Psyllid ID: psy3928

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-----
Protein Sequence
MAELVENNKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTTSRLSFGITPLGFESGGWWFKSSHEI
Secondary Structure (PSIPRED)
cccccccccccccEEEEccccccccHHHHHHHHHccccEEEEEccccccccccccEEEEEEccHHHHHHHHHHccccccccccccEEEEEccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccHcccccccEEEEEcccccccHHHHHHHHHHcccEEEEEEccccccccccEEEEEEEccHHHHHHHHHHHcccccHHccccEEEEEEEccccEcccccccccEEEEccccc
Coil and Loop (DISEMBL)
MAELVENNKKYGRVVLkeklppeaehdYIESVFSKYgkvtyvslpkfkstgklkgfafVEFSTKEEATKALElglnpcptdyqssiltttsrlsfgitplgfesggwwfksshei
Flexible Loop (DISEMBL)
maelvennkkygrvvlkeklppeaehDYIESVFSKYGKVTYVSlpkfkstgklKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTTSRLSFGITPLgfesggwwfksshei
Low Complexity Region (SEG)
MAELVENNKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTTSRLSFGITPLGFESGGWWFKSSHEI
Disordered region (IsUnstruct)
*************VVL*******AEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTTSRLSFGITPLGFESGGWWF******
Disordered Region (DISOPRED)
**************VLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTD**********************************
Disordered Region (DISEMBL)
MAELVENNKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTTSRLSFGITPLGFESGGWWFKSSHEI
Disordered Region (DISPRO)
******N*KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTTSRLSFGITPLGFESGGWWFK*****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAELVENNKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTTSRLSFGITPLGFESGGWWFKSSHEI
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	115	2.2.26 [Sep-21-2011]
Q28G87	593	La-related protein 7 OS=X	yes	N/A	0.573	0.111	0.560	2e-14
Q4G0J3	582	La-related protein 7 OS=H	yes	N/A	0.565	0.111	0.569	1e-13
Q4R627	581	La-related protein 7 OS=M	N/A	N/A	0.565	0.111	0.569	2e-13
Q05CL8	570	La-related protein 7 OS=M	yes	N/A	0.565	0.114	0.569	2e-13
Q5XI01	571	La-related protein 7 OS=R	yes	N/A	0.565	0.113	0.569	3e-13
Q7ZWE3	555	La-related protein 7 OS=D	yes	N/A	0.6	0.124	0.528	1e-12
A4QUF0	762	Polyadenylate-binding pro	N/A	N/A	0.478	0.072	0.418	1e-06
Q9WX39	105	Putative RNA-binding prot	yes	N/A	0.486	0.533	0.456	3e-06
Q0U6E7	281	Eukaryotic translation in	N/A	N/A	0.426	0.174	0.469	6e-06
A4RHN3	303	Eukaryotic translation in	N/A	N/A	0.417	0.158	0.437	2e-05

>sp|Q28G87|LARP7_XENTR La-related protein 7 OS=Xenopus tropicalis GN=larp7 PE=2 SV=1

 Score = 77.8 bits (190), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 37/66 (56%), Positives = 46/66 (69%)

Query: 12  GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
            R V  E LP    H +IE VF KYG V YVS+P++KSTG  KGFAF+EF T+E+A KA+
Sbjct: 126 SRTVYVELLPKNVTHSWIERVFGKYGMVVYVSIPRYKSTGDPKGFAFIEFETQEQAAKAI 185

Query: 72  ELGLNP 77
           E+  NP
Sbjct: 186 EVLNNP 191

Xenopus tropicalis (taxid: 8364)

>sp|Q4G0J3|LARP7_HUMAN La-related protein 7 OS=Homo sapiens GN=LARP7 PE=1 SV=1

 Score = 74.7 bits (182), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 37/65 (56%), Positives = 43/65 (66%)

Query: 13  RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
           R V  E LP    H +IE VF K G V Y+S+P +KSTG  KGFAFVEF TKE+A KA+E
Sbjct: 125 RTVYVELLPKNVNHSWIERVFGKCGNVVYISIPHYKSTGDPKGFAFVEFETKEQAAKAIE 184

Query: 73  LGLNP 77
              NP
Sbjct: 185 FLNNP 189

Negative transcriptional regulator of polymerase II genes, acting by means of the 7SK RNP system. Within the 7SK RNP complex, the positive transcription elongation factor b (P-TEFb) is sequestered in an inactive form, preventing RNA polymerase II phosphorylation and subsequent transcriptional elongation.

Homo sapiens (taxid: 9606)

>sp|Q4R627|LARP7_MACFA La-related protein 7 OS=Macaca fascicularis GN=LARP7 PE=2 SV=1

 Score = 74.7 bits (182), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 37/65 (56%), Positives = 43/65 (66%)

Query: 13  RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
           R V  E LP    H +IE VF K G V Y+S+P +KSTG  KGFAFVEF TKE+A KA+E
Sbjct: 125 RTVYVELLPKNVNHSWIERVFGKCGNVVYISIPHYKSTGDPKGFAFVEFETKEQAAKAIE 184

Query: 73  LGLNP 77
              NP
Sbjct: 185 FLNNP 189

Negative transcriptional regulator of polymerase II genes, acting by means of the 7SK RNP system. Within the 7SK RNP complex, the positive transcription elongation factor b (P-TEFb) is sequestered in an inactive form, preventing RNA polymerase II phosphorylation and subsequent transcriptional elongation.

Macaca fascicularis (taxid: 9541)

>sp|Q05CL8|LARP7_MOUSE La-related protein 7 OS=Mus musculus GN=Larp7 PE=1 SV=2

 Score = 73.9 bits (180), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 37/65 (56%), Positives = 43/65 (66%)

Query: 13  RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
           R V  E LP    H +IE VF K G V Y+S+P +KSTG  KGFAFVEF TKE+A KA+E
Sbjct: 119 RTVYVELLPKNVTHSWIERVFGKCGNVVYISIPHYKSTGDPKGFAFVEFETKEQAAKAIE 178

Query: 73  LGLNP 77
              NP
Sbjct: 179 FLNNP 183

Negative transcriptional regulator of polymerase II genes, acting by means of the 7SK RNP system. Within the 7SK RNP complex, the positive transcription elongation factor b (P-TEFb) is sequestered in an inactive form, preventing RNA polymerase II phosphorylation and subsequent transcriptional elongation.

Mus musculus (taxid: 10090)

>sp|Q5XI01|LARP7_RAT La-related protein 7 OS=Rattus norvegicus GN=Larp7 PE=1 SV=2

 Score = 73.6 bits (179), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 37/65 (56%), Positives = 43/65 (66%)

Query: 13  RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
           R V  E LP    H +IE VF K G V Y+S+P +KSTG  KGFAFVEF TKE+A KA+E
Sbjct: 120 RTVYVELLPKNVTHSWIERVFGKCGNVVYISIPHYKSTGDPKGFAFVEFETKEQAAKAIE 179

Query: 73  LGLNP 77
              NP
Sbjct: 180 FLNNP 184

Negative transcriptional regulator of polymerase II genes, acting by means of the 7SK RNP system. Within the 7SK RNP complex, the positive transcription elongation factor b (P-TEFb) is sequestered in an inactive form, preventing RNA polymerase II phosphorylation and subsequent transcriptional elongation.

Rattus norvegicus (taxid: 10116)

>sp|Q7ZWE3|LARP7_DANRE La-related protein 7 OS=Danio rerio GN=larp7 PE=2 SV=1

 Score = 71.6 bits (174), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 37/70 (52%), Positives = 47/70 (67%), Gaps = 1/70 (1%)

Query: 12  GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
            R V  E LP    H ++E VFSK G V Y+S+P++KST   KGFAFVEF T+E+A KA+
Sbjct: 132 SRTVYVELLPKTVTHIWLERVFSKCGHVVYISIPRYKSTRHSKGFAFVEFETQEQAQKAV 191

Query: 72  ELGLNPCPTD 81
           E+  NP P D
Sbjct: 192 EMLNNP-PED 200

Danio rerio (taxid: 7955)

>sp|A4QUF0|PABP_MAGO7 Polyadenylate-binding protein, cytoplasmic and nuclear OS=Magnaporthe oryzae (strain 70-15 / ATCC MYA-4617 / FGSC 8958) GN=PAB1 PE=3 SV=1

 Score = 51.6 bits (122), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 23/55 (41%), Positives = 36/55 (65%)

Query: 18  EKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
           + + PE   D   ++F KYG VT  SL + + TGK +GF FV F++ E+A+KA++
Sbjct: 247 KNINPEVTDDEFRTLFEKYGDVTSSSLARDQETGKSRGFGFVNFTSHEDASKAVQ 301

Binds the poly(A) tail of mRNA. Appears to be an important mediator of the multiple roles of the poly(A) tail in mRNA biogenesis, stability and translation. In the nucleus, involved in both mRNA cleavage and polyadenylation. Is also required for efficient mRNA export to the cytoplasm. Acts in concert with a poly(A)-specific nuclease (PAN) to affect poly(A) tail shortening, which may occur concomitantly with either nucleocytoplasmic mRNA transport or translational initiation. In the cytoplasm, stimulates translation initiation and regulates mRNA decay through translation termination-coupled poly(A) shortening, probably mediated by PAN.

Magnaporthe oryzae (strain 70-15 / ATCC MYA-4617 / FGSC 8958) (taxid: 242507)

>sp|Q9WX39|RBPF_NOSS1 Putative RNA-binding protein RbpF OS=Nostoc sp. (strain PCC 7120 / UTEX 2576) GN=rbpF PE=3 SV=3

 Score = 50.4 bits (119), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 26/57 (45%), Positives = 36/57 (63%), Gaps = 1/57 (1%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          L  E   + I +VF++YG V  V LP  + TG+L+GFAFVE  +  E T A+E GL+
Sbjct: 8  LSYEVTQEDISNVFAEYGSVKRVVLPTDRETGRLRGFAFVEMGSDAEETAAIE-GLD 63

Nostoc sp. (strain PCC 7120 / UTEX 2576) (taxid: 103690)

>sp|Q0U6E7|EIF3G_PHANO Eukaryotic translation initiation factor 3 subunit G OS=Phaeosphaeria nodorum (strain SN15 / ATCC MYA-4574 / FGSC 10173) GN=TIF35 PE=3 SV=2

 Score = 49.7 bits (117), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 23/49 (46%), Positives = 32/49 (65%)

Query: 24  AEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
           AE   +  +FS+YG VT V L K + TG+ KGFAFV ++ + +A KA E
Sbjct: 213 AEEQDLRDMFSRYGHVTRVFLAKDRETGRAKGFAFVSYADRTDAAKACE 261

Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome. This subunit can bind 18S rRNA.

Phaeosphaeria nodorum (strain SN15 / ATCC MYA-4574 / FGSC 10173) (taxid: 321614)

>sp|A4RHN3|EIF3G_MAGO7 Eukaryotic translation initiation factor 3 subunit G OS=Magnaporthe oryzae (strain 70-15 / ATCC MYA-4617 / FGSC 8958) GN=TIF35 PE=3 SV=1

 Score = 47.8 bits (112), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 21/48 (43%), Positives = 31/48 (64%)

Query: 24  AEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
           AE   +  +F ++G+VT V L K + TG  KGFAF+ F+ +E+A KA 
Sbjct: 234 AEEQELRDMFERFGRVTRVFLAKDRDTGLAKGFAFISFADREDAVKAC 281

Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome. This subunit can bind 18S rRNA.

Magnaporthe oryzae (strain 70-15 / ATCC MYA-4617 / FGSC 8958) (taxid: 242507)

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	115
225708530	220	La protein homolog [Osmerus mordax]	0.591	0.309	0.565	6e-13
113931440	593	la-related protein 7 [Xenopus (Silurana)	0.573	0.111	0.560	8e-13
390333306	643	PREDICTED: uncharacterized protein LOC58	0.756	0.135	0.471	9e-13
163916279	233	Unknown (protein for IMAGE:7537566) [Xen	0.565	0.278	0.569	9e-13
326919006	597	PREDICTED: la-related protein 7-like [Me	0.565	0.108	0.584	2e-12
363733597	647	PREDICTED: la-related protein 7 [Gallus	0.565	0.100	0.584	2e-12
449265844	585	La-related protein 7 [Columba livia]	0.573	0.112	0.575	2e-12
53134741	233	hypothetical protein RCJMB04_23k13 [Gall	0.565	0.278	0.584	3e-12
345326822	678	PREDICTED: la-related protein 7 [Ornitho	0.565	0.095	0.569	3e-12
449499453	590	PREDICTED: la-related protein 7-like [Ta	0.573	0.111	0.560	4e-12

>gi|225708530|gb|ACO10111.1| La protein homolog [Osmerus mordax]

 Score = 78.2 bits (191), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 39/69 (56%), Positives = 51/69 (73%), Gaps = 1/69 (1%)

Query: 13  RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
           R V  E LP + +H +IE VFSK G V YVS+PK+K++G+ KGFAFVEF T+E+A KA+E
Sbjct: 122 RTVYVELLPKDVKHGWIERVFSKCGNVVYVSIPKYKTSGQSKGFAFVEFETEEQAQKAIE 181

Query: 73  LGLNPCPTD 81
           +  NP P D
Sbjct: 182 MLNNP-PED 189

Source: Osmerus mordax

Species: Osmerus mordax

Genus: Osmerus

Family: Osmeridae

Order: Osmeriformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|113931440|ref|NP_001039168.1| la-related protein 7 [Xenopus (Silurana) tropicalis] gi|123910245|sp|Q28G87.1|LARP7_XENTR RecName: Full=La-related protein 7; AltName: Full=La ribonucleoprotein domain family member 7 gi|89266879|emb|CAJ83882.1| novel La domain and RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) containing protein [Xenopus (Silurana) tropicalis]

 Score = 77.8 bits (190), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 37/66 (56%), Positives = 46/66 (69%)

Query: 12  GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
            R V  E LP    H +IE VF KYG V YVS+P++KSTG  KGFAF+EF T+E+A KA+
Sbjct: 126 SRTVYVELLPKNVTHSWIERVFGKYGMVVYVSIPRYKSTGDPKGFAFIEFETQEQAAKAI 185

Query: 72  ELGLNP 77
           E+  NP
Sbjct: 186 EVLNNP 191

Source: Xenopus (Silurana) tropicalis

Species: Xenopus (Silurana) tropicalis

Genus: Xenopus

Family: Pipidae

Order: Anura

Class: Amphibia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|390333306|ref|XP_793889.3| PREDICTED: uncharacterized protein LOC589145 [Strongylocentrotus purpuratus]

 Score = 77.4 bits (189), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 41/87 (47%), Positives = 52/87 (59%)

Query: 18  EKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNP 77
           E LP +A+HD +   FS  GKV YVSLP++KST  +KGFAF+EF T EEA +A EL  NP
Sbjct: 130 ECLPKKADHDLLRKAFSYCGKVVYVSLPRYKSTSDIKGFAFIEFETPEEADQACELMNNP 189

Query: 78  CPTDYQSSILTTTSRLSFGITPLGFES 104
            P     +      R +  I PL F+ 
Sbjct: 190 PPDMMDRAGKFPKMRGNKRIVPLEFDQ 216

Source: Strongylocentrotus purpuratus

Species: Strongylocentrotus purpuratus

Genus: Strongylocentrotus

Family: Strongylocentrotidae

Order: Echinoida

Class: Echinoidea

Phylum: Echinodermata

Superkingdom: Eukaryota

>gi|163916279|gb|AAI57142.1| Unknown (protein for IMAGE:7537566) [Xenopus (Silurana) tropicalis]

 Score = 77.4 bits (189), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 37/65 (56%), Positives = 46/65 (70%)

Query: 13  RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
           R V  E LP    H +IE VF KYG V YVS+P++KSTG  KGFAF+EF T+E+A KA+E
Sbjct: 127 RTVYVELLPKNVTHSWIERVFGKYGMVVYVSIPRYKSTGDPKGFAFIEFETQEQAAKAIE 186

Query: 73  LGLNP 77
           +  NP
Sbjct: 187 VLNNP 191

Source: Xenopus (Silurana) tropicalis

Species: Xenopus (Silurana) tropicalis

Genus: Xenopus

Family: Pipidae

Order: Anura

Class: Amphibia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|326919006|ref|XP_003205775.1| PREDICTED: la-related protein 7-like [Meleagris gallopavo]

 Score = 76.3 bits (186), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 38/65 (58%), Positives = 44/65 (67%)

Query: 13  RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
           R V  E LP    H +IE VF K G V YVS+P++KSTG  KGFAFVEF TKE+A KA+E
Sbjct: 127 RTVYVELLPKNVNHSWIERVFGKCGNVVYVSIPRYKSTGDPKGFAFVEFETKEQAEKAIE 186

Query: 73  LGLNP 77
              NP
Sbjct: 187 FLNNP 191

Source: Meleagris gallopavo

Species: Meleagris gallopavo

Genus: Meleagris

Family: Phasianidae

Order: Galliformes

Class: Aves

Phylum: Chordata

Superkingdom: Eukaryota

>gi|363733597|ref|XP_420643.3| PREDICTED: la-related protein 7 [Gallus gallus]

 Score = 76.3 bits (186), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 38/65 (58%), Positives = 44/65 (67%)

Query: 13  RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
           R V  E LP    H +IE VF K G V YVS+P++KSTG  KGFAFVEF TKE+A KA+E
Sbjct: 179 RTVYVELLPKNVNHSWIERVFGKCGNVVYVSIPRYKSTGDPKGFAFVEFETKEQAEKAIE 238

Query: 73  LGLNP 77
              NP
Sbjct: 239 FLNNP 243

Source: Gallus gallus

Species: Gallus gallus

Genus: Gallus

Family: Phasianidae

Order: Galliformes

Class: Aves

Phylum: Chordata

Superkingdom: Eukaryota

>gi|449265844|gb|EMC76974.1| La-related protein 7 [Columba livia]

 Score = 76.3 bits (186), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 38/66 (57%), Positives = 44/66 (66%)

Query: 12  GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
            R V  E LP    H +IE VF K G V YVS+P++KSTG  KGFAFVEF TKE+A KA+
Sbjct: 123 SRTVYVELLPKNVNHSWIERVFGKCGNVVYVSIPRYKSTGNPKGFAFVEFETKEQAEKAI 182

Query: 72  ELGLNP 77
           E   NP
Sbjct: 183 EFLNNP 188

Source: Columba livia

Species: Columba livia

Genus: Columba

Family: Columbidae

Order: Columbiformes

Class: Aves

Phylum: Chordata

Superkingdom: Eukaryota

>gi|53134741|emb|CAG32359.1| hypothetical protein RCJMB04_23k13 [Gallus gallus]

 Score = 76.3 bits (186), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 38/65 (58%), Positives = 44/65 (67%)

Query: 13  RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
           R V  E LP    H +IE VF K G V YVS+P++KSTG  KGFAFVEF TKE+A KA+E
Sbjct: 127 RTVYVELLPKNVNHSWIERVFGKCGNVVYVSIPRYKSTGDPKGFAFVEFETKEQAEKAIE 186

Query: 73  LGLNP 77
              NP
Sbjct: 187 FLNNP 191

Source: Gallus gallus

Species: Gallus gallus

Genus: Gallus

Family: Phasianidae

Order: Galliformes

Class: Aves

Phylum: Chordata

Superkingdom: Eukaryota

>gi|345326822|ref|XP_001507431.2| PREDICTED: la-related protein 7 [Ornithorhynchus anatinus]

 Score = 75.9 bits (185), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 37/65 (56%), Positives = 44/65 (67%)

Query: 13  RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
           R V  E LP +  H +IE VF K G V Y+S+P +KSTG  KGFAFVEF TKE+A KA+E
Sbjct: 125 RTVYVELLPKDVNHSWIERVFGKCGNVVYISIPHYKSTGDPKGFAFVEFETKEQADKAIE 184

Query: 73  LGLNP 77
              NP
Sbjct: 185 FLNNP 189

Source: Ornithorhynchus anatinus

Species: Ornithorhynchus anatinus

Genus: Ornithorhynchus

Family: Ornithorhynchidae

Order: Monotremata

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|449499453|ref|XP_002196501.2| PREDICTED: la-related protein 7-like [Taeniopygia guttata]

 Score = 75.5 bits (184), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 37/66 (56%), Positives = 44/66 (66%)

Query: 12  GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
            R V  E LP    H +IE VF K G V YVS+P+++STG  KGFAFVEF TKE+A KA+
Sbjct: 126 SRTVYVELLPKNVNHSWIERVFGKCGNVVYVSIPRYRSTGDPKGFAFVEFETKEQAEKAI 185

Query: 72  ELGLNP 77
           E   NP
Sbjct: 186 EFLNNP 191

Source: Taeniopygia guttata

Species: Taeniopygia guttata

Genus: Taeniopygia

Family: Estrildidae

Order: Passeriformes

Class: Aves

Phylum: Chordata

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	115
UNIPROTKB|F1NJ86	233	LARP7 "Uncharacterized protein	0.565	0.278	0.584	6.9e-15
UNIPROTKB|D6RFF0	299	LARP7 "La-related protein 7" [	0.565	0.217	0.569	2e-14
UNIPROTKB|E1BQG3	602	LARP7 "Uncharacterized protein	0.565	0.107	0.584	7.2e-14
UNIPROTKB|F1MR14	578	F1MR14 "Uncharacterized protei	0.565	0.112	0.569	1.4e-13
UNIPROTKB|I3LNK9	580	I3LNK9 "Uncharacterized protei	0.565	0.112	0.569	1.4e-13
UNIPROTKB|E2QW27	582	LARP7 "Uncharacterized protein	0.565	0.111	0.569	1.4e-13
UNIPROTKB|Q4G0J3	582	LARP7 "La-related protein 7" [	0.565	0.111	0.569	1.4e-13
UNIPROTKB|F1S150	582	LARP7 "Uncharacterized protein	0.565	0.111	0.569	1.4e-13
MGI|MGI:107634	570	Larp7 "La ribonucleoprotein do	0.565	0.114	0.569	1.8e-13
RGD|1592474	571	Larp7 "La ribonucleoprotein do	0.565	0.113	0.569	1.8e-13

UNIPROTKB|F1NJ86 LARP7 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 189 (71.6 bits), Expect = 6.9e-15, P = 6.9e-15
 Identities = 38/65 (58%), Positives = 44/65 (67%)

Query:    13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
             R V  E LP    H +IE VF K G V YVS+P++KSTG  KGFAFVEF TKE+A KA+E
Sbjct:   127 RTVYVELLPKNVNHSWIERVFGKCGNVVYVSIPRYKSTGDPKGFAFVEFETKEQAEKAIE 186

Query:    73 LGLNP 77
                NP
Sbjct:   187 FLNNP 191

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006396 "RNA processing" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

UNIPROTKB|D6RFF0 LARP7 "La-related protein 7" [Homo sapiens (taxid:9606)]

 Score = 186 (70.5 bits), Expect = 2.0e-14, P = 2.0e-14
 Identities = 37/65 (56%), Positives = 43/65 (66%)

Query:    13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
             R V  E LP    H +IE VF K G V Y+S+P +KSTG  KGFAFVEF TKE+A KA+E
Sbjct:   125 RTVYVELLPKNVNHSWIERVFGKCGNVVYISIPHYKSTGDPKGFAFVEFETKEQAAKAIE 184

Query:    73 LGLNP 77
                NP
Sbjct:   185 FLNNP 189

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0006396 "RNA processing" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

UNIPROTKB|E1BQG3 LARP7 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 189 (71.6 bits), Expect = 7.2e-14, P = 7.2e-14
 Identities = 38/65 (58%), Positives = 44/65 (67%)

Query:    13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
             R V  E LP    H +IE VF K G V YVS+P++KSTG  KGFAFVEF TKE+A KA+E
Sbjct:   127 RTVYVELLPKNVNHSWIERVFGKCGNVVYVSIPRYKSTGDPKGFAFVEFETKEQAEKAIE 186

Query:    73 LGLNP 77
                NP
Sbjct:   187 FLNNP 191

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0006396 "RNA processing" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

UNIPROTKB|F1MR14 F1MR14 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 186 (70.5 bits), Expect = 1.4e-13, P = 1.4e-13
 Identities = 37/65 (56%), Positives = 43/65 (66%)

Query:    13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
             R V  E LP    H +IE VF K G V Y+S+P +KSTG  KGFAFVEF TKE+A KA+E
Sbjct:   123 RTVYVELLPKNVNHSWIERVFGKCGNVVYISIPHYKSTGDPKGFAFVEFETKEQAAKAIE 182

Query:    73 LGLNP 77
                NP
Sbjct:   183 FLNNP 187

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0006396 "RNA processing" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|I3LNK9 I3LNK9 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 186 (70.5 bits), Expect = 1.4e-13, P = 1.4e-13
 Identities = 37/65 (56%), Positives = 43/65 (66%)

Query:    13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
             R V  E LP    H +IE VF K G V Y+S+P +KSTG  KGFAFVEF TKE+A KA+E
Sbjct:   125 RTVYVELLPKNVNHSWIERVFGKCGNVVYISIPHYKSTGDPKGFAFVEFETKEQAAKAIE 184

Query:    73 LGLNP 77
                NP
Sbjct:   185 FLNNP 189

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0006396 "RNA processing" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|E2QW27 LARP7 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 186 (70.5 bits), Expect = 1.4e-13, P = 1.4e-13
 Identities = 37/65 (56%), Positives = 43/65 (66%)

Query:    13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
             R V  E LP    H +IE VF K G V Y+S+P +KSTG  KGFAFVEF TKE+A KA+E
Sbjct:   124 RTVYVELLPKNVNHSWIERVFGKCGNVVYISIPHYKSTGDPKGFAFVEFETKEQAAKAIE 183

Query:    73 LGLNP 77
                NP
Sbjct:   184 FLNNP 188

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0006396 "RNA processing" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|Q4G0J3 LARP7 "La-related protein 7" [Homo sapiens (taxid:9606)]

 Score = 186 (70.5 bits), Expect = 1.4e-13, P = 1.4e-13
 Identities = 37/65 (56%), Positives = 43/65 (66%)

Query:    13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
             R V  E LP    H +IE VF K G V Y+S+P +KSTG  KGFAFVEF TKE+A KA+E
Sbjct:   125 RTVYVELLPKNVNHSWIERVFGKCGNVVYISIPHYKSTGDPKGFAFVEFETKEQAAKAIE 184

Query:    73 LGLNP 77
                NP
Sbjct:   185 FLNNP 189

GO:0000166 "nucleotide binding" evidence=IEA

GO:0006396 "RNA processing" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005654 "nucleoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

UNIPROTKB|F1S150 LARP7 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 186 (70.5 bits), Expect = 1.4e-13, P = 1.4e-13
 Identities = 37/65 (56%), Positives = 43/65 (66%)

Query:    13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
             R V  E LP    H +IE VF K G V Y+S+P +KSTG  KGFAFVEF TKE+A KA+E
Sbjct:   125 RTVYVELLPKNVNHSWIERVFGKCGNVVYISIPHYKSTGDPKGFAFVEFETKEQAAKAIE 184

Query:    73 LGLNP 77
                NP
Sbjct:   185 FLNNP 189

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0006396 "RNA processing" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

MGI|MGI:107634 Larp7 "La ribonucleoprotein domain family, member 7" [Mus musculus (taxid:10090)]

 Score = 185 (70.2 bits), Expect = 1.8e-13, P = 1.8e-13
 Identities = 37/65 (56%), Positives = 43/65 (66%)

Query:    13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
             R V  E LP    H +IE VF K G V Y+S+P +KSTG  KGFAFVEF TKE+A KA+E
Sbjct:   119 RTVYVELLPKNVTHSWIERVFGKCGNVVYISIPHYKSTGDPKGFAFVEFETKEQAAKAIE 178

Query:    73 LGLNP 77
                NP
Sbjct:   179 FLNNP 183

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IGI

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003674 "molecular_function" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006396 "RNA processing" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0035562 "negative regulation of chromatin binding" evidence=IGI

GO:0036093 "germ cell proliferation" evidence=IMP

GO:1900087 "positive regulation of G1/S transition of mitotic cell cycle" evidence=IMP

RGD|1592474 Larp7 "La ribonucleoprotein domain family, member 7" [Rattus norvegicus (taxid:10116)]

 Score = 185 (70.2 bits), Expect = 1.8e-13, P = 1.8e-13
 Identities = 37/65 (56%), Positives = 43/65 (66%)

Query:    13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
             R V  E LP    H +IE VF K G V Y+S+P +KSTG  KGFAFVEF TKE+A KA+E
Sbjct:   120 RTVYVELLPKNVTHSWIERVFGKCGNVVYISIPHYKSTGDPKGFAFVEFETKEQAAKAIE 179

Query:    73 LGLNP 77
                NP
Sbjct:   180 FLNNP 184

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=ISO

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISO

GO:0005654 "nucleoplasm" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISO

GO:0006396 "RNA processing" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0035562 "negative regulation of chromatin binding" evidence=ISO

GO:0036093 "germ cell proliferation" evidence=ISO

GO:1900087 "positive regulation of G1/S transition of mitotic cell cycle" evidence=ISO

---

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)
Q05CL8	LARP7_MOUSE	No assigned EC number	0.5692	0.5652	0.1140	yes	N/A
Q4G0J3	LARP7_HUMAN	No assigned EC number	0.5692	0.5652	0.1116	yes	N/A
Q28G87	LARP7_XENTR	No assigned EC number	0.5606	0.5739	0.1112	yes	N/A
Q7ZWE3	LARP7_DANRE	No assigned EC number	0.5285	0.6	0.1243	yes	N/A
Q5XI01	LARP7_RAT	No assigned EC number	0.5692	0.5652	0.1138	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	115
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	5e-25
smart00360	73	smart00360, RRM, RNA recognition motif	1e-15
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	5e-14
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	7e-14
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	4e-13
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	6e-13
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	7e-13
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	2e-12
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	4e-12
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	3e-11
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	5e-11
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	2e-10
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	2e-10
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	3e-10
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	9e-10
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	2e-09
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	4e-09
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	4e-09
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	5e-09
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	6e-09
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	6e-09
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	6e-09
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	7e-09
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	8e-09
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-08
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	1e-08
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	1e-08
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	2e-08
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	2e-08
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	3e-08
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	4e-08
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	4e-08
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	4e-08
cd12291	72	cd12291, RRM1_La, RNA recognition motif 1 in La au	4e-08
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	5e-08
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	6e-08
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	6e-08
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	1e-07
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	1e-07
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	1e-07
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	1e-07
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	2e-07
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	2e-07
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	2e-07
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	3e-07
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	3e-07
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	3e-07
cd12561	81	cd12561, RRM1_RBM5_like, RNA recognition motif 1 i	4e-07
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	5e-07
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	6e-07
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	6e-07
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	6e-07
cd12753	85	cd12753, RRM1_RBM10, RNA recognition motif 1 in ve	6e-07
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	7e-07
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	8e-07
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	8e-07
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	8e-07
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	9e-07
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	1e-06
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	1e-06
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	2e-06
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	2e-06
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	2e-06
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	2e-06
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	2e-06
cd12466	70	cd12466, RRM2_AtRSp31_like, RNA recognition motif	3e-06
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	3e-06
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	3e-06
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	3e-06
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	3e-06
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	3e-06
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	3e-06
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	4e-06
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	4e-06
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	5e-06
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	6e-06
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	6e-06
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	6e-06
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	6e-06
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	7e-06
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	7e-06
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	8e-06
cd12401	76	cd12401, RRM_eIF4H, RNA recognition motif in eukar	9e-06
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	1e-05
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	1e-05
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	1e-05
cd12597	73	cd12597, RRM1_SRSF1, RNA recognition motif 1 in se	1e-05
cd12247	72	cd12247, RRM2_U1A_like, RNA recognition motif 2 in	1e-05
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-05
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	2e-05
cd12611	81	cd12611, RRM1_NGR1_NAM8_like, RNA recognition moti	2e-05
cd12238	73	cd12238, RRM1_RBM40_like, RNA recognition motif 1	2e-05
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	2e-05
cd12257	72	cd12257, RRM1_RBM26_like, RNA recognition motif 1	2e-05
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	2e-05
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	3e-05
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	3e-05
cd12426	79	cd12426, RRM4_PTBPH3, RNA recognition motif 4 in p	3e-05
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	4e-05
cd12429	74	cd12429, RRM_DNAJC17, RNA recognition motif in the	4e-05
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	5e-05
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	6e-05
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	6e-05
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	6e-05
cd12405	72	cd12405, RRM3_NCL, RNA recognition motif 3 in vert	6e-05
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	6e-05
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	8e-05
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	8e-05
cd12484	78	cd12484, RRM1_RBM46, RNA recognition motif 1 found	8e-05
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	1e-04
cd12583	75	cd12583, RRM2_hnRNPD, RNA recognition motif 2 in h	1e-04
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	1e-04
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	1e-04
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	1e-04
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	1e-04
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	1e-04
cd12385	76	cd12385, RRM1_hnRNPM_like, RNA recognition motif 1	1e-04
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	2e-04
cd12431	80	cd12431, RRM_ALKBH8, RNA recognition motif in alky	2e-04
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	2e-04
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	2e-04
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	2e-04
cd12603	71	cd12603, RRM_hnRNPC, RNA recognition motif in vert	2e-04
cd12755	86	cd12755, RRM2_RBM5, RNA recognition motif 2 in ver	3e-04
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	3e-04
cd12230	82	cd12230, RRM1_U2AF65, RNA recognition motif 1 foun	3e-04
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	3e-04
cd12562	86	cd12562, RRM2_RBM5_like, RNA recognition motif 2 i	3e-04
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	3e-04
cd12239	82	cd12239, RRM2_RBM40_like, RNA recognition motif 2	3e-04
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	3e-04
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	3e-04
cd12584	80	cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in	4e-04
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	4e-04
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	4e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	5e-04
cd12585	75	cd12585, RRM2_hnRPDL, RNA recognition motif 2 in h	5e-04
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	5e-04
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	5e-04
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	5e-04
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	5e-04
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	6e-04
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	6e-04
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	6e-04
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	7e-04
cd12551	77	cd12551, RRM_II_PABPN1L, RNA recognition motif in	7e-04
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	8e-04
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	8e-04
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	8e-04
cd12582	80	cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in	8e-04
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	9e-04
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	0.001
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	0.001
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	0.001
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	0.001
cd12402	77	cd12402, RRM_eIF4B, RNA recognition motif in eukar	0.001
cd12232	89	cd12232, RRM3_U2AF65, RNA recognition motif 3 foun	0.002
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	0.002
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	0.002
cd12467	78	cd12467, RRM_Srp1p_like, RNA recognition motif 1 i	0.002
cd12288	93	cd12288, RRM_La_like_plant, RNA recognition motif	0.002
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	0.003
cd12357	89	cd12357, RRM_PPARGC1A_like, RNA recognition motif	0.003
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	0.003
cd12404	77	cd12404, RRM2_NCL, RNA recognition motif 2 in vert	0.003
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	0.003
cd12598	72	cd12598, RRM1_SRSF9, RNA recognition motif 1 in ve	0.004
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	0.004
cd12322	71	cd12322, RRM2_TDP43, RNA recognition motif 2 in TA	0.004
cd12483	79	cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in v	0.004
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	0.004

