329 PDPEVMAKVKVL 340

Heterogenous nuclear ribonucleoprotein (hnRNP) implicated in mRNA processing mechanisms. Component of the CRD-mediated complex that promotes MYC mRNA stability. Isoform 1, isoform 2 and isoform 3 are associated in vitro with pre-mRNA, splicing intermediates and mature mRNA protein complexes. Isoform 1 binds to apoB mRNA AU-rich sequences. Isoform 1 is part of the APOB mRNA editosome complex and may modulate the postranscriptional C to U RNA-editing of the APOB mRNA through either by binding to A1CF (APOBEC1 complementation factor), to APOBEC1 or to RNA itself. May be involved in translationally coupled mRNA turnover. Implicated with other RNA-binding proteins in the cytoplasmic deadenylation/translational and decay interplay of the FOS mRNA mediated by the major coding-region determinant of instability (mCRD) domain. Interacts in vitro preferentially with poly(A) and poly(U) RNA sequences. Isoform 3 may be involved in cytoplasmic vesicle-based mRNA transport through interaction with synaptotagmins.

Homo sapiens (taxid: 9606)

>sp|Q7TP47|HNRPQ_RAT Heterogeneous nuclear ribonucleoprotein Q OS=Rattus norvegicus GN=Syncrip PE=2 SV=1

 Score =  101 bits (252), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 43/72 (59%), Positives = 57/72 (79%)

Query: 56  GLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEE 115
           GL+ VI+Y  PDD KKNRGFCFLEY+ HK+A+ A++RL +G++KVWG    V+WADP E+
Sbjct: 179 GLTDVILYHQPDDKKKNRGFCFLEYEDHKTAAQARRRLMSGKVKVWGNVGTVEWADPIED 238

Query: 116 PDTETMSKVLML 127
           PD E M+KV +L
Sbjct: 239 PDPEVMAKVKVL 250

Heterogenous nuclear ribonucleoprotein (hnRNP) implicated in mRNA processing mechanisms. Component of the CRD-mediated complex that promotes MYC mRNA stability. Is associated in vitro with pre-mRNA, splicing intermediates and mature mRNA protein complexes. Binds to apoB mRNA AU-rich sequences. Part of the APOB mRNA editosome complex and may modulate the postranscriptional C to U RNA-editing of the APOB mRNA through either by binding to A1CF (APOBEC1 complementation factor), to APOBEC1 or to RNA itself. May be involved in translationally coupled mRNA turnover. Implicated with other RNA-binding proteins in the cytoplasmic deadenylation/translational and decay interplay of the FOS mRNA mediated by the major coding-region determinant of instability (mCRD) domain. Interacts in vitro preferentially with poly(A) and poly(U) RNA sequences. May be involved in cytoplasmic vesicle-based mRNA transport through interaction with synaptotagmins.

Rattus norvegicus (taxid: 10116)

>sp|Q9NQ94|A1CF_HUMAN APOBEC1 complementation factor OS=Homo sapiens GN=A1CF PE=1 SV=1

 Score = 87.0 bits (214), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 36/72 (50%), Positives = 54/72 (75%)

Query: 56  GLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEE 115
           G+  VI+Y S  D  KNRGF F+EY+SH++A++A+++L  GR+++WG  I VDWA+P+ E
Sbjct: 162 GVVDVIVYPSAADKTKNRGFAFVEYESHRAAAMARRKLLPGRIQLWGHGIAVDWAEPEVE 221

Query: 116 PDTETMSKVLML 127
            D +TMS V +L
Sbjct: 222 VDEDTMSSVKIL 233

Essential component of the apolipoprotein B mRNA editing enzyme complex which is responsible for the postranscriptional editing of a CAA codon for Gln to a UAA codon for stop in APOB mRNA. Binds to APOB mRNA and is probably responsible for docking the catalytic subunit, APOBEC1, to the mRNA to allow it to deaminate its target cytosine. The complex also protects the edited APOB mRNA from nonsense-mediated decay.

Homo sapiens (taxid: 9606)

>sp|Q5R9H4|A1CF_PONAB APOBEC1 complementation factor OS=Pongo abelii GN=A1CF PE=2 SV=1

 Score = 87.0 bits (214), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 36/72 (50%), Positives = 54/72 (75%)

Query: 56  GLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEE 115
           G+  VI+Y S  D  KNRGF F+EY+SH++A++A+++L  GR+++WG  I VDWA+P+ E
Sbjct: 162 GVVDVIVYPSAADKTKNRGFAFVEYESHRAAAMARRKLLPGRIQLWGHPIAVDWAEPEVE 221

Query: 116 PDTETMSKVLML 127
            D +TMS V +L
Sbjct: 222 VDEDTMSSVKIL 233

Essential component of the apolipoprotein B mRNA editing enzyme complex which is responsible for the postranscriptional editing of a CAA codon for Gln to a UAA codon for stop in APOB mRNA. Binds to APOB mRNA and is probably responsible for docking the catalytic subunit, APOBEC1, to the mRNA to allow it to deaminate its target cytosine. The complex also seems to protect the edited APOB mRNA from nonsense-mediated decay.

Pongo abelii (taxid: 9601)

>sp|P86049|RBM46_MOUSE Probable RNA-binding protein 46 OS=Mus musculus GN=Rbm46 PE=4 SV=1

 Score = 85.9 bits (211), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 36/72 (50%), Positives = 53/72 (73%)

Query: 56  GLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEE 115
           G+  VI+Y S  D  KNRGF F+EY+SH++A++A+++L  G  ++WG  I VDWADP++E
Sbjct: 167 GVVDVIVYPSATDKTKNRGFAFVEYESHRAAAMARRKLIPGTFQLWGHTIQVDWADPEKE 226

Query: 116 PDTETMSKVLML 127
            D ETM +V +L
Sbjct: 227 VDEETMQRVKVL 238

Mus musculus (taxid: 10090)

>sp|Q4R2Z0|RBM46_MACFA Probable RNA-binding protein 46 OS=Macaca fascicularis GN=RBM46 PE=2 SV=2

 Score = 85.9 bits (211), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 36/72 (50%), Positives = 53/72 (73%)

Query: 56  GLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEE 115
           G+  VI+Y S  D  KNRGF F+EY+SH++A++A+++L  G  ++WG  I VDWADP++E
Sbjct: 167 GVVDVIVYPSATDKTKNRGFAFVEYESHRAAAMARRKLIPGTFQLWGHTIQVDWADPEKE 226

Query: 116 PDTETMSKVLML 127
            D ETM +V +L
Sbjct: 227 VDEETMQRVKVL 238

Macaca fascicularis (taxid: 9541)

>sp|Q8TBY0|RBM46_HUMAN Probable RNA-binding protein 46 OS=Homo sapiens GN=RBM46 PE=2 SV=1

 Score = 85.9 bits (211), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 36/72 (50%), Positives = 53/72 (73%)

Query: 56  GLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEE 115
           G+  VI+Y S  D  KNRGF F+EY+SH++A++A+++L  G  ++WG  I VDWADP++E
Sbjct: 167 GVVDVIVYPSATDKTKNRGFAFVEYESHRAAAMARRKLIPGTFQLWGHTIQVDWADPEKE 226

Query: 116 PDTETMSKVLML 127
            D ETM +V +L
Sbjct: 227 VDEETMQRVKVL 238

Homo sapiens (taxid: 9606)

>sp|Q08BH5|RBM46_DANRE Probable RNA-binding protein 46 OS=Danio rerio GN=rbm46 PE=2 SV=1

 Score = 85.5 bits (210), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 40/83 (48%), Positives = 60/83 (72%), Gaps = 1/83 (1%)

Query: 46  EDRQEAITVT-GLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCD 104
           E ++E + VT G+  VI+Y S  D  KNRGF F+EY+SHK+A++A+++L  G  ++WG  
Sbjct: 140 EIQEEMMKVTEGVMDVIVYPSAVDRMKNRGFAFVEYESHKAAAMARRKLIPGTFQLWGHT 199

Query: 105 IIVDWADPQEEPDTETMSKVLML 127
           I VDWA+P++E D ETM +V +L
Sbjct: 200 IQVDWAEPEKELDEETMQRVRVL 222

Danio rerio (taxid: 7955)

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	131
242011880	548	Heterogeneous nuclear ribonucleoprotein	0.564	0.135	0.824	4e-31
391324923	558	PREDICTED: heterogeneous nuclear ribonuc	0.488	0.114	0.810	4e-31
195113079	721	GI10594 [Drosophila mojavensis] gi|19391	0.488	0.088	0.824	4e-31
195390987	789	GJ22950 [Drosophila virilis] gi|19415223	0.488	0.081	0.824	5e-31
332026895	724	Heterogeneous nuclear ribonucleoprotein	0.564	0.102	0.810	5e-31
307212325	649	Heterogeneous nuclear ribonucleoprotein	0.564	0.114	0.810	6e-31
350409228	664	PREDICTED: heterogeneous nuclear ribonuc	0.564	0.111	0.810	6e-31
328789990	664	PREDICTED: heterogeneous nuclear ribonuc	0.564	0.111	0.810	6e-31
195449649	731	GK22469 [Drosophila willistoni] gi|19416	0.488	0.087	0.824	6e-31
383847619	664	PREDICTED: heterogeneous nuclear ribonuc	0.564	0.111	0.810	6e-31

>gi|242011880|ref|XP_002426671.1| Heterogeneous nuclear ribonucleoprotein Q, putative [Pediculus humanus corporis] gi|212510842|gb|EEB13933.1| Heterogeneous nuclear ribonucleoprotein Q, putative [Pediculus humanus corporis]

 Score =  139 bits (350), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 61/74 (82%), Positives = 68/74 (91%)

Query: 54  VTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQ 113
             GL++VIIYSSPDD KKNRGFCFLEY+SHK+ASLAK+RL TGR+KVWGCDIIVDWADPQ
Sbjct: 282 AAGLTKVIIYSSPDDKKKNRGFCFLEYESHKAASLAKRRLGTGRVKVWGCDIIVDWADPQ 341

Query: 114 EEPDTETMSKVLML 127
           EEPD ETMSKV +L
Sbjct: 342 EEPDAETMSKVKVL 355

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|391324923|ref|XP_003736991.1| PREDICTED: heterogeneous nuclear ribonucleoprotein Q [Metaseiulus occidentalis]

 Score =  139 bits (349), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 60/74 (81%), Positives = 69/74 (93%)

Query: 54  VTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQ 113
             GL+ VIIY+SPDD KKNRGFCFLEY+SHK+ASLAK+RL+TGR+KVWGCDIIVDWADPQ
Sbjct: 278 APGLTDVIIYTSPDDKKKNRGFCFLEYESHKAASLAKRRLSTGRIKVWGCDIIVDWADPQ 337

Query: 114 EEPDTETMSKVLML 127
           EEPD+ETMSKV +L
Sbjct: 338 EEPDSETMSKVKVL 351

Source: Metaseiulus occidentalis

Species: Metaseiulus occidentalis

Genus: Metaseiulus

Family: Phytoseiidae

Order: Mesostigmata

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195113079|ref|XP_002001097.1| GI10594 [Drosophila mojavensis] gi|193917691|gb|EDW16558.1| GI10594 [Drosophila mojavensis]

 Score =  139 bits (349), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 61/74 (82%), Positives = 67/74 (90%)

Query: 54  VTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQ 113
             GL +VIIYSSPDD KKNRGFCFLEYDSHK+ASLAK+RL TGR+KVWGCDIIVDWADPQ
Sbjct: 328 TAGLYEVIIYSSPDDKKKNRGFCFLEYDSHKAASLAKRRLGTGRIKVWGCDIIVDWADPQ 387

Query: 114 EEPDTETMSKVLML 127
           EEPD +TMSKV +L
Sbjct: 388 EEPDEQTMSKVKVL 401

Source: Drosophila mojavensis

Species: Drosophila mojavensis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195390987|ref|XP_002054147.1| GJ22950 [Drosophila virilis] gi|194152233|gb|EDW67667.1| GJ22950 [Drosophila virilis]

 Score =  139 bits (349), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 61/74 (82%), Positives = 67/74 (90%)

Query: 54  VTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQ 113
             GL +VIIYSSPDD KKNRGFCFLEYDSHK+ASLAK+RL TGR+KVWGCDIIVDWADPQ
Sbjct: 272 TAGLYEVIIYSSPDDKKKNRGFCFLEYDSHKAASLAKRRLGTGRIKVWGCDIIVDWADPQ 331

Query: 114 EEPDTETMSKVLML 127
           EEPD +TMSKV +L
Sbjct: 332 EEPDEQTMSKVKVL 345

Source: Drosophila virilis

Species: Drosophila virilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332026895|gb|EGI66996.1| Heterogeneous nuclear ribonucleoprotein Q [Acromyrmex echinatior]

 Score =  139 bits (349), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 60/74 (81%), Positives = 69/74 (93%)

Query: 54  VTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQ 113
             GL++VIIYSSPDD KKNRGFCFLEY+SHK+ASLAK+RL+TGR+KVWGCDIIVDWADPQ
Sbjct: 312 APGLTEVIIYSSPDDKKKNRGFCFLEYESHKAASLAKRRLSTGRIKVWGCDIIVDWADPQ 371

Query: 114 EEPDTETMSKVLML 127
           EEPD +TMSKV +L
Sbjct: 372 EEPDEQTMSKVRVL 385

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307212325|gb|EFN88129.1| Heterogeneous nuclear ribonucleoprotein Q [Harpegnathos saltator]

 Score =  138 bits (348), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 60/74 (81%), Positives = 69/74 (93%)

Query: 54  VTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQ 113
             GL++VIIYSSPDD KKNRGFCFLEY+SHK+ASLAK+RL+TGR+KVWGCDIIVDWADPQ
Sbjct: 259 TAGLTEVIIYSSPDDKKKNRGFCFLEYESHKAASLAKRRLSTGRIKVWGCDIIVDWADPQ 318

Query: 114 EEPDTETMSKVLML 127
           EEPD +TMSKV +L
Sbjct: 319 EEPDEQTMSKVRVL 332

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350409228|ref|XP_003488661.1| PREDICTED: heterogeneous nuclear ribonucleoprotein Q-like [Bombus impatiens]

 Score =  138 bits (348), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 60/74 (81%), Positives = 69/74 (93%)

Query: 54  VTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQ 113
             GL++VIIYSSPDD KKNRGFCFLEY+SHK+ASLAK+RL+TGR+KVWGCDIIVDWADPQ
Sbjct: 268 TAGLTEVIIYSSPDDKKKNRGFCFLEYESHKAASLAKRRLSTGRIKVWGCDIIVDWADPQ 327

Query: 114 EEPDTETMSKVLML 127
           EEPD +TMSKV +L
Sbjct: 328 EEPDEQTMSKVRVL 341

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328789990|ref|XP_392307.4| PREDICTED: heterogeneous nuclear ribonucleoprotein Q-like [Apis mellifera]

 Score =  138 bits (348), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 60/74 (81%), Positives = 69/74 (93%)

Query: 54  VTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQ 113
             GL++VIIYSSPDD KKNRGFCFLEY+SHK+ASLAK+RL+TGR+KVWGCDIIVDWADPQ
Sbjct: 268 TAGLTEVIIYSSPDDKKKNRGFCFLEYESHKAASLAKRRLSTGRIKVWGCDIIVDWADPQ 327

Query: 114 EEPDTETMSKVLML 127
           EEPD +TMSKV +L
Sbjct: 328 EEPDEQTMSKVRVL 341

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195449649|ref|XP_002072163.1| GK22469 [Drosophila willistoni] gi|194168248|gb|EDW83149.1| GK22469 [Drosophila willistoni]

 Score =  138 bits (348), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 61/74 (82%), Positives = 67/74 (90%)

Query: 54  VTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQ 113
             GL +VIIYSSPDD KKNRGFCFLEYDSHK+ASLAK+RL TGR+KVWGCDIIVDWADPQ
Sbjct: 272 TAGLYEVIIYSSPDDKKKNRGFCFLEYDSHKAASLAKRRLGTGRIKVWGCDIIVDWADPQ 331

Query: 114 EEPDTETMSKVLML 127
           EEPD +TMSKV +L
Sbjct: 332 EEPDEQTMSKVKVL 345

Source: Drosophila willistoni

Species: Drosophila willistoni

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383847619|ref|XP_003699450.1| PREDICTED: heterogeneous nuclear ribonucleoprotein Q-like [Megachile rotundata]

 Score =  138 bits (348), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 60/74 (81%), Positives = 69/74 (93%)

Query: 54  VTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQ 113
             GL++VIIYSSPDD KKNRGFCFLEY+SHK+ASLAK+RL+TGR+KVWGCDIIVDWADPQ
Sbjct: 268 TAGLTEVIIYSSPDDKKKNRGFCFLEYESHKAASLAKRRLSTGRIKVWGCDIIVDWADPQ 327

Query: 114 EEPDTETMSKVLML 127
           EEPD +TMSKV +L
Sbjct: 328 EEPDEQTMSKVRVL 341

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	131
FB|FBgn0038826	711	Syp "Syncrip" [Drosophila mela	0.549	0.101	0.833	9.5e-31
UNIPROTKB|F1NWI9	622	SYNCRIP "Uncharacterized prote	0.603	0.127	0.575	3.3e-22
UNIPROTKB|F1LUZ6	381	Hnrnpr "Protein Hnrnpr" [Rattu	0.603	0.207	0.6	5.5e-22
RGD|1305683	533	Syncrip "synaptotagmin binding	0.603	0.148	0.575	9e-22
UNIPROTKB|Q7TP47	533	Syncrip "Heterogeneous nuclear	0.603	0.148	0.575	9e-22
UNIPROTKB|F6XIK8	562	SYNCRIP "Uncharacterized prote	0.603	0.140	0.575	1.2e-21
UNIPROTKB|E2QVD3	622	SYNCRIP "Uncharacterized prote	0.603	0.127	0.575	1.9e-21
UNIPROTKB|O60506	623	SYNCRIP "Heterogeneous nuclear	0.603	0.126	0.575	1.9e-21
MGI|MGI:1891690	623	Syncrip "synaptotagmin binding	0.603	0.126	0.575	1.9e-21
UNIPROTKB|F2Z5D4	627	SYNCRIP "Uncharacterized prote	0.603	0.125	0.575	1.9e-21

FB|FBgn0038826 Syp "Syncrip" [Drosophila melanogaster (taxid:7227)]

 Score = 332 (121.9 bits), Expect = 9.5e-31, Sum P(2) = 9.5e-31
 Identities = 60/72 (83%), Positives = 67/72 (93%)

Query:    56 GLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEE 115
             GL +VIIYSSPDD KKNRGFCFLEY+SHK+ASLAK+RL TGR+KVWGCDIIVDWADPQEE
Sbjct:   271 GLYEVIIYSSPDDKKKNRGFCFLEYESHKAASLAKRRLGTGRIKVWGCDIIVDWADPQEE 330

Query:   116 PDTETMSKVLML 127
             PD +TMSKV +L
Sbjct:   331 PDEQTMSKVKVL 342

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

GO:0000166 "nucleotide binding" evidence=IEA

GO:0071011 "precatalytic spliceosome" evidence=IDA

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

GO:0022008 "neurogenesis" evidence=IMP

GO:0046011 "regulation of oskar mRNA translation" evidence=IMP

GO:0007310 "oocyte dorsal/ventral axis specification" evidence=IMP

GO:0046843 "dorsal appendage formation" evidence=IMP

GO:0035770 "ribonucleoprotein granule" evidence=IDA

UNIPROTKB|F1NWI9 SYNCRIP "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 252 (93.8 bits), Expect = 3.3e-22, Sum P(2) = 3.3e-22
 Identities = 46/80 (57%), Positives = 62/80 (77%)

Query:    49 QEAITVT-GLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIV 107
             +E   VT GL+ VI+Y  PDD KKNRGFCFLEY+ HK+A+ A++RL +G++KVWG  + V
Sbjct:   260 EEFSKVTEGLTDVILYHQPDDKKKNRGFCFLEYEDHKTAAQARRRLMSGKVKVWGNVVTV 319

Query:   108 DWADPQEEPDTETMSKVLML 127
             +WADP E+PD E M+KV +L
Sbjct:   320 EWADPIEDPDPEVMAKVKVL 339

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0070934 "CRD-mediated mRNA stabilization" evidence=IEA

GO:0070937 "CRD-mediated mRNA stability complex" evidence=IEA

GO:0071013 "catalytic step 2 spliceosome" evidence=IEA

GO:0071204 "histone pre-mRNA 3'end processing complex" evidence=IEA

UNIPROTKB|F1LUZ6 Hnrnpr "Protein Hnrnpr" [Rattus norvegicus (taxid:10116)]

 Score = 256 (95.2 bits), Expect = 5.5e-22, P = 5.5e-22
 Identities = 48/80 (60%), Positives = 61/80 (76%)

Query:    49 QEAITVT-GLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIV 107
             +E   VT GL  VI+Y  PDD KKNRGFCFLEY+ HKSA+ A++RL +G++KVWG  + V
Sbjct:   233 EEFSKVTEGLVDVILYHQPDDKKKNRGFCFLEYEDHKSAAQARRRLMSGKVKVWGNVVTV 292

Query:   108 DWADPQEEPDTETMSKVLML 127
             +WADP EEPD E M+KV +L
Sbjct:   293 EWADPVEEPDPEVMAKVKVL 312

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

RGD|1305683 Syncrip "synaptotagmin binding, cytoplasmic RNA interacting protein" [Rattus norvegicus (taxid:10116)]

 Score = 245 (91.3 bits), Expect = 9.0e-22, Sum P(2) = 9.0e-22
 Identities = 46/80 (57%), Positives = 61/80 (76%)

Query:    49 QEAITVT-GLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIV 107
             +E   VT GL+ VI+Y  PDD KKNRGFCFLEY+ HK+A+ A++RL +G++KVWG    V
Sbjct:   171 EEFSKVTEGLTDVILYHQPDDKKKNRGFCFLEYEDHKTAAQARRRLMSGKVKVWGNVGTV 230

Query:   108 DWADPQEEPDTETMSKVLML 127
             +WADP E+PD E M+KV +L
Sbjct:   231 EWADPIEDPDPEVMAKVKVL 250

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005654 "nucleoplasm" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISO

GO:0006397 "mRNA processing" evidence=IEA

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

GO:0008380 "RNA splicing" evidence=IEA

GO:0017148 "negative regulation of translation" evidence=ISO

GO:0030529 "ribonucleoprotein complex" evidence=ISO;ISS

GO:0070934 "CRD-mediated mRNA stabilization" evidence=ISO

GO:0070937 "CRD-mediated mRNA stability complex" evidence=ISO;ISS

GO:0071013 "catalytic step 2 spliceosome" evidence=ISO

GO:0071204 "histone pre-mRNA 3'end processing complex" evidence=ISO;ISS

GO:0071346 "cellular response to interferon-gamma" evidence=ISO

UNIPROTKB|Q7TP47 Syncrip "Heterogeneous nuclear ribonucleoprotein Q" [Rattus norvegicus (taxid:10116)]

 Score = 245 (91.3 bits), Expect = 9.0e-22, Sum P(2) = 9.0e-22
 Identities = 46/80 (57%), Positives = 61/80 (76%)

Query:    49 QEAITVT-GLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIV 107
             +E   VT GL+ VI+Y  PDD KKNRGFCFLEY+ HK+A+ A++RL +G++KVWG    V
Sbjct:   171 EEFSKVTEGLTDVILYHQPDDKKKNRGFCFLEYEDHKTAAQARRRLMSGKVKVWGNVGTV 230

Query:   108 DWADPQEEPDTETMSKVLML 127
             +WADP E+PD E M+KV +L
Sbjct:   231 EWADPIEDPDPEVMAKVKVL 250

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|F6XIK8 SYNCRIP "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 245 (91.3 bits), Expect = 1.2e-21, Sum P(2) = 1.2e-21
 Identities = 46/80 (57%), Positives = 61/80 (76%)

Query:    49 QEAITVT-GLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIV 107
             +E   VT GL+ VI+Y  PDD KKNRGFCFLEY+ HK+A+ A++RL +G++KVWG    V
Sbjct:   261 EEFSKVTEGLTDVILYHQPDDKKKNRGFCFLEYEDHKTAAQARRRLMSGKVKVWGNVGTV 320

Query:   108 DWADPQEEPDTETMSKVLML 127
             +WADP E+PD E M+KV +L
Sbjct:   321 EWADPIEDPDPEVMAKVKVL 340

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|E2QVD3 SYNCRIP "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 245 (91.3 bits), Expect = 1.9e-21, Sum P(2) = 1.9e-21
 Identities = 46/80 (57%), Positives = 61/80 (76%)

Query:    49 QEAITVT-GLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIV 107
             +E   VT GL+ VI+Y  PDD KKNRGFCFLEY+ HK+A+ A++RL +G++KVWG    V
Sbjct:   261 EEFSKVTEGLTDVILYHQPDDKKKNRGFCFLEYEDHKTAAQARRRLMSGKVKVWGNVGTV 320

Query:   108 DWADPQEEPDTETMSKVLML 127
             +WADP E+PD E M+KV +L
Sbjct:   321 EWADPIEDPDPEVMAKVKVL 340

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|O60506 SYNCRIP "Heterogeneous nuclear ribonucleoprotein Q" [Homo sapiens (taxid:9606)]

 Score = 245 (91.3 bits), Expect = 1.9e-21, Sum P(2) = 1.9e-21
 Identities = 46/80 (57%), Positives = 61/80 (76%)

Query:    49 QEAITVT-GLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIV 107
             +E   VT GL+ VI+Y  PDD KKNRGFCFLEY+ HK+A+ A++RL +G++KVWG    V
Sbjct:   261 EEFSKVTEGLTDVILYHQPDDKKKNRGFCFLEYEDHKTAAQARRRLMSGKVKVWGNVGTV 320

Query:   108 DWADPQEEPDTETMSKVLML 127
             +WADP E+PD E M+KV +L
Sbjct:   321 EWADPIEDPDPEVMAKVKVL 340

GO:0000166 "nucleotide binding" evidence=IEA

GO:0019048 "virus-host interaction" evidence=IEA

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

GO:0005654 "nucleoplasm" evidence=IEA

GO:0005783 "endoplasmic reticulum" evidence=IEA

GO:0071013 "catalytic step 2 spliceosome" evidence=IDA

GO:0071204 "histone pre-mRNA 3'end processing complex" evidence=ISS

GO:0070937 "CRD-mediated mRNA stability complex" evidence=IDA

GO:0070934 "CRD-mediated mRNA stabilization" evidence=IMP

GO:0030529 "ribonucleoprotein complex" evidence=IDA

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

GO:0017148 "negative regulation of translation" evidence=IDA;IMP

GO:0071346 "cellular response to interferon-gamma" evidence=IDA

GO:0003723 "RNA binding" evidence=TAS

GO:0005634 "nucleus" evidence=TAS

GO:0006396 "RNA processing" evidence=TAS

GO:0008380 "RNA splicing" evidence=TAS

GO:0005515 "protein binding" evidence=IPI

MGI|MGI:1891690 Syncrip "synaptotagmin binding, cytoplasmic RNA interacting protein" [Mus musculus (taxid:10090)]

 Score = 245 (91.3 bits), Expect = 1.9e-21, Sum P(2) = 1.9e-21
 Identities = 46/80 (57%), Positives = 61/80 (76%)

Query:    49 QEAITVT-GLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIV 107
             +E   VT GL+ VI+Y  PDD KKNRGFCFLEY+ HK+A+ A++RL +G++KVWG    V
Sbjct:   261 EEFSKVTEGLTDVILYHQPDDKKKNRGFCFLEYEDHKTAAQARRRLMSGKVKVWGNVGTV 320

Query:   108 DWADPQEEPDTETMSKVLML 127
             +WADP E+PD E M+KV +L
Sbjct:   321 EWADPIEDPDPEVMAKVKVL 340

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:0005681 "spliceosomal complex" evidence=IEA

GO:0005737 "cytoplasm" evidence=IDA

GO:0006397 "mRNA processing" evidence=IEA

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

GO:0008380 "RNA splicing" evidence=IEA

GO:0017148 "negative regulation of translation" evidence=ISO

GO:0030529 "ribonucleoprotein complex" evidence=ISO

GO:0070934 "CRD-mediated mRNA stabilization" evidence=ISO

GO:0070937 "CRD-mediated mRNA stability complex" evidence=ISO

GO:0071013 "catalytic step 2 spliceosome" evidence=ISO

GO:0071204 "histone pre-mRNA 3'end processing complex" evidence=IDA

GO:0071346 "cellular response to interferon-gamma" evidence=ISO

UNIPROTKB|F2Z5D4 SYNCRIP "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 245 (91.3 bits), Expect = 1.9e-21, Sum P(2) = 1.9e-21
 Identities = 46/80 (57%), Positives = 61/80 (76%)

Query:    49 QEAITVT-GLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIV 107
             +E   VT GL+ VI+Y  PDD KKNRGFCFLEY+ HK+A+ A++RL +G++KVWG    V
Sbjct:   265 EEFSKVTEGLTDVILYHQPDDKKKNRGFCFLEYEDHKTAAQARRRLMSGKVKVWGNVGTV 324

Query:   108 DWADPQEEPDTETMSKVLML 127
             +WADP E+PD E M+KV +L
Sbjct:   325 EWADPIEDPDPEVMAKVKVL 344

GO:0071204 "histone pre-mRNA 3'end processing complex" evidence=IEA

GO:0071013 "catalytic step 2 spliceosome" evidence=IEA

GO:0070937 "CRD-mediated mRNA stability complex" evidence=IEA

GO:0070934 "CRD-mediated mRNA stabilization" evidence=IEA

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

GO:0000166 "nucleotide binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
O43390	HNRPR_HUMAN	No assigned EC number	0.625	0.5496	0.1137	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	131
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	3e-30
cd12250	82	cd12250, RRM2_hnRNPR_like, RNA recognition motif 2	1e-26
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	2e-25
cd12488	85	cd12488, RRM2_hnRNPR, RNA recognition motif 2 in v	4e-22
cd12489	85	cd12489, RRM2_hnRNPQ, RNA recognition motif 2 in v	2e-21
cd12491	89	cd12491, RRM2_RBM47, RNA recognition motif 2 in ve	1e-18
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	2e-18
cd12490	85	cd12490, RRM2_ACF, RNA recognition motif 2 in vert	2e-18
cd12492	85	cd12492, RRM2_RBM46, RNA recognition motif 2 found	3e-17
cd12494	72	cd12494, RRM3_hnRNPR, RNA recognition motif 3 in v	2e-16
cd12495	72	cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in v	3e-16
cd12498	83	cd12498, RRM3_ACF, RNA recognition motif 3 in vert	2e-14
cd12497	74	cd12497, RRM3_RBM47, RNA recognition motif 3 in ve	4e-14
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	6e-14
cd12496	74	cd12496, RRM3_RBM46, RNA recognition motif 3 in ve	1e-13
smart00360	73	smart00360, RRM, RNA recognition motif	4e-13
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	8e-12
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	2e-11
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	1e-09
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	7e-09
cd12607	67	cd12607, RRM2_RBM4, RNA recognition motif 2 in ver	7e-09
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	2e-08
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	2e-08
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	3e-08
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	3e-08
cd12421	74	cd12421, RRM1_PTBP1_hnRNPL_like, RNA recognition m	4e-08
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	6e-08
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	1e-07
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	1e-07
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	1e-07
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	1e-07
cd12523	78	cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA	2e-07
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	2e-07
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	3e-07
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	3e-07
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	3e-07
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	3e-07
cd12686	81	cd12686, RRM1_PTBPH1_PTBPH2, RNA recognition motif	4e-07
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	4e-07
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	5e-07
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	7e-07
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	1e-06
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	1e-06
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	1e-06
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	1e-06
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	2e-06
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	3e-06
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	3e-06
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	4e-06
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	5e-06
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	5e-06
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	6e-06
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	7e-06
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	7e-06
cd12689	80	cd12689, RRM1_hnRNPL_like, RNA recognition motif 1	9e-06
cd12522	79	cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA	9e-06
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	1e-05
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-05
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	2e-05
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	2e-05
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	2e-05
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	2e-05
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	2e-05
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	2e-05
cd12247	72	cd12247, RRM2_U1A_like, RNA recognition motif 2 in	3e-05
cd12493	83	cd12493, RRM2_DND1, RNA recognition motif 2 found	5e-05
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	5e-05
cd12416	98	cd12416, RRM4_RBM28_like, RNA recognition motif 4	5e-05
cd12322	71	cd12322, RRM2_TDP43, RNA recognition motif 2 in TA	6e-05
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	7e-05
cd12333	80	cd12333, RRM2_p54nrb_like, RNA recognition motif 2	7e-05
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	8e-05
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	8e-05
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	8e-05
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	9e-05
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-04
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	1e-04
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	1e-04
TIGR01649	481	TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus spl	1e-04
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	1e-04
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	1e-04
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	2e-04
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	2e-04
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	2e-04
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	2e-04
cd12348	75	cd12348, RRM1_SHARP, RNA recognition motif 1 in SM	2e-04
cd12234	72	cd12234, RRM1_AtRSp31_like, RNA recognition motif	3e-04
cd12317	72	cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition mot	3e-04
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	3e-04
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	3e-04
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	3e-04
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	3e-04
cd12590	80	cd12590, RRM2_PSF, RNA recognition motif 2 in vert	3e-04
cd12294	102	cd12294, RRM_Rrp7A, RNA recognition motif in ribos	3e-04
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	4e-04
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	4e-04
cd12591	80	cd12591, RRM2_p54nrb, RNA recognition motif 2 in v	4e-04
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	4e-04
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	5e-04
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	5e-04
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	5e-04
cd12257	72	cd12257, RRM1_RBM26_like, RNA recognition motif 1	5e-04
cd12431	80	cd12431, RRM_ALKBH8, RNA recognition motif in alky	6e-04
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	6e-04
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	6e-04
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	7e-04
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	7e-04
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	8e-04
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	8e-04
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	8e-04
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	9e-04
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	0.001
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	0.001
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	0.001
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	0.001
cd12466	70	cd12466, RRM2_AtRSp31_like, RNA recognition motif	0.001
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	0.001
cd12443	73	cd12443, RRM_MCM3A_like, RNA recognition motif in	0.001
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	0.001
cd12405	72	cd12405, RRM3_NCL, RNA recognition motif 3 in vert	0.001
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	0.002
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	0.002
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	0.002
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	0.002
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	0.002
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	0.002
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	0.002
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	0.002
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	0.002
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	0.002
cd12357	89	cd12357, RRM_PPARGC1A_like, RNA recognition motif	0.003
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	0.003
cd12622	74	cd12622, RRM3_PUB1, RNA recognition motif 3 in yea	0.003
cd12615	74	cd12615, RRM1_TIA1, RNA recognition motif 1 in nuc	0.003
cd12643	77	cd12643, RRM_CFIm68, RNA recognition motif of pre-	0.004
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	0.004
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	0.004
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	0.004

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

 Score =  112 bits (282), Expect = 3e-30
 Identities = 40/80 (50%), Positives = 60/80 (75%), Gaps = 1/80 (1%)

Query: 49  QEAITVT-GLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIV 107
           +E   VT G+  VI+Y S  D KKNRGF F+EY+SH++A++A+++L  GR+++WG  I V
Sbjct: 157 EEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAV 216

Query: 108 DWADPQEEPDTETMSKVLML 127
           DWA+P+EE D + M+KV +L
Sbjct: 217 DWAEPEEEVDEDVMAKVKIL 236

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|240696 cd12250, RRM2_hnRNPR_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 94.7 bits (236), Expect = 1e-26
 Identities = 29/57 (50%), Positives = 44/57 (77%)

Query: 54  VTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWA 110
             G+  VI+Y SPDD  KNRGF F+EY+SH++A++A+++L  GR+ +WG ++ VDWA
Sbjct: 26  TEGVVDVIVYRSPDDKNKNRGFAFVEYESHRAAAMARRKLVPGRILLWGHEVAVDWA 82

This subfamily corresponds to the RRM2 in hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF), and dead end protein homolog 1 (DND1). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches. It has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. DND1 is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members in this family, except for DND1, contain three conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains); DND1 harbors only two RRMs. . Length = 82

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

 Score = 90.8 bits (226), Expect = 2e-25
 Identities = 34/50 (68%), Positives = 41/50 (82%)

Query: 4  VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAIT 53
          VKVLYVRNL    TEE+L+E F +YG VERVK+IKDYAFVHFE+R +A+ 
Sbjct: 1  VKVLYVRNLPLSTTEEQLRELFSEYGEVERVKKIKDYAFVHFEERDDAVK 50

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

>gnl|CDD|240932 cd12488, RRM2_hnRNPR, RNA recognition motif 2 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 83.2 bits (205), Expect = 4e-22
 Identities = 36/57 (63%), Positives = 46/57 (80%)

Query: 56  GLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADP 112
           GL  VI+Y  PDD KKNRGFCFLEY+ HKSA+ A++RL +G++KVWG  + V+WADP
Sbjct: 29  GLVDVILYHQPDDKKKNRGFCFLEYEDHKSAAQARRRLMSGKVKVWGNVVTVEWADP 85

This subgroup corresponds to the RRM2 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. It 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 = 85

>gnl|CDD|240933 cd12489, RRM2_hnRNPQ, RNA recognition motif 2 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 81.7 bits (201), Expect = 2e-21
 Identities = 35/57 (61%), Positives = 47/57 (82%)

Query: 56  GLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADP 112
           GL+ VI+Y  PDD KKNRGFCFLEY+ HK+A+ A++RL +G++KVWG  + V+WADP
Sbjct: 29  GLTDVILYHQPDDKKKNRGFCFLEYEDHKTAAQARRRLMSGKVKVWGNVVTVEWADP 85

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 = 85

>gnl|CDD|240935 cd12491, RRM2_RBM47, RNA recognition motif 2 in vertebrate RNA-binding protein 47 (RBM47)

 Score = 74.3 bits (182), Expect = 1e-18
 Identities = 30/67 (44%), Positives = 49/67 (73%)

Query: 51  AITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWA 110
           +    G+  VI+Y+S  D  KNRGF F+EY+SH++A++A+++L  GR+++WG  I VDWA
Sbjct: 23  SKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWA 82

Query: 111 DPQEEPD 117
           +P+ + D
Sbjct: 83  EPEIDVD 89

This subgroup corresponds to the RRM2 of RBM47, a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM47 contains two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 89

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

 Score = 79.3 bits (195), Expect = 2e-18
 Identities = 32/54 (59%), Positives = 46/54 (85%), Gaps = 2/54 (3%)

Query: 1   MSKVKVLYVRNLTQYCTEEKLKEAFEQY--GRVERVKRIKDYAFVHFEDRQEAI 52
           M+KVK+LYVRNL    TEE ++++F ++  G+VERVK+I+DYAFVHFEDR++A+
Sbjct: 230 MAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIRDYAFVHFEDREDAV 283

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|240934 cd12490, RRM2_ACF, RNA recognition motif 2 in vertebrate APOBEC-1 complementation factor (ACF)

 Score = 73.6 bits (180), Expect = 2e-18
 Identities = 29/57 (50%), Positives = 44/57 (77%)

Query: 56  GLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADP 112
           G+  VI+Y S  D  KNRGF F+EY+SH++A++A+++L  GR+++WG  I VDWA+P
Sbjct: 29  GVLDVIVYPSAADKAKNRGFAFVEYESHRAAAMARRKLLPGRIQLWGHPIAVDWAEP 85

This subgroup corresponds to the RRM2 of ACF, also termed APOBEC-1-stimulating protein, an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. ACF shuttles between the cytoplasm and nucleus. ACF contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which display high affinity for an 11 nucleotide AU-rich mooring sequence 3' of the edited cytidine in apoB mRNA. All three RRMs may be required for complementation of editing activity in living cells. RRM2/3 are implicated in ACF interaction with APOBEC-1. . Length = 85

>gnl|CDD|240936 cd12492, RRM2_RBM46, RNA recognition motif 2 found in vertebrate RNA-binding protein 46 (RBM46)

 Score = 70.4 bits (172), Expect = 3e-17
 Identities = 32/68 (47%), Positives = 46/68 (67%), Gaps = 1/68 (1%)

Query: 46  EDRQEAITVT-GLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCD 104
           E  +E   VT G+  VI+Y S  D  KNRGF F+EY+SH++A++A+++L  G  ++WG  
Sbjct: 18  EILEEMKKVTEGVMDVIVYPSATDRTKNRGFAFVEYESHRAAAMARRKLIPGTFQLWGHT 77

Query: 105 IIVDWADP 112
           I VDWA P
Sbjct: 78  IQVDWACP 85

This subgroup corresponds to the RRM2 of RBM46, also termed cancer/testis antigen 68 (CT68). It is a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM46 contains two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 85

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

 Score = 68.1 bits (166), Expect = 2e-16
 Identities = 29/49 (59%), Positives = 41/49 (83%)

Query: 4  VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAI 52
          VKVL+VRNL    TEE L+++F ++G++ERVK++KDYAFVHFE+R  A+
Sbjct: 1  VKVLFVRNLATTVTEEILEKSFSEFGKLERVKKLKDYAFVHFEERDAAV 49

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

 Score = 67.7 bits (165), Expect = 3e-16
 Identities = 29/49 (59%), Positives = 41/49 (83%)

Query: 4  VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAI 52
          VKVL+VRNL    TEE L++AF Q+G++ERVK++KDYAF+HF++R  A+
Sbjct: 1  VKVLFVRNLANTVTEEILEKAFGQFGKLERVKKLKDYAFIHFDERDGAV 49

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|240942 cd12498, RRM3_ACF, RNA recognition motif 3 in vertebrate APOBEC-1 complementation factor (ACF)

 Score = 63.5 bits (154), Expect = 2e-14
 Identities = 34/69 (49%), Positives = 48/69 (69%), Gaps = 3/69 (4%)

Query: 1  MSKVKVLYVRNLTQYCTEEKLKEAFE--QYGRVERVKRIKDYAFVHFEDRQEAI-TVTGL 57
          MS VK+LYVRNL    TEE +++ F   + G VERVK+I+DYAFVHF +R++A+  +  L
Sbjct: 5  MSSVKILYVRNLMLSTTEETIEKEFNSIKPGAVERVKKIRDYAFVHFSNREDAVDAMNAL 64

Query: 58 SQVIIYSSP 66
          +  +I  SP
Sbjct: 65 NGKVIDGSP 73

This subgroup corresponds to the RRM3 of ACF, also termed APOBEC-1-stimulating protein, an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. ACF shuttles between the cytoplasm and nucleus. ACF contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which display high affinity for an 11 nucleotide AU-rich mooring sequence 3' of the edited cytidine in apoB mRNA. All three RRMs may be required for complementation of editing activity in living cells. RRM2/3 are implicated in ACF interaction with APOBEC-1. . Length = 83

>gnl|CDD|240941 cd12497, RRM3_RBM47, RNA recognition motif 3 in vertebrate RNA-binding protein 47 (RBM47)

 Score = 62.4 bits (151), Expect = 4e-14
 Identities = 28/51 (54%), Positives = 39/51 (76%), Gaps = 2/51 (3%)

Query: 4  VKVLYVRNLTQYCTEEKLKEAFEQY--GRVERVKRIKDYAFVHFEDRQEAI 52
          VK+LYVRNL    +E+ +K+ F Q+  G VERVK+I+DYAFVHF  R++A+
Sbjct: 1  VKILYVRNLMIETSEDTIKKTFGQFNPGCVERVKKIRDYAFVHFTSREDAV 51

This subgroup corresponds to the RRM3 of RBM47, a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM47 contains two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 74

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

 Score = 61.8 bits (151), Expect = 6e-14
 Identities = 20/87 (22%), Positives = 37/87 (42%), Gaps = 28/87 (32%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
          L+V NL    TEE LK+ F ++G +E ++ +                             
Sbjct: 1  LFVGNLPPDTTEEDLKDLFSKFGPIESIRIV----------------------------R 32

Query: 67 DDNKKNRGFCFLEYDSHKSASLAKKRL 93
          D+  +++GF F+E++  + A  A + L
Sbjct: 33 DETGRSKGFAFVEFEDEEDAEKALEAL 59

(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|240940 cd12496, RRM3_RBM46, RNA recognition motif 3 in vertebrate RNA-binding protein 46 (RBM46)

 Score = 61.2 bits (148), Expect = 1e-13
 Identities = 29/51 (56%), Positives = 39/51 (76%), Gaps = 2/51 (3%)

Query: 4  VKVLYVRNLTQYCTEEKLKEAFEQY--GRVERVKRIKDYAFVHFEDRQEAI 52
          VKVLYVRNL    TEE +K  F ++  G VERVK+++DYAFVHF +R++A+
Sbjct: 1  VKVLYVRNLMISTTEETIKAEFNKFKPGVVERVKKLRDYAFVHFFNREDAV 51

This subgroup corresponds to the RRM3 of RBM46, also termed cancer/testis antigen 68 (CT68), is a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM46 contains two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 74

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

 Score = 59.9 bits (146), Expect = 4e-13
 Identities = 21/54 (38%), Positives = 33/54 (61%), Gaps = 8/54 (14%)

Query: 6  VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
           L+V NL    TEE+L+E F ++G+VE V+ ++D        +AFV FE  ++A
Sbjct: 1  TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDA 54

Length = 73

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

 Score = 56.1 bits (136), Expect = 8e-12
 Identities = 19/45 (42%), Positives = 28/45 (62%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEA 51
          L+V NL    T E+L+  FE+YG V     +K+Y FVH E+ ++A
Sbjct: 2  LFVGNLPDATTSEELRALFEKYGTVTECDVVKNYGFVHMEEEEDA 46

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

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

 Score = 55.4 bits (134), Expect = 2e-11
 Identities = 20/52 (38%), Positives = 31/52 (59%), Gaps = 7/52 (13%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEA 51
          L+V NL    TEE L+E F ++G +E V+ ++D       +AFV FE  ++A
Sbjct: 1  LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDA 52

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|241050 cd12606, RRM1_RBM4, RNA recognition motif 1 in vertebrate RNA-binding protein 4 (RBM4)

 Score = 50.3 bits (120), Expect = 1e-09
 Identities = 20/45 (44%), Positives = 29/45 (64%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEA 51
          L+V NL    TE++++  FEQYG+V     IK+Y FVH +D+  A
Sbjct: 3  LFVGNLPPEATEQEIRSLFEQYGKVLECDIIKNYGFVHMDDKTAA 47

This subgroup corresponds to the RRM1 of RBM4, a ubiquitously expressed splicing factor that has two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may function as a translational regulator of stress-associated mRNAs and also plays a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. The C-terminal region may be crucial for nuclear localization and protein-protein interaction. The RRMs, in combination with the C-terminal region, are responsible for the splicing function of RBM4. . Length = 67

>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 = 48.8 bits (117), Expect = 7e-09
 Identities = 22/54 (40%), Positives = 30/54 (55%), Gaps = 8/54 (14%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERV--------KRIKDYAFVHFEDRQEAI 52
          L+VRNL    TEE+L+E FE +G +  V        KR K +AFV F   + A+
Sbjct: 2  LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAV 55

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|241051 cd12607, RRM2_RBM4, RNA recognition motif 2 in vertebrate RNA-binding protein 4 (RBM4)

 Score = 48.5 bits (115), Expect = 7e-09
 Identities = 20/46 (43%), Positives = 31/46 (67%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAI 52
          L+V N++  CT ++L+  FE+YG V     +KDYAFVH E  ++A+
Sbjct: 3  LHVGNISSSCTNQELRAKFEEYGPVIECDIVKDYAFVHMERAEDAV 48

This subgroup corresponds to the RRM2 of RBM4, a ubiquitously expressed splicing factor that has two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may function as a translational regulator of stress-associated mRNAs and also plays a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. The C-terminal region may be crucial for nuclear localization and protein-protein interaction. The RRMs, in combination with the C-terminal region, are responsible for the splicing function of RBM4. . Length = 67

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

 Score = 47.5 bits (113), Expect = 2e-08
 Identities = 20/45 (44%), Positives = 32/45 (71%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEA 51
          ++V N++  CT ++L+  FE++GRV    ++KDYAFVH E  +EA
Sbjct: 3  IFVGNVSATCTSDELRGLFEEFGRVVECDKVKDYAFVHMEREEEA 47

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

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

 Score = 47.0 bits (112), Expect = 2e-08
 Identities = 20/46 (43%), Positives = 27/46 (58%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAI 52
          LYVR      +E  ++E F  YG V+ VK I ++AFV FE  + AI
Sbjct: 2  LYVRPFPPDTSESAIREIFSPYGAVKEVKMISNFAFVEFESLESAI 47

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

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

 Score = 47.2 bits (113), Expect = 3e-08
 Identities = 20/55 (36%), Positives = 32/55 (58%), Gaps = 8/55 (14%)

Query: 5  KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
          + +++RNL    TEE+LKE F Q+G V+  + +KD         AFV F+ ++ A
Sbjct: 1  RTVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESA 55

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

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

 Score = 46.8 bits (112), Expect = 3e-08
 Identities = 23/51 (45%), Positives = 30/51 (58%), Gaps = 6/51 (11%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVK------RIKDYAFVHFEDRQEA 51
          LYVRNL    TEE L+E F  YG+VE V+      R + +AFV F   ++A
Sbjct: 1  LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDA 51

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

>gnl|CDD|240867 cd12421, RRM1_PTBP1_hnRNPL_like, RNA recognition motif in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins

 Score = 46.8 bits (112), Expect = 4e-08
 Identities = 14/56 (25%), Positives = 24/56 (42%), Gaps = 2/56 (3%)

Query: 6  VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDY--AFVHFEDRQEAITVTGLSQ 59
          VL++RNL    TE  L      +G+V  V  ++    A V  +  + A ++     
Sbjct: 1  VLHLRNLPPDVTESDLIALVSPFGKVTNVLLLRGKNQALVEMDSVESAKSMVDYYL 56

This subfamily corresponds to the RRM1 of the majority of family members that include polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), polypyrimidine tract-binding protein homolog 3 (PTBPH3), polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2), and similar proteins. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. Rod1 is a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL protein plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. The family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to other family members, all of which contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although their biological roles remain unclear, both PTBPH1 and PTBPH2 show significant sequence similarity to PTB. However, in contrast to PTB, they have three RRMs. In addition, this family also includes RNA-binding motif protein 20 (RBM20) that is an alternative splicing regulator associated with dilated cardiomyopathy (DCM) and contains only one RRM. . Length = 74

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

 Score = 46.4 bits (111), Expect = 6e-08
 Identities = 24/109 (22%), Positives = 39/109 (35%), Gaps = 30/109 (27%)

Query: 5   KVLYVRNLTQYCTEEKLKEAFEQYGR--VERVKRIKDYAFVHFEDRQEAITVTGLSQVII 62
             L +R L    TEE + +A        ++ V+ I+D              +TG S    
Sbjct: 3   NTLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRD-------------KLTGTS---- 45

Query: 63  YSSPDDNKKNRGFCFLEYDSHKSASLAKKRL-ATGRLKVWGCDIIVDWA 110
                     RGF F+E+ S + A+     L       + G  + V +A
Sbjct: 46  ----------RGFAFVEFPSLEDATQWMDALNNLDPFVIDGRVVRVSYA 84

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

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

 Score = 46.0 bits (110), Expect = 1e-07
 Identities = 31/105 (29%), Positives = 43/105 (40%), Gaps = 33/105 (31%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
           LYV NL+ Y TEE++ E F + G ++R+                   + GL         
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDIKRI-------------------IMGL--------- 32

Query: 67  DDNKKNR--GFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDW 109
            D       GFCF+EY + + A  A K L   +L      I VDW
Sbjct: 33  -DRFTKTPCGFCFVEYYTREDAENAVKYLNGTKLD--DRIIRVDW 74

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

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

 Score = 45.7 bits (109), Expect = 1e-07
 Identities = 32/107 (29%), Positives = 41/107 (38%), Gaps = 31/107 (28%)

Query: 6   VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSS 65
           +L V NL    T+E+ +E    +G VER        F                  ++YS 
Sbjct: 1   LLCVGNLPLEFTDEQFRELVSPFGAVER-------CF------------------LVYSE 35

Query: 66  PDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDII-VDWAD 111
                K  GF   EY S  SA  AK +L     K  G   + VDWAD
Sbjct: 36  STGESKGYGFV--EYASKASALKAKNQLDG---KQIGGRKLQVDWAD 77

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

 Score = 45.7 bits (109), Expect = 1e-07
 Identities = 31/105 (29%), Positives = 48/105 (45%), Gaps = 29/105 (27%)

Query: 6   VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSS 65
            L V  L+ Y TE  L+E F +YG +E+V+ +         D++     TG S       
Sbjct: 1   CLGVFGLSLYTTERDLREVFSRYGPIEKVQVVY--------DQK-----TGRS------- 40

Query: 66  PDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWA 110
                  RGF F+ ++S + A  AK+RL    +   G  I VD++
Sbjct: 41  -------RGFGFVYFESVEDAKEAKERLNGMEI--DGRRIRVDYS 76

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

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

 Score = 45.7 bits (109), Expect = 1e-07
 Identities = 21/53 (39%), Positives = 26/53 (49%), Gaps = 8/53 (15%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
          LYV NL    TEE LK+ F Q+G V   + I D        + FV  E  +EA
Sbjct: 2  LYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEA 54

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|240967 cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA-binding protein MRN1 and similar proteins

 Score = 45.1 bits (107), Expect = 2e-07
 Identities = 21/56 (37%), Positives = 35/56 (62%), Gaps = 3/56 (5%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--YAFVHFEDRQEAI-TVTGLSQ 59
          +Y+ NL +  +EE+L+E  E++G ++++K +K+   AFVHF     AI  VT L  
Sbjct: 6  VYIGNLPESYSEEELREDLEKFGPIDQIKIVKEKNIAFVHFLSIANAIKVVTTLPC 61

This subgroup corresponds to the RRM2 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 78

>gnl|CDD|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 = 44.9 bits (107), Expect = 2e-07
 Identities = 21/49 (42%), Positives = 29/49 (59%), Gaps = 2/49 (4%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVE--RVKRIKDYAFVHFEDRQEAIT 53
          +YV NL    TEE+L+  F  +G +E  RV + K YAFV F+  + A T
Sbjct: 3  VYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKDKGYAFVRFDTHEAAAT 51

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

 Score = 44.6 bits (106), Expect = 3e-07
 Identities = 30/104 (28%), Positives = 38/104 (36%), Gaps = 30/104 (28%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
           L VRNL   CTE  LK+ F  +G V  V                           I   P
Sbjct: 2   LIVRNLPFKCTEADLKKLFSPFGFVWEVT--------------------------IPRKP 35

Query: 67  DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWA 110
           D   K +GF F+++ S   A   K        K+ G  + VDWA
Sbjct: 36  D--GKKKGFAFVQFTSKADA--EKAIKGVNGKKIKGRPVAVDWA 75

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

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

 Score = 44.6 bits (106), Expect = 3e-07
 Identities = 19/53 (35%), Positives = 28/53 (52%), Gaps = 8/53 (15%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
          LYV NL    TE+ L+  FE +G +E V+  +D        Y F+ F D ++A
Sbjct: 1  LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDA 53

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

 Score = 44.5 bits (106), Expect = 3e-07
 Identities = 18/48 (37%), Positives = 29/48 (60%), Gaps = 3/48 (6%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERV---KRIKDYAFVHFEDRQEA 51
          +YV NL    T+ +L++ FE+YG +  V   +    +AFV FED ++A
Sbjct: 2  VYVGNLGPRATKRELEDEFEKYGPLRSVWVARNPPGFAFVEFEDPRDA 49

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

 Score = 44.2 bits (105), Expect = 3e-07
 Identities = 20/50 (40%), Positives = 28/50 (56%), Gaps = 5/50 (10%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-----YAFVHFEDRQEA 51
          LYV NL +  TE+ L E F Q G ++  K I++     YAFV + D + A
Sbjct: 1  LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGNDPYAFVEYYDHRSA 50

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

>gnl|CDD|241130 cd12686, RRM1_PTBPH1_PTBPH2, RNA recognition motif 1 in plant polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2)

 Score = 44.5 bits (105), Expect = 4e-07
 Identities = 28/81 (34%), Positives = 44/81 (54%), Gaps = 10/81 (12%)

Query: 5  KVLYVRNLTQYCTEEKLKEAFEQYGRVERVK----RIKDYAFVHFEDRQEAITVTGLSQV 60
          KVL++RNL   CTEE+L E  + +G++   K      ++ AFV F D  +AI     + V
Sbjct: 3  KVLHLRNLPWECTEEELIELCKPFGKIVNTKCNVGANRNQAFVEFADLNQAI-----AMV 57

Query: 61 IIYSSPDDNKKNRG-FCFLEY 80
            Y+S  +  + RG   +L+Y
Sbjct: 58 SYYASSSEPAQVRGKTVYLQY 78

This subfamily corresponds to the RRM1 of PTBPH1 and PTBPH2. Although their biological roles remain unclear, PTBPH1 and PTBPH2 show significant sequence similarity to polypyrimidine tract binding protein (PTB) that is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. Both, PTBPH1 and PTBPH2, contain three RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 81

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

 Score = 44.1 bits (105), Expect = 4e-07
 Identities = 21/92 (22%), Positives = 36/92 (39%), Gaps = 27/92 (29%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
          L+V  LT+   ++ LKE F  YG V+ V    D                           
Sbjct: 1  LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPID--------------------------- 33

Query: 67 DDNKKNRGFCFLEYDSHKSASLAKKRLATGRL 98
           +    RG+ ++E++S + A  A K +  G++
Sbjct: 34 REVNLPRGYAYVEFESPEDAEKAIKHMDGGQI 65

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|241081 cd12637, RRM2_FCA, RNA recognition motif 2 in plant flowering time control protein FCA and similar proteins

 Score = 44.1 bits (104), Expect = 5e-07
 Identities = 34/108 (31%), Positives = 49/108 (45%), Gaps = 31/108 (28%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
           L+V  L +  TE++++E F  YGRVE                             IY   
Sbjct: 2   LFVGCLNKQATEKEVEEVFSPYGRVED----------------------------IYMMR 33

Query: 67  DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCD--IIVDWADP 112
           D+ K++RG  F++Y S + A  A K L  G   + GCD  +IV +ADP
Sbjct: 34  DEMKQSRGCAFVKYSSKEMAQAAIKAL-NGVYTMRGCDQPLIVRFADP 80

This subgroup corresponds to the RRM2 of FCA, a gene controlling flowering time in Arabidopsis, which encodes a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. The flowering time control protein FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain. . Length = 80

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

 Score = 44.2 bits (105), Expect = 7e-07
 Identities = 28/104 (26%), Positives = 46/104 (44%), Gaps = 29/104 (27%)

Query: 5   KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYS 64
             L+V  L+   TEE L+E F +YG + R++ ++D              VTG S      
Sbjct: 4   LTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRD-------------IVTGFS------ 44

Query: 65  SPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVD 108
                   +G+ F+EY+  + A  A +     +L + G +I VD
Sbjct: 45  --------KGYAFVEYEHERDALRAYR--DAHKLVIDGSEIFVD 78

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

 Score = 43.2 bits (102), Expect = 1e-06
 Identities = 18/47 (38%), Positives = 27/47 (57%), Gaps = 8/47 (17%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERV--------KRIKDYAFVHF 45
          L++RNL   CTEE L++ F +YG +  V        K+ K +AFV +
Sbjct: 5  LFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTY 51

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

 Score = 43.3 bits (103), Expect = 1e-06
 Identities = 20/52 (38%), Positives = 32/52 (61%), Gaps = 7/52 (13%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEA 51
          +YV+NL +   +EKLKE F +YG++   K +KD       + FV+FE+ + A
Sbjct: 4  VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAA 55

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

 Score = 42.9 bits (102), Expect = 1e-06
 Identities = 18/54 (33%), Positives = 29/54 (53%), Gaps = 8/54 (14%)

Query: 6  VLYVRNLTQYCTEEKLKEAFEQYGRVERVK--------RIKDYAFVHFEDRQEA 51
          V+Y+ +L     E +L++ F Q+G V R++        + K YAFV FE  + A
Sbjct: 1  VVYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVA 54

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

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

 Score = 42.6 bits (101), Expect = 1e-06
 Identities = 16/46 (34%), Positives = 29/46 (63%), Gaps = 1/46 (2%)

Query: 7  LYVRNL-TQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEA 51
          ++V NL T   ++E L+E F +YG++  +   K Y FV F++ ++A
Sbjct: 3  VFVGNLNTDKVSKEDLEEIFSKYGKILGISLHKGYGFVQFDNEEDA 48

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

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

 Score = 42.2 bits (100), Expect = 2e-06
 Identities = 22/68 (32%), Positives = 33/68 (48%), Gaps = 8/68 (11%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEAI-TVTGLS 58
          LYV+NL     +E+L+E F  +G +   K + D       + FV F   +EA   VT ++
Sbjct: 4  LYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAVTEMN 63

Query: 59 QVIIYSSP 66
            II   P
Sbjct: 64 GRIIGGKP 71

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|241058 cd12614, RRM1_PUB1, RNA recognition motif 1 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 42.1 bits (99), Expect = 3e-06
 Identities = 31/104 (29%), Positives = 43/104 (41%), Gaps = 30/104 (28%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
           LYV NL    TE+ LK+ F+  G V+ VK I                            P
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKII----------------------------P 32

Query: 67  DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWA 110
           D N K   + F+EY     A +A + L  GR ++   +I V+WA
Sbjct: 33  DKNNKGVNYGFVEYHQSHDAEIALQTL-NGR-QIENNEIRVNWA 74

This subgroup corresponds to the RRM1 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 = 74

>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 = 42.1 bits (100), Expect = 3e-06
 Identities = 21/53 (39%), Positives = 29/53 (54%), Gaps = 8/53 (15%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDY--------AFVHFEDRQEA 51
          L+V  L +  TEE ++  FE+YG +E V  I+D         AFV F  R+EA
Sbjct: 2  LFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEA 54

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

 Score = 41.8 bits (99), Expect = 4e-06
 Identities = 18/51 (35%), Positives = 27/51 (52%), Gaps = 8/51 (15%)

Query: 9  VRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
          V NL++   E+ L+E F  +G + RV   KD        +AFV F  R++A
Sbjct: 4  VTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDA 54

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

 Score = 43.8 bits (102), Expect = 5e-06
 Identities = 20/58 (34%), Positives = 30/58 (51%), Gaps = 8/58 (13%)

Query: 5   KVLYVRNLTQYCTEEKLKEAFEQYGRVERV--------KRIKDYAFVHFEDRQEAITV 54
             L+V NL    TEE L+E F+++G V+RV         + + +AFV FE  + A   
Sbjct: 116 NTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKA 173

Length = 306

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

 Score = 41.5 bits (98), Expect = 5e-06
 Identities = 19/51 (37%), Positives = 29/51 (56%), Gaps = 8/51 (15%)

Query: 5  KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFED 47
          K L+V  L    TE KL+  FE+YG ++R++ ++D        YAF+ FE 
Sbjct: 2  KTLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEH 52

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

 Score = 41.2 bits (97), Expect = 6e-06
 Identities = 17/54 (31%), Positives = 30/54 (55%), Gaps = 8/54 (14%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERV--------KRIKDYAFVHFEDRQEAI 52
          L+VRNL   C E+ L++ F ++G +  V         + K +A+V F D ++A+
Sbjct: 5  LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAV 58

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

 Score = 41.1 bits (97), Expect = 7e-06
 Identities = 18/51 (35%), Positives = 29/51 (56%), Gaps = 7/51 (13%)

Query: 8  YVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEA 51
          +V  +    TEE+L++ F ++G V+ VK I D       Y FV FE +++A
Sbjct: 6  FVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVSKGYGFVTFETQEDA 56

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

 Score = 41.0 bits (97), Expect = 7e-06
 Identities = 18/52 (34%), Positives = 30/52 (57%), Gaps = 7/52 (13%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEA 51
          + V+NL +Y TE++L+E FE  G V  VK ++        + FV F+  ++A
Sbjct: 3  IIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRDGKSRRFGFVGFKSEEDA 54

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

>gnl|CDD|241133 cd12689, RRM1_hnRNPL_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and similar proteins

 Score = 40.8 bits (96), Expect = 9e-06
 Identities = 19/56 (33%), Positives = 27/56 (48%), Gaps = 2/56 (3%)

Query: 6  VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--KDYAFVHFEDRQEAITVTGLSQ 59
          V++VR L    TE  L EA  ++G +  V  +  K  A V FED  +A      +Q
Sbjct: 4  VVHVRGLPDGVTEADLVEALSEFGPISYVTMMPKKRQALVEFEDISDAKACVNHAQ 59

This subfamily corresponds to the RRM1 of heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), and similar proteins. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. It is closely related in domain structure and sequence to hnRNP-L, which contains three RNA-recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 80

>gnl|CDD|240966 cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA-binding protein MRN1 and similar proteins

 Score = 40.9 bits (96), Expect = 9e-06
 Identities = 21/48 (43%), Positives = 29/48 (60%), Gaps = 2/48 (4%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVK--RIKDYAFVHFEDRQEAI 52
          +Y+ N+    TEEKL+  F QYG +E V   R K+ AFV+F +   AI
Sbjct: 6  VYIGNIDDSLTEEKLRNDFSQYGEIESVNYLREKNCAFVNFTNISNAI 53

This subgroup corresponds to the RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 79

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

 Score = 40.7 bits (96), Expect = 1e-05
 Identities = 18/56 (32%), Positives = 27/56 (48%), Gaps = 11/56 (19%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-----------YAFVHFEDRQEA 51
          +YVRNL     E+ L+  F ++G VE ++  K            +AFV F+D   A
Sbjct: 3  IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSA 58

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

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

 Score = 42.5 bits (100), Expect = 1e-05
 Identities = 21/73 (28%), Positives = 35/73 (47%), Gaps = 8/73 (10%)

Query: 2   SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVK-------RIKDYAFVHFEDRQEAI-T 53
           ++   LYV+NL    T+EKL+E F + G +   K         + + FV F + +EA   
Sbjct: 283 AQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRA 342

Query: 54  VTGLSQVIIYSSP 66
           VT +   ++   P
Sbjct: 343 VTEMHGRMLGGKP 355

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

 Score = 40.0 bits (94), Expect = 2e-05
 Identities = 18/47 (38%), Positives = 25/47 (53%), Gaps = 2/47 (4%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERV--KRIKDYAFVHFEDRQEA 51
          L+V NL    TEE+ KE F +YG V  V   + K + F+  + R  A
Sbjct: 4  LFVGNLPNDITEEEFKELFSKYGEVSEVFLNKEKGFGFIRLDTRTNA 50

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|241052 cd12608, RRM1_CoAA, RNA recognition motif 1 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 39.8 bits (93), Expect = 2e-05
 Identities = 14/45 (31%), Positives = 25/45 (55%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEA 51
          ++V N+ +  ++E+L+  FE YG V     ++ +AFVH      A
Sbjct: 3  IFVGNVDEDTSQEELRALFEAYGAVLSCAVMRQFAFVHLRGEAAA 47

This subgroup corresponds to the RRM1 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs. . Length = 69

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

 Score = 39.4 bits (93), Expect = 2e-05
 Identities = 15/47 (31%), Positives = 24/47 (51%), Gaps = 4/47 (8%)

Query: 21 LKEAFEQYGRVERVKRIKD---YAFVHFEDRQEAIT-VTGLSQVIIY 63
          L + F  +G VE++K +K    +AFV F   + A   V  L+ V+  
Sbjct: 1  LYKLFSPFGNVEKIKLLKKKPGFAFVEFSTEEAAEKAVQYLNGVLFG 47

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

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

 Score = 39.9 bits (94), Expect = 2e-05
 Identities = 19/53 (35%), Positives = 30/53 (56%), Gaps = 8/53 (15%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
          L+V  L+   TE++L+  F ++GRVE V  +KD        + FV FE  ++A
Sbjct: 4  LFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDA 56

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 = 39.5 bits (93), Expect = 2e-05
 Identities = 16/53 (30%), Positives = 28/53 (52%), Gaps = 8/53 (15%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
          ++V  L  + T++ L++ F Q+G +E    I D        Y FV F+D++ A
Sbjct: 3  IFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESA 55

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

 Score = 39.6 bits (93), Expect = 2e-05
 Identities = 16/50 (32%), Positives = 27/50 (54%), Gaps = 2/50 (4%)

Query: 4  VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--KDYAFVHFEDRQEA 51
          +  LYV  L +  TE+ L++ F Q+G +  +  +  +  AFV F  R+ A
Sbjct: 1  ITTLYVGGLGERVTEKDLRDHFYQFGEIRSITVVPRQQCAFVTFTTREAA 50

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

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

 Score = 39.1 bits (92), Expect = 3e-05
 Identities = 17/45 (37%), Positives = 27/45 (60%), Gaps = 2/45 (4%)

Query: 5  KVLYVRNLTQYCTEEKLKEAFEQY-GRVE-RVKRIKDYAFVHFED 47
          K+L+++NL +  T+E L+  F Q+ G  E R+   +  AFV FE 
Sbjct: 3  KILFLQNLPEETTKEMLEMLFNQFPGFKEVRLVPRRGIAFVEFET 47

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

>gnl|CDD|240937 cd12493, RRM2_DND1, RNA recognition motif 2 found in vertebrate dead end protein homolog 1 (DND1)

 Score = 39.0 bits (91), Expect = 5e-05
 Identities = 18/57 (31%), Positives = 32/57 (56%), Gaps = 2/57 (3%)

Query: 56  GLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADP 112
           G+  V+++ SP   K       ++Y SH++A++AKK L  G   ++G  + V+W  P
Sbjct: 29  GVEDVLLHPSP--GKGKGVVALVKYSSHRAAAMAKKALVEGFRNLYGISVTVEWLKP 83

This subgroup corresponds to the RRM2 of DND1, also termed RNA-binding motif, single-stranded-interacting protein 4. It is an RNA-binding protein that is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. For instance, DND1 binds cell cycle inhibitor, P27 (p27Kip1, CDKN1B), and cell cycle regulator and tumor suppressor, LATS2 (large tumor suppressor, homolog 2 of Drosophila). It helps maintain their protein expression through blocking the inhibitory function of microRNAs (miRNA) from these transcripts. DND1 may also impose another level of translational regulation to modulate expression of critical factors in embryonic stem (ES) cells. Moreover, DND1 interacts specifically with apolipoprotein B editing complex 3 (APOBEC3), a multi-functional protein inhibiting retroviral replication. The DND1-APOBEC3 interaction may play a role in maintaining viability of germ cells and for preventing germ cell tumor development. DND1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 83

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

 Score = 38.9 bits (91), Expect = 5e-05
 Identities = 18/47 (38%), Positives = 30/47 (63%), Gaps = 2/47 (4%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--KDYAFVHFEDRQEA 51
          L++ +L++  TEE LK  FE+YG ++ +  I  +  A+V  E RQ+A
Sbjct: 5  LWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIPPRGCAYVCMETRQDA 51

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

>gnl|CDD|240862 cd12416, RRM4_RBM28_like, RNA recognition motif 4 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 39.1 bits (92), Expect = 5e-05
 Identities = 21/83 (25%), Positives = 35/83 (42%), Gaps = 18/83 (21%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVK---RIKDYAFVHFEDRQEAITVTGLSQVIIY 63
          L +RNL +   E+KLKE F +       K   +IK    +    R               
Sbjct: 3  LSIRNLPKSVDEKKLKELFLKAVSERAGKKKPKIKQVKIMRDLKR--------------- 47

Query: 64 SSPDDNKKNRGFCFLEYDSHKSA 86
            P+   K++G+ F+E+ +H+ A
Sbjct: 48 VDPNGKGKSKGYGFVEFTNHEHA 70

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

 Score = 38.4 bits (90), Expect = 6e-05
 Identities = 21/58 (36%), Positives = 32/58 (55%), Gaps = 3/58 (5%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDY---AFVHFEDRQEAITVTGLSQVI 61
          ++V  LT+  TEE L++ F Q+G V  V   K +   AFV F D + A ++ G   +I
Sbjct: 3  VFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKPFRAFAFVTFADPEVAQSLCGEDHII 60

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

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

 Score = 38.5 bits (90), Expect = 7e-05
 Identities = 15/52 (28%), Positives = 29/52 (55%), Gaps = 7/52 (13%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRI-------KDYAFVHFEDRQEA 51
          L+V  L    T+E+L++ F+++G V+ V+ +       K  A+V +E+   A
Sbjct: 5  LFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSA 56

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

>gnl|CDD|240779 cd12333, RRM2_p54nrb_like, RNA recognition motif 2 in the p54nrb/PSF/PSP1 family

 Score = 38.4 bits (90), Expect = 7e-05
 Identities = 15/33 (45%), Positives = 22/33 (66%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD 39
          L V+NL+ + + E L++AF Q+G VER   I D
Sbjct: 2  LRVKNLSPFVSNELLEQAFSQFGEVERAVVIVD 34

This subfamily corresponds to the RRM2 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. The family 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 contains 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 = 80

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

 Score = 38.0 bits (89), Expect = 8e-05
 Identities = 26/71 (36%), Positives = 33/71 (46%), Gaps = 13/71 (18%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHF---EDRQEAITVT 55
          +YV NL +  TEE L E F Q G V  V   KD        Y FV F   ED   AI + 
Sbjct: 1  VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKI- 59

Query: 56 GLSQVIIYSSP 66
           ++ + +Y  P
Sbjct: 60 -MNMIKLYGKP 69

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

 Score = 38.4 bits (90), Expect = 8e-05
 Identities = 16/54 (29%), Positives = 30/54 (55%), Gaps = 8/54 (14%)

Query: 6  VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
          VL+V  L    T+E L+  F ++G+++  + I+D        YAF+ FE +++ 
Sbjct: 5  VLFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDC 58

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

 Score = 38.5 bits (90), Expect = 8e-05
 Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 8/53 (15%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERV--------KRIKDYAFVHFEDRQEA 51
          LYVRN+      + L+  F +YG +  V        +R + +A+V FED ++A
Sbjct: 3  LYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDA 55

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

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

 Score = 38.0 bits (89), Expect = 9e-05
 Identities = 11/48 (22%), Positives = 27/48 (56%), Gaps = 2/48 (4%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVK--RIKDYAFVHFEDRQEAI 52
          L+V  L  + +  +L+  F+++G + R+     ++YA++ +E  + A 
Sbjct: 1  LWVGGLGPWTSLAELEREFDRFGAIRRIDYDPGRNYAYIEYESIEAAQ 48

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

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

 Score = 39.8 bits (93), Expect = 1e-04
 Identities = 19/52 (36%), Positives = 30/52 (57%), Gaps = 7/52 (13%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEA 51
           LYV+NL     E+KL+E F ++G +     +KD       +AFV+FE  ++A
Sbjct: 181 LYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDA 232

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

 Score = 37.8 bits (88), Expect = 1e-04
 Identities = 16/46 (34%), Positives = 25/46 (54%), Gaps = 1/46 (2%)

Query: 7  LYVRNL-TQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEA 51
          L+V         EE +++ FE +G + R    K +AFV FED ++A
Sbjct: 2  LFVVGFDPGTTREEDIEKLFEPFGPLVRCDIRKTFAFVEFEDSEDA 47

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

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

 Score = 38.0 bits (89), Expect = 1e-04
 Identities = 19/56 (33%), Positives = 27/56 (48%), Gaps = 11/56 (19%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVK-----------RIKDYAFVHFEDRQEA 51
          LYV NL    TEE L + F ++G +  VK           R ++  FV F +R +A
Sbjct: 4  LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADA 59

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

>gnl|CDD|233508 TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus splicing factor family

 Score = 39.8 bits (93), Expect = 1e-04
 Identities = 24/62 (38%), Positives = 30/62 (48%), Gaps = 3/62 (4%)

Query: 5  KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--KDYAFVHFEDRQEAIT-VTGLSQVI 61
           V++VRNL Q   E  L EA   +G V  V  +  K  A V FED + A   V   + V 
Sbjct: 3  PVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPGKRQALVEFEDEESAKACVNFATSVP 62

Query: 62 IY 63
          IY
Sbjct: 63 IY 64

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). Length = 481

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

 Score = 38.0 bits (88), Expect = 1e-04
 Identities = 21/64 (32%), Positives = 36/64 (56%), Gaps = 9/64 (14%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAI-TVTGL 57
          LYV NL +  TE++L++ FE YG + +   ++D         AFV ++ R+EA   ++ L
Sbjct: 3  LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSL 62

Query: 58 SQVI 61
          +  I
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|240689 cd12243, RRM1_MSSP, RNA recognition motif 1 in the c-myc gene single-strand binding proteins (MSSP) family

 Score = 37.2 bits (87), Expect = 1e-04
 Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 9/60 (15%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYAFVHFEDRQEA-ITVTGL 57
          +Y+R L    T+E L++  + +G++   K I        K Y FV F+  + A   + GL
Sbjct: 3  VYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIEGL 62

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

 Score = 37.3 bits (87), Expect = 2e-04
 Identities = 20/48 (41%), Positives = 25/48 (52%), Gaps = 7/48 (14%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVK-------RIKDYAFVHFED 47
          L+V NL    TEE L E F Q G +E VK       + K +AFV F+ 
Sbjct: 4  LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGKPKSFAFVTFKH 51

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|240818 cd12372, RRM_CFIm68_CFIm59, RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6), pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7), and similar proteins

 Score = 37.3 bits (87), Expect = 2e-04
 Identities = 25/87 (28%), Positives = 41/87 (47%), Gaps = 25/87 (28%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
          LYV NLT + T+E L+ A  + G V+    +K   F  FE +                  
Sbjct: 1  LYVGNLTWWTTDEDLEGALAEAGVVD----VKSIKF--FEHKA----------------- 37

Query: 67 DDNKKNRGFCFLEYDSHKSASLAKKRL 93
            N K++GF ++E+ S  +A+  K++L
Sbjct: 38 --NGKSKGFAYVEFASEAAAAAVKEKL 62

This subfamily corresponds to the RRM of cleavage factor Im (CFIm) subunits. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the regulation of alternative poly(A) site selection, mRNA export, and mRNA splicing. It is a complex composed of a small 25 kDa (CFIm25) subunit and a larger 59/68/72 kDa subunit. Two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. Structurally related CFIm68 and CFIm59, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF7), or cleavage and polyadenylation specificity factor 59 kDa subunit (CPSF59), are functionally redundant. Both contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a central proline-rich region, and a C-terminal RS-like domain. Their N-terminal RRM mediates the interaction with CFIm25, and also serves to enhance RNA binding and facilitate RNA looping. . Length = 76

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

 Score = 37.2 bits (87), Expect = 2e-04
 Identities = 19/58 (32%), Positives = 31/58 (53%), Gaps = 11/58 (18%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHF---EDRQEAIT 53
          L+VRNL    T+E+L+E F + G ++R   +KD        + +V F   ED + A+ 
Sbjct: 2  LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALE 59

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

 Score = 37.2 bits (87), Expect = 2e-04
 Identities = 15/53 (28%), Positives = 24/53 (45%), Gaps = 8/53 (15%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
          L++ +L  +  E  +  AF + G V  VK I++        Y FV F   + A
Sbjct: 2  LWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAA 54

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|240794 cd12348, RRM1_SHARP, RNA recognition motif 1 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 37.0 bits (86), Expect = 2e-04
 Identities = 21/52 (40%), Positives = 29/52 (55%), Gaps = 7/52 (13%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDY-------AFVHFEDRQEA 51
          L+V NL +   EE++ E F++YGRVE VK +          AFV F D + A
Sbjct: 2  LWVGNLPENVREERISEHFKRYGRVESVKILPKRGSDGGVAAFVDFVDIKSA 53

This subfamily corresponds to the RRM1 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins. . Length = 75

>gnl|CDD|240680 cd12234, RRM1_AtRSp31_like, RNA recognition motif in Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins from plants

 Score = 36.7 bits (85), Expect = 3e-04
 Identities = 14/47 (29%), Positives = 27/47 (57%)

Query: 5  KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEA 51
          + ++  N      + +++  F +YGRV+RV     +AFV+ ED ++A
Sbjct: 1  RPVFCGNFEYDARQSEIERLFGKYGRVDRVDMKSGFAFVYMEDERDA 47

This subfamily corresponds to the RRM1in a family that represents a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at their N-terminus, and an RS domain at their C-terminus. Length = 72

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

 Score = 36.8 bits (86), Expect = 3e-04
 Identities = 17/49 (34%), Positives = 28/49 (57%), Gaps = 2/49 (4%)

Query: 5  KVLYVRNLTQYCTEEKLKEAFEQYGRVERV--KRIKDYAFVHFEDRQEA 51
           V+ V+NL    TEE+L+E FE++G + R+     +  A V F +  +A
Sbjct: 1  TVILVKNLPFGTTEEELRELFEKFGSLGRLLLPPSRTIALVEFLEPSDA 49

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

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

 Score = 36.9 bits (86), Expect = 3e-04
 Identities = 24/80 (30%), Positives = 32/80 (40%), Gaps = 27/80 (33%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
          L+V  L +  TEE L+E F QYG VE V+ + D               TG          
Sbjct: 2  LFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKE-------------TG---------- 38

Query: 67 DDNKKNRGFCFLEYDSHKSA 86
              K RGF F+ +D +   
Sbjct: 39 ----KKRGFAFVTFDDYDPV 54

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

 Score = 36.9 bits (86), Expect = 3e-04
 Identities = 15/52 (28%), Positives = 29/52 (55%), Gaps = 7/52 (13%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVK-------RIKDYAFVHFEDRQEA 51
          L V+NL +   E+KL++ FE +G +  V+       + + + FV ++  +EA
Sbjct: 3  LIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEA 54

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

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

 Score = 37.0 bits (86), Expect = 3e-04
 Identities = 18/49 (36%), Positives = 28/49 (57%), Gaps = 8/49 (16%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERV--------KRIKDYAFVHFED 47
          L+V NL    TE++LKE F+++G V  V         R+ ++ FV F+D
Sbjct: 6  LFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDD 54

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

 Score = 36.9 bits (86), Expect = 3e-04
 Identities = 18/83 (21%), Positives = 35/83 (42%), Gaps = 27/83 (32%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
          +YV ++    +E+ +K  FE +G+++      D               TG          
Sbjct: 3  IYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPD-------------PETG---------- 39

Query: 67 DDNKKNRGFCFLEYDSHKSASLA 89
              K++G+ F+EY++ +SA  A
Sbjct: 40 ----KHKGYGFIEYENPQSAQDA 58

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

>gnl|CDD|241034 cd12590, RRM2_PSF, RNA recognition motif 2 in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)

 Score = 36.6 bits (84), Expect = 3e-04
 Identities = 18/33 (54%), Positives = 22/33 (66%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD 39
          L VRNL+ Y + E L+EAF Q+G VER   I D
Sbjct: 2  LSVRNLSPYVSNELLEEAFSQFGPVERAVVIVD 34

This subgroup corresponds to the RRM2 of PSF, also termed proline- and glutamine-rich splicing factor, or 100 kDa DNA-pairing protein (POMp100), or 100 kDa subunit of DNA-binding p52/p100 complex, a multifunctional protein that mediates diverse activities in the cell. It is ubiquitously expressed and highly conserved in vertebrates. PSF binds not only RNA but also both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) and facilitates the renaturation of complementary ssDNAs. It promotes the formation of D-loops in superhelical duplex DNA, and is involved in cell proliferation. PSF can also interact with multiple factors. It is an RNA-binding component of spliceosomes and binds to insulin-like growth factor response element (IGFRE). Moreover, PSF functions as a transcriptional repressor interacting with Sin3A and mediating silencing through the recruitment of histone deacetylases (HDACs) to the DNA binding domain (DBD) of nuclear hormone receptors. PSF is an essential pre-mRNA splicing factor and is dissociated from PTB and binds to U1-70K and serine-arginine (SR) proteins during apoptosis. PSF forms a heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO). The PSF/p54nrb complex displays a variety of functions, such as DNA recombination and RNA synthesis, processing, and transport. PSF contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for interactions with RNA and for the localization of the protein in speckles. It also contains an N-terminal region rich in proline, glycine, and glutamine residues, which may play a role in interactions recruiting other molecules. . Length = 80

>gnl|CDD|240740 cd12294, RRM_Rrp7A, RNA recognition motif in ribosomal RNA-processing protein 7 homolog A (Rrp7A) and similar proteins

 Score = 36.9 bits (86), Expect = 3e-04
 Identities = 15/30 (50%), Positives = 20/30 (66%)

Query: 5  KVLYVRNLTQYCTEEKLKEAFEQYGRVERV 34
          + L+V N+  YCTEE LK  F + G+VE V
Sbjct: 1  RTLFVLNVPPYCTEESLKRLFSRCGKVESV 30

This subfamily corresponds to the RRM of Rrp7A, also termed gastric cancer antigen Zg14, a homolog of yeast ribosomal RNA-processing protein 7 (Rrp7p), and mainly found in Metazoa. Rrp7p is an essential yeast protein involved in pre-rRNA processing and ribosome assembly, and is speculated to be required for correct assembly of rpS27 into the pre-ribosomal particle. In contrast, the cellular function of Rrp7A remains unclear currently. Rrp7A harbors an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal Rrp7 domain. . Length = 102

>gnl|CDD|240895 cd12449, RRM_CIRBP_RBM3, RNA recognition motif in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins

 Score = 36.4 bits (84), Expect = 4e-04
 Identities = 15/53 (28%), Positives = 28/53 (52%), Gaps = 8/53 (15%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
          L++  L+    E+ L++ F +YG++  V  +KD        + FV FE+  +A
Sbjct: 3  LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDA 55

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

 Score = 36.5 bits (85), Expect = 4e-04
 Identities = 23/104 (22%), Positives = 43/104 (41%), Gaps = 26/104 (25%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
           L++ NL    TE  L + F +YG++++   +                         + S 
Sbjct: 2   LWIGNLDSRLTEFHLLKLFSKYGKIKKFDFL------------------------FHKSG 37

Query: 67  DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWA 110
               + RG+CF+ +++ + A  A K L  G+    G  ++V WA
Sbjct: 38  PLKGQPRGYCFVTFETKEEAEKALKSL-NGKT-ALGKKLVVRWA 79

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

>gnl|CDD|241035 cd12591, RRM2_p54nrb, RNA recognition motif 2 in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb)

 Score = 36.5 bits (84), Expect = 4e-04
 Identities = 16/33 (48%), Positives = 22/33 (66%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD 39
          L V+NL Q+ + E L+EAF  +G+VER   I D
Sbjct: 2  LTVKNLPQFVSNELLEEAFSMFGQVERAVVIVD 34

This subgroup corresponds to the RRM2 of p54nrb, also termed non-POU domain-containing octamer-binding protein (NonO), or 55 kDa nuclear protein (NMT55), or DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a multifunctional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. It is ubiquitously expressed and highly conserved in vertebrates. It binds both, single- and double-stranded RNA and DNA, and also possesses inherent carbonic anhydrase activity. p54nrb forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manner. It also forms a heterodimer with polypyrimidine tract-binding protein-associated-splicing factor (PSF). p54nrb contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 80

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

 Score = 36.1 bits (84), Expect = 4e-04
 Identities = 19/53 (35%), Positives = 28/53 (52%), Gaps = 8/53 (15%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERV--------KRIKDYAFVHFEDRQEA 51
          L V NLT   T + L+  FE+YG V  V        +  + +AFV F D+++A
Sbjct: 1  LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDA 53

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

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

 Score = 36.1 bits (84), Expect = 5e-04
 Identities = 17/67 (25%), Positives = 33/67 (49%), Gaps = 7/67 (10%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEAITVTGLSQ 59
          ++V NL     E++L++ F + G +  V+ +K+       YA+V FE+ +       L +
Sbjct: 2  VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVEFENEESVQEALKLDR 61

Query: 60 VIIYSSP 66
           +I   P
Sbjct: 62 ELIKGRP 68

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

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

 Score = 36.0 bits (84), Expect = 5e-04
 Identities = 17/53 (32%), Positives = 26/53 (49%), Gaps = 8/53 (15%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
          LYV +L    TE  L E F   G V  ++  +D        YA+V+F++  +A
Sbjct: 2  LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADA 54

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

 Score = 36.2 bits (84), Expect = 5e-04
 Identities = 16/53 (30%), Positives = 27/53 (50%), Gaps = 8/53 (15%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
          L V  L Q  T+++++  F   G +E  K I+D        Y FV++ D ++A
Sbjct: 4  LIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDA 56

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

 Score = 36.0 bits (84), Expect = 5e-04
 Identities = 15/48 (31%), Positives = 23/48 (47%), Gaps = 3/48 (6%)

Query: 7  LYVRNL-TQYCTEEKLKEAFEQYGRVE--RVKRIKDYAFVHFEDRQEA 51
          L VRN+  +     KL E F ++G +   +V    + A V F   +EA
Sbjct: 4  LEVRNIPPELNNITKLNEHFSKFGTIVNIQVNYNPESALVQFSTSEEA 51

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

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

 Score = 36.1 bits (84), Expect = 6e-04
 Identities = 16/56 (28%), Positives = 23/56 (41%), Gaps = 2/56 (3%)

Query: 17 TEEKLKEAFEQYGRVERVKRI--KDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNK 70
          + E+L   FE+YG VE +     K Y FV +   ++A              P  NK
Sbjct: 16 SREELLRVFEKYGTVEDLVMPPGKPYCFVSYSSIEDAAAAYDALNGKELELPQQNK 71

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

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

 Score = 38.1 bits (88), Expect = 6e-04
 Identities = 21/64 (32%), Positives = 35/64 (54%), Gaps = 9/64 (14%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAI-TVTGL 57
           LYV NL +  T+++L   F +YG++ +   ++D         AFV F  R+EA   ++ L
Sbjct: 196 LYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISAL 255

Query: 58  SQVI 61
           + VI
Sbjct: 256 NNVI 259

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

 Score = 36.2 bits (84), Expect = 6e-04
 Identities = 17/51 (33%), Positives = 28/51 (54%), Gaps = 6/51 (11%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD------YAFVHFEDRQEA 51
          ++V  L+   T+E+L E F ++G++  V  IK       +AF+ FE  Q A
Sbjct: 6  IFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNAFAFIKFEREQAA 56

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

 Score = 35.8 bits (83), Expect = 7e-04
 Identities = 14/53 (26%), Positives = 26/53 (49%), Gaps = 8/53 (15%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
          ++V +L+     E L+ AF  +G +   + +KD        Y FV F  +++A
Sbjct: 2  IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDA 54

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|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 37.6 bits (87), Expect = 7e-04
 Identities = 20/54 (37%), Positives = 30/54 (55%), Gaps = 8/54 (14%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVK--------RIKDYAFVHFEDRQEAI 52
           LYV NL    TE++L++ FE +G +E V+        R K + F+ F D +EA 
Sbjct: 189 LYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAK 242

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

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

 Score = 35.5 bits (82), Expect = 8e-04
 Identities = 16/59 (27%), Positives = 28/59 (47%), Gaps = 8/59 (13%)

Query: 6  VLYVRNLTQYCTEEKLKEAFEQYGRVERVK--------RIKDYAFVHFEDRQEAITVTG 56
          V+Y+ +L     E++LK+ F Q+G V+ V+          K Y F+ F + + A     
Sbjct: 1  VIYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAK 59

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

 Score = 35.2 bits (82), Expect = 8e-04
 Identities = 15/52 (28%), Positives = 26/52 (50%), Gaps = 8/52 (15%)

Query: 8  YVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
          +V NL     EE+L++ FE  G VE V+ ++D        + +V F+ +   
Sbjct: 3  FVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSV 54

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|241085 cd12641, RRM_TRA2B, RNA recognition motif in Transformer-2 protein homolog beta (TRA-2 beta) and similar proteins

 Score = 35.8 bits (82), Expect = 8e-04
 Identities = 19/53 (35%), Positives = 29/53 (54%), Gaps = 8/53 (15%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERV--------KRIKDYAFVHFEDRQEA 51
          L V  L+ Y TE  L+E F +YG +  V        +R + +AFV+FE+  +A
Sbjct: 12 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDA 64

This subgroup corresponds to the RRM of TRA2-beta or TRA-2-beta, also termed splicing factor, arginine/serine-rich 10 (SFRS10), or transformer-2 protein homolog B, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. It contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. TRA2-beta specifically binds to two types of RNA sequences, the CAA and (GAA)2 sequences, through the RRMs in different RNA binding modes. . Length = 89

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

 Score = 35.4 bits (82), Expect = 9e-04
 Identities = 20/56 (35%), Positives = 26/56 (46%), Gaps = 8/56 (14%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERV--------KRIKDYAFVHFEDRQEAITV 54
          +YV  L +  T E LK  F +YG V  V          IK +AF+ FE  +EA   
Sbjct: 2  VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKA 57

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

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

 Score = 35.7 bits (83), Expect = 0.001
 Identities = 24/89 (26%), Positives = 34/89 (38%), Gaps = 22/89 (24%)

Query: 5  KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYS 64
            L+V+NL    TEE LK+ FE+ G V  V   K                          
Sbjct: 1  TTLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKD----------------------P 38

Query: 65 SPDDNKKNRGFCFLEYDSHKSASLAKKRL 93
                 + G+ F+E+ S ++A  A KRL
Sbjct: 39 KGPGKLLSMGYGFVEFKSKEAAQKALKRL 67

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

 Score = 35.3 bits (82), Expect = 0.001
 Identities = 19/52 (36%), Positives = 29/52 (55%), Gaps = 5/52 (9%)

Query: 5  KVLYVRNLTQYCTEEKLKEAFEQYG-----RVERVKRIKDYAFVHFEDRQEA 51
          ++LYVRNL    + E+L + F +YG     R+   K  +  AFV +ED  +A
Sbjct: 3  RILYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKETRGTAFVVYEDIYDA 54

This subfamily corresponds to the RRM of SF3B14 (also termed p14), a 14 kDa protein subunit of SF3B which is a multiprotein complex that is an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA and has been involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B14 associates directly with another SF3B subunit called SF3B155. It is also present in both U2- and U12-dependent spliceosomes and may contribute to branch site positioning in both the major and minor spliceosome. Moreover, SF3B14 interacts directly with the pre-mRNA branch adenosine early in spliceosome assembly and within the fully assembled spliceosome. SF3B14 contains one well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 77

>gnl|CDD|240755 cd12309, RRM2_Spen, RNA recognition motif 2 in the Spen (split end) protein family

 Score = 35.5 bits (82), Expect = 0.001
 Identities = 23/49 (46%), Positives = 28/49 (57%), Gaps = 9/49 (18%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIK--------DYAFVHFED 47
          L+V NL    TEE+L+ AFE+YG VE V  IK         YAFV F +
Sbjct: 5  LFVGNLEITITEEELRRAFERYGVVEDVD-IKRPPRGQGNAYAFVKFLN 52

This subfamily corresponds to the RRM2 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B), and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which share a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 79

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

 Score = 35.4 bits (82), Expect = 0.001
 Identities = 18/53 (33%), Positives = 26/53 (49%), Gaps = 8/53 (15%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
          L V  L Q  T+E+L+  FE  G +E  K ++D        Y FV + D  +A
Sbjct: 3  LIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDA 55

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

 Score = 34.8 bits (80), Expect = 0.001
 Identities = 15/46 (32%), Positives = 28/46 (60%), Gaps = 1/46 (2%)

Query: 7  LYVRNLTQYCTEEK-LKEAFEQYGRVERVKRIKDYAFVHFEDRQEA 51
          L+V N     T  + L+  FE YG++  V+  +++AFV +E +++A
Sbjct: 2  LFVINFDPINTRTRDLERHFEPYGKLVNVRIRRNFAFVQYETQEDA 47

This subgroup corresponds to the RRM2 in a family that represents a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at their N-terminus, and an RS domain at their C-terminus. Length = 70

>gnl|CDD|240766 cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition motif 6 in RNA-binding protein 19 (RBM19 or RBD-1) and RNA recognition motif 5 in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 34.9 bits (81), Expect = 0.001
 Identities = 18/52 (34%), Positives = 30/52 (57%), Gaps = 7/52 (13%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVK-------RIKDYAFVHFEDRQEA 51
          L VRN+    T+++L+E F  +G+V+ V+         + +AFV F  +QEA
Sbjct: 3  LIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEA 54

This subfamily corresponds to the RRM6 of RBM19 and RRM5 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 76

>gnl|CDD|240889 cd12443, RRM_MCM3A_like, RNA recognition motif in 80 kDa MCM3-associated protein (Map80) and similar proteins

 Score = 35.1 bits (81), Expect = 0.001
 Identities = 14/50 (28%), Positives = 23/50 (46%), Gaps = 3/50 (6%)

Query: 5  KVLYVRNLTQYCTE-EKLKEAFEQYGRVERV--KRIKDYAFVHFEDRQEA 51
            +  +N+     + + L+  F ++G+V RV     K  A VHF D   A
Sbjct: 1  TTIQCKNIPDELNDKDWLERHFGKFGKVARVYCNPRKKSAVVHFFDHASA 50

This subfamily corresponds to the RRM of Map80, also termed germinal center-associated nuclear protein (GANP), involved in the nuclear localization pathway of MCM3, a protein necessary for the initiation of DNA replication and also involves in controls that ensure DNA replication is initiated once per cell cycle. Map80 contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 73

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

 Score = 35.0 bits (81), Expect = 0.001
 Identities = 13/48 (27%), Positives = 24/48 (50%), Gaps = 8/48 (16%)

Query: 8  YVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFED 47
          +V N+    T E+L+E F+  G + R+  + D        +A++ F D
Sbjct: 3  FVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLD 50

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

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

 Score = 34.9 bits (80), Expect = 0.001
 Identities = 22/54 (40%), Positives = 31/54 (57%), Gaps = 6/54 (11%)

Query: 5  KVLYVRNLTQYCTEEKLKEAFEQYGRV---ERVKRIKDYAFVHF---EDRQEAI 52
          KVL V NL+   +E+ L+E FE+   +   +   R K YAFV F   ED +EA+
Sbjct: 2  KVLVVNNLSYSASEDSLQEVFEKATSIRIPQNNGRPKGYAFVEFESAEDAKEAL 55

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

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

 Score = 34.9 bits (81), Expect = 0.002
 Identities = 12/54 (22%), Positives = 28/54 (51%), Gaps = 8/54 (14%)

Query: 6  VLYVRNLTQYCTEEKLKEAFEQYGRVE--------RVKRIKDYAFVHFEDRQEA 51
          +++V  + +   EE + + F ++G ++        R   +K YA + +E ++EA
Sbjct: 8  IIFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEA 61

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

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

 Score = 34.6 bits (80), Expect = 0.002
 Identities = 16/48 (33%), Positives = 23/48 (47%), Gaps = 4/48 (8%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRI---KDYAFVHFEDRQEA 51
          ++V  L    TE++L+  F  +G +  VK I   K   FV F  R  A
Sbjct: 4  VFVGGLDPAVTEDELRSLFGPFGEIVYVK-IPPGKGCGFVQFVHRAAA 50

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

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

 Score = 34.9 bits (81), Expect = 0.002
 Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 8/49 (16%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFED 47
          ++V +L    T+E L  AF +Y   ++ K ++D        Y FV F D
Sbjct: 9  IFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSD 57

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

 Score = 34.6 bits (80), Expect = 0.002
 Identities = 19/53 (35%), Positives = 28/53 (52%), Gaps = 8/53 (15%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
          +YV NL    T   L + F +YG+V +V  +KD         AF+ F DR++A
Sbjct: 4  VYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDA 56

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

 Score = 34.6 bits (80), Expect = 0.002
 Identities = 20/83 (24%), Positives = 33/83 (39%), Gaps = 27/83 (32%)

Query: 3  KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVII 62
          + K ++V  L    TE  L++ F Q+G V  V                         V++
Sbjct: 1  RTKKIFVGGLPPNVTETDLRKYFSQFGTVTEV-------------------------VVM 35

Query: 63 YSSPDDNKKNRGFCFLEYDSHKS 85
          Y    + K+ RGF F+ ++S  S
Sbjct: 36 YDH--EKKRPRGFGFITFESEDS 56

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

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

 Score = 34.5 bits (80), Expect = 0.002
 Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 8/53 (15%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDY--------AFVHFEDRQEA 51
          LYV  L +   E+ L  AF  +G ++ ++   DY        AFV FE+ ++A
Sbjct: 1  LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDA 53

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

 Score = 34.3 bits (79), Expect = 0.002
 Identities = 16/51 (31%), Positives = 29/51 (56%), Gaps = 7/51 (13%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD------YAFVHFEDRQEA 51
          +YV NL     E  +++ F +YG ++ +  +K+      +AFV FED ++A
Sbjct: 2  IYVGNLPGDIRERDIEDLFYKYGPIKAID-LKNRRRGPPFAFVEFEDPRDA 51

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

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

 Score = 34.3 bits (79), Expect = 0.002
 Identities = 19/53 (35%), Positives = 31/53 (58%), Gaps = 8/53 (15%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVK--------RIKDYAFVHFEDRQEA 51
          L+V NL+   TE++L+  F + GR+ RV+        + K +AFV FE+ + A
Sbjct: 1  LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFA 53

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

 Score = 34.6 bits (79), Expect = 0.002
 Identities = 27/109 (24%), Positives = 46/109 (42%), Gaps = 32/109 (29%)

Query: 5   KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYS 64
           K L+V+ L++  TEE LKE+F+       V            DR                
Sbjct: 1   KTLFVKGLSEDTTEETLKESFDGSIAARIVT-----------DR---------------- 33

Query: 65  SPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQ 113
              D   ++GF F+++ S + A  AK+ +  G +   G  + +D+A P+
Sbjct: 34  ---DTGSSKGFGFVDFSSEEDAKAAKEAMEDGEID--GNKVTLDFAKPK 77

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|240822 cd12376, RRM2_Hu_like, RNA recognition motif 2 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 34.5 bits (79), Expect = 0.002
 Identities = 19/64 (29%), Positives = 33/64 (51%), Gaps = 9/64 (14%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAI-TVTGL 57
          LYV  L +  T+++L++ F QYGR+   + ++D          F+ F+ R EA   + GL
Sbjct: 3  LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKGL 62

Query: 58 SQVI 61
          +   
Sbjct: 63 NGQK 66

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

 Score = 34.6 bits (80), Expect = 0.003
 Identities = 13/56 (23%), Positives = 24/56 (42%), Gaps = 7/56 (12%)

Query: 5  KVLYVRNLTQYCTEEKLKEAFEQYGRVE------RVKRIKDYAFVHFEDRQEAITV 54
          +V+YV  +    T  +L++ F+ +G +E      R      Y FV +    +A   
Sbjct: 3  RVIYVGKIPIDTTRSELRQRFQPFGEIEEITLHFRDDGDN-YGFVTYRYACDAFRA 57

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

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

 Score = 33.8 bits (78), Expect = 0.003
 Identities = 13/45 (28%), Positives = 23/45 (51%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEA 51
          +Y+  L     E  ++  F+ YGR+  +     + FV FED ++A
Sbjct: 2  VYIGRLPYRARERDVERFFKGYGRIREINLKNGFGFVEFEDPRDA 46

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

>gnl|CDD|241066 cd12622, RRM3_PUB1, RNA recognition motif 3 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 34.0 bits (78), Expect = 0.003
 Identities = 18/82 (21%), Positives = 30/82 (36%), Gaps = 33/82 (40%)

Query: 8  YVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPD 67
          YV N+  Y T+  L   F+ +G                E R +                 
Sbjct: 4  YVGNIPPYTTQADLIPLFQNFGY-------------ILEFRHQP---------------- 34

Query: 68 DNKKNRGFCFLEYDSHKSASLA 89
              +RGF F++ D+H+ A++A
Sbjct: 35 ----DRGFAFVKLDTHEQAAMA 52

This subfamily corresponds to the RRM3 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. 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 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 = 74

>gnl|CDD|241059 cd12615, RRM1_TIA1, RNA recognition motif 1 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 34.2 bits (78), Expect = 0.003
 Identities = 27/104 (25%), Positives = 43/104 (41%), Gaps = 31/104 (29%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
           LYV NL++  TE  + + F Q G  +  K I D A                         
Sbjct: 2   LYVGNLSRDVTEALILQLFSQIGPCKSCKMIMDTA------------------------- 36

Query: 67  DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWA 110
                N  +CF+E+  H+ A+ +   +  GR K+ G ++ V+WA
Sbjct: 37  ----GNDPYCFVEFFEHRHAAASLAAM-NGR-KIMGKEVKVNWA 74

This subgroup corresponds to the RRM1 of 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 functions 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 = 74

>gnl|CDD|241087 cd12643, RRM_CFIm68, RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6) and similar proteins

 Score = 33.9 bits (78), Expect = 0.004
 Identities = 22/89 (24%), Positives = 35/89 (39%), Gaps = 25/89 (28%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
          LYV NLT + T++ L EA +  G    V  + +  F  FE+R                  
Sbjct: 2  LYVGNLTWWTTDQDLTEAIQSIG----VNDLLEIKF--FENRA----------------- 38

Query: 67 DDNKKNRGFCFLEYDSHKSASLAKKRLAT 95
            N +++GF  +   S  S+     +L  
Sbjct: 39 --NGQSKGFALIVLGSESSSRKLMDKLPK 65

This subgroup corresponds to the RRM of CFIm68. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the regulation of alternative poly(A) site selection, mRNA export, and mRNA splicing. It is a complex composed of a small 25 kDa (CFIm25) subunit and a larger 59/68/72 kDa subunit. Two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. The family includes CFIm68, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF6), or cleavage and polyadenylation specificity factor 68 kDa subunit (CPSF68), or protein HPBRII-4/7. CFIm68 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a central proline-rich region, and a C-terminal RS-like domain. The N-terminal RRM of CFIm68 mediates the interaction with CFIm25. It also serves to enhance RNA binding and facilitate RNA looping. . Length = 77

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

 Score = 33.9 bits (78), Expect = 0.004
 Identities = 16/53 (30%), Positives = 27/53 (50%), Gaps = 8/53 (15%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVK--------RIKDYAFVHFEDRQEA 51
          L+V NL+    +E LK  FE++G V   +        R + + +V FE  ++A
Sbjct: 2  LFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDA 54

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

 Score = 34.1 bits (78), Expect = 0.004
 Identities = 17/53 (32%), Positives = 23/53 (43%), Gaps = 8/53 (15%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
          L+VRNL    TEE L   F ++G V     + D          FV F+D+   
Sbjct: 4  LFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTY 56

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|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 = 33.8 bits (78), Expect = 0.004
 Identities = 17/53 (32%), Positives = 24/53 (45%), Gaps = 8/53 (15%)

Query: 8  YVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAI 52
          +V N+    TEE+L E F + G V   + + D        Y F  FED + A 
Sbjct: 2  FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAA 54

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	131
KOG0117|consensus	506		99.94
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.87
KOG0144|consensus	510		99.86
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.86
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.85
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.84
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.83
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.8
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.78
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.77
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.77
KOG0109|consensus	346		99.77
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.77
KOG0131|consensus	203		99.74
KOG0122|consensus	270		99.73
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.73
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.72
KOG0145|consensus	360		99.72
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.72
PLN03120	260	nucleic acid binding protein; Provisional	99.72
KOG0127|consensus	678		99.71
KOG0149|consensus	247		99.68
KOG0121|consensus	153		99.68
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.68
KOG0117|consensus	506		99.67
KOG0148|consensus	321		99.67
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.63
KOG0107|consensus	195		99.63
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.61
KOG0145|consensus	360		99.61
KOG0148|consensus	321		99.61
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.61
PLN03213	759	repressor of silencing 3; Provisional	99.6
KOG0113|consensus	335		99.59
KOG4207|consensus	256		99.59
smart00362	72	RRM_2 RNA recognition motif.	99.58
KOG0125|consensus	376		99.57
KOG0146|consensus	371		99.57
PLN03121	243	nucleic acid binding protein; Provisional	99.56
KOG0111|consensus	298		99.53
KOG0126|consensus	219		99.53
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.52
KOG0105|consensus	241		99.52
KOG0124|consensus	544		99.51
KOG0108|consensus	435		99.51
smart00360	71	RRM RNA recognition motif.	99.5
KOG0127|consensus	678		99.5
KOG0130|consensus	170		99.5
KOG0114|consensus	124		99.5
KOG0144|consensus	510		99.49
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.49
KOG0110|consensus	725		99.48
KOG0123|consensus	369		99.45
KOG4206|consensus	221		99.44
KOG0123|consensus	369		99.42
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.42
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.41
KOG4205|consensus	311		99.41
KOG0132|consensus	894		99.32
KOG0153|consensus	377		99.3
smart00361	70	RRM_1 RNA recognition motif.	99.28
KOG0146|consensus	371		99.21
KOG4661|consensus	940		99.16
KOG0415|consensus	479		99.14
KOG0106|consensus	216		99.14
KOG0147|consensus	549		99.13
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.11
KOG4208|consensus	214		99.08
KOG0147|consensus	549		99.06
KOG0110|consensus	725		99.03
KOG4212|consensus	608		99.01
KOG4212|consensus	608		98.93
KOG1190|consensus	492		98.92
KOG0151|consensus	877		98.89
KOG1456|consensus	494		98.89
KOG1548|consensus	382		98.88
KOG0116|consensus	419		98.88
KOG1457|consensus	284		98.81
KOG0533|consensus	243		98.76
KOG0124|consensus	544		98.75
KOG4211|consensus	510		98.73
KOG0109|consensus	346		98.73
KOG4660|consensus	549		98.73
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.66
KOG4209|consensus	231		98.64
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.6
KOG0120|consensus	500		98.52
KOG0226|consensus	290		98.51
KOG1190|consensus	492		98.5
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.43
KOG4454|consensus	267		98.41
KOG4205|consensus	311		98.29
KOG0129|consensus	520		98.24
KOG1457|consensus	284		98.19
KOG4206|consensus	221		98.12
KOG4210|consensus	285		97.93
KOG0112|consensus	975		97.88
KOG1995|consensus	351		97.8
KOG0120|consensus	500		97.79
KOG3152|consensus	278		97.77
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.74
KOG1365|consensus	508		97.7
KOG0128|consensus	881		97.69
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.69
KOG2193|consensus	584		97.64
KOG4211|consensus	510		97.63
KOG0131|consensus	203		97.55
KOG1548|consensus	382		97.53
KOG1855|consensus	484		97.45
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.4
KOG2314|consensus	698		97.31
KOG4849|consensus	498		97.25
KOG4307|consensus	944		97.16
KOG1456|consensus	494		97.01
KOG1996|consensus	378		96.74
KOG4676|consensus	479		96.72
KOG2416|consensus	718		96.59
KOG2202|consensus	260		96.37
KOG0106|consensus	216		96.35
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	96.2
KOG0115|consensus	275		96.18
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	96.14
KOG4574|consensus	1007		95.97
KOG0129|consensus	520		95.74
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	95.54
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	95.45
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	94.73
KOG0105|consensus	241		94.66
KOG4307|consensus	944		94.6
KOG2068|consensus	327		94.2
KOG2591|consensus	684		94.01
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	93.8
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	93.44
KOG0112|consensus	975		93.17
KOG4660|consensus	549		93.02
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	92.77
KOG0128|consensus	881		92.64
KOG1365|consensus	508		92.24
KOG2253|consensus	668		91.44
KOG0804|consensus	493		91.24
smart00361	70	RRM_1 RNA recognition motif.	90.81
KOG0125|consensus	376		90.73
KOG2135|consensus	526		90.65
KOG4285|consensus	350		89.25
KOG4410|consensus	396		88.47
KOG4210|consensus	285		87.41
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	87.21
KOG0149|consensus	247		87.03
KOG0122|consensus	270		86.35
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	86.19
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	85.24
KOG0107|consensus	195		85.24
KOG4208|consensus	214		85.11

>KOG0117|consensus

Probab=99.94  E-value=5.4e-26  Score=171.08  Aligned_cols=125  Identities=43%  Similarity=0.851  Sum_probs=118.7

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe--------cCeEEEEECCHHHHHh---------------------
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYAFVHFEDRQEAIT---------------------   53 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~--------~~~~fv~~~~~~~a~~---------------------   53 (131)
                      .-|.||||.||.++.|++|..||++.|+|.++++|        ||||||+|++.+.|+.                     
T Consensus        82 ~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~S  161 (506)
T KOG0117|consen   82 RGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCVS  161 (506)
T ss_pred             CCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEEe
Confidence            35789999999999999999999999999999998        8999999999999988                     


Q ss_pred             ---------------------------hcCCceeEEecCCCCCCCCcceEEEEeCCHHhHHHHHHHHhCCcceecCcEEE
Q psy1185          54 ---------------------------VTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDII  106 (131)
Q Consensus        54 ---------------------------~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~~~~~g~~l~  106 (131)
                                                 ..|+..++++..+....++||||||+|.+|..|..|.+.|-...+.++|..+.
T Consensus       162 van~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g~~klwgn~~t  241 (506)
T KOG0117|consen  162 VANCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMPGKIKLWGNAIT  241 (506)
T ss_pred             eecceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhccCCceeecCCcce
Confidence                                       46899999999999999999999999999999999999998878999999999


Q ss_pred             EEecCCCCCCChHHHHhHhhh
Q psy1185         107 VDWADPQEEPDTETMSKVLML  127 (131)
Q Consensus       107 v~~a~~~~~~~~~~~~~~~~~  127 (131)
                      |+||.|+.+++.+.|+++|.|
T Consensus       242 VdWAep~~e~ded~ms~VKvL  262 (506)
T KOG0117|consen  242 VDWAEPEEEPDEDTMSKVKVL  262 (506)
T ss_pred             eeccCcccCCChhhhhheeee
Confidence            999999999999999999976

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

Probab=99.87  E-value=2.2e-21  Score=153.59  Aligned_cols=121  Identities=40%  Similarity=0.776  Sum_probs=100.7

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe-------cCeEEEEECCHHHHHhhc---------------------
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI-------KDYAFVHFEDRQEAITVT---------------------   55 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~-------~~~~fv~~~~~~~a~~~~---------------------   55 (131)
                      .++|||+|||+++++++|+++|++||.|.+++++       +|||||+|.+.++|+.+.                     
T Consensus        58 ~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~S~~  137 (578)
T TIGR01648        58 GCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCISVD  137 (578)
T ss_pred             CCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEECCCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCcccccccccc
Confidence            5799999999999999999999999999999986       799999999999999810                     


Q ss_pred             ---------------------------CCceeEEecCCCCCCCCcceEEEEeCCHHhHHHHHHHHhCCcceecCcEEEEE
Q psy1185          56 ---------------------------GLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVD  108 (131)
Q Consensus        56 ---------------------------g~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~~~~~g~~l~v~  108 (131)
                                                 ++..++++..+...+++++||||+|.++++|.+|++.|+...+.++|+.|.|+
T Consensus       138 ~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~gki~l~Gr~I~Vd  217 (578)
T TIGR01648       138 NCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAVD  217 (578)
T ss_pred             CceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhccceEecCceEEEE
Confidence                                       22233333334445678999999999999999999999876678999999999


Q ss_pred             ecCCCCCCChHHHHhH
Q psy1185         109 WADPQEEPDTETMSKV  124 (131)
Q Consensus       109 ~a~~~~~~~~~~~~~~  124 (131)
                      |+.+..+.+++.++..
T Consensus       218 wA~p~~~~d~~~~~~~  233 (578)
T TIGR01648       218 WAEPEEEVDEDVMAKV  233 (578)
T ss_pred             eecccccccccccccc
Confidence            9998877766655543

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.

>KOG0144|consensus

Probab=99.86  E-value=2.3e-21  Score=145.86  Aligned_cols=116  Identities=29%  Similarity=0.534  Sum_probs=101.8

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe--------cCeEEEEECCHHHHHh----------------------
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYAFVHFEDRQEAIT----------------------   53 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~--------~~~~fv~~~~~~~a~~----------------------   53 (131)
                      .-++|||.+|+.++|.+|+++|++||.|.+|.++        +|||||.|...++|.+                      
T Consensus        34 ~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqvk~  113 (510)
T KOG0144|consen   34 AVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQVKY  113 (510)
T ss_pred             hhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceeecc
Confidence            3479999999999999999999999999999988        7999999999999988                      


Q ss_pred             ---------------------------------hcC-CceeEEecCCCCCCCCcceEEEEeCCHHhHHHHHHHHhCCcce
Q psy1185          54 ---------------------------------VTG-LSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLK   99 (131)
Q Consensus        54 ---------------------------------~~g-~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~~~   99 (131)
                                                       .+| |+.+.+..++  .+.+||||||.|.+++-|..|++.|||. .+
T Consensus       114 Ad~E~er~~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~--~~~sRGcaFV~fstke~A~~Aika~ng~-~t  190 (510)
T KOG0144|consen  114 ADGERERIVEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDP--DGLSRGCAFVKFSTKEMAVAAIKALNGT-QT  190 (510)
T ss_pred             cchhhhccccchhhhhhhccccccHHHHHHHHHhhCccchhhheecc--cccccceeEEEEehHHHHHHHHHhhccc-ee
Confidence                                             356 5555555555  5889999999999999999999999996 48


Q ss_pred             ecCcE--EEEEecCCCCCCChHHHH
Q psy1185         100 VWGCD--IIVDWADPQEEPDTETMS  122 (131)
Q Consensus       100 ~~g~~--l~v~~a~~~~~~~~~~~~  122 (131)
                      +.||.  |.|+||+++++++.+.++
T Consensus       191 meGcs~PLVVkFADtqkdk~~~~lq  215 (510)
T KOG0144|consen  191 MEGCSQPLVVKFADTQKDKDGKRLQ  215 (510)
T ss_pred             eccCCCceEEEecccCCCchHHHHH
Confidence            88986  999999999988876653

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.86  E-value=1.4e-20  Score=141.99  Aligned_cols=113  Identities=21%  Similarity=0.259  Sum_probs=91.9

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe--------cCeEEEEECCHHHHHh---------------------
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYAFVHFEDRQEAIT---------------------   53 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~--------~~~~fv~~~~~~~a~~---------------------   53 (131)
                      ..++|||+|||+++++++|+++|++||+|.+|+++        ++||||+|.++++|+.                     
T Consensus       106 ~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~~a~  185 (346)
T TIGR01659       106 SGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYAR  185 (346)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeeeccc
Confidence            46799999999999999999999999999999987        4899999999999988                     


Q ss_pred             ------------------------------hcC-CceeEEecCCCCCCCCcceEEEEeCCHHhHHHHHHHHhCCcceecC
Q psy1185          54 ------------------------------VTG-LSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWG  102 (131)
Q Consensus        54 ------------------------------~~g-~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~~~~~g  102 (131)
                                                    .+| +..+.+..+ ..+++++++|||+|.++++|++|++.|++..+...+
T Consensus       186 p~~~~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d-~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~  264 (346)
T TIGR01659       186 PGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRD-KLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGS  264 (346)
T ss_pred             ccccccccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeec-CCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCc
Confidence                                          223 222333322 237888999999999999999999999998333344


Q ss_pred             cEEEEEecCCCCCC
Q psy1185         103 CDIIVDWADPQEEP  116 (131)
Q Consensus       103 ~~l~v~~a~~~~~~  116 (131)
                      +.|+|.||+.+...
T Consensus       265 ~~l~V~~a~~~~~~  278 (346)
T TIGR01659       265 QPLTVRLAEEHGKA  278 (346)
T ss_pred             eeEEEEECCccccc
Confidence            78999999876543

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

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

Probab=99.85  E-value=2.9e-20  Score=147.69  Aligned_cols=111  Identities=21%  Similarity=0.372  Sum_probs=93.4

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe--------cCeEEEEECCHHHHHhh--------------------
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYAFVHFEDRQEAITV--------------------   54 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~--------~~~~fv~~~~~~~a~~~--------------------   54 (131)
                      ..++|||||||+++++++|+++|++||+|.+++++        +|||||+|.+.++|+.+                    
T Consensus       106 ~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp~  185 (612)
T TIGR01645       106 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS  185 (612)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeecccc
Confidence            46899999999999999999999999999999986        89999999999999981                    


Q ss_pred             ------------------------------------------cC-CceeEEecCCCCCCCCcceEEEEeCCHHhHHHHHH
Q psy1185          55 ------------------------------------------TG-LSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKK   91 (131)
Q Consensus        55 ------------------------------------------~g-~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~   91 (131)
                                                                +| +..+.+..++ .++.++|||||+|.+.++|.+|+.
T Consensus       186 ~~p~a~~~~~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~-~tgksKGfGFVeFe~~e~A~kAI~  264 (612)
T TIGR01645       186 NMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAP-TGRGHKGYGFIEYNNLQSQSEAIA  264 (612)
T ss_pred             cccccccccccccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecC-CCCCcCCeEEEEECCHHHHHHHHH
Confidence                                                      22 1222222222 356789999999999999999999


Q ss_pred             HHhCCcceecCcEEEEEecCCCCCC
Q psy1185          92 RLATGRLKVWGCDIIVDWADPQEEP  116 (131)
Q Consensus        92 ~l~~~~~~~~g~~l~v~~a~~~~~~  116 (131)
                      .+|+.  .++|+.|+|.++.++++.
T Consensus       265 amNg~--elgGr~LrV~kAi~pP~~  287 (612)
T TIGR01645       265 SMNLF--DLGGQYLRVGKCVTPPDA  287 (612)
T ss_pred             HhCCC--eeCCeEEEEEecCCCccc
Confidence            99997  899999999999875543

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=99.84  E-value=7.6e-20  Score=137.78  Aligned_cols=110  Identities=25%  Similarity=0.367  Sum_probs=89.2

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe--------cCeEEEEECCHHHHHhh--------------------
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYAFVHFEDRQEAITV--------------------   54 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~--------~~~~fv~~~~~~~a~~~--------------------   54 (131)
                      ..++|||+|||.++++++|+++|++||+|.+++++        +|||||+|.+.++|+.+                    
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            46799999999999999999999999999999997        48999999999999981                    


Q ss_pred             -------------------------------cC-CceeEEecCCCCCCCCcceEEEEeCCHHhHHHHHHHHhCCcceecC
Q psy1185          55 -------------------------------TG-LSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWG  102 (131)
Q Consensus        55 -------------------------------~g-~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~~~~~g  102 (131)
                                                     +| +..+.+..+ ..++.++|||||+|.+.++|..|++.|+|.  .+.|
T Consensus        82 ~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~-~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~--~~~g  158 (352)
T TIGR01661        82 PSSDSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSD-NVTGLSKGVGFIRFDKRDEADRAIKTLNGT--TPSG  158 (352)
T ss_pred             ccccccccceEEECCccccCCHHHHHHHHhccCCEEEEEEEec-CCCCCcCcEEEEEECCHHHHHHHHHHhCCC--ccCC
Confidence                                           11 111111111 135678999999999999999999999998  5555


Q ss_pred             --cEEEEEecCCCCC
Q psy1185         103 --CDIIVDWADPQEE  115 (131)
Q Consensus       103 --~~l~v~~a~~~~~  115 (131)
                        ..|.|.|+..+..
T Consensus       159 ~~~~i~v~~a~~~~~  173 (352)
T TIGR01661       159 CTEPITVKFANNPSS  173 (352)
T ss_pred             CceeEEEEECCCCCc
Confidence              5689999986653

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

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

Probab=99.83  E-value=1.1e-19  Score=122.00  Aligned_cols=84  Identities=24%  Similarity=0.416  Sum_probs=76.6

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||+++++++|+++|++||.|.++.++..                           ..++.+++||||+|.+
T Consensus        33 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d---------------------------~~tg~~kGfaFV~F~~   85 (144)
T PLN03134         33 MSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVD---------------------------RETGRSRGFGFVNFND   85 (144)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEec---------------------------CCCCCcceEEEEEECC
Confidence            3678999999999999999999999999999998854                           3478899999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEE  115 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~  115 (131)
                      .++|+.|++.|++.  .++|+.|+|+|+.++..
T Consensus        86 ~e~A~~Al~~lng~--~i~Gr~l~V~~a~~~~~  116 (144)
T PLN03134         86 EGAATAAISEMDGK--ELNGRHIRVNPANDRPS  116 (144)
T ss_pred             HHHHHHHHHHcCCC--EECCEEEEEEeCCcCCC
Confidence            99999999999998  89999999999987654

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

Probab=99.80  E-value=1.9e-18  Score=134.32  Aligned_cols=107  Identities=26%  Similarity=0.433  Sum_probs=89.7

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe--------cCeEEEEECCHHHHHhh---------------------
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYAFVHFEDRQEAITV---------------------   54 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~--------~~~~fv~~~~~~~a~~~---------------------   54 (131)
                      .++|||+|||..+++++|+++|++||.|..+.++        +|||||+|.+.++|..+                     
T Consensus        89 ~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~l~g~~~~g~~i~v~~~~~~  168 (457)
T TIGR01622        89 DRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALALTGQMLLGRPIIVQSSQAE  168 (457)
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHHhCCCEECCeeeEEeecchh
Confidence            5789999999999999999999999999999987        68999999999999772                     


Q ss_pred             -----------------------------------------cC-CceeEEecCCCCCCCCcceEEEEeCCHHhHHHHHHH
Q psy1185          55 -----------------------------------------TG-LSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKR   92 (131)
Q Consensus        55 -----------------------------------------~g-~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~   92 (131)
                                                               +| +..+.+..+. .+|.++|||||+|.+.++|.+|+..
T Consensus       169 ~~~~~~~~~~~~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~-~~g~~~g~afV~f~~~e~A~~A~~~  247 (457)
T TIGR01622       169 KNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDP-ETGRSKGFGFIQFHDAEEAKEALEV  247 (457)
T ss_pred             hhhhhhcccccCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcC-CCCccceEEEEEECCHHHHHHHHHh
Confidence                                                     22 1122222222 3567899999999999999999999


Q ss_pred             HhCCcceecCcEEEEEecCCC
Q psy1185          93 LATGRLKVWGCDIIVDWADPQ  113 (131)
Q Consensus        93 l~~~~~~~~g~~l~v~~a~~~  113 (131)
                      |+|.  .+.|+.|.|.|+...
T Consensus       248 l~g~--~i~g~~i~v~~a~~~  266 (457)
T TIGR01622       248 MNGF--ELAGRPIKVGYAQDS  266 (457)
T ss_pred             cCCc--EECCEEEEEEEccCC
Confidence            9997  899999999998743

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.