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

 Score = 89.7 bits (223), Expect = 5e-25
 Identities = 33/55 (60%), Positives = 43/55 (78%)

Query: 18 EKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          E LP  A H+++++VFSKYG V YVSLP++K TG +KGFAF+EF T EEA KA +
Sbjct: 5  ECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACK 59

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|214636 smart00360, RRM, RNA recognition motif

 Score = 65.7 bits (161), Expect = 1e-15
 Identities = 29/54 (53%), Positives = 38/54 (70%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
          LPP+   + +  +FSK+GKV  V L + K TGK KGFAFVEF ++E+A KALE 
Sbjct: 7  LPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Length = 73

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

 Score = 61.5 bits (150), Expect = 5e-14
 Identities = 26/58 (44%), Positives = 36/58 (62%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNP 77
          LP +A  + ++ +FS++G+V Y  + K K TG  KG AFV+F TKE A K LE   N 
Sbjct: 8  LPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAADNA 65

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

 Score = 61.2 bits (149), Expect = 7e-14
 Identities = 22/55 (40%), Positives = 34/55 (61%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELG 74
          L  +A+ D I   F +YG+++ V LP    +G+ KGF +VEFS++E A  AL+  
Sbjct: 6  LSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

This subfamily corresponds to the RRM2 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues. . Length = 73

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

 Score = 59.2 bits (144), Expect = 4e-13
 Identities = 24/53 (45%), Positives = 35/53 (66%), Gaps = 1/53 (1%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          LPP+   + +  +FSK+G++  V + +    GK KGFAFVEF + E+A KALE
Sbjct: 6  LPPDTTEEDLRELFSKFGEIESVRIVR-DKDGKSKGFAFVEFESPEDAEKALE 57

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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 58.8 bits (143), Expect = 6e-13
 Identities = 23/53 (43%), Positives = 36/53 (67%), Gaps = 1/53 (1%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          LPP+   + ++ +FSK+G +  + + +   TG+ KGFAFVEF  +E+A KALE
Sbjct: 6  LPPDTTEEDLKDLFSKFGPIESIRIVR-DETGRSKGFAFVEFEDEEDAEKALE 57

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

 Score = 58.7 bits (143), Expect = 7e-13
 Identities = 22/53 (41%), Positives = 35/53 (66%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L  +A+ D +  +F  +G ++ V L K K TG+ +GFAFV F T+E+A +A+E
Sbjct: 7  LSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIE 59

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

 Score = 57.7 bits (140), Expect = 2e-12
 Identities = 24/53 (45%), Positives = 34/53 (64%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L P  +  YI S F++ G+VT V + + K TGK  G+ FVEF+T E A +AL+
Sbjct: 7  LEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQ 59

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

 Score = 56.9 bits (138), Expect = 4e-12
 Identities = 24/57 (42%), Positives = 39/57 (68%), Gaps = 2/57 (3%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          LP +     ++ +FS +G V  V++P+ K  GK KGFAFV+F++K +A KA++ G+N
Sbjct: 7  LPFKCTEADLKKLFSPFGFVWEVTIPR-KPDGKKKGFAFVQFTSKADAEKAIK-GVN 61

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

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

 Score = 54.1 bits (131), Expect = 3e-11
 Identities = 20/55 (36%), Positives = 32/55 (58%)

Query: 18 EKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
           KL      D+++ +FS YG V  V LP  +     +G+A+VEF + E+A KA++
Sbjct: 4  GKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIK 58

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|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 = 53.8 bits (130), Expect = 5e-11
 Identities = 26/53 (49%), Positives = 34/53 (64%), Gaps = 1/53 (1%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          +P EA    +  +FS +G+V  V LPK K  G  +GFAFVEF TK+EA  A+E
Sbjct: 8  VPFEATKKELRELFSPFGQVKSVRLPK-KFDGSHRGFAFVEFVTKQEAQNAME 59

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|240729 cd12283, RRM1_RBM39_like, RNA recognition motif 1 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins

 Score = 52.2 bits (126), Expect = 2e-10
 Identities = 19/59 (32%), Positives = 30/59 (50%)

Query: 15 VLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
          V   +L  +     +   FSK GKV  V + + +++ + KG A+VEF  +E    AL L
Sbjct: 2  VFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLALGL 60

This subfamily corresponds to the RRM1 of RNA-binding protein 39 (RBM39), RNA-binding protein 23 (RBM23) and similar proteins. RBM39 (also termed HCC1) is a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor. . Length = 73

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

 Score = 52.2 bits (126), Expect = 2e-10
 Identities = 17/53 (32%), Positives = 28/53 (52%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L  E +   + + F  +G +  + +P    T K +GFAFVEF   E+A  A++
Sbjct: 6  LAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAID 58

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

 Score = 51.9 bits (125), Expect = 3e-10
 Identities = 17/46 (36%), Positives = 30/46 (65%)

Query: 27 DYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          D +  +F  +G++ +V L +   TG+ KG+ F++F+  E+A KALE
Sbjct: 13 DDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALE 58

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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 50.2 bits (121), Expect = 9e-10
 Identities = 22/54 (40%), Positives = 32/54 (59%), Gaps = 2/54 (3%)

Query: 19 KLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
           LPP    + +   FS YGKV  V L +  +  + +GFAFVEF++ E+A  AL+
Sbjct: 5  NLPPSVTEEDLREFFSPYGKVEGVRLVR--NKDRPRGFAFVEFASPEDAEAALK 56

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

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

 Score = 53.0 bits (126), Expect = 2e-09
 Identities = 24/72 (33%), Positives = 40/72 (55%)

Query: 1   MAELVENNKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVE 60
             +  + +K+    +    LP +   + +  +F K+G V  V L + + TGK +GFAFVE
Sbjct: 104 SPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVE 163

Query: 61  FSTKEEATKALE 72
           F ++E A KA+E
Sbjct: 164 FESEESAEKAIE 175

Length = 306

>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 = 49.1 bits (118), Expect = 4e-09
 Identities = 22/57 (38%), Positives = 32/57 (56%), Gaps = 1/57 (1%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          L        +E++FSK+G+V  V L K   TG+ +GF FV F + E+A  A+   LN
Sbjct: 9  LSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR-DLN 64

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

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

 Score = 49.2 bits (118), Expect = 4e-09
 Identities = 20/64 (31%), Positives = 33/64 (51%), Gaps = 3/64 (4%)

Query: 13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLK---GFAFVEFSTKEEATK 69
          R +    L  + + D +  +FSK+G+V  + +PK +   + +   GFAFV F     A  
Sbjct: 1  REIYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAEN 60

Query: 70 ALEL 73
          AL+L
Sbjct: 61 ALQL 64

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

 Score = 48.8 bits (117), Expect = 5e-09
 Identities = 19/52 (36%), Positives = 31/52 (59%)

Query: 19 KLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKA 70
          KL P    + +E +FS++GK+    + + K TG    +AF+EF TKE+  +A
Sbjct: 10 KLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEA 61

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|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 = 48.7 bits (117), Expect = 6e-09
 Identities = 23/53 (43%), Positives = 37/53 (69%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          LP  A  + + ++F +YG +  V++ + K TG+ KG AFV+FS++EEA KA+E
Sbjct: 7  LPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIE 59

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

 Score = 48.4 bits (116), Expect = 6e-09
 Identities = 19/53 (35%), Positives = 31/53 (58%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          LP     + ++ +F ++G+VT   +   + TG+ +GF FVE  T EEA  A+E
Sbjct: 7  LPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIE 59

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

 Score = 48.4 bits (116), Expect = 6e-09
 Identities = 20/53 (37%), Positives = 28/53 (52%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          LP     + +  +F  +G+++ V LP  K T + KGFAFV F   E A KA  
Sbjct: 7  LPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYS 59

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|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like proteins mainly from plants

 Score = 48.5 bits (116), Expect = 7e-09
 Identities = 20/45 (44%), Positives = 29/45 (64%)

Query: 29 IESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
          +   FS  G++T VS+P  + TG  KGFA++EF + +   KALEL
Sbjct: 20 LTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEKALEL 64

This subfamily corresponds to the RRM2 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 48.2 bits (115), Expect = 8e-09
 Identities = 22/59 (37%), Positives = 35/59 (59%), Gaps = 1/59 (1%)

Query: 15 VLKEKLPPEAEHDYIESVFSKYGKVTYVSLP-KFKSTGKLKGFAFVEFSTKEEATKALE 72
          +L   +P EA    +  +FS +G++  V LP K   TG  +GF FV+F TK++A +A +
Sbjct: 3  ILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAFK 61

This subgroup corresponds to the RRM6 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 51.0 bits (122), Expect = 1e-08
 Identities = 24/70 (34%), Positives = 39/70 (55%), Gaps = 2/70 (2%)

Query: 3   ELVENNKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFS 62
                 KK+  + +K  L P    D +  +F+K+G++T  ++ K  S G+ +GFAFV F 
Sbjct: 170 REAAPLKKFTNLYVKN-LDPSVNEDKLRELFAKFGEITSAAVMKDGS-GRSRGFAFVNFE 227

Query: 63  TKEEATKALE 72
             E+A KA+E
Sbjct: 228 KHEDAAKAVE 237

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

 Score = 47.8 bits (114), Expect = 1e-08
 Identities = 24/60 (40%), Positives = 38/60 (63%), Gaps = 1/60 (1%)

Query: 12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
          GR+ ++  LP   + D +E +FSK+G+++ V +   K +GK KGFA+V F   E+A KA 
Sbjct: 3  GRLFVR-NLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAY 61

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

 Score = 47.6 bits (114), Expect = 1e-08
 Identities = 18/61 (29%), Positives = 37/61 (60%)

Query: 12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
          G ++    +  EA+ + +   F+++G++  + L   + TG +KG+A +E+ TK+EA  A+
Sbjct: 6  GWIIFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAI 65

Query: 72 E 72
          E
Sbjct: 66 E 66

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

 Score = 47.3 bits (113), Expect = 2e-08
 Identities = 23/59 (38%), Positives = 35/59 (59%), Gaps = 2/59 (3%)

Query: 13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
          R+++K  LP   + D +  +F  +G +T V L K+   GK + F FV + T+EEA KAL
Sbjct: 2  RLIVKN-LPKGIKEDKLRKLFEAFGTITDVQL-KYTKDGKFRKFGFVGYKTEEEAQKAL 58

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

 Score = 46.9 bits (112), Expect = 2e-08
 Identities = 19/52 (36%), Positives = 28/52 (53%)

Query: 21 PPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
           P+   D I+SVF  +GK+   SL     TGK KG+ F+E+   + A  A+ 
Sbjct: 9  HPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIA 60

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

 Score = 46.5 bits (111), Expect = 3e-08
 Identities = 19/46 (41%), Positives = 29/46 (63%)

Query: 27 DYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          D +  VF KYG+V  V +P+ + T + +GFAFV F  K +A  A++
Sbjct: 13 DDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMD 58

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

 Score = 46.5 bits (111), Expect = 4e-08
 Identities = 19/61 (31%), Positives = 31/61 (50%), Gaps = 3/61 (4%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCP 79
          LP     D +   FS++G++    +   + TGK +G+ FV F  KE A +A +   +P P
Sbjct: 8  LPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK---DPNP 64

Query: 80 T 80
           
Sbjct: 65 I 65

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

 Score = 46.5 bits (111), Expect = 4e-08
 Identities = 23/55 (41%), Positives = 31/55 (56%), Gaps = 1/55 (1%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELG 74
          L   AE D +E  F + G+V  V + +    G+ KGF  VEF+T+E A KALE  
Sbjct: 7  LSWSAEQDDLEEFFKECGEVVDVRIAQDDD-GRSKGFGHVEFATEEGAQKALEKS 60

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

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

 Score = 46.6 bits (111), Expect = 4e-08
 Identities = 25/60 (41%), Positives = 34/60 (56%), Gaps = 1/60 (1%)

Query: 12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
          GR+ ++  L      + +E +FSKYG ++ V LP  K T K KGFAFV +   E A KA 
Sbjct: 3  GRLFIR-NLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAF 61

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|240737 cd12291, RRM1_La, RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins

 Score = 46.4 bits (111), Expect = 4e-08
 Identities = 22/54 (40%), Positives = 30/54 (55%), Gaps = 1/54 (1%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
           P +A  D I+  F K+GKV  + + +     K KG  FVEF T+E+A K LE 
Sbjct: 7  FPKDATLDDIQEFFEKFGKVNNIRMRRDL-DKKFKGSVFVEFKTEEDAKKFLEK 59

This subfamily corresponds to the RRM1 of La autoantigen, also termed Lupus La protein, or La ribonucleoprotein, or Sjoegren syndrome type B antigen (SS-B), a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from exonucleolytic degradation by 3' exonucleases. In addition, La can directly facilitate the translation and/or metabolism of many UUU-3' OH-lacking cellular and viral mRNAs, through binding internal RNA sequences within the untranslated regions of target mRNAs. La contains an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It also possesses a short basic motif (SBM) and a nuclear localization signal (NLS) at the C-terminus. . Length = 72

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

 Score = 46.3 bits (110), Expect = 5e-08
 Identities = 25/61 (40%), Positives = 38/61 (62%), Gaps = 2/61 (3%)

Query: 12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
           ++++K  LP EA    + ++FS YG++  V +PK K     +GFAFVEFST +EA  A+
Sbjct: 1  TKILVK-NLPFEATKKDVRTLFSSYGQLKSVRVPK-KFDQSARGFAFVEFSTAKEALNAM 58

Query: 72 E 72
           
Sbjct: 59 N 59

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

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

 Score = 46.0 bits (110), Expect = 6e-08
 Identities = 16/55 (29%), Positives = 29/55 (52%), Gaps = 5/55 (9%)

Query: 21 PPEAEHDYIESVFSKYGKVTYVSLP--KFKSTGKLKGFAFVEFSTKEEATKALEL 73
          PP  +   I  +F +YG++  +  P  +F  T   + F +V+F++ E A  A+ L
Sbjct: 9  PPSFDQSDIRDLFEQYGEILSIRFPSLRFNKT---RRFCYVQFTSPESAAAAVAL 60

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

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

 Score = 45.6 bits (109), Expect = 6e-08
 Identities = 19/35 (54%), Positives = 25/35 (71%)

Query: 33 FSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEA 67
          FS++G VT + L + K TGK KG+AFVEF + E A
Sbjct: 20 FSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVA 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|240717 cd12271, RRM1_PHIP1, RNA recognition motif 1 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 45.4 bits (108), Expect = 1e-07
 Identities = 21/54 (38%), Positives = 31/54 (57%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
          +P  +  D I S FS  G++  + L  F  TG+ +G AF+ F T+E A +AL L
Sbjct: 6  IPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRALAL 59

This subfamily corresponds to the RRM1 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA. . Length = 72

>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 = 45.7 bits (109), Expect = 1e-07
 Identities = 17/54 (31%), Positives = 30/54 (55%)

Query: 19 KLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          +L  +   + +  VFS+YG +  + L +   TG  KG+AFVE+  + +A +A  
Sbjct: 10 RLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYR 63

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

 Score = 45.6 bits (109), Expect = 1e-07
 Identities = 19/55 (34%), Positives = 27/55 (49%), Gaps = 2/55 (3%)

Query: 20 LPPEAEHDYIESVFSKYGKVTY--VSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L      + I    S    V    V L + K TG  +GFAFVEF + E+AT+ ++
Sbjct: 10 LDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMD 64

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

 Score = 45.3 bits (107), Expect = 1e-07
 Identities = 19/53 (35%), Positives = 29/53 (54%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          LP +   D +  +F  YG +   +L + KSTG  +G AFV +  +EEA  A+ 
Sbjct: 8  LPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAIS 60

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

 Score = 44.9 bits (107), Expect = 2e-07
 Identities = 24/61 (39%), Positives = 28/61 (45%)

Query: 13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
            V    +P     D+I  +  K GKV      K  STGKLK F F EF   E A +AL 
Sbjct: 1  TTVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALR 60

Query: 73 L 73
          L
Sbjct: 61 L 61

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

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

 Score = 44.5 bits (106), Expect = 2e-07
 Identities = 21/53 (39%), Positives = 30/53 (56%), Gaps = 1/53 (1%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L  + + + ++ +F KYGK+T   + K    GK KGF FV F   E A KA+E
Sbjct: 9  LGEDMDDEKLKELFGKYGKITSAKVMK-DDEGKSKGFGFVNFENHEAAQKAVE 60

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

 Score = 44.5 bits (106), Expect = 2e-07
 Identities = 19/55 (34%), Positives = 28/55 (50%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELG 74
          LP + E + +   F   G V  V + + + TG  KGF +V F TK+    AL+L 
Sbjct: 7  LPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALKLN 61

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

 Score = 44.0 bits (104), Expect = 3e-07
 Identities = 20/52 (38%), Positives = 30/52 (57%)

Query: 23 EAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELG 74
          E   D + + F + G++  V +  F+ +GK KGFAFV+F   E AT AL+  
Sbjct: 9  ETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNALKGK 60

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

 Score = 43.8 bits (104), Expect = 3e-07
 Identities = 17/44 (38%), Positives = 26/44 (59%), Gaps = 8/44 (18%)

Query: 29 IESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          +E +FSKYGK+  +SL         KG+ FV+F  +E+A  A+ 
Sbjct: 18 LEEIFSKYGKILGISL--------HKGYGFVQFDNEEDARAAVA 53

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

 Score = 44.2 bits (105), Expect = 3e-07
 Identities = 19/51 (37%), Positives = 28/51 (54%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKA 70
          LP E   +    + S +G V    L   +STG+ KG+ FVE+++K  A KA
Sbjct: 7  LPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKA 57

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

 Score = 43.9 bits (104), Expect = 4e-07
 Identities = 23/56 (41%), Positives = 32/56 (57%), Gaps = 3/56 (5%)

Query: 20 LPPEAEHDYIESVFSKYGKVTY--VSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
          LP     + I +    +G V    V L + K+TG  +GFAFVEF + EEAT+ +EL
Sbjct: 10 LPLSVTEEDIRNALVSHG-VEPKDVRLMRRKTTGASRGFAFVEFMSLEEATRWMEL 64

This subgroup corresponds to the RRM1 of RNA-binding protein 5 (RBM5 or LUCA15 or H37), RNA-binding protein 10 (RBM10 or S1-1) and similar proteins. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor; it specifically binds poly(G) RNA. RBM10, a paralog of RBM5, may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. Both, RBM5 and RBM10, contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain. . Length = 81

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

 Score = 43.5 bits (103), Expect = 5e-07
 Identities = 16/52 (30%), Positives = 26/52 (50%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
          +      D +  +F KYG +  V +P    T + +GFA+V+F    +A  AL
Sbjct: 8  VADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDAL 59

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

 Score = 46.2 bits (109), Expect = 6e-07
 Identities = 18/69 (26%), Positives = 37/69 (53%), Gaps = 1/69 (1%)

Query: 3   ELVENNKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFS 62
            + E  KK+ R+ +    P  +E D I+SVF  +G++    L +  +    KG+ F+E++
Sbjct: 196 MVQEEAKKFNRIYVASVHPDLSETD-IKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYN 254

Query: 63  TKEEATKAL 71
             +  ++A+
Sbjct: 255 NLQSQSEAI 263

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

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

 Score = 43.4 bits (103), Expect = 6e-07
 Identities = 21/54 (38%), Positives = 30/54 (55%), Gaps = 1/54 (1%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
          L      D +  +FSK G++T V L      GK KG+A+VEF  +E   +AL+L
Sbjct: 7  LDYSVPEDELRKLFSKCGEITDVRLV-KNYKGKSKGYAYVEFENEESVQEALKL 59

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

 Score = 43.4 bits (103), Expect = 6e-07
 Identities = 17/41 (41%), Positives = 26/41 (63%)

Query: 32 VFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          VFS+YG +  V +   + TG+ +GF FV F + E+A +A E
Sbjct: 19 VFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKE 59

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|241197 cd12753, RRM1_RBM10, RNA recognition motif 1 in vertebrate RNA-binding protein 10 (RBM10)

 Score = 43.5 bits (102), Expect = 6e-07
 Identities = 20/60 (33%), Positives = 35/60 (58%), Gaps = 1/60 (1%)

Query: 14 VVLKEKLPPEAEHDYIESVFSKYG-KVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          +++   LP  A    I     ++G +   V L + KS+G+ +GFAFVEF+  ++AT+ +E
Sbjct: 4  IIMLRMLPQNATETDIRGQLQEHGIQPREVRLMRNKSSGQSRGFAFVEFNHLQDATRWME 63

This subgroup corresponds to the RRM1 of RBM10, also termed G patch domain-containing protein 9, or RNA-binding protein S1-1 (S1-1), a paralog of putative tumor suppressor RNA-binding protein 5 (RBM5 or LUCA15 or H37). 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. RBM10 is structurally related to RBM5 and RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). It contains 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 = 85

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

 Score = 43.0 bits (102), Expect = 7e-07
 Identities = 18/53 (33%), Positives = 29/53 (54%), Gaps = 8/53 (15%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          LP     + +  +FS+YG+V  V         K+K +AFV F  +++A KA+E
Sbjct: 9  LPLSTTEEQLRELFSEYGEVERVK--------KIKDYAFVHFEERDDAVKAME 53

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|241077 cd12633, RRM1_FCA, RNA recognition motif 1 in plant flowering time control protein FCA and similar proteins

 Score = 43.0 bits (101), Expect = 8e-07
 Identities = 17/52 (32%), Positives = 31/52 (59%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
          +P       +  +F ++G V  V++ K K TG  +G  FV++ST++EA +A+
Sbjct: 7  VPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAI 58

This subgroup corresponds to the RRM1 of FCA, a gene controlling flowering time in Arabidopsis, encoding a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain. . Length = 80

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

 Score = 43.0 bits (102), Expect = 8e-07
 Identities = 19/44 (43%), Positives = 27/44 (61%), Gaps = 3/44 (6%)

Query: 32 VFSKYGKV---TYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          +FSKYGK+    ++        G+ +G+ FV F TKEEA KAL+
Sbjct: 19 LFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKALK 62

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

 Score = 43.0 bits (102), Expect = 8e-07
 Identities = 20/48 (41%), Positives = 25/48 (52%), Gaps = 1/48 (2%)

Query: 24 AEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
           E D  E  FS+YG V  V +   K TGK +GFAFV F   +   K +
Sbjct: 12 TEEDLRE-YFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIV 58

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

 Score = 43.0 bits (102), Expect = 9e-07
 Identities = 18/53 (33%), Positives = 31/53 (58%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          LP +   + +E  FS+ G +    + K K + K +GF +V F+ +E+A +ALE
Sbjct: 7  LPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALE 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|240836 cd12390, RRM3_RAVER, RNA recognition motif 3 in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins

 Score = 43.0 bits (102), Expect = 1e-06
 Identities = 21/61 (34%), Positives = 34/61 (55%), Gaps = 2/61 (3%)

Query: 11 YGRVVLKEKLPPEAEHDYIES-VFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATK 69
          + R +  ++LP       I   +FS+ GK T+  L      G+ +GFAFVE++T E+A +
Sbjct: 1  HSRCLFVDRLPKTFRDVSILRKLFSQVGKPTFCQL-AIAPNGQPRGFAFVEYATAEDAEE 59

Query: 70 A 70
          A
Sbjct: 60 A 60

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

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

 Score = 42.4 bits (100), Expect = 1e-06
 Identities = 18/52 (34%), Positives = 26/52 (50%), Gaps = 3/52 (5%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
          LP +     IE +F KYG +  + L   K+  +   FAFVEF    +A  A+
Sbjct: 7  LPGDIRERDIEDLFYKYGPIKAIDL---KNRRRGPPFAFVEFEDPRDAEDAV 55

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

 Score = 42.0 bits (99), Expect = 2e-06
 Identities = 18/52 (34%), Positives = 31/52 (59%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
          L PE + + + + F+ +G+++   + K   TGK KG+ FV F  KE+A  A+
Sbjct: 7  LSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAI 58

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

 Score = 42.0 bits (99), Expect = 2e-06
 Identities = 19/52 (36%), Positives = 28/52 (53%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
          LP     D I S+FS  G++    L + K TG+  G+ FV +   E+A KA+
Sbjct: 9  LPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAI 60

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

 Score = 41.9 bits (99), Expect = 2e-06
 Identities = 20/41 (48%), Positives = 28/41 (68%)

Query: 32 VFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          +FSKYGKV  V++ K K T K KG AF+ F  +E+A K ++
Sbjct: 21 IFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVK 61

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

 Score = 42.0 bits (99), Expect = 2e-06
 Identities = 20/53 (37%), Positives = 28/53 (52%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L PE   + I   F K+G +  + LP  K T K +GF F+ F ++E   K LE
Sbjct: 7  LSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKILE 59

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

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

 Score = 41.8 bits (99), Expect = 2e-06
 Identities = 21/46 (45%), Positives = 30/46 (65%), Gaps = 3/46 (6%)

Query: 29 IESVFSKYGKVTYVSL--PKFKSTGKLKGFAFVEFSTKEEATKALE 72
          +  +FSK+G    V +  P    TGK KG+AFVEF+T EEA +A++
Sbjct: 24 LRKIFSKFGVGKIVGIYMP-VDETGKTKGYAFVEFATPEEAKEAVK 68

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

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

 Score = 41.4 bits (97), Expect = 3e-06
 Identities = 19/48 (39%), Positives = 27/48 (56%), Gaps = 9/48 (18%)

Query: 25 EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
            D +E  F  YGK+  V + +         FAFV++ T+E+ATKALE
Sbjct: 14 TRD-LERHFEPYGKLVNVRIRR--------NFAFVQYETQEDATKALE 52

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

 Score = 41.5 bits (98), Expect = 3e-06
 Identities = 17/39 (43%), Positives = 25/39 (64%)

Query: 33 FSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
          FS++GKV   ++P  K TG  KG+ FV FS+++    AL
Sbjct: 20 FSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENAL 58

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

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

 Score = 43.9 bits (103), Expect = 3e-06
 Identities = 19/52 (36%), Positives = 33/52 (63%)

Query: 20  LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
           LP     D ++++F KYG++   ++ + K TG  +G AFV F+ +EEA +A+
Sbjct: 201 LPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAI 252

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

 Score = 44.1 bits (104), Expect = 3e-06
 Identities = 17/46 (36%), Positives = 26/46 (56%)

Query: 27  DYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
             +  +F  +G +  V L +   TG+ KGF F++F   EEA +ALE
Sbjct: 201 QELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALE 246

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|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 = 41.8 bits (98), Expect = 3e-06
 Identities = 17/45 (37%), Positives = 28/45 (62%)

Query: 27 DYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
            +E VFSKYG+++ V + K + T + +GF FV F   ++A  A+
Sbjct: 15 QSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAM 59

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

 Score = 41.5 bits (97), Expect = 3e-06
 Identities = 18/57 (31%), Positives = 32/57 (56%), Gaps = 1/57 (1%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          LP       +E +FS+YG++    + + + TG  +G  F+ F  + EA +A++ GLN
Sbjct: 8  LPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIK-GLN 63

This subfamily corresponds to the RRM2 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. Also included in this subfamily is the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 79

>gnl|CDD|240813 cd12367, RRM2_RBM45, RNA recognition motif 2 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 41.2 bits (97), Expect = 3e-06
 Identities = 19/52 (36%), Positives = 30/52 (57%)

Query: 21 PPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          P     + +   F ++G + YVS+ K K+TG+ KGF +V+F    +A  ALE
Sbjct: 9  PKSYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVALE 60

This subfamily corresponds to the RRM2 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 74

>gnl|CDD|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 = 41.1 bits (97), Expect = 4e-06
 Identities = 18/51 (35%), Positives = 25/51 (49%), Gaps = 6/51 (11%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKA 70
          LP     + ++  FS +G +  V +  FK     KG+AFV F T E A  A
Sbjct: 8  LPHGLTEEELQRTFSPFGAIEEVRV--FKD----KGYAFVRFDTHEAAATA 52

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

 Score = 41.1 bits (97), Expect = 4e-06
 Identities = 18/51 (35%), Positives = 23/51 (45%), Gaps = 5/51 (9%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKA 70
          L P A    +E  F KYG +  V + +        GFAFVEF    +A  A
Sbjct: 7  LGPRATKRELEDEFEKYGPLRSVWVAR-----NPPGFAFVEFEDPRDAEDA 52

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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 40.6 bits (96), Expect = 5e-06
 Identities = 22/47 (46%), Positives = 27/47 (57%), Gaps = 6/47 (12%)

Query: 33 FSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCP 79
          FS +G V  + L K K      GFAFVEFST+E A KA++  LN   
Sbjct: 5  FSPFGNVEKIKLLKKK-----PGFAFVEFSTEEAAEKAVQY-LNGVL 45

(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|240823 cd12377, RRM3_Hu, RNA recognition motif 3 in the Hu proteins family

 Score = 40.8 bits (96), Expect = 6e-06
 Identities = 20/52 (38%), Positives = 31/52 (59%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
          LPP+A+   +  +FS +G VT V + +  +T K KG+ FV  +  EEA  A+
Sbjct: 9  LPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAI 60

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

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

 Score = 40.6 bits (96), Expect = 6e-06
 Identities = 17/53 (32%), Positives = 25/53 (47%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L  +   + +   FSKYG+V    + K   TG+ +GF FV F+      K L 
Sbjct: 6  LSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLA 58

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

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

 Score = 41.0 bits (96), Expect = 6e-06
 Identities = 19/44 (43%), Positives = 28/44 (63%), Gaps = 1/44 (2%)

Query: 29 IESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          ++ +F +YGKV   ++P+ K  GKL GFAFV    ++ A  ALE
Sbjct: 18 LKKIFGRYGKVREATIPR-KRGGKLCGFAFVTMKKRKNAEIALE 60

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

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

 Score = 41.1 bits (97), Expect = 6e-06
 Identities = 17/37 (45%), Positives = 26/37 (70%), Gaps = 1/37 (2%)

Query: 25 EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEF 61
          E D +  VFS+YG++  ++L + K TGK KGFAF+ +
Sbjct: 23 EGDIL-CVFSQYGEIVDINLVRDKKTGKSKGFAFLAY 58

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

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

 Score = 40.7 bits (96), Expect = 7e-06
 Identities = 18/38 (47%), Positives = 23/38 (60%), Gaps = 1/38 (2%)

Query: 33 FSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKA 70
          FS +G +T   +      G+ KGF FV FS+ EEATKA
Sbjct: 22 FSPFGTITSAKVMT-DEKGRSKGFGFVCFSSPEEATKA 58

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

 Score = 40.8 bits (95), Expect = 7e-06
 Identities = 20/52 (38%), Positives = 31/52 (59%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
          L PE   + I+S F+ +GK++   + K  +TGK KG+ FV F  K +A  A+
Sbjct: 9  LSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAI 60

This subgroup corresponds to the RRM2 of nucleolysin TIAR, also termed TIA-1-related protein, a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal, highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 80

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

 Score = 40.3 bits (95), Expect = 8e-06
 Identities = 18/52 (34%), Positives = 27/52 (51%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
          +P +A  + +  +FS+ G V    L   + TGK KG+ F EF   E A  A+
Sbjct: 6  IPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAI 57

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

>gnl|CDD|240847 cd12401, RRM_eIF4H, RNA recognition motif in eukaryotic translation initiation factor 4H (eIF-4H) and similar proteins

 Score = 40.4 bits (95), Expect = 9e-06
 Identities = 17/45 (37%), Positives = 24/45 (53%), Gaps = 1/45 (2%)

Query: 29 IESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
          ++++F     V  V L + K T K KGF +VEF   E   +ALE 
Sbjct: 18 LDAIFKDL-SVKSVRLVRDKETDKFKGFCYVEFEDVESLKEALEY 61

This subfamily corresponds to the RRM of eIF-4H, also termed Williams-Beuren syndrome chromosomal region 1 protein, which, together with elf-4B/eIF-4G, serves as the accessory protein of RNA helicase eIF-4A. eIF-4H contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It stimulates protein synthesis by enhancing the helicase activity of eIF-4A in the initiation step of mRNA translation. . Length = 76

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

 Score = 40.1 bits (94), Expect = 1e-05
 Identities = 20/50 (40%), Positives = 25/50 (50%)

Query: 23 EAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          E   D I   FS +G +  + +     T K KGFAFVE+   E A  ALE
Sbjct: 11 ELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALE 60

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

>gnl|CDD|240846 cd12400, RRM_Nop6, RNA recognition motif in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and similar proteins

 Score = 40.0 bits (94), Expect = 1e-05
 Identities = 24/54 (44%), Positives = 29/54 (53%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
          LP +   + + + F   G    V L   K TGK KG AFVEF T E  TKAL+L
Sbjct: 8  LPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALKL 61

This subfamily corresponds to the RRM of Nop6, also known as Ydl213c, a component of 90S pre-ribosomal particles in yeast S. cerevisiae. It is enriched in the nucleolus and is required for 40S ribosomal subunit biogenesis. Nop6 is a non-essential putative RNA-binding protein with two N-terminal putative nuclear localisation sequences (NLS-1 and NLS-2) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It binds to the pre-rRNA early during transcription and plays an essential role in pre-rRNA processing. . Length = 74

>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 = 40.1 bits (94), Expect = 1e-05
 Identities = 19/52 (36%), Positives = 30/52 (57%), Gaps = 1/52 (1%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
          LP     + +E +F K+G V  V L   +S GK KG A+VE+  +  A++A+
Sbjct: 10 LPFSVTKEELEKLFKKHGVVKSVRLVTNRS-GKPKGLAYVEYENESSASQAV 60

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

 Score = 39.8 bits (93), Expect = 1e-05
 Identities = 18/52 (34%), Positives = 25/52 (48%), Gaps = 4/52 (7%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
          LPP+     IE +F KYG +  + L   +       FAFVEF    +A  A+
Sbjct: 7  LPPDIRTKDIEDLFYKYGAIRDIDLKNRRG----PPFAFVEFEDPRDAEDAV 54

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

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

 Score = 39.5 bits (93), Expect = 1e-05
 Identities = 20/57 (35%), Positives = 31/57 (54%), Gaps = 10/57 (17%)

Query: 18 EKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTG--KLKGFAFVEFSTKEEATKALE 72
          + LP E   + +E +F+++        P FK       +G AFVEF T+E+AT AL+
Sbjct: 8  QNLPEETTKEMLEMLFNQF--------PGFKEVRLVPRRGIAFVEFETEEQATVALQ 56

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

 Score = 41.7 bits (98), Expect = 2e-05
 Identities = 15/39 (38%), Positives = 22/39 (56%), Gaps = 1/39 (2%)

Query: 33  FSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
           FS+ G++T   +      G  +GF FV FS  EEA +A+
Sbjct: 306 FSECGEITSAKV-MLDEKGVSRGFGFVCFSNPEEANRAV 343

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

 Score = 41.8 bits (98), Expect = 2e-05
 Identities = 23/61 (37%), Positives = 31/61 (50%)

Query: 13  RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
           R V   +L  +A    +   FSK GKV  V   K +++ + KG A+VEF   E   KAL 
Sbjct: 90  RTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA 149

Query: 73  L 73
           L
Sbjct: 150 L 150

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|241055 cd12611, RRM1_NGR1_NAM8_like, RNA recognition motif 1 in yeast negative growth regulatory protein NGR1, yeast protein NAM8 and similar proteins

 Score = 39.7 bits (93), Expect = 2e-05
 Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 1/74 (1%)

Query: 20 LPPEAEHDYIESVFSKYGKVTY-VSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPC 78
          L P  + ++I+ V++  G     V + + +++G   G+ FVEF +   A  AL L   P 
Sbjct: 7  LEPWMDENFIKQVWASLGLEPVNVKVIRSRNSGLNAGYCFVEFPSPHAAQNALSLNGTPI 66

Query: 79 PTDYQSSILTTTSR 92
          P   ++  L   S 
Sbjct: 67 PNSNRTFKLNWASG 80

This subgroup corresponds to the RRM1 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), 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 carboxyl terminus which also harbors a methionine-rich region. The subgroup also includes NAM8, 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 = 81

>gnl|CDD|240684 cd12238, RRM1_RBM40_like, RNA recognition motif 1 in RNA-binding protein 40 (RBM40) and similar proteins

 Score = 39.5 bits (93), Expect = 2e-05
 Identities = 18/54 (33%), Positives = 24/54 (44%), Gaps = 7/54 (12%)

Query: 20 LPPEAEHDYIESVFSKYG--KVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
          LPPE   D  E +   +G   V           GKLK  AF  F  ++ A++AL
Sbjct: 7  LPPELSEDDKEDLLKHFGASSVRV-----MSRRGKLKNTAFATFDNEQAASQAL 55

This subfamily corresponds to the RRM1 of RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein), It serves as a bridging factor between the U11 and U12 snRNPs. It contains two repeats of RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions. . Length = 73

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

 Score = 39.6 bits (93), Expect = 2e-05
 Identities = 16/53 (30%), Positives = 29/53 (54%), Gaps = 2/53 (3%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L P+   + +   FS++GK+  V+L   K       FAF++F  ++ A +A+E
Sbjct: 11 LSPDVTKEELNERFSRHGKILEVNL--IKRANHTNAFAFIKFEREQAAARAVE 61

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

 Score = 39.1 bits (92), Expect = 2e-05
 Identities = 18/57 (31%), Positives = 27/57 (47%), Gaps = 11/57 (19%)

Query: 18 EKLPPEAEHDYIESV---FSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
            +PPE   + I  +   FSK+G +  + +     +      A V+FST EEA KA 
Sbjct: 7  RNIPPE--LNNITKLNEHFSKFGTIVNIQVNYNPES------ALVQFSTSEEAKKAY 55

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

 Score = 39.3 bits (92), Expect = 2e-05
 Identities = 15/57 (26%), Positives = 30/57 (52%), Gaps = 1/57 (1%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          LP +   + + S+F   G +    + + + TG+  G+ FV++  + +A KA+   LN
Sbjct: 8  LPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAIN-TLN 63

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

>gnl|CDD|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 = 39.2 bits (92), Expect = 3e-05
 Identities = 18/47 (38%), Positives = 27/47 (57%), Gaps = 4/47 (8%)

Query: 29 IESVFSKYGKVTYVSLPKF---KSTGKLKGFAFVEFSTKEEATKALE 72
          +E   ++ G V   S+ KF   K+ GK KGFA+VEF+++  A    E
Sbjct: 15 LEGALAEAGVVDVKSI-KFFEHKANGKSKGFAYVEFASEAAAAAVKE 60

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

 Score = 39.3 bits (91), Expect = 3e-05
 Identities = 19/53 (35%), Positives = 32/53 (60%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L PE   D I++ F+ +G+++   + K  +TGK KG+ FV F  K +A  A++
Sbjct: 9  LSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQ 61

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

>gnl|CDD|240872 cd12426, RRM4_PTBPH3, RNA recognition motif 4 in plant polypyrimidine tract-binding protein homolog 3 (PTBPH3)

 Score = 39.0 bits (91), Expect = 3e-05
 Identities = 24/76 (31%), Positives = 43/76 (56%), Gaps = 11/76 (14%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCP 79
          LP +   + + +  +++G +  V +  F+S GK +  A VEF+T+E+AT+AL        
Sbjct: 15 LPSDVTEEDVINHLAEHGVIVNVKV--FESNGKKQ--ALVEFATEEQATEAL-------A 63

Query: 80 TDYQSSILTTTSRLSF 95
            + SS+  +T RL+F
Sbjct: 64 CKHASSLNGSTIRLAF 79

This subfamily corresponds to the RRM4 of PTBPH3. Although its biological roles remain unclear, PTBPH3 shows 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. Like PTB, PTBPH3 contains four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 79

>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 = 38.6 bits (90), Expect = 4e-05
 Identities = 20/48 (41%), Positives = 25/48 (52%), Gaps = 9/48 (18%)

Query: 25 EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          E D IE +F  +G +    + K         FAFVEF   E+ATKALE
Sbjct: 14 EED-IEKLFEPFGPLVRCDIRK--------TFAFVEFEDSEDATKALE 52

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|240875 cd12429, RRM_DNAJC17, RNA recognition motif in the DnaJ homolog subfamily C member 17

 Score = 38.4 bits (90), Expect = 4e-05
 Identities = 25/74 (33%), Positives = 35/74 (47%), Gaps = 10/74 (13%)

Query: 13 RVVLKEKLPPEAE---HDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATK 69
          R+ +K K          D +  +FSKYG V+ V +   K     KG A VEF++K+ A  
Sbjct: 2  RLKVKWKRKKGNGDYSEDELRKIFSKYGDVSDVVVSSKK-----KGSAIVEFASKKAAEA 56

Query: 70 AL--ELGLNPCPTD 81
          A+  E GL   P  
Sbjct: 57 AVENECGLPSNPLL 70

The CD corresponds to the RRM of some eukaryotic DnaJ homolog subfamily C member 17 and similar proteins. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Members in this family contains an N-terminal DnaJ domain or J-domain, which mediates the interaction with Hsp70. They also contains a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the C-terminus, which may play an essential role in RNA binding. . Length = 74

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

 Score = 38.1 bits (89), Expect = 5e-05
 Identities = 18/52 (34%), Positives = 28/52 (53%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
          LP +     ++  FS +G++  V + K   TG+ KGF FV F+  E+  K L
Sbjct: 7  LPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVL 58

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

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

 Score = 38.3 bits (90), Expect = 6e-05
 Identities = 19/59 (32%), Positives = 29/59 (49%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPC 78
          L P      +E  FS++G V+ V + K K  G  +GFA+++  T E   K  +  LN  
Sbjct: 7  LSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKSTLNGT 65

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

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

 Score = 38.1 bits (89), Expect = 6e-05
 Identities = 16/53 (30%), Positives = 23/53 (43%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          LP +   D ++  F ++G V  V +      G+L  F FV F   E   K L 
Sbjct: 11 LPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILA 63

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|241086 cd12642, RRM_TRA2A, RNA recognition motif in transformer-2 protein homolog alpha (TRA-2 alpha) and similar proteins

 Score = 38.4 bits (89), Expect = 6e-05
 Identities = 16/44 (36%), Positives = 29/44 (65%)

Query: 29 IESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          +  VFS+YG +  V++   + TG+ +GFAFV F   +++ +A+E
Sbjct: 16 LREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAME 59

This subgroup corresponds to the RRM of TRA2-alpha or TRA-2-alpha, also termed transformer-2 protein homolog A, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein (SRp40) 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-alpha 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 = 79

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

 Score = 38.0 bits (88), Expect = 6e-05
 Identities = 21/60 (35%), Positives = 35/60 (58%), Gaps = 5/60 (8%)

Query: 13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          +V++   L   A  D ++ VF K    T + +P+  + G+ KG+AFVEF + E+A +AL 
Sbjct: 2  KVLVVNNLSYSASEDSLQEVFEK---ATSIRIPQ--NNGRPKGYAFVEFESAEDAKEALN 56

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

 Score = 38.3 bits (90), Expect = 6e-05
 Identities = 20/57 (35%), Positives = 30/57 (52%), Gaps = 3/57 (5%)

Query: 16 LKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L EK+  +     + ++FS++G V  +   K   T K++G AFV F   E AT AL 
Sbjct: 7  LNEKIKKDELKRSLYALFSQFGPVLDIVASK---TLKMRGQAFVVFKDVESATNALR 60

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

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

 Score = 37.6 bits (88), Expect = 8e-05
 Identities = 15/41 (36%), Positives = 26/41 (63%)

Query: 33 FSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
          F + G V  V +PK + T   +G+ FVEF ++E+A  A+++
Sbjct: 19 FIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKI 59

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|240718 cd12272, RRM2_PHIP1, RNA recognition motif 2 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 37.8 bits (88), Expect = 8e-05
 Identities = 17/42 (40%), Positives = 24/42 (57%)

Query: 32 VFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
           F K  ++T V L   K TG+ KGF  V+F+ +E    AL+L
Sbjct: 18 EFFKGCEITSVRLATDKETGEFKGFGHVDFADEESLDAALKL 59

The CD corresponds to the RRM2 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA. . Length = 72

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

 Score = 38.0 bits (88), Expect = 8e-05
 Identities = 20/62 (32%), Positives = 35/62 (56%), Gaps = 1/62 (1%)

Query: 12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
          G  V   K+P +   D +  +F + GK+    L   + +G+ +G+AFV ++TKEEA  A+
Sbjct: 1  GCEVFVGKIPRDMYEDELVPLFERAGKIYEFRL-MMEFSGENRGYAFVMYTTKEEAQLAI 59

Query: 72 EL 73
           +
Sbjct: 60 RI 61

This subgroup corresponds to the RRM1 of RBM46, also termed cancer/testis antigen 68 (CT68), a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM46 contains two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 78

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

 Score = 37.6 bits (88), Expect = 1e-04
 Identities = 21/61 (34%), Positives = 33/61 (54%), Gaps = 3/61 (4%)

Query: 13 RVVLKEKLPPEAEHDYIESVFSK-YGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
          R+++K  LP       ++  FSK  G++T V L      GK +  AF+ + T+EEA KA 
Sbjct: 2  RLIVKN-LPASLTEAELKEHFSKHGGEITDVKL-LRTEDGKSRRIAFIGYKTEEEAQKAK 59

Query: 72 E 72
          +
Sbjct: 60 D 60

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

>gnl|CDD|241027 cd12583, RRM2_hnRNPD, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 37.7 bits (87), Expect = 1e-04
 Identities = 20/64 (31%), Positives = 31/64 (48%), Gaps = 5/64 (7%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE-----LG 74
          L P+   + I   F  +G+V  + LP    T K +GF F+ F  +E   K +E     +G
Sbjct: 7  LSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVG 66

Query: 75 LNPC 78
          L+ C
Sbjct: 67 LSKC 70

This subgroup corresponds to the RRM2 of hnRNP D0, also termed AU-rich element RNA-binding protein 1, a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP D0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), in the middle and an RGG box rich in glycine and arginine residues in the C-terminal part. Each of RRMs can bind solely to the UUAG sequence specifically. . Length = 75

>gnl|CDD|241099 cd12655, RRM3_HuC, RNA recognition motif 3 in vertebrate Hu-antigen C (HuC)

 Score = 37.8 bits (87), Expect = 1e-04
 Identities = 20/60 (33%), Positives = 31/60 (51%)

Query: 12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
          G  +    L PEA+   +  +F  +G VT V + +  +T K KGF FV  +  +EA  A+
Sbjct: 1  GWCIFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAI 60

This subgroup corresponds to the RRM3 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 85

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

 Score = 37.4 bits (87), Expect = 1e-04
 Identities = 15/46 (32%), Positives = 30/46 (65%)

Query: 27 DYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          +++++ F K+G V    +   + TG+ +GF +V+F + E+A KA+E
Sbjct: 14 EWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIE 59

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

 Score = 37.3 bits (87), Expect = 1e-04
 Identities = 15/52 (28%), Positives = 25/52 (48%)

Query: 22 PEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
               + ++  F   G +  +++   K TG+ KGFA++EF  K     AL L
Sbjct: 9  YGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALLL 60

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

 Score = 37.0 bits (86), Expect = 1e-04
 Identities = 18/53 (33%), Positives = 25/53 (47%), Gaps = 8/53 (15%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
           PP+     I  +FS YG V  V +        +  FAFVEF + E A +A +
Sbjct: 7  FPPDTSESAIREIFSPYGAVKEVKM--------ISNFAFVEFESLESAIRAKD 51

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

 Score = 37.2 bits (86), Expect = 1e-04
 Identities = 18/53 (33%), Positives = 25/53 (47%), Gaps = 8/53 (15%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          LPPEA    I S+F +YGKV    +        +K + FV    K  A +A+ 
Sbjct: 8  LPPEATEQEIRSLFEQYGKVLECDI--------IKNYGFVHMDDKTAADEAIR 52

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

 Score = 37.0 bits (86), Expect = 1e-04
 Identities = 20/40 (50%), Positives = 22/40 (55%), Gaps = 1/40 (2%)

Query: 34 SKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
           K G+VTYV L K    GK +G   VEF  KE   KALE 
Sbjct: 22 EKVGEVTYVELFK-DEEGKSRGCGVVEFKDKESVQKALET 60

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

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

 Score = 37.0 bits (86), Expect = 2e-04
 Identities = 17/56 (30%), Positives = 29/56 (51%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGL 75
          LPP+   +  +  FS++GKV    L +   TG+ +GF FV F ++    +    G+
Sbjct: 7  LPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSAGM 62

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

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

 Score = 37.2 bits (87), Expect = 2e-04
 Identities = 14/45 (31%), Positives = 22/45 (48%), Gaps = 6/45 (13%)

Query: 29 IESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
          +  VF KYG V  + +P  K       + FV +S+ E+A  A + 
Sbjct: 20 LLRVFEKYGTVEDLVMPPGKP------YCFVSYSSIEDAAAAYDA 58

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

 Score = 36.7 bits (85), Expect = 2e-04
 Identities = 16/54 (29%), Positives = 26/54 (48%)

Query: 14 VVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEA 67
          V+    LP       ++  FS++G V  V + + K TG  K + F++F   E A
Sbjct: 1  VIYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVA 54

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

 Score = 36.7 bits (85), Expect = 2e-04
 Identities = 20/50 (40%), Positives = 31/50 (62%), Gaps = 6/50 (12%)

Query: 29 IESVFSKYGKV--TYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          +E VFS YG+V   Y+   + K +   +G AFV++S+KE A  A++  LN
Sbjct: 16 VEEVFSPYGRVEDIYMMRDEMKQS---RGCAFVKYSSKEMAQAAIK-ALN 61

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

 Score = 36.9 bits (85), Expect = 2e-04
 Identities = 17/44 (38%), Positives = 27/44 (61%)

Query: 29 IESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          +  VFSKYG +  VS+   + + + +GFAFV F   ++A +A E
Sbjct: 26 LREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 69

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

 Score = 36.5 bits (84), Expect = 2e-04
 Identities = 16/43 (37%), Positives = 25/43 (58%), Gaps = 8/43 (18%)

Query: 29 IESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
          +E++FSKYGK+   S+         KGFAFV++  +  A  A+
Sbjct: 19 VEAIFSKYGKIVGCSVH--------KGFAFVQYVNERNARAAV 53

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

>gnl|CDD|241199 cd12755, RRM2_RBM5, RNA recognition motif 2 in vertebrate RNA-binding protein 5 (RBM5)

 Score = 36.8 bits (85), Expect = 3e-04
 Identities = 21/71 (29%), Positives = 36/71 (50%), Gaps = 4/71 (5%)

Query: 11 YGRVVLKEKLPPEAEHDYIESVFSKYGK--VTYVSLPKFKSTGKLKGFAFVEFSTKEEAT 68
          Y   ++   + P    D I +  + Y    V  + L K K T + +GFAFV+ S+  EA+
Sbjct: 1  YCDTIILRNIAPHTVVDSILTALAPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSALEAS 60

Query: 69 KALEL--GLNP 77
          + L++   L+P
Sbjct: 61 QLLQILQSLHP 71

This subgroup corresponds to the RRM2 of RBM5, also termed protein G15, or putative tumor suppressor LUCA15, or renal carcinoma antigen NY-REN-9, a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM5 shows high sequence similarity to RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). Both, RBM5 and RBM6, specifically bind poly(G) RNA. They contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain. . Length = 86

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

 Score = 36.4 bits (85), Expect = 3e-04
 Identities = 19/60 (31%), Positives = 33/60 (55%), Gaps = 2/60 (3%)

Query: 13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          R+++K  LP     D +   F   G+VT V + +    GK + F FV F ++E+A +A++
Sbjct: 2  RIIVK-NLPKYVTEDRLREHFESKGEVTDVKVMR-TRDGKSRRFGFVGFKSEEDAQQAVK 59

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|240676 cd12230, RRM1_U2AF65, RNA recognition motif 1 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 36.4 bits (85), Expect = 3e-04
 Identities = 15/20 (75%), Positives = 15/20 (75%)

Query: 54 KGFAFVEFSTKEEATKALEL 73
          K FAFVEF T EEAT AL L
Sbjct: 48 KNFAFVEFRTVEEATAALAL 67

The subfamily corresponds to the RRM1 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs. Length = 82

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

 Score = 36.5 bits (85), Expect = 3e-04
 Identities = 19/55 (34%), Positives = 30/55 (54%), Gaps = 1/55 (1%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELG 74
          +PP+   + +   FS++G V  V +      G  KG+ FV F T+E+A K L +G
Sbjct: 10 IPPDTTEEELRDFFSRFGSVKDVKI-ITDRAGVSKGYGFVTFETQEDAEKILAMG 63

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|241006 cd12562, RRM2_RBM5_like, RNA recognition motif 2 in RNA-binding protein 5 (RBM5) and similar proteins

 Score = 36.8 bits (85), Expect = 3e-04
 Identities = 21/71 (29%), Positives = 36/71 (50%), Gaps = 4/71 (5%)

Query: 11 YGRVVLKEKLPPEAEHDYIESVFSKYGK--VTYVSLPKFKSTGKLKGFAFVEFSTKEEAT 68
              ++   + P    D I S  + Y    V+ + L K K T + +GFAFV+ S+  EA+
Sbjct: 1  ANDTIILRNIAPHTVVDSILSALAPYASLSVSNIRLIKDKQTQQNRGFAFVQLSSALEAS 60

Query: 69 KALEL--GLNP 77
          + L++   L+P
Sbjct: 61 QLLQILQALHP 71

This subgroup corresponds to the RRM2 of RNA-binding protein 5 (RBM5 or LUCA15 or H37), RNA-binding protein 10 (RBM10 or S1-1) and similar proteins. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor; it specifically binds poly(G) RNA. RBM10, a paralog of RBM5, may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. Both, RBM5 and RBM10, contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain. . Length = 86

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

 Score = 36.6 bits (84), Expect = 3e-04
 Identities = 19/60 (31%), Positives = 31/60 (51%)

Query: 12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
          G  +    L P+A+   +  +F  +G VT V + +  +T K KGF FV  +  +EA  A+
Sbjct: 3  GWCIFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAI 62

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

>gnl|CDD|240685 cd12239, RRM2_RBM40_like, RNA recognition motif 2 in RNA-binding protein 40 (RBM40) and similar proteins

 Score = 36.4 bits (85), Expect = 3e-04
 Identities = 17/58 (29%), Positives = 28/58 (48%), Gaps = 4/58 (6%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFK----STGKLKGFAFVEFSTKEEATKALEL 73
          L      + +  +F ++   +      F     + G++KG AFV F ++E ATKAL L
Sbjct: 9  LSKRVTEEDLVYIFGRFVDSSSEEKNMFDIRLMTEGRMKGQAFVTFPSEEIATKALNL 66

This subfamily corresponds to the RRM2 of RBM40 and the RRM of RBM41. RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein). It serves as a bridging factor between the U11 and U12 snRNPs. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions. RBM41 contains only one RRM. Its biological function remains unclear. . Length = 82

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

 Score = 36.3 bits (84), Expect = 3e-04
 Identities = 18/52 (34%), Positives = 29/52 (55%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
          +P EA  + ++ +FS+ G V    L   + TGK KG+ F E+  +E A  A+
Sbjct: 6  IPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAM 57

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

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

 Score = 36.8 bits (85), Expect = 3e-04
 Identities = 19/52 (36%), Positives = 25/52 (48%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
          LP +A  + +   FSK+G V Y      KSTG+ KG  FV F  +      L
Sbjct: 9  LPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACL 60

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|241028 cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 36.1 bits (83), Expect = 4e-04
 Identities = 18/53 (33%), Positives = 28/53 (52%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L PEA  + I   F ++G++  + LP    T K +GF F+ F  ++   K LE
Sbjct: 12 LNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEEDPVKKVLE 64

This subgroup corresponds to the RRM2 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 80

>gnl|CDD|241024 cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 36.1 bits (83), Expect = 4e-04
 Identities = 14/47 (29%), Positives = 25/47 (53%)

Query: 23 EAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATK 69
          + E  ++   F +YGK+  + +   + +GK +GFAFV F   +   K
Sbjct: 11 DTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDK 57

This subgroup corresponds to the RRM2 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A1 has been characterized as a splicing silencer, often acting in opposition to an activating hnRNP H. It silences exons when bound to exonic elements in the alternatively spliced transcripts of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle between the nucleus and the cytoplasm. Thus, it may be involved in transport of cellular RNAs, including the packaging of pre-mRNA into hnRNP particles and transport of poly A+ mRNA from the nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has high affinity with AU-rich elements, whereas the nuclear hnRNP A1 has high affinity with a polypyrimidine stretch bordered by AG at the 3' ends of introns. hnRNP A1 is also involved in the replication of an RNA virus, such as mouse hepatitis virus (MHV), through an interaction with the transcription-regulatory region of viral RNA. Moreover, hnRNP A1, together with the scaffold protein septin 6, serves as host proteins to form a complex with NS5b and viral RNA, and further play important roles in the replication of Hepatitis C virus (HCV). hnRNP A1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The RRMs of hnRNP A1 play an important role in silencing the exon and the glycine-rich domain is responsible for protein-protein interactions. . Length = 77

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

 Score = 35.9 bits (83), Expect = 4e-04
 Identities = 16/53 (30%), Positives = 26/53 (49%), Gaps = 3/53 (5%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          LP +     +E +F KYG +  + L   K   +  G+AF+EF    +A  A+ 
Sbjct: 7  LPGDIREREVEDLFYKYGPIVDIDL---KLPPRPPGYAFIEFEDARDAEDAIR 56

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

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

 Score = 37.9 bits (88), Expect = 5e-04
 Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 2/61 (3%)

Query: 12  GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
           G + +K  L    ++  +   FSK+G +    +      GK +G+ FV F  +E A  A+
Sbjct: 89  GNIFVK-NLDKSVDNKALFDTFSKFGNILSCKVAT-DENGKSRGYGFVHFEKEESAKAAI 146

Query: 72  E 72
           +
Sbjct: 147 Q 147

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|241029 cd12585, RRM2_hnRPDL, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP DL) and similar proteins

 Score = 35.8 bits (82), Expect = 5e-04
 Identities = 16/53 (30%), Positives = 28/53 (52%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L P+   + I+  F  +G++  + LP    T + +GF FV ++ +E   K LE
Sbjct: 7  LSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQKLLE 59

This subgroup corresponds to the RRM2 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 75

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

 Score = 36.0 bits (84), Expect = 5e-04
 Identities = 18/49 (36%), Positives = 25/49 (51%), Gaps = 5/49 (10%)

Query: 29 IESVFSKYGKVTYVSLPKFKSTGKLK-----GFAFVEFSTKEEATKALE 72
          ++  F K G V  V++ K K           G+ FVEF +KE A KAL+
Sbjct: 17 LKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQKALK 65

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

 Score = 35.7 bits (83), Expect = 5e-04
 Identities = 19/51 (37%), Positives = 27/51 (52%), Gaps = 6/51 (11%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKA 70
          LP +   +  + +FSKYG+V+ V L       K KGF F+   T+  A KA
Sbjct: 9  LPNDITEEEFKELFSKYGEVSEVFLN------KEKGFGFIRLDTRTNAEKA 53

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

 Score = 35.3 bits (82), Expect = 5e-04
 Identities = 16/57 (28%), Positives = 26/57 (45%), Gaps = 9/57 (15%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          LP     + + ++F KYG VT            +K + FV    +E+A  A++  LN
Sbjct: 7  LPDATTSEELRALFEKYGTVT--------ECDVVKNYGFVHMEEEEDAEDAIK-ALN 54

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

 Score = 35.8 bits (83), Expect = 5e-04
 Identities = 14/49 (28%), Positives = 27/49 (55%)

Query: 24 AEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
             D +   F+ +G++  + + K K T + KG A+V+F+    A +A+E
Sbjct: 14 VTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAME 62

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

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

 Score = 37.4 bits (86), Expect = 6e-04
 Identities = 20/50 (40%), Positives = 27/50 (54%)

Query: 23  EAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
           E   D I   F  +G +  +++    +TGK KGFAFVE+   E A  ALE
Sbjct: 118 ELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALE 167

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

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

 Score = 35.4 bits (82), Expect = 6e-04
 Identities = 16/52 (30%), Positives = 30/52 (57%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
          L  E   D +++ FS++G++T   + K  +T + +GF FV F++  E   A+
Sbjct: 7  LSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAM 58

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

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

 Score = 35.7 bits (82), Expect = 6e-04
 Identities = 20/54 (37%), Positives = 27/54 (50%), Gaps = 1/54 (1%)

Query: 24 AEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNP 77
           E D  E  FS++G V    +   K TGK +GF FV F   + A KA  +  +P
Sbjct: 12 GEGDLTEH-FSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAVVKFHP 64

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

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

 Score = 35.3 bits (82), Expect = 7e-04
 Identities = 22/57 (38%), Positives = 31/57 (54%), Gaps = 1/57 (1%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          LPP    + +E +   +GK+        K T K KG+ FV+F + E A KA+E GLN
Sbjct: 8  LPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIE-GLN 63

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|240995 cd12551, RRM_II_PABPN1L, RNA recognition motif in vertebrate type II embryonic polyadenylate-binding protein 2 (ePABP-2)

 Score = 35.2 bits (81), Expect = 7e-04
 Identities = 15/47 (31%), Positives = 29/47 (61%)

Query: 27 DYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
          + +E+ FS  G +  V++   K +G  KG+A++EF+T++    A+ L
Sbjct: 14 EELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFATRDSVEAAVAL 60

This subgroup corresponds to the RRM of ePABP-2, also termed embryonic poly(A)-binding protein 2, or poly(A)-binding protein nuclear-like 1 (PABPN1L). ePABP-2 is a novel embryonic-specific cytoplasmic type II poly(A)-binding protein that is expressed during the early stages of vertebrate development and in adult ovarian tissue. It may play an important role in the poly(A) metabolism of stored mRNAs during early vertebrate development. ePABP-2 shows significant sequence similarity to the ubiquitously expressed nuclear polyadenylate-binding protein 2 (PABP-2 or PABPN1). Like PABP-2, ePABP-2 contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, it possesses an acidic N-terminal domain predicted to form a coiled-coil and an arginine-rich C-terminal domain. . Length = 77

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

 Score = 35.2 bits (82), Expect = 8e-04
 Identities = 14/53 (26%), Positives = 26/53 (49%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L P+     +  +FS  G V  + + +   T +  G+A+V F    +A +AL+
Sbjct: 7  LHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALD 59

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

 Score = 35.2 bits (81), Expect = 8e-04
 Identities = 13/52 (25%), Positives = 24/52 (46%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
          L      + +   FS    + +  +     TG+ +G+ FV F+  E+A +AL
Sbjct: 7  LAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEAL 58

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

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

 Score = 35.0 bits (81), Expect = 8e-04
 Identities = 16/52 (30%), Positives = 23/52 (44%), Gaps = 8/52 (15%)

Query: 19 KLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKA 70
          +LP  A    +E  F  YG++  ++L          GF FVEF    +A  A
Sbjct: 6  RLPYRARERDVERFFKGYGRIREINLK--------NGFGFVEFEDPRDADDA 49

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|241026 cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 35.3 bits (81), Expect = 8e-04
 Identities = 15/47 (31%), Positives = 26/47 (55%)

Query: 23 EAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATK 69
          + E  ++   F KYGK+  + + + + +GK +GFAFV F   +   K
Sbjct: 11 DTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDK 57

This subgroup corresponds to the RRM2 of hnRNP A3, a novel RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE) independently of hnRNP A2 and participates in the trafficking of A2RE-containing RNA. hnRNP A3 can shuttle between the nucleus and the cytoplasm. It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

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

 Score = 35.1 bits (81), Expect = 9e-04
 Identities = 16/47 (34%), Positives = 26/47 (55%)

Query: 27 DYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
          D ++  FS++GKV    L   K T + +GF FV F +++   K  E+
Sbjct: 14 DDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCEI 60

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

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

 Score = 36.8 bits (85), Expect = 0.001
 Identities = 17/52 (32%), Positives = 28/52 (53%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
          LP     + I S+F+  G++    L + K TG+  G+ FV +   E+A KA+
Sbjct: 11 LPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAV 62

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

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

 Score = 36.5 bits (84), Expect = 0.001
 Identities = 18/57 (31%), Positives = 30/57 (52%), Gaps = 1/57 (1%)

Query: 20  LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
           LP       +ES+FS +G++    +     TG  KG  F+ F  ++EA +A++  LN
Sbjct: 97  LPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIK-TLN 152

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

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

 Score = 36.5 bits (84), Expect = 0.001
 Identities = 17/57 (29%), Positives = 30/57 (52%), Gaps = 1/57 (1%)

Query: 20  LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
           L P+ +   +  +F  +G V  V + +  +T + KG+ FV  +  +EA  A+ L LN
Sbjct: 277 LSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAI-LSLN 332

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

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

 Score = 35.3 bits (82), Expect = 0.001
 Identities = 13/34 (38%), Positives = 22/34 (64%)

Query: 33 FSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEE 66
          F +YG +  + L + K TGK +G+AF+EF  + +
Sbjct: 22 FEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERD 55

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

 Score = 34.7 bits (80), Expect = 0.001
 Identities = 17/55 (30%), Positives = 29/55 (52%), Gaps = 2/55 (3%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKS-TGKLKGFAFVEFSTKEEATKALEL 73
          LP +   + I+  F +   V+ V LP+     G+L+GF + EF  ++   +AL L
Sbjct: 9  LPYDVTEEDIKEFF-RGLNVSSVRLPREPGDPGRLRGFGYAEFEDRDSLLQALSL 62