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.78  E-value=2.5e-18  Score=129.54  Aligned_cols=82  Identities=22%  Similarity=0.301  Sum_probs=75.8

Q ss_pred             eEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHH
Q psy1185           5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHK   84 (131)
Q Consensus         5 ~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~   84 (131)
                      .+|||+|||+++++++|+++|++||.|.++++++.                           ..++.++|||||.|.+.+
T Consensus       270 ~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d---------------------------~~t~~skG~aFV~F~~~~  322 (352)
T TIGR01661       270 YCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRD---------------------------LTTNQCKGYGFVSMTNYD  322 (352)
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEc---------------------------CCCCCccceEEEEECCHH
Confidence            36999999999999999999999999999999854                           347889999999999999


Q ss_pred             hHHHHHHHHhCCcceecCcEEEEEecCCCCC
Q psy1185          85 SASLAKKRLATGRLKVWGCDIIVDWADPQEE  115 (131)
Q Consensus        85 ~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~  115 (131)
                      +|.+|+..|||.  .++|+.|+|.|+.++..
T Consensus       323 ~A~~Ai~~lnG~--~~~gr~i~V~~~~~~~~  351 (352)
T TIGR01661       323 EAAMAILSLNGY--TLGNRVLQVSFKTNKAY  351 (352)
T ss_pred             HHHHHHHHhCCC--EECCeEEEEEEccCCCC
Confidence            999999999998  89999999999988764

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

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

Probab=99.77  E-value=8.3e-18  Score=133.96  Aligned_cols=107  Identities=26%  Similarity=0.423  Sum_probs=89.5

Q ss_pred             EEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe--------cCeEEEEECCHHHHHhh-----------------------
Q psy1185           6 VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYAFVHFEDRQEAITV-----------------------   54 (131)
Q Consensus         6 ~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~--------~~~~fv~~~~~~~a~~~-----------------------   54 (131)
                      +|||||||.++|+++|+++|++||+|.+++++        +|||||+|.+.++|+++                       
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            79999999999999999999999999999997        48999999999999991                       


Q ss_pred             ------------------------------cC-CceeEEecCCCCCCCCcceEEEEeCCHHhHHHHHHHHhCCcceecCc
Q psy1185          55 ------------------------------TG-LSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGC  103 (131)
Q Consensus        55 ------------------------------~g-~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~~~~~g~  103 (131)
                                                    +| +..+.+..  ...|+++|||||+|.+.++|.+|+..++|.  .+.|+
T Consensus        82 ~~~~~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~--~~~g~skg~afV~F~~~e~A~~Ai~~lng~--~~~~~  157 (562)
T TIGR01628        82 SLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVAT--DENGKSRGYGFVHFEKEESAKAAIQKVNGM--LLNDK  157 (562)
T ss_pred             cccccCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeee--cCCCCcccEEEEEECCHHHHHHHHHHhccc--EecCc
Confidence                                          12 22222222  235778999999999999999999999998  88999


Q ss_pred             EEEEEecCCCCCC
Q psy1185         104 DIIVDWADPQEEP  116 (131)
Q Consensus       104 ~l~v~~a~~~~~~  116 (131)
                      .|.|.....+.++
T Consensus       158 ~i~v~~~~~~~~~  170 (562)
T TIGR01628       158 EVYVGRFIKKHER  170 (562)
T ss_pred             eEEEecccccccc
Confidence            9999877655544

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

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

Probab=99.77  E-value=9.1e-18  Score=131.74  Aligned_cols=111  Identities=30%  Similarity=0.353  Sum_probs=85.0

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe--cCeEEEEECCHHHHHhhc------C--CceeEE-----------
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--KDYAFVHFEDRQEAITVT------G--LSQVII-----------   62 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~--~~~~fv~~~~~~~a~~~~------g--~~~~~~-----------   62 (131)
                      +++|||+|||+++++++|+++|++||.|.++.++  ++||||+|.+.++|+.+.      +  +.++.+           
T Consensus         2 s~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~~k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~s~~~~~~   81 (481)
T TIGR01649         2 SPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPGKRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYSTSQEIK   81 (481)
T ss_pred             ccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEECCCCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEecCCcccc
Confidence            5799999999999999999999999999999988  689999999999998821      0  111111           


Q ss_pred             ------------------ecC-CC-----------------------CCCCCcceEEEEeCCHHhHHHHHHHHhCCccee
Q psy1185          63 ------------------YSS-PD-----------------------DNKKNRGFCFLEYDSHKSASLAKKRLATGRLKV  100 (131)
Q Consensus        63 ------------------~~~-~~-----------------------~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~~~~  100 (131)
                                        ++. +.                       .....+++|||+|.+.++|.+|+..|||..+.-
T Consensus        82 ~~~~~~~~~~~~~~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~~~~~afVef~~~~~A~~A~~~Lng~~i~~  161 (481)
T TIGR01649        82 RDGNSDFDSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKNNVFQALVEFESVNSAQHAKAALNGADIYN  161 (481)
T ss_pred             cCCCCcccCCCCCceEEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecCCceEEEEEECCHHHHHHHHHHhcCCcccC
Confidence                              100 00                       011124689999999999999999999994322


Q ss_pred             cCcEEEEEecCCCC
Q psy1185         101 WGCDIIVDWADPQE  114 (131)
Q Consensus       101 ~g~~l~v~~a~~~~  114 (131)
                      +++.|+|.|+++..
T Consensus       162 ~~~~l~v~~sk~~~  175 (481)
T TIGR01649       162 GCCTLKIEYAKPTR  175 (481)
T ss_pred             CceEEEEEEecCCC
Confidence            34689999998643

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).

>KOG0109|consensus

Probab=99.77  E-value=8.7e-19  Score=126.57  Aligned_cols=113  Identities=27%  Similarity=0.424  Sum_probs=91.2

Q ss_pred             eEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcC------CceeEEecCCC-----------
Q psy1185           5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTG------LSQVIIYSSPD-----------   67 (131)
Q Consensus         5 ~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g------~~~~~~~~~~~-----------   67 (131)
                      .++||||||..+++.+|+.||++||.|.+|.|+++||||+.++...|+.+..      +++..+-+...           
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKNYgFVHiEdktaaedairNLhgYtLhg~nInVeaSksKsk~stkl~   82 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVKNYGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSKSKASTKLH   82 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeecccceEEeecccccHHHHhhcccceecceEEEEEeccccCCCccccc
Confidence            4799999999999999999999999999999999999999999988877211      22222111000           


Q ss_pred             ------------------------CCCCCcceEEEEeCCHHhHHHHHHHHhCCcceecCcEEEEEecCCCCCCChH
Q psy1185          68 ------------------------DNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPDTE  119 (131)
Q Consensus        68 ------------------------~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~~~  119 (131)
                                              ....-++|+||+|.-.++|..|++.|++.  .+.|++++|+.+.++..+.+.
T Consensus        83 vgNis~tctn~ElRa~fe~ygpviecdivkdy~fvh~d~~eda~~air~l~~~--~~~gk~m~vq~stsrlrtapg  156 (346)
T KOG0109|consen   83 VGNISPTCTNQELRAKFEKYGPVIECDIVKDYAFVHFDRAEDAVEAIRGLDNT--EFQGKRMHVQLSTSRLRTAPG  156 (346)
T ss_pred             cCCCCccccCHHHhhhhcccCCceeeeeecceeEEEEeeccchHHHHhccccc--ccccceeeeeeeccccccCCC
Confidence                                    12235899999999999999999999998  899999999998877655443

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

Probab=99.77  E-value=1.3e-17  Score=132.75  Aligned_cols=109  Identities=26%  Similarity=0.489  Sum_probs=91.9

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe-------cCeEEEEECCHHHHHhhc---------------------
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI-------KDYAFVHFEDRQEAITVT---------------------   55 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~-------~~~~fv~~~~~~~a~~~~---------------------   55 (131)
                      .++|||+|||.++++++|+++|++||.|.++.++       +|||||+|.+.++|..+.                     
T Consensus       178 ~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~~~~~g~~~G~afV~F~~~e~A~~Av~~l~g~~i~~~~~g~~l~v~~  257 (562)
T TIGR01628       178 FTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGR  257 (562)
T ss_pred             CCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCcEecccccceeeEeec
Confidence            4679999999999999999999999999999887       679999999999998721                     


Q ss_pred             ----------------------------------------------------C-CceeEEecCCCCCCCCcceEEEEeCC
Q psy1185          56 ----------------------------------------------------G-LSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus        56 ----------------------------------------------------g-~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                                                                          | +..+.+..+  .+|.++|||||+|.+
T Consensus       258 a~~k~er~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d--~~g~~~g~gfV~f~~  335 (562)
T TIGR01628       258 AQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLD--EKGVSRGFGFVCFSN  335 (562)
T ss_pred             ccChhhhHHHHHhhHHhhhhhhhcccCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEEC--CCCCcCCeEEEEeCC
Confidence                                                                1 111222222  467889999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEEP  116 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~  116 (131)
                      .++|.+|+..+||.  .++|+.|.|.||..+.++
T Consensus       336 ~~~A~~A~~~~~g~--~~~gk~l~V~~a~~k~~~  367 (562)
T TIGR01628       336 PEEANRAVTEMHGR--MLGGKPLYVALAQRKEQR  367 (562)
T ss_pred             HHHHHHHHHHhcCC--eeCCceeEEEeccCcHHH
Confidence            99999999999998  899999999999876644

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

>KOG0131|consensus

Probab=99.74  E-value=1.8e-17  Score=112.77  Aligned_cols=112  Identities=26%  Similarity=0.369  Sum_probs=93.8

Q ss_pred             CCceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe--------cCeEEEEECCHHHHHh--------------------
Q psy1185           2 SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYAFVHFEDRQEAIT--------------------   53 (131)
Q Consensus         2 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~--------~~~~fv~~~~~~~a~~--------------------   53 (131)
                      +...|||||||+...+++.|+++|-+.|+|.+++++        +||||++|.++++|+-                    
T Consensus         7 nqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~ka   86 (203)
T KOG0131|consen    7 NQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKA   86 (203)
T ss_pred             CCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEec
Confidence            356799999999999999999999999999999998        7999999999999998                    


Q ss_pred             --------------------------------hcCCc---eeEEecCCCCCCCCcceEEEEeCCHHhHHHHHHHHhCCcc
Q psy1185          54 --------------------------------VTGLS---QVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRL   98 (131)
Q Consensus        54 --------------------------------~~g~~---~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~~   98 (131)
                                                      ++|..   ..+++ + ..+|.++++||+.|.+.+.+.+|+.+++|.  
T Consensus        87 s~~~~nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~r-d-~~tg~~~~~g~i~~~sfeasd~ai~s~ngq--  162 (203)
T KOG0131|consen   87 SAHQKNLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMR-D-PDTGNPKGFGFINYASFEASDAAIGSMNGQ--  162 (203)
T ss_pred             ccccccccccccccccccCcchhHHHHHHHHHhccccccCCcccc-c-ccCCCCCCCeEEechhHHHHHHHHHHhccc--
Confidence                                            23311   11111 1 246889999999999999999999999998  


Q ss_pred             eecCcEEEEEecCCCCCCC
Q psy1185          99 KVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        99 ~~~g~~l~v~~a~~~~~~~  117 (131)
                      .+..++++|.|+..+....
T Consensus       163 ~l~nr~itv~ya~k~~~kg  181 (203)
T KOG0131|consen  163 YLCNRPITVSYAFKKDTKG  181 (203)
T ss_pred             hhcCCceEEEEEEecCCCc
Confidence            8889999999997655443

>KOG0122|consensus

Probab=99.73  E-value=2.5e-17  Score=116.50  Aligned_cols=82  Identities=26%  Similarity=0.449  Sum_probs=76.8

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      .+++|=|.|||.++++++|.+||.+||.|.++++.++                           +.+|.++|||||.|.+
T Consensus       188 D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylard---------------------------K~TG~~kGFAFVtF~s  240 (270)
T KOG0122|consen  188 DEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARD---------------------------KETGLSKGFAFVTFES  240 (270)
T ss_pred             ccceeEEecCccccChhHHHHHhhccCccceeEEEEc---------------------------cccCcccceEEEEEec
Confidence            3568999999999999999999999999999999976                           6799999999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQ  113 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~  113 (131)
                      +++|++|++.|+|.  .++.-.|+|+|++|+
T Consensus       241 RddA~rAI~~LnG~--gyd~LILrvEwskP~  269 (270)
T KOG0122|consen  241 RDDAARAIADLNGY--GYDNLILRVEWSKPS  269 (270)
T ss_pred             HHHHHHHHHHccCc--ccceEEEEEEecCCC
Confidence            99999999999997  788889999999986

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

Probab=99.73  E-value=1.4e-16  Score=125.40  Aligned_cols=107  Identities=25%  Similarity=0.419  Sum_probs=84.8

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe--------cCeEEEEECCHHHHHhhc--------------------
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYAFVHFEDRQEAITVT--------------------   55 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~--------~~~~fv~~~~~~~a~~~~--------------------   55 (131)
                      .++|||+|||..+++++|+++|++||.|..+.++        +|||||+|.+.++|..+.                    
T Consensus       295 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~  374 (509)
T TIGR01642       295 KDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACV  374 (509)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECcc
Confidence            4689999999999999999999999999999886        699999999999988710                    


Q ss_pred             ---------------------------------------------------------------------C-CceeEEecC
Q psy1185          56 ---------------------------------------------------------------------G-LSQVIIYSS   65 (131)
Q Consensus        56 ---------------------------------------------------------------------g-~~~~~~~~~   65 (131)
                                                                                           | +..+.+...
T Consensus       375 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~~~  454 (509)
T TIGR01642       375 GANQATIDTSNGMAPVTLLAKALSQSILQIGGKPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRP  454 (509)
T ss_pred             CCCCCCccccccccccccccccchhhhccccCCCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEeecc
Confidence                                                                                 0 000011100


Q ss_pred             C--CCCCCCcceEEEEeCCHHhHHHHHHHHhCCcceecCcEEEEEecCC
Q psy1185          66 P--DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADP  112 (131)
Q Consensus        66 ~--~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~  112 (131)
                      .  ..++...|++||+|.+.++|.+|+..|||.  .++|+.|.|.|...
T Consensus       455 ~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnGr--~~~gr~v~~~~~~~  501 (509)
T TIGR01642       455 NGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGR--KFNDRVVVAAFYGE  501 (509)
T ss_pred             CcCCCcCCCcceEEEEECCHHHHHHHHHHcCCC--EECCeEEEEEEeCH
Confidence            0  012334689999999999999999999998  89999999999653

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

>PF00076 RRM_1: RNA recognition motif

Probab=99.72  E-value=5.7e-17  Score=95.13  Aligned_cols=70  Identities=36%  Similarity=0.650  Sum_probs=64.2

Q ss_pred             EEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHHhH
Q psy1185           7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSA   86 (131)
Q Consensus         7 l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a   86 (131)
                      |||+|||.++++++|+++|++||.+..+.+...                            .++..+++|||+|.++++|
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~----------------------------~~~~~~~~a~V~F~~~~~a   52 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRN----------------------------SSGKSKGYAFVEFESEEDA   52 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEE----------------------------TTSSEEEEEEEEESSHHHH
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhccccccccc----------------------------ccccccceEEEEEcCHHHH
Confidence            799999999999999999999999999988742                            3678899999999999999


Q ss_pred             HHHHHHHhCCcceecCcEEE
Q psy1185          87 SLAKKRLATGRLKVWGCDII  106 (131)
Q Consensus        87 ~~a~~~l~~~~~~~~g~~l~  106 (131)
                      .+|+..++|.  .++|+.|+
T Consensus        53 ~~a~~~l~g~--~~~~~~ir   70 (70)
T PF00076_consen   53 EKALEELNGK--KINGRKIR   70 (70)
T ss_dssp             HHHHHHHTTE--EETTEEEE
T ss_pred             HHHHHHcCCC--EECccCcC
Confidence            9999999998  89998875

(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 ....

>KOG0145|consensus

Probab=99.72  E-value=4.2e-17  Score=116.61  Aligned_cols=110  Identities=27%  Similarity=0.399  Sum_probs=91.4

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe--------cCeEEEEECCHHHHHh----------------------
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYAFVHFEDRQEAIT----------------------   53 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~--------~~~~fv~~~~~~~a~~----------------------   53 (131)
                      .+.|.|.-||..+|+++++.||++.|+|.+|+++        .|||||+|.++++|++                      
T Consensus        41 kTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSyARP  120 (360)
T KOG0145|consen   41 KTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSYARP  120 (360)
T ss_pred             cceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEeccC
Confidence            4578999999999999999999999999999998        6999999999999999                      


Q ss_pred             -----------------------------hcC-CceeEEecCCCCCCCCcceEEEEeCCHHhHHHHHHHHhCCcceecCc
Q psy1185          54 -----------------------------VTG-LSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGC  103 (131)
Q Consensus        54 -----------------------------~~g-~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~~~~~g~  103 (131)
                                                   .+| +.-..+..+ ..+|.++|.|||.|..+.+|..|+..|||.  ..-|+
T Consensus       121 Ss~~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~d-qvtg~srGVgFiRFDKr~EAe~AIk~lNG~--~P~g~  197 (360)
T KOG0145|consen  121 SSDSIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVD-QVTGLSRGVGFIRFDKRIEAEEAIKGLNGQ--KPSGC  197 (360)
T ss_pred             ChhhhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhh-cccceecceeEEEecchhHHHHHHHhccCC--CCCCC
Confidence                                         233 221122222 257899999999999999999999999998  66666


Q ss_pred             E--EEEEecCCCCCC
Q psy1185         104 D--IIVDWADPQEEP  116 (131)
Q Consensus       104 ~--l~v~~a~~~~~~  116 (131)
                      .  |.|.||..+...
T Consensus       198 tepItVKFannPsq~  212 (360)
T KOG0145|consen  198 TEPITVKFANNPSQK  212 (360)
T ss_pred             CCCeEEEecCCcccc
Confidence            4  999999876543

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

Probab=99.72  E-value=2.9e-16  Score=123.56  Aligned_cols=108  Identities=23%  Similarity=0.295  Sum_probs=85.0

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhcc------------CCeeEEEEe--cCeEEEEECCHHHHHhhcCCce----------
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQY------------GRVERVKRI--KDYAFVHFEDRQEAITVTGLSQ----------   59 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~------------G~v~~~~i~--~~~~fv~~~~~~~a~~~~g~~~----------   59 (131)
                      .++|||||||+++++++|+++|+++            +.|..+.+.  +|||||+|.+.++|..++.+.+          
T Consensus       175 ~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~~~~kg~afVeF~~~e~A~~Al~l~g~~~~g~~l~v  254 (509)
T TIGR01642       175 ARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNINKEKNFAFLEFRTVEEATFAMALDSIIYSNVFLKI  254 (509)
T ss_pred             ccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEECCCCCEEEEEeCCHHHHhhhhcCCCeEeeCceeEe
Confidence            5789999999999999999999975            345555554  7999999999999987322110          


Q ss_pred             -----------------------------------------eEEec--C--------------------------CCCCC
Q psy1185          60 -----------------------------------------VIIYS--S--------------------------PDDNK   70 (131)
Q Consensus        60 -----------------------------------------~~~~~--~--------------------------~~~~~   70 (131)
                                                               ..|++  .                          ...+|
T Consensus       255 ~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g  334 (509)
T TIGR01642       255 RRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATG  334 (509)
T ss_pred             cCccccCCccccCCCCCCCCCcccccccccccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCC
Confidence                                                     01111  0                          01357


Q ss_pred             CCcceEEEEeCCHHhHHHHHHHHhCCcceecCcEEEEEecCCC
Q psy1185          71 KNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQ  113 (131)
Q Consensus        71 ~~~~~~fv~f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~  113 (131)
                      .++|||||+|.+.+.|..|+..|+|.  .++|+.|.|.+|...
T Consensus       335 ~~~g~afv~f~~~~~a~~A~~~l~g~--~~~~~~l~v~~a~~~  375 (509)
T TIGR01642       335 LSKGYAFCEYKDPSVTDVAIAALNGK--DTGDNKLHVQRACVG  375 (509)
T ss_pred             CcCeEEEEEECCHHHHHHHHHHcCCC--EECCeEEEEEECccC
Confidence            78999999999999999999999998  899999999998643

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

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.72  E-value=1.1e-16  Score=115.24  Aligned_cols=80  Identities=19%  Similarity=0.289  Sum_probs=71.5

Q ss_pred             CCCceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEe
Q psy1185           1 MSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEY   80 (131)
Q Consensus         1 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f   80 (131)
                      |+..++|||+|||+.+++++|+++|+.||.|.++.+++.                              +..++||||+|
T Consensus         1 ~~~~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d------------------------------~~~~GfAFVtF   50 (260)
T PLN03120          1 VMQVRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSE------------------------------NERSQIAYVTF   50 (260)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeec------------------------------CCCCCEEEEEe
Confidence            355789999999999999999999999999999998753                              23579999999


Q ss_pred             CCHHhHHHHHHHHhCCcceecCcEEEEEecCCC
Q psy1185          81 DSHKSASLAKKRLATGRLKVWGCDIIVDWADPQ  113 (131)
Q Consensus        81 ~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~  113 (131)
                      .++++|..|+. |+|.  .++|+.|.|.++..-
T Consensus        51 ~d~eaAe~All-LnG~--~l~gr~V~Vt~a~~~   80 (260)
T PLN03120         51 KDPQGAETALL-LSGA--TIVDQSVTITPAEDY   80 (260)
T ss_pred             CcHHHHHHHHH-hcCC--eeCCceEEEEeccCC
Confidence            99999999995 9998  999999999998743

>KOG0127|consensus

Probab=99.71  E-value=1.4e-16  Score=123.27  Aligned_cols=109  Identities=25%  Similarity=0.425  Sum_probs=92.4

Q ss_pred             eEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe--------cCeEEEEECCHHHHHh-----------------------
Q psy1185           5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYAFVHFEDRQEAIT-----------------------   53 (131)
Q Consensus         5 ~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~--------~~~~fv~~~~~~~a~~-----------------------   53 (131)
                      .||||++||++++.++|.++|+.+|+|..|.++        ||||||+|.-.++++.                       
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            899999999999999999999999999999988        8999999999999988                       


Q ss_pred             ------------------------------------------------------hcCCc-eeEEecCCCCCCCCcceEEE
Q psy1185          54 ------------------------------------------------------VTGLS-QVIIYSSPDDNKKNRGFCFL   78 (131)
Q Consensus        54 ------------------------------------------------------~~g~~-~~~~~~~~~~~~~~~~~~fv   78 (131)
                                                                            .+|-. ++.++  ....|.-.|||||
T Consensus        86 ~r~e~~~~~e~~~veK~~~q~~~~k~~v~~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP--~k~dgklcGFaFV  163 (678)
T KOG0127|consen   86 ARSEEVEKGENKAVEKPIEQKRPTKAKVDLPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIP--RKKDGKLCGFAFV  163 (678)
T ss_pred             ccchhcccccchhhhcccccCCcchhhccCccceEEeecCCcccCcHHHHHHHhhcceEEEEEcc--cCCCCCccceEEE
Confidence                                                                  23322 22222  1234555699999


Q ss_pred             EeCCHHhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          79 EYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        79 ~f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      .|.+..+|..|++.+|+.  .++|++|.|.||.++..-.
T Consensus       164 ~fk~~~dA~~Al~~~N~~--~i~gR~VAVDWAV~Kd~ye  200 (678)
T KOG0127|consen  164 QFKEKKDAEKALEFFNGN--KIDGRPVAVDWAVDKDTYE  200 (678)
T ss_pred             EEeeHHHHHHHHHhccCc--eecCceeEEeeeccccccc
Confidence            999999999999999998  9999999999999876543

>KOG0149|consensus

Probab=99.68  E-value=7.8e-17  Score=113.41  Aligned_cols=79  Identities=22%  Similarity=0.366  Sum_probs=71.0

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      +.++||||+|+|.|..+.|++.|++||+|.+..++..                           +.+|+++|||||+|.+
T Consensus        11 ~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd---------------------------~~t~rskGyGfVTf~d   63 (247)
T KOG0149|consen   11 TFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITD---------------------------KNTGRSKGYGFVTFRD   63 (247)
T ss_pred             eEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEec---------------------------cCCccccceeeEEeec
Confidence            3579999999999999999999999999999988843                           4589999999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWAD  111 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~  111 (131)
                      .++|.+|+..-+-   .++||+-.++.|.
T Consensus        64 ~~aa~rAc~dp~p---iIdGR~aNcnlA~   89 (247)
T KOG0149|consen   64 AEAATRACKDPNP---IIDGRKANCNLAS   89 (247)
T ss_pred             HHHHHHHhcCCCC---cccccccccchhh
Confidence            9999999988776   7999998888764

>KOG0121|consensus

Probab=99.68  E-value=1.7e-16  Score=102.53  Aligned_cols=80  Identities=34%  Similarity=0.515  Sum_probs=70.6

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      +++|||||||++.++|+.|.+||+++|+|..+-+-.+                           +.+..+-|||||+|.+
T Consensus        35 ~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLd---------------------------r~kktpCGFCFVeyy~   87 (153)
T KOG0121|consen   35 KSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLD---------------------------RFKKTPCGFCFVEYYS   87 (153)
T ss_pred             hcceEEEeeeeeeecHHHHHHHHHhccchheeEeccc---------------------------cCCcCccceEEEEEec
Confidence            5789999999999999999999999999999754321                           2255678999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWAD  111 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~  111 (131)
                      .++|..|++.+++.  .++.+.|++.|.-
T Consensus        88 ~~dA~~Alryisgt--rLddr~ir~D~D~  114 (153)
T KOG0121|consen   88 RDDAEDALRYISGT--RLDDRPIRIDWDA  114 (153)
T ss_pred             chhHHHHHHHhccC--cccccceeeeccc
Confidence            99999999999998  8999999999964

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

Probab=99.68  E-value=1.5e-15  Score=119.32  Aligned_cols=108  Identities=27%  Similarity=0.325  Sum_probs=85.0

Q ss_pred             ceEEEEeCCCC-CCCHHHHHHHhhccCCeeEEEEe---cCeEEEEECCHHHHHhhc----C--Cce--------------
Q psy1185           4 VKVLYVRNLTQ-YCTEEKLKEAFEQYGRVERVKRI---KDYAFVHFEDRQEAITVT----G--LSQ--------------   59 (131)
Q Consensus         4 ~~~l~v~nLp~-~~t~~~l~~~F~~~G~v~~~~i~---~~~~fv~~~~~~~a~~~~----g--~~~--------------   59 (131)
                      .++|||+|||+ .+++++|+++|++||.|.+++++   +|||||+|.+.++|..+.    |  +.+              
T Consensus       275 ~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~~~~~~  354 (481)
T TIGR01649       275 GSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNKKETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQNVQ  354 (481)
T ss_pred             CCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEccccccc
Confidence            56999999998 69999999999999999999988   699999999999999910    0  000              


Q ss_pred             ----------------------------------------eEEecC--CC--------------------------CCCC
Q psy1185          60 ----------------------------------------VIIYSS--PD--------------------------DNKK   71 (131)
Q Consensus        60 ----------------------------------------~~~~~~--~~--------------------------~~~~   71 (131)
                                                              ..|+..  +.                          ..+.
T Consensus       355 ~~~~~~~~~~~~~~~d~~~~~~~r~~~~~~~~~~~~~~ps~~L~v~NLp~~~tee~L~~lF~~~G~~~i~~ik~~~~~~~  434 (481)
T TIGR01649       355 PPREGQLDDGLTSYKDYSSSRNHRFKKPGSANKNNIQPPSATLHLSNIPLSVSEEDLKELFAENGVHKVKKFKFFPKDNE  434 (481)
T ss_pred             CCCCCcCcCCCcccccccCCccccCCCcccccccccCCCCcEEEEecCCCCCCHHHHHHHHHhcCCccceEEEEecCCCC
Confidence                                                    111110  00                          0112


Q ss_pred             CcceEEEEeCCHHhHHHHHHHHhCCcceecCcE------EEEEecCCC
Q psy1185          72 NRGFCFLEYDSHKSASLAKKRLATGRLKVWGCD------IIVDWADPQ  113 (131)
Q Consensus        72 ~~~~~fv~f~~~~~a~~a~~~l~~~~~~~~g~~------l~v~~a~~~  113 (131)
                      .+++|||+|.+.++|..|+..||+.  .++++.      |+|.||+++
T Consensus       435 ~~~~gfVeF~~~e~A~~Al~~ln~~--~l~~~~~~~~~~lkv~fs~~~  480 (481)
T TIGR01649       435 RSKMGLLEWESVEDAVEALIALNHH--QLNEPNGSAPYHLKVSFSTSR  480 (481)
T ss_pred             cceeEEEEcCCHHHHHHHHHHhcCC--ccCCCCCCccceEEEEeccCC
Confidence            3689999999999999999999998  788874      999999875

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

>KOG0117|consensus

Probab=99.67  E-value=8e-16  Score=116.56  Aligned_cols=109  Identities=21%  Similarity=0.298  Sum_probs=91.4

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCC-eeEEEEe---------cCeEEEEECCHHHHHh--------------------
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGR-VERVKRI---------KDYAFVHFEDRQEAIT--------------------   53 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~-v~~~~i~---------~~~~fv~~~~~~~a~~--------------------   53 (131)
                      .+.|||||+|...++++|.+.+++.++ |+.+-+.         ||||||+|.++..|..                    
T Consensus       164 n~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g~~klwgn~~tVd  243 (506)
T KOG0117|consen  164 NCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMPGKIKLWGNAITVD  243 (506)
T ss_pred             cceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhccCCceeecCCcceee
Confidence            578999999999999999999999987 4444443         8999999999998887                    


Q ss_pred             -----------------------------------hcCCceeEEecCCCCCCCCcceEEEEeCCHHhHHHHHHHHhCCcc
Q psy1185          54 -----------------------------------VTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRL   98 (131)
Q Consensus        54 -----------------------------------~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~~   98 (131)
                                                         .++.++++.++.     +.+.||||+|.++++|.+|++.++++  
T Consensus       244 WAep~~e~ded~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVk-----k~rDYaFVHf~eR~davkAm~~~ngk--  316 (506)
T KOG0117|consen  244 WAEPEEEPDEDTMSKVKVLYVRNLMESTTEETLKKLFNEFGKVERVK-----KPRDYAFVHFAEREDAVKAMKETNGK--  316 (506)
T ss_pred             ccCcccCCChhhhhheeeeeeeccchhhhHHHHHHHHHhccceEEee-----cccceeEEeecchHHHHHHHHHhcCc--
Confidence                                               334445554442     34789999999999999999999999  


Q ss_pred             eecCcEEEEEecCCCCCCChH
Q psy1185          99 KVWGCDIIVDWADPQEEPDTE  119 (131)
Q Consensus        99 ~~~g~~l~v~~a~~~~~~~~~  119 (131)
                      .++|..|.|.+|+|..+...+
T Consensus       317 eldG~~iEvtLAKP~~k~k~~  337 (506)
T KOG0117|consen  317 ELDGSPIEVTLAKPVDKKKKE  337 (506)
T ss_pred             eecCceEEEEecCChhhhccc
Confidence            999999999999998876654

>KOG0148|consensus

Probab=99.67  E-value=8.9e-16  Score=110.15  Aligned_cols=102  Identities=26%  Similarity=0.527  Sum_probs=88.5

Q ss_pred             eEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe--------cCeEEEEECCHHHHHh-----------------------
Q psy1185           5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYAFVHFEDRQEAIT-----------------------   53 (131)
Q Consensus         5 ~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~--------~~~~fv~~~~~~~a~~-----------------------   53 (131)
                      -.+|||-|...++-+.|++.|.+||+|.+++++        +|||||.|-+.++|++                       
T Consensus        63 fhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATRK  142 (321)
T KOG0148|consen   63 FHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATRK  142 (321)
T ss_pred             eeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeeccccccC
Confidence            369999999999999999999999999999998        7999999999999999                       


Q ss_pred             --------------------------------------------hcC-CceeEEecCCCCCCCCcceEEEEeCCHHhHHH
Q psy1185          54 --------------------------------------------VTG-LSQVIIYSSPDDNKKNRGFCFLEYDSHKSASL   88 (131)
Q Consensus        54 --------------------------------------------~~g-~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~   88 (131)
                                                                  .+| |.++.       .-+.+||+||.|.+++.|.+
T Consensus       143 p~e~n~~~ltfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVR-------vFk~qGYaFVrF~tkEaAah  215 (321)
T KOG0148|consen  143 PSEMNGKPLTFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVR-------VFKDQGYAFVRFETKEAAAH  215 (321)
T ss_pred             ccccCCCCccHHHHhccCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEE-------EecccceEEEEecchhhHHH
Confidence                                                        233 11222       12358999999999999999


Q ss_pred             HHHHHhCCcceecCcEEEEEecCCCCC
Q psy1185          89 AKKRLATGRLKVWGCDIIVDWADPQEE  115 (131)
Q Consensus        89 a~~~l~~~~~~~~g~~l~v~~a~~~~~  115 (131)
                      ||..+|+.  .+.|..+++.|.+....
T Consensus       216 AIv~mNnt--ei~G~~VkCsWGKe~~~  240 (321)
T KOG0148|consen  216 AIVQMNNT--EIGGQLVRCSWGKEGDD  240 (321)
T ss_pred             HHHHhcCc--eeCceEEEEeccccCCC
Confidence            99999999  99999999999986544

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.63  E-value=3e-15  Score=88.27  Aligned_cols=70  Identities=34%  Similarity=0.602  Sum_probs=61.3

Q ss_pred             EEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHHhH
Q psy1185           7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSA   86 (131)
Q Consensus         7 l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a   86 (131)
                      |||+|||+++++++|.++|+.||.|..+++.++                           . .+..+++|||+|.+.++|
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~---------------------------~-~~~~~~~a~v~f~~~~~a   52 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKN---------------------------K-DGQSRGFAFVEFSSEEDA   52 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEES---------------------------T-TSSEEEEEEEEESSHHHH
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEee---------------------------e-ccccCCEEEEEeCCHHHH
Confidence            799999999999999999999999999988854                           2 367899999999999999


Q ss_pred             HHHHHHHhCCcceecCcEEE
Q psy1185          87 SLAKKRLATGRLKVWGCDII  106 (131)
Q Consensus        87 ~~a~~~l~~~~~~~~g~~l~  106 (131)
                      .+|+..+++.  .++|+.|.
T Consensus        53 ~~al~~~~~~--~~~g~~l~   70 (70)
T PF14259_consen   53 KRALELLNGK--EIDGRKLR   70 (70)
T ss_dssp             HHHHHHHTTE--EETTEEEE
T ss_pred             HHHHHHCCCc--EECCEEcC
Confidence            9999999976  88998874

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 ....

>KOG0107|consensus

Probab=99.63  E-value=2.5e-15  Score=101.79  Aligned_cols=78  Identities=27%  Similarity=0.452  Sum_probs=70.8

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .++||||||+..+++.||+..|..||++..+-+-+                                .+.|||||+|++.
T Consensus        10 ~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvAr--------------------------------nPPGfAFVEFed~   57 (195)
T KOG0107|consen   10 NTKVYVGNLGSRATKRELERAFSKYGPLRSVWVAR--------------------------------NPPGFAFVEFEDP   57 (195)
T ss_pred             CceEEeccCCCCcchHHHHHHHHhcCcceeEEEee--------------------------------cCCCceEEeccCc
Confidence            67999999999999999999999999999986653                                3689999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCCCCC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADPQEE  115 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~  115 (131)
                      .+|..|+..|+|+  .+.|..+.|+.+.....
T Consensus        58 RDA~DAvr~LDG~--~~cG~r~rVE~S~G~~r   87 (195)
T KOG0107|consen   58 RDAEDAVRYLDGK--DICGSRIRVELSTGRPR   87 (195)
T ss_pred             ccHHHHHhhcCCc--cccCceEEEEeecCCcc
Confidence            9999999999999  89999999999876554

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

Probab=99.61  E-value=5e-15  Score=117.73  Aligned_cols=78  Identities=40%  Similarity=0.697  Sum_probs=71.0

Q ss_pred             CCCceEEEEeCCCCCCCHHHHHHHhhcc--CCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEE
Q psy1185           1 MSKVKVLYVRNLTQYCTEEKLKEAFEQY--GRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFL   78 (131)
Q Consensus         1 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~--G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv   78 (131)
                      |++.++|||+|||.++++++|+++|++|  |.|.++.++                                   ++||||
T Consensus       230 ~~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~-----------------------------------rgfAFV  274 (578)
T TIGR01648       230 MAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI-----------------------------------RDYAFV  274 (578)
T ss_pred             cccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee-----------------------------------cCeEEE
Confidence            4556899999999999999999999999  999998765                                   568999


Q ss_pred             EeCCHHhHHHHHHHHhCCcceecCcEEEEEecCCCCC
Q psy1185          79 EYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEE  115 (131)
Q Consensus        79 ~f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~  115 (131)
                      +|.++++|.+|+..|++.  .++|+.|.|.||+++..
T Consensus       275 eF~s~e~A~kAi~~lnG~--~i~Gr~I~V~~Akp~~~  309 (578)
T TIGR01648       275 HFEDREDAVKAMDELNGK--ELEGSEIEVTLAKPVDK  309 (578)
T ss_pred             EeCCHHHHHHHHHHhCCC--EECCEEEEEEEccCCCc
Confidence            999999999999999998  89999999999988654

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.

>KOG0145|consensus

Probab=99.61  E-value=5.7e-15  Score=105.79  Aligned_cols=107  Identities=22%  Similarity=0.362  Sum_probs=90.2

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe--------cCeEEEEECCHHHHHh----------------------
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYAFVHFEDRQEAIT----------------------   53 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~--------~~~~fv~~~~~~~a~~----------------------   53 (131)
                      ...|||.+||..+|..+|+++|++||.|..-++.        +|-|||.|+....|+.                      
T Consensus       127 ~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~P~g~tepItVKFa  206 (360)
T KOG0145|consen  127 DANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQKPSGCTEPITVKFA  206 (360)
T ss_pred             ccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhccCCCCCCCCCCeEEEec
Confidence            4579999999999999999999999998776665        8999999999999988                      


Q ss_pred             --------------------------------------------------------------------------------
Q psy1185          54 --------------------------------------------------------------------------------   53 (131)
Q Consensus        54 --------------------------------------------------------------------------------   53 (131)
                                                                                                      
T Consensus       207 nnPsq~t~~a~ls~ly~sp~rr~~Gp~hh~~~r~r~~~~~~~~~~~~rfsP~~~d~m~~l~~~~lp~~~~~g~ciFvYNL  286 (360)
T KOG0145|consen  207 NNPSQKTNQALLSQLYQSPARRYGGPMHHQAQRFRLDNLLNPHAAQARFSPMTIDGMSGLAGVNLPGGPGGGWCIFVYNL  286 (360)
T ss_pred             CCcccccchhhhHHhhcCccccCCCcccchhhhhccccccchhhhhccCCCccccccceeeeeccCCCCCCeeEEEEEec
Confidence                                                                                            


Q ss_pred             -----------hcCCc----eeEEecCCCCCCCCcceEEEEeCCHHhHHHHHHHHhCCcceecCcEEEEEecCCC
Q psy1185          54 -----------VTGLS----QVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQ  113 (131)
Q Consensus        54 -----------~~g~~----~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~  113 (131)
                                 .+|.+    .+.+..+.. +++.+|||||...+-++|.+|+..|||-  .++++.|.|.|-.++
T Consensus       287 spd~de~~LWQlFgpFGAv~nVKvirD~t-tnkCKGfgFVtMtNYdEAamAi~sLNGy--~lg~rvLQVsFKtnk  358 (360)
T KOG0145|consen  287 SPDADESILWQLFGPFGAVTNVKVIRDFT-TNKCKGFGFVTMTNYDEAAMAIASLNGY--RLGDRVLQVSFKTNK  358 (360)
T ss_pred             CCCchHhHHHHHhCcccceeeEEEEecCC-cccccceeEEEecchHHHHHHHHHhcCc--cccceEEEEEEecCC
Confidence                       33433    333444443 6788999999999999999999999998  999999999985543

>KOG0148|consensus

Probab=99.61  E-value=2.9e-15  Score=107.53  Aligned_cols=109  Identities=26%  Similarity=0.394  Sum_probs=88.2

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe--------------------cCe--EEEE-------ECCHHHHHh
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------------------KDY--AFVH-------FEDRQEAIT   53 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~--------------------~~~--~fv~-------~~~~~~a~~   53 (131)
                      .-+|||||||..++||+-|..||++.|++..|+++                    +.+  -||.       +++..+|=.
T Consensus         5 ~prtlyvgnld~~vte~~i~~lf~qig~v~~~k~i~~e~~v~wa~~p~nQsk~t~~~hfhvfvgdls~eI~~e~lr~aF~   84 (321)
T KOG0148|consen    5 EPRTLYVGNLDSTVTEDFIATLFNQIGSVTKTKVIFDELKVNWATAPGNQSKPTSNQHFHVFVGDLSPEIDNEKLREAFA   84 (321)
T ss_pred             CCceEEeeccChhhHHHHHHHHHHhccccccceeehhhhccccccCcccCCCCccccceeEEehhcchhcchHHHHHHhc
Confidence            46899999999999999999999999999999987                    111  1221       222233333


Q ss_pred             hcC-CceeEEecCCCCCCCCcceEEEEeCCHHhHHHHHHHHhCCcceecCcEEEEEecCCCC
Q psy1185          54 VTG-LSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQE  114 (131)
Q Consensus        54 ~~g-~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~  114 (131)
                      .+| +..+.+..+.. +++++||+||.|.+.++|+.|+..|+|.  =|++|.|+-.||--++
T Consensus        85 pFGevS~akvirD~~-T~KsKGYgFVSf~~k~dAEnAI~~MnGq--WlG~R~IRTNWATRKp  143 (321)
T KOG0148|consen   85 PFGEVSDAKVIRDMN-TGKSKGYGFVSFPNKEDAENAIQQMNGQ--WLGRRTIRTNWATRKP  143 (321)
T ss_pred             cccccccceEeeccc-CCcccceeEEeccchHHHHHHHHHhCCe--eeccceeeccccccCc
Confidence            677 77777777776 8899999999999999999999999998  7899999999997554

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

Probab=99.61  E-value=2.1e-14  Score=111.79  Aligned_cols=50  Identities=38%  Similarity=0.636  Sum_probs=47.2

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe--------cCeEEEEECCHHHHHh
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYAFVHFEDRQEAIT   53 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~--------~~~~fv~~~~~~~a~~   53 (131)
                      .++|||+|||..+++++|+++|++||.|..+.++        +|||||+|.+.++|..
T Consensus       186 ~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~  243 (457)
T TIGR01622       186 FLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKE  243 (457)
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHH
Confidence            4789999999999999999999999999999887        5899999999999997

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.

>PLN03213 repressor of silencing 3; Provisional

Probab=99.60  E-value=7.2e-15  Score=113.07  Aligned_cols=78  Identities=17%  Similarity=0.230  Sum_probs=70.9

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ...+||||||++.+++++|+.+|++||.|.++.|+|-                             +|  ||||||+|.+
T Consensus         9 ~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRE-----------------------------TG--RGFAFVEMss   57 (759)
T PLN03213          9 GGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRT-----------------------------KG--RSFAYIDFSP   57 (759)
T ss_pred             cceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecc-----------------------------cC--CceEEEEecC
Confidence            3568999999999999999999999999999999853                             55  9999999998


Q ss_pred             H--HhHHHHHHHHhCCcceecCcEEEEEecCCC
Q psy1185          83 H--KSASLAKKRLATGRLKVWGCDIIVDWADPQ  113 (131)
Q Consensus        83 ~--~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~  113 (131)
                      .  .++.+|+..|+|.  .+.|+.|+|..|++.
T Consensus        58 dddaEeeKAISaLNGA--EWKGR~LKVNKAKP~   88 (759)
T PLN03213         58 SSTNSLTKLFSTYNGC--VWKGGRLRLEKAKEH   88 (759)
T ss_pred             CcHHHHHHHHHHhcCC--eecCceeEEeeccHH
Confidence            7  6899999999999  899999999999853

>KOG0113|consensus

Probab=99.59  E-value=9.9e-15  Score=105.92  Aligned_cols=79  Identities=32%  Similarity=0.561  Sum_probs=74.2

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .+||||+-|+.+++|+.|++.|+.||+|..+++++.                           ..+|+++|||||+|..+
T Consensus       101 y~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d---------------------------~vTgkskGYAFIeye~e  153 (335)
T KOG0113|consen  101 YKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRD---------------------------KVTGKSKGYAFIEYEHE  153 (335)
T ss_pred             cceeeeeeccccccHHHHHHHHHhcCcceeEEEeee---------------------------cccCCccceEEEEeccH
Confidence            689999999999999999999999999999999976                           56899999999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWAD  111 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~  111 (131)
                      .+..+|.+...|.  .|+|+.|.|.+-.
T Consensus       154 rdm~~AYK~adG~--~Idgrri~VDvER  179 (335)
T KOG0113|consen  154 RDMKAAYKDADGI--KIDGRRILVDVER  179 (335)
T ss_pred             HHHHHHHHhccCc--eecCcEEEEEecc
Confidence            9999999999997  9999999998854

>KOG4207|consensus

Probab=99.59  E-value=4.3e-15  Score=103.14  Aligned_cols=82  Identities=28%  Similarity=0.430  Sum_probs=76.1

Q ss_pred             CCceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeC
Q psy1185           2 SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYD   81 (131)
Q Consensus         2 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~   81 (131)
                      +.+.+|-|-||...|+.++|+.+|++||.|.+++|++.                           ..++.++|||||.|+
T Consensus        11 ~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrd---------------------------r~Tr~sRgFaFVrf~   63 (256)
T KOG4207|consen   11 EGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRD---------------------------RYTRQSRGFAFVRFH   63 (256)
T ss_pred             ccceeEEecceeccCCHHHHHHHHHHhCcccceecccc---------------------------cccccccceeEEEee
Confidence            45789999999999999999999999999999999965                           458899999999999


Q ss_pred             CHHhHHHHHHHHhCCcceecCcEEEEEecCC
Q psy1185          82 SHKSASLAKKRLATGRLKVWGCDIIVDWADP  112 (131)
Q Consensus        82 ~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~  112 (131)
                      +..+|+.|++.|.|.  .|+|+.|.|++|.=
T Consensus        64 ~k~daedA~damDG~--~ldgRelrVq~ary   92 (256)
T KOG4207|consen   64 DKRDAEDALDAMDGA--VLDGRELRVQMARY   92 (256)
T ss_pred             ecchHHHHHHhhcce--eeccceeeehhhhc
Confidence            999999999999998  99999999988763

>smart00362 RRM_2 RNA recognition motif

Probab=99.58  E-value=3e-14  Score=82.82  Aligned_cols=72  Identities=40%  Similarity=0.605  Sum_probs=64.7

Q ss_pred             EEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHHh
Q psy1185           6 VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKS   85 (131)
Q Consensus         6 ~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~~   85 (131)
                      +|||+|||..+++++|+++|.+||.+..+.+.+.                             .+.++++|||+|.+.+.
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~-----------------------------~~~~~~~~~v~f~~~~~   51 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKD-----------------------------TGKSKGFAFVEFESEED   51 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecC-----------------------------CCCCCceEEEEeCCHHH
Confidence            5899999999999999999999999999988753                             25678999999999999


Q ss_pred             HHHHHHHHhCCcceecCcEEEEE
Q psy1185          86 ASLAKKRLATGRLKVWGCDIIVD  108 (131)
Q Consensus        86 a~~a~~~l~~~~~~~~g~~l~v~  108 (131)
                      |..|+..+++.  .+.|+.+.|+
T Consensus        52 a~~a~~~~~~~--~~~~~~i~v~   72 (72)
T smart00362       52 AEKAIEALNGT--KLGGRPLRVE   72 (72)
T ss_pred             HHHHHHHhCCc--EECCEEEeeC
Confidence            99999999987  8899988763

>KOG0125|consensus

Probab=99.57  E-value=1e-14  Score=107.04  Aligned_cols=80  Identities=28%  Similarity=0.384  Sum_probs=72.6

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      +.+.|+|.|||+..-+.||+..|++||.|.++.|+.+                             ...+||||||+|.+
T Consensus        95 ~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfN-----------------------------ERGSKGFGFVTmen  145 (376)
T KOG0125|consen   95 TPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFN-----------------------------ERGSKGFGFVTMEN  145 (376)
T ss_pred             CCceeEeecCCccccCccHHHHHHhhCceeeEEEEec-----------------------------cCCCCccceEEecC
Confidence            4578999999999999999999999999999999843                             33479999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQ  113 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~  113 (131)
                      .++|.+|..+|||.  .+.||+|.|+.|-.+
T Consensus       146 ~~dadRARa~LHgt--~VEGRkIEVn~ATar  174 (376)
T KOG0125|consen  146 PADADRARAELHGT--VVEGRKIEVNNATAR  174 (376)
T ss_pred             hhhHHHHHHHhhcc--eeeceEEEEeccchh
Confidence            99999999999998  999999999988644

>KOG0146|consensus

Probab=99.57  E-value=4.7e-15  Score=106.57  Aligned_cols=94  Identities=21%  Similarity=0.457  Sum_probs=84.1

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      +.++||||.|.+.-+|+|++++|..||.+.+|.+.+|                            -.|.++||+||.|.+
T Consensus        18 ~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg----------------------------~dg~sKGCAFVKf~s   69 (371)
T KOG0146|consen   18 DDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRG----------------------------PDGNSKGCAFVKFSS   69 (371)
T ss_pred             cchhhhhhhhcccccHHHHHHHhcccCCcceeEEecC----------------------------CCCCCCCceEEEecc
Confidence            3689999999999999999999999999999999987                            368899999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCc--EEEEEecCCCCCCChHHHHhHh
Q psy1185          83 HKSASLAKKRLATGRLKVWGC--DIIVDWADPQEEPDTETMSKVL  125 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~--~l~v~~a~~~~~~~~~~~~~~~  125 (131)
                      +.+|++|++.|||.. ++-|-  .|+|.||+..+|+.-..|+++-
T Consensus        70 ~~eAqaAI~aLHgSq-TmpGASSSLVVK~ADTdkER~lRRMQQma  113 (371)
T KOG0146|consen   70 HAEAQAAINALHGSQ-TMPGASSSLVVKFADTDKERTLRRMQQMA  113 (371)
T ss_pred             chHHHHHHHHhcccc-cCCCCccceEEEeccchHHHHHHHHHHHH
Confidence            999999999999975 44444  4999999999999888888764

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.56  E-value=6.7e-14  Score=99.72  Aligned_cols=75  Identities=16%  Similarity=0.200  Sum_probs=67.1

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      ..+|||+||++.+|+++|+++|+.||+|.++++++                              .+..+++|||+|.++
T Consensus         5 g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~------------------------------D~et~gfAfVtF~d~   54 (243)
T PLN03121          5 GYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIR------------------------------SGEYACTAYVTFKDA   54 (243)
T ss_pred             ceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEec------------------------------CCCcceEEEEEECCH
Confidence            57999999999999999999999999999999885                              245578999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWAD  111 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~  111 (131)
                      ++|..|+ .|+|.  .|.++.|.|.-+.
T Consensus        55 ~aaetAl-lLnGa--~l~d~~I~It~~~   79 (243)
T PLN03121         55 YALETAV-LLSGA--TIVDQRVCITRWG   79 (243)
T ss_pred             HHHHHHH-hcCCC--eeCCceEEEEeCc
Confidence            9999998 79998  8999999887543

>KOG0111|consensus

Probab=99.53  E-value=6.4e-15  Score=103.26  Aligned_cols=85  Identities=29%  Similarity=0.567  Sum_probs=78.0

Q ss_pred             CCceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeC
Q psy1185           2 SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYD   81 (131)
Q Consensus         2 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~   81 (131)
                      ++.++||||+|...+++.-|...|-+||.|..+.++..|                           .+++.||||||+|.
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDy---------------------------esqkHRgFgFVefe   60 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDY---------------------------ESQKHRGFGFVEFE   60 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccccccchhhcccccch---------------------------hcccccceeEEEee
Confidence            346899999999999999999999999999999998664                           37888999999999


Q ss_pred             CHHhHHHHHHHHhCCcceecCcEEEEEecCCCCC
Q psy1185          82 SHKSASLAKKRLATGRLKVWGCDIIVDWADPQEE  115 (131)
Q Consensus        82 ~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~  115 (131)
                      ..++|.+|+..+++.  .|.|+.|+|.+|+|..-
T Consensus        61 ~aEDAaaAiDNMnes--EL~GrtirVN~AkP~ki   92 (298)
T KOG0111|consen   61 EAEDAAAAIDNMNES--ELFGRTIRVNLAKPEKI   92 (298)
T ss_pred             ccchhHHHhhcCchh--hhcceeEEEeecCCccc
Confidence            999999999999998  89999999999997654

>KOG0126|consensus

Probab=99.53  E-value=2e-15  Score=102.93  Aligned_cols=84  Identities=31%  Similarity=0.504  Sum_probs=75.6

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      +.-|||||||+..||.+|.-+|++||+|+.+.++|.                           ..+|+++||||+.|.+.
T Consensus        35 sA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRD---------------------------k~TGKSKGFaFLcYEDQ   87 (219)
T KOG0126|consen   35 SAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRD---------------------------KKTGKSKGFAFLCYEDQ   87 (219)
T ss_pred             ceEEEECCCcccccCCcEEEEeeccCceEEEEEEec---------------------------CCCCcccceEEEEecCc
Confidence            456999999999999999999999999999999976                           56999999999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCCCCCC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADPQEEP  116 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~  116 (131)
                      .+...|+..|||-  .+.||.|+|.....-..+
T Consensus        88 RSTILAVDN~NGi--ki~gRtirVDHv~~Yk~p  118 (219)
T KOG0126|consen   88 RSTILAVDNLNGI--KILGRTIRVDHVSNYKKP  118 (219)
T ss_pred             cceEEEEeccCCc--eecceeEEeeecccccCC
Confidence            9999999999997  999999999875544433

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

Probab=99.52  E-value=1.3e-13  Score=98.52  Aligned_cols=80  Identities=38%  Similarity=0.610  Sum_probs=73.0

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .++|||+|||.++++++|.++|.+||.+..+.+...                           ..++.++|+|||+|.+.
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d---------------------------~~~~~~~g~~~v~f~~~  167 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRD---------------------------RETGKSRGFAFVEFESE  167 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeec---------------------------cccCccCceEEEEecCH
Confidence            389999999999999999999999999999888743                           24789999999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADP  112 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~  112 (131)
                      ++|..|+..+++.  .+.|+.|.|.++.+
T Consensus       168 ~~~~~a~~~~~~~--~~~~~~~~v~~~~~  194 (306)
T COG0724         168 ESAEKAIEELNGK--ELEGRPLRVQKAQP  194 (306)
T ss_pred             HHHHHHHHHcCCC--eECCceeEeecccc
Confidence            9999999999987  99999999999653

>KOG0105|consensus

Probab=99.52  E-value=4e-14  Score=96.95  Aligned_cols=79  Identities=22%  Similarity=0.384  Sum_probs=70.6

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      +.++|||||||.++-+.+|.++|.+||.|.++.+..                              ......||||+|.+
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~------------------------------r~g~ppfafVeFEd   54 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKN------------------------------RPGPPPFAFVEFED   54 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhhcceEEEEecc------------------------------CCCCCCeeEEEecC
Confidence            478999999999999999999999999999998763                              23347899999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQ  113 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~  113 (131)
                      ..+|..|+..-+|-  .++|++|+|+++..-
T Consensus        55 ~RDAeDAiygRdGY--dydg~rLRVEfprgg   83 (241)
T KOG0105|consen   55 PRDAEDAIYGRDGY--DYDGCRLRVEFPRGG   83 (241)
T ss_pred             ccchhhhhhccccc--ccCcceEEEEeccCC
Confidence            99999999999997  899999999998754

>KOG0124|consensus

Probab=99.51  E-value=4.8e-14  Score=105.18  Aligned_cols=108  Identities=21%  Similarity=0.380  Sum_probs=95.5

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe--------cCeEEEEECCHHHHHh----------------------
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYAFVHFEDRQEAIT----------------------   53 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~--------~~~~fv~~~~~~~a~~----------------------   53 (131)
                      +|.||||.+.+...|+-|+..|.+||+|+++.+.        +||+||+|+-+++|.-                      
T Consensus       113 McRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPsN  192 (544)
T KOG0124|consen  113 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSN  192 (544)
T ss_pred             hHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCCC
Confidence            6889999999999999999999999999999876        8999999999999987                      


Q ss_pred             ----------------------------------------hcC-CceeEEecCCCCCCCCcceEEEEeCCHHhHHHHHHH
Q psy1185          54 ----------------------------------------VTG-LSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKR   92 (131)
Q Consensus        54 ----------------------------------------~~g-~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~   92 (131)
                                                              ++| +..|.+...+. .+..+||||++|.+.++...|+..
T Consensus       193 mpQAQpiID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt-~~~HkGyGfiEy~n~qs~~eAias  271 (544)
T KOG0124|consen  193 MPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPT-GRGHKGYGFIEYNNLQSQSEAIAS  271 (544)
T ss_pred             CcccchHHHHHHHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCC-CCCccceeeEEeccccchHHHhhh
Confidence                                                    566 66777777775 455699999999999999999999


Q ss_pred             HhCCcceecCcEEEEEecCCCC
Q psy1185          93 LATGRLKVWGCDIIVDWADPQE  114 (131)
Q Consensus        93 l~~~~~~~~g~~l~v~~a~~~~  114 (131)
                      +|-.  .++|..|+|..+..++
T Consensus       272 MNlF--DLGGQyLRVGk~vTPP  291 (544)
T KOG0124|consen  272 MNLF--DLGGQYLRVGKCVTPP  291 (544)
T ss_pred             cchh--hcccceEecccccCCC
Confidence            9975  8999999998776443

>KOG0108|consensus

Probab=99.51  E-value=8e-14  Score=107.47  Aligned_cols=86  Identities=23%  Similarity=0.397  Sum_probs=78.9

Q ss_pred             eEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHH
Q psy1185           5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHK   84 (131)
Q Consensus         5 ~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~   84 (131)
                      +.+||||+|+++++++|.++|+..|.|.+++++..                           ..+|..+||||++|.+.+
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D---------------------------~~tG~~~G~~f~~~~~~~   71 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYD---------------------------RETGKPKGFGFCEFTDEE   71 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeeccc---------------------------ccCCCcCceeeEecCchh
Confidence            78999999999999999999999999999998854                           568999999999999999


Q ss_pred             hHHHHHHHHhCCcceecCcEEEEEecCCCCCCChH
Q psy1185          85 SASLAKKRLATGRLKVWGCDIIVDWADPQEEPDTE  119 (131)
Q Consensus        85 ~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~~~  119 (131)
                      ++..|++.|+|.  .+.|++|+|.|+...+.....
T Consensus        72 ~~~~a~~~lNg~--~~~gr~l~v~~~~~~~~~~~~  104 (435)
T KOG0108|consen   72 TAERAIRNLNGA--EFNGRKLRVNYASNRKNAERS  104 (435)
T ss_pred             hHHHHHHhcCCc--ccCCceEEeecccccchhHHH
Confidence            999999999998  999999999999877765433

>smart00360 RRM RNA recognition motif

Probab=99.50  E-value=2.2e-13  Score=78.80  Aligned_cols=71  Identities=35%  Similarity=0.612  Sum_probs=62.5

Q ss_pred             EeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHHhHHH
Q psy1185           9 VRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASL   88 (131)
Q Consensus         9 v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~   88 (131)
                      |+|||..+++++|+++|++||.|..+.+...                           ..++.++++|||+|.+.++|..
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~---------------------------~~~~~~~~~a~v~f~~~~~a~~   53 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRD---------------------------KDTGKSKGFAFVEFESEEDAEK   53 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeC---------------------------CCCCCCCceEEEEeCCHHHHHH
Confidence            5899999999999999999999999988743                           2256788999999999999999


Q ss_pred             HHHHHhCCcceecCcEEEEE
Q psy1185          89 AKKRLATGRLKVWGCDIIVD  108 (131)
Q Consensus        89 a~~~l~~~~~~~~g~~l~v~  108 (131)
                      |+..+++.  .++|+.+.|+
T Consensus        54 a~~~~~~~--~~~~~~~~v~   71 (71)
T smart00360       54 ALEALNGK--ELDGRPLKVK   71 (71)
T ss_pred             HHHHcCCC--eeCCcEEEeC
Confidence            99999987  7889888763

>KOG0127|consensus

Probab=99.50  E-value=2.6e-13  Score=105.37  Aligned_cols=112  Identities=23%  Similarity=0.385  Sum_probs=94.6

Q ss_pred             EEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe-------cCeEEEEECCHHHHHh-------------------------
Q psy1185           6 VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI-------KDYAFVHFEDRQEAIT-------------------------   53 (131)
Q Consensus         6 ~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~-------~~~~fv~~~~~~~a~~-------------------------   53 (131)
                      .|.|.|||+.|.+.+|+.+|++||.|.++.|+       +|||||+|....+|+.                         
T Consensus       119 rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd~  198 (678)
T KOG0127|consen  119 RLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDKDT  198 (678)
T ss_pred             eEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeeccccc
Confidence            68899999999999999999999999999998       7999999999999998                         


Q ss_pred             --------------------------------------------------------------------------------
Q psy1185          54 --------------------------------------------------------------------------------   53 (131)
Q Consensus        54 --------------------------------------------------------------------------------   53 (131)
                                                                                                      
T Consensus       199 ye~ta~~~~~s~Kk~~~eEed~e~~~d~~~~~~~Ed~e~d~edeEe~D~~se~~ee~~~~Eee~~~vDd~e~S~~~~~~k  278 (678)
T KOG0127|consen  199 YEDTAHEEKQSLKKAVKEEEDKEADEDDGKDFDEEDGEEDSEDEEETDGNSEAFEEGEESEEEEDDVDDEESSGKKESDK  278 (678)
T ss_pred             ccccchhhhhhhhhccchhhhcccccccccccchhcccccccccccccccchhhhccccccccccccccccccccCcccc
Confidence                                                                                            


Q ss_pred             ------------------------------------hcCCceeEEecCCCCCCCCcceEEEEeCCHHhHHHHHHHH----
Q psy1185          54 ------------------------------------VTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRL----   93 (131)
Q Consensus        54 ------------------------------------~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l----   93 (131)
                                                          .+|-....+.+..+.+++++|.|||.|.+..+++.||...    
T Consensus       279 ~~q~k~~~en~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~  358 (678)
T KOG0127|consen  279 KAQNKTTRENITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAASPAS  358 (678)
T ss_pred             hhccccccccccccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcCccC
Confidence                                                4563333333333469999999999999999999999987    


Q ss_pred             hCCcceecCcEEEEEecCCCCCCC
Q psy1185          94 ATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        94 ~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      -...+.++|+.|.|..|.++.+..
T Consensus       359 e~g~~ll~GR~Lkv~~Av~RkeA~  382 (678)
T KOG0127|consen  359 EDGSVLLDGRLLKVTLAVTRKEAA  382 (678)
T ss_pred             CCceEEEeccEEeeeeccchHHHH
Confidence            222367899999999999887654

>KOG0130|consensus

Probab=99.50  E-value=5.9e-14  Score=91.65  Aligned_cols=81  Identities=23%  Similarity=0.502  Sum_probs=73.9

Q ss_pred             EEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHHh
Q psy1185           6 VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKS   85 (131)
Q Consensus         6 ~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~~   85 (131)
                      .|||.++...++++++.+.|..||+|+++++-..                           .++|..+|||+|+|.+.+.
T Consensus        74 Ii~VtgvHeEatEedi~d~F~dyGeiKNihLNLD---------------------------RRtGy~KGYaLvEYet~ke  126 (170)
T KOG0130|consen   74 IIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLD---------------------------RRTGYVKGYALVEYETLKE  126 (170)
T ss_pred             EEEEeccCcchhHHHHHHHHhhcccccceeeccc---------------------------cccccccceeeeehHhHHH
Confidence            5899999999999999999999999999987633                           4588899999999999999


Q ss_pred             HHHHHHHHhCCcceecCcEEEEEecCCCCC
Q psy1185          86 ASLAKKRLATGRLKVWGCDIIVDWADPQEE  115 (131)
Q Consensus        86 a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~  115 (131)
                      |++|+..+||.  .+.|..|.|.|+..+.+
T Consensus       127 Aq~A~~~~Ng~--~ll~q~v~VDw~Fv~gp  154 (170)
T KOG0130|consen  127 AQAAIDALNGA--ELLGQNVSVDWCFVKGP  154 (170)
T ss_pred             HHHHHHhccch--hhhCCceeEEEEEecCC
Confidence            99999999998  88999999999876655

>KOG0114|consensus

Probab=99.50  E-value=3e-13  Score=84.59  Aligned_cols=79  Identities=27%  Similarity=0.445  Sum_probs=70.6

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .+-|||.|||+++|.++..++|++||.|.++++-.                              +..-+|.|||.|.+.
T Consensus        18 nriLyirNLp~~ITseemydlFGkyg~IrQIRiG~------------------------------~k~TrGTAFVVYedi   67 (124)
T KOG0114|consen   18 NRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGN------------------------------TKETRGTAFVVYEDI   67 (124)
T ss_pred             heeEEEecCCccccHHHHHHHhhcccceEEEEecC------------------------------ccCcCceEEEEehHh
Confidence            46799999999999999999999999999998753                              345589999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCCCC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADPQE  114 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~  114 (131)
                      .+|.+|++.|.|-  .+.++.+.|-|-.+..
T Consensus        68 ~dAk~A~dhlsg~--n~~~ryl~vlyyq~~~   96 (124)
T KOG0114|consen   68 FDAKKACDHLSGY--NVDNRYLVVLYYQPED   96 (124)
T ss_pred             hhHHHHHHHhccc--ccCCceEEEEecCHHH
Confidence            9999999999997  8999999999877544

>KOG0144|consensus

Probab=99.49  E-value=4.6e-14  Score=106.79  Aligned_cols=50  Identities=30%  Similarity=0.652  Sum_probs=47.8

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe-------cCeEEEEECCHHHHHh
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI-------KDYAFVHFEDRQEAIT   53 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~-------~~~~fv~~~~~~~a~~   53 (131)
                      .++||||.|+..+||.+++++|++||.|.+|+|+       ||||||+|+..+.|..
T Consensus       124 e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fstke~A~~  180 (510)
T KOG0144|consen  124 ERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFSTKEMAVA  180 (510)
T ss_pred             chhhhhhhccccccHHHHHHHHHhhCccchhhheecccccccceeEEEEehHHHHHH
Confidence            6799999999999999999999999999999998       7999999999998887

>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=99.49  E-value=7.8e-13  Score=77.13  Aligned_cols=74  Identities=34%  Similarity=0.640  Sum_probs=65.5

Q ss_pred             EEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHHh
Q psy1185           6 VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKS   85 (131)
Q Consensus         6 ~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~~   85 (131)
                      +|+|+|||..+++++|+++|+.+|.|..+.+...                            ..+.++++|||+|.+.+.
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~----------------------------~~~~~~~~~~v~f~s~~~   52 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRD----------------------------KDTKSKGFAFVEFEDEED   52 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeC----------------------------CCCCcceEEEEEECCHHH
Confidence            4899999999999999999999999999888742                            123568999999999999


Q ss_pred             HHHHHHHHhCCcceecCcEEEEEe
Q psy1185          86 ASLAKKRLATGRLKVWGCDIIVDW  109 (131)
Q Consensus        86 a~~a~~~l~~~~~~~~g~~l~v~~  109 (131)
                      |..|++.+++.  .++|+.+.|.|
T Consensus        53 a~~a~~~~~~~--~~~~~~~~v~~   74 (74)
T cd00590          53 AEKALEALNGK--ELGGRPLRVEF   74 (74)
T ss_pred             HHHHHHHhCCC--eECCeEEEEeC
Confidence            99999999997  68999998875

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).

>KOG0110|consensus

Probab=99.48  E-value=1.5e-13  Score=109.09  Aligned_cols=108  Identities=24%  Similarity=0.426  Sum_probs=89.4

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe-----------cCeEEEEECCHHHHHh-------------------
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI-----------KDYAFVHFEDRQEAIT-------------------   53 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~-----------~~~~fv~~~~~~~a~~-------------------   53 (131)
                      .+++||.||+++++.+++..+|...|.|.++.|.           .|||||+|.++++|+.                   
T Consensus       515 ~t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~  594 (725)
T KOG0110|consen  515 ETKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKI  594 (725)
T ss_pred             chhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEe
Confidence            3449999999999999999999999999999776           2999999999999998                   


Q ss_pred             -----------------------------------------hcCCc-eeEEecCCCCCCCCcceEEEEeCCHHhHHHHHH
Q psy1185          54 -----------------------------------------VTGLS-QVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKK   91 (131)
Q Consensus        54 -----------------------------------------~~g~~-~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~   91 (131)
                                                               .+|.. -+.+... ...+..+|||||+|-++.+|..|.+
T Consensus       595 S~~k~~~~~gK~~~~kk~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK-~~k~a~rGF~Fv~f~t~~ea~nA~~  673 (725)
T KOG0110|consen  595 SENKPASTVGKKKSKKKKGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKK-IGKGAHRGFGFVDFLTPREAKNAFD  673 (725)
T ss_pred             ccCccccccccccccccccceeeeeccchHHHHHHHHHHHhcccceeeeccchh-hcchhhccceeeeccCcHHHHHHHH
Confidence                                                     23322 2222222 3445669999999999999999999


Q ss_pred             HHhCCcceecCcEEEEEecCCCC
Q psy1185          92 RLATGRLKVWGCDIIVDWADPQE  114 (131)
Q Consensus        92 ~l~~~~~~~~g~~l~v~~a~~~~  114 (131)
                      .|.+.  -++|++|+++||++..
T Consensus       674 al~ST--HlyGRrLVLEwA~~d~  694 (725)
T KOG0110|consen  674 ALGST--HLYGRRLVLEWAKSDN  694 (725)
T ss_pred             hhccc--ceechhhheehhccch
Confidence            99976  8999999999998754

>KOG0123|consensus

Probab=99.45  E-value=1.1e-12  Score=99.91  Aligned_cols=104  Identities=26%  Similarity=0.400  Sum_probs=89.8

Q ss_pred             eEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe-----cCeEEEEECCHHHHHh--------------------------
Q psy1185           5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI-----KDYAFVHFEDRQEAIT--------------------------   53 (131)
Q Consensus         5 ~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~-----~~~~fv~~~~~~~a~~--------------------------   53 (131)
                      ..+|||   +++|+..|.++|+++|++.++++.     .|||||+|.++++|++                          
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~tslgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd~~~   78 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDATSLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRDPSL   78 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecCCccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccCCce
Confidence            468999   999999999999999999999988     5899999999999999                          


Q ss_pred             --------------------hcC-CceeEEecCCCCCCCCcceEEEEeCCHHhHHHHHHHHhCCcceecCcEEEEEecCC
Q psy1185          54 --------------------VTG-LSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADP  112 (131)
Q Consensus        54 --------------------~~g-~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~  112 (131)
                                          .+| +..|.+-.+..  | ++|| ||+|.+++.|.+|+..+||.  .+.|+.|-|.....
T Consensus        79 ~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~--g-~kg~-FV~f~~e~~a~~ai~~~ng~--ll~~kki~vg~~~~  152 (369)
T KOG0123|consen   79 VFIKNLDESIDNKSLYDTFSEFGNILSCKVATDEN--G-SKGY-FVQFESEESAKKAIEKLNGM--LLNGKKIYVGLFER  152 (369)
T ss_pred             eeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCC--C-ceee-EEEeCCHHHHHHHHHHhcCc--ccCCCeeEEeeccc
Confidence                                234 55555555443  3 8999 99999999999999999998  88999999998887


Q ss_pred             CCCCC
Q psy1185         113 QEEPD  117 (131)
Q Consensus       113 ~~~~~  117 (131)
                      +.++.
T Consensus       153 ~~er~  157 (369)
T KOG0123|consen  153 KEERE  157 (369)
T ss_pred             hhhhc
Confidence            77655

>KOG4206|consensus

Probab=99.44  E-value=6e-13  Score=93.38  Aligned_cols=83  Identities=24%  Similarity=0.456  Sum_probs=74.4

Q ss_pred             CCCceEEEEeCCCCCCCHHHHHH----HhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceE
Q psy1185           1 MSKVKVLYVRNLTQYCTEEKLKE----AFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFC   76 (131)
Q Consensus         1 ~~~~~~l~v~nLp~~~t~~~l~~----~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~   76 (131)
                      |+...||||.||+..+..++|++    ||++||.|..+...+                              +.+.+|-|
T Consensus         6 ~~pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~k------------------------------t~KmRGQA   55 (221)
T KOG4206|consen    6 VNPNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFK------------------------------TPKMRGQA   55 (221)
T ss_pred             cCCCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecC------------------------------CCCccCce
Confidence            45667999999999999999988    999999999987653                              57789999


Q ss_pred             EEEeCCHHhHHHHHHHHhCCcceecCcEEEEEecCCCCC
Q psy1185          77 FLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEE  115 (131)
Q Consensus        77 fv~f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~  115 (131)
                      ||.|.+.+.|..|++.|+|-  .+.|+.++++||..+..
T Consensus        56 ~VvFk~~~~As~A~r~l~gf--pFygK~mriqyA~s~sd   92 (221)
T KOG4206|consen   56 FVVFKETEAASAALRALQGF--PFYGKPMRIQYAKSDSD   92 (221)
T ss_pred             EEEecChhHHHHHHHHhcCC--cccCchhheecccCccc
Confidence            99999999999999999997  78999999999987653

>KOG0123|consensus

Probab=99.42  E-value=1.7e-12  Score=98.84  Aligned_cols=109  Identities=22%  Similarity=0.396  Sum_probs=87.9

Q ss_pred             EEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe------cCeEEEEECCHHHHHhh----c--------------------
Q psy1185           6 VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI------KDYAFVHFEDRQEAITV----T--------------------   55 (131)
Q Consensus         6 ~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~------~~~~fv~~~~~~~a~~~----~--------------------   55 (131)
                      .+||.||+++++..+|.++|+.||.|.+|++.      +|| ||+|+++++|.+.    .                    
T Consensus        78 ~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~er  156 (369)
T KOG0123|consen   78 LVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENGSKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERKEER  156 (369)
T ss_pred             eeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCCceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccchhhh
Confidence            48999999999999999999999999999998      789 9999999999990    0                    


Q ss_pred             --------------------------------CCce--eEEecCCCCCCCCcceEEEEeCCHHhHHHHHHHHhCCcceec
Q psy1185          56 --------------------------------GLSQ--VIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVW  101 (131)
Q Consensus        56 --------------------------------g~~~--~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~~~~~  101 (131)
                                                      ...+  ..+...++..+.+++|+||.|.+++.|..|+..+++.  ..+
T Consensus       157 ~~~~~~~~~~~t~v~vk~~~~~~~~~~l~~~f~~~g~i~s~~v~~~~~g~~~~~gfv~f~~~e~a~~av~~l~~~--~~~  234 (369)
T KOG0123|consen  157 EAPLGEYKKRFTNVYVKNLEEDSTDEELKDLFSAYGSITSVAVMRDSIGKSKGFGFVNFENPEDAKKAVETLNGK--IFG  234 (369)
T ss_pred             cccccchhhhhhhhheeccccccchHHHHHhhcccCcceEEEEeecCCCCCCCccceeecChhHHHHHHHhccCC--cCC
Confidence                                            0000  0111122345778999999999999999999999998  677


Q ss_pred             CcEEEEEecCCCCCCC
Q psy1185         102 GCDIIVDWADPQEEPD  117 (131)
Q Consensus       102 g~~l~v~~a~~~~~~~  117 (131)
                      +..+.|.-+..+.+..
T Consensus       235 ~~~~~V~~aqkk~e~~  250 (369)
T KOG0123|consen  235 DKELYVGRAQKKSERE  250 (369)
T ss_pred             ccceeecccccchhhH
Confidence            8888888887755444

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

Probab=99.42  E-value=6.7e-12  Score=100.41  Aligned_cols=50  Identities=22%  Similarity=0.506  Sum_probs=47.2

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe--------cCeEEEEECCHHHHHh
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYAFVHFEDRQEAIT   53 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~--------~~~~fv~~~~~~~a~~   53 (131)
                      .++|||+|||.++++++|+++|++||.|.++++.        +|||||+|.+.++|..
T Consensus       204 ~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~k  261 (612)
T TIGR01645       204 FNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSE  261 (612)
T ss_pred             cceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHH
Confidence            4689999999999999999999999999999987        6899999999999887

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.

>PF13893 RRM_5: RNA recognition motif

Probab=99.41  E-value=2.6e-12  Score=72.67  Aligned_cols=56  Identities=34%  Similarity=0.581  Sum_probs=49.9

Q ss_pred             HHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHHhHHHHHHHHhCCccee
Q psy1185          21 LKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKV  100 (131)
Q Consensus        21 l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~~~~  100 (131)
                      |+++|++||+|.++.+.+.                               . +++|||+|.+.++|..|++.|||.  .+
T Consensus         1 L~~~f~~fG~V~~i~~~~~-------------------------------~-~~~a~V~f~~~~~A~~a~~~l~~~--~~   46 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKK-------------------------------K-RGFAFVEFASVEDAQKAIEQLNGR--QF   46 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETT-------------------------------S-TTEEEEEESSHHHHHHHHHHHTTS--EE
T ss_pred             ChHHhCCcccEEEEEEEeC-------------------------------C-CCEEEEEECCHHHHHHHHHHhCCC--EE
Confidence            6789999999999988742                               1 699999999999999999999998  89


Q ss_pred             cCcEEEEEec
Q psy1185         101 WGCDIIVDWA  110 (131)
Q Consensus       101 ~g~~l~v~~a  110 (131)
                      +|++|+|+||
T Consensus        47 ~g~~l~V~~a   56 (56)
T PF13893_consen   47 NGRPLKVSYA   56 (56)
T ss_dssp             TTEEEEEEEE
T ss_pred             CCcEEEEEEC
Confidence            9999999996

(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 ....

>KOG4205|consensus

Probab=99.41  E-value=4.9e-13  Score=99.27  Aligned_cols=112  Identities=24%  Similarity=0.356  Sum_probs=91.6

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe--------cCeEEEEECCHHHHHh---------------------
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYAFVHFEDRQEAIT---------------------   53 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~--------~~~~fv~~~~~~~a~~---------------------   53 (131)
                      ..+++|||+|+++++++.|++.|++||+|.+|.++        ++|+||+|.+.+....                     
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            57899999999999999999999999999999999        4999999997766555                     


Q ss_pred             -----------------------------------hcCCceeEEecCCCCCCCCcceEEEEeCCHHhHHHHHHHHhCCcc
Q psy1185          54 -----------------------------------VTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRL   98 (131)
Q Consensus        54 -----------------------------------~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~~   98 (131)
                                                         .+|....++......+..+++|+||.|.+++++.+++..--.   
T Consensus        85 r~~~~~~~~~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~~~f~---  161 (311)
T KOG4205|consen   85 REDQTKVGRHLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTLQKFH---  161 (311)
T ss_pred             cccccccccccceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceeccccee---
Confidence                                               345444444444456788999999999999888877554332   


Q ss_pred             eecCcEEEEEecCCCCCCC
Q psy1185          99 KVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        99 ~~~g~~l~v~~a~~~~~~~  117 (131)
                      .+.|+.+.|.-|.|+....
T Consensus       162 ~~~gk~vevkrA~pk~~~~  180 (311)
T KOG4205|consen  162 DFNGKKVEVKRAIPKEVMQ  180 (311)
T ss_pred             eecCceeeEeeccchhhcc
Confidence            8999999999999877654

>KOG0132|consensus

Probab=99.32  E-value=7.3e-12  Score=100.49  Aligned_cols=79  Identities=25%  Similarity=0.437  Sum_probs=72.2

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      ++|||||+|+..+++.+|..+|+.||+|.++.++                                 .+++||||....+
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li---------------------------------~~R~cAfI~M~~R  467 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILI---------------------------------PPRGCAFIKMVRR  467 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEeec---------------------------------cCCceeEEEEeeh
Confidence            6899999999999999999999999999999776                                 3589999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      ++|.+|+..|.+.  .+.++.|++.||..+-.++
T Consensus       468 qdA~kalqkl~n~--kv~~k~Iki~Wa~g~G~ks  499 (894)
T KOG0132|consen  468 QDAEKALQKLSNV--KVADKTIKIAWAVGKGPKS  499 (894)
T ss_pred             hHHHHHHHHHhcc--cccceeeEEeeeccCCcch
Confidence            9999999999976  8899999999998766554

>KOG0153|consensus

Probab=99.30  E-value=1.1e-11  Score=91.81  Aligned_cols=76  Identities=22%  Similarity=0.581  Sum_probs=69.0

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++||||+|....++.+|++.|.+||+|.++.+.-                                 .+++|||+|.+
T Consensus       227 ~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~---------------------------------~~~CAFv~ftT  273 (377)
T KOG0153|consen  227 SIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILP---------------------------------RKGCAFVTFTT  273 (377)
T ss_pred             ceeEEEecccccchhHHHHHHHHhhcCCeeeEEeec---------------------------------ccccceeeehh
Confidence            367999999999999999999999999999998873                                 26799999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADP  112 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~  112 (131)
                      +.+|+.|....-+ .+.++|++|.|.|+.+
T Consensus       274 R~aAE~Aae~~~n-~lvI~G~Rl~i~Wg~~  302 (377)
T KOG0153|consen  274 REAAEKAAEKSFN-KLVINGFRLKIKWGRP  302 (377)
T ss_pred             hHHHHHHHHhhcc-eeeecceEEEEEeCCC
Confidence            9999999888877 4799999999999998

>smart00361 RRM_1 RNA recognition motif

Probab=99.28  E-value=3e-11  Score=71.40  Aligned_cols=62  Identities=18%  Similarity=0.356  Sum_probs=51.9

Q ss_pred             HHHHHHHhh----ccCCeeEEE-EecCeEEEEECCHHHHHhhcCCceeEEecCCCCC--CCCcceEEEEeCCHHhHHHHH
Q psy1185          18 EEKLKEAFE----QYGRVERVK-RIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDN--KKNRGFCFLEYDSHKSASLAK   90 (131)
Q Consensus        18 ~~~l~~~F~----~~G~v~~~~-i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~--~~~~~~~fv~f~~~~~a~~a~   90 (131)
                      +++|+++|+    +||.|.++. ++..                           ..+  +.++|+|||+|.+.++|.+|+
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~---------------------------~~~~~~~~rG~~fV~f~~~~dA~~A~   54 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYID---------------------------NVGYENHKRGNVYITFERSEDAARAI   54 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeC---------------------------CCCCCCCCcEEEEEEECCHHHHHHHH
Confidence            578888888    999999985 4321                           123  788999999999999999999


Q ss_pred             HHHhCCcceecCcEEEEE
Q psy1185          91 KRLATGRLKVWGCDIIVD  108 (131)
Q Consensus        91 ~~l~~~~~~~~g~~l~v~  108 (131)
                      +.|+|+  .++|+.|+++
T Consensus        55 ~~l~g~--~~~gr~l~~~   70 (70)
T smart00361       55 VDLNGR--YFDGRTVKAE   70 (70)
T ss_pred             HHhCCC--EECCEEEEeC
Confidence            999998  8999998763

>KOG0146|consensus

Probab=99.21  E-value=2.4e-11  Score=87.63  Aligned_cols=85  Identities=19%  Similarity=0.286  Sum_probs=75.7

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..|+|||..||....+.||...|-.||.|.+.++--.                           +.++.+++|+||.|++
T Consensus       284 eGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvD---------------------------RATNQSKCFGFVSfDN  336 (371)
T KOG0146|consen  284 EGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVD---------------------------RATNQSKCFGFVSFDN  336 (371)
T ss_pred             CcceEEEEeCchhhccHHHHHHhccccceeeeeeeeh---------------------------hccccccceeeEecCC
Confidence            4689999999999999999999999999999876522                           2378999999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEEP  116 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~  116 (131)
                      ..+|+.|+..+||.  .++-++|+|..-+|+.+.
T Consensus       337 p~SaQaAIqAMNGF--QIGMKRLKVQLKRPkdan  368 (371)
T KOG0146|consen  337 PASAQAAIQAMNGF--QIGMKRLKVQLKRPKDAN  368 (371)
T ss_pred             chhHHHHHHHhcch--hhhhhhhhhhhcCccccC
Confidence            99999999999996  999999999998887653

>KOG4661|consensus

Probab=99.16  E-value=1.1e-10  Score=91.61  Aligned_cols=84  Identities=21%  Similarity=0.317  Sum_probs=74.9

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .+++||.+|+..|-..+|+.||++||.|+..+++.+                           .++...++|+||+..+.
T Consensus       405 gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTN---------------------------aRsPGaRCYGfVTMSts  457 (940)
T KOG4661|consen  405 GRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTN---------------------------ARSPGARCYGFVTMSTS  457 (940)
T ss_pred             ccceeeeccccchhhhHHHHHHHHhcceeceeeeec---------------------------CCCCCcceeEEEEecch
Confidence            568999999999999999999999999999998854                           34556699999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCCCCCC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADPQEEP  116 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~  116 (131)
                      +.|.+||..||-.  .|.|+.|.|..+++.+..
T Consensus       458 ~eAtkCI~hLHrT--ELHGrmISVEkaKNEp~G  488 (940)
T KOG4661|consen  458 AEATKCIEHLHRT--ELHGRMISVEKAKNEPGG  488 (940)
T ss_pred             HHHHHHHHHhhhh--hhcceeeeeeecccCccc
Confidence            9999999999987  899999999999876543

>KOG0415|consensus

Probab=99.14  E-value=1.2e-10  Score=86.75  Aligned_cols=80  Identities=23%  Similarity=0.414  Sum_probs=74.4

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      ...|||..|.+-|+.++|.-+|+.||.|.+|.+++.                           ..+|.+-.||||+|.+.
T Consensus       239 eNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD---------------------------~ktgdsLqyaFiEFen~  291 (479)
T KOG0415|consen  239 ENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRD---------------------------RKTGDSLQYAFIEFENK  291 (479)
T ss_pred             cceEEEEecCCcccccchhhHHhhcccceeeeEEec---------------------------ccccchhheeeeeecch
Confidence            567999999999999999999999999999999976                           45899999999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADP  112 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~  112 (131)
                      ++..+|...|.+.  .++.++|.|.|+.+
T Consensus       292 escE~AyFKMdNv--LIDDrRIHVDFSQS  318 (479)
T KOG0415|consen  292 ESCEQAYFKMDNV--LIDDRRIHVDFSQS  318 (479)
T ss_pred             hhHHHHHhhhcce--eeccceEEeehhhh
Confidence            9999999999986  89999999999764

>KOG0106|consensus

Probab=99.14  E-value=6.9e-11  Score=83.47  Aligned_cols=103  Identities=23%  Similarity=0.394  Sum_probs=82.2

Q ss_pred             eEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhh---------cCCc-----------------
Q psy1185           5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITV---------TGLS-----------------   58 (131)
Q Consensus         5 ~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~---------~g~~-----------------   58 (131)
                      ..+|||+||+...+.++.++|..||.+..+.+..+|+||+|.+..+|..+         .|..                 
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~~~~~g~~~   81 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMKNGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGKRRGRGRPR   81 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceeecccceeccCchhhhhcccchhcCceecceeeeeecccccccccCCCC
Confidence            57999999999999999999999999999999999999999999999981         1111                 


Q ss_pred             -----------------eeEEecCCC--------------CCCC------CcceEEEEeCCHHhHHHHHHHHhCCcceec
Q psy1185          59 -----------------QVIIYSSPD--------------DNKK------NRGFCFLEYDSHKSASLAKKRLATGRLKVW  101 (131)
Q Consensus        59 -----------------~~~~~~~~~--------------~~~~------~~~~~fv~f~~~~~a~~a~~~l~~~~~~~~  101 (131)
                                       .+.+...+.              .-|.      ..+++||+|.+..+|..|+..|++.  .+.
T Consensus        82 ~g~r~~~~~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~~~~~~~v~Fs~~~da~ra~~~l~~~--~~~  159 (216)
T KOG0106|consen   82 GGDRRSDSRRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDARRNFAFVEFSEQEDAKRALEKLDGK--KLN  159 (216)
T ss_pred             CCCccchhhccCCcccccceeeeccchhhhhHHHHhhhhcccCCCchhhhhccccceeehhhhhhhhcchhccch--hhc
Confidence                             000000000              0011      3689999999999999999999998  899


Q ss_pred             CcEEEEEe
Q psy1185         102 GCDIIVDW  109 (131)
Q Consensus       102 g~~l~v~~  109 (131)
                      ++.|.+..
T Consensus       160 ~~~l~~~~  167 (216)
T KOG0106|consen  160 GRRISVEK  167 (216)
T ss_pred             Cceeeecc
Confidence            99999944

>KOG0147|consensus

Probab=99.13  E-value=8.7e-11  Score=91.33  Aligned_cols=111  Identities=22%  Similarity=0.338  Sum_probs=88.6

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe--------cCeEEEEECCHHHHHh----------------------
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYAFVHFEDRQEAIT----------------------   53 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~--------~~~~fv~~~~~~~a~~----------------------   53 (131)
                      .+|+|+..|+...++.+|.++|+..|.|..++++        +|.|||.|.+.++...                      
T Consensus       179 ~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aiaLsGqrllg~pv~vq~sEae  258 (549)
T KOG0147|consen  179 QRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIALSGQRLLGVPVIVQLSEAE  258 (549)
T ss_pred             HHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhhhcCCcccCceeEecccHHH
Confidence            3578888889999999999999999999999988        7999999998866554                      


Q ss_pred             ------------------------------------------hcCCceeEEecCCCCCCCCcceEEEEeCCHHhHHHHHH
Q psy1185          54 ------------------------------------------VTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKK   91 (131)
Q Consensus        54 ------------------------------------------~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~   91 (131)
                                                                .+|-.+.+......++|.++||||++|.+.+.|.+|+.
T Consensus       259 knr~a~~s~a~~~k~~~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e  338 (549)
T KOG0147|consen  259 KNRAANASPALQGKGFTGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALE  338 (549)
T ss_pred             HHHHHhccccccccccccchhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHH
Confidence                                                      22322222222223489999999999999999999999


Q ss_pred             HHhCCcceecCcEEEEEecCCCCCC
Q psy1185          92 RLATGRLKVWGCDIIVDWADPQEEP  116 (131)
Q Consensus        92 ~l~~~~~~~~g~~l~v~~a~~~~~~  116 (131)
                      .|||  |.+-|+.|+|....-+-..
T Consensus       339 ~lng--felAGr~ikV~~v~~r~~~  361 (549)
T KOG0147|consen  339 QLNG--FELAGRLIKVSVVTERVDT  361 (549)
T ss_pred             Hhcc--ceecCceEEEEEeeeeccc
Confidence            9999  5999999999876544443

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.11  E-value=2.2e-10  Score=86.76  Aligned_cols=51  Identities=33%  Similarity=0.584  Sum_probs=47.7

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe--------cCeEEEEECCHHHHHhh
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYAFVHFEDRQEAITV   54 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~--------~~~~fv~~~~~~~a~~~   54 (131)
                      .++|||+|||.++++++|+++|++||.|..++++        ++||||+|.+.++|+.+
T Consensus       193 ~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~A  251 (346)
T TIGR01659       193 DTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEA  251 (346)
T ss_pred             cceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHH
Confidence            5689999999999999999999999999999887        47999999999999994

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).

>KOG4208|consensus

Probab=99.08  E-value=6.5e-10  Score=77.33  Aligned_cols=81  Identities=20%  Similarity=0.387  Sum_probs=72.6

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhcc-CCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQY-GRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~-G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..-+|++.+|....+.++..+|.++ |.+...++.|+                           .++|+++|||||+|.+
T Consensus        49 ~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRn---------------------------krTGNSKgYAFVEFEs  101 (214)
T KOG4208|consen   49 EGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRN---------------------------KRTGNSKGYAFVEFES  101 (214)
T ss_pred             ccceeecccccchhHHHHhhhhhhcCCeeEEEEeecc---------------------------cccCCcCceEEEEecc
Confidence            3468999999999999999999998 77888888776                           6799999999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQ  113 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~  113 (131)
                      .+.|.=|-+.||+-  .++|+.|.+.+-.|.
T Consensus       102 ~eVA~IaAETMNNY--Ll~e~lL~c~vmppe  130 (214)
T KOG4208|consen  102 EEVAKIAAETMNNY--LLMEHLLECHVMPPE  130 (214)
T ss_pred             HHHHHHHHHHhhhh--hhhhheeeeEEeCch
Confidence            99999999999996  789999999987765

>KOG0147|consensus

Probab=99.06  E-value=6.7e-10  Score=86.49  Aligned_cols=48  Identities=35%  Similarity=0.654  Sum_probs=45.4

Q ss_pred             EEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe--------cCeEEEEECCHHHHHh
Q psy1185           6 VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYAFVHFEDRQEAIT   53 (131)
Q Consensus         6 ~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~--------~~~~fv~~~~~~~a~~   53 (131)
                      .+|||||.++++++.|+..|++||.|..+.+.        +|||||+|.+.++|..
T Consensus       280 rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~  335 (549)
T KOG0147|consen  280 RLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARK  335 (549)
T ss_pred             hhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHH
Confidence            38999999999999999999999999998776        7999999999999998

>KOG0110|consensus

Probab=99.03  E-value=4.4e-09  Score=84.06  Aligned_cols=105  Identities=29%  Similarity=0.358  Sum_probs=83.7

Q ss_pred             eEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe--cCeEEEEECCHHHHHh-----------------------------
Q psy1185           5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--KDYAFVHFEDRQEAIT-----------------------------   53 (131)
Q Consensus         5 ~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~--~~~~fv~~~~~~~a~~-----------------------------   53 (131)
                      +.++++|||..+..++|...|..||+|..+.++  -..++|+|.++.+|..                             
T Consensus       386 ~vil~kNlpa~t~~~elt~~F~~fG~i~rvllp~~G~~aiv~fl~p~eAr~Afrklaysr~k~~plyle~aP~dvf~~~p  465 (725)
T KOG0110|consen  386 TVILVKNLPAGTLSEELTEAFLRFGEIGRVLLPPGGTGAIVEFLNPLEARKAFRKLAYSRFKSAPLYLEWAPEDVFTEDP  465 (725)
T ss_pred             ceeeeccCccccccHHHHHHhhcccccceeecCcccceeeeeecCccchHHHHHHhchhhhccCccccccChhhhccCCc
Confidence            578999999999999999999999999999665  2458999999999988                             


Q ss_pred             ------------------------------------------------------------------------hcC-Ccee
Q psy1185          54 ------------------------------------------------------------------------VTG-LSQV   60 (131)
Q Consensus        54 ------------------------------------------------------------------------~~g-~~~~   60 (131)
                                                                                              ..| +..+
T Consensus       466 ka~~~~~e~~~~~ee~~~Er~s~~d~~v~eD~d~te~ss~a~~a~~~~~~t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~  545 (725)
T KOG0110|consen  466 KADDLSAESRSKMEENPSERVSAEDGQVEEDKDPTEESSLARVAEDEETETKLFVKNLNFDTTLEDLEDLFSKQGTVLSI  545 (725)
T ss_pred             cccccccccccccccCcceecccccccccccCCccccccchhhhhccccchhhhhhcCCcccchhHHHHHHHhcCeEEEE
Confidence                                                                                    122 1122


Q ss_pred             EEecCCC--CCCCCcceEEEEeCCHHhHHHHHHHHhCCcceecCcEEEEEecC
Q psy1185          61 IIYSSPD--DNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWAD  111 (131)
Q Consensus        61 ~~~~~~~--~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~  111 (131)
                      .+...++  ...-+.|||||+|.+.++|+.|++.|+|.  .++|+.|.|+++.
T Consensus       546 ~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgt--vldGH~l~lk~S~  596 (725)
T KOG0110|consen  546 EISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGT--VLDGHKLELKISE  596 (725)
T ss_pred             EEeccccccccccccceeEEEecCHHHHHHHHHHhcCc--eecCceEEEEecc
Confidence            2222111  11224599999999999999999999998  9999999999998

>KOG4212|consensus

Probab=99.01  E-value=2.3e-09  Score=82.00  Aligned_cols=79  Identities=22%  Similarity=0.357  Sum_probs=70.0

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhc-cCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQ-YGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYD   81 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~-~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~   81 (131)
                      +.+.+||.|+|++..=.+|++||.. .|+|..|.+.-                            +..|++++||.|+|+
T Consensus        43 r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~----------------------------D~~GK~rGcavVEFk   94 (608)
T KOG4212|consen   43 RDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLF----------------------------DESGKARGCAVVEFK   94 (608)
T ss_pred             ccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeec----------------------------ccCCCcCCceEEEee
Confidence            4677999999999999999999985 68999987763                            357999999999999


Q ss_pred             CHHhHHHHHHHHhCCcceecCcEEEEEecC
Q psy1185          82 SHKSASLAKKRLATGRLKVWGCDIIVDWAD  111 (131)
Q Consensus        82 ~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~  111 (131)
                      +++.+++|++.||..  .+.|+.|.|.-..
T Consensus        95 ~~E~~qKa~E~lnk~--~~~GR~l~vKEd~  122 (608)
T KOG4212|consen   95 DPENVQKALEKLNKY--EVNGRELVVKEDH  122 (608)
T ss_pred             CHHHHHHHHHHhhhc--cccCceEEEeccC
Confidence            999999999999987  8999999997643

>KOG4212|consensus

Probab=98.93  E-value=3.1e-09  Score=81.27  Aligned_cols=74  Identities=24%  Similarity=0.310  Sum_probs=66.9

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      +.|+|+|.|||.++|=+.|++-|..||.|..+.|+-                              .|++++  .|.|.+
T Consensus       535 Ka~qIiirNlP~dfTWqmlrDKfre~G~v~yadime------------------------------~GkskG--VVrF~s  582 (608)
T KOG4212|consen  535 KACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIME------------------------------NGKSKG--VVRFFS  582 (608)
T ss_pred             cccEEEEecCCccccHHHHHHHHHhccceehhhhhc------------------------------cCCccc--eEEecC
Confidence            468899999999999999999999999999988873                              355666  889999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEec
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWA  110 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a  110 (131)
                      +++|++|+..+++.  .++|+.|.|.|+
T Consensus       583 ~edAEra~a~Mngs--~l~Gr~I~V~y~  608 (608)
T KOG4212|consen  583 PEDAERACALMNGS--RLDGRNIKVTYF  608 (608)
T ss_pred             HHHHHHHHHHhccC--cccCceeeeeeC
Confidence            99999999999998  999999999884

>KOG1190|consensus

Probab=98.92  E-value=2.5e-09  Score=81.05  Aligned_cols=103  Identities=31%  Similarity=0.424  Sum_probs=85.0

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe--cCeEEEEECCHHHHHh----------------------------
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--KDYAFVHFEDRQEAIT----------------------------   53 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~--~~~~fv~~~~~~~a~~----------------------------   53 (131)
                      ++.|.++|||++++|.++.+++.+||.|..+.+.  ++.||++|.+.++|..                            
T Consensus        28 SkV~HlRnlp~e~tE~elI~Lg~pFG~vtn~~~lkGknQAflem~d~~sAvtmv~~y~~~~p~lr~~~~yiq~sn~~~lk  107 (492)
T KOG1190|consen   28 SKVVHLRNLPWEVTEEELISLGLPFGKVTNLLMLKGKNQAFLEMADEESAVTMVNYYTSVTPVLRGQPIYIQYSNHSELK  107 (492)
T ss_pred             cceeEeccCCccccHHHHHHhcccccceeeeeeeccchhhhhhhcchhhhhheeecccccCccccCcceeehhhhHHHHh
Confidence            5789999999999999999999999999999877  7899999999999987                            


Q ss_pred             -----------------------------------------------------------------hcCCceeEEecCCCC
Q psy1185          54 -----------------------------------------------------------------VTGLSQVIIYSSPDD   68 (131)
Q Consensus        54 -----------------------------------------------------------------~~g~~~~~~~~~~~~   68 (131)
                                                                                       .+|....|+..    
T Consensus       108 t~s~p~q~r~~~vy~~~s~~q~~~~~~s~~~~~~G~~~~~n~vLr~iie~m~ypVslDVLHqvFS~fG~VlKIiTF----  183 (492)
T KOG1190|consen  108 TDSQPNQIRGQAVYQAVSSVQEIVLPLSASAVVVGNEDGPNPVLRTIIENMFYPVSLDVLHQVFSKFGFVLKIITF----  183 (492)
T ss_pred             ccCchhhhhhhhHHhhhhcccccccccccccccccccCCCceeEEEEeccceeeeEHHHHHHHHhhcceeEEEEEE----
Confidence                                                                             22322222211    


Q ss_pred             CCCCcce-EEEEeCCHHhHHHHHHHHhCCcceecCcEEEEEecC
Q psy1185          69 NKKNRGF-CFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWAD  111 (131)
Q Consensus        69 ~~~~~~~-~fv~f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~  111 (131)
                       .++.+| |.|.|.+.+.|+.|.-.|.|..+.=++|.|+++|++
T Consensus       184 -~Knn~FQALvQy~d~~sAq~AK~aLdGqnIyngcCtLrId~Sk  226 (492)
T KOG1190|consen  184 -TKNNGFQALVQYTDAVSAQAAKLALDGQNIYNGCCTLRIDFSK  226 (492)
T ss_pred             -ecccchhhhhhccchhhHHHHHHhccCCcccCceeEEEeehhh
Confidence             233454 899999999999999999999877778889999886

>KOG0151|consensus

Probab=98.89  E-value=4.1e-09  Score=84.43  Aligned_cols=82  Identities=23%  Similarity=0.380  Sum_probs=70.1

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .+++||+||++.++++.|-..|++||+|.+++++..-                        .-......+.||||.|.++
T Consensus       174 TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpR------------------------tEeEk~r~r~cgfvafmnR  229 (877)
T KOG0151|consen  174 TTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPR------------------------TEEEKRRERNCGFVAFMNR  229 (877)
T ss_pred             ccceeeecCCccccHHHHHHHhcccCcccceeeeccc------------------------chhhhccccccceeeehhh
Confidence            4689999999999999999999999999999988210                        0011234578999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWAD  111 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~  111 (131)
                      .+|++|+..|+|.  .+.+..+++.|++
T Consensus       230 ~D~era~k~lqg~--iv~~~e~K~gWgk  255 (877)
T KOG0151|consen  230 ADAERALKELQGI--IVMEYEMKLGWGK  255 (877)
T ss_pred             hhHHHHHHHhcce--eeeeeeeeecccc
Confidence            9999999999997  8899999999995

>KOG1456|consensus

Probab=98.89  E-value=1.7e-08  Score=75.96  Aligned_cols=109  Identities=28%  Similarity=0.358  Sum_probs=86.7

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe--cCeEEEEECCHHHHHh----------------------------
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--KDYAFVHFEDRQEAIT----------------------------   53 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~--~~~~fv~~~~~~~a~~----------------------------   53 (131)
                      +-.|.|.+|-...+|.+|.+..+.||+|..+..+  +..+.|.|++.+.|+.                            
T Consensus        31 spvvhvr~l~~~v~eadl~eal~~fG~i~yvt~~P~~r~alvefedi~~akn~Vnfaa~n~i~i~gq~Al~NyStsq~i~  110 (494)
T KOG1456|consen   31 SPVVHVRGLHQGVVEADLVEALSNFGPIAYVTCMPHKRQALVEFEDIEGAKNCVNFAADNQIYIAGQQALFNYSTSQCIE  110 (494)
T ss_pred             CceEEEeccccccchhHHHHHHhcCCceEEEEeccccceeeeeeccccchhhheehhccCcccccCchhhcccchhhhhc
Confidence            4468999999999999999999999999998877  7889999999998888                            


Q ss_pred             -------------------------------hcCCceeEEecCCCCCCCCcceEEEEeCCHHhHHHHHHHHhCCcceecC
Q psy1185          54 -------------------------------VTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWG  102 (131)
Q Consensus        54 -------------------------------~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~~~~~g  102 (131)
                                                     +....+.++++-.  ..++.-.|.|+|.+.+.|++|...|||.++.-+.
T Consensus       111 R~g~es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvI--fkkngVQAmVEFdsv~~AqrAk~alNGADIYsGC  188 (494)
T KOG1456|consen  111 RPGDESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVI--FKKNGVQAMVEFDSVEVAQRAKAALNGADIYSGC  188 (494)
T ss_pred             cCCCCCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEE--EeccceeeEEeechhHHHHHHHhhcccccccccc
Confidence                                           1111111111110  1123346999999999999999999999999899


Q ss_pred             cEEEEEecCCCC
Q psy1185         103 CDIIVDWADPQE  114 (131)
Q Consensus       103 ~~l~v~~a~~~~  114 (131)
                      |.|+|+||+|..
T Consensus       189 CTLKIeyAkP~r  200 (494)
T KOG1456|consen  189 CTLKIEYAKPTR  200 (494)
T ss_pred             eeEEEEecCcce
Confidence            999999999754

>KOG1548|consensus

Probab=98.88  E-value=5.6e-09  Score=77.63  Aligned_cols=90  Identities=26%  Similarity=0.280  Sum_probs=73.5

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .+.|||.|||.++|-+++.++|++||-|.+-  +                ..|-..+.+|.+.  .|+.+|-|.+.|...
T Consensus       134 Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d--~----------------~t~epk~KlYrd~--~G~lKGDaLc~y~K~  193 (382)
T KOG1548|consen  134 NTSVYVSGLPLDITVDEFAEVMSKCGIIMRD--P----------------QTGEPKVKLYRDN--QGKLKGDALCCYIKR  193 (382)
T ss_pred             CceEEecCCCCcccHHHHHHHHHhcceEecc--C----------------CCCCeeEEEEecC--CCCccCceEEEeecc
Confidence            4579999999999999999999999987652  1                1223345555544  489999999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCCCCC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADPQEE  115 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~  115 (131)
                      +++..|+..|++.  .+.|+.|+|+-|+-+..
T Consensus       194 ESVeLA~~ilDe~--~~rg~~~rVerAkfq~K  223 (382)
T KOG1548|consen  194 ESVELAIKILDED--ELRGKKLRVERAKFQMK  223 (382)
T ss_pred             cHHHHHHHHhCcc--cccCcEEEEehhhhhhc
Confidence            9999999999998  78899999999874443

>KOG0116|consensus

Probab=98.88  E-value=7.5e-09  Score=79.83  Aligned_cols=80  Identities=24%  Similarity=0.331  Sum_probs=65.5

Q ss_pred             eEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHH
Q psy1185           5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHK   84 (131)
Q Consensus         5 ~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~   84 (131)
                      .+|||+|||.+++..+|+++|.+||.|+...|...                           ...+...+||||+|.+..
T Consensus       289 ~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr---------------------------~~~~~~~~fgFV~f~~~~  341 (419)
T KOG0116|consen  289 LGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVR---------------------------SPGGKNPCFGFVEFENAA  341 (419)
T ss_pred             cceEeecCCCCCCHHHHHHHHhhcccccccceEEe---------------------------ccCCCcCceEEEEEeecc
Confidence            46999999999999999999999999999877621                           012344499999999999


Q ss_pred             hHHHHHHHHhCCcceecCcEEEEEecCCCC
Q psy1185          85 SASLAKKRLATGRLKVWGCDIIVDWADPQE  114 (131)
Q Consensus        85 ~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~  114 (131)
                      .++.|+.+-   ++.++++++.|+--++..
T Consensus       342 ~~~~~i~As---p~~ig~~kl~Veek~~~~  368 (419)
T KOG0116|consen  342 AVQNAIEAS---PLEIGGRKLNVEEKRPGF  368 (419)
T ss_pred             hhhhhhhcC---ccccCCeeEEEEeccccc
Confidence            999988775   679999999998765533

>KOG1457|consensus

Probab=98.81  E-value=4.6e-08  Score=69.21  Aligned_cols=86  Identities=17%  Similarity=0.253  Sum_probs=64.5

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .+||||.+||.++...+|..||..|---..+.+...                          .+.....+-+||+.|.++
T Consensus        34 VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~T--------------------------sk~~~~~~pvaFatF~s~   87 (284)
T KOG1457|consen   34 VRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYT--------------------------SKGDQVCKPVAFATFTSH   87 (284)
T ss_pred             cceeeeccCCcccCHHHHHHHhccCCCccceeeeec--------------------------cCCCccccceEEEEecch
Confidence            689999999999999999999999855555444310                          011122357899999999


Q ss_pred             HhHHHHHHHHhCCcceec-CcEEEEEecCCCCC
Q psy1185          84 KSASLAKKRLATGRLKVW-GCDIIVDWADPQEE  115 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~-g~~l~v~~a~~~~~  115 (131)
                      +.|++|.+.|||-.+... +..|++++|++...
T Consensus        88 q~A~aamnaLNGvrFDpE~~stLhiElAKSNtK  120 (284)
T KOG1457|consen   88 QFALAAMNALNGVRFDPETGSTLHIELAKSNTK  120 (284)
T ss_pred             HHHHHHHHHhcCeeeccccCceeEeeehhcCcc
Confidence            999999999999733322 55699999876544

>KOG0533|consensus

Probab=98.76  E-value=7.5e-08  Score=69.44  Aligned_cols=83  Identities=19%  Similarity=0.300  Sum_probs=70.1

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      +.++|+|.|||..+++++|++||+.||.+..+-+-       |                     ...|.+.|.|-|.|..
T Consensus        82 ~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vh-------y---------------------~~~G~s~Gta~v~~~r  133 (243)
T KOG0533|consen   82 RSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVH-------Y---------------------DRAGRSLGTADVSFNR  133 (243)
T ss_pred             CcceeeeecCCcCcchHHHHHHHHHhccceEEeec-------c---------------------CCCCCCCccceeeecc
Confidence            45789999999999999999999999966654332       1                     4578899999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEE  115 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~  115 (131)
                      .++|.+|++.+++-  .++|+.+.+....+...
T Consensus       134 ~~DA~~avk~~~gv--~ldG~~mk~~~i~~~~~  164 (243)
T KOG0533|consen  134 RDDAERAVKKYNGV--ALDGRPMKIEIISSPSQ  164 (243)
T ss_pred             hHhHHHHHHHhcCc--ccCCceeeeEEecCccc
Confidence            99999999999995  99999998887665443

>KOG0124|consensus

Probab=98.75  E-value=1.1e-07  Score=71.69  Aligned_cols=50  Identities=22%  Similarity=0.506  Sum_probs=45.0

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe--------cCeEEEEECCHHHHHh
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYAFVHFEDRQEAIT   53 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~--------~~~~fv~~~~~~~a~~   53 (131)
                      ...|||..+.++.++++|+.+|+-||+|..|.+-        +||||++|.+..+...
T Consensus       210 fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~e  267 (544)
T KOG0124|consen  210 FNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSE  267 (544)
T ss_pred             hheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHH
Confidence            3579999999999999999999999999999987        8999999998765544

>KOG4211|consensus

Probab=98.73  E-value=2.9e-07  Score=71.28  Aligned_cols=103  Identities=21%  Similarity=0.310  Sum_probs=77.6

Q ss_pred             CCceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe------cCeEEEEECCHHHHHh----------------------
Q psy1185           2 SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI------KDYAFVHFEDRQEAIT----------------------   53 (131)
Q Consensus         2 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~------~~~~fv~~~~~~~a~~----------------------   53 (131)
                      ++.--|=+.+|||++|+++|.++|+.|+ |.++.+.      .|=|||+|.+.++++.                      
T Consensus         8 ~~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r~~Gr~sGeA~Ve~~seedv~~AlkkdR~~mg~RYIEVf~~~~~   86 (510)
T KOG4211|consen    8 STAFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPRRNGRPSGEAYVEFTSEEDVEKALKKDRESMGHRYIEVFTAGGA   86 (510)
T ss_pred             CcceEEEecCCCccccHHHHHHHHhcCc-eeEEEEeccCCCcCcceEEEeechHHHHHHHHhhHHHhCCceEEEEccCCc
Confidence            3445577889999999999999999996 6666555      6899999999999988                      


Q ss_pred             -------------------------------------hcCCc----eeEEecCCCCCCCCcceEEEEeCCHHhHHHHHHH
Q psy1185          54 -------------------------------------VTGLS----QVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKR   92 (131)
Q Consensus        54 -------------------------------------~~g~~----~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~   92 (131)
                                                           +.||.    +..+..+.  .+++.+-|||.|.+.+.|+.|+..
T Consensus        87 e~d~~~~~~g~~s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~--rgR~tGEAfVqF~sqe~ae~Al~r  164 (510)
T KOG4211|consen   87 EADWVMRPGGPNSSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQ--RGRPTGEAFVQFESQESAEIALGR  164 (510)
T ss_pred             cccccccCCCCCCCCCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccC--CCCcccceEEEecCHHHHHHHHHH
Confidence                                                 22322    22233333  356789999999999999999888


Q ss_pred             HhCCcceecCcEEEEEec
Q psy1185          93 LATGRLKVWGCDIIVDWA  110 (131)
Q Consensus        93 l~~~~~~~~g~~l~v~~a  110 (131)
                      -..   .++-+-|.|-.+
T Consensus       165 hre---~iGhRYIEvF~S  179 (510)
T KOG4211|consen  165 HRE---NIGHRYIEVFRS  179 (510)
T ss_pred             HHH---hhccceEEeehh
Confidence            665   566666776443

>KOG0109|consensus

Probab=98.73  E-value=6.7e-09  Score=75.77  Aligned_cols=50  Identities=40%  Similarity=0.751  Sum_probs=47.7

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHh
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAIT   53 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~   53 (131)
                      +++++|||+.+.|+.++|+..|++||+|.+|.|+++|+||+|.-.++|..
T Consensus        78 stkl~vgNis~tctn~ElRa~fe~ygpviecdivkdy~fvh~d~~eda~~  127 (346)
T KOG0109|consen   78 STKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKDYAFVHFDRAEDAVE  127 (346)
T ss_pred             ccccccCCCCccccCHHHhhhhcccCCceeeeeecceeEEEEeeccchHH
Confidence            56899999999999999999999999999999999999999999988877

>KOG4660|consensus

Probab=98.73  E-value=1.4e-08  Score=79.39  Aligned_cols=70  Identities=26%  Similarity=0.423  Sum_probs=62.9

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|+|-|||..+++++|..+|+.||+|.+++.                                +...++..||+|.|
T Consensus        74 ~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~--------------------------------t~~~~~~~~v~FyD  121 (549)
T KOG4660|consen   74 NQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRE--------------------------------TPNKRGIVFVEFYD  121 (549)
T ss_pred             ccceEEEEecCCcCCHHHHHHHHHhhcchhhhhc--------------------------------ccccCceEEEEEee
Confidence            3679999999999999999999999999999654                                44568999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEE
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDII  106 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~  106 (131)
                      ..+|++|+++|++.  .+.|+.|.
T Consensus       122 vR~A~~Alk~l~~~--~~~~~~~k  143 (549)
T KOG4660|consen  122 VRDAERALKALNRR--EIAGKRIK  143 (549)
T ss_pred             hHhHHHHHHHHHHH--Hhhhhhhc
Confidence            99999999999998  78888877

>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=98.66  E-value=3.6e-07  Score=55.35  Aligned_cols=70  Identities=27%  Similarity=0.439  Sum_probs=49.5

Q ss_pred             eEEEEeCCCCCCCHHH----HHHHhhccC-CeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEE
Q psy1185           5 KVLYVRNLTQYCTEEK----LKEAFEQYG-RVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLE   79 (131)
Q Consensus         5 ~~l~v~nLp~~~t~~~----l~~~F~~~G-~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~   79 (131)
                      +.|||.|||.+.+...    |++|+..|| .|.++                                     ..+.|.|.
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v-------------------------------------~~~tAilr   45 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV-------------------------------------SGGTAILR   45 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE---------------------------------------TT-EEEE
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE-------------------------------------eCCEEEEE
Confidence            5799999999988765    667888886 66664                                     25789999


Q ss_pred             eCCHHhHHHHHHHHhCCcceecCcEEEEEecCCC
Q psy1185          80 YDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQ  113 (131)
Q Consensus        80 f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~  113 (131)
                      |.+++.|.+|.+.|.|.  .+.|.+|.|+|....
T Consensus        46 F~~~~~A~RA~KRmegE--dVfG~kI~v~~~~~~   77 (90)
T PF11608_consen   46 FPNQEFAERAQKRMEGE--DVFGNKISVSFSPKN   77 (90)
T ss_dssp             ESSHHHHHHHHHHHTT----SSSS--EEESS--S
T ss_pred             eCCHHHHHHHHHhhccc--ccccceEEEEEcCCc
Confidence            99999999999999998  889999999997433

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

>KOG4209|consensus

Probab=98.64  E-value=7.1e-08  Score=69.38  Aligned_cols=81  Identities=26%  Similarity=0.340  Sum_probs=71.5

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      +.+.+||||+...++.+++...|+.||.+..+.+...                           ...+++++|+||+|.+
T Consensus       100 d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d---------------------------~~~~~~k~~~yvef~~  152 (231)
T KOG4209|consen  100 DAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKD---------------------------KFRGHPKGFAYVEFSS  152 (231)
T ss_pred             CCceEEEeccccccccchhhheeeccCCccceeeecc---------------------------ccCCCcceeEEEeccc
Confidence            4578999999999999999999999999998888754                           2367789999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQ  113 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~  113 (131)
                      .+.+..|+. |++.  .+.|+.+.|.+..-.
T Consensus       153 ~~~~~~ay~-l~gs--~i~~~~i~vt~~r~~  180 (231)
T KOG4209|consen  153 YELVEEAYK-LDGS--EIPGPAIEVTLKRTN  180 (231)
T ss_pred             HhhhHHHhh-cCCc--ccccccceeeeeeee
Confidence            999999999 9998  899999999887644

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

Probab=98.60  E-value=7.6e-07  Score=55.76  Aligned_cols=83  Identities=20%  Similarity=0.242  Sum_probs=64.3

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhcc--CCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeC
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQY--GRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYD   81 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~--G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~   81 (131)
                      .+||-|.|+|...|.++|.+++...  |...-++++-.                           ..++.+.|||||.|.
T Consensus         1 RTTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiD---------------------------f~~~~N~GYAFVNf~   53 (97)
T PF04059_consen    1 RTTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPID---------------------------FKNKCNLGYAFVNFT   53 (97)
T ss_pred             CeeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeee---------------------------ccCCCceEEEEEEcC
Confidence            3789999999999999999998864  44555555522                           135678999999999


Q ss_pred             CHHhHHHHHHHHhCCcceec--CcEEEEEecCCC
Q psy1185          82 SHKSASLAKKRLATGRLKVW--GCDIIVDWADPQ  113 (131)
Q Consensus        82 ~~~~a~~a~~~l~~~~~~~~--g~~l~v~~a~~~  113 (131)
                      +++.|.+-.+..+|..|...  .+...|.||.-+
T Consensus        54 ~~~~~~~F~~~f~g~~w~~~~s~Kvc~i~yAriQ   87 (97)
T PF04059_consen   54 SPQAAIRFYKAFNGKKWPNFNSKKVCEISYARIQ   87 (97)
T ss_pred             CHHHHHHHHHHHcCCccccCCCCcEEEEehhHhh
Confidence            99999999999999866322  445688888754

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

>KOG0120|consensus

Probab=98.52  E-value=9.7e-07  Score=69.35  Aligned_cols=106  Identities=23%  Similarity=0.402  Sum_probs=82.9

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe--------cCeEEEEECCHHHHHh----------------------
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYAFVHFEDRQEAIT----------------------   53 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~--------~~~~fv~~~~~~~a~~----------------------   53 (131)
                      .+++||++||...++..+.++...||++....++        ++|+|-.|.++.....                      
T Consensus       289 ~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~  368 (500)
T KOG0120|consen  289 PNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIV  368 (500)
T ss_pred             cchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhc
Confidence            5689999999999999999999999999887766        7999999999977755                      


Q ss_pred             ---------------------------------------------------------------hcCCc-eeEEecC-CC-
Q psy1185          54 ---------------------------------------------------------------VTGLS-QVIIYSS-PD-   67 (131)
Q Consensus        54 ---------------------------------------------------------------~~g~~-~~~~~~~-~~-   67 (131)
                                                                                     -+|.. .+.+... +. 
T Consensus       369 g~~~~~~~~~~~~~~~~~i~~~~~q~~g~~t~Vl~L~n~Vt~deLkdd~EyeeIlEdvr~ec~k~g~v~~v~ipr~~~~~  448 (500)
T KOG0120|consen  369 GASNANVNFNISQSQVPGIPLLMTQMAGIPTEVLCLTNVVTPDELKDDEEYEEILEDVRTECAKFGAVRSVEIPRPYPDE  448 (500)
T ss_pred             cchhccccCCccccccccchhhhcccCCCcchhhhhhhcCCHHHhcchHHHHHHHHHHHHHhcccCceeEEecCCCCCCC
Confidence                                                                           12322 2222111 11 


Q ss_pred             CCCCCcceEEEEeCCHHhHHHHHHHHhCCcceecCcEEEEEecC
Q psy1185          68 DNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWAD  111 (131)
Q Consensus        68 ~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~  111 (131)
                      ...-..|..||+|.+.+++++|...|+|.  .+.++.+...|-.
T Consensus       449 ~~~~G~GkVFVefas~ed~qrA~~~L~Gr--KF~nRtVvtsYyd  490 (500)
T KOG0120|consen  449 NPVPGTGKVFVEFADTEDSQRAMEELTGR--KFANRTVVASYYD  490 (500)
T ss_pred             CcCCCcccEEEEecChHHHHHHHHHccCc--eeCCcEEEEEecC
Confidence            12223577899999999999999999999  9999999988854

>KOG0226|consensus

Probab=98.51  E-value=1.5e-07  Score=67.65  Aligned_cols=82  Identities=17%  Similarity=0.285  Sum_probs=72.1

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .-.||.|-|..+.+.+.|-+.|.+|-.-...+++|.                           .++|+++||+||.|.+.
T Consensus       190 DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRd---------------------------kRTgKSkgygfVSf~~p  242 (290)
T KOG0226|consen  190 DFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRD---------------------------KRTGKSKGYGFVSFRDP  242 (290)
T ss_pred             cceeecccccccccHHHHHHHHHhccchhhcccccc---------------------------ccccccccceeeeecCH
Confidence            457999999999999999999999987777777765                           57899999999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCCCC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADPQE  114 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~  114 (131)
                      .++.+|++.++|+  .++.+.|.++-+.-+.
T Consensus       243 ad~~rAmrem~gk--yVgsrpiklRkS~wke  271 (290)
T KOG0226|consen  243 ADYVRAMREMNGK--YVGSRPIKLRKSEWKE  271 (290)
T ss_pred             HHHHHHHHhhccc--ccccchhHhhhhhHHh
Confidence            9999999999999  8899998887655443

>KOG1190|consensus

Probab=98.50  E-value=1.2e-06  Score=66.72  Aligned_cols=75  Identities=28%  Similarity=0.397  Sum_probs=66.5

Q ss_pred             ceEEEEeCCCC-CCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           4 VKVLYVRNLTQ-YCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         4 ~~~l~v~nLp~-~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      .+.|.|.||.. .+|.+.|.-+|+-||.|.+++|..+                                .+.-|.|.|.+
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~n--------------------------------kkd~ALIQmsd  344 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYN--------------------------------KKDNALIQMSD  344 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeec--------------------------------CCcceeeeecc
Confidence            46788888865 5899999999999999999999843                                24779999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADP  112 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~  112 (131)
                      ...|+.|+..|.|.  .++||+|+|.+++.
T Consensus       345 ~~qAqLA~~hL~g~--~l~gk~lrvt~SKH  372 (492)
T KOG1190|consen  345 GQQAQLAMEHLEGH--KLYGKKLRVTLSKH  372 (492)
T ss_pred             hhHHHHHHHHhhcc--eecCceEEEeeccC
Confidence            99999999999999  99999999999873

>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=98.43  E-value=1.1e-06  Score=55.86  Aligned_cols=72  Identities=24%  Similarity=0.391  Sum_probs=45.9

Q ss_pred             eEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHH
Q psy1185           5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHK   84 (131)
Q Consensus         5 ~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~   84 (131)
                      +.|.+.+++..++.++|++.|++||.|..+.+.+|                                 ...|+|.|.+.+
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G---------------------------------~~~g~VRf~~~~   48 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRG---------------------------------DTEGYVRFKTPE   48 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT----------------------------------SEEEEEESS--
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCC---------------------------------CCEEEEEECCcc
Confidence            46889999999999999999999999998877754                                 467999999999


Q ss_pred             hHHHHHHHHhCC---cceecCcEEEEEe
Q psy1185          85 SASLAKKRLATG---RLKVWGCDIIVDW  109 (131)
Q Consensus        85 ~a~~a~~~l~~~---~~~~~g~~l~v~~  109 (131)
                      .|+.|+..+...   .+.+.+..+.++.
T Consensus        49 ~A~~a~~~~~~~~~~~~~i~~~~~~~~v   76 (105)
T PF08777_consen   49 AAQKALEKLKEANDGKLKIKGKEVTLEV   76 (105)
T ss_dssp             -HHHHHHHHHHTTTS-B-TTSSSEEEE-
T ss_pred             hHHHHHHHHHhccCCceEEcCceEEEEE
Confidence            999999888654   5667776665554

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

>KOG4454|consensus

Probab=98.41  E-value=1.1e-07  Score=67.03  Aligned_cols=77  Identities=21%  Similarity=0.214  Sum_probs=67.0

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .+||||+|+...++|+-|.++|-+-|+|..+.|..+                            ..++.+ ||||.|.++
T Consensus         9 drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~----------------------------~d~~~k-Fa~v~f~~E   59 (267)
T KOG4454|consen    9 DRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSG----------------------------QDQEQK-FAYVFFPNE   59 (267)
T ss_pred             hhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCC----------------------------ccCCCc-eeeeecccc
Confidence            579999999999999999999999999999988754                            245555 999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWAD  111 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~  111 (131)
                      .+..-|++-++|-  .+.+..+.+.+-.
T Consensus        60 ~sv~~a~~L~ng~--~l~~~e~q~~~r~   85 (267)
T KOG4454|consen   60 NSVQLAGQLENGD--DLEEDEEQRTLRC   85 (267)
T ss_pred             cchhhhhhhcccc--hhccchhhccccc
Confidence            9999999999997  7888888777643

>KOG4205|consensus

Probab=98.29  E-value=1e-06  Score=65.86  Aligned_cols=50  Identities=32%  Similarity=0.587  Sum_probs=46.7

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe--------cCeEEEEECCHHHHHh
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYAFVHFEDRQEAIT   53 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~--------~~~~fv~~~~~~~a~~   53 (131)
                      .++||||+||.++++.++++.|++||.|..+.++        ++||||.|.++++.+.
T Consensus        97 tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdk  154 (311)
T KOG4205|consen   97 TKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDK  154 (311)
T ss_pred             eeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccce
Confidence            5689999999999999999999999988888776        8999999999999998

>KOG0129|consensus

Probab=98.24  E-value=6.1e-06  Score=64.45  Aligned_cols=89  Identities=24%  Similarity=0.351  Sum_probs=69.7

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEE---E-------EecC---eEEEEECCHHHHHh-----------------
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERV---K-------RIKD---YAFVHFEDRQEAIT-----------------   53 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~---~-------i~~~---~~fv~~~~~~~a~~-----------------   53 (131)
                      +++||||+||++++|+.|...|..||.+.--   +       ..+|   |.|..|+++.+...                 
T Consensus       259 S~KVFvGGlp~dise~~i~~~F~~FGs~~VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~~~~~~yf~vs  338 (520)
T KOG0129|consen  259 SRKVFVGGLPWDITEAQINASFGQFGSVKVDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSEGEGNYYFKVS  338 (520)
T ss_pred             ccceeecCCCccccHHHHHhhcccccceEeecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHhhcccceEEEEe
Confidence            5789999999999999999999999975321   0       1167   99999999998887                 


Q ss_pred             ----------------------------------------------------hcCCceeEEecCCC---CCCCCcceEEE
Q psy1185          54 ----------------------------------------------------VTGLSQVIIYSSPD---DNKKNRGFCFL   78 (131)
Q Consensus        54 ----------------------------------------------------~~g~~~~~~~~~~~---~~~~~~~~~fv   78 (131)
                                                                          +.++.+.+++..++   +-+.++|-|-|
T Consensus       339 s~~~k~k~VQIrPW~laDs~fv~d~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRV  418 (520)
T KOG0129|consen  339 SPTIKDKEVQIRPWVLADSDFVLDHNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRV  418 (520)
T ss_pred             cCcccccceeEEeeEeccchhhhccCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCccee
Confidence                                                                12355555554332   45788999999


Q ss_pred             EeCCHHhHHHHHHH
Q psy1185          79 EYDSHKSASLAKKR   92 (131)
Q Consensus        79 ~f~~~~~a~~a~~~   92 (131)
                      +|.+.++-.+||..
T Consensus       419 tFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  419 TFSNQQAYIKAISA  432 (520)
T ss_pred             eecccHHHHHHHhh
Confidence            99999998888875

>KOG1457|consensus

Probab=98.19  E-value=2.3e-06  Score=60.74  Aligned_cols=62  Identities=23%  Similarity=0.395  Sum_probs=51.5

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      ..|+||.||..+++|++|+.+|+.|.-...+++-.                               ...-..||++|.+.
T Consensus       210 cstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~-------------------------------~~g~~vaf~~~~~~  258 (284)
T KOG1457|consen  210 CSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRA-------------------------------RGGMPVAFADFEEI  258 (284)
T ss_pred             hhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEec-------------------------------CCCcceEeecHHHH
Confidence            46899999999999999999999997655555441                               11246799999999


Q ss_pred             HhHHHHHHHHhCC
Q psy1185          84 KSASLAKKRLATG   96 (131)
Q Consensus        84 ~~a~~a~~~l~~~   96 (131)
                      +.|..|+..|+|.
T Consensus       259 ~~at~am~~lqg~  271 (284)
T KOG1457|consen  259 EQATDAMNHLQGN  271 (284)
T ss_pred             HHHHHHHHHhhcc
Confidence            9999999999996

>KOG4206|consensus

Probab=98.12  E-value=2.1e-05  Score=55.69  Aligned_cols=75  Identities=23%  Similarity=0.412  Sum_probs=64.3

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      ...+|+.|||..++.+.+..+|.+|.-..+++++.+                                .++.|||+|.+.
T Consensus       146 n~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~--------------------------------~~~iAfve~~~d  193 (221)
T KOG4206|consen  146 NNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPP--------------------------------RSGIAFVEFLSD  193 (221)
T ss_pred             ceEEEEecCCcchhHHHHHHHHhhCcccceeEeccC--------------------------------CCceeEEecchh
Confidence            468999999999999999999999999999988732                                378999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWAD  111 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~  111 (131)
                      ..|..|...+++..++- ...+.|.+|+
T Consensus       194 ~~a~~a~~~lq~~~it~-~~~m~i~~a~  220 (221)
T KOG4206|consen  194 RQASAAQQALQGFKITK-KNTMQITFAK  220 (221)
T ss_pred             hhhHHHhhhhccceecc-CceEEecccC
Confidence            99999999999974444 6678887764

>KOG4210|consensus

Probab=97.93  E-value=8.8e-06  Score=60.36  Aligned_cols=84  Identities=23%  Similarity=0.446  Sum_probs=72.0

Q ss_pred             ceEEE-EeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           4 VKVLY-VRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         4 ~~~l~-v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++| +++++.++++++|+..|..+|.|..+++...                           ..++..+++|++.|.+
T Consensus       184 s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~---------------------------~~s~~~kg~a~~~~~~  236 (285)
T KOG4210|consen  184 SDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTD---------------------------EESGDSKGFAYVDFSA  236 (285)
T ss_pred             cccceeecccccccchHHHhhhccCcCcceeeccCCC---------------------------CCccchhhhhhhhhhh
Confidence            34566 9999999999999999999999999887732                           3478889999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      ...+.+++.. +..  .++++.+.+.+..++...+
T Consensus       237 ~~~~~~~~~~-~~~--~~~~~~~~~~~~~~~~~~~  268 (285)
T KOG4210|consen  237 GNSKKLALND-QTR--SIGGRPLRLEEDEPRPKSD  268 (285)
T ss_pred             chhHHHHhhc-ccC--cccCcccccccCCCCcccc
Confidence            9999999888 776  8899999999998876543

>KOG0112|consensus

Probab=97.88  E-value=5.1e-06  Score=68.55  Aligned_cols=109  Identities=23%  Similarity=0.330  Sum_probs=84.5

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe-------cCeEEEEECCHHHHHhh----------------------
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI-------KDYAFVHFEDRQEAITV----------------------   54 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~-------~~~~fv~~~~~~~a~~~----------------------   54 (131)
                      .+|||+|||+...++.+|+..|..+|.+.++.|.       .-|+|+.|.+-.++-..                      
T Consensus       372 trTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~glG~~k  451 (975)
T KOG0112|consen  372 TRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHIKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGLGQPK  451 (975)
T ss_pred             hhhhhhcCcccchhhhhhhhhhhhhccccccccccCCCCcccchhhhhhhccccCcccchhhcCCccccCcccccccccc
Confidence            5789999999999999999999999999998887       57999999998877761                      


Q ss_pred             ------------------------cCCceeEEecCCCCCCCCcceEEEEeCCHHhHHHHHHHHhCCcceecCcEEEEEec
Q psy1185          55 ------------------------TGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWA  110 (131)
Q Consensus        55 ------------------------~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a  110 (131)
                                              ++-++.+-.++.   .+...|+++.|.+...|++|+..+.|.++.-..+++.|.||
T Consensus       452 st~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy---~hgq~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvdla  528 (975)
T KOG0112|consen  452 STPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDY---RHGQPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVDLA  528 (975)
T ss_pred             cccceeeccCCCCCCChHHHHHHHhhccCcceeeec---ccCCcceeeecccCccchhhHHHHhcCcCCCCCcccccccc
Confidence                                    111111111111   23457999999999999999999999866555667999998


Q ss_pred             CCCCC
Q psy1185         111 DPQEE  115 (131)
Q Consensus       111 ~~~~~  115 (131)
                      .+.-.
T Consensus       529 ~~~~~  533 (975)
T KOG0112|consen  529 SPPGA  533 (975)
T ss_pred             cCCCC
Confidence            85443

>KOG1995|consensus

Probab=97.80  E-value=3.7e-05  Score=57.75  Aligned_cols=92  Identities=22%  Similarity=0.324  Sum_probs=71.9

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ...+|||-+||..++++++.++|.+||.|..-+--                  +--.+-++.+. .++.+++-|.|.|.+
T Consensus        65 ~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t------------------~kPki~~y~dk-eT~~~KGeatvS~~D  125 (351)
T KOG1995|consen   65 DNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRT------------------GKPKIKIYTDK-ETGAPKGEATVSYED  125 (351)
T ss_pred             ccccceeeccCccchHHHHHHHHhhcceeccCCCC------------------CCcchhccccc-cccCcCCceeeeecC
Confidence            35689999999999999999999999987642111                  00011223333 688999999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEE  115 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~  115 (131)
                      ...|+.|+..+.++  .+.+..|+|..|..+..
T Consensus       126 ~~~akaai~~~agk--df~gn~ikvs~a~~r~~  156 (351)
T KOG1995|consen  126 PPAAKAAIEWFAGK--DFCGNTIKVSLAERRTG  156 (351)
T ss_pred             hhhhhhhhhhhccc--cccCCCchhhhhhhccC
Confidence            99999999999999  67788899988876653

>KOG0120|consensus

Probab=97.79  E-value=5.2e-05  Score=59.80  Aligned_cols=106  Identities=25%  Similarity=0.338  Sum_probs=81.8

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhcc-----------C-CeeEEEEe--cCeEEEEECCHHHHHh----------------
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQY-----------G-RVERVKRI--KDYAFVHFEDRQEAIT----------------   53 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~-----------G-~v~~~~i~--~~~~fv~~~~~~~a~~----------------   53 (131)
                      .+.+||+++|..+++++.-.+|..-           | .+..+.+-  .+++|++|.+.+.|..                
T Consensus       175 ~~r~~v~~~~~~~~e~~~~~f~~~~~~~~gl~~~~~g~~~~s~~~n~~~nfa~ie~~s~~~at~~~~~~~~~f~g~~~~~  254 (500)
T KOG0120|consen  175 ARRLYVGNIPFTSNEESMMSFFNSRMHASGLNQAPDGPSFVSVQLNLEKNFAFIEFRSISEATEAMALDGIIFEGRPLKI  254 (500)
T ss_pred             hhhhcccccCCccCcHhhhhhhhhhhhhcccccCCCCCceeeeeecccccceeEEecCCCchhhhhcccchhhCCCCcee
Confidence            3568999999999999999888854           2 25555443  8999999999999988                


Q ss_pred             ---------------------------------------------------------hcC-CceeEEecCCCCCCCCcce
Q psy1185          54 ---------------------------------------------------------VTG-LSQVIIYSSPDDNKKNRGF   75 (131)
Q Consensus        54 ---------------------------------------------------------~~g-~~~~~~~~~~~~~~~~~~~   75 (131)
                                                                               .+| +..-.+..+. .+|.+++|
T Consensus       255 ~r~~d~~~~p~~~~~~~~~~~~~~~~~~t~~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~-~~g~skg~  333 (500)
T KOG0120|consen  255 RRPHDYQPVPGITLSPSQLGKVGLLPASTDVPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDS-ATGNSKGF  333 (500)
T ss_pred             cccccccCCccchhhhccccccCCcccccCcccccchhhhccCcCccCHHHHHHHHHhcccchhheeeccc-ccccccce
Confidence                                                                     112 1111112222 34789999


Q ss_pred             EEEEeCCHHhHHHHHHHHhCCcceecCcEEEEEecCC
Q psy1185          76 CFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADP  112 (131)
Q Consensus        76 ~fv~f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~  112 (131)
                      ||.+|.+......|+..|||.  .+++..|+|+.|-.
T Consensus       334 af~ey~dpsvtd~A~agLnGm--~lgd~~lvvq~A~~  368 (500)
T KOG0120|consen  334 AFCEYCDPSVTDQAIAGLNGM--QLGDKKLVVQRAIV  368 (500)
T ss_pred             eeeeeeCCcchhhhhcccchh--hhcCceeEeehhhc
Confidence            999999999999999999998  89999999988753

>KOG3152|consensus

Probab=97.77  E-value=2.9e-05  Score=56.06  Aligned_cols=84  Identities=24%  Similarity=0.308  Sum_probs=58.4

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .-.||+++||+.+...-|+++|+.||.|-++++-..       +........+-        ....+..-.-|.|+|.+.
T Consensus        74 ~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE-------~~s~~~~r~~~--------~~n~~~~y~EGWvEF~~K  138 (278)
T KOG3152|consen   74 TGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPE-------DDSKRAARKRK--------GGNYKKLYSEGWVEFISK  138 (278)
T ss_pred             ceEEEeccCCCccCHHHHHHHHHhccccceEEecch-------hhHHHHHHhhc--------CCCccccchhHHHHHHHH
Confidence            457999999999999999999999999999987611       00000000000        000111123378899999


Q ss_pred             HhHHHHHHHHhCCcceecCcE
Q psy1185          84 KSASLAKKRLATGRLKVWGCD  104 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~  104 (131)
                      ..|.++...||+.  .++|+.
T Consensus       139 rvAK~iAe~Lnn~--~Iggkk  157 (278)
T KOG3152|consen  139 RVAKRIAELLNNT--PIGGKK  157 (278)
T ss_pred             HHHHHHHHHhCCC--ccCCCC
Confidence            9999999999998  778875

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

Probab=97.74  E-value=0.00014  Score=40.55  Aligned_cols=32  Identities=16%  Similarity=0.253  Sum_probs=25.4

Q ss_pred             eEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe
Q psy1185           5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI   37 (131)
Q Consensus         5 ~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~   37 (131)
                      +.|-|.+.|.+..+ .+.+.|.+||+|..+.+.
T Consensus         2 ~wI~V~Gf~~~~~~-~vl~~F~~fGeI~~~~~~   33 (53)
T PF14605_consen    2 TWISVSGFPPDLAE-EVLEHFASFGEIVDIYVP   33 (53)
T ss_pred             cEEEEEeECchHHH-HHHHHHHhcCCEEEEEcC
Confidence            56788899888754 455589999999998765

>KOG1365|consensus

Probab=97.70  E-value=0.00021  Score=54.49  Aligned_cols=102  Identities=20%  Similarity=0.143  Sum_probs=73.6

Q ss_pred             EEEEeCCCCCCCHHHHHHHhhcc----CCeeEEEEe-------cCeEEEEECCHHHHHh---------------------
Q psy1185           6 VLYVRNLTQYCTEEKLKEAFEQY----GRVERVKRI-------KDYAFVHFEDRQEAIT---------------------   53 (131)
Q Consensus         6 ~l~v~nLp~~~t~~~l~~~F~~~----G~v~~~~i~-------~~~~fv~~~~~~~a~~---------------------   53 (131)
                      .|=+.+||+++++.++.++|.+-    |....+.++       .|-|||.|..+++|..                     
T Consensus       163 ivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~ee~aq~aL~khrq~iGqRYIElFRSTa  242 (508)
T KOG1365|consen  163 IVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACEEDAQFALRKHRQNIGQRYIELFRSTA  242 (508)
T ss_pred             EEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCHHHHHHHHHHHHHHHhHHHHHHHHHhH
Confidence            34567999999999999999742    233444444       5899999999999988                     


Q ss_pred             ---------------------------------------------------------hcC-----CceeEEecCCCCCCC
Q psy1185          54 ---------------------------------------------------------VTG-----LSQVIIYSSPDDNKK   71 (131)
Q Consensus        54 ---------------------------------------------------------~~g-----~~~~~~~~~~~~~~~   71 (131)
                                                                               ++|     +.-.-+++..+..|+
T Consensus       243 aEvqqvlnr~~s~pLi~~~~sp~~p~~p~~~~p~~~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~qGr  322 (508)
T KOG1365|consen  243 AEVQQVLNREVSEPLIPGLTSPLLPGGPARLVPPTRSKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNGQGR  322 (508)
T ss_pred             HHHHHHHHhhccccccCCCCCCCCCCCccccCCCCCCCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcCCCC
Confidence                                                                     111     111112222335688


Q ss_pred             CcceEEEEeCCHHhHHHHHHHHhCCcceecCcEEEEEe
Q psy1185          72 NRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDW  109 (131)
Q Consensus        72 ~~~~~fv~f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~  109 (131)
                      +.|-|||.+.+.+.|.+|....+.+  .+.++.|.|--
T Consensus       323 PSGeAFIqm~nae~a~aaaqk~hk~--~mk~RYiEvfp  358 (508)
T KOG1365|consen  323 PSGEAFIQMRNAERARAAAQKCHKK--LMKSRYIEVFP  358 (508)
T ss_pred             cChhhhhhhhhhHHHHHHHHHHHHh--hcccceEEEee
Confidence            8999999999999999999999986  44577776643

>KOG0128|consensus

Probab=97.69  E-value=2.6e-06  Score=69.79  Aligned_cols=107  Identities=21%  Similarity=0.273  Sum_probs=80.8

Q ss_pred             eEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe--------cCeEEEEECCHHHHHhh----------------cC-Cc-
Q psy1185           5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYAFVHFEDRQEAITV----------------TG-LS-   58 (131)
Q Consensus         5 ~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~--------~~~~fv~~~~~~~a~~~----------------~g-~~-   58 (131)
                      .++|+.||+..+.+.+|...|+.+|.+..+.+.        +|+||+.|..+++|.++                .| .+ 
T Consensus       668 ~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~gK~~v~i~g~pf~  747 (881)
T KOG0128|consen  668 IKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFGKISVAISGPPFQ  747 (881)
T ss_pred             HHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhhhhhhheeCCCCC
Confidence            478999999999999999999999877665544        89999999999998881                11 00 


Q ss_pred             ---------------eeEEecCCCCCCCCcceEEEEeCCHHhHHHHHHHHhCCcceecCcEEEEEecCCC
Q psy1185          59 ---------------QVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQ  113 (131)
Q Consensus        59 ---------------~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~  113 (131)
                                     ...+.....+.|+++|-++|.|.+..++.+++......  .+....+.|..++|.
T Consensus       748 gt~e~~k~l~~~~gn~~~~~~vt~r~gkpkg~a~v~y~~ea~~s~~~~s~d~~--~~rE~~~~v~vsnp~  815 (881)
T KOG0128|consen  748 GTKEELKSLASKTGNVTSLRLVTVRAGKPKGKARVDYNTEADASRKVASVDVA--GKRENNGEVQVSNPE  815 (881)
T ss_pred             CchHHHHhhccccCCccccchhhhhccccccceeccCCCcchhhhhcccchhh--hhhhcCccccccCCc
Confidence                           00111111245788999999999999999998888776  666666777776653

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.69  E-value=0.00019  Score=54.00  Aligned_cols=79  Identities=18%  Similarity=0.328  Sum_probs=59.6

Q ss_pred             EEEEeCCCCCCCHHH----H--HHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcce-EEE
Q psy1185           6 VLYVRNLTQYCTEEK----L--KEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGF-CFL   78 (131)
Q Consensus         6 ~l~v~nLp~~~t~~~----l--~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~-~fv   78 (131)
                      -+||-+||+....++    |  .++|++||.|..+.+-+.-                         +.-...+..+ .||
T Consensus       116 LvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt-------------------------~s~nst~~h~gvYI  170 (480)
T COG5175         116 LVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKT-------------------------SSLNSTASHAGVYI  170 (480)
T ss_pred             eeEEecCCCCCCcccccccccchhhhhhccceeEEEecccc-------------------------cccccccccceEEE
Confidence            489999988876665    3  3899999999998665320                         0000111223 499


Q ss_pred             EeCCHHhHHHHHHHHhCCcceecCcEEEEEecC
Q psy1185          79 EYDSHKSASLAKKRLATGRLKVWGCDIIVDWAD  111 (131)
Q Consensus        79 ~f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~  111 (131)
                      +|.+.++|.+|+....|.  .++|+.|+..|.-
T Consensus       171 Ty~~kedAarcIa~vDgs--~~DGr~lkatYGT  201 (480)
T COG5175         171 TYSTKEDAARCIAEVDGS--LLDGRVLKATYGT  201 (480)
T ss_pred             EecchHHHHHHHHHhccc--cccCceEeeecCc
Confidence            999999999999999998  8999999999874

>KOG2193|consensus

Probab=97.64  E-value=3.9e-05  Score=59.09  Aligned_cols=78  Identities=19%  Similarity=0.286  Sum_probs=63.1

Q ss_pred             eEEEEeCCCCCCCHHHHHHHhhccCC-eeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           5 KVLYVRNLTQYCTEEKLKEAFEQYGR-VERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         5 ~~l~v~nLp~~~t~~~l~~~F~~~G~-v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .++|+|||.+..+.++|+.+|..-.- ...-.++                                  ..+|+||.+.+.
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~----------------------------------k~gyafvd~pdq   47 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLV----------------------------------KSGYAFVDCPDQ   47 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceee----------------------------------ecceeeccCCch
Confidence            57899999999999999999985411 1111122                                  268999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      .+|.+|++.++|+ ..+.|.++.+.++.++..+.
T Consensus        48 ~wa~kaie~~sgk-~elqGkr~e~~~sv~kkqrs   80 (584)
T KOG2193|consen   48 QWANKAIETLSGK-VELQGKRQEVEHSVPKKQRS   80 (584)
T ss_pred             hhhhhhHHhhchh-hhhcCceeeccchhhHHHHh
Confidence            9999999999996 69999999999998877654

>KOG4211|consensus

Probab=97.63  E-value=0.00045  Score=54.03  Aligned_cols=50  Identities=32%  Similarity=0.379  Sum_probs=40.5

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeE-EEEe-------cCeEEEEECCHHHHHh
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVER-VKRI-------KDYAFVHFEDRQEAIT   53 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~-~~i~-------~~~~fv~~~~~~~a~~   53 (131)
                      ...|=+.+||+.||+++|.++|+..--+.. +.++       .+=|||+|++.++|++
T Consensus       103 d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~  160 (510)
T KOG4211|consen  103 DGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEI  160 (510)
T ss_pred             CceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHH
Confidence            346778999999999999999997643333 3333       6889999999999999

>KOG0131|consensus

Probab=97.55  E-value=0.00015  Score=50.01  Aligned_cols=42  Identities=31%  Similarity=0.483  Sum_probs=38.4

Q ss_pred             CCCCCcceEEEEeCCHHhHHHHHHHHhCCcceecCcEEEEEecC
Q psy1185          68 DNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWAD  111 (131)
Q Consensus        68 ~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~  111 (131)
                      .+...+||||++|.++++|.-|++.|+.  +.+.|++|+|..+.
T Consensus        46 v~~~~qGygF~Ef~~eedadYAikiln~--VkLYgrpIrv~kas   87 (203)
T KOG0131|consen   46 VTQKHQGYGFAEFRTEEDADYAIKILNM--VKLYGRPIRVNKAS   87 (203)
T ss_pred             hcccccceeEEEEechhhhHHHHHHHHH--HHhcCceeEEEecc
Confidence            4566899999999999999999999995  59999999999987

>KOG1548|consensus

Probab=97.53  E-value=0.00066  Score=51.11  Aligned_cols=76  Identities=16%  Similarity=0.252  Sum_probs=60.3

Q ss_pred             CceEEEEeCCC----CCCC-------HHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCC
Q psy1185           3 KVKVLYVRNLT----QYCT-------EEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKK   71 (131)
Q Consensus         3 ~~~~l~v~nLp----~~~t-------~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~   71 (131)
                      ..++|.+.|+=    ...+       .++|++-.++||.|.++.+.                               ..+
T Consensus       264 ~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~-------------------------------d~h  312 (382)
T KOG1548|consen  264 ADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVY-------------------------------DRH  312 (382)
T ss_pred             CCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEe-------------------------------ccC
Confidence            35678888772    1233       24566668899999998776                               356


Q ss_pred             CcceEEEEeCCHHhHHHHHHHHhCCcceecCcEEEEEecC
Q psy1185          72 NRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWAD  111 (131)
Q Consensus        72 ~~~~~fv~f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~  111 (131)
                      +.|.+-|.|.+.+.|..|++.|+|+  .++||.|..+...
T Consensus       313 PdGvvtV~f~n~eeA~~ciq~m~GR--~fdgRql~A~i~D  350 (382)
T KOG1548|consen  313 PDGVVTVSFRNNEEADQCIQTMDGR--WFDGRQLTASIWD  350 (382)
T ss_pred             CCceeEEEeCChHHHHHHHHHhcCe--eecceEEEEEEeC
Confidence            7899999999999999999999999  8999999887544

>KOG1855|consensus

Probab=97.45  E-value=0.00012  Score=56.29  Aligned_cols=77  Identities=18%  Similarity=0.284  Sum_probs=56.3

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCC--CCCcceEEEEe
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDN--KKNRGFCFLEY   80 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~--~~~~~~~fv~f   80 (131)
                      .+++|.+.|||.+-.-+.|.++|+.+|.|..++|+..                |.........+...  -..+-+|+|+|
T Consensus       230 ~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckP----------------gaip~d~r~~~~~~~~~~tk~~AlvEy  293 (484)
T KOG1855|consen  230 PSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKP----------------GAIPEDVRGFPKKYFELQTKECALVEY  293 (484)
T ss_pred             ccceEEEecCCcchHHHHHHHHhhcccceeeeeecCC----------------CCCCcccccCCccchhhhhhhhhhhhh
Confidence            3689999999999988999999999999999999842                11111111111100  11267899999


Q ss_pred             CCHHhHHHHHHHHhC
Q psy1185          81 DSHKSASLAKKRLAT   95 (131)
Q Consensus        81 ~~~~~a~~a~~~l~~   95 (131)
                      ...+.|.+|.+.++.
T Consensus       294 e~~~~A~KA~e~~~~  308 (484)
T KOG1855|consen  294 EEVEAARKARELLNP  308 (484)
T ss_pred             hhhHHHHHHHHhhch
Confidence            999999999998854

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

Probab=97.40  E-value=0.00087  Score=42.21  Aligned_cols=84  Identities=14%  Similarity=0.147  Sum_probs=50.1

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .+.|-|-+.|+.. .+.+.+.|++||.|.+..-..+-             ..|+..       .......++-.|.|.++
T Consensus         6 ~~wVtVFGfp~~~-~~~Vl~~F~~~G~Ile~~~~~~~-------------~~~~~~-------~~~~~~~NWi~I~Y~~~   64 (100)
T PF05172_consen    6 ETWVTVFGFPPSA-SNQVLRHFSSFGTILEHFEVLRS-------------SSGINP-------YPIPSGGNWIHITYDNP   64 (100)
T ss_dssp             CCEEEEE---GGG-HHHHHHHHHCCS-EECEEGGG------------------------------E-CCTTEEEEEESSH
T ss_pred             CeEEEEEccCHHH-HHHHHHHHHhcceEEEeeccccc-------------cccccc-------ccCCCCCCEEEEECCCH
Confidence            4567888999984 56777899999999887522000             000000       00123468899999999


Q ss_pred             HhHHHHHHHHhCCcceecCc-EEEEEecC
Q psy1185          84 KSASLAKKRLATGRLKVWGC-DIIVDWAD  111 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~-~l~v~~a~  111 (131)
                      .+|.+||.. ||.  .++|. .+-|.|.+
T Consensus        65 ~~A~rAL~~-NG~--i~~g~~mvGV~~~~   90 (100)
T PF05172_consen   65 LSAQRALQK-NGT--IFSGSLMVGVKPCD   90 (100)
T ss_dssp             HHHHHHHTT-TTE--EETTCEEEEEEE-H
T ss_pred             HHHHHHHHh-CCe--EEcCcEEEEEEEcH
Confidence            999999876 554  67665 45677764

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.

>KOG2314|consensus

Probab=97.31  E-value=0.001  Score=53.03  Aligned_cols=75  Identities=21%  Similarity=0.309  Sum_probs=57.8

Q ss_pred             eEEEEeCCCCCCCH------HHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEE
Q psy1185           5 KVLYVRNLTQYCTE------EKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFL   78 (131)
Q Consensus         5 ~~l~v~nLp~~~t~------~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv   78 (131)
                      .-|+|.|+|.-=..      ..|..+|+++|++....++-                            ...|..+||.|+
T Consensus        59 ~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~----------------------------~e~ggtkG~lf~  110 (698)
T KOG2314|consen   59 SVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPI----------------------------DEEGGTKGYLFV  110 (698)
T ss_pred             eEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeecc----------------------------CccCCeeeEEEE
Confidence            45788888875333      35778999999999887762                            234568999999


Q ss_pred             EeCCHHhHHHHHHHHhCCcceec-CcEEEEEe
Q psy1185          79 EYDSHKSASLAKKRLATGRLKVW-GCDIIVDW  109 (131)
Q Consensus        79 ~f~~~~~a~~a~~~l~~~~~~~~-g~~l~v~~  109 (131)
                      +|.+..+|+.|++.|+|+  .++ .+++.|..
T Consensus       111 E~~~~~~A~~aVK~l~G~--~ldknHtf~v~~  140 (698)
T KOG2314|consen  111 EYASMRDAKKAVKSLNGK--RLDKNHTFFVRL  140 (698)
T ss_pred             EecChhhHHHHHHhcccc--eecccceEEeeh
Confidence            999999999999999998  444 44566653

>KOG4849|consensus

Probab=97.25  E-value=0.00031  Score=53.08  Aligned_cols=77  Identities=22%  Similarity=0.395  Sum_probs=59.7

Q ss_pred             EEEEeCCCCCCCHHHHHHHhhccCC--eeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           6 VLYVRNLTQYCTEEKLKEAFEQYGR--VERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         6 ~l~v~nLp~~~t~~~l~~~F~~~G~--v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .+|||||-|++|+++|.+...+-|.  +.++++.-+                           +..|+++|||+|...+.
T Consensus        82 ~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFEN---------------------------R~NGQSKG~AL~~~~Sd  134 (498)
T KOG4849|consen   82 CCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFEN---------------------------RTNGQSKGYALLVLNSD  134 (498)
T ss_pred             EEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhc---------------------------ccCCcccceEEEEecch
Confidence            5899999999999999998888774  333333221                           34789999999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcE-EEEEecC
Q psy1185          84 KSASLAKKRLATGRLKVWGCD-IIVDWAD  111 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~-l~v~~a~  111 (131)
                      .+..+-++.|..+  ++.|+. .+..|-+
T Consensus       135 Aa~Kq~MeiLP~k--~iHGQ~P~V~~~NK  161 (498)
T KOG4849|consen  135 AAVKQTMEILPTK--TIHGQSPTVLSYNK  161 (498)
T ss_pred             HHHHHHHHhcccc--eecCCCCeeeccch
Confidence            8888999999888  888886 3444443

>KOG4307|consensus

Probab=97.16  E-value=0.0021  Score=52.53  Aligned_cols=74  Identities=22%  Similarity=0.323  Sum_probs=62.2

Q ss_pred             eEEEEeCCCCCCCHHHHHHHhhccCCeeE-EEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           5 KVLYVRNLTQYCTEEKLKEAFEQYGRVER-VKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         5 ~~l~v~nLp~~~t~~~l~~~F~~~G~v~~-~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      +.|-+.|+|++++-+||-++|.-|-.+-. +.+.+                            .+.|...|-|-|.|.+.
T Consensus       868 ~V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~----------------------------nd~G~pTGe~mvAfes~  919 (944)
T KOG4307|consen  868 RVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRR----------------------------NDDGVPTGECMVAFESQ  919 (944)
T ss_pred             eEEEecCCCccccHHHHHHHhcccccCCCceeEee----------------------------cCCCCcccceeEeecCH
Confidence            46888999999999999999999965543 33333                            35788999999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEE
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVD  108 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~  108 (131)
                      +.|.+|...|+++  .+..+.+.+.
T Consensus       920 ~eAr~A~~dl~~~--~i~nr~V~l~  942 (944)
T KOG4307|consen  920 EEARRASMDLDGQ--KIRNRVVSLR  942 (944)
T ss_pred             HHHHhhhhccccC--cccceeEEEE
Confidence            9999999999999  8888887765

>KOG1456|consensus

Probab=97.01  E-value=0.0065  Score=46.48  Aligned_cols=74  Identities=26%  Similarity=0.281  Sum_probs=63.9

Q ss_pred             ceEEEEeCCCCC-CCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           4 VKVLYVRNLTQY-CTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         4 ~~~l~v~nLp~~-~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      .+.+.|.+|... ++.+.|..+|=.||.|.++++++.                                ..|-|.|+..+
T Consensus       287 g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkT--------------------------------k~gtamVemgd  334 (494)
T KOG1456|consen  287 GCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKT--------------------------------KPGTAMVEMGD  334 (494)
T ss_pred             CcEEEEEeccccccchhhhhhhhhhcCceeeEEEeec--------------------------------ccceeEEEcCc
Confidence            456888999776 777889999999999999999852                                36889999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWAD  111 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~  111 (131)
                      ..+.++|+..||+.  .+-|.+|.|..++
T Consensus       335 ~~aver~v~hLnn~--~lfG~kl~v~~Sk  361 (494)
T KOG1456|consen  335 AYAVERAVTHLNNI--PLFGGKLNVCVSK  361 (494)
T ss_pred             HHHHHHHHHHhccC--ccccceEEEeecc
Confidence            99999999999997  6688888888776

>KOG1996|consensus

Probab=96.74  E-value=0.0077  Score=44.71  Aligned_cols=66  Identities=24%  Similarity=0.282  Sum_probs=49.6

Q ss_pred             HHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHHhHHHHHHHHhCCc
Q psy1185          18 EEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGR   97 (131)
Q Consensus        18 ~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~   97 (131)
                      ++++++-.++||.|..|.|-                          ..+.-+-...--.||+|...++|.+|+-.|||. 
T Consensus       300 ede~keEceKyg~V~~viif--------------------------eip~~p~deavRiFveF~r~e~aiKA~VdlnGR-  352 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIF--------------------------EIPSQPEDEAVRIFVEFERVESAIKAVVDLNGR-  352 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEE--------------------------ecCCCccchhheeeeeeccHHHHHHHHHhcCCc-
Confidence            35667777888888876443                          222222233345799999999999999999999 


Q ss_pred             ceecCcEEEEEecC
Q psy1185          98 LKVWGCDIIVDWAD  111 (131)
Q Consensus        98 ~~~~g~~l~v~~a~  111 (131)
                       .++|+.++..|-+
T Consensus       353 -yFGGr~v~A~Fyn  365 (378)
T KOG1996|consen  353 -YFGGRVVSACFYN  365 (378)
T ss_pred             -eecceeeeheecc
Confidence             9999999988755

>KOG4676|consensus

Probab=96.72  E-value=0.005  Score=47.26  Aligned_cols=85  Identities=14%  Similarity=0.297  Sum_probs=59.9

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      +...|-|.||.+.++.+.+..||+..|.|.++.++-+                        +++.........|||.|.+
T Consensus         6 ~~~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~------------------------~~d~~~pv~sRtcyVkf~d   61 (479)
T KOG4676|consen    6 SLGVIQVANISPSATKDQMQTLFGNLGKIPELRLYPN------------------------VDDSKIPVISRTCYVKFLD   61 (479)
T ss_pred             CCceeeecccCchhhHHHHHHHHhhccccccccccCC------------------------CCCccCcceeeeEEEeccC
Confidence            4557899999999999999999999999999987722                        1111223445679999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcE-EEEEecCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCD-IIVDWADPQE  114 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~-l~v~~a~~~~  114 (131)
                      .+.+..|- .|.+.  .+-++. |++-|+.+..
T Consensus        62 ~~sv~vaQ-hLtnt--vfvdraliv~p~~~~~~   91 (479)
T KOG4676|consen   62 SQSVTVAQ-HLTNT--VFVDRALIVRPYGDEVI   91 (479)
T ss_pred             CcceeHHh-hhccc--eeeeeeEEEEecCCCCC
Confidence            88887664 44443  444554 5555655433

>KOG2416|consensus

Probab=96.59  E-value=0.0029  Score=50.84  Aligned_cols=49  Identities=31%  Similarity=0.391  Sum_probs=36.6

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhh-ccCCeeEEEEe---cCeEEEEECCHHHHHh
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFE-QYGRVERVKRI---KDYAFVHFEDRQEAIT   53 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~-~~G~v~~~~i~---~~~~fv~~~~~~~a~~   53 (131)
                      ++.|||.||=.-.|...|+.|+. .+|.|.+. .|   +..|||.|.+.+.|..
T Consensus       444 SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~-WmDkIKShCyV~yss~eEA~a  496 (718)
T KOG2416|consen  444 SNVLHIDNLVRPFTLGQLKELLGRTGGNVEEF-WMDKIKSHCYVSYSSVEEAAA  496 (718)
T ss_pred             cceEeeecccccchHHHHHHHHhhccCchHHH-HHHHhhcceeEecccHHHHHH
Confidence            46799999999999999999999 56667665 33   5566666666655555

>KOG2202|consensus

Probab=96.37  E-value=0.0023  Score=46.41  Aligned_cols=62  Identities=18%  Similarity=0.286  Sum_probs=49.3

Q ss_pred             HHHHHhh-ccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHHhHHHHHHHHhCCcc
Q psy1185          20 KLKEAFE-QYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRL   98 (131)
Q Consensus        20 ~l~~~F~-~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~~   98 (131)
                      ++...++ +||+|.++.+..+-                            ..+-.|-++|.|...++|++|+..||+.  
T Consensus        84 d~f~E~~~kygEiee~~Vc~Nl----------------------------~~hl~GNVYV~f~~Ee~ae~a~~~lnnR--  133 (260)
T KOG2202|consen   84 DVFTELEDKYGEIEELNVCDNL----------------------------GDHLVGNVYVKFRSEEDAEAALEDLNNR--  133 (260)
T ss_pred             HHHHHHHHHhhhhhhhhhhccc----------------------------chhhhhhhhhhcccHHHHHHHHHHHcCc--
Confidence            4444444 89999998766431                            2345788999999999999999999998  


Q ss_pred             eecCcEEEEEecC
Q psy1185          99 KVWGCDIIVDWAD  111 (131)
Q Consensus        99 ~~~g~~l~v~~a~  111 (131)
                      -+.|++|...+..
T Consensus       134 w~~G~pi~ae~~p  146 (260)
T KOG2202|consen  134 WYNGRPIHAELSP  146 (260)
T ss_pred             cccCCcceeeecC
Confidence            8899999988865

>KOG0106|consensus

Probab=96.35  E-value=0.0025  Score=45.41  Aligned_cols=51  Identities=31%  Similarity=0.472  Sum_probs=46.3

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhh
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITV   54 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~   54 (131)
                      .+.+.+.+++..++.++|.+.|.++|++....+..+++||.|+..++|..+
T Consensus        99 ~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~~~~~~~v~Fs~~~da~ra  149 (216)
T KOG0106|consen   99 HFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDARRNFAFVEFSEQEDAKRA  149 (216)
T ss_pred             cceeeeccchhhhhHHHHhhhhcccCCCchhhhhccccceeehhhhhhhhc
Confidence            456889999999999999999999999977777899999999999999983

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=96.20  E-value=0.065  Score=35.92  Aligned_cols=73  Identities=15%  Similarity=0.243  Sum_probs=56.4

Q ss_pred             ceEEEEeCCCCCCCH----HHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEE
Q psy1185           4 VKVLYVRNLTQYCTE----EKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLE   79 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~----~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~   79 (131)
                      +.||.|.=|+.++..    ..+..-++.||+|.++...                                  .+..|.|.
T Consensus        86 MsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~c----------------------------------GrqsavVv  131 (166)
T PF15023_consen   86 MSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLC----------------------------------GRQSAVVV  131 (166)
T ss_pred             ceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeec----------------------------------CCceEEEE
Confidence            567888777666554    3355566789999998654                                  26779999


Q ss_pred             eCCHHhHHHHHHHHhCCcceecCcEEEEEecCCC
Q psy1185          80 YDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQ  113 (131)
Q Consensus        80 f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~  113 (131)
                      |.+..+|=.|+++++.   ..-|..+.+.|-..-
T Consensus       132 F~d~~SAC~Av~Af~s---~~pgtm~qCsWqqrF  162 (166)
T PF15023_consen  132 FKDITSACKAVSAFQS---RAPGTMFQCSWQQRF  162 (166)
T ss_pred             ehhhHHHHHHHHhhcC---CCCCceEEeeccccc
Confidence            9999999999999988   457888999996543

>KOG0115|consensus

Probab=96.18  E-value=0.0091  Score=43.42  Aligned_cols=64  Identities=31%  Similarity=0.442  Sum_probs=54.4

Q ss_pred             eEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHH
Q psy1185           5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHK   84 (131)
Q Consensus         5 ~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~   84 (131)
                      ..|||.||+..++.+.+.+-|+.||+|....++-                            +..++..+-++|.|.+.-
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~v----------------------------D~r~k~t~eg~v~~~~k~   83 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKV----------------------------DDRGKPTREGIVEFAKKP   83 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeee----------------------------cccccccccchhhhhcch
Confidence            5799999999999999999999999998865552                            224667788999999999


Q ss_pred             hHHHHHHHHhCC
Q psy1185          85 SASLAKKRLATG   96 (131)
Q Consensus        85 ~a~~a~~~l~~~   96 (131)
                      .|.+|++.+...
T Consensus        84 ~a~~a~rr~~~~   95 (275)
T KOG0115|consen   84 NARKAARRCREG   95 (275)
T ss_pred             hHHHHHHHhccC
Confidence            999999998554

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

Probab=96.14  E-value=0.058  Score=32.82  Aligned_cols=57  Identities=16%  Similarity=0.307  Sum_probs=41.2

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      +.+..|++ .|..+-..||.++|+.||.|. +..+                                  +-..|||...+
T Consensus         8 RdHVFhlt-FPkeWK~~DI~qlFspfG~I~-VsWi----------------------------------~dTSAfV~l~~   51 (87)
T PF08675_consen    8 RDHVFHLT-FPKEWKTSDIYQLFSPFGQIY-VSWI----------------------------------NDTSAFVALHN   51 (87)
T ss_dssp             GCCEEEEE---TT--HHHHHHHCCCCCCEE-EEEE----------------------------------CTTEEEEEECC
T ss_pred             cceEEEEe-CchHhhhhhHHHHhccCCcEE-EEEE----------------------------------cCCcEEEEeec
Confidence            34556666 999999999999999999863 3333                                  24569999999


Q ss_pred             HHhHHHHHHHHhC
Q psy1185          83 HKSASLAKKRLAT   95 (131)
Q Consensus        83 ~~~a~~a~~~l~~   95 (131)
                      ++.|..+++.+..
T Consensus        52 r~~~~~v~~~~~~   64 (87)
T PF08675_consen   52 RDQAKVVMNTLKK   64 (87)
T ss_dssp             CHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHhcc
Confidence            9999998888864

; 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.

>KOG4574|consensus

Probab=95.97  E-value=0.0054  Score=51.12  Aligned_cols=75  Identities=23%  Similarity=0.254  Sum_probs=65.4

Q ss_pred             EEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHHh
Q psy1185           6 VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKS   85 (131)
Q Consensus         6 ~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~~   85 (131)
                      +.++-|.+-..+...|..+++.||.|.+....|+                                 -..|.|+|.+.+.
T Consensus       300 ~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~---------------------------------~N~alvs~~s~~s  346 (1007)
T KOG4574|consen  300 KQSLENNAVNLTSSSLATLCSDYGSVASAWTLRD---------------------------------LNMALVSFSSVES  346 (1007)
T ss_pred             hhhhhcccccchHHHHHHHHHhhcchhhheeccc---------------------------------ccchhhhhHHHHH
Confidence            3456677778899999999999999999877654                                 4779999999999


Q ss_pred             HHHHHHHHhCCcceecCcEEEEEecCCC
Q psy1185          86 ASLAKKRLATGRLKVWGCDIIVDWADPQ  113 (131)
Q Consensus        86 a~~a~~~l~~~~~~~~g~~l~v~~a~~~  113 (131)
                      |..|+++++|+++...|-..+|.+|++-
T Consensus       347 ai~a~dAl~gkevs~~g~Ps~V~~ak~~  374 (1007)
T KOG4574|consen  347 AILALDALQGKEVSVTGAPSRVSFAKTL  374 (1007)
T ss_pred             HHHhhhhhcCCcccccCCceeEEecccc
Confidence            9999999999999999999999999853

>KOG0129|consensus

Probab=95.74  E-value=0.028  Score=44.52  Aligned_cols=51  Identities=27%  Similarity=0.296  Sum_probs=44.1

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhh-ccCCeeEEEEe--------cCeEEEEECCHHHHHh
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFE-QYGRVERVKRI--------KDYAFVHFEDRQEAIT   53 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~-~~G~v~~~~i~--------~~~~fv~~~~~~~a~~   53 (131)
                      ..+|||||+||.-++..+|-.+|+ -||.|..+-|-        +|-|-|+|++..+=.+
T Consensus       369 prrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~  428 (520)
T KOG0129|consen  369 PRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIK  428 (520)
T ss_pred             ccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHH
Confidence            468999999999999999999999 59988776553        8999999999877655

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

Probab=95.54  E-value=0.16  Score=29.15  Aligned_cols=55  Identities=18%  Similarity=0.316  Sum_probs=41.2

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhcc---CCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEe
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQY---GRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEY   80 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~---G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f   80 (131)
                      ..+|+|.|+ .+++.++++.+|..|   .....+..+.                                  -..|-|.|
T Consensus         5 peavhirGv-d~lsT~dI~~y~~~y~~~~~~~~IEWId----------------------------------DtScNvvf   49 (62)
T PF10309_consen    5 PEAVHIRGV-DELSTDDIKAYFSEYFDEEGPFRIEWID----------------------------------DTSCNVVF   49 (62)
T ss_pred             eceEEEEcC-CCCCHHHHHHHHHHhcccCCCceEEEec----------------------------------CCcEEEEE
Confidence            458999999 457889999999998   1234555542                                  24477889


Q ss_pred             CCHHhHHHHHHHH
Q psy1185          81 DSHKSASLAKKRL   93 (131)
Q Consensus        81 ~~~~~a~~a~~~l   93 (131)
                      .+...|.+|+..|
T Consensus        50 ~d~~~A~~AL~~L   62 (62)
T PF10309_consen   50 KDEETAARALVAL   62 (62)
T ss_pred             CCHHHHHHHHHcC
Confidence            9999999998764

>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=95.45  E-value=0.075  Score=37.11  Aligned_cols=63  Identities=21%  Similarity=0.234  Sum_probs=45.3

Q ss_pred             CHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHHhHHHHHHHHh--
Q psy1185          17 TEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLA--   94 (131)
Q Consensus        17 t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~--   94 (131)
                      ..+.|+++|.+++.+.+....++                                 -+-..|.|.+.+.|.+|...|+  
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~s---------------------------------FrRi~v~f~~~~~A~~~r~~l~~~   54 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKS---------------------------------FRRIRVVFESPESAQRARQLLHWD   54 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETT---------------------------------TTEEEEE-SSTTHHHHHHHTST--
T ss_pred             hHHHHHHHHHhcCCceEEEEcCC---------------------------------CCEEEEEeCCHHHHHHHHHHhccc
Confidence            35789999999999988877654                                 3457889999999999999998  


Q ss_pred             CCcceecCcEEEEEecCCCC
Q psy1185          95 TGRLKVWGCDIIVDWADPQE  114 (131)
Q Consensus        95 ~~~~~~~g~~l~v~~a~~~~  114 (131)
                      +.  .+.|..+++-|+.+..
T Consensus        55 ~~--~~~g~~l~~yf~~~~~   72 (184)
T PF04847_consen   55 GT--SFNGKRLRVYFGQPTP   72 (184)
T ss_dssp             TS--EETTEE-EEE----SS
T ss_pred             cc--ccCCCceEEEEccccc
Confidence            76  8899999999985433

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.

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

Probab=94.73  E-value=0.24  Score=33.24  Aligned_cols=54  Identities=24%  Similarity=0.303  Sum_probs=40.1

Q ss_pred             HHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHHhHHHHHHHHhCCcce
Q psy1185          20 KLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLK   99 (131)
Q Consensus        20 ~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~~~   99 (131)
                      +|.+.|++||.+.-++++                                   .+.-.|+|.+-+.|.+|+. ++|.  +
T Consensus        52 ~ll~~~~~~GevvLvRfv-----------------------------------~~~mwVTF~dg~sALaals-~dg~--~   93 (146)
T PF08952_consen   52 ELLQKFAQYGEVVLVRFV-----------------------------------GDTMWVTFRDGQSALAALS-LDGI--Q   93 (146)
T ss_dssp             HHHHHHHCCS-ECEEEEE-----------------------------------TTCEEEEESSCHHHHHHHH-GCCS--E
T ss_pred             HHHHHHHhCCceEEEEEe-----------------------------------CCeEEEEECccHHHHHHHc-cCCc--E
Confidence            677888899988877776                                   3567889998888887765 4565  8


Q ss_pred             ecCcEEEEEecC
Q psy1185         100 VWGCDIIVDWAD  111 (131)
Q Consensus       100 ~~g~~l~v~~a~  111 (131)
                      ++|+.|+|+.-.
T Consensus        94 v~g~~l~i~LKt  105 (146)
T PF08952_consen   94 VNGRTLKIRLKT  105 (146)
T ss_dssp             ETTEEEEEEE--
T ss_pred             ECCEEEEEEeCC
Confidence            999999997643

; PDB: 1UFW_A 2DNR_A.

>KOG0105|consensus

Probab=94.66  E-value=0.39  Score=33.69  Aligned_cols=65  Identities=18%  Similarity=0.232  Sum_probs=53.5

Q ss_pred             EEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHHh
Q psy1185           6 VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKS   85 (131)
Q Consensus         6 ~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~~   85 (131)
                      .|.|.+||.+-+=++|++...+-|.|-...+.+                                  -+++.|+|...++
T Consensus       117 RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~r----------------------------------Dg~GvV~~~r~eD  162 (241)
T KOG0105|consen  117 RVVVSGLPPSGSWQDLKDHMREAGDVCFADVQR----------------------------------DGVGVVEYLRKED  162 (241)
T ss_pred             eEEEecCCCCCchHHHHHHHHhhCCeeeeeeec----------------------------------ccceeeeeeehhh
Confidence            578999999999999999999999987766553                                  3588999999999


Q ss_pred             HHHHHHHHhCCcceecCcE
Q psy1185          86 ASLAKKRLATGRLKVWGCD  104 (131)
Q Consensus        86 a~~a~~~l~~~~~~~~g~~  104 (131)
                      ..-|++.|....+.-.|..
T Consensus       163 MkYAvr~ld~~~~~seGe~  181 (241)
T KOG0105|consen  163 MKYAVRKLDDQKFRSEGET  181 (241)
T ss_pred             HHHHHHhhccccccCcCcE
Confidence            9999999987654444544

>KOG4307|consensus

Probab=94.60  E-value=0.026  Score=46.44  Aligned_cols=75  Identities=17%  Similarity=0.012  Sum_probs=55.1

Q ss_pred             eEEEEeCCCCCCCHHHHHHHhhccCCeeE-EEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           5 KVLYVRNLTQYCTEEKLKEAFEQYGRVER-VKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         5 ~~l~v~nLp~~~t~~~l~~~F~~~G~v~~-~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      -.|||..||..+++.++.+.|..-..|.+ |.+.++                            -++..++.|||.|..+
T Consensus       435 ~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~----------------------------P~~~~~~~afv~F~~~  486 (944)
T KOG4307|consen  435 GALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRL----------------------------PTDLLRPAAFVAFIHP  486 (944)
T ss_pred             ceEEeccCCccccccchhhhhhhhhhhhheeEeccC----------------------------Ccccccchhhheeccc
Confidence            36999999999999999999998766655 555432                            2455677888888887


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEe
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDW  109 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~  109 (131)
                      +++..|...-+..  .++-+.|+|.-
T Consensus       487 ~a~~~a~~~~~k~--y~G~r~irv~s  510 (944)
T KOG4307|consen  487 TAPLTASSVKTKF--YPGHRIIRVDS  510 (944)
T ss_pred             cccchhhhccccc--ccCceEEEeec
Confidence            7777776665554  66666677753

>KOG2068|consensus

Probab=94.20  E-value=0.024  Score=42.63  Aligned_cols=81  Identities=19%  Similarity=0.286  Sum_probs=55.9

Q ss_pred             EEEEeCCCCCCCH-HHHH--HHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           6 VLYVRNLTQYCTE-EKLK--EAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         6 ~l~v~nLp~~~t~-~~l~--~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      -+||-+||...-. ..|+  +.|.+||.|..+.+-++-.                       .....+ ...-++|+|..
T Consensus        79 lvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S-----------------------~~s~~~-~~~s~yITy~~  134 (327)
T KOG2068|consen   79 LVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPS-----------------------SSSSSG-GTCSVYITYEE  134 (327)
T ss_pred             hhhhhCCCccccchhhhhCcccccccccceEEeecCCcc-----------------------cccCCC-CCCcccccccc
Confidence            4678888876444 4444  6888999998876554300                       000111 12238999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADP  112 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~  112 (131)
                      .++|..|+..++|.  .++|+.++..++..
T Consensus       135 ~eda~rci~~v~g~--~~dg~~lka~~gtt  162 (327)
T KOG2068|consen  135 EEDADRCIDDVDGF--VDDGRALKASLGTT  162 (327)
T ss_pred             hHhhhhHHHHhhhH--HhhhhhhHHhhCCC
Confidence            99999999999996  78888877777653

>KOG2591|consensus

Probab=94.01  E-value=0.14  Score=41.26  Aligned_cols=69  Identities=19%  Similarity=0.206  Sum_probs=51.8

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhc--cCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEe
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQ--YGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEY   80 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~--~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f   80 (131)
                      +.|.|.++.||..+-.++++.||..  |-.+.+|.+--                                  ..-=||+|
T Consensus       174 kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~----------------------------------N~nWyITf  219 (684)
T KOG2591|consen  174 KRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAH----------------------------------NDNWYITF  219 (684)
T ss_pred             ceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeee----------------------------------cCceEEEe
Confidence            4678999999999999999999985  77888886541                                  23358899


Q ss_pred             CCHHhHHHHHHHHhCCcceecCcEE
Q psy1185          81 DSHKSASLAKKRLATGRLKVWGCDI  105 (131)
Q Consensus        81 ~~~~~a~~a~~~l~~~~~~~~g~~l  105 (131)
                      .+..+|+.|...|...--++.|+.|
T Consensus       220 esd~DAQqAykylreevk~fqgKpI  244 (684)
T KOG2591|consen  220 ESDTDAQQAYKYLREEVKTFQGKPI  244 (684)
T ss_pred             ecchhHHHHHHHHHHHHHhhcCcch
Confidence            9999999888777553224455443

>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=93.80  E-value=1.1  Score=28.69  Aligned_cols=66  Identities=15%  Similarity=0.223  Sum_probs=44.9

Q ss_pred             ceEEEEeCCCCC-CCHHHHHHHhhccC-CeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeC
Q psy1185           4 VKVLYVRNLTQY-CTEEKLKEAFEQYG-RVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYD   81 (131)
Q Consensus         4 ~~~l~v~nLp~~-~t~~~l~~~F~~~G-~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~   81 (131)
                      .+++.+=-.|.. ++.++|..+.+.+- .|..++++|.                             ...++-.+.+.|.
T Consensus        12 ~~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird-----------------------------~~pnrymVLikF~   62 (110)
T PF07576_consen   12 RSTLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRD-----------------------------GTPNRYMVLIKFR   62 (110)
T ss_pred             CceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeC-----------------------------CCCceEEEEEEEC
Confidence            344444445555 55566666666654 4667777753                             2234556999999


Q ss_pred             CHHhHHHHHHHHhCCcc
Q psy1185          82 SHKSASLAKKRLATGRL   98 (131)
Q Consensus        82 ~~~~a~~a~~~l~~~~~   98 (131)
                      +.+.|..-....||+++
T Consensus        63 ~~~~Ad~Fy~~fNGk~F   79 (110)
T PF07576_consen   63 DQESADEFYEEFNGKPF   79 (110)
T ss_pred             CHHHHHHHHHHhCCCcc
Confidence            99999999999999865

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

>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=93.44  E-value=0.87  Score=26.73  Aligned_cols=59  Identities=20%  Similarity=0.223  Sum_probs=34.8

Q ss_pred             CCCCHHHHHHHhhccCC-----eeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHHhHHH
Q psy1185          14 QYCTEEKLKEAFEQYGR-----VERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASL   88 (131)
Q Consensus        14 ~~~t~~~l~~~F~~~G~-----v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~   88 (131)
                      ...+..+|..++..-+.     |-.+.+.                                   ..|+||+-.. +.|..
T Consensus        11 dg~~~~~iv~~i~~~~gi~~~~IG~I~I~-----------------------------------~~~S~vev~~-~~a~~   54 (74)
T PF03880_consen   11 DGLTPRDIVGAICNEAGIPGRDIGRIDIF-----------------------------------DNFSFVEVPE-EVAEK   54 (74)
T ss_dssp             GT--HHHHHHHHHTCTTB-GGGEEEEEE------------------------------------SS-EEEEE-T-T-HHH
T ss_pred             cCCCHHHHHHHHHhccCCCHHhEEEEEEe-----------------------------------eeEEEEEECH-HHHHH
Confidence            45778888888887653     4455554                                   4677777776 57888


Q ss_pred             HHHHHhCCcceecCcEEEEEec
Q psy1185          89 AKKRLATGRLKVWGCDIIVDWA  110 (131)
Q Consensus        89 a~~~l~~~~~~~~g~~l~v~~a  110 (131)
                      ++..|++.  .+.|++++|+.|
T Consensus        55 v~~~l~~~--~~~gk~v~ve~A   74 (74)
T PF03880_consen   55 VLEALNGK--KIKGKKVRVERA   74 (74)
T ss_dssp             HHHHHTT----SSS----EEE-
T ss_pred             HHHHhcCC--CCCCeeEEEEEC
Confidence            99999998  899999998865

; PDB: 2G0C_A 3MOJ_B.

>KOG0112|consensus

Probab=93.17  E-value=0.11  Score=43.86  Aligned_cols=50  Identities=18%  Similarity=0.428  Sum_probs=45.7

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe--cCeEEEEECCHHHHHh
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--KDYAFVHFEDRQEAIT   53 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~--~~~~fv~~~~~~~a~~   53 (131)
                      .+.+|+|+|+.++....|...|..||.|..+.+-  ..|+||+|++...|..
T Consensus       455 ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~hgq~yayi~yes~~~aq~  506 (975)
T KOG0112|consen  455 TTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRHGQPYAYIQYESPPAAQA  506 (975)
T ss_pred             ceeeccCCCCCCChHHHHHHHhhccCcceeeecccCCcceeeecccCccchh
Confidence            3569999999999999999999999999998776  6899999999988887

>KOG4660|consensus

Probab=93.02  E-value=0.32  Score=39.10  Aligned_cols=46  Identities=22%  Similarity=0.224  Sum_probs=34.8

Q ss_pred             CCCCcceEEEEeCCHHhHHHHHHHHhCCcc-eecCcE-EEEEecCCCC
Q psy1185          69 NKKNRGFCFLEYDSHKSASLAKKRLATGRL-KVWGCD-IIVDWADPQE  114 (131)
Q Consensus        69 ~~~~~~~~fv~f~~~~~a~~a~~~l~~~~~-~~~g~~-l~v~~a~~~~  114 (131)
                      ...+.|||||.|-+.+++..+.++.||+.| .+++.+ ..+.||+.+.
T Consensus       427 nkcNvGYAFINm~sp~ai~~F~kAFnGk~W~~FnS~Kia~itYArIQG  474 (549)
T KOG4660|consen  427 NKCNVGYAFINMTSPEAIIRFYKAFNGKKWEKFNSEKIASITYARIQG  474 (549)
T ss_pred             cccccceeEEeecCHHHHHHHHHHHcCCchhhhcceeeeeeehhhhhc
Confidence            445679999999999999999999999876 344443 4666776544

>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=92.77  E-value=0.17  Score=35.09  Aligned_cols=85  Identities=12%  Similarity=0.059  Sum_probs=44.5

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhc-cCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQ-YGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~-~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..+|-|++||++.|++++.+.+++ ++.-..-+..      .+..                ..........+-|+|.|.+
T Consensus         7 ~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~------~g~~----------------~~~~~~~~~~SRaYi~F~~   64 (176)
T PF03467_consen    7 GTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYF------QGKY----------------GKKSFKPPTYSRAYINFKN   64 (176)
T ss_dssp             --EEEEEEE-TTS-HHHHCCCCSS--SSE---EEE------EEEE----------------S-SSSTTS--EEEEEEESS
T ss_pred             CceEEEeCCCCCCCHHHHHHHhhhhcccccceEEE------ecCC----------------CCccCCCCcceEEEEEeCC
Confidence            458999999999999999887776 5554221111      1000                0000011123558888888


Q ss_pred             HHhHHHHHHHHhCCcceecCc----EEEEEecC
Q psy1185          83 HKSASLAKKRLATGRLKVWGC----DIIVDWAD  111 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~----~l~v~~a~  111 (131)
                      .+++..-...++|..+ .+.+    .-.|.+|-
T Consensus        65 ~~~~~~F~~~~~g~~F-~D~kg~~~~~~VE~Ap   96 (176)
T PF03467_consen   65 PEDLLEFRDRFDGHVF-VDSKGNEYPAVVEFAP   96 (176)
T ss_dssp             CHHHHHHHHHCTTEEE-E-TTS-EEEEEEEE-S
T ss_pred             HHHHHHHHHhcCCcEE-ECCCCCCcceeEEEcc
Confidence            8888888888877532 2222    24566654

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.

>KOG0128|consensus

Probab=92.64  E-value=0.073  Score=44.60  Aligned_cols=49  Identities=20%  Similarity=0.222  Sum_probs=45.4

Q ss_pred             eEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe-------cCeEEEEECCHHHHHh
Q psy1185           5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI-------KDYAFVHFEDRQEAIT   53 (131)
Q Consensus         5 ~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~-------~~~~fv~~~~~~~a~~   53 (131)
                      ..|+|.|.|+..|.++++.++...|.+.+.+++       +|.++|.|.++.+|.+
T Consensus       737 ~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r~gkpkg~a~v~y~~ea~~s~  792 (881)
T KOG0128|consen  737 ISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVRAGKPKGKARVDYNTEADASR  792 (881)
T ss_pred             hhhheeCCCCCCchHHHHhhccccCCccccchhhhhccccccceeccCCCcchhhh
Confidence            468999999999999999999999999998766       7899999999999998

>KOG1365|consensus

Probab=92.24  E-value=1.2  Score=34.55  Aligned_cols=88  Identities=15%  Similarity=0.246  Sum_probs=59.4

Q ss_pred             EEEeCCCCCCCHHHHHHHhhcc----CCeeEEEEe----cCeEEEEECCHHHHHh-------------------------
Q psy1185           7 LYVRNLTQYCTEEKLKEAFEQY----GRVERVKRI----KDYAFVHFEDRQEAIT-------------------------   53 (131)
Q Consensus         7 l~v~nLp~~~t~~~l~~~F~~~----G~v~~~~i~----~~~~fv~~~~~~~a~~-------------------------   53 (131)
                      +=..+|||..++.++-.+|.--    |-+.=|...    +|.+.|.|.+++.-+.                         
T Consensus        63 vRaRglpwq~Sd~~ia~ff~gl~ia~gg~aKOG~~qgrRnge~lvrf~d~e~RdlalkRhkhh~g~ryievYka~ge~f~  142 (508)
T KOG1365|consen   63 VRARGLPWQSSDQDIARFFKGLNIANGGRALCLNAQGRRNGEALVRFVDPEGRDLALKRHKHHMGTRYIEVYKATGEEFL  142 (508)
T ss_pred             EEecCCCCCcccCCHHHHHhhhhccccceeeeehhhhccccceEEEecCchhhhhhhHhhhhhccCCceeeeccCchhhe
Confidence            4456999999999999998743    222222222    7899999998654333                         


Q ss_pred             --------------------------------------hcC-------CceeEEecCCCCCCCCcceEEEEeCCHHhHHH
Q psy1185          54 --------------------------------------VTG-------LSQVIIYSSPDDNKKNRGFCFLEYDSHKSASL   88 (131)
Q Consensus        54 --------------------------------------~~g-------~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~   88 (131)
                                                            ++|       ...-++.+.. -.|+..|-||+-|..+++|+.
T Consensus       143 ~iagg~s~e~~~flsk~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~r-pdgrpTGdAFvlfa~ee~aq~  221 (508)
T KOG1365|consen  143 KIAGGTSNEAAPFLSKENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTR-PDGRPTGDAFVLFACEEDAQF  221 (508)
T ss_pred             EecCCccccCCCCCCcccceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEEC-CCCCcccceEEEecCHHHHHH
Confidence                                                  121       2222333321 258889999999999999999


Q ss_pred             HHHHHhC
Q psy1185          89 AKKRLAT   95 (131)
Q Consensus        89 a~~~l~~   95 (131)
                      |+..-..
T Consensus       222 aL~khrq  228 (508)
T KOG1365|consen  222 ALRKHRQ  228 (508)
T ss_pred             HHHHHHH
Confidence            9988654

>KOG2253|consensus

Probab=91.44  E-value=0.12  Score=42.31  Aligned_cols=68  Identities=22%  Similarity=0.233  Sum_probs=56.7

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .-++||||+...++..-++.+...||.|.++...                                    .|||.+|.++
T Consensus        40 ~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~------------------------------------~fgf~~f~~~   83 (668)
T KOG2253|consen   40 RDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRD------------------------------------KFGFCEFLKH   83 (668)
T ss_pred             CceeEecchhhhhhHHHHHHHHhhCCcchhhhhh------------------------------------hhcccchhhH
Confidence            5689999999999999999999999998887433                                    2888899999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEe
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDW  109 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~  109 (131)
                      ..+.+|++.++..  .++|..+.+.-
T Consensus        84 ~~~~ra~r~~t~~--~~~~~kl~~~~  107 (668)
T KOG2253|consen   84 IGDLRASRLLTEL--NIDDQKLIENV  107 (668)
T ss_pred             HHHHHHHHHhccc--CCCcchhhccc
Confidence            9999999998875  77777765544

>KOG0804|consensus

Probab=91.24  E-value=0.92  Score=35.81  Aligned_cols=65  Identities=9%  Similarity=0.279  Sum_probs=54.8

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhcc-CCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcce-EEEEeC
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQY-GRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGF-CFLEYD   81 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~-G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~-~fv~f~   81 (131)
                      .+.|+|-.+|-.++..||..+...+ ..|.+++++|.                              |.+..| ..|.|.
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd------------------------------~~pnrymvLIkFr  123 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRD------------------------------GMPNRYMVLIKFR  123 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeec------------------------------CCCceEEEEEEec
Confidence            5678999999999999999999876 56888988853                              444454 899999


Q ss_pred             CHHhHHHHHHHHhCCcc
Q psy1185          82 SHKSASLAKKRLATGRL   98 (131)
Q Consensus        82 ~~~~a~~a~~~l~~~~~   98 (131)
                      +..+|..-...+||+.+
T Consensus       124 ~q~da~~Fy~efNGk~F  140 (493)
T KOG0804|consen  124 DQADADTFYEEFNGKQF  140 (493)
T ss_pred             cchhHHHHHHHcCCCcC
Confidence            99999999999999844

>smart00361 RRM_1 RNA recognition motif

Probab=90.81  E-value=0.24  Score=28.60  Aligned_cols=32  Identities=16%  Similarity=0.449  Sum_probs=24.5

Q ss_pred             HhhccCCee--EEE------EecCeEEEEECCHHHHHhhc
Q psy1185          24 AFEQYGRVE--RVK------RIKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        24 ~F~~~G~v~--~~~------i~~~~~fv~~~~~~~a~~~~   55 (131)
                      .|..++.|.  .+.      -.+|||||+|.+.++|..+.
T Consensus        15 ~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~   54 (70)
T smart00361       15 YFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAI   54 (70)
T ss_pred             hcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHH
Confidence            678888763  331      24899999999999999854

>KOG0125|consensus

Probab=90.73  E-value=0.22  Score=37.67  Aligned_cols=45  Identities=24%  Similarity=0.270  Sum_probs=30.9

Q ss_pred             HHHHHhhccCCeeEEEEe---cCeEEEEECCHHHHHhh----cC--CceeEEec
Q psy1185          20 KLKEAFEQYGRVERVKRI---KDYAFVHFEDRQEAITV----TG--LSQVIIYS   64 (131)
Q Consensus        20 ~l~~~F~~~G~v~~~~i~---~~~~fv~~~~~~~a~~~----~g--~~~~~~~~   64 (131)
                      ...+-|++.-.|.=|.--   +|||||+|++++||+++    -|  ++++++.+
T Consensus       115 aMF~kfG~VldVEIIfNERGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEV  168 (376)
T KOG0125|consen  115 AMFEKFGKVLDVEIIFNERGSKGFGFVTMENPADADRARAELHGTVVEGRKIEV  168 (376)
T ss_pred             HHHHhhCceeeEEEEeccCCCCccceEEecChhhHHHHHHHhhcceeeceEEEE
Confidence            334556666666655443   89999999999999993    33  55555554

>KOG2135|consensus

Probab=90.65  E-value=0.23  Score=39.29  Aligned_cols=66  Identities=17%  Similarity=0.179  Sum_probs=49.8

Q ss_pred             CCCCCC-CHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHHhHHHH
Q psy1185          11 NLTQYC-TEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLA   89 (131)
Q Consensus        11 nLp~~~-t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a   89 (131)
                      -.|+.. +-.+|...|.+||.|..|.+-                                 .+.-.|.|+|.++.+|-.|
T Consensus       379 k~~~glnt~a~ln~hfA~fG~i~n~qv~---------------------------------~~~~~a~vTF~t~aeag~a  425 (526)
T KOG2135|consen  379 KSPFGLNTIADLNPHFAQFGEIENIQVD---------------------------------YSSLHAVVTFKTRAEAGEA  425 (526)
T ss_pred             ccCCCCchHhhhhhhhhhcCcccccccc---------------------------------Cchhhheeeeeccccccch
Confidence            344443 347889999999999998653                                 2245689999999888666


Q ss_pred             HHHHhCCcceecCcEEEEEecCC
Q psy1185          90 KKRLATGRLKVWGCDIIVDWADP  112 (131)
Q Consensus        90 ~~~l~~~~~~~~g~~l~v~~a~~  112 (131)
                      -. .++.  .|+++-|+|.|-++
T Consensus       426 ~~-s~~a--vlnnr~iKl~whnp  445 (526)
T KOG2135|consen  426 YA-SHGA--VLNNRFIKLFWHNP  445 (526)
T ss_pred             hc-cccc--eecCceeEEEEecC
Confidence            43 4555  89999999999876

>KOG4285|consensus

Probab=89.25  E-value=2.9  Score=31.50  Aligned_cols=50  Identities=18%  Similarity=0.216  Sum_probs=36.3

Q ss_pred             EeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHHhHHH
Q psy1185           9 VRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASL   88 (131)
Q Consensus         9 v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~   88 (131)
                      |-+.|+.-. .-+..+|++||.|.....                                 +...++-+|.|.++-.|++
T Consensus       202 VfGFppg~~-s~vL~~F~~cG~Vvkhv~---------------------------------~~ngNwMhirYssr~~A~K  247 (350)
T KOG4285|consen  202 VFGFPPGQV-SIVLNLFSRCGEVVKHVT---------------------------------PSNGNWMHIRYSSRTHAQK  247 (350)
T ss_pred             EeccCccch-hHHHHHHHhhCeeeeeec---------------------------------CCCCceEEEEecchhHHHH
Confidence            446666643 556679999999988632                                 3445678888888888888


Q ss_pred             HHHH
Q psy1185          89 AKKR   92 (131)
Q Consensus        89 a~~~   92 (131)
                      ||..
T Consensus       248 ALsk  251 (350)
T KOG4285|consen  248 ALSK  251 (350)
T ss_pred             hhhh
Confidence            8765

>KOG4410|consensus

Probab=88.47  E-value=0.85  Score=34.09  Aligned_cols=27  Identities=15%  Similarity=0.156  Sum_probs=23.4

Q ss_pred             eEEEEeCCCCCCCHHHHHHHhhccCCe
Q psy1185           5 KVLYVRNLTQYCTEEKLKEAFEQYGRV   31 (131)
Q Consensus         5 ~~l~v~nLp~~~t~~~l~~~F~~~G~v   31 (131)
                      +-||++|||.++...+|+..+.+-|.+
T Consensus       331 ~di~~~nl~rd~rv~dlk~~lr~~~~~  357 (396)
T KOG4410|consen  331 TDIKLTNLSRDIRVKDLKSELRKRECT  357 (396)
T ss_pred             cceeeccCccccchHHHHHHHHhcCCC
Confidence            459999999999999999998887653

>KOG4210|consensus

Probab=87.41  E-value=0.46  Score=35.45  Aligned_cols=76  Identities=12%  Similarity=0.063  Sum_probs=56.9

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .++.|+|++.+.+.+.+...++..+|....+.....                           .....+++++.+.|...
T Consensus        88 ~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~---------------------------~~~~~sk~~~s~~f~~k  140 (285)
T KOG4210|consen   88 SSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSL---------------------------EDSLSSKGGLSVHFAGK  140 (285)
T ss_pred             cccccccccccchhhccccccchhhcCcccchhhhh---------------------------ccccccccceeeccccH
Confidence            578999999999999988899999998777665532                           23566788899999998


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEE
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVD  108 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~  108 (131)
                      +.+..++......  .+.++.+...
T Consensus       141 s~~~~~l~~s~~~--~~~~~~~~~d  163 (285)
T KOG4210|consen  141 SQFFAALEESGSK--VLDGNKGEKD  163 (285)
T ss_pred             HHHHHHHHhhhcc--ccccccccCc
Confidence            8888888776654  4455544433

>PF00076 RRM_1: RNA recognition motif

Probab=87.21  E-value=0.61  Score=26.06  Aligned_cols=20  Identities=40%  Similarity=0.604  Sum_probs=17.1

Q ss_pred             ecCeEEEEECCHHHHHhhcC
Q psy1185          37 IKDYAFVHFEDRQEAITVTG   56 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~g   56 (131)
                      .++||||.|.+.++|+.+..
T Consensus        38 ~~~~a~V~F~~~~~a~~a~~   57 (70)
T PF00076_consen   38 SKGYAFVEFESEEDAEKALE   57 (70)
T ss_dssp             EEEEEEEEESSHHHHHHHHH
T ss_pred             ccceEEEEEcCHHHHHHHHH
Confidence            37999999999999998543

(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 ....

>KOG0149|consensus

Probab=87.03  E-value=0.49  Score=34.23  Aligned_cols=17  Identities=41%  Similarity=0.718  Sum_probs=16.1

Q ss_pred             cCeEEEEECCHHHHHhh
Q psy1185          38 KDYAFVHFEDRQEAITV   54 (131)
Q Consensus        38 ~~~~fv~~~~~~~a~~~   54 (131)
                      +|||||+|.+.++|.++
T Consensus        54 kGyGfVTf~d~~aa~rA   70 (247)
T KOG0149|consen   54 KGYGFVTFRDAEAATRA   70 (247)
T ss_pred             cceeeEEeecHHHHHHH
Confidence            89999999999999993

>KOG0122|consensus

Probab=86.35  E-value=1  Score=32.85  Aligned_cols=36  Identities=36%  Similarity=0.503  Sum_probs=26.6

Q ss_pred             HHHHHHhhccCCeeEEE-----EecCeEEEEECCHHHHHhh
Q psy1185          19 EKLKEAFEQYGRVERVK-----RIKDYAFVHFEDRQEAITV   54 (131)
Q Consensus        19 ~~l~~~F~~~G~v~~~~-----i~~~~~fv~~~~~~~a~~~   54 (131)
                      .+|..-|...-.|.=++     +.+|||||+|.+.++|.++
T Consensus       207 ~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rA  247 (270)
T KOG0122|consen  207 EELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARA  247 (270)
T ss_pred             HHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHH
Confidence            56666667666554333     3499999999999999994

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

Probab=86.19  E-value=0.69  Score=30.86  Aligned_cols=19  Identities=26%  Similarity=0.564  Sum_probs=16.9

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .++||||+|.+.++|+.+.
T Consensus        75 ~kGfaFV~F~~~e~A~~Al   93 (144)
T PLN03134         75 SRGFGFVNFNDEGAATAAI   93 (144)
T ss_pred             cceEEEEEECCHHHHHHHH
Confidence            3899999999999999954

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

Probab=85.24  E-value=1.4  Score=27.53  Aligned_cols=47  Identities=23%  Similarity=0.296  Sum_probs=29.6

Q ss_pred             cCeEEEEECCHHHHHhhcCC-ceeEEecCCCCCCCCcceEEEEeCCHHhHHHH
Q psy1185          38 KDYAFVHFEDRQEAITVTGL-SQVIIYSSPDDNKKNRGFCFLEYDSHKSASLA   89 (131)
Q Consensus        38 ~~~~fv~~~~~~~a~~~~g~-~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a   89 (131)
                      .|||||+|.++++|...... .+....     ...+...|=|.|...+.-.+-
T Consensus        45 ~GYAFVNf~~~~~~~~F~~~f~g~~w~-----~~~s~Kvc~i~yAriQG~~al   92 (97)
T PF04059_consen   45 LGYAFVNFTSPQAAIRFYKAFNGKKWP-----NFNSKKVCEISYARIQGKDAL   92 (97)
T ss_pred             eEEEEEEcCCHHHHHHHHHHHcCCccc-----cCCCCcEEEEehhHhhCHHHH
Confidence            79999999999999995542 222211     122455666777665554433

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

>KOG0107|consensus

Probab=85.24  E-value=1  Score=31.35  Aligned_cols=35  Identities=26%  Similarity=0.365  Sum_probs=28.1

Q ss_pred             HHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHh
Q psy1185          19 EKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAIT   53 (131)
Q Consensus        19 ~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~   53 (131)
                      +.+...|.+.=.|.=...+.|||||+|+++.+|+.
T Consensus        28 E~~F~~yG~lrsvWvArnPPGfAFVEFed~RDA~D   62 (195)
T KOG0107|consen   28 ERAFSKYGPLRSVWVARNPPGFAFVEFEDPRDAED   62 (195)
T ss_pred             HHHHHhcCcceeEEEeecCCCceEEeccCcccHHH
Confidence            44555667766666677899999999999999998

>KOG4208|consensus

Probab=85.11  E-value=0.74  Score=32.67  Aligned_cols=16  Identities=50%  Similarity=0.735  Sum_probs=15.3

Q ss_pred             cCeEEEEECCHHHHHh
Q psy1185          38 KDYAFVHFEDRQEAIT   53 (131)
Q Consensus        38 ~~~~fv~~~~~~~a~~   53 (131)
                      +|||||+|++++.|..
T Consensus        92 KgYAFVEFEs~eVA~I  107 (214)
T KOG4208|consen   92 KGYAFVEFESEEVAKI  107 (214)
T ss_pred             CceEEEEeccHHHHHH
Confidence            7999999999999988

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	131
2dis_A	109	Solution Structure Of The Rrm Domain Of Unnamed Pro		3e-16
2dgu_A	103	Solution Structure Of The Rna Binding Domain In Het		2e-15
2dk2_A	97	Solution Structure Of Rrm Domain In Heterogeneous N		5e-15
2cpd_A	99	Solution Structure Of The Rna Recognition Motif Of		1e-11
2dnq_A	90	Solution Structure Of Rna Binding Domain 1 In Rna-B		1e-06
2dgt_A	92	Solution Structure Of The Second Rna Binding Domain		2e-06
2dnp_A	90	Solution Structure Of Rna Binding Domain 2 In Rna-B		7e-06
2fc8_A	102	Solution Structure Of The Rrm_1 Domain Of Ncl Prote		1e-04

>pdb|2DIS|A Chain A, Solution Structure Of The Rrm Domain Of Unnamed Protein Product Length = 109

Iteration: 1
 Score = 80.1 bits (196), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 32/69 (46%), Positives = 51/69 (73%)
Query: 56  GLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEE 115
           G+  VI+Y+S  D  KNRGF F+EY+SH++A++A+++L  GR+++WG  I VDWA+P+ +
Sbjct: 35  GVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEID 94
Query: 116 PDTETMSKV 124
            D + M  V
Sbjct: 95  VDEDVMETV 103

>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In Heterogeneous Nuclear Ribonucleoprotein Q Length = 103

Iteration: 1
 Score = 77.4 bits (189), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 36/80 (45%), Positives = 55/80 (68%), Gaps = 9/80 (11%)
Query: 1  MSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAIT------- 53
          M+KVKVL+VRNL    TEE L++AF Q+G++ERVK++KDYAF+HF++R  A+        
Sbjct: 8  MAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKDYAFIHFDERDGAVKAMEEMNG 67
Query: 54 --VTGLSQVIIYSSPDDNKK 71
            + G +  I+++ P D K+
Sbjct: 68 KDLEGENIEIVFAKPPDQKR 87

>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear Ribonucleoprotein R (Hnrnp R) Length = 97

Iteration: 1
 Score = 75.9 bits (185), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 32/52 (61%), Positives = 44/52 (84%)
Query: 1  MSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAI 52
          M+KVKVL+VRNL    TEE L+++F ++G++ERVK++KDYAFVHFEDR  A+
Sbjct: 12 MAKVKVLFVRNLATTVTEEILEKSFSEFGKLERVKKLKDYAFVHFEDRGAAV 63

>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human Apobec-1 Complementation Factor, Acf Length = 99

Iteration: 1
 Score = 65.1 bits (157), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 32/69 (46%), Positives = 47/69 (68%), Gaps = 3/69 (4%)
Query: 1  MSKVKVLYVRNLTQYCTEEKLKEAFEQY--GRVERVKRIKDYAFVHFEDRQEAI-TVTGL 57
          MS VK+LYVRNL    +EE +++ F     G VERVK+I+DYAFVHF +R++A+  +  L
Sbjct: 12 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKAL 71
Query: 58 SQVIIYSSP 66
          +  ++  SP
Sbjct: 72 NGKVLDGSP 80

>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding Protein 30 Length = 90

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 20/45 (44%), Positives = 30/45 (66%)
Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEA 51
          L++ NL +  TE++++  FEQYG+V     IK+Y FVH ED+  A
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDIIKNYGFVHIEDKTAA 55

>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In Rna- Binding Protein 30 Length = 92

Iteration: 1
 Score = 47.8 bits (112), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 22/52 (42%), Positives = 34/52 (65%), Gaps = 1/52 (1%)
Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAI-TVTGL 57
          L+V N++  CT ++L+  FE+YG V     +KDYAFVH E  ++A+  + GL
Sbjct: 13 LHVGNISPTCTNQELRAKFEEYGPVIECDIVKDYAFVHMERAEDAVEAIRGL 64

>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding Protein 14 Length = 90

Iteration: 1
 Score = 45.8 bits (107), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 19/45 (42%), Positives = 29/45 (64%)
Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEA 51
          ++V N++  CT ++L+  FE+ GRV     +KDYAFVH E   +A
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDVVKDYAFVHMEKEADA 56

>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein Length = 102

Iteration: 1
 Score = 42.0 bits (97), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 31/109 (28%), Positives = 50/109 (45%), Gaps = 32/109 (29%)
Query: 5   KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYS 64
           K L+V+ L++  TEE LKE+F+   R   V            DR+     TG S      
Sbjct: 16  KTLFVKGLSEDTTEETLKESFDGSVRARIVT-----------DRE-----TGSS------ 53
Query: 65  SPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQ 113
                   +GF F++++S + A  AK+ +  G +   G  + +DWA P+
Sbjct: 54  --------KGFGFVDFNSEEDAKAAKEAMEDGEID--GNKVTLDWAKPK 92

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	131
2dis_A	109	Unnamed protein product; structural genomics, RRM	7e-31
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	7e-25
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	5e-23
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-22
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	5e-12
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-19
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	3e-13
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	3e-19
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	8e-19
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	4e-18
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	2e-17
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	5e-17
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	9e-17
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	2e-15
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	4e-15
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	4e-15
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	5e-15
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	1e-14
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	2e-14
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	3e-14
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-09
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	4e-14
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	4e-14
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	7e-10
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	5e-14
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	6e-14
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	6e-14
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	8e-14
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	8e-14
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	9e-14
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	1e-13
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	2e-13
1x4e_A	85	RNA binding motif, single-stranded interacting pro	3e-13
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	3e-13
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	4e-13
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	4e-13
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	4e-13
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	6e-13
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	6e-13
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	6e-13
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	7e-13
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	7e-13
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	8e-13
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	8e-13
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	8e-13
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	1e-12
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	1e-12
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	1e-12
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	1e-12
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	1e-12
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	2e-12
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	2e-12
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	2e-12
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	2e-12
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	2e-12
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-12
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-07
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	3e-12
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	3e-12
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	4e-12
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	4e-12
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	5e-12
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	5e-12
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	6e-12
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	7e-12
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	8e-12
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	1e-11
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	1e-11
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	1e-11
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	1e-11
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	1e-11
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	1e-11
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	1e-11
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	6e-11
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-11
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-10
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-11
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-11
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	5e-10
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	2e-11
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	2e-11
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	2e-11
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-11
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-11
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	2e-11
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	2e-11
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	3e-11
1x5o_A	114	RNA binding motif, single-stranded interacting pro	3e-11
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	3e-11
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	3e-11
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	4e-11
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	9e-10
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	4e-11
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	5e-11
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	5e-11
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	5e-11
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	5e-11
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	4e-07
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	6e-11
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	7e-11
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	1e-10
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	1e-10
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	2e-10
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	1e-08
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	2e-10
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-10
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-10
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	2e-10
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	2e-10
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	2e-10
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	2e-10
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	3e-10
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	3e-10
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	3e-09
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	3e-10
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	3e-10
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	4e-10
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	4e-10
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	5e-10
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	6e-10
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-07
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	6e-10
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	7e-10
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	9e-10
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	1e-09
1x5p_A	97	Negative elongation factor E; structure genomics,	1e-09
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	1e-09
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	1e-09
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	1e-09
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	1e-09
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	1e-09
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-09
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	3e-09
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	3e-09
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	3e-08
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	3e-09
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	3e-09
2div_A	99	TRNA selenocysteine associated protein; structural	4e-09
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	4e-09
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	1e-08
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	1e-08
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	1e-08
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	2e-08
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	2e-08
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	3e-08
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	4e-08
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	4e-08
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	5e-08
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	5e-08
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	5e-08
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	6e-08
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	6e-08
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	9e-08
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	1e-07
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	2e-07
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	3e-07
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	3e-07
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	3e-07
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	4e-07
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	4e-07
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	5e-07
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	6e-07
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	6e-07
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	7e-07
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	8e-07
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	9e-07
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	1e-06
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	1e-06
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	1e-06
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	1e-06
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	1e-06
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	2e-06
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	2e-06
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	3e-06
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	4e-06
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	5e-06
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	7e-06
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	1e-05
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	3e-05
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	3e-05
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	6e-05
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	2e-04
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	2e-04
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	2e-04
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	2e-04
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	6e-04
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	8e-04

>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 =  105 bits (264), Expect = 7e-31
 Identities = 35/118 (29%), Positives = 61/118 (51%), Gaps = 25/118 (21%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
           L++  + +    E++ E   +                            G+  VI+Y+S 
Sbjct: 11  LFIGGIPKMKKREEILEEIAKVT-------------------------EGVLDVIVYASA 45

Query: 67  DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPDTETMSKV 124
            D  KNRGF F+EY+SH++A++A+++L  GR+++WG  I VDWA+P+ + D + M  V
Sbjct: 46  ADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMETV 103

>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 = 90.0 bits (224), Expect = 7e-25
 Identities = 31/51 (60%), Positives = 43/51 (84%)

Query: 1  MSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEA 51
          M+KVKVL+VRNL    TEE L++AF Q+G++ERVK++KDYAF+HF++R  A
Sbjct: 8  MAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKDYAFIHFDERDGA 58

>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 = 85.0 bits (211), Expect = 5e-23
 Identities = 28/54 (51%), Positives = 39/54 (72%), Gaps = 2/54 (3%)

Query: 1  MSKVKVLYVRNLTQYCTEEKLKEAFEQYG--RVERVKRIKDYAFVHFEDRQEAI 52
          MS VK+LYVRNL    +EE +++ F       VERVK+I+DYAFVHF +R++A+
Sbjct: 12 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAV 65

>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 = 88.9 bits (221), Expect = 1e-22
 Identities = 23/168 (13%), Positives = 49/168 (29%), Gaps = 55/168 (32%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD------YAFVHFEDRQEA--------- 51
           + V+NL +   + K+ + F+  G +  V           +A + F     A         
Sbjct: 44  VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKTHK 103

Query: 52  ------ITV------------------------------TGLSQVIIYSSPDDNKKNRGF 75
                 I V                                   + + S       +R F
Sbjct: 104 VVGQNEIIVSHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPS--LRFNTSRRF 161

Query: 76  CFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPDTETMSK 123
            +++  S + A    ++L    LK+ G  ++   ++P E+      + 
Sbjct: 162 AYIDVTSKEDARYCVEKL--NGLKIEGYTLVTKVSNPLEKSKRTDSAT 207

>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 = 60.0 bits (146), Expect = 5e-12
 Identities = 15/61 (24%), Positives = 30/61 (49%), Gaps = 10/61 (16%)

Query: 1   MSKVKVLYVRNLTQYCTEEK-LKEAFEQYGRVERVK---------RIKDYAFVHFEDRQE 50
             + + + +RNL+    +E  L+E+FE +G +E++               AF+ FE++  
Sbjct: 207 TLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDS 266

Query: 51  A 51
           A
Sbjct: 267 A 267

>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 = 80.4 bits (199), Expect = 1e-19
 Identities = 28/172 (16%), Positives = 52/172 (30%), Gaps = 52/172 (30%)

Query: 2   SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVE-RVKRIKDYAFVHFEDRQEA--------- 51
              + + +R L    T +++ +    Y      V + K  AFV   + ++A         
Sbjct: 20  RNRRKILIRGLPGDVTNQEVHDLLSDYELKYCFVDKYKGTAFVTLLNGEQAEAAINAFHQ 79

Query: 52  ------------------ITVTGLSQ--------------------VIIYSSPDDNKKNR 73
                             + V  L                       ++YS  +   +++
Sbjct: 80  SRLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYS--ERTGQSK 137

Query: 74  GFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPDTETMSKVL 125
           G+ F EY    SA+ AK  L      +    + V W D  +       S+ L
Sbjct: 138 GYGFAEYMKKDSAARAKSDL--LGKPLGPRTLYVHWTDAGQLTPALLHSRCL 187

>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 = 63.5 bits (155), Expect = 3e-13
 Identities = 9/59 (15%), Positives = 20/59 (33%), Gaps = 8/59 (13%)

Query: 1   MSKVKVLYVRNLTQYCTE-EKLKEAFEQYGRVERVK-------RIKDYAFVHFEDRQEA 51
           +   + L V  L     + + L  A          +       ++K +A + +E  + A
Sbjct: 181 LLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMA 239

>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 = 75.3 bits (186), Expect = 3e-19
 Identities = 20/45 (44%), Positives = 30/45 (66%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEA 51
          L+V N++  CT ++L+  FE+YG V     +KDYAFVH E  ++A
Sbjct: 13 LHVGNISPTCTNQELRAKFEEYGPVIECDIVKDYAFVHMERAEDA 57

>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 = 74.2 bits (183), Expect = 8e-19
 Identities = 19/45 (42%), Positives = 29/45 (64%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEA 51
          ++V N++  CT ++L+  FE+ GRV     +KDYAFVH E   +A
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDVVKDYAFVHMEKEADA 56

>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 = 72.2 bits (178), Expect = 4e-18
 Identities = 21/50 (42%), Positives = 32/50 (64%)

Query: 2  SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEA 51
          S +  L++ NL +  TE++++  FEQYG+V     IK+Y FVH ED+  A
Sbjct: 6  SGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKNYGFVHIEDKTAA 55

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 71.2 bits (175), Expect = 2e-17
 Identities = 16/45 (35%), Positives = 25/45 (55%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEA 51
          L+VR       E +L E F  +G ++ VK +  +AFV FE+ + A
Sbjct: 34 LFVRPFPLDVQESELNEIFGPFGPMKEVKILNGFAFVEFEEAESA 78

>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 = 70.0 bits (172), Expect = 5e-17
 Identities = 18/47 (38%), Positives = 27/47 (57%), Gaps = 2/47 (4%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--YAFVHFEDRQEA 51
          L+V NL    TEE++++ FE+YG+   V   KD  + F+  E R  A
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLA 64

>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 = 69.6 bits (171), Expect = 9e-17
 Identities = 20/116 (17%), Positives = 44/116 (37%), Gaps = 27/116 (23%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
           + VRN+     + +++E F  +G ++ V+  K                            
Sbjct: 18  ILVRNIPFQANQREIRELFSTFGELKTVRLPKK--------------------------M 51

Query: 67  DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPDTETMS 122
                +RGF F+++ + + A  A   L      ++G  ++++WAD +    +   S
Sbjct: 52  TGTGAHRGFGFVDFITKQDAKKAFNALCHST-HLYGRRLVLEWADSEVTVQSGPSS 106

>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 = 65.7 bits (161), Expect = 2e-15
 Identities = 16/53 (30%), Positives = 25/53 (47%), Gaps = 5/53 (9%)

Query: 1  MSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVE--RVKRIKDYAFVHFEDRQEA 51
          M+K   LY+ NL+   T + L++ F         +V     YAFV + D+  A
Sbjct: 8  MNK---LYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWA 57

>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 = 65.0 bits (159), Expect = 4e-15
 Identities = 10/50 (20%), Positives = 22/50 (44%), Gaps = 2/50 (4%)

Query: 5  KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--YAFVHFEDRQEAI 52
            L+V  L    +   L   F+++G +  +  +K   +A++ +E    A 
Sbjct: 18 TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQ 67

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 65.2 bits (159), Expect = 4e-15
 Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 2/51 (3%)

Query: 5  KVLYVRNLTQYCTEEKLKEAFEQYGRVERVK--RIKDYAFVHFEDRQEAIT 53
           V++VR L +   E  L EA E++G +  V     K  A V FE+   A  
Sbjct: 16 PVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKE 66

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

 Score = 64.7 bits (158), Expect = 5e-15
 Identities = 24/110 (21%), Positives = 38/110 (34%), Gaps = 31/110 (28%)

Query: 5   KVLYVRNLTQYCTEEKLKEAFEQYGR--VERVKRIKDYAFVHFEDRQEAITVTGLSQVII 62
             + +RN+  +   + +  A   Y    V  ++ IKD               T  +    
Sbjct: 10  DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKD-------------KQTQQN---- 52

Query: 63  YSSPDDNKKNRGFCFLEYDSHKSASLAKKRL--ATGRLKVWGCDIIVDWA 110
                     RGF F++  S   AS   + L      LK+ G  I VD+A
Sbjct: 53  ----------RGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGVDFA 92

>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 = 63.8 bits (156), Expect = 1e-14
 Identities = 17/56 (30%), Positives = 28/56 (50%), Gaps = 6/56 (10%)

Query: 2  SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD------YAFVHFEDRQEA 51
           + + LYV NL++  TE  + + F Q G  +  K I +      Y FV F + ++A
Sbjct: 13 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDA 68

>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 = 63.5 bits (155), Expect = 2e-14
 Identities = 20/111 (18%), Positives = 41/111 (36%), Gaps = 31/111 (27%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
           L+V  L +  +EE +   F+ +G ++    ++                            
Sbjct: 18  LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLR---------------------------- 49

Query: 67  DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCD--IIVDWADPQEE 115
             +  ++G  F+++ SH  A  A   L  G   + G    ++V +AD  +E
Sbjct: 50  GPDGSSKGCAFVKFSSHTEAQAAIHAL-HGSQTMPGASSSLVVKFADTDKE 99

>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 = 64.1 bits (157), Expect = 3e-14
 Identities = 26/114 (22%), Positives = 39/114 (34%), Gaps = 29/114 (25%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
           L V  L Q  T+E+ +  F   G +E  K ++D              +TG S        
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDK-------------ITGQS-------- 43

Query: 67  DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPDTET 120
                  G+ F+ Y   K A  A   L    L++    I V +A P      + 
Sbjct: 44  ------LGYGFVNYIDPKDAEKAINTL--NGLRLQTKTIKVSYARPSSASIRDA 89

>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 = 51.4 bits (124), Expect = 2e-09
 Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 8/53 (15%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
           LYV  L +  T+++L++ F QYGR+   + + D          F+ F+ R EA
Sbjct: 91  LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEA 143

>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 = 64.1 bits (156), Expect = 4e-14
 Identities = 29/109 (26%), Positives = 41/109 (37%), Gaps = 29/109 (26%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
           LYV NL+ Y TEE++ E F + G ++++    D                           
Sbjct: 42  LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLD--------------------------- 74

Query: 67  DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEE 115
              K   GFCF+EY S   A  A + +   RL      I  DW    +E
Sbjct: 75  KMKKTACGFCFVEYYSRADAENAMRYINGTRLD--DRIIRTDWDAGFKE 121

>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 = 64.1 bits (157), Expect = 4e-14
 Identities = 25/114 (21%), Positives = 40/114 (35%), Gaps = 29/114 (25%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
           L V  L Q  T+ +L   F   G +   + ++DY              TG S        
Sbjct: 6   LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDY-------------KTGYS-------- 44

Query: 67  DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPDTET 120
                  G+ F+++ S   +  A K L    + V    + V +A P  E   +T
Sbjct: 45  ------YGYAFVDFTSEMDSQRAIKVL--NGITVRNKRLKVSYARPGGESIKDT 90

>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 = 53.0 bits (128), Expect = 7e-10
 Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 8/53 (15%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
           LYV NL +  T+++L   F +YG + +   ++D         AFV +  R+EA
Sbjct: 92  LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEA 144

>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 = 5e-14
 Identities = 30/117 (25%), Positives = 43/117 (36%), Gaps = 27/117 (23%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
           LY+ NLT + T+E L EA    G  + +  IK   F  FE+R       G S        
Sbjct: 71  LYIGNLTWWTTDEDLTEAVHSLGVND-ILEIK---F--FENR-----ANGQS-------- 111

Query: 67  DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPDTETMSK 123
                 +GF  +   S  S+      L    L   G + +V   + Q     E  S+
Sbjct: 112 ------KGFALVGVGSEASSKKLMDLLPKRELH--GQNPVVTPVNKQFLSQFEMQSR 160

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

 Score = 61.9 bits (151), Expect = 6e-14
 Identities = 10/47 (21%), Positives = 22/47 (46%), Gaps = 2/47 (4%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--YAFVHFEDRQEA 51
           Y+ N+  + TE  L   F+ +G +   K   +    F+ ++  ++A
Sbjct: 30 AYIGNIPHFATEADLIPLFQNFGFILDFKHYPEKGCCFIKYDTHEQA 76

>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 = 6e-14
 Identities = 28/116 (24%), Positives = 40/116 (34%), Gaps = 37/116 (31%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
           L V NLT   + + L+  FE+YGRV  V   +D               T  S        
Sbjct: 50  LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRY-------------TKES-------- 88

Query: 67  DDNKKNRGFCFLEYDSHKSASLAKKRL----ATGRLKVWGCDIIVDWADPQEEPDT 118
                 RGF F+ +   + A  A   +      GR      ++ V  A     PD+
Sbjct: 89  ------RGFAFVRFHDKRDAEDAMDAMDGAVLDGR------ELRVQMARYGRPPDS 132

>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 = 62.0 bits (151), Expect = 8e-14
 Identities = 9/47 (19%), Positives = 24/47 (51%), Gaps = 2/47 (4%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--YAFVHFEDRQEA 51
          +Y   +    T++ +++ F  +G++  ++   +  Y+FV F   + A
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESA 74

>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 = 61.9 bits (151), Expect = 8e-14
 Identities = 26/116 (22%), Positives = 39/116 (33%), Gaps = 30/116 (25%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
           L V NLT   + + L+  FE+YGRV  V   ++               T           
Sbjct: 16  LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREP-------------HTKAP-------- 54

Query: 67  DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPDTETMS 122
                 RGF F+ +   + A  A+  +    L   G ++ V  A      D    S
Sbjct: 55  ------RGFAFVRFHDRRDAQDAEAAMDGAELD--GRELRVQVARYG-RRDLSGPS 101

>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 = 64.7 bits (158), Expect = 9e-14
 Identities = 35/159 (22%), Positives = 55/159 (34%), Gaps = 48/159 (30%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--YAFVHFEDRQEA------------- 51
           L+V NL    TEE  K  FE+YG    V   +D  + F+  E R  A             
Sbjct: 25  LFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELDGTILK 84

Query: 52  --------------ITVTGLSQVI--------------IYSS---PDDNKKNRGFCFLEY 80
                         +TV  LS V+              +  +    DD  +  G  F+E+
Sbjct: 85  SRPLRIRFATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEF 144

Query: 81  DSHKSASLAKKRLATGRLKVWGCD--IIVDWADPQEEPD 117
            +   A  A +R   G   +      +IV+  +  ++ D
Sbjct: 145 AAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFDDED 183

>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 = 61.1 bits (149), Expect = 1e-13
 Identities = 16/53 (30%), Positives = 27/53 (50%), Gaps = 8/53 (15%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
          + V NL++   E  L+E F  +G + R+   KD        +AF+ F  R++A
Sbjct: 18 IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDA 70

>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 = 60.8 bits (148), Expect = 2e-13
 Identities = 16/56 (28%), Positives = 29/56 (51%), Gaps = 6/56 (10%)

Query: 2  SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD------YAFVHFEDRQEA 51
          S  K L+V N+     +  L++ F Q+G++  V+ I +      + FV FE+  +A
Sbjct: 13 STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADA 68

>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 = 59.8 bits (146), Expect = 3e-13
 Identities = 16/53 (30%), Positives = 24/53 (45%), Gaps = 8/53 (15%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
          LY+R L    T++ L +  + YG++   K I D        Y FV F+    A
Sbjct: 8  LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAA 60

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 60.3 bits (146), Expect = 3e-13
 Identities = 14/119 (11%), Positives = 41/119 (34%), Gaps = 33/119 (27%)

Query: 5   KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYS 64
           +V+++R L    TE ++      +G+V  +  +K                          
Sbjct: 17  RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------------------------- 51

Query: 65  SPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPDTETMSK 123
                   +   F+E ++ ++A+       +    + G  I + +++ +E     + ++
Sbjct: 52  --------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKTDSSPNQ 102

>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 = 4e-13
 Identities = 28/113 (24%), Positives = 40/113 (35%), Gaps = 29/113 (25%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
           L V NLT   + + L+  FE+YGRV  V   +D               T  S        
Sbjct: 73  LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRY-------------TKES-------- 111

Query: 67  DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPDTE 119
                 RGF F+ +   + A  A   +    L   G ++ V  A     PD+ 
Sbjct: 112 ------RGFAFVRFHDKRDAEDAMDAMDGAVLD--GRELRVQMARYGRPPDSH 156

>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 = 59.6 bits (145), Expect = 4e-13
 Identities = 16/47 (34%), Positives = 23/47 (48%), Gaps = 2/47 (4%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--YAFVHFEDRQEA 51
          LYV  L    TE  L+  F Q+G +  +  ++    AF+ F  RQ A
Sbjct: 15 LYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAA 61

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 101

 Score = 59.8 bits (145), Expect = 4e-13
 Identities = 14/52 (26%), Positives = 27/52 (51%), Gaps = 2/52 (3%)

Query: 5  KVLYVRNLTQYCTEEKLKEAFEQYGRVERVK--RIKDYAFVHFEDRQEAITV 54
          +VL++R L    TE ++      +G+V  +   + K+ AF+     + AIT+
Sbjct: 16 RVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITM 67

>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 = 59.6 bits (145), Expect = 6e-13
 Identities = 24/112 (21%), Positives = 43/112 (38%), Gaps = 30/112 (26%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
           L++  + +   E+ LK  FE++G++  +  +KD               TG+         
Sbjct: 16  LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRF-------------TGMH-------- 54

Query: 67  DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCD--IIVDWADPQEEP 116
                 +G  FL Y   +SA  A+  L   +  + G +  I V  AD +   
Sbjct: 55  ------KGCAFLTYCERESALKAQSAL-HEQKTLPGMNRPIQVKPADSESRG 99

>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 = 59.2 bits (144), Expect = 6e-13
 Identities = 16/52 (30%), Positives = 23/52 (44%), Gaps = 7/52 (13%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEA 51
          ++V NL     EE L E F Q G + +V   KD       + FV F+  +  
Sbjct: 19 VFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESV 70

>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 = 60.1 bits (146), Expect = 6e-13
 Identities = 27/113 (23%), Positives = 41/113 (36%), Gaps = 37/113 (32%)

Query: 5   KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYS 64
             L V  L+ Y TE  L+E F +YG +  V  + D               +  S      
Sbjct: 47  CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQ-------------QSRRS------ 87

Query: 65  SPDDNKKNRGFCFLEYDSHKSASLAKKRLA----TGRLKVWGCDIIVDWADPQ 113
                   RGF F+ +++   A  AK+R       GR       I VD++  +
Sbjct: 88  --------RGFAFVYFENVDDAKEAKERANGMELDGR------RIRVDFSITK 126

>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 = 59.2 bits (144), Expect = 7e-13
 Identities = 17/51 (33%), Positives = 28/51 (54%), Gaps = 4/51 (7%)

Query: 5  KVLYVRNLTQYCTEEKLKEAFEQYGRVERVK----RIKDYAFVHFEDRQEA 51
          K L + NL+   TEE L+E FE+   ++  +    + K YAF+ F   ++A
Sbjct: 16 KTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDA 66

>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 = 59.1 bits (144), Expect = 7e-13
 Identities = 19/55 (34%), Positives = 28/55 (50%), Gaps = 8/55 (14%)

Query: 5  KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
            L V  L+ Y TE  L+E F +YG +  V  + D        +AFV+FE+  +A
Sbjct: 16 CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDA 70

>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 = 59.2 bits (144), Expect = 8e-13
 Identities = 17/53 (32%), Positives = 26/53 (49%), Gaps = 8/53 (15%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
          L+VRNL+   +EE L++ F  YG +  +    D        +AFV F   + A
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHA 63

>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 = 59.3 bits (144), Expect = 8e-13
 Identities = 14/46 (30%), Positives = 24/46 (52%), Gaps = 1/46 (2%)

Query: 7  LYVRNL-TQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEA 51
          +++ NL T    +  ++  F +YGRV      K YAFV + + + A
Sbjct: 30 VFIGNLNTALVKKSDVETIFSKYGRVAGCSVHKGYAFVQYSNERHA 75

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 119

 Score = 59.5 bits (144), Expect = 8e-13
 Identities = 14/119 (11%), Positives = 41/119 (34%), Gaps = 33/119 (27%)

Query: 5   KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYS 64
           +V+++R L    TE ++      +G+V  +  +K                          
Sbjct: 32  RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------------------------- 66

Query: 65  SPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPDTETMSK 123
                   +   F+E ++ ++A+       +    + G  I + +++ +E     + ++
Sbjct: 67  --------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKTDSSPNQ 117

>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 = 58.8 bits (143), Expect = 1e-12
 Identities = 27/109 (24%), Positives = 39/109 (35%), Gaps = 29/109 (26%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
           +YV  L +  +E  L E F Q G V      KD              VTG          
Sbjct: 18  VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDR-------------VTGQH-------- 56

Query: 67  DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEE 115
                 +G+ F+E+ S + A  A K +   +L   G  I V+ A    +
Sbjct: 57  ------QGYGFVEFLSEEDADYAIKIMDMIKLY--GKPIRVNKASAHNK 97

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 58.9 bits (143), Expect = 1e-12
 Identities = 14/50 (28%), Positives = 25/50 (50%), Gaps = 5/50 (10%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVK-----RIKDYAFVHFEDRQEA 51
          +YV NL      + +++ F +YG +  +          +AFV FED ++A
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDA 74

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 58.6 bits (142), Expect = 1e-12
 Identities = 16/52 (30%), Positives = 23/52 (44%), Gaps = 2/52 (3%)

Query: 5  KVLYVRNLTQYCTEEKLKEAFEQYGRVERVK--RIKDYAFVHFEDRQEAITV 54
           V+++R L     E  L EA +++G +  V     K  A V FED   A   
Sbjct: 22 PVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNA 73

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

 Score = 58.4 bits (142), Expect = 1e-12
 Identities = 13/52 (25%), Positives = 29/52 (55%), Gaps = 7/52 (13%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEA 51
          L++  L   CT+E+L+E  + +G V+ ++ + +        A+V +E+  +A
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQA 71

>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 = 58.4 bits (142), Expect = 1e-12
 Identities = 24/111 (21%), Positives = 39/111 (35%), Gaps = 29/111 (26%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
           LYV  L +   ++ L  AF  +G +  ++   DY              T           
Sbjct: 15  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDY-------------ETEKH-------- 53

Query: 67  DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD 117
                 RGF F+E++  + A+ A   +    L   G  I V+ A P    +
Sbjct: 54  ------RGFAFVEFELAEDAAAAIDNMNESELF--GRTIRVNLAKPMRIKE 96

>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 = 58.0 bits (141), Expect = 2e-12
 Identities = 19/119 (15%), Positives = 43/119 (36%), Gaps = 37/119 (31%)

Query: 5   KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYS 64
           +V+Y+ ++    TEE++ +     G V  +K +         D Q     TG        
Sbjct: 3   RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMF--------DPQ-----TG-------- 41

Query: 65  SPDDNKKNRGFCFLEYDSHKSASLAKKRL----ATGRLKVWGCDIIVDWADPQEEPDTE 119
                 +++G+ F+E+   +S++ A + L       R       +   ++   +     
Sbjct: 42  ------RSKGYAFIEFRDLESSASAVRNLNGYQLGSR------FLKCGYSSNSDISGVS 88

>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 = 57.9 bits (141), Expect = 2e-12
 Identities = 18/109 (16%), Positives = 41/109 (37%), Gaps = 28/109 (25%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
           +++  LT+  T++ + E F  YG+++ +            +R        LS        
Sbjct: 7   VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPV--------ERMH----PHLS-------- 46

Query: 67  DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEE 115
                 +G+ ++E+++   A  A K +  G++   G +I          
Sbjct: 47  ------KGYAYVEFENPDEAEKALKHMDGGQID--GQEITATAVLAPWP 87

>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 = 58.5 bits (142), Expect = 2e-12
 Identities = 24/115 (20%), Positives = 44/115 (38%), Gaps = 31/115 (26%)

Query: 5   KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYS 64
           K +++RNL+    EE L E  +Q+G ++ V+ +                 T  S      
Sbjct: 16  KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPD-------------TEHS------ 56

Query: 65  SPDDNKKNRGFCFLEYDSHKSASLA----KKRLATGRLKVWGCDIIVDWADPQEE 115
                   +G  F ++ + ++A             G LK+ G  + VD A  ++E
Sbjct: 57  --------KGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDE 103

>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 = 58.4 bits (142), Expect = 2e-12
 Identities = 26/113 (23%), Positives = 42/113 (37%), Gaps = 37/113 (32%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
           L+V  L+    E+ L++ F +YG++  V  +K        DR+     T  S        
Sbjct: 15  LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVK--------DRE-----TQRS-------- 53

Query: 67  DDNKKNRGFCFLEYDSHKSASLAKKRL----ATGRLKVWGCDIIVDWADPQEE 115
                 RGF F+ +++   A  A   +      GR       I VD A    +
Sbjct: 54  ------RGFGFVTFENIDDAKDAMMAMNGKSVDGR------QIRVDQAGKSSD 94

>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 = 58.1 bits (141), Expect = 2e-12
 Identities = 11/46 (23%), Positives = 23/46 (50%), Gaps = 1/46 (2%)

Query: 7  LYVRNL-TQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEA 51
          L++ NL  +  ++E L   F  YG + ++     + F+ F++ Q  
Sbjct: 25 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSV 70

>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 = 59.5 bits (145), Expect = 3e-12
 Identities = 27/120 (22%), Positives = 51/120 (42%), Gaps = 30/120 (25%)

Query: 5   KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYS 64
           +VLYV NL +  TE+ LK+ F+  G +  +K                         I+  
Sbjct: 1   RVLYVGNLDKAITEDILKQYFQVGGPIANIK-------------------------IMI- 34

Query: 65  SPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPDTETMSKV 124
             D N KN  + F+EY     A++A + L  G+ ++    + ++WA   ++  ++    +
Sbjct: 35  --DKNNKNVNYAFVEYHQSHDANIALQTL-NGK-QIENNIVKINWAFQSQQSSSDDTFNL 90

>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 = 46.0 bits (110), Expect = 2e-07
 Identities = 13/53 (24%), Positives = 22/53 (41%), Gaps = 8/53 (15%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
           L+V +L     +E L+ AF+ +        + D        Y FV F  + +A
Sbjct: 90  LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDA 142

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 57.5 bits (139), Expect = 3e-12
 Identities = 12/56 (21%), Positives = 24/56 (42%), Gaps = 5/56 (8%)

Query: 1  MSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-----YAFVHFEDRQEA 51
            +++ L +RN+  +   E L     QYG VE  +++          V +  + +A
Sbjct: 12 RQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQA 67

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 57.3 bits (139), Expect = 3e-12
 Identities = 17/48 (35%), Positives = 27/48 (56%), Gaps = 3/48 (6%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD---YAFVHFEDRQEA 51
          +YV NL     + +L+ AF  YG +  V   ++   +AFV FED ++A
Sbjct: 3  VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDA 50

>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 = 57.3 bits (139), Expect = 4e-12
 Identities = 27/117 (23%), Positives = 47/117 (40%), Gaps = 37/117 (31%)

Query: 5   KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYS 64
           + ++V N+    TEE+LK+ F + G V   + +         DR+     TG        
Sbjct: 9   RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVY--------DRE-----TG-------- 47

Query: 65  SPDDNKKNRGFCFLEYDSHKSASLAKKRL----ATGRLKVWGCDIIVDWADPQEEPD 117
                 K +G+ F EY   ++A  A + L     +GR       + VD A  ++  +
Sbjct: 48  ------KPKGYGFCEYQDQETALSAMRNLNGREFSGR------ALRVDNAASEKNKE 92

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 56.9 bits (138), Expect = 4e-12
 Identities = 16/64 (25%), Positives = 25/64 (39%), Gaps = 3/64 (4%)

Query: 2  SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD---YAFVHFEDRQEAITVTGLS 58
          S ++ ++V    +     +L E F  +G V  V   KD   +A V   D      V   S
Sbjct: 6  SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAVLSQS 65

Query: 59 QVII 62
          Q  +
Sbjct: 66 QHSL 69

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

 Score = 56.8 bits (138), Expect = 5e-12
 Identities = 17/60 (28%), Positives = 28/60 (46%), Gaps = 9/60 (15%)

Query: 1  MSKVKV-LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
          M+  K  LYV  L +   ++ L  AF  +G +  ++   D        +AFV FE  ++A
Sbjct: 3  MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 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 = 56.6 bits (137), Expect = 5e-12
 Identities = 12/46 (26%), Positives = 23/46 (50%), Gaps = 1/46 (2%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYG-RVERVKRIKDYAFVHFEDRQEA 51
          + V+NL Q    +++ +  + Y  +   V R K  AFV   + ++A
Sbjct: 8  ILVKNLPQDSNCQEVHDLLKDYDLKYCYVDRNKRTAFVTLLNGEQA 53

>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 = 56.9 bits (138), Expect = 6e-12
 Identities = 14/52 (26%), Positives = 25/52 (48%), Gaps = 7/52 (13%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEA 51
          L V NL    ++  ++E F ++G +++     D        A VHFE + +A
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADA 83

>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 = 58.3 bits (141), Expect = 7e-12
 Identities = 24/115 (20%), Positives = 46/115 (40%), Gaps = 29/115 (25%)

Query: 5   KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYS 64
            +L+V ++ +   E++++E F  YG ++ +    D               TG        
Sbjct: 73  WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRR-------------TG-------- 111

Query: 65  SPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPDTE 119
                  ++G+  +EY++HK A  AK+ L    +   G  I VDW   +     +
Sbjct: 112 ------FSKGYALVEYETHKQALAAKEALNGAEIM--GQTIQVDWCFVKGPKRVK 158

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

 Score = 56.4 bits (137), Expect = 8e-12
 Identities = 11/46 (23%), Positives = 23/46 (50%), Gaps = 1/46 (2%)

Query: 7  LYVRNL-TQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEA 51
          L++ NL  +  ++E L   F  YG + ++     + F+ F++ Q  
Sbjct: 13 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSV 58

>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 = 56.1 bits (136), Expect = 1e-11
 Identities = 18/53 (33%), Positives = 25/53 (47%), Gaps = 8/53 (15%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
          +YV NL    T   L   F +YG+V +V  +KD         AF+ F D+  A
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSA 71

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

 Score = 56.5 bits (137), Expect = 1e-11
 Identities = 14/55 (25%), Positives = 24/55 (43%), Gaps = 8/55 (14%)

Query: 5  KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
          KVLY++NL+   TE  L   F ++   +                AF+ F +++ A
Sbjct: 26 KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIA 80

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 57.6 bits (139), Expect = 1e-11
 Identities = 19/121 (15%), Positives = 38/121 (31%), Gaps = 35/121 (28%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
           +YV + + + T+++L +     G  +    + +  F   E+R       G S        
Sbjct: 58  VYVGSFSWWTTDQQLIQVIRSIGVYD----VVELKFA--ENRA-----NGQS-------- 98

Query: 67  DDNKKNRGFCFLEYDSHKSASLAKKRLAT----GRLKVWGCDIIVDWADPQEEPDTETMS 122
                 +G+  +   S  S     + L      G        + V  A  Q     E  +
Sbjct: 99  ------KGYAEVVVASENSVHKLLELLPGKVLNGE------KVDVRPATRQNLSQFEAQA 146

Query: 123 K 123
           +
Sbjct: 147 R 147

>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 = 57.0 bits (138), Expect = 1e-11
 Identities = 15/52 (28%), Positives = 25/52 (48%), Gaps = 7/52 (13%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEA 51
          L V NL    ++  ++E F ++G +++     D        A VHFE R +A
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADA 89

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

 Score = 56.3 bits (136), Expect = 1e-11
 Identities = 16/89 (17%), Positives = 26/89 (29%), Gaps = 27/89 (30%)

Query: 5  KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYS 64
          K +    L     E  LK+   +YG VE V+ +                           
Sbjct: 7  KEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLH------------------------- 41

Query: 65 SPDDNKKNRGFCFLEYDSHKSASLAKKRL 93
               +K+ G   + + S + A    K L
Sbjct: 42 --PRTRKHLGLARVLFTSTRGAKETVKNL 68

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

 Score = 57.1 bits (138), Expect = 1e-11
 Identities = 15/53 (28%), Positives = 25/53 (47%), Gaps = 8/53 (15%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
           LYV  L +   ++ L  AF  +G +  ++   D        +AFV FE  ++A
Sbjct: 66  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 118

>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 = 57.6 bits (140), Expect = 1e-11
 Identities = 18/107 (16%), Positives = 41/107 (38%), Gaps = 31/107 (28%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
           L++  +++ CTE  ++  F  +G++E  + ++                            
Sbjct: 98  LFIGMISKKCTENDIRVMFSSFGQIEECRILR---------------------------- 129

Query: 67  DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCD--IIVDWAD 111
             +  +RG  F+ + +   A  A K +      + GC   ++V +AD
Sbjct: 130 GPDGLSRGCAFVTFTTRAMAQTAIKAM-HQAQTMEGCSSPMVVKFAD 175

>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 = 56.1 bits (136), Expect = 6e-11
 Identities = 23/120 (19%), Positives = 44/120 (36%), Gaps = 34/120 (28%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
           ++V  + +  +E+ L+E FEQYG V  +  ++D                   Q       
Sbjct: 6   MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDR-------------SQNPPQ------- 45

Query: 67  DDNKKNRGFCFLEYDSHKSASLA-----KKRLATGRLKVWGCDIIVDWADPQEEPDTETM 121
                ++G CF+ + + K+A  A       ++  G        I +  AD ++    E  
Sbjct: 46  -----SKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHP----IQMKPADSEKNNAVEDR 96

>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 = 57.6 bits (140), Expect = 1e-11
 Identities = 17/123 (13%), Positives = 40/123 (32%), Gaps = 31/123 (25%)