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

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

 Score = 34.8 bits (81), Expect = 0.002
 Identities = 17/43 (39%), Positives = 23/43 (53%), Gaps = 3/43 (6%)

Query: 33 FSKYGKVTYVSLPKFKSTGKLK---GFAFVEFSTKEEATKALE 72
            KYGKV  V +P+ ++ G      G  FVEF+  E+A KA  
Sbjct: 32 CGKYGKVLSVVIPRPEAEGVDVPGVGKVFVEFADVEDAQKAQL 74

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

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

 Score = 34.6 bits (80), Expect = 0.002
 Identities = 17/57 (29%), Positives = 29/57 (50%), Gaps = 1/57 (1%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          LP       +E++FS YG++    +     TG  +G  F+ F  + EA +A++  LN
Sbjct: 8  LPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIK-ALN 63

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

>gnl|CDD|241076 cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 34.3 bits (79), Expect = 0.002
 Identities = 17/52 (32%), Positives = 30/52 (57%)

Query: 19 KLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKA 70
          ++P   E   +  +F ++GK+  +++ K K TG  KG AF+ +  +E A KA
Sbjct: 12 QIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALKA 63

This subfamily corresponds to the RRM1 of CELF-3, CELF-4, CELF-5, CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein.The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in an muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In additiona to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 87

>gnl|CDD|240913 cd12467, RRM_Srp1p_like, RNA recognition motif 1 in fission yeast pre-mRNA-splicing factor Srp1p and similar proteins

 Score = 34.4 bits (79), Expect = 0.002
 Identities = 13/41 (31%), Positives = 23/41 (56%), Gaps = 1/41 (2%)

Query: 33 FSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
          F +YG++    +P  + T + + FAFVE+ +  +A  A E 
Sbjct: 20 FERYGRLVRCDIPPPR-TFQSRPFAFVEYESHRDAEDAYEE 59

This subgroup corresponds to the RRM domain in Srp1p encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but not essential for growth. Srp1p is closely related to the SR protein family found in metazoa. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine hinge and a RS domain in the middle, and a C-terminal domain. Some family members also contain another RRM domain. Length = 78

>gnl|CDD|240734 cd12288, RRM_La_like_plant, RNA recognition motif in plant proteins related to the La autoantigen

 Score = 34.4 bits (79), Expect = 0.002
 Identities = 22/73 (30%), Positives = 29/73 (39%), Gaps = 15/73 (20%)

Query: 13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSL------------PKFKSTGKL---KGFA 57
          R V+ E LP +   + +E +F   G V  V +             K K    L   K  A
Sbjct: 1  RTVVAENLPEDHSIENLEEIFGTVGSVKNVRICDPGRVGSGSTASKAKKPDTLVSNKLHA 60

Query: 58 FVEFSTKEEATKA 70
           VE+ T E A KA
Sbjct: 61 LVEYETVEAAEKA 73

This subfamily corresponds to the RRM of plant La-like proteins related to the La autoantigen. A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes. Members in this family contain an LAM domain followed by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 93

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

 Score = 33.7 bits (78), Expect = 0.003
 Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 1/57 (1%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          LP     D ++ +   +GK+   +L K  +TG  KG+AF E+       +A+  GLN
Sbjct: 8  LPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIA-GLN 63

This subfamily corresponds to the RRM2 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs. Length = 77

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

 Score = 33.8 bits (78), Expect = 0.003
 Identities = 15/62 (24%), Positives = 30/62 (48%), Gaps = 3/62 (4%)

Query: 13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          RV+   K+P +     +   F  +G++  ++L  F+  G    + FV +    +A +A+E
Sbjct: 3  RVIYVGKIPIDTTRSELRQRFQPFGEIEEITL-HFRDDGD--NYGFVTYRYACDAFRAIE 59

Query: 73 LG 74
           G
Sbjct: 60 HG 61

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|241025 cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 33.9 bits (77), Expect = 0.003
 Identities = 13/47 (27%), Positives = 24/47 (51%)

Query: 23 EAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATK 69
          + E  ++   F +YGK+  + +   + +GK +GF FV F   +   K
Sbjct: 11 DTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDK 57

This subgroup corresponds to the RRM2 of hnRNP A2/B1, an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

>gnl|CDD|240850 cd12404, RRM2_NCL, RNA recognition motif 2 in vertebrate nucleolin

 Score = 33.7 bits (77), Expect = 0.003
 Identities = 20/60 (33%), Positives = 28/60 (46%), Gaps = 4/60 (6%)

Query: 13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          R +  + LP     D ++ VF     +   S       G  KG A++EF T+ EA KALE
Sbjct: 4  RTLFVKNLPYNITVDELKEVFEDAVDIRLPS----GKDGSSKGIAYIEFKTEAEAEKALE 59

This subfamily corresponds to the RRM2 of ubiquitously expressed protein nucleolin, also termed protein C23, 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.RRM2, together with RRM1, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop. . Length = 77

>gnl|CDD|241100 cd12656, RRM3_HuD, RNA recognition motif 3 in vertebrate Hu-antigen D (HuD)

 Score = 33.9 bits (77), Expect = 0.003
 Identities = 17/60 (28%), Positives = 30/60 (50%)

Query: 12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
          G  +    L P+++   +  +F  +G V  V + +  +T K KGF FV  +  +EA  A+
Sbjct: 3  GWCIFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAI 62

This subgroup corresponds to the RRM3 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells. And it also regulates the neurite elongation and morphological differentiation. HuD specifically bound poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 86

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

 Score = 33.2 bits (76), Expect = 0.004
 Identities = 17/52 (32%), Positives = 26/52 (50%), Gaps = 3/52 (5%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
          LP +     +E +F KYG++  + L   K+   L  FAFV F    +A  A+
Sbjct: 7  LPSDVREKDLEDLFYKYGRIRDIEL---KNRRGLVPFAFVRFEDPRDAEDAV 55

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

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

 Score = 33.4 bits (77), Expect = 0.004
 Identities = 16/46 (34%), Positives = 24/46 (52%)

Query: 27 DYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          + +   FSKY       + + K TGK KG+ FV FS   +  KA++
Sbjct: 21 EVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAMK 66

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

 Score = 33.4 bits (77), Expect = 0.004
 Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 5/49 (10%)

Query: 19 KLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEA 67
          +L  +   + +   FS++G+VT V +PK       + FAFV F+  E A
Sbjct: 7  RLTEDMTEEDLRQYFSQFGEVTDVYIPK-----PFRAFAFVTFADPEVA 50

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

 Score = 33.4 bits (76), Expect = 0.004
 Identities = 21/62 (33%), Positives = 33/62 (53%)

Query: 12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
          G  +   K+P +   D +  +F K G +  + L     TG  +G+AFV F TKE A +A+
Sbjct: 1  GTEIFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEAV 60

Query: 72 EL 73
          +L
Sbjct: 61 KL 62

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

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

 Score = 33.4 bits (76), Expect = 0.004
 Identities = 18/57 (31%), Positives = 31/57 (54%), Gaps = 1/57 (1%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          LP       +E +FS+YG++    +   + TG  +G  F+ F  + EA +A++ GLN
Sbjct: 9  LPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIK-GLN 64

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	115
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.82
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.75
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.73
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.73
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.72
KOG0121|consensus	153		99.68
KOG0122|consensus	270		99.67
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.66
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.65
KOG0117|consensus	506		99.65
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.65
KOG0113|consensus	335		99.65
KOG0149|consensus	247		99.64
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.63
KOG0125|consensus	376		99.63
KOG0107|consensus	195		99.63
PLN03120	260	nucleic acid binding protein; Provisional	99.59
KOG4207|consensus	256		99.58
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.58
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.58
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.56
PLN03213	759	repressor of silencing 3; Provisional	99.56
smart00362	72	RRM_2 RNA recognition motif.	99.55
KOG0111|consensus	298		99.54
KOG0126|consensus	219		99.54
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.54
KOG0144|consensus	510		99.53
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.53
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.53
smart00360	71	RRM RNA recognition motif.	99.52
PLN03121	243	nucleic acid binding protein; Provisional	99.51
KOG0130|consensus	170		99.51
KOG0131|consensus	203		99.5
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.49
KOG0105|consensus	241		99.49
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.48
KOG0117|consensus	506		99.46
KOG0114|consensus	124		99.45
KOG0145|consensus	360		99.45
KOG0108|consensus	435		99.45
KOG0148|consensus	321		99.45
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.44
KOG0148|consensus	321		99.43
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.43
KOG0144|consensus	510		99.39
KOG0146|consensus	371		99.36
KOG0109|consensus	346		99.35
smart00361	70	RRM_1 RNA recognition motif.	99.33
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.33
KOG0124|consensus	544		99.33
KOG0145|consensus	360		99.32
KOG0127|consensus	678		99.31
KOG0127|consensus	678		99.31
KOG4208|consensus	214		99.3
KOG0146|consensus	371		99.28
KOG0147|consensus	549		99.27
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.2
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.19
KOG0131|consensus	203		99.19
KOG0415|consensus	479		99.19
KOG1457|consensus	284		99.16
KOG0124|consensus	544		99.15
KOG4212|consensus	608		99.15
KOG0123|consensus	369		99.14
KOG0533|consensus	243		99.14
KOG4206|consensus	221		99.11
KOG4205|consensus	311		99.08
KOG0123|consensus	369		99.01
KOG0109|consensus	346		98.99
KOG4661|consensus	940		98.96
KOG4205|consensus	311		98.96
KOG4660|consensus	549		98.95
KOG0132|consensus	894		98.93
KOG0153|consensus	377		98.84
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.84
KOG4212|consensus	608		98.84
KOG4209|consensus	231		98.83
KOG1548|consensus	382		98.81
KOG0116|consensus	419		98.79
KOG0110|consensus	725		98.77
KOG0226|consensus	290		98.71
KOG0151|consensus	877		98.69
KOG0110|consensus	725		98.69
KOG4211|consensus	510		98.64
KOG0106|consensus	216		98.57
KOG4454|consensus	267		98.52
KOG0120|consensus	500		98.5
KOG3152|consensus	278		98.23
KOG1457|consensus	284		98.22
KOG2314|consensus	698		98.15
KOG1995|consensus	351		98.15
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.06
KOG4211|consensus	510		98.05
KOG0147|consensus	549		98.05
KOG4206|consensus	221		98.02
KOG1190|consensus	492		97.98
KOG4849|consensus	498		97.87
KOG4307|consensus	944		97.86
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.79
KOG0129|consensus	520		97.66
KOG4210|consensus	285		97.65
KOG0129|consensus	520		97.65
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.63
KOG0105|consensus	241		97.57
KOG0106|consensus	216		97.56
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.52
KOG1855|consensus	484		97.51
KOG1365|consensus	508		97.32
KOG1190|consensus	492		97.31
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	97.14
KOG1456|consensus	494		97.09
KOG1365|consensus	508		97.06
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	96.97
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	96.88
KOG0120|consensus	500		96.87
KOG1548|consensus	382		96.78
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	96.74
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	96.65
KOG0128|consensus	881		96.58
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	96.46
KOG0115|consensus	275		96.44
KOG4676|consensus	479		96.29
KOG0128|consensus	881		96.15
KOG0112|consensus	975		96.13
KOG0112|consensus	975		95.74
KOG0804|consensus	493		95.7
KOG2202|consensus	260		95.4
KOG4307|consensus	944		95.22
KOG2416|consensus	718		95.18
KOG1456|consensus	494		95.09
KOG1996|consensus	378		94.5
KOG4660|consensus	549		94.19
KOG2068|consensus	327		93.89
KOG2193|consensus	584		93.17
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	92.93
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	92.3
KOG4210|consensus	285		92.12
KOG4285|consensus	350		91.48
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	90.8
KOG2253|consensus	668		90.79
KOG4483|consensus	528		88.68
KOG2591|consensus	684		87.59
KOG4410|consensus	396		87.54
KOG2318|consensus	650		86.7
KOG4574|consensus	1007		85.65
smart00596	69	PRE_C2HC PRE_C2HC domain.	81.91
KOG4019|consensus	193		80.72

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

Probab=99.82  E-value=3.6e-19  Score=110.86  Aligned_cols=85  Identities=18%  Similarity=0.247  Sum_probs=78.3

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      ....++|||+|||..+++++|+++|.+||.|..+.++.++.+++++|||||+|.+.++|+.|++.|++..++++.+.|..
T Consensus        31 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~  110 (144)
T PLN03134         31 RLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNP  110 (144)
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            34467899999999999999999999999999999999988999999999999999999999999999999999999887


Q ss_pred             eeecc
Q psy3928          89 TTSRL   93 (115)
Q Consensus        89 ~~~~~   93 (115)
                      ++.+.
T Consensus       111 a~~~~  115 (144)
T PLN03134        111 ANDRP  115 (144)
T ss_pred             CCcCC
Confidence            76543

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.75  E-value=1.2e-17  Score=116.91  Aligned_cols=81  Identities=20%  Similarity=0.298  Sum_probs=77.0

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEeee
Q psy3928          12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTTS   91 (115)
Q Consensus        12 ~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~~   91 (115)
                      +..|||+|||..+++++|+++|++||.|..++++.++.++.++|||||+|.+.++|..|+..|||..++|+.++|..++.
T Consensus       269 ~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~~  348 (352)
T TIGR01661       269 GYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKTN  348 (352)
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEccC
Confidence            44799999999999999999999999999999999998999999999999999999999999999999999999998876


Q ss_pred             c
Q psy3928          92 R   92 (115)
Q Consensus        92 ~   92 (115)
                      +
T Consensus       349 ~  349 (352)
T TIGR01661       349 K  349 (352)
T ss_pred             C
Confidence            4

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

>PF00076 RRM_1: RNA recognition motif

Probab=99.73  E-value=3.6e-17  Score=89.61  Aligned_cols=70  Identities=33%  Similarity=0.534  Sum_probs=65.5

Q ss_pred             EEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceee
Q psy3928          15 VLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSS   85 (115)
Q Consensus        15 l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~   85 (115)
                      |||+|||.++++.+|+++|.+||.+..+.+..+ .++..+++|||+|.+.++|++|++.+++..+.+..++
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~-~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRN-SSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEE-TTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhccccccccc-ccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            799999999999999999999999999998887 4889999999999999999999999999998888764

(a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.73  E-value=3.3e-17  Score=114.70  Aligned_cols=81  Identities=21%  Similarity=0.283  Sum_probs=76.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEee
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTT   90 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~   90 (115)
                      ...+|||+|||..+++++|+++|..||.|..++|+.++.+|+++|||||+|.+.++|++|+..|++..+.|+.+.+....
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            45789999999999999999999999999999999998899999999999999999999999999999999999887665


Q ss_pred             e
Q psy3928          91 S   91 (115)
Q Consensus        91 ~   91 (115)
                      +
T Consensus        82 ~   82 (352)
T TIGR01661        82 P   82 (352)
T ss_pred             c
Confidence            4

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

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.72  E-value=6.3e-17  Score=113.23  Aligned_cols=84  Identities=15%  Similarity=0.265  Sum_probs=77.4

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      .....++|||++||.++++++|+++|..||.|..++|+.++.+++++|||||+|.++++|++|++.|++..+.++.+.+.
T Consensus       103 ~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~  182 (346)
T TIGR01659       103 TNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVS  182 (346)
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeee
Confidence            34467899999999999999999999999999999999998899999999999999999999999999999999998887


Q ss_pred             Eeee
Q psy3928          88 TTTS   91 (115)
Q Consensus        88 ~~~~   91 (115)
                      .+++
T Consensus       183 ~a~p  186 (346)
T TIGR01659       183 YARP  186 (346)
T ss_pred             cccc
Confidence            6543

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).

>KOG0121|consensus

Probab=99.68  E-value=1.5e-16  Score=95.27  Aligned_cols=80  Identities=21%  Similarity=0.204  Sum_probs=74.5

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      ....++||||||+..++|+.|.++|..+|.|+.+.|-.++.+-.++|||||+|.+.++|..|++.+++..++.+.|++..
T Consensus        33 ~r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~  112 (153)
T KOG0121|consen   33 LRKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDW  112 (153)
T ss_pred             HhhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeec
Confidence            44678999999999999999999999999999999999998888999999999999999999999999999999887654

>KOG0122|consensus

Probab=99.67  E-value=4.5e-16  Score=102.08  Aligned_cols=85  Identities=25%  Similarity=0.335  Sum_probs=78.2

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      .+++..+|-|.||+.+++|.+|+++|.+||.+..+.+.+++.+|.++|||||.|.+.++|++|+..|||+-++.--+++.
T Consensus       185 ~R~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvE  264 (270)
T KOG0122|consen  185 ERDDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVE  264 (270)
T ss_pred             cCCccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEE
Confidence            45567889999999999999999999999999999999999999999999999999999999999999998888877777


Q ss_pred             Eeeec
Q psy3928          88 TTTSR   92 (115)
Q Consensus        88 ~~~~~   92 (115)
                      -.+|+
T Consensus       265 wskP~  269 (270)
T KOG0122|consen  265 WSKPS  269 (270)
T ss_pred             ecCCC
Confidence            66654

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.66  E-value=9.6e-16  Score=84.27  Aligned_cols=69  Identities=39%  Similarity=0.580  Sum_probs=62.6

Q ss_pred             EEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCcee
Q psy3928          15 VLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQS   84 (115)
Q Consensus        15 l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~   84 (115)
                      |||+|||+++++++|+++|..+|.+..+.+..++. +..+++|||+|.+.++|.+|++.+++..++|+.+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~-~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l   69 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKD-GQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKL   69 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTT-SSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeec-cccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEc
Confidence            79999999999999999999999999999998875 8999999999999999999999999888888765

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

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.65  E-value=2.5e-15  Score=105.23  Aligned_cols=81  Identities=26%  Similarity=0.415  Sum_probs=73.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCC--ceeeEEE
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTD--YQSSILT   88 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~--~~~~v~~   88 (115)
                      ...+|||+|||..+++++|+++|.+||.|..+.++.++.+++++++|||+|.+.++|++|++.||+..+.+  ..+.|..
T Consensus       192 ~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~  271 (346)
T TIGR01659       192 KDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRL  271 (346)
T ss_pred             ccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEE
Confidence            45689999999999999999999999999999999998899999999999999999999999999998876  4666665


Q ss_pred             eee
Q psy3928          89 TTS   91 (115)
Q Consensus        89 ~~~   91 (115)
                      ++.
T Consensus       272 a~~  274 (346)
T TIGR01659       272 AEE  274 (346)
T ss_pred             CCc
Confidence            554

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).

>KOG0117|consensus

Probab=99.65  E-value=1.3e-15  Score=106.97  Aligned_cols=94  Identities=29%  Similarity=0.315  Sum_probs=84.0

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCC-ceeeEE-
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTD-YQSSIL-   87 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~-~~~~v~-   87 (115)
                      ..++.||||.||.++.|++|.-+|.+.|.|..++|++++.+|.++|||||.|++.+.|+.|++.||++.|.. +.|.+. 
T Consensus        81 ~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~  160 (506)
T KOG0117|consen   81 PRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCV  160 (506)
T ss_pred             CCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEE
Confidence            346899999999999999999999999999999999999999999999999999999999999999997754 555554 


Q ss_pred             -EeeeccccCCCCCCCC
Q psy3928          88 -TTTSRLSFGITPLGFE  103 (115)
Q Consensus        88 -~~~~~~~~~~~~~~~~  103 (115)
                       .+..|.+.|+.|+.+.
T Consensus       161 Svan~RLFiG~IPK~k~  177 (506)
T KOG0117|consen  161 SVANCRLFIGNIPKTKK  177 (506)
T ss_pred             eeecceeEeccCCcccc
Confidence             4567899999998764

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

Probab=99.65  E-value=2e-15  Score=111.47  Aligned_cols=81  Identities=15%  Similarity=0.198  Sum_probs=76.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEee
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTT   90 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~   90 (115)
                      ..++|||+|||.++++++|+++|+.||.+..+++.+++.+++++|||||+|.+.++|.+|+..||+..++|+.++|....
T Consensus       203 ~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi  282 (612)
T TIGR01645       203 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCV  282 (612)
T ss_pred             ccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecC
Confidence            34789999999999999999999999999999999998889999999999999999999999999999999999988766


Q ss_pred             e
Q psy3928          91 S   91 (115)
Q Consensus        91 ~   91 (115)
                      .
T Consensus       283 ~  283 (612)
T TIGR01645       283 T  283 (612)
T ss_pred             C
Confidence            4

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.

>KOG0113|consensus

Probab=99.65  E-value=1.7e-15  Score=101.80  Aligned_cols=84  Identities=20%  Similarity=0.288  Sum_probs=77.7

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      .+..++|||+-|+.+++|..|+..|..||.|+.+.|+.++.+|+++|||||+|..+.+...|.+..+|..|+++.|-|..
T Consensus        98 gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDv  177 (335)
T KOG0113|consen   98 GDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDV  177 (335)
T ss_pred             CCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEe
Confidence            45668999999999999999999999999999999999999999999999999999999999999999999999887765


Q ss_pred             eeec
Q psy3928          89 TTSR   92 (115)
Q Consensus        89 ~~~~   92 (115)
                      -..+
T Consensus       178 ERgR  181 (335)
T KOG0113|consen  178 ERGR  181 (335)
T ss_pred             cccc
Confidence            5443

>KOG0149|consensus

Probab=99.64  E-value=9.5e-16  Score=100.08  Aligned_cols=77  Identities=22%  Similarity=0.317  Sum_probs=68.8

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceee
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSS   85 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~   85 (115)
                      .|..-.+||||+|++.+..+.|+++|++||+|.+..++.|+.+|+++||+||.|.+.+.|.+|++..+ -.|+|++-.
T Consensus         8 ~DT~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~-piIdGR~aN   84 (247)
T KOG0149|consen    8 GDTTFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPN-PIIDGRKAN   84 (247)
T ss_pred             CCceEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCC-Ccccccccc
Confidence            34556799999999999999999999999999999999999999999999999999999999999655 467887543

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

Probab=99.63  E-value=1.6e-15  Score=111.93  Aligned_cols=79  Identities=27%  Similarity=0.283  Sum_probs=74.5

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      ...++|||+|||..+++++|+++|.+||.|..+.++.++.+++++|||||+|.+.++|+.|++.|||..+.|+.+++..
T Consensus       105 ~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~r  183 (612)
T TIGR01645       105 AIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGR  183 (612)
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeecc
Confidence            4567999999999999999999999999999999999998999999999999999999999999999999999888764

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.

>KOG0125|consensus

Probab=99.63  E-value=1.7e-15  Score=102.98  Aligned_cols=98  Identities=19%  Similarity=0.234  Sum_probs=85.0

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      ..+..++|+|+|+|....+-+|+.+|.+||.|..|.|+.+  ...++||+||+|++.++|++|-.+|||..+.|++|.|.
T Consensus        92 s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfN--ERGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn  169 (376)
T KOG0125|consen   92 SKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFN--ERGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVN  169 (376)
T ss_pred             CCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEec--cCCCCccceEEecChhhHHHHHHHhhcceeeceEEEEe
Confidence            3456789999999999999999999999999999999987  46678999999999999999999999999999999999


Q ss_pred             EeeeccccCCCCCCCCCcce
Q psy3928          88 TTTSRLSFGITPLGFESGGW  107 (115)
Q Consensus        88 ~~~~~~~~~~~~~~~~~~g~  107 (115)
                      .++.|+......-.....||
T Consensus       170 ~ATarV~n~K~~v~p~~~g~  189 (376)
T KOG0125|consen  170 NATARVHNKKKKVLPYPNGW  189 (376)
T ss_pred             ccchhhccCCcccCCCcccc
Confidence            99988765444444444555

>KOG0107|consensus

Probab=99.63  E-value=1.9e-15  Score=94.92  Aligned_cols=77  Identities=27%  Similarity=0.298  Sum_probs=70.2

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEee
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTT   90 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~   90 (115)
                      -.++||||||+..+++.+|...|..||.+..+.|-.+     +.|||||+|.++.+|+.|+..|+|..+.|..++|...+
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn-----PPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~   83 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARN-----PPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELST   83 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeec-----CCCceEEeccCcccHHHHHhhcCCccccCceEEEEeec
Confidence            3689999999999999999999999999999887554     47899999999999999999999999999999998876


Q ss_pred             ec
Q psy3928          91 SR   92 (115)
Q Consensus        91 ~~   92 (115)
                      .+
T Consensus        84 G~   85 (195)
T KOG0107|consen   84 GR   85 (195)
T ss_pred             CC
Confidence            54

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.59  E-value=2e-14  Score=96.12  Aligned_cols=76  Identities=22%  Similarity=0.234  Sum_probs=68.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEee
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTT   90 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~   90 (115)
                      ..++|||+|||+.+++++|+++|+.||.|..+.|+.++   .++|||||+|.+++.|+.|+. |++..+.|+.+.|....
T Consensus         3 ~~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~---~~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~   78 (260)
T PLN03120          3 QVRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSEN---ERSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAE   78 (260)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecC---CCCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEecc
Confidence            35799999999999999999999999999999998764   356899999999999999995 99999999999887765

>KOG4207|consensus

Probab=99.58  E-value=6.5e-15  Score=94.81  Aligned_cols=84  Identities=25%  Similarity=0.335  Sum_probs=78.1

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      +.+....|-|-||...++.++|+.+|++||.|-.|.|++++.++.++|||||.|....+|+.|+++|+|..++|+.++|.
T Consensus         9 dv~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq   88 (256)
T KOG4207|consen    9 DVEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQ   88 (256)
T ss_pred             CcccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeeh
Confidence            34455789999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             Eeee
Q psy3928          88 TTTS   91 (115)
Q Consensus        88 ~~~~   91 (115)
                      .++.
T Consensus        89 ~ary   92 (256)
T KOG4207|consen   89 MARY   92 (256)
T ss_pred             hhhc
Confidence            7764

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

Probab=99.58  E-value=2.6e-14  Score=104.39  Aligned_cols=81  Identities=20%  Similarity=0.228  Sum_probs=75.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEee
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTT   90 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~   90 (115)
                      ...+|||+|||..+++++|+++|..||.+..+.++.++.+|.++|||||+|.+.+.|..|+..|++..+.+..+.|..+.
T Consensus       294 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~  373 (509)
T TIGR01642       294 SKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRAC  373 (509)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECc
Confidence            45799999999999999999999999999999999888889999999999999999999999999999999998887765


Q ss_pred             e
Q psy3928          91 S   91 (115)
Q Consensus        91 ~   91 (115)
                      .
T Consensus       374 ~  374 (509)
T TIGR01642       374 V  374 (509)
T ss_pred             c
Confidence            3

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

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

Probab=99.58  E-value=1.3e-14  Score=107.27  Aligned_cols=76  Identities=20%  Similarity=0.263  Sum_probs=72.1

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          14 VVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        14 ~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      +|||+|||.++++++|+++|..||.|..+++.+++.+++++|||||+|.+.++|++|+..+++..+.|+.+++...
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   77 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWS   77 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeecc
Confidence            6999999999999999999999999999999999888999999999999999999999999999999999888654

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

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

Probab=99.56  E-value=3.3e-14  Score=102.76  Aligned_cols=79  Identities=23%  Similarity=0.278  Sum_probs=74.7

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEee
Q psy3928          12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTT   90 (115)
Q Consensus        12 ~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~   90 (115)
                      ..+|||+|||..+++++|+++|..||.|..+.+..++.+|.++|||||+|.+.++|..|+..|+|..+.|..+.|..+.
T Consensus       186 ~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~  264 (457)
T TIGR01622       186 FLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQ  264 (457)
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEcc
Confidence            5799999999999999999999999999999999998888999999999999999999999999999999999888754

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=99.56  E-value=2.5e-14  Score=102.16  Aligned_cols=79  Identities=19%  Similarity=0.215  Sum_probs=71.6

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCH--HHHHHHHHhhCCCCCCCceeeE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK--EEATKALELGLNPCPTDYQSSI   86 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~--~~a~~al~~l~~~~~~~~~~~v   86 (115)
                      .....+||||||++.+++++|...|..||.|..+.|++  .+|  +|||||+|...  .++.+|+..|||..++|+.++|
T Consensus         7 ~~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpR--ETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKV   82 (759)
T PLN03213          7 GGGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVR--TKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRL   82 (759)
T ss_pred             CCcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEec--ccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEE
Confidence            34557999999999999999999999999999999984  466  89999999977  7899999999999999999999


Q ss_pred             EEeee
Q psy3928          87 LTTTS   91 (115)
Q Consensus        87 ~~~~~   91 (115)
                      ..+++
T Consensus        83 NKAKP   87 (759)
T PLN03213         83 EKAKE   87 (759)
T ss_pred             eeccH
Confidence            88876

>smart00362 RRM_2 RNA recognition motif

Probab=99.55  E-value=5.9e-14  Score=76.27  Aligned_cols=71  Identities=35%  Similarity=0.581  Sum_probs=63.7

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeE
Q psy3928          14 VVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSI   86 (115)
Q Consensus        14 ~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v   86 (115)
                      +|||+|||..++..+|+++|..||.+..+.+..++  +.+++++||+|.+.+.|+.|+..+++..+.+..+.+
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v   71 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT--GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRV   71 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC--CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEee
Confidence            48999999999999999999999999999887765  678899999999999999999999998887776553

>KOG0111|consensus

Probab=99.54  E-value=6.5e-15  Score=95.72  Aligned_cols=98  Identities=18%  Similarity=0.308  Sum_probs=86.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      ...++||||+|...+++.-|..-|-+||.|..++++.+..+++.+||+||+|...++|.+|+..||+..+-|+.|+|-.+
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~A   87 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLA   87 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeec
Confidence            45689999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             ee-ccccCCCCCCCCCcce
Q psy3928          90 TS-RLSFGITPLGFESGGW  107 (115)
Q Consensus        90 ~~-~~~~~~~~~~~~~~g~  107 (115)
                      +| +...+....-|....|
T Consensus        88 kP~kikegsqkPvWADDdW  106 (298)
T KOG0111|consen   88 KPEKIKEGSQKPVWADDDW  106 (298)
T ss_pred             CCccccCCCCCCcccCcHH
Confidence            87 4444445555655555

>KOG0126|consensus

Probab=99.54  E-value=6.4e-16  Score=97.62  Aligned_cols=81  Identities=25%  Similarity=0.279  Sum_probs=76.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEee
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTT   90 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~   90 (115)
                      +..=|||||||...+|.+|...|++||.+..+.+++++.||+++||||+.|.+..+.--|+..|||..+.|+.++|..+.
T Consensus        34 dsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv~  113 (219)
T KOG0126|consen   34 DSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHVS  113 (219)
T ss_pred             cceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeecc
Confidence            44569999999999999999999999999999999999999999999999999999999999999999999999998775


Q ss_pred             e
Q psy3928          91 S   91 (115)
Q Consensus        91 ~   91 (115)
                      .
T Consensus       114 ~  114 (219)
T KOG0126|consen  114 N  114 (219)
T ss_pred             c
Confidence            4

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

Probab=99.54  E-value=5.2e-14  Score=103.73  Aligned_cols=73  Identities=30%  Similarity=0.335  Sum_probs=66.9

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCC-Ccee
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPT-DYQS   84 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~-~~~~   84 (115)
                      ..++|||+|||.+++|++|.++|.++|.|..++|+++ .+++++|||||+|.+.++|++|++.||+..+. ++.+
T Consensus        57 ~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l  130 (578)
T TIGR01648        57 RGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLL  130 (578)
T ss_pred             CCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC-CCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCccc
Confidence            4589999999999999999999999999999999998 59999999999999999999999999998875 4443

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=99.53  E-value=2.8e-14  Score=100.15  Aligned_cols=73  Identities=30%  Similarity=0.412  Sum_probs=67.7

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCC
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPT   80 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~   80 (115)
                      .+.+.-++|||.+|+.++|.+|+.+|++||.|.+|.|++|+.++.++|||||.|.+..+|.+|+.+|++...-
T Consensus        30 ~d~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktl  102 (510)
T KOG0144|consen   30 PDGSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTL  102 (510)
T ss_pred             CCchhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhccccc
Confidence            4555679999999999999999999999999999999999999999999999999999999999999987533

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

Probab=99.53  E-value=7.5e-14  Score=100.88  Aligned_cols=79  Identities=28%  Similarity=0.275  Sum_probs=72.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      ...++|||+|||..+++.+|+++|..||.|..+.++.++.++.++|||||+|.+.++|++|+. +++..+.|..+.+...
T Consensus        87 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~~~  165 (457)
T TIGR01622        87 RDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQSS  165 (457)
T ss_pred             cCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEeec
Confidence            346799999999999999999999999999999999998899999999999999999999997 8999999988877654

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

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

Probab=99.53  E-value=9.8e-14  Score=102.66  Aligned_cols=82  Identities=22%  Similarity=0.261  Sum_probs=75.2

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      .....+|||+||+..+++++|+++|..||.|..++++.+ .++.++|++||+|.+.++|.+|+..+|+..+.|+.+.|..
T Consensus       282 ~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d-~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~  360 (562)
T TIGR01628       282 KAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLD-EKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVAL  360 (562)
T ss_pred             ccCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEEC-CCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEe
Confidence            345678999999999999999999999999999999988 4899999999999999999999999999999999998876


Q ss_pred             eee
Q psy3928          89 TTS   91 (115)
Q Consensus        89 ~~~   91 (115)
                      +..
T Consensus       361 a~~  363 (562)
T TIGR01628       361 AQR  363 (562)
T ss_pred             ccC
Confidence            653