Query: 2   SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVI 61
           +    L++ NL    +  +LK A  +      +                          +
Sbjct: 11  TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLA-------------------------V 45

Query: 62  IYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPDTETM 121
           +         NR F +++++S +    A +   TG  KV+G +I ++    ++       
Sbjct: 46  VD---VRTGTNRKFGYVDFESAEDLEKALE--LTGL-KVFGNEIKLEKPKGRDSKKVRAA 99

Query: 122 SKV 124
             +
Sbjct: 100 RTL 102

>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 = 54.9 bits (133), Expect = 1e-10
 Identities = 15/48 (31%), Positives = 25/48 (52%), Gaps = 3/48 (6%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVK---RIKDYAFVHFEDRQEA 51
           L  +NL+   TE++LKE FE    +  V    + K  A++ F+   +A
Sbjct: 102 LLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADA 149

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 56.0 bits (135), Expect = 1e-11
 Identities = 13/49 (26%), Positives = 22/49 (44%), Gaps = 2/49 (4%)

Query: 5  KVLYVRNLTQYCTEEKLKEAFEQYGRVERVK--RIKDYAFVHFEDRQEA 51
           V+  +NL       +++E F ++G + RV        A V F +  EA
Sbjct: 11 TVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEA 59

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

 Score = 57.2 bits (139), Expect = 2e-11
 Identities = 17/118 (14%), Positives = 37/118 (31%), Gaps = 25/118 (21%)

Query: 1   MSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQV 60
           +   + LYV N+    TEE + + F    R+  + +                        
Sbjct: 1   LGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPG--------------------N 40

Query: 61  IIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPDT 118
            + +      +++ F FLE+ S    + A   +A   +   G  + +      +    
Sbjct: 41  PVLA--VQINQDKNFAFLEFRSVDETTQA---MAFDGIIFQGQSLKIRRPHDYQPLPG 93

>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 = 53.4 bits (129), Expect = 5e-10
 Identities = 12/53 (22%), Positives = 23/53 (43%), Gaps = 8/53 (15%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
           L++  L  Y  ++++KE    +G ++    +KD        YAF  + D    
Sbjct: 97  LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVT 149

>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 = 55.8 bits (135), Expect = 2e-11
 Identities = 26/112 (23%), Positives = 49/112 (43%), Gaps = 29/112 (25%)

Query: 5   KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYS 64
            +L+V ++ +   E++++E F  YG ++ +    D        R+     TG        
Sbjct: 27  WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLD--------RR-----TG-------- 65

Query: 65  SPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEP 116
                  ++G+  +EY++HK A  AK+ L  G  ++ G  I VDW   +   
Sbjct: 66  ------FSKGYALVEYETHKQALAAKEAL-NGA-EIMGQTIQVDWCFVKGPK 109

>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 = 56.7 bits (137), Expect = 2e-11
 Identities = 24/109 (22%), Positives = 38/109 (34%), Gaps = 29/109 (26%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
           L V  +     E +L++ FE+YG +E VK + D               T  S        
Sbjct: 45  LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRE-------------TRQS-------- 83

Query: 67  DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEE 115
                 RG+ F+++ S  SA  A   L    +      + V  A    +
Sbjct: 84  ------RGYGFVKFQSGSSAQQAIAGLNGFNIL--NKRLKVALAASGHQ 124

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 55.8 bits (135), Expect = 2e-11
 Identities = 14/51 (27%), Positives = 27/51 (52%), Gaps = 6/51 (11%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD------YAFVHFEDRQEA 51
          L+V N+     +  L++ F Q+G++  V+ I +      + FV FE+  +A
Sbjct: 32 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADA 82

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

 Score = 55.3 bits (134), Expect = 2e-11
 Identities = 14/51 (27%), Positives = 21/51 (41%), Gaps = 6/51 (11%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD------YAFVHFEDRQEA 51
          ++VRNL    T + LK+ F + G V       +         V FE  + A
Sbjct: 11 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVA 61

>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 = 55.8 bits (135), Expect = 2e-11
 Identities = 17/52 (32%), Positives = 22/52 (42%), Gaps = 7/52 (13%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEA 51
          ++V NL      +KLKE F   G V R   ++D          V FE   EA
Sbjct: 18 VFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEA 69

>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 = 55.3 bits (134), Expect = 2e-11
 Identities = 26/109 (23%), Positives = 41/109 (37%), Gaps = 27/109 (24%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
           LY+ NLT + T+E L EA    G  + +  IK      FE+R                  
Sbjct: 4   LYIGNLTWWTTDEDLTEAVHSLGVND-ILEIK-----FFENR------------------ 39

Query: 67  DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEE 115
             N +++GF  +   S  S+      L    L   G + +V  ++  E 
Sbjct: 40  -ANGQSKGFALVGVGSEASSKKLMDLLPKRELH--GQNPVVTPSNKLEH 85

>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 = 56.4 bits (136), Expect = 2e-11
 Identities = 17/48 (35%), Positives = 27/48 (56%), Gaps = 3/48 (6%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD---YAFVHFEDRQEA 51
           +YV NL     + +L+ AF  YG +  V   ++   +AFV FED ++A
Sbjct: 76  VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDA 123

>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 = 55.8 bits (135), Expect = 3e-11
 Identities = 26/110 (23%), Positives = 46/110 (41%), Gaps = 29/110 (26%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
           L+V  + +  TEE + + F +YG ++ +            DR+     TG          
Sbjct: 25  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNL--------DRR-----TGYL-------- 63

Query: 67  DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEP 116
                 +G+  +EY+++K A  A + L  G+  + G  I VDW   +  P
Sbjct: 64  ------KGYTLVEYETYKEAQAAMEGL-NGQ-DLMGQPISVDWCFVRGPP 105

>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 = 55.3 bits (134), Expect = 3e-11
 Identities = 11/52 (21%), Positives = 23/52 (44%), Gaps = 7/52 (13%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEA 51
          LY+ NL     E++L+   + +G+V   + ++D         F   E  ++ 
Sbjct: 28 LYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKC 79

>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 = 54.9 bits (133), Expect = 3e-11
 Identities = 14/57 (24%), Positives = 24/57 (42%), Gaps = 7/57 (12%)

Query: 2  SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEA 51
               ++V  +     E +++  F +YG V+ VK I D       Y FV F +  + 
Sbjct: 7  IMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDV 63

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

 Score = 54.9 bits (133), Expect = 3e-11
 Identities = 23/113 (20%), Positives = 42/113 (37%), Gaps = 37/113 (32%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
           LYV +L    TE+ L+  FE +G+++ +  +K        D       TG S        
Sbjct: 8   LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMK--------DSD-----TGRS-------- 46

Query: 67  DDNKKNRGFCFLEYDSHKSASLAKKRL----ATGRLKVWGCDIIVDWADPQEE 115
                 +G+ F+ +   + A  A ++L      GR       + V     + +
Sbjct: 47  ------KGYGFITFSDSECARRALEQLNGFELAGR------PMRVGHVTERLD 87

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

 Score = 56.9 bits (138), Expect = 4e-11
 Identities = 20/109 (18%), Positives = 44/109 (40%), Gaps = 29/109 (26%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
           +YV ++     E+ +++AF  +G ++ +    D             +VT           
Sbjct: 31  VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWD-------------SVTMKH-------- 69

Query: 67  DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEE 115
                 +GF F+EY+  ++A LA +++    + + G +I V       +
Sbjct: 70  ------KGFAFVEYEVPEAAQLALEQM--NSVMLGGRNIKVGRPSNIGQ 110

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

 Score = 53.1 bits (128), Expect = 9e-10
 Identities = 12/53 (22%), Positives = 27/53 (50%), Gaps = 8/53 (15%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
           +YV ++ Q  +++ +K  FE +G+++     +D        Y F+ +E  Q +
Sbjct: 128 IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSS 180

>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 = 55.0 bits (133), Expect = 4e-11
 Identities = 16/52 (30%), Positives = 27/52 (51%), Gaps = 7/52 (13%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEA 51
          L++  L +   E+ LK  F ++G +  V  IKD       +AF+ FE+  +A
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADA 61

>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 = 54.6 bits (132), Expect = 5e-11
 Identities = 24/113 (21%), Positives = 43/113 (38%), Gaps = 37/113 (32%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
           LYV +L    TE+ L+  FE +GR+E ++ +         D +     TG S        
Sbjct: 29  LYVGSLHFNITEDMLRGIFEPFGRIESIQLMM--------DSE-----TGRS-------- 67

Query: 67  DDNKKNRGFCFLEYDSHKSASLAKKRL----ATGRLKVWGCDIIVDWADPQEE 115
                 +G+ F+ +   + A  A ++L      GR       + V     + +
Sbjct: 68  ------KGYGFITFSDSECAKKALEQLNGFELAGR------PMKVGHVTERTD 108

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

 Score = 54.2 bits (131), Expect = 5e-11
 Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 3/50 (6%)

Query: 5  KVLYVRNLTQYCTEEKLKEAFEQYGRVERVK---RIKDYAFVHFEDRQEA 51
          + L  +NL+   TE++LKE FE    +  V    + K  A++ F+   +A
Sbjct: 17 RTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADA 66

>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 = 54.6 bits (132), Expect = 5e-11
 Identities = 15/61 (24%), Positives = 26/61 (42%), Gaps = 11/61 (18%)

Query: 2  SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-----------YAFVHFEDRQE 50
          S    L+++NL    TEE LK  F + G ++     K            + FV ++  ++
Sbjct: 3  SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQ 62

Query: 51 A 51
          A
Sbjct: 63 A 63

>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 = 56.1 bits (136), Expect = 5e-11
 Identities = 27/122 (22%), Positives = 48/122 (39%), Gaps = 30/122 (24%)

Query: 2   SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVI 61
             VK ++V  + +   E  L++ FEQYG++E ++ + D                      
Sbjct: 102 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR--------------------- 140

Query: 62  IYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPDTETM 121
                  + K RGF F+ +D H S     K +      V G +  V  A  ++E  + + 
Sbjct: 141 ------GSGKKRGFAFVTFDDHDS---VDKIVIQKYHTVNGHNCEVRKALSKQEMASASS 191

Query: 122 SK 123
           S+
Sbjct: 192 SQ 193

>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 = 45.7 bits (109), Expect = 4e-07
 Identities = 13/56 (23%), Positives = 25/56 (44%), Gaps = 8/56 (14%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITV 54
          L++  L+   T+E L+  FEQ+G +     ++D        + FV +   +E    
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 71

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

 Score = 54.6 bits (132), Expect = 6e-11
 Identities = 26/110 (23%), Positives = 46/110 (41%), Gaps = 29/110 (26%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
           L+V  + +  TEE + + F +YG ++ +    D        R+     TG          
Sbjct: 26  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLD--------RR-----TG---------- 62

Query: 67  DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEP 116
                 +G+  +EY+++K A  A + L  G+  + G  I VDW   +  P
Sbjct: 63  ----YLKGYTLVEYETYKEAQAAMEGL-NGQ-DLMGQPISVDWCFVRGPP 106

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 56.0 bits (135), Expect = 7e-11
 Identities = 15/52 (28%), Positives = 25/52 (48%), Gaps = 7/52 (13%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEA 51
           L V NL    ++  ++E F ++G +++     D        A VHFE R +A
Sbjct: 91  LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADA 142

>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 = 54.0 bits (130), Expect = 1e-10
 Identities = 22/111 (19%), Positives = 40/111 (36%), Gaps = 21/111 (18%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
           +YV+ L    T + L + F+Q G V+  KR        + D++     TG          
Sbjct: 18  IYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKE-----TG---------- 62

Query: 67  DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD 117
               K +G   + Y+   +A  A +       +  G  + V  A  +   +
Sbjct: 63  ----KPKGDATVSYEDPPTAKAAVEWFDGKDFQ--GSKLKVSLARKKPPMN 107

>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 = 52.9 bits (128), Expect = 1e-10
 Identities = 15/55 (27%), Positives = 26/55 (47%), Gaps = 8/55 (14%)

Query: 5  KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
          + +YV N+    T E+L+  F   G V RV  + D        +A++ F D++  
Sbjct: 7  RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESV 61

>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 = 55.4 bits (134), Expect = 2e-10
 Identities = 16/53 (30%), Positives = 25/53 (47%), Gaps = 8/53 (15%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
          LYV +L    TE  L E F   G +  ++  +D        YA+V+F+   +A
Sbjct: 18 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADA 70

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 50.0 bits (120), Expect = 1e-08
 Identities = 14/51 (27%), Positives = 26/51 (50%), Gaps = 6/51 (11%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD------YAFVHFEDRQEA 51
           ++++NL +    + L + F  +G +   K + D      Y FVHFE ++ A
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAA 156

>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 = 53.5 bits (129), Expect = 2e-10
 Identities = 15/52 (28%), Positives = 30/52 (57%), Gaps = 5/52 (9%)

Query: 5  KVLYVRNLTQYCTEEKLKEAFEQYGRVERVK-----RIKDYAFVHFEDRQEA 51
          ++LY+RNL    T E++ + F +YG + +++       +  A+V +ED  +A
Sbjct: 9  RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDA 60

>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 = 55.4 bits (133), Expect = 2e-10
 Identities = 12/53 (22%), Positives = 22/53 (41%), Gaps = 4/53 (7%)

Query: 5   KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI----KDYAFVHFEDRQEAIT 53
             L++ N+    +EE LK  F   G V +  +     +  A +     +EA+ 
Sbjct: 152 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQ 204

>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 = 54.6 bits (131), Expect = 3e-10
 Identities = 21/70 (30%), Positives = 32/70 (45%), Gaps = 5/70 (7%)

Query: 2   SKVKVLYVRNLTQY-CTEEKLKEAFEQYGRVERVKRI---KDYAFVHFEDRQEAIT-VTG 56
           +   VL V NL     T + L   F  YG V+RVK +   K+ A V   D  +A   ++ 
Sbjct: 32  AGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSH 91

Query: 57  LSQVIIYSSP 66
           L+   ++  P
Sbjct: 92  LNGHKLHGKP 101

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 53.6 bits (129), Expect = 2e-10
 Identities = 22/111 (19%), Positives = 41/111 (36%), Gaps = 21/111 (18%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
           ++V+ L +  T E + + F+Q G ++  K+        + DR+     TG          
Sbjct: 10  IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRE-----TG---------- 54

Query: 67  DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD 117
               K +G   + +D   SA  A            G  I V +A  + + +
Sbjct: 55  ----KLKGEATVSFDDPPSAKAAIDWFDGKEFS--GNPIKVSFATRRADFN 99

>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 = 55.0 bits (133), Expect = 2e-10
 Identities = 12/53 (22%), Positives = 23/53 (43%), Gaps = 8/53 (15%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
           L++  L  Y  ++++KE    +G ++    +KD        YAF  + D    
Sbjct: 117 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVT 169

>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 = 54.7 bits (132), Expect = 2e-10
 Identities = 17/117 (14%), Positives = 37/117 (31%), Gaps = 25/117 (21%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
           LYV N+    TEE + + F    R+  + +                         + +  
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGN--------------------PVLA-- 44

Query: 67  DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPDTETMSK 123
               +++ F FLE+ S    + A   +A   +   G  + +      +     + + 
Sbjct: 45  VQINQDKNFAFLEFRSVDETTQA---MAFDGIIFQGQSLKIRRPHDYQPLPGMSENP 98

>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 = 53.0 bits (128), Expect = 2e-10
 Identities = 14/51 (27%), Positives = 26/51 (50%), Gaps = 6/51 (11%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD------YAFVHFEDRQEA 51
          ++++NL +    + L + F  +G +   K + D      Y FVHFE ++ A
Sbjct: 8  IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAA 58

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 53.1 bits (128), Expect = 3e-10
 Identities = 14/53 (26%), Positives = 22/53 (41%), Gaps = 8/53 (15%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
          L++ +L Q  T+  L   F  +G V   K   D        + FV F++   A
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSA 95

>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 = 54.5 bits (131), Expect = 3e-10
 Identities = 18/51 (35%), Positives = 23/51 (45%), Gaps = 4/51 (7%)

Query: 5  KVLYVRNLTQY-CTEEKLKEAFEQYGRVERVKRIKD---YAFVHFEDRQEA 51
           VL V NL     T + L   F  YG V+RVK + +    A V   D  +A
Sbjct: 4  SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQA 54

>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 = 51.8 bits (124), Expect = 3e-09
 Identities = 12/53 (22%), Positives = 22/53 (41%), Gaps = 4/53 (7%)

Query: 5   KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI----KDYAFVHFEDRQEAIT 53
             L++ N+    +EE LK  F   G V +  +     +  A +     +EA+ 
Sbjct: 121 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQ 173

>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 = 52.7 bits (127), Expect = 3e-10
 Identities = 12/53 (22%), Positives = 23/53 (43%), Gaps = 8/53 (15%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
          L++ +L Q   ++ L + F  +G V   K   D        + FV +++   A
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSA 80

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A Length = 115

 Score = 52.7 bits (127), Expect = 3e-10
 Identities = 16/53 (30%), Positives = 28/53 (52%), Gaps = 8/53 (15%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
          ++V +L+   T E +K AF  +GR+   + +KD        Y FV F ++ +A
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDA 70

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 52.2 bits (126), Expect = 4e-10
 Identities = 16/51 (31%), Positives = 27/51 (52%), Gaps = 6/51 (11%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD------YAFVHFEDRQEA 51
          LYV+NL     +E+L++AF  +G +   K + +      + FV F   +EA
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEA 68

>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 = 51.8 bits (125), Expect = 4e-10
 Identities = 14/53 (26%), Positives = 26/53 (49%), Gaps = 8/53 (15%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
          ++V +L+   T   +  AF  +GR+   + +KD        Y FV F ++ +A
Sbjct: 9  VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDA 61

>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 = 54.5 bits (130), Expect = 6e-10
 Identities = 15/70 (21%), Positives = 32/70 (45%), Gaps = 10/70 (14%)

Query: 7  LYVRNLTQYCTEEKLKEA----FEQYGRVERVKRIKD-----YAFVHFEDRQEAIT-VTG 56
          +Y+ NL +   +++LK++    F Q+G++  +   +       AFV F++   A   +  
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 71

Query: 57 LSQVIIYSSP 66
          +     Y  P
Sbjct: 72 MQGFPFYDKP 81

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

 Score = 46.8 bits (110), Expect = 2e-07
 Identities = 12/47 (25%), Positives = 22/47 (46%), Gaps = 3/47 (6%)

Query: 8   YVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD---YAFVHFEDRQEA 51
           ++ NL +   E  L   F Q+   + V+ +      AFV F++  +A
Sbjct: 211 FLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQA 257

>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 = 52.9 bits (128), Expect = 6e-10
 Identities = 18/112 (16%), Positives = 36/112 (32%), Gaps = 30/112 (26%)

Query: 1   MSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQV 60
             K   ++V  +      ++ +E F Q+G +   + + D                     
Sbjct: 84  QDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDK-------------------- 123

Query: 61  IIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADP 112
                  D  ++RGF F+ YDS  +     +      +      I +  A+P
Sbjct: 124 -------DTGQSRGFGFVTYDSADA---VDRVCQNKFIDFKDRKIEIKRAEP 165

>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 = 51.1 bits (123), Expect = 7e-10
 Identities = 22/58 (37%), Positives = 31/58 (53%), Gaps = 3/58 (5%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD---YAFVHFEDRQEAITVTGLSQVI 61
          ++V   T   TE++L+E F QYG V  V   K    +AFV F D Q A ++ G   +I
Sbjct: 8  VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCGEDLII 65

>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 = 51.0 bits (123), Expect = 9e-10
 Identities = 21/59 (35%), Positives = 31/59 (52%), Gaps = 10/59 (16%)

Query: 4  VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDR--QEAI 52
          ++ +YV NL    T E++KE F Q+G+V  VK I D        + FV  ++    EAI
Sbjct: 1  MRNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAI 59

>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 = 51.6 bits (124), Expect = 1e-09
 Identities = 14/62 (22%), Positives = 24/62 (38%), Gaps = 8/62 (12%)

Query: 5  KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITVTG 56
          + ++   L        L++ F   G+V  V+ I D         A+V F + Q      G
Sbjct: 26 RTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG 85

Query: 57 LS 58
          L+
Sbjct: 86 LT 87

>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 = 51.1 bits (123), Expect = 1e-09
 Identities = 13/47 (27%), Positives = 19/47 (40%), Gaps = 4/47 (8%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--YAFVHFEDRQEA 51
          LYV       T   L+ AF  +G +  +        AFV +E  + A
Sbjct: 18 LYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESA 62

>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 = 51.1 bits (123), Expect = 1e-09
 Identities = 32/113 (28%), Positives = 51/113 (45%), Gaps = 32/113 (28%)

Query: 5   KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYS 64
           K L+V+ L++  TEE LKE+F+   R   V            DR+     TG S      
Sbjct: 16  KTLFVKGLSEDTTEETLKESFDGSVRARIVT-----------DRE-----TGSS------ 53

Query: 65  SPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD 117
                   +GF F++++S + A  AK+ +  G +   G  + +DWA P+ E  
Sbjct: 54  --------KGFGFVDFNSEEDAKAAKEAMEDGEID--GNKVTLDWAKPKGEGG 96

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 51.6 bits (123), Expect = 1e-09
 Identities = 15/55 (27%), Positives = 23/55 (41%), Gaps = 3/55 (5%)

Query: 1  MSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD---YAFVHFEDRQEAI 52
           +KV +L ++N     T + L       G+V+R+   K     A V FE    A 
Sbjct: 22 GNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESVLCAQ 76

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 51.6 bits (124), Expect = 1e-09
 Identities = 13/53 (24%), Positives = 23/53 (43%), Gaps = 8/53 (15%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
          +YV N+    T + L+  F   G + R+  + D        YA++ F +R   
Sbjct: 39 VYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSV 91

>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 = 51.1 bits (122), Expect = 1e-09
 Identities = 12/53 (22%), Positives = 22/53 (41%), Gaps = 4/53 (7%)

Query: 5  KVLYVRN--LTQYCTEEKLKEAFEQYGRVERVKRI--KDYAFVHFEDRQEAIT 53
          + L V N  L    +  +L    E+ G V+ +     K Y+F  +   +E+  
Sbjct: 26 QSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKR 78

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 112

 Score = 51.1 bits (122), Expect = 1e-09
 Identities = 13/53 (24%), Positives = 30/53 (56%), Gaps = 3/53 (5%)

Query: 5  KVLYVRNL-TQYCTEEKLKEAFEQYGRVERVK--RIKDYAFVHFEDRQEAITV 54
          +V+++ NL     ++  + +  E YG+++     R+K  AF+  E R++A+ +
Sbjct: 26 RVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAM 78

>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 = 50.2 bits (121), Expect = 2e-09
 Identities = 13/53 (24%), Positives = 22/53 (41%), Gaps = 8/53 (15%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
          L+V +L     +E L+ AF+ +        + D        Y FV F  + +A
Sbjct: 4  LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDA 56

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

 Score = 49.8 bits (119), Expect = 3e-09
 Identities = 14/48 (29%), Positives = 21/48 (43%), Gaps = 3/48 (6%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRV---ERVKRIKDYAFVHFEDRQEA 51
          +YV NL +      LK A  + G V      +  +  AF+H+ D   A
Sbjct: 22 VYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRAFLHYPDSAAA 69

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 52.0 bits (124), Expect = 3e-09
 Identities = 15/51 (29%), Positives = 20/51 (39%), Gaps = 4/51 (7%)

Query: 5  KVLYVRNL-TQYCTEEKLKEAFEQYGRVERVKRIKD---YAFVHFEDRQEA 51
           VL V  L       +++   F  YG VE+VK +K     A V   D    
Sbjct: 5  PVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAV 55

>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 = 48.9 bits (116), Expect = 3e-08
 Identities = 9/55 (16%), Positives = 18/55 (32%), Gaps = 8/55 (14%)

Query: 6   VLYVRNLTQYCTEEKLKEAFEQYGRVERVK--------RIKDYAFVHFEDRQEAI 52
           VL+  N     TEE   E  ++ G                     + ++ + +A+
Sbjct: 125 VLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDAL 179

>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 = 50.0 bits (120), Expect = 3e-09
 Identities = 16/56 (28%), Positives = 24/56 (42%), Gaps = 8/56 (14%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITV 54
          ++V  L  + T+  L++ FE +G +E    I D        Y FV   DR  A   
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERA 75

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

 Score = 50.3 bits (120), Expect = 3e-09
 Identities = 9/56 (16%), Positives = 21/56 (37%), Gaps = 9/56 (16%)

Query: 5  KVLYVRNLTQYCTEEKLKEA----FEQYGRVERVK-----RIKDYAFVHFEDRQEA 51
          +V+ + N+     +EKL+          G +  +           A++ F  ++ A
Sbjct: 30 QVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQESA 85

>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 = 49.6 bits (119), Expect = 4e-09
 Identities = 17/54 (31%), Positives = 23/54 (42%), Gaps = 9/54 (16%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYG-RVERVKRIKD--------YAFVHFEDRQEA 51
          L++ +L  Y  E  +  AF   G  V  VK I++        Y FV F D   A
Sbjct: 12 LWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATA 65

>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 = 49.5 bits (119), Expect = 4e-09
 Identities = 22/114 (19%), Positives = 44/114 (38%), Gaps = 30/114 (26%)

Query: 2   SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVI 61
           SK   ++V  +   C E +L+E F+++G V  V  I D                      
Sbjct: 8   SKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDA--------------------- 46

Query: 62  IYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEE 115
                 + ++ RGF F+ ++  +S     + +      + G  + V  A+P++ 
Sbjct: 47  ------EKQRPRGFGFITFEDEQS---VDQAVNMHFHDIMGKKVEVKRAEPRDS 91

>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 = 48.1 bits (115), Expect = 1e-08
 Identities = 16/87 (18%), Positives = 31/87 (35%), Gaps = 19/87 (21%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
          ++V+ L +  T E + + F+Q G ++  K+        + DR                  
Sbjct: 16 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDR------------------ 57

Query: 67 DDNKKNRGFCFLEYDSHKSASLAKKRL 93
           +  K +G   + +D   SA  A    
Sbjct: 58 -ETGKLKGEATVSFDDPPSAKAAIDWF 83

>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 = 49.3 bits (117), Expect = 1e-08
 Identities = 14/55 (25%), Positives = 24/55 (43%), Gaps = 4/55 (7%)

Query: 2  SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERV----KRIKDYAFVHFEDRQEAI 52
          S V  + V NL    T + L + F ++G V ++    K  +  A + + D   A 
Sbjct: 44 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQ 98

>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 = 48.0 bits (115), Expect = 1e-08
 Identities = 12/54 (22%), Positives = 24/54 (44%), Gaps = 9/54 (16%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRI---------KDYAFVHFEDRQEA 51
          +++ NL     E+ L + F  +G + +  +I         K YAF++F     +
Sbjct: 8  IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDAS 61

>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 = 48.3 bits (115), Expect = 2e-08
 Identities = 9/46 (19%), Positives = 18/46 (39%), Gaps = 1/46 (2%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-YAFVHFEDRQEA 51
          + V  L    + + LK+   + G V      +D    V F  +++ 
Sbjct: 18 VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDGTGVVEFVRKEDM 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 = 47.1 bits (113), Expect = 2e-08
 Identities = 15/53 (28%), Positives = 24/53 (45%), Gaps = 8/53 (15%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
          ++V  L+   T E +K  FEQ+G+V+    + D        + FV FE     
Sbjct: 2  IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIV 54

>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 = 46.7 bits (112), Expect = 3e-08
 Identities = 18/80 (22%), Positives = 30/80 (37%), Gaps = 27/80 (33%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
          ++V  L+    EEK++E F  +G VE ++   D                           
Sbjct: 2  IFVGGLSPDTPEEKIREYFGGFGEVESIELPMD--------------------------N 35

Query: 67 DDNKKNRGFCFLEYDSHKSA 86
            NK+ RGFCF+ +   +  
Sbjct: 36 KTNKR-RGFCFITFKEEEPV 54

>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 = 46.9 bits (112), Expect = 4e-08
 Identities = 13/54 (24%), Positives = 23/54 (42%), Gaps = 8/54 (14%)

Query: 6  VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
          V+ V+N+    + +++ + F  Y  +     +K          A V FE R EA
Sbjct: 17 VIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEA 70

>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 = 46.9 bits (112), Expect = 4e-08
 Identities = 9/52 (17%), Positives = 20/52 (38%), Gaps = 7/52 (13%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVK-------RIKDYAFVHFEDRQEA 51
          L++ NL    +  +LK A  +      +          + + +V FE  ++ 
Sbjct: 20 LFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDL 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 = 46.4 bits (111), Expect = 5e-08
 Identities = 20/58 (34%), Positives = 31/58 (53%), Gaps = 3/58 (5%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD---YAFVHFEDRQEAITVTGLSQVI 61
          ++V   T+  T E+L++ F QYG V  V   K    +AFV F D + A ++ G   +I
Sbjct: 14 VFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQSLCGEDLII 71

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 47.3 bits (112), Expect = 5e-08
 Identities = 14/56 (25%), Positives = 24/56 (42%), Gaps = 4/56 (7%)

Query: 2  SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERV----KRIKDYAFVHFEDRQEAIT 53
          S V  + V NL    T + L + F ++G V ++    K  +  A + + D   A  
Sbjct: 26 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQH 81

>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 = 46.5 bits (111), Expect = 5e-08
 Identities = 12/54 (22%), Positives = 23/54 (42%), Gaps = 8/54 (14%)

Query: 6  VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
          ++ V+N+    + +++ + F  Y  +     +K          A V FE R EA
Sbjct: 17 IIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEA 70

>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 = 46.5 bits (111), Expect = 6e-08
 Identities = 18/56 (32%), Positives = 25/56 (44%), Gaps = 8/56 (14%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITV 54
          L V  L    TE+ LKE F  +G V  V+  KD        + FV F + +  + V
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKV 73

>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 = 48.7 bits (115), Expect = 6e-08
 Identities = 24/113 (21%), Positives = 40/113 (35%), Gaps = 29/113 (25%)

Query: 5   KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYS 64
           K L+V  +    TE KL+  FE YG ++R+  +                           
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYS------------------------- 137

Query: 65  SPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD 117
               + K RG+ F+EY+  +    A K       K+ G  ++VD    +    
Sbjct: 138 --KRSGKPRGYAFIEYEHERDMHSAYKHA--DGKKIDGRRVLVDVERGRTVKG 186

>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 = 46.7 bits (111), Expect = 9e-08
 Identities = 14/60 (23%), Positives = 24/60 (40%), Gaps = 13/60 (21%)

Query: 5   KVLYVRNLTQYCTEEKLKEAFEQYGRVERVK-------------RIKDYAFVHFEDRQEA 51
             +YV+NL ++  E+ LK  F +Y                    R+K  AF+   + + A
Sbjct: 46  CRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAA 105

>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 = 45.7 bits (109), Expect = 1e-07
 Identities = 22/113 (19%), Positives = 40/113 (35%), Gaps = 30/113 (26%)

Query: 5   KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYS 64
              ++ NL    TEE +KE F     +  V+  ++                         
Sbjct: 16  YTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPRE------------------------- 49

Query: 65  SPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD 117
            P + ++ +GF + E++   S   A   L+     +    I VD AD  ++ D
Sbjct: 50  -PSNPERLKGFGYAEFEDLDSLLSA---LSLNEESLGNKRIRVDVADQAQDKD 98

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

 Score = 44.9 bits (107), Expect = 2e-07
 Identities = 14/93 (15%), Positives = 33/93 (35%), Gaps = 34/93 (36%)

Query: 5  KVLYVRNLTQYCTEEKLKEA----FEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQV 60
            +Y+ NL +   +++LK++    F ++G++  +   +                      
Sbjct: 9  HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL-------------------- 48

Query: 61 IIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRL 93
                    K RG  F+ +    SA+ A + +
Sbjct: 49 ----------KMRGQAFVIFKEVSSATNALRSM 71

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 44.0 bits (105), Expect = 3e-07
 Identities = 15/56 (26%), Positives = 27/56 (48%), Gaps = 8/56 (14%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITV 54
          +++  L+   T+E L+E F Q+G V+    ++D        + FV F D+     V
Sbjct: 3  MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKV 58

>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 = 44.5 bits (106), Expect = 3e-07
 Identities = 21/111 (18%), Positives = 39/111 (35%), Gaps = 30/111 (27%)

Query: 5   KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYS 64
              ++ NL    TEE +KE F     +  V+  ++                         
Sbjct: 20  YTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPRE------------------------- 53

Query: 65  SPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEE 115
            P + ++ +GF + E++   S   A   L+     +    I VD AD  ++
Sbjct: 54  -PSNPERLKGFGYAEFEDLDSLLSA---LSLNEESLGNRRIRVDVADQAQD 100

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 44.3 bits (105), Expect = 3e-07
 Identities = 14/56 (25%), Positives = 24/56 (42%), Gaps = 7/56 (12%)

Query: 3  KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERV-------KRIKDYAFVHFEDRQEA 51
          K + +Y++      T + +KE  E  G+V  +       K  K   FV F+  + A
Sbjct: 10 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESA 65

>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 = 4e-07
 Identities = 11/60 (18%), Positives = 25/60 (41%), Gaps = 14/60 (23%)

Query: 6  VLYVRNLTQYCTEE---KLKEAFEQYGRVERVKRIKD-----------YAFVHFEDRQEA 51
          +++V  L+Q   +    K  E F ++G++ +V                 A+V +   ++A
Sbjct: 17 LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 76

>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 = 44.7 bits (106), Expect = 4e-07
 Identities = 8/55 (14%), Positives = 18/55 (32%), Gaps = 8/55 (14%)

Query: 5  KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
             ++ N+    T+  + +  E     E    +           A V F++  +A
Sbjct: 16 VCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDA 70

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 44.2 bits (105), Expect = 5e-07
 Identities = 9/55 (16%), Positives = 20/55 (36%), Gaps = 9/55 (16%)

Query: 5  KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
             YV NL     +  +   F+    +  V+ ++D        + +V F++    
Sbjct: 16 YTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSL 69

>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 = 43.8 bits (104), Expect = 6e-07
 Identities = 19/56 (33%), Positives = 25/56 (44%), Gaps = 8/56 (14%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITV 54
          L+V  L    T+E L+  F QYG V     +KD        + FV F+D     TV
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTV 74

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115

 Score = 44.0 bits (104), Expect = 6e-07
 Identities = 9/46 (19%), Positives = 18/46 (39%), Gaps = 1/46 (2%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-YAFVHFEDRQEA 51
          + V  L    + + LK+   + G V      +D    V F  +++ 
Sbjct: 19 VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDGTGVVEFVRKEDM 64

>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 Length = 102

 Score = 43.7 bits (103), Expect = 7e-07
 Identities = 7/53 (13%), Positives = 20/53 (37%), Gaps = 3/53 (5%)

Query: 5  KVLYVRNL-TQYCTEEKLKEAFEQYGRVERVKRIKD--YAFVHFEDRQEAITV 54
          +V+++ +         +L +  E +G +     +     AF+     ++A   
Sbjct: 16 RVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAA 68

>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 = 43.2 bits (102), Expect = 8e-07
 Identities = 15/83 (18%), Positives = 28/83 (33%), Gaps = 22/83 (26%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
          LYV N+    TEE + + F    R+  + +      +  +                    
Sbjct: 9  LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN------------------ 50

Query: 67 DDNKKNRGFCFLEYDSHKSASLA 89
              +++ F FLE+ S    + A
Sbjct: 51 ----QDKNFAFLEFRSVDETTQA 69

>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 = 43.6 bits (103), Expect = 9e-07
 Identities = 11/55 (20%), Positives = 21/55 (38%), Gaps = 8/55 (14%)

Query: 5  KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
            + +R L   C++E++ + F     V     +           AFV F  ++ A
Sbjct: 16 GFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIA 70

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 45.2 bits (106), Expect = 1e-06
 Identities = 14/63 (22%), Positives = 26/63 (41%), Gaps = 11/63 (17%)

Query: 1   MSKVKVLYVRNLTQYCT---------EEKLKEAFEQYGRVERVK--RIKDYAFVHFEDRQ 49
             K K LYV  +              E +++  F + G ++R++    K+  FV F+ + 
Sbjct: 131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGFVKFKYQA 190

Query: 50  EAI 52
            A 
Sbjct: 191 NAE 193

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 43.0 bits (102), Expect = 1e-06
 Identities = 16/53 (30%), Positives = 21/53 (39%), Gaps = 8/53 (15%)

Query: 7  LYVRNLTQYCTEEKLKEAF-EQYGRVERVKRIKD-------YAFVHFEDRQEA 51
          L+V +LT    +  L E F + Y      K + D       Y FV F D  E 
Sbjct: 12 LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQ 64

>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 = 43.4 bits (103), Expect = 1e-06
 Identities = 14/53 (26%), Positives = 25/53 (47%), Gaps = 8/53 (15%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
          L++  L+   TEE L+  +EQ+G++     ++D        + FV F    E 
Sbjct: 30 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEV 82

>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 = 43.0 bits (102), Expect = 1e-06
 Identities = 15/56 (26%), Positives = 27/56 (48%), Gaps = 8/56 (14%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITV 54
          +++  L+   T+E L+E F Q+G V+    ++D        + FV F D+     V
Sbjct: 28 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKV 83

>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 = 42.6 bits (101), Expect = 1e-06
 Identities = 12/56 (21%), Positives = 24/56 (42%), Gaps = 8/56 (14%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITV 54
          ++V  L+   +++ LK+ F ++G V       D        + F+ F+D      V
Sbjct: 14 MFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKV 69

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 124

 Score = 42.9 bits (101), Expect = 2e-06
 Identities = 9/54 (16%), Positives = 19/54 (35%), Gaps = 8/54 (14%)

Query: 6  VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYAFVHFEDRQEA 51
           +Y++ L      + + + F++   VE    I            FV F +  + 
Sbjct: 27 CVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADY 80

>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 = 42.9 bits (101), Expect = 2e-06
 Identities = 12/54 (22%), Positives = 21/54 (38%), Gaps = 8/54 (14%)

Query: 6  VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
           + +R L   CT+E++ + F     V     +           AFV F  ++ A
Sbjct: 44 FVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELA 97

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

 Score = 42.0 bits (99), Expect = 3e-06
 Identities = 13/88 (14%), Positives = 24/88 (27%), Gaps = 27/88 (30%)

Query: 6  VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSS 65
             + +      ++ L   F + G+V  ++   D                          
Sbjct: 14 APVIPSAKVPVLKKALTSLFSKAGKVVNMEFPID-------------------------- 47

Query: 66 PDDNKKNRGFCFLEYDSHKSASLAKKRL 93
           +   K +GF F+E  S   A    K  
Sbjct: 48 -EATGKTKGFLFVECGSMNDAKKIIKSF 74

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 43.3 bits (101), Expect = 4e-06
 Identities = 13/54 (24%), Positives = 23/54 (42%), Gaps = 7/54 (12%)

Query: 5   KVLYVRNLTQYCTEEKLKEAFEQYGRVERV-------KRIKDYAFVHFEDRQEA 51
           + +Y++      T + +KE  E  G+V  +       K  K   FV F+  + A
Sbjct: 110 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESA 163

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 41.6 bits (98), Expect = 5e-06
 Identities = 11/54 (20%), Positives = 17/54 (31%), Gaps = 8/54 (14%)

Query: 5  KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEA 51
            +++R L    TE  +   F       RV             A V F   ++A
Sbjct: 16 HCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVTGEADVEFATHEDA 68

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 41.8 bits (98), Expect = 7e-06
 Identities = 13/53 (24%), Positives = 19/53 (35%), Gaps = 6/53 (11%)

Query: 5  KVLYVRNLTQYCTEEKLKEAFEQYG--RVERVK----RIKDYAFVHFEDRQEA 51
            +++R L    TE  +   F      RV        R+   A V F   +EA
Sbjct: 47 HCVHMRGLPYKATENDIYNFFSPLNPVRVHIEIGPDGRVTGEADVEFATHEEA 99

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 40.5 bits (95), Expect = 1e-05
 Identities = 11/54 (20%), Positives = 19/54 (35%), Gaps = 8/54 (14%)

Query: 5  KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEA 51
            + V  +     E  +++ F    RV+ V  +KD          V F   Q+ 
Sbjct: 17 LYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDT 69

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 39.2 bits (92), Expect = 3e-05
 Identities = 9/54 (16%), Positives = 20/54 (37%), Gaps = 8/54 (14%)

Query: 5  KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEA 51
            + +R      TE+ + E          ++ +++       Y FV F + +E 
Sbjct: 11 HTVKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNAHGNKTGYIFVDFSNEEEV 63

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 39.9 bits (93), Expect = 3e-05
 Identities = 12/87 (13%), Positives = 27/87 (31%), Gaps = 24/87 (27%)

Query: 6  VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSS 65
          ++ +R L    T E++   F Q+  +   K       + F                    
Sbjct: 25 IVRMRGLPFTATAEEVVAFFGQHCPITGGKEG-----ILFVT------------------ 61

Query: 66 PDDNKKNRGFCFLEYDSHKSASLAKKR 92
             + +  G  F+ +   + A  A ++
Sbjct: 62 -YPDGRPTGDAFVLFACEEYAQNALRK 87

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 38.8 bits (90), Expect = 6e-05
 Identities = 13/55 (23%), Positives = 20/55 (36%), Gaps = 5/55 (9%)

Query: 5  KVLYVRNLTQYCTEEKLKEAFEQY-----GRVERVKRIKDYAFVHFEDRQEAITV 54
            + VR L     +E L   FE       G V   +R+     + F +  +A  V
Sbjct: 9  VAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLGCGGVLTFREPADAERV 63

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 118

 Score = 37.6 bits (87), Expect = 2e-04
 Identities = 10/56 (17%), Positives = 18/56 (32%), Gaps = 10/56 (17%)

Query: 6  VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI----------KDYAFVHFEDRQEA 51
          V+ +R L   C+ E ++         + V  +             AFV  E   + 
Sbjct: 19 VVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDV 74

>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 = 2e-04
 Identities = 13/77 (16%), Positives = 25/77 (32%), Gaps = 29/77 (37%)

Query: 17 TEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFC 76
           +  + + F ++G++                                  P+++ K +G+ 
Sbjct: 20 LKNVIHKIFSKFGKITNDFY-----------------------------PEEDGKTKGYI 50

Query: 77 FLEYDSHKSASLAKKRL 93
          FLEY S   A  A K  
Sbjct: 51 FLEYASPAHAVDAVKNA 67

>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 Length = 96

 Score = 36.9 bits (85), Expect = 2e-04
 Identities = 14/57 (24%), Positives = 28/57 (49%), Gaps = 9/57 (15%)

Query: 7  LYVRNLTQYCTEEKLKE----AFEQYGRVERV-----KRIKDYAFVHFEDRQEAITV 54
          + V N+    + ++L++    AF ++G+V+ V        +  A V  E+ Q+AI  
Sbjct: 12 VQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGA 68

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 37.0 bits (86), Expect = 2e-04
 Identities = 16/95 (16%), Positives = 30/95 (31%), Gaps = 35/95 (36%)

Query: 5  KVLYVRNL------TQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLS 58
           V+ V N+           +  + + F ++G++                           
Sbjct: 16 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFY---------------------- 53

Query: 59 QVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRL 93
                 P+++ K +G+ FLEY S   A  A K  
Sbjct: 54 -------PEEDGKTKGYIFLEYASPAHAVDAVKNA 81

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens} Length = 107

 Score = 36.0 bits (83), Expect = 6e-04
 Identities = 10/61 (16%), Positives = 18/61 (29%), Gaps = 10/61 (16%)

Query: 1  MSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI----------KDYAFVHFEDRQE 50
          +  V ++  + L   CT E +   F           I          +  A +  E  Q+
Sbjct: 8  VDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQD 67

Query: 51 A 51
           
Sbjct: 68 V 68

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 35.7 bits (82), Expect = 8e-04
 Identities = 10/58 (17%), Positives = 23/58 (39%), Gaps = 10/58 (17%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERV----------KRIKDYAFVHFEDRQEAITV 54
          ++V  L     E+++  +F ++G +                K YAF+ F++      +
Sbjct: 11 VFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQAL 68

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	131
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.92
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.91
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.91
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.91
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.9
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.9
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.9
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.9
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.89
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.89
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.89
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.89
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.88
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.88
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.88
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.88
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.88
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.87
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.87
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.87
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.87
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.87
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.87
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.86
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.86
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.86
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.86
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.86
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.86
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.86
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.86
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.86
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.86
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.86
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.86
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.86
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.86
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.86
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.86
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.86
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.85
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.85
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.85
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.85
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.85
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.85
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.85
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.85
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.85
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.85
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.85
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.85
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.85
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.85
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.85
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.85
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.85
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.85
2div_A	99	TRNA selenocysteine associated protein; structural	99.85
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.85
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.85
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.85
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.84
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.84
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.84
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.84
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.84
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.84
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.84
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.84
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.84
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.84
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.84
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.84
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.84
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.84
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.84
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.84
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.83
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.83
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.83
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.83
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.83
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.83
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.83
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.83
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.83
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.83
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.83
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.83
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.83
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.83
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.83
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.83
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.83
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.83
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.83
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.83
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.83
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.83
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.83
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.83
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.83
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.83
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.82
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.82
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.82
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.82
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.82
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.82
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.82
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.82
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.82
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.82
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.82
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.82
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.82
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.82
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.82
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.82
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.82
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.82
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.82
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.81
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.81
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.81
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.81
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.81
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.81
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.81
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.81
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.81
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.81
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.81
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.81
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.8
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.8
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.8
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.8
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.79
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.79
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.79
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.79
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.79
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.79
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.79
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.78
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.78
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.78
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.78
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.78
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.78
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.78
1x5p_A	97	Negative elongation factor E; structure genomics,	99.77
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.77
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.77
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.64
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.77
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.77
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.77
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.77
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.76
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.76
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.76
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.76
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.76
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.75
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.75
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.75
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.74
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.73
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.73
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.73
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.73
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.72
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.72
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.72
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.71
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.71
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.71
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.67
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.67
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.65
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.61
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.57
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.53
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.53
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.51
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.49
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.41
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.39
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.25
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.24
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.24
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.21
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.21
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.19
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.18
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.18
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.18
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.17
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.16
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.09
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.09
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.08
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	99.02
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.0
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.91
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.5
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.97
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.64
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.61
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.24
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.16
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.13
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	96.72
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	96.51
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	95.79
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	95.05
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	95.0
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	93.4
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	93.36
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	93.26
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	93.0
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	92.78
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	92.66
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	92.64
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	92.29
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	92.23
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	92.02
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	91.95
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	91.76
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	91.71
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	91.64
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	91.52
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	91.44
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	91.33
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	91.05
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	91.05
1x4e_A	85	RNA binding motif, single-stranded interacting pro	91.01
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	90.93
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	90.77
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	90.71
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	90.68
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	90.56
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	90.5
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	90.46
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	90.46
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	90.45
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	90.36
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	90.35
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	90.34
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	90.32
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	90.3
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	90.28
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	90.14
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	90.07
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	90.03
2dis_A	109	Unnamed protein product; structural genomics, RRM	90.0
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	90.0
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	89.94
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	89.92
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	89.87
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	89.69
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	89.64
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	89.59
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	89.58
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	89.52
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	89.52
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	89.49
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	89.45
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	89.43
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	89.41
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	89.4
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	89.37
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	89.37
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	89.35
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	89.29
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	89.24
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	89.23
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	89.18
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	89.11
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	89.09
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	89.04
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	88.99
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	88.99
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	88.94
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	88.8
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	88.79
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	88.79
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	88.78
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	88.77
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	88.69
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	88.65
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	88.64
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	88.61
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	88.61
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	88.59
2div_A	99	TRNA selenocysteine associated protein; structural	88.56
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	88.54
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	88.52
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	88.5
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	88.47
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	88.44
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	88.44
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	88.39
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	88.38
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	88.28
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	88.17
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	88.14
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	88.13
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	88.11
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	88.11
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	88.09
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	87.89
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	87.88
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	87.7
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	87.68
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	87.55
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	87.49
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	87.35
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	87.18
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	87.03
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	86.87
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	86.8
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	86.79
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	86.72
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	86.57
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	86.43
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	86.35
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	86.34
1x5o_A	114	RNA binding motif, single-stranded interacting pro	86.34
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	86.25
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	85.69
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	85.16
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	85.06
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	84.57
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	84.27
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	84.12
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	83.59
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	83.43
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	83.37
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	82.99
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	82.68
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	82.38
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	82.33
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	82.3
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	81.51
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	81.2
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	80.63
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	80.55
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	80.45

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.92  E-value=3.6e-25  Score=155.54  Aligned_cols=109  Identities=20%  Similarity=0.370  Sum_probs=93.2

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe--------cCeEEEEECCHHHHHh----------------------
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYAFVHFEDRQEAIT----------------------   53 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~--------~~~~fv~~~~~~~a~~----------------------   53 (131)
                      .++|||||||+++++++|+++|++||+|.+++++        +|||||+|.+.++|+.                      
T Consensus        15 ~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~~~   94 (213)
T 4f02_A           15 MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQR   94 (213)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcccccccccc
Confidence            5799999999999999999999999999999987        5899999999999998                      


Q ss_pred             -------------------------------hcC-CceeEEecCCCCCCCCcceEEEEeCCHHhHHHHHHHHhCCcceec
Q psy1185          54 -------------------------------VTG-LSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVW  101 (131)
Q Consensus        54 -------------------------------~~g-~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~~~~~  101 (131)
                                                     .+| +..+.+..+   .+.++|||||+|.+.++|.+|++.|||.  .++
T Consensus        95 ~~~~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d---~~~~~g~~fV~f~~~~~a~~Ai~~lng~--~~~  169 (213)
T 4f02_A           95 DPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD---ENGSKGYGFVHFETQEAAERAIEKMNGM--LLN  169 (213)
T ss_dssp             CTHHHHHCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEE---TTEEEEEEEEEESSHHHHHHHHHHHTTC--EET
T ss_pred             cccccccccccceECCcccccHHHHHHHHHhhcCCeEEEEeecc---CCCCceEEEEEeCCHHHHHHHHHHhCCC--EEC
Confidence                                           234 333333332   3457899999999999999999999998  899


Q ss_pred             CcEEEEEecCCCCCCC
Q psy1185         102 GCDIIVDWADPQEEPD  117 (131)
Q Consensus       102 g~~l~v~~a~~~~~~~  117 (131)
                      |+.|.|.||.++.++.
T Consensus       170 g~~i~V~~a~~~~~~~  185 (213)
T 4f02_A          170 DRKVFVGRFKSRKERE  185 (213)
T ss_dssp             TEECEEEECCCHHHHH
T ss_pred             CEEEEEEEcCCCcccc
Confidence            9999999999765443

>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=99.91  E-value=1.1e-23  Score=141.82  Aligned_cols=108  Identities=23%  Similarity=0.389  Sum_probs=91.9

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe--------cCeEEEEECCHHHHHh---------------------
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYAFVHFEDRQEAIT---------------------   53 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~--------~~~~fv~~~~~~~a~~---------------------   53 (131)
                      ..++|||+|||.++++++|+++|++||.|.+++++        +|||||+|.+.++|+.                     
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            36899999999999999999999999999999987        4899999999999987                     


Q ss_pred             ----------------------------hcC-CceeEEecCCCCCCCCcceEEEEeCCHHhHHHHHHHHhCCcceecCcE
Q psy1185          54 ----------------------------VTG-LSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCD  104 (131)
Q Consensus        54 ----------------------------~~g-~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~~~~~g~~  104 (131)
                                                  .+| +..+.+..+. .+|.++|+|||+|.+.++|.+|+. +++.  .++|+.
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 DEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDK-DTGQSRGFGFVTYDSADAVDRVCQ-NKFI--DFKDRK  157 (167)
T ss_dssp             HHHHHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSS-SSSTTSEEEEEEESSHHHHHHHHH-CSEE--CSSSSC
T ss_pred             hhccCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcC-CCCccceEEEEEECCHHHHHHHHh-CCCE--EeCCeE
Confidence                                        234 3333333332 468889999999999999999998 7776  899999


Q ss_pred             EEEEecCCCC
Q psy1185         105 IIVDWADPQE  114 (131)
Q Consensus       105 l~v~~a~~~~  114 (131)
                      |.|.||.|+.
T Consensus       158 i~V~~a~pk~  167 (167)
T 2cjk_A          158 IEIKRAEPRH  167 (167)
T ss_dssp             EEEEECCCCC
T ss_pred             EEEeecCCCC
Confidence            9999999863

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

Probab=99.91  E-value=1.5e-23  Score=140.48  Aligned_cols=105  Identities=26%  Similarity=0.420  Sum_probs=90.8

Q ss_pred             eEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe-------cCeEEEEECCHHHHHh------------------------
Q psy1185           5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI-------KDYAFVHFEDRQEAIT------------------------   53 (131)
Q Consensus         5 ~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~-------~~~~fv~~~~~~~a~~------------------------   53 (131)
                      ++|||+|||.++++++|+++|++||.|.++.++       +|||||+|.+.++|..                        
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~~   80 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQ   80 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCCCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCCC
Confidence            689999999999999999999999999999987       6899999999999988                        


Q ss_pred             -----------------------------hcC-CceeEEecCCCCCCCCcceEEEEeCCHHhHHHHHHHHhCCcceecCc
Q psy1185          54 -----------------------------VTG-LSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGC  103 (131)
Q Consensus        54 -----------------------------~~g-~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~~~~~g~  103 (131)
                                                   .+| +..+.+..++ .++.++|+|||+|.+.++|.+|+..|+|.  .++|+
T Consensus        81 ~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~-~~~~~~g~afV~f~~~~~A~~A~~~l~g~--~~~g~  157 (166)
T 3md3_A           81 QSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDM-QTGSSRGYGFVSFTSQDDAQNAMDSMQGQ--DLNGR  157 (166)
T ss_dssp             CCCCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECT-TTCCEEEEEEEEESCHHHHHHHHHHHTTC--EETTE
T ss_pred             CCCCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecC-CCCCcceEEEEEeCCHHHHHHHHHHhCCC--ccCCc
Confidence                                         233 2233333332 46788999999999999999999999998  89999


Q ss_pred             EEEEEecCC
Q psy1185         104 DIIVDWADP  112 (131)
Q Consensus       104 ~l~v~~a~~  112 (131)
                      .|.|.||++
T Consensus       158 ~i~v~~a~~  166 (166)
T 3md3_A          158 PLRINWAAK  166 (166)
T ss_dssp             ECEEEESCC
T ss_pred             EEEEEecCC
Confidence            999999863

>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=99.91  E-value=1e-23  Score=132.20  Aligned_cols=81  Identities=30%  Similarity=0.395  Sum_probs=75.1

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++|+++|+++|++||+|.++++++.                           ..+|.++|||||+|.+
T Consensus        18 ~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d---------------------------~~tg~~kG~afV~f~~   70 (99)
T 4fxv_A           18 QGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRD---------------------------KVAGHSLGYGFVNYVT   70 (99)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEC---------------------------SSSCCEEEEEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeec---------------------------CCCCcccccEEEEECC
Confidence            3578999999999999999999999999999998854                           3468899999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADP  112 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~  112 (131)
                      .++|.+|++.|+|.  .++|+.|+|+||+|
T Consensus        71 ~~~A~~Ai~~lng~--~~~gr~l~V~~AkP   98 (99)
T 4fxv_A           71 AKDAERAINTLNGL--RLQSKTIKVSYARP   98 (99)
T ss_dssp             HHHHHHHHHHHTTC--EETTEECEEEECCB
T ss_pred             HHHHHHHHHHhCCC--EECCEEEEEEEeeC
Confidence            99999999999998  89999999999986

>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=99.90  E-value=6.7e-23  Score=141.09  Aligned_cols=111  Identities=24%  Similarity=0.411  Sum_probs=89.1

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe--------cCeEEEEECCHHHHHh----------------------
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYAFVHFEDRQEAIT----------------------   53 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~--------~~~~fv~~~~~~~a~~----------------------   53 (131)
                      .++|||+|||+++++++|+++|++||.|.++.++        +|||||+|.+.++|+.                      
T Consensus        13 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~g~~l~v~~~~~~   92 (196)
T 1l3k_A           13 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSR   92 (196)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECCC-
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhcCCCEECCEEeeeecccCc
Confidence            6799999999999999999999999999999987        5799999999999998                      


Q ss_pred             ----------------------------------hcC-CceeEEecCCCCCCCCcceEEEEeCCHHhHHHHHHHHhCCcc
Q psy1185          54 ----------------------------------VTG-LSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRL   98 (131)
Q Consensus        54 ----------------------------------~~g-~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~~   98 (131)
                                                        .+| +..+.+..+. .++.++|||||+|.+.++|.+|+.. ++.  
T Consensus        93 ~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~~g~~~g~afV~F~~~~~A~~A~~~-~~~--  168 (196)
T 1l3k_A           93 EDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR-GSGKKRGFAFVTFDDHDSVDKIVIQ-KYH--  168 (196)
T ss_dssp             ----------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECT-TTCCEEEEEEEEESSHHHHHHHHHC-SCC--
T ss_pred             ccccccccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecC-CCCCccceEEEEECCHHHHHHHHHh-CCc--
Confidence                                              223 2233333322 3678899999999999999999987 676  


Q ss_pred             eecCcEEEEEecCCCCCCCh
Q psy1185          99 KVWGCDIIVDWADPQEEPDT  118 (131)
Q Consensus        99 ~~~g~~l~v~~a~~~~~~~~  118 (131)
                      .++|+.|.|.||.++.+...
T Consensus       169 ~~~G~~i~v~~a~~k~~~~~  188 (196)
T 1l3k_A          169 TVNGHNCEVRKALSKQEMAS  188 (196)
T ss_dssp             EETTEECEEEECC-------
T ss_pred             EECCEEEEEEecCChhHhcc
Confidence            89999999999998877653

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

Probab=99.90  E-value=1.1e-22  Score=141.98  Aligned_cols=111  Identities=23%  Similarity=0.376  Sum_probs=94.7

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe--------cCeEEEEECCHHHHHh----------------------
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYAFVHFEDRQEAIT----------------------   53 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~--------~~~~fv~~~~~~~a~~----------------------   53 (131)
                      .++|||+|||.++++++|+++|++||.|.+++++        +|||||+|.+.++|..                      
T Consensus        28 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~  107 (216)
T 2qfj_A           28 MSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSN  107 (216)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCSC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCCC
Confidence            5799999999999999999999999999999985        7999999999999998                      


Q ss_pred             ----------------------------------------hcC-CceeEEecCCCCCCCCcceEEEEeCCHHhHHHHHHH
Q psy1185          54 ----------------------------------------VTG-LSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKR   92 (131)
Q Consensus        54 ----------------------------------------~~g-~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~   92 (131)
                                                              .+| +..+.+..+. .++.++|+|||+|.+.++|.+|+..
T Consensus       108 ~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~-~~g~~~g~afV~F~~~~~A~~A~~~  186 (216)
T 2qfj_A          108 IGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDP-TTGKHKGYGFIEYEKAQSSQDAVSS  186 (216)
T ss_dssp             CGGGHHHHHHHHHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECT-TTCCEEEEEEEEESSHHHHHHHHHH
T ss_pred             ccccchhhhhhhcccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecC-CCCCcCceEEEEecCHHHHHHHHHH
Confidence                                                    123 2223333322 3678899999999999999999999


Q ss_pred             HhCCcceecCcEEEEEecCCCCCCC
Q psy1185          93 LATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        93 l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      |++.  .++|+.|.|.||.++..+.
T Consensus       187 l~g~--~~~g~~i~V~~a~~~~~~~  209 (216)
T 2qfj_A          187 MNLF--DLGGQYLRVGKAVTPPMPL  209 (216)
T ss_dssp             HTTC--BCSSSBCEEEECSSCSSTT
T ss_pred             ccCC--EeCCcEEEEEEecCCCCCC
Confidence            9998  8999999999999876554

>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=99.90  E-value=1.2e-22  Score=137.24  Aligned_cols=106  Identities=26%  Similarity=0.472  Sum_probs=89.7

Q ss_pred             CCceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe----------cCeEEEEECCHHHHHh------------------
Q psy1185           2 SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI----------KDYAFVHFEDRQEAIT------------------   53 (131)
Q Consensus         2 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~----------~~~~fv~~~~~~~a~~------------------   53 (131)
                      |..++|||+|||+++++++|+++|++||+|.+++++          +|||||+|.+.++|+.                  
T Consensus         1 s~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~   80 (175)
T 3nmr_A            1 SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPI   80 (175)
T ss_dssp             CCCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCC
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccce
Confidence            567999999999999999999999999999999886          4799999999999988                  


Q ss_pred             -------------------------------------hcC-CceeEEecCCCCCCCCcceEEEEeCCHHhHHHHHHHHhC
Q psy1185          54 -------------------------------------VTG-LSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLAT   95 (131)
Q Consensus        54 -------------------------------------~~g-~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~   95 (131)
                                                           .+| +..+.+..+  ..|.++|+|||+|.+.++|.+|+..|+|
T Consensus        81 ~~~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~--~~g~~~g~afV~f~~~~~A~~A~~~l~g  158 (175)
T 3nmr_A           81 QMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRG--PDGLSRGCAFVTFTTRAMAQTAIKAMHQ  158 (175)
T ss_dssp             EEEECGGGCCSCGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEC--TTSCEEEEEEEEESSHHHHHHHHHHHTT
T ss_pred             EEccccccccccCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEEC--CCCCEEEEEEEEECCHHHHHHHHHHhcC
Confidence                                                 234 333334333  3578899999999999999999999999


Q ss_pred             Ccceec---CcEEEEEecC
Q psy1185          96 GRLKVW---GCDIIVDWAD  111 (131)
Q Consensus        96 ~~~~~~---g~~l~v~~a~  111 (131)
                      .  .+.   ++.|.|.||+
T Consensus       159 ~--~~~~g~~~~l~V~~ad  175 (175)
T 3nmr_A          159 A--QTMEGCSSPMVVKFAD  175 (175)
T ss_dssp             S--CCCTTCSSCCEEEECC
T ss_pred             C--cccCCCCCCeEEEecC
Confidence            7  344   4899999985

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.90  E-value=1.2e-23  Score=129.95  Aligned_cols=87  Identities=20%  Similarity=0.454  Sum_probs=77.1

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccC-CeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYG-RVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G-~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      +++|||+|||+++|+++|+++|++|| .|.++++++.                           ..+|.++|||||+|.+
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d---------------------------~~t~~~rg~aFV~F~~   53 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRN---------------------------KSSGQSRGFAFVEFSH   53 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSC---------------------------SSSCCCSSEEEEECSS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEec---------------------------CCCCCcCceEEEEecC
Confidence            47899999999999999999999999 7999988854                           3478899999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCCCCh
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPDT  118 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~~  118 (131)
                      .++|.+|++.+++. ..++|+.|.|+||.+++....
T Consensus        54 ~~~A~~Ai~~~~~~-~~~~gr~i~V~~a~~~~~~~~   88 (91)
T 2lxi_A           54 LQDATRWMEANQHS-LNILGQKVSMHYSDPKPKINE   88 (91)
T ss_dssp             HHHHHHHHHTTTTE-EEETTEEEEEECCCSCCCCSC
T ss_pred             HHHHHHHHHhcCCC-eEECCEEEEEEEcCCCCCCCC
Confidence            99999999988653 479999999999998877654

>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=99.89  E-value=1.5e-22  Score=136.12  Aligned_cols=105  Identities=25%  Similarity=0.313  Sum_probs=88.3

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe--------cCeEEEEECCHHHHHh---------------------
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYAFVHFEDRQEAIT---------------------   53 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~--------~~~~fv~~~~~~~a~~---------------------   53 (131)
                      ..++|||+|||.++++++|+++|++||+|.++.++        +|||||+|.+.++|+.                     
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            56899999999999999999999999999999887        4799999999999998                     


Q ss_pred             ------------------------------hcC-CceeEEecCCCCCCCCcceEEEEeCCHHhHHHHHHHHhCCcceecC
Q psy1185          54 ------------------------------VTG-LSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWG  102 (131)
Q Consensus        54 ------------------------------~~g-~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~~~~~g  102 (131)
                                                    .+| +..+.+..+ ..++.++|+|||+|.+.++|.+|++.|+|.  .++|
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 PGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRD-KLTGRPRGVAFVRYNKREEAQEAISALNNV--IPEG  158 (168)
T ss_dssp             CCSSTTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEEC-TTTCCEEEEEEEEESSHHHHHHHHHHHTTC--CCTT
T ss_pred             CCcccCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEc-CCCCCcceEEEEEECCHHHHHHHHHHhcCC--EecC
Confidence                                          123 222222222 236778999999999999999999999998  6766


Q ss_pred             --cEEEEEec
Q psy1185         103 --CDIIVDWA  110 (131)
Q Consensus       103 --~~l~v~~a  110 (131)
                        +.|+|+||
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

>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=99.89  E-value=3.3e-22  Score=134.04  Aligned_cols=104  Identities=29%  Similarity=0.388  Sum_probs=88.0

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe--------cCeEEEEECCHHHHHh----------------------
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYAFVHFEDRQEAIT----------------------   53 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~--------~~~~fv~~~~~~~a~~----------------------   53 (131)
                      .++|||+|||+++++++|+++|++||.|.++.++        +|||||+|.+.++|..                      
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            5899999999999999999999999999999987        3899999999999998                      


Q ss_pred             -----------------------------hcC-CceeEEecCCCCCCCCcceEEEEeCCHHhHHHHHHHHhCCcceecCc
Q psy1185          54 -----------------------------VTG-LSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGC  103 (131)
Q Consensus        54 -----------------------------~~g-~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~~~~~g~  103 (131)
                                                   .+| +..+.+..+. .+|.++|+|||+|.+.++|.+|++.|+|.  .++|+
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 SSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQ-VTGVSRGVGFIRFDKRIEAEEAIKGLNGQ--KPSGA  158 (167)
T ss_dssp             CCGGGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TTCCEEEEEEEEESSHHHHHHHHHHHTTC--CCTTC
T ss_pred             CcccCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecC-CCCCccceEEEEeCCHHHHHHHHHHhcCC--ccCCC
Confidence                                         233 2233333322 36778999999999999999999999998  78886


Q ss_pred             E--EEEEec
Q psy1185         104 D--IIVDWA  110 (131)
Q Consensus       104 ~--l~v~~a  110 (131)
                      .  |.|+||
T Consensus       159 ~~~i~v~~A  167 (167)
T 1fxl_A          159 TEPITVKFA  167 (167)
T ss_dssp             SSCCEEEEC
T ss_pred             ccceEEEeC
Confidence            4  899986

>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=99.89  E-value=1.1e-22  Score=130.46  Aligned_cols=85  Identities=16%  Similarity=0.384  Sum_probs=75.1

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .++|||+|||+++++++|+++|++||.|.++++++.                             .+.++|||||+|.+.
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d-----------------------------~~~~kg~afV~f~~~   55 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD-----------------------------ENGSKGYGFVHFETQ   55 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEE-----------------------------TTEEEEEEEEEESCH
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeec-----------------------------CCCCCceEEEEECCH
Confidence            578999999999999999999999999999998853                             355789999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCCCCCCChH
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADPQEEPDTE  119 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~~~  119 (131)
                      ++|.+|++.|++.  .++|+.|.|.|+.++.++...
T Consensus        56 ~~A~~Ai~~l~~~--~~~g~~i~V~~a~~~~~~~~~   89 (115)
T 4f25_A           56 EAAERAIEKMNGM--LLNDRKVFVGRFKSRKEREAE   89 (115)
T ss_dssp             HHHHHHHHHHTTC--EETTEECEEEESSCCCC----
T ss_pred             HHHHHHHHHcCCC--EECCEEEEEEECCCccccccc
Confidence            9999999999998  899999999999987765544

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

Probab=99.89  E-value=8.1e-23  Score=127.31  Aligned_cols=83  Identities=29%  Similarity=0.455  Sum_probs=74.2

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCC--eeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEe
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGR--VERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEY   80 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~--v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f   80 (131)
                      .+.||||+|||+++|+++|+++|++||.  +.+++++++                           ..+|.++|||||+|
T Consensus         8 ~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d---------------------------~~tg~srG~aFV~f   60 (95)
T 2lkz_A            8 HMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKD---------------------------KQTQQNRGFAFVQL   60 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCC---------------------------SSSSSCSSEEEEEC
T ss_pred             ccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEec---------------------------CCCCCCceEeEEEE
Confidence            4779999999999999999999999995  678888764                           44789999999999


Q ss_pred             CCHHhHHHHHHHHhCCc--ceecCcEEEEEecCC
Q psy1185          81 DSHKSASLAKKRLATGR--LKVWGCDIIVDWADP  112 (131)
Q Consensus        81 ~~~~~a~~a~~~l~~~~--~~~~g~~l~v~~a~~  112 (131)
                      .+.++|.+|++.|++.+  +.++|+.|.|+||++
T Consensus        61 ~~~~~A~~Ai~~lng~~~~~~i~Gr~i~V~~Aks   94 (95)
T 2lkz_A           61 SSAMDASQLLQILQSLHPPLKIDGKTIGVDFAKS   94 (95)
T ss_dssp             SSSHHHHHHHHHHHSSSSCEEETTEEEEEEECCC
T ss_pred             CCHHHHHHHHHHhcCCCCCceECCEEEEEEEccC
Confidence            99999999999999963  468999999999985

>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=99.88  E-value=2.3e-22  Score=136.37  Aligned_cols=108  Identities=17%  Similarity=0.250  Sum_probs=88.6

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeE-----EEEe--cCeEEEEECCHHHHHh----------------------
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVER-----VKRI--KDYAFVHFEDRQEAIT----------------------   53 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~-----~~i~--~~~~fv~~~~~~~a~~----------------------   53 (131)
                      ..++|||+|||.++++++|+++|++||.+..     ...-  +|||||+|.+.++|..                      
T Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~v~~~~~~   91 (175)
T 1fje_B           12 TPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPKGR   91 (175)
T ss_dssp             SSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHHGGGEEETTEEEEEECCCCS
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEECCCCccccEEEEEECCHHHHHHHHhcCCCEeCCeEEEEecCCCc
Confidence            4789999999999999999999999986544     2211  7999999999999998                      


Q ss_pred             ---------------------------hcCCceeEEecCCCCCCCCcceEEEEeCCHHhHHHHHHHHhCCcceecCcEEE
Q psy1185          54 ---------------------------VTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDII  106 (131)
Q Consensus        54 ---------------------------~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~~~~~g~~l~  106 (131)
                                                 .+.-.+.+...  ..++.++|+|||+|.+.++|.+|+..|+|.  .++|+.|.
T Consensus        92 ~~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~--~~~~~~~g~afV~f~~~~~A~~A~~~l~g~--~~~g~~i~  167 (175)
T 1fje_B           92 DSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV--SQDGKSKGIAYIEFKSEADAEKNLEEKQGA--EIDGRSVS  167 (175)
T ss_dssp             SCSTTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE--CSSSSCCSEEEEECSSHHHHHHHHHHHTEE--EETTEEEE
T ss_pred             cccccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe--cCCCCCceEEEEEECCHHHHHHHHHHhCCC--EECCeEEE
Confidence                                       12222222222  456788999999999999999999999998  89999999


Q ss_pred             EEecCCCC
Q psy1185         107 VDWADPQE  114 (131)
Q Consensus       107 v~~a~~~~  114 (131)
                      |+||.+++
T Consensus       168 v~~a~~k~  175 (175)
T 1fje_B          168 LYYTGEKG  175 (175)
T ss_dssp             EEECSSCC
T ss_pred             EEecCCCC
Confidence            99998764

>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=99.88  E-value=8.3e-22  Score=119.98  Aligned_cols=84  Identities=21%  Similarity=0.382  Sum_probs=73.9

Q ss_pred             CCceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeC
Q psy1185           2 SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYD   81 (131)
Q Consensus         2 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~   81 (131)
                      +..++|||+|||.++++++|+++|++||.|.++.++++                           ..++.++|||||+|.
T Consensus         4 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~---------------------------~~~~~~~g~afV~f~   56 (87)
T 3bs9_A            4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKD---------------------------MATGKSKGYGFVSFF   56 (87)
T ss_dssp             --CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEC---------------------------TTTCCEEEEEEEEES
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEec---------------------------CCCCccceEEEEEEC
Confidence            35689999999999999999999999999999998854                           346788999999999


Q ss_pred             CHHhHHHHHHHHhCCcceecCcEEEEEecCCCC
Q psy1185          82 SHKSASLAKKRLATGRLKVWGCDIIVDWADPQE  114 (131)
Q Consensus        82 ~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~  114 (131)
                      +.++|.+|++.|++.  .++|+.|.|+||++++
T Consensus        57 ~~~~A~~A~~~l~g~--~~~g~~l~v~~a~~kp   87 (87)
T 3bs9_A           57 NKWDAENAIQQMGGQ--WLGGRQIRTNWATRKP   87 (87)
T ss_dssp             SHHHHHHHHHHHTTC--EETTEECEEEEEC---
T ss_pred             CHHHHHHHHHHcCCC--EECCeEEEEEecCCCC
Confidence            999999999999998  8999999999998753

>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=99.88  E-value=1.2e-21  Score=118.27  Aligned_cols=82  Identities=22%  Similarity=0.375  Sum_probs=75.4

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      ..+|||+|||.++++++|+++|++||.|.++.+++.                           ..++.++|||||+|.+.
T Consensus         1 t~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~---------------------------~~~~~~~g~afV~f~~~   53 (83)
T 3md1_A            1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWD---------------------------MQTGSSRGYGFVSFTSQ   53 (83)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEEC---------------------------TTTCCEEEEEEEEESCH
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEc---------------------------CCCCCccceEEEEECCH
Confidence            368999999999999999999999999999998854                           34688899999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCCCC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADPQE  114 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~  114 (131)
                      ++|.+|+..|+|.  .++|+.|.|+||.+++
T Consensus        54 ~~a~~a~~~l~g~--~~~g~~l~v~~a~~~~   82 (83)
T 3md1_A           54 DDAQNAMDSMQGQ--DLNGRPLRINWAAKLE   82 (83)
T ss_dssp             HHHHHHHHHHTTC--EETTEECEEEECCCCC
T ss_pred             HHHHHHHHHhcCC--eeCCcEEEEEecCcCC
Confidence            9999999999998  8999999999999865

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.88  E-value=9.8e-22  Score=123.25  Aligned_cols=79  Identities=20%  Similarity=0.322  Sum_probs=73.0

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      .+++|||+|||+++|+++|+++|++||.|.++.+++                                 .+|+|||+|.+
T Consensus        20 ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~---------------------------------~kg~AFVef~~   66 (100)
T 3r27_A           20 ASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP---------------------------------KKRQALVEFED   66 (100)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEET---------------------------------TTTEEEEEESS
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEc---------------------------------CCCEEEEEECC
Confidence            367999999999999999999999999999998874                                 37999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQE  114 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~  114 (131)
                      .++|.+|++.+++.++.+.|+.|.|+||+++.
T Consensus        67 ~~~A~~Av~~ln~~~~~i~Gr~i~V~~S~~k~   98 (100)
T 3r27_A           67 VLGACNAVNYAADNQIYIAGHPAFVNYSTSQK   98 (100)
T ss_dssp             HHHHHHHHHHHHHSCEEETTEEEEEEECSCSC
T ss_pred             HHHHHHHHHHhcCCCceeCCcEEEEEeccccc
Confidence            99999999999998777999999999998764

>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=99.88  E-value=1.8e-21  Score=131.40  Aligned_cols=107  Identities=24%  Similarity=0.336  Sum_probs=90.4

Q ss_pred             CCceEEEEeCCCCCCCHHHHHHHhhcc----C-------CeeEEEEe--cCeEEEEECCHHHHHh---------------
Q psy1185           2 SKVKVLYVRNLTQYCTEEKLKEAFEQY----G-------RVERVKRI--KDYAFVHFEDRQEAIT---------------   53 (131)
Q Consensus         2 ~~~~~l~v~nLp~~~t~~~l~~~F~~~----G-------~v~~~~i~--~~~~fv~~~~~~~a~~---------------   53 (131)
                      ...++|||+|||.++++++|+++|++|    |       .|.++.+.  +|||||+|.+.++|+.               
T Consensus         2 r~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~~~g~afV~f~~~~~A~~A~~~~~~~~~g~~i~   81 (172)
T 2g4b_A            2 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLK   81 (172)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEETTTTEEEEEESSHHHHHHHGGGTTCEETTEECE
T ss_pred             CcccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecCCCCEEEEEeCCHHHHHHHHHhCCcEecCceee
Confidence            357899999999999999999999999    7       78888776  8999999999999998               


Q ss_pred             -----------------------------------hcC-CceeEEecCCCCCCCCcceEEEEeCCHHhHHHHHHHHhCCc
Q psy1185          54 -----------------------------------VTG-LSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGR   97 (131)
Q Consensus        54 -----------------------------------~~g-~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~   97 (131)
                                                         .+| +..+.+..++ .+|.++|+|||+|.+.++|.+|+..|+|. 
T Consensus        82 v~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~-  159 (172)
T 2g4b_A           82 IRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDS-ATGLSKGYAFCEYVDINVTDQAIAGLNGM-  159 (172)
T ss_dssp             EECCSSCCCCTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TTCSEEEEEEEEESSTTHHHHHHHHHTTC-
T ss_pred             ecCCcccCCCCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecC-CCCCcceEEEEEeCCHHHHHHHHHHcCCC-
Confidence                                               223 2223332322 36788999999999999999999999998 


Q ss_pred             ceecCcEEEEEecC
Q psy1185          98 LKVWGCDIIVDWAD  111 (131)
Q Consensus        98 ~~~~g~~l~v~~a~  111 (131)
                       .++|+.|.|+||.
T Consensus       160 -~~~g~~l~V~~As  172 (172)
T 2g4b_A          160 -QLGDKKLLVQRAS  172 (172)
T ss_dssp             -EETTEECEEEECC
T ss_pred             -EECCeEEEEEeCC
Confidence             8999999999983

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.87  E-value=4.3e-22  Score=125.97  Aligned_cols=83  Identities=17%  Similarity=0.261  Sum_probs=74.4

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||+++++++|+++|++||.|.+++++++                                 +|||||+|.+
T Consensus        15 ~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~---------------------------------kGfaFVeF~~   61 (105)
T 1sjq_A           15 PSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG---------------------------------KNQAFIEMNT   61 (105)
T ss_dssp             CCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT---------------------------------TTEEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC---------------------------------CCEEEEEECC
Confidence            4689999999999999999999999999999998842                                 7999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCCCCh
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPDT  118 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~~  118 (131)
                      .++|.+|++.+++.+..++|+.|.|.||+++.....
T Consensus        62 ~~~A~~Ai~~l~~~~~~l~Gr~l~V~~A~~~~~~~~   97 (105)
T 1sjq_A           62 EEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKTD   97 (105)
T ss_dssp             HHHHHHHHHHHTTSCCEETTEECCBCCCSSSSCCCT
T ss_pred             HHHHHHHHHHhccCCceECCEEEEEEEcCCCCCCcc
Confidence            999999999998644489999999999998776553

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

Probab=99.87  E-value=2.5e-21  Score=133.38  Aligned_cols=113  Identities=23%  Similarity=0.307  Sum_probs=90.9

Q ss_pred             CCCceEEEEeCCCCCCCHHHHHHHhhcc----C-------CeeEEEEe--cCeEEEEECCHHHHHhhc------------
Q psy1185           1 MSKVKVLYVRNLTQYCTEEKLKEAFEQY----G-------RVERVKRI--KDYAFVHFEDRQEAITVT------------   55 (131)
Q Consensus         1 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~----G-------~v~~~~i~--~~~~fv~~~~~~~a~~~~------------   55 (131)
                      |...++|||+|||.++++++|+++|++|    |       .|.++.+.  +|||||+|.+.++|+.+.            
T Consensus         1 ~~~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~~~~~g~afV~F~~~~~A~~Al~l~g~~~~g~~i   80 (198)
T 2yh0_A            1 GAMARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSL   80 (198)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEEETTTTEEEEEESCSHHHHHHGGGTTEEETTEEE
T ss_pred             CCceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEecCCCCEEEEEeCCHHHHHHHHHhcCCEEcCceE
Confidence            3467899999999999999999999999    6       67777766  899999999999999821            


Q ss_pred             ----------------------------------------------------------C-CceeEEecCCCCCCCCcceE
Q psy1185          56 ----------------------------------------------------------G-LSQVIIYSSPDDNKKNRGFC   76 (131)
Q Consensus        56 ----------------------------------------------------------g-~~~~~~~~~~~~~~~~~~~~   76 (131)
                                                                                | +..+.+..+ ..++.++|||
T Consensus        81 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~-~~~~~~~g~a  159 (198)
T 2yh0_A           81 KIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKD-SATGLSKGYA  159 (198)
T ss_dssp             EEECCCCCCCCCCSSSCSSCCCTTSSCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEEC-TTTCSEEEEE
T ss_pred             EEeCCCCCCCCCCCcCCCcCCCCCCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeec-CCCCCcceEE
Confidence                                                                      1 111111111 1367779999


Q ss_pred             EEEeCCHHhHHHHHHHHhCCcceecCcEEEEEecCCCCCC
Q psy1185          77 FLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEP  116 (131)
Q Consensus        77 fv~f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~  116 (131)
                      ||+|.+.++|.+|+..|+|.  .++|+.|.|.||.++...
T Consensus       160 fV~f~~~~~a~~A~~~l~g~--~~~g~~l~v~~a~~~~~~  197 (198)
T 2yh0_A          160 FCEYVDINVTDQAIAGLNGM--QLGDKKLLVQRASVGAKN  197 (198)
T ss_dssp             EEEESSSSHHHHHHHHHTTC--EETTEECEEEESCCCCCC
T ss_pred             EEEECCHHHHHHHHHHcCCC--EECCEEEEEEECCCCCCC
Confidence            99999999999999999998  899999999999987653

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

Probab=99.87  E-value=2.7e-21  Score=119.55  Aligned_cols=87  Identities=24%  Similarity=0.411  Sum_probs=79.1

Q ss_pred             CCceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeC
Q psy1185           2 SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYD   81 (131)
Q Consensus         2 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~   81 (131)
                      +..++|||+|||.++++++|+++|++||.|.++.+++.                           ..++.+++||||+|.
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~---------------------------~~~~~~~g~afV~f~   55 (95)
T 2dnz_A            3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKD---------------------------SDTGRSKGYGFITFS   55 (95)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECC---------------------------SSSCCCCSEEEEEES
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeec---------------------------CCCCceeeEEEEEEC
Confidence            35789999999999999999999999999999998854                           346788999999999


Q ss_pred             CHHhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          82 SHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        82 ~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      +.++|.+|+..|++.  .++|+.|+|+|+.++..+.
T Consensus        56 ~~~~a~~A~~~l~g~--~~~g~~l~V~~a~~~~~~~   89 (95)
T 2dnz_A           56 DSECARRALEQLNGF--ELAGRPMRVGHVTERLDGG   89 (95)
T ss_dssp             CHHHHHHHHHHHTTC--CSSSSCCEEEESSCCCCCC
T ss_pred             CHHHHHHHHHHhCCC--eeCCcEEEEEEcccccCCC
Confidence            999999999999998  8899999999999887654

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

Probab=99.87  E-value=3.1e-21  Score=120.25  Aligned_cols=86  Identities=26%  Similarity=0.310  Sum_probs=78.1

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||.|.++.+++.                           ..++.+++||||+|.+
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~---------------------------~~~~~~~g~afV~f~~   59 (99)
T 1whw_A            7 GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPID---------------------------SLTKKPKGFAFVTFMF   59 (99)
T ss_dssp             SCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCC---------------------------TTTCCCCSEEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEec---------------------------CCCCCcCeEEEEEECC
Confidence            4689999999999999999999999999999988753                           3368889999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      .++|.+|+..|++.  .++|+.|.|.|+.++.+..
T Consensus        60 ~~~a~~A~~~l~g~--~~~g~~l~V~~a~~~~~~~   92 (99)
T 1whw_A           60 PEHAVKAYAEVDGQ--VFQGRMLHVLPSTIKKEAS   92 (99)
T ss_dssp             HHHHHHHHHHTTTE--ESSSCEEEEEECCCCSTTC
T ss_pred             HHHHHHHHHHhCCC--EECCcEEEEEEcCCCcccc
Confidence            99999999999997  8899999999999887653

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

Probab=99.87  E-value=2.1e-21  Score=123.79  Aligned_cols=83  Identities=23%  Similarity=0.266  Sum_probs=76.1

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||+++++++|+++|++||.|.++++++.                           ..++.++|||||+|.+
T Consensus         5 p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d---------------------------~~tg~~rG~aFV~f~~   57 (110)
T 3s8s_A            5 PLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLH---------------------------PRTRKHLGLARVLFTS   57 (110)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEEC---------------------------TTTCCEEEEEEEEESS
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEC---------------------------CCCCceeeEEEEEECC
Confidence            3579999999999999999999999999999998854                           3468899999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQE  114 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~  114 (131)
                      .++|.+|++.|||.  .++|+.|.|.+|....
T Consensus        58 ~~~A~~Ai~~lng~--~~~gr~i~V~~a~~~~   87 (110)
T 3s8s_A           58 TRGAKETVKNLHLT--SVMGNIIHAQLDIKGQ   87 (110)
T ss_dssp             HHHHHHHHHHHTTC--EETTEECEEEECSTTH
T ss_pred             HHHHHHHHHHhCCC--EECCeEEEEEECCCCc
Confidence            99999999999998  8999999999997543

>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=99.87  E-value=5.4e-22  Score=125.72  Aligned_cols=96  Identities=33%  Similarity=0.652  Sum_probs=82.6

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCC-eeEEEEe-cCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEe
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGR-VERVKRI-KDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEY   80 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~-v~~~~i~-~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f   80 (131)
                      ..++|||+|||.++++++|+++|++||. |.++.++ +.                           ..++.++|||||+|
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~---------------------------~~~g~~~g~afV~f   59 (109)
T 2dis_A            7 GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASA---------------------------ADKMKNRGFAFVEY   59 (109)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSS---------------------------CTTTTTCCEEEEEE
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccC---------------------------CCCCCcCcEEEEEe
Confidence            3679999999999999999999999998 9999877 32                           34678899999999


Q ss_pred             CCHHhHHHHHHHHhCCcceecCcEEEEEecCCCCCCChHHHHhHh
Q psy1185          81 DSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPDTETMSKVL  125 (131)
Q Consensus        81 ~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~  125 (131)
                      .+.++|.+|+..|++....++|+.|.|.||.++.+++.+.+++++
T Consensus        60 ~~~~~A~~A~~~l~~g~~~~~g~~l~V~~a~~~~~~~~~~~~~~k  104 (109)
T 2dis_A           60 ESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMETVS  104 (109)
T ss_dssp             SSHHHHHHHHTTTTTCCSCBTTBCCEEEESCSSCSTTTCCSSCCS
T ss_pred             cCHHHHHHHHHHhhCCCceecCCeEEEEEcCCCCCcCHHHHHhcc
Confidence            999999999999962113899999999999999988877776654

>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=99.86  E-value=3.6e-21  Score=119.47  Aligned_cols=86  Identities=17%  Similarity=0.307  Sum_probs=78.2

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .++|||+|||.++++++|+++|++||.|.+++++++                           ..+|.++|||||+|.+.
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~---------------------------~~~g~~~g~afV~f~~~   54 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFD---------------------------PQTGRSKGYAFIEFRDL   54 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBC---------------------------TTTCCBCSEEEEEESSH
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeC---------------------------CCCCccceEEEEEECCH
Confidence            579999999999999999999999999999998854                           34678899999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCCCCCCCh
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADPQEEPDT  118 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~~  118 (131)
                      ++|.+|+..|+|.  .++|+.|.|.||.++.....
T Consensus        55 ~~A~~Ai~~l~g~--~~~g~~l~V~~a~~~~~~~~   87 (96)
T 2x1f_A           55 ESSASAVRNLNGY--QLGSRFLKCGYSSNSDISGV   87 (96)
T ss_dssp             HHHHHHHHHHTTC--EETTEECEEEECSCSSGGGH
T ss_pred             HHHHHHHHHhCCC--eECCeEEEEEEcCCCCCCCc
Confidence            9999999999998  89999999999998776543

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.86  E-value=1.8e-21  Score=120.61  Aligned_cols=87  Identities=20%  Similarity=0.375  Sum_probs=78.7

Q ss_pred             CCceEEEEeCCCCCCCHHHHHHHhhccCCeeEE-EEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEe
Q psy1185           2 SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERV-KRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEY   80 (131)
Q Consensus         2 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~-~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f   80 (131)
                      +..++|||+|||.++++++|+++|++||.|.++ ++++.                           ..++.+++||||+|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~---------------------------~~~g~~~g~afV~f   55 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRD---------------------------PDTGNSKGYAFINF   55 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCC---------------------------TTTCSCCSEEEEEB
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEc---------------------------CCCCCcCeEEEEEE
Confidence            457899999999999999999999999999998 88753                           34788899999999


Q ss_pred             CCHHhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          81 DSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        81 ~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      .+.++|.+|+..|++.  .++|+.|.|.|+.++..+.
T Consensus        56 ~~~~~A~~A~~~l~g~--~~~g~~l~v~~a~~~~~~~   90 (96)
T 1x5t_A           56 ASFDASDAAIEAMNGQ--YLCNRPITVSYAFKKDSKG   90 (96)
T ss_dssp             SSHHHHHHHHHTTTTC--EETTEECEEEESCCCCCCC
T ss_pred             CCHHHHHHHHHHcCCC--EECCEEEEEEEecccCCCC
Confidence            9999999999999998  8999999999999877654

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

Probab=99.86  E-value=2.1e-21  Score=122.38  Aligned_cols=85  Identities=26%  Similarity=0.472  Sum_probs=77.1

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||.|.++.++++                           ..++.++|||||+|.+
T Consensus        22 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~---------------------------~~~~~~~g~afV~f~~   74 (106)
T 1p27_B           22 EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLD---------------------------RRTGYLKGYTLVEYET   74 (106)
T ss_dssp             TBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEEC---------------------------TTTSSEEEEEEEEESC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEec---------------------------CCCCceeeEEEEEECC
Confidence            3578999999999999999999999999999998854                           3467889999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEEP  116 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~  116 (131)
                      .++|.+|+..|+|.  .++|+.|.|+||.++.++
T Consensus        75 ~~~a~~A~~~l~g~--~~~g~~l~V~~a~~~~~~  106 (106)
T 1p27_B           75 YKEAQAAMEGLNGQ--DLMGQPISVDWCFVRGPP  106 (106)
T ss_dssp             HHHHHHHHHHHTTC--BSSSSBCEEEESEESSCC
T ss_pred             HHHHHHHHHHhcCC--EECCcEEEEEeecCCCCC
Confidence            99999999999998  889999999999887653

>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=99.86  E-value=2.8e-21  Score=117.17  Aligned_cols=80  Identities=28%  Similarity=0.512  Sum_probs=73.5

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||.|.++.+++.                           ..++.++|||||+|.+
T Consensus         6 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~---------------------------~~~~~~~g~afV~f~~   58 (85)
T 3mdf_A            6 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLD---------------------------YETEKHRGFAFVEFEL   58 (85)
T ss_dssp             CSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEE---------------------------TTTTEECSEEEEEESS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEEC---------------------------CCCCccccEEEEEECC
Confidence            5689999999999999999999999999999988743                           3467889999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWAD  111 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~  111 (131)
                      .++|.+|++.|+|.  .++|+.|+|+||+
T Consensus        59 ~~~a~~A~~~l~g~--~~~g~~l~v~~ak   85 (85)
T 3mdf_A           59 AEDAAAAIDNMNES--ELFGRTIRVNLAK   85 (85)
T ss_dssp             HHHHHHHHHHHTTC--EETTEECEEEECC
T ss_pred             HHHHHHHHHHhCCC--EECCcEEEEEEcC
Confidence            99999999999998  8999999999985

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

Probab=99.86  E-value=2.6e-21  Score=121.48  Aligned_cols=86  Identities=23%  Similarity=0.411  Sum_probs=78.5

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||.|..+.+++.                           ..++.++|||||+|.+
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~---------------------------~~~~~~~g~afV~f~~   66 (103)
T 2cq0_A           14 DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKD---------------------------KTTGQSKGFAFISFHR   66 (103)
T ss_dssp             SSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEEC---------------------------SSSCSEEEEEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeec---------------------------CCCCceeeEEEEEECC
Confidence            4689999999999999999999999999999998854                           3467889999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      .++|.+|+..|++.  .++|+.|.|.|+.++....
T Consensus        67 ~~~A~~A~~~l~g~--~~~g~~l~v~~a~~~~~~~   99 (103)
T 2cq0_A           67 REDAARAIAGVSGF--GYDHLILNVEWAKPSTNSG   99 (103)
T ss_dssp             HHHHHHHHHHTTTC--EETTEECEEEESSCCCCSC
T ss_pred             HHHHHHHHHHcCCC--eeCCcEEEEEECCCCCCCC
Confidence            99999999999998  8999999999999887654

>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=99.86  E-value=4.1e-22  Score=122.52  Aligned_cols=84  Identities=25%  Similarity=0.380  Sum_probs=69.7

Q ss_pred             eEEEEeCCCCCCCHHHHHHHhhccC--CeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           5 KVLYVRNLTQYCTEEKLKEAFEQYG--RVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         5 ~~l~v~nLp~~~t~~~l~~~F~~~G--~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      .+|||+|||.++++++|+++|++||  .|.++++++.                           ..+|.++|||||+|.+
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~---------------------------~~~g~~kG~afV~f~~   54 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFEN---------------------------RANGQSKGFALVGVGS   54 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEEC---------------------------TTTCCEEEEEEECC-C
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEec---------------------------CCCCccCcEEEEEECC
Confidence            5899999999999999999999999  9999998854                           3478899999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      .++|.+|++.|+|.  .++|+.|+|.++.++.++.
T Consensus        55 ~~~a~~Ai~~l~g~--~~~gr~i~V~~~~~~~~~~   87 (90)
T 3p5t_L           55 EASSKKLMDLLPKR--ELHGQNPVVTPSNKLEHHH   87 (90)
T ss_dssp             HHHHHHHHHHGGGS--CSSSCCCEECCC-------
T ss_pred             HHHHHHHHHHcCCC--eeCCEEEEEEECCCCcccc
Confidence            99999999999998  8999999999999876654

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.86  E-value=4.7e-21  Score=119.46  Aligned_cols=85  Identities=26%  Similarity=0.542  Sum_probs=77.1

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||.|.++.+++.                           ..++.++|||||+|.+
T Consensus         9 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~---------------------------~~~~~~~g~afV~f~~   61 (99)
T 2dgs_A            9 KSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYD---------------------------AEKQRPRGFGFITFED   61 (99)
T ss_dssp             SCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCC---------------------------TTTCSCCSEEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeC---------------------------CCCCCCCceEEEEECC
Confidence            4689999999999999999999999999999998853                           3467889999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      .++|.+|++ +++.  .++|+.|.|.|+.++....
T Consensus        62 ~~~a~~A~~-~~~~--~~~g~~l~V~~a~~~~~~~   93 (99)
T 2dgs_A           62 EQSVDQAVN-MHFH--DIMGKKVEVKRAEPRDSKS   93 (99)
T ss_dssp             HHHHHHHHH-HCCC--BSSSCBCEEEECCCCCCCC
T ss_pred             HHHHHHHHH-hCCC--EECCeEEEEEECCCCcccC
Confidence            999999998 9998  8899999999999877654

>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=99.86  E-value=8.9e-21  Score=137.69  Aligned_cols=111  Identities=21%  Similarity=0.348  Sum_probs=95.3

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe--------cCeEEEEECCHHHHHh---------------------
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYAFVHFEDRQEAIT---------------------   53 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~--------~~~~fv~~~~~~~a~~---------------------   53 (131)
                      ..++|||+|||.++++++|+++|++||.|.++.++        +|||||+|.+.++|..                     
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            35789999999999999999999999999999887        5799999999999988                     


Q ss_pred             ----------------------------------hcC-CceeEEecCCCCCCCCcceEEEEeCCHHhHHHHHHHHhCCcc
Q psy1185          54 ----------------------------------VTG-LSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRL   98 (131)
Q Consensus        54 ----------------------------------~~g-~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~~   98 (131)
                                                        .+| +..+.+..++  +|.++|+|||+|.+.++|.+|+..|+|.  
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--DGQLKGFAVLEYETAEMAEEAQQQADGL--  249 (284)
T ss_dssp             GGGCCTTTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECS--SCCEEEEEEEECSSHHHHHHHHHHHTTC--
T ss_pred             CCCCCcccCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECC--CCCcccEEEEEeCCHHHHHHHHHHhCCC--
Confidence                                              123 3334433333  5778999999999999999999999998  


Q ss_pred             eecCcEEEEEecCCCCCCC
Q psy1185          99 KVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        99 ~~~g~~l~v~~a~~~~~~~  117 (131)
                      .++|+.|.|.|+.++.++.
T Consensus       250 ~~~g~~l~v~~a~~~~~~~  268 (284)
T 3smz_A          250 SLGGSHLRVSFCAPGPPGR  268 (284)
T ss_dssp             EETTEECEEEECCSSSCHH
T ss_pred             ccCCeEEEEEEecCCCccc
Confidence            8899999999999887654

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

Probab=99.86  E-value=5.6e-21  Score=119.93  Aligned_cols=85  Identities=28%  Similarity=0.532  Sum_probs=76.5

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||.|.++++++.                             .+.+++||||+|.+
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~-----------------------------~~~~~g~afV~f~~   64 (103)
T 2cqi_A           14 QPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITE-----------------------------HTSNDPYCFVEFYE   64 (103)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECC-----------------------------CCSSCCEEEEEESS
T ss_pred             CCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEec-----------------------------CCCCCCEEEEEECC
Confidence            3689999999999999999999999999999998853                             34468999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCCCCh
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPDT  118 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~~  118 (131)
                      .++|.+|+..|++.  .++|+.|.|.|+.++.....
T Consensus        65 ~~~a~~A~~~l~g~--~~~g~~l~V~~a~~~~~~~~   98 (103)
T 2cqi_A           65 HRDAAAALAAMNGR--KILGKEVKVNWATTPSSQKS   98 (103)
T ss_dssp             HHHHHHHHHHHTTE--EETTEEEEEEECCCTTCCCC
T ss_pred             HHHHHHHHHHhCCC--CcCCCeEEEEECCCCccccc
Confidence            99999999999998  89999999999998776543

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.86  E-value=7.4e-21  Score=121.58  Aligned_cols=86  Identities=23%  Similarity=0.402  Sum_probs=78.2

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||.|..+++++.                           ..++.++|||||+|.+
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~---------------------------~~~~~~~g~afV~f~~   66 (115)
T 2dgo_A           14 NHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKD---------------------------MATGKSKGYGFVSFFN   66 (115)
T ss_dssp             TCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEC---------------------------TTTCCEEEEEEEEESS
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEc---------------------------CCCCCcceEEEEEECC
Confidence            4689999999999999999999999999999998854                           2367889999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      .++|.+|++.|++.  .++|+.|.|.|+.++....
T Consensus        67 ~~~a~~A~~~l~g~--~~~g~~l~V~~a~~~~~~~   99 (115)
T 2dgo_A           67 KWDAENAIQQMGGQ--WLGGRQIRTNWATRKPPAP   99 (115)
T ss_dssp             HHHHHHHHHHTTTC--EETTEECEEEESSCCCCCS
T ss_pred             HHHHHHHHHHhCCC--EECCEEEEEEEccCCCCCC
Confidence            99999999999998  8999999999999877654

>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=99.86  E-value=3.6e-21  Score=117.25  Aligned_cols=84  Identities=19%  Similarity=0.357  Sum_probs=74.6

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCC-CcceEEEEeC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKK-NRGFCFLEYD   81 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~-~~~~~fv~f~   81 (131)
                      +.++|||+|||.++++++|+++|++||.|.++.++..                           ..++. ++|+|||+|.
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~---------------------------~~~~~~~~g~afV~f~   55 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVE---------------------------RMHPHLSKGYAYVEFE   55 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEE---------------------------TTEEEEECSEEEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeC---------------------------CCCCCCCCcEEEEEEe
Confidence            4689999999999999999999999999999988743                           11223 7899999999


Q ss_pred             CHHhHHHHHHHHhCCcceecCcEEEEEecCCCCC
Q psy1185          82 SHKSASLAKKRLATGRLKVWGCDIIVDWADPQEE  115 (131)
Q Consensus        82 ~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~  115 (131)
                      +.++|.+|+..|+|.  .++|+.|.|+++.++.+
T Consensus        56 ~~~~a~~A~~~l~g~--~~~g~~l~v~~a~~~~~   87 (88)
T 4a8x_A           56 NPDEAEKALKHMDGG--QIDGQEITATAVLAPWP   87 (88)
T ss_dssp             SHHHHHHHHHHHTTC--EETTEECEEEEECCCCC
T ss_pred             cHHHHHHHHHHcCCC--eECCeEEEEEECCCCCC
Confidence            999999999999998  89999999999988765

>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=99.86  E-value=5.6e-21  Score=121.24  Aligned_cols=85  Identities=26%  Similarity=0.501  Sum_probs=77.2

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||.|.++.+++.                           ..+|.++|||||+|.+
T Consensus        25 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~---------------------------~~~~~~~g~afV~f~~   77 (110)
T 1oo0_B           25 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLD---------------------------RRTGFSKGYALVEYET   77 (110)
T ss_dssp             TBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBC---------------------------TTTSSBCSEEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEec---------------------------CCCCCcceEEEEEECC
Confidence            3678999999999999999999999999999988753                           3468889999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEEP  116 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~  116 (131)
                      .++|.+|+..|+|.  .++|+.|.|.|+.++.++
T Consensus        78 ~~~A~~Ai~~l~g~--~~~g~~l~V~~a~~~~~~  109 (110)
T 1oo0_B           78 HKQALAAKEALNGA--EIMGQTIQVDWCFVKGPK  109 (110)
T ss_dssp             HHHHHHHHHHHTTC--EETTEECEEEESEESSCC
T ss_pred             HHHHHHHHHHcCCC--EECCcEEEEEEcccCCCC
Confidence            99999999999998  899999999999887654

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.86  E-value=7.4e-21  Score=118.20  Aligned_cols=84  Identities=20%  Similarity=0.204  Sum_probs=75.4

Q ss_pred             CCceEEEEeCCCCCCCHHHHH----HHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEE
Q psy1185           2 SKVKVLYVRNLTQYCTEEKLK----EAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCF   77 (131)
Q Consensus         2 ~~~~~l~v~nLp~~~t~~~l~----~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~f   77 (131)
                      +..++|||+|||+++++++|+    ++|++||.|.++++++.                             ... ++|||
T Consensus         7 ~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~-----------------------------~~~-rg~af   56 (96)
T 2dgx_A            7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPH-----------------------------TDY-QLKAV   56 (96)
T ss_dssp             SSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSC-----------------------------CST-TCCEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeC-----------------------------CCC-CeEEE
Confidence            457899999999999999999    99999999999998853                             122 89999


Q ss_pred             EEeCCHHhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          78 LEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        78 v~f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      |+|.+.++|.+|++.|+|.  .++|+.|+|+||+++..+.
T Consensus        57 V~f~~~~~A~~Ai~~l~g~--~~~gr~l~V~~a~~~~~~~   94 (96)
T 2dgx_A           57 VQMENLQDAIGAVNSLHRY--KIGSKKILVSLATGASGPS   94 (96)
T ss_dssp             EEESSHHHHHHHHHHHTTE--EETTEEEEEEECCCSSCCC
T ss_pred             EEECCHHHHHHHHHHhCCC--EECCeEEEEEEcCCCCCCC
Confidence            9999999999999999998  8999999999999877654

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

Probab=99.86  E-value=3.5e-21  Score=120.89  Aligned_cols=86  Identities=27%  Similarity=0.389  Sum_probs=77.9

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||.|..+.+++.                           ..++.+++||||+|.+
T Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~---------------------------~~~~~~~g~afV~f~~   64 (103)
T 2dnm_A           12 GMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPRE---------------------------PHTKAPRGFAFVRFHD   64 (103)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBC---------------------------SSSCSBCSCEEEEESS
T ss_pred             CCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeC---------------------------CCCCCCCeEEEEEECC
Confidence            4689999999999999999999999999999988754                           3467889999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      .++|.+|+..|++.  .++|+.|.|.||++.....
T Consensus        65 ~~~A~~A~~~l~g~--~~~g~~l~V~~a~~~~~~~   97 (103)
T 2dnm_A           65 RRDAQDAEAAMDGA--ELDGRELRVQVARYGRRDL   97 (103)
T ss_dssp             SSHHHHHHHHHSSC--CBTTBCCEEEECSSCCSCC
T ss_pred             HHHHHHHHHHcCCC--EECCcEEEEEECCcCCCCC
Confidence            99999999999998  8999999999999776544

>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=99.86  E-value=1.1e-21  Score=123.65  Aligned_cols=82  Identities=15%  Similarity=0.180  Sum_probs=73.4

Q ss_pred             CceEEEEeCCCC-CCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeC
Q psy1185           3 KVKVLYVRNLTQ-YCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYD   81 (131)
Q Consensus         3 ~~~~l~v~nLp~-~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~   81 (131)
                      ..++|||+|||+ ++++++|+++|++||.|.++.++++                                 ++||||+|.
T Consensus        14 p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~---------------------------------kg~aFVef~   60 (102)
T 1x4d_A           14 TRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK---------------------------------INEAFIEMA   60 (102)
T ss_dssp             CCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS---------------------------------SSCEEEEES
T ss_pred             CCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC---------------------------------CCEEEEEEC
Confidence            367999999999 9999999999999999999998743                                 689999999


Q ss_pred             CHHhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          82 SHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        82 ~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      +.++|.+|++.|++.+..+.|+.|.|.||+.+....
T Consensus        61 ~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~~~~~~   96 (102)
T 1x4d_A           61 TTEDAQAAVDYYTTTPALVFGKPVRVHLSQKYKRIK   96 (102)
T ss_dssp             SHHHHHHHHHHHHHSCCEETTEECEEEEECCCTTSS
T ss_pred             CHHHHHHHHHHHcCCCceECCcEEEEEECCCCCCCC
Confidence            999999999999986557999999999999765543

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.86  E-value=4.1e-21  Score=120.28  Aligned_cols=86  Identities=27%  Similarity=0.435  Sum_probs=77.8

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||.|..+.+++.                           ..++.+++||||+|.+
T Consensus        11 ~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~---------------------------~~~~~~~g~afV~f~~   63 (102)
T 1x5s_A           11 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKD---------------------------RETQRSRGFGFVTFEN   63 (102)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCC---------------------------SSSCSCCSEEEEECSS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeC---------------------------CCCCCcccEEEEEECC
Confidence            4689999999999999999999999999999998853                           3467789999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      .++|.+|++.|++.  .++|+.|+|.|+.++....
T Consensus        64 ~~~A~~A~~~l~g~--~~~g~~l~v~~a~~~~~~~   96 (102)
T 1x5s_A           64 IDDAKDAMMAMNGK--SVDGRQIRVDQAGKSSDNR   96 (102)
T ss_dssp             HHHHHHHHHHHTTC--CTTSCCCEEEEEECCCCCC
T ss_pred             HHHHHHHHHHhCCC--EECCeEEEEEECCCCCCCC
Confidence            99999999999998  8899999999998877644

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

Probab=99.86  E-value=6.5e-21  Score=119.04  Aligned_cols=83  Identities=22%  Similarity=0.366  Sum_probs=76.4

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .++|||+|||.++++++|+++|++||.|.+++++..                            .++.+++||||+|.+.
T Consensus        17 ~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~----------------------------~~g~~~g~afV~f~~~   68 (100)
T 2do4_A           17 KHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTN----------------------------RAGKPKGLAYVEYENE   68 (100)
T ss_dssp             CSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEEC----------------------------TTSCEEEEEEEEESSH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEEC----------------------------CCCCEEeEEEEEECCH
Confidence            678999999999999999999999999999998854                            2678899999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCCCCCC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADPQEEP  116 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~  116 (131)
                      ++|.+|+..|++.  .++|+.|.|.|+.++...
T Consensus        69 ~~a~~A~~~l~g~--~~~g~~l~v~~a~~~~~~   99 (100)
T 2do4_A           69 SQASQAVMKMDGM--TIKENIIKVAISNSGPSS   99 (100)
T ss_dssp             HHHHHHHHHHTTE--ESSSCEEEEEECCCCSCC
T ss_pred             HHHHHHHHHhCCC--EECCEEEEEEECCCCCCC
Confidence            9999999999997  899999999999987754

>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=99.85  E-value=6.1e-21  Score=120.08  Aligned_cols=85  Identities=28%  Similarity=0.342  Sum_probs=77.4

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||.|..+.+++.                           ..++.++|||||+|.+
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~---------------------------~~~~~~~g~afV~f~~   66 (105)
T 1x5u_A           14 QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKD---------------------------RVTGQHQGYGFVEFLS   66 (105)
T ss_dssp             TTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBC---------------------------SSSCSBCSCEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEec---------------------------CCCCcCCcEEEEEECC
Confidence            4679999999999999999999999999999998754                           3367889999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEEP  116 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~  116 (131)
                      .++|.+|+..|++.  .++|+.|.|.||.++...
T Consensus        67 ~~~a~~A~~~l~g~--~~~g~~l~v~~a~~~~~~   98 (105)
T 1x5u_A           67 EEDADYAIKIMDMI--KLYGKPIRVNKASAHNKN   98 (105)
T ss_dssp             HHHHHHHHHHSSSC--BCSSCBCEEEETTTTSCC
T ss_pred             HHHHHHHHHHhCCC--eECCeEEEEEECCCCCcC
Confidence            99999999999998  899999999999987654

>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=99.85  E-value=1.5e-20  Score=136.52  Aligned_cols=109  Identities=22%  Similarity=0.342  Sum_probs=93.2

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe--cCeEEEEECCHHHHHh---------------------------
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--KDYAFVHFEDRQEAIT---------------------------   53 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~--~~~~fv~~~~~~~a~~---------------------------   53 (131)
                      ..++|||+|||.++++++|+++|++|| |.++.+.  +|||||+|.+.++|..                           
T Consensus        21 ~~~~l~V~nLp~~~te~~l~~~F~~~G-i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~~~~~~~l~   99 (284)
T 3smz_A           21 NRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPTDALLC   99 (284)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHTTTSC-EEEEEEETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCSCEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcC-CEEEEEecCCCEEEEEeCCHHHHHHHHHHcCCCeeCCeEEEEEecCCCCEEE
Confidence            468999999999999999999999999 9999886  7999999999999988                           


Q ss_pred             ------------------hcC-CceeEEecCCCCCCCCcceEEEEeCCHHhHHHHHHHHhCCcceecCcEEEEEecCCCC
Q psy1185          54 ------------------VTG-LSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQE  114 (131)
Q Consensus        54 ------------------~~g-~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~  114 (131)
                                        .+| +..+.+..+ ..+|.++|+|||+|.+.++|.+|+..++|.  .++|+.|.|.|+.++.
T Consensus       100 v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~-~~~g~~~g~afV~f~~~~~a~~A~~~l~~~--~~~g~~i~v~~a~~~~  176 (284)
T 3smz_A          100 VANLPPSLTQQQFEELVRPFGSLERCFLVYS-ERTGQSKGYGFAEYMKKDSAARAKSDLLGK--PLGPRTLYVHWTDAGQ  176 (284)
T ss_dssp             EESCCTTCCHHHHHHHHGGGSCEEEEEEEEC-TTTCCEEEEEEEEESSHHHHHHHHHHHTTC--EETTEECEEEECCGGG
T ss_pred             EcCCCCcCCHHHHHHHHHhcCCeeEEEEEee-CCCCccceEEEEEECCHHHHHHHHHHhCCC--EeCCcEEEEEECCCCC
Confidence                              234 223333322 346888999999999999999999999998  8999999999998765


Q ss_pred             C
Q psy1185         115 E  115 (131)
Q Consensus       115 ~  115 (131)
                      .
T Consensus       177 ~  177 (284)
T 3smz_A          177 L  177 (284)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A

Probab=99.85  E-value=5.1e-21  Score=122.41  Aligned_cols=85  Identities=20%  Similarity=0.280  Sum_probs=77.7

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .++|||+|||.++++++|+++|++||.|.++++++.                           ..++.+++||||+|.+.
T Consensus        25 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~---------------------------~~~g~~~g~afV~f~~~   77 (115)
T 2cpz_A           25 GANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFID---------------------------KQTNLSKCFGFVSYDNP   77 (115)
T ss_dssp             TCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEEC---------------------------SSSCSEEEEEEEECSSH
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC---------------------------CCCCCcCccEEEEECCH
Confidence            579999999999999999999999999999998854                           33678899999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      ++|.+|++.|++.  .++|+.|+|+|++++....
T Consensus        78 ~~a~~A~~~l~g~--~~~g~~l~V~~a~~~~~~~  109 (115)
T 2cpz_A           78 VSAQAAIQSMNGF--QIGMKRLKVQLKRSKNDSK  109 (115)
T ss_dssp             HHHHHHHHHHTTC--EETTEECEEECCCCSCCCC
T ss_pred             HHHHHHHHHcCCC--EECCEEEEEEEcCCCCcCC
Confidence            9999999999998  8999999999999877654

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

Probab=99.85  E-value=3.5e-21  Score=120.60  Aligned_cols=86  Identities=27%  Similarity=0.501  Sum_probs=77.9

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||.|.++.+++.                           ..++.+++||||+|.+
T Consensus        11 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~---------------------------~~~~~~~g~afV~f~~   63 (102)
T 2cqb_A           11 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLD---------------------------YETEKHRGFAFVEFEL   63 (102)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCC---------------------------SSSCCCSSEEEECCSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEec---------------------------CCCCCcceEEEEEECC
Confidence            4679999999999999999999999999999988753                           3467889999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      .++|.+|+..|++.  .++|+.|.|.|+.++....
T Consensus        64 ~~~A~~A~~~l~g~--~~~g~~l~V~~a~~~~~~~   96 (102)
T 2cqb_A           64 AEDAAAAIDNMNES--ELFGRTIRVNLAKPMRIKE   96 (102)
T ss_dssp             HHHHHHHHHHHTTE--EETTEEEEEEECCCCCCCC
T ss_pred             HHHHHHHHHHhCCC--EECCcEEEEEeCCCCCCCC
Confidence            99999999999997  8999999999999877654

>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=99.85  E-value=5.2e-21  Score=138.03  Aligned_cols=109  Identities=26%  Similarity=0.379  Sum_probs=92.0

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe--cCeEEEEECCHHHHHh---------------------------
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--KDYAFVHFEDRQEAIT---------------------------   53 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~--~~~~fv~~~~~~~a~~---------------------------   53 (131)
                      ..++|||+|||.++|+++|+++|++||.|.++.+.  +|||||+|.+.++|..                           
T Consensus        21 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~a~~~~~l~  100 (261)
T 3sde_A           21 QRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATHGAALT  100 (261)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETTTTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCSSEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCCCcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeecccCCccc
Confidence            46799999999999999999999999999999988  8999999999999998                           


Q ss_pred             ------------------hcC-CceeEEecCCCCCCCCcceEEEEeCCHHhHHHHHHHHhCCcceec---CcEEEEEecC
Q psy1185          54 ------------------VTG-LSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVW---GCDIIVDWAD  111 (131)
Q Consensus        54 ------------------~~g-~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~~~~~---g~~l~v~~a~  111 (131)
                                        .+| +..+.+..+  .+|.++|+|||+|.+.++|.+|+..++++. .+.   ++.|.|.++.
T Consensus       101 v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~--~~g~~~g~afV~f~~~~~A~~A~~~l~~~~-~~~~~~~r~i~v~~~~  177 (261)
T 3sde_A          101 VKNLSPVVSNELLEQAFSQFGPVEKAVVVVD--DRGRATGKGFVEFAAKPPARKALERCGDGA-FLLTTTPRPVIVEPME  177 (261)
T ss_dssp             EESCCTTCCHHHHHHHHGGGSCEEEEEEEEE--TTSCEEEEEEEEESSHHHHHHHHHHHHHSC-EESSSSCCBCEEEECC
T ss_pred             ccCCCCCCCHHHHHHHHHhcCCeEEEEeeeC--CCCCcCcEEEEEeCCHHHHHHHHHHhcCCe-EEecCCCceEEEeecc
Confidence                              344 334444444  378889999999999999999999996542 333   8899999998


Q ss_pred             CCC
Q psy1185         112 PQE  114 (131)
Q Consensus       112 ~~~  114 (131)
                      +..
T Consensus       178 ~~~  180 (261)
T 3sde_A          178 QFD  180 (261)
T ss_dssp             CEE
T ss_pred             ccC
Confidence            654

>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=99.85  E-value=1.6e-20  Score=117.78  Aligned_cols=84  Identities=25%  Similarity=0.392  Sum_probs=76.4

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||.|.++++++.                             .+.+++||||+|.+
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~-----------------------------~~~~~g~afV~f~~   64 (103)
T 2cq3_A           14 TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN-----------------------------ERGSKGFGFVTFEN   64 (103)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECC-----------------------------TTTTCCEEEEEESC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEec-----------------------------CCCCcEEEEEEECC
Confidence            4689999999999999999999999999999998853                             33479999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      .++|.+|+..|++.  .++|+.|.|.|+.++....
T Consensus        65 ~~~a~~A~~~l~g~--~~~g~~l~v~~a~~~~~~~   97 (103)
T 2cq3_A           65 SADADRAREKLHGT--VVEGRKIEVNNATARVMTN   97 (103)
T ss_dssp             HHHHHHHHHHHTTC--EETTEECEEEECCSSCCCC
T ss_pred             HHHHHHHHHHhCCC--EECCEEEEEEEcccCCCCC
Confidence            99999999999998  8999999999999877654

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.85  E-value=8.1e-21  Score=120.54  Aligned_cols=86  Identities=24%  Similarity=0.394  Sum_probs=77.7

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||+++++++|+++|++||.|..+++++.                           ..++.++|||||+|.+
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~---------------------------~~~g~~~g~afV~f~~   66 (111)
T 1x4h_A           14 EGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLH---------------------------PDTEHSKGCAFAQFMT   66 (111)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBC---------------------------SSSCCBCSEEEEEESS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEec---------------------------CCCCCCccEEEEEECC
Confidence            3679999999999999999999999999999998854                           3467889999999999


Q ss_pred             HHhHHHHHHHHh------CCcceecCcEEEEEecCCCCCCC
Q psy1185          83 HKSASLAKKRLA------TGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        83 ~~~a~~a~~~l~------~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      .++|.+|+..++      +.  .++|+.|.|.|+.++.+..
T Consensus        67 ~~~A~~A~~~~~~~~~~~~~--~~~g~~l~v~~a~~~~~~~  105 (111)
T 1x4h_A           67 QEAAQKCLAAASLEAEGGGL--KLDGRQLKVDLAVTRDEAA  105 (111)
T ss_dssp             HHHHHHHHHHHCTTTTTCCE--ESSSCEEEEECCCCCCCCC
T ss_pred             HHHHHHHHHHhccccccCCc--EEcCEEEEEEECCCCccCC
Confidence            999999999999      76  8999999999999887654

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

Probab=99.85  E-value=5.6e-21  Score=117.49  Aligned_cols=85  Identities=26%  Similarity=0.296  Sum_probs=77.5

Q ss_pred             CCceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeC
Q psy1185           2 SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYD   81 (131)
Q Consensus         2 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~   81 (131)
                      +..++|||+|||.++++++|+++|++||.|..+.+++.                             ++.+++||||+|.
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~-----------------------------~g~~~g~afV~f~   56 (92)
T 2dgv_A            6 SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-----------------------------NGKSKGCGVVKFE   56 (92)
T ss_dssp             SSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES-----------------------------SSCEEEEEEEEES
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc-----------------------------CCCcceEEEEEEC
Confidence            35689999999999999999999999999999988742                             6778999999999


Q ss_pred             CHHhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          82 SHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        82 ~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      +.++|.+|+..|++.  .++|+.|.|+|+++...+.
T Consensus        57 ~~~~a~~a~~~l~g~--~~~g~~l~v~~a~~~~~~~   90 (92)
T 2dgv_A           57 SPEVAERACRMMNGM--KLSGREIDVRIDRNASGPS   90 (92)
T ss_dssp             SHHHHHHHHHHHTTC--CBTTBCCCCEECSCCSSCC
T ss_pred             CHHHHHHHHHHhCCC--EECCcEEEEEEcCCCCCCC
Confidence            999999999999998  8999999999999877653

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

Probab=99.85  E-value=5.1e-21  Score=121.55  Aligned_cols=83  Identities=24%  Similarity=0.422  Sum_probs=76.2

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||.|.++.+++.                           ..++.++|||||+|.+
T Consensus        25 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~---------------------------~~~g~~~g~afV~F~~   77 (108)
T 2jrs_A           25 GPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMD---------------------------SETGRSKGYGFITFSD   77 (108)
T ss_dssp             SCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEE---------------------------TTTTEEEEEEEEEESC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEc---------------------------CCCCccceEEEEEECC
Confidence            4689999999999999999999999999999998853                           3467889999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQE  114 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~  114 (131)
                      .++|.+|++.++|.  .++|+.|+|+|++++.
T Consensus        78 ~~~A~~Ai~~l~g~--~i~g~~l~V~~a~~k~  107 (108)
T 2jrs_A           78 SECAKKALEQLNGF--ELAGRPMKVGHVTERT  107 (108)
T ss_dssp             HHHHHHHHHHHTTC--CSSSSCCEEECSCSSC
T ss_pred             HHHHHHHHHHcCCC--EECCEEEEEEEcccCC
Confidence            99999999999998  8999999999999875

>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=99.85  E-value=9.8e-21  Score=115.64  Aligned_cols=82  Identities=24%  Similarity=0.355  Sum_probs=74.9

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .++|||+|||.++++++|+++|++||.|.++.+++.                           ..++.++|||||+|.+.
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~---------------------------~~~~~~~g~afV~f~~~   58 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCD---------------------------KFSGHPKGFAYIEFSDK   58 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEES---------------------------CSSSSCCEEEEEEESST
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEec---------------------------CCCCCcceEEEEEECCH
Confidence            579999999999999999999999999999998854                           34688899999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCCCCC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADPQEE  115 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~  115 (131)
                      ++|.+|+ .+++.  .++|+.|.|.|++++.+
T Consensus        59 ~~a~~a~-~~~g~--~~~g~~l~V~~a~~~~p   87 (89)
T 3ucg_A           59 ESVRTSL-ALDES--LFRGRQIKVIPKRTNRP   87 (89)
T ss_dssp             HHHHHHG-GGTTC--EETTEECEEEETTTTSC
T ss_pred             HHHHHHH-hcCCC--EECCcEEEEEEccCCCC
Confidence            9999999 99998  89999999999987653

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

Probab=99.85  E-value=4.8e-21  Score=119.17  Aligned_cols=90  Identities=28%  Similarity=0.355  Sum_probs=77.3

Q ss_pred             CCceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeC
Q psy1185           2 SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYD   81 (131)
Q Consensus         2 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~   81 (131)
                      +..++|||+|||.++++++|+++|++||.|..+.+++..                        ....++.+++||||+|.
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~------------------------~~~gt~~~~g~afV~f~   58 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKK------------------------NKAGVLLSMGFGFVEYK   58 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEE------------------------CTTCCEEEEEEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecC------------------------CCCCCcCcccEEEEEEC
Confidence            356899999999999999999999999999999888430                        00013378899999999


Q ss_pred             CHHhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          82 SHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        82 ~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      +.++|.+|+..|++.  .++|+.|.|+|+.++..+.
T Consensus        59 ~~~~a~~A~~~l~g~--~~~g~~l~V~~a~~~~~~~   92 (98)
T 2cpf_A           59 KPEQAQKALKQLQGH--TVDGHKLEVRISERATKPA   92 (98)
T ss_dssp             SHHHHHHHHHHSTTC--EETTEECEEECSSCSSCCC
T ss_pred             CHHHHHHHHHHhCCC--eeCCeEEEEEEccCCCCCC
Confidence            999999999999998  8999999999999877654

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.85  E-value=6.3e-21  Score=119.69  Aligned_cols=84  Identities=27%  Similarity=0.443  Sum_probs=77.4