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

>smart00360 RRM RNA recognition motif

Probab=99.52  E-value=1.7e-13  Score=74.19  Aligned_cols=70  Identities=40%  Similarity=0.580  Sum_probs=63.6

Q ss_pred             EcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeE
Q psy3928          17 KEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSI   86 (115)
Q Consensus        17 V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v   86 (115)
                      |+|||..+++++|+++|++||.+..+.+..++.++.++++|||+|.+.+.|..|+..+++..+.+..+.+
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v   70 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV   70 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEe
Confidence            5799999999999999999999999998887767889999999999999999999999988888876654

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.51  E-value=2.5e-13  Score=89.76  Aligned_cols=77  Identities=21%  Similarity=0.213  Sum_probs=67.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      ..+.+|||+||++.+++++|+++|+.||.|..+.|+++   +...++|||+|.++..++.|+ .|+|..+.+..+.|...
T Consensus         3 ~~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D---~et~gfAfVtF~d~~aaetAl-lLnGa~l~d~~I~It~~   78 (243)
T PLN03121          3 PGGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRS---GEYACTAYVTFKDAYALETAV-LLSGATIVDQRVCITRW   78 (243)
T ss_pred             CCceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecC---CCcceEEEEEECCHHHHHHHH-hcCCCeeCCceEEEEeC
Confidence            35689999999999999999999999999999999876   444579999999999999999 59999999998877654


Q ss_pred             e
Q psy3928          90 T   90 (115)
Q Consensus        90 ~   90 (115)
                      .
T Consensus        79 ~   79 (243)
T PLN03121         79 G   79 (243)
T ss_pred             c
Confidence            3

>KOG0130|consensus

Probab=99.51  E-value=1.4e-13  Score=83.45  Aligned_cols=82  Identities=24%  Similarity=0.313  Sum_probs=75.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      ..+.+|||.++....+|+++...|..||.|+.+.+-.++.+|..+||++|+|.+..+|++|+..+|+..+.+..+.|.-.
T Consensus        70 VEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~  149 (170)
T KOG0130|consen   70 VEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWC  149 (170)
T ss_pred             eeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEE
Confidence            34679999999999999999999999999999999999889999999999999999999999999999999998887655


Q ss_pred             ee
Q psy3928          90 TS   91 (115)
Q Consensus        90 ~~   91 (115)
                      ..
T Consensus       150 Fv  151 (170)
T KOG0130|consen  150 FV  151 (170)
T ss_pred             Ee
Confidence            54

>KOG0131|consensus

Probab=99.50  E-value=4.9e-14  Score=89.06  Aligned_cols=83  Identities=19%  Similarity=0.283  Sum_probs=77.6

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      +.....+|||+||+..+++..|.++|-+.|++..+.+++++-+...+||||++|.++++|+.|++.||...+-|++|++.
T Consensus         5 ~rnqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~   84 (203)
T KOG0131|consen    5 ERNQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVN   84 (203)
T ss_pred             ccCCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEE
Confidence            34567899999999999999999999999999999999999899999999999999999999999999989999999988


Q ss_pred             Eee
Q psy3928          88 TTT   90 (115)
Q Consensus        88 ~~~   90 (115)
                      .+.
T Consensus        85 kas   87 (203)
T KOG0131|consen   85 KAS   87 (203)
T ss_pred             ecc
Confidence            776

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

Probab=99.49  E-value=2.8e-13  Score=90.42  Aligned_cols=79  Identities=29%  Similarity=0.432  Sum_probs=75.0

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEee
Q psy3928          12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTT   90 (115)
Q Consensus        12 ~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~   90 (115)
                      ..+|||+|||..+++++|+++|..||.+..+.+..++.++.++|+|||+|.+.+.|..|+..+++..+.|+.+.+....
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~  193 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQ  193 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeeccc
Confidence            5899999999999999999999999999999999988899999999999999999999999999999999999988754

>KOG0105|consensus

Probab=99.49  E-value=1.8e-13  Score=86.94  Aligned_cols=79  Identities=23%  Similarity=0.280  Sum_probs=70.1

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      ...+.|||+|||.++.+.+|..+|-+||.|..+.+...   -.+.+||||+|++..+|+.|+..-+++.+++..++|.+.
T Consensus         4 r~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r---~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfp   80 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNR---PGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFP   80 (241)
T ss_pred             cccceEEecCCCcchhhccHHHHHhhhcceEEEEeccC---CCCCCeeEEEecCccchhhhhhcccccccCcceEEEEec
Confidence            35678999999999999999999999999999887443   234569999999999999999999999999999999987


Q ss_pred             ee
Q psy3928          90 TS   91 (115)
Q Consensus        90 ~~   91 (115)
                      ..
T Consensus        81 rg   82 (241)
T KOG0105|consen   81 RG   82 (241)
T ss_pred             cC
Confidence            64

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

Probab=99.48  E-value=4.4e-13  Score=98.88  Aligned_cols=76  Identities=22%  Similarity=0.298  Sum_probs=68.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhc--CCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKY--GKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~--g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      ..++|||+||+.++++++|+++|..|  |.|..+.++        ++||||+|.+.++|++|++.||+..++++.+.|..
T Consensus       232 ~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~--------rgfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~  303 (578)
T TIGR01648       232 KVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI--------RDYAFVHFEDREDAVKAMDELNGKELEGSEIEVTL  303 (578)
T ss_pred             cccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee--------cCeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            45789999999999999999999999  999988764        35999999999999999999999999999999998


Q ss_pred             eeeccc
Q psy3928          89 TTSRLS   94 (115)
Q Consensus        89 ~~~~~~   94 (115)
                      ++++..
T Consensus       304 Akp~~~  309 (578)
T TIGR01648       304 AKPVDK  309 (578)
T ss_pred             ccCCCc
Confidence            877543

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.

>KOG0117|consensus

Probab=99.46  E-value=1.8e-13  Score=96.42  Aligned_cols=80  Identities=21%  Similarity=0.321  Sum_probs=72.0

Q ss_pred             hhcccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCcee
Q psy3928           5 VENNKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQS   84 (115)
Q Consensus         5 ~~~~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~   84 (115)
                      +++.....+.|||.||+.+++++.|+++|+.||.+.+|+.++|        ||||+|.+.++|-+|++.+|++.++|..+
T Consensus       252 ded~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD--------YaFVHf~eR~davkAm~~~ngkeldG~~i  323 (506)
T KOG0117|consen  252 DEDTMSKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD--------YAFVHFAEREDAVKAMKETNGKELDGSPI  323 (506)
T ss_pred             ChhhhhheeeeeeeccchhhhHHHHHHHHHhccceEEeecccc--------eeEEeecchHHHHHHHHHhcCceecCceE
Confidence            3344556789999999999999999999999999999877654        99999999999999999999999999999


Q ss_pred             eEEEeeec
Q psy3928          85 SILTTTSR   92 (115)
Q Consensus        85 ~v~~~~~~   92 (115)
                      .+..++|.
T Consensus       324 EvtLAKP~  331 (506)
T KOG0117|consen  324 EVTLAKPV  331 (506)
T ss_pred             EEEecCCh
Confidence            99988874

>KOG0114|consensus

Probab=99.45  E-value=9.6e-13  Score=76.39  Aligned_cols=78  Identities=19%  Similarity=0.257  Sum_probs=70.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEee
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTT   90 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~   90 (115)
                      -.+.|||.|||..++.++..++|..||.|..+++-..   ...+|-|||.|++..+|.+|++.|.|..+++..+.++.-.
T Consensus        17 vnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~---k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq   93 (124)
T KOG0114|consen   17 VNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNT---KETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQ   93 (124)
T ss_pred             hheeEEEecCCccccHHHHHHHhhcccceEEEEecCc---cCcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecC
Confidence            3578999999999999999999999999999998654   4567899999999999999999999999999998888765


Q ss_pred             e
Q psy3928          91 S   91 (115)
Q Consensus        91 ~   91 (115)
                      +
T Consensus        94 ~   94 (124)
T KOG0114|consen   94 P   94 (124)
T ss_pred             H
Confidence            4

>KOG0145|consensus

Probab=99.45  E-value=3.9e-13  Score=89.50  Aligned_cols=83  Identities=19%  Similarity=0.280  Sum_probs=75.6

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      ++....+.|.-||..+++++++.+|.+.|+|..|++++|+.+|.+.||+||.|.++.+|++|+..|||..+-.+.|.|.+
T Consensus        38 ~~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSy  117 (360)
T KOG0145|consen   38 DESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSY  117 (360)
T ss_pred             CcccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEe
Confidence            44556899999999999999999999999999999999999999999999999999999999999999877777777776


Q ss_pred             eee
Q psy3928          89 TTS   91 (115)
Q Consensus        89 ~~~   91 (115)
                      +.|
T Consensus       118 ARP  120 (360)
T KOG0145|consen  118 ARP  120 (360)
T ss_pred             ccC
Confidence            665

>KOG0108|consensus

Probab=99.45  E-value=4.4e-13  Score=95.84  Aligned_cols=80  Identities=28%  Similarity=0.341  Sum_probs=76.9

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEeeec
Q psy3928          13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTTSR   92 (115)
Q Consensus        13 ~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~~~   92 (115)
                      +.+||||+|.+++++.|..+|...|.+..++++.|+.+|+++||+|++|.+.+.++.|++.||+..+.|+.+++.....+
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~~   98 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASNR   98 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeeccccc
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999877653

>KOG0148|consensus

Probab=99.45  E-value=1e-12  Score=87.74  Aligned_cols=81  Identities=23%  Similarity=0.251  Sum_probs=72.4

Q ss_pred             hhhhcccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCc
Q psy3928           3 ELVENNKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDY   82 (115)
Q Consensus         3 ~~~~~~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~   82 (115)
                      |+..+...+.++|||||++..++++++++.|.+||+|.++++..+      +||+||.|.+.+.|..|+..+|+..+.|.
T Consensus       155 eV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~------qGYaFVrF~tkEaAahAIv~mNntei~G~  228 (321)
T KOG0148|consen  155 EVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD------QGYAFVRFETKEAAAHAIVQMNNTEIGGQ  228 (321)
T ss_pred             HHhccCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc------cceEEEEecchhhHHHHHHHhcCceeCce
Confidence            555667788899999999999999999999999999999998765      58999999999999999999999999998


Q ss_pred             eeeEEEe
Q psy3928          83 QSSILTT   89 (115)
Q Consensus        83 ~~~v~~~   89 (115)
                      .++..=-
T Consensus       229 ~VkCsWG  235 (321)
T KOG0148|consen  229 LVRCSWG  235 (321)
T ss_pred             EEEEecc
Confidence            7775533

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

Probab=99.44  E-value=2.2e-12  Score=70.33  Aligned_cols=72  Identities=36%  Similarity=0.514  Sum_probs=64.4

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeE
Q psy3928          14 VVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSI   86 (115)
Q Consensus        14 ~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v   86 (115)
                      +|+|+|||..+++.+|+++|+.+|.+..+.+..++ .+.+++++||+|.+.+.|+.|+..+++..+.+..+.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~-~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v   72 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDK-DTKSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRV   72 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            48999999999999999999999999999888766 3377899999999999999999999998888877654

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).

>KOG0148|consensus

Probab=99.43  E-value=3.9e-13  Score=89.67  Aligned_cols=77  Identities=25%  Similarity=0.353  Sum_probs=71.8

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        13 ~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      .-+||+.|...++-+.|++.|.+||.|+.+++++|..+++++||+||.|.+.++|+.|++.|||.=+.++.||.-=+
T Consensus        63 fhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWA  139 (321)
T KOG0148|consen   63 FHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWA  139 (321)
T ss_pred             eeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeecccc
Confidence            36899999999999999999999999999999999999999999999999999999999999999888888875433

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

Probab=99.43  E-value=1.5e-12  Score=94.96  Aligned_cols=77  Identities=22%  Similarity=0.193  Sum_probs=69.4

Q ss_pred             CCCCEEEEcCCCC-CCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928          10 KYGRVVLKEKLPP-EAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus        10 ~~~~~l~V~~l~~-~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      ....+|||+|||. .+++++|+++|..||.|..++++.++     +|+|||+|.+.++|+.|+..||+..+.|+.+.|..
T Consensus       273 ~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~-----~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~  347 (481)
T TIGR01649       273 GPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNK-----KETALIEMADPYQAQLALTHLNGVKLFGKPLRVCP  347 (481)
T ss_pred             CCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEE
Confidence            3567999999997 69999999999999999999997753     58999999999999999999999999999999876


Q ss_pred             eee
Q psy3928          89 TTS   91 (115)
Q Consensus        89 ~~~   91 (115)
                      .+.
T Consensus       348 s~~  350 (481)
T TIGR01649       348 SKQ  350 (481)
T ss_pred             ccc
Confidence            543

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).

>KOG0144|consensus

Probab=99.39  E-value=3.9e-13  Score=94.48  Aligned_cols=68  Identities=25%  Similarity=0.354  Sum_probs=64.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCC
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCP   79 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~   79 (115)
                      +.++||||.|++.++|.+++++|.+||.|..|+|+++. .+.++||+||.|.+.+.|..|++.||+...
T Consensus       123 ~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~-~~~sRGcaFV~fstke~A~~Aika~ng~~t  190 (510)
T KOG0144|consen  123 EERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDP-DGLSRGCAFVKFSTKEMAVAAIKALNGTQT  190 (510)
T ss_pred             cchhhhhhhccccccHHHHHHHHHhhCccchhhheecc-cccccceeEEEEehHHHHHHHHHhhcccee
Confidence            46889999999999999999999999999999999987 889999999999999999999999999853

>KOG0146|consensus

Probab=99.36  E-value=1.6e-12  Score=86.84  Aligned_cols=83  Identities=23%  Similarity=0.295  Sum_probs=71.5

Q ss_pred             hhcccC-CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCce
Q psy3928           5 VENNKK-YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQ   83 (115)
Q Consensus         5 ~~~~~~-~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~   83 (115)
                      +.+.+. +.+++|||.|.+.-+|++++++|+.||.+.+|.+++.+ .|.++||+||.|.+..+|+.|+..|+|.......
T Consensus        11 dsesrg~~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~-dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGA   89 (371)
T KOG0146|consen   11 DSESRGGDDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGP-DGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGA   89 (371)
T ss_pred             ccccCCccchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCC-CCCCCCceEEEeccchHHHHHHHHhcccccCCCC
Confidence            333333 67899999999999999999999999999999999887 8899999999999999999999999999766654


Q ss_pred             eeEEE
Q psy3928          84 SSILT   88 (115)
Q Consensus        84 ~~v~~   88 (115)
                      ...+.
T Consensus        90 SSSLV   94 (371)
T KOG0146|consen   90 SSSLV   94 (371)
T ss_pred             ccceE
Confidence            44333

>KOG0109|consensus

Probab=99.35  E-value=1.1e-12  Score=88.28  Aligned_cols=72  Identities=24%  Similarity=0.316  Sum_probs=68.2

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEeeec
Q psy3928          13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTTSR   92 (115)
Q Consensus        13 ~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~~~   92 (115)
                      .++||||||..+++.+|+.+|++||.+.+|.|+.+        |+||..++...++.|++.|++++++|..|.|...+.+
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN--------YgFVHiEdktaaedairNLhgYtLhg~nInVeaSksK   74 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVKN--------YGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSK   74 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeecc--------cceEEeecccccHHHHhhcccceecceEEEEEecccc
Confidence            47999999999999999999999999999999876        9999999999999999999999999999999988876

>smart00361 RRM_1 RNA recognition motif

Probab=99.33  E-value=9.4e-12  Score=68.51  Aligned_cols=61  Identities=16%  Similarity=0.193  Sum_probs=52.7

Q ss_pred             HHHHHHHhh----hcCCeEEEE-eceeCCC--CCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeE
Q psy3928          26 HDYIESVFS----KYGKVTYVS-LPKFKST--GKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSI   86 (115)
Q Consensus        26 ~~~l~~~f~----~~g~i~~~~-i~~~~~~--~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v   86 (115)
                      +++|+++|.    .||.+..+. +..++.+  +.++|++||+|.+.++|++|+..|||..+.|+.+.+
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence            567888888    999999884 6666655  889999999999999999999999999999887654

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

Probab=99.33  E-value=1.3e-11  Score=90.03  Aligned_cols=79  Identities=15%  Similarity=0.184  Sum_probs=66.9

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhcCC--eEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCce------
Q psy3928          12 GRVVLKEKLPPEAEHDYIESVFSKYGK--VTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQ------   83 (115)
Q Consensus        12 ~~~l~V~~l~~~~~~~~l~~~f~~~g~--i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~------   83 (115)
                      ..+|||+|||..+++++|+++|+.||.  +..+++...+ + ..+++|||+|.+.++|..|+..||+..+.+..      
T Consensus       394 s~~L~v~NLp~~~tee~L~~lF~~~G~~~i~~ik~~~~~-~-~~~~~gfVeF~~~e~A~~Al~~ln~~~l~~~~~~~~~~  471 (481)
T TIGR01649       394 SATLHLSNIPLSVSEEDLKELFAENGVHKVKKFKFFPKD-N-ERSKMGLLEWESVEDAVEALIALNHHQLNEPNGSAPYH  471 (481)
T ss_pred             CcEEEEecCCCCCCHHHHHHHHHhcCCccceEEEEecCC-C-CcceeEEEEcCCHHHHHHHHHHhcCCccCCCCCCccce
Confidence            468999999999999999999999997  7778775433 3 35789999999999999999999999999875      


Q ss_pred             eeEEEeeec
Q psy3928          84 SSILTTTSR   92 (115)
Q Consensus        84 ~~v~~~~~~   92 (115)
                      +++.+.+++
T Consensus       472 lkv~fs~~~  480 (481)
T TIGR01649       472 LKVSFSTSR  480 (481)
T ss_pred             EEEEeccCC
Confidence            666666543

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).

>KOG0124|consensus

Probab=99.33  E-value=1.5e-12  Score=90.28  Aligned_cols=75  Identities=28%  Similarity=0.319  Sum_probs=72.0

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928          13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus        13 ~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      +.+|||.+.....|+.|+.-|.+||+|+.+.+.+++.+++.+||+||+|+-++.|+-|++.||+.-+.|+.+.|-
T Consensus       114 cRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVg  188 (544)
T KOG0124|consen  114 CRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVG  188 (544)
T ss_pred             HheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCcccccc
Confidence            789999999999999999999999999999999999999999999999999999999999999999999887765

>KOG0145|consensus

Probab=99.32  E-value=1.7e-11  Score=81.76  Aligned_cols=82  Identities=26%  Similarity=0.304  Sum_probs=75.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      ..+.-|||=||.++.+|..|+.+|.+||.+..+++++|..+.+.+||+||...+-++|..|+..|||+.+.++.+.|.+.
T Consensus       276 ~~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsFK  355 (360)
T KOG0145|consen  276 GGGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFK  355 (360)
T ss_pred             CCeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccceEEEEEEe
Confidence            34567999999999999999999999999999999999988999999999999999999999999999999988777766


Q ss_pred             ee
Q psy3928          90 TS   91 (115)
Q Consensus        90 ~~   91 (115)
                      +.
T Consensus       356 tn  357 (360)
T KOG0145|consen  356 TN  357 (360)
T ss_pred             cC
Confidence            54

>KOG0127|consensus

Probab=99.31  E-value=9.9e-12  Score=89.75  Aligned_cols=87  Identities=29%  Similarity=0.406  Sum_probs=74.0

Q ss_pred             cccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhC-----C-CCCC
Q psy3928           7 NNKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGL-----N-PCPT   80 (115)
Q Consensus         7 ~~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~-----~-~~~~   80 (115)
                      ++...+.+|||+|||.++++++|...|++||.+..+.++.++.|+.+.|.|||.|.+...++.|+..-.     + ..++
T Consensus       287 en~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~  366 (678)
T KOG0127|consen  287 ENITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLLD  366 (678)
T ss_pred             ccccccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcCccCCCceEEEe
Confidence            345567899999999999999999999999999999999999999999999999999999999998762     2 3466


Q ss_pred             CceeeEEEeeecc
Q psy3928          81 DYQSSILTTTSRL   93 (115)
Q Consensus        81 ~~~~~v~~~~~~~   93 (115)
                      |+.+.+..+-.|.
T Consensus       367 GR~Lkv~~Av~Rk  379 (678)
T KOG0127|consen  367 GRLLKVTLAVTRK  379 (678)
T ss_pred             ccEEeeeeccchH
Confidence            6776666655543

>KOG0127|consensus

Probab=99.31  E-value=6.6e-12  Score=90.65  Aligned_cols=85  Identities=21%  Similarity=0.310  Sum_probs=78.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      ..+.+|||++||.+++.+.|.++|+.+|+|..+.++.++.++..+||+||.|+..+++++|+....+..+.|+.+++..+
T Consensus         3 ~~g~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A   82 (678)
T KOG0127|consen    3 KSGATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDPA   82 (678)
T ss_pred             CCCceEEEecCCCccchhHHHHhhhcccCcceeEEecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceecccccc
Confidence            34589999999999999999999999999999999999888889999999999999999999999999999999998887


Q ss_pred             eeccc
Q psy3928          90 TSRLS   94 (115)
Q Consensus        90 ~~~~~   94 (115)
                      +.|..
T Consensus        83 ~~R~r   87 (678)
T KOG0127|consen   83 KKRAR   87 (678)
T ss_pred             ccccc
Confidence            76543

>KOG4208|consensus

Probab=99.30  E-value=1.6e-11  Score=79.09  Aligned_cols=80  Identities=30%  Similarity=0.322  Sum_probs=70.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhc-CCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKY-GKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~-g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      .....+|+..+|..+.+..+..+|.++ |.+..+++.+++.||.++|||||+|.+++.|.-|.++||++-+.++.+.+-.
T Consensus        47 ~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~v  126 (214)
T KOG4208|consen   47 EIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHV  126 (214)
T ss_pred             CCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEE
Confidence            344678999999999999999999998 5677888889999999999999999999999999999999998887665444


Q ss_pred             e
Q psy3928          89 T   89 (115)
Q Consensus        89 ~   89 (115)
                      .
T Consensus       127 m  127 (214)
T KOG4208|consen  127 M  127 (214)
T ss_pred             e
Confidence            3

>KOG0146|consensus

Probab=99.28  E-value=6e-12  Score=84.17  Aligned_cols=86  Identities=16%  Similarity=0.148  Sum_probs=79.8

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      +..+++.|||=-||....+.+|..+|-+||.|...++..|+.+..+++|+||.|.++.+++.|+..|||..|.-+++.|.
T Consensus       281 eGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQ  360 (371)
T KOG0146|consen  281 EGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQ  360 (371)
T ss_pred             cCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhh
Confidence            56788999999999999999999999999999999999999999999999999999999999999999999999988887


Q ss_pred             Eeeecc
Q psy3928          88 TTTSRL   93 (115)
Q Consensus        88 ~~~~~~   93 (115)
                      ..+++.
T Consensus       361 LKRPkd  366 (371)
T KOG0146|consen  361 LKRPKD  366 (371)
T ss_pred             hcCccc
Confidence            777654

>KOG0147|consensus

Probab=99.27  E-value=1.1e-11  Score=89.35  Aligned_cols=82  Identities=29%  Similarity=0.381  Sum_probs=76.6

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEeeecc
Q psy3928          14 VVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTTSRL   93 (115)
Q Consensus        14 ~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~~~~   93 (115)
                      .+|||||..++++++|+.+|.+||.|..+.+..+..+|.++||+|++|...+.|..|+..|||..+-|+.+.|..++.+.
T Consensus       280 rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r~  359 (549)
T KOG0147|consen  280 RLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTERV  359 (549)
T ss_pred             hhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeeeec
Confidence            39999999999999999999999999999999988899999999999999999999999999999999999998887765


Q ss_pred             cc
Q psy3928          94 SF   95 (115)
Q Consensus        94 ~~   95 (115)
                      ..
T Consensus       360 ~~  361 (549)
T KOG0147|consen  360 DT  361 (549)
T ss_pred             cc
Confidence            43

>PF13893 RRM_5: RNA recognition motif

Probab=99.20  E-value=9.3e-11  Score=61.67  Aligned_cols=55  Identities=35%  Similarity=0.457  Sum_probs=47.5

Q ss_pred             HHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928          29 IESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus        29 l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      |+++|++||.|..+.+....     +++|||+|.+.++|+.|++.||+..+.|+.+++..
T Consensus         1 L~~~f~~fG~V~~i~~~~~~-----~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~   55 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK-----RGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSY   55 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS-----TTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            67899999999999885432     57999999999999999999999999999888764

(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 ....

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

Probab=99.19  E-value=7.4e-11  Score=86.39  Aligned_cols=74  Identities=28%  Similarity=0.301  Sum_probs=59.3

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcC------------CeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhC
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYG------------KVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGL   75 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g------------~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~   75 (115)
                      .....++|||+|||..+++.+|.++|..++            .+..+.      .+..+|||||+|.+.++|..|+ .|+
T Consensus       171 ~~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~------~~~~kg~afVeF~~~e~A~~Al-~l~  243 (509)
T TIGR01642       171 ATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVN------INKEKNFAFLEFRTVEEATFAM-ALD  243 (509)
T ss_pred             CCccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEE------ECCCCCEEEEEeCCHHHHhhhh-cCC
Confidence            345568999999999999999999999751            223332      2345789999999999999999 599


Q ss_pred             CCCCCCceeeEEE
Q psy3928          76 NPCPTDYQSSILT   88 (115)
Q Consensus        76 ~~~~~~~~~~v~~   88 (115)
                      +..+.|..+.+..
T Consensus       244 g~~~~g~~l~v~r  256 (509)
T TIGR01642       244 SIIYSNVFLKIRR  256 (509)
T ss_pred             CeEeeCceeEecC
Confidence            9999998877653

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

>KOG0131|consensus

Probab=99.19  E-value=8.3e-11  Score=74.60  Aligned_cols=86  Identities=17%  Similarity=0.276  Sum_probs=76.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEE-EEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTY-VSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~-~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      .-+..+||+||.+.++|..|...|+.||.+.. .++++++.+|.+++++|+.|++.+.+.+|+..+|+..+..+++++..
T Consensus        94 ~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~y  173 (203)
T KOG0131|consen   94 DVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPITVSY  173 (203)
T ss_pred             cccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCceEEEE
Confidence            34578999999999999999999999997744 58889998999999999999999999999999999999999999888


Q ss_pred             eeecccc
Q psy3928          89 TTSRLSF   95 (115)
Q Consensus        89 ~~~~~~~   95 (115)
                      +......
T Consensus       174 a~k~~~k  180 (203)
T KOG0131|consen  174 AFKKDTK  180 (203)
T ss_pred             EEecCCC
Confidence            7764443

>KOG0415|consensus

Probab=99.19  E-value=5.2e-11  Score=82.35  Aligned_cols=83  Identities=27%  Similarity=0.332  Sum_probs=77.5

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      .++...|||..|.+.++.++|.-+|+.||.|..|.+++++.+|.+..||||+|.+..+.++|.-+|++..++.+.|+|.+
T Consensus       236 ~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDF  315 (479)
T KOG0415|consen  236 KPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDF  315 (479)
T ss_pred             CCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeeh
Confidence            45668999999999999999999999999999999999999999999999999999999999999999999999999876


Q ss_pred             eee
Q psy3928          89 TTS   91 (115)
Q Consensus        89 ~~~   91 (115)
                      ..+
T Consensus       316 SQS  318 (479)
T KOG0415|consen  316 SQS  318 (479)
T ss_pred             hhh
Confidence            543

>KOG1457|consensus

Probab=99.16  E-value=3.2e-10  Score=74.18  Aligned_cols=81  Identities=17%  Similarity=0.108  Sum_probs=61.6

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCC-CeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeE
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTG-KLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSI   86 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~-~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v   86 (115)
                      .....+++||++||.++...+|+.+|+.|.......+..-...+ -.+.++|+.|.+.+.|.+|+..|||..++.....+
T Consensus        30 ~~~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~st  109 (284)
T KOG1457|consen   30 EPGAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGST  109 (284)
T ss_pred             cccccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCce
Confidence            34567999999999999999999999998655444332211111 23469999999999999999999999988865444


Q ss_pred             EE
Q psy3928          87 LT   88 (115)
Q Consensus        87 ~~   88 (115)
                      +.
T Consensus       110 Lh  111 (284)
T KOG1457|consen  110 LH  111 (284)
T ss_pred             eE
Confidence            43

>KOG0124|consensus

Probab=99.15  E-value=1.7e-10  Score=80.25  Aligned_cols=80  Identities=15%  Similarity=0.194  Sum_probs=74.7

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEee
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTT   90 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~   90 (115)
                      .-..|||..+.++.++++|+..|+.||.|..|.+-+.+.++..+||+|++|.+....+.|+..||-..+.|..++|-..-
T Consensus       209 ~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~v  288 (544)
T KOG0124|consen  209 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCV  288 (544)
T ss_pred             hhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEeccccc
Confidence            44689999999999999999999999999999999999888899999999999999999999999999999999987654

>KOG4212|consensus

Probab=99.15  E-value=2.1e-10  Score=81.24  Aligned_cols=76  Identities=26%  Similarity=0.314  Sum_probs=69.7

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhh-cCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928          12 GRVVLKEKLPPEAEHDYIESVFSK-YGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus        12 ~~~l~V~~l~~~~~~~~l~~~f~~-~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      .+.+||.|+|.+....+|++++.. .|.+..|.++.+. +|+++||+.|+|.+++.+++|++.||.+.++|+.+.+-.
T Consensus        44 ~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~-~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKE  120 (608)
T KOG4212|consen   44 DRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDE-SGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKE  120 (608)
T ss_pred             cceEEEecCcchhhhHhHHHHHHHhcCceEeeeeeccc-CCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEec
Confidence            466999999999999999999985 7899999999987 999999999999999999999999999999999876543

>KOG0123|consensus

Probab=99.14  E-value=3.5e-10  Score=80.04  Aligned_cols=76  Identities=21%  Similarity=0.309  Sum_probs=69.2

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEeee
Q psy3928          13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTTS   91 (115)
Q Consensus        13 ~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~~   91 (115)
                      ..+||-||+++++...|.++|..||.|.+|++..+. .| ++|| ||+|.+++.|.+|+..+||..+.+..+-+.....
T Consensus        77 ~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~-~g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~  152 (369)
T KOG0123|consen   77 SLVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDE-NG-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFER  152 (369)
T ss_pred             ceeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcC-CC-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccc
Confidence            449999999999999999999999999999999987 45 8899 9999999999999999999999999988765544

>KOG0533|consensus

Probab=99.14  E-value=5.3e-10  Score=74.67  Aligned_cols=83  Identities=19%  Similarity=0.241  Sum_probs=74.7

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      ......+|+|.|||..+.+.+|+++|..|+.+..+.+.+++ .|.+.|.|-|.|...++|.++++.+++..++|+.+.+.
T Consensus        79 ~~~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~-~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~  157 (243)
T KOG0533|consen   79 NETRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDR-AGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIE  157 (243)
T ss_pred             cCCCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCC-CCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeE
Confidence            34455789999999999999999999999988888888887 89999999999999999999999999999999998877


Q ss_pred             Eeee
Q psy3928          88 TTTS   91 (115)
Q Consensus        88 ~~~~   91 (115)
                      .+.+
T Consensus       158 ~i~~  161 (243)
T KOG0533|consen  158 IISS  161 (243)
T ss_pred             EecC
Confidence            6654

>KOG4206|consensus

Probab=99.11  E-value=5.8e-10  Score=72.81  Aligned_cols=77  Identities=27%  Similarity=0.289  Sum_probs=69.6

Q ss_pred             CEEEEcCCCCCCCHHHHHH----HhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928          13 RVVLKEKLPPEAEHDYIES----VFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus        13 ~~l~V~~l~~~~~~~~l~~----~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      .+|||.||+..+..++|++    +|++||.+..+....   +.+-+|-|||.|.+.+.|..|++.|+|..+-|+.+++.+
T Consensus        10 ~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~k---t~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriqy   86 (221)
T KOG4206|consen   10 GTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFK---TPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQY   86 (221)
T ss_pred             ceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecC---CCCccCceEEEecChhHHHHHHHHhcCCcccCchhheec
Confidence            4999999999999988777    999999999887642   778899999999999999999999999999999999998


Q ss_pred             eeec
Q psy3928          89 TTSR   92 (115)
Q Consensus        89 ~~~~   92 (115)
                      ++..
T Consensus        87 A~s~   90 (221)
T KOG4206|consen   87 AKSD   90 (221)
T ss_pred             ccCc
Confidence            8764

>KOG4205|consensus

Probab=99.08  E-value=2e-10  Score=79.28  Aligned_cols=85  Identities=24%  Similarity=0.259  Sum_probs=74.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEee
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTT   90 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~   90 (115)
                      +.+++||++|++.++++.|+++|.+||.+..+.+++++.++.+++|+||+|++.....+++..-. ..++++.+.+..+.
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~~~-h~~dgr~ve~k~av   83 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNART-HKLDGRSVEPKRAV   83 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecccc-cccCCccccceecc
Confidence            67899999999999999999999999999999999999999999999999999888888877544 46788888887777


Q ss_pred             eccccC
Q psy3928          91 SRLSFG   96 (115)
Q Consensus        91 ~~~~~~   96 (115)
                      +|....
T Consensus        84 ~r~~~~   89 (311)
T KOG4205|consen   84 SREDQT   89 (311)
T ss_pred             Cccccc
Confidence            765543

>KOG0123|consensus

Probab=99.01  E-value=1.8e-09  Score=76.43  Aligned_cols=71  Identities=20%  Similarity=0.235  Sum_probs=65.4

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        13 ~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      ..+|||   +++++.+|.+.|.++|.+..+++.++. +  +.|||||.|.++.+|++|++++|...+.|+.+++...
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~-t--slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s   72 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDA-T--SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWS   72 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecC-C--ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehh
Confidence            468998   889999999999999999999999986 5  9999999999999999999999999999999887643

>KOG0109|consensus

Probab=98.99  E-value=9.6e-10  Score=74.35  Aligned_cols=78  Identities=24%  Similarity=0.293  Sum_probs=71.7

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEee
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTT   90 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~   90 (115)
                      ...+++|+|+.+.++..+++..|++||.+.++.|+.+        |+||.|.-.++|..|++.|++..+.|+++.|...+
T Consensus        77 ~stkl~vgNis~tctn~ElRa~fe~ygpviecdivkd--------y~fvh~d~~eda~~air~l~~~~~~gk~m~vq~st  148 (346)
T KOG0109|consen   77 ASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKD--------YAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLST  148 (346)
T ss_pred             CccccccCCCCccccCHHHhhhhcccCCceeeeeecc--------eeEEEEeeccchHHHHhcccccccccceeeeeeec
Confidence            4578999999999999999999999999999999865        99999999999999999999999999999999988


Q ss_pred             eccccC
Q psy3928          91 SRLSFG   96 (115)
Q Consensus        91 ~~~~~~   96 (115)
                      +|...+
T Consensus       149 srlrta  154 (346)
T KOG0109|consen  149 SRLRTA  154 (346)
T ss_pred             cccccC
Confidence            875543

>KOG4661|consensus

Probab=98.96  E-value=2.3e-09  Score=78.42  Aligned_cols=81  Identities=25%  Similarity=0.281  Sum_probs=73.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEee
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTT   90 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~   90 (115)
                      -++.+||++|...+...+|+.+|.+||.|.-.+++.+-.+...++|+||++++.++|.+|+..|+...+.|+-|.|..++
T Consensus       404 ~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaK  483 (940)
T KOG4661|consen  404 LGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAK  483 (940)
T ss_pred             cccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeecc
Confidence            35789999999999999999999999999988888876666778999999999999999999999999999999998876


Q ss_pred             e
Q psy3928          91 S   91 (115)
Q Consensus        91 ~   91 (115)
                      .
T Consensus       484 N  484 (940)
T KOG4661|consen  484 N  484 (940)
T ss_pred             c
Confidence            4

>KOG4205|consensus

Probab=98.96  E-value=1.4e-09  Score=75.18  Aligned_cols=83  Identities=19%  Similarity=0.326  Sum_probs=73.3

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEeee
Q psy3928          12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTTS   91 (115)
Q Consensus        12 ~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~~   91 (115)
                      ..++||++||.++++.+++++|.+||.+..+.++.+..+..+++++||.|.+++.+.+++. ..-..++++.+.+..+.+
T Consensus        97 tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~-~~f~~~~gk~vevkrA~p  175 (311)
T KOG4205|consen   97 TKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL-QKFHDFNGKKVEVKRAIP  175 (311)
T ss_pred             eeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecc-cceeeecCceeeEeeccc
Confidence            3599999999999999999999999999999999999899999999999999999998887 455678889999988887


Q ss_pred             cccc
Q psy3928          92 RLSF   95 (115)
Q Consensus        92 ~~~~   95 (115)
                      +...
T Consensus       176 k~~~  179 (311)
T KOG4205|consen  176 KEVM  179 (311)
T ss_pred             hhhc
Confidence            6443

>KOG4660|consensus

Probab=98.95  E-value=6.9e-10  Score=80.29  Aligned_cols=74  Identities=20%  Similarity=0.289  Sum_probs=64.7

Q ss_pred             cccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceee
Q psy3928           7 NNKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSS   85 (115)
Q Consensus         7 ~~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~   85 (115)
                      +.+...++|+|-|||..+++++|+.+|..||+|+.++.     +...++.+||+|.+..+|++|++.|++..+-++++.
T Consensus        70 ~~~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~-----t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   70 EKDMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRE-----TPNKRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             cccCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhc-----ccccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            34566789999999999999999999999999999765     445588999999999999999999999887777654

>KOG0132|consensus

Probab=98.93  E-value=3.9e-09  Score=79.11  Aligned_cols=70  Identities=21%  Similarity=0.356  Sum_probs=62.7

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928          12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus        12 ~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      .++||||+|+..+++.+|..+|+.||.|.++.+..+      ++||||.....++|.+|+++|.+..+.++.+++.
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~------R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~  490 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP------RGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIA  490 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEeeccC------CceeEEEEeehhHHHHHHHHHhcccccceeeEEe
Confidence            479999999999999999999999999999987654      6899999999999999999999888777766544

>KOG0153|consensus

Probab=98.84  E-value=1.2e-08  Score=70.40  Aligned_cols=76  Identities=26%  Similarity=0.340  Sum_probs=61.9

Q ss_pred             hcccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCC-CCCCCcee
Q psy3928           6 ENNKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN-PCPTDYQS   84 (115)
Q Consensus         6 ~~~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~-~~~~~~~~   84 (115)
                      +..+..-.+|||++|...+++.+|++.|.+||++..+.+...      +++|||+|.+...|+.|....-. ..++|+++
T Consensus       222 pPeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~------~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl  295 (377)
T KOG0153|consen  222 PPEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR------KGCAFVTFTTREAAEKAAEKSFNKLVINGFRL  295 (377)
T ss_pred             CCcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc------cccceeeehhhHHHHHHHHhhcceeeecceEE
Confidence            334566689999999999999999999999999999988754      35999999999999988865544 34677766


Q ss_pred             eEE
Q psy3928          85 SIL   87 (115)
Q Consensus        85 ~v~   87 (115)
                      .+.
T Consensus       296 ~i~  298 (377)
T KOG0153|consen  296 KIK  298 (377)
T ss_pred             EEE
Confidence            554

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

Probab=98.84  E-value=7.1e-08  Score=56.09  Aligned_cols=70  Identities=17%  Similarity=0.275  Sum_probs=62.6

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhh--cCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCc
Q psy3928          13 RVVLKEKLPPEAEHDYIESVFSK--YGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDY   82 (115)
Q Consensus        13 ~~l~V~~l~~~~~~~~l~~~f~~--~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~   82 (115)
                      ++|.+.|+|...+..+|.+.+..  .|....+.++.|..++.+.|||||.|.+++.|.+..+.++|..+...
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~   73 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNF   73 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccC
Confidence            68999999999999999998876  35667789999988899999999999999999999999999987654

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

>KOG4212|consensus

Probab=98.84  E-value=1.5e-08  Score=72.13  Aligned_cols=74  Identities=22%  Similarity=0.313  Sum_probs=66.1

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      .+.++|||.|||.+++...|++-|..+|.+....|+-   .|+++|  .|.|.++++|+.|+..|++..++|+.|.|.+
T Consensus       534 rKa~qIiirNlP~dfTWqmlrDKfre~G~v~yadime---~GkskG--VVrF~s~edAEra~a~Mngs~l~Gr~I~V~y  607 (608)
T KOG4212|consen  534 RKACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIME---NGKSKG--VVRFFSPEDAERACALMNGSRLDGRNIKVTY  607 (608)
T ss_pred             ccccEEEEecCCccccHHHHHHHHHhccceehhhhhc---cCCccc--eEEecCHHHHHHHHHHhccCcccCceeeeee
Confidence            4457899999999999999999999999999888742   577766  8999999999999999999999999988764

>KOG4209|consensus

Probab=98.83  E-value=2.3e-08  Score=66.75  Aligned_cols=84  Identities=24%  Similarity=0.213  Sum_probs=75.5

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      ...+...+||+|+...++..++...|+.||.+..+.++.++..+.++|++||+|.+...++.+++ |++..+.+..+.+.
T Consensus        97 ~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt  175 (231)
T KOG4209|consen   97 KEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVT  175 (231)
T ss_pred             hccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceee
Confidence            34567899999999999998899999999999999999998888899999999999999999999 99999999998877


Q ss_pred             Eeeec
Q psy3928          88 TTTSR   92 (115)
Q Consensus        88 ~~~~~   92 (115)
                      ....+
T Consensus       176 ~~r~~  180 (231)
T KOG4209|consen  176 LKRTN  180 (231)
T ss_pred             eeeee
Confidence            66544

>KOG1548|consensus

Probab=98.81  E-value=3.9e-08  Score=67.97  Aligned_cols=85  Identities=21%  Similarity=0.188  Sum_probs=73.4

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhcCCeEE--------EEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCce
Q psy3928          12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTY--------VSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQ   83 (115)
Q Consensus        12 ~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~--------~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~   83 (115)
                      ...|||+|||.+++-+++.++|..+|-|..        |++.++. .|+.+|=+.+.|...+++.-|+..|++..+.|..
T Consensus       134 Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~-~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~~  212 (382)
T KOG1548|consen  134 NTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDN-QGKLKGDALCCYIKRESVELAIKILDEDELRGKK  212 (382)
T ss_pred             CceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecC-CCCccCceEEEeecccHHHHHHHHhCcccccCcE
Confidence            356999999999999999999999986643        6777776 6999999999999999999999999999999999


Q ss_pred             eeEEEeeeccccCC
Q psy3928          84 SSILTTTSRLSFGI   97 (115)
Q Consensus        84 ~~v~~~~~~~~~~~   97 (115)
                      ++|..++-.....+
T Consensus       213 ~rVerAkfq~Kge~  226 (382)
T KOG1548|consen  213 LRVERAKFQMKGEY  226 (382)
T ss_pred             EEEehhhhhhccCc
Confidence            99998876444333

>KOG0116|consensus

Probab=98.79  E-value=3.7e-08  Score=70.55  Aligned_cols=80  Identities=23%  Similarity=0.332  Sum_probs=65.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEee
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTT   90 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~   90 (115)
                      ....|||.|||.+++..+|.+.|.+||.|+...|....-.++..+|+||+|.+.+.++.++.+- -..++++++.|...+
T Consensus       287 ~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~As-p~~ig~~kl~Veek~  365 (419)
T KOG0116|consen  287 DGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEAS-PLEIGGRKLNVEEKR  365 (419)
T ss_pred             cccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhcC-ccccCCeeEEEEecc
Confidence            3456999999999999999999999999998776543223444489999999999999999875 556777888887766


Q ss_pred             e
Q psy3928          91 S   91 (115)
Q Consensus        91 ~   91 (115)
                      +
T Consensus       366 ~  366 (419)
T KOG0116|consen  366 P  366 (419)
T ss_pred             c
Confidence            5

>KOG0110|consensus

Probab=98.77  E-value=3.8e-08  Score=73.22  Aligned_cols=78  Identities=24%  Similarity=0.314  Sum_probs=66.6

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCC---CeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTG---KLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        13 ~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~---~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      .++||.||+.+++...+...|...|.+..+.|...+...   -+.||+||+|.+.++|+.|++.|+|..++|..+.+...
T Consensus       516 t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S  595 (725)
T KOG0110|consen  516 TKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKIS  595 (725)
T ss_pred             hhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEec
Confidence            349999999999999999999999999988776554222   14599999999999999999999999999998877665


Q ss_pred             e
Q psy3928          90 T   90 (115)
Q Consensus        90 ~   90 (115)
                      .
T Consensus       596 ~  596 (725)
T KOG0110|consen  596 E  596 (725)
T ss_pred             c
Confidence            5

>KOG0226|consensus

Probab=98.71  E-value=1.8e-08  Score=67.10  Aligned_cols=83  Identities=18%  Similarity=0.223  Sum_probs=72.6

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      +....+||.|.|...++.+.|-+.|.+|-.....++++++.+|+++||+||.|.+..++-.|++.|+|.-++.+.|..+.
T Consensus       187 ~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRk  266 (290)
T KOG0226|consen  187 DEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRK  266 (290)
T ss_pred             ccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhh
Confidence            44567899999999999999999999998777778899988999999999999999999999999999988887776554


Q ss_pred             eee
Q psy3928          89 TTS   91 (115)
Q Consensus        89 ~~~   91 (115)
                      ...
T Consensus       267 S~w  269 (290)
T KOG0226|consen  267 SEW  269 (290)
T ss_pred             hhH
Confidence            443

>KOG0151|consensus

Probab=98.69  E-value=4.5e-08  Score=73.06  Aligned_cols=81  Identities=15%  Similarity=0.268  Sum_probs=69.2

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCC---CCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceee
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKST---GKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSS   85 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~---~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~   85 (115)
                      ++..+.+||+||++.++++.|...|..||++..+++++.+..   ...+.|+||.|-+..+|++|++.|+|..+....++
T Consensus       171 DP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K  250 (877)
T KOG0151|consen  171 DPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMK  250 (877)
T ss_pred             CCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeee
Confidence            455689999999999999999999999999999999887632   34467999999999999999999999988777666


Q ss_pred             EEEe
Q psy3928          86 ILTT   89 (115)
Q Consensus        86 v~~~   89 (115)
                      +.-.
T Consensus       251 ~gWg  254 (877)
T KOG0151|consen  251 LGWG  254 (877)
T ss_pred             eccc
Confidence            5443

>KOG0110|consensus

Probab=98.69  E-value=2.5e-08  Score=74.14  Aligned_cols=79  Identities=27%  Similarity=0.406  Sum_probs=69.2

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEee
Q psy3928          12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTT   90 (115)
Q Consensus        12 ~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~   90 (115)
                      ..+|.|.|+|...+-.+++.+|..||+++.++++.-...+..+|+|||+|-++++|..|...|.+..+-|+++-+..++
T Consensus       613 ~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEwA~  691 (725)
T KOG0110|consen  613 GTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEWAK  691 (725)
T ss_pred             cceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhcccceechhhheehhc
Confidence            4689999999999999999999999999999998754455679999999999999999999999888888876655543

>KOG4211|consensus

Probab=98.64  E-value=2.7e-07  Score=66.39  Aligned_cols=80  Identities=25%  Similarity=0.333  Sum_probs=65.7

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      +.+....|-+.+||+++++++|+++|+.++ |..+.+.+  .+|++.|-|||+|.+.++++.|+++ +...+..+.|.|.
T Consensus         6 e~~~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r--~~Gr~sGeA~Ve~~seedv~~Alkk-dR~~mg~RYIEVf   81 (510)
T KOG4211|consen    6 EGSTAFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPR--RNGRPSGEAYVEFTSEEDVEKALKK-DRESMGHRYIEVF   81 (510)
T ss_pred             CCCcceEEEecCCCccccHHHHHHHHhcCc-eeEEEEec--cCCCcCcceEEEeechHHHHHHHHh-hHHHhCCceEEEE
Confidence            344566788899999999999999999996 77766554  3799999999999999999999984 5456677778887


Q ss_pred             Eeee
Q psy3928          88 TTTS   91 (115)
Q Consensus        88 ~~~~   91 (115)
                      .+..
T Consensus        82 ~~~~   85 (510)
T KOG4211|consen   82 TAGG   85 (510)
T ss_pred             ccCC
Confidence            7654

>KOG0106|consensus

Probab=98.57  E-value=1e-07  Score=62.71  Aligned_cols=70  Identities=24%  Similarity=0.319  Sum_probs=61.4

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEee
Q psy3928          13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTT   90 (115)
Q Consensus        13 ~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~   90 (115)
                      ..+||++||..+.+.++..+|..||.+..+.+.        .+|+||+|.+..+|..|+..+|+..+.+..+.+..++
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk--------~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r   71 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMK--------NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHAR   71 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceee--------cccceeccCchhhhhcccchhcCceecceeeeeeccc
Confidence            368999999999999999999999999888764        3588999999999999999999999999885555554

>KOG4454|consensus

Probab=98.52  E-value=5.2e-08  Score=63.77  Aligned_cols=73  Identities=19%  Similarity=0.273  Sum_probs=63.9

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceee
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSS   85 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~   85 (115)
                      ..++|||+|+...++|+.|.++|-+.|+|..+.|...+ .++.+ ||||.|.++....-|+..+||..+.+..+.
T Consensus         8 ~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~-d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q   80 (267)
T KOG4454|consen    8 MDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQ-DQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQ   80 (267)
T ss_pred             hhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCc-cCCCc-eeeeecccccchhhhhhhcccchhccchhh
Confidence            35789999999999999999999999999999998776 45555 999999999999999999999987776543

>KOG0120|consensus

Probab=98.50  E-value=1.3e-07  Score=68.83  Aligned_cols=81  Identities=20%  Similarity=0.234  Sum_probs=73.7

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEee
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTT   90 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~   90 (115)
                      ...++||++||....+..+++++..||.++...+..+..+|.++||||.+|.+......|+..|||+.+.+..+.+..+.
T Consensus       288 ~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~  367 (500)
T KOG0120|consen  288 SPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAI  367 (500)
T ss_pred             ccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhh
Confidence            45789999999999999999999999999999888888789999999999999999999999999999998887776554


Q ss_pred             e
Q psy3928          91 S   91 (115)
Q Consensus        91 ~   91 (115)
                      .
T Consensus       368 ~  368 (500)
T KOG0120|consen  368 V  368 (500)
T ss_pred             c
Confidence            3

>KOG3152|consensus

Probab=98.23  E-value=1.8e-06  Score=57.76  Aligned_cols=75  Identities=27%  Similarity=0.276  Sum_probs=62.9

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCC--------CCeee----EEEEEecCHHHHHHHHHhhCCCC
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKST--------GKLKG----FAFVEFSTKEEATKALELGLNPC   78 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~--------~~~~g----~~fv~f~~~~~a~~al~~l~~~~   78 (115)
                      ....||++++|+.+....|+++|..||.|-.+.+.....+        |....    -+.|+|.+...|..+...||+.+
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~  152 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTP  152 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCc
Confidence            5579999999999999999999999999999988766443        23222    36699999999999999999999


Q ss_pred             CCCceee
Q psy3928          79 PTDYQSS   85 (115)
Q Consensus        79 ~~~~~~~   85 (115)
                      +.|+.-.
T Consensus       153 Iggkk~S  159 (278)
T KOG3152|consen  153 IGGKKKS  159 (278)
T ss_pred             cCCCCCC
Confidence            9997643

>KOG1457|consensus

Probab=98.22  E-value=1.9e-06  Score=56.80  Aligned_cols=64  Identities=20%  Similarity=0.340  Sum_probs=53.3

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCC
Q psy3928          13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPT   80 (115)
Q Consensus        13 ~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~   80 (115)
                      .++||.||...++|++|+.+|..|.....++|.. + +|.  ..+|++|++.+.|..|+..|+|..+.
T Consensus       211 stlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~-~-~g~--~vaf~~~~~~~~at~am~~lqg~~~s  274 (284)
T KOG1457|consen  211 STLFIANLGPNCTEDELKQLLSRYPGFHILKIRA-R-GGM--PVAFADFEEIEQATDAMNHLQGNLLS  274 (284)
T ss_pred             hhHhhhccCCCCCHHHHHHHHHhCCCceEEEEec-C-CCc--ceEeecHHHHHHHHHHHHHhhcceec
Confidence            4799999999999999999999997766666532 2 444  48999999999999999999997543

>KOG2314|consensus

Probab=98.15  E-value=1.1e-05  Score=59.33  Aligned_cols=71  Identities=27%  Similarity=0.383  Sum_probs=59.0

Q ss_pred             CCCEEEEcCCCCCCCHH------HHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCc
Q psy3928          11 YGRVVLKEKLPPEAEHD------YIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDY   82 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~------~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~   82 (115)
                      ....|+|.|+|..-...      -|.++|+++|.+..+.++.+..+| ++||.|++|.+..+|+.|++.+||+.++..
T Consensus        57 ~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~gg-tkG~lf~E~~~~~~A~~aVK~l~G~~ldkn  133 (698)
T KOG2314|consen   57 FDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGG-TKGYLFVEYASMRDAKKAVKSLNGKRLDKN  133 (698)
T ss_pred             cceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCC-eeeEEEEEecChhhHHHHHHhcccceeccc
Confidence            34678899999754332      378889999999999888877444 899999999999999999999999987765

>KOG1995|consensus

Probab=98.15  E-value=5.4e-06  Score=57.76  Aligned_cols=86  Identities=17%  Similarity=0.129  Sum_probs=74.4

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEE--------EEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCC
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTY--------VSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCP   79 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~--------~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~   79 (115)
                      ......+|||.+||..++++.+..+|.+++.|+.        +.+..++.|+++++-|.|.|.+...|++|+.-+++..+
T Consensus        62 ~~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf  141 (351)
T KOG1995|consen   62 DKSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDF  141 (351)
T ss_pred             cccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccc
Confidence            3556679999999999999999999999986643        56677788999999999999999999999999999999


Q ss_pred             CCceeeEEEeeecc
Q psy3928          80 TDYQSSILTTTSRL   93 (115)
Q Consensus        80 ~~~~~~v~~~~~~~   93 (115)
                      .+..+.|..++.+.
T Consensus       142 ~gn~ikvs~a~~r~  155 (351)
T KOG1995|consen  142 CGNTIKVSLAERRT  155 (351)
T ss_pred             cCCCchhhhhhhcc
Confidence            99888877766543

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

Probab=98.06  E-value=5.3e-05  Score=42.75  Aligned_cols=69  Identities=20%  Similarity=0.249  Sum_probs=45.4

Q ss_pred             CEEEEcCCCCCCCHHH----HHHHhhhcC-CeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928          13 RVVLKEKLPPEAEHDY----IESVFSKYG-KVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus        13 ~~l~V~~l~~~~~~~~----l~~~f~~~g-~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      ..|+|.|||.+.+...    |+.++..+| .+..+       ++   +-|++.|.+.+.|.+|.+.|+|-.+-|..|.+.
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v-------~~---~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~   72 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV-------SG---GTAILRFPNQEFAERAQKRMEGEDVFGNKISVS   72 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE---------T---T-EEEEESSHHHHHHHHHHHTT--SSSS--EEE
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE-------eC---CEEEEEeCCHHHHHHHHHhhcccccccceEEEE
Confidence            3689999999988766    555666776 34433       22   479999999999999999999999999998887


Q ss_pred             Eeee
Q psy3928          88 TTTS   91 (115)
Q Consensus        88 ~~~~   91 (115)
                      +...
T Consensus        73 ~~~~   76 (90)
T PF11608_consen   73 FSPK   76 (90)
T ss_dssp             SS--
T ss_pred             EcCC
Confidence            6643

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

>KOG4211|consensus

Probab=98.05  E-value=1.7e-05  Score=57.43  Aligned_cols=77  Identities=25%  Similarity=0.250  Sum_probs=59.2

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEE-EEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTY-VSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~-~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      ....|-+.+||..+++++|.++|+..--+.. +.++.++ .+++.|-|||.|++.+.|+.|+.... ..+..+.|.|...
T Consensus       102 ~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~-rgR~tGEAfVqF~sqe~ae~Al~rhr-e~iGhRYIEvF~S  179 (510)
T KOG4211|consen  102 NDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQ-RGRPTGEAFVQFESQESAEIALGRHR-ENIGHRYIEVFRS  179 (510)
T ss_pred             CCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccC-CCCcccceEEEecCHHHHHHHHHHHH-HhhccceEEeehh
Confidence            4468889999999999999999998743333 4455555 67789999999999999999998654 3456666666544

>KOG0147|consensus

Probab=98.05  E-value=1.7e-06  Score=63.11  Aligned_cols=78  Identities=22%  Similarity=0.222  Sum_probs=69.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      .+.+++|+-.++...++.+|.++|..+|.|..+.++.++.++.++|.+||+|.+.+.+..|+ .|.|..+.|.++-+..
T Consensus       177 Rd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~ai-aLsGqrllg~pv~vq~  254 (549)
T KOG0147|consen  177 RDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAI-ALSGQRLLGVPVIVQL  254 (549)
T ss_pred             HhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHh-hhcCCcccCceeEecc
Confidence            34577888888888999999999999999999999999999999999999999999999998 5899888888776654

>KOG4206|consensus

Probab=98.02  E-value=3.2e-05  Score=50.91  Aligned_cols=67  Identities=21%  Similarity=0.328  Sum_probs=58.7

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCC
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPT   80 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~   80 (115)
                      -....++|+.|+|..++...+..+|.+|...+.++++..+     .+.+||+|.+...+..|...+++..+.
T Consensus       143 ~ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~~-----~~iAfve~~~d~~a~~a~~~lq~~~it  209 (221)
T KOG4206|consen  143 APPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPPR-----SGIAFVEFLSDRQASAAQQALQGFKIT  209 (221)
T ss_pred             CCCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccCC-----CceeEEecchhhhhHHHhhhhccceec
Confidence            3456789999999999999999999999999999887654     569999999999999999999997655

>KOG1190|consensus

Probab=97.98  E-value=5e-05  Score=54.09  Aligned_cols=75  Identities=20%  Similarity=0.189  Sum_probs=65.6

Q ss_pred             CCEEEEcCCCC-CCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEee
Q psy3928          12 GRVVLKEKLPP-EAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTT   90 (115)
Q Consensus        12 ~~~l~V~~l~~-~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~   90 (115)
                      ...|.|.||.. .++.+.|..+|..||.+.+++|+.++.     --|.|.+++...|+-|+..|+|..+-|+.+++...+
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkk-----d~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SK  371 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKK-----DNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSK  371 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCC-----cceeeeecchhHHHHHHHHhhcceecCceEEEeecc
Confidence            46788888864 578899999999999999999998752     379999999999999999999999999999987765


Q ss_pred             e
Q psy3928          91 S   91 (115)
Q Consensus        91 ~   91 (115)
                      .
T Consensus       372 H  372 (492)
T KOG1190|consen  372 H  372 (492)
T ss_pred             C
Confidence            4

>KOG4849|consensus

Probab=97.87  E-value=2.1e-05  Score=55.04  Aligned_cols=76  Identities=9%  Similarity=0.132  Sum_probs=64.9

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcC--CeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeE
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYG--KVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSI   86 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g--~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v   86 (115)
                      ...-+|||||-+.++.++|.+.+.+.|  ++..+++.-++.+|+++|||++...+....++.++.|-...+.|..-.|
T Consensus        79 rk~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V  156 (498)
T KOG4849|consen   79 RKYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTV  156 (498)
T ss_pred             ceEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCee
Confidence            345689999999999999999998876  5667777888889999999999999999999999999888888765444

>KOG4307|consensus

Probab=97.86  E-value=0.0001  Score=55.77  Aligned_cols=83  Identities=22%  Similarity=0.201  Sum_probs=65.6

Q ss_pred             hhhcccCCCC-EEEEcCCCCCCCHHHHHHHhhhcCCeE-EEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCC
Q psy3928           4 LVENNKKYGR-VVLKEKLPPEAEHDYIESVFSKYGKVT-YVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTD   81 (115)
Q Consensus         4 ~~~~~~~~~~-~l~V~~l~~~~~~~~l~~~f~~~g~i~-~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~   81 (115)
                      +.+...+.+. .|-+.|+|.+++-++|.++|..|-.+. .+.+-++ +.|...|-|.|.|++.++|.+|...+++.+|..
T Consensus       858 ~~~~~~~pGp~V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~n-d~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~n  936 (944)
T KOG4307|consen  858 LMELIKSPGPRVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRN-DDGVPTGECMVAFESQEEARRASMDLDGQKIRN  936 (944)
T ss_pred             HHHhcCCCCCeEEEecCCCccccHHHHHHHhcccccCCCceeEeec-CCCCcccceeEeecCHHHHHhhhhccccCcccc
Confidence            3444444444 788999999999999999999996543 3444443 489999999999999999999999999988877


Q ss_pred             ceeeEE
Q psy3928          82 YQSSIL   87 (115)
Q Consensus        82 ~~~~v~   87 (115)
                      +.+.+.
T Consensus       937 r~V~l~  942 (944)
T KOG4307|consen  937 RVVSLR  942 (944)
T ss_pred             eeEEEE
Confidence            766543

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

Probab=97.79  E-value=0.00013  Score=43.11  Aligned_cols=59  Identities=31%  Similarity=0.459  Sum_probs=38.5

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCC
Q psy3928          13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNP   77 (115)
Q Consensus        13 ~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~   77 (115)
                      ..|.+.+++..++.++|+..|..||.|..+.+..    |..  -|+|.|.+.+.|+.|+..+...
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~----G~~--~g~VRf~~~~~A~~a~~~~~~~   60 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSR----GDT--EGYVRFKTPEAAQKALEKLKEA   60 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--T----T-S--EEEEEESS---HHHHHHHHHHT
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecC----CCC--EEEEEECCcchHHHHHHHHHhc
Confidence            5788989999999999999999999998887643    333  7899999999999999877665

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

>KOG0129|consensus

Probab=97.66  E-value=0.00022  Score=52.04  Aligned_cols=65  Identities=23%  Similarity=0.277  Sum_probs=57.6

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhh-hcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHH
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFS-KYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE   72 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~-~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~   72 (115)
                      .-+..++||||+||.-++..+|-.+|. -||.|..+-|-.|++-..++|=+-|.|++.+.--+|+.
T Consensus       366 ~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIs  431 (520)
T KOG0129|consen  366 PIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAIS  431 (520)
T ss_pred             ccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHh
Confidence            345678999999999999999999998 59999999998887778899999999999988888875

>KOG4210|consensus

Probab=97.65  E-value=6.3e-05  Score=51.89  Aligned_cols=80  Identities=24%  Similarity=0.312  Sum_probs=70.6

Q ss_pred             CEEE-EcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEeee
Q psy3928          13 RVVL-KEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTTS   91 (115)
Q Consensus        13 ~~l~-V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~~   91 (115)
                      .++| |++++..+++++|+..|..+|.+..+++..++.++...+++++.|........++.. +...+.+..+.+....+
T Consensus       185 ~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~  263 (285)
T KOG4210|consen  185 DTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEEDEP  263 (285)
T ss_pred             ccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCcccccccCCC
Confidence            4555 999999999999999999999999999999988999999999999999999999887 77788888877777766


Q ss_pred             cc
Q psy3928          92 RL   93 (115)
Q Consensus        92 ~~   93 (115)
                      +.
T Consensus       264 ~~  265 (285)
T KOG4210|consen  264 RP  265 (285)
T ss_pred             Cc
Confidence            53

>KOG0129|consensus

Probab=97.65  E-value=0.00019  Score=52.39  Aligned_cols=65  Identities=25%  Similarity=0.411  Sum_probs=49.7

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCC--C-CCeee---EEEEEecCHHHHHHHHHhhCC
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKS--T-GKLKG---FAFVEFSTKEEATKALELGLN   76 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~--~-~~~~g---~~fv~f~~~~~a~~al~~l~~   76 (115)
                      ..++||||+||++++|+.|...|..||.+ .+.++....  . --++|   |+|+.|.++..++..+.++..
T Consensus       258 ~S~KVFvGGlp~dise~~i~~~F~~FGs~-~VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~  328 (520)
T KOG0129|consen  258 YSRKVFVGGLPWDITEAQINASFGQFGSV-KVDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSE  328 (520)
T ss_pred             cccceeecCCCccccHHHHHhhcccccce-EeecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHhh
Confidence            45799999999999999999999999944 344442111  1 11345   999999999999998887765

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

Probab=97.63  E-value=0.00034  Score=36.21  Aligned_cols=52  Identities=17%  Similarity=0.517  Sum_probs=41.0

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHH
Q psy3928          13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL   71 (115)
Q Consensus        13 ~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al   71 (115)
                      +.|-|.|.+.+.. +.++..|.+||.|....+.      ......++.|.+..+|++||
T Consensus         2 ~wI~V~Gf~~~~~-~~vl~~F~~fGeI~~~~~~------~~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLA-EEVLEHFASFGEIVDIYVP------ESTNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHH-HHHHHHHHhcCCEEEEEcC------CCCcEEEEEECCHHHHHhhC
Confidence            4577888888755 4567789999999998774      22348999999999999885

>KOG0105|consensus

Probab=97.57  E-value=0.0018  Score=41.94  Aligned_cols=67  Identities=18%  Similarity=0.260  Sum_probs=57.8

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCC
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTD   81 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~   81 (115)
                      .+.....|.|++||++.+..+|+..+..-|.++...+.++       |.+.|+|-..++.+.|+..|....+..
T Consensus       111 srrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD-------g~GvV~~~r~eDMkYAvr~ld~~~~~s  177 (241)
T KOG0105|consen  111 SRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD-------GVGVVEYLRKEDMKYAVRKLDDQKFRS  177 (241)
T ss_pred             ccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc-------cceeeeeeehhhHHHHHHhhccccccC
Confidence            3445578999999999999999999999999998877654       388999999999999999999876555

>KOG0106|consensus

Probab=97.56  E-value=6.7e-05  Score=49.55  Aligned_cols=68  Identities=29%  Similarity=0.348  Sum_probs=59.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeE
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSI   86 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v   86 (115)
                      ..+.+.|.+++..+.+.+|...|.++|.+....+        ..+.+||+|....++..|+..+++..+.+..+.+
T Consensus        98 s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~--------~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~  165 (216)
T KOG0106|consen   98 THFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA--------RRNFAFVEFSEQEDAKRALEKLDGKKLNGRRISV  165 (216)
T ss_pred             ccceeeeccchhhhhHHHHhhhhcccCCCchhhh--------hccccceeehhhhhhhhcchhccchhhcCceeee
Confidence            4578889999999999999999999998843322        2458999999999999999999999999998887