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||+++++++|+++|++||.|.++.+++.                             ++.+++||||+|.+
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~-----------------------------~g~~~g~afV~f~~   64 (103)
T 2d9p_A           14 QVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-----------------------------GGRSKGFGFVCFSS   64 (103)
T ss_dssp             SCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC-----------------------------SSSEEEEEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC-----------------------------CCCcCEEEEEEECC
Confidence            4789999999999999999999999999999988742                             67889999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      .++|.+|+..|++.  .++|+.|.|.|+.++.++.
T Consensus        65 ~~~A~~A~~~l~g~--~~~g~~l~V~~a~~~~~~~   97 (103)
T 2d9p_A           65 PEEATKAVTEMNGR--IVATKPLYVALAQRKEERQ   97 (103)
T ss_dssp             HHHHHHHHHHHTTC--BSSSSBCEEEECSSCCCCC
T ss_pred             HHHHHHHHHHhCCC--EeCCcEEEEEEecccccCC
Confidence            99999999999998  8899999999999887764

>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=99.85  E-value=9.3e-21  Score=119.20  Aligned_cols=81  Identities=19%  Similarity=0.255  Sum_probs=72.6

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .++|||+|||+++++++|+++|++||.|.++.++++                                 +|||||+|.+.
T Consensus        15 ~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~---------------------------------kg~aFVef~~~   61 (101)
T 2cq1_A           15 SRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG---------------------------------KNQAFLELATE   61 (101)
T ss_dssp             CSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT---------------------------------TTEEEEEESSH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC---------------------------------CCEEEEEECCH
Confidence            579999999999999999999999999999988742                                 89999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      ++|.+|++.+++.+..+.|+.|.|.||+++....
T Consensus        62 ~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~~~~~~   95 (101)
T 2cq1_A           62 EAAITMVNYYSAVTPHLRNQPIYIQYSNHKELKT   95 (101)
T ss_dssp             HHHHHHHHHHHHSCCEETTEECEEEECSCSSCCC
T ss_pred             HHHHHHHHHhccCCceECCcEEEEEEcCcccCcC
Confidence            9999999998754458999999999999876554

>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=99.85  E-value=1.6e-20  Score=136.77  Aligned_cols=109  Identities=18%  Similarity=0.304  Sum_probs=87.3

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe------cCeEEEEECCHHHHHh------------------------
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI------KDYAFVHFEDRQEAIT------------------------   53 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~------~~~~fv~~~~~~~a~~------------------------   53 (131)
                      .++|||+|||.++++++|+++|++||.|.++.++      +|||||+|.+.++|..                        
T Consensus        41 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~A~~A~~~~~~~~~g~~i~v~~~~~~~l  120 (292)
T 2ghp_A           41 LTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKTHKVVGQNEIIVSHLTECTL  120 (292)
T ss_dssp             -CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHHTTTTCEETTEECEEEECCSCEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEEECCHHHHHHHHHhCCcEeCCcEEEEEECCCCEE
Confidence            6799999999999999999999999999999987      5899999999999998                        


Q ss_pred             -------------------hcC--CceeEEecCCCCCCCCcceEEEEeCCHHhHHHHHHHHhCCcceecCcEEEEEecCC
Q psy1185          54 -------------------VTG--LSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADP  112 (131)
Q Consensus        54 -------------------~~g--~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~  112 (131)
                                         .+|  +..+.+..  ...+.++|||||+|.+.++|.+|+..|+|.  .++|+.|.|.|+.+
T Consensus       121 ~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~--~~~~~~~g~afV~f~~~~~a~~A~~~l~g~--~~~g~~l~v~~a~~  196 (292)
T 2ghp_A          121 WMTNFPPSYTQRNIRDLLQDINVVALSIRLPS--LRFNTSRRFAYIDVTSKEDARYCVEKLNGL--KIEGYTLVTKVSNP  196 (292)
T ss_dssp             EEECCCTTCCHHHHHHHHHHTTCCCCEEECC---------CCEEEEECSSHHHHHHHHHHHTTC--EETTEECEEEECCC
T ss_pred             EEECCCCCCCHHHHHHHHHHhCCCeEEEEEEe--CCCCCcceEEEEEECCHHHHHHHHHHhCCC--EeCCcEEEEEECCC
Confidence                               233  22222222  223678999999999999999999999998  89999999999987


Q ss_pred             CCCC
Q psy1185         113 QEEP  116 (131)
Q Consensus       113 ~~~~  116 (131)
                      +...
T Consensus       197 ~~~~  200 (292)
T 2ghp_A          197 LEKS  200 (292)
T ss_dssp             C---
T ss_pred             Cccc
Confidence            6643

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

Probab=99.85  E-value=1.1e-20  Score=119.06  Aligned_cols=86  Identities=26%  Similarity=0.369  Sum_probs=77.2

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||.|.++++++.                           ..++.++|||||+|.+
T Consensus        12 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~---------------------------~~~g~~~g~afV~f~~   64 (106)
T 2dgp_A           12 DAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKD---------------------------RFTGMHKGCAFLTYCE   64 (106)
T ss_dssp             TCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCC---------------------------SSSCSCCSEEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEec---------------------------CCCCCcceEEEEEECC
Confidence            4689999999999999999999999999999998854                           3468889999999999


Q ss_pred             HHhHHHHHHHHhCCccee---cCcEEEEEecCCCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKV---WGCDIIVDWADPQEEPD  117 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~---~g~~l~v~~a~~~~~~~  117 (131)
                      .++|.+|++.|++.  .+   .|+.|.|.|+.++....
T Consensus        65 ~~~A~~A~~~l~g~--~~~~~~g~~l~v~~a~~~~~~~  100 (106)
T 2dgp_A           65 RESALKAQSALHEQ--KTLPGMNRPIQVKPADSESRGG  100 (106)
T ss_dssp             HHHHHHHHHHHTTT--CCCTTCSSCCEEEECCCCSCCC
T ss_pred             HHHHHHHHHHhcCC--cccCCCCceEEEEECCcccccC
Confidence            99999999999997  55   88999999999877644

>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=99.85  E-value=8.8e-21  Score=119.87  Aligned_cols=80  Identities=20%  Similarity=0.260  Sum_probs=72.5

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .++|||+|||+++++++|+++|++||.|.++.+++                                 .+|||||+|.+.
T Consensus        15 ~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~---------------------------------~kg~aFVef~~~   61 (104)
T 1wex_A           15 SPVVHVRGLCESVVEADLVEALEKFGTICYVMMMP---------------------------------FKRQALVEFENI   61 (104)
T ss_dssp             CSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEET---------------------------------TTTEEEEEESSH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEC---------------------------------CCCEEEEEECCH
Confidence            67999999999999999999999999999998873                                 279999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCCCCCC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADPQEEP  116 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~  116 (131)
                      ++|.+|++.+++.++.++|+.|.|.||.++...
T Consensus        62 ~~A~~Ai~~l~~~~~~i~Gr~l~V~~a~~~~~~   94 (104)
T 1wex_A           62 DSAKECVTFAADVPVYIAGQQAFFNYSTSKRIT   94 (104)
T ss_dssp             HHHHHHHHHHHHSCCBSSSSBCEEEECSSSSCC
T ss_pred             HHHHHHHHHhccCCceECCEEEEEEEccCcccc
Confidence            999999999988656799999999999876543

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

Probab=99.85  E-value=1e-20  Score=116.71  Aligned_cols=80  Identities=28%  Similarity=0.448  Sum_probs=73.3

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||.|.++.+++.                           ..++.+++||||+|.+
T Consensus        15 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~---------------------------~~~~~~~g~afV~f~~   67 (94)
T 2e5h_A           15 SKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKD---------------------------KDTRKSKGVAFILFLD   67 (94)
T ss_dssp             CTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCC---------------------------SSSCCCTTCEEEEESC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeC---------------------------CCCCCcccEEEEEECC
Confidence            3679999999999999999999999999999998854                           3357889999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWAD  111 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~  111 (131)
                      .++|.+|++.|++.  .++|+.|+|+||+
T Consensus        68 ~~~A~~A~~~l~g~--~~~g~~l~v~~ak   94 (94)
T 2e5h_A           68 KDSAQNCTRAINNK--QLFGRVIKASIAI   94 (94)
T ss_dssp             HHHHHHHHHHTTTE--EETTEEEEEEECC
T ss_pred             HHHHHHHHHHcCCC--eeCCcEEEEEecC
Confidence            99999999999997  8999999999985

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

Probab=99.85  E-value=1.2e-20  Score=118.73  Aligned_cols=85  Identities=21%  Similarity=0.445  Sum_probs=76.9

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||.|.++.++++                            .++.++|||||+|.+
T Consensus        14 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~----------------------------~~g~~~g~afV~f~~   65 (105)
T 2dnh_A           14 RDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRG----------------------------PDGSSKGCAFVKFSS   65 (105)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEEC----------------------------SSSCEEEEEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC----------------------------CCCCcCcEEEEEeCC
Confidence            3689999999999999999999999999999998854                            267889999999999


Q ss_pred             HHhHHHHHHHHhCCcceecC---cEEEEEecCCCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWG---CDIIVDWADPQEEPD  117 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g---~~l~v~~a~~~~~~~  117 (131)
                      .++|.+|++.|++.  .+.|   +.|.|.||.++.++.
T Consensus        66 ~~~A~~Ai~~l~g~--~~~gg~~~~l~V~~a~~~~~~~  101 (105)
T 2dnh_A           66 HTEAQAAIHALHGS--QTMPGASSSLVVKFADTDKESG  101 (105)
T ss_dssp             HHHHHHHHHHHSSC--CCCTTCSSCCEEEESCSSCCCS
T ss_pred             HHHHHHHHHHHcCC--ccCCCCCccEEEEECccCcccC
Confidence            99999999999998  6777   999999999887654

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.85  E-value=7.5e-21  Score=118.47  Aligned_cols=85  Identities=20%  Similarity=0.368  Sum_probs=76.9

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCee-EEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVE-RVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYD   81 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~-~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~   81 (131)
                      ..++|||+|||.++++++|+++|++||.|. ++++++.                           ..++.++|||||+|.
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~---------------------------~~~g~~~g~afV~f~   60 (99)
T 2div_A            8 MAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRN---------------------------RLTGIPAGYCFVEFA   60 (99)
T ss_dssp             SSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEEC---------------------------SSSCCEEEEEEEECS
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeec---------------------------CCCCCcCCEEEEEeC
Confidence            368999999999999999999999999999 9998854                           346788999999999


Q ss_pred             CHHhHHHHHHHHhCCcceecCcE----EEEEecCCCCCC
Q psy1185          82 SHKSASLAKKRLATGRLKVWGCD----IIVDWADPQEEP  116 (131)
Q Consensus        82 ~~~~a~~a~~~l~~~~~~~~g~~----l~v~~a~~~~~~  116 (131)
                      +.++|.+|+..|++.  .++|+.    |+|.||.+...+
T Consensus        61 ~~~~a~~A~~~l~g~--~~~g~~~~~~l~v~~a~~~~~~   97 (99)
T 2div_A           61 DLATAEKCLHKINGK--PLPGATPAKRFKLNYATYSGPS   97 (99)
T ss_dssp             CHHHHHHHHHTTTTS--EESSCSSCEECCEEETTCCSSS
T ss_pred             CHHHHHHHHHHHcCC--ccCCCCcceeEEEeecCCCCCC
Confidence            999999999999998  899999    999999987644

>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=99.85  E-value=1.4e-20  Score=120.85  Aligned_cols=84  Identities=27%  Similarity=0.402  Sum_probs=76.8

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||.|.++.++++                            .++.++|||||+|.+
T Consensus         6 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~----------------------------~~g~~~g~afV~F~~   57 (116)
T 2fy1_A            6 HPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD----------------------------RTSKSRGFAFITFEN   57 (116)
T ss_dssp             SCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECS----------------------------TTTTCCCEEEEECSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEEC----------------------------CCCCcccEEEEEECC
Confidence            4689999999999999999999999999999998854                            268889999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEEP  116 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~  116 (131)
                      .++|.+|+..|+|.  .++|+.|.|.||+++...
T Consensus        58 ~~~A~~Ai~~l~g~--~~~g~~l~V~~a~~~~~~   89 (116)
T 2fy1_A           58 PADAKNAAKDMNGK--SLHGKAIKVEQAKKPSFQ   89 (116)
T ss_dssp             HHHHHHHHHHCSSC--BCSSSBCEEEECCCSSCS
T ss_pred             HHHHHHHHHHhCCC--EECCEEEEEEECCCCCCC
Confidence            99999999999998  899999999999876643

>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=99.85  E-value=6e-21  Score=123.27  Aligned_cols=81  Identities=17%  Similarity=0.270  Sum_probs=73.1

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .++|||+|||+++++++|+++|++||.|.++.++++                                 +|||||+|.+.
T Consensus        31 s~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~---------------------------------kG~AFVeF~~~   77 (119)
T 2ad9_A           31 SRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG---------------------------------KNQAFIEMNTE   77 (119)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG---------------------------------GTEEEEECSCH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC---------------------------------CCEEEEEECCH
Confidence            679999999999999999999999999999998842                                 79999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      ++|.+|+..+++.+..++|+.|.|.||+++....
T Consensus        78 e~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~k~~~~  111 (119)
T 2ad9_A           78 EAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKT  111 (119)
T ss_dssp             HHHHHHHHHHHHHCCCBTTBCCEEEECSSSSCCC
T ss_pred             HHHHHHHHHhccCCceECCeEEEEEEccCCCCCc
Confidence            9999999999863347999999999999877654

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=2.6e-20  Score=118.01  Aligned_cols=83  Identities=17%  Similarity=0.279  Sum_probs=75.4

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||.|..+.+..                              ++.+++||||+|.+
T Consensus        21 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~------------------------------~~~~~g~afV~f~~   70 (109)
T 1x4a_A           21 NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN------------------------------RRGGPPFAFVEFED   70 (109)
T ss_dssp             CSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECC------------------------------SSSSSCCEEEEESC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEE------------------------------CCCCCcEEEEEECC
Confidence            367999999999999999999999999999998863                              35579999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      .++|.+|++.|++.  .++|+.|.|+|++++....
T Consensus        71 ~~~A~~A~~~l~g~--~~~g~~l~V~~a~~~~~~~  103 (109)
T 1x4a_A           71 PRDAEDAVYGRDGY--DYDGYRLRVEFPRSGRGTG  103 (109)
T ss_dssp             HHHHHHHHHHHTTC--EETTEECEEECCCCCCCCC
T ss_pred             HHHHHHHHHHcCCC--EECCeEEEEEEcccCCCCC
Confidence            99999999999998  8999999999999876543

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

Probab=99.84  E-value=1.6e-21  Score=122.15  Aligned_cols=81  Identities=17%  Similarity=0.178  Sum_probs=74.5

Q ss_pred             ceEEEEeCCCC------CCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEE
Q psy1185           4 VKVLYVRNLTQ------YCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCF   77 (131)
Q Consensus         4 ~~~l~v~nLp~------~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~f   77 (131)
                      .++|||+|||.      ++++++|+++|++||.|.++++++.                           ..+|.++||||
T Consensus         6 ~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d---------------------------~~tg~~kG~af   58 (100)
T 3ns6_A            6 DQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPID---------------------------EATGKTKGFLF   58 (100)
T ss_dssp             GGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEE---------------------------TTTTEECSEEE
T ss_pred             CcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEc---------------------------CCCCccceEEE
Confidence            67999999999      9999999999999999999998854                           34688999999


Q ss_pred             EEeCCHHhHHHHHHHHhCCcceecC-cEEEEEecCCC
Q psy1185          78 LEYDSHKSASLAKKRLATGRLKVWG-CDIIVDWADPQ  113 (131)
Q Consensus        78 v~f~~~~~a~~a~~~l~~~~~~~~g-~~l~v~~a~~~  113 (131)
                      |+|.+.++|.+|+..|+|.  .++| +.|.|.||.++
T Consensus        59 V~f~~~~~A~~Ai~~lng~--~~~g~r~l~V~~a~~~   93 (100)
T 3ns6_A           59 VECGSMNDAKKIIKSFHGK--RLDLKHRLFLYTMKDV   93 (100)
T ss_dssp             EEESSHHHHHHHHHHHTTC--BSSSSCBCEEEESHHH
T ss_pred             EEECCHHHHHHHHHHhCCc--ccCCCeEEEEEECchh
Confidence            9999999999999999998  8899 99999999753

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

Probab=99.84  E-value=1.4e-20  Score=116.19  Aligned_cols=81  Identities=30%  Similarity=0.440  Sum_probs=74.1

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||.|.++.+++.                           ..++.+++||||+|.+
T Consensus        14 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~---------------------------~~~~~~~g~afV~f~~   66 (95)
T 2cqc_A           14 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYD---------------------------QQSRRSRGFAFVYFEN   66 (95)
T ss_dssp             GGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEEC---------------------------SSSSSEEEEEEEEESS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEc---------------------------CCCCCcccEEEEEECC
Confidence            3678999999999999999999999999999998853                           3357889999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADP  112 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~  112 (131)
                      .++|.+|+..|++.  .++|+.|.|+||++
T Consensus        67 ~~~A~~A~~~l~g~--~~~g~~l~v~~a~~   94 (95)
T 2cqc_A           67 VDDAKEAKERANGM--ELDGRRIRVSGPSS   94 (95)
T ss_dssp             HHHHHHHHHHHTTE--EETTEEEEEECCSC
T ss_pred             HHHHHHHHHHhCCC--EECCEEEEEEecCC
Confidence            99999999999997  89999999999975

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

Probab=99.84  E-value=2.2e-20  Score=117.75  Aligned_cols=87  Identities=22%  Similarity=0.487  Sum_probs=77.4

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||.|..+++++.                          ...++.+++||||+|.+
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--------------------------~~~~~~~~g~afV~f~~   67 (107)
T 2cph_A           14 TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKK--------------------------MTGTGAHRGFGFVDFIT   67 (107)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCC--------------------------CSSSCSSCSEEEEEESS
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecC--------------------------CCCCCCcCceEEEEECC
Confidence            3679999999999999999999999999999988742                          01267889999999999


Q ss_pred             HHhHHHHHHHH-hCCcceecCcEEEEEecCCCCCCC
Q psy1185          83 HKSASLAKKRL-ATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        83 ~~~a~~a~~~l-~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      .++|.+|+..| ++.  .++|+.|.|.||.++.+..
T Consensus        68 ~~~a~~A~~~l~~~~--~~~g~~l~v~~a~~~~~~~  101 (107)
T 2cph_A           68 KQDAKKAFNALCHST--HLYGRRLVLEWADSEVTVQ  101 (107)
T ss_dssp             HHHHHHHHHHHHTCC--BSSSCBCEEEECCCCCCCC
T ss_pred             HHHHHHHHHHhccCC--eECCCEEEEEeCCCCCCCC
Confidence            99999999999 887  8899999999999887654

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=1.9e-20  Score=119.34  Aligned_cols=86  Identities=21%  Similarity=0.306  Sum_probs=77.4

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCee--------EEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcc
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVE--------RVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRG   74 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~--------~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~   74 (131)
                      ..++|||+|||.++++++|+++|++||.|.        .++++..                           ..++.++|
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~---------------------------~~~g~~~g   66 (113)
T 2cpe_A           14 DNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLD---------------------------KETGKPKG   66 (113)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBC---------------------------TTTCSBCS
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEe---------------------------CCCCCeee
Confidence            468999999999999999999999999998        5777643                           34788899


Q ss_pred             eEEEEeCCHHhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          75 FCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        75 ~~fv~f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      ||||+|.+.++|.+|+..|++.  .++|+.|+|.|+.++.+..
T Consensus        67 ~afV~f~~~~~A~~Ai~~l~g~--~~~g~~l~V~~a~~~~~~~  107 (113)
T 2cpe_A           67 DATVSYEDPPTAKAAVEWFDGK--DFQGSKLKVSLARKKPPMN  107 (113)
T ss_dssp             EEEEEBSSHHHHHHHHHHHTTC--EETTEECEEECSSCCCCST
T ss_pred             EEEEEECCHHHHHHHHHHcCCC--ccCCCEEEEEECCCCCCCC
Confidence            9999999999999999999998  8999999999999887654

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=2.9e-20  Score=116.87  Aligned_cols=84  Identities=26%  Similarity=0.348  Sum_probs=75.6

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCC-CCCcceEEEEeC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDN-KKNRGFCFLEYD   81 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~-~~~~~~~fv~f~   81 (131)
                      ..++|||+|||.++++++|+++|++|| |.++.+++.                           ..+ +.++|||||+|.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~---------------------------~~~~g~~~g~afV~f~   65 (104)
T 1wi8_A           14 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPRE---------------------------PSNPERLKGFGYAEFE   65 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBC---------------------------SSCTTSBCSCEEEEES
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecC---------------------------CCCCCCcCeEEEEEEC
Confidence            468999999999999999999999999 999988753                           223 788999999999


Q ss_pred             CHHhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          82 SHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        82 ~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      +.++|.+|+ .+++.  .++|+.|.|.|+.++.+..
T Consensus        66 ~~~~a~~A~-~l~g~--~~~g~~l~V~~a~~~~~~~   98 (104)
T 1wi8_A           66 DLDSLLSAL-SLNEE--SLGNKRIRVDVADQAQDKD   98 (104)
T ss_dssp             SHHHHHHHH-GGGTC--EETTEECEEEECCCCCCCC
T ss_pred             CHHHHHHHH-hcCCC--EeCCcEEEEEEccCCCCCC
Confidence            999999999 99998  8999999999999887654

>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=99.84  E-value=2.1e-20  Score=117.47  Aligned_cols=80  Identities=38%  Similarity=0.671  Sum_probs=73.4

Q ss_pred             CCCceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEe
Q psy1185           1 MSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEY   80 (131)
Q Consensus         1 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f   80 (131)
                      |+..++|||+|||.++++++|+++|++||.|..+.++                                   ++||||+|
T Consensus         8 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~-----------------------------------~~~afV~f   52 (103)
T 2dgu_A            8 MAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL-----------------------------------KDYAFIHF   52 (103)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC-----------------------------------SSCEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE-----------------------------------CCEEEEEe
Confidence            5678899999999999999999999999999999876                                   46899999


Q ss_pred             CCHHhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          81 DSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        81 ~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      .+.++|.+|+..|++.  .++|+.|.|.|+.++....
T Consensus        53 ~~~~~a~~A~~~l~g~--~~~g~~l~v~~a~~~~~~~   87 (103)
T 2dgu_A           53 DERDGAVKAMEEMNGK--DLEGENIEIVFAKPPDQKR   87 (103)
T ss_dssp             SSHHHHHHHHHHHTTE--EETTEEEEEEECCCCCCCC
T ss_pred             CCHHHHHHHHHHHCCC--ccCCCEEEEEEcCCCcccc
Confidence            9999999999999998  8999999999999877654

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=1.9e-20  Score=118.96  Aligned_cols=81  Identities=26%  Similarity=0.411  Sum_probs=74.2

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||.|.++.+++.                             .+.++|||||+|.+
T Consensus        28 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----------------------------~~~~kg~afV~f~~   78 (109)
T 2err_A           28 QPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN-----------------------------ERGSKGFGFVTFEN   78 (109)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCB-----------------------------TTBCTTEEEEECCC
T ss_pred             CCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEEC-----------------------------CCCCceEEEEEECC
Confidence            4689999999999999999999999999999998853                             34579999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQE  114 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~  114 (131)
                      .++|.+|+..|+|.  .++|+.|.|+||.++.
T Consensus        79 ~~~A~~Ai~~l~g~--~~~g~~l~V~~a~~~~  108 (109)
T 2err_A           79 SADADRAREKLHGT--VVEGRKIEVNNATARV  108 (109)
T ss_dssp             SHHHHHHHHHHTTC--EETTEECEEEECCCSC
T ss_pred             HHHHHHHHHHcCCC--EECCEEEEEEECCCCc
Confidence            99999999999998  8999999999998763

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

Probab=99.84  E-value=1.2e-20  Score=123.41  Aligned_cols=84  Identities=30%  Similarity=0.462  Sum_probs=76.7

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||.|..+.+++.                           ..++.++|||||+|.+
T Consensus        45 ~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d---------------------------~~tg~~~G~afV~F~~   97 (129)
T 2kxn_B           45 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYD---------------------------QQSRRSRGFAFVYFEN   97 (129)
T ss_dssp             CSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECC---------------------------SSSSCCCCEEEEEESC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEec---------------------------CCCCccceEEEEEECC
Confidence            3678999999999999999999999999999998854                           3467889999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEE  115 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~  115 (131)
                      .++|.+|+..|++.  .++|+.|.|+|+.++.+
T Consensus        98 ~~~A~~Ai~~lng~--~i~g~~l~V~~a~~~~p  128 (129)
T 2kxn_B           98 VDDAKEAKERANGM--ELDGRRIRVDFSITKRP  128 (129)
T ss_dssp             HHHHHHHHHHHTTC--CSSSSCCEESCCSSSSC
T ss_pred             HHHHHHHHHHhCCC--EECCEEEEEEEecCCCC
Confidence            99999999999998  88999999999998764

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.84  E-value=2.2e-20  Score=116.48  Aligned_cols=80  Identities=23%  Similarity=0.325  Sum_probs=73.1

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeE--------EEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcc
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVER--------VKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRG   74 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~--------~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~   74 (131)
                      ..++|||+|||.++++++|+++|++||.|.+        +++++.                           ..+|.++|
T Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~---------------------------~~~g~~~G   64 (99)
T 2la6_A           12 DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTD---------------------------RETGKLKG   64 (99)
T ss_dssp             CCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEEC---------------------------TTTCSEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEec---------------------------CCCCCeee
Confidence            3679999999999999999999999999999        887753                           34688899


Q ss_pred             eEEEEeCCHHhHHHHHHHHhCCcceecCcEEEEEecC
Q psy1185          75 FCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWAD  111 (131)
Q Consensus        75 ~~fv~f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~  111 (131)
                      ||||+|.+.++|.+|++.|+|.  .++|+.|+|+||+
T Consensus        65 ~afV~f~~~~~a~~Ai~~l~g~--~~~g~~l~V~~A~   99 (99)
T 2la6_A           65 EATVSFDDPPSAKAAIDWFDGK--EFSGNPIKVSFAT   99 (99)
T ss_dssp             EEEEEBSSHHHHHHHHHHHTTC--BSSSSBCEEEECC
T ss_pred             EEEEEECCHHHHHHHHHHhCCC--EeCCcEEEEEecC
Confidence            9999999999999999999998  8899999999984

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.84  E-value=5e-20  Score=112.97  Aligned_cols=78  Identities=26%  Similarity=0.446  Sum_probs=72.1

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||.|.++.++                                   ++||||+|.+
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~-----------------------------------~g~afV~f~~   51 (90)
T 2dnq_A            7 GMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII-----------------------------------KNYGFVHIED   51 (90)
T ss_dssp             CCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE-----------------------------------TTEEEEEESS
T ss_pred             CCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE-----------------------------------CCEEEEEECC
Confidence            47899999999999999999999999999999876                                   5789999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      .++|.+|+..+++.  .++|+.|+|+|+.++....
T Consensus        52 ~~~A~~A~~~l~g~--~~~g~~l~v~~a~~~~~~~   84 (90)
T 2dnq_A           52 KTAAEDAIRNLHHY--KLHGVNINVEASKNKSKAS   84 (90)
T ss_dssp             HHHHHHHHHHHTTC--BCSSCBCEEECSSCCCCCC
T ss_pred             HHHHHHHHHHhcCC--ccCCcEEEEEECCCCCCCC
Confidence            99999999999998  8999999999999877654

>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=99.84  E-value=3.6e-20  Score=115.09  Aligned_cols=79  Identities=19%  Similarity=0.365  Sum_probs=72.1

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||.|.++.++++                                 ++||||+|.+
T Consensus        16 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~---------------------------------~g~afV~f~~   62 (97)
T 1why_A           16 PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG---------------------------------DSFAYIQYES   62 (97)
T ss_dssp             CCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS---------------------------------SCCEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC---------------------------------CCEEEEEECC
Confidence            3579999999999999999999999999999988632                                 7899999999


Q ss_pred             HHhHHHHHHHHhCCcceec--CcEEEEEecCCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVW--GCDIIVDWADPQEEP  116 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~--g~~l~v~~a~~~~~~  116 (131)
                      .++|.+|++.|++.  .++  |+.|+|+|+.++...
T Consensus        63 ~~~A~~A~~~l~g~--~~~~~g~~l~V~~a~~~~~~   96 (97)
T 1why_A           63 LDAAQAACAKMRGF--PLGGPDRRLRVDFAKSGPSS   96 (97)
T ss_dssp             HHHHHHHHHHHTTC--BCSSSSCBCEEEECCCCCCC
T ss_pred             HHHHHHHHHHHCCC--EeCCCCcEEEEEECCCCCCC
Confidence            99999999999998  778  999999999987654

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.84  E-value=7.4e-21  Score=128.20  Aligned_cols=83  Identities=19%  Similarity=0.249  Sum_probs=75.0

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccC--CeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEe
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYG--RVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEY   80 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G--~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f   80 (131)
                      ..++|||||||+++++++|+++|++||  .|.+++++++                           ..+|.++|||||+|
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d---------------------------~~tg~skGfaFV~f  106 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAEN---------------------------RANGQSKGYAEVVV  106 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEEC---------------------------TTTCCEEEEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEec---------------------------CCCCccceEEEEEE
Confidence            357999999999999999999999999  9999998854                           34788999999999


Q ss_pred             CCHHhHHHHHHHHhCCcceecCcEEEEEecCCCC
Q psy1185          81 DSHKSASLAKKRLATGRLKVWGCDIIVDWADPQE  114 (131)
Q Consensus        81 ~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~  114 (131)
                      .+.++|.+|+..|+|.  .++|+.|.|.+|.++.
T Consensus       107 ~~~~~A~~Ai~~lng~--~~~Gr~l~V~~a~~~~  138 (156)
T 3n9u_C          107 ASENSVHKLLELLPGK--VLNGEKVDVRPATRQN  138 (156)
T ss_dssp             SCHHHHHHHHHHSTTC--EETTEECEEEECCHHH
T ss_pred             CCHHHHHHHHHHcCCC--EECCeEeEEEEcCCCc
Confidence            9999999999999998  8999999999998654

>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=99.84  E-value=3.5e-20  Score=114.51  Aligned_cols=80  Identities=29%  Similarity=0.345  Sum_probs=73.4

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||.|.++++++.                            ..+.+++||||+|.+
T Consensus        15 ~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~----------------------------~~g~~~g~afV~f~~   66 (95)
T 2ywk_A           15 ADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKD----------------------------REGKPKSFGFVCFKH   66 (95)
T ss_dssp             GGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEEC----------------------------TTSCEEEEEEEEESS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEEC----------------------------CCCCCceEEEEEECC
Confidence            3679999999999999999999999999999998853                            247789999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADP  112 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~  112 (131)
                      .++|.+|+..|++.  .++|+.|.|+||++
T Consensus        67 ~~~a~~A~~~l~g~--~~~g~~l~V~~a~~   94 (95)
T 2ywk_A           67 PESVSYAIALLNGI--RLYGRPINVSGPSS   94 (95)
T ss_dssp             THHHHHHHHHHTTC--EETTEECEEECCCC
T ss_pred             HHHHHHHHHHhCCC--EECCCEEEEEEcCC
Confidence            99999999999998  89999999999875

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.84  E-value=4.4e-20  Score=115.90  Aligned_cols=84  Identities=23%  Similarity=0.391  Sum_probs=75.7

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++|| |.++++++.                           ..++.++|||||+|.+
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~---------------------------~~~g~~~g~afV~f~~   65 (103)
T 2dng_A           14 PPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRD---------------------------KDTDKFKGFCYVEFDE   65 (103)
T ss_dssp             SCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEEC---------------------------SSSCSEEEEEEEEESS
T ss_pred             CCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeec---------------------------CCCCccceEEEEEECC
Confidence            468999999999999999999999997 999998854                           3467889999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      .++|.+|+ .|++.  .++|+.|.|.|+.++....
T Consensus        66 ~~~a~~A~-~l~g~--~~~g~~l~V~~a~~~~~~~   97 (103)
T 2dng_A           66 VDSLKEAL-TYDGA--LLGDRSLRVDIAEGRKQDK   97 (103)
T ss_dssp             HHHHHHHG-GGTTC--EETTEECEEEECCCCCCCC
T ss_pred             HHHHHHHH-hhCCC--eECCeEEEEEEecCCCCCC
Confidence            99999999 89998  8999999999999877654

>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=99.84  E-value=4.8e-20  Score=123.68  Aligned_cols=86  Identities=33%  Similarity=0.459  Sum_probs=77.7

Q ss_pred             CCceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeC
Q psy1185           2 SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYD   81 (131)
Q Consensus         2 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~   81 (131)
                      +..++|||+|||.++++++|+++|++||.|.++.++..                           ..++.+++||||+|.
T Consensus        37 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~---------------------------~~~~~~~g~afV~f~   89 (156)
T 1h2v_Z           37 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLD---------------------------KMKKTACGFCFVEYY   89 (156)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEC---------------------------TTTCCEEEEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEec---------------------------CCCCccceEEEEEEC
Confidence            45789999999999999999999999999999998854                           336778999999999


Q ss_pred             CHHhHHHHHHHHhCCcceecCcEEEEEecCCCCCC
Q psy1185          82 SHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEP  116 (131)
Q Consensus        82 ~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~  116 (131)
                      +.++|.+|+..|++.  .++|+.|.|.||.+..+.
T Consensus        90 ~~~~A~~Ai~~l~g~--~~~g~~l~V~~a~~~~~~  122 (156)
T 1h2v_Z           90 SRADAENAMRYINGT--RLDDRIIRTDWDAGFKEG  122 (156)
T ss_dssp             SHHHHHHHHHHTTTS--EETTEECEEEEESCCCTT
T ss_pred             CHHHHHHHHHHhCCC--EECCeEEEEEECCCCCCc
Confidence            999999999999998  899999999999876653

>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=99.84  E-value=3e-20  Score=120.48  Aligned_cols=86  Identities=26%  Similarity=0.469  Sum_probs=77.5

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||.|.++.++..                           ..++.++|||||+|.+
T Consensus        21 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~---------------------------~~~~~~~g~afV~f~~   73 (126)
T 3ex7_B           21 EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLD---------------------------RRTGYLKGYTLVEYET   73 (126)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBC---------------------------TTTSSBCSCEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEec---------------------------CCCCccceEEEEEECC
Confidence            4679999999999999999999999999999988753                           3478889999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      .++|.+|+..|++.  .++|+.|.|.||.++..+.
T Consensus        74 ~~~a~~A~~~l~g~--~~~g~~l~v~~a~~~~~~~  106 (126)
T 3ex7_B           74 YKEAQAAMEGLNGQ--DLMGQPISVDWCFVRGPPK  106 (126)
T ss_dssp             HHHHHHHHHHHTTC--BSSSSBCEEEESEESSSCC
T ss_pred             HHHHHHHHHHhCCC--eeCCeEEEEEEecCCCCCC
Confidence            99999999999998  8899999999998766544

>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=99.83  E-value=5e-20  Score=134.22  Aligned_cols=109  Identities=15%  Similarity=0.289  Sum_probs=88.9

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccC-CeeEEEEe-------cCeEEEEECCHHHHHhh--------------------
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYG-RVERVKRI-------KDYAFVHFEDRQEAITV--------------------   54 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G-~v~~~~i~-------~~~~fv~~~~~~~a~~~--------------------   54 (131)
                      ..++|||+|||.++++++|+++|++|| .|..+.++       +|||||+|.+.++|..+                    
T Consensus       116 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~  195 (292)
T 2ghp_A          116 TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSN  195 (292)
T ss_dssp             CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECC
Confidence            468999999999999999999999999 99999986       69999999999999981                    


Q ss_pred             ---------------------------------------cC-CceeEEecCCCCCCCCcceEEEEeCCHHhHHHHHHHHh
Q psy1185          55 ---------------------------------------TG-LSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLA   94 (131)
Q Consensus        55 ---------------------------------------~g-~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~   94 (131)
                                                             +| +..+.+..+...+|.++|+|||+|.+.++|.+|+ .|+
T Consensus       196 ~~~~~~~~~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~  274 (292)
T 2ghp_A          196 PLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMN  274 (292)
T ss_dssp             CC---------CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGT
T ss_pred             CCcccccccccCCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-Hhc
Confidence                                                   11 1111111111113788999999999999999999 999


Q ss_pred             CCcceecCcEEEEEecCCCC
Q psy1185          95 TGRLKVWGCDIIVDWADPQE  114 (131)
Q Consensus        95 ~~~~~~~g~~l~v~~a~~~~  114 (131)
                      |.  .++|+.|.|.||.+++
T Consensus       275 g~--~~~g~~i~V~~a~~k~  292 (292)
T 2ghp_A          275 RS--LLGNREISVSLADKKP  292 (292)
T ss_dssp             TE--EETTEEEEEEECCCCC
T ss_pred             CC--EECCcEEEEEEecCCC
Confidence            98  8999999999999864

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

Probab=99.83  E-value=2.9e-20  Score=122.44  Aligned_cols=86  Identities=26%  Similarity=0.404  Sum_probs=77.8

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||.|.++++++.                           ..++.++|||||+|.+
T Consensus        41 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~---------------------------~~~~~~~g~afV~f~~   93 (139)
T 1u6f_A           41 VLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCD---------------------------RETRQSRGYGFVKFQS   93 (139)
T ss_dssp             TTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEE---------------------------TTTTEEEEEEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEc---------------------------CCCCCcceEEEEEECC
Confidence            3579999999999999999999999999999998854                           3367889999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      .++|.+|+..|++.  .++|+.|+|.||.++..+.
T Consensus        94 ~~~a~~A~~~l~g~--~~~g~~l~v~~a~~~~~~~  126 (139)
T 1u6f_A           94 GSSAQQAIAGLNGF--NILNKRLKVALAASGHQRP  126 (139)
T ss_dssp             HHHHHHHHHHTTTE--ECSSCEEEEEESSCCCCCC
T ss_pred             HHHHHHHHHHhCCC--EECCeEEEEEECCCCCCCC
Confidence            99999999999997  8999999999999877654

>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=99.83  E-value=3.2e-20  Score=124.56  Aligned_cols=85  Identities=31%  Similarity=0.464  Sum_probs=77.9

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .++|||+|||+++++++|+++|++||.|.+++++++                           ..+|.++|||||+|.+.
T Consensus        70 ~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~---------------------------~~~g~~~g~afV~f~~~  122 (158)
T 2kn4_A           70 MTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRD---------------------------RYTKESRGFAFVRFHDK  122 (158)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCC---------------------------SSCTTSCCEEEEEESBH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeec---------------------------CCCCccceEEEEEECCH
Confidence            579999999999999999999999999999998854                           34788999999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      ++|.+|+..|+|.  .++|+.|.|.||.++.++.
T Consensus       123 ~~a~~A~~~l~g~--~~~g~~l~v~~a~~~~~~~  154 (158)
T 2kn4_A          123 RDAEDAMDAMDGA--VLDGRELRVQMARYGRPPD  154 (158)
T ss_dssp             HHHHHHHHHSTTE--ESSSSEEEEEEECCSSCCC
T ss_pred             HHHHHHHHHhCCC--EECCeEEEEEECCCCCCCC
Confidence            9999999999998  8999999999999876654

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.83  E-value=3.4e-20  Score=117.87  Aligned_cols=84  Identities=21%  Similarity=0.294  Sum_probs=74.5

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||.|.+++++++                           ..+|.++|||||+|.+
T Consensus        24 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~---------------------------~~tg~~kg~afV~f~~   76 (109)
T 2rs2_A           24 SGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRD---------------------------PLTKRSRGFGFVTFMD   76 (109)
T ss_dssp             --CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCC---------------------------TTTCCCTTCEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEEC---------------------------CCCCCcCcEEEEEECC
Confidence            3679999999999999999999999999999998854                           3468899999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEEP  116 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~  116 (131)
                      .++|.+|+..++ .  .++|+.|.|.++.++...
T Consensus        77 ~~~A~~Ai~~~~-~--~l~g~~l~V~~a~~~~~~  107 (109)
T 2rs2_A           77 QAGVDKVLAQSR-H--ELDSKTIDPKVAFPRRAQ  107 (109)
T ss_dssp             HHHHHHHHHSSC-E--EETTEEEEEEECCCCCCC
T ss_pred             HHHHHHHHHHCC-C--cCCCEEEEEEEccCCCCC
Confidence            999999999874 4  899999999999987754

>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=99.83  E-value=6.5e-20  Score=115.68  Aligned_cols=80  Identities=16%  Similarity=0.219  Sum_probs=73.9

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||..+++++|+++|++||.|.++.+++.                            .++.++|||||+|.+
T Consensus        28 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~----------------------------~~g~~~g~afV~f~~   79 (107)
T 3ulh_A           28 TGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD----------------------------RSGRSLGTADVHFER   79 (107)
T ss_dssp             CSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEC----------------------------TTSCEEEEEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC----------------------------CCCCcceEEEEEECC
Confidence            4689999999999999999999999999999998854                            277889999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADP  112 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~  112 (131)
                      .++|.+|+..|++.  .++|+.|.|+||.+
T Consensus        80 ~~~a~~A~~~l~g~--~~~g~~l~V~~a~s  107 (107)
T 3ulh_A           80 KADALKAMKQYNGV--PLDGRPMNIQLVTS  107 (107)
T ss_dssp             HHHHHHHHHHHTTC--EETTEECEEEEECC
T ss_pred             HHHHHHHHHHhCCC--EeCCcEEEEEEeCC
Confidence            99999999999998  89999999999863

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.83  E-value=1.9e-20  Score=117.59  Aligned_cols=85  Identities=18%  Similarity=0.200  Sum_probs=77.1

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhc-cCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQ-YGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYD   81 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~-~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~   81 (131)
                      ..++|||+|||.++++++|+++|++ ||.|.++++++.                           . ++.++|||||+|.
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~---------------------------~-~g~~~g~afV~f~   59 (104)
T 2dhg_A            8 PEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLD---------------------------Q-TGVSKGYGFVKFT   59 (104)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEEC---------------------------T-TCCEEEEEEEEES
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEEC---------------------------C-CCCccceEEEEEC
Confidence            4679999999999999999999999 999999998854                           2 7788999999999


Q ss_pred             CHHhHHHHHHHHhCCcce-ecCcEEEEEecCCCCCCC
Q psy1185          82 SHKSASLAKKRLATGRLK-VWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        82 ~~~~a~~a~~~l~~~~~~-~~g~~l~v~~a~~~~~~~  117 (131)
                      +.++|.+|+..|++.  . ++|+.|.|.|+.++....
T Consensus        60 ~~~~a~~A~~~l~g~--~~~~g~~l~v~~a~~~~~~~   94 (104)
T 2dhg_A           60 DELEQKRALTECQGA--VGLGSKPVRLSVAIPKASRV   94 (104)
T ss_dssp             CHHHHHHHHHHTTTC--CSSSSSCCCCCBCCCCCSCC
T ss_pred             CHHHHHHHHHHccCC--cccCCEeEEEEEccCCCcCC
Confidence            999999999999998  7 899999999998776543

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.83  E-value=2.1e-20  Score=117.89  Aligned_cols=78  Identities=22%  Similarity=0.307  Sum_probs=71.3

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .++|||+|||+++|+++|+++|++||+|.++++++.                           . .+.++|||||+|.+.
T Consensus        11 ~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d---------------------------~-~g~~rG~aFV~F~~~   62 (103)
T 1s79_A           11 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT---------------------------L-HKAFKGSIFVVFDSI   62 (103)
T ss_dssp             GGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECC---------------------------C-TTSCCCEEEEEESSH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEEC---------------------------C-CCCCccEEEEEECCH
Confidence            579999999999999999999999999999998864                           2 388999999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADP  112 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~  112 (131)
                      ++|.+|+. +++.  .++|+.|.|.|+..
T Consensus        63 e~a~~Ai~-~~~~--~~~gr~l~V~~~~~   88 (103)
T 1s79_A           63 ESAKKFVE-TPGQ--KYKETDLLILFKDD   88 (103)
T ss_dssp             HHHHHHHT-SSCC--CCTTTTCEEEEHHH
T ss_pred             HHHHHHHH-cCCC--EECCEEEEEEEchH
Confidence            99999999 8887  89999999999763

>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=99.83  E-value=2.8e-21  Score=118.50  Aligned_cols=84  Identities=36%  Similarity=0.525  Sum_probs=71.5

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .++|||+|||.++++++|+++|++||.|.++.+++.                           ..++.++|||||+|.+.
T Consensus         1 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~---------------------------~~~~~~~g~afV~f~~~   53 (90)
T 2ki2_A            1 MRNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYD---------------------------RETKKPKGFGFVEMQEE   53 (90)
T ss_dssp             CEEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCC---------------------------SSSCCCCEEEEEEECTT
T ss_pred             CcEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEc---------------------------CCCCCcceEEEEEECCH
Confidence            479999999999999999999999999999998854                           34688899999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      + |.+|+..++|.  .++|+.|+|+||.++....
T Consensus        54 ~-a~~a~~~l~g~--~~~g~~l~V~~a~~~~~~~   84 (90)
T 2ki2_A           54 S-VSEAIAKLDNT--DFMGRTIRVTEANPKKSLE   84 (90)
T ss_dssp             H-HHHHHHTSCSS--CCSSSSCSEEEC-------
T ss_pred             H-HHHHHHHhCCC--EECCeEEEEEEcCCCCCCC
Confidence            9 99999999998  8899999999998876543

>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=99.83  E-value=1.4e-20  Score=118.14  Aligned_cols=84  Identities=27%  Similarity=0.446  Sum_probs=76.3

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .++|||+|||.++++++|+++|++||.|.++.+++.                           ..+|.++|||||+|.+.
T Consensus         8 ~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~---------------------------~~~g~~~g~afV~f~~~   60 (104)
T 1p1t_A            8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYD---------------------------RETGKPKGYGFCEYQDQ   60 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEE---------------------------TTTTEEEEEEEEECSCH
T ss_pred             ccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeC---------------------------CCCCccceEEEEEECCH
Confidence            579999999999999999999999999999998853                           33678899999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCCCCCC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADPQEEP  116 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~  116 (131)
                      ++|.+|++.++|.  .++|+.|.|.||.++...
T Consensus        61 ~~a~~A~~~l~g~--~~~g~~l~v~~a~~~~~~   91 (104)
T 1p1t_A           61 ETALSAMRNLNGR--EFSGRALRVDNAASEKNK   91 (104)
T ss_dssp             HHHHHHHHHSSSB--SCSSSCBEEEETTCTTHH
T ss_pred             HHHHHHHHHhCCC--eeCCcEEEEEeCCCccch
Confidence            9999999999998  889999999999986643

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.83  E-value=4.6e-20  Score=118.09  Aligned_cols=84  Identities=25%  Similarity=0.356  Sum_probs=75.3

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||.|.++++++.                           ..++.+++||||+|.+
T Consensus        16 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~---------------------------~~~~~~~g~afV~f~~   68 (116)
T 2cqd_A           16 TFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITD---------------------------RQTGKSRGYGFVTMAD   68 (116)
T ss_dssp             SSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCC---------------------------SSSCCCCSEEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEc---------------------------CCCCccceEEEEEECC
Confidence            4689999999999999999999999999999998854                           3468889999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEEP  116 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~  116 (131)
                      .++|.+|+..+++   .++|+.|.|+||.+...+
T Consensus        69 ~~~a~~Ai~~~~~---~~~g~~l~V~~a~~~~~~   99 (116)
T 2cqd_A           69 RAAAERACKDPNP---IIDGRKANVNLAYLGAKP   99 (116)
T ss_dssp             HHHHHHHHTCSSC---EETTEECEEEESTTTCCC
T ss_pred             HHHHHHHHHhCCC---cCCCEEEEEEEcccCCCc
Confidence            9999999999997   689999999999765443

>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=99.83  E-value=1.2e-20  Score=120.60  Aligned_cols=81  Identities=16%  Similarity=0.239  Sum_probs=72.8

Q ss_pred             CceEEEEeCCCCC-CCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeC
Q psy1185           3 KVKVLYVRNLTQY-CTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYD   81 (131)
Q Consensus         3 ~~~~l~v~nLp~~-~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~   81 (131)
                      ..++|||+|||++ +++++|+++|++||.|.++.+++                                 ++|||||+|.
T Consensus        24 p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~---------------------------------~kg~aFVef~   70 (112)
T 1x4f_A           24 LGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR---------------------------------MKSQAFIEME   70 (112)
T ss_dssp             CCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET---------------------------------TTTEEEEECS
T ss_pred             CCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec---------------------------------CCCEEEEEEC
Confidence            3679999999998 99999999999999999999874                                 3899999999


Q ss_pred             CHHhHHHHHHHHhCCcceecCcEEEEEecCCCCCC
Q psy1185          82 SHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEP  116 (131)
Q Consensus        82 ~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~  116 (131)
                      +.++|.+|++.|++....++|+.|.|+||..+...
T Consensus        71 ~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~~~~~  105 (112)
T 1x4f_A           71 TREDAMAMVDHCLKKALWFQGRCVKVDLSEKYKKL  105 (112)
T ss_dssp             SHHHHHHHHHHHHHSCCCSSSSCCEEEEECSCSSS
T ss_pred             CHHHHHHHHHHhccCCceECCEEEEEEECcccccc
Confidence            99999999999987545799999999999876654

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.83  E-value=8.3e-20  Score=112.42  Aligned_cols=78  Identities=22%  Similarity=0.387  Sum_probs=71.6

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||.|.++.++                                   ++||||+|.+
T Consensus         9 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~-----------------------------------~~~afV~f~~   53 (92)
T 2dgt_A            9 ASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV-----------------------------------KDYAFVHMER   53 (92)
T ss_dssp             SSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEEC-----------------------------------SSEEEEEESC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEE-----------------------------------CCEEEEEECC
Confidence            46899999999999999999999999999999886                                   4589999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      .++|.+|+..|++.  .++|+.|.|+|+.++....
T Consensus        54 ~~~a~~A~~~l~g~--~~~g~~l~V~~a~~~~~~~   86 (92)
T 2dgt_A           54 AEDAVEAIRGLDNT--EFQGKRMHVQLSTSRLRTA   86 (92)
T ss_dssp             HHHHHHHHHHHTTE--EETTEEEEEEESSCCCSCC
T ss_pred             HHHHHHHHHHhCCC--eeCCcEEEEEEccCCCCCC
Confidence            99999999999998  8999999999999876654

>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=99.83  E-value=1.5e-19  Score=127.99  Aligned_cols=109  Identities=28%  Similarity=0.356  Sum_probs=88.5

Q ss_pred             CceEEEEeCCCC-CCCHHHHHHHhhccCCeeEEEEe---cCeEEEEECCHHHHHhhc----C--Cc--------------
Q psy1185           3 KVKVLYVRNLTQ-YCTEEKLKEAFEQYGRVERVKRI---KDYAFVHFEDRQEAITVT----G--LS--------------   58 (131)
Q Consensus         3 ~~~~l~v~nLp~-~~t~~~l~~~F~~~G~v~~~~i~---~~~~fv~~~~~~~a~~~~----g--~~--------------   58 (131)
                      ..++|||+|||. ++++++|+++|++||.|.+++++   +|||||+|.+.++|+.+.    |  +.              
T Consensus        33 ~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~~  112 (229)
T 2adc_A           33 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNV  112 (229)
T ss_dssp             CCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTTSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCCCC
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEecCccc
Confidence            368999999999 99999999999999999999998   799999999999999811    0  00              


Q ss_pred             --------------------------------------eeEEec--CCC------------CC----------CCCcceE
Q psy1185          59 --------------------------------------QVIIYS--SPD------------DN----------KKNRGFC   76 (131)
Q Consensus        59 --------------------------------------~~~~~~--~~~------------~~----------~~~~~~~   76 (131)
                                                            ...+++  .+.            ..          ...+|+|
T Consensus       113 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~g~a  192 (229)
T 2adc_A          113 QLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMA  192 (229)
T ss_dssp             CCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSSTTCE
T ss_pred             cCccccccccccccccccCcccccCCccccccccCCCCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEECCCcEE
Confidence                                                  011211  111            01          2257999


Q ss_pred             EEEeCCHHhHHHHHHHHhCCcceec-CcEEEEEecCCC
Q psy1185          77 FLEYDSHKSASLAKKRLATGRLKVW-GCDIIVDWADPQ  113 (131)
Q Consensus        77 fv~f~~~~~a~~a~~~l~~~~~~~~-g~~l~v~~a~~~  113 (131)
                      ||+|.+.++|.+|+..|+|.  .++ |+.|+|.||+++
T Consensus       193 fV~f~~~~~A~~Ai~~l~g~--~~~~g~~l~v~~a~~~  228 (229)
T 2adc_A          193 LIQMGSVEEAVQALIDLHNH--DLGENHHLRVSFSKST  228 (229)
T ss_dssp             EEEESSHHHHHHHHHHHTTC--BSSSSCBCEEEECSSC
T ss_pred             EEEECCHHHHHHHHHHHCCC--ccCCCCeEEEEEecCC
Confidence            99999999999999999998  778 999999999875

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

Probab=99.83  E-value=7.4e-20  Score=115.98  Aligned_cols=80  Identities=16%  Similarity=0.419  Sum_probs=73.8

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||.|.++.+++.                                 ++||||+|.+
T Consensus        24 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~---------------------------------~g~afV~f~~   70 (109)
T 1x4g_A           24 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE---------------------------------KGYSFVRFST   70 (109)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT---------------------------------TTEEEEEESS
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC---------------------------------CCEEEEEECC
Confidence            4679999999999999999999999999999998742                                 8999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      .++|.+|+..|++.  .++|+.|+|.|++++....
T Consensus        71 ~~~a~~A~~~l~g~--~~~g~~l~v~~a~~~~~~~  103 (109)
T 1x4g_A           71 HESAAHAIVSVNGT--TIEGHVVKCYWGKESPDMT  103 (109)
T ss_dssp             HHHHHHHHHHHTTC--EETTEECEEECCCCCCSSC
T ss_pred             HHHHHHHHHHcCCC--EECCcEEEEEecCCCCCCC
Confidence            99999999999998  8999999999999877654

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.83  E-value=2.5e-20  Score=119.59  Aligned_cols=80  Identities=24%  Similarity=0.300  Sum_probs=72.9

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||.|.++++++.                           ..++.++|||||+|.+
T Consensus        39 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~---------------------------~~~g~~~g~afV~f~~   91 (118)
T 2khc_A           39 EGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFID---------------------------KQTSLSKCFGFVSFDN   91 (118)
T ss_dssp             CSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCC---------------------------SSSSCCCCEEEEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeC---------------------------CCCCCcCcEEEEEECC
Confidence            3589999999999999999999999999999998853                           3467889999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWAD  111 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~  111 (131)
                      .++|.+|++.|++.  .++|+.|+|+|++
T Consensus        92 ~~~A~~A~~~l~g~--~~~g~~l~V~~ak  118 (118)
T 2khc_A           92 PDSAQVAIKAMNGF--QVGTKRLKVQLKK  118 (118)
T ss_dssp             SHHHHHHHHHCCCC--EETTEECCEEEC-
T ss_pred             HHHHHHHHHHcCCC--EECCEEEEEEecC
Confidence            99999999999998  8999999999985

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.83  E-value=4.1e-20  Score=118.10  Aligned_cols=80  Identities=21%  Similarity=0.195  Sum_probs=70.6

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccC-CeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYG-RVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYD   81 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G-~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~   81 (131)
                      ..++|||+|||+++++++|+++|++|| .|..+.+..                               +.++|||||+|.
T Consensus        27 ~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~-------------------------------~~~rGfaFV~F~   75 (111)
T 2jvr_A           27 KRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNT-------------------------------RDFDGTGALEFP   75 (111)
T ss_dssp             CCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSS-------------------------------CSSSCCEEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEc-------------------------------CCCCCEEEEEEC
Confidence            357999999999999999999999999 899988752                               347899999999


Q ss_pred             CHHhHHHHHHHHhCCcceecCcEEEEEecCCCCC
Q psy1185          82 SHKSASLAKKRLATGRLKVWGCDIIVDWADPQEE  115 (131)
Q Consensus        82 ~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~  115 (131)
                      +.++|.+|++.|+|.  .++|+.|.|.++..+++
T Consensus        76 ~~e~A~~Ai~~lng~--~l~Gr~i~V~~a~~~p~  107 (111)
T 2jvr_A           76 SEEILVEALERLNNI--EFRGSVITVERDDNPPP  107 (111)
T ss_dssp             SHHHHHHHHHHTTTE--EETTEEEEEEESCC---
T ss_pred             CHHHHHHHHHHcCCC--EECCeEEEEEECCCCCC
Confidence            999999999999998  89999999999986543

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.83  E-value=2.9e-20  Score=117.35  Aligned_cols=80  Identities=23%  Similarity=0.276  Sum_probs=73.2

Q ss_pred             ceEEEEeCCCCCC------CHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEE
Q psy1185           4 VKVLYVRNLTQYC------TEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCF   77 (131)
Q Consensus         4 ~~~l~v~nLp~~~------t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~f   77 (131)
                      .++|||+|||+.+      ++++|+++|++||.|.++.+++                             .+|.++||||
T Consensus        15 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~-----------------------------~~g~~~G~af   65 (105)
T 2nlw_A           15 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE-----------------------------EDGKTKGYIF   65 (105)
T ss_dssp             CSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCC-----------------------------BTTBSCCEEE
T ss_pred             CCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeC-----------------------------CCCCeeeEEE
Confidence            5799999999999      7899999999999999998873                             3788999999


Q ss_pred             EEeCCHHhHHHHHHHHhCCcceecCc-EEEEEecCCCC
Q psy1185          78 LEYDSHKSASLAKKRLATGRLKVWGC-DIIVDWADPQE  114 (131)
Q Consensus        78 v~f~~~~~a~~a~~~l~~~~~~~~g~-~l~v~~a~~~~  114 (131)
                      |+|.+.++|.+|+..|+|.  .++|+ .|+|.||....
T Consensus        66 V~f~~~~~A~~Ai~~l~g~--~~~g~~~l~V~~a~~~~  101 (105)
T 2nlw_A           66 LEYASPAHAVDAVKNADGY--KLDKQHTFRVNLFTDFD  101 (105)
T ss_dssp             EEECSSSHHHHHHHHCSSE--ECSTTCEEEEECSCCCC
T ss_pred             EEECCHHHHHHHHHHhCCc--ccCCCceEEEEEcchHh
Confidence            9999999999999999998  89998 99999997654

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.83  E-value=1.1e-19  Score=117.56  Aligned_cols=86  Identities=16%  Similarity=0.207  Sum_probs=77.5

Q ss_pred             CCceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeC
Q psy1185           2 SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYD   81 (131)
Q Consensus         2 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~   81 (131)
                      +..++|||+|||.++++++|+++|++||.|.++++++.                            .+|.++|||||+|.
T Consensus        33 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~----------------------------~~g~~~g~afV~f~   84 (124)
T 2kt5_A           33 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD----------------------------RSGRSLGTADVHFE   84 (124)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECC----------------------------SSSSCCSEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEC----------------------------CCCCEeeEEEEEEC
Confidence            34689999999999999999999999999999998854                            26788999999999


Q ss_pred             CHHhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          82 SHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        82 ~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      +.++|.+|+..+++.  .++|+.|.|+||.+.....
T Consensus        85 ~~~~A~~Ai~~l~g~--~~~g~~l~V~~a~~~~~~~  118 (124)
T 2kt5_A           85 RRADALKAMKQYKGV--PLDGRPMDIQLVASQIDLE  118 (124)
T ss_dssp             SHHHHHHHHHHHTTE--ESSSCEEEEEEECCTTCCC
T ss_pred             CHHHHHHHHHHcCCC--EECCcEEEEEEeCCCCCCC
Confidence            999999999999998  8999999999998766543

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

Probab=99.83  E-value=3.7e-20  Score=115.76  Aligned_cols=76  Identities=26%  Similarity=0.580  Sum_probs=70.7

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||.|.++++.+                                 ++|||||+|.+
T Consensus        26 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~---------------------------------~~g~afV~f~~   72 (101)
T 2la4_A           26 RVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYP---------------------------------EKGCCFIKYDT   72 (101)
T ss_dssp             SCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEET---------------------------------TTTEEEEECSS
T ss_pred             CCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEec---------------------------------CCCEEEEEECC
Confidence            368999999999999999999999999999998863                                 48999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQ  113 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~  113 (131)
                      .++|.+|+..|++.  .++|+.|+|.||+++
T Consensus        73 ~~~A~~Ai~~l~g~--~~~g~~l~V~~a~~~  101 (101)
T 2la4_A           73 HEQAAVCIVALANF--PFQGRNLRTGWGKER  101 (101)
T ss_dssp             HHHHHHHHHHHTTC--EETTEECCCCBCCCC
T ss_pred             HHHHHHHHHHhCCC--eECCeEEEEEeccCC
Confidence            99999999999998  899999999999874

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.83  E-value=8.9e-20  Score=111.85  Aligned_cols=78  Identities=23%  Similarity=0.412  Sum_probs=71.5

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||.|.++.++                                   ++||||+|.+
T Consensus         8 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~-----------------------------------~~~afV~f~~   52 (90)
T 2dnp_A            8 NTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV-----------------------------------KDYAFVHMEK   52 (90)
T ss_dssp             CSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEEC-----------------------------------SSCEEEEESC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEE-----------------------------------CCEEEEEECC
Confidence            46899999999999999999999999999999886                                   4589999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      .++|.+|+..|++.  .++|+.|.|.|+.++....
T Consensus        53 ~~~a~~A~~~l~g~--~~~g~~l~v~~a~~~~~~~   85 (90)
T 2dnp_A           53 EADAKAAIAQLNGK--EVKGKRINVELSTKGQKKS   85 (90)
T ss_dssp             HHHHHHHHHHHTTC--EETTEECEEEESCCCCCCC
T ss_pred             HHHHHHHHHHhCCC--EECCcEEEEEECCCCCCCC
Confidence            99999999999998  8999999999999876543

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.83  E-value=2.2e-20  Score=117.54  Aligned_cols=85  Identities=24%  Similarity=0.359  Sum_probs=76.7

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||+++++++|+++|++||.|.++.+++.                           ..++.++|||||+|.+
T Consensus        15 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~---------------------------~~~g~~~g~afV~f~~   67 (105)
T 2dh8_A           15 EIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKD---------------------------KTTNQSRGFGFVKFKD   67 (105)
T ss_dssp             SSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEEC---------------------------SSSCCEEEEEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---------------------------CCCCCcceEEEEEECC
Confidence            4689999999999999999999999999999998853                           3467889999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      .++|.+|+.. ++.  .++|+.|.|.|+.++.+..
T Consensus        68 ~~~a~~a~~~-~~~--~~~g~~l~V~~a~~~~~~~   99 (105)
T 2dh8_A           68 PNCVGTVLAS-RPH--TLDGRNIDPKPCTPRGMQP   99 (105)
T ss_dssp             TTHHHHHHHH-CSE--EETTEEEBCCCSCCSSCCT
T ss_pred             HHHHHHHHHh-CCC--eECCEEEEEEEccCCCCCC
Confidence            9999999999 886  9999999999999877654

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.83  E-value=5.6e-20  Score=112.25  Aligned_cols=72  Identities=19%  Similarity=0.231  Sum_probs=68.1

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      +.-||||||++.+|+++|+++|.+||+|.++++..                                 ++|||||+|.+.
T Consensus         7 ~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~---------------------------------~kGfaFVey~~~   53 (89)
T 2wbr_A            7 SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL---------------------------------NQGIALCKYTTR   53 (89)
T ss_dssp             CCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET---------------------------------TTTEEEEEESSH
T ss_pred             cceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC---------------------------------CCcEEEEEECCH
Confidence            45799999999999999999999999999998862                                 599999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEec
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWA  110 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a  110 (131)
                      ++|.+|++.||+.  .++|+.|+|++|
T Consensus        54 ~eA~~Ai~~Ln~~--~l~gr~I~V~~A   78 (89)
T 2wbr_A           54 EEANKAQMALNNC--VLANTTIFAESP   78 (89)
T ss_dssp             HHHHHHHHHHTTE--EETTEEEEEECC
T ss_pred             HHHHHHHHHhcCC--EECCcEEEEEEC
Confidence            9999999999997  999999999999

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

Probab=99.83  E-value=1.1e-19  Score=115.79  Aligned_cols=83  Identities=22%  Similarity=0.254  Sum_probs=75.2

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .++|||+|||.++++++|+++|++||.|.++.+++.                            .++.+++||||+|.+.
T Consensus        15 ~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~----------------------------~~g~~~g~afV~f~~~   66 (114)
T 2do0_A           15 GSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILED----------------------------KDGKSRGIGTVTFEQS   66 (114)
T ss_dssp             CSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEEC----------------------------TTCSEEEEEEEEESSH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC----------------------------CCCCeeeEEEEEECCH
Confidence            579999999999999999999999999999988853                            2578899999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCCCCCC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADPQEEP  116 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~  116 (131)
                      ++|.+|+..|++.  .++|+.|.|.|++...+.
T Consensus        67 ~~a~~A~~~l~g~--~~~g~~l~v~~a~~~~~~   97 (114)
T 2do0_A           67 IEAVQAISMFNGQ--LLFDRPMHVKMDERALPK   97 (114)
T ss_dssp             HHHHHHHHHHTTC--EETTEECEEEECSCCCCC
T ss_pred             HHHHHHHHHhCCC--EeCCCEEEEEEcccCCCC
Confidence            9999999999998  899999999999865443

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

Probab=99.83  E-value=3.7e-20  Score=115.09  Aligned_cols=78  Identities=24%  Similarity=0.261  Sum_probs=70.7

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .++|||+|||.++++++|+++|++||.|. +.++.                               +.++|||||+|.+.
T Consensus        19 ~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~-------------------------------~~~~g~afV~f~~~   66 (97)
T 2e5j_A           19 AADVYVGNLPRDARVSDLKRALRELGSVP-LRLTW-------------------------------QGPRRRAFLHYPDS   66 (97)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEE-------------------------------ETTTTEEEEECSSH
T ss_pred             CCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEc-------------------------------CCCCcEEEEEECCH
Confidence            67999999999999999999999999996 55552                               35789999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCCCCC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADPQEE  115 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~  115 (131)
                      ++|.+|+..|++.  .++|+.|.|.|+.++.+
T Consensus        67 ~~a~~A~~~l~g~--~~~g~~l~V~~a~~~~~   96 (97)
T 2e5j_A           67 AAAQQAVSCLQGL--RLGTDTLRVALARQQRD   96 (97)
T ss_dssp             HHHHHHHHHHTTC--CSSSSCCEEEECCCCCC
T ss_pred             HHHHHHHHHhCCC--EECCcEEEEEEcCCCCC
Confidence            9999999999998  88999999999998764

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

Probab=99.83  E-value=5.8e-20  Score=119.97  Aligned_cols=79  Identities=14%  Similarity=0.260  Sum_probs=71.8

Q ss_pred             ceEEEEeCCCCCCCHHHHH----HHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEE
Q psy1185           4 VKVLYVRNLTQYCTEEKLK----EAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLE   79 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~----~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~   79 (131)
                      .++|||+|||+.+++++|+    ++|++||.|.++.+.+                              ++.++|||||+
T Consensus        29 ~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~------------------------------~~~~rG~aFV~   78 (127)
T 2a3j_A           29 SQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL------------------------------SDDNSGKAYIV   78 (127)
T ss_dssp             CSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC------------------------------CCSSCCCEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc------------------------------CCCcCCEEEEE
Confidence            5799999999999999876    6999999999987753                              56789999999


Q ss_pred             eCCHHhHHHHHHHHhCCcceecCcEEEEEecCCCC
Q psy1185          80 YDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQE  114 (131)
Q Consensus        80 f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~  114 (131)
                      |.+.++|..|+..|+|.  .+.|+.|+|.||+++.
T Consensus        79 F~~~~~A~~Ai~~lng~--~l~gr~l~V~~a~~~~  111 (127)
T 2a3j_A           79 FATQESAQAFVEAFQGY--PFQGNPLVITFSETPQ  111 (127)
T ss_dssp             ESSHHHHHHHHHHSTTC--CCTTSCCEEEECCCCC
T ss_pred             ECCHHHHHHHHHHHCCC--EeCCCEEEEEEccCcc
Confidence            99999999999999998  8899999999999765

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.83  E-value=1.4e-19  Score=112.77  Aligned_cols=80  Identities=39%  Similarity=0.586  Sum_probs=72.1

Q ss_pred             CCCceEEEEeCCCCCCCHHHHHHHhhcc--CCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEE
Q psy1185           1 MSKVKVLYVRNLTQYCTEEKLKEAFEQY--GRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFL   78 (131)
Q Consensus         1 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~--G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv   78 (131)
                      |...++|||+|||.++++++|+++|++|  |.|..+.+.                                   ++||||
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~-----------------------------------~g~afV   56 (99)
T 2cpd_A           12 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI-----------------------------------RDYAFV   56 (99)
T ss_dssp             SSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC-----------------------------------SSEEEE
T ss_pred             cCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe-----------------------------------CCeEEE
Confidence            3567899999999999999999999999  899988764                                   679999


Q ss_pred             EeCCHHhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          79 EYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        79 ~f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      +|.+.++|.+|+..|++.  .++|+.|.|.||+++....
T Consensus        57 ~f~~~~~A~~A~~~l~g~--~~~g~~l~v~~a~~~~~~~   93 (99)
T 2cpd_A           57 HFSNREDAVEAMKALNGK--VLDGSPIEVTLAKPVDKDS   93 (99)
T ss_dssp             EESSHHHHHHHHHHHSSE--EETTEEEEEECCCCCCCCC
T ss_pred             EeCCHHHHHHHHHHhCCC--EeCCcEEEEEECCCCCCCC
Confidence            999999999999999998  8999999999999876543

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.82  E-value=1.8e-20  Score=111.21  Aligned_cols=75  Identities=23%  Similarity=0.370  Sum_probs=68.6

Q ss_pred             EEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHHh
Q psy1185           6 VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKS   85 (131)
Q Consensus         6 ~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~~   85 (131)
                      +|||+|||+++++++|+++|++||+|.++.+++.                           ..++.++|||||+|.+.++
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~---------------------------~~~~~~~g~afV~f~~~~~   53 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFD---------------------------KTTNRHRGFGFVTFESEDI   53 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBC---------------------------SSSTTSCBEEEEECSCHHH
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEec---------------------------CCCCCcCcEEEEEECCHHH
Confidence            5899999999999999999999999999988754                           3368889999999999999


Q ss_pred             HHHHHHHHhCCcceecCcEEEEEec
Q psy1185          86 ASLAKKRLATGRLKVWGCDIIVDWA  110 (131)
Q Consensus        86 a~~a~~~l~~~~~~~~g~~l~v~~a  110 (131)
                      |.+|+. +++.  .++|+.|.|+||
T Consensus        54 a~~a~~-~~~~--~~~g~~l~v~~A   75 (75)
T 2mss_A           54 VEKVCE-IHFH--EINNKMVECKKA   75 (75)
T ss_dssp             HHHHHS-SSCC--CSSSCCCEEECC
T ss_pred             HHHHHH-CCCC--EECCEEEEEEeC
Confidence            999998 8988  899999999986

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.82  E-value=6.8e-20  Score=117.30  Aligned_cols=84  Identities=25%  Similarity=0.404  Sum_probs=76.1

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .++|||+|||.++++++|+++|++||.|..+.+++.                           ..++.++|||||+|.+.
T Consensus        27 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~---------------------------~~~g~~~g~afV~f~~~   79 (116)
T 1x4b_A           27 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRD---------------------------PASKRSRGFGFVTFSSM   79 (116)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECC---------------------------TTTSSCCSEEEEECSSH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEEC---------------------------CCCCCcCceEEEEeCCH
Confidence            479999999999999999999999999999998854                           34688899999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      ++|.+|+.. ++.  .++|+.|.|.|+.++.+..
T Consensus        80 ~~a~~Ai~~-~~~--~~~g~~l~V~~a~~~~~~~  110 (116)
T 1x4b_A           80 AEVDAAMAA-RPH--SIDGRVVEPKRAVAREESG  110 (116)
T ss_dssp             HHHHHHHTS-CSE--EETTEEEEEECCSSCCCCC
T ss_pred             HHHHHHHHh-CCc--EECCEEEEEEECCCCccCC
Confidence            999999998 776  8999999999999887654

>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=99.82  E-value=3.5e-20  Score=114.91  Aligned_cols=81  Identities=19%  Similarity=0.365  Sum_probs=73.7

Q ss_pred             CceEEEEeCCCCCCCHHHHH----HHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEE
Q psy1185           3 KVKVLYVRNLTQYCTEEKLK----EAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFL   78 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~----~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv   78 (131)
                      ..++|||+|||.++++++|+    ++|++||.|.++.+++                              ++.++|||||
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~------------------------------~~~~~g~afV   56 (97)
T 1nu4_A            7 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR------------------------------SLKMRGQAFV   56 (97)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH------------------------------HHHHTTCEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc------------------------------CCCcCcEEEE
Confidence            46899999999999999999    9999999999998763                              3567899999


Q ss_pred             EeCCHHhHHHHHHHHhCCcceecCcEEEEEecCCCCC
Q psy1185          79 EYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEE  115 (131)
Q Consensus        79 ~f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~  115 (131)
                      +|.+.++|.+|+..|+|.  .++|+.|.|.|+.++.+
T Consensus        57 ~f~~~~~A~~A~~~l~g~--~~~g~~l~v~~a~~~~~   91 (97)
T 1nu4_A           57 IFKEVSSATNALRSMQGF--PFYDKPMRIQYAKTDSD   91 (97)
T ss_dssp             EESSHHHHHHHHHHHTTC--EETTEECEEEECSSCCT
T ss_pred             EeCCHHHHHHHHHHhCCC--EECCcEEEEEEccCCCc
Confidence            999999999999999998  88999999999998653

>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=99.82  E-value=7.4e-20  Score=111.42  Aligned_cols=78  Identities=21%  Similarity=0.303  Sum_probs=70.2

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||.|.++++++.                           ..++.++|||||+|.+
T Consensus        10 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~---------------------------~~~g~~~g~afV~f~~   62 (87)
T 3s7r_A           10 DAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMD---------------------------PNTGRSRGFGFILFKD   62 (87)
T ss_dssp             CTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEEC---------------------------TTTCCEEEEEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeec---------------------------CCCCccccEEEEEECC
Confidence            4679999999999999999999999999999998854                           3468889999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEec
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWA  110 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a  110 (131)
                      .++|.+|+.. ++.  .++|+.|.|++|
T Consensus        63 ~~~a~~A~~~-~~~--~~~g~~i~v~~A   87 (87)
T 3s7r_A           63 AASVEKVLDQ-KEH--RLDGRVIDPKKA   87 (87)
T ss_dssp             THHHHHHHHS-SCE--EETTEEEEEEEC
T ss_pred             HHHHHHHHHh-CCC--EECCEEEEEEeC
Confidence            9999999965 665  799999999986

>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=99.82  E-value=1.5e-20  Score=117.64  Aligned_cols=81  Identities=25%  Similarity=0.323  Sum_probs=72.7

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCC-CCCCCcceEEEEeC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPD-DNKKNRGFCFLEYD   81 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~-~~~~~~~~~fv~f~   81 (131)
                      ..++|||+|||.++++++|+++|++|| |.++++++.                           . .+|.++|||||+|.
T Consensus        18 ~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~---------------------------~~~~g~~~g~afV~f~   69 (100)
T 2j76_E           18 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPRE---------------------------PSNPERLKGFGYAEFE   69 (100)
T ss_dssp             --CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCC---------------------------TTTTCCCCSCEEEEEC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEec---------------------------CCcCCccCeEEEEEEC
Confidence            468999999999999999999999999 999988753                           2 36888999999999


Q ss_pred             CHHhHHHHHHHHhCCcceecCcEEEEEecCCCC
Q psy1185          82 SHKSASLAKKRLATGRLKVWGCDIIVDWADPQE  114 (131)
Q Consensus        82 ~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~  114 (131)
                      +.++|.+|+ .++|.  .++|+.|.|+||.++.
T Consensus        70 ~~~~a~~Ai-~l~g~--~~~g~~l~V~~a~~~~   99 (100)
T 2j76_E           70 DLDSLLSAL-SLNEE--SLGNRRIRVDVADQAQ   99 (100)
T ss_dssp             CHHHHHHHH-HTTTC--CBTTBCCCCEECCCSC
T ss_pred             CHHHHHHHH-hcCCC--EECCeEEEEEeccCCC
Confidence            999999999 99998  8999999999998865

>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=99.82  E-value=7.3e-20  Score=114.09  Aligned_cols=80  Identities=29%  Similarity=0.436  Sum_probs=73.2

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||.|..+++++                                 +++||||+|.+
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~---------------------------------~kg~afV~f~~   60 (99)
T 2cpj_A           14 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHK---------------------------------DKGFGFIRLET   60 (99)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEET---------------------------------TTTEEEEECSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEec---------------------------------CCCEEEEEECC
Confidence            467999999999999999999999999999998874                                 37999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      .++|.+|++.|++.  .++|+.|.|.|+.++....
T Consensus        61 ~~~a~~a~~~l~g~--~~~g~~l~v~~a~~~~~~~   93 (99)
T 2cpj_A           61 RTLAEIAKVELDNM--PLRGKQLRVRFACHSASLT   93 (99)
T ss_dssp             SHHHHHHHHHHTTC--CBTTBCCEEEESSCCSCCC
T ss_pred             HHHHHHHHHHhCCC--EeCCceEEEEEcCCCCCCC
Confidence            99999999999998  8899999999999876543

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

Probab=99.82  E-value=2.7e-20  Score=115.72  Aligned_cols=83  Identities=12%  Similarity=0.160  Sum_probs=73.7

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||.|..+.++..                           ..++.++|||||+|.+
T Consensus        14 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~---------------------------~~~g~~~g~afV~f~~   66 (98)
T 2cqp_A           14 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKY---------------------------NEKGMPTGEAMVAFES   66 (98)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEE---------------------------CSSSCEEEEEEEEESC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEE---------------------------CCCCCeeeEEEEEECC
Confidence            4689999999999999999999999999987666532                           3467889999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQE  114 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~  114 (131)
                      .++|.+|++.|++.  .++|+.|+|+|+..+.
T Consensus        67 ~~~a~~Ai~~l~g~--~~~g~~l~V~~a~~~~   96 (98)
T 2cqp_A           67 RDEATAAVIDLNDR--PIGSRKVKLVLGSGPS   96 (98)
T ss_dssp             HHHHHHHHHHTTTC--EETTEECEEEESSCSS
T ss_pred             HHHHHHHHHHhCCC--eeCCeEEEEEEcCCCC
Confidence            99999999999998  8999999999998654

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.82  E-value=1.4e-20  Score=123.16  Aligned_cols=84  Identities=26%  Similarity=0.384  Sum_probs=75.3

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeE--EEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeC
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVER--VKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYD   81 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~--~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~   81 (131)
                      .++|||+|||+++++++|+++|++||.|..  +++++.                           ..+|.++|||||+|.
T Consensus        23 ~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d---------------------------~~tg~~rG~aFV~f~   75 (131)
T 2m2b_A           23 NDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKD---------------------------KQTQLNRGFAFIQLS   75 (131)
T ss_dssp             CCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBC---------------------------SSSSSBCSCEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEc---------------------------CCCCCcceEEEEEEC
Confidence            579999999999999999999999999976  888854                           347889999999999


Q ss_pred             CHHhHHHHHHHHhCC--cceecCcEEEEEecCCCCC
Q psy1185          82 SHKSASLAKKRLATG--RLKVWGCDIIVDWADPQEE  115 (131)
Q Consensus        82 ~~~~a~~a~~~l~~~--~~~~~g~~l~v~~a~~~~~  115 (131)
                      +. +|.+|+..|++.  ++.++|+.|.|+|+.++..
T Consensus        76 ~~-~a~~Ai~~l~g~~~~~~~~gr~l~V~~a~~~~~  110 (131)
T 2m2b_A           76 TI-EAAQLLQILQALHPPLTIDGKTINVEFAKGSKR  110 (131)
T ss_dssp             HH-HHHHHHHHHTTCCCSCCGGGCCCCCEECCCSCC
T ss_pred             CH-HHHHHHHHhcCCCCCccCCCEEEEEEECCCCCC
Confidence            99 999999999996  4478999999999988754

>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=99.82  E-value=1.4e-19  Score=113.49  Aligned_cols=84  Identities=24%  Similarity=0.285  Sum_probs=74.5

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||.|..+++++.                           ..++.++|||||+|.+
T Consensus        14 ~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~---------------------------~~~g~~~g~afV~f~~   66 (103)
T 2cqg_A           14 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKD---------------------------LKTGHSKGFGFVRFTE   66 (103)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEEC---------------------------SSSCSEEEEEEEEESS
T ss_pred             CCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEec---------------------------CCCCCccceEEEEECC
Confidence            4678999999999999999999999999999998854                           3468889999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      .++|.+|+..  +.  .++|+.|.|.|+.++.+..
T Consensus        67 ~~~a~~A~~~--~~--~~~g~~l~v~~a~~~~~~~   97 (103)
T 2cqg_A           67 YETQVKVMSQ--RH--MIDGRWCDCKLPNSKQSQD   97 (103)
T ss_dssp             HHHHHHHHHS--CE--EETTEEEEEECCCTTCCCC
T ss_pred             HHHHHHHHHc--CC--eeCCeEEEEEecCCCCcCC
Confidence            9999999984  54  8999999999999877654

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.82  E-value=1.9e-20  Score=111.45  Aligned_cols=76  Identities=22%  Similarity=0.318  Sum_probs=70.1

Q ss_pred             eEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHH
Q psy1185           5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHK   84 (131)
Q Consensus         5 ~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~   84 (131)
                      ++|||+|||.++++++|+++|++||+|.++.++++                           ..++.++|+|||+|.+.+
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~---------------------------~~~~~~~g~afV~f~~~~   53 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRD---------------------------PLTKRSRGFGFVTFMDQA   53 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECC---------------------------CCSSSCSSEEEECCCCTT
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecC---------------------------CCCCCcCceEEEEEcCHH
Confidence            58999999999999999999999999999998854                           346888999999999999


Q ss_pred             hHHHHHHHHhCCcceecCcEEEEEec
Q psy1185          85 SASLAKKRLATGRLKVWGCDIIVDWA  110 (131)
Q Consensus        85 ~a~~a~~~l~~~~~~~~g~~l~v~~a  110 (131)
                      +|.+|+..++ .  .++|+.|.|+||
T Consensus        54 ~a~~a~~~~~-~--~~~g~~l~v~~a   76 (77)
T 1uaw_A           54 GVDKVLAQSR-H--ELDSKTIDPKVA   76 (77)
T ss_dssp             HHHHHHHTTT-C--CCSSCCCEEEEC
T ss_pred             HHHHHHHhCC-C--ccCCEEEEEEec
Confidence            9999999999 5  899999999997

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

Probab=99.82  E-value=1.3e-20  Score=114.39  Aligned_cols=81  Identities=25%  Similarity=0.348  Sum_probs=73.1

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||+++++++|+++|++||.|.++.++..                           ..++.++|||||+|.+
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~---------------------------~~~~~~~g~afV~f~~   56 (85)
T 1x4e_A            4 GSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILD---------------------------KTTNKCKGYGFVDFDS   56 (85)
T ss_dssp             CCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECC---------------------------SSSCSCCSEEEEEESC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEec---------------------------CCCCCcCcEEEEEECC
Confidence            4689999999999999999999999999999998853                           3468889999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADP  112 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~  112 (131)
                      .++|.+|++.|+|.  .++|+.++++|+.+
T Consensus        57 ~~~a~~A~~~l~g~--~~~g~~~~~~~~~s   84 (85)
T 1x4e_A           57 PSAAQKAVTALKAS--GVQAQMAKQSGPSS   84 (85)
T ss_dssp             HHHHHHHHHHHHHH--TCCEESCCSSCCCC
T ss_pred             HHHHHHHHHHhcCC--eEeeEEEeecCCCC
Confidence            99999999999998  88999998888653

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

Probab=99.82  E-value=2.4e-20  Score=122.81  Aligned_cols=85  Identities=31%  Similarity=0.464  Sum_probs=77.5

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .++|||+|||.++++++|+++|++||.|..+.+++.                           ..++.++|||||+|.+.
T Consensus        47 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~---------------------------~~~g~~~G~afV~F~~~   99 (135)
T 2lea_A           47 MTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRD---------------------------RYTKESRGFAFVRFHDK   99 (135)
T ss_dssp             CCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCC---------------------------SSSSSCCSCCEEECSCH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEec---------------------------CCCCccceEEEEEECCH
Confidence            578999999999999999999999999999988753                           33678899999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      ++|.+|+..|++.  .++|+.|.|+|++++.++.
T Consensus       100 ~~A~~Ai~~l~g~--~i~g~~l~V~~a~~~~~~~  131 (135)
T 2lea_A          100 RDAEDAMDAMDGA--VLDGRELRVQMARYGRPPD  131 (135)
T ss_dssp             HHHHHHHTTTTTC--CSSSSCCEEEECCCCCCCT
T ss_pred             HHHHHHHHHcCCC--EECCEEEEEEECCCCCCCc
Confidence            9999999999998  8899999999999877654

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.82  E-value=8.1e-20  Score=118.14  Aligned_cols=83  Identities=19%  Similarity=0.296  Sum_probs=75.3

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .++|||+|||.++++++|+++|++||.|.++.+++.                           ..++.++|||||+|.+.
T Consensus        36 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~---------------------------~~~~~~~g~afV~f~~~   88 (124)
T 2jwn_A           36 KRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCD---------------------------KFSGHPKGYAYIEFAER   88 (124)
T ss_dssp             HTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEE---------------------------CTTSSCEEEEEEEESSH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEec---------------------------CCCCCcccEEEEEECCH
Confidence            579999999999999999999999999999998853                           34688899999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCCCCCC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADPQEEP  116 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~  116 (131)
                      ++|.+|+ .+++.  .++|+.|.|.|+++..+.
T Consensus        89 ~~a~~A~-~l~g~--~~~g~~l~V~~a~~~~~~  118 (124)
T 2jwn_A           89 NSVDAAV-AMDET--VFRGRTIKVLPKRTNMPG  118 (124)
T ss_dssp             HHHHHHH-TTTTC--EETTEECEEEESSCCCSS
T ss_pred             HHHHHHH-hcCCC--eECCeEEEEEECCCCCCC
Confidence            9999999 89998  899999999999876654

>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=99.82  E-value=4.8e-20  Score=117.65  Aligned_cols=81  Identities=22%  Similarity=0.458  Sum_probs=73.5

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .++|||+|||.++++++|+++|++||.|..+.+++.                           ..++.++|||||+|.+.
T Consensus        25 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~---------------------------~~~g~~~g~afV~f~~~   77 (114)
T 2cq4_A           25 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISD---------------------------RNSRRSKGIAYVEFCEI   77 (114)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCS---------------------------CCSSSCCCCEEEEESCG
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEec---------------------------CCCCccCcEEEEEeCcH
Confidence            479999999999999999999999999999998854                           33578899999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCCCC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADPQE  114 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~  114 (131)
                      ++|.+|+ .+++.  .++|+.|.|.|+.++.
T Consensus        78 ~~a~~A~-~l~g~--~~~g~~l~V~~a~~~~  105 (114)
T 2cq4_A           78 QSVPLAI-GLTGQ--RLLGVPIIVQASQAEK  105 (114)
T ss_dssp             GGHHHHH-HHTTE--EETTEEEEEEEHHHHH
T ss_pred             HHHHHHH-HcCCC--EeCCeEEEEEecCCCc
Confidence            9999999 99998  8999999999987543

>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=99.82  E-value=1.1e-19  Score=123.06  Aligned_cols=86  Identities=26%  Similarity=0.489  Sum_probs=75.9

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .++|||+|||..+++++|+++|++||.|..+.+++.                           ..+|.++|||||+|.+.
T Consensus        72 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~---------------------------~~~g~~~g~afV~f~~~  124 (165)
T 1rk8_A           72 GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLD---------------------------RRTGFSKGYALVEYETH  124 (165)
T ss_dssp             CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEC---------------------------TTTSSEEEEEEEEESSH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEec---------------------------CCCCcEeeEEEEEECCH
Confidence            568999999999999999999999999999998854                           34788899999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCCCCCCCh
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADPQEEPDT  118 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~~  118 (131)
                      ++|.+|+..|+|.  .++|+.|.|.||.++.++..
T Consensus       125 ~~A~~Ai~~l~g~--~~~g~~l~V~~a~~~~~~~~  157 (165)
T 1rk8_A          125 KQALAAKEALNGA--EIMGQTIQVDWCFVKGPKRV  157 (165)
T ss_dssp             HHHHHHHHHHTTC--EETTEECEEEESEECC----
T ss_pred             HHHHHHHHHhCCC--EECCEEEEEEEecCCCCCCC
Confidence            9999999999998  89999999999988776543

>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=99.82  E-value=5.2e-20  Score=117.26  Aligned_cols=87  Identities=15%  Similarity=0.190  Sum_probs=74.8

Q ss_pred             CceEEEEeCCCCCCCHHHHH---HHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEE
Q psy1185           3 KVKVLYVRNLTQYCTEEKLK---EAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLE   79 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~---~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~   79 (131)
                      ..++|||+|||+++++++|+   ++|++||.|.++.+++.-                        ....++.++|||||+
T Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~------------------------~~~~~~~~~G~afV~   69 (111)
T 2cpi_A           14 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNST------------------------SYAGSQGPSASAYVT   69 (111)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCS------------------------SCCSSSCCCEEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCC------------------------CcCccCCCCeEEEEE
Confidence            35789999999999999999   999999999999988430                        001133567999999


Q ss_pred             eCCHHhHHHHHHHHhCCcceecCcEEEEEecCCCCC
Q psy1185          80 YDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEE  115 (131)
Q Consensus        80 f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~  115 (131)
                      |.+.++|.+|+..|++.  .++|+.|+|.||.++..
T Consensus        70 f~~~~~A~~Ai~~lng~--~~~gr~l~V~~a~~k~~  103 (111)
T 2cpi_A           70 YIRSEDALRAIQCVNNV--VVDGRTLKASLGTTKYC  103 (111)
T ss_dssp             ESSHHHHHHHHHHHTTE--EETTEEEEEESCCCCSC
T ss_pred             ECcHHHHHHHHHHhCCC--EECCEEEEEEecccccc
Confidence            99999999999999998  89999999999998764

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.82  E-value=1.2e-19  Score=109.92  Aligned_cols=74  Identities=23%  Similarity=0.476  Sum_probs=68.6

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||.|.++.+++                                 ++|||||+|.+
T Consensus        11 ~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~---------------------------------~kg~afV~f~~   57 (85)
T 2ytc_A           11 TITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQ---------------------------------RQQCAFIQFAT   57 (85)
T ss_dssp             SCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEG---------------------------------GGTEEEEEESS
T ss_pred             CccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEEC---------------------------------CCCEEEEEECC
Confidence            467999999999999999999999999999999874                                 37999999999


Q ss_pred             HHhHHHHHHHH-hCCcceecCcEEEEEecC
Q psy1185          83 HKSASLAKKRL-ATGRLKVWGCDIIVDWAD  111 (131)
Q Consensus        83 ~~~a~~a~~~l-~~~~~~~~g~~l~v~~a~  111 (131)
                      .++|.+|++.| ++.  .++|+.|+|+||+
T Consensus        58 ~~~A~~a~~~l~~~~--~~~g~~l~v~~ak   85 (85)
T 2ytc_A           58 RQAAEVAAEKSFNKL--IVNGRRLNVKWGR   85 (85)
T ss_dssp             HHHHHHHHHTTTTTC--EETTEECCEEECC
T ss_pred             HHHHHHHHHHhcCCe--eECCCEEEEEecC
Confidence            99999999999 877  8999999999985

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.82  E-value=1.7e-19  Score=110.69  Aligned_cols=81  Identities=14%  Similarity=0.207  Sum_probs=74.0

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++| .|.+++++++                            .+|.++|+|||+|.+
T Consensus         9 ~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~----------------------------~~g~~~g~afV~f~~   59 (91)
T 2dgw_A            9 TCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN----------------------------AHGNKTGYIFVDFSN   59 (91)
T ss_dssp             CCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC----------------------------TTSCEEEEEEEECSS
T ss_pred             CccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC----------------------------CCCCCceEEEEEECC
Confidence            46799999999999999999999999 9999988853                            367889999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEE  115 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~  115 (131)
                      .++|.+|+. +++.  .++|+.|.|.+|.++++
T Consensus        60 ~~~a~~A~~-~~g~--~~~gr~i~v~~a~~~~~   89 (91)
T 2dgw_A           60 EEEVKQALK-CNRE--YMGGRYIEVFREKSGPS   89 (91)
T ss_dssp             HHHHHHHHH-SCSE--EETTEEEEEEEESSCCC
T ss_pred             HHHHHHHHH-hCCc--eeCCcEEEEEECCcCCC
Confidence            999999999 9997  89999999999998764

>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=99.82  E-value=4.2e-20  Score=114.18  Aligned_cols=81  Identities=14%  Similarity=0.173  Sum_probs=71.7

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||.|..+.++..                           ..++.+++||||+|.+
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~---------------------------~~~g~~~g~afV~f~~   66 (95)
T 2ek1_A           14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKY---------------------------NEKGMPTGEAMVAFES   66 (95)
T ss_dssp             -CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEE---------------------------CTTSCEEEEEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEe---------------------------CCCCCEeeEEEEEECC
Confidence            3589999999999999999999999999988766632                           3467889999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADP  112 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~  112 (131)
                      +++|.+|++.|++.  .++|+.|+|.++.+
T Consensus        67 ~~~a~~Ai~~l~g~--~~~gr~l~v~~a~s   94 (95)
T 2ek1_A           67 RDEATAAVIDLNDR--PIGSRKVKLSGPSS   94 (95)
T ss_dssp             HHHHHHHHHHHTTC--EETTEECEEECCC-
T ss_pred             HHHHHHHHHHhCCC--eECCcEEEEEeccC
Confidence            99999999999998  89999999999864

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.81  E-value=1.5e-19  Score=124.81  Aligned_cols=109  Identities=27%  Similarity=0.334  Sum_probs=88.1

Q ss_pred             CceEEEEeCCCC-CCCHHHHHHHhhccCCeeEEEEe---cCeEEEEECCHHHHHhhc----C--Cc--------------
Q psy1185           3 KVKVLYVRNLTQ-YCTEEKLKEAFEQYGRVERVKRI---KDYAFVHFEDRQEAITVT----G--LS--------------   58 (131)
Q Consensus         3 ~~~~l~v~nLp~-~~t~~~l~~~F~~~G~v~~~~i~---~~~~fv~~~~~~~a~~~~----g--~~--------------   58 (131)
                      ..++|||+|||. ++++++|+++|++||.|.+++++   +|||||+|.+.++|+.+.    |  +.              
T Consensus         2 ~~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~~~~~   81 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNV   81 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTCSSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECCCCSC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEecCCCc
Confidence            368999999999 99999999999999999999998   799999999999999811    0  00              


Q ss_pred             --------------------------------------eeEEec--CCC--------------C--------CCCCcceE
Q psy1185          59 --------------------------------------QVIIYS--SPD--------------D--------NKKNRGFC   76 (131)
Q Consensus        59 --------------------------------------~~~~~~--~~~--------------~--------~~~~~~~~   76 (131)
                                                            ...+++  .+.              .        ....+|+|
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~~~g~a  161 (198)
T 1qm9_A           82 QLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMA  161 (198)
T ss_dssp             CCSSSSSSSSSCEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESSTTSSCE
T ss_pred             CCCCcCCccccccccccCCchhhccCccccccccCCCCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeCCCcEE
Confidence                                                  111111  110              0        02257999


Q ss_pred             EEEeCCHHhHHHHHHHHhCCcceec-CcEEEEEecCCC
Q psy1185          77 FLEYDSHKSASLAKKRLATGRLKVW-GCDIIVDWADPQ  113 (131)
Q Consensus        77 fv~f~~~~~a~~a~~~l~~~~~~~~-g~~l~v~~a~~~  113 (131)
                      ||+|.+.++|.+|+..|+|.  .++ |+.|+|.|++++
T Consensus       162 fV~f~~~~~A~~A~~~l~g~--~~~~g~~l~v~~a~~~  197 (198)
T 1qm9_A          162 LIQMGSVEEAVQALIDLHNH--DLGENHHLRVSFSKST  197 (198)
T ss_dssp             EEECSSHHHHHHHHHHHTSS--CCSSCCSCCEEEECCC
T ss_pred             EEEeCCHHHHHHHHHHhcCC--ccCCCCeEEEEeeccc
Confidence            99999999999999999998  778 999999999875

>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=99.81  E-value=3.2e-19  Score=111.12  Aligned_cols=75  Identities=20%  Similarity=0.371  Sum_probs=69.4

Q ss_pred             CceEEEEeCCCC-CCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeC
Q psy1185           3 KVKVLYVRNLTQ-YCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYD   81 (131)
Q Consensus         3 ~~~~l~v~nLp~-~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~   81 (131)
                      ..++|||+|||. ++++++|+++|++||.|.++.+.                                   +|||||+|.
T Consensus        21 ~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~-----------------------------------~g~afV~f~   65 (97)
T 2xnq_A           21 MKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-----------------------------------NAFGFIQFD   65 (97)
T ss_dssp             TTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC-----------------------------------SSEEEEEES
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe-----------------------------------CCEEEEEEC
Confidence            478999999998 99999999999999999998764                                   689999999


Q ss_pred             CHHhHHHHHHHHhCCcceecCcEEEEEecCCCC
Q psy1185          82 SHKSASLAKKRLATGRLKVWGCDIIVDWADPQE  114 (131)
Q Consensus        82 ~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~  114 (131)
                      +.++|.+|+..++|.  .++|+.|+|+|++++.
T Consensus        66 ~~~~A~~Ai~~l~g~--~~~g~~l~V~~a~~~~   96 (97)
T 2xnq_A           66 NPQSVRDAIEXESQE--MNFGKKLILEVSSSNA   96 (97)
T ss_dssp             SHHHHHHHHHHHTTS--EETTEECEEEECCCCC
T ss_pred             CHHHHHHHHHHcCCC--EECCEEEEEEecCCCC
Confidence            999999999999998  8999999999998754

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} SCOP: d.58.7.1 PDB: 2f9d_A 2f9j_A 2fho_B

Probab=99.81  E-value=1.7e-19  Score=115.24  Aligned_cols=80  Identities=23%  Similarity=0.377  Sum_probs=73.0

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||.|.++.+++                              .+.++|||||+|.+
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~------------------------------~~~~~g~afV~f~~   56 (115)
T 3lqv_A            7 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN------------------------------TPETRGTAYVVYED   56 (115)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEC------------------------------STTTTTCEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEee------------------------------CCCCCcEEEEEECC
Confidence            367999999999999999999999999999999874                              35569999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQE  114 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~  114 (131)
                      .++|.+|+..|+|.  .++|+.|.|.|+.++.
T Consensus        57 ~~~A~~A~~~l~g~--~~~g~~l~v~~a~~~~   86 (115)
T 3lqv_A           57 IFDAKNAVDHLSGF--NVSNRYLVVLYYNANR   86 (115)
T ss_dssp             HHHHHHHHHHHTTC--BSSSCBCEEEECCHHH
T ss_pred             HHHHHHHHHHcCCC--EECCeEEEEEEecCCh
Confidence            99999999999998  8899999999998643

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

Probab=99.81  E-value=1.2e-19  Score=112.62  Aligned_cols=79  Identities=20%  Similarity=0.376  Sum_probs=70.5

Q ss_pred             CceEEEEeCCCC-CCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeC
Q psy1185           3 KVKVLYVRNLTQ-YCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYD   81 (131)
Q Consensus         3 ~~~~l~v~nLp~-~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~   81 (131)
                      ..++|||+|||. ++++++|+++|++||.|.++.+.                                   +|||||+|.
T Consensus         9 ~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~-----------------------------------~g~afV~f~   53 (96)
T 2kvi_A            9 PKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-----------------------------------NAFGFIQFD   53 (96)
T ss_dssp             CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE-----------------------------------TTEEEEEES
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe-----------------------------------CCEEEEEEC
Confidence            478999999998 99999999999999999999875                                   688999999


Q ss_pred             CHHhHHHHHHHHhCCcceecCcEEEEEecCCCCCCCh
Q psy1185          82 SHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPDT  118 (131)
Q Consensus        82 ~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~~  118 (131)
                      +.++|.+|+..|++.  .++|+.|.|.|+.++..+..
T Consensus        54 ~~~~A~~A~~~l~g~--~~~g~~l~V~~a~~~~~~~~   88 (96)
T 2kvi_A           54 NPQSVRDAIECESQE--MNFGKKLILEVSSSNARPQF   88 (96)
T ss_dssp             CHHHHHHHHHHHTCS--SCBTTTBCEEEEECCCC---
T ss_pred             CHHHHHHHHHHcCCC--eeCCcEEEEEEcCcCCCCCC
Confidence            999999999999998  88999999999987766543

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.81  E-value=1.2e-19  Score=113.43  Aligned_cols=78  Identities=24%  Similarity=0.385  Sum_probs=71.7

Q ss_pred             eEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHH
Q psy1185           5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHK   84 (131)
Q Consensus         5 ~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~   84 (131)
                      ++|||+|||.++++++|+++|++||.|.++.+++                               . +++||||+|.+.+
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~-------------------------------~-~~g~afV~f~~~~   48 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIAR-------------------------------N-PPGFAFVEFEDPR   48 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEES-------------------------------S-SSSEEEEECSSHH
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEee-------------------------------C-CCCEEEEEECCHH
Confidence            5899999999999999999999999999998873                               1 6899999999999


Q ss_pred             hHHHHHHHHhCCcceecCcEEEEEecCCCCCC
Q psy1185          85 SASLAKKRLATGRLKVWGCDIIVDWADPQEEP  116 (131)
Q Consensus        85 ~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~  116 (131)
                      +|.+|+..|++.  .++|+.|.|+|+.++...
T Consensus        49 ~a~~A~~~l~g~--~~~g~~l~V~~a~~~~~~   78 (101)
T 2hvz_A           49 DAEDAVRGLDGK--VICGSRVRVELSTGMPRR   78 (101)
T ss_dssp             HHHHHHHHHHHS--CSSSCCCEEEESSSCCCS
T ss_pred             HHHHHHHHHCCC--eECCcEEEEEEccCCCCc
Confidence            999999999998  889999999999876643

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.81  E-value=3.4e-20  Score=111.68  Aligned_cols=73  Identities=25%  Similarity=0.309  Sum_probs=66.5

Q ss_pred             ceEEEEeCCCCCC------CHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEE
Q psy1185           4 VKVLYVRNLTQYC------TEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCF   77 (131)
Q Consensus         4 ~~~l~v~nLp~~~------t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~f   77 (131)
                      .++|||+|||..+      ++++|+++|++||.|.++.+++                             .+|.++||||
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~~-----------------------------~~g~~~g~af   51 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE-----------------------------EDGKTKGYIF   51 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCC-----------------------------BTTBCCCEEE
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecC-----------------------------CCCcEeEEEE
Confidence            4789999999999      7799999999999999998763                             3788999999


Q ss_pred             EEeCCHHhHHHHHHHHhCCcceecCc-EEEE
Q psy1185          78 LEYDSHKSASLAKKRLATGRLKVWGC-DIIV  107 (131)
Q Consensus        78 v~f~~~~~a~~a~~~l~~~~~~~~g~-~l~v  107 (131)
                      |+|.+.++|.+|+..|+|.  .++|+ .|+|
T Consensus        52 V~f~~~~~A~~Ai~~lng~--~~~g~~~l~V   80 (81)
T 2krb_A           52 LEYASPAHAVDAVKNADGY--KLDKQHTFRV   80 (81)
T ss_dssp             EEESSHHHHHHHHTTSSSC--CCSSSSCCCC
T ss_pred             EEECCHHHHHHHHHHhcCc--ccCCceeEEe
Confidence            9999999999999999998  88998 7776

>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=99.81  E-value=1.6e-19  Score=115.06  Aligned_cols=76  Identities=21%  Similarity=0.288  Sum_probs=69.8

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .++|||+|||.++++++|+++|++||.|..+.+++                                 +++||||+|.+.
T Consensus        10 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~---------------------------------~~g~afV~f~~~   56 (111)
T 1whx_A           10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE---------------------------------GGITAIVEFLEP   56 (111)
T ss_dssp             EEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS---------------------------------SSSCEEEEESCH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC---------------------------------CCCEEEEEeCCH
Confidence            57999999999999999999999999999988763                                 478999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCCCC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADPQE  114 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~  114 (131)
                      ++|.+|+..|||.  .++|+.|.|.||....
T Consensus        57 ~~A~~Ai~~l~g~--~~~g~~l~V~~a~~~~   85 (111)
T 1whx_A           57 LEARKAFRHLAYS--KFHHVPLYLEWAPIGV   85 (111)
T ss_dssp             HHHHHHHHHHTTC--BSSSSBCEEEEEETTT
T ss_pred             HHHHHHHHHhCCC--EECCeEEEEEECCCCc
Confidence            9999999999998  8899999999997543

>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=99.81  E-value=1.2e-19  Score=111.78  Aligned_cols=79  Identities=20%  Similarity=0.325  Sum_probs=70.3

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCC-eeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGR-VERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYD   81 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~-v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~   81 (131)
                      ..++|||+|||.++++++|+++|++||. |..+.+.                                  +++||||+|.
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~----------------------------------~~g~afV~f~   52 (93)
T 2cqh_A            7 GMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL----------------------------------KSGYAFVDYP   52 (93)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE----------------------------------ETTEEEECCS
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc----------------------------------CCCEEEEEEC
Confidence            4689999999999999999999999999 5555443                                  3799999999


Q ss_pred             CHHhHHHHHHHHhC-CcceecCcEEEEEecCCCCCCC
Q psy1185          82 SHKSASLAKKRLAT-GRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        82 ~~~~a~~a~~~l~~-~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      +.++|.+|+..|++ .  .++|+.|.|+|+.++.++.
T Consensus        53 ~~~~A~~A~~~l~g~~--~~~g~~l~v~~a~~~~~~~   87 (93)
T 2cqh_A           53 DQNWAIRAIETLSGKV--ELHGKIMEVDYSVSKKLRS   87 (93)
T ss_dssp             CHHHHHHHHHHHTTTC--EETTEECEEEECCCCCCCC
T ss_pred             CHHHHHHHHHHccCCe--eECCEEEEEEEccCccccC
Confidence            99999999999999 7  8999999999999877654

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.81  E-value=2.6e-19  Score=113.67  Aligned_cols=77  Identities=23%  Similarity=0.378  Sum_probs=70.2

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||.|.++.++                                   +|||||+|.+
T Consensus        30 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~-----------------------------------kg~afV~f~~   74 (108)
T 2jvo_A           30 SNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-----------------------------------NGFAFVEFEE   74 (108)
T ss_dssp             SCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE-----------------------------------TTEEEEECSS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE-----------------------------------CCEEEEEECC
Confidence            36899999999999999999999999999999875                                   6899999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEEP  116 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~  116 (131)
                      .++|.+|+..|+|.  .++|+.|.|.|++++..+
T Consensus        75 ~~~A~~Ai~~l~g~--~~~g~~l~V~~a~~~~~r  106 (108)
T 2jvo_A           75 AESAAKAIEEVHGK--SFANQPLEVVYSKLPAKR  106 (108)
T ss_dssp             HHHHHHHHHHHTTC--EETTEECEEESCSCCC--
T ss_pred             HHHHHHHHHHcCCC--EECCeEEEEEEecCCCCC
Confidence            99999999999998  889999999999987654

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

Probab=99.81  E-value=2e-19  Score=118.24  Aligned_cols=79  Identities=28%  Similarity=0.516  Sum_probs=72.0

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||.|.++++++.                           ..++.++|||||+|.+
T Consensus        62 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~---------------------------~~~~~~~g~afV~f~~  114 (140)
T 2ku7_A           62 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLD---------------------------YETEKHRGFAFVEFEL  114 (140)
T ss_dssp             SCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCC---------------------------TTTCCCCSEEEEEESC
T ss_pred             CCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeec---------------------------CCCCCcCcEEEEEECC
Confidence            4689999999999999999999999999999988753                           3467889999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEec
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWA  110 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a  110 (131)
                      .++|.+|++.|++.  .++|+.|+|+||
T Consensus       115 ~~~a~~A~~~l~g~--~~~g~~l~v~~A  140 (140)
T 2ku7_A          115 AEDAAAAIDNMNES--ELFGRTIRVNLA  140 (140)
T ss_dssp             HHHHHHHHHHSTEE--EETTEEEEEEC-
T ss_pred             HHHHHHHHHHhCCC--EECCEEEEEEeC
Confidence            99999999999997  899999999986

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

Probab=99.81  E-value=1.2e-19  Score=115.86  Aligned_cols=81  Identities=21%  Similarity=0.409  Sum_probs=72.6

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCee----EEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEE
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVE----RVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLE   79 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~----~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~   79 (131)
                      .++|||+|||.++++++|+++|++||.|.    .+++.                               ++.++|||||+
T Consensus        25 ~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~-------------------------------~g~~~g~afV~   73 (115)
T 2cpx_A           25 NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMM-------------------------------TGRMRGQAFIT   73 (115)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEE-------------------------------CSSSCSEEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcC-------------------------------CCccceEEEEE
Confidence            57999999999999999999999999984    44443                               56789999999


Q ss_pred             eCCHHhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          80 YDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        80 f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      |.+.++|.+|+..|++.  .++|+.|.|.||.++..+.
T Consensus        74 f~~~~~a~~Ai~~l~g~--~~~g~~l~v~~a~~~~~~~  109 (115)
T 2cpx_A           74 FPNKEIAWQALHLVNGY--KLYGKILVIEFGKNKKQRS  109 (115)
T ss_dssp             CSSHHHHHHHHHHSTTC--BCSSCBCEEEECCCCSCCC
T ss_pred             ECCHHHHHHHHHHhCCC--EeCCcEEEEEEccCCCCCC
Confidence            99999999999999998  8899999999999877654

>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=99.81  E-value=2.2e-19  Score=114.46  Aligned_cols=82  Identities=17%  Similarity=0.334  Sum_probs=73.8

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||.|.+++++++                           . ++.++|||||+|.+
T Consensus        24 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~---------------------------~-~g~~~g~afV~f~~   75 (114)
T 1x5o_A           24 DPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD---------------------------S-SGTSRGVGFARMES   75 (114)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEEC---------------------------S-SSCEEEEEEEEESC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEEC---------------------------C-CCCcceEEEEEECC
Confidence            3579999999999999999999999999999998854                           2 67889999999999


Q ss_pred             HHhHHHHHHHHhCCccee--------cCcEEEEEecCCCC
Q psy1185          83 HKSASLAKKRLATGRLKV--------WGCDIIVDWADPQE  114 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~--------~g~~l~v~~a~~~~  114 (131)
                      .++|.+|+..|+|.  .+        .++.|.|.||.|+.
T Consensus        76 ~~~a~~A~~~l~g~--~~~~~~~~~~~~~~l~v~~a~p~~  113 (114)
T 1x5o_A           76 TEKCEAVIGHFNGK--FIKTPPGVSAPTEPLLCKFSGPSS  113 (114)
T ss_dssp             HHHHHHHHHHHBTC--CCCCCTTSCCCSSCBEEEECCCSC
T ss_pred             HHHHHHHHHHhCCC--EEcCCccccCCCCceeEEccCCCC
Confidence            99999999999998  56        58889999999753

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus}

Probab=99.80  E-value=5e-19  Score=108.67  Aligned_cols=76  Identities=29%  Similarity=0.401  Sum_probs=64.5

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .++|||||||+++++++|+++|++||.|.++++++                                .++|||||+|.+.
T Consensus        11 ~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~--------------------------------~srGfaFV~F~~~   58 (89)
T 3d2w_A           11 GSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPK--------------------------------PFRAFAFVTFADD   58 (89)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCS--------------------------------SCCSEEEEEESCH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEee--------------------------------CCCCEEEEEECCH
Confidence            57999999999999999999999999999998873                                2689999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCCCCC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADPQEE  115 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~  115 (131)
                      ++|.    .+++..+.+.|+.|.|.+|.++.+
T Consensus        59 ~~A~----~~~~~~~~~~g~~v~v~~a~~k~~   86 (89)
T 3d2w_A           59 KVAQ----SLCGEDLIIKGISVHISNAEPKHN   86 (89)
T ss_dssp             HHHH----HHTTCEEEETTEEEEEEECC----
T ss_pred             HHHH----HHcCCCcccCCEEEEEEEcCCCCc
Confidence            9987    367776677799999999998654

>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=99.80  E-value=8.5e-19  Score=111.02  Aligned_cols=78  Identities=18%  Similarity=0.228  Sum_probs=71.5

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||+++++++|+++|++||.|..+.+++                              .    +||||+|.+
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~------------------------------~----g~afV~f~~   59 (108)
T 1x4c_A           14 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR------------------------------D----GTGVVEFVR   59 (108)
T ss_dssp             CCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEET------------------------------T----TEEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEec------------------------------C----CEEEEEECC
Confidence            467999999999999999999999999999998873                              1    899999999


Q ss_pred             HHhHHHHHHHHhCCcceecC-----cEEEEEecCCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWG-----CDIIVDWADPQEEP  116 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g-----~~l~v~~a~~~~~~  116 (131)
                      .++|.+|++.|++.  .++|     +.|.|.+|.++...
T Consensus        60 ~~~a~~Ai~~l~g~--~~~g~~~~~~~i~V~~a~~~~~~   96 (108)
T 1x4c_A           60 KEDMTYAVRKLDNT--KFRSHEGETAYIRVKVDGPRSPS   96 (108)
T ss_dssp             HHHHHHHHHHSSSE--EEECTTSCEEEEEEEESSCCSCC
T ss_pred             HHHHHHHHHHHCcC--CccCCcCcceEEEEEeCCCCCCC
Confidence            99999999999998  8899     99999999987654

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

Probab=99.80  E-value=3.8e-19  Score=111.11  Aligned_cols=82  Identities=29%  Similarity=0.466  Sum_probs=72.0

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||.|   ++++                            ..++.+++||||+|.+
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~----------------------------~~~g~~~g~afV~f~~   62 (101)
T 2fc9_A           14 ESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQ----------------------------NQNGKSKGYAFIEFAS   62 (101)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCB----------------------------CSSSCBCSEEEEECSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEE----------------------------CCCCCEeeEEEEEECC
Confidence            36899999999999999999999999977   3442                            1367889999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      .++|.+|+..|++.  .++|+.|.|.|+.++..+.
T Consensus        63 ~~~A~~A~~~l~g~--~~~g~~l~v~~a~~~~~~~   95 (101)
T 2fc9_A           63 FEDAKEALNSCNKR--EIEGRAIRLELQGPRGSPN   95 (101)
T ss_dssp             HHHHHHHHHHTSSE--EETTEEEEEEECSSCCCCC
T ss_pred             HHHHHHHHHHhCCC--EeCCeEEEEEEcCCCCCCC
Confidence            99999999999997  8999999999999876543

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.80  E-value=2.8e-20  Score=116.30  Aligned_cols=83  Identities=20%  Similarity=0.266  Sum_probs=72.2

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||.|.. .++..                           ..++.++|||||+|.+
T Consensus        16 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~---------------------------~~~g~~~g~afV~f~~   67 (101)
T 1fj7_A           16 TPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVD---------------------------VRTGTNRKFGYVDFES   67 (101)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCE---------------------------EEEETTTTEEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEec---------------------------CCCCCcCcEEEEEECC
Confidence            4679999999999999999999999998877 33321                           1256789999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEEP  116 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~  116 (131)
                      .++|.+|++ +++.  .++|+.|.|.||.++.++
T Consensus        68 ~~~a~~A~~-l~g~--~~~g~~l~V~~a~~~~~~   98 (101)
T 1fj7_A           68 AEDLEKALE-LTGL--KVFGNEIKLEKPKGRDGT   98 (101)
T ss_dssp             HHHHHHHHH-GGGC--CBTTBCCEEECCSCCCCS
T ss_pred             HHHHHHHHh-cCCc--EECCcEEEEEEcCCCCCC
Confidence            999999998 9998  889999999999987754

>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=99.79  E-value=3.8e-19  Score=118.59  Aligned_cols=78  Identities=26%  Similarity=0.466  Sum_probs=72.0

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||+++++++|+++|++||.|.+++++++                                ++|||||+|.+
T Consensus        72 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~--------------------------------~~g~afV~f~~  119 (150)
T 2i2y_A           72 LDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN--------------------------------PPGFAFVEFED  119 (150)
T ss_dssp             TSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS--------------------------------SCSEEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC--------------------------------CCcEEEEEECC
Confidence            3589999999999999999999999999999988732                                58999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQE  114 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~  114 (131)
                      .++|.+|+..|+|.  .++|+.|+|+|+.++.
T Consensus       120 ~~~a~~A~~~l~g~--~~~g~~l~v~~a~~~~  149 (150)
T 2i2y_A          120 PRDAADAVRELDGR--TLCGCRVRVELSNGEK  149 (150)
T ss_dssp             HHHHHHHHHHHSSS--CSSSSCCEEEECCCCC
T ss_pred             HHHHHHHHHHcCCC--EECCeEEEEEEcCCCC
Confidence            99999999999998  8899999999998864

>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=99.79  E-value=1.2e-19  Score=107.56  Aligned_cols=75  Identities=25%  Similarity=0.455  Sum_probs=67.7

Q ss_pred             EEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHHh
Q psy1185           6 VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKS   85 (131)
Q Consensus         6 ~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~~   85 (131)
                      +|||+|||.++++++|+++|++||+|.++.+++.                           ..++.++|||||+|.+.++
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~---------------------------~~~~~~~g~afV~f~~~~~   53 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMD---------------------------NKTNKRRGFCFITFKEEEP   53 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCS---------------------------CCCSSSCCCEEEECSSSHH
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEec---------------------------CCCCCcCCEEEEEECCHHH
Confidence            6899999999999999999999999999988754                           3468889999999999999


Q ss_pred             HHHHHHHHhCCcceecCcEEEEEec
Q psy1185          86 ASLAKKRLATGRLKVWGCDIIVDWA  110 (131)
Q Consensus        86 a~~a~~~l~~~~~~~~g~~l~v~~a  110 (131)
                      |.+|+.. ++.  .++|+.|.|++|
T Consensus        54 a~~Ai~~-~~~--~~~g~~l~v~~a   75 (75)
T 1iqt_A           54 VKKIMEK-KYH--NVGLSKCEIKVA   75 (75)
T ss_dssp             HHHHHTT-SSC--CBTTBCCCEEEC
T ss_pred             HHHHHHh-CCC--eECCEEEEEEEC
Confidence            9999986 666  899999999886

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A

Probab=99.79  E-value=5.7e-19  Score=119.50  Aligned_cols=79  Identities=25%  Similarity=0.375  Sum_probs=70.2

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      +..+|||+|||+.+++++|+++|++||.|.++.+..                               ..++++|||+|.+
T Consensus        45 ~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~-------------------------------k~~rgfAFVeF~d   93 (164)
T 1sjr_A           45 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFT-------------------------------KNNQFQALLQYAD   93 (164)
T ss_dssp             CEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEE-------------------------------SSSCEEEEEEESC
T ss_pred             ceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEe-------------------------------CCCCCEEEEEECC
Confidence            457899999999999999999999999999998762                               2357899999999


Q ss_pred             HHhHHHHHHHHhCCcceec--CcEEEEEecCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVW--GCDIIVDWADPQE  114 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~--g~~l~v~~a~~~~  114 (131)
                      .++|.+|++.|+|.  .++  |+.|+|+||+++.
T Consensus        94 ~~~A~~Ai~~LnG~--~i~g~g~~L~V~~Ak~~~  125 (164)
T 1sjr_A           94 PVSAQHAKLSLDGQ--NIYNACCTLRIDFSKLTS  125 (164)
T ss_dssp             HHHHHHHHHHSTTB--CSSSSCSCEEEEECSSSS
T ss_pred             HHHHHHHHHHhCCC--EecCCCcEEEEEEecCCc
Confidence            99999999999998  664  4999999999764

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=2.1e-19  Score=114.94  Aligned_cols=80  Identities=14%  Similarity=0.153  Sum_probs=72.3

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCe-eEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRV-ERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYD   81 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v-~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~   81 (131)
                      ..++|||+|||+++++++|+++|++||.| ..+++++.                            .++.++|||||+|.
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d----------------------------~~g~~~G~afV~F~   65 (114)
T 2cpy_A           14 AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVD----------------------------NNGQGLGQALVQFK   65 (114)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCC----------------------------TTSSCSSCEEEECS
T ss_pred             CccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEEC----------------------------CCCCcceEEEEEEC
Confidence            36799999999999999999999999999 88888753                            27889999999999


Q ss_pred             CHHhHHHHHHHHhCCcceecCcEEEEEecCCC
Q psy1185          82 SHKSASLAKKRLATGRLKVWGCDIIVDWADPQ  113 (131)
Q Consensus        82 ~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~  113 (131)
                      +.++|.+|+.. ++.  .++|+.|.|.||.++
T Consensus        66 ~~~~a~~Al~~-~~~--~~~gr~i~v~~a~~~   94 (114)
T 2cpy_A           66 NEDDARKSERL-HRK--KLNGREAFVHVVTLE   94 (114)
T ss_dssp             SHHHHHHHGGG-CSE--EETTEEEEEEEECHH
T ss_pred             CHHHHHHHHHh-CCC--ccCCeEEEEEECCHH
Confidence            99999999988 886  899999999999754

>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=99.79  E-value=3.9e-19  Score=117.66  Aligned_cols=83  Identities=22%  Similarity=0.332  Sum_probs=72.1

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEE--------EEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcc
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERV--------KRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRG   74 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~--------~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~   74 (131)
                      ..++|||+|||+++++++|+++|++||.|..+        ++.                              .++.++|
T Consensus        44 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~------------------------------~~g~~~g   93 (143)
T 3egn_A           44 PNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLM------------------------------KEGRMKG   93 (143)
T ss_dssp             CCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEE------------------------------EETTTEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEec------------------------------cCCCccc
Confidence            35799999999999999999999999998774        222                              2578899


Q ss_pred             eEEEEeCCHHhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          75 FCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        75 ~~fv~f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      ||||+|.+.++|.+|+..|||.  .++|+.|.|.||++..++.
T Consensus        94 ~afV~f~~~~~A~~Ai~~lng~--~~~g~~l~V~~a~~~~~~~  134 (143)
T 3egn_A           94 QAFIGLPNEKAAAKALKEANGY--VLFGKPMVVQFARSARPKQ  134 (143)
T ss_dssp             EEEEECSSHHHHHHHHHHHTTB--EETTEECEEEECCCSCC--
T ss_pred             EEEEEeCCHHHHHHHHHHhCCC--EeCCcEEEEEECCCCCCcc
Confidence            9999999999999999999998  8999999999998876554

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=6.7e-19  Score=110.83  Aligned_cols=81  Identities=19%  Similarity=0.199  Sum_probs=72.0

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeE-EEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVER-VKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYD   81 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~-~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~   81 (131)
                      ..++|||+|||+++++++|+++|++||.|.. ++++..                            .++.++|||||+|.
T Consensus        14 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~----------------------------~~g~~~G~afV~F~   65 (104)
T 1wg5_A           14 NDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD----------------------------FQGRSTGEAFVQFA   65 (104)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC----------------------------SSSCBCSEEEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC----------------------------CCCCcceEEEEEEC
Confidence            4689999999999999999999999999987 766642                            36888999999999


Q ss_pred             CHHhHHHHHHHHhCCcceecCcEEEEEecCCCC
Q psy1185          82 SHKSASLAKKRLATGRLKVWGCDIIVDWADPQE  114 (131)
Q Consensus        82 ~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~  114 (131)
                      +.++|.+|+.. ++.  .++|+.|.|.++.++.
T Consensus        66 ~~~~a~~A~~~-~~~--~~~gr~i~v~~~~~~~   95 (104)
T 1wg5_A           66 SQEIAEKALKK-HKE--RIGHRYIEIFKSSRAE   95 (104)
T ss_dssp             SHHHHHHHHTT-TTC--CSSSSCCEEEEECTTT
T ss_pred             CHHHHHHHHHh-Ccc--hhCCcEEEEEECCHHH
Confidence            99999999998 887  8999999999987654