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.52  E-value=0.00049  Score=48.24  Aligned_cols=78  Identities=18%  Similarity=0.256  Sum_probs=57.4

Q ss_pred             CCEEEEcCCCCCCCHHH------HHHHhhhcCCeEEEEeceeC-CCCCeeeE--EEEEecCHHHHHHHHHhhCCCCCCCc
Q psy3928          12 GRVVLKEKLPPEAEHDY------IESVFSKYGKVTYVSLPKFK-STGKLKGF--AFVEFSTKEEATKALELGLNPCPTDY   82 (115)
Q Consensus        12 ~~~l~V~~l~~~~~~~~------l~~~f~~~g~i~~~~i~~~~-~~~~~~g~--~fv~f~~~~~a~~al~~l~~~~~~~~   82 (115)
                      ...+||-+||+.+..++      -.++|.+||.|..+.+-..- ......++  .||.|.+.++|.+|+...+|..++|+
T Consensus       114 KNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr  193 (480)
T COG5175         114 KNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGR  193 (480)
T ss_pred             cceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCc
Confidence            35689999987765544      36899999999987653321 11122233  49999999999999999999999999


Q ss_pred             eeeEEEe
Q psy3928          83 QSSILTT   89 (115)
Q Consensus        83 ~~~v~~~   89 (115)
                      .++..+-
T Consensus       194 ~lkatYG  200 (480)
T COG5175         194 VLKATYG  200 (480)
T ss_pred             eEeeecC
Confidence            8776543

>KOG1855|consensus

Probab=97.51  E-value=0.00018  Score=51.59  Aligned_cols=68  Identities=26%  Similarity=0.335  Sum_probs=55.8

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEecee---CCC--CC--------eeeEEEEEecCHHHHHHHHHhhCC
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKF---KST--GK--------LKGFAFVEFSTKEEATKALELGLN   76 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~---~~~--~~--------~~g~~fv~f~~~~~a~~al~~l~~   76 (115)
                      -..++|.+.|||.+-.-+.|.++|..+|.|+.++|...   +.+  +.        .+-+|+|+|.....|.+|.+.++.
T Consensus       229 l~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~~  308 (484)
T KOG1855|consen  229 LPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLNP  308 (484)
T ss_pred             cccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhch
Confidence            36789999999998777889999999999999998765   221  11        245899999999999999998865


Q ss_pred             C
Q psy3928          77 P   77 (115)
Q Consensus        77 ~   77 (115)
                      .
T Consensus       309 e  309 (484)
T KOG1855|consen  309 E  309 (484)
T ss_pred             h
Confidence            4

>KOG1365|consensus

Probab=97.32  E-value=0.00031  Score=49.91  Aligned_cols=76  Identities=18%  Similarity=0.227  Sum_probs=62.3

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhcCC-eEE--EEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          13 RVVLKEKLPPEAEHDYIESVFSKYGK-VTY--VSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        13 ~~l~V~~l~~~~~~~~l~~~f~~~g~-i~~--~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      .-|-+++||...+.++|..+|..|.. +..  +.++.+. .|.+.|-|||++.+.+.|.+|.+..+....+.+.+.+...
T Consensus       281 dcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~-qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp~  359 (508)
T KOG1365|consen  281 DCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNG-QGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFPC  359 (508)
T ss_pred             CeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcC-CCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEeec
Confidence            45789999999999999999999863 443  6777765 8899999999999999999999998887666666666543

>KOG1190|consensus

Probab=97.31  E-value=0.0011  Score=47.49  Aligned_cols=75  Identities=17%  Similarity=0.198  Sum_probs=59.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCC-eEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCc-eeeEEE
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGK-VTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDY-QSSILT   88 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~-i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~-~~~v~~   88 (115)
                      ...++.++|+|.+++|++++..|..-|. ++..+.     -++.+.++.+.+.+.++|-.|+..++...+.+. .+||-+
T Consensus       413 psatlHlsnip~svsee~lk~~f~~~g~~vkafkf-----f~kd~kmal~q~~sveeA~~ali~~hnh~lgen~hlRvSF  487 (492)
T KOG1190|consen  413 PSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKF-----FQKDRKMALPQLESVEEAIQALIDLHNHYLGENHHLRVSF  487 (492)
T ss_pred             chhheeeccCCcccchhHHHHhhhcCCceEEeeee-----cCCCcceeecccCChhHhhhhccccccccCCCCceEEEEe
Confidence            3458899999999999999999998764 455544     344566999999999999999999998877665 456655


Q ss_pred             ee
Q psy3928          89 TT   90 (115)
Q Consensus        89 ~~   90 (115)
                      .+
T Consensus       488 Sk  489 (492)
T KOG1190|consen  488 SK  489 (492)
T ss_pred             ec
Confidence            44

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

Probab=97.14  E-value=0.018  Score=34.36  Aligned_cols=76  Identities=9%  Similarity=0.052  Sum_probs=52.4

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhhcC-CeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCc---eeeEEEe
Q psy3928          14 VVLKEKLPPEAEHDYIESVFSKYG-KVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDY---QSSILTT   89 (115)
Q Consensus        14 ~l~V~~l~~~~~~~~l~~~f~~~g-~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~---~~~v~~~   89 (115)
                      .+.+...|..+..+.|..+.+.+- .+..++++++  ....+..+.+.|.+...|......+||..++..   ..++.++
T Consensus        15 ~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird--~~pnrymVLikF~~~~~Ad~Fy~~fNGk~FnslEpE~ChvvfV   92 (110)
T PF07576_consen   15 LCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRD--GTPNRYMVLIKFRDQESADEFYEEFNGKPFNSLEPETCHVVFV   92 (110)
T ss_pred             EEEEEeCcccccHHHHHHhhhcccccEEEEEEeeC--CCCceEEEEEEECCHHHHHHHHHHhCCCccCCCCCceeEEEEE
Confidence            333434444455556665555553 5677888775  344677899999999999999999999987663   4555555


Q ss_pred             ee
Q psy3928          90 TS   91 (115)
Q Consensus        90 ~~   91 (115)
                      +.
T Consensus        93 ~~   94 (110)
T PF07576_consen   93 KS   94 (110)
T ss_pred             EE
Confidence            44

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

>KOG1456|consensus

Probab=97.09  E-value=0.0056  Score=43.60  Aligned_cols=77  Identities=22%  Similarity=0.176  Sum_probs=65.0

Q ss_pred             cCCCCEEEEcCCCCC-CCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928           9 KKYGRVVLKEKLPPE-AEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~-~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      ...+..+.|-+|... +..+.|..+|-.||.+.++++++-+     .|-|.|+..+....++|+..||+..+-|.++.+.
T Consensus       284 ~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk-----~gtamVemgd~~aver~v~hLnn~~lfG~kl~v~  358 (494)
T KOG1456|consen  284 GAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK-----PGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVC  358 (494)
T ss_pred             CCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc-----cceeEEEcCcHHHHHHHHHHhccCccccceEEEe
Confidence            445678899999865 5667899999999999999987644     4679999999999999999999999999888876


Q ss_pred             Eee
Q psy3928          88 TTT   90 (115)
Q Consensus        88 ~~~   90 (115)
                      ..+
T Consensus       359 ~Sk  361 (494)
T KOG1456|consen  359 VSK  361 (494)
T ss_pred             ecc
Confidence            544

>KOG1365|consensus

Probab=97.06  E-value=0.0036  Score=44.72  Aligned_cols=63  Identities=27%  Similarity=0.231  Sum_probs=49.6

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhc----CCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhC
Q psy3928          12 GRVVLKEKLPPEAEHDYIESVFSKY----GKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGL   75 (115)
Q Consensus        12 ~~~l~V~~l~~~~~~~~l~~~f~~~----g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~   75 (115)
                      .-.|-.++||.+.++.++..+|.+-    +....+.++..+ +|+..|-|||.|..+++|+.||.+-.
T Consensus       161 qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rp-dgrpTGdAFvlfa~ee~aq~aL~khr  227 (508)
T KOG1365|consen  161 QVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRP-DGRPTGDAFVLFACEEDAQFALRKHR  227 (508)
T ss_pred             ceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECC-CCCcccceEEEecCHHHHHHHHHHHH
Confidence            3466678999999999999999632    234455555544 78999999999999999999997543

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

Probab=96.97  E-value=0.0037  Score=36.63  Aligned_cols=71  Identities=14%  Similarity=0.129  Sum_probs=46.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEE-eceeCC------CCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCce
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVS-LPKFKS------TGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQ   83 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~-i~~~~~------~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~   83 (115)
                      ...-|.|-+.|+. ....+.+.|++||.|.+.. +..+..      ......+-.+.|.++.+|++||. -||..+.|..
T Consensus         5 ~~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~~   82 (100)
T PF05172_consen    5 SETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGSL   82 (100)
T ss_dssp             GCCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTCE
T ss_pred             CCeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCcE
Confidence            4456888899998 5577899999999987653 111100      01123489999999999999998 5887777654

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.

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

Probab=96.88  E-value=0.014  Score=31.17  Aligned_cols=56  Identities=21%  Similarity=0.129  Sum_probs=43.7

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhc---CCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhh
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKY---GKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELG   74 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~---g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l   74 (115)
                      .+.+|+|.|+.. ++.++++.+|..|   .....+.++.+.       -|-|.|.+...|.+||..|
T Consensus         4 rpeavhirGvd~-lsT~dI~~y~~~y~~~~~~~~IEWIdDt-------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    4 RPEAVHIRGVDE-LSTDDIKAYFSEYFDEEGPFRIEWIDDT-------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eeceEEEEcCCC-CCHHHHHHHHHHhcccCCCceEEEecCC-------cEEEEECCHHHHHHHHHcC
Confidence            346799999865 6778899999988   135567777653       4789999999999999864

>KOG0120|consensus

Probab=96.87  E-value=0.0055  Score=45.30  Aligned_cols=60  Identities=22%  Similarity=0.253  Sum_probs=47.0

Q ss_pred             HHHHhhhcCCeEEEEeceeCCC---CCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928          29 IESVFSKYGKVTYVSLPKFKST---GKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus        29 l~~~f~~~g~i~~~~i~~~~~~---~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      ++.-+..||.+..|.+.++...   .-..|..||+|.+.++++.|...|+|..+.++.+-..+
T Consensus       426 vr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsY  488 (500)
T KOG0120|consen  426 VRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASY  488 (500)
T ss_pred             HHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEe
Confidence            4445567888999988876222   33467899999999999999999999999998765443

>KOG1548|consensus

Probab=96.78  E-value=0.0077  Score=42.40  Aligned_cols=74  Identities=19%  Similarity=0.202  Sum_probs=55.5

Q ss_pred             CCCEEEEcCCCC----CCC-------HHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCC
Q psy3928          11 YGRVVLKEKLPP----EAE-------HDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCP   79 (115)
Q Consensus        11 ~~~~l~V~~l~~----~~~-------~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~   79 (115)
                      ..++|.+.|+-.    ..+       .++|++--..||.+..+.+.    ...+.|.+-|.|.+...|+.|++.|+|.-+
T Consensus       264 ~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~----d~hPdGvvtV~f~n~eeA~~ciq~m~GR~f  339 (382)
T KOG1548|consen  264 ADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVY----DRHPDGVVTVSFRNNEEADQCIQTMDGRWF  339 (382)
T ss_pred             CCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEe----ccCCCceeEEEeCChHHHHHHHHHhcCeee
Confidence            457788877631    112       12355556789999998764    345678999999999999999999999999


Q ss_pred             CCceeeEEE
Q psy3928          80 TDYQSSILT   88 (115)
Q Consensus        80 ~~~~~~v~~   88 (115)
                      +|+++....
T Consensus       340 dgRql~A~i  348 (382)
T KOG1548|consen  340 DGRQLTASI  348 (382)
T ss_pred             cceEEEEEE
Confidence            999876543

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

Probab=96.74  E-value=0.0064  Score=37.91  Aligned_cols=80  Identities=19%  Similarity=0.152  Sum_probs=50.6

Q ss_pred             hhhhcccCCCCEEEEcCCC------CCCCH---HHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHh
Q psy3928           3 ELVENNKKYGRVVLKEKLP------PEAEH---DYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL   73 (115)
Q Consensus         3 ~~~~~~~~~~~~l~V~~l~------~~~~~---~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~   73 (115)
                      ++.....+...+|.|.-..      ....+   .+|.+.|..||.+.-+++..+        .-.|+|.+-..|.+|+. 
T Consensus        18 eVi~~~GPpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaals-   88 (146)
T PF08952_consen   18 EVISSQGPPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAALS-   88 (146)
T ss_dssp             --S-----TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHHH-
T ss_pred             HHHHhcCCCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHHc-
Confidence            3444455666777776555      22333   257778888998776666432        57899999999999998 


Q ss_pred             hCCCCCCCceeeEEEeee
Q psy3928          74 GLNPCPTDYQSSILTTTS   91 (115)
Q Consensus        74 l~~~~~~~~~~~v~~~~~   91 (115)
                      ++|..+.|..+.+...++
T Consensus        89 ~dg~~v~g~~l~i~LKtp  106 (146)
T PF08952_consen   89 LDGIQVNGRTLKIRLKTP  106 (146)
T ss_dssp             GCCSEETTEEEEEEE---
T ss_pred             cCCcEECCEEEEEEeCCc
Confidence            899999999988887765

; PDB: 1UFW_A 2DNR_A.

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

Probab=96.65  E-value=0.018  Score=32.56  Aligned_cols=56  Identities=23%  Similarity=0.297  Sum_probs=41.8

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCC
Q psy3928          12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN   76 (115)
Q Consensus        12 ~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~   76 (115)
                      .+..+|+ .|..+...+|.++|++||.|. +.++.+-       =|||.....+.+..++..+.-
T Consensus         9 dHVFhlt-FPkeWK~~DI~qlFspfG~I~-VsWi~dT-------SAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen    9 DHVFHLT-FPKEWKTSDIYQLFSPFGQIY-VSWINDT-------SAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             CCEEEEE---TT--HHHHHHHCCCCCCEE-EEEECTT-------EEEEEECCCHHHHHHHHHHTT
T ss_pred             ceEEEEe-CchHhhhhhHHHHhccCCcEE-EEEEcCC-------cEEEEeecHHHHHHHHHHhcc
Confidence            4566776 999999999999999999764 4555432       589999999999999998864

; 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.

>KOG0128|consensus

Probab=96.58  E-value=0.0011  Score=51.20  Aligned_cols=76  Identities=22%  Similarity=0.250  Sum_probs=64.9

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928          12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus        12 ~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      ..+++|+|.|...+.++++.++..+|.+..++++..+ .|+++|.+++.|.++.++.+++.......+.-..+.+..
T Consensus       736 K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r-~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~v  811 (881)
T KOG0128|consen  736 KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVR-AGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQV  811 (881)
T ss_pred             hhhhheeCCCCCCchHHHHhhccccCCccccchhhhh-ccccccceeccCCCcchhhhhcccchhhhhhhcCccccc
Confidence            4689999999999999999999999999988877776 899999999999999999999988777765555444433

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

Probab=96.46  E-value=0.0055  Score=39.51  Aligned_cols=75  Identities=17%  Similarity=0.134  Sum_probs=46.8

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhh-cCCe---EEEE--eceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCce
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSK-YGKV---TYVS--LPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQ   83 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~-~g~i---~~~~--i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~   83 (115)
                      ....+|.|+.||++++++++.+.+.+ ++.-   ..+.  ............-||+.|.+.+++......++|..+.+..
T Consensus         5 ~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~k   84 (176)
T PF03467_consen    5 KEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSK   84 (176)
T ss_dssp             ----EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TT
T ss_pred             ccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCC
Confidence            34568999999999999998887776 5544   3332  1111111123457999999999999999999997755544


Q ss_pred             e
Q psy3928          84 S   84 (115)
Q Consensus        84 ~   84 (115)
                      .
T Consensus        85 g   85 (176)
T PF03467_consen   85 G   85 (176)
T ss_dssp             S
T ss_pred             C
Confidence            3

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.

>KOG0115|consensus

Probab=96.44  E-value=0.0055  Score=41.45  Aligned_cols=65  Identities=23%  Similarity=0.240  Sum_probs=55.0

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCC
Q psy3928          13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPC   78 (115)
Q Consensus        13 ~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~   78 (115)
                      ..|||.||+..++-+.+..-|+.||++....+..+- .++..+-.+|+|.....|..|+..+....
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~-r~k~t~eg~v~~~~k~~a~~a~rr~~~~g   96 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDD-RGKPTREGIVEFAKKPNARKAARRCREGG   96 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeecc-cccccccchhhhhcchhHHHHHHHhccCc
Confidence            679999999999999999999999998765444442 67888899999999999999999886544

>KOG4676|consensus

Probab=96.29  E-value=0.0098  Score=42.60  Aligned_cols=75  Identities=19%  Similarity=0.220  Sum_probs=56.9

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCC---CCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeE
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKST---GKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSI   86 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~---~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v   86 (115)
                      ....|-|.||.+.++.++++.+|...|.|..+.|+.+...   ......|||.|.+.+.+..|.. |.+..+-+..+-|
T Consensus         6 ~~~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQh-Ltntvfvdraliv   83 (479)
T KOG4676|consen    6 SLGVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQH-LTNTVFVDRALIV   83 (479)
T ss_pred             CCceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhh-hccceeeeeeEEE
Confidence            3458999999999999999999999999999988764322   2345689999999888876665 5555555554433

>KOG0128|consensus

Probab=96.15  E-value=0.00014  Score=55.79  Aligned_cols=67  Identities=22%  Similarity=0.307  Sum_probs=56.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCC
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNP   77 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~   77 (115)
                      ...++||+||+..+.+.+|...|..+|.+..+++......+..+|+|+++|..+.++.+++......
T Consensus       666 ~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~  732 (881)
T KOG0128|consen  666 DLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSC  732 (881)
T ss_pred             HHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhh
Confidence            3467899999999999999999999998877776655567889999999999999999999755544

>KOG0112|consensus

Probab=96.13  E-value=0.0015  Score=50.72  Aligned_cols=80  Identities=18%  Similarity=0.145  Sum_probs=64.1

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      .....+||+|||+..+++.+|+..|..+|.+..|.|-..+ -+.-.-|+|+.|.+.+.+..++..+.+..|....+++..
T Consensus       369 ~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~-~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~gl  447 (975)
T KOG0112|consen  369 FRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPH-IKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGL  447 (975)
T ss_pred             hhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCC-CCcccchhhhhhhccccCcccchhhcCCccccCcccccc
Confidence            3456799999999999999999999999999988876553 222234999999999999999999998877766555444


Q ss_pred             e
Q psy3928          89 T   89 (115)
Q Consensus        89 ~   89 (115)
                      -
T Consensus       448 G  448 (975)
T KOG0112|consen  448 G  448 (975)
T ss_pred             c
Confidence            4

>KOG0112|consensus

Probab=95.74  E-value=0.022  Score=44.66  Aligned_cols=73  Identities=11%  Similarity=0.153  Sum_probs=60.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCce--eeEEE
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQ--SSILT   88 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~--~~v~~   88 (115)
                      ..+.+++++|+.+.....+...|..||.+..+.+-    -|.  .|+++.|.+...++.|+..+.+.++.+..  ++|.+
T Consensus       454 ~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~----hgq--~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvdl  527 (975)
T KOG0112|consen  454 PTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYR----HGQ--PYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVDL  527 (975)
T ss_pred             cceeeccCCCCCCChHHHHHHHhhccCcceeeecc----cCC--cceeeecccCccchhhHHHHhcCcCCCCCccccccc
Confidence            34679999999999999999999999999886542    233  39999999999999999999999988854  44444


Q ss_pred             e
Q psy3928          89 T   89 (115)
Q Consensus        89 ~   89 (115)
                      +
T Consensus       528 a  528 (975)
T KOG0112|consen  528 A  528 (975)
T ss_pred             c
Confidence            4

>KOG0804|consensus

Probab=95.70  E-value=0.11  Score=38.06  Aligned_cols=69  Identities=6%  Similarity=0.020  Sum_probs=58.7

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhcC-CeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCc
Q psy3928          12 GRVVLKEKLPPEAEHDYIESVFSKYG-KVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDY   82 (115)
Q Consensus        12 ~~~l~V~~l~~~~~~~~l~~~f~~~g-~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~   82 (115)
                      ...|.|=.+|..++-.+|..|...+- .|..++++++  ....+-...+.|.+..+|..+...+||..++..
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd--~~pnrymvLIkFr~q~da~~Fy~efNGk~Fn~l  143 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRD--GMPNRYMVLIKFRDQADADTFYEEFNGKQFNSL  143 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeec--CCCceEEEEEEeccchhHHHHHHHcCCCcCCCC
Confidence            67788888999999999999999864 6788999885  344566899999999999999999999987664

>KOG2202|consensus

Probab=95.40  E-value=0.012  Score=39.76  Aligned_cols=60  Identities=22%  Similarity=0.226  Sum_probs=46.3

Q ss_pred             HHHHhh-hcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          29 IESVFS-KYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        29 l~~~f~-~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      +...|. +||.+..+.+-.+. .-.-.|-++|.|...++|++|+..||+.-+.|+++.....
T Consensus        85 ~f~E~~~kygEiee~~Vc~Nl-~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~  145 (260)
T KOG2202|consen   85 VFTELEDKYGEIEELNVCDNL-GDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELS  145 (260)
T ss_pred             HHHHHHHHhhhhhhhhhhccc-chhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeec
Confidence            434444 78988887654432 3345678999999999999999999999999999876654

>KOG4307|consensus

Probab=95.22  E-value=0.016  Score=44.49  Aligned_cols=79  Identities=18%  Similarity=0.109  Sum_probs=56.6

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEE-EEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTY-VSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~-~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      ..-+..|||.+||..+.+.++.++|.....+.. +.|.+.+ ++..++-|||+|..++.+..|+..-...-+..+.|+|.
T Consensus       431 ~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~P-~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~  509 (944)
T KOG4307|consen  431 GGAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRLP-TDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVD  509 (944)
T ss_pred             CCccceEEeccCCccccccchhhhhhhhhhhhheeEeccCC-cccccchhhheeccccccchhhhcccccccCceEEEee
Confidence            344578999999999999999999987555544 7776666 77788899999999777777765433333333444544


Q ss_pred             E
Q psy3928          88 T   88 (115)
Q Consensus        88 ~   88 (115)
                      .
T Consensus       510 s  510 (944)
T KOG4307|consen  510 S  510 (944)
T ss_pred             c
Confidence            3

>KOG2416|consensus

Probab=95.18  E-value=0.027  Score=42.43  Aligned_cols=74  Identities=18%  Similarity=0.085  Sum_probs=56.7

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhh-cCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCC---Cceee
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSK-YGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPT---DYQSS   85 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~-~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~---~~~~~   85 (115)
                      ...+.|||.||-.-++...|+.++.. .|.|... |+ +    +-+.+|||.|.+.++|.+...+|||....   ++.+.
T Consensus       442 ~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~-Wm-D----kIKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~  515 (718)
T KOG2416|consen  442 EPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEF-WM-D----KIKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLI  515 (718)
T ss_pred             CccceEeeecccccchHHHHHHHHhhccCchHHH-HH-H----HhhcceeEecccHHHHHHHHHHHhccccCCCCCceeE
Confidence            44579999999999999999999995 5555555 32 2    23459999999999999999999998643   34555


Q ss_pred             EEEe
Q psy3928          86 ILTT   89 (115)
Q Consensus        86 v~~~   89 (115)
                      +.+.
T Consensus       516 adf~  519 (718)
T KOG2416|consen  516 ADFV  519 (718)
T ss_pred             eeec
Confidence            5444

>KOG1456|consensus

Probab=95.09  E-value=0.13  Score=36.89  Aligned_cols=73  Identities=15%  Similarity=0.064  Sum_probs=55.7

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCC-eEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCce
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGK-VTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQ   83 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~-i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~   83 (115)
                      ....++|..-|.|..++|+.|..++..-+. ...+++...+  .....-+.+||++.++|-.++-.+|+.++.+..
T Consensus       403 q~Ps~vLHffNaP~~vtEe~l~~i~nek~v~~~svkvFp~k--serSssGllEfe~~s~Aveal~~~NH~pi~~p~  476 (494)
T KOG1456|consen  403 QPPSNVLHFFNAPLGVTEEQLIGICNEKDVPPTSVKVFPLK--SERSSSGLLEFENKSDAVEALMKLNHYPIEGPN  476 (494)
T ss_pred             cCCcceeEEecCCCccCHHHHHHHhhhcCCCcceEEeeccc--ccccccceeeeehHHHHHHHHHHhccccccCCC
Confidence            345678999999999999999999987652 3445554333  222335788999999999999999999887753

>KOG1996|consensus

Probab=94.50  E-value=0.2  Score=34.95  Aligned_cols=62  Identities=27%  Similarity=0.115  Sum_probs=47.3

Q ss_pred             HHHHHHhhhcCCeEEEEeceeCCCCCe-eeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928          27 DYIESVFSKYGKVTYVSLPKFKSTGKL-KGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus        27 ~~l~~~f~~~g~i~~~~i~~~~~~~~~-~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      +++.+-..+||.+..|.|.-.+..-.. .---||+|...++|.+|+..|||.-+.|+.++..+
T Consensus       301 de~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~F  363 (378)
T KOG1996|consen  301 DETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACF  363 (378)
T ss_pred             HHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeehee
Confidence            457777889999988876555422221 23579999999999999999999999998766544

>KOG4660|consensus

Probab=94.19  E-value=0.099  Score=39.04  Aligned_cols=70  Identities=11%  Similarity=0.162  Sum_probs=48.5

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhh-hcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCc
Q psy3928          13 RVVLKEKLPPEAEHDYIESVFS-KYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDY   82 (115)
Q Consensus        13 ~~l~V~~l~~~~~~~~l~~~f~-~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~   82 (115)
                      .++.+-|+|...+...|.+... ..|.-..+.++.+-.+....|||||.|.+...+..+.+++||+..+.+
T Consensus       389 tt~~iknipNK~T~~ml~~~d~~~~gtYDFlYLPiDF~nkcNvGYAFINm~sp~ai~~F~kAFnGk~W~~F  459 (549)
T KOG4660|consen  389 TTLMIKNIPNKYTSKMLLAADEKNKGTYDFLYLPIDFKNKCNVGYAFINMTSPEAIIRFYKAFNGKKWEKF  459 (549)
T ss_pred             hhhHhhccCchhhHHhhhhhhccccCccceEEeccccccccccceeEEeecCHHHHHHHHHHHcCCchhhh
Confidence            3444445554444444433322 245556677777776778899999999999999999999999975543

>KOG2068|consensus

Probab=93.89  E-value=0.023  Score=39.82  Aligned_cols=73  Identities=15%  Similarity=0.215  Sum_probs=52.0

Q ss_pred             CEEEEcCCCCCCCHHHH---HHHhhhcCCeEEEEeceeCC--CC-CeeeEEEEEecCHHHHHHHHHhhCCCCCCCceee
Q psy3928          13 RVVLKEKLPPEAEHDYI---ESVFSKYGKVTYVSLPKFKS--TG-KLKGFAFVEFSTKEEATKALELGLNPCPTDYQSS   85 (115)
Q Consensus        13 ~~l~V~~l~~~~~~~~l---~~~f~~~g~i~~~~i~~~~~--~~-~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~   85 (115)
                      ..+||-+|+.......+   .++|.+||.+..+.+-.++.  .+ ....-++|.|...++|..|+...+|...+++.+.
T Consensus        78 nlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lk  156 (327)
T KOG2068|consen   78 NLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALK  156 (327)
T ss_pred             hhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhH
Confidence            45677788876644433   46788888888887655442  01 1122489999999999999999999988887644

>KOG2193|consensus

Probab=93.17  E-value=0.13  Score=37.49  Aligned_cols=67  Identities=21%  Similarity=0.244  Sum_probs=49.4

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhcC--CeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCC-CCCceeeEE
Q psy3928          13 RVVLKEKLPPEAEHDYIESVFSKYG--KVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPC-PTDYQSSIL   87 (115)
Q Consensus        13 ~~l~V~~l~~~~~~~~l~~~f~~~g--~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~-~~~~~~~v~   87 (115)
                      .++|++||.+.++..++..+|....  .-..+.+        ..||+|+.+.+..-|.++.+.+++.. +-|.+..+.
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~--------k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~   71 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLV--------KSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVE   71 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceee--------ecceeeccCCchhhhhhhHHhhchhhhhcCceeecc
Confidence            4689999999999999999987541  1111111        24799999999999999999999875 444444443

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=92.93  E-value=1.2  Score=27.95  Aligned_cols=61  Identities=20%  Similarity=0.175  Sum_probs=45.4

Q ss_pred             CCCCEEEEcCCCCCCCHH----HHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCC
Q psy3928          10 KYGRVVLKEKLPPEAEHD----YIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNP   77 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~----~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~   77 (115)
                      ..-.+|.|.=|..++...    .+...++.||+|..+.+     .|+.  -|.|.|.+..+|=.|+.+++..
T Consensus        84 pPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~-----cGrq--savVvF~d~~SAC~Av~Af~s~  148 (166)
T PF15023_consen   84 PPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTL-----CGRQ--SAVVVFKDITSACKAVSAFQSR  148 (166)
T ss_pred             CCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeee-----cCCc--eEEEEehhhHHHHHHHHhhcCC
Confidence            445678888777666442    35556678999998865     3443  6999999999999999998864

>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=92.30  E-value=0.35  Score=31.47  Aligned_cols=59  Identities=20%  Similarity=0.090  Sum_probs=41.8

Q ss_pred             HHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhC--CCCCCCceeeEEEee
Q psy3928          26 HDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGL--NPCPTDYQSSILTTT   90 (115)
Q Consensus        26 ~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~--~~~~~~~~~~v~~~~   90 (115)
                      ...|+++|..++.+..+..+..      -+-..|.|.+.+.|.++...|+  +..+.|..+++.+..
T Consensus         9 ~~~l~~l~~~~~~~~~~~~L~s------FrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~   69 (184)
T PF04847_consen    9 LAELEELFSTYDPPVQFSPLKS------FRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQ   69 (184)
T ss_dssp             HHHHHHHHHTT-SS-EEEEETT------TTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE---
T ss_pred             HHHHHHHHHhcCCceEEEEcCC------CCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEcc
Confidence            3678999999997766654432      2357899999999999999999  888888888887663

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.

>KOG4210|consensus

Probab=92.12  E-value=0.17  Score=35.22  Aligned_cols=73  Identities=16%  Similarity=0.062  Sum_probs=56.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCce
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQ   83 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~   83 (115)
                      ...+.|++++...+.+.....++...|......+........+++++.+.|...+.+..++.......+.+..
T Consensus        87 ~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~  159 (285)
T KOG4210|consen   87 SSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNK  159 (285)
T ss_pred             ccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhcccccccc
Confidence            4578899999999888877788888886666555554557788899999999999999999866654544443

>KOG4285|consensus

Probab=91.48  E-value=1.3  Score=31.03  Aligned_cols=63  Identities=21%  Similarity=0.277  Sum_probs=46.8

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCc
Q psy3928          12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDY   82 (115)
Q Consensus        12 ~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~   82 (115)
                      ..=|-|-++|+. .-..+...|.+||.|......      ....+-+|.|.+..+|++||. .+|+.|++.
T Consensus       197 D~WVTVfGFppg-~~s~vL~~F~~cG~Vvkhv~~------~ngNwMhirYssr~~A~KALs-kng~ii~g~  259 (350)
T KOG4285|consen  197 DTWVTVFGFPPG-QVSIVLNLFSRCGEVVKHVTP------SNGNWMHIRYSSRTHAQKALS-KNGTIIDGD  259 (350)
T ss_pred             cceEEEeccCcc-chhHHHHHHHhhCeeeeeecC------CCCceEEEEecchhHHHHhhh-hcCeeeccc
Confidence            344566688886 446788999999988775432      223488999999999999998 477766664

>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=90.80  E-value=1.7  Score=23.77  Aligned_cols=58  Identities=17%  Similarity=0.104  Sum_probs=34.1

Q ss_pred             CCCCHHHHHHHhhhcC-----CeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928          22 PEAEHDYIESVFSKYG-----KVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus        22 ~~~~~~~l~~~f~~~g-----~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      ..++..+|..++..-+     .|-.+.+..+        |+||+... +.|+.++..|++..+.|+.+.+..
T Consensus        11 dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~~--------~S~vev~~-~~a~~v~~~l~~~~~~gk~v~ve~   73 (74)
T PF03880_consen   11 DGLTPRDIVGAICNEAGIPGRDIGRIDIFDN--------FSFVEVPE-EVAEKVLEALNGKKIKGKKVRVER   73 (74)
T ss_dssp             GT--HHHHHHHHHTCTTB-GGGEEEEEE-SS---------EEEEE-T-T-HHHHHHHHTT--SSS----EEE
T ss_pred             cCCCHHHHHHHHHhccCCCHHhEEEEEEeee--------EEEEEECH-HHHHHHHHHhcCCCCCCeeEEEEE
Confidence            4567778888887654     3445665432        88999887 478899999999999999888764

; PDB: 2G0C_A 3MOJ_B.