>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=99.79  E-value=9.9e-19  Score=110.94  Aligned_cols=76  Identities=18%  Similarity=0.343  Sum_probs=69.7

Q ss_pred             ceEEEEeCCCCC-CCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           4 VKVLYVRNLTQY-CTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         4 ~~~l~v~nLp~~-~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      .++|||+|||++ +++++|+++|++||.|.++.+.                                   ++||||+|.+
T Consensus        27 ~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i~-----------------------------------~g~afV~f~~   71 (110)
T 1wf1_A           27 NSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVH-----------------------------------KGYAFVQYSN   71 (110)
T ss_dssp             SSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEEE-----------------------------------TTEEEEECSS
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEe-----------------------------------CCEEEEEECC
Confidence            479999999999 9999999999999999998763                                   6899999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEEP  116 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~  116 (131)
                      .++|.+|++.|++.  .++|+.|.|.|+.++.+.
T Consensus        72 ~~~A~~A~~~l~g~--~~~g~~l~V~~a~~~~~~  103 (110)
T 1wf1_A           72 ERHARAAVLGENGR--VLAGQTLDINMAGEPKPD  103 (110)
T ss_dssp             SHHHHHHHHHHTTC--EETTEECCEEESCCCCSC
T ss_pred             HHHHHHHHHHcCCC--EECCeEEEEEECCCCCCC
Confidence            99999999999998  899999999999865543

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.78  E-value=2.1e-18  Score=112.75  Aligned_cols=79  Identities=27%  Similarity=0.432  Sum_probs=70.0

Q ss_pred             CCceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcce-EEEEe
Q psy1185           2 SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGF-CFLEY   80 (131)
Q Consensus         2 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~-~fv~f   80 (131)
                      |+.-.|||+|||+.+|+++|+++|++||.|.++.+...                                .+++ |||+|
T Consensus        26 s~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~--------------------------------~~gfqAFVef   73 (130)
T 3zzy_A           26 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK--------------------------------NNQFQALLQY   73 (130)
T ss_dssp             CSEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE--------------------------------TTEEEEEEEE
T ss_pred             CceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC--------------------------------CCCcEEEEEE
Confidence            35568999999999999999999999999999987631                                3577 99999


Q ss_pred             CCHHhHHHHHHHHhCCcceecC--cEEEEEecCCCC
Q psy1185          81 DSHKSASLAKKRLATGRLKVWG--CDIIVDWADPQE  114 (131)
Q Consensus        81 ~~~~~a~~a~~~l~~~~~~~~g--~~l~v~~a~~~~  114 (131)
                      .+.++|..|++.|+|.  .++|  +.|+|+||+++.
T Consensus        74 ~~~~~A~~Ai~~LnG~--~i~g~~~~LrI~~ak~~~  107 (130)
T 3zzy_A           74 ADPVSAQHAKLSLDGQ--NIYNACCTLRIDFSKLTS  107 (130)
T ss_dssp             SCHHHHHHHHHHHTTC--EEETTEEEEEEEECSCSS
T ss_pred             CCHHHHHHHHHHcCCC--eecCCCcEEEEEecCCCc
Confidence            9999999999999999  7777  899999998764

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

Probab=99.78  E-value=1.1e-18  Score=109.19  Aligned_cols=83  Identities=33%  Similarity=0.632  Sum_probs=72.1

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|+.|+   .+.+++.                           ..++.+++||||+|.+
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~---------------------------~~~~~~~g~afV~f~~   63 (102)
T 2fc8_A           14 PSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTD---------------------------RETGSSKGFGFVDFNS   63 (102)
T ss_dssp             CCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEEC---------------------------SSSCSEEEEEEEECSS
T ss_pred             CCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEec---------------------------CCCCCcCcEEEEEECC
Confidence            467999999999999999999999874   4555532                           2367889999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      .++|.+|+..|++.  .++|+.|.|.||+++.++.
T Consensus        64 ~~~A~~A~~~l~g~--~~~g~~l~V~~a~~~~~~~   96 (102)
T 2fc8_A           64 EEDAKAAKEAMEDG--EIDGNKVTLDWAKPKGEGG   96 (102)
T ss_dssp             HHHHHHHHHHHTTC--EETTEECEEEECCCCCSSS
T ss_pred             HHHHHHHHHHhCCC--eECCeEEEEEEecCCCCCC
Confidence            99999999999998  8999999999999887654

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

Probab=99.78  E-value=4.6e-19  Score=109.72  Aligned_cols=79  Identities=22%  Similarity=0.360  Sum_probs=71.1

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .++|||+|||.++++++|+++|++||.|..+  .                              .++.++|||||+|.+.
T Consensus        16 ~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~--~------------------------------~~~~~~g~afV~f~~~   63 (96)
T 1fjc_A           16 ARTLLAKNLSFNITEDELKEVFEDALEIRLV--S------------------------------QDGKSKGIAYIEFKSE   63 (96)
T ss_dssp             GGEEEEESCCSSCCHHHHHHHHCSEEEECCE--E------------------------------ETTEEEEEEEEEESSH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe--C------------------------------CCCCcceEEEEEECCH
Confidence            6799999999999999999999999987765  1                              1577899999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCCCCCC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADPQEEP  116 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~  116 (131)
                      ++|.+|+..+++.  .++|+.|.|.|+.++...
T Consensus        64 ~~a~~A~~~l~g~--~~~g~~l~v~~a~~~~~~   94 (96)
T 1fjc_A           64 ADAEKNLEEKQGA--EIDGRSVSLYYTGEKGGT   94 (96)
T ss_dssp             HHHHHHHHHTTEE--EETTEEEEEEECSSSCCC
T ss_pred             HHHHHHHHHhCCC--EECCeEEEEEEcCCCCCC
Confidence            9999999999997  899999999999887653

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.78  E-value=1.3e-18  Score=107.66  Aligned_cols=79  Identities=22%  Similarity=0.260  Sum_probs=69.8

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEE-EecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVK-RIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYD   81 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~-i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~   81 (131)
                      ..++|||+|||+++++++|+++|++||.|.+++ ++..                               ...+.|||+|.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~-------------------------------~~~~~afV~f~   62 (96)
T 2e44_A           14 RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTD-------------------------------SETAVVNVTYS   62 (96)
T ss_dssp             SCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCS-------------------------------SSSEEEEEEES
T ss_pred             CCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecC-------------------------------CCCCEEEEEEC
Confidence            367999999999999999999999999999994 6632                               12344999999


Q ss_pred             CHHhHHHHHHHHhCCcceecCcEEEEEecCCCC
Q psy1185          82 SHKSASLAKKRLATGRLKVWGCDIIVDWADPQE  114 (131)
Q Consensus        82 ~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~  114 (131)
                      +.++|.+|+..|+|.  .++|+.|.|.||.++.
T Consensus        63 ~~~~a~~Ai~~l~g~--~~~g~~l~V~~a~~~~   93 (96)
T 2e44_A           63 SKDQARQALDKLNGF--QLENFTLKVAYIPDEM   93 (96)
T ss_dssp             SHHHHHHHHHHHTTC--BCSSCBCEEEECCCCC
T ss_pred             CHHHHHHHHHHhCCC--EECCcEEEEEEcCccc
Confidence            999999999999998  8899999999999874

>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=99.78  E-value=3.6e-19  Score=126.66  Aligned_cols=82  Identities=27%  Similarity=0.394  Sum_probs=74.1

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccC--CeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEe
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYG--RVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEY   80 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G--~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f   80 (131)
                      ..++|||+|||+++++++|+++|++||  .|.+++|++.                           ..++.++|||||+|
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d---------------------------~~tg~skGfaFV~f  119 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFEN---------------------------RANGQSKGFALVGV  119 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEEC---------------------------TTTCCEEEEEEEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEec---------------------------CCCCccceEEEEEE
Confidence            457899999999999999999999999  9999998854                           34788999999999


Q ss_pred             CCHHhHHHHHHHHhCCcceecCcEEEEEecCCC
Q psy1185          81 DSHKSASLAKKRLATGRLKVWGCDIIVDWADPQ  113 (131)
Q Consensus        81 ~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~  113 (131)
                      .+.++|.+|+..|++.  .++|+.|.|.||.+.
T Consensus       120 ~~~~~a~~Ai~~lng~--~~~Gr~l~V~~a~~~  150 (229)
T 3q2s_C          120 GSEASSKKLMDLLPKR--ELHGQNPVVTPVNKQ  150 (229)
T ss_dssp             SCTTHHHHHHTTSTTS--CBTTBCCEEEECCHH
T ss_pred             CCHHHHHHHHHHcCCC--eECCEEeEEEECCCC
Confidence            9999999999999998  899999999998753

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.78  E-value=5.4e-19  Score=110.59  Aligned_cols=81  Identities=17%  Similarity=0.303  Sum_probs=72.3

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .++|||+|||.++++++|+++|++||.|.++++++.                           . ++.++|||||+|.+.
T Consensus         9 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~---------------------------~-~g~~~g~afV~f~~~   60 (102)
T 2xs2_A            9 PNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD---------------------------R-TGVSKGYGFVSFYND   60 (102)
T ss_dssp             EEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEEC---------------------------T-TSCEEEEEEEEESSC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEEC---------------------------C-CCCccceEEEEECCH
Confidence            579999999999999999999999999999998864                           2 678899999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCCCCCC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADPQEEP  116 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~  116 (131)
                      ++|.+|+.  ++.  .++|+.|.|.++.++...
T Consensus        61 ~~a~~Ai~--~~~--~~~g~~l~v~~a~~~~~~   89 (102)
T 2xs2_A           61 VDVQKIVE--SQI--NFHGKKLKLGPAIRKQNL   89 (102)
T ss_dssp             CCHHHHTT--CCC--EETTEECEEEEEEECC--
T ss_pred             HHHHHHHh--CCC--eECCEEEEEEECCcCcch
Confidence            99999999  776  899999999999876654

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.78  E-value=6.6e-19  Score=113.37  Aligned_cols=79  Identities=22%  Similarity=0.185  Sum_probs=71.4

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCC---eeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEE
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGR---VERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLE   79 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~---v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~   79 (131)
                      ..++|||+|||+++++++|+++|++||.   |..+++++.                            ..|.++|||||+
T Consensus        16 ~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~----------------------------~~g~~~G~afV~   67 (118)
T 2db1_A           16 EGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYT----------------------------REGRQSGEAFVE   67 (118)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEEC----------------------------SSSCEEEEEEEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEEC----------------------------CCCCCCeEEEEE
Confidence            3578999999999999999999999999   889988753                            247889999999


Q ss_pred             eCCHHhHHHHHHHHhCCcceecCcEEEEEecCC
Q psy1185          80 YDSHKSASLAKKRLATGRLKVWGCDIIVDWADP  112 (131)
Q Consensus        80 f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~  112 (131)
                      |.+.++|.+|+. +++.  .++|+.|.|.++.+
T Consensus        68 F~~~~~a~~Al~-~~g~--~~~gr~i~V~~a~~   97 (118)
T 2db1_A           68 LESEDDVKLALK-KDRE--SMGHRYIEVFKSHR   97 (118)
T ss_dssp             BSSHHHHHHHGG-GTTE--EETTEEEEEEEECH
T ss_pred             ECCHHHHHHHHh-cCCC--eECCeEEEEEECCH
Confidence            999999999999 9987  89999999999863

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

Probab=99.77  E-value=4.2e-18  Score=105.71  Aligned_cols=78  Identities=27%  Similarity=0.302  Sum_probs=70.7

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+||  ++++++|+++|++||.|.++.+.                                 .+++||||+|.+
T Consensus        14 ~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~---------------------------------~~~g~afV~f~~   58 (97)
T 1x5p_A           14 KGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD---------------------------------PPRNCAFVTYEK   58 (97)
T ss_dssp             CCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE---------------------------------TTTTEEEEEESS
T ss_pred             CCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec---------------------------------CCCCEEEEEECC
Confidence            3579999996  89999999999999999999875                                 358999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      .++|.+|+..|++.  .++|+.|.|.|+.++....
T Consensus        59 ~~~a~~Ai~~l~g~--~~~g~~l~v~~a~~~~~~~   91 (97)
T 1x5p_A           59 MESADQAVAELNGT--QVESVQLKVNIARKQPMLD   91 (97)
T ss_dssp             HHHHHHHHHHTTTE--EETTEEEEEECCSSCCCCC
T ss_pred             HHHHHHHHHHhCCC--eECCeEEEEEECCCCCCCC
Confidence            99999999999998  8899999999999877654

>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=99.77  E-value=9.8e-19  Score=109.94  Aligned_cols=81  Identities=15%  Similarity=0.119  Sum_probs=71.4

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||+++++++|+++|++||.+ ++++++.                            .++.++|||||+|.+
T Consensus        14 ~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d----------------------------~~g~~~G~afV~F~~   64 (102)
T 1wez_A           14 TGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIG----------------------------PDGRVTGEADVEFAT   64 (102)
T ss_dssp             SSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEES----------------------------SSSCEEEEEEEECSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEEC----------------------------CCCCEeeEEEEEECC
Confidence            36799999999999999999999999954 8888753                            278899999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEE  115 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~  115 (131)
                      .++|.+|+ .+++.  .++|+.|.|.++.+...
T Consensus        65 ~~~a~~Al-~~~~~--~~~gr~i~V~~~~~~~~   94 (102)
T 1wez_A           65 HEDAVAAM-AKDKA--NMQHRYVELFLNSTAGT   94 (102)
T ss_dssp             SHHHHHHH-TTSSC--CSSSSCCEEEEECCCCC
T ss_pred             HHHHHHHH-HhCCC--eECCcEEEEEECCCCCC
Confidence            99999999 47887  89999999999887654

>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=99.77  E-value=4.5e-19  Score=116.99  Aligned_cols=79  Identities=19%  Similarity=0.153  Sum_probs=71.6

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCC---eeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEE
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGR---VERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLE   79 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~---v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~   79 (131)
                      ..++|||+|||+++|+++|+++|++||.   |.++++++.                            ..|.++|||||+
T Consensus        43 ~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d----------------------------~~g~srG~aFV~   94 (136)
T 2hgl_A           43 EGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYT----------------------------REGRQSGEAFVE   94 (136)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEEC----------------------------SSSCEEEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEEC----------------------------CCCCCCeEEEEE
Confidence            3678999999999999999999999999   889988854                            248889999999


Q ss_pred             eCCHHhHHHHHHHHhCCcceecCcEEEEEecCC
Q psy1185          80 YDSHKSASLAKKRLATGRLKVWGCDIIVDWADP  112 (131)
Q Consensus        80 f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~  112 (131)
                      |.+.++|.+|+. +++.  .++|+.|.|.++.+
T Consensus        95 F~~~e~a~~Al~-~~g~--~l~gr~i~V~~a~~  124 (136)
T 2hgl_A           95 LGSEDDVKMALK-KDRE--SMGHRYIEVFKSHR  124 (136)
T ss_dssp             CSSHHHHHHHHT-TTEE--ESSSSEEEEEECCH
T ss_pred             ECCHHHHHHHHh-cCCC--EECCEEEEEEECCh
Confidence            999999999999 9997  89999999999863

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.64  E-value=2e-20  Score=119.86  Aligned_cols=86  Identities=21%  Similarity=0.309  Sum_probs=76.4

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeE--------EEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcc
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVER--------VKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRG   74 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~--------~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~   74 (131)
                      ..++|||+|||.++++++|+++|++||.|..        +.+++.                           ..++.++|
T Consensus         6 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~---------------------------~~~g~~~g   58 (116)
T 2lcw_A            6 DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTD---------------------------RETGKLKG   58 (116)
Confidence            4689999999999999999999999999988        666642                           23678899


Q ss_pred             eEEEEeCCHHhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          75 FCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        75 ~~fv~f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      ||||+|.+.++|.+|+..|++.  .++|+.|.|.||.++....
T Consensus        59 ~afV~f~~~~~A~~Ai~~l~g~--~~~g~~l~V~~a~~~~~~~   99 (116)
T 2lcw_A           59 EATVSFDDPPSAKAAIDWFDGK--EFSGNPIKVSFATRRADFN   99 (116)
Confidence            9999999999999999999998  8899999999999877654

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.77  E-value=6.5e-18  Score=109.73  Aligned_cols=78  Identities=26%  Similarity=0.452  Sum_probs=68.4

Q ss_pred             CCceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcce-EEEEe
Q psy1185           2 SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGF-CFLEY   80 (131)
Q Consensus         2 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~-~fv~f   80 (131)
                      ++...|||+|||+.+++++|+++|++||.|.++.+..                                + .|+ |||+|
T Consensus        23 s~vl~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~--------------------------------~-~Gf~aFVef   69 (124)
T 2e5i_A           23 NKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFK--------------------------------R-NGIQAMVEF   69 (124)
T ss_dssp             CSEEEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEE--------------------------------S-SSEEEEEEE
T ss_pred             CcEEEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEe--------------------------------C-CCCEEEEEE
Confidence            3455689999999999999999999999999998762                                1 385 99999


Q ss_pred             CCHHhHHHHHHHHhCCcceecC--cEEEEEecCCCC
Q psy1185          81 DSHKSASLAKKRLATGRLKVWG--CDIIVDWADPQE  114 (131)
Q Consensus        81 ~~~~~a~~a~~~l~~~~~~~~g--~~l~v~~a~~~~  114 (131)
                      .+.++|..|++.|+|.  .++|  +.|+|.||+++.
T Consensus        70 ~~~~~A~~A~~~LnG~--~i~g~~~~l~V~~Ak~~~  103 (124)
T 2e5i_A           70 ESVLCAQKAKAALNGA--DIYAGCCTLKIEYARPTR  103 (124)
T ss_dssp             SSHHHHHHHHHHHTTC--CCBTTBSEEEEECCSCSC
T ss_pred             CCHHHHHHHHHHhCCC--EecCCCeEEEEEEecCCc
Confidence            9999999999999998  6666  689999999775

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.77  E-value=3e-18  Score=117.56  Aligned_cols=83  Identities=17%  Similarity=0.212  Sum_probs=75.6

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||.|.++.++..                            .++.++|||||+|.+
T Consensus        87 ~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d----------------------------~~g~~kG~afV~F~~  138 (177)
T 2f3j_A           87 TGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD----------------------------RSGRSLGTADVHFER  138 (177)
T ss_dssp             TCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCC----------------------------TTSSCSCCEEEEESC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC----------------------------CCCCEeeEEEEEeCC
Confidence            4689999999999999999999999999999998753                            267889999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEE  115 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~  115 (131)
                      .++|.+|+..+++.  .++|+.|.|.||.+...
T Consensus       139 ~~~A~~Ai~~lng~--~l~Gr~l~V~~a~~~~~  169 (177)
T 2f3j_A          139 RADALKAMKQYKGV--PLDGRPMDIQLVASQID  169 (177)
T ss_dssp             HHHHHHHHHHSTTC--BCSSSBCEEEEESSGGG
T ss_pred             HHHHHHHHHHhCCC--EECCEEEEEEEecCCCC
Confidence            99999999999998  89999999999986543

>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=99.77  E-value=2.2e-18  Score=105.28  Aligned_cols=76  Identities=17%  Similarity=0.209  Sum_probs=69.3

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||+++++++|+++|++| .|.++++.                                 .++|||||+|.+
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~---------------------------------~~~g~afV~f~~   49 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD---------------------------------RNKRTAFVTLLN   49 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE---------------------------------GGGTEEEECCSC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe---------------------------------CCCcEEEEEECC
Confidence            46799999999999999999999999 99998774                                 358999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQE  114 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~  114 (131)
                      .++|.+|++.+++.  .++|+.|+|+||....
T Consensus        50 ~~~a~~Ai~~l~g~--~~~g~~l~V~~a~~~~   79 (88)
T 1wg1_A           50 GEQAQNAIQMFHQY--SFRGKDLIVQLQPTDA   79 (88)
T ss_dssp             HHHHHHHHHHHTTE--EETTEEEEEEECCCCC
T ss_pred             HHHHHHHHHHhCCC--eECCcEEEEEEcCCCc
Confidence            99999999999998  8999999999997643

>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=99.77  E-value=3.1e-18  Score=104.52  Aligned_cols=80  Identities=29%  Similarity=0.404  Sum_probs=69.5

Q ss_pred             CCceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeC
Q psy1185           2 SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYD   81 (131)
Q Consensus         2 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~   81 (131)
                      +..++|||+|||.++++++|+++|++||.|.++++++                                .++|||||+|.
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~--------------------------------~~~g~afV~f~   50 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK--------------------------------PFRAFAFVTFA   50 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCS--------------------------------SCCSCCEEECS
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEec--------------------------------CCCCEEEEEEC
Confidence            4578999999999999999999999999999998863                                26899999999


Q ss_pred             CHHhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          82 SHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        82 ~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      +.++|++    +++..+.+.|+.|.|.|+.++....
T Consensus        51 ~~~~a~~----~~~~~~~~~g~~l~v~~a~~~~~~~   82 (88)
T 1wf0_A           51 DDQIAQS----LCGEDLIIKGISVHISNAEPKHNSN   82 (88)
T ss_dssp             CHHHHHH----TTTCEEEETTEEEEEECCCCCCCCC
T ss_pred             CHHHHHH----HhcCCceeCCEEEEEEecCCCCCCC
Confidence            9999875    4565667899999999999887654

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.76  E-value=3.8e-18  Score=105.37  Aligned_cols=80  Identities=16%  Similarity=0.239  Sum_probs=68.5

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||+++++++|+++|++||.|.++ +..                            ..++.   ||||+|.+
T Consensus         7 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v-~~~----------------------------~~~g~---~afV~f~~   54 (94)
T 2e5g_A            7 GLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV-VMD----------------------------KDKGV---FAIVEMGD   54 (94)
T ss_dssp             TCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE-EEC----------------------------SSSCC---EEEEEESS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE-EEc----------------------------CCCCc---EEEEEECC
Confidence            46799999999999999999999999999987 331                            11222   99999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      .++|.+|+. +++.  .++|+.|.|+++.++....
T Consensus        55 ~~~a~~ai~-l~g~--~~~g~~l~V~~a~~~~~~~   86 (94)
T 2e5g_A           55 VGAREAVLS-QSQH--SLGGHRLRVRPREQKEFQS   86 (94)
T ss_dssp             HHHHHHHHT-CSCC--EETTEECCCBCSCCSCCCC
T ss_pred             HHHHHHHHh-cCCe--EECCEEEEEEECCcCCCCC
Confidence            999999999 9998  8999999999998766543

>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=99.76  E-value=2.8e-18  Score=109.84  Aligned_cols=77  Identities=17%  Similarity=0.243  Sum_probs=68.0

Q ss_pred             ceEEEE--eCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeC
Q psy1185           4 VKVLYV--RNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYD   81 (131)
Q Consensus         4 ~~~l~v--~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~   81 (131)
                      .++|||  ||||+++++++|+++|++||.|.++.++.                                 .+|||||+|.
T Consensus        25 t~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~---------------------------------~rgfaFV~f~   71 (114)
T 2cq2_A           25 TQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP---------------------------------NKPYSFARYR   71 (114)
T ss_dssp             CSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT---------------------------------TCSCEEEEES
T ss_pred             CCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC---------------------------------CCCEEEEEEC
Confidence            568999  77999999999999999999999987652                                 3799999999


Q ss_pred             CHHhHHHHHHHHhCCccee-----cCcEEEEEecCCCCC
Q psy1185          82 SHKSASLAKKRLATGRLKV-----WGCDIIVDWADPQEE  115 (131)
Q Consensus        82 ~~~~a~~a~~~l~~~~~~~-----~g~~l~v~~a~~~~~  115 (131)
                      +.++|.+|++.|||+  .+     .|+.|.|.|+...+.
T Consensus        72 ~~~~A~~Ai~~lnG~--~~~~~lg~g~~l~v~~a~~~p~  108 (114)
T 2cq2_A           72 TTEESKRAYVTLNGK--EVVDDLGQKITLYLNFVEKVQW  108 (114)
T ss_dssp             SHHHHHHHHHHTTTC--EEECTTSCEEECEEEEESCCCC
T ss_pred             CHHHHHHHHHHhCCC--EEccccCCCcEEEEEecccCcc
Confidence            999999999999998  55     588899999986554

>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=99.76  E-value=4.3e-19  Score=112.28  Aligned_cols=79  Identities=16%  Similarity=0.136  Sum_probs=71.4

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCC---eeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEE
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGR---VERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLE   79 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~---v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~   79 (131)
                      ..++|||+|||+++++++|+++|++||.   |.++++++.                           . .|.++|||||+
T Consensus        10 ~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~---------------------------~-~g~~~G~afV~   61 (107)
T 2lmi_A           10 DVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLN---------------------------R-DGKRRGDALIE   61 (107)
T ss_dssp             SCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCC---------------------------T-TSTTCSEEEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEEC---------------------------C-CCCEeeEEEEE
Confidence            4679999999999999999999999998   889988753                           2 48899999999


Q ss_pred             eCCHHhHHHHHHHHhCCcceecCcEEEEEecCC
Q psy1185          80 YDSHKSASLAKKRLATGRLKVWGCDIIVDWADP  112 (131)
Q Consensus        80 f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~  112 (131)
                      |.+.++|.+|+. +++.  .++|+.|.|.++.+
T Consensus        62 F~~~~~a~~Al~-~~~~--~~~gr~i~V~~a~~   91 (107)
T 2lmi_A           62 MESEQDVQKALE-KHRM--YMGQRYVEVYEINN   91 (107)
T ss_dssp             BSSHHHHHHHHT-TTTC--CSSSSCCCCEECCH
T ss_pred             ECCHHHHHHHHH-hCcc--eeCCeEEEEEECCH
Confidence            999999999999 9997  89999999999875

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.76  E-value=2.3e-18  Score=123.07  Aligned_cols=81  Identities=22%  Similarity=0.541  Sum_probs=69.4

Q ss_pred             CCceEEEEeCCCCCC---------CHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCC
Q psy1185           2 SKVKVLYVRNLTQYC---------TEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKN   72 (131)
Q Consensus         2 ~~~~~l~v~nLp~~~---------t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~   72 (131)
                      ...++|||||||..+         ++++|+++|++||+|.+++++.                                 +
T Consensus       132 ~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~---------------------------------~  178 (240)
T 3u1l_A          132 KKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE---------------------------------S  178 (240)
T ss_dssp             CCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEG---------------------------------G
T ss_pred             cCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEEC---------------------------------C
Confidence            357899999999998         7999999999999999999874                                 3


Q ss_pred             cceEEEEeCCHHhHHHHHHHHhCCccee------------cCcEEEEEecCCCCCCC
Q psy1185          73 RGFCFLEYDSHKSASLAKKRLATGRLKV------------WGCDIIVDWADPQEEPD  117 (131)
Q Consensus        73 ~~~~fv~f~~~~~a~~a~~~l~~~~~~~------------~g~~l~v~~a~~~~~~~  117 (131)
                      +|||||+|.+.++|+.|++.|+|.  .+            .|+.|.|.||.+.+.+.
T Consensus       179 kG~AFV~F~~~~~Ae~A~~am~g~--~l~~~~~~e~~~~~~gr~L~V~wA~~~pnp~  233 (240)
T 3u1l_A          179 KNCGFVKFKYQANAEFAKEAMSNQ--TLLLPSDKEWDDRREGTGLLVKWANEDPDPA  233 (240)
T ss_dssp             GTEEEEEESSHHHHHHHHHHHTTC--CCCCTTSTTGGGGGGSCCCEEEECC------
T ss_pred             CCEEEEEeCCHHHHHHHHHHhCCC--EEeccccccccccCCCCEEEEEEccCCCCHH
Confidence            899999999999999999999998  55            89999999999876554

>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=99.76  E-value=3.7e-19  Score=115.25  Aligned_cols=80  Identities=18%  Similarity=0.096  Sum_probs=70.1

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||+++++++|+++|++||.|..+.++..                           ..+|.++|||||+|.+
T Consensus        24 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~---------------------------~~~g~~~G~afV~F~~   76 (124)
T 1wel_A           24 AGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAY---------------------------GPNGKATGEGFVEFRN   76 (124)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEE---------------------------CTTSSEEEEEEEEBSS
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEE---------------------------CCCCCCCeEEEEEECC
Confidence            3579999999999999999999999999987433321                           2368889999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADP  112 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~  112 (131)
                      .++|.+|+. +++.  .++|+.|.|.+|.+
T Consensus        77 ~~~a~~Al~-~~g~--~~~gr~i~V~~a~~  103 (124)
T 1wel_A           77 EADYKAALC-RHKQ--YMGNRFIQVHPITK  103 (124)
T ss_dssp             SHHHHHHHT-SCSB--CSTTSCBEEEEECH
T ss_pred             HHHHHHHHH-hCCC--eECCcEEEEEECCH
Confidence            999999999 9997  89999999999975

>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=99.75  E-value=8.8e-18  Score=117.59  Aligned_cols=78  Identities=23%  Similarity=0.290  Sum_probs=71.3

Q ss_pred             CCceEEEEeCCC-CCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEe
Q psy1185           2 SKVKVLYVRNLT-QYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEY   80 (131)
Q Consensus         2 ~~~~~l~v~nLp-~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f   80 (131)
                      ...++|||+||| +.+++++|+++|++||.|.++++++.                                .+|||||+|
T Consensus         2 ~~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~--------------------------------~~g~afV~f   49 (205)
T 3tyt_A            2 ADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS--------------------------------KPGAAMVEM   49 (205)
T ss_dssp             CCCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTT--------------------------------STTCEEEEE
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecC--------------------------------CCCEEEEEE
Confidence            356899999999 89999999999999999999998742                                479999999


Q ss_pred             CCHHhHHHHHHHHhCCcceecCcEEEEEecCCC
Q psy1185          81 DSHKSASLAKKRLATGRLKVWGCDIIVDWADPQ  113 (131)
Q Consensus        81 ~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~  113 (131)
                      .+.++|.+|++.|||.  .+.|+.|.|.|++.+
T Consensus        50 ~~~~~A~~Ai~~lng~--~~~g~~l~v~~s~~~   80 (205)
T 3tyt_A           50 ADGYAVDRAITHLNNN--FMFGQKMNVCVSKQP   80 (205)
T ss_dssp             SSHHHHHHHHHHHTTC--EETTEECEEEECSCS
T ss_pred             CCHHHHHHHHHHhCCC--EECCceEEEEEccCC
Confidence            9999999999999998  899999999999743

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.75  E-value=8.6e-18  Score=106.91  Aligned_cols=77  Identities=18%  Similarity=0.153  Sum_probs=69.3

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .++|||+|||+++++++|+++|++| .|.+++++++                            ..|+++|+|||+|.++
T Consensus        16 ~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d----------------------------~~g~~~G~afV~F~~~   66 (109)
T 2dnn_A           16 DLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKD----------------------------HVGRNNGNGLVKFLSP   66 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCC----------------------------TTCCCCSEEEEECSSH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEEC----------------------------CCCCCCeEEEEEECCH
Confidence            4689999999999999999999999 8999988853                            2488899999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADP  112 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~  112 (131)
                      ++|.+|+ .+++.  .++|+.|.|..+.+
T Consensus        67 ~~a~~Al-~~~~~--~~~gr~i~V~~a~~   92 (109)
T 2dnn_A           67 QDTFEAL-KRNRM--LMIQRYVEVSPATE   92 (109)
T ss_dssp             HHHHHHH-HTTTE--EETTEEEEEEECCH
T ss_pred             HHHHHHH-hcCCC--eECCeEEEEEECCc
Confidence            9999999 68987  89999999988753

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.75  E-value=1.2e-17  Score=102.94  Aligned_cols=73  Identities=27%  Similarity=0.406  Sum_probs=65.3

Q ss_pred             eEEEEeCCCCCCCHHH----HHHHhhcc-CCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEE
Q psy1185           5 KVLYVRNLTQYCTEEK----LKEAFEQY-GRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLE   79 (131)
Q Consensus         5 ~~l~v~nLp~~~t~~~----l~~~F~~~-G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~   79 (131)
                      +.|||+|||+++++++    |+++|++| |+|.++                                  ++   |+|||.
T Consensus        10 T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V----------------------------------tg---G~AfV~   52 (96)
T 2diu_A           10 TLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI----------------------------------TG---CSAILR   52 (96)
T ss_dssp             EEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC----------------------------------CT---TCEEEE
T ss_pred             eEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE----------------------------------ec---CEEEEE
Confidence            3499999999999988    55899999 599996                                  23   999999


Q ss_pred             eCCHHhHHHHHHHHhCCcceecCcEEEEEecCCCCCC
Q psy1185          80 YDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEP  116 (131)
Q Consensus        80 f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~  116 (131)
                      |.+.++|.+|++.|+|.  .+.|+.|+|+||+.+.+.
T Consensus        53 F~~~esA~~A~~~l~G~--~l~gr~i~v~~A~~~sd~   87 (96)
T 2diu_A           53 FINQDSAERAQKRMENE--DVFGNRIIVSFTPKNREL   87 (96)
T ss_dssp             ESSHHHHHHHHHHHTTC--CSSSSCCEEESSCCSCCC
T ss_pred             ECCHHHHHHHHHHhcCC--ccCCceEEEEecCCCcce
Confidence            99999999999999998  899999999999987754

>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=99.74  E-value=1.5e-17  Score=128.10  Aligned_cols=83  Identities=29%  Similarity=0.493  Sum_probs=75.8

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .++|||+|||..+|+++|.++|++||.|..|.|+..                           ..++.++|||||+|.+.
T Consensus       102 ~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d---------------------------~~tg~~kG~aFV~F~~~  154 (437)
T 3pgw_S          102 FKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYS---------------------------KRSGKPRGYAFIEYEHE  154 (437)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeecc---------------------------CCCCCccceEEEeeccH
Confidence            479999999999999999999999999999998853                           24688899999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCCCCC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADPQEE  115 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~  115 (131)
                      ++|.+|+..|||.  .|+|+.|.|.||.+...
T Consensus       155 e~A~~Ai~~lng~--~i~gr~i~V~~a~~~~~  184 (437)
T 3pgw_S          155 RDMHSAYKHADGK--KIDGRRVLVDVERGRTV  184 (437)
T ss_pred             HHHHHHHHHcCCC--EECCEEEEEEEeCCCCC
Confidence            9999999999998  89999999999987654

>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=99.73  E-value=2.1e-18  Score=114.12  Aligned_cols=81  Identities=16%  Similarity=0.104  Sum_probs=71.8

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||+++|+++|+++|++|| +.++++++.                            ..+.++|||||+|.+
T Consensus        45 ~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d----------------------------~~g~srGfaFV~F~~   95 (139)
T 2hgn_A           45 TGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIG----------------------------PDGRVTGEADVEFAT   95 (139)
T ss_dssp             CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCS----------------------------SSSCSSCCCEEECSH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEEC----------------------------CCCCCceEEEEEeCC
Confidence            357899999999999999999999999 668888753                            248899999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEE  115 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~  115 (131)
                      .++|.+|+ .+++.  .++|+.|.|.++.++..
T Consensus        96 ~e~A~~Al-~~~g~--~l~gR~i~V~~a~~~~~  125 (139)
T 2hgn_A           96 HEEAVAAM-SKDRA--NMQHRYIELFLNSTTGA  125 (139)
T ss_dssp             HHHHHHHT-TCCSC--SSSSCCCCCEECCCSCC
T ss_pred             HHHHHHHH-hhCCC--EECCEEEEEEECCCCCC
Confidence            99999999 78887  89999999999887654

>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=99.73  E-value=2.8e-17  Score=99.72  Aligned_cols=71  Identities=25%  Similarity=0.331  Sum_probs=65.0

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhcc----C-------CeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQY----G-------RVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKK   71 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~----G-------~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~   71 (131)
                      ..++|||+|||.++++++|+++|++|    |       .|.++.+.+                                 
T Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~---------------------------------   51 (87)
T 2hzc_A            5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQ---------------------------------   51 (87)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECS---------------------------------
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecC---------------------------------
Confidence            46899999999999999999999999    8       899988763                                 


Q ss_pred             CcceEEEEeCCHHhHHHHHHHHhCCcceecCcEEEEEe
Q psy1185          72 NRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDW  109 (131)
Q Consensus        72 ~~~~~fv~f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~  109 (131)
                      ++|||||+|.+.++|.+|+ .+++.  .++|+.|+|+.
T Consensus        52 ~kg~afV~f~~~~~a~~A~-~l~g~--~~~g~~l~V~r   86 (87)
T 2hzc_A           52 DKNFAFLEFRSVDETTQAM-AFDGI--IFQGQSLKIRR   86 (87)
T ss_dssp             SSSEEEEEESSHHHHHHHG-GGTTC--EETTEECEEEC
T ss_pred             CCcEEEEEcCCHHHHHHHH-hcCCC--EECCeEEEEeC
Confidence            3899999999999999999 99998  89999999874

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.73  E-value=1.8e-17  Score=105.86  Aligned_cols=77  Identities=14%  Similarity=0.236  Sum_probs=63.5

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCC---CCCcceEEEE
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDN---KKNRGFCFLE   79 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~---~~~~~~~fv~   79 (131)
                      ..++|||+|||+++++++|+++|++||.|. +.++..                           ..+   |.++|||||+
T Consensus         7 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~---------------------------~~~~~~g~~~G~aFV~   58 (114)
T 2dnl_A            7 GSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHK---------------------------AESKSYFPPKGYAFLL   58 (114)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTS---------------------------SSSCCCSCTTSEEEEC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeec---------------------------CCCCCCCCcccEEEEE
Confidence            468999999999999999999999999999 766632                           122   6889999999


Q ss_pred             eCCHHhHHHHHHHHhCCcceecCcEEEEEecC
Q psy1185          80 YDSHKSASLAKKRLATGRLKVWGCDIIVDWAD  111 (131)
Q Consensus        80 f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~  111 (131)
                      |.+.++|.+|++.++    .++|+.+.+..+.
T Consensus        59 f~~~~~a~~Ai~~~~----~~~G~~~~~~~~~   86 (114)
T 2dnl_A           59 FQEESSVQALIDACL----EEDGKLYLCVSSP   86 (114)
T ss_dssp             CSSHHHHHHHHHHSE----EETTEEEEEECCS
T ss_pred             ECCHHHHHHHHHhhh----hcCCcEEEeccCC
Confidence            999999999999984    3566666665443

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=4.6e-18  Score=110.36  Aligned_cols=78  Identities=15%  Similarity=0.121  Sum_probs=69.0

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCe----eEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEE
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRV----ERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFL   78 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v----~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv   78 (131)
                      ..++|||+|||+++|+++|+++|++||.|    ..++++..                            .+|+++|||||
T Consensus        22 ~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d----------------------------~~gr~~G~aFV   73 (123)
T 2dha_A           22 NQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTY----------------------------PDGRPTGDAFV   73 (123)
T ss_dssp             SCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEEC----------------------------TTSCEEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEEC----------------------------CCCCEeeEEEE
Confidence            35799999999999999999999999985    57877742                            36889999999


Q ss_pred             EeCCHHhHHHHHHHHhCCcceecCcEEEEEecC
Q psy1185          79 EYDSHKSASLAKKRLATGRLKVWGCDIIVDWAD  111 (131)
Q Consensus        79 ~f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~  111 (131)
                      +|.+.++|.+|+.. ++.  .++|+.|.|..+.
T Consensus        74 ~F~~~~~A~~Al~~-~~~--~l~gR~i~V~~a~  103 (123)
T 2dha_A           74 LFACEEYAQNALRK-HKD--LLGKRYIELFRST  103 (123)
T ss_dssp             CCSSHHHHHHHHTT-TTE--ESSSCEECCEEEC
T ss_pred             EECCHHHHHHHHHh-CCC--eeCCeEEEEEECC
Confidence            99999999999997 776  8999999998875

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.72  E-value=2.1e-17  Score=107.32  Aligned_cols=79  Identities=16%  Similarity=0.193  Sum_probs=68.8

Q ss_pred             eEEEEeCC----CCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEe
Q psy1185           5 KVLYVRNL----TQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEY   80 (131)
Q Consensus         5 ~~l~v~nL----p~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f   80 (131)
                      ++||||||    |+.+++.+|+++|++||+|.++.++.+                           +.+|.++|||||+|
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~D---------------------------p~Tg~slGfgfVef   55 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFND---------------------------PNSALPLHVYLIKY   55 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEEC---------------------------TTTCCEEEEEEEEC
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEec---------------------------CCCCceeeEEEEEE
Confidence            68999999    999999999999999999999998854                           55899999999999


Q ss_pred             CC----HHh----HHHHHH--HHhCCcceecCcEEEEEecCC
Q psy1185          81 DS----HKS----ASLAKK--RLATGRLKVWGCDIIVDWADP  112 (131)
Q Consensus        81 ~~----~~~----a~~a~~--~l~~~~~~~~g~~l~v~~a~~  112 (131)
                      .+    +..    |.+|+.  .++|.  .++|+.|+|.+...
T Consensus        56 ~d~~g~~d~a~kAA~kAi~~~~lng~--~I~Gr~irV~ln~~   95 (136)
T 2j8a_A           56 ASSDGKINDAAKAAFSAVRKHESSGC--FIMGFKFEVILNKH   95 (136)
T ss_dssp             C------CCHHHHHHHHHHHTTTTCE--EETTEEEEEEECCT
T ss_pred             CCCCCCcchHHHHHHHHHHHhhhcCC--eecCcEEEEEECcc
Confidence            96    333    788888  67887  99999999998664

>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=99.72  E-value=2e-17  Score=105.85  Aligned_cols=77  Identities=18%  Similarity=0.234  Sum_probs=65.4

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||+++++++|+++|++||.|..+.++.                                  .+||||+|.+
T Consensus        15 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~----------------------------------~g~afV~f~~   60 (115)
T 3beg_B           15 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR----------------------------------DGTGVVEFVR   60 (115)
T ss_dssp             --CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECT----------------------------------TSEEEEEESS
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEec----------------------------------CCEEEEEECC
Confidence            357899999999999999999999999999998862                                  1999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcE-----EEEEecCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCD-----IIVDWADPQEE  115 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~-----l~v~~a~~~~~  115 (131)
                      .++|.+|++.|++.  .++|+.     +.|..+.++..
T Consensus        61 ~~~a~~Ai~~l~g~--~~~gr~~~~~~i~v~~~~~~~~   96 (115)
T 3beg_B           61 KEDMTYAVRKLDNT--KFRSHEGETAYIRVKVDGPRSP   96 (115)
T ss_dssp             HHHHHHHHHHHTTC--BCCCTTSCCCBCEEEECC----
T ss_pred             HHHHHHHHHHhCCC--EECCcEeeeEEEEeccCCCCCC
Confidence            99999999999998  889988     77777765443

>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=99.71  E-value=2.1e-17  Score=107.59  Aligned_cols=78  Identities=19%  Similarity=0.193  Sum_probs=67.9

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCee--EEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEe
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVE--RVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEY   80 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~--~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f   80 (131)
                      ..++|||+|||+++++++|+++|++| .|.  +++++++                            ..|.++|||||+|
T Consensus        41 ~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d----------------------------~~GrsrGfaFV~F   91 (126)
T 2hgm_A           41 NDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVD----------------------------PEGKITGEAFVQF   91 (126)
T ss_dssp             SCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCC----------------------------SSSSSCSEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEEC----------------------------CCCCCceEEEEEE
Confidence            36789999999999999999999999 566  7887753                            2488999999999


Q ss_pred             CCHHhHHHHHHHHhCCcceecCcEEEEEecCC
Q psy1185          81 DSHKSASLAKKRLATGRLKVWGCDIIVDWADP  112 (131)
Q Consensus        81 ~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~  112 (131)
                      .+.++|.+|+.. ++.  .++|+.|.|.++.+
T Consensus        92 ~~~e~A~~Al~~-~~~--~l~gR~I~V~~a~~  120 (126)
T 2hgm_A           92 ASQELAEKALGK-HKE--RIGHRYIEVFKSSQ  120 (126)
T ss_dssp             SSTTHHHHHHTT-TTC--CBTTBCCCCEEECH
T ss_pred             CCHHHHHHHHHH-CCC--EECCEEEEEEECCH
Confidence            999999999986 566  89999999998753

>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=99.71  E-value=8.2e-17  Score=116.62  Aligned_cols=81  Identities=20%  Similarity=0.370  Sum_probs=73.7

Q ss_pred             CceEEEEeCCCCCCCHHHHH----HHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEE
Q psy1185           3 KVKVLYVRNLTQYCTEEKLK----EAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFL   78 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~----~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv   78 (131)
                      ..++|||+|||.++++++|+    ++|++||.|.++++++                              ++.++|||||
T Consensus         8 ~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~------------------------------~~~~~g~afV   57 (282)
T 3pgw_A            8 PNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR------------------------------SLKMRGQAFV   57 (282)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC------------------------------CCCcceEEEE
Confidence            37899999999999999976    8999999999998873                              5778999999


Q ss_pred             EeCCHHhHHHHHHHHhCCcceecCcEEEEEecCCCCC
Q psy1185          79 EYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEE  115 (131)
Q Consensus        79 ~f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~  115 (131)
                      +|.+.++|.+|++.++|.  .+.|+.|+|.|++.+..
T Consensus        58 ~f~~~~~a~~A~~~l~g~--~~~g~~l~v~~a~~~~~   92 (282)
T 3pgw_A           58 IFKEVSSATNALRSMQGF--PFYDKPMRIQYAKTDSD   92 (282)
T ss_pred             EECCHHHHHHHHHHhcCC--eeCCcEEEEEEeccCcc
Confidence            999999999999999998  89999999999976553

>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=99.71  E-value=7.2e-17  Score=112.01  Aligned_cols=80  Identities=21%  Similarity=0.280  Sum_probs=70.6

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .++|||+|||+++++++|+++|++||.|.++++++.                            .++.++|||||+|.+.
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~----------------------------~~~~~kG~aFVeF~~~  160 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT----------------------------LHKAFKGSIFVVFDSI  160 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEEC----------------------------TTCCEEEEEEEEESSH
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEEC----------------------------CCCCcccEEEEEECCH
Confidence            478999999999999999999999999999998853                            2477899999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCCCC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADPQE  114 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~  114 (131)
                      ++|.+|+..++.   .++|+.|.|.|+..-.
T Consensus       161 e~A~~A~~~~~~---~~~Gr~l~V~~~~~y~  188 (193)
T 2voo_A          161 ESAKKFVETPGQ---KYKETDLLILFKDDYF  188 (193)
T ss_dssp             HHHHHHHHCTTC---EETTEECEEEETTTC-
T ss_pred             HHHHHHHHhCCC---eECCEEEEEEEhHHHH
Confidence            999999987653   8999999999987543

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.67  E-value=9.5e-16  Score=96.79  Aligned_cols=82  Identities=24%  Similarity=0.243  Sum_probs=69.5

Q ss_pred             CceEEEEeCCCC-----CCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEE
Q psy1185           3 KVKVLYVRNLTQ-----YCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCF   77 (131)
Q Consensus         3 ~~~~l~v~nLp~-----~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~f   77 (131)
                      .+++|+|.|+..     +-++++|++.|++||.|.++.+++.                          +..++.++|+||
T Consensus         7 ~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~--------------------------~~~~~~~~G~~F   60 (105)
T 2pe8_A            7 PTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEI--------------------------PGAPDDEAVRIF   60 (105)
T ss_dssp             CCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEEC--------------------------SSCCTTTSEEEE
T ss_pred             CCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecC--------------------------CCCCCCCcEEEE
Confidence            367899999963     2378999999999999999998853                          111357899999


Q ss_pred             EEeCCHHhHHHHHHHHhCCcceecCcEEEEEecCC
Q psy1185          78 LEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADP  112 (131)
Q Consensus        78 v~f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~  112 (131)
                      |+|.+.++|.+|+..|||+  .++|+.|.|.|+.+
T Consensus        61 V~f~~~~~A~~Ai~~lnG~--~~~Gr~i~v~~a~~   93 (105)
T 2pe8_A           61 LEFERVESAIKAVVDLNGR--YFGGRVVKACFYNL   93 (105)
T ss_dssp             EEESSHHHHHHHHHHHTTC--EETTEECEEEECCH
T ss_pred             EEECCHHHHHHHHHHHCCC--EECCcEEEEEEcCH
Confidence            9999999999999999999  89999999999864

>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=99.67  E-value=4.6e-16  Score=112.64  Aligned_cols=74  Identities=22%  Similarity=0.366  Sum_probs=68.7

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .++|||+|||.++++++|+++|++||.|.+++++.+                                .+|+|||+|.+.
T Consensus       207 ~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~--------------------------------~~g~afV~f~~~  254 (282)
T 3pgw_A          207 NHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPG--------------------------------RHDIAFVEFDNE  254 (282)
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecC--------------------------------CCcEEEEEeCCH
Confidence            578999999999999999999999999999998743                                268999999999


Q ss_pred             HhHHHHHHHHhCCcceec-CcEEEEEecC
Q psy1185          84 KSASLAKKRLATGRLKVW-GCDIIVDWAD  111 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~-g~~l~v~~a~  111 (131)
                      ++|.+|+..|+|.  .++ |+.|+|+||+
T Consensus       255 ~~A~~A~~~l~g~--~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          255 VQAGAARDALQGF--KITQNNAMKISFAK  281 (282)
T ss_pred             HHHHHHHHHcCCc--EeCCCCEEEEEEec
Confidence            9999999999998  888 9999999986

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=1.5e-15  Score=96.58  Aligned_cols=81  Identities=14%  Similarity=0.247  Sum_probs=69.2

Q ss_pred             CceEEEEeCCCCCCC-----------HHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCC
Q psy1185           3 KVKVLYVRNLTQYCT-----------EEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKK   71 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t-----------~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~   71 (131)
                      ..++|+|.||.....           +++|+++|++||.|.++.+.                               ...
T Consensus        14 ~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i~-------------------------------~~~   62 (112)
T 2dit_A           14 HERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLF-------------------------------DRH   62 (112)
T ss_dssp             SCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEE-------------------------------TTC
T ss_pred             CceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEEe-------------------------------cCC
Confidence            367899999944432           58999999999999999664                               234


Q ss_pred             CcceEEEEeCCHHhHHHHHHHHhCCcceecCcEEEEEecCCCCCC
Q psy1185          72 NRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEP  116 (131)
Q Consensus        72 ~~~~~fv~f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~  116 (131)
                      ++|||||+|.+.++|.+|+..|+|.  .++|+.|.|.|+.++...
T Consensus        63 ~~G~afV~f~~~~~A~~Ai~~lng~--~~~gr~l~v~~a~~~~~~  105 (112)
T 2dit_A           63 PDGVASVSFRDPEEADYCIQTLDGR--WFGGRQITAQAWDGTTDY  105 (112)
T ss_dssp             TTCEEEEECSCHHHHHHHHHHSTTC--EETTEECEEEECCSCCCS
T ss_pred             CCEEEEEEECCHHHHHHHHHHcCCC--EECCcEEEEEEeCCCCCc
Confidence            7999999999999999999999998  899999999999886543

>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=99.61  E-value=2e-15  Score=105.54  Aligned_cols=76  Identities=21%  Similarity=0.142  Sum_probs=65.8

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCe--eEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeC
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRV--ERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYD   81 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v--~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~   81 (131)
                      .++|||+|||+++++++|+++|++||.|  .+++++..                             .+.++|+|||+|.
T Consensus       123 ~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~-----------------------------~~~~~g~gfV~f~  173 (205)
T 3tyt_A          123 SNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSG-----------------------------KSERSSSGLLEWD  173 (205)
T ss_dssp             CSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSC-----------------------------CSSSSEEEEEECS
T ss_pred             cceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcC-----------------------------CCCCceEEEEEeC
Confidence            4689999999999999999999999999  88887742                             3556799999999


Q ss_pred             CHHhHHHHHHHHhCCcceecCc----EEEEEec
Q psy1185          82 SHKSASLAKKRLATGRLKVWGC----DIIVDWA  110 (131)
Q Consensus        82 ~~~~a~~a~~~l~~~~~~~~g~----~l~v~~a  110 (131)
                      +.++|.+|+..|||.  .+.|.    .+.|.||
T Consensus       174 ~~~~A~~Ai~~lng~--~~~g~~~~~p~~vk~~  204 (205)
T 3tyt_A          174 SKSDALETLGFLNHY--QMKNPNGPYPYTLKLC  204 (205)
T ss_dssp             SHHHHHHHHHHHTTC--EECCSSSSSCEECEEE
T ss_pred             CHHHHHHHHHHhCCC--CccCCCCCcceEEEec
Confidence            999999999999998  77766    4777765

>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=99.57  E-value=1.4e-15  Score=95.82  Aligned_cols=71  Identities=18%  Similarity=0.289  Sum_probs=60.6

Q ss_pred             eCCCCCCCHHHHHHHh------------hccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEE
Q psy1185          10 RNLTQYCTEEKLKEAF------------EQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCF   77 (131)
Q Consensus        10 ~nLp~~~t~~~l~~~F------------~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~f   77 (131)
                      .|||+.+++++|++.|            ++||.|.++.++++                            ..+.++||||
T Consensus        21 ~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~----------------------------~~~~~~G~~f   72 (104)
T 1jmt_A           21 DGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN----------------------------LGDHLVGNVY   72 (104)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCS----------------------------SSSSSEEEEE
T ss_pred             CCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeC----------------------------CCCCccEEEE
Confidence            4555666777666666            99999999998854                            2467899999


Q ss_pred             EEeCCHHhHHHHHHHHhCCcceecCcEEEEEec
Q psy1185          78 LEYDSHKSASLAKKRLATGRLKVWGCDIIVDWA  110 (131)
Q Consensus        78 v~f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a  110 (131)
                      |+|.+.++|.+|+..|||.  .++|+.|.|.|+
T Consensus        73 V~f~~~~~A~~A~~~lng~--~~~Gr~i~v~~s  103 (104)
T 1jmt_A           73 VKFRREEDAEKAVIDLNNR--WFNGQPIHAELS  103 (104)
T ss_dssp             EEESCHHHHHHHHHHHTTC--EETTEECCEEEC
T ss_pred             EEECCHHHHHHHHHHHCCC--EECCEEEEEEEc
Confidence            9999999999999999998  899999999986

>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=99.53  E-value=5e-14  Score=88.81  Aligned_cols=82  Identities=20%  Similarity=0.285  Sum_probs=66.9

Q ss_pred             ceEEEEeCC--CCCCC--------HHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCc
Q psy1185           4 VKVLYVRNL--TQYCT--------EEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNR   73 (131)
Q Consensus         4 ~~~l~v~nL--p~~~t--------~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~   73 (131)
                      ++.|.+.|+  |.+..        +++|++.|++||.|.++++++..                         ...++.++
T Consensus         5 s~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~-------------------------~~~~~~~~   59 (105)
T 3v4m_A            5 TEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPV-------------------------DGVEVPGC   59 (105)
T ss_dssp             CSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCB-------------------------TTBCCTTT
T ss_pred             CeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccC-------------------------CCCCcCCc
Confidence            567888888  44443        36899999999999999988530                         00123578


Q ss_pred             ceEEEEeCCHHhHHHHHHHHhCCcceecCcEEEEEecCC
Q psy1185          74 GFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADP  112 (131)
Q Consensus        74 ~~~fv~f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~  112 (131)
                      |++||+|.+.++|.+|+..|||+  .++|+.|+|.|+..
T Consensus        60 G~~fV~f~~~~~A~~Ai~~lnG~--~f~GR~i~v~~~~~   96 (105)
T 3v4m_A           60 GKIFVEFTSVFDCQKAMQGLTGR--KFANRVVVTKYCDP   96 (105)
T ss_dssp             TEEEEEESSHHHHHHHHHHHTTC--EETTEECEEEEECH
T ss_pred             EEEEEEECCHHHHHHHHHHhCCC--EeCCCEEEEEEeCH
Confidence            99999999999999999999999  89999999999763

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.53  E-value=1.9e-13  Score=85.49  Aligned_cols=67  Identities=19%  Similarity=0.311  Sum_probs=58.5

Q ss_pred             CCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHHhHHHHHHHH
Q psy1185          14 QYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRL   93 (131)
Q Consensus        14 ~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l   93 (131)
                      .++++++|+++|++||.|.+++++                                +.++|||||+|.++++|..|++.+
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~--------------------------------~~~rGfaFVeF~~~~~A~~Ai~~~   74 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLS--------------------------------SKKPGTAVVEFATVKAAELAVQNE   74 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEE--------------------------------SSSSSEEEEEESCHHHHHHHHHTC
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEc--------------------------------cCCCCEEEEEECCHHHHHHHHHhc
Confidence            568999999999999999999886                                256899999999999999999985


Q ss_pred             hCCcceecCcEEEEEecCCCCCC
Q psy1185          94 ATGRLKVWGCDIIVDWADPQEEP  116 (131)
Q Consensus        94 ~~~~~~~~g~~l~v~~a~~~~~~  116 (131)
                      ++    +.|+.|+|.|+.++...
T Consensus        75 ~~----~~g~~l~V~~a~~~~~~   93 (100)
T 2d9o_A           75 VG----LVDNPLKISWLEGQPQD   93 (100)
T ss_dssp             CB----CSSSBCEEECSSCCCCC
T ss_pred             CC----CCCCeEEEEEccCCCCC
Confidence            54    57999999999877644

>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=99.51  E-value=7.7e-14  Score=104.35  Aligned_cols=75  Identities=19%  Similarity=0.293  Sum_probs=62.8

Q ss_pred             ceEEEEeC--CCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeC
Q psy1185           4 VKVLYVRN--LTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYD   81 (131)
Q Consensus         4 ~~~l~v~n--Lp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~   81 (131)
                      .++|||||  |+.++|+++|+++|++||.|.++.+..                                 +||||||+|.
T Consensus        18 s~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~---------------------------------~kgfaFV~f~   64 (345)
T 3tht_A           18 TQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP---------------------------------NKPYSFARYR   64 (345)
T ss_dssp             CSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT---------------------------------TCSEEEEEES
T ss_pred             CCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC---------------------------------CCCEEEEEEC
Confidence            57999999  588999999999999999999986642                                 4799999999


Q ss_pred             CHHhHHHHHHHHhCCcce-ecCc--EEEEEecC
Q psy1185          82 SHKSASLAKKRLATGRLK-VWGC--DIIVDWAD  111 (131)
Q Consensus        82 ~~~~a~~a~~~l~~~~~~-~~g~--~l~v~~a~  111 (131)
                      +.++|++|++.|||+++. ..|+  .+.+.|++
T Consensus        65 ~~~~A~~Ai~~lnG~~~~~~~g~~~~ly~~~~~   97 (345)
T 3tht_A           65 TTEESKRAYVTLNGKEVVDDLGQKITLYLNFVE   97 (345)
T ss_dssp             SHHHHHHHHHHTTTCEEECTTSCEEECEEEECS
T ss_pred             CHHHHHHHHHHhCCCccccccCCceEEEEEEee
Confidence            999999999999998541 1245  47778874

>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=99.49  E-value=1.3e-13  Score=88.60  Aligned_cols=84  Identities=18%  Similarity=0.247  Sum_probs=67.8

Q ss_pred             CceEEEEeCCC--CC---CCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEE
Q psy1185           3 KVKVLYVRNLT--QY---CTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCF   77 (131)
Q Consensus         3 ~~~~l~v~nLp--~~---~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~f   77 (131)
                      .+++|++.|+-  .+   -.+++|++.|++||.|.++.+++..                       .....++.++|++|
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~-----------------------~~~~~~~~~~G~~F   75 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEK-----------------------QGEEEDAEIIVKIF   75 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEE-----------------------ESSSTTCEEEEEEE
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecC-----------------------CCcccCCcceEEEE
Confidence            36789999983  22   2368999999999999999988531                       00011345679999


Q ss_pred             EEeCCHHhHHHHHHHHhCCcceecCcEEEEEecC
Q psy1185          78 LEYDSHKSASLAKKRLATGRLKVWGCDIIVDWAD  111 (131)
Q Consensus        78 v~f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~  111 (131)
                      |+|.+.++|.+|+..|||+  .++|+.|.|.|+.
T Consensus        76 V~F~~~e~A~~Ai~~LnGr--~f~GR~i~v~~~~  107 (118)
T 3ue2_A           76 VEFSIASETHKAIQALNGR--WFAGRKVVAEVYD  107 (118)
T ss_dssp             EEESSHHHHHHHHHHHTTC--EETTEECEEEEEC
T ss_pred             EEECCHHHHHHHHHHHCCC--EECCcEEEEEEcC
Confidence            9999999999999999999  8999999999975

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.41  E-value=1.8e-12  Score=83.52  Aligned_cols=81  Identities=12%  Similarity=0.101  Sum_probs=70.3

Q ss_pred             CCCceEEEEeCCCCC-CCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEE
Q psy1185           1 MSKVKVLYVRNLTQY-CTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLE   79 (131)
Q Consensus         1 ~~~~~~l~v~nLp~~-~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~   79 (131)
                      |.+.+.|||+|||.+ +++++|+++|++||+|..|.+.++                                 ...|||.
T Consensus        15 ~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g---------------------------------~~tgfVr   61 (121)
T 1owx_A           15 EKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG---------------------------------AKEGIIL   61 (121)
T ss_dssp             CCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT---------------------------------CSEEEEE
T ss_pred             ccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecC---------------------------------CCEEEEE
Confidence            456788999999999 999999999999999999998865                                 3369999


Q ss_pred             eCC-HHhHHHHHHHHhCCcceecCcEEEEEecCCCC
Q psy1185          80 YDS-HKSASLAKKRLATGRLKVWGCDIIVDWADPQE  114 (131)
Q Consensus        80 f~~-~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~  114 (131)
                      |.+ ..+|..|++.++...+.+.|..++++......
T Consensus        62 f~~~~~~A~~av~~ln~~~~~i~g~~~~~evL~Gee   97 (121)
T 1owx_A           62 FKEKAKEALGKAKDANNGNLQLRNKEVTWEVLEGEV   97 (121)
T ss_dssp             ESSCHHHHHHHHHHTTTSCBCTTSSSEEEEECCHHH
T ss_pred             ECCChHHHHHHHHHhhcCCcEEeCcEEEEEECCCHH
Confidence            999 89999999999877789999888887765433

>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=99.39  E-value=1.6e-12  Score=83.04  Aligned_cols=75  Identities=16%  Similarity=0.141  Sum_probs=62.1

Q ss_pred             ceEEEEeCCCCCC----------CHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCc
Q psy1185           4 VKVLYVRNLTQYC----------TEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNR   73 (131)
Q Consensus         4 ~~~l~v~nLp~~~----------t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~   73 (131)
                      ++.|.+.|+=..-          .+++|++.|++||.|.++.+.+.                               .++
T Consensus         7 s~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~-------------------------------~~~   55 (114)
T 3s6e_A            7 TQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKN-------------------------------SAQ   55 (114)
T ss_dssp             CSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTT-------------------------------CTT
T ss_pred             CcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecC-------------------------------CCc
Confidence            4567777772211          12578999999999999988743                               258


Q ss_pred             ceEEEEeCCHHhHHHHHHHHhCCcceecCcEEEEEecC
Q psy1185          74 GFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWAD  111 (131)
Q Consensus        74 ~~~fv~f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~  111 (131)
                      |++||+|.+.++|.+|++.|||.  .++|+.|.|.|+.
T Consensus        56 G~~fV~f~~~e~A~~Ai~~lnG~--~f~GR~i~v~~~~   91 (114)
T 3s6e_A           56 GNVYVKCPSIAAAIAAVNALHGR--WFAGKMITAAYVP   91 (114)
T ss_dssp             CCEEEECSSHHHHHHHHHHHTTC--EETTEECEEEEEC
T ss_pred             EEEEEEECCHHHHHHHHHHhCCC--EECCEEEEEEEEc
Confidence            99999999999999999999999  8999999999985

>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=99.25  E-value=2e-11  Score=83.33  Aligned_cols=52  Identities=31%  Similarity=0.668  Sum_probs=48.6

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe--------cCeEEEEECCHHHHHhhc
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYAFVHFEDRQEAITVT   55 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~--------~~~~fv~~~~~~~a~~~~   55 (131)
                      .++|||+|||.++++++|+++|++||.|..+.++        +|||||+|.+.++|..+.
T Consensus       104 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~  163 (196)
T 1l3k_A          104 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV  163 (196)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHH
T ss_pred             cceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHH
Confidence            4799999999999999999999999999999987        679999999999999855

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.24  E-value=2.1e-11  Score=85.12  Aligned_cols=52  Identities=29%  Similarity=0.585  Sum_probs=48.7

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe------cCeEEEEECCHHHHHhhc
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI------KDYAFVHFEDRQEAITVT   55 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~------~~~~fv~~~~~~~a~~~~   55 (131)
                      .++|||+|||+++++++|+++|++||.|.+++++      +|||||+|.+.++|+.+.
T Consensus       103 ~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~~~~~g~~fV~f~~~~~a~~Ai  160 (213)
T 4f02_A          103 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAI  160 (213)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESSHHHHHHHH
T ss_pred             cccceECCcccccHHHHHHHHHhhcCCeEEEEeeccCCCCceEEEEEeCCHHHHHHHH
Confidence            5689999999999999999999999999999987      789999999999999954

>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=99.24  E-value=2.5e-11  Score=81.29  Aligned_cols=53  Identities=26%  Similarity=0.575  Sum_probs=48.9

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe-------cCeEEEEECCHHHHHhhc
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI-------KDYAFVHFEDRQEAITVT   55 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~-------~~~~fv~~~~~~~a~~~~   55 (131)
                      ..++|||+|||.++++++|+++|++||.|.++.++       +|||||+|.+.++|..+.
T Consensus        94 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~~~~~A~~A~  153 (175)
T 3nmr_A           94 EDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAI  153 (175)
T ss_dssp             GGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHH
T ss_pred             CCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEECCHHHHHHHH
Confidence            35789999999999999999999999999999987       579999999999999954

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

Probab=99.21  E-value=4.5e-11  Score=79.31  Aligned_cols=53  Identities=23%  Similarity=0.423  Sum_probs=48.9

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe--------cCeEEEEECCHHHHHhhc
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYAFVHFEDRQEAITVT   55 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~--------~~~~fv~~~~~~~a~~~~   55 (131)
                      ..++|||+|||.++++++|+++|++||.|.++.++        +|||||+|.+.++|..+.
T Consensus        86 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~  146 (166)
T 3md3_A           86 DTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM  146 (166)
T ss_dssp             TCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHH
T ss_pred             CCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHH
Confidence            36789999999999999999999999999999987        579999999999999954

>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=99.21  E-value=2e-11  Score=81.37  Aligned_cols=53  Identities=15%  Similarity=0.380  Sum_probs=49.0

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe--------cCeEEEEECCHHHHHhhcC
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYAFVHFEDRQEAITVTG   56 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~--------~~~~fv~~~~~~~a~~~~g   56 (131)
                      .++|||+|||.++++++|+++|++||.|.++.++        +|||||+|.+.++|..+..
T Consensus        87 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~  147 (167)
T 2cjk_A           87 TGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ  147 (167)
T ss_dssp             CEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH
T ss_pred             CCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh
Confidence            5689999999999999999999999999999987        4799999999999999654

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

Probab=99.19  E-value=6.7e-11  Score=80.87  Aligned_cols=52  Identities=21%  Similarity=0.487  Sum_probs=48.4

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe--------cCeEEEEECCHHHHHhh
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYAFVHFEDRQEAITV   54 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~--------~~~~fv~~~~~~~a~~~   54 (131)
                      ..++|||+|||.++++++|+++|++||.|.+++++        +|||||+|.+.++|..+
T Consensus       113 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A  172 (198)
T 2yh0_A          113 SAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQA  172 (198)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHH
Confidence            35899999999999999999999999999999987        67999999999999984

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.18  E-value=1.1e-10  Score=71.13  Aligned_cols=72  Identities=15%  Similarity=0.217  Sum_probs=59.7

Q ss_pred             ceEEEEeCCCC----CCCH----HHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcce
Q psy1185           4 VKVLYVRNLTQ----YCTE----EKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGF   75 (131)
Q Consensus         4 ~~~l~v~nLp~----~~t~----~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~   75 (131)
                      ..||+|.-.|.    ...+    .+|.+.|++||.|..++++.+                                   .
T Consensus         7 d~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d-----------------------------------~   51 (91)
T 2dnr_A            7 GGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVED-----------------------------------K   51 (91)
T ss_dssp             SCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSS-----------------------------------S
T ss_pred             CCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecC-----------------------------------C
Confidence            35777877662    3333    679999999999999998843                                   3


Q ss_pred             EEEEeCCHHhHHHHHHHHhCCcceecCcEEEEEecCCC
Q psy1185          76 CFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQ  113 (131)
Q Consensus        76 ~fv~f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~  113 (131)
                      +||+|.+.++|.+|++ |+|.  .++|+.|+|+++.+.
T Consensus        52 ~fVtF~d~~sAlaAi~-mnG~--~v~Gr~LkV~lkt~d   86 (91)
T 2dnr_A           52 MWVTFLEGSSALNVLS-LNGK--ELLNRTITIALKSPS   86 (91)
T ss_dssp             EEEEESSHHHHHHGGG-GTTC--EETTEEEEEEECCCS
T ss_pred             EEEEECChHHHHHHHh-cCCe--EeCCeEEEEEeCCCC
Confidence            8999999999999998 9998  999999999998764

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

Probab=99.18  E-value=7e-11  Score=81.78  Aligned_cols=51  Identities=24%  Similarity=0.561  Sum_probs=48.0

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe--------cCeEEEEECCHHHHHhh
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYAFVHFEDRQEAITV   54 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~--------~~~~fv~~~~~~~a~~~   54 (131)
                      .++|||+|||.++++++|+++|++||.|..++++        +|||||+|.+.++|..+
T Consensus       125 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A  183 (216)
T 2qfj_A          125 FNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDA  183 (216)
T ss_dssp             SCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHH
T ss_pred             CcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHH
Confidence            5799999999999999999999999999999987        57999999999999984

>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=99.18  E-value=4.5e-11  Score=80.03  Aligned_cols=52  Identities=21%  Similarity=0.482  Sum_probs=48.1

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe--------cCeEEEEECCHHHHHhhc
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYAFVHFEDRQEAITVT   55 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~--------~~~~fv~~~~~~~a~~~~   55 (131)
                      .++|||+|||.++++++|+++|++||.|.++.++        +|||||+|.+.++|..+.
T Consensus        94 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~  153 (172)
T 2g4b_A           94 AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI  153 (172)
T ss_dssp             TTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHH
T ss_pred             CCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHH
Confidence            4789999999999999999999999999999987        579999999999999844

>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=99.17  E-value=9.3e-11  Score=78.10  Aligned_cols=53  Identities=32%  Similarity=0.555  Sum_probs=48.7

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe--------cCeEEEEECCHHHHHhhc
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYAFVHFEDRQEAITVT   55 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~--------~~~~fv~~~~~~~a~~~~   55 (131)
                      ..++|||+|||.++++++|+++|++||.|..+.++        +|||||+|.+.++|..+.
T Consensus        88 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~  148 (168)
T 1b7f_A           88 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI  148 (168)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHH
T ss_pred             CCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHH
Confidence            35789999999999999999999999999999887        479999999999999954

>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=99.16  E-value=1.1e-10  Score=77.49  Aligned_cols=52  Identities=31%  Similarity=0.545  Sum_probs=48.3

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe--------cCeEEEEECCHHHHHhhc
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYAFVHFEDRQEAITVT   55 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~--------~~~~fv~~~~~~~a~~~~   55 (131)
                      .++|||+|||.++++++|+++|++||.|..++++        +|||||+|.+.++|..+.
T Consensus        88 ~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~  147 (167)
T 1fxl_A           88 DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI  147 (167)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHH
T ss_pred             CCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHH
Confidence            5789999999999999999999999999999886        589999999999999954

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.09  E-value=2.2e-10  Score=78.53  Aligned_cols=52  Identities=25%  Similarity=0.359  Sum_probs=48.8

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccC-CeeEEEEe---cCeEEEEECCHHHHHhhc
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYG-RVERVKRI---KDYAFVHFEDRQEAITVT   55 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G-~v~~~~i~---~~~~fv~~~~~~~a~~~~   55 (131)
                      .++|||+|||.++++++|+++|++|| .|.+++++   +|||||+|.+.++|..+.
T Consensus       120 ~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~~~g~afV~f~~~~~A~~A~  175 (198)
T 1qm9_A          120 SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQAL  175 (198)
T ss_dssp             CCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESSTTSSCEEEECSSHHHHHHHH
T ss_pred             ccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeCCCcEEEEEeCCHHHHHHHH
Confidence            67899999999999999999999999 99999995   799999999999999954

>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=99.09  E-value=3.3e-10  Score=79.78  Aligned_cols=52  Identities=25%  Similarity=0.359  Sum_probs=48.6

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccC-CeeEEEEe---cCeEEEEECCHHHHHhhc
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYG-RVERVKRI---KDYAFVHFEDRQEAITVT   55 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G-~v~~~~i~---~~~~fv~~~~~~~a~~~~   55 (131)
                      .++|||+|||.++++++|+++|++|| .|..++++   +|||||+|.+.++|..+.
T Consensus       151 ~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~g~afV~f~~~~~A~~Ai  206 (229)
T 2adc_A          151 SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQAL  206 (229)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSSTTCEEEEESSHHHHHHHH
T ss_pred             CCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEECCCcEEEEEECCHHHHHHHH
Confidence            57899999999999999999999999 99999994   799999999999999953

>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=99.08  E-value=3e-10  Score=81.52  Aligned_cols=51  Identities=31%  Similarity=0.485  Sum_probs=48.1

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe-------cCeEEEEECCHHHHHhh
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI-------KDYAFVHFEDRQEAITV   54 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~-------~~~~fv~~~~~~~a~~~   54 (131)
                      .++|||+|||..+++++|+++|++||.|.++.++       +|||||+|.+.++|..+
T Consensus        96 ~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A  153 (261)
T 3sde_A           96 GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKA  153 (261)
T ss_dssp             SSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHHHHHH
T ss_pred             CCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHHHHHH
Confidence            5689999999999999999999999999999987       78999999999999994

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=99.02  E-value=1.1e-09  Score=76.83  Aligned_cols=71  Identities=17%  Similarity=0.211  Sum_probs=59.6

Q ss_pred             CCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHHhHHHHHHHHhC
Q psy1185          16 CTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLAT   95 (131)
Q Consensus        16 ~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~   95 (131)
                      -.+++|++.|++||.|.++.++++.                       .....++.++|++||+|.+.++|.+|+..|+|
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~-----------------------~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~g  197 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEK-----------------------QGEEEDAEIIVKIFVEFSIASETHKAIQALNG  197 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEE-----------------------CCSSTTCCEEEEEEEEESSHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCC-----------------------CCcccCcCceeEEEEEECCHHHHHHHHHHhcC
Confidence            4567899999999999999887431                       11123568899999999999999999999999


Q ss_pred             CcceecCcEEEEEecC
Q psy1185          96 GRLKVWGCDIIVDWAD  111 (131)
Q Consensus        96 ~~~~~~g~~l~v~~a~  111 (131)
                      +  .++||.|.+.|+.
T Consensus       198 r--~~~gr~i~~~~~~  211 (222)
T 3dxb_A          198 R--WFAGRKVVAEVYD  211 (222)
T ss_dssp             C--BSSSSBCEEEECC
T ss_pred             c--eECCeEEEEEEcC
Confidence            9  8999999999975

>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=99.00  E-value=5.6e-10  Score=74.97  Aligned_cols=53  Identities=28%  Similarity=0.411  Sum_probs=46.5

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEE---ecCeEEEEECCHHHHHhhcC
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKR---IKDYAFVHFEDRQEAITVTG   56 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i---~~~~~fv~~~~~~~a~~~~g   56 (131)
                      .++|||+|||.++++++|+++|++||.|..+..   .+|||||+|.+.++|..+..
T Consensus        99 ~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~~~~~~~~g~afV~f~~~~~A~~A~~  154 (175)
T 1fje_B           99 ARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLE  154 (175)
T ss_dssp             GGEEEEESCCSSCCHHHHHHHCTTCSEEEEECSSSSCCSEEEEECSSHHHHHHHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCeEEEecCCCCCceEEEEEECCHHHHHHHHH
Confidence            579999999999999999999999998887711   17999999999999999543

>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=98.91  E-value=7.1e-09  Score=63.52  Aligned_cols=70  Identities=14%  Similarity=0.114  Sum_probs=58.3

Q ss_pred             ceEEEEeCCCCC-----CCH----HHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcc
Q psy1185           4 VKVLYVRNLTQY-----CTE----EKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRG   74 (131)
Q Consensus         4 ~~~l~v~nLp~~-----~t~----~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~   74 (131)
                      ..||+|.-++.+     +.+    .+|.+.|++||.|..+++..+                                   
T Consensus        15 D~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d-----------------------------------   59 (95)
T 1ufw_A           15 DATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG-----------------------------------   59 (95)
T ss_dssp             TCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT-----------------------------------
T ss_pred             CCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecC-----------------------------------
Confidence            458889888643     222    568899999999999998843                                   


Q ss_pred             eEEEEeCCHHhHHHHHHHHhCCcceecCcEEEEEecC
Q psy1185          75 FCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWAD  111 (131)
Q Consensus        75 ~~fv~f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~  111 (131)
                      -+||+|.+.++|.+|++ |+|.  .++||.|+|++-.
T Consensus        60 ~~fVtF~d~~sAl~AI~-ldG~--~v~Gr~L~V~~k~   93 (95)
T 1ufw_A           60 QMLVTFADSHSALSVLD-VDGM--KVKGRAVKISGPS   93 (95)
T ss_dssp             EEEEECSCSHHHHHHHH-GGGS--EETTEEEEEECCC
T ss_pred             cEEEEEcChHHHHHHHh-cCCe--eeCCeEEEEeccC
Confidence            29999999999999998 9998  9999999999743

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.50  E-value=1.4e-06  Score=54.63  Aligned_cols=72  Identities=10%  Similarity=0.043  Sum_probs=64.5

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhcc-----CCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEE
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQY-----GRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCF   77 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~-----G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~f   77 (131)
                      ..++|-+-|||..+++..|+.+.+++     |.+..+.+...                                 .+-|+
T Consensus        20 ~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pD---------------------------------H~GAi   66 (117)
T 2l9w_A           20 LETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSD---------------------------------FNGAI   66 (117)
T ss_dssp             TTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETT---------------------------------TTEEE
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecC---------------------------------CCceE
Confidence            36889999999999999999999999     99999987732                                 56699


Q ss_pred             EEeCCHHhHHHHHHHHhCCcceecCcEEEEEe
Q psy1185          78 LEYDSHKSASLAKKRLATGRLKVWGCDIIVDW  109 (131)
Q Consensus        78 v~f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~  109 (131)
                      |+|.+...|-+|.-.|+|.  .+.|++|++.-
T Consensus        67 vef~d~~~AgKasLaL~G~--ef~gr~Lr~gT   96 (117)
T 2l9w_A           67 IIFRDSKFAAKMLMILNGS--QFQGKVIRSGT   96 (117)
T ss_dssp             EECSCHHHHHHHHHHHSSE--EETTEEEEEEC
T ss_pred             EEEccchhhHHHHhhcCCe--eecCeEEEecC
Confidence            9999999999999999998  88999999864

>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=97.97  E-value=4.8e-05  Score=47.22  Aligned_cols=76  Identities=17%  Similarity=0.187  Sum_probs=62.1

Q ss_pred             ceEEEEeCCCCCC-CH----HHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEE
Q psy1185           4 VKVLYVRNLTQYC-TE----EKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFL   78 (131)
Q Consensus         4 ~~~l~v~nLp~~~-t~----~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv   78 (131)
                      .++|+|.||+.++ ..    ..++++|.+|+++......+.                                 -.-..|
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkS---------------------------------FRRirv   51 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS---------------------------------FKRVRI   51 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT---------------------------------TTEEEE
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCc---------------------------------ceEEEE
Confidence            4689999998864 22    467899999999888766543                                 234688


Q ss_pred             EeCCHHhHHHHHHHHhCCcceecCcEEEEEecCCCC
Q psy1185          79 EYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQE  114 (131)
Q Consensus        79 ~f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~  114 (131)
                      .|.+.++|.+|...||+.  .++|+.++|-|+.+-.
T Consensus        52 ~F~~~~~A~~AR~~Lh~~--~f~g~~~r~YFgq~~~   85 (104)
T 1wey_A           52 NFSNPLSAADARLRLHKT--EFLGKEMKLYFAQTLH   85 (104)
T ss_dssp             ECSSTTHHHHHHHTSTTS--EETTEECEEECCCCSS
T ss_pred             EeCChHHHHHHHHHhccc--eecCceeEEEecCCCC
Confidence            999999999999999998  8999999999998543

>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=97.64  E-value=0.00061  Score=41.31  Aligned_cols=67  Identities=12%  Similarity=0.177  Sum_probs=52.2

Q ss_pred             eEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHH
Q psy1185           5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHK   84 (131)
Q Consensus         5 ~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~   84 (131)
                      ++|-|++||+..|++++.+.++....+.....+.|-                         ........+-|+|.|.+.+
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~-------------------------~s~~~~~~SRaYi~f~~~e   56 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSND-------------------------TSLYPHMYARAYINFKNQE   56 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESC-------------------------CSSTTCCCEEEEEEESSSH
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCc-------------------------cCCCCCcceEEEEEeCCHH
Confidence            689999999999999999999998876665555440                         0001123466999999999


Q ss_pred             hHHHHHHHHhCC
Q psy1185          85 SASLAKKRLATG   96 (131)
Q Consensus        85 ~a~~a~~~l~~~   96 (131)
                      ++..-.+.++|.
T Consensus        57 ~v~~f~~~~~g~   68 (91)
T 1uw4_A           57 DIILFRDRFDGY   68 (91)
T ss_dssp             HHHHHHHHHTTC
T ss_pred             HHHHHHHHhCCc
Confidence            999999999997

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.61  E-value=0.0011  Score=40.98  Aligned_cols=70  Identities=20%  Similarity=0.165  Sum_probs=54.8

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhcc-----CCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEE
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQY-----GRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCF   77 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~-----G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~f   77 (131)
                      -.++|.|.|||..++++.|.-+|++-     |+|..+...                                   .+-|+
T Consensus         7 ~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~-----------------------------------~~~Av   51 (104)
T 2dhx_A            7 GGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRL-----------------------------------GCGGV   51 (104)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEE-----------------------------------TTEEE
T ss_pred             CccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEc-----------------------------------CCcEE
Confidence            35789999999999999999999982     578777543                                   26789


Q ss_pred             EEeCCHHhHHHHHHHHhCCcceecCcEEEEEec
Q psy1185          78 LEYDSHKSASLAKKRLATGRLKVWGCDIIVDWA  110 (131)
Q Consensus        78 v~f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a  110 (131)
                      |+|.+.+.|++.+..-..   .+++..|.|.-.
T Consensus        52 ItF~d~~va~rVL~k~~H---~L~~~~LsV~P~   81 (104)
T 2dhx_A           52 LTFREPADAERVLAQADH---ELHGAQLSLRPA   81 (104)
T ss_dssp             EEESSHHHHHHHHTCSCC---BSSSSBCEEEEC
T ss_pred             EEEcChHHHHHHhcCCcc---eecCeEEEEEcC
Confidence            999999998877665332   778888888543

>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=97.24  E-value=0.0013  Score=40.32  Aligned_cols=56  Identities=16%  Similarity=0.267  Sum_probs=44.8

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      +.+.+++ +.|..+...||.++|++||. ..+..+.                                  -..|||.|.+
T Consensus        15 r~HVf~l-~FP~ewKt~DI~~lFs~fgg-v~I~Wid----------------------------------DTsAlvvf~~   58 (100)
T 1whv_A           15 RDHVLHV-TFPKEWKTSDLYQLFSAFGN-IQISWID----------------------------------DTSAFVSLSQ   58 (100)
T ss_dssp             CCSEEEE-ECCTTCCHHHHHHHHTTTCS-CCCEEEE----------------------------------TTEEEEECSC
T ss_pred             CCeEEEE-eCChhhhhHHHHHHhhccCC-EEEEEEc----------------------------------CCeEEEEecC
Confidence            4556677 99999999999999999983 3344442                                  3569999999


Q ss_pred             HHhHHHHHHHHh
Q psy1185          83 HKSASLAKKRLA   94 (131)
Q Consensus        83 ~~~a~~a~~~l~   94 (131)
                      ++.|..|++.+.
T Consensus        59 ~~~a~~al~~i~   70 (100)
T 1whv_A           59 PEQVQIAVNTSK   70 (100)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcc
Confidence            999999999774

>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=97.16  E-value=0.00087  Score=41.14  Aligned_cols=57  Identities=16%  Similarity=0.234  Sum_probs=45.3

Q ss_pred             CCceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeC
Q psy1185           2 SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYD   81 (131)
Q Consensus         2 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~   81 (131)
                      ++.+.+++ +.|..+...||..+|++|| -..+..+.                                  -..|||.|.
T Consensus         4 ~R~HV~~l-~FP~ewKt~Di~~lFs~fg-gv~I~Wid----------------------------------DTsAlvvf~   47 (101)
T 3ctr_A            4 GSDHVLHV-TFPKEWKTSDLYQLFSAFG-NIQISWID----------------------------------DTSAFVSLS   47 (101)
T ss_dssp             EEEEEEEE-ECCTTCCHHHHHHHTTTSE-EEEEEEEE----------------------------------TTEEEEEEE
T ss_pred             CCCeEEEE-eCChhhhhHHHHHHHhccC-CEEEEEEc----------------------------------CCeEEEEec
Confidence            34566777 9999999999999999999 33444442                                  356999999


Q ss_pred             CHHhHHHHHHHHh
Q psy1185          82 SHKSASLAKKRLA   94 (131)
Q Consensus        82 ~~~~a~~a~~~l~   94 (131)
                      +++.|..|++.+.
T Consensus        48 ~~~~a~~al~~i~   60 (101)
T 3ctr_A           48 QPEQVKIAVNTSK   60 (101)
T ss_dssp             EECHHHHHHHHHT
T ss_pred             CHHHHHHHHHhcc
Confidence            9999999998774

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=97.13  E-value=0.0039  Score=39.53  Aligned_cols=69  Identities=17%  Similarity=0.090  Sum_probs=52.8

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .+.|-|-+.|... .+.+.+.|++||.|.+....                                 ...++-.|.|.++
T Consensus        24 ~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~---------------------------------~~~NWihI~Y~s~   69 (119)
T 1wwh_A           24 DTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMS---------------------------------NTGNWMHIRYQSK   69 (119)
T ss_dssp             GGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEEC---------------------------------SSSSEEEEEESSH
T ss_pred             CCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccC---------------------------------CCCCeEEEEeCCH
Confidence            4567888999885 56677789999999987643                                 2368899999999


Q ss_pred             HhHHHHHHHHhCCcceecC-cEEEEEe
Q psy1185          84 KSASLAKKRLATGRLKVWG-CDIIVDW  109 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g-~~l~v~~  109 (131)
                      .+|++||.. ||.  .++| ..|-|..
T Consensus        70 ~~A~rAL~k-NG~--ii~g~~mIGV~p   93 (119)
T 1wwh_A           70 LQARKALSK-DGR--IFGESIMIGVKP   93 (119)
T ss_dssp             HHHHHHHTT-TTC--EETTTEECEEEE
T ss_pred             HHHHHHHHh-CCe--EecCCEEEEEEE
Confidence            999999887 665  6664 4555554

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=96.72  E-value=0.0012  Score=51.07  Aligned_cols=33  Identities=12%  Similarity=0.231  Sum_probs=27.2

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI   37 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~   37 (131)
                      .++|||. .|..+++.+|.++|++||+|.++...
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~   85 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFFY   85 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEE
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEE
Confidence            4789997 79999999999999999999998776

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=96.51  E-value=0.008  Score=36.71  Aligned_cols=68  Identities=12%  Similarity=0.134  Sum_probs=46.0

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      +-+|-|+.||+.+|++++.+.++..-++.....+.|                         +.......-+-|+|.|.+.
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G-------------------------~~s~~~~~~SRAYI~F~~~   63 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAA-------------------------DLSLYPHLYSRAYINFRNP   63 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCC-------------------------CSSSCCSCCCCCEEEESCH
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCC-------------------------ccCCCCCcceEEEEEeCCH
Confidence            457899999999999998877776544322222222                         0000112235689999999


Q ss_pred             HhHHHHHHHHhCC
Q psy1185          84 KSASLAKKRLATG   96 (131)
Q Consensus        84 ~~a~~a~~~l~~~   96 (131)
                      ++...-.+..+|.
T Consensus        64 edv~~F~~~f~g~   76 (97)
T 2l08_A           64 DDILLFRDRFDGY   76 (97)
T ss_dssp             HHHHHHHHHSTTE
T ss_pred             HHHHHHHHHcCCc
Confidence            9999888888886

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=95.79  E-value=0.016  Score=37.31  Aligned_cols=89  Identities=11%  Similarity=-0.000  Sum_probs=52.7

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEE-EecCeEEEEECCHHHHHhhcCCceeEEecCCCCCC-CCcceEEEEe
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVK-RIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNK-KNRGFCFLEY   80 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~-i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~-~~~~~~fv~f   80 (131)
                      ....|-|-+.|++.+ ..+.+.|++||.|.+-. ..++..   ..         .+..   ....+.+. ...++..|.|
T Consensus         6 ~e~~VtVFGFp~~~~-~~VI~~Fs~~G~IlE~~~~~~~~~---~~---------~~~~---~~~k~yP~f~g~NWikItY   69 (132)
T 3p3d_A            6 GELAILVFGYPETMA-NQVIAYFQEFGTILEDFEVLRKPQ---AM---------TVGL---QDRQFVPIFSGNSWTKITY   69 (132)
T ss_dssp             --CEEEEECCCGGGH-HHHHHHHGGGSCBCSCCGGGCCC--------------------------CCCCCEETTEEEEEB
T ss_pred             CceEEEEEecCHHHH-HHHHHHHHhhceEeeecccccccc---cc---------cccc---ccccccCccCCCcEEEEEc
Confidence            356677889988864 56667899999987732 111100   00         0000   00000111 2357889999


Q ss_pred             CCHHhHHHHHHHHhCCcceecCcEEEEEec
Q psy1185          81 DSHKSASLAKKRLATGRLKVWGCDIIVDWA  110 (131)
Q Consensus        81 ~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a  110 (131)
                      .++.+|.+||.. ||.  .++|..|-|..-
T Consensus        70 ds~~~A~rAL~~-NG~--ii~G~mIGV~Py   96 (132)
T 3p3d_A           70 DNPASAVDALLE-NGA--VFNGVLLGVIPY   96 (132)
T ss_dssp             SSHHHHHHHHTT-TTC--EETTEECEEEEC
T ss_pred             CCHHHHHHHHHh-CCe--EeCcEEEEEEEC
Confidence            999999999875 555  788887766553

>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=95.05  E-value=0.01  Score=38.45  Aligned_cols=40  Identities=23%  Similarity=0.063  Sum_probs=35.7

Q ss_pred             CCCcceEEEEeCCHHhHHHHHHHH-hCCcceecCcEEEEEecCC
Q psy1185          70 KKNRGFCFLEYDSHKSASLAKKRL-ATGRLKVWGCDIIVDWADP  112 (131)
Q Consensus        70 ~~~~~~~fv~f~~~~~a~~a~~~l-~~~~~~~~g~~l~v~~a~~  112 (131)
                      ...+|+++++|.+.+.|++|+..+ +|.  .++| .+.+.++.+
T Consensus        10 ~~l~G~~~ve~~~~~~A~~a~~~~~ng~--~~~G-~~~~~~a~~   50 (150)
T 2i2y_A           10 KTLKGETTTEAVDAATAEKVFKQYANDN--GVDG-EWTYDDATK   50 (150)
T ss_dssp             SSSCEEEEEECSSHHHHTTTHHHHHHHH--TCCC-EEEEETTTT
T ss_pred             ccccccceeeecCHHHHHHHHHHHhcCC--CCCC-ceecccccC
Confidence            355899999999999999999999 887  8899 999999875

>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=95.00  E-value=0.029  Score=36.39  Aligned_cols=26  Identities=23%  Similarity=0.078  Sum_probs=23.2

Q ss_pred             CCCcceEEEEeCCHHhHHHHHHHHhC
Q psy1185          70 KKNRGFCFLEYDSHKSASLAKKRLAT   95 (131)
Q Consensus        70 ~~~~~~~fv~f~~~~~a~~a~~~l~~   95 (131)
                      ..++|||||+|.+.++|.+|+..+++
T Consensus        10 ~~~~G~~fV~f~~~~~A~~al~~~~~   35 (158)
T 2kn4_A           10 KTLKGETTTEAVDAATAEKVFKQYAN   35 (158)
T ss_dssp             SSCEEEEEEECSSHHHHHHHHHHHHH
T ss_pred             ccccchhHHHHHHHHhHHHHHHhhcc
Confidence            35789999999999999999988874

>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=93.40  E-value=0.5  Score=36.89  Aligned_cols=58  Identities=16%  Similarity=0.256  Sum_probs=46.0

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      +.+.++++ +|..+...+|.++|+.||. .+++.+                                  ....|||.+.+
T Consensus       439 R~~vl~v~-f~~~~~~~~i~~~fs~fg~-v~V~wi----------------------------------ddt~a~V~~~~  482 (507)
T 3d45_A          439 RDHVLHVT-FPKEWKTSDLYQLFSAFGN-IQISWI----------------------------------DDTSAFVSLSQ  482 (507)
T ss_dssp             GGGEEEEE-CCTTCCHHHHHHHGGGGCC-CEEEEC----------------------------------SSSEEEEECSC
T ss_pred             cCcEEEEe-CCCCCCHHHHHHHHHhcCC-EEEEEE----------------------------------cCCeEEEEECC
Confidence            45667776 8899999999999999994 344443                                  24669999999


Q ss_pred             HHhHHHHHHHHhCC
Q psy1185          83 HKSASLAKKRLATG   96 (131)
Q Consensus        83 ~~~a~~a~~~l~~~   96 (131)
                      ++.|..+++.+...
T Consensus       483 ~~~a~~~l~~~~~~  496 (507)
T 3d45_A          483 PEQVQIAVNTSKYA  496 (507)
T ss_dssp             HHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHhC
Confidence            99999999988643

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=93.36  E-value=0.047  Score=32.29  Aligned_cols=19  Identities=32%  Similarity=0.501  Sum_probs=16.8

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|+.+.
T Consensus        43 ~rg~aFV~F~~~~~A~~Ai   61 (91)
T 2lxi_A           43 SRGFAFVEFSHLQDATRWM   61 (91)
T ss_dssp             CSSEEEEECSSHHHHHHHH
T ss_pred             cCceEEEEecCHHHHHHHH
Confidence            4899999999999999853

>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=93.26  E-value=0.056  Score=31.84  Aligned_cols=20  Identities=35%  Similarity=0.698  Sum_probs=18.0

Q ss_pred             ecCeEEEEECCHHHHHhhcC
Q psy1185          37 IKDYAFVHFEDRQEAITVTG   56 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~g   56 (131)
                      .+|||||+|.+.++|+.+.|
T Consensus        47 srGfaFV~F~~~~~A~~~~~   66 (89)
T 3d2w_A           47 FRAFAFVTFADDKVAQSLCG   66 (89)
T ss_dssp             CCSEEEEEESCHHHHHHHTT
T ss_pred             CCCEEEEEECCHHHHHHHcC
Confidence            68999999999999998665

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=93.00  E-value=0.069  Score=32.01  Aligned_cols=18  Identities=22%  Similarity=0.385  Sum_probs=15.0

Q ss_pred             cCeEEEEECCHHHHHhhc
Q psy1185          38 KDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        38 ~~~~fv~~~~~~~a~~~~   55 (131)
                      +|||||+|.++++|+.+.
T Consensus        43 kGfaFVey~~~~eA~~Ai   60 (89)
T 2wbr_A           43 QGIALCKYTTREEANKAQ   60 (89)
T ss_dssp             TTEEEEEESSHHHHHHHH
T ss_pred             CcEEEEEECCHHHHHHHH
Confidence            069999999999999843

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

Probab=92.78  E-value=0.13  Score=30.59  Aligned_cols=19  Identities=26%  Similarity=0.455  Sum_probs=16.5

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|+.+.
T Consensus        57 ~~g~afV~f~~~~~a~~A~   75 (100)
T 2do4_A           57 PKGLAYVEYENESQASQAV   75 (100)
T ss_dssp             EEEEEEEEESSHHHHHHHH
T ss_pred             EEeEEEEEECCHHHHHHHH
Confidence            3799999999999999843

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

Probab=92.66  E-value=0.054  Score=32.55  Aligned_cols=18  Identities=22%  Similarity=0.469  Sum_probs=16.3

Q ss_pred             ecCeEEEEECCHHHHHhh
Q psy1185          37 IKDYAFVHFEDRQEAITV   54 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~   54 (131)
                      .+|||||+|.+.++|+.+
T Consensus        52 srG~aFV~f~~~~~A~~A   69 (95)
T 2lkz_A           52 NRGFAFVQLSSAMDASQL   69 (95)
T ss_dssp             CSSEEEEECSSSHHHHHH
T ss_pred             CceEeEEEECCHHHHHHH
Confidence            489999999999999984

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=92.64  E-value=0.23  Score=30.65  Aligned_cols=50  Identities=10%  Similarity=0.030  Sum_probs=35.1

Q ss_pred             ecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHHhHHHHHHHHhC
Q psy1185          37 IKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLAT   95 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~   95 (131)
                      .+|||||+|.+.++|+.+..+.+..+.         .....|.+.+..+...++.....
T Consensus        60 ~~G~afV~F~~~~~a~~Al~~~g~~~~---------gr~i~V~~a~~~~~~~~~~~~~~  109 (118)
T 2db1_A           60 QSGEAFVELESEDDVKLALKKDRESMG---------HRYIEVFKSHRTEMDWVLKHSGP  109 (118)
T ss_dssp             EEEEEEEEBSSHHHHHHHGGGTTEEET---------TEEEEEEEECHHHHHHHHHTTSS
T ss_pred             CCeEEEEEECCHHHHHHHHhcCCCeEC---------CeEEEEEECCHHHHHHHHHHhCC
Confidence            479999999999999997765543321         12456677777777777665543

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=92.29  E-value=0.099  Score=29.88  Aligned_cols=20  Identities=20%  Similarity=0.473  Sum_probs=17.4

Q ss_pred             ecCeEEEEECCHHHHHhhcC
Q psy1185          37 IKDYAFVHFEDRQEAITVTG   56 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~g   56 (131)
                      .+|||||+|.+.++|+.+..
T Consensus        46 ~~g~afV~f~~~~~A~~Ai~   65 (81)
T 2krb_A           46 TKGYIFLEYASPAHAVDAVK   65 (81)
T ss_dssp             CCCEEEEEESSHHHHHHHHT
T ss_pred             EeEEEEEEECCHHHHHHHHH
Confidence            47999999999999999554

>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=92.23  E-value=0.23  Score=31.79  Aligned_cols=46  Identities=9%  Similarity=0.012  Sum_probs=32.2

Q ss_pred             ecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHHhHHHHHH
Q psy1185          37 IKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKK   91 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~   91 (131)
                      .+|||||+|.+.++|+.+..+.+..+.         ....-|...+..+...+++
T Consensus        87 srG~aFV~F~~~e~a~~Al~~~g~~l~---------gr~i~V~~a~~~e~~~~~~  132 (136)
T 2hgl_A           87 QSGEAFVELGSEDDVKMALKKDRESMG---------HRYIEVFKSHRTEMDWVLK  132 (136)
T ss_dssp             EEEEEEEECSSHHHHHHHHTTTEEESS---------SSEEEEEECCHHHHHHHHT
T ss_pred             CCeEEEEEECCHHHHHHHHhcCCCEEC---------CEEEEEEECChHHHHHHHh
Confidence            479999999999999997765553321         1245667777777666554

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=92.02  E-value=0.11  Score=31.64  Aligned_cols=32  Identities=13%  Similarity=0.090  Sum_probs=22.1

Q ss_pred             HHhhccCCeeEEEEecCeEEEEECCHHHHHhh
Q psy1185          23 EAFEQYGRVERVKRIKDYAFVHFEDRQEAITV   54 (131)
Q Consensus        23 ~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~   54 (131)
                      .-|...-.|.=+.-.+|||||+|.+.++|+.+
T Consensus        39 ~~~G~V~~v~i~~~~rGfaFVeF~~~~~A~~A   70 (100)
T 2d9o_A           39 QKYGEVLNLVLSSKKPGTAVVEFATVKAAELA   70 (100)
T ss_dssp             HTTSCEEEEEEESSSSSEEEEEESCHHHHHHH
T ss_pred             HhcCCEEEEEEccCCCCEEEEEECCHHHHHHH
Confidence            33443333333345799999999999999984

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=91.95  E-value=0.099  Score=32.22  Aligned_cols=24  Identities=13%  Similarity=0.188  Sum_probs=19.7

Q ss_pred             ecCeEEEEECCHHHHHhhcCCcee
Q psy1185          37 IKDYAFVHFEDRQEAITVTGLSQV   60 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~g~~~~   60 (131)
                      .+|||||+|.+.++|+.+..+.+.
T Consensus        55 ~~G~afV~F~~~~~a~~Al~~~~~   78 (109)
T 2dnn_A           55 NNGNGLVKFLSPQDTFEALKRNRM   78 (109)
T ss_dssp             CCSEEEEECSSHHHHHHHHHTTTE
T ss_pred             CCeEEEEEECCHHHHHHHHhcCCC
Confidence            479999999999999997654443

>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=91.76  E-value=0.31  Score=30.21  Aligned_cols=47  Identities=11%  Similarity=0.051  Sum_probs=32.4

Q ss_pred             cCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHHhHHHHHHHH
Q psy1185          38 KDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRL   93 (131)
Q Consensus        38 ~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l   93 (131)
                      +|||||+|.+.++|+.+..+.+..+.         .....|.+.+.......+..+
T Consensus        67 ~G~afV~F~~~~~a~~Al~~~g~~~~---------gr~i~V~~a~~~~~~~~~~~~  113 (124)
T 1wel_A           67 TGEGFVEFRNEADYKAALCRHKQYMG---------NRFIQVHPITKKGMLEKIDMI  113 (124)
T ss_dssp             EEEEEEEBSSSHHHHHHHTSCSBCST---------TSCBEEEEECHHHHHHHHHHH
T ss_pred             CeEEEEEECCHHHHHHHHHhCCCeEC---------CcEEEEEECCHHHHHHHHHHH
Confidence            79999999999999997765442211         124566777777766555544

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=91.71  E-value=0.12  Score=31.37  Aligned_cols=22  Identities=23%  Similarity=0.282  Sum_probs=18.8

Q ss_pred             ecCeEEEEECCHHHHHhhcCCc
Q psy1185          37 IKDYAFVHFEDRQEAITVTGLS   58 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~g~~   58 (131)
                      .+|||||+|.+.++|..+....
T Consensus        51 ~rG~aFV~F~~~e~a~~Ai~~~   72 (103)
T 1s79_A           51 FKGSIFVVFDSIESAKKFVETP   72 (103)
T ss_dssp             CCCEEEEEESSHHHHHHHHTSS
T ss_pred             CccEEEEEECCHHHHHHHHHcC
Confidence            4899999999999999976543

>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=91.64  E-value=0.1  Score=31.34  Aligned_cols=19  Identities=21%  Similarity=0.385  Sum_probs=16.6

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|+.+.
T Consensus        60 ~kG~afV~f~~~~~A~~Ai   78 (99)
T 4fxv_A           60 SLGYGFVNYVTAKDAERAI   78 (99)
T ss_dssp             EEEEEEEEESSHHHHHHHH
T ss_pred             ccccEEEEECCHHHHHHHH
Confidence            3799999999999999843

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=91.52  E-value=0.12  Score=30.87  Aligned_cols=20  Identities=15%  Similarity=0.411  Sum_probs=17.4

Q ss_pred             ecCeEEEEECCHHHHHhhcC
Q psy1185          37 IKDYAFVHFEDRQEAITVTG   56 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~g   56 (131)
                      .+|||||+|.+.++|+.+..
T Consensus        55 ~~g~afV~f~~~~~a~~A~~   74 (103)
T 2dng_A           55 FKGFCYVEFDEVDSLKEALT   74 (103)
T ss_dssp             EEEEEEEEESSHHHHHHHGG
T ss_pred             cceEEEEEECCHHHHHHHHh
Confidence            37899999999999999654

>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=91.44  E-value=0.11  Score=32.03  Aligned_cols=18  Identities=44%  Similarity=0.733  Sum_probs=16.2

Q ss_pred             ecCeEEEEECCHHHHHhh
Q psy1185          37 IKDYAFVHFEDRQEAITV   54 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~   54 (131)
                      .+|||||+|.+.++|+.+
T Consensus        44 ~kg~afV~f~~~~~A~~A   61 (115)
T 4f25_A           44 SKGYGFVHFETQEAAERA   61 (115)
T ss_dssp             EEEEEEEEESCHHHHHHH
T ss_pred             CCceEEEEECCHHHHHHH
Confidence            379999999999999984

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

Probab=91.33  E-value=0.14  Score=30.62  Aligned_cols=19  Identities=21%  Similarity=0.368  Sum_probs=16.9

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|+.+.
T Consensus        53 ~kG~afV~f~~~~~A~~Ai   71 (100)
T 3ns6_A           53 TKGFLFVECGSMNDAKKII   71 (100)
T ss_dssp             ECSEEEEEESSHHHHHHHH
T ss_pred             cceEEEEEECCHHHHHHHH
Confidence            4899999999999999854

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=91.05  E-value=0.13  Score=28.72  Aligned_cols=22  Identities=23%  Similarity=0.428  Sum_probs=18.4

Q ss_pred             ecCeEEEEECCHHHHHhhcCCc
Q psy1185          37 IKDYAFVHFEDRQEAITVTGLS   58 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~g~~   58 (131)
                      .+|||||+|.+.++|+.+..+.
T Consensus        40 ~~g~afV~f~~~~~a~~a~~~~   61 (75)
T 2mss_A           40 HRGFGFVTFESEDIVEKVCEIH   61 (75)
T ss_dssp             SCBEEEEECSCHHHHHHHHSSS
T ss_pred             cCcEEEEEECCHHHHHHHHHCC
Confidence            3799999999999999976543

>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=91.05  E-value=0.16  Score=31.10  Aligned_cols=46  Identities=15%  Similarity=0.126  Sum_probs=31.3

Q ss_pred             ecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHHhHHHHHH
Q psy1185          37 IKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKK   91 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~   91 (131)
                      .+|||||+|.+.++|+.+....+..+.         .....|.+.+......+..
T Consensus        56 ~~G~afV~F~~~~~a~~Al~~~~~~~~---------gr~i~v~~a~~~~~~~~~~  101 (114)
T 2cpy_A           56 GLGQALVQFKNEDDARKSERLHRKKLN---------GREAFVHVVTLEDMREIEK  101 (114)
T ss_dssp             CSSCEEEECSSHHHHHHHGGGCSEEET---------TEEEEEEEECHHHHHHHHH
T ss_pred             cceEEEEEECCHHHHHHHHHhCCCccC---------CeEEEEEECCHHHHHHHHh
Confidence            479999999999999997655433221         1345677777766655543

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

Probab=91.01  E-value=0.16  Score=29.09  Aligned_cols=18  Identities=33%  Similarity=0.584  Sum_probs=16.1

Q ss_pred             ecCeEEEEECCHHHHHhh
Q psy1185          37 IKDYAFVHFEDRQEAITV   54 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~   54 (131)
                      .+|||||+|.+.++|+.+
T Consensus        46 ~~g~afV~f~~~~~a~~A   63 (85)
T 1x4e_A           46 CKGYGFVDFDSPSAAQKA   63 (85)
T ss_dssp             CCSEEEEEESCHHHHHHH
T ss_pred             cCcEEEEEECCHHHHHHH
Confidence            379999999999999984

>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=90.93  E-value=0.15  Score=30.50  Aligned_cols=20  Identities=20%  Similarity=0.564  Sum_probs=17.3

Q ss_pred             ecCeEEEEECCHHHHHhhcC
Q psy1185          37 IKDYAFVHFEDRQEAITVTG   56 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~g   56 (131)
                      .+|||||+|.+.++|+.+..
T Consensus        56 ~~g~afV~f~~~~~a~~A~~   75 (104)
T 1wi8_A           56 LKGFGYAEFEDLDSLLSALS   75 (104)
T ss_dssp             BCSCEEEEESSHHHHHHHHG
T ss_pred             cCeEEEEEECCHHHHHHHHh
Confidence            37899999999999999654

>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=90.77  E-value=0.15  Score=29.45  Aligned_cols=21  Identities=29%  Similarity=0.616  Sum_probs=17.7

Q ss_pred             cCeEEEEECCHHHHHhhcCCc
Q psy1185          38 KDYAFVHFEDRQEAITVTGLS   58 (131)
Q Consensus        38 ~~~~fv~~~~~~~a~~~~g~~   58 (131)
                      +|||||+|.+.++|+.+..+.
T Consensus        48 ~g~afV~f~~~~~a~~a~~~~   68 (89)
T 3ucg_A           48 KGFAYIEFSDKESVRTSLALD   68 (89)
T ss_dssp             CEEEEEEESSTHHHHHHGGGT
T ss_pred             ceEEEEEECCHHHHHHHHhcC
Confidence            799999999999999965433

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=90.71  E-value=0.17  Score=30.05  Aligned_cols=18  Identities=17%  Similarity=0.512  Sum_probs=16.5

Q ss_pred             cCeEEEEECCHHHHHhhc
Q psy1185          38 KDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        38 ~~~~fv~~~~~~~a~~~~   55 (131)
                      +|||||+|.+.++|+.+.
T Consensus        58 ~g~afV~f~~~~~a~~A~   75 (101)
T 1fj7_A           58 RKFGYVDFESAEDLEKAL   75 (101)
T ss_dssp             TTEEEEEESSHHHHHHHH
T ss_pred             CcEEEEEECCHHHHHHHH
Confidence            899999999999999954

>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=90.68  E-value=0.19  Score=28.75  Aligned_cols=19  Identities=32%  Similarity=0.545  Sum_probs=16.8

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|+.+.
T Consensus        48 ~~g~afV~f~~~~~a~~A~   66 (85)
T 3mdf_A           48 HRGFAFVEFELAEDAAAAI   66 (85)
T ss_dssp             ECSEEEEEESSHHHHHHHH
T ss_pred             cccEEEEEECCHHHHHHHH
Confidence            4899999999999999854

>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=90.56  E-value=0.11  Score=28.96  Aligned_cols=21  Identities=10%  Similarity=0.414  Sum_probs=18.0

Q ss_pred             ecCeEEEEECCHHHHHhhcCC
Q psy1185          37 IKDYAFVHFEDRQEAITVTGL   57 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~g~   57 (131)
                      .+|||||+|.+.++|+.+...
T Consensus        40 ~~g~afV~f~~~~~a~~Ai~~   60 (75)
T 1iqt_A           40 RRGFCFITFKEEEPVKKIMEK   60 (75)
T ss_dssp             SCCCEEEECSSSHHHHHHHTT
T ss_pred             cCCEEEEEECCHHHHHHHHHh
Confidence            389999999999999996543

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

Probab=90.50  E-value=0.15  Score=31.26  Aligned_cols=19  Identities=21%  Similarity=0.083  Sum_probs=16.7

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|+.+.
T Consensus        47 ~rG~aFV~f~~~~~A~~Ai   65 (110)
T 3s8s_A           47 HLGLARVLFTSTRGAKETV   65 (110)
T ss_dssp             EEEEEEEEESSHHHHHHHH
T ss_pred             eeeEEEEEECCHHHHHHHH
Confidence            4799999999999999953

>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=90.46  E-value=0.16  Score=29.16  Aligned_cols=19  Identities=32%  Similarity=0.487  Sum_probs=16.6

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|+.+.
T Consensus        47 ~~g~afV~f~~~~~A~~A~   65 (87)
T 3bs9_A           47 SKGYGFVSFFNKWDAENAI   65 (87)
T ss_dssp             EEEEEEEEESSHHHHHHHH
T ss_pred             cceEEEEEECCHHHHHHHH
Confidence            3799999999999999844

>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=90.46  E-value=0.19  Score=30.23  Aligned_cols=20  Identities=25%  Similarity=0.255  Sum_probs=17.4

Q ss_pred             ecCeEEEEECCHHHHHhhcC
Q psy1185          37 IKDYAFVHFEDRQEAITVTG   56 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~g   56 (131)
                      .+|||||+|.+.++|+.+..
T Consensus        56 ~~G~afV~F~~~~~a~~A~~   75 (104)
T 1wg5_A           56 STGEAFVQFASQEIAEKALK   75 (104)
T ss_dssp             BCSEEEEEESSHHHHHHHHT
T ss_pred             cceEEEEEECCHHHHHHHHH
Confidence            47999999999999999654

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=90.45  E-value=0.17  Score=29.66  Aligned_cols=19  Identities=26%  Similarity=0.450  Sum_probs=16.6

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|+.+.
T Consensus        47 ~~g~afV~f~~~~~A~~A~   65 (96)
T 1x5t_A           47 SKGYAFINFASFDASDAAI   65 (96)
T ss_dssp             CCSEEEEEBSSHHHHHHHH
T ss_pred             cCeEEEEEECCHHHHHHHH
Confidence            3799999999999999943

>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=90.36  E-value=0.17  Score=30.89  Aligned_cols=18  Identities=17%  Similarity=0.322  Sum_probs=15.9

Q ss_pred             ecCeEEEEECCHHHHHhh
Q psy1185          37 IKDYAFVHFEDRQEAITV   54 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~   54 (131)
                      .+|||||+|.+.++|+.+
T Consensus        62 ~~G~afV~f~~~~~A~~A   79 (111)
T 2cpi_A           62 PSASAYVTYIRSEDALRA   79 (111)
T ss_dssp             CCEEEEEEESSHHHHHHH
T ss_pred             CCeEEEEEECcHHHHHHH
Confidence            368999999999999983

>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=90.35  E-value=0.2  Score=28.72  Aligned_cols=18  Identities=44%  Similarity=0.684  Sum_probs=16.5

Q ss_pred             ecCeEEEEECCHHHHHhh
Q psy1185          37 IKDYAFVHFEDRQEAITV   54 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~   54 (131)
                      .+|||||+|.+.++|+.+
T Consensus        46 ~~g~afV~f~~~~~a~~A   63 (88)
T 4a8x_A           46 SKGYAYVEFENPDEAEKA   63 (88)
T ss_dssp             ECSEEEEEESSHHHHHHH
T ss_pred             CCcEEEEEEecHHHHHHH
Confidence            589999999999999984

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

Probab=90.34  E-value=0.31  Score=28.40  Aligned_cols=19  Identities=32%  Similarity=0.553  Sum_probs=16.6

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|+.+.
T Consensus        56 ~~g~afV~f~~~~~A~~A~   74 (95)
T 2cqc_A           56 SRGFAFVYFENVDDAKEAK   74 (95)
T ss_dssp             EEEEEEEEESSHHHHHHHH
T ss_pred             cccEEEEEECCHHHHHHHH
Confidence            3789999999999999943

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

Probab=90.32  E-value=0.17  Score=32.03  Aligned_cols=19  Identities=16%  Similarity=0.274  Sum_probs=16.8

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|..+.
T Consensus        71 ~rG~aFV~F~~~~~A~~Ai   89 (127)
T 2a3j_A           71 NSGKAYIVFATQESAQAFV   89 (127)
T ss_dssp             SCCCEEEEESSHHHHHHHH
T ss_pred             cCCEEEEEECCHHHHHHHH
Confidence            4899999999999999854

>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=90.30  E-value=0.12  Score=29.93  Aligned_cols=20  Identities=40%  Similarity=0.705  Sum_probs=17.9

Q ss_pred             ecCeEEEEECCHHHHHhhcC
Q psy1185          37 IKDYAFVHFEDRQEAITVTG   56 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~g   56 (131)
                      .+|||||+|.+.++|+.+.+
T Consensus        41 ~~g~afV~f~~~~~a~~~~~   60 (88)
T 1wf0_A           41 FRAFAFVTFADDQIAQSLCG   60 (88)
T ss_dssp             CCSCCEEECSCHHHHHHTTT
T ss_pred             CCCEEEEEECCHHHHHHHhc
Confidence            68999999999999998655

>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=90.28  E-value=0.097  Score=30.62  Aligned_cols=18  Identities=17%  Similarity=0.263  Sum_probs=15.1

Q ss_pred             ecCeEEEEECCHHHHHhh
Q psy1185          37 IKDYAFVHFEDRQEAITV   54 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~   54 (131)
                      .+|||||+|.+.++|+.+
T Consensus        44 ~kG~afV~f~~~~~a~~A   61 (90)
T 3p5t_L           44 SKGFALVGVGSEASSKKL   61 (90)
T ss_dssp             EEEEEEECC-CHHHHHHH
T ss_pred             cCcEEEEEECCHHHHHHH
Confidence            389999999999999984

>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=90.14  E-value=0.18  Score=28.69  Aligned_cols=19  Identities=26%  Similarity=0.571  Sum_probs=16.6

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|+.+.
T Consensus        42 ~~g~afV~f~~~~~a~~a~   60 (83)
T 3md1_A           42 SRGYGFVSFTSQDDAQNAM   60 (83)
T ss_dssp             EEEEEEEEESCHHHHHHHH
T ss_pred             ccceEEEEECCHHHHHHHH
Confidence            3799999999999999843

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=90.07  E-value=0.22  Score=29.48  Aligned_cols=19  Identities=26%  Similarity=0.538  Sum_probs=16.7

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|+.+.
T Consensus        51 ~~g~afV~f~~~~~a~~A~   69 (99)
T 2dgs_A           51 PRGFGFITFEDEQSVDQAV   69 (99)
T ss_dssp             CCSEEEEEESSHHHHHHHH
T ss_pred             CCceEEEEECCHHHHHHHH
Confidence            3799999999999999954

>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=90.03  E-value=0.19  Score=29.67  Aligned_cols=17  Identities=35%  Similarity=0.364  Sum_probs=15.7

Q ss_pred             cCeEEEEECCHHHHHhh
Q psy1185          38 KDYAFVHFEDRQEAITV   54 (131)
Q Consensus        38 ~~~~fv~~~~~~~a~~~   54 (131)
                      ++||||+|.+.++|+.+
T Consensus        52 rg~afV~f~~~~~A~~A   68 (96)
T 2dgx_A           52 QLKAVVQMENLQDAIGA   68 (96)
T ss_dssp             TCCEEEEESSHHHHHHH
T ss_pred             CeEEEEEECCHHHHHHH
Confidence            89999999999999984

>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=90.00  E-value=0.21  Score=30.02  Aligned_cols=20  Identities=25%  Similarity=0.492  Sum_probs=17.2

Q ss_pred             ecCeEEEEECCHHHHHhhcC
Q psy1185          37 IKDYAFVHFEDRQEAITVTG   56 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~g   56 (131)
                      .+|||||+|.+.++|+.+..
T Consensus        51 ~~g~afV~f~~~~~A~~A~~   70 (109)
T 2dis_A           51 NRGFAFVEYESHRAAAMARR   70 (109)
T ss_dssp             TCCEEEEEESSHHHHHHHHT
T ss_pred             cCcEEEEEecCHHHHHHHHH
Confidence            37999999999999999543

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=90.00  E-value=0.19  Score=31.02  Aligned_cols=19  Identities=5%  Similarity=0.127  Sum_probs=16.8

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|+.+.
T Consensus        66 ~rGfaFV~F~~~e~A~~Ai   84 (111)
T 2jvr_A           66 FDGTGALEFPSEEILVEAL   84 (111)
T ss_dssp             SSCCEEEEESSHHHHHHHH
T ss_pred             CCCEEEEEECCHHHHHHHH
Confidence            6899999999999999843

>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=89.94  E-value=0.22  Score=29.36  Aligned_cols=19  Identities=32%  Similarity=0.419  Sum_probs=16.7

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|+.+.
T Consensus        49 ~~g~afV~f~~~~~a~~A~   67 (99)
T 1whw_A           49 PKGFAFVTFMFPEHAVKAY   67 (99)
T ss_dssp             CCSEEEEEESSHHHHHHHH
T ss_pred             cCeEEEEEECCHHHHHHHH
Confidence            4799999999999999944

>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=89.92  E-value=0.23  Score=29.24  Aligned_cols=19  Identities=32%  Similarity=0.630  Sum_probs=16.6

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|+.+.
T Consensus        43 ~~g~afV~f~~~~~A~~Ai   61 (96)
T 2x1f_A           43 SKGYAFIEFRDLESSASAV   61 (96)
T ss_dssp             BCSEEEEEESSHHHHHHHH
T ss_pred             cceEEEEEECCHHHHHHHH
Confidence            3799999999999999843

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=89.87  E-value=0.24  Score=30.59  Aligned_cols=21  Identities=24%  Similarity=0.607  Sum_probs=18.0

Q ss_pred             cCeEEEEECCHHHHHhhcCCc
Q psy1185          38 KDYAFVHFEDRQEAITVTGLS   58 (131)
Q Consensus        38 ~~~~fv~~~~~~~a~~~~g~~   58 (131)
                      +|||||+|.+.++|+.+..+.
T Consensus        78 ~g~afV~f~~~~~a~~A~~l~   98 (124)
T 2jwn_A           78 KGYAYIEFAERNSVDAAVAMD   98 (124)
T ss_dssp             EEEEEEEESSHHHHHHHHTTT
T ss_pred             ccEEEEEECCHHHHHHHHhcC
Confidence            799999999999999965444

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

Probab=89.69  E-value=0.2  Score=29.42  Aligned_cols=20  Identities=20%  Similarity=0.375  Sum_probs=17.3

Q ss_pred             EecCeEEEEECCHHHHHhhc
Q psy1185          36 RIKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        36 i~~~~~fv~~~~~~~a~~~~   55 (131)
                      ..+|||||+|.+.++|+.+.
T Consensus        51 ~~~g~afV~f~~~~~a~~A~   70 (96)
T 1fjc_A           51 KSKGIAYIEFKSEADAEKNL   70 (96)
T ss_dssp             EEEEEEEEEESSHHHHHHHH
T ss_pred             CcceEEEEEECCHHHHHHHH
Confidence            35799999999999999954

>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=89.64  E-value=0.36  Score=30.37  Aligned_cols=18  Identities=33%  Similarity=0.582  Sum_probs=16.2

Q ss_pred             ecCeEEEEECCHHHHHhh
Q psy1185          37 IKDYAFVHFEDRQEAITV   54 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~   54 (131)
                      .+|||||+|.+.++|+.+
T Consensus        87 ~~G~afV~F~~~~~A~~A  104 (129)
T 2kxn_B           87 SRGFAFVYFENVDDAKEA  104 (129)
T ss_dssp             CCCEEEEEESCHHHHHHH
T ss_pred             cceEEEEEECCHHHHHHH
Confidence            489999999999999984

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=89.59  E-value=0.21  Score=30.33  Aligned_cols=19  Identities=26%  Similarity=0.447  Sum_probs=16.9

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|+.+.
T Consensus        66 ~kg~afV~f~~~~~A~~Ai   84 (109)
T 2rs2_A           66 SRGFGFVTFMDQAGVDKVL   84 (109)
T ss_dssp             CTTCEEEEESSHHHHHHHH
T ss_pred             cCcEEEEEECCHHHHHHHH
Confidence            4899999999999999954

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=89.58  E-value=0.15  Score=31.21  Aligned_cols=19  Identities=26%  Similarity=0.527  Sum_probs=16.5

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|+.+.
T Consensus        51 ~~G~aFV~f~~~~~a~~Ai   69 (114)
T 2dnl_A           51 PKGYAFLLFQEESSVQALI   69 (114)
T ss_dssp             TTSEEEECCSSHHHHHHHH
T ss_pred             cccEEEEEECCHHHHHHHH
Confidence            4799999999999998843

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

Probab=89.52  E-value=0.25  Score=28.84  Aligned_cols=18  Identities=33%  Similarity=0.554  Sum_probs=16.1