>KOG2253|consensus

Probab=90.79  E-value=0.27  Score=37.64  Aligned_cols=68  Identities=19%  Similarity=0.154  Sum_probs=56.7

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCcee
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQS   84 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~   84 (115)
                      ..+...++||+|+...+....++.++..+|.+..+...  .       |+|.+|.++.....++..++-..+++..+
T Consensus        36 ~~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~--~-------fgf~~f~~~~~~~ra~r~~t~~~~~~~kl  103 (668)
T KOG2253|consen   36 PLPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRD--K-------FGFCEFLKHIGDLRASRLLTELNIDDQKL  103 (668)
T ss_pred             CCCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhh--h-------hcccchhhHHHHHHHHHHhcccCCCcchh
Confidence            34566799999999999999999999999977665332  1       89999999999999999999888877654

>KOG4483|consensus

Probab=88.68  E-value=1.6  Score=31.88  Aligned_cols=58  Identities=21%  Similarity=0.229  Sum_probs=48.0

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCC-eEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHh
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGK-VTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL   73 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~-i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~   73 (115)
                      .+-.+.|-|-++|......+|...|..|+. ...++|+-+.       ++|..|.+...|..||..
T Consensus       388 ~dlpHVlEIydfp~efkteDll~~f~~yq~kgfdIkWvDdt-------halaVFss~~~AaeaLt~  446 (528)
T KOG4483|consen  388 SDLPHVLEIYDFPDEFKTEDLLKAFETYQNKGFDIKWVDDT-------HALAVFSSVNRAAEALTL  446 (528)
T ss_pred             ccccceeEeccCchhhccHHHHHHHHHhhcCCceeEEeecc-------eeEEeecchHHHHHHhhc
Confidence            345688889999999888999999999973 4567777654       899999999999999975

>KOG2591|consensus

Probab=87.59  E-value=2.6  Score=32.10  Aligned_cols=59  Identities=14%  Similarity=0.247  Sum_probs=45.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhh--cCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCC
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSK--YGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN   76 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~--~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~   76 (115)
                      +.++|.++-||..+..++++.+|..  +-.+-.|.+-.+.       -=||.|.+..+|+.|.+.|..
T Consensus       174 kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~-------nWyITfesd~DAQqAykylre  234 (684)
T KOG2591|consen  174 KRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND-------NWYITFESDTDAQQAYKYLRE  234 (684)
T ss_pred             ceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC-------ceEEEeecchhHHHHHHHHHH
Confidence            4578999999999999999999976  4445555443332       358999999999999876543

>KOG4410|consensus

Probab=87.54  E-value=2.1  Score=29.94  Aligned_cols=46  Identities=15%  Similarity=0.148  Sum_probs=34.6

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhcCCe-EEEEeceeCCCCCeeeEEEEEecCH
Q psy3928          13 RVVLKEKLPPEAEHDYIESVFSKYGKV-TYVSLPKFKSTGKLKGFAFVEFSTK   64 (115)
Q Consensus        13 ~~l~V~~l~~~~~~~~l~~~f~~~g~i-~~~~i~~~~~~~~~~g~~fv~f~~~   64 (115)
                      .-|+++||+.++.-.+|+.-+...+.+ ..+.+      ..+.|-||+.|-+.
T Consensus       331 ~di~~~nl~rd~rv~dlk~~lr~~~~~pm~isw------kg~~~k~flh~~~~  377 (396)
T KOG4410|consen  331 TDIKLTNLSRDIRVKDLKSELRKRECTPMSISW------KGHFGKCFLHFGNR  377 (396)
T ss_pred             cceeeccCccccchHHHHHHHHhcCCCceeEee------ecCCcceeEecCCc
Confidence            459999999999999999999988743 33443      12356799999654

>KOG2318|consensus

Probab=86.70  E-value=10  Score=29.16  Aligned_cols=76  Identities=13%  Similarity=0.056  Sum_probs=56.1

Q ss_pred             cCCCCEEEEcCCCCC-CCHHHHHHHhhhc----CCeEEEEeceeCC----------CCC---------------------
Q psy3928           9 KKYGRVVLKEKLPPE-AEHDYIESVFSKY----GKVTYVSLPKFKS----------TGK---------------------   52 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~-~~~~~l~~~f~~~----g~i~~~~i~~~~~----------~~~---------------------   52 (115)
                      ....+.|-|-|+.|+ +...+|..+|.+|    |.|..|.|.....          .|.                     
T Consensus       171 ~~~T~RLAVvNMDWd~v~AkDL~v~~nSFlP~gGsilSV~IYpSeFGkeRM~eEeV~GP~~el~~~~e~~~~s~sD~ee~  250 (650)
T KOG2318|consen  171 GEETKRLAVVNMDWDRVKAKDLFVLFNSFLPKGGSILSVKIYPSEFGKERMKEEEVHGPPKELFKPVEEYKESESDDEEE  250 (650)
T ss_pred             ccccceeeEeccccccccHHHHHHHHHhhcCCCCceeEEEechhhhhHHHhhhhcccCChhhhccccccCcccccchhhh
Confidence            345678999999986 6778898888876    4677777643210          011                     


Q ss_pred             ----------------eeeEEEEEecCHHHHHHHHHhhCCCCCCCcee
Q psy3928          53 ----------------LKGFAFVEFSTKEEATKALELGLNPCPTDYQS   84 (115)
Q Consensus        53 ----------------~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~   84 (115)
                                      ...||.|+|.+...|...+..|+|..+.....
T Consensus       251 ~~~~~~kLR~Yq~~rLkYYyAVvecDsi~tA~~vYe~CDG~EfEsS~~  298 (650)
T KOG2318|consen  251 EDVDREKLRQYQLNRLKYYYAVVECDSIETAKAVYEECDGIEFESSAN  298 (650)
T ss_pred             hhHHHHHHHHHHhhhheeEEEEEEecCchHHHHHHHhcCcceeccccc
Confidence                            13589999999999999999999998766543

>KOG4574|consensus

Probab=85.65  E-value=0.87  Score=36.13  Aligned_cols=76  Identities=20%  Similarity=0.117  Sum_probs=58.2

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCC--CCCceeeEEEeee
Q psy3928          14 VVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPC--PTDYQSSILTTTS   91 (115)
Q Consensus        14 ~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~--~~~~~~~v~~~~~   91 (115)
                      +.++.|.+-..+...|-.++..||.+.....+++      ..++.|+|...+.|-.|+.+++|..  ..|-+.+|..++.
T Consensus       300 ~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~------~N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~  373 (1007)
T KOG4574|consen  300 KQSLENNAVNLTSSSLATLCSDYGSVASAWTLRD------LNMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKT  373 (1007)
T ss_pred             hhhhhcccccchHHHHHHHHHhhcchhhheeccc------ccchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEeccc
Confidence            3445566666777778999999999988776654      2489999999999999999999986  4456667777776


Q ss_pred             cccc
Q psy3928          92 RLSF   95 (115)
Q Consensus        92 ~~~~   95 (115)
                      ...+
T Consensus       374 ~~~~  377 (1007)
T KOG4574|consen  374 LPMY  377 (1007)
T ss_pred             cccc
Confidence            5444

>smart00596 PRE_C2HC PRE_C2HC domain

Probab=81.91  E-value=3  Score=22.73  Aligned_cols=61  Identities=11%  Similarity=0.075  Sum_probs=40.4

Q ss_pred             HHHHHHhhhcC-CeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEee
Q psy3928          27 DYIESVFSKYG-KVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTT   90 (115)
Q Consensus        27 ~~l~~~f~~~g-~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~   90 (115)
                      .+|.+-|...| ++..+..+..++++.+...-+|+.....+...   .++-..+.+..+.|....
T Consensus         2 ~~I~~~L~~~G~~v~~i~~m~~~~~r~P~nmf~vel~~~~~~~~---Il~ik~Lg~~~V~VEr~~   63 (69)
T smart00596        2 SQIEEALKDIGFPVLFIHNMLNRDTKNPQNMFEVELVPAANGKE---ILNIKTLGGQRVTVERPH   63 (69)
T ss_pred             HHHHHHHHHcCCceeEEEcccccCCCCcceeEEEEeeecCCCcc---eEeehhhCCeeEEEecCc
Confidence            35677787777 77888888888777888888888876443332   344445566666655443

>KOG4019|consensus

Probab=80.72  E-value=5  Score=26.18  Aligned_cols=73  Identities=12%  Similarity=0.046  Sum_probs=48.1

Q ss_pred             CCCEEEEcCCCCCCCH-----HHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCc-ee
Q psy3928          11 YGRVVLKEKLPPEAEH-----DYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDY-QS   84 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~-----~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~-~~   84 (115)
                      -...+.+.+++..+-.     .....+|.++.......+.+.      .+..-|.|.++..|..|...++...+.+. .+
T Consensus         9 lp~~~~~c~i~~~VF~~~~~k~~~~~lFrq~n~~~~fq~lrs------frrvRi~f~~p~~a~~a~i~~~~~~f~~~~~~   82 (193)
T KOG4019|consen    9 LPTAIIACDIHEEVFVNREDKALFENLFRQINEDATFQLLRS------FRRVRINFSNPEAAADARIKLHSTSFNGKNEL   82 (193)
T ss_pred             ccceeeeecccHHhhccHHHHHHHHhHHhhhCcchHHHHHHh------hceeEEeccChhHHHHHHHHhhhcccCCCceE
Confidence            3455777777755422     224566666655544444432      34567899999999999999999999998 44


Q ss_pred             eEEEe
Q psy3928          85 SILTT   89 (115)
Q Consensus        85 ~v~~~   89 (115)
                      ....+
T Consensus        83 k~yfa   87 (193)
T KOG4019|consen   83 KLYFA   87 (193)
T ss_pred             EEEEc
Confidence            44333

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	115
2cph_A	107	Solution Structure Of The C-Terminal Rna Recognitio		7e-06
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		8e-06
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		9e-06
1sxl_A	97	Resonance Assignments And Solution Structure Of The		1e-05
2lxi_A	91	Nmr Structure Of The N-Terminal Rna Binding Domain		1e-05
2lea_A	135	Solution Structure Of Human Srsf2 (Sc35) Rrm Length		1e-05
2kn4_A	158	The Structure Of The Rrm Domain Of Sc35 Length = 15		3e-05
4a8x_A	88	Structure Of The Core Asap Complex Length = 88		7e-05
2cq0_A	103	Solution Structure Of Rna Binding Domain In Eukaryo		7e-05
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		9e-05
2j0q_D	109	The Crystal Structure Of The Exon Junction Complex		1e-04
2j0s_D	89	The Crystal Structure Of The Exon Junction Complex		1e-04
3ex7_B	126	The Crystal Structure Of Ejc In Its Transition Stat		1e-04
1p27_B	106	Crystal Structure Of The Human Y14MAGOH COMPLEX Len		1e-04
2xb2_D	90	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		2e-04
2hyi_B	91	Structure Of The Human Exon Junction Complex With A		2e-04
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		2e-04
2ku7_A	140	Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric		2e-04
3lpy_A	79	Crystal Structure Of The Rrm Domain Of Cyp33 Length		2e-04
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		2e-04
2cqb_A	102	Solution Structure Of The Rna Recognition Motif In		2e-04
3mdf_A	85	Crystal Structure Of The Rrm Domain Of Cyclophilin		2e-04
2kyx_A	83	Solution Structure Of The Rrm Domain Of Cyp33 Lengt		3e-04
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		3e-04
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		3e-04
2e5h_A	94	Solution Structure Of Rna Binding Domain In Zinc Fi		3e-04
2dnm_A	103	Solution Structure Of Rna Binding Domain In Srp46 S		3e-04
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		4e-04
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		6e-04
1oo0_B	110	Crystal Structure Of The Drosophila Mago Nashi-Y14		7e-04
1hl6_A	165	A Novel Mode Of Rbd-Protein Recognition In The Y14-		8e-04
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		9e-04

>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif Of Hypothetical Rna-Binding Protein Rbm19 Length = 107

Iteration: 1
 Score = 45.8 bits (107), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 23/59 (38%), Positives = 34/59 (57%), Gaps = 1/59 (1%)
Query: 15 VLKEKLPPEAEHDYIESVFSKYGKVTYVSLPK-FKSTGKLKGFAFVEFSTKEEATKALE 72
          +L   +P +A    I  +FS +G++  V LPK    TG  +GF FV+F TK++A KA  
Sbjct: 18 ILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFN 76

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 45.4 bits (106), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 20/61 (32%), Positives = 35/61 (57%)
Query: 19  KLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPC 78
            LP     D ++++F KYG +   ++ + K TG+ +G AFV ++ +EEA +A+    N  
Sbjct: 96  NLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVI 155
Query: 79  P 79
           P
Sbjct: 156 P 156

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 45.1 bits (105), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 20/61 (32%), Positives = 35/61 (57%)
Query: 19  KLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPC 78
            LP     D ++++F KYG +   ++ + K TG+ +G AFV ++ +EEA +A+    N  
Sbjct: 107 NLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVI 166
Query: 79  P 79
           P
Sbjct: 167 P 167

>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second Rna-Binding Domain Of Sex-Lethal Determined By Multidimensional Heteronuclear Magnetic Resonance Spectroscopy Length = 97

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 20/60 (33%), Positives = 35/60 (58%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCP 79
          LP     D ++++F KYG +   ++ + K TG+ +G AFV ++ +EEA +A+    N  P
Sbjct: 21 LPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIP 80

>pdb|2LXI|A Chain A, Nmr Structure Of The N-Terminal Rna Binding Domain 1 (Rrm1) Of The Protein Rbm10 From Homo Sapiens Length = 91

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 23/60 (38%), Positives = 35/60 (58%), Gaps = 1/60 (1%)
Query: 14 VVLKEKLPPEAEHDYIESVFSKYG-KVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          +V+   LP  A  D I      +G +   V L + KS+G+ +GFAFVEFS  ++AT+ +E
Sbjct: 3  IVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWME 62

>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm Length = 135

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 19/46 (41%), Positives = 29/46 (63%)
Query: 27  DYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
           D +  VF KYG+V  V +P+ + T + +GFAFV F  K +A  A++
Sbjct: 62  DTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 107

>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35 Length = 158

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 19/46 (41%), Positives = 29/46 (63%)
Query: 27  DYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
           D +  VF KYG+V  V +P+ + T + +GFAFV F  K +A  A++
Sbjct: 85  DTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 130

>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex Length = 88

Iteration: 1
 Score = 42.4 bits (98), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 20/47 (42%), Positives = 30/47 (63%), Gaps = 1/47 (2%)
Query: 27 DYIESVFSKYGKVTYVSLPKFKSTGKL-KGFAFVEFSTKEEATKALE 72
          D+I  +FS YGK+  + +P  +    L KG+A+VEF   +EA KAL+
Sbjct: 19 DHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65

>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic Translation Initiation Factor 3 Subunit 4 Length = 103

Iteration: 1
 Score = 42.4 bits (98), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 16/43 (37%), Positives = 30/43 (69%)
Query: 29 IESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
          ++ +F  +G ++ + L K K+TG+ KGFAF+ F  +E+A +A+
Sbjct: 32 LQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAI 74

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 42.0 bits (97), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 18/46 (39%), Positives = 27/46 (58%)
Query: 27 DYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          D +  +F  +GK+  + L K   TG+ KG+ F+ FS  E A +ALE
Sbjct: 20 DMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65

>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 109

Iteration: 1
 Score = 41.6 bits (96), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/65 (35%), Positives = 37/65 (56%), Gaps = 1/65 (1%)
Query: 12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
          G ++    +  EA  + I   F++YG++  + L   + TG LKG+  VE+ T +EA  A+
Sbjct: 7  GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 66
Query: 72 ELGLN 76
          E GLN
Sbjct: 67 E-GLN 70

>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2 A Resolution Length = 89

Iteration: 1
 Score = 41.2 bits (95), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/65 (35%), Positives = 37/65 (56%), Gaps = 1/65 (1%)
Query: 12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
          G ++    +  EA  + I   F++YG++  + L   + TG LKG+  VE+ T +EA  A+
Sbjct: 7  GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 66
Query: 72 ELGLN 76
          E GLN
Sbjct: 67 E-GLN 70

>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State Length = 126

Iteration: 1
 Score = 41.2 bits (95), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/65 (35%), Positives = 37/65 (56%), Gaps = 1/65 (1%)
Query: 12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
          G ++    +  EA  + I   F++YG++  + L   + TG LKG+  VE+ T +EA  A+
Sbjct: 22 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 81
Query: 72 ELGLN 76
          E GLN
Sbjct: 82 E-GLN 85

>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX Length = 106

Iteration: 1
 Score = 41.2 bits (95), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 22/54 (40%), Positives = 33/54 (61%), Gaps = 1/54 (1%)
Query: 23 EAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          EA  + I   F++YG++  + L   + TG LKG+  VE+ T +EA  A+E GLN
Sbjct: 34 EATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME-GLN 86

>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd Machinery Length = 90

Iteration: 1
 Score = 41.2 bits (95), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/54 (40%), Positives = 33/54 (61%), Gaps = 1/54 (1%)
Query: 23 EAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          EA  + I   F++YG++  + L   + TG LKG+  VE+ T +EA  A+E GLN
Sbjct: 18 EATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME-GLN 70

>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A Trapped Dead-Box Helicase Bound To Rna Length = 91

Iteration: 1
 Score = 41.2 bits (95), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/54 (40%), Positives = 33/54 (61%), Gaps = 1/54 (1%)
Query: 23 EAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          EA  + I   F++YG++  + L   + TG LKG+  VE+ T +EA  A+E GLN
Sbjct: 20 EATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME-GLN 72

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 41.2 bits (95), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 19/53 (35%), Positives = 32/53 (60%), Gaps = 1/53 (1%)
Query: 29 IESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTD 81
          +E VFSKYG+++ V + K + T + +GF FV F   ++A  A+ + +N    D
Sbjct: 29 LEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAM-MAMNGKSVD 80

>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein Length = 140

Iteration: 1
 Score = 41.2 bits (95), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 20/60 (33%), Positives = 32/60 (53%)
Query: 13  RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
           RV+    L  E +   + + F  +G +T + +P    T K +GFAFVEF   E+A  A++
Sbjct: 64  RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 123

>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33 Length = 79

Iteration: 1
 Score = 40.4 bits (93), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 20/60 (33%), Positives = 32/60 (53%)
Query: 13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          RV+    L  E +   + + F  +G +T + +P    T K +GFAFVEF   E+A  A++
Sbjct: 3  RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 62

>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To Ssdna From A Portion Of Fuse Length = 216

Iteration: 1
 Score = 40.4 bits (93), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 19/69 (27%), Positives = 38/69 (55%), Gaps = 1/69 (1%)
Query: 3   ELVENNKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFS 62
           +L E  + + R+ +   +  +   D I+SVF  +GK+   +L +  +TGK KG+ F+E+ 
Sbjct: 117 QLAEEARAFNRIYVAS-VHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYE 175
Query: 63  TKEEATKAL 71
             + +  A+
Sbjct: 176 KAQSSQDAV 184

>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In Peptidyl- Prolyl Cis-Trans Isomerase E Length = 102

Iteration: 1
 Score = 40.4 bits (93), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 20/60 (33%), Positives = 32/60 (53%)
Query: 13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          RV+    L  E +   + + F  +G +T + +P    T K +GFAFVEF   E+A  A++
Sbjct: 13 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 72

>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33 Length = 85

Iteration: 1
 Score = 40.4 bits (93), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 20/60 (33%), Positives = 32/60 (53%)
Query: 13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          RV+    L  E +   + + F  +G +T + +P    T K +GFAFVEF   E+A  A++
Sbjct: 8  RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 67

>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33 Length = 83

Iteration: 1
 Score = 40.4 bits (93), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 20/60 (33%), Positives = 32/60 (53%)
Query: 13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          RV+    L  E +   + + F  +G +T + +P    T K +GFAFVEF   E+A  A++
Sbjct: 6  RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 65

>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U Binding Splicing Factor 60kda (Puf60) From Homo Sapiens At 2.50 A Resolution Length = 200

Iteration: 1
 Score = 40.4 bits (93), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 19/71 (26%), Positives = 39/71 (54%), Gaps = 1/71 (1%)
Query: 1   MAELVENNKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVE 60
           + +L E  + + R+ +   +  +   D I+SVF  +GK+   +L +  +TGK KG+ F+E
Sbjct: 99  IDQLAEEARAFNRIYVAS-VHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIE 157
Query: 61  FSTKEEATKAL 71
           +   + +  A+
Sbjct: 158 YEKAQSSQDAV 168

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 40.0 bits (92), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 19/69 (27%), Positives = 38/69 (55%), Gaps = 1/69 (1%)
Query: 3   ELVENNKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFS 62
           +L E  + + R+ +   +  +   D I+SVF  +GK+   +L +  +TGK KG+ F+E+ 
Sbjct: 102 QLAEEARAFNRIYVAS-VHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYE 160
Query: 63  TKEEATKAL 71
             + +  A+
Sbjct: 161 KAQSSQDAV 169

>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger Cchc-Type And Rna Binding Motif 1 Length = 94

Iteration: 1
 Score = 40.0 bits (92), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 23/56 (41%), Positives = 33/56 (58%), Gaps = 3/56 (5%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEA---TKALE 72
          LP    ++ +  +FSKYGKV  V++ K K T K KG AF+ F  K+ A   T+A+ 
Sbjct: 24 LPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAIN 79

>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing Factor Length = 103

Iteration: 1
 Score = 40.0 bits (92), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 18/44 (40%), Positives = 25/44 (56%)
Query: 27 DYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKA 70
          D +  VF KYG+V  V +P+   T   +GFAFV F  + +A  A
Sbjct: 28 DSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDA 71

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 40.0 bits (92), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 21/57 (36%), Positives = 32/57 (56%)
Query: 15 VLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
          V    L PE   + I+S F+ +GK++   + K  +TGK KG+ FV F  K +A  A+
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAI 74

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 39.3 bits (90), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 17/46 (36%), Positives = 26/46 (56%)
Query: 27 DYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          D +  +F  +G++  + L     TG+ KG+ F+ FS  E A KALE
Sbjct: 41 DMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALE 86

>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex Length = 110

Iteration: 1
 Score = 38.9 bits (89), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 20/61 (32%), Positives = 33/61 (54%)
Query: 12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
          G ++    +  EA+ D I+  F  YG++  + L   + TG  KG+A VE+ T ++A  A 
Sbjct: 26 GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAK 85
Query: 72 E 72
          E
Sbjct: 86 E 86

>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago Complex Length = 165

Iteration: 1
 Score = 38.9 bits (89), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 19/53 (35%), Positives = 30/53 (56%)
Query: 20  LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
           +  EA+ D I+  F  YG++  + L   + TG  KG+A VE+ T ++A  A E
Sbjct: 80  IHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 132

>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In Cytotoxic Granule-Associated Rna Binding Protein 1 Length = 115

Iteration: 1
 Score = 38.5 bits (88), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 19/58 (32%), Positives = 33/58 (56%)
Query: 15 VLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          V    L PE   + I++ F+ +G+++   + K  +TGK KG+ FV F  K +A  A++
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQ 75

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	115
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	7e-17
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	9e-17
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	1e-16
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	1e-16
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	2e-16
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	2e-16
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	2e-16
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	3e-16
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	6e-16
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	6e-16
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	1e-15
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	1e-15
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	1e-15
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	1e-15
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	2e-15
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	2e-15
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	1e-10
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	3e-15
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	4e-15
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	5e-15
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	6e-15
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	7e-15
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	9e-15
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	1e-14
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	1e-14
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	2e-14
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	2e-14
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	2e-14
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	3e-14
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	4e-14
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	5e-14
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	6e-14
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	3e-11
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	7e-14
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	7e-14
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	8e-14
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	8e-14
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	4e-07
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	9e-14
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	3e-11
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-10
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	9e-14
1x4e_A	85	RNA binding motif, single-stranded interacting pro	1e-13
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	1e-13
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	2e-13
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-13
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-13
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	1e-04
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	2e-13
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-13
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	5e-09
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	3e-13
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	6e-11
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	3e-13
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	1e-09
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	3e-13
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	4e-13
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	4e-13
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	5e-13
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	6e-13
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	7e-10
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	7e-13
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	1e-12
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	1e-12
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	1e-12
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	1e-12
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	1e-12
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	1e-12
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	4e-11
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	2e-12
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	2e-12
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	3e-12
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	3e-12
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	3e-12
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	4e-12
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	5e-12
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	5e-12
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	6e-12
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	7e-12
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	7e-12
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	9e-11
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	7e-12
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-11
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	7e-09
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	1e-11
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	1e-11
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	2e-11
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	2e-11
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	2e-11
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	2e-11
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	2e-11
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	3e-11
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	3e-11
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	3e-11
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	4e-11
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	4e-11
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	4e-11
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	4e-11
2div_A	99	TRNA selenocysteine associated protein; structural	5e-11
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	5e-11
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	5e-11
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	6e-11
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	6e-11
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	7e-11
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	8e-11
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	9e-11
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	9e-11
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	1e-10
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	1e-10
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	1e-10
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	1e-10
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	2e-10
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-10
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-10
1x5o_A	114	RNA binding motif, single-stranded interacting pro	2e-10
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	2e-10
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	3e-10
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	3e-10
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	3e-10
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	8e-10
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	3e-10
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-10
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	4e-10
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	4e-10
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	3e-07
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	4e-10
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	4e-10
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	5e-10
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	5e-10
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	5e-10
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	5e-10
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	6e-10
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	7e-10
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	7e-10
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	9e-10
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	9e-10
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	1e-09
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-07
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	1e-09
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	1e-09
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	1e-09
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	1e-09
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	4e-09
1x5p_A	97	Negative elongation factor E; structure genomics,	5e-09
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	5e-09
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	6e-09
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	6e-09
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	7e-09
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	8e-09
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	8e-09
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	1e-08
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	1e-08
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	1e-08
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	1e-08
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	2e-08
2dis_A	109	Unnamed protein product; structural genomics, RRM	2e-08
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	2e-08
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	2e-08
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	3e-08
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	3e-08
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	2e-04
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	4e-08
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	4e-08
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	4e-08
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	5e-08
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	5e-08
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	6e-08
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-04
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	8e-08
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	8e-08
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	1e-07
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	1e-07
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	2e-07
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	2e-07
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	2e-07
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	2e-07
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-07
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	3e-07
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	4e-07
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	5e-07
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	6e-07
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	7e-07
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	8e-07
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	3e-06
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	3e-06
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	7e-06
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	9e-06
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	1e-05
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	2e-05
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	3e-05
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	3e-05
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	5e-05
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	6e-05
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	6e-05
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	8e-05
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	1e-04
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	4e-04

>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 = 70.6 bits (173), Expect = 7e-17
 Identities = 21/57 (36%), Positives = 32/57 (56%), Gaps = 1/57 (1%)

Query: 20  LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
           +  EA+ D I+  F  YG++  + L   + TG  KG+A VE+ T ++A  A E  LN
Sbjct: 80  IHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE-ALN 135

>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 = 69.3 bits (170), Expect = 9e-17
 Identities = 22/57 (38%), Positives = 34/57 (59%), Gaps = 1/57 (1%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          +  EA  + I   F++YG++  + L   + TG LKG+  VE+ T +EA  A+E GLN
Sbjct: 30 VHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME-GLN 85

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 68.4 bits (168), Expect = 1e-16
 Identities = 22/57 (38%), Positives = 34/57 (59%), Gaps = 1/57 (1%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          +  EA  + I   F++YG++  + L   + TG LKG+  VE+ T +EA  A+E GLN
Sbjct: 31 VHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME-GLN 86

>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 = 68.5 bits (168), Expect = 1e-16
 Identities = 21/57 (36%), Positives = 32/57 (56%), Gaps = 1/57 (1%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          +  EA+ D I+  F  YG++  + L   + TG  KG+A VE+ T ++A  A E  LN
Sbjct: 34 IHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE-ALN 89

>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 = 68.1 bits (167), Expect = 2e-16
 Identities = 22/54 (40%), Positives = 32/54 (59%), Gaps = 1/54 (1%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPK-FKSTGKLKGFAFVEFSTKEEATKALE 72
          +P +A    I  +FS +G++  V LPK    TG  +GF FV+F TK++A KA  
Sbjct: 23 IPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFN 76

>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 = 67.2 bits (165), Expect = 2e-16
 Identities = 19/54 (35%), Positives = 29/54 (53%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
          +   A  + +E+ F   G V  V++   K +G  KGFA++EFS KE    +L L
Sbjct: 14 VDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLAL 67

>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 = 67.6 bits (166), Expect = 2e-16
 Identities = 18/57 (31%), Positives = 35/57 (61%), Gaps = 1/57 (1%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          L  +     ++ +F  +G ++ + L K K+TG+ KGFAF+ F  +E+A +A+  G++
Sbjct: 23 LSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIA-GVS 78

>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 = 67.3 bits (165), Expect = 3e-16
 Identities = 19/57 (33%), Positives = 28/57 (49%), Gaps = 1/57 (1%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          L      D +  VF KYG+V  V +P+   T   +GFAFV F  + +A  A    ++
Sbjct: 21 LTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEA-AMD 76

>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 = 66.0 bits (162), Expect = 6e-16
 Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 1/57 (1%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          L  E +   + + F  +G +T + +P    T K +GFAFVEF   E+A  A++  +N
Sbjct: 15 LAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID-NMN 70

>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 = 67.0 bits (164), Expect = 6e-16
 Identities = 17/53 (32%), Positives = 27/53 (50%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L  ++E + +  V  ++G + YV +     T   KG AF +F T+E A K L 
Sbjct: 23 LSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 75

>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 = 65.7 bits (161), Expect = 1e-15
 Identities = 21/57 (36%), Positives = 30/57 (52%), Gaps = 1/57 (1%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          L      D +  +F  +GK+  + L K   TG+ KG+ F+ FS  E A +ALE  LN
Sbjct: 13 LHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE-QLN 68

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 67.1 bits (164), Expect = 1e-15
 Identities = 20/57 (35%), Positives = 32/57 (56%), Gaps = 1/57 (1%)

Query: 20  LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
           L      D +  VF KYG+V  V +P+ + T + +GFAFV F  K +A  A++  ++
Sbjct: 55  LTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD-AMD 110

>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 = 65.3 bits (160), Expect = 1e-15
 Identities = 22/57 (38%), Positives = 31/57 (54%), Gaps = 1/57 (1%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          LP    ++ +  +FSKYGKV  V++ K K T K KG AF+ F  K+ A       +N
Sbjct: 24 LPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTR-AIN 79

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 66.7 bits (163), Expect = 1e-15
 Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 1/57 (1%)

Query: 20  LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
           L  E +   + + F  +G +T + +P    T K +GFAFVEF   E+A  A++  +N
Sbjct: 71  LAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID-NMN 126

>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 = 65.3 bits (160), Expect = 2e-15
 Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 1/57 (1%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          L  E +   + + F  +G +T + +P    T K +GFAFVEF   E+A  A++  +N
Sbjct: 20 LAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID-NMN 75

>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 = 67.4 bits (165), Expect = 2e-15
 Identities = 17/57 (29%), Positives = 29/57 (50%), Gaps = 1/57 (1%)

Query: 20  LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
           LP     D ++ + + +G +   +L K  +TG  KG+AF E+       +A+  GLN
Sbjct: 122 LPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA-GLN 177

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 55.0 bits (133), Expect = 1e-10
 Identities = 11/59 (18%), Positives = 25/59 (42%), Gaps = 5/59 (8%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKF-----KSTGKLKGFAFVEFSTKEEATKALEL 73
          +P     + +   F+   ++  ++             + K FAF+EF + +E T+A+  
Sbjct: 12 IPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAF 70

>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 = 65.5 bits (160), Expect = 3e-15
 Identities = 12/54 (22%), Positives = 28/54 (51%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
          +   +    +E+ FS  G +  +++   K +G  KG+A++EF+ +     A+ +
Sbjct: 44 VDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAM 97

>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 = 64.6 bits (158), Expect = 4e-15
 Identities = 20/57 (35%), Positives = 29/57 (50%), Gaps = 1/57 (1%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          L      D +  +F  +G++  + L     TG+ KG+ F+ FS  E A KALE  LN
Sbjct: 34 LHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALE-QLN 89

>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 = 64.2 bits (157), Expect = 5e-15
 Identities = 20/53 (37%), Positives = 27/53 (50%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L   +  + +E +FS YG ++ +  P    T K KGFAFV F   E A KA  
Sbjct: 16 LSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

>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 = 64.3 bits (157), Expect = 6e-15
 Identities = 16/54 (29%), Positives = 25/54 (46%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
          L        +E  FS  GKV  V +   +++ + KG A+VEF   +    A+ L
Sbjct: 33 LAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGL 86

>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 = 63.8 bits (156), Expect = 7e-15
 Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 1/57 (1%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          +P +   + I  + S  G V  + +     TG+ KG+AF+EF   E +  A+   LN
Sbjct: 10 IPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR-NLN 65

>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 = 64.9 bits (158), Expect = 9e-15
 Identities = 20/57 (35%), Positives = 32/57 (56%), Gaps = 1/57 (1%)

Query: 20  LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
           L      D +  VF KYG+V  V +P+ + T + +GFAFV F  K +A  A++  ++
Sbjct: 78  LTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD-AMD 133

>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 = 63.4 bits (155), Expect = 1e-14
 Identities = 20/57 (35%), Positives = 31/57 (54%), Gaps = 1/57 (1%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          +P EA  + ++ +FS+ G V    L   + TGK KG+ F E+  +E A  A+   LN
Sbjct: 16 IPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR-NLN 71

>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 = 64.0 bits (156), Expect = 1e-14
 Identities = 19/57 (33%), Positives = 29/57 (50%), Gaps = 1/57 (1%)

Query: 20  LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
           L        +  VFSKYG +  VS+   + + + +GFAFV F   ++A +A E   N
Sbjct: 54  LSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE-RAN 109

>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 = 63.0 bits (154), Expect = 