Q ss_pred             ecCeEEEEECCHHHHHhh
Q psy1185          37 IKDYAFVHFEDRQEAITV   54 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~   54 (131)
                      .++||||+|.+.++|+.+
T Consensus        46 ~~g~afV~f~~~~~a~~A   63 (95)
T 2dnz_A           46 SKGYGFITFSDSECARRA   63 (95)
T ss_dssp             CCSEEEEEESCHHHHHHH
T ss_pred             eeeEEEEEECCHHHHHHH
Confidence            379999999999999983

>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=89.52  E-value=0.22  Score=29.65  Aligned_cols=22  Identities=23%  Similarity=0.587  Sum_probs=18.2

Q ss_pred             ecCeEEEEECCHHHHHhhcCCc
Q psy1185          37 IKDYAFVHFEDRQEAITVTGLS   58 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~g~~   58 (131)
                      .+|||||+|.+.++|+.+..+.
T Consensus        60 ~~g~afV~f~~~~~a~~Ai~l~   81 (100)
T 2j76_E           60 LKGFGYAEFEDLDSLLSALSLN   81 (100)
T ss_dssp             CCSCEEEEECCHHHHHHHHHTT
T ss_pred             cCeEEEEEECCHHHHHHHHhcC
Confidence            3799999999999999965433

>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=89.49  E-value=0.25  Score=29.41  Aligned_cols=17  Identities=29%  Similarity=0.647  Sum_probs=15.7

Q ss_pred             cCeEEEEECCHHHHHhh
Q psy1185          38 KDYAFVHFEDRQEAITV   54 (131)
Q Consensus        38 ~~~~fv~~~~~~~a~~~   54 (131)
                      ++||||+|.+.++|+.+
T Consensus        55 ~g~afV~f~~~~~a~~A   71 (103)
T 2cqi_A           55 DPYCFVEFYEHRDAAAA   71 (103)
T ss_dssp             CCEEEEEESSHHHHHHH
T ss_pred             CCEEEEEECCHHHHHHH
Confidence            79999999999999984

>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=89.45  E-value=0.21  Score=30.37  Aligned_cols=19  Identities=16%  Similarity=0.366  Sum_probs=16.7

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||.|.+.++|..+.
T Consensus        67 ~~G~~fV~f~~~~~A~~A~   85 (104)
T 1jmt_A           67 LVGNVYVKFRREEDAEKAV   85 (104)
T ss_dssp             SEEEEEEEESCHHHHHHHH
T ss_pred             ccEEEEEEECCHHHHHHHH
Confidence            4899999999999999843

>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=89.43  E-value=0.18  Score=28.98  Aligned_cols=21  Identities=19%  Similarity=0.401  Sum_probs=17.8

Q ss_pred             ecCeEEEEECCHHHHHhhcCC
Q psy1185          37 IKDYAFVHFEDRQEAITVTGL   57 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~g~   57 (131)
                      .+|||||+|.+.++|+.+...
T Consensus        52 ~~g~afV~f~~~~~a~~A~~~   72 (87)
T 3s7r_A           52 SRGFGFILFKDAASVEKVLDQ   72 (87)
T ss_dssp             EEEEEEEEESSTHHHHHHHHS
T ss_pred             cccEEEEEECCHHHHHHHHHh
Confidence            379999999999999996543

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

Probab=89.41  E-value=0.18  Score=29.99  Aligned_cols=18  Identities=28%  Similarity=0.595  Sum_probs=16.0

Q ss_pred             ecCeEEEEECCHHHHHhh
Q psy1185          37 IKDYAFVHFEDRQEAITV   54 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~   54 (131)
                      .++||||+|.+.++|+.+
T Consensus        53 ~~g~afV~f~~~~~A~~A   70 (102)
T 2fc8_A           53 SKGFGFVDFNSEEDAKAA   70 (102)
T ss_dssp             EEEEEEEECSSHHHHHHH
T ss_pred             cCcEEEEEECCHHHHHHH
Confidence            378999999999999984

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

Probab=89.40  E-value=0.26  Score=29.49  Aligned_cols=18  Identities=28%  Similarity=0.554  Sum_probs=16.1

Q ss_pred             ecCeEEEEECCHHHHHhh
Q psy1185          37 IKDYAFVHFEDRQEAITV   54 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~   54 (131)
                      .+|||||+|.+.++|+.+
T Consensus        57 ~~g~afV~f~~~~~a~~A   74 (107)
T 2cph_A           57 HRGFGFVDFITKQDAKKA   74 (107)
T ss_dssp             SCSEEEEEESSHHHHHHH
T ss_pred             cCceEEEEECCHHHHHHH
Confidence            379999999999999983

>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=89.37  E-value=0.23  Score=29.11  Aligned_cols=19  Identities=26%  Similarity=0.433  Sum_probs=16.5

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|+.+.
T Consensus        50 ~~g~afV~f~~~~~A~~A~   68 (97)
T 1nu4_A           50 MRGQAFVIFKEVSSATNAL   68 (97)
T ss_dssp             HTTCEEEEESSHHHHHHHH
T ss_pred             cCcEEEEEeCCHHHHHHHH
Confidence            3799999999999999843

>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=89.37  E-value=0.24  Score=29.61  Aligned_cols=19  Identities=26%  Similarity=0.426  Sum_probs=16.7

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|+.+.
T Consensus        56 ~~g~afV~f~~~~~a~~A~   74 (105)
T 1x5u_A           56 HQGYGFVEFLSEEDADYAI   74 (105)
T ss_dssp             BCSCEEEEESSHHHHHHHH
T ss_pred             CCcEEEEEECCHHHHHHHH
Confidence            4799999999999999943

>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=89.35  E-value=0.26  Score=29.69  Aligned_cols=18  Identities=28%  Similarity=0.381  Sum_probs=16.2

Q ss_pred             ecCeEEEEECCHHHHHhh
Q psy1185          37 IKDYAFVHFEDRQEAITV   54 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~   54 (131)
                      .+|||||+|.+.++|+.+
T Consensus        56 ~~g~afV~f~~~~~A~~A   73 (111)
T 1x4h_A           56 SKGCAFAQFMTQEAAQKC   73 (111)
T ss_dssp             BCSEEEEEESSHHHHHHH
T ss_pred             CccEEEEEECCHHHHHHH
Confidence            489999999999999984

>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=89.29  E-value=0.27  Score=29.42  Aligned_cols=18  Identities=28%  Similarity=0.525  Sum_probs=16.1

Q ss_pred             ecCeEEEEECCHHHHHhh
Q psy1185          37 IKDYAFVHFEDRQEAITV   54 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~   54 (131)
                      .+|||||+|.+.++|+.+
T Consensus        54 ~~g~afV~f~~~~~A~~A   71 (106)
T 2dgp_A           54 HKGCAFLTYCERESALKA   71 (106)
T ss_dssp             CCSEEEEEESSHHHHHHH
T ss_pred             cceEEEEEECCHHHHHHH
Confidence            379999999999999984

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

Probab=89.24  E-value=0.24  Score=28.87  Aligned_cols=19  Identities=37%  Similarity=0.478  Sum_probs=16.8

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .++||||+|.+.++|+.+.
T Consensus        57 ~~g~afV~f~~~~~A~~A~   75 (94)
T 2e5h_A           57 SKGVAFILFLDKDSAQNCT   75 (94)
T ss_dssp             CTTCEEEEESCHHHHHHHH
T ss_pred             cccEEEEEECCHHHHHHHH
Confidence            3799999999999999854

>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=89.23  E-value=0.24  Score=29.93  Aligned_cols=48  Identities=10%  Similarity=0.098  Sum_probs=31.4

Q ss_pred             ecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHHhHHHHHHHH
Q psy1185          37 IKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRL   93 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l   93 (131)
                      .+|||||+|.+.++|+.+..+.+..+.         .....|.+.+......+++..
T Consensus        54 ~~G~afV~F~~~~~a~~Al~~~~~~~~---------gr~i~V~~a~~~~~~~~~~~~  101 (107)
T 2lmi_A           54 RRGDALIEMESEQDVQKALEKHRMYMG---------QRYVEVYEINNEDVDALMKSL  101 (107)
T ss_dssp             TCSEEEEEBSSHHHHHHHHTTTTCCSS---------SSCCCCEECCHHHHHHHHHTT
T ss_pred             EeeEEEEEECCHHHHHHHHHhCcceeC---------CeEEEEEECCHHHHHHHHHhh
Confidence            379999999999999997764432211         123445666776666665543

>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=89.18  E-value=0.23  Score=29.62  Aligned_cols=19  Identities=26%  Similarity=0.585  Sum_probs=16.7

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|+.+.
T Consensus        56 ~~g~afV~f~~~~~a~~A~   74 (103)
T 2cqg_A           56 SKGFGFVRFTEYETQVKVM   74 (103)
T ss_dssp             EEEEEEEEESSHHHHHHHH
T ss_pred             ccceEEEEECCHHHHHHHH
Confidence            3799999999999999954

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

Probab=89.11  E-value=0.23  Score=29.23  Aligned_cols=20  Identities=15%  Similarity=0.331  Sum_probs=17.1

Q ss_pred             EecCeEEEEECCHHHHHhhc
Q psy1185          36 RIKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        36 i~~~~~fv~~~~~~~a~~~~   55 (131)
                      ..++||||+|.+.++|+.+.
T Consensus        48 ~~~g~afV~f~~~~~a~~A~   67 (98)
T 2cpf_A           48 LSMGFGFVEYKKPEQAQKAL   67 (98)
T ss_dssp             EEEEEEEEEESSHHHHHHHH
T ss_pred             CcccEEEEEECCHHHHHHHH
Confidence            35799999999999999943

>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=89.09  E-value=0.21  Score=31.65  Aligned_cols=22  Identities=32%  Similarity=0.400  Sum_probs=18.5

Q ss_pred             ecCeEEEEECCHHHHHhhcCCc
Q psy1185          37 IKDYAFVHFEDRQEAITVTGLS   58 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~g~~   58 (131)
                      .+|||||+|.+.++|+.+....
T Consensus        83 srGfaFV~F~~~e~A~~Al~~~  104 (126)
T 2hgm_A           83 ITGEAFVQFASQELAEKALGKH  104 (126)
T ss_dssp             SCSEEEEEESSTTHHHHHHTTT
T ss_pred             CceEEEEEECCHHHHHHHHHHC
Confidence            4799999999999999966543

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

Probab=89.04  E-value=0.24  Score=29.38  Aligned_cols=19  Identities=32%  Similarity=0.525  Sum_probs=16.7

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .++||||+|.+.++|+.+.
T Consensus        52 ~~g~afV~f~~~~~A~~A~   70 (101)
T 2fc9_A           52 SKGYAFIEFASFEDAKEAL   70 (101)
T ss_dssp             BCSEEEEECSSHHHHHHHH
T ss_pred             EeeEEEEEECCHHHHHHHH
Confidence            4799999999999999943

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=88.99  E-value=0.38  Score=29.28  Aligned_cols=20  Identities=20%  Similarity=0.385  Sum_probs=17.3

Q ss_pred             ecCeEEEEECCHHHHHhhcC
Q psy1185          37 IKDYAFVHFEDRQEAITVTG   56 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~g   56 (131)
                      .+|||||+|.+.++|+.+..
T Consensus        68 ~~g~afV~f~~~~~a~~Ai~   87 (116)
T 1x4b_A           68 SRGFGFVTFSSMAEVDAAMA   87 (116)
T ss_dssp             CCSEEEEECSSHHHHHHHHT
T ss_pred             cCceEEEEeCCHHHHHHHHH
Confidence            37999999999999999653

>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=88.99  E-value=0.24  Score=28.94  Aligned_cols=19  Identities=37%  Similarity=0.428  Sum_probs=16.5

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .++||||+|.+.++|+.+.
T Consensus        56 ~~g~afV~f~~~~~a~~Ai   74 (95)
T 2ek1_A           56 PTGEAMVAFESRDEATAAV   74 (95)
T ss_dssp             EEEEEEEEESSHHHHHHHH
T ss_pred             EeeEEEEEECCHHHHHHHH
Confidence            3799999999999999843

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=88.94  E-value=0.24  Score=29.54  Aligned_cols=18  Identities=39%  Similarity=0.600  Sum_probs=16.3

Q ss_pred             ecCeEEEEECCHHHHHhh
Q psy1185          37 IKDYAFVHFEDRQEAITV   54 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~   54 (131)
                      .+|||||+|.+.++|+.+
T Consensus        50 ~~g~afV~f~~~~~a~~A   67 (104)
T 2dhg_A           50 SKGYGFVKFTDELEQKRA   67 (104)
T ss_dssp             EEEEEEEEESCHHHHHHH
T ss_pred             ccceEEEEECCHHHHHHH
Confidence            479999999999999984

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

Probab=88.80  E-value=0.25  Score=28.64  Aligned_cols=18  Identities=28%  Similarity=0.283  Sum_probs=16.1

Q ss_pred             ecCeEEEEECCHHHHHhh
Q psy1185          37 IKDYAFVHFEDRQEAITV   54 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~   54 (131)
                      .++||||+|.+.++|+.+
T Consensus        47 ~~g~afV~f~~~~~a~~a   64 (92)
T 2dgv_A           47 SKGCGVVKFESPEVAERA   64 (92)
T ss_dssp             EEEEEEEEESSHHHHHHH
T ss_pred             cceEEEEEECCHHHHHHH
Confidence            479999999999999983

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=88.79  E-value=0.15  Score=28.59  Aligned_cols=18  Identities=28%  Similarity=0.505  Sum_probs=16.4

Q ss_pred             cCeEEEEECCHHHHHhhc
Q psy1185          38 KDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        38 ~~~~fv~~~~~~~a~~~~   55 (131)
                      +|||||+|.+.++|+.+.
T Consensus        42 ~g~afV~f~~~~~a~~a~   59 (77)
T 1uaw_A           42 RGFGFVTFMDQAGVDKVL   59 (77)
T ss_dssp             SSEEEECCCCTTHHHHHH
T ss_pred             CceEEEEEcCHHHHHHHH
Confidence            799999999999999854

>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=88.79  E-value=0.25  Score=29.50  Aligned_cols=17  Identities=41%  Similarity=0.575  Sum_probs=15.7

Q ss_pred             cCeEEEEECCHHHHHhh
Q psy1185          38 KDYAFVHFEDRQEAITV   54 (131)
Q Consensus        38 ~~~~fv~~~~~~~a~~~   54 (131)
                      +|||||+|.+.++|+.+
T Consensus        56 ~g~afV~f~~~~~A~~A   72 (105)
T 2dnh_A           56 KGCAFVKFSSHTEAQAA   72 (105)
T ss_dssp             EEEEEEEESSHHHHHHH
T ss_pred             CcEEEEEeCCHHHHHHH
Confidence            78999999999999984

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=88.78  E-value=0.27  Score=29.82  Aligned_cols=18  Identities=33%  Similarity=0.270  Sum_probs=16.2

Q ss_pred             ecCeEEEEECCHHHHHhh
Q psy1185          37 IKDYAFVHFEDRQEAITV   54 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~   54 (131)
                      .+|||||+|.+.++|+.+
T Consensus        64 ~~g~afV~f~~~~~A~~A   81 (113)
T 2cpe_A           64 PKGDATVSYEDPPTAKAA   81 (113)
T ss_dssp             BCSEEEEEBSSHHHHHHH
T ss_pred             eeeEEEEEECCHHHHHHH
Confidence            379999999999999984

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=88.77  E-value=0.26  Score=29.25  Aligned_cols=18  Identities=28%  Similarity=0.576  Sum_probs=16.1

Q ss_pred             ecCeEEEEECCHHHHHhh
Q psy1185          37 IKDYAFVHFEDRQEAITV   54 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~   54 (131)
                      .++||||+|.+.++|+.+
T Consensus        53 ~~g~afV~f~~~~~A~~A   70 (102)
T 1x5s_A           53 SRGFGFVTFENIDDAKDA   70 (102)
T ss_dssp             CCSEEEEECSSHHHHHHH
T ss_pred             cccEEEEEECCHHHHHHH
Confidence            479999999999999984

>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=88.69  E-value=0.25  Score=29.05  Aligned_cols=19  Identities=37%  Similarity=0.428  Sum_probs=16.6

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|+.+.
T Consensus        56 ~~g~afV~f~~~~~a~~Ai   74 (98)
T 2cqp_A           56 PTGEAMVAFESRDEATAAV   74 (98)
T ss_dssp             EEEEEEEEESCHHHHHHHH
T ss_pred             eeeEEEEEECCHHHHHHHH
Confidence            3799999999999999844

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

Probab=88.65  E-value=0.26  Score=29.06  Aligned_cols=19  Identities=26%  Similarity=0.417  Sum_probs=16.9

Q ss_pred             EecCeEEEEECCHHHHHhh
Q psy1185          36 RIKDYAFVHFEDRQEAITV   54 (131)
Q Consensus        36 i~~~~~fv~~~~~~~a~~~   54 (131)
                      -.+|||||+|.+.++|+.+
T Consensus        54 ~~~g~afV~f~~~~~a~~A   72 (97)
T 2e5j_A           54 GPRRRAFLHYPDSAAAQQA   72 (97)
T ss_dssp             TTTTEEEEECSSHHHHHHH
T ss_pred             CCCcEEEEEECCHHHHHHH
Confidence            4589999999999999984

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

Probab=88.64  E-value=0.44  Score=29.95  Aligned_cols=18  Identities=28%  Similarity=0.547  Sum_probs=16.2

Q ss_pred             ecCeEEEEECCHHHHHhh
Q psy1185          37 IKDYAFVHFEDRQEAITV   54 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~   54 (131)
                      .+|||||+|.+.++|+.+
T Consensus        83 ~~g~afV~f~~~~~a~~A  100 (139)
T 1u6f_A           83 SRGYGFVKFQSGSSAQQA  100 (139)
T ss_dssp             EEEEEEEEESSHHHHHHH
T ss_pred             cceEEEEEECCHHHHHHH
Confidence            389999999999999984

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=88.61  E-value=0.23  Score=29.37  Aligned_cols=19  Identities=32%  Similarity=0.364  Sum_probs=16.6

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|+.+.
T Consensus        62 ~~G~afV~f~~~~~a~~Ai   80 (99)
T 2la6_A           62 LKGEATVSFDDPPSAKAAI   80 (99)
T ss_dssp             EEEEEEEEBSSHHHHHHHH
T ss_pred             eeeEEEEEECCHHHHHHHH
Confidence            3799999999999999844

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=88.61  E-value=0.2  Score=30.14  Aligned_cols=19  Identities=21%  Similarity=0.517  Sum_probs=16.6

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|..+.
T Consensus        60 ~~G~afV~f~~~~~A~~Ai   78 (105)
T 2nlw_A           60 TKGYIFLEYASPAHAVDAV   78 (105)
T ss_dssp             SCCEEEEEECSSSHHHHHH
T ss_pred             eeeEEEEEECCHHHHHHHH
Confidence            4799999999999999843

>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=88.59  E-value=0.17  Score=30.46  Aligned_cols=20  Identities=20%  Similarity=0.341  Sum_probs=17.3

Q ss_pred             ecCeEEEEECCHHHHHhhcC
Q psy1185          37 IKDYAFVHFEDRQEAITVTG   56 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~g   56 (131)
                      .+|||||+|.+.++|+.+..
T Consensus        54 ~~G~afV~F~~~~~a~~Al~   73 (102)
T 1wez_A           54 VTGEADVEFATHEDAVAAMA   73 (102)
T ss_dssp             EEEEEEEECSSSHHHHHHHT
T ss_pred             EeeEEEEEECCHHHHHHHHH
Confidence            47999999999999999553

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=88.56  E-value=0.22  Score=29.39  Aligned_cols=19  Identities=32%  Similarity=0.420  Sum_probs=16.7

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|+.+.
T Consensus        51 ~~g~afV~f~~~~~a~~A~   69 (99)
T 2div_A           51 PAGYCFVEFADLATAEKCL   69 (99)
T ss_dssp             EEEEEEEECSCHHHHHHHH
T ss_pred             cCCEEEEEeCCHHHHHHHH
Confidence            3799999999999999954

>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=88.54  E-value=0.32  Score=28.94  Aligned_cols=18  Identities=33%  Similarity=0.571  Sum_probs=16.1

Q ss_pred             ecCeEEEEECCHHHHHhh
Q psy1185          37 IKDYAFVHFEDRQEAITV   54 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~   54 (131)
                      .++||||+|.+.++|+.+
T Consensus        54 ~~g~afV~f~~~~~a~~A   71 (103)
T 2cq3_A           54 SKGFGFVTFENSADADRA   71 (103)
T ss_dssp             TCCEEEEEESCHHHHHHH
T ss_pred             CcEEEEEEECCHHHHHHH
Confidence            379999999999999984

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=88.52  E-value=0.28  Score=29.11  Aligned_cols=18  Identities=39%  Similarity=0.623  Sum_probs=16.6

Q ss_pred             ecCeEEEEECCHHHHHhh
Q psy1185          37 IKDYAFVHFEDRQEAITV   54 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~   54 (131)
                      .+|||||+|.+.++|+.+
T Consensus        36 ~~g~afV~f~~~~~a~~A   53 (101)
T 2hvz_A           36 PPGFAFVEFEDPRDAEDA   53 (101)
T ss_dssp             SSSEEEEECSSHHHHHHH
T ss_pred             CCCEEEEEECCHHHHHHH
Confidence            789999999999999983

>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=88.50  E-value=0.27  Score=29.86  Aligned_cols=19  Identities=21%  Similarity=0.450  Sum_probs=16.7

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|+.+.
T Consensus        66 ~~g~afV~f~~~~~a~~Ai   84 (115)
T 2cpx_A           66 MRGQAFITFPNKEIAWQAL   84 (115)
T ss_dssp             SCSEEEEECSSHHHHHHHH
T ss_pred             cceEEEEEECCHHHHHHHH
Confidence            4899999999999999843

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=88.47  E-value=0.23  Score=28.85  Aligned_cols=21  Identities=24%  Similarity=0.449  Sum_probs=17.7

Q ss_pred             cCeEEEEECCHHHHHhhcCCc
Q psy1185          38 KDYAFVHFEDRQEAITVTGLS   58 (131)
Q Consensus        38 ~~~~fv~~~~~~~a~~~~g~~   58 (131)
                      +|||||+|.+.++|+.+..+.
T Consensus        50 ~g~afV~f~~~~~a~~A~~~~   70 (91)
T 2dgw_A           50 TGYIFVDFSNEEEVKQALKCN   70 (91)
T ss_dssp             EEEEEEECSSHHHHHHHHHSC
T ss_pred             ceEEEEEECCHHHHHHHHHhC
Confidence            789999999999999965433

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

Probab=88.44  E-value=0.27  Score=29.26  Aligned_cols=19  Identities=32%  Similarity=0.632  Sum_probs=16.5

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|+.+.
T Consensus        56 ~~g~afV~f~~~~~A~~A~   74 (103)
T 2cq0_A           56 SKGFAFISFHRREDAARAI   74 (103)
T ss_dssp             EEEEEEEEESSHHHHHHHH
T ss_pred             eeeEEEEEECCHHHHHHHH
Confidence            3789999999999999843

>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=88.44  E-value=0.29  Score=29.49  Aligned_cols=19  Identities=37%  Similarity=0.543  Sum_probs=16.7

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .++||||+|.+.++|+.+.
T Consensus        60 ~~g~afV~f~~~~~A~~A~   78 (109)
T 1x4a_A           60 GPPFAFVEFEDPRDAEDAV   78 (109)
T ss_dssp             SSCCEEEEESCHHHHHHHH
T ss_pred             CCcEEEEEECCHHHHHHHH
Confidence            4799999999999999843

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=88.39  E-value=0.33  Score=29.60  Aligned_cols=20  Identities=30%  Similarity=0.471  Sum_probs=17.3

Q ss_pred             ecCeEEEEECCHHHHHhhcC
Q psy1185          37 IKDYAFVHFEDRQEAITVTG   56 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~g   56 (131)
                      .++||||+|.+.++|+.+..
T Consensus        58 ~~g~afV~f~~~~~a~~Ai~   77 (116)
T 2cqd_A           58 SRGYGFVTMADRAAAERACK   77 (116)
T ss_dssp             CCSEEEEEESSHHHHHHHHT
T ss_pred             cceEEEEEECCHHHHHHHHH
Confidence            47999999999999999543

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

Probab=88.38  E-value=0.27  Score=29.38  Aligned_cols=18  Identities=33%  Similarity=0.558  Sum_probs=16.1

Q ss_pred             cCeEEEEECCHHHHHhhc
Q psy1185          38 KDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        38 ~~~~fv~~~~~~~a~~~~   55 (131)
                      +|||||+|.+.++|+.+.
T Consensus        65 ~g~afV~f~~~~~a~~A~   82 (106)
T 1p27_B           65 KGYTLVEYETYKEAQAAM   82 (106)
T ss_dssp             EEEEEEEESCHHHHHHHH
T ss_pred             eeEEEEEECCHHHHHHHH
Confidence            799999999999999843

>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=88.28  E-value=0.24  Score=28.91  Aligned_cols=19  Identities=21%  Similarity=0.375  Sum_probs=16.6

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .++||||+|.+.++|+.+.
T Consensus        56 ~~g~afV~f~~~~~a~~A~   74 (95)
T 2ywk_A           56 PKSFGFVCFKHPESVSYAI   74 (95)
T ss_dssp             EEEEEEEEESSTHHHHHHH
T ss_pred             CceEEEEEECCHHHHHHHH
Confidence            4789999999999999943

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=88.17  E-value=0.22  Score=29.78  Aligned_cols=19  Identities=32%  Similarity=0.483  Sum_probs=16.5

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|+.+.
T Consensus        57 ~~g~afV~f~~~~~a~~a~   75 (105)
T 2dh8_A           57 SRGFGFVKFKDPNCVGTVL   75 (105)
T ss_dssp             EEEEEEEEESSTTHHHHHH
T ss_pred             cceEEEEEECCHHHHHHHH
Confidence            3799999999999999843

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

Probab=88.14  E-value=0.22  Score=29.53  Aligned_cols=19  Identities=32%  Similarity=0.545  Sum_probs=16.7

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .++||||+|.+.++|+.+.
T Consensus        53 ~~g~afV~f~~~~~A~~A~   71 (102)
T 2cqb_A           53 HRGFAFVEFELAEDAAAAI   71 (102)
T ss_dssp             CSSEEEECCSSHHHHHHHH
T ss_pred             cceEEEEEECCHHHHHHHH
Confidence            4899999999999999843

>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=88.13  E-value=0.35  Score=29.11  Aligned_cols=19  Identities=32%  Similarity=0.632  Sum_probs=16.5

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|+.+.
T Consensus        67 ~~g~afV~f~~~~~A~~Ai   85 (110)
T 1oo0_B           67 SKGYALVEYETHKQALAAK   85 (110)
T ss_dssp             BCSEEEEEESSHHHHHHHH
T ss_pred             cceEEEEEECCHHHHHHHH
Confidence            3799999999999999843

>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=88.11  E-value=0.29  Score=30.10  Aligned_cols=18  Identities=28%  Similarity=0.623  Sum_probs=16.1

Q ss_pred             ecCeEEEEECCHHHHHhh
Q psy1185          37 IKDYAFVHFEDRQEAITV   54 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~   54 (131)
                      .+|||||+|.+.++|+.+
T Consensus        47 ~~g~afV~F~~~~~A~~A   64 (116)
T 2fy1_A           47 SRGFAFITFENPADAKNA   64 (116)
T ss_dssp             CCCEEEEECSSHHHHHHH
T ss_pred             cccEEEEEECCHHHHHHH
Confidence            379999999999999984

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=88.11  E-value=0.29  Score=29.77  Aligned_cols=18  Identities=33%  Similarity=0.547  Sum_probs=16.2

Q ss_pred             cCeEEEEECCHHHHHhhc
Q psy1185          38 KDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        38 ~~~~fv~~~~~~~a~~~~   55 (131)
                      +|||||+|.+.++|+.+.
T Consensus        57 ~g~afV~f~~~~~a~~A~   74 (115)
T 2dgo_A           57 KGYGFVSFFNKWDAENAI   74 (115)
T ss_dssp             EEEEEEEESSHHHHHHHH
T ss_pred             ceEEEEEECCHHHHHHHH
Confidence            799999999999999843

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=88.09  E-value=0.29  Score=29.09  Aligned_cols=18  Identities=33%  Similarity=0.562  Sum_probs=16.1

Q ss_pred             ecCeEEEEECCHHHHHhh
Q psy1185          37 IKDYAFVHFEDRQEAITV   54 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~   54 (131)
                      .++||||+|.+.++|+.+
T Consensus        54 ~~g~afV~f~~~~~A~~A   71 (103)
T 2d9p_A           54 SKGFGFVCFSSPEEATKA   71 (103)
T ss_dssp             EEEEEEEEESSHHHHHHH
T ss_pred             cCEEEEEEECCHHHHHHH
Confidence            478999999999999983

>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=87.89  E-value=0.26  Score=29.34  Aligned_cols=18  Identities=28%  Similarity=0.737  Sum_probs=16.6

Q ss_pred             cCeEEEEECCHHHHHhhc
Q psy1185          38 KDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        38 ~~~~fv~~~~~~~a~~~~   55 (131)
                      +|||||+|.+.++|+.+.
T Consensus        50 ~g~afV~f~~~~~a~~A~   67 (104)
T 1p1t_A           50 KGYGFCEYQDQETALSAM   67 (104)
T ss_dssp             EEEEEEECSCHHHHHHHH
T ss_pred             ceEEEEEECCHHHHHHHH
Confidence            799999999999999955

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=87.88  E-value=0.32  Score=29.58  Aligned_cols=18  Identities=28%  Similarity=0.373  Sum_probs=16.2

Q ss_pred             cCeEEEEECCHHHHHhhc
Q psy1185          38 KDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        38 ~~~~fv~~~~~~~a~~~~   55 (131)
                      +|||||+|.+.++|..+.
T Consensus        56 ~G~~FV~f~~~~~A~~Ai   73 (105)
T 2pe8_A           56 AVRIFLEFERVESAIKAV   73 (105)
T ss_dssp             SEEEEEEESSHHHHHHHH
T ss_pred             cEEEEEEECCHHHHHHHH
Confidence            799999999999999843

>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=87.70  E-value=0.31  Score=29.54  Aligned_cols=19  Identities=32%  Similarity=0.513  Sum_probs=16.6

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|+.+.
T Consensus        67 ~~g~afV~F~~~~~A~~Ai   85 (108)
T 2jrs_A           67 SKGYGFITFSDSECAKKAL   85 (108)
T ss_dssp             EEEEEEEEESCHHHHHHHH
T ss_pred             cceEEEEEECCHHHHHHHH
Confidence            4799999999999999843

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=87.68  E-value=0.25  Score=29.98  Aligned_cols=19  Identities=32%  Similarity=0.538  Sum_probs=16.7

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|+.+.
T Consensus        68 ~kg~afV~f~~~~~A~~Ai   86 (109)
T 2err_A           68 SKGFGFVTFENSADADRAR   86 (109)
T ss_dssp             CTTEEEEECCCSHHHHHHH
T ss_pred             CceEEEEEECCHHHHHHHH
Confidence            4899999999999999843

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

Probab=87.55  E-value=0.24  Score=29.49  Aligned_cols=18  Identities=39%  Similarity=0.746  Sum_probs=16.1

Q ss_pred             ecCeEEEEECCHHHHHhh
Q psy1185          37 IKDYAFVHFEDRQEAITV   54 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~   54 (131)
                      .+|||||+|.+.++|+.+
T Consensus        54 ~~g~afV~f~~~~~A~~A   71 (103)
T 2dnm_A           54 PRGFAFVRFHDRRDAQDA   71 (103)
T ss_dssp             BCSCEEEEESSSSHHHHH
T ss_pred             CCeEEEEEECCHHHHHHH
Confidence            479999999999999983

>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=87.49  E-value=0.31  Score=29.60  Aligned_cols=23  Identities=30%  Similarity=0.380  Sum_probs=18.8

Q ss_pred             ecCeEEEEECCHHHHHhhcCCce
Q psy1185          37 IKDYAFVHFEDRQEAITVTGLSQ   59 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~g~~~   59 (131)
                      .+|||||+|.+.++|+.+..+.+
T Consensus        66 ~~g~afV~f~~~~~a~~A~~l~g   88 (114)
T 2cq4_A           66 SKGIAYVEFCEIQSVPLAIGLTG   88 (114)
T ss_dssp             CCCCEEEEESCGGGHHHHHHHTT
T ss_pred             cCcEEEEEeCcHHHHHHHHHcCC
Confidence            47999999999999999664444

>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=87.35  E-value=0.34  Score=29.50  Aligned_cols=19  Identities=32%  Similarity=0.218  Sum_probs=16.8

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|+.+.
T Consensus        63 ~~G~afV~f~~~~~A~~Ai   81 (112)
T 2dit_A           63 PDGVASVSFRDPEEADYCI   81 (112)
T ss_dssp             TTCEEEEECSCHHHHHHHH
T ss_pred             CCEEEEEEECCHHHHHHHH
Confidence            5899999999999999843

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=87.18  E-value=0.33  Score=31.67  Aligned_cols=19  Identities=21%  Similarity=0.170  Sum_probs=16.8

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|+.+.
T Consensus        98 skGfaFV~f~~~~~A~~Ai  116 (156)
T 3n9u_C           98 SKGYAEVVVASENSVHKLL  116 (156)
T ss_dssp             EEEEEEEEESCHHHHHHHH
T ss_pred             cceEEEEEECCHHHHHHHH
Confidence            3899999999999999954

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

Probab=87.03  E-value=0.42  Score=29.90  Aligned_cols=19  Identities=32%  Similarity=0.545  Sum_probs=17.1

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|+.+.
T Consensus       104 ~~g~afV~f~~~~~a~~A~  122 (140)
T 2ku7_A          104 HRGFAFVEFELAEDAAAAI  122 (140)
T ss_dssp             CCSEEEEEESCHHHHHHHH
T ss_pred             cCcEEEEEECCHHHHHHHH
Confidence            4799999999999999965

>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=86.87  E-value=0.38  Score=28.75  Aligned_cols=19  Identities=32%  Similarity=0.385  Sum_probs=16.5

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|+.+.
T Consensus        69 ~~g~afV~f~~~~~a~~A~   87 (107)
T 3ulh_A           69 SLGTADVHFERKADALKAM   87 (107)
T ss_dssp             EEEEEEEEESSHHHHHHHH
T ss_pred             cceEEEEEECCHHHHHHHH
Confidence            3789999999999999843

>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=86.80  E-value=0.46  Score=28.83  Aligned_cols=18  Identities=17%  Similarity=0.167  Sum_probs=16.3

Q ss_pred             cCeEEEEECCHHHHHhhc
Q psy1185          38 KDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        38 ~~~~fv~~~~~~~a~~~~   55 (131)
                      +|++||+|.+.++|.++.
T Consensus        59 ~G~~fV~f~~~~~A~~Ai   76 (105)
T 3v4m_A           59 CGKIFVEFTSVFDCQKAM   76 (105)
T ss_dssp             TTEEEEEESSHHHHHHHH
T ss_pred             cEEEEEEECCHHHHHHHH
Confidence            799999999999999853

>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=86.79  E-value=0.41  Score=29.04  Aligned_cols=18  Identities=28%  Similarity=0.405  Sum_probs=16.3

Q ss_pred             cCeEEEEECCHHHHHhhc
Q psy1185          38 KDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        38 ~~~~fv~~~~~~~a~~~~   55 (131)
                      +|||||+|.+.++|..+.
T Consensus        47 ~g~afV~f~~~~~A~~A~   64 (115)
T 3lqv_A           47 RGTAYVVYEDIFDAKNAV   64 (115)
T ss_dssp             TTCEEEEESSHHHHHHHH
T ss_pred             CcEEEEEECCHHHHHHHH
Confidence            799999999999999854

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=86.72  E-value=0.46  Score=29.29  Aligned_cols=18  Identities=39%  Similarity=0.455  Sum_probs=16.2

Q ss_pred             ecCeEEEEECCHHHHHhh
Q psy1185          37 IKDYAFVHFEDRQEAITV   54 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~   54 (131)
                      .+|||||+|.+.++|+.+
T Consensus        75 ~~g~afV~f~~~~~A~~A   92 (124)
T 2kt5_A           75 SLGTADVHFERRADALKA   92 (124)
T ss_dssp             CCSEEEEEESSHHHHHHH
T ss_pred             EeeEEEEEECCHHHHHHH
Confidence            379999999999999984

>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=86.57  E-value=0.34  Score=29.49  Aligned_cols=18  Identities=22%  Similarity=0.449  Sum_probs=16.1

Q ss_pred             cCeEEEEECCHHHHHhhc
Q psy1185          38 KDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        38 ~~~~fv~~~~~~~a~~~~   55 (131)
                      ++||||+|.+.++|+.+.
T Consensus        67 ~g~afV~f~~~~~a~~A~   84 (115)
T 2cpz_A           67 KCFGFVSYDNPVSAQAAI   84 (115)
T ss_dssp             EEEEEEECSSHHHHHHHH
T ss_pred             CccEEEEECCHHHHHHHH
Confidence            789999999999999843

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=86.43  E-value=0.26  Score=31.00  Aligned_cols=50  Identities=14%  Similarity=0.092  Sum_probs=33.0

Q ss_pred             ecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHHhHHHHHHHHhC
Q psy1185          37 IKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLAT   95 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~   95 (131)
                      .+|||||+|.+.++|+.+....+..+.         ..+.-|...+..+...++.....
T Consensus        67 ~~G~aFV~F~~~~~A~~Al~~~~~~l~---------gR~i~V~~a~~~e~~~~~~~~~~  116 (123)
T 2dha_A           67 PTGDAFVLFACEEYAQNALRKHKDLLG---------KRYIELFRSTAAEVQQVLNRFSS  116 (123)
T ss_dssp             EEEEEEECCSSHHHHHHHHTTTTEESS---------SCEECCEEECHHHHHHHHHHHTT
T ss_pred             EeeEEEEEECCHHHHHHHHHhCCCeeC---------CeEEEEEECCHHHHHHHHHhccC
Confidence            379999999999999997654443211         11344455677777777665443

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

Probab=86.35  E-value=0.42  Score=28.92  Aligned_cols=18  Identities=28%  Similarity=0.377  Sum_probs=15.9

Q ss_pred             ecCeEEEEECCHHHHHhh
Q psy1185          37 IKDYAFVHFEDRQEAITV   54 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~   54 (131)
                      .++||||+|.+.++|+.+
T Consensus        55 ~~g~afV~f~~~~~a~~A   72 (114)
T 2do0_A           55 SRGIGTVTFEQSIEAVQA   72 (114)
T ss_dssp             EEEEEEEEESSHHHHHHH
T ss_pred             eeeEEEEEECCHHHHHHH
Confidence            378999999999999884

>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=86.34  E-value=0.45  Score=29.36  Aligned_cols=17  Identities=35%  Similarity=0.602  Sum_probs=15.8

Q ss_pred             cCeEEEEECCHHHHHhh
Q psy1185          38 KDYAFVHFEDRQEAITV   54 (131)
Q Consensus        38 ~~~~fv~~~~~~~a~~~   54 (131)
                      +|||||+|.+.++|+.+
T Consensus        64 ~g~afV~f~~~~~a~~A   80 (126)
T 3ex7_B           64 KGYTLVEYETYKEAQAA   80 (126)
T ss_dssp             CSCEEEEESSHHHHHHH
T ss_pred             ceEEEEEECCHHHHHHH
Confidence            79999999999999984

>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=86.34  E-value=0.41  Score=28.98  Aligned_cols=19  Identities=16%  Similarity=0.312  Sum_probs=16.6

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|+.+.
T Consensus        65 ~~g~afV~f~~~~~a~~A~   83 (114)
T 1x5o_A           65 SRGVGFARMESTEKCEAVI   83 (114)
T ss_dssp             EEEEEEEEESCHHHHHHHH
T ss_pred             cceEEEEEECCHHHHHHHH
Confidence            3799999999999999954

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=86.25  E-value=0.22  Score=29.59  Aligned_cols=20  Identities=25%  Similarity=0.468  Sum_probs=17.6

Q ss_pred             ecCeEEEEECCHHHHHhhcC
Q psy1185          37 IKDYAFVHFEDRQEAITVTG   56 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~g   56 (131)
                      .+|||||+|.+.++|+.+..
T Consensus        49 ~~g~afV~f~~~~~a~~Ai~   68 (102)
T 2xs2_A           49 SKGYGFVSFYNDVDVQKIVE   68 (102)
T ss_dssp             EEEEEEEEESSCCCHHHHTT
T ss_pred             ccceEEEEECCHHHHHHHHh
Confidence            37999999999999999765

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=85.69  E-value=0.39  Score=29.31  Aligned_cols=19  Identities=26%  Similarity=0.459  Sum_probs=16.8

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|+.+.
T Consensus        81 ~~g~afV~f~~~~~A~~A~   99 (118)
T 2khc_A           81 SKCFGFVSFDNPDSAQVAI   99 (118)
T ss_dssp             CCCEEEEEEESSHHHHHHH
T ss_pred             cCcEEEEEECCHHHHHHHH
Confidence            3799999999999999854

>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=85.16  E-value=0.61  Score=28.07  Aligned_cols=17  Identities=12%  Similarity=0.225  Sum_probs=13.9

Q ss_pred             CeEEEEECCHHHHHhhc
Q psy1185          39 DYAFVHFEDRQEAITVT   55 (131)
Q Consensus        39 ~~~fv~~~~~~~a~~~~   55 (131)
                      +||||+|.+.++|+.+.
T Consensus        51 g~afV~f~~~~~a~~Ai   67 (108)
T 1x4c_A           51 GTGVVEFVRKEDMTYAV   67 (108)
T ss_dssp             TEEEEEESSHHHHHHHH
T ss_pred             CEEEEEECCHHHHHHHH
Confidence            06999999999999843

>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=85.06  E-value=0.62  Score=28.48  Aligned_cols=16  Identities=13%  Similarity=0.239  Sum_probs=13.5

Q ss_pred             CeEEEEECCHHHHHhh
Q psy1185          39 DYAFVHFEDRQEAITV   54 (131)
Q Consensus        39 ~~~fv~~~~~~~a~~~   54 (131)
                      +||||+|.+.++|+.+
T Consensus        52 g~afV~f~~~~~a~~A   67 (115)
T 3beg_B           52 GTGVVEFVRKEDMTYA   67 (115)
T ss_dssp             SEEEEEESSHHHHHHH
T ss_pred             CEEEEEECCHHHHHHH
Confidence            0599999999999984

>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=84.57  E-value=0.43  Score=27.77  Aligned_cols=17  Identities=41%  Similarity=0.681  Sum_probs=14.2

Q ss_pred             cCeEEEEECCHHHHHhh
Q psy1185          38 KDYAFVHFEDRQEAITV   54 (131)
Q Consensus        38 ~~~~fv~~~~~~~a~~~   54 (131)
                      ++||||+|.+.++|+.+
T Consensus        44 ~g~afV~f~~~~~A~~A   60 (93)
T 2cqh_A           44 SGYAFVDYPDQNWAIRA   60 (93)
T ss_dssp             TTEEEECCSCHHHHHHH
T ss_pred             CCEEEEEECCHHHHHHH
Confidence            04899999999999884

>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=84.27  E-value=0.49  Score=29.97  Aligned_cols=18  Identities=22%  Similarity=0.420  Sum_probs=16.2

Q ss_pred             ecCeEEEEECCHHHHHhh
Q psy1185          37 IKDYAFVHFEDRQEAITV   54 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~   54 (131)
                      .+|||||+|.+.++|..+
T Consensus        91 ~~g~afV~f~~~~~A~~A  108 (143)
T 3egn_A           91 MKGQAFIGLPNEKAAAKA  108 (143)
T ss_dssp             TEEEEEEECSSHHHHHHH
T ss_pred             cccEEEEEeCCHHHHHHH
Confidence            379999999999999984

>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=84.12  E-value=0.83  Score=25.97  Aligned_cols=22  Identities=23%  Similarity=0.516  Sum_probs=17.2

Q ss_pred             cCeEEEEECCHHHHHhhcCCce
Q psy1185          38 KDYAFVHFEDRQEAITVTGLSQ   59 (131)
Q Consensus        38 ~~~~fv~~~~~~~a~~~~g~~~   59 (131)
                      +|||||+|.+.++|+.+..+.+
T Consensus        53 kg~afV~f~~~~~a~~A~~l~g   74 (87)
T 2hzc_A           53 KNFAFLEFRSVDETTQAMAFDG   74 (87)
T ss_dssp             SSEEEEEESSHHHHHHHGGGTT
T ss_pred             CcEEEEEcCCHHHHHHHHhcCC
Confidence            0489999999999999665444

>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=83.59  E-value=0.36  Score=31.01  Aligned_cols=20  Identities=25%  Similarity=0.355  Sum_probs=17.6

Q ss_pred             ecCeEEEEECCHHHHHhhcC
Q psy1185          37 IKDYAFVHFEDRQEAITVTG   56 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~g   56 (131)
                      .+|||||+|.+.++|+.+..
T Consensus        85 srGfaFV~F~~~e~A~~Al~  104 (139)
T 2hgn_A           85 VTGEADVEFATHEEAVAAMS  104 (139)
T ss_dssp             SSCCCEEECSHHHHHHHHTT
T ss_pred             CceEEEEEeCCHHHHHHHHh
Confidence            48999999999999999654

>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=83.43  E-value=0.65  Score=29.84  Aligned_cols=18  Identities=22%  Similarity=0.433  Sum_probs=16.1

Q ss_pred             ecCeEEEEECCHHHHHhh
Q psy1185          37 IKDYAFVHFEDRQEAITV   54 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~   54 (131)
                      .++||||+|.+.++|+.+
T Consensus        80 ~~g~afV~f~~~~~A~~A   97 (156)
T 1h2v_Z           80 ACGFCFVEYYSRADAENA   97 (156)
T ss_dssp             EEEEEEEEESSHHHHHHH
T ss_pred             cceEEEEEECCHHHHHHH
Confidence            478999999999999994

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=83.37  E-value=0.43  Score=29.87  Aligned_cols=16  Identities=25%  Similarity=0.497  Sum_probs=14.3

Q ss_pred             ecCeEEEEECCHHHHHh
Q psy1185          37 IKDYAFVHFEDRQEAIT   53 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~   53 (131)
                      .+|||||+|.+. +|..
T Consensus        66 ~rG~aFV~f~~~-~a~~   81 (131)
T 2m2b_A           66 NRGFAFIQLSTI-EAAQ   81 (131)
T ss_dssp             BCSCEEEECCHH-HHHH
T ss_pred             cceEEEEEECCH-HHHH
Confidence            389999999999 8887

>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=82.99  E-value=0.66  Score=28.70  Aligned_cols=18  Identities=17%  Similarity=0.244  Sum_probs=16.3

Q ss_pred             cCeEEEEECCHHHHHhhc
Q psy1185          38 KDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        38 ~~~~fv~~~~~~~a~~~~   55 (131)
                      +|++||.|.+.++|..+.
T Consensus        55 ~G~~fV~f~~~e~A~~Ai   72 (114)
T 3s6e_A           55 QGNVYVKCPSIAAAIAAV   72 (114)
T ss_dssp             TCCEEEECSSHHHHHHHH
T ss_pred             cEEEEEEECCHHHHHHHH
Confidence            899999999999999843

>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=82.68  E-value=0.76  Score=28.60  Aligned_cols=18  Identities=22%  Similarity=0.141  Sum_probs=16.0

Q ss_pred             cCeEEEEECCHHHHHhhc
Q psy1185          38 KDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        38 ~~~~fv~~~~~~~a~~~~   55 (131)
                      +|++||.|.+.++|..+.
T Consensus        71 ~G~~FV~F~~~e~A~~Ai   88 (118)
T 3ue2_A           71 IVKIFVEFSIASETHKAI   88 (118)
T ss_dssp             EEEEEEEESSHHHHHHHH
T ss_pred             eEEEEEEECCHHHHHHHH
Confidence            699999999999999843

>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=82.38  E-value=0.73  Score=31.04  Aligned_cols=20  Identities=25%  Similarity=0.325  Sum_probs=17.4

Q ss_pred             ecCeEEEEECCHHHHHhhcC
Q psy1185          37 IKDYAFVHFEDRQEAITVTG   56 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~g   56 (131)
                      .+|||||+|.+.++|+.+..
T Consensus       149 ~kG~aFVeF~~~e~A~~A~~  168 (193)
T 2voo_A          149 FKGSIFVVFDSIESAKKFVE  168 (193)
T ss_dssp             EEEEEEEEESSHHHHHHHHH
T ss_pred             cccEEEEEECCHHHHHHHHH
Confidence            48999999999999999543

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=82.33  E-value=0.88  Score=27.52  Aligned_cols=17  Identities=18%  Similarity=0.165  Sum_probs=14.5

Q ss_pred             cCeEEEEECCHHHHHhh
Q psy1185          38 KDYAFVHFEDRQEAITV   54 (131)
Q Consensus        38 ~~~~fv~~~~~~~a~~~   54 (131)
                      .|+|||.|.+.++|+++
T Consensus        46 gG~AfV~F~~~esA~~A   62 (96)
T 2diu_A           46 GCSAILRFINQDSAERA   62 (96)
T ss_dssp             TTCEEEEESSHHHHHHH
T ss_pred             cCEEEEEECCHHHHHHH
Confidence            06899999999999883

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

Probab=82.30  E-value=0.58  Score=29.59  Aligned_cols=19  Identities=32%  Similarity=0.662  Sum_probs=16.7

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|+.+.
T Consensus        88 ~~G~afV~F~~~~~A~~Ai  106 (135)
T 2lea_A           88 SRGFAFVRFHDKRDAEDAM  106 (135)
T ss_dssp             CCSCCEEECSCHHHHHHHH
T ss_pred             cceEEEEEECCHHHHHHHH
Confidence            4799999999999999944

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=81.51  E-value=1.5  Score=25.49  Aligned_cols=19  Identities=26%  Similarity=0.268  Sum_probs=16.1

Q ss_pred             eEEEEECCHHHHHhhcCCc
Q psy1185          40 YAFVHFEDRQEAITVTGLS   58 (131)
Q Consensus        40 ~~fv~~~~~~~a~~~~g~~   58 (131)
                      ||||+|.+.++|+.+..+.
T Consensus        47 ~afV~f~~~~~a~~ai~l~   65 (94)
T 2e5g_A           47 FAIVEMGDVGAREAVLSQS   65 (94)
T ss_dssp             EEEEEESSHHHHHHHHTCS
T ss_pred             EEEEEECCHHHHHHHHhcC
Confidence            9999999999999965444

>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=81.20  E-value=0.91  Score=30.13  Aligned_cols=35  Identities=11%  Similarity=0.146  Sum_probs=23.2

Q ss_pred             HHHHHhhccCCeeEEEE-ecCeEEEEECCHHHHHhh
Q psy1185          20 KLKEAFEQYGRVERVKR-IKDYAFVHFEDRQEAITV   54 (131)
Q Consensus        20 ~l~~~F~~~G~v~~~~i-~~~~~fv~~~~~~~a~~~   54 (131)
                      ++..-|...-.|.=..- .++||||+|.+.++|+.+
T Consensus        65 ~~Fs~fG~V~~V~i~~k~~rgfAFVeF~d~~~A~~A  100 (164)
T 1sjr_A           65 QIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHA  100 (164)
T ss_dssp             HHHHHHSCEEEEEEEESSSCEEEEEEESCHHHHHHH
T ss_pred             HHHHhcCCEEEEEEEeCCCCCEEEEEECCHHHHHHH
Confidence            34444555444433322 478999999999999984

>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=80.63  E-value=1  Score=28.02  Aligned_cols=23  Identities=17%  Similarity=0.342  Sum_probs=17.8

Q ss_pred             eEEEEECCHHHHHhhcC-CceeEE
Q psy1185          40 YAFVHFEDRQEAITVTG-LSQVII   62 (131)
Q Consensus        40 ~~fv~~~~~~~a~~~~g-~~~~~~   62 (131)
                      ||||+|.+.++|+.+.. +.+..+
T Consensus        65 faFV~f~~~~~A~~Ai~~lnG~~~   88 (114)
T 2cq2_A           65 YSFARYRTTEESKRAYVTLNGKEV   88 (114)
T ss_dssp             CEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             EEEEEECCHHHHHHHHHHhCCCEE
Confidence            99999999999998543 555443

>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=80.55  E-value=0.95  Score=29.44  Aligned_cols=18  Identities=33%  Similarity=0.665  Sum_probs=16.1

Q ss_pred             ecCeEEEEECCHHHHHhh
Q psy1185          37 IKDYAFVHFEDRQEAITV   54 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~   54 (131)
                      .+|||||+|.+.++|+.+
T Consensus       113 ~~g~afV~f~~~~~A~~A  130 (165)
T 1rk8_A          113 SKGYALVEYETHKQALAA  130 (165)
T ss_dssp             EEEEEEEEESSHHHHHHH
T ss_pred             EeeEEEEEECCHHHHHHH
Confidence            379999999999999984

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=80.45  E-value=1.1  Score=27.29  Aligned_cols=16  Identities=25%  Similarity=0.453  Sum_probs=13.3

Q ss_pred             CeEEEEECCHHHHHhh
Q psy1185          39 DYAFVHFEDRQEAITV   54 (131)
Q Consensus        39 ~~~fv~~~~~~~a~~~   54 (131)
                      |||||+|.+.++|+.+
T Consensus        53 GfaFVeF~~~~~A~~A   68 (105)
T 1sjq_A           53 NQAFIEMNTEEAANTM   68 (105)
T ss_dssp             TEEEEEESSHHHHHHH
T ss_pred             CEEEEEECCHHHHHHH
Confidence            0599999999999883

---

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	131
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	2e-19
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	7e-12
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-11
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	5e-10
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	2e-09
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	4e-09
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	5e-09
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	1e-08
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	6e-08
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	7e-08
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	7e-08
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	1e-07
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	1e-07
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	1e-07
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	1e-07
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	2e-07
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	2e-07
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	5e-07
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	5e-07
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	5e-07
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	5e-07
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	6e-07
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	8e-07
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	8e-07
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	1e-06
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-06
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	2e-06
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-06
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	4e-06
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	6e-06
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	6e-06
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	6e-06
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	1e-05
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	1e-05
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	1e-05
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-05
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	2e-05
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	2e-05
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	3e-05
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	5e-05
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	5e-05
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	6e-05
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	7e-05
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	7e-05
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	8e-05
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	9e-05
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	9e-05
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	1e-04
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	1e-04
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	1e-04
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	2e-04
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	3e-04
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	4e-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:) 4e-04
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	6e-04
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	0.001
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	0.001
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	0.001
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	0.002
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	0.002
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	0.002
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	0.004
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	0.004

>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 = 75.1 bits (184), Expect = 2e-19
 Identities = 34/118 (28%), Positives = 59/118 (50%), Gaps = 25/118 (21%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
           L++  + +    E++ E   +                                VI+Y+S 
Sbjct: 4   LFIGGIPKMKKREEILEEIAKVTEGVL-------------------------DVIVYASA 38

Query: 67  DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPDTETMSKV 124
            D  KNRGF F+EY+SH++A++A+++L  GR+++WG  I VDWA+P+ + D + M  V
Sbjct: 39  ADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMETV 96

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 55.3 bits (133), Expect = 7e-12
 Identities = 19/109 (17%), Positives = 42/109 (38%), Gaps = 27/109 (24%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
           + VRN+     + +++E F  +G ++ V+  K                            
Sbjct: 11  ILVRNIPFQANQREIRELFSTFGELKTVRLPKK--------------------------M 44

Query: 67  DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEE 115
                +RGF F+++ + + A  A   L      ++G  ++++WAD +  
Sbjct: 45  TGTGAHRGFGFVDFITKQDAKKAFNALCHST-HLYGRRLVLEWADSEVT 92

>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 = 53.7 bits (129), Expect = 3e-11
 Identities = 10/46 (21%), Positives = 23/46 (50%), Gaps = 1/46 (2%)

Query: 7  LYVRNLTQY-CTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEA 51
          +++ NL      +  ++  F +YG++      K +AFV + + + A
Sbjct: 18 VFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNERNA 63

>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 = 50.4 bits (120), Expect = 5e-10
 Identities = 26/53 (49%), Positives = 36/53 (67%), Gaps = 2/53 (3%)

Query: 1  MSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVE--RVKRIKDYAFVHFEDRQEA 51
          MS VK+LYVRNL    +EE +++ F         RVK+I+DYAFVHF +R++A
Sbjct: 5  MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDA 57

>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 = 49.2 bits (117), Expect = 2e-09
 Identities = 21/113 (18%), Positives = 35/113 (30%), Gaps = 31/113 (27%)

Query: 2   SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVI 61
           S V  + V NL    T + L + F ++G V ++                           
Sbjct: 5   SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITF------------------------ 40

Query: 62  IYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQE 114
                   K N+    L+Y    SA  AK  L    +    C + +D++    
Sbjct: 41  -------TKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTS 86

>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 = 48.1 bits (114), Expect = 4e-09
 Identities = 22/110 (20%), Positives = 39/110 (35%), Gaps = 26/110 (23%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
           L+++NL    TEE LK  F + G ++                           +    + 
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSC------------------------TISKKKNK 36

Query: 67  DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEP 116
                + GF F+EY   + A  A K+L    +   G  + V  ++   +P
Sbjct: 37  AGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVD--GHKLEVRISERATKP 84

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 47.6 bits (113), Expect = 5e-09
 Identities = 16/53 (30%), Positives = 27/53 (50%), Gaps = 8/53 (15%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYAFVHFEDRQEA 51
          LYV NL +  T+++L   F +YG + +   +        +  AFV +  R+EA
Sbjct: 9  LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEA 61

>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 = 46.7 bits (110), Expect = 1e-08
 Identities = 16/109 (14%), Positives = 37/109 (33%), Gaps = 28/109 (25%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
           +++ NL     E+ L + F  +G + +  +I                             
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRD-------------------------- 34

Query: 67  DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEE 115
            D   ++G+ F+ + S  ++  A +  A     +    I V +A  ++ 
Sbjct: 35  PDTGNSKGYAFINFASFDASDAAIE--AMNGQYLCNRPITVSYAFKKDS 81

>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 = 45.1 bits (106), Expect = 6e-08
 Identities = 19/115 (16%), Positives = 41/115 (35%), Gaps = 37/115 (32%)

Query: 1   MSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQV 60
           M+K   LY+ NL+   T + L++ F         + +                       
Sbjct: 1   MNK---LYIGNLSPAVTADDLRQLFGDRKLPLAGQVL----------------------- 34

Query: 61  IIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEE 115
                        G+ F++Y     A  A + L +G++++ G  + VD++  ++ 
Sbjct: 35  ----------LKSGYAFVDYPDQNWAIRAIETL-SGKVELHGKIMEVDYSVSKKL 78

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]} Length = 114

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.4 bits (107), Expect = 7e-08
 Identities = 15/52 (28%), Positives = 28/52 (53%), Gaps = 5/52 (9%)

Query: 5  KVLYVRNLTQYCTEEKLKEAFEQYGRVER-----VKRIKDYAFVHFEDRQEA 51
          ++LY+RNL    T E++ + F +YG + +         +  A+V +ED  +A
Sbjct: 8  RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDA 59

>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 = 45.0 bits (106), Expect = 7e-08
 Identities = 10/47 (21%), Positives = 24/47 (51%), Gaps = 2/47 (4%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVK--RIKDYAFVHFEDRQEA 51
          +Y   +    T++ +++ F  +G++  ++    K Y+FV F   + A
Sbjct: 21 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESA 67

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 44.2 bits (104), Expect = 1e-07
 Identities = 20/106 (18%), Positives = 35/106 (33%), Gaps = 29/106 (27%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
           L V  L Q  T+ +L   F   G +   + ++DY                          
Sbjct: 5   LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDY-------------------------- 38

Query: 67  DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADP 112
                + G+ F+++ S   +  A K L    + V    + V +A P
Sbjct: 39  -KTGYSYGYAFVDFTSEMDSQRAIKVL--NGITVRNKRLKVSYARP 81

>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 = 44.1 bits (104), Expect = 1e-07
 Identities = 16/104 (15%), Positives = 33/104 (31%), Gaps = 29/104 (27%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
           LYV +L    TE  L E F   G +  ++  +D                           
Sbjct: 3   LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDM-------------------------- 36

Query: 67  DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWA 110
              +++ G+ ++ +     A  A   +      + G  + + W+
Sbjct: 37  -ITRRSLGYAYVNFQQPADAERALDTM--NFDVIKGKPVRIMWS 77

>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 = 44.2 bits (104), Expect = 1e-07
 Identities = 17/82 (20%), Positives = 29/82 (35%), Gaps = 13/82 (15%)

Query: 5   KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITVTG 56
           + ++   L        L++ F   G+V  V+ I D         A+V F + Q      G
Sbjct: 19  RTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG 78

Query: 57  LSQVIIYS-----SPDDNKKNR 73
           L+   +            +KNR
Sbjct: 79  LTGQRLLGVPIIVQASQAEKNR 100

>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 = 43.8 bits (103), Expect = 1e-07
 Identities = 12/53 (22%), Positives = 26/53 (49%), Gaps = 8/53 (15%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYAFVHFEDRQEA 51
          ++V  L+    EEK++E F  +G VE ++          + + F+ F++ +  
Sbjct: 2  IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPV 54

>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 = 43.9 bits (103), Expect = 2e-07
 Identities = 23/104 (22%), Positives = 37/104 (35%), Gaps = 27/104 (25%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
           LYV  L +  T+++L++ F QYGR+   + + D                           
Sbjct: 9   LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGV---------------------- 46

Query: 67  DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWA 110
                +RG  F+ +D    A  A K L   +       I V +A
Sbjct: 47  -----SRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA 85

>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 = 43.8 bits (103), Expect = 2e-07
 Identities = 21/117 (17%), Positives = 36/117 (30%), Gaps = 31/117 (26%)

Query: 1   MSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQV 60
           + K   L V  L    TE+ LKE F  +G V  V+  KD                     
Sbjct: 5   VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDL-------------------- 44

Query: 61  IIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD 117
                      ++GF F+ +  +++           R  + G        + ++  D
Sbjct: 45  -------KTGHSKGFGFVRFTEYETQVKVMS----QRHMIDGRWCDCKLPNSKQSQD 90

>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 = 42.6 bits (100), Expect = 5e-07
 Identities = 13/52 (25%), Positives = 24/52 (46%), Gaps = 7/52 (13%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIK-------DYAFVHFEDRQEA 51
          L V NL    ++  ++E F ++G +++              A VHFE + +A
Sbjct: 3  LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADA 54

>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 = 42.3 bits (99), Expect = 5e-07
 Identities = 14/53 (26%), Positives = 26/53 (49%), Gaps = 8/53 (15%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
          +++  L+   T+E L+E F Q+G V+    ++D        + FV F D+   
Sbjct: 3  MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGV 55

>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 = 42.8 bits (100), Expect = 5e-07
 Identities = 20/108 (18%), Positives = 36/108 (33%), Gaps = 21/108 (19%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
           +YV+ L    T + L + F+Q G V+  KR        + D++                 
Sbjct: 11  IYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKE----------------- 53

Query: 67  DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQE 114
               K +G   + Y+   +A  A +          G  + V  A  + 
Sbjct: 54  --TGKPKGDATVSYEDPPTAKAAVEWF--DGKDFQGSKLKVSLARKKP 97

>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 = 42.6 bits (100), Expect = 5e-07
 Identities = 27/110 (24%), Positives = 41/110 (37%), Gaps = 29/110 (26%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
           LYV NL+ Y TEE++ E F + G ++++    D                           
Sbjct: 10  LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDK-------------------------- 43

Query: 67  DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEP 116
              K   GFCF+EY S   A  A + +     ++    I  DW    +E 
Sbjct: 44  -MKKTACGFCFVEYYSRADAENAMRYI--NGTRLDDRIIRTDWDAGFKEG 90

>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 = 42.3 bits (99), Expect = 6e-07
 Identities = 24/109 (22%), Positives = 40/109 (36%), Gaps = 29/109 (26%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
           +YV  L +  +E  L E F Q G V      KD                           
Sbjct: 12  VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDR-------------------------- 45

Query: 67  DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEE 115
               +++G+ F+E+ S + A  A K +    +K++G  I V+ A    +
Sbjct: 46  -VTGQHQGYGFVEFLSEEDADYAIKIM--DMIKLYGKPIRVNKASAHNK 91

>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 = 42.0 bits (98), Expect = 8e-07
 Identities = 15/83 (18%), Positives = 28/83 (33%), Gaps = 22/83 (26%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
          LYV N+    TEE + + F    R+  + +      +  +                    
Sbjct: 4  LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQ-------------------- 43

Query: 67 DDNKKNRGFCFLEYDSHKSASLA 89
              +++ F FLE+ S    + A
Sbjct: 44 --INQDKNFAFLEFRSVDETTQA 64

>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 = 41.9 bits (98), Expect = 8e-07
 Identities = 17/47 (36%), Positives = 27/47 (57%), Gaps = 2/47 (4%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERV--KRIKDYAFVHFEDRQEA 51
          L+V NL    TEE++++ FE+YG+   V   + K + F+  E R  A
Sbjct: 11 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLA 57

>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 = 41.2 bits (96), Expect = 1e-06
 Identities = 19/55 (34%), Positives = 27/55 (49%), Gaps = 8/55 (14%)

Query: 5  KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDY--------AFVHFEDRQEA 51
            L V  L+ Y TE  L+E F +YG +  V  + D         AFV+FE+  +A
Sbjct: 10 CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDA 64

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.7 bits (97), Expect = 2e-06
 Identities = 18/54 (33%), Positives = 26/54 (48%), Gaps = 2/54 (3%)

Query: 1  MSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERV--KRIKDYAFVHFEDRQEAI 52
          +S   V++VR L +   E  L EA E++G +  V     K  A V FE+   A 
Sbjct: 12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAK 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 = 41.2 bits (96), Expect = 2e-06
 Identities = 20/48 (41%), Positives = 26/48 (54%), Gaps = 3/48 (6%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD---YAFVHFEDRQEA 51
          ++V   T   TE++L+E F QYG V  V   K    +AFV F D Q A
Sbjct: 8  VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIA 55

>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 = 40.4 bits (94), Expect = 3e-06
 Identities = 11/53 (20%), Positives = 24/53 (45%), Gaps = 8/53 (15%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
          +++  L+   T++ LK+ F ++G V       D        + FV F++ +  
Sbjct: 2  MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESV 54

>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 = 40.0 bits (93), Expect = 4e-06
 Identities = 14/57 (24%), Positives = 28/57 (49%), Gaps = 8/57 (14%)

Query: 3  KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERV--------KRIKDYAFVHFEDRQEA 51
          +++ L++  L+   T+E L+  FEQ+G +           KR + + FV +   +E 
Sbjct: 5  QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 61

>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 = 40.0 bits (93), Expect = 6e-06
 Identities = 16/114 (14%), Positives = 41/114 (35%), Gaps = 31/114 (27%)

Query: 2   SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVI 61
           S V  ++++NL +    + L + F  +G +   K + D                      
Sbjct: 6   SGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--------------------- 44

Query: 62  IYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEE 115
                     ++G+ F+ +++ ++A  A +++    L      + V     ++E
Sbjct: 45  --------NGSKGYGFVHFETQEAAERAIEKMNGMLLN--DRKVFVGRFKSRKE 88

>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 = 40.0 bits (93), Expect = 6e-06
 Identities = 25/116 (21%), Positives = 44/116 (37%), Gaps = 30/116 (25%)

Query: 1   MSKVK-VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQ 59
           M+  K VLYV  L +   ++ L  AF  +G +  ++   DY                   
Sbjct: 1   MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEK--------------- 45

Query: 60  VIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEE 115
                       +RGF F+E++  + A+ A   +     +++G  I V+ A P   
Sbjct: 46  ------------HRGFAFVEFELAEDAAAAIDNM--NESELFGRTIRVNLAKPMRI 87

>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 = 6e-06
 Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 6/53 (11%)

Query: 5  KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD------YAFVHFEDRQEA 51
          + LYV NL++  TE  + + F Q G  +  K I +      Y FV F + ++A
Sbjct: 9  RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDA 61

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.3 bits (91), Expect = 1e-05
 Identities = 6/48 (12%), Positives = 18/48 (37%), Gaps = 3/48 (6%)

Query: 5  KVLYVRNL-TQYCTEEKLKEAFEQYGRVERVKR--IKDYAFVHFEDRQ 49
          +V+++ +         +L +  E +G +         + AF+     +
Sbjct: 9  RVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTE 56

>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 = 39.3 bits (91), Expect = 1e-05
 Identities = 14/50 (28%), Positives = 25/50 (50%), Gaps = 5/50 (10%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-----YAFVHFEDRQEA 51
          +YV NL      + +++ F +YG +  +          +AFV FED ++A
Sbjct: 17 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDA 66

>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 = 38.9 bits (90), Expect = 1e-05
 Identities = 21/113 (18%), Positives = 40/113 (35%), Gaps = 30/113 (26%)

Query: 3   KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVII 62
           + + L++  L+   TEE L+  +EQ+G++                               
Sbjct: 19  QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCV--------------------------- 51

Query: 63  YSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEE 115
                 +K++RGF F+ + S      A   +A     + G  +    A  +EE
Sbjct: 52  VMRDPASKRSRGFGFVTFSSMAEVDAA---MAARPHSIDGRVVEPKRAVAREE 101

>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 = 38.5 bits (89), Expect = 2e-05
 Identities = 11/53 (20%), Positives = 21/53 (39%), Gaps = 8/53 (15%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVK--------RIKDYAFVHFEDRQEA 51
          L++  L  Y  ++++KE    +G ++             K YAF  + D    
Sbjct: 4  LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVT 56

>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 = 38.9 bits (90), Expect = 2e-05
 Identities = 17/109 (15%), Positives = 36/109 (33%), Gaps = 34/109 (31%)

Query: 5   KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYS 64
           + L  +NL+   TE++LKE FE    +  V                              
Sbjct: 17  RTLLAKNLSFNITEDELKEVFEDALEIRLV------------------------------ 46

Query: 65  SPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQ 113
               + K++G  ++E+ S   A    +       ++ G  + + +   +
Sbjct: 47  --SQDGKSKGIAYIEFKSEADAEKNLEEK--QGAEIDGRSVSLYYTGEK 91

>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 = 39.0 bits (90), Expect = 2e-05
 Identities = 7/53 (13%), Positives = 15/53 (28%), Gaps = 7/53 (13%)

Query: 7  LYVRNL-----TQYCTEEKLKEAFEQYGRVERVKRI--KDYAFVHFEDRQEAI 52
          L          ++  T  K +  F  Y +    +         ++F +   A 
Sbjct: 8  LIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFKRVRINFSNPLSAA 60

>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 = 38.1 bits (88), Expect = 3e-05
 Identities = 16/56 (28%), Positives = 29/56 (51%), Gaps = 6/56 (10%)

Query: 2  SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD------YAFVHFEDRQEA 51
          S  K L+V N+     +  L++ F Q+G++  V+ I +      + FV FE+  +A
Sbjct: 9  STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADA 64

>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 = 38.8 bits (89), Expect = 5e-05
 Identities = 25/115 (21%), Positives = 43/115 (37%), Gaps = 30/115 (26%)

Query: 1   MSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQV 60
              VK ++V  + +   E  L++ FEQYG++E ++ + D                     
Sbjct: 94  HLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR-------------------- 133

Query: 61  IIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEE 115
                   + K RGF F+ +D H S       +      V G +  V  A  ++E
Sbjct: 134 -------GSGKKRGFAFVTFDDHDSVDKI---VIQKYHTVNGHNCEVRKALSKQE 178

>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 = 38.8 bits (89), Expect = 5e-05
 Identities = 15/82 (18%), Positives = 31/82 (37%), Gaps = 8/82 (9%)

Query: 4  VKVLYVRNLTQYCTEEKLKEAFEQYGRVERV--------KRIKDYAFVHFEDRQEAITVT 55
          ++ L++  L+   T+E L+  FEQ+G +           KR + + FV +   +E     
Sbjct: 6  LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM 65

Query: 56 GLSQVIIYSSPDDNKKNRGFCF 77
                +     + K+      
Sbjct: 66 NARPHKVDGRVVEPKRAVSRED 87

>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 = 37.4 bits (86), Expect = 6e-05
 Identities = 20/111 (18%), Positives = 36/111 (32%), Gaps = 29/111 (26%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
           L+VRNL+   +EE L++ F  YG +  +    D                           
Sbjct: 11  LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKK---------------------- 48

Query: 67  DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD 117
                 +GF F+ +   + A  A   +        G  + V  +  ++E  
Sbjct: 49  -----PKGFAFVTFMFPEHAVKAYAEV--DGQVFQGRMLHVLPSTIKKEAS 92

>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 = 37.4 bits (86), Expect = 7e-05
 Identities = 21/112 (18%), Positives = 37/112 (33%), Gaps = 30/112 (26%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
            ++ NL    TEE +KE F                                  V +   P
Sbjct: 18  AFLGNLPYDVTEESIKEFFRGLNIS---------------------------AVRLPREP 50

Query: 67  DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPDT 118
            + ++ +GF + E++   S       L+     +    I VD AD  ++ D+
Sbjct: 51  SNPERLKGFGYAEFEDLDS---LLSALSLNEESLGNKRIRVDVADQAQDKDS 99

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.0 bits (85), Expect = 7e-05
 Identities = 12/52 (23%), Positives = 22/52 (42%), Gaps = 4/52 (7%)

Query: 5  KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI----KDYAFVHFEDRQEAI 52
            L++ N+    +EE LK  F   G V +  +     +  A +     +EA+
Sbjct: 11 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAV 62

>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 = 37.0 bits (85), Expect = 8e-05
 Identities = 10/52 (19%), Positives = 22/52 (42%), Gaps = 2/52 (3%)

Query: 2  SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERV--KRIKDYAFVHFEDRQEA 51
          ++  V+    L    +  +L    E+ G V+ +     K Y+F  +   +E+
Sbjct: 18 TQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEES 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 = 36.6 bits (84), Expect = 9e-05
 Identities = 20/108 (18%), Positives = 38/108 (35%), Gaps = 29/108 (26%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
           + V NL++   E  L+E F  +G + R+   KD                           
Sbjct: 11  IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDK-------------------------- 44

Query: 67  DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQE 114
               +++GF F+ +   + A+ A   ++          + V+WA P  
Sbjct: 45  -TTGQSKGFAFISFHRREDAARAIAGVS--GFGYDHLILNVEWAKPST 89

>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 = 36.6 bits (84), Expect = 9e-05
 Identities = 23/106 (21%), Positives = 36/106 (33%), Gaps = 29/106 (27%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
           L V  L Q  T+E+ +  F   G +E  K ++D                           
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDK-------------------------- 38

Query: 67  DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADP 112
               ++ G+ F+ Y   K A  A   L    L++    I V +A P
Sbjct: 39  -ITGQSLGYGFVNYIDPKDAEKAINTLN--GLRLQTKTIKVSYARP 81

>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 = 36.6 bits (84), Expect = 1e-04
 Identities = 15/112 (13%), Positives = 36/112 (32%), Gaps = 28/112 (25%)

Query: 5   KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYS 64
             +Y+ NL +   +++LK++                 F  F    + +            
Sbjct: 4   HTIYINNLNEKIKKDELKKSLHAI-------------FSRFGQILDILV----------- 39

Query: 65  SPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEP 116
               + K RG  F+ +    SA+ A + +       +   + + +A    + 
Sbjct: 40  --SRSLKMRGQAFVIFKEVSSATNALRSM--QGFPFYDKPMRIQYAKTDSDI 87

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.6 bits (84), Expect = 1e-04
 Identities = 9/49 (18%), Positives = 21/49 (42%), Gaps = 2/49 (4%)

Query: 5  KVLYVRNLTQYCTEEKLKEAFEQYGRVERV--KRIKDYAFVHFEDRQEA 51
            L+V  L    +   L   F+++G +  +   +   +A++ +E    A
Sbjct: 18 TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAA 66

>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 = 35.9 bits (82), Expect = 1e-04
 Identities = 17/67 (25%), Positives = 32/67 (47%), Gaps = 8/67 (11%)

Query: 4  VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITVT 55
          VK ++V  + +   E  L++ FEQYG++E ++ + D        +AFV F+D      + 
Sbjct: 2  VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 61

Query: 56 GLSQVII 62
                +
Sbjct: 62 IQKYHTV 68

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 35.9 bits (82), Expect = 2e-04
 Identities = 16/64 (25%), Positives = 26/64 (40%), Gaps = 8/64 (12%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIK--------DYAFVHFEDRQEAITVTGLS 58
          ++V  L+   T E +K  FEQ+G+V+    +          + FV FE       V  + 
Sbjct: 2  IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61

Query: 59 QVII 62
             I
Sbjct: 62 FHEI 65

>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 = 35.5 bits (81), Expect = 3e-04
 Identities = 22/108 (20%), Positives = 44/108 (40%), Gaps = 29/108 (26%)

Query: 6   VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSS 65
           +L+V ++ +   E++++E F  YG ++ +    D                          
Sbjct: 9   ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGF--------------------- 47

Query: 66  PDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQ 113
                 ++G+  +EY++HK A  AK+ L     ++ G  I VDW   +
Sbjct: 48  ------SKGYALVEYETHKQALAAKEALN--GAEIMGQTIQVDWCFVK 87

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.1 bits (80), Expect = 4e-04
 Identities = 10/51 (19%), Positives = 20/51 (39%), Gaps = 1/51 (1%)

Query: 2  SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-YAFVHFEDRQEA 51
          S    + V+NL Q    +++ +  + Y             AFV   + ++A
Sbjct: 3  SGSSGILVKNLPQDSNCQEVHDLLKDYDLKYCYVDRNKRTAFVTLLNGEQA 53

>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 = 35.0 bits (80), Expect = 4e-04
 Identities = 12/56 (21%), Positives = 20/56 (35%), Gaps = 7/56 (12%)

Query: 1  MSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVK-------RIKDYAFVHFEDRQ 49
           S V  + ++       EE   E  E+YG VE +         +    +V F   +
Sbjct: 24 RSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREE 79

>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 = 34.7 bits (79), Expect = 6e-04
 Identities = 22/115 (19%), Positives = 42/115 (36%), Gaps = 29/115 (25%)

Query: 3   KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVII 62
            ++ ++V N+    TEE+LK+ F + G V   + + D                       
Sbjct: 7   SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKP----------------- 49

Query: 63  YSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD 117
                     +G+ F EY   ++A  A + L     +  G  + VD A  ++  +
Sbjct: 50  ----------KGYGFCEYQDQETALSAMRNL--NGREFSGRALRVDNAASEKNKE 92

>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 = 34.3 bits (78), Expect = 0.001
 Identities = 18/115 (15%), Positives = 37/115 (32%), Gaps = 30/115 (26%)

Query: 2   SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVI 61
           +    ++V  L  + T+  L++ FE +G +                           +  
Sbjct: 8   TTFTKIFVGGLPYHTTDASLRKYFEGFGDI---------------------------EEA 40

Query: 62  IYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEP 116
           +  +     K+RG+ F+      +A  A K        + G    V+ A    +P
Sbjct: 41  VVITDRQTGKSRGYGFVTMADRAAAERACKDPNP---IIDGRKANVNLAYLGAKP 92

>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 = 33.6 bits (76), Expect = 0.001
 Identities = 14/106 (13%), Positives = 34/106 (32%), Gaps = 29/106 (27%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
           L++ N     T+  +++  +    V    R+                             
Sbjct: 4   LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSL-------------------------- 37

Query: 67  DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADP 112
                +R F +++  S + A    ++L    LK+ G  ++   ++P
Sbjct: 38  -RFNTSRRFAYIDVTSKEDARYCVEKL--NGLKIEGYTLVTKVSNP 80

>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 = 33.9 bits (77), Expect = 0.001
 Identities = 10/52 (19%), Positives = 21/52 (40%), Gaps = 8/52 (15%)

Query: 6  VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQ 49
          ++ V+N+    + +++ + F  Y  +     +K          A V FE R 
Sbjct: 11 IIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRD 62

>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 = 33.1 bits (75), Expect = 0.002
 Identities = 17/109 (15%), Positives = 35/109 (32%), Gaps = 29/109 (26%)

Query: 7   LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
           L++ +L Q   ++ L + F  +G V   K   D                           
Sbjct: 21  LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDK-------------------------- 54

Query: 67  DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEE 115
                ++ F F+ YD+  SA  A + +     ++    + V     + +
Sbjct: 55  -QTNLSKCFGFVSYDNPVSAQAAIQSM--NGFQIGMKRLKVQLKRSKND 100

>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 = 33.2 bits (75), Expect = 0.002
 Identities = 23/115 (20%), Positives = 44/115 (38%), Gaps = 31/115 (26%)

Query: 5   KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYS 64
           K +++RNL+    EE L E  +Q+G ++ V+ +      H                    
Sbjct: 9   KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEH-------------------- 48

Query: 65  SPDDNKKNRGFCFLEYDSHKSASLAKKRL----ATGRLKVWGCDIIVDWADPQEE 115
                  ++G  F ++ + ++A             G LK+ G  + VD A  ++E
Sbjct: 49  -------SKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDE 96

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 32.7 bits (74), Expect = 0.002
 Identities = 14/55 (25%), Positives = 21/55 (38%), Gaps = 7/55 (12%)

Query: 3  KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--YAFVHF---EDRQEAI 52
          K   LYV       T   L+ AF  +G +  +        AFV +   E   +A+
Sbjct: 4  KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAV 56

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 32.1 bits (72), Expect = 0.004
 Identities = 9/50 (18%), Positives = 19/50 (38%), Gaps = 6/50 (12%)

Query: 7  LYVRNLTQYCTEEKLKEAFEQYGRVERVKRI------KDYAFVHFEDRQE 50
          + V+NL +   + K+ + F+  G +  V           +A + F     
Sbjct: 3  VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDG 52

>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 = 33.0 bits (74), Expect = 0.004
 Identities = 20/111 (18%), Positives = 35/111 (31%), Gaps = 29/111 (26%)

Query: 5   KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYS 64
           + L V  +     E +L++ FE+YG +E VK + D                         
Sbjct: 43  RNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRG----------------- 85

Query: 65  SPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEE 115
                     + F+++ S  SA  A   L      +    + V  A    +
Sbjct: 86  ----------YGFVKFQSGSSAQQAIAGL--NGFNILNKRLKVALAASGHQ 124

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	131
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.91
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.91
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.91
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.91
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.91
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.9
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.9
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.9
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.9
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.89
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.89
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.89
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.89
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.89
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.89
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.89
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.89
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.89
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.89
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.88
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.88
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.88
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.88
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.88
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.88
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.88
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.88
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.88
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.87
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.87
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.87
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.87
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.87
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.87
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.87
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.87
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.86
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.86
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.86
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.86
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.86
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.86
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.86
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.86
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.85
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.85
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.85
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.84
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.84
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.84
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.84
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.84
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.84
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.84
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.83
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.83
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.83
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.83
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.83
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.83
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.83
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.82
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.82
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.82
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.82
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.82
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.81
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.81
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.8
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.8
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.8
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.8
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.8
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.79
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.77
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.76
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.76
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.76
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.71
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.7
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.68
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	99.63
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.62
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.59
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.54
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.34
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.25
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.72
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.53
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	96.46
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	94.92
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	94.17
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	93.85
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	93.62
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	93.6
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	93.46
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	93.39
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	93.28
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	93.08
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	93.04
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	92.84
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	92.84
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	92.81
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	92.81
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	92.68
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	92.68
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	92.52
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	92.51
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	92.49
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	92.47
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	92.4
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	92.23
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	92.13
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	91.88
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	91.7
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	91.66
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	91.66
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	91.62
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	91.5
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	91.46
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	91.42
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	91.38
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	91.36
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	91.32
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	91.21
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	91.16
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	91.13
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	91.12
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	91.09
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	91.03
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	90.92
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	90.92
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	90.72
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	90.54
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	90.37
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	90.35
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	90.33
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	90.33
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	90.24
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	90.21
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	90.18
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	90.08
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	90.06
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	90.01
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	89.91
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	89.9
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	89.77
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	89.76
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	88.97
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	88.79
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	88.43
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	87.93
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	87.66
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	87.42
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	86.84
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	86.28
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	85.59
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	82.24
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	82.19

>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=99.91  E-value=6e-25  Score=135.67  Aligned_cols=95  Identities=34%  Similarity=0.672  Sum_probs=83.9

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCC-eeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGR-VERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~-v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      .|+|||||||.++++++|+++|++||+ |.++.+++.                          +...+.++|||||+|.+
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~--------------------------~~~~~~~rg~aFV~F~~   54 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYAS--------------------------AADKMKNRGFAFVEYES   54 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSS--------------------------SCTTTTTCCEEEEEESS
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeee--------------------------ccccccCCCeEEEEEcC
Confidence            478999999999999999999999996 888877642                          23467889999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCCCChHHHHhH
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPDTETMSKV  124 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~~~~~~~~  124 (131)
                      +++|.+|++.|++..+.++|+.|.|+||+|+.+++.+.|+++
T Consensus        55 ~~~A~~Ai~~l~~~~~~~~g~~i~V~~A~p~~~~~~~~~~~v   96 (96)
T d2disa1          55 HRAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMETV   96 (96)
T ss_dssp             HHHHHHHHTTTTTCCSCBTTBCCEEEESCSSCSTTTCCSSCC
T ss_pred             HHHHHHHHHHHcCCCeEECCEEEEEEEcCCCCCCChHHhccC
Confidence            999999999998877788999999999999999998888764

>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=99.91  E-value=1.9e-24  Score=131.73  Aligned_cols=85  Identities=27%  Similarity=0.497  Sum_probs=77.1

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      +.++|||+|||+++++++|+++|++||+|.++++++.                           ..+|.++|||||+|.+
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d---------------------------~~~~~~kg~afV~f~~   56 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLD---------------------------YETEKHRGFAFVEFEL   56 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCC---------------------------SSSCCCSSEEEECCSS
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccc---------------------------cccccccceeEEEECC
Confidence            3678999999999999999999999999999998854                           3468899999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEEP  116 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~  116 (131)
                      .++|.+|+..+++.  .++|+.|.|+||+|+..+
T Consensus        57 ~~~A~~ai~~l~~~--~i~g~~l~v~~a~p~~~k   88 (89)
T d2cqba1          57 AEDAAAAIDNMNES--ELFGRTIRVNLAKPMRIK   88 (89)
T ss_dssp             HHHHHHHHHHHTTE--EETTEEEEEEECCCCCCC
T ss_pred             HHHHHHHHHHcCCC--EECCEEEEEEEeCCCCCC
Confidence            99999999999997  899999999999987543

>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=99.91  E-value=3.2e-24  Score=128.63  Aligned_cols=80  Identities=24%  Similarity=0.331  Sum_probs=74.3

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .++|||+|||+++++++|+++|++||+|.++++++.                           ..+|.++|||||+|.++
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~---------------------------~~~g~~~g~afV~f~~~   54 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRD---------------------------YKTGYSYGYAFVDFTSE   54 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEE---------------------------TTTTEECSEEEEEESSH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeee---------------------------cccCCccccceEEECCH
Confidence            568999999999999999999999999999988754                           34788899999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADP  112 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~  112 (131)
                      ++|.+|++.|+|.  .++|+.|+|+||+|
T Consensus        55 ~~A~~ai~~lng~--~~~g~~l~v~~a~p   81 (82)
T d1b7fa1          55 MDSQRAIKVLNGI--TVRNKRLKVSYARP   81 (82)
T ss_dssp             HHHHHHHHHHTTC--EETTEECEEEECCC
T ss_pred             HHHHHHHHHhCCC--EECCEEEEEEEcCC
Confidence            9999999999998  89999999999986

>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=99.91  E-value=7.4e-24  Score=130.05  Aligned_cols=87  Identities=32%  Similarity=0.464  Sum_probs=78.5

Q ss_pred             CCCceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEe
Q psy1185           1 MSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEY   80 (131)
Q Consensus         1 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f   80 (131)
                      +..++||||+|||.++|+++|+++|++||+|.++.+++.                           ..++.++|||||+|
T Consensus         4 ~~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~---------------------------~~~~~~kg~afV~f   56 (93)
T d1h2vz_           4 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLD---------------------------KMKKTACGFCFVEY   56 (93)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEC---------------------------TTTCCEEEEEEEEE
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccc---------------------------cccccccceEEEEE
Confidence            356889999999999999999999999999999998854                           34678899999999


Q ss_pred             CCHHhHHHHHHHHhCCcceecCcEEEEEecCCCCCC
Q psy1185          81 DSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEP  116 (131)
Q Consensus        81 ~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~  116 (131)
                      .+.++|..|++.|+|.  .++|+.|+|+||.+..+.
T Consensus        57 ~~~~~A~~Ai~~l~g~--~~~gr~i~V~~a~~~~~g   90 (93)
T d1h2vz_          57 YSRADAENAMRYINGT--RLDDRIIRTDWDAGFKEG   90 (93)
T ss_dssp             SSHHHHHHHHHHTTTS--EETTEECEEEEESCCCTT
T ss_pred             CCHHHHHHHHHHhCCC--EECCEEEEEEEcCCCCCC
Confidence            9999999999999998  899999999999876544

>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=99.91  E-value=8.8e-24  Score=126.65  Aligned_cols=80  Identities=28%  Similarity=0.375  Sum_probs=73.8

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .++|||+|||.++++++|+++|++||+|.++++++.                           ...+.++|||||+|.++
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~---------------------------~~~~~~~g~afv~f~~~   54 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRD---------------------------KITGQSLGYGFVNYIDP   54 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEC---------------------------TTTCCEEEEEEEEESSH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceee---------------------------ccCCCceeeEEEEECCH
Confidence            457999999999999999999999999999998854                           34678899999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADP  112 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~  112 (131)
                      ++|..|++.|+|.  .++|+.|+|+||+|
T Consensus        55 ~~a~~a~~~l~g~--~~~g~~l~v~~AkP   81 (82)
T d1fxla1          55 KDAEKAINTLNGL--RLQTKTIKVSYARP   81 (82)
T ss_dssp             HHHHHHHHHHTTC--EETTEECEEEECCC
T ss_pred             HHHHHHHHHhCCC--EECCEEEEEEEeeC
Confidence            9999999999998  89999999999986

>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=99.90  E-value=8e-24  Score=129.88  Aligned_cols=84  Identities=29%  Similarity=0.349  Sum_probs=77.1

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||.|.++++++.                           ..+|.++|||||+|.+
T Consensus         8 ~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d---------------------------~~tg~~kg~afV~f~~   60 (93)
T d1x5ua1           8 QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKD---------------------------RVTGQHQGYGFVEFLS   60 (93)
T ss_dssp             TTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBC---------------------------SSSCSBCSCEEEEESS
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeec---------------------------ccccccccceEEEECC
Confidence            4679999999999999999999999999999998854                           3478899999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEE  115 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~  115 (131)
                      .++|.+|++.|++.  .++|+.|+|+||.++..
T Consensus        61 ~~~A~~Ai~~l~g~--~~~g~~l~V~~A~~~~~   91 (93)
T d1x5ua1          61 EEDADYAIKIMDMI--KLYGKPIRVNKASAHNK   91 (93)
T ss_dssp             HHHHHHHHHHSSSC--BCSSCBCEEEETTTTSC
T ss_pred             HHHHHHHHHHcCCC--EECCEEEEEEEcCCCCC
Confidence            99999999999998  89999999999998763

>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=99.90  E-value=1.4e-23  Score=128.05  Aligned_cols=83  Identities=24%  Similarity=0.420  Sum_probs=76.4

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||.|.++++++.                           ..+|.++|||||+|.+
T Consensus         7 ~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d---------------------------~~t~~~rg~afV~f~~   59 (90)
T d2cq0a1           7 DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKD---------------------------KTTGQSKGFAFISFHR   59 (90)
T ss_dssp             SSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEEC---------------------------SSSCSEEEEEEEEESS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhccccccccccc---------------------------ccccccccceeEEECC
Confidence            4679999999999999999999999999999998853                           3468899999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQE  114 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~  114 (131)
                      .++|.+|++.|+|.  .++|+.|+|+||+|+.
T Consensus        60 ~~~A~~Ai~~l~g~--~~~g~~i~v~~akp~~   89 (90)
T d2cq0a1          60 REDAARAIAGVSGF--GYDHLILNVEWAKPST   89 (90)
T ss_dssp             HHHHHHHHHHTTTC--EETTEECEEEESSCCC
T ss_pred             HHHHHHHHHHhCCC--EECCEEEEEEeeeCCC
Confidence            99999999999998  8999999999999875

>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=99.90  E-value=2.1e-23  Score=127.12  Aligned_cols=85  Identities=27%  Similarity=0.441  Sum_probs=77.3

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||||||+++++++|+++|++||.|..+.+++.                           ..++.++|||||+|.+
T Consensus         4 ~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~---------------------------~~~~~~~g~afV~f~~   56 (90)
T d1x5sa1           4 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKD---------------------------RETQRSRGFGFVTFEN   56 (90)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCC---------------------------SSSCSCCSEEEEECSS
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccceeeccc---------------------------cccccccceEEEEECC
Confidence            4678999999999999999999999999999987743                           3578899999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEEP  116 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~  116 (131)
                      +++|.+|++.|++.  .++|+.|.|+||.++.+.
T Consensus        57 ~~~a~~Ai~~l~~~--~~~g~~l~V~~a~~~~~~   88 (90)
T d1x5sa1          57 IDDAKDAMMAMNGK--SVDGRQIRVDQAGKSSDN   88 (90)
T ss_dssp             HHHHHHHHHHHTTC--CTTSCCCEEEEEECCCCC
T ss_pred             HHHHHHHHHHcCCC--EECCEEEEEEEcCCCCCC
Confidence            99999999999998  899999999999887654

>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=99.90  E-value=1.3e-23  Score=142.47  Aligned_cols=107  Identities=24%  Similarity=0.411  Sum_probs=90.9

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe--------cCeEEEEECCHHHHHh----------------------
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYAFVHFEDRQEAIT----------------------   53 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~--------~~~~fv~~~~~~~a~~----------------------   53 (131)
                      .++|||||||+++|+++|+++|++||.|.++.++        +|||||+|.+.++|..                      
T Consensus         6 ~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~~~~~~~~~   85 (183)
T d1u1qa_           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSR   85 (183)
T ss_dssp             HHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECCCT
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHhcCCcccccchhhhhhhhc
Confidence            4799999999999999999999999999999886        7899999999999997                      


Q ss_pred             ----------------------------------hcC-CceeEEecCCCCCCCCcceEEEEeCCHHhHHHHHHHHhCCcc
Q psy1185          54 ----------------------------------VTG-LSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRL   98 (131)
Q Consensus        54 ----------------------------------~~g-~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~~   98 (131)
                                                        .+| +..+.+..+ ..+|.++|||||+|.++++|.+|+. +++.  
T Consensus        86 ~~~~~~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~-~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~--  161 (183)
T d1u1qa_          86 EDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTD-RGSGKKRGFAFVTFDDHDSVDKIVI-QKYH--  161 (183)
T ss_dssp             TGGGSTTTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEEC-TTTCCEEEEEEEEESCHHHHHHHHT-SSCE--
T ss_pred             ccccccccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecc-cccCccceeEEEEECCHHHHHHHHH-hCCC--
Confidence                                              244 333333333 3468889999999999999999997 6776  


Q ss_pred             eecCcEEEEEecCCCC
Q psy1185          99 KVWGCDIIVDWADPQE  114 (131)
Q Consensus        99 ~~~g~~l~v~~a~~~~  114 (131)
                      .++|+.|.|.||.++.
T Consensus       162 ~~~G~~i~V~~A~~k~  177 (183)
T d1u1qa_         162 TVNGHNCEVRKALSKQ  177 (183)
T ss_dssp             EETTEEEEEEECCCHH
T ss_pred             eECCEEEEEEecCCcc
Confidence            8899999999998754

>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=99.89  E-value=1.6e-23  Score=126.53  Aligned_cols=82  Identities=20%  Similarity=0.371  Sum_probs=76.0

Q ss_pred             eEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHH
Q psy1185           5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHK   84 (131)
Q Consensus         5 ~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~   84 (131)
                      ++|||+|||.++|+++|+++|++||+|.+++++++                           ..+|.++|||||+|.+++
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d---------------------------~~tg~~rg~aFV~f~~~~   54 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKD---------------------------SATGLSKGYAFCEYVDIN   54 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECC---------------------------CSSSCCCCEEEEEESSSH
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeecc---------------------------ccccccceeEEEEECCHH
Confidence            57999999999999999999999999999999864                           457899999999999999


Q ss_pred             hHHHHHHHHhCCcceecCcEEEEEecCCCCC
Q psy1185          85 SASLAKKRLATGRLKVWGCDIIVDWADPQEE  115 (131)
Q Consensus        85 ~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~  115 (131)
                      +|..|++.+++.  .++|+.|.|+||.+...
T Consensus        55 ~A~~a~~~l~~~--~l~g~~l~V~~A~~~~~   83 (85)
T d2u2fa_          55 VTDQAIAGLNGM--QLGDKKLLVQRASVGAK   83 (85)
T ss_dssp             HHHHHHHTSSSC--CCSSSCCEEEECCCCCC
T ss_pred             HHHHHHHHhCCC--EECCEEEEEEECCCCCC
Confidence            999999999998  89999999999987654

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.89  E-value=5.4e-23  Score=127.39  Aligned_cols=86  Identities=26%  Similarity=0.310  Sum_probs=78.3

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||+++++++|+++|++||.|.++++++.                           ..++.++|||||+|.+
T Consensus         7 ~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d---------------------------~~tg~~~g~afV~f~~   59 (99)
T d1whwa_           7 GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPID---------------------------SLTKKPKGFAFVTFMF   59 (99)
T ss_dssp             SCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCC---------------------------TTTCCCCSEEEEEESS
T ss_pred             CCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeeccc---------------------------ccccccCcceEEEECC
Confidence            4678999999999999999999999999999998754                           3478899999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      .++|.+|+..|++.  .++|+.|+|.||.++.+..
T Consensus        60 ~~~a~~A~~~l~g~--~~~gr~i~V~~a~~~~~~~   92 (99)
T d1whwa_          60 PEHAVKAYAEVDGQ--VFQGRMLHVLPSTIKKEAS   92 (99)
T ss_dssp             HHHHHHHHHHTTTE--ESSSCEEEEEECCCCSTTC
T ss_pred             HHHHHHHHHHcCCC--EECCEEEEEEECCCCCccC
Confidence            99999999999998  8999999999999877654

>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=99.89  E-value=7.4e-23  Score=124.75  Aligned_cols=83  Identities=29%  Similarity=0.537  Sum_probs=74.6

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||||||.++++++|+++|++||+|.++.+++.                             ....++||||+|.+
T Consensus         7 ~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d-----------------------------~~~~~~~afV~f~~   57 (90)
T d2cqia1           7 QPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITE-----------------------------HTSNDPYCFVEFYE   57 (90)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECC-----------------------------CCSSCCEEEEEESS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecc-----------------------------cCccceeeEEEECC
Confidence            3679999999999999999999999999999998743                             33458999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEEP  116 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~  116 (131)
                      .++|..|++.++|.  .++|+.|+|.||.++...
T Consensus        58 ~~~A~~A~~~l~~~--~~~g~~i~v~~a~~~~~~   89 (90)
T d2cqia1          58 HRDAAAALAAMNGR--KILGKEVKVNWATTPSSQ   89 (90)
T ss_dssp             HHHHHHHHHHHTTE--EETTEEEEEEECCCTTCC
T ss_pred             HHHHHHHHHHcCCC--EECCEEEEEEEcCCCCCC
Confidence            99999999999998  899999999999876643

>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=99.89  E-value=1.7e-23  Score=127.35  Aligned_cols=83  Identities=17%  Similarity=0.379  Sum_probs=75.6

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ...+|||+|||+++++++|+++|++||.|.+++++..                             .+.++|||||+|.+
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-----------------------------~~~~kg~afV~f~~   57 (89)
T d1cvja2           7 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD-----------------------------ENGSKGYGFVHFET   57 (89)
T ss_dssp             TTTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCB-----------------------------TTBCCSCEEEEESC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEee-----------------------------cCCCcceeEEEECC
Confidence            4568999999999999999999999999999998853                             45578999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEEP  116 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~  116 (131)
                      .++|.+|++.|+|.  .++|+.|.|+||+++.++
T Consensus        58 ~~~A~~Ai~~l~g~--~~~g~~i~V~~a~~~~~R   89 (89)
T d1cvja2          58 QEAAERAIEKMNGM--LLNDRKVFVGRFKSRKER   89 (89)
T ss_dssp             HHHHHHHTTSSSEE--EETTEEEEEEECCCTTTC
T ss_pred             HHHHHHHHHHcCCC--EECCEEEEEEECCCCCCC
Confidence            99999999999998  899999999999987753

>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=99.89  E-value=2.8e-23  Score=124.27  Aligned_cols=80  Identities=16%  Similarity=0.309  Sum_probs=68.9

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .+||||+|||+++|+++|+++|++||.|..+.++..                           ...|.++|||||+|.++
T Consensus         1 d~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~---------------------------~~~~~~~g~afV~f~~~   53 (81)
T d2ghpa1           1 ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPS---------------------------LRFNTSRRFAYIDVTSK   53 (81)
T ss_dssp             SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC----------------------------------CCEEEEECSSH
T ss_pred             CcEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecc---------------------------cccccccceeEEEECCH
Confidence            479999999999999999999999999988776632                           33678899999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADP  112 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~  112 (131)
                      ++|.+|++.|||.  .++|+.|+|+||+|
T Consensus        54 e~A~~Ai~~l~g~--~~~g~~i~V~~a~P   80 (81)
T d2ghpa1          54 EDARYCVEKLNGL--KIEGYTLVTKVSNP   80 (81)
T ss_dssp             HHHHHHHHHHTTC--EETTEECEEEECCC
T ss_pred             HHHHHHHHHhCCC--EECCEEEEEEEccC
Confidence            9999999999998  99999999999987

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.89  E-value=4.4e-23  Score=125.30  Aligned_cols=81  Identities=27%  Similarity=0.528  Sum_probs=74.9

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .++|||+|||.++++++|+++|++||.|.++++++.                           ..+|.++|||||+|.+.
T Consensus         7 ~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d---------------------------~~tg~~~g~afV~f~~~   59 (88)
T d1rk8a_           7 GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLD---------------------------RRTGFSKGYALVEYETH   59 (88)
T ss_dssp             CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEC---------------------------TTTSSEEEEEEEEESSH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHcCCccccccccc---------------------------ccccccccceeEEECCH
Confidence            468999999999999999999999999999998854                           34788999999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCCC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADPQ  113 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~  113 (131)
                      ++|.+|+..|||.  .++|+.|+|+||.++
T Consensus        60 ~~A~~A~~~lng~--~l~g~~l~V~~a~~k   87 (88)
T d1rk8a_          60 KQALAAKEALNGA--EIMGQTIQVDWCFVK   87 (88)
T ss_dssp             HHHHHHHHHHTTC--EETTEECEEEESEEC
T ss_pred             HHHHHHHHHcCCC--EECCEEEEEEEecCC
Confidence            9999999999998  899999999999865

>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=99.89  E-value=7.4e-23  Score=125.74  Aligned_cols=85  Identities=22%  Similarity=0.502  Sum_probs=75.8

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||.|.++++++.                          ...+|.++|||||+|.+
T Consensus         7 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~--------------------------~~~~g~~rg~afV~f~~   60 (94)
T d2cpha1           7 TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKK--------------------------MTGTGAHRGFGFVDFIT   60 (94)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCC--------------------------CSSSCSSCSEEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEec--------------------------cccCCCcccEEEEEECC
Confidence            4678999999999999999999999999999988743                          13368899999999999


Q ss_pred             HHhHHHHHHHH-hCCcceecCcEEEEEecCCCCC
Q psy1185          83 HKSASLAKKRL-ATGRLKVWGCDIIVDWADPQEE  115 (131)
Q Consensus        83 ~~~a~~a~~~l-~~~~~~~~g~~l~v~~a~~~~~  115 (131)
                      .++|.+|++.| ++.  .++|+.|.|+||+++..
T Consensus        61 ~~~A~~Ai~~l~~~~--~~~Gr~l~V~~A~~~~~   92 (94)
T d2cpha1          61 KQDAKKAFNALCHST--HLYGRRLVLEWADSEVT   92 (94)
T ss_dssp             HHHHHHHHHHHHTCC--BSSSCBCEEEECCCCCC
T ss_pred             HHHHHHHHHHccCCc--EECCEEEEEEEcCCCCC
Confidence            99999999999 676  78999999999998764

>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=99.89  E-value=5.4e-23  Score=128.13  Aligned_cols=84  Identities=20%  Similarity=0.281  Sum_probs=77.1

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .++|||+|||+++++++|+++|++||.|.++.++..                           ..+|.++|||||+|.+.
T Consensus        18 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~---------------------------~~~g~~kG~afV~f~~~   70 (102)
T d2cpza1          18 GANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFID---------------------------KQTNLSKCFGFVSYDNP   70 (102)
T ss_dssp             TCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEEC---------------------------SSSCSEEEEEEEECSSH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhhccccccceeee---------------------------cccCCCccceEEEeCCH
Confidence            468999999999999999999999999999988743                           34688899999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCCCCCC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADPQEEP  116 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~  116 (131)
                      ++|..|++.|+|.  .++|+.|+|+||.++.+.
T Consensus        71 ~~A~~Ai~~lng~--~~~g~~i~V~~a~~k~~~  101 (102)
T d2cpza1          71 VSAQAAIQSMNGF--QIGMKRLKVQLKRSKNDS  101 (102)
T ss_dssp             HHHHHHHHHHTTC--EETTEECEEECCCCSCCC
T ss_pred             HHHHHHHHHhCCC--EECCEEEEEEEeCCCCCC
Confidence            9999999999998  899999999999998764

>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=99.89  E-value=1.5e-22  Score=124.12  Aligned_cols=82  Identities=26%  Similarity=0.392  Sum_probs=75.0

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||+++++++|+++|++||+|.+++++++                             .+.++|||||+|.+
T Consensus        10 ~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~-----------------------------~~~~kg~afV~f~~   60 (93)
T d2cq3a1          10 TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN-----------------------------ERGSKGFGFVTFEN   60 (93)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECC-----------------------------TTTTCCEEEEEESC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcceeeecccccc-----------------------------ccCCcceeEEEECC
Confidence            4678999999999999999999999999999998853                             34578999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEE  115 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~  115 (131)
                      +++|.+|+..+++.  .++|+.|+|+||.++..
T Consensus        61 ~~~a~~Ai~~l~~~--~~~g~~l~V~~A~~r~~   91 (93)
T d2cq3a1          61 SADADRAREKLHGT--VVEGRKIEVNNATARVM   91 (93)
T ss_dssp             HHHHHHHHHHHTTC--EETTEECEEEECCSSCC
T ss_pred             HHHHHHHHHHcCCC--EECCEEEEEEecCcCCC
Confidence            99999999999998  99999999999998764

>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=99.89  E-value=5.5e-23  Score=122.75  Aligned_cols=77  Identities=21%  Similarity=0.387  Sum_probs=72.2

Q ss_pred             EEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHHh
Q psy1185           6 VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKS   85 (131)
Q Consensus         6 ~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~~   85 (131)
                      +|||||||+++|+++|+++|++||+|.++++++.                           ..+|.++|||||+|.++++
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d---------------------------~~tg~~~g~aFV~f~~~~~   54 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRD---------------------------MITRRSLGYAYVNFQQPAD   54 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEC---------------------------TTTCCEEEEEEEEESSHHH
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEec---------------------------ccccCCCCceEEEECCHHH
Confidence            6999999999999999999999999999999864                           3468889999999999999


Q ss_pred             HHHHHHHHhCCcceecCcEEEEEecC
Q psy1185          86 ASLAKKRLATGRLKVWGCDIIVDWAD  111 (131)
Q Consensus        86 a~~a~~~l~~~~~~~~g~~l~v~~a~  111 (131)
                      |..|++.|+|.  .++|+.|+|+||+
T Consensus        55 a~~ai~~l~g~--~~~gr~i~v~~a~   78 (80)
T d1cvja1          55 AERALDTMNFD--VIKGKPVRIMWSQ   78 (80)
T ss_dssp             HHHHHTTSTTC--EETTEECEEEECC
T ss_pred             HHHHHHHcCCC--EECCEEEEEEEeC
Confidence            99999999998  8999999999986

>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=99.88  E-value=1e-22  Score=122.92  Aligned_cols=79  Identities=32%  Similarity=0.444  Sum_probs=71.3

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      +.++|||+|||+++|+++|+++|++||+|.+++++++                           ..+|.++|||||+|.+
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d---------------------------~~~g~~kg~afV~f~~   57 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVD---------------------------QVTGVSRGVGFIRFDK   57 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEC---------------------------TTTCCEEEEEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccc---------------------------cccccCCCeeEEEEcC
Confidence            4578999999999999999999999999999999854                           3468899999999999


Q ss_pred             HHhHHHHHHHHhCCcceecC--cEEEEEec
Q psy1185          83 HKSASLAKKRLATGRLKVWG--CDIIVDWA  110 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g--~~l~v~~a  110 (131)
                      +++|.+|++.|||.  .++|  ++|+|+||
T Consensus        58 ~~~a~~Ai~~lng~--~~~G~~~~i~V~~A   85 (85)
T d1fxla2          58 RIEAEEAIKGLNGQ--KPSGATEPITVKFA   85 (85)
T ss_dssp             HHHHHHHHHHHTTC--CCTTCSSCCEEEEC
T ss_pred             HHHHHHHHHHhCCC--EeCCCCEEEEEEeC
Confidence            99999999999998  7776  55999997

>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=99.88  E-value=1.1e-22  Score=126.88  Aligned_cols=84  Identities=25%  Similarity=0.356  Sum_probs=74.9

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      +.++|||+|||+.+++++|+++|++||+|.++++++.                           ..+|.++|||||+|.+
T Consensus         9 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d---------------------------~~tg~~kg~afV~f~~   61 (103)
T d2cqda1           9 TFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITD---------------------------RQTGKSRGYGFVTMAD   61 (103)
T ss_dssp             SSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCC---------------------------SSSCCCCSEEEEEESS
T ss_pred             CCcEEEEeCCCCcCcHHHHHHHHhhcccccceecccc---------------------------ccccccCCeEEEEECC
Confidence            4578999999999999999999999999999998854                           3468899999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEEP  116 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~  116 (131)
                      +++|.+|++.+++   .++|+.|.|+||.++..+
T Consensus        62 ~~~A~~Ai~~~~~---~l~Gr~l~V~~a~~~~~p   92 (103)
T d2cqda1          62 RAAAERACKDPNP---IIDGRKANVNLAYLGAKP   92 (103)
T ss_dssp             HHHHHHHHTCSSC---EETTEECEEEESTTTCCC
T ss_pred             HHHHHHHHHHCCC---cCCCEEEEEEEcCCCCCC
Confidence            9999999999875   789999999999865443

>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=99.88  E-value=8.7e-23  Score=122.57  Aligned_cols=81  Identities=20%  Similarity=0.415  Sum_probs=72.7

Q ss_pred             EEEeCCCCCCCHHHHHHHhhccCCeeEE-EEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHHh
Q psy1185           7 LYVRNLTQYCTEEKLKEAFEQYGRVERV-KRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKS   85 (131)
Q Consensus         7 l~v~nLp~~~t~~~l~~~F~~~G~v~~~-~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~~   85 (131)
                      |||+|||+++++++|+++|++||.|.++ ++++.                           ..+|+++|||||+|.+.++
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~---------------------------~~~g~~~g~afV~f~~~~~   53 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRD---------------------------PDTGNSKGYAFINFASFDA   53 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCC---------------------------TTTCSCCSEEEEEBSSHHH
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEee---------------------------ccccccCceEEEEECCHHH
Confidence            7999999999999999999999998765 55543                           3478899999999999999


Q ss_pred             HHHHHHHHhCCcceecCcEEEEEecCCCCCC
Q psy1185          86 ASLAKKRLATGRLKVWGCDIIVDWADPQEEP  116 (131)
Q Consensus        86 a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~  116 (131)
                      |.+|++.++|.  .++|+.|+|+||.++.++
T Consensus        54 a~~Ai~~~~g~--~~~gr~l~v~~a~~k~~k   82 (83)
T d1x5ta1          54 SDAAIEAMNGQ--YLCNRPITVSYAFKKDSK   82 (83)
T ss_dssp             HHHHHHTTTTC--EETTEECEEEESCCCCCC
T ss_pred             HHHHHHhCCCc--EECCEEEEEEEecCCCcC
Confidence            99999999998  899999999999987754

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.88  E-value=1.5e-22  Score=123.44  Aligned_cols=83  Identities=23%  Similarity=0.262  Sum_probs=74.3

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||+++|+++|+++|++||.|.++++++.                           ..+|.++|||||+|.+
T Consensus         7 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d---------------------------~~tg~srG~aFV~f~~   59 (90)
T d2cqga1           7 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKD---------------------------LKTGHSKGFGFVRFTE   59 (90)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEEC---------------------------SSSCSEEEEEEEEESS
T ss_pred             CCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccC---------------------------CCCcccCCEEEEEECC
Confidence            4678999999999999999999999999999999864                           3478999999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEEP  116 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~  116 (131)
                      .++|.+|++..  .  .++|+.|.|++|.++..+
T Consensus        60 ~~~a~~al~~~--~--~l~Gr~i~v~~a~~k~~~   89 (90)
T d2cqga1          60 YETQVKVMSQR--H--MIDGRWCDCKLPNSKQSQ   89 (90)
T ss_dssp             HHHHHHHHHSC--E--EETTEEEEEECCCTTCCC
T ss_pred             HHHHHHHHhcC--C--ccCCEEeEEEeCCCCCCC
Confidence            99999999843  3  789999999999988765

>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=99.88  E-value=2e-22  Score=121.77  Aligned_cols=80  Identities=31%  Similarity=0.416  Sum_probs=73.0

Q ss_pred             CCCceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEe
Q psy1185           1 MSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEY   80 (131)
Q Consensus         1 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f   80 (131)
                      |++.++|||+|||.++++++|+++|++||.+..+.+.                                 .++|||||+|
T Consensus         5 ~~~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~---------------------------------~~rg~afV~f   51 (86)
T d2cpda1           5 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK---------------------------------KIRDYAFVHF   51 (86)
T ss_dssp             SSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEE---------------------------------ECSSEEEEEE
T ss_pred             ccCCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEc---------------------------------cccEEEEEEe
Confidence            6778999999999999999999999999998877654                                 3589999999


Q ss_pred             CCHHhHHHHHHHHhCCcceecCcEEEEEecCCCCC
Q psy1185          81 DSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEE  115 (131)
Q Consensus        81 ~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~  115 (131)
                      .++++|.+|+..|||.  .++|+.|.|+||+|+..
T Consensus        52 ~~~~~A~~Ai~~l~~~--~i~g~~i~V~~akP~~~   84 (86)
T d2cpda1          52 SNREDAVEAMKALNGK--VLDGSPIEVTLAKPVDK   84 (86)
T ss_dssp             SSHHHHHHHHHHHSSE--EETTEEEEEECCCCCCC
T ss_pred             CCHHHHHHHHHHcCCC--EECCEEEEEEeccCCCC
Confidence            9999999999999997  89999999999997664

>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=99.88  E-value=1.3e-22  Score=122.38  Aligned_cols=81  Identities=26%  Similarity=0.363  Sum_probs=71.5

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      +.++|||+|||+++++++|+++|++||+|.++++++.                           ..+|.++|||||+|.+
T Consensus         5 ~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d---------------------------~~~g~~~g~afV~f~~   57 (85)
T d1b7fa2           5 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRD---------------------------KLTGRPRGVAFVRYNK   57 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEEC---------------------------TTTCCEEEEEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecc---------------------------cccccCceeEEEEECC
Confidence            4678999999999999999999999999999998854                           3478899999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEec
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWA  110 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a  110 (131)
                      +++|.+|++.+|+..+...+++|.|+||
T Consensus        58 ~~~A~~Ai~~l~g~~~~g~~~~l~V~~A   85 (85)
T d1b7fa2          58 REEAQEAISALNNVIPEGGSQPLSVRLA   85 (85)
T ss_dssp             HHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             HHHHHHHHHHHCCCEeCCCCeEEEEEEC
Confidence            9999999999999833323488999997

>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=99.88  E-value=3.5e-22  Score=118.72  Aligned_cols=77  Identities=17%  Similarity=0.245  Sum_probs=71.8

Q ss_pred             EEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHHh
Q psy1185           6 VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKS   85 (131)
Q Consensus         6 ~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~~   85 (131)
                      +|||+|||+++++++|+++|++||+|.+++++.+                            .+++++|||||+|.+.++
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~----------------------------~~g~~~g~afV~f~~~~~   53 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD----------------------------RSGRSLGTADVHFERKAD   53 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCS----------------------------SCCCSCCEEEEEESCHHH
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEe----------------------------eccccceeEEEEECCHHH
Confidence            6999999999999999999999999999998753                            378889999999999999


Q ss_pred             HHHHHHHHhCCcceecCcEEEEEecCC
Q psy1185          86 ASLAKKRLATGRLKVWGCDIIVDWADP  112 (131)
Q Consensus        86 a~~a~~~l~~~~~~~~g~~l~v~~a~~  112 (131)
                      |.+|++.+||.  .++|+.|+|++|.+
T Consensus        54 A~~Ai~~l~g~--~l~g~~l~V~~a~S   78 (78)
T d1no8a_          54 ALKAMKQYNGV--PLDGRPMNIQLVTS   78 (78)
T ss_dssp             HHHHHHHHTTC--EETTEECEEEEECC
T ss_pred             HHHHHHHhCCC--EECCEEEEEEEeeC
Confidence            99999999998  89999999999864

>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=99.88  E-value=3.9e-22  Score=123.00  Aligned_cols=88  Identities=25%  Similarity=0.416  Sum_probs=76.5

Q ss_pred             CCceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeC
Q psy1185           2 SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYD   81 (131)
Q Consensus         2 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~   81 (131)
                      +..++|||||||+++|+++|+++|++||+|.++.++..                           ..++.++|||||+|.
T Consensus         6 ~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~---------------------------~~~~~~~g~afV~F~   58 (98)
T d1x4ha1           6 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLH---------------------------PDTEHSKGCAFAQFM   58 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBC---------------------------SSSCCBCSEEEEEES
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccc---------------------------cccccccceEEEEEc
Confidence            45789999999999999999999999999999887743                           346778999999999


Q ss_pred             CHHhHHHHHHHHhCC----cceecCcEEEEEecCCCCCC
Q psy1185          82 SHKSASLAKKRLATG----RLKVWGCDIIVDWADPQEEP  116 (131)
Q Consensus        82 ~~~~a~~a~~~l~~~----~~~~~g~~l~v~~a~~~~~~  116 (131)
                      ++++|.+|++.+++.    ...++|+.|+|+||.++.+.
T Consensus        59 ~~~~a~~ai~~l~~~~~~~g~~~~gr~l~v~~a~~k~~a   97 (98)
T d1x4ha1          59 TQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEA   97 (98)
T ss_dssp             SHHHHHHHHHHHCTTTTTCCEESSSCEEEEECCCCCCCC
T ss_pred             CHHHHHHHHHHcccccccCCcEECCEEEEEEECCCCCcC
Confidence            999999999999732    23789999999999987654

>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=99.88  E-value=2.2e-22  Score=125.55  Aligned_cols=83  Identities=25%  Similarity=0.406  Sum_probs=74.9

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .++|||||||+++++++|+++|++||.|..+.++++                           ..++.++|||||+|.+.
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d---------------------------~~~~~~kg~aFV~f~~~   72 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRD---------------------------PASKRSRGFGFVTFSSM   72 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECC---------------------------TTTSSCCSEEEEECSSH
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeeccc---------------------------ccCCCccCeEEEEECCH
Confidence            478999999999999999999999999999999854                           34678899999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCCCCCC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADPQEEP  116 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~  116 (131)
                      ++|.+|+. +++.  .++|+.|.|++|.++.+.
T Consensus        73 ~~a~~al~-~~~~--~l~G~~i~V~~a~~ke~~  102 (103)
T d1x4ba1          73 AEVDAAMA-ARPH--SIDGRVVEPKRAVAREES  102 (103)
T ss_dssp             HHHHHHHT-SCSE--EETTEEEEEECCSSCCCC
T ss_pred             HHHHHHHH-hCCC--eECCEEEEEEECcccCCC
Confidence            99999986 6776  899999999999998764

>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=99.87  E-value=5.2e-22  Score=122.35  Aligned_cols=78  Identities=17%  Similarity=0.432  Sum_probs=72.1

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||+|.++++++                                 .+|||||+|.+
T Consensus        17 ~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~---------------------------------~kg~afV~f~~   63 (96)
T d1x4ga1          17 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFP---------------------------------EKGYSFVRFST   63 (96)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEET---------------------------------TTTEEEEEESS
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEe---------------------------------cceEEEEEECC
Confidence            357899999999999999999999999999999884                                 28999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEE  115 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~  115 (131)
                      .++|.+|+..|+|.  .++|+.|+|.||++++.
T Consensus        64 ~~~A~~Ai~~l~~~--~i~g~~l~v~~ak~~p~   94 (96)
T d1x4ga1          64 HESAAHAIVSVNGT--TIEGHVVKCYWGKESPD   94 (96)
T ss_dssp             HHHHHHHHHHHTTC--EETTEECEEECCCCCCS
T ss_pred             HHHHHHHHHHhCCC--EECCEEEEEEEcCCCCC
Confidence            99999999999998  89999999999987654

>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=99.87  E-value=2.6e-22  Score=131.19  Aligned_cols=84  Identities=26%  Similarity=0.423  Sum_probs=76.5

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .++|||+|||+++++++|+++|++||.|.++++++.                           ..+|.++|||||+|.+.
T Consensus        42 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d---------------------------~~t~~~rg~afV~f~~~   94 (139)
T d1u6fa1          42 LRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCD---------------------------RETRQSRGYGFVKFQSG   94 (139)
T ss_dssp             TSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEE---------------------------TTTTEEEEEEEEEESSH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhhccccccccccc---------------------------cccccccceeeEEECCH
Confidence            468999999999999999999999999999998853                           34678899999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCCCCCC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADPQEEP  116 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~  116 (131)
                      ++|..|++.|+|.  .++|+.|+|+||.++.++
T Consensus        95 ~~A~~Ai~~lng~--~~~gr~l~V~~a~~~~~~  125 (139)
T d1u6fa1          95 SSAQQAIAGLNGF--NILNKRLKVALAASGHQR  125 (139)
T ss_dssp             HHHHHHHHHTTTE--ECSSCEEEEEESSCCCCC
T ss_pred             HHHHHHHHHhCCC--EECCEEEEEEEcCCCCCC
Confidence            9999999999998  899999999999876654

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.87  E-value=3.2e-22  Score=120.54  Aligned_cols=84  Identities=29%  Similarity=0.394  Sum_probs=71.7

Q ss_pred             EEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHHhH
Q psy1185           7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSA   86 (131)
Q Consensus         7 l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a   86 (131)
                      |||+|||+++|+++|+++|++||.|.++.+++.-                        .....+.++|||||+|.++++|
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~------------------------~~~~~~~~kG~afV~f~~~~~A   56 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKK------------------------NKAGVLLSMGFGFVEYKKPEQA   56 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEE------------------------CTTCCEEEEEEEEEEESSHHHH
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceeccc------------------------ccccccccceEEEEEECCHHHH
Confidence            7999999999999999999999999999987420                        0011235689999999999999


Q ss_pred             HHHHHHHhCCcceecCcEEEEEecCCCCCC
Q psy1185          87 SLAKKRLATGRLKVWGCDIIVDWADPQEEP  116 (131)
Q Consensus        87 ~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~  116 (131)
                      .+|++.++|.  .++|+.|.|+||++...+
T Consensus        57 ~~A~~~~~~~--~~~g~~i~V~~a~~~~kp   84 (85)
T d2cpfa1          57 QKALKQLQGH--TVDGHKLEVRISERATKP   84 (85)
T ss_dssp             HHHHHHSTTC--EETTEECEEECSSCSSCC
T ss_pred             HHHHHHhCCC--EECCEEEEEEECCCCCCC
Confidence            9999999998  899999999999765543

>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=99.87  E-value=1.1e-22  Score=121.40  Aligned_cols=78  Identities=21%  Similarity=0.315  Sum_probs=69.9

Q ss_pred             eEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHH
Q psy1185           5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHK   84 (131)
Q Consensus         5 ~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~   84 (131)
                      ++|||||||.++++++|+++|++||.|.++.+.                                 .++|||||+|.+.+
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~---------------------------------~~rg~aFV~f~~~~   48 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL---------------------------------LKSGYAFVDYPDQN   48 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEE---------------------------------EETTEEEECCSCHH
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEe---------------------------------cccceEEEEECCHH
Confidence            469999999999999999999999998776554                                 24799999999999


Q ss_pred             hHHHHHHHHhCCcceecCcEEEEEecCCCCCC
Q psy1185          85 SASLAKKRLATGRLKVWGCDIIVDWADPQEEP  116 (131)
Q Consensus        85 ~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~  116 (131)
                      +|.+|++.|+|. +.++|+.|+|+||.|+.++
T Consensus        49 ~A~~Ai~~lng~-~~~~G~~i~V~~a~~k~~r   79 (80)
T d2cqha1          49 WAIRAIETLSGK-VELHGKIMEVDYSVSKKLR   79 (80)
T ss_dssp             HHHHHHHHHTTT-CEETTEECEEEECCCCCCC
T ss_pred             HHHHHHHHhCCC-eEECCEEEEEEEcCCcCcC
Confidence            999999999985 3699999999999998765

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=1.5e-22  Score=126.39  Aligned_cols=82  Identities=28%  Similarity=0.456  Sum_probs=75.1

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .++|||+|||.++++++|+++|++||.|.+++++++                           ..+|.++|||||+|.+.
T Consensus         8 ~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~---------------------------~~tg~~~g~afV~f~~~   60 (104)
T d1p1ta_           8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYD---------------------------RETGKPKGYGFCEYQDQ   60 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEE---------------------------TTTTEEEEEEEEECSCH
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccccccccc---------------------------cceeccCCceEEEECCH
Confidence            468999999999999999999999999999998854                           34688899999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCCCC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADPQE  114 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~  114 (131)
                      ++|.+|++.|++.  .++|+.|.|+||.++.
T Consensus        61 ~~a~~ai~~l~~~--~~~g~~i~V~~a~~~~   89 (104)
T d1p1ta_          61 ETALSAMRNLNGR--EFSGRALRVDNAASEK   89 (104)
T ss_dssp             HHHHHHHHHSSSB--SCSSSCBEEEETTCTT
T ss_pred             HHHHHHHHHcCCC--EECCEEEEEEECCCCC
Confidence            9999999999998  8899999999998754

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=1.1e-21  Score=120.57  Aligned_cols=82  Identities=17%  Similarity=0.285  Sum_probs=73.9

Q ss_pred             CCceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeC
Q psy1185           2 SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYD   81 (131)
Q Consensus         2 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~   81 (131)
                      +..++|||+|||+++++++|+++|++||.|..+.+.+                              .+.+++||||+|.
T Consensus        12 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~------------------------------~~~~~g~afV~f~   61 (95)
T d1x4aa1          12 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN------------------------------RRGGPPFAFVEFE   61 (95)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECC------------------------------SSSSSCCEEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEecc------------------------------cccccceEEEEEC
Confidence            3567899999999999999999999999999988763                              3567899999999


Q ss_pred             CHHhHHHHHHHHhCCcceecCcEEEEEecCCCCC
Q psy1185          82 SHKSASLAKKRLATGRLKVWGCDIIVDWADPQEE  115 (131)
Q Consensus        82 ~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~  115 (131)
                      ++++|..|++.|++.  .++|+.|+|+||++...
T Consensus        62 ~~e~a~~Ai~~l~g~--~~~g~~l~V~~a~~~r~   93 (95)
T d1x4aa1          62 DPRDAEDAVYGRDGY--DYDGYRLRVEFPRSGRG   93 (95)
T ss_dssp             CHHHHHHHHHHHTTC--EETTEECEEECCCCCCC
T ss_pred             CHHHHHHHHHHhCCC--EECCEEEEEEeccCCCC
Confidence            999999999999998  89999999999987543

>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=99.87  E-value=1.3e-22  Score=120.34  Aligned_cols=76  Identities=22%  Similarity=0.320  Sum_probs=70.0

Q ss_pred             eEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHH
Q psy1185           5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHK   84 (131)
Q Consensus         5 ~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~   84 (131)
                      |+|||+|||+++++++|+++|++||.|.++++++.                           +.+|.++|||||+|.+++
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d---------------------------~~tg~~kG~aFV~f~~~~   53 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRD---------------------------PLTKRSRGFGFVTFMDQA   53 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECC---------------------------CCSSSCSSEEEECCCCTT
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecc---------------------------cCCCCccceEEEEECCHH
Confidence            68999999999999999999999999999998864                           457889999999999999


Q ss_pred             hHHHHHHHHhCCcceecCcEEEEEec
Q psy1185          85 SASLAKKRLATGRLKVWGCDIIVDWA  110 (131)
Q Consensus        85 ~a~~a~~~l~~~~~~~~g~~l~v~~a  110 (131)
                      +|.+|+. ++++  .++|+.|.|+.|
T Consensus        54 ~a~~al~-~~~~--~i~Gr~i~V~~A   76 (77)
T d1uawa_          54 GVDKVLA-QSRH--ELDSKTIDPKVA   76 (77)
T ss_dssp             HHHHHHH-TTTC--CCSSCCCEEEEC
T ss_pred             HHHHHHH-cCCC--EECCeEEEEEEC
Confidence            9999997 6887  899999999987

>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=99.87  E-value=4.6e-22  Score=125.95  Aligned_cols=77  Identities=23%  Similarity=0.399  Sum_probs=71.7

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .++|||+|||.++++++|+++|++||.|.++++..                              ++.++|||||+|.+.
T Consensus         7 ~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~------------------------------~~~~kG~afV~f~~~   56 (114)
T d2f9da1           7 NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN------------------------------TPETRGTAYVVYEDI   56 (114)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEC------------------------------STTTTTEEEEEESSH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccc------------------------------cCCcCCeEEEEECCH
Confidence            57999999999999999999999999999998874                              456789999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADP  112 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~  112 (131)
                      ++|..|++.|+|.  .++|+.|.|.|+.+
T Consensus        57 ~~A~~Ai~~l~g~--~~~gr~l~V~~a~~   83 (114)
T d2f9da1          57 FDAKNACDHLSGF--NVCNRYLVVLYYNA   83 (114)
T ss_dssp             HHHHHHHHHHTTC--EETTEECEEEECCH
T ss_pred             HHHHHHHHHhCCC--EECCEEEEEEEcCC
Confidence            9999999999998  89999999999874

>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=99.86  E-value=1.1e-21  Score=118.10  Aligned_cols=80  Identities=26%  Similarity=0.429  Sum_probs=71.9

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||||||+++++++|+++|++||+|.++++++.                           ..+|.++|||||+|.+
T Consensus         5 ~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d---------------------------~~tg~~kG~afV~f~~   57 (84)
T d1l3ka1           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRD---------------------------PNTKRSRGFGFVTYAT   57 (84)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEC---------------------------TTTCCEEEEEEEEESS
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhhccccceeeccc---------------------------ccCCCcccEEEEEEcC
Confidence            3579999999999999999999999999999998854                           3478999999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADP  112 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~  112 (131)
                      .+.|.+|++ ++++  .++|+.|.|+.|.+
T Consensus        58 ~~~a~~ai~-~~~~--~i~Gr~i~V~~A~s   84 (84)
T d1l3ka1          58 VEEVDAAMN-ARPH--KVDGRVVEPKRAVS   84 (84)
T ss_dssp             HHHHHHHHH-TCSC--EETTEECEEEECCC
T ss_pred             HHHHHHHHH-hCCC--EECCEEEEEEeeeC
Confidence            999999997 4777  89999999998864

>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=99.86  E-value=9e-22  Score=118.97  Aligned_cols=78  Identities=29%  Similarity=0.463  Sum_probs=72.0

Q ss_pred             CCceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeC
Q psy1185           2 SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYD   81 (131)
Q Consensus         2 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~   81 (131)
                      +..++|||+|||.++++++|+++|++||+|.++++.+                                 .++||||+|.
T Consensus         6 ~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~---------------------------------~k~~afV~f~   52 (86)
T d2cpja1           6 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHK---------------------------------DKGFGFIRLE   52 (86)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEET---------------------------------TTTEEEEECS
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeec---------------------------------ccceEEEEEC
Confidence            4467899999999999999999999999999998874                                 3789999999


Q ss_pred             CHHhHHHHHHHHhCCcceecCcEEEEEecCCCC
Q psy1185          82 SHKSASLAKKRLATGRLKVWGCDIIVDWADPQE  114 (131)
Q Consensus        82 ~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~  114 (131)
                      +.++|.+|++.|+|.  .++|+.|+|+||.+..
T Consensus        53 ~~~~A~~A~~~l~g~--~i~g~~l~V~~A~~~~   83 (86)
T d2cpja1          53 TRTLAEIAKVELDNM--PLRGKQLRVRFACHSA   83 (86)
T ss_dssp             SSHHHHHHHHHHTTC--CBTTBCCEEEESSCCS
T ss_pred             CHHHHHHHHHHhCCC--EECCEEEEEEECCCcC
Confidence            999999999999998  8899999999998765

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=4e-22  Score=123.93  Aligned_cols=79  Identities=23%  Similarity=0.457  Sum_probs=72.6

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .++|||+|||.++++++|+++|++||.|.++++++.                           ..+|.++|||||+|.+.
T Consensus        18 ~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d---------------------------~~tg~~kG~afV~F~~~   70 (101)
T d2cq4a1          18 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISD---------------------------RNSRRSKGIAYVEFCEI   70 (101)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCS---------------------------CCSSSCCCCEEEEESCG
T ss_pred             CCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeec---------------------------CCCccccceEEEEECCH
Confidence            468999999999999999999999999999999864                           34789999999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADP  112 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~  112 (131)
                      ++|.+|+. ++|.  .++|+.|.|++|.+
T Consensus        71 e~a~~A~~-l~g~--~~~G~~l~V~~a~~   96 (101)
T d2cq4a1          71 QSVPLAIG-LTGQ--RLLGVPIIVQASQA   96 (101)
T ss_dssp             GGHHHHHH-HTTE--EETTEEEEEEEHHH
T ss_pred             HHHHHHHH-HCCC--EECCEEEEEEECCC
Confidence            99999995 9997  89999999999864

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=9.4e-22  Score=118.01  Aligned_cols=75  Identities=32%  Similarity=0.488  Sum_probs=69.2

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .++|||+|||.++|+++|+++|++||.|.++.+++.                           ..++.++|||||+|.+.
T Consensus         9 ~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~---------------------------~~~~~~~g~afV~f~~~   61 (83)
T d2cqca1           9 NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYD---------------------------QQSRRSRGFAFVYFENV   61 (83)
T ss_dssp             GGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEEC---------------------------SSSSSEEEEEEEEESSH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCCcccccccc---------------------------ccccccccceEEEECCH
Confidence            578999999999999999999999999999998853                           34688899999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEE
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIV  107 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v  107 (131)
                      ++|.+|+..|++.  .++|+.|+|
T Consensus        62 ~~A~~Ai~~l~g~--~~~gr~i~V   83 (83)
T d2cqca1          62 DDAKEAKERANGM--ELDGRRIRV   83 (83)
T ss_dssp             HHHHHHHHHHTTE--EETTEEEEE
T ss_pred             HHHHHHHHHcCCC--EECCEEeEC
Confidence            9999999999998  899999986

>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=99.86  E-value=4e-22  Score=120.49  Aligned_cols=83  Identities=23%  Similarity=0.374  Sum_probs=70.2

Q ss_pred             CceEEEEeCCCCCCC-HHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeC
Q psy1185           3 KVKVLYVRNLTQYCT-EEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYD   81 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t-~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~   81 (131)
                      ..++|||+|||++++ +++|+++|++||.|.+++++..                          ...++.++|||||+|.
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~--------------------------~~~~~~~kg~afV~f~   56 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAG--------------------------QKEHSFNNCCAFMVFE   56 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSC--------------------------CC---CCCEEEEEEES
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecc--------------------------cCCccccceeeeEEEC
Confidence            367999999999875 5679999999999999988642                          1246788999999999


Q ss_pred             CHHhHHHHHHHHhCCcceecCcEEEEEecCCCC
Q psy1185          82 SHKSASLAKKRLATGRLKVWGCDIIVDWADPQE  114 (131)
Q Consensus        82 ~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~  114 (131)
                      +.++|.+|+. +++.  .++|+.|+|+||++++
T Consensus        57 ~~~~a~~Al~-~n~~--~~~gr~l~V~~a~~kP   86 (86)
T d2ghpa3          57 NKDSAERALQ-MNRS--LLGNREISVSLADKKP   86 (86)
T ss_dssp             SHHHHHHHGG-GTTE--EETTEEEEEEECCCCC
T ss_pred             CHHHHHHHHh-cCCC--EECCEEEEEEEcCCCC
Confidence            9999999995 9997  8999999999999764

>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=99.86  E-value=1.5e-21  Score=120.98  Aligned_cols=94  Identities=22%  Similarity=0.319  Sum_probs=75.8

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||+|..+.+...                  ....+.. ...+|.+++||||+|.+
T Consensus         7 ~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~------------------~~~~~~~-d~~~~~~~g~afV~f~~   67 (101)
T d2cpea1           7 DNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQ------------------PMIHIYL-DKETGKPKGDATVSYED   67 (101)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCC------------------BSEECCB-CTTTCSBCSEEEEEBSS
T ss_pred             CCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeeccc------------------ceeEEee-ccccccccceeeEEecC
Confidence            4679999999999999999999999999865433311                  0011111 13468889999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      +++|.+|++.|+|.  .++|+.|+|+||+++.++.
T Consensus        68 ~~~a~~Ai~~l~g~--~~~gr~i~V~~a~~~~p~~  100 (101)
T d2cpea1          68 PPTAKAAVEWFDGK--DFQGSKLKVSLARKKPPMN  100 (101)
T ss_dssp             HHHHHHHHHHHTTC--EETTEECEEECSSCCCCST
T ss_pred             HHHHHHHHHHhCCC--EECCEEEEEEEcCCCCCCC
Confidence            99999999999998  8999999999999877653

>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=99.86  E-value=1.4e-21  Score=116.21  Aligned_cols=78  Identities=31%  Similarity=0.502  Sum_probs=70.0

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      +.++|||||||+++|+++|+++|++||.|..+.++..                           ..++.++|+|||+|.+
T Consensus         1 t~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~---------------------------~~~~~~~g~afV~f~~   53 (79)
T d1l3ka2           1 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTD---------------------------RGSGKKRGFAFVTFDD   53 (79)
T ss_dssp             CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEEC---------------------------TTTCCEEEEEEEEESS
T ss_pred             CCCEEEECCCCCcCCHHHHHHHHHHhccccccccccC---------------------------CCCcccccEEEEEEcC
Confidence            4689999999999999999999999999999988743                           3467889999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEec
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWA  110 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a  110 (131)
                      +++|.+|+. +++.  .++|+.|.|+.|
T Consensus        54 ~e~~~~al~-~~~~--~l~Gr~i~V~~A   78 (79)
T d1l3ka2          54 HDSVDKIVI-QKYH--TVNGHNCEVRKA   78 (79)
T ss_dssp             HHHHHHHHH-CSCC--EETTEECEEEEC
T ss_pred             HHHHHHHHH-hCCC--EECCEEEEEEEC
Confidence            999998885 7988  899999999987

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=1.3e-21  Score=115.37  Aligned_cols=75  Identities=23%  Similarity=0.302  Sum_probs=67.7

Q ss_pred             EEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHHh
Q psy1185           6 VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKS   85 (131)
Q Consensus         6 ~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~~   85 (131)
                      +|||||||+++++++|+++|++||+|.++++++.                           ..++.++|||||+|.+.++
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d---------------------------~~t~~~kg~afV~f~~~~~   53 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLD---------------------------PITGRSRGFGFVLFKESES   53 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCB---------------------------TTTTBCCSEEEEEESSHHH
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccC---------------------------CCCCCcCceEEEEECCHHH
Confidence            5899999999999999999999999999998854                           3478899999999999999


Q ss_pred             HHHHHHHHhCCcceecCcEEEEEec
Q psy1185          86 ASLAKKRLATGRLKVWGCDIIVDWA  110 (131)
Q Consensus        86 a~~a~~~l~~~~~~~~g~~l~v~~a  110 (131)
                      |.+|+. +++.  .++|+.|.|+.|
T Consensus        54 a~~Al~-~~~~--~l~Gr~i~V~rA   75 (75)
T d1hd0a_          54 VDKVMD-QKEH--KLNGKVIDPKRA   75 (75)
T ss_dssp             HHHHHH-TCCC--CBTTBCCEECCC
T ss_pred             HHHHHh-cCCC--EECCCEEEeeEC
Confidence            999997 6776  889999998764

>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=99.85  E-value=4.6e-21  Score=116.13  Aligned_cols=78  Identities=21%  Similarity=0.246  Sum_probs=69.8

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      .+++|||+|||.++++++|+++|++||.|..+.+.                               .++++++|||+|.+
T Consensus         9 Ps~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~-------------------------------~~~~~~~afV~f~~   57 (88)
T d2adca2           9 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKF-------------------------------FQKDRKMALIQMGS   57 (88)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEE-------------------------------CSSSTTCEEEEESS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEe-------------------------------eecccceeEEEECC
Confidence            36799999999999999999999999999887665                               34568999999999


Q ss_pred             HHhHHHHHHHHhCCccee-cCcEEEEEecCCC
Q psy1185          83 HKSASLAKKRLATGRLKV-WGCDIIVDWADPQ  113 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~-~g~~l~v~~a~~~  113 (131)
                      .++|.+|+..|+|.  .+ +|+.|+|+|++++
T Consensus        58 ~~~A~~A~~~l~~~--~i~~g~~l~v~~sk~~   87 (88)
T d2adca2          58 VEEAVQALIDLHNH--DLGENHHLRVSFSKST   87 (88)
T ss_dssp             HHHHHHHHHHHTTC--BSSSSCBCEEEECSSC
T ss_pred             HHHHHHHHHhccCC--EecCCCEEEEEeCCCC
Confidence            99999999999998  55 6899999999875

>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=99.85  E-value=3.8e-22  Score=123.99  Aligned_cols=84  Identities=20%  Similarity=0.304  Sum_probs=75.5

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .++|||+|||.++++++|+++|++||.|..+.++..                           ..+|.+++||||+|.+.
T Consensus        18 s~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~---------------------------~~~g~~~g~~fV~f~~~   70 (102)
T d2cpxa1          18 NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFR---------------------------MMTGRMRGQAFITFPNK   70 (102)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEE---------------------------EECSSSCSEEEEECSSH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecc---------------------------cccccccccceEEeccH
Confidence            579999999999999999999999999988776632                           12678899999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCCCCCC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADPQEEP  116 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~  116 (131)
                      ++|..|++.|+|.  .++|+.|+|+||+++.++
T Consensus        71 ~~A~~Ai~~l~g~--~~~g~~l~V~~ak~k~~r  101 (102)
T d2cpxa1          71 EIAWQALHLVNGY--KLYGKILVIEFGKNKKQR  101 (102)
T ss_dssp             HHHHHHHHHSTTC--BCSSCBCEEEECCCCSCC
T ss_pred             HHHHHHHHHhCCC--EECCEEEEEEeCCCcccC
Confidence            9999999999998  889999999999998765

>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=99.85  E-value=1.2e-21  Score=115.51  Aligned_cols=75  Identities=25%  Similarity=0.455  Sum_probs=67.3

Q ss_pred             EEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHHh
Q psy1185           6 VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKS   85 (131)
Q Consensus         6 ~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~~   85 (131)
                      +|||||||+++|+++|+++|++||+|.++++++.                           +.++.++|||||+|.+.++
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d---------------------------~~t~~~rG~~FV~f~~~~~   53 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMD---------------------------NKTNKRRGFCFITFKEEEP   53 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCC---------------------------TTTCCTTCCEEEEESSSHH
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCccccccccc---------------------------ccccccccEEEEEECCHHH
Confidence            5999999999999999999999999999998854                           4578999999999999999


Q ss_pred             HHHHHHHHhCCcceecCcEEEEEec
Q psy1185          86 ASLAKKRLATGRLKVWGCDIIVDWA  110 (131)
Q Consensus        86 a~~a~~~l~~~~~~~~g~~l~v~~a  110 (131)
                      |.+|++. ++.  .++|+.|.|+.|
T Consensus        54 a~~al~~-~~~--~i~g~~i~vk~A   75 (75)
T d1x0fa1          54 VKKIMEK-KYH--NVGLSKCEIKVA   75 (75)
T ss_dssp             HHHHTTC-SSC--CBTTBCCEEECC
T ss_pred             HHHHHhh-CCC--EECCEEeEEEEC
Confidence            9999975 444  789999999875

>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=99.84  E-value=2.8e-21  Score=113.66  Aligned_cols=75  Identities=23%  Similarity=0.370  Sum_probs=68.3

Q ss_pred             EEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHHh
Q psy1185           6 VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKS   85 (131)
Q Consensus         6 ~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~~   85 (131)
                      +|||||||.++|+++|+++|++||.+..+.++..                           ..++.++++|||+|.+.++
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~---------------------------~~~~~~~~~afV~F~~~~~   53 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFD---------------------------KTTNRHRGFGFVTFESEDI   53 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCC---------------------------TTCTTSCCEEEEECSCHHH
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeee---------------------------ccccccCceeEEEECCHHH
Confidence            4899999999999999999999999999887643                           3467889999999999999


Q ss_pred             HHHHHHHHhCCcceecCcEEEEEec
Q psy1185          86 ASLAKKRLATGRLKVWGCDIIVDWA  110 (131)
Q Consensus        86 a~~a~~~l~~~~~~~~g~~l~v~~a  110 (131)
                      |.+|++ +++.  .++|+.|+|++|
T Consensus        54 a~~al~-~~~~--~l~gr~i~V~~A   75 (75)
T d2msta_          54 VEKVCE-IHFH--EINNKMVECKKA   75 (75)
T ss_dssp             HHHHHH-CSSC--CBTTBCCEEEEC
T ss_pred             HHHHHh-cCCC--EECCeEEEEEEC
Confidence            999996 9998  899999999986

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=5.1e-21  Score=113.84  Aligned_cols=75  Identities=27%  Similarity=0.325  Sum_probs=68.5

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      +.++|||+|+|  +|+++|+++|++||.|.++++.+                                 .++||||+|.+
T Consensus         4 ~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~---------------------------------~~~~afV~f~~   48 (79)
T d2bz2a1           4 KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDP---------------------------------PRNCAFVTYEK   48 (79)
T ss_dssp             CCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEET---------------------------------TTTEEEEECSS
T ss_pred             CCCEEEEECCC--CCHHHHHHHHhccCccceeeecc---------------------------------CCCEEEEEEcc
Confidence            45799999996  89999999999999999998864                                 37899999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQE  114 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~  114 (131)
                      .++|..|+..|+|.  .++|+.|+|+||++++
T Consensus        49 ~~~A~~Ai~~lng~--~~~g~~l~V~~a~~~P   78 (79)
T d2bz2a1          49 MESADQAVAELNGT--QVESVQLKVNIARKQP   78 (79)
T ss_dssp             HHHHHHHHHHHTTC--BCSSCBCEEEECCSSC
T ss_pred             cHHHHHHHHHhCCC--EECCEEEEEEEecCCC
Confidence            99999999999998  8899999999998754

>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=99.84  E-value=7.4e-21  Score=119.60  Aligned_cols=76  Identities=21%  Similarity=0.288  Sum_probs=69.5

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .++|||+|||.++++++|+++|++||+|.++.+.                                 ..++||||+|.+.
T Consensus        10 ~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~---------------------------------~~kg~afV~f~~~   56 (111)
T d1whxa_          10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP---------------------------------EGGITAIVEFLEP   56 (111)
T ss_dssp             EEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC---------------------------------SSSSCEEEEESCH
T ss_pred             CCEEEEECCCCCCCHHHHHhhhhccCCccEEEee---------------------------------ccCceEEEEEcCH
Confidence            4689999999999999999999999999998764                                 3479999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCCCC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADPQE  114 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~  114 (131)
                      ++|.+|+..|||.  .+.|+.|.|+||....
T Consensus        57 ~~A~~A~~~lng~--~~~gr~l~v~~a~~~~   85 (111)
T d1whxa_          57 LEARKAFRHLAYS--KFHHVPLYLEWAPIGV   85 (111)
T ss_dssp             HHHHHHHHHHTTC--BSSSSBCEEEEEETTT
T ss_pred             HHHHHHHHHHcCC--ccCCCeEEEEECCCCc
Confidence            9999999999998  8899999999996544

>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=99.84  E-value=3.9e-21  Score=117.19  Aligned_cols=80  Identities=19%  Similarity=0.377  Sum_probs=71.1

Q ss_pred             ceEEEEeCCCCCCCHHHHHH----HhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEE
Q psy1185           4 VKVLYVRNLTQYCTEEKLKE----AFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLE   79 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~----~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~   79 (131)
                      +++|||+|||+++++++|++    +|++||+|.++++.+                              ++.++|||||+
T Consensus         3 ~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~------------------------------~~~~~g~afV~   52 (91)
T d1nu4a_           3 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR------------------------------SLKMRGQAFVI   52 (91)
T ss_dssp             CSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH------------------------------HHHHTTCEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee------------------------------eccCCCceEEE
Confidence            57999999999999998864    689999999988763                              35678999999


Q ss_pred             eCCHHhHHHHHHHHhCCcceecCcEEEEEecCCCCC
Q psy1185          80 YDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEE  115 (131)
Q Consensus        80 f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~  115 (131)
                      |.+.++|.+|+..+||.  .++|+.|.|.||+++.+
T Consensus        53 F~~~~~A~~A~~~~~~~--~~~g~~l~v~~ak~~~~   86 (91)
T d1nu4a_          53 FKEVSSATNALRSMQGF--PFYDKPMRIQYAKTDSD   86 (91)
T ss_dssp             ESSHHHHHHHHHHHTTC--EETTEECEEEECSSCCT
T ss_pred             ECCHHHHHHHHHHhCCC--EECCEEEEEEEeCCCch
Confidence            99999999999999998  89999999999987653

>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=99.84  E-value=1.5e-20  Score=112.72  Aligned_cols=74  Identities=20%  Similarity=0.351  Sum_probs=67.6

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      +++|||+|||.++++++|+++|++||.|.+++++++                                .+|||||+|.+.
T Consensus         8 ~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~--------------------------------~~g~afV~f~~~   55 (83)
T d2b0ga1           8 NQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN--------------------------------RHDIAFVEFTTE   55 (83)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT--------------------------------TCSCEEEEESSH
T ss_pred             CCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc--------------------------------cceeEEEecCCH
Confidence            579999999999999999999999999999988742                                478999999999


Q ss_pred             HhHHHHHHHHhCCccee-cCcEEEEEecC
Q psy1185          84 KSASLAKKRLATGRLKV-WGCDIIVDWAD  111 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~-~g~~l~v~~a~  111 (131)
                      ++|.+|++.|+|.  .+ +|+.|+|+||+
T Consensus        56 ~~A~~A~~~l~g~--~~~~~~~i~v~~ak   82 (83)
T d2b0ga1          56 LQSNAAKEALQGF--KITPTHAMKITFAK   82 (83)
T ss_dssp             HHHHHHHHHHTTC--BSSTTCBCEEEECC
T ss_pred             HHHHHHHHHhCCc--EeCCCcEEEEEEec
Confidence            9999999999997  55 57899999986

>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=99.84  E-value=1.5e-20  Score=113.89  Aligned_cols=79  Identities=19%  Similarity=0.265  Sum_probs=71.8

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      +++|||+|||.++++++|+++|++||.|.++.+.+                                 .+++|||+|.+.
T Consensus         8 s~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~---------------------------------~~~~afV~f~~~   54 (88)
T d2cq1a1           8 SRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLK---------------------------------GKNQAFLELATE   54 (88)
T ss_dssp             CSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEET---------------------------------TTTEEEEEESSH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcccccccccccc---------------------------------cceEEEEEeCCH
Confidence            68999999999999999999999999999998874                                 368999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCCCCC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADPQEE  115 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~  115 (131)
                      ++|.+|+..+++.+..++|+.|.|+|++.+..
T Consensus        55 e~A~~a~~~~~~~~~~~~g~~l~v~~sk~~~l   86 (88)
T d2cq1a1          55 EAAITMVNYYSAVTPHLRNQPIYIQYSNHKEL   86 (88)
T ss_dssp             HHHHHHHHHHHHSCCEETTEECEEEECSCSSC
T ss_pred             HHHHHHHHHHccCCCccCCCEEEEEECCCCCC
Confidence            99999999887666699999999999987653

>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=99.84  E-value=7.1e-22  Score=120.64  Aligned_cols=80  Identities=20%  Similarity=0.266  Sum_probs=71.6

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||+++++++|+++|++||.|..+.++..                            .+|.++|||||+|.+
T Consensus        12 ~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~----------------------------~~g~~kg~afv~F~~   63 (91)
T d1fjeb1          12 TPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV----------------------------RTGTNRKFGYVDFES   63 (91)
T ss_dssp             SSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE----------------------------EEETTTTEEEEEESS
T ss_pred             CCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec----------------------------CCCCccEEeEEeeCC
Confidence            4578999999999999999999999999988776532                            367889999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQ  113 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~  113 (131)
                      .++|.+|++ +++.  .++|+.|.|.||+++
T Consensus        64 ~e~a~~Al~-~~g~--~~~g~~i~V~~ak~k   91 (91)
T d1fjeb1          64 AEDLEKALE-LTGL--KVFGNEIKLEKPKGR   91 (91)
T ss_dssp             HHHHHHHHH-GGGE--EETTEEEEEECCCCS
T ss_pred             HHHHHHHHh-cCCc--EECCEEEEEEecCCC
Confidence            999999995 9998  999999999999864

>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=99.83  E-value=2.2e-20  Score=115.10  Aligned_cols=79  Identities=20%  Similarity=0.352  Sum_probs=69.2

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .++|||+|||+++++++|+++|++||+|..+++.+                                 .+++|||+|.+.
T Consensus        17 s~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~---------------------------------~~~~afV~f~~~   63 (97)
T d1whya_          17 TTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVK---------------------------------GDSFAYIQYESL   63 (97)
T ss_dssp             CSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECS---------------------------------SSCCEEEEESSH
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeec---------------------------------cccEEEeccCCH
Confidence            57999999999999999999999999999998864                                 378999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCCCCC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADPQEE  115 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~  115 (131)
                      ++|.+|++.|++..+...+++|+|+||++.+.
T Consensus        64 ~~A~~A~~~l~~~~i~g~~~~l~v~~ak~~~~   95 (97)
T d1whya_          64 DAAQAACAKMRGFPLGGPDRRLRVDFAKSGPS   95 (97)
T ss_dssp             HHHHHHHHHHTTCBCSSSSCBCEEEECCCCCC
T ss_pred             HHHHHHHHHhCCCEeCCCceEEEEEeCCCCCC
Confidence            99999999999984333346899999997653

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.83  E-value=6.4e-21  Score=117.31  Aligned_cols=80  Identities=21%  Similarity=0.364  Sum_probs=71.9

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||.|..+..                                ++.+++||||+|.+
T Consensus        15 ~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~--------------------------------~~~~~~~afV~f~~   62 (96)
T d1fjca_          15 AARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ--------------------------------DGKSKGIAYIEFKS   62 (96)
T ss_dssp             GGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE--------------------------------TTEEEEEEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee--------------------------------cCccccEEEEEeCC
Confidence            3679999999999999999999999998766532                                46779999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEEP  116 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~  116 (131)
                      .++|.+|++.|++.  .++|+.|.|.||.++...
T Consensus        63 ~~~A~~A~~~l~~~--~~~gr~i~V~~a~~k~~~   94 (96)
T d1fjca_          63 EADAEKNLEEKQGA--EIDGRSVSLYYTGEKGGT   94 (96)
T ss_dssp             HHHHHHHHHHTTEE--EETTEEEEEEECSSSCCC
T ss_pred             HHHHHHHHHHcCCC--EECCEEEEEEEeCCCCCC
Confidence            99999999999998  999999999999987754

>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=99.83  E-value=4.9e-21  Score=116.12  Aligned_cols=80  Identities=26%  Similarity=0.338  Sum_probs=70.1

Q ss_pred             CCceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeC
Q psy1185           2 SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYD   81 (131)
Q Consensus         2 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~   81 (131)
                      +..++|||+|||+++++++|+++|++||.|.+++++                                ..+++||||+|.
T Consensus         3 ~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~--------------------------------~~~~gfafV~f~   50 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIP--------------------------------KPFRAFAFVTFA   50 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECC--------------------------------SSCCSCCEEECS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEe--------------------------------eccCceEEEEEC
Confidence            457899999999999999999999999999998764                                346899999999


Q ss_pred             CHHhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          82 SHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        82 ~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      +.++|++|+.  ++.  .++|+.|.|+||.++....
T Consensus        51 ~~~~a~~a~~--~~~--~i~g~~l~v~~a~~k~~~~   82 (88)
T d1wf0a_          51 DDQIAQSLCG--EDL--IIKGISVHISNAEPKHNSN   82 (88)
T ss_dssp             CHHHHHHTTT--CEE--EETTEEEEEECCCCCCCCC
T ss_pred             CHHHHHHHHh--CCC--EECCEEeEEEeCCCCCCCC
Confidence            9999999975  444  8999999999998876544

>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=99.83  E-value=2.3e-20  Score=117.02  Aligned_cols=77  Identities=29%  Similarity=0.348  Sum_probs=69.6

Q ss_pred             ceEEEEeCCCC-CCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           4 VKVLYVRNLTQ-YCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         4 ~~~l~v~nLp~-~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      +++|||+|||+ .+++++|+++|++||.|.++.+++.                                .+|+|||+|.+
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~--------------------------------~kg~afV~f~~   49 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN--------------------------------KKENALVQMAD   49 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCT--------------------------------TSCCEEEEESC
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEec--------------------------------ccceEEEEECC
Confidence            57999999955 6999999999999999999998742                                37899999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQE  114 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~  114 (131)
                      .++|.+|+..++|.  .++|+.|+|+|++.+.
T Consensus        50 ~~~A~~ai~~lng~--~l~g~~l~v~~s~~~~   79 (109)
T d2adca1          50 GNQAQLAMSHLNGH--KLHGKPIRITLSKHQN   79 (109)
T ss_dssp             HHHHHHHHHHHTTC--BCSSSBCEEECCSCCC
T ss_pred             HHHHHHHHHHhCCC--EECCEEEEEEECCCCC
Confidence            99999999999998  8899999999997543

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=2.1e-20  Score=112.63  Aligned_cols=77  Identities=22%  Similarity=0.314  Sum_probs=69.7

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .++|||+|||.++|+++|+++|++||+|..+++.+.                            .+|.++|||||+|.++
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~----------------------------~~~~~kG~afV~f~~~   57 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT----------------------------LHKAFKGSIFVVFDSI   57 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEEC----------------------------TTCCEEEEEEEEESCH
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeee----------------------------ccCCcceEEEEEEcCH
Confidence            579999999999999999999999999999988753                            3678899999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWAD  111 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~  111 (131)
                      ++|.+|++ +++.  .++|+.|.|.|++
T Consensus        58 e~a~~al~-~~~~--~~~g~~l~v~~~~   82 (85)
T d1zh5a2          58 ESAKKFVE-TPGQ--KYKETDLLILFKD   82 (85)
T ss_dssp             HHHHHHHT-CCCC--EETTEECEEEEGG
T ss_pred             HHHHHHHH-HCCC--EECCEEEEEEEcC
Confidence            99999996 5776  8999999999964

>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=99.83  E-value=5.1e-21  Score=118.81  Aligned_cols=79  Identities=18%  Similarity=0.285  Sum_probs=71.8

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .++|||+|||.++++++|+++|++||.|..+.+...                            .++.++|||||+|.+.
T Consensus        18 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~----------------------------~~~~~~g~afV~f~~~   69 (101)
T d1x5oa1          18 PTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD----------------------------SSGTSRGVGFARMEST   69 (101)
T ss_dssp             TTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEEC----------------------------SSSCEEEEEEEEESCH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecc----------------------------cccccccceeEEeCCH
Confidence            568999999999999999999999999999887742                            3677899999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADP  112 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~  112 (131)
                      ++|.+|++.|||.  .+.|+.+.|.+++|
T Consensus        70 ~~A~~Ai~~lng~--~i~gr~~~v~~~~P   96 (101)
T d1x5oa1          70 EKCEAVIGHFNGK--FIKTPPGVSAPTEP   96 (101)
T ss_dssp             HHHHHHHHHHBTC--CCCCCTTSCCCSSC
T ss_pred             HHHHHHHHHhCCC--EECCcCCccCCCCC
Confidence            9999999999998  89999999988775

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=1.7e-20  Score=113.67  Aligned_cols=78  Identities=18%  Similarity=0.204  Sum_probs=67.5

Q ss_pred             CCceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeC
Q psy1185           2 SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYD   81 (131)
Q Consensus         2 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~   81 (131)
                      +..++|||+|||+++++++|+++|++||. ..+.+                                 +..++||||+|.
T Consensus         3 s~s~~i~V~nLp~~~t~~~l~~lF~~~G~-~~~~~---------------------------------~~~kg~afV~f~   48 (88)
T d1wg1a_           3 SGSSGILVKNLPQDSNCQEVHDLLKDYDL-KYCYV---------------------------------DRNKRTAFVTLL   48 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSSCC-CCEEE---------------------------------EGGGTEEEECCS
T ss_pred             CCCCEEEEeCCCCccChHHHHHHHHhcCc-eeeee---------------------------------eccCCceEEEEC
Confidence            45789999999999999999999999992 23332                                 245899999999


Q ss_pred             CHHhHHHHHHHHhCCcceecCcEEEEEecCCCCC
Q psy1185          82 SHKSASLAKKRLATGRLKVWGCDIIVDWADPQEE  115 (131)
Q Consensus        82 ~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~  115 (131)
                      +.++|++|++.||+.  .++|+.|.|+|++++..
T Consensus        49 ~~~~A~~Ai~~ln~~--~~~G~~l~V~~a~~~~~   80 (88)
T d1wg1a_          49 NGEQAQNAIQMFHQY--SFRGKDLIVQLQPTDAL   80 (88)
T ss_dssp             CHHHHHHHHHHHTTE--EETTEEEEEEECCCCCC
T ss_pred             CHHHHHHHHHHhCCC--EECCEEEEEEEcCCCCC
Confidence            999999999999998  89999999999976554

>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=99.82  E-value=6.3e-20  Score=114.22  Aligned_cols=84  Identities=26%  Similarity=0.373  Sum_probs=71.7

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .++|||+|||+++++++|+++|++|| +.++.++..                          ...++.++|||||+|.+.
T Consensus        15 ~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~--------------------------~~~~g~~~g~afV~f~~~   67 (104)
T d1wi8a_          15 PYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPRE--------------------------PSNPERLKGFGYAEFEDL   67 (104)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBC--------------------------SSCTTSBCSCEEEEESSH
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeee--------------------------eccCCCcceeeeEEECCH
Confidence            57999999999999999999999999 777766632                          134678899999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      ++|++|+ .+++.  .++|+.|+|.||.++.+..
T Consensus        68 e~a~~~~-~~~~~--~~~gr~l~V~~a~~~~~~~   98 (104)
T d1wi8a_          68 DSLLSAL-SLNEE--SLGNKRIRVDVADQAQDKD   98 (104)
T ss_dssp             HHHHHHH-GGGTC--EETTEECEEEECCCCCCCC
T ss_pred             HHHHHHH-HcCCC--EECCEEEEEEECCCCCCCC
Confidence            9998666 69998  8999999999999877654

>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=99.82  E-value=1.9e-20  Score=115.67  Aligned_cols=75  Identities=17%  Similarity=0.324  Sum_probs=67.8

Q ss_pred             ceEEEEeCCC-CCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           4 VKVLYVRNLT-QYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         4 ~~~l~v~nLp-~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      .++|||+||| ..+++++|+++|++||.|.++.+.                                   ++||||+|.+
T Consensus        15 ~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~-----------------------------------rg~aFV~f~~   59 (98)
T d1wf2a_          15 NSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH-----------------------------------KGFAFVQYVN   59 (98)
T ss_dssp             CCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE-----------------------------------TEEEEEEESS
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe-----------------------------------CCeEEEEECC
Confidence            5679999997 578899999999999999999875                                   6889999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEE  115 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~  115 (131)
                      .++|.+|++.|+|.  .++|+.|+|+||.++..
T Consensus        60 ~~~A~~Ai~~lng~--~~~g~~l~V~~a~~~~~   90 (98)
T d1wf2a_          60 ERNARAAVAGEDGR--MIAGQVLDINLAAEPKV   90 (98)
T ss_dssp             HHHHHHHHHTTTTC--EETTEECEEEETTSCCC
T ss_pred             HHHHHHHHHHcCCC--EECCEEEEEEECCCCCC
Confidence            99999999999998  89999999999986544

>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=99.82  E-value=1.3e-20  Score=118.22  Aligned_cols=82  Identities=23%  Similarity=0.287  Sum_probs=72.5

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ...+|||+|||+.+|+++|+++|++||.|.++.+.+.                               +++|+|||+|.+
T Consensus         6 ~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~-------------------------------~~~g~aFV~f~~   54 (108)
T d2adba1           6 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK-------------------------------NNQFQALLQYAD   54 (108)
T ss_dssp             CEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEE-------------------------------TTEEEEEEEESC
T ss_pred             CeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEee-------------------------------CCCCeEEEEECC
Confidence            4568999999999999999999999999999988742                               358999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEE  115 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~  115 (131)
                      .++|..|+..|+|.++...|+.|.|.|++++..
T Consensus        55 ~e~A~~Ai~~ln~~~l~~~~~~l~v~~s~~~~~   87 (108)
T d2adba1          55 PVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSL   87 (108)
T ss_dssp             HHHHHHHHHHHHSCCSSTTCCCCEEEECSSCSC
T ss_pred             HHHHHHHHHHHCCCEeccCCcEEEEEecCCccc
Confidence            999999999999996655788999999987553

>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=99.82  E-value=3e-20  Score=112.87  Aligned_cols=81  Identities=15%  Similarity=0.185  Sum_probs=71.9

Q ss_pred             CCceEEEEeCCCCC-CCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEe
Q psy1185           2 SKVKVLYVRNLTQY-CTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEY   80 (131)
Q Consensus         2 ~~~~~l~v~nLp~~-~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f   80 (131)
                      +.+++|||+|||.. +|+++|.++|++||.|.++.+++                                 .+++|||+|
T Consensus         6 ~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~---------------------------------~k~~afV~f   52 (89)
T d1x4da1           6 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILN---------------------------------KINEAFIEM   52 (89)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECS---------------------------------SSSCEEEEE
T ss_pred             CCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeec---------------------------------cceEEEEEE
Confidence            35789999999997 78999999999999999998874                                 368999999


Q ss_pred             CCHHhHHHHHHHHhCCcceecCcEEEEEecCCCCC
Q psy1185          81 DSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEE  115 (131)
Q Consensus        81 ~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~  115 (131)
                      .+.++|..|++.+++.++.++|++|.|+||++..+
T Consensus        53 ~~~~~A~~A~~~l~~~~~~~~gr~l~V~~s~~~~~   87 (89)
T d1x4da1          53 ATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKYKR   87 (89)
T ss_dssp             SSHHHHHHHHHHHHHSCCEETTEECEEEEECCCTT
T ss_pred             cchhhHHHHHHHHhhCCCccCCceEEEEECCCccc
Confidence            99999999999987666689999999999987553

>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=99.82  E-value=4.9e-20  Score=108.52  Aligned_cols=74  Identities=24%  Similarity=0.266  Sum_probs=66.1

Q ss_pred             eEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHH
Q psy1185           5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHK   84 (131)
Q Consensus         5 ~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~   84 (131)
                      ++|||+|||+++++++|+++|++||+|..++++++                             .+..+++|||+|.+++
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~-----------------------------~~~~~~~afV~F~~~~   51 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS-----------------------------LKKNFRFARIEFARYD   51 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEEC-----------------------------TTSSSEEEEEEESSHH
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEee-----------------------------ccccceEEEEEEcchH
Confidence            58999999999999999999999999999998853                             3445689999999999


Q ss_pred             hHHHHHHHHhCCcceecCcEEEEEec
Q psy1185          85 SASLAKKRLATGRLKVWGCDIIVDWA  110 (131)
Q Consensus        85 ~a~~a~~~l~~~~~~~~g~~l~v~~a  110 (131)
                      +|.+|+. ++++  .++|+.|.|..+
T Consensus        52 ~a~~Al~-~~~~--~i~g~~i~V~~~   74 (75)
T d2ghpa2          52 GALAAIT-KTHK--VVGQNEIIVSHL   74 (75)
T ss_dssp             HHHHHHT-TTTC--EETTEECEEEEC
T ss_pred             HhHHHHH-hcCc--EECCEEEEEEEC
Confidence            9999984 7988  899999999864

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.81  E-value=1.5e-19  Score=106.45  Aligned_cols=71  Identities=14%  Similarity=0.256  Sum_probs=63.6

Q ss_pred             EEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHHhH
Q psy1185           7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSA   86 (131)
Q Consensus         7 l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a   86 (131)
                      |||+|||+++++++|+++|++|| +..+.+                                 +.++|+|||+|.+.++|
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~---------------------------------~~~~g~afv~f~~~~~A   46 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV---------------------------------DKYKGTAFVTLLNGEQA   46 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE---------------------------------ETTTTEEEEEESSHHHH
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee---------------------------------cccceeEEEEECCHHHH
Confidence            79999999999999999999999 444443                                 34689999999999999


Q ss_pred             HHHHHHHhCCcceecCcEEEEEecCCC
Q psy1185          87 SLAKKRLATGRLKVWGCDIIVDWADPQ  113 (131)
Q Consensus        87 ~~a~~~l~~~~~~~~g~~l~v~~a~~~  113 (131)
                      .+|++.|||.  .+.|++|.|+||.+.
T Consensus        47 ~~Ai~~ln~~--~~~g~~l~V~~a~~d   71 (75)
T d1wi6a1          47 EAAINTFHQS--RLRERELSVQLQPTD   71 (75)
T ss_dssp             HHHHHHHTTE--ESSSCEEEEEECCST
T ss_pred             HHHHHHhCCc--cCCCCEEEEEEeCCC
Confidence            9999999998  899999999999764

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.81  E-value=1.2e-19  Score=113.09  Aligned_cols=80  Identities=20%  Similarity=0.252  Sum_probs=72.1

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..++|||+|||.++++++|+++|++||.|.++.+.+                                 .+++|||+|.+
T Consensus        14 ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~---------------------------------~k~~AfV~f~~   60 (104)
T d1wexa_          14 VSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMP---------------------------------FKRQALVEFEN   60 (104)
T ss_dssp             CCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEET---------------------------------TTTEEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEe---------------------------------cceeEEEEeCC
Confidence            367899999999999999999999999999998864                                 37899999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEE  115 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~  115 (131)
                      .++|++|+..+++.++.++|++|.|+|++.+..
T Consensus        61 ~e~A~~ai~~~~~~~~~~~g~~l~v~~s~~~~~   93 (104)
T d1wexa_          61 IDSAKECVTFAADVPVYIAGQQAFFNYSTSKRI   93 (104)
T ss_dssp             HHHHHHHHHHHHHSCCBSSSSBCEEEECSSSSC
T ss_pred             HHHHHHHHHHHcCCCcEEeeEEEEEEEcCCCcc
Confidence            999999999998766789999999999986543

>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=99.80  E-value=7.6e-20  Score=112.90  Aligned_cols=78  Identities=17%  Similarity=0.153  Sum_probs=71.0

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .++|||+|||+++++++|+++|++||.|.++.+.                                  .+|||||+|.+.
T Consensus        15 ~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~----------------------------------~~g~afV~f~~~   60 (98)
T d1wg4a_          15 DFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQ----------------------------------KDGMGMVEYLRK   60 (98)
T ss_dssp             SCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEE----------------------------------TTTEEEEEESSH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhhccccccccc----------------------------------ccceEEEEECCH
Confidence            5689999999999999999999999999999875                                  258999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      ++|++|++.||+.  .++|+.|.|.|++++.++.
T Consensus        61 ~~a~~Ai~~lng~--~~~g~~i~v~~~~~~~~~~   92 (98)
T d1wg4a_          61 EDMEYALRKLDDT--KFRSHEGETSYIRVYPERS   92 (98)
T ss_dssp             HHHHHHHHHHSSE--EEECTTSCEEEEEEECCCS
T ss_pred             HHHHHHHHHhCCC--EeCCeEEEEEEEecCCCCC
Confidence            9999999999998  9999999999998766543

>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=99.80  E-value=1.6e-20  Score=113.58  Aligned_cols=75  Identities=15%  Similarity=0.180  Sum_probs=67.7

Q ss_pred             eEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHH
Q psy1185           5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHK   84 (131)
Q Consensus         5 ~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~   84 (131)
                      .+|||+|||+++++++|+++|++||+|.++.+.+                                  .|||||+|.+.+
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~----------------------------------~g~afV~f~~~~   46 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR----------------------------------DGTGVVEFVRKE   46 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECT----------------------------------TSEEEEEESSHH
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhcccccccccc----------------------------------cceeeEEeCCHH
Confidence            3699999999999999999999999999998752                                  489999999999


Q ss_pred             hHHHHHHHHhCCcceecCcEEEEEecCCCCC
Q psy1185          85 SASLAKKRLATGRLKVWGCDIIVDWADPQEE  115 (131)
Q Consensus        85 ~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~  115 (131)
                      +|.+|+..|+|.  .++|+.|.|.++.++.+
T Consensus        47 ~a~~Ai~~l~g~--~~~g~~i~v~~~~~~~~   75 (87)
T d3begb1          47 DMTYAVRKLDNT--KFRSHEGETAYIRVKVD   75 (87)
T ss_dssp             HHHHHHHHHTTC--BCCCTTSCCCBCEEEEC
T ss_pred             HHHHHHHHhCCC--EECCcEeEEeEEecCcC
Confidence            999999999998  88999999988765543

>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=99.80  E-value=6.1e-20  Score=110.61  Aligned_cols=78  Identities=12%  Similarity=0.139  Sum_probs=68.6

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEE-EEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERV-KRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYD   81 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~-~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~   81 (131)
                      ..++|||+|||.++++++|+++|+.||.+... .+..                            ..++.++|+|||+|.
T Consensus         8 ~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~----------------------------~~~g~~~G~afV~f~   59 (86)
T d2cqpa1           8 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKY----------------------------NEKGMPTGEAMVAFE   59 (86)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEE----------------------------CSSSCEEEEEEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEe----------------------------CCCCCcceEEEEEEc
Confidence            45689999999999999999999999998663 3332                            246888999999999


Q ss_pred             CHHhHHHHHHHHhCCcceecCcEEEEEec
Q psy1185          82 SHKSASLAKKRLATGRLKVWGCDIIVDWA  110 (131)
Q Consensus        82 ~~~~a~~a~~~l~~~~~~~~g~~l~v~~a  110 (131)
                      +.++|.+|++.+|+.  .++|++|+|.+|
T Consensus        60 ~~e~a~~Ai~~l~~~--~l~gr~i~v~l~   86 (86)
T d2cqpa1          60 SRDEATAAVIDLNDR--PIGSRKVKLVLG   86 (86)
T ss_dssp             CHHHHHHHHHHTTTC--EETTEECEEEES
T ss_pred             CcHHHHHHHHHcCCC--EECCEEEEEEEC
Confidence            999999999999998  999999999875

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.80  E-value=8e-20  Score=112.98  Aligned_cols=79  Identities=16%  Similarity=0.264  Sum_probs=69.5

Q ss_pred             ceEEEEeCCCCC-CCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           4 VKVLYVRNLTQY-CTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         4 ~~~l~v~nLp~~-~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      .++|||+|||.+ +|+++|.++|++||.|.++.+++                                 ++++|||+|.+
T Consensus        18 ~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~---------------------------------~k~~afV~f~~   64 (99)
T d1x4fa1          18 GRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR---------------------------------MKSQAFIEMET   64 (99)
T ss_dssp             CCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET---------------------------------TTTEEEEECSS
T ss_pred             CCEEEEeCCcCCccCHHHHHhhhccccceeEEEEee---------------------------------cCCcEEEEecc
Confidence            578999999985 89999999999999999998874                                 37999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEE  115 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~  115 (131)
                      .++|.+|++.++..++.++|+.|.|+||+.+.+
T Consensus        65 ~~~A~~Ai~~~~~~~~~~~gr~l~V~~s~~~~~   97 (99)
T d1x4fa1          65 REDAMAMVDHCLKKALWFQGRCVKVDLSEKYKK   97 (99)
T ss_dssp             HHHHHHHHHHHHHSCCCSSSSCCEEEEECSCSS
T ss_pred             hHHHHHHHHHHhcCCceECCEEEEEEEcCCccc
Confidence            999999999765555689999999999976553

>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=99.80  E-value=3.6e-20  Score=108.10  Aligned_cols=70  Identities=29%  Similarity=0.455  Sum_probs=63.6

Q ss_pred             EEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHHhH
Q psy1185           7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSA   86 (131)
Q Consensus         7 l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a   86 (131)
                      |||+|||.++++++|+++|++||+|..+++.+.                           ..++.++|+|||+|.+.++|
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~---------------------------~~~~~~~g~afV~f~~~~~A   53 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILD---------------------------KTTNKCKGYGFVDFDSPSAA   53 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECC---------------------------SSSCSCCSEEEEEESCHHHH
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccc---------------------------cccccccceeEEEECCHHHH
Confidence            799999999999999999999999999988753                           34678899999999999999


Q ss_pred             HHHHHHHhCCcceecCcEE
Q psy1185          87 SLAKKRLATGRLKVWGCDI  105 (131)
Q Consensus        87 ~~a~~~l~~~~~~~~g~~l  105 (131)
                      .+|+..|||.  .++|+.+
T Consensus        54 ~~Ai~~lng~--~~~Gr~~   70 (72)
T d1x4ea1          54 QKAVTALKAS--GVQAQMA   70 (72)
T ss_dssp             HHHHHHHHHH--TCCEESC
T ss_pred             HHHHHHhCCC--EECCEEC
Confidence            9999999998  7888765

>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=8.5e-20  Score=110.80  Aligned_cols=79  Identities=16%  Similarity=0.227  Sum_probs=66.4

Q ss_pred             ceEEEEeCCCCCCCHHHH---HHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEe
Q psy1185           4 VKVLYVRNLTQYCTEEKL---KEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEY   80 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l---~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f   80 (131)
                      .++|||+|||+++++++|   +++|++||+|.++.+++.-                        .....+..+|||||+|
T Consensus         8 ~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~------------------------~~~~~~~~~g~aFV~f   63 (89)
T d2cpia1           8 KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNST------------------------SYAGSQGPSASAYVTY   63 (89)
T ss_dssp             SSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCS------------------------SCCSSSCCCEEEEEEE
T ss_pred             cCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeecc------------------------CcCCCCCcceEEEEec
Confidence            467999999999999999   6789999999999988430                        0012234468999999


Q ss_pred             CCHHhHHHHHHHHhCCcceecCcEEEEE
Q psy1185          81 DSHKSASLAKKRLATGRLKVWGCDIIVD  108 (131)
Q Consensus        81 ~~~~~a~~a~~~l~~~~~~~~g~~l~v~  108 (131)
                      .++++|.+|++.|||.  .++|+.|+|+
T Consensus        64 ~~~~~A~~Ai~~lng~--~~~gr~lkvS   89 (89)
T d2cpia1          64 IRSEDALRAIQCVNNV--VVDGRTLKAS   89 (89)
T ss_dssp             SSHHHHHHHHHHHTTE--EETTEEEEEE
T ss_pred             ccchhHHHHHHHhCCC--EECCEEEEEC
Confidence            9999999999999998  8999999985

>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=99.77  E-value=1.2e-18  Score=108.45  Aligned_cols=84  Identities=18%  Similarity=0.158  Sum_probs=71.7

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      +..+|||+|||+++|+++|+++|+.+|.+....++..                           ..++.++|+|||+|.+
T Consensus        14 ~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~---------------------------~~~~~~kG~afV~F~~   66 (104)
T d1wg5a_          14 NDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPV---------------------------DFQGRSTGEAFVQFAS   66 (104)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCB---------------------------CSSSCBCSEEEEEESS
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEe---------------------------CCCCCcceEEEEEeCC
Confidence            4568999999999999999999999998887544421                           3467889999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEEP  116 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~  116 (131)
                      +++|++|++ +++.  .++|+.|.|.++.+++..
T Consensus        67 ~e~a~~a~~-~~~~--~i~gR~i~V~~~~~~~~~   97 (104)
T d1wg5a_          67 QEIAEKALK-KHKE--RIGHRYIEIFKSSRAEVR   97 (104)
T ss_dssp             HHHHHHHHT-TTTC--CSSSSCCEEEEECTTTSC
T ss_pred             HHHHHHHHh-hCCC--EEcceEEEEEECCHHHhc
Confidence            999999986 8887  889999999999876544

>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=99.76  E-value=1e-18  Score=108.47  Aligned_cols=77  Identities=16%  Similarity=0.192  Sum_probs=67.5

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEE-EEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERV-KRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~-~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ..+|||+|||+++++++|+++|+.||.+..+ .+..                            ..+|.++|+|||+|.+
T Consensus         8 ~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~----------------------------~~~g~~~G~afV~F~s   59 (103)
T d2cpya1           8 KVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLV----------------------------DNNGQGLGQALVQFKN   59 (103)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECC----------------------------CTTSSCSSCEEEECSS
T ss_pred             ceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEe----------------------------CCCCCcCccEEEEECC
Confidence            4579999999999999999999999988764 3332                            3478899999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWAD  111 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~  111 (131)
                      +++|.+|+. +++.  .++|+.|.|.++.
T Consensus        60 ~~~a~~Al~-~n~~--~i~gr~i~V~~~~   85 (103)
T d2cpya1          60 EDDARKSER-LHRK--KLNGREAFVHVVT   85 (103)
T ss_dssp             HHHHHHHGG-GCSE--EETTEEEEEEEEC
T ss_pred             HHHHHHHHh-cCCC--eECCcEEEEEECC
Confidence            999999996 8987  8999999999875

>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=99.76  E-value=1.3e-18  Score=107.97  Aligned_cols=82  Identities=15%  Similarity=0.120  Sum_probs=70.0

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      ...+|||+|||+++|+++|+++|+.||.+ .+.++..                            ..+..+|||||+|.+
T Consensus        14 ~~~~v~v~nLp~~~te~dl~~~F~~~~~~-~v~~~~~----------------------------~~g~~~G~afVeF~~   64 (102)
T d1weza_          14 TGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIG----------------------------PDGRVTGEADVEFAT   64 (102)
T ss_dssp             SSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEES----------------------------SSSCEEEEEEEECSS
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHhccCcc-eeeeEEe----------------------------cCCcceEEEEEEECC
Confidence            35689999999999999999999999854 5655532                            357889999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcEEEEEecCCCCCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCDIIVDWADPQEEP  116 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~  116 (131)
                      .++|++|+. +++.  .++|+.|.|.|+.++...
T Consensus        65 ~~~a~~Al~-~~~~--~i~gR~I~V~~s~~~~~~   95 (102)
T d1weza_          65 HEDAVAAMA-KDKA--NMQHRYVELFLNSTAGTS   95 (102)
T ss_dssp             SHHHHHHHT-TSSC--CSSSSCCEEEEECCCCCC
T ss_pred             HHHHHHHHH-cCCC--EECCEEEEEEEcCCCCCC
Confidence            999999986 8998  899999999999876543

>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=99.76  E-value=7.5e-19  Score=109.47  Aligned_cols=81  Identities=17%  Similarity=0.166  Sum_probs=71.2

Q ss_pred             CCceEEEEeCCCCCC-CH----HHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceE
Q psy1185           2 SKVKVLYVRNLTQYC-TE----EKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFC   76 (131)
Q Consensus         2 ~~~~~l~v~nLp~~~-t~----~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~   76 (131)
                      +..++|||+||+.++ ++    ++|+++|++||.|.++.+.+                                 ++++|
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k---------------------------------~~~~a   49 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK---------------------------------SFKRV   49 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET---------------------------------TTTEE
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEec---------------------------------CCCEE
Confidence            567899999999885 33    56999999999999998874                                 37899


Q ss_pred             EEEeCCHHhHHHHHHHHhCCcceecCcEEEEEecCCCCCCC
Q psy1185          77 FLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD  117 (131)
Q Consensus        77 fv~f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~~~  117 (131)
                      ||+|.+.++|.+|++.|||.  .++|+.|+|.||+++...+
T Consensus        50 fV~f~~~~~A~~Ai~~lng~--~~~g~~l~v~~a~~~~~~~   88 (104)
T d1weya_          50 RINFSNPLSAADARLRLHKT--EFLGKEMKLYFAQTLHIGS   88 (104)
T ss_dssp             EEECSSTTHHHHHHHTSTTS--EETTEECEEECCCCSSCCS
T ss_pred             EEEECCHHHHHHHHHHhccc--ccCCCEeEEeecccCCCCC
Confidence            99999999999999999998  8999999999998766543

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=1.9e-19  Score=109.27  Aligned_cols=84  Identities=19%  Similarity=0.253  Sum_probs=68.4

Q ss_pred             eEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHH
Q psy1185           5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHK   84 (131)
Q Consensus         5 ~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~   84 (131)
                      ++|||||||.++++++|+++|++||.+..+.+.......                      ...++.++|||||+|.+.+
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~----------------------~~~~~~~kg~afV~f~~~e   59 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVL----------------------AVQINQDKNFAFLEFRSVD   59 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEE----------------------ECCEETTTTEEEEEESSCT
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceee----------------------ecccCCCceEEEEEeCCHH
Confidence            689999999999999999999999998877655221000                      0235678999999999999


Q ss_pred             hHHHHHHHHhCCcceecCcEEEEEecCCC
Q psy1185          85 SASLAKKRLATGRLKVWGCDIIVDWADPQ  113 (131)
Q Consensus        85 ~a~~a~~~l~~~~~~~~g~~l~v~~a~~~  113 (131)
                      +|.+|+. |+|.  .++|+.|+|+.++.-
T Consensus        60 ~a~~a~~-l~g~--~~~Gr~l~V~r~k~~   85 (90)
T d1u2fa_          60 ETTQAMA-FDGI--IFQGQSLKIRRPHDY   85 (90)
T ss_dssp             TTTTGGG-GSSC--CSSSSCCCCBCTTCC
T ss_pred             HHHHHHh-hCCc--EECCEEEEECCCCCC
Confidence            9999985 9998  889999999876653

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=7.1e-18  Score=106.40  Aligned_cols=77  Identities=16%  Similarity=0.203  Sum_probs=63.7

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      ...+||||||+++|+++|+++|++||+|.++.++++                                 ++||||.|.++
T Consensus        11 ~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~---------------------------------kg~gfV~F~~~   57 (113)
T d1owxa_          11 CLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG---------------------------------AKEGIILFKEK   57 (113)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT---------------------------------CSEEEEEESSC
T ss_pred             CeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC---------------------------------CceEEEEecCc
Confidence            346799999999999999999999999999998853                                 79999999996


Q ss_pred             -HhHHHHHHHHhCCcceecCcEEEEEecCCCCC
Q psy1185          84 -KSASLAKKRLATGRLKVWGCDIIVDWADPQEE  115 (131)
Q Consensus        84 -~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~~  115 (131)
                       ++|..|+..+++.  .+.++.+.|.|+....+
T Consensus        58 ~~~A~~a~~~~~~~--~l~~~~~~v~~~~~~~~   88 (113)
T d1owxa_          58 AKEALGKAKDANNG--NLQLRNKEVTWEVLEGE   88 (113)
T ss_dssp             HHHHHHHHHHTTTS--CBCTTSSSEEEEECCHH
T ss_pred             HHHHHHHHHHhcCC--ceecCceEEEEeeccch
Confidence             6788999999998  55555556666554433

>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=1e-17  Score=105.41  Aligned_cols=80  Identities=18%  Similarity=0.104  Sum_probs=67.9

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      .++|||+|||+++|+++|+++|+.||.+..+.++..                           ..+|.++|+|||+|.+.
T Consensus        18 ~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~---------------------------~~~g~~~G~afVeF~~~   70 (112)
T d1wela1          18 GFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAY---------------------------GPNGKATGEGFVEFRNE   70 (112)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEE---------------------------CTTSSEEEEEEEEBSSS
T ss_pred             CeEEEEecCCCcCcHHHHhhHHhhccccccceeeec---------------------------CcccceeeEEEEEECCH
Confidence            568999999999999999999999998866433311                           24788999999999999


Q ss_pred             HhHHHHHHHHhCCcceecCcEEEEEecCCC
Q psy1185          84 KSASLAKKRLATGRLKVWGCDIIVDWADPQ  113 (131)
Q Consensus        84 ~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~  113 (131)
                      ++|++|+. +++.  .|+|+.|.|..+.++
T Consensus        71 e~a~~al~-~~~~--~i~gR~i~V~~~~~~   97 (112)
T d1wela1          71 ADYKAALC-RHKQ--YMGNRFIQVHPITKK   97 (112)
T ss_dssp             HHHHHHHT-SCSB--CSTTSCBEEEEECHH
T ss_pred             HHHHHHHH-cCCC--cCCCEEEEEEEcChH
Confidence            99999996 8998  899999999987643

>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=99.63  E-value=2.2e-17  Score=102.65  Aligned_cols=75  Identities=19%  Similarity=0.188  Sum_probs=67.5

Q ss_pred             EEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHHh
Q psy1185           6 VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKS   85 (131)
Q Consensus         6 ~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~~   85 (131)
                      .++|++++.++++++|+++|++||+|.+++|+++                            .+++++|+|||+|.+.++
T Consensus        29 ~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~----------------------------~~~~~~G~~fV~f~~~~~   80 (104)
T d1jmta_          29 DVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN----------------------------LGDHLVGNVYVKFRREED   80 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCS----------------------------SSSSSEEEEEEEESCHHH
T ss_pred             hHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecC----------------------------CCCCEeeEEEEEEechhH
Confidence            4566777778889999999999999999998853                            478899999999999999


Q ss_pred             HHHHHHHHhCCcceecCcEEEEEec
Q psy1185          86 ASLAKKRLATGRLKVWGCDIIVDWA  110 (131)
Q Consensus        86 a~~a~~~l~~~~~~~~g~~l~v~~a  110 (131)
                      |.+|++.|+|+  .++|+.|.|+|+
T Consensus        81 A~~Ai~~lng~--~~~gr~i~v~~s  103 (104)
T d1jmta_          81 AEKAVIDLNNR--WFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHTTC--EETTEECCEEEC
T ss_pred             HHHHHHHHCCC--EECCEEEEEEEC
Confidence            99999999999  999999999985

>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=99.62  E-value=1.4e-15  Score=93.88  Aligned_cols=61  Identities=20%  Similarity=0.269  Sum_probs=54.8

Q ss_pred             ceEEEEe--CCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeC
Q psy1185           4 VKVLYVR--NLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYD   81 (131)
Q Consensus         4 ~~~l~v~--nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~   81 (131)
                      .+++||+  |||.++|+++|+++|++||.|..+++++                                 .++||||+|.
T Consensus        18 t~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~---------------------------------~k~~aFV~f~   64 (101)
T d2cq2a1          18 TQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP---------------------------------NKPYSFARYR   64 (101)
T ss_dssp             CSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT---------------------------------TCSCEEEEES
T ss_pred             CceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeecc---------------------------------CccEEEEEEC
Confidence            4678884  5999999999999999999999998763                                 3789999999


Q ss_pred             CHHhHHHHHHHHhCCc
Q psy1185          82 SHKSASLAKKRLATGR   97 (131)
Q Consensus        82 ~~~~a~~a~~~l~~~~   97 (131)
                      +.++|.+|++.|||..
T Consensus        65 ~~e~A~~A~~~lng~~   80 (101)
T d2cq2a1          65 TTEESKRAYVTLNGKE   80 (101)
T ss_dssp             SHHHHHHHHHHTTTCE
T ss_pred             CHHHHHHHHHHhCCCC
Confidence            9999999999999983

>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=99.59  E-value=4.4e-15  Score=91.29  Aligned_cols=79  Identities=14%  Similarity=0.249  Sum_probs=68.3

Q ss_pred             CceEEEEeCC--CCCCC---------HHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCC
Q psy1185           3 KVKVLYVRNL--TQYCT---------EEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKK   71 (131)
Q Consensus         3 ~~~~l~v~nL--p~~~t---------~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~   71 (131)
                      .+++|+|.|+  |.+..         .++|++.|++||.|..+.+..                               +.
T Consensus         7 ~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~-------------------------------~~   55 (99)
T d2dita1           7 HERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFD-------------------------------RH   55 (99)
T ss_dssp             SCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEET-------------------------------TC
T ss_pred             CccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccC-------------------------------CC
Confidence            4789999999  65431         267999999999999998873                               35


Q ss_pred             CcceEEEEeCCHHhHHHHHHHHhCCcceecCcEEEEEecCCCC
Q psy1185          72 NRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQE  114 (131)
Q Consensus        72 ~~~~~fv~f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~~~  114 (131)
                      ++|+|||+|.+.++|.+|+..|||.  .++|+.|+|.|+.++.
T Consensus        56 ~~G~~fV~f~~~e~A~~A~~~lng~--~~~gr~i~v~~~~g~~   96 (99)
T d2dita1          56 PDGVASVSFRDPEEADYCIQTLDGR--WFGGRQITAQAWDGTT   96 (99)
T ss_dssp             TTCEEEEECSCHHHHHHHHHHSTTC--EETTEECEEEECCSCC
T ss_pred             CccEEEEEECCHHHHHHHHHHhCCc--EECCEEEEEEEeCCcC
Confidence            6899999999999999999999998  8999999999988764

>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=99.54  E-value=1.1e-14  Score=86.41  Aligned_cols=73  Identities=18%  Similarity=0.055  Sum_probs=60.8

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCC
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDS   82 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~   82 (131)
                      +.+.|+|+++|++++++.| +.|++||+|.++++.                                 .+++||||+|.+
T Consensus         3 ~~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~---------------------------------~~~~~~fV~f~~   48 (81)
T d1wwha1           3 DDTWVTVFGFPQASASYIL-LQFAQYGNILKHVMS---------------------------------NTGNWMHIRYQS   48 (81)
T ss_dssp             GGGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEEC---------------------------------SSSSEEEEEESS
T ss_pred             cccEEEEECCChHHHHHHH-HHHHhhhhhheEEec---------------------------------CCCCEEEEEEcc
Confidence            3577999999999986655 589999999998764                                 348999999999


Q ss_pred             HHhHHHHHHHHhCCcceecCcE-EEEEecCC
Q psy1185          83 HKSASLAKKRLATGRLKVWGCD-IIVDWADP  112 (131)
Q Consensus        83 ~~~a~~a~~~l~~~~~~~~g~~-l~v~~a~~  112 (131)
                      +++|.+|++ +||.  .++|+. +.|.....
T Consensus        49 ~~~A~~Al~-~nG~--~~~g~~~vgV~~~~~   76 (81)
T d1wwha1          49 KLQARKALS-KDGR--IFGESIMIGVKPCID   76 (81)
T ss_dssp             HHHHHHHHT-TTTC--EETTTEECEEEECCC
T ss_pred             cHHHHHHHh-cCCC--eECCcEEEEEEeCCC
Confidence            999999995 8998  899975 56776543

>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=99.34  E-value=1.2e-12  Score=80.85  Aligned_cols=82  Identities=20%  Similarity=0.285  Sum_probs=66.0

Q ss_pred             ceEEEEeCC--CCCCC--------HHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCc
Q psy1185           4 VKVLYVRNL--TQYCT--------EEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNR   73 (131)
Q Consensus         4 ~~~l~v~nL--p~~~t--------~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~   73 (131)
                      ++.|.+.|+  |....        .++|++.|++||.|.++.+++..                         ........
T Consensus         4 s~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~-------------------------~~~~~~~~   58 (104)
T d1o0pa_           4 TEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPV-------------------------DGVEVPGC   58 (104)
T ss_dssp             CSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCT-------------------------TSSSCTTC
T ss_pred             CcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecC-------------------------CCCccCCc
Confidence            567899999  55543        25689999999999999887420                         01123456


Q ss_pred             ceEEEEeCCHHhHHHHHHHHhCCcceecCcEEEEEecCC
Q psy1185          74 GFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADP  112 (131)
Q Consensus        74 ~~~fv~f~~~~~a~~a~~~l~~~~~~~~g~~l~v~~a~~  112 (131)
                      |++||+|.+.++|.+|+..|+|+  .++||.|.+.|+.+
T Consensus        59 g~vfV~f~~~e~A~~A~~~l~Gr--~f~gR~v~v~f~~~   95 (104)
T d1o0pa_          59 GKIFVEFTSVFDCQKAMQGLTGR--KFANRVVVTKYCDP   95 (104)
T ss_dssp             CEEEEEESCHHHHHHHHHHHSSC--CSSSSCCEEEEECH
T ss_pred             eEEEEEECCHHHHHHHHHHHCCC--EECCeEEEEEEcCH
Confidence            89999999999999999999999  89999999999763

>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=99.25  E-value=1.8e-11  Score=81.63  Aligned_cols=56  Identities=29%  Similarity=0.585  Sum_probs=50.5

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEe--------cCeEEEEECCHHHHHhhcCCc
Q psy1185           3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYAFVHFEDRQEAITVTGLS   58 (131)
Q Consensus         3 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~--------~~~~fv~~~~~~~a~~~~g~~   58 (131)
                      ..++|||+|||+.+++++|+++|+.||.|..+.++        +|||||+|.+.++|.++....
T Consensus        96 ~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~~~  159 (183)
T d1u1qa_          96 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQK  159 (183)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHTSS
T ss_pred             ccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHHhC
Confidence            46799999999999999999999999999999877        579999999999999975433

>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=97.72  E-value=0.00019  Score=42.08  Aligned_cols=66  Identities=14%  Similarity=0.248  Sum_probs=53.5

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCC--CCcceEEEEeC
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNK--KNRGFCFLEYD   81 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~--~~~~~~fv~f~   81 (131)
                      .++|-|+.||+..|++++.+.++..|.+.......|                           +.+.  ..-+-|+|.|.
T Consensus         1 ~tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~G---------------------------k~s~~~~~~SRAYi~F~   53 (91)
T d1uw4a_           1 LSKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSN---------------------------DTSLYPHMYARAYINFK   53 (91)
T ss_dssp             CCEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEES---------------------------CCSSTTCCCEEEEEEES
T ss_pred             CceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCC---------------------------CcCCCCCcceEEEEEeC
Confidence            368999999999999999999998888877666644                           1121  22356999999


Q ss_pred             CHHhHHHHHHHHhCC
Q psy1185          82 SHKSASLAKKRLATG   96 (131)
Q Consensus        82 ~~~~a~~a~~~l~~~   96 (131)
                      +.++...-.+..+|.
T Consensus        54 ~~~~v~~F~~~f~g~   68 (91)
T d1uw4a_          54 NQEDIILFRDRFDGY   68 (91)
T ss_dssp             SSHHHHHHHHHHTTC
T ss_pred             CHHHHHHHHHHcCCc
Confidence            999999999999997

>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=97.53  E-value=0.00058  Score=37.87  Aligned_cols=60  Identities=23%  Similarity=0.227  Sum_probs=49.6

Q ss_pred             HHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHHhHHHHHHHHhCCcce
Q psy1185          20 KLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLK   99 (131)
Q Consensus        20 ~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~~~   99 (131)
                      -|...|.++|.|.++.+.-                              .....-.|-|...+.++|.-|+..||-.  .
T Consensus        12 ~L~~~f~~h~~V~sv~l~~------------------------------~~dg~~~A~V~v~~~q~A~~~v~~LhR~--K   59 (73)
T d2dgxa1          12 LLQEAFARHGKVKSVELSP------------------------------HTDYQLKAVVQMENLQDAIGAVNSLHRY--K   59 (73)
T ss_dssp             HHHHHHHHHSCEEEEEECS------------------------------CCSTTCCEEEEESSHHHHHHHHHHHTTE--E
T ss_pred             HHHHHHHhheeEEEEEEEe------------------------------ccCCcEEEEEEcCCHHHHHHHHHHHHHH--h
Confidence            4567788999999987751                              1223456999999999999999999998  9


Q ss_pred             ecCcEEEEEecC
Q psy1185         100 VWGCDIIVDWAD  111 (131)
Q Consensus       100 ~~g~~l~v~~a~  111 (131)
                      +++++|.|.++.
T Consensus        60 iG~KRI~Vs~~~   71 (73)
T d2dgxa1          60 IGSKKILVSLAT   71 (73)
T ss_dssp             ETTEEEEEEECC
T ss_pred             cCCeEEEEEEec
Confidence            999999999975

>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=96.46  E-value=0.0078  Score=34.82  Aligned_cols=54  Identities=19%  Similarity=0.245  Sum_probs=42.6

Q ss_pred             HHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHHhHHHHHHHHhCCcc
Q psy1185          19 EKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRL   98 (131)
Q Consensus        19 ~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~~~~~   98 (131)
                      .+|.+.|++||+|.-++++                                   .+--.|+|.+-+.|.+|++ +++.  
T Consensus        39 ~~Llq~l~~~GeViLvRFv-----------------------------------~d~mwVTF~dG~SAL~al~-l~g~--   80 (95)
T d1ufwa_          39 TELMQTLGSYGTIVLVRIN-----------------------------------QGQMLVTFADSHSALSVLD-VDGM--   80 (95)
T ss_dssp             HHHHHHHHHHSCCSEEEEE-----------------------------------TTEEEEECSCSHHHHHHHH-GGGS--
T ss_pred             HHHHHHHhhCCeEEEEEEe-----------------------------------CCeEEEEECCcHHHHHHhc-cCCe--
Confidence            4678889999999999888                                   3557788888888887765 4555  


Q ss_pred             eecCcEEEEEec
Q psy1185          99 KVWGCDIIVDWA  110 (131)
Q Consensus        99 ~~~g~~l~v~~a  110 (131)
                      ++.|+.|.|.--
T Consensus        81 ~v~G~~l~It~~   92 (95)
T d1ufwa_          81 KVKGRAVKISGP   92 (95)
T ss_dssp             EETTEEEEEECC
T ss_pred             EEcceEEEEecC
Confidence            889999888753

>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=94.92  E-value=0.01  Score=33.18  Aligned_cols=19  Identities=26%  Similarity=0.450  Sum_probs=16.7

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|+.+.
T Consensus        40 ~~g~afV~f~~~~~a~~Ai   58 (83)
T d1x5ta1          40 SKGYAFINFASFDASDAAI   58 (83)
T ss_dssp             CCSEEEEEBSSHHHHHHHH
T ss_pred             cCceEEEEECCHHHHHHHH
Confidence            3799999999999999943

>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=94.17  E-value=0.026  Score=33.08  Aligned_cols=20  Identities=20%  Similarity=0.385  Sum_probs=17.5

Q ss_pred             ecCeEEEEECCHHHHHhhcC
Q psy1185          37 IKDYAFVHFEDRQEAITVTG   56 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~g   56 (131)
                      .+|||||+|.+.++|+.+..
T Consensus        61 ~kg~aFV~f~~~~~a~~al~   80 (103)
T d1x4ba1          61 SRGFGFVTFSSMAEVDAAMA   80 (103)
T ss_dssp             CCSEEEEECSSHHHHHHHHT
T ss_pred             ccCeEEEEECCHHHHHHHHH
Confidence            38999999999999999654

>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=93.85  E-value=0.18  Score=29.31  Aligned_cols=56  Identities=9%  Similarity=0.137  Sum_probs=43.8

Q ss_pred             ceEEEEeCCCCCCCHHHHHHHhhccCCeeEEEEecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCH
Q psy1185           4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSH   83 (131)
Q Consensus         4 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~   83 (131)
                      ...||.-..|..+...+|.++|++||.|.=--|                                   .-.-|||...+.
T Consensus        15 RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswI-----------------------------------ddTSa~V~L~~~   59 (100)
T d1whva_          15 RDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWI-----------------------------------DDTSAFVSLSQP   59 (100)
T ss_dssp             CCSEEEEECCTTCCHHHHHHHHTTTCSCCCEEE-----------------------------------ETTEEEEECSCH
T ss_pred             cceeEEEeCCcccchhHHHHHhcCCCceEEEEe-----------------------------------cCceEEEEecCH
Confidence            446888899999999999999999997642222                                   134689999999


Q ss_pred             HhHHHHHHHHh
Q psy1185          84 KSASLAKKRLA   94 (131)
Q Consensus        84 ~~a~~a~~~l~   94 (131)
                      ++|..++..+.
T Consensus        60 e~~~~v~~~~~   70 (100)
T d1whva_          60 EQVQIAVNTSK   70 (100)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHhc
Confidence            99888877654

>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=93.62  E-value=0.011  Score=33.69  Aligned_cols=21  Identities=24%  Similarity=0.556  Sum_probs=17.7

Q ss_pred             cCeEEEEECCHHHHHhhcCCc
Q psy1185          38 KDYAFVHFEDRQEAITVTGLS   58 (131)
Q Consensus        38 ~~~~fv~~~~~~~a~~~~g~~   58 (131)
                      +|||||+|.+.++|+.+..+.
T Consensus        48 kg~afV~f~~~e~a~~a~~l~   68 (90)
T d1u2fa_          48 KNFAFLEFRSVDETTQAMAFD   68 (90)
T ss_dssp             TTEEEEEESSCTTTTTGGGGS
T ss_pred             ceEEEEEeCCHHHHHHHHhhC
Confidence            899999999999999855443

>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=93.60  E-value=0.028  Score=31.13  Aligned_cols=19  Identities=26%  Similarity=0.443  Sum_probs=16.9

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.++++|+.+.
T Consensus        43 ~~g~afV~f~~~~~A~~ai   61 (82)
T d1b7fa1          43 SYGYAFVDFTSEMDSQRAI   61 (82)
T ss_dssp             ECSEEEEEESSHHHHHHHH
T ss_pred             ccccceEEECCHHHHHHHH
Confidence            4899999999999999943

>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=93.46  E-value=0.042  Score=30.99  Aligned_cols=24  Identities=33%  Similarity=0.654  Sum_probs=19.4

Q ss_pred             cCeEEEEECCHHHHHhhcC-CceeE
Q psy1185          38 KDYAFVHFEDRQEAITVTG-LSQVI   61 (131)
Q Consensus        38 ~~~~fv~~~~~~~a~~~~g-~~~~~   61 (131)
                      +|||||+|.+.++|+.+.. +.+..
T Consensus        48 kg~afV~f~~~~~A~~Ai~~l~g~~   72 (89)
T d1cvja2          48 KGYGFVHFETQEAAERAIEKMNGML   72 (89)
T ss_dssp             CSCEEEEESCHHHHHHHTTSSSEEE
T ss_pred             cceeEEEECCHHHHHHHHHHcCCCE
Confidence            7999999999999999664 44433

>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=93.39  E-value=0.03  Score=31.46  Aligned_cols=23  Identities=22%  Similarity=0.326  Sum_probs=18.9

Q ss_pred             ecCeEEEEECCHHHHHhhcCCce
Q psy1185          37 IKDYAFVHFEDRQEAITVTGLSQ   59 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~g~~~   59 (131)
                      .+|||||+|.+.++|+.+..+.+
T Consensus        47 ~kg~afV~f~~~~~a~~Al~~n~   69 (86)
T d2ghpa3          47 NNCCAFMVFENKDSAERALQMNR   69 (86)
T ss_dssp             CCEEEEEEESSHHHHHHHGGGTT
T ss_pred             cceeeeEEECCHHHHHHHHhcCC
Confidence            48999999999999999655443

>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=93.28  E-value=0.032  Score=31.31  Aligned_cols=22  Identities=23%  Similarity=0.282  Sum_probs=18.7

Q ss_pred             ecCeEEEEECCHHHHHhhcCCc
Q psy1185          37 IKDYAFVHFEDRQEAITVTGLS   58 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~g~~   58 (131)
                      .+|||||+|.++++|+.+....
T Consensus        46 ~kG~afV~f~~~e~a~~al~~~   67 (85)
T d1zh5a2          46 FKGSIFVVFDSIESAKKFVETP   67 (85)
T ss_dssp             EEEEEEEEESCHHHHHHHHTCC
T ss_pred             cceEEEEEEcCHHHHHHHHHHC
Confidence            4799999999999999976543

>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=93.08  E-value=0.026  Score=31.58  Aligned_cols=19  Identities=16%  Similarity=0.387  Sum_probs=16.7

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|+.+.
T Consensus        42 ~kG~afV~f~~~~~A~~A~   60 (85)
T d2cpfa1          42 SMGFGFVEYKKPEQAQKAL   60 (85)
T ss_dssp             EEEEEEEEESSHHHHHHHH
T ss_pred             cceEEEEEECCHHHHHHHH
Confidence            4799999999999999843

>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=93.04  E-value=0.044  Score=30.86  Aligned_cols=22  Identities=41%  Similarity=0.676  Sum_probs=18.5

Q ss_pred             EEecCeEEEEECCHHHHHhhcC
Q psy1185          35 KRIKDYAFVHFEDRQEAITVTG   56 (131)
Q Consensus        35 ~i~~~~~fv~~~~~~~a~~~~g   56 (131)
                      .-.++||||+|.+.++|+.+..
T Consensus        39 ~~~~gfafV~f~~~~~a~~a~~   60 (88)
T d1wf0a_          39 KPFRAFAFVTFADDQIAQSLCG   60 (88)
T ss_dssp             SSCCSCCEEECSCHHHHHHTTT
T ss_pred             eccCceEEEEECCHHHHHHHHh
Confidence            3468999999999999999654

>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=92.84  E-value=0.037  Score=30.26  Aligned_cols=20  Identities=20%  Similarity=0.451  Sum_probs=17.4

Q ss_pred             ecCeEEEEECCHHHHHhhcC
Q psy1185          37 IKDYAFVHFEDRQEAITVTG   56 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~g   56 (131)
                      .+|||||+|.+.++|+.+..
T Consensus        40 ~kg~afV~f~~~~~a~~Al~   59 (75)
T d1hd0a_          40 SRGFGFVLFKESESVDKVMD   59 (75)
T ss_dssp             CCSEEEEEESSHHHHHHHHH
T ss_pred             cCceEEEEECCHHHHHHHHh
Confidence            37999999999999999644

>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=92.84  E-value=0.039  Score=31.16  Aligned_cols=18  Identities=33%  Similarity=0.586  Sum_probs=16.3

Q ss_pred             ecCeEEEEECCHHHHHhh
Q psy1185          37 IKDYAFVHFEDRQEAITV   54 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~   54 (131)
                      .+|||||+|.+.++|+.+
T Consensus        46 ~kg~afV~f~~~~~A~~a   63 (89)
T d2cqba1          46 HRGFAFVEFELAEDAAAA   63 (89)
T ss_dssp             CSSEEEECCSSHHHHHHH
T ss_pred             ccceeEEEECCHHHHHHH
Confidence            489999999999999994

>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=92.81  E-value=0.036  Score=31.73  Aligned_cols=19  Identities=26%  Similarity=0.487  Sum_probs=16.7

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|..+.
T Consensus        50 ~rg~afV~f~~~~~A~~Ai   68 (94)
T d2cpha1          50 HRGFGFVDFITKQDAKKAF   68 (94)
T ss_dssp             SCSEEEEEESSHHHHHHHH
T ss_pred             cccEEEEEECCHHHHHHHH
Confidence            3899999999999999843

>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=92.81  E-value=0.029  Score=31.96  Aligned_cols=19  Identities=26%  Similarity=0.585  Sum_probs=16.8

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|+.+.
T Consensus        49 srG~aFV~f~~~~~a~~al   67 (90)
T d2cqga1          49 SKGFGFVRFTEYETQVKVM   67 (90)
T ss_dssp             EEEEEEEEESSHHHHHHHH
T ss_pred             cCCEEEEEECCHHHHHHHH
Confidence            3899999999999999854

>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=92.68  E-value=0.035  Score=32.22  Aligned_cols=20  Identities=20%  Similarity=0.564  Sum_probs=16.8

Q ss_pred             ecCeEEEEECCHHHHHhhcC
Q psy1185          37 IKDYAFVHFEDRQEAITVTG   56 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~g   56 (131)
                      .+|||||+|.+.++|+.+..
T Consensus        56 ~~g~afV~f~~~e~a~~~~~   75 (104)
T d1wi8a_          56 LKGFGYAEFEDLDSLLSALS   75 (104)
T ss_dssp             BCSCEEEEESSHHHHHHHHG
T ss_pred             cceeeeEEECCHHHHHHHHH
Confidence            37899999999999988543

>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=92.68  E-value=0.032  Score=30.65  Aligned_cols=23  Identities=22%  Similarity=0.381  Sum_probs=18.5

Q ss_pred             ecCeEEEEECCHHHHHhhcCCce
Q psy1185          37 IKDYAFVHFEDRQEAITVTGLSQ   59 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~g~~~   59 (131)
                      .+|||||+|.++++|..+....+
T Consensus        43 ~~g~afV~f~~~e~~~~al~~~~   65 (79)
T d1l3ka2          43 KRGFAFVTFDDHDSVDKIVIQKY   65 (79)
T ss_dssp             EEEEEEEEESSHHHHHHHHHCSC
T ss_pred             cccEEEEEEcCHHHHHHHHHhCC
Confidence            37899999999999998655443

>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=92.52  E-value=0.03  Score=30.80  Aligned_cols=20  Identities=10%  Similarity=0.469  Sum_probs=17.7

Q ss_pred             ecCeEEEEECCHHHHHhhcC
Q psy1185          37 IKDYAFVHFEDRQEAITVTG   56 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~g   56 (131)
                      .+|||||+|.+.++|+++..
T Consensus        40 ~rG~~FV~f~~~~~a~~al~   59 (75)
T d1x0fa1          40 RRGFCFITFKEEEPVKKIME   59 (75)
T ss_dssp             TTCCEEEEESSSHHHHHHTT
T ss_pred             cccEEEEEECCHHHHHHHHh
Confidence            38999999999999999764

>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=92.51  E-value=0.043  Score=31.80  Aligned_cols=43  Identities=14%  Similarity=0.107  Sum_probs=29.2

Q ss_pred             ecCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHHhHHH
Q psy1185          37 IKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASL   88 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~   88 (131)
                      .+|||||+|.+.++|+.+..+.+..+.         .....|...+......
T Consensus        49 ~~G~afV~F~s~~~a~~Al~~n~~~i~---------gr~i~V~~~~~~~~~~   91 (103)
T d2cpya1          49 GLGQALVQFKNEDDARKSERLHRKKLN---------GREAFVHVVTLEDMRE   91 (103)
T ss_dssp             CSSCEEEECSSHHHHHHHGGGCSEEET---------TEEEEEEEECHHHHHH
T ss_pred             cCccEEEEECCHHHHHHHHhcCCCeEC---------CcEEEEEECCHHHhhh
Confidence            389999999999999998776554321         1245556666555443

>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=92.49  E-value=0.034  Score=31.16  Aligned_cols=20  Identities=15%  Similarity=0.366  Sum_probs=17.4

Q ss_pred             ecCeEEEEECCHHHHHhhcC
Q psy1185          37 IKDYAFVHFEDRQEAITVTG   56 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~g   56 (131)
                      .+|||||+|.+.++|+.+..
T Consensus        47 ~kG~afV~f~~~~~a~~ai~   66 (84)
T d1l3ka1          47 SRGFGFVTYATVEEVDAAMN   66 (84)
T ss_dssp             EEEEEEEEESSHHHHHHHHH
T ss_pred             cccEEEEEEcCHHHHHHHHH
Confidence            48999999999999999554

>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=92.47  E-value=0.041  Score=31.47  Aligned_cols=18  Identities=28%  Similarity=0.617  Sum_probs=16.3

Q ss_pred             cCeEEEEECCHHHHHhhc
Q psy1185          38 KDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        38 ~~~~fv~~~~~~~a~~~~   55 (131)
                      +|||||+|.++++|..+.
T Consensus        45 rg~aFV~F~~~~~A~~Ai   62 (96)
T d2disa1          45 RGFAFVEYESHRAAAMAR   62 (96)
T ss_dssp             CCEEEEEESSHHHHHHHH
T ss_pred             CCeEEEEEcCHHHHHHHH
Confidence            799999999999999853

>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=92.40  E-value=0.026  Score=32.89  Aligned_cols=23  Identities=30%  Similarity=0.380  Sum_probs=18.9

Q ss_pred             ecCeEEEEECCHHHHHhhcCCce
Q psy1185          37 IKDYAFVHFEDRQEAITVTGLSQ   59 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~g~~~   59 (131)
                      .+|||||+|.+.++|..+..+.+
T Consensus        59 ~kG~afV~F~~~e~a~~A~~l~g   81 (101)
T d2cq4a1          59 SKGIAYVEFCEIQSVPLAIGLTG   81 (101)
T ss_dssp             CCCCEEEEESCGGGHHHHHHHTT
T ss_pred             ccceEEEEECCHHHHHHHHHHCC
Confidence            48999999999999999655444

>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=92.23  E-value=0.079  Score=30.16  Aligned_cols=17  Identities=41%  Similarity=0.694  Sum_probs=15.6

Q ss_pred             cCeEEEEECCHHHHHhh
Q psy1185          38 KDYAFVHFEDRQEAITV   54 (131)
Q Consensus        38 ~~~~fv~~~~~~~a~~~   54 (131)
                      ++||||+|.+.++|+.+
T Consensus        53 ~g~afV~f~~~e~a~~A   69 (95)
T d1x4aa1          53 PPFAFVEFEDPRDAEDA   69 (95)
T ss_dssp             SCCEEEEESCHHHHHHH
T ss_pred             cceEEEEECCHHHHHHH
Confidence            78999999999999983

>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=92.13  E-value=0.051  Score=29.21  Aligned_cols=19  Identities=32%  Similarity=0.553  Sum_probs=16.5

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|+.+.
T Consensus        39 ~~g~afV~f~~~~~A~~Ai   57 (72)
T d1x4ea1          39 CKGYGFVDFDSPSAAQKAV   57 (72)
T ss_dssp             CCSEEEEEESCHHHHHHHH
T ss_pred             ccceeEEEECCHHHHHHHH
Confidence            4799999999999998843

>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=91.88  E-value=0.045  Score=30.54  Aligned_cols=19  Identities=32%  Similarity=0.508  Sum_probs=16.8

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|..+.
T Consensus        47 ~~g~afV~f~~~~~A~~Ai   65 (85)
T d1b7fa2          47 PRGVAFVRYNKREEAQEAI   65 (85)
T ss_dssp             EEEEEEEEESSHHHHHHHH
T ss_pred             CceeEEEEECCHHHHHHHH
Confidence            4799999999999999954

>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=91.70  E-value=0.092  Score=29.99  Aligned_cols=17  Identities=35%  Similarity=0.337  Sum_probs=15.5

Q ss_pred             cCeEEEEECCHHHHHhh
Q psy1185          38 KDYAFVHFEDRQEAITV   54 (131)
Q Consensus        38 ~~~~fv~~~~~~~a~~~   54 (131)
                      ++||||+|.+.++|..+
T Consensus        58 ~g~afV~f~~~~~a~~A   74 (101)
T d2cpea1          58 KGDATVSYEDPPTAKAA   74 (101)
T ss_dssp             CSEEEEEBSSHHHHHHH
T ss_pred             cceeeEEecCHHHHHHH
Confidence            68999999999999983

>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=91.66  E-value=0.061  Score=30.52  Aligned_cols=19  Identities=16%  Similarity=0.471  Sum_probs=16.9

Q ss_pred             cCeEEEEECCHHHHHhhcC
Q psy1185          38 KDYAFVHFEDRQEAITVTG   56 (131)
Q Consensus        38 ~~~~fv~~~~~~~a~~~~g   56 (131)
                      +|||||+|.+.++|+.+..
T Consensus        54 kg~afv~F~~~e~a~~Al~   72 (91)
T d1fjeb1          54 RKFGYVDFESAEDLEKALE   72 (91)
T ss_dssp             TTEEEEEESSHHHHHHHHH
T ss_pred             cEEeEEeeCCHHHHHHHHh
Confidence            8999999999999999543

>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=91.66  E-value=0.061  Score=29.52  Aligned_cols=19  Identities=32%  Similarity=0.385  Sum_probs=16.6

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|+.+.
T Consensus        40 ~~g~afV~f~~~~~A~~Ai   58 (78)
T d1no8a_          40 SLGTADVHFERKADALKAM   58 (78)
T ss_dssp             SCCEEEEEESCHHHHHHHH
T ss_pred             cceeEEEEECCHHHHHHHH
Confidence            3789999999999998854

>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=91.62  E-value=0.1  Score=29.28  Aligned_cols=17  Identities=29%  Similarity=0.647  Sum_probs=15.8

Q ss_pred             cCeEEEEECCHHHHHhh
Q psy1185          38 KDYAFVHFEDRQEAITV   54 (131)
Q Consensus        38 ~~~~fv~~~~~~~a~~~   54 (131)
                      ++||||+|.+.++|+.+
T Consensus        48 ~~~afV~f~~~~~A~~A   64 (90)
T d2cqia1          48 DPYCFVEFYEHRDAAAA   64 (90)
T ss_dssp             CCEEEEEESSHHHHHHH
T ss_pred             ceeeEEEECCHHHHHHH
Confidence            78999999999999994

>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=91.50  E-value=0.076  Score=28.93  Aligned_cols=23  Identities=13%  Similarity=0.180  Sum_probs=18.9

Q ss_pred             cCeEEEEECCHHHHHhhcCCcee
Q psy1185          38 KDYAFVHFEDRQEAITVTGLSQV   60 (131)
Q Consensus        38 ~~~~fv~~~~~~~a~~~~g~~~~   60 (131)
                      ++||||+|.++++|.++....+.
T Consensus        40 ~~~afV~F~~~~~a~~Al~~~~~   62 (75)
T d2ghpa2          40 FRFARIEFARYDGALAAITKTHK   62 (75)
T ss_dssp             SEEEEEEESSHHHHHHHHTTTTC
T ss_pred             ceEEEEEEcchHHhHHHHHhcCc
Confidence            57999999999999997655443

>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=91.46  E-value=0.055  Score=29.80  Aligned_cols=19  Identities=11%  Similarity=0.394  Sum_probs=16.4

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|+.+.
T Consensus        42 ~~g~afV~f~~~e~A~~Ai   60 (81)
T d2ghpa1          42 SRRFAYIDVTSKEDARYCV   60 (81)
T ss_dssp             -CCEEEEECSSHHHHHHHH
T ss_pred             ccceeEEEECCHHHHHHHH
Confidence            4899999999999999943

>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=91.42  E-value=0.064  Score=30.49  Aligned_cols=18  Identities=28%  Similarity=0.381  Sum_probs=16.2

Q ss_pred             ecCeEEEEECCHHHHHhh
Q psy1185          37 IKDYAFVHFEDRQEAITV   54 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~   54 (131)
                      .+|||||+|.+.++|..+
T Consensus        49 ~~g~afV~F~~~~~a~~a   66 (98)
T d1x4ha1          49 SKGCAFAQFMTQEAAQKC   66 (98)
T ss_dssp             BCSEEEEEESSHHHHHHH
T ss_pred             ccceEEEEEcCHHHHHHH
Confidence            379999999999999984

>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=91.38  E-value=0.056  Score=29.80  Aligned_cols=24  Identities=21%  Similarity=0.333  Sum_probs=19.0

Q ss_pred             ecCeEEEEECCHHHHHhhcC-Ccee
Q psy1185          37 IKDYAFVHFEDRQEAITVTG-LSQV   60 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~g-~~~~   60 (131)
                      .+|||||+|.++++|..+.. +.+.
T Consensus        41 ~~g~aFV~f~~~~~a~~ai~~l~g~   65 (80)
T d1cvja1          41 SLGYAYVNFQQPADAERALDTMNFD   65 (80)
T ss_dssp             EEEEEEEEESSHHHHHHHHTTSTTC
T ss_pred             CCCceEEEECCHHHHHHHHHHcCCC
Confidence            37999999999999999653 4443

>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=91.36  E-value=0.18  Score=29.55  Aligned_cols=47  Identities=11%  Similarity=0.051  Sum_probs=32.3

Q ss_pred             cCeEEEEECCHHHHHhhcCCceeEEecCCCCCCCCcceEEEEeCCHHhHHHHHHHH
Q psy1185          38 KDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRL   93 (131)
Q Consensus        38 ~~~~fv~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l   93 (131)
                      +|||||+|.+.++|+.++.+.+..+.         ..+..|...+......++...
T Consensus        60 ~G~afVeF~~~e~a~~al~~~~~~i~---------gR~i~V~~~~~~~~~~~~~~~  106 (112)
T d1wela1          60 TGEGFVEFRNEADYKAALCRHKQYMG---------NRFIQVHPITKKGMLEKIDMI  106 (112)
T ss_dssp             EEEEEEEBSSSHHHHHHHTSCSBCST---------TSCBEEEEECHHHHHHHHHHH
T ss_pred             eeEEEEEECCHHHHHHHHHcCCCcCC---------CEEEEEEEcChHHHHHHHHHH
Confidence            79999999999999998776654321         223455666766666555543

>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=91.32  E-value=0.057  Score=29.74  Aligned_cols=19  Identities=26%  Similarity=0.454  Sum_probs=16.7

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.++++|+.+.
T Consensus        43 ~~g~afv~f~~~~~a~~a~   61 (82)
T d1fxla1          43 SLGYGFVNYIDPKDAEKAI   61 (82)
T ss_dssp             EEEEEEEEESSHHHHHHHH
T ss_pred             ceeeEEEEECCHHHHHHHH
Confidence            4789999999999999943

>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=91.21  E-value=0.033  Score=30.70  Aligned_cols=20  Identities=25%  Similarity=0.433  Sum_probs=17.3

Q ss_pred             ecCeEEEEECCHHHHHhhcC
Q psy1185          37 IKDYAFVHFEDRQEAITVTG   56 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~g   56 (131)
                      .+|||||+|.+.++|..+..
T Consensus        41 ~kG~aFV~f~~~~~a~~al~   60 (77)
T d1uawa_          41 SRGFGFVTFMDQAGVDKVLA   60 (77)
T ss_dssp             CSSEEEECCCCTTHHHHHHH
T ss_pred             ccceEEEEECCHHHHHHHHH
Confidence            38999999999999999653

>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=91.16  E-value=0.057  Score=30.19  Aligned_cols=18  Identities=28%  Similarity=0.399  Sum_probs=16.4

Q ss_pred             cCeEEEEECCHHHHHhhc
Q psy1185          38 KDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        38 ~~~~fv~~~~~~~a~~~~   55 (131)
                      +|||||+|.++++|+.+.
T Consensus        43 rg~aFV~f~~~~~A~~a~   60 (85)
T d2u2fa_          43 KGYAFCEYVDINVTDQAI   60 (85)
T ss_dssp             CCEEEEEESSSHHHHHHH
T ss_pred             ceeEEEEECCHHHHHHHH
Confidence            899999999999999943

>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=91.13  E-value=0.065  Score=30.47  Aligned_cols=19  Identities=26%  Similarity=0.426  Sum_probs=16.8

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|+.+.
T Consensus        50 ~kg~afV~f~~~~~A~~Ai   68 (93)
T d1x5ua1          50 HQGYGFVEFLSEEDADYAI   68 (93)
T ss_dssp             BCSCEEEEESSHHHHHHHH
T ss_pred             cccceEEEECCHHHHHHHH
Confidence            4799999999999999953

>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=91.12  E-value=0.06  Score=30.27  Aligned_cols=19  Identities=32%  Similarity=0.632  Sum_probs=16.7

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|+.+.
T Consensus        48 ~~g~afV~f~~~~~A~~A~   66 (88)
T d1rk8a_          48 SKGYALVEYETHKQALAAK   66 (88)
T ss_dssp             EEEEEEEEESSHHHHHHHH
T ss_pred             cccceeEEECCHHHHHHHH
Confidence            3799999999999999954

>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=91.09  E-value=0.06  Score=30.36  Aligned_cols=19  Identities=32%  Similarity=0.632  Sum_probs=16.6

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|+.+.
T Consensus        49 ~rg~afV~f~~~~~A~~Ai   67 (90)
T d2cq0a1          49 SKGFAFISFHRREDAARAI   67 (90)
T ss_dssp             EEEEEEEEESSHHHHHHHH
T ss_pred             cccceeEEECCHHHHHHHH
Confidence            3789999999999999943

>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=91.03  E-value=0.055  Score=31.42  Aligned_cols=21  Identities=24%  Similarity=0.210  Sum_probs=17.9

Q ss_pred             ecCeEEEEECCHHHHHhhcCC
Q psy1185          37 IKDYAFVHFEDRQEAITVTGL   57 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~g~   57 (131)
                      .+|||||+|.++++|+++..+
T Consensus        56 ~kG~afV~F~~~e~a~~a~~~   76 (104)
T d1wg5a_          56 STGEAFVQFASQEIAEKALKK   76 (104)
T ss_dssp             BCSEEEEEESSHHHHHHHHTT
T ss_pred             cceEEEEEeCCHHHHHHHHhh
Confidence            479999999999999995543

>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=90.92  E-value=0.033  Score=32.37  Aligned_cols=21  Identities=19%  Similarity=0.292  Sum_probs=17.8

Q ss_pred             ecCeEEEEECCHHHHHhhcCC
Q psy1185          37 IKDYAFVHFEDRQEAITVTGL   57 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~g~   57 (131)
                      .+|||||+|.+.++|+.+...
T Consensus        54 ~~G~afVeF~~~~~a~~Al~~   74 (102)
T d1weza_          54 VTGEADVEFATHEDAVAAMAK   74 (102)
T ss_dssp             EEEEEEEECSSSHHHHHHHTT
T ss_pred             ceEEEEEEECCHHHHHHHHHc
Confidence            379999999999999996543

>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=90.92  E-value=0.061  Score=31.42  Aligned_cols=17  Identities=18%  Similarity=0.210  Sum_probs=15.9

Q ss_pred             cCeEEEEECCHHHHHhh
Q psy1185          38 KDYAFVHFEDRQEAITV   54 (131)
Q Consensus        38 ~~~~fv~~~~~~~a~~~   54 (131)
                      +|||||+|.+.++|+.+
T Consensus        45 ~g~aFV~f~~~e~A~~A   61 (108)
T d2adba1          45 QFQALLQYADPVSAQHA   61 (108)
T ss_dssp             EEEEEEEESCHHHHHHH
T ss_pred             CCeEEEEECCHHHHHHH
Confidence            78999999999999994

>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=90.72  E-value=0.082  Score=30.62  Aligned_cols=20  Identities=30%  Similarity=0.471  Sum_probs=17.4

Q ss_pred             ecCeEEEEECCHHHHHhhcC
Q psy1185          37 IKDYAFVHFEDRQEAITVTG   56 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~g   56 (131)
                      .+|||||+|.+.++|+.+..
T Consensus        51 ~kg~afV~f~~~~~A~~Ai~   70 (103)
T d2cqda1          51 SRGYGFVTMADRAAAERACK   70 (103)
T ss_dssp             CCSEEEEEESSHHHHHHHHT
T ss_pred             cCCeEEEEECCHHHHHHHHH
Confidence            48999999999999999543

>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=90.54  E-value=0.075  Score=29.84  Aligned_cols=17  Identities=29%  Similarity=0.645  Sum_probs=15.8

Q ss_pred             cCeEEEEECCHHHHHhh
Q psy1185          38 KDYAFVHFEDRQEAITV   54 (131)
Q Consensus        38 ~~~~fv~~~~~~~a~~~   54 (131)
                      +|||||.|.++++|+.+
T Consensus        47 ~g~afV~f~~~~~a~~A   63 (90)
T d1x5sa1          47 RGFGFVTFENIDDAKDA   63 (90)
T ss_dssp             CSEEEEECSSHHHHHHH
T ss_pred             cceEEEEECCHHHHHHH
Confidence            89999999999999993

>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=90.37  E-value=0.078  Score=29.56  Aligned_cols=19  Identities=26%  Similarity=0.471  Sum_probs=16.8

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|+.+.
T Consensus        47 ~kg~afV~f~~~~~a~~Ai   65 (85)
T d1fxla2          47 SRGVGFIRFDKRIEAEEAI   65 (85)
T ss_dssp             EEEEEEEEESSHHHHHHHH
T ss_pred             CCCeeEEEEcCHHHHHHHH
Confidence            4789999999999999954

>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=90.35  E-value=0.079  Score=29.29  Aligned_cols=19  Identities=32%  Similarity=0.553  Sum_probs=16.6

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|+.+.
T Consensus        50 ~~g~afV~f~~~~~A~~Ai   68 (83)
T d2cqca1          50 SRGFAFVYFENVDDAKEAK   68 (83)
T ss_dssp             EEEEEEEEESSHHHHHHHH
T ss_pred             cccceEEEECCHHHHHHHH
Confidence            3789999999999999854

>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=90.33  E-value=0.089  Score=30.84  Aligned_cols=18  Identities=28%  Similarity=0.396  Sum_probs=16.3

Q ss_pred             cCeEEEEECCHHHHHhhc
Q psy1185          38 KDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        38 ~~~~fv~~~~~~~a~~~~   55 (131)
                      +|||||+|.+.++|..+.
T Consensus        46 kG~afV~f~~~~~A~~Ai   63 (114)
T d2f9da1          46 RGTAYVVYEDIFDAKNAC   63 (114)
T ss_dssp             TTEEEEEESSHHHHHHHH
T ss_pred             CCeEEEEECCHHHHHHHH
Confidence            799999999999999953

>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=90.33  E-value=0.093  Score=30.03  Aligned_cols=18  Identities=33%  Similarity=0.477  Sum_probs=16.1

Q ss_pred             ecCeEEEEECCHHHHHhh
Q psy1185          37 IKDYAFVHFEDRQEAITV   54 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~   54 (131)
                      .+|||||+|.+.++|+.+
T Consensus        49 ~~g~afV~f~~~~~a~~A   66 (99)
T d1whwa_          49 PKGFAFVTFMFPEHAVKA   66 (99)
T ss_dssp             CCSEEEEEESSHHHHHHH
T ss_pred             cCcceEEEECCHHHHHHH
Confidence            489999999999999883

>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=90.24  E-value=0.083  Score=30.64  Aligned_cols=34  Identities=24%  Similarity=0.268  Sum_probs=22.4

Q ss_pred             HHHHhhccCCeeEEEEecCeEEEEECCHHHHHhh
Q psy1185          21 LKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITV   54 (131)
Q Consensus        21 l~~~F~~~G~v~~~~i~~~~~fv~~~~~~~a~~~   54 (131)
                      +..-|+..-.+.=+.-.+|||||+|.+.++|..+
T Consensus        23 ~F~~fG~I~~v~i~~~~kg~afV~f~~~~~A~~a   56 (109)
T d2adca1          23 LFGVYGDVQRVKILFNKKENALVQMADGNQAQLA   56 (109)
T ss_dssp             HHHHHTCEEEEEECCTTSCCEEEEESCHHHHHHH
T ss_pred             HHhhccccceEEEEecccceEEEEECCHHHHHHH
Confidence            3344444433332323489999999999999983

>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=90.21  E-value=0.088  Score=29.42  Aligned_cols=18  Identities=17%  Similarity=0.383  Sum_probs=16.3

Q ss_pred             cCeEEEEECCHHHHHhhc
Q psy1185          38 KDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        38 ~~~~fv~~~~~~~a~~~~   55 (131)
                      ++||||+|.+.++|..+.
T Consensus        48 ~~~afV~f~~~~~A~~A~   65 (88)
T d2adca2          48 RKMALIQMGSVEEAVQAL   65 (88)
T ss_dssp             TTCEEEEESSHHHHHHHH
T ss_pred             cceeEEEECCHHHHHHHH
Confidence            789999999999999954

>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=90.18  E-value=0.13  Score=31.26  Aligned_cols=35  Identities=26%  Similarity=0.395  Sum_probs=23.9

Q ss_pred             HHHHHhhccCCeeEEE-----EecCeEEEEECCHHHHHhh
Q psy1185          20 KLKEAFEQYGRVERVK-----RIKDYAFVHFEDRQEAITV   54 (131)
Q Consensus        20 ~l~~~F~~~G~v~~~~-----i~~~~~fv~~~~~~~a~~~   54 (131)
                      ++.+-|+..-.|.=++     ..+|||||+|.+.++|+.+
T Consensus        61 ~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~A  100 (139)
T d1u6fa1          61 QLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQA  100 (139)
T ss_dssp             HHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHH
T ss_pred             HHHHhhccccccccccccccccccceeeEEECCHHHHHHH
Confidence            3444555554444333     2489999999999999994

>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=90.08  E-value=0.094  Score=29.01  Aligned_cols=19  Identities=26%  Similarity=0.385  Sum_probs=16.8

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|..+.
T Consensus        44 ~~g~afV~f~~~~~A~~A~   62 (83)
T d2b0ga1          44 RHDIAFVEFTTELQSNAAK   62 (83)
T ss_dssp             TCSCEEEEESSHHHHHHHH
T ss_pred             cceeEEEecCCHHHHHHHH
Confidence            4799999999999999954

>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=90.06  E-value=0.084  Score=29.97  Aligned_cols=19  Identities=21%  Similarity=0.399  Sum_probs=16.6

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|..+.
T Consensus        48 ~kg~afV~f~~~~~A~~Ai   66 (93)
T d1h2vz_          48 ACGFCFVEYYSRADAENAM   66 (93)
T ss_dssp             EEEEEEEEESSHHHHHHHH
T ss_pred             ccceEEEEECCHHHHHHHH
Confidence            3789999999999999944

>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=90.01  E-value=0.093  Score=29.59  Aligned_cols=18  Identities=28%  Similarity=0.410  Sum_probs=16.3

Q ss_pred             cCeEEEEECCHHHHHhhc
Q psy1185          38 KDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        38 ~~~~fv~~~~~~~a~~~~   55 (131)
                      +|||||.|.+.++|..+.
T Consensus        46 ~g~afV~F~~~~~A~~A~   63 (91)
T d1nu4a_          46 RGQAFVIFKEVSSATNAL   63 (91)
T ss_dssp             TTCEEEEESSHHHHHHHH
T ss_pred             CCceEEEECCHHHHHHHH
Confidence            789999999999999954

>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=89.91  E-value=0.093  Score=29.54  Aligned_cols=18  Identities=17%  Similarity=0.359  Sum_probs=15.9

Q ss_pred             cCeEEEEECCHHHHHhhc
Q psy1185          38 KDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        38 ~~~~fv~~~~~~~a~~~~   55 (131)
                      ++||||+|.+.++|..+.
T Consensus        56 ~g~aFV~f~~~~~A~~Ai   73 (89)
T d2cpia1          56 SASAYVTYIRSEDALRAI   73 (89)
T ss_dssp             CEEEEEEESSHHHHHHHH
T ss_pred             ceEEEEecccchhHHHHH
Confidence            589999999999999843

>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=89.90  E-value=0.11  Score=29.48  Aligned_cols=19  Identities=32%  Similarity=0.538  Sum_probs=16.6

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||.|.+.++|+.+.
T Consensus        50 ~kg~afV~f~~~~~a~~Ai   68 (93)
T d2cq3a1          50 SKGFGFVTFENSADADRAR   68 (93)
T ss_dssp             TCCEEEEEESCHHHHHHHH
T ss_pred             CcceeEEEECCHHHHHHHH
Confidence            3799999999999999943

>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=89.77  E-value=0.074  Score=30.74  Aligned_cols=19  Identities=26%  Similarity=0.653  Sum_probs=16.8

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|+.+.
T Consensus        49 ~~g~afV~f~~~~~a~~ai   67 (104)
T d1p1ta_          49 PKGYGFCEYQDQETALSAM   67 (104)
T ss_dssp             EEEEEEEECSCHHHHHHHH
T ss_pred             cCCceEEEECCHHHHHHHH
Confidence            3799999999999999954

>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=89.76  E-value=0.076  Score=30.72  Aligned_cols=33  Identities=15%  Similarity=0.177  Sum_probs=22.3

Q ss_pred             HHHhhccCCeeEEEE-----ecCeEEEEECCHHHHHhh
Q psy1185          22 KEAFEQYGRVERVKR-----IKDYAFVHFEDRQEAITV   54 (131)
Q Consensus        22 ~~~F~~~G~v~~~~i-----~~~~~fv~~~~~~~a~~~   54 (131)
                      ..-|...-.+.-+.-     .+|||||+|.+.++|+.+
T Consensus        39 F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~A   76 (102)
T d2cpza1          39 FMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAA   76 (102)
T ss_dssp             HGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHH
T ss_pred             HHhhccccccceeeecccCCCccceEEEeCCHHHHHHH
Confidence            334444444444432     378999999999999994

>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=88.97  E-value=0.11  Score=28.74  Aligned_cols=19  Identities=37%  Similarity=0.428  Sum_probs=16.7

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|+|||.|.+.++|+.+.
T Consensus        50 ~~G~afV~f~~~e~a~~Ai   68 (86)
T d2cqpa1          50 PTGEAMVAFESRDEATAAV   68 (86)
T ss_dssp             EEEEEEEEESCHHHHHHHH
T ss_pred             cceEEEEEEcCcHHHHHHH
Confidence            3799999999999999853

>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=88.79  E-value=0.12  Score=27.66  Aligned_cols=23  Identities=22%  Similarity=0.372  Sum_probs=18.5

Q ss_pred             ecCeEEEEECCHHHHHhhcCCce
Q psy1185          37 IKDYAFVHFEDRQEAITVTGLSQ   59 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~g~~~   59 (131)
                      .++||||+|.+.++|+.+..+.+
T Consensus        40 ~~~~afV~F~~~~~a~~al~~~~   62 (75)
T d2msta_          40 HRGFGFVTFESEDIVEKVCEIHF   62 (75)
T ss_dssp             SCCEEEEECSCHHHHHHHHHCSS
T ss_pred             cCceeEEEECCHHHHHHHHhcCC
Confidence            37899999999999998654443

>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=88.43  E-value=0.13  Score=29.60  Aligned_cols=18  Identities=17%  Similarity=0.362  Sum_probs=16.2

Q ss_pred             cCeEEEEECCHHHHHhhc
Q psy1185          38 KDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        38 ~~~~fv~~~~~~~a~~~~   55 (131)
                      +|||||+|.+.++|..+.
T Consensus        59 ~g~afV~f~~~~~A~~Ai   76 (101)
T d1x5oa1          59 RGVGFARMESTEKCEAVI   76 (101)
T ss_dssp             EEEEEEEESCHHHHHHHH
T ss_pred             ccceeEEeCCHHHHHHHH
Confidence            789999999999999854

>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=87.93  E-value=0.22  Score=27.53  Aligned_cols=22  Identities=5%  Similarity=0.214  Sum_probs=18.5

Q ss_pred             CeEEEEECCHHHHHhhcCCcee
Q psy1185          39 DYAFVHFEDRQEAITVTGLSQV   60 (131)
Q Consensus        39 ~~~fv~~~~~~~a~~~~g~~~~   60 (131)
                      |||||.|.++++|+++..+.+.
T Consensus        40 ~~~fV~f~~~~~A~~Al~~nG~   61 (81)
T d1wwha1          40 NWMHIRYQSKLQARKALSKDGR   61 (81)
T ss_dssp             SEEEEEESSHHHHHHHHTTTTC
T ss_pred             CEEEEEEcccHHHHHHHhcCCC
Confidence            7999999999999997655443

>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=87.66  E-value=0.19  Score=27.99  Aligned_cols=16  Identities=13%  Similarity=0.239  Sum_probs=13.4

Q ss_pred             CeEEEEECCHHHHHhh
Q psy1185          39 DYAFVHFEDRQEAITV   54 (131)
Q Consensus        39 ~~~fv~~~~~~~a~~~   54 (131)
                      |||||+|.+.++|+.+
T Consensus        36 g~afV~f~~~~~a~~A   51 (87)
T d3begb1          36 GTGVVEFVRKEDMTYA   51 (87)
T ss_dssp             SEEEEEESSHHHHHHH
T ss_pred             ceeeEEeCCHHHHHHH
Confidence            0489999999999984

>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=87.42  E-value=0.16  Score=29.52  Aligned_cols=19  Identities=16%  Similarity=0.366  Sum_probs=16.6

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|||||+|.+.++|..+.
T Consensus        67 ~~G~~fV~f~~~~~A~~Ai   85 (104)
T d1jmta_          67 LVGNVYVKFRREEDAEKAV   85 (104)
T ss_dssp             SEEEEEEEESCHHHHHHHH
T ss_pred             EeeEEEEEEechhHHHHHH
Confidence            3799999999999999843

>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=86.84  E-value=0.18  Score=28.55  Aligned_cols=19  Identities=21%  Similarity=0.347  Sum_probs=16.7

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .++||||+|.+.++|+.+.
T Consensus        52 ~~~~afV~f~~~~~A~~A~   70 (96)
T d1fjca_          52 SKGIAYIEFKSEADAEKNL   70 (96)
T ss_dssp             EEEEEEEEESSHHHHHHHH
T ss_pred             cccEEEEEeCCHHHHHHHH
Confidence            5789999999999999854

>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=86.28  E-value=0.21  Score=28.46  Aligned_cols=18  Identities=22%  Similarity=0.429  Sum_probs=16.5

Q ss_pred             cCeEEEEECCHHHHHhhc
Q psy1185          38 KDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        38 ~~~~fv~~~~~~~a~~~~   55 (131)
                      ++||||.|.+.++|..+.
T Consensus        60 ~g~~fV~f~~~~~A~~Ai   77 (102)
T d2cpxa1          60 RGQAFITFPNKEIAWQAL   77 (102)
T ss_dssp             CSEEEEECSSHHHHHHHH
T ss_pred             cccceEEeccHHHHHHHH
Confidence            899999999999999954

>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=85.59  E-value=0.23  Score=28.44  Aligned_cols=19  Identities=32%  Similarity=0.218  Sum_probs=16.6

Q ss_pred             ecCeEEEEECCHHHHHhhc
Q psy1185          37 IKDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        37 ~~~~~fv~~~~~~~a~~~~   55 (131)
                      .+|++||.|.++++|..+.
T Consensus        56 ~~G~~fV~f~~~e~A~~A~   74 (99)
T d2dita1          56 PDGVASVSFRDPEEADYCI   74 (99)
T ss_dssp             TTCEEEEECSCHHHHHHHH
T ss_pred             CccEEEEEECCHHHHHHHH
Confidence            3699999999999999943

>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=82.24  E-value=0.45  Score=27.01  Aligned_cols=18  Identities=6%  Similarity=0.167  Sum_probs=14.9

Q ss_pred             cCeEEEEECCHHHHHhhc
Q psy1185          38 KDYAFVHFEDRQEAITVT   55 (131)
Q Consensus        38 ~~~~fv~~~~~~~a~~~~   55 (131)
                      +|||||+|.+.++|+.+.
T Consensus        50 ~g~afV~f~~~~~a~~Ai   67 (98)
T d1wg4a_          50 DGMGMVEYLRKEDMEYAL   67 (98)
T ss_dssp             TTEEEEEESSHHHHHHHH
T ss_pred             cceEEEEECCHHHHHHHH
Confidence            048999999999999954

>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=82.19  E-value=0.43  Score=27.10  Aligned_cols=16  Identities=25%  Similarity=0.586  Sum_probs=13.7

Q ss_pred             CeEEEEECCHHHHHhh
Q psy1185          39 DYAFVHFEDRQEAITV   54 (131)
Q Consensus        39 ~~~fv~~~~~~~a~~~   54 (131)
                      |||||+|.+.++|+.+
T Consensus        51 g~aFV~f~~~~~A~~A   66 (98)
T d1wf2a_          51 GFAFVQYVNERNARAA   66 (98)
T ss_dssp             EEEEEEESSHHHHHHH
T ss_pred             CeEEEEECCHHHHHHH
Confidence            0699999999999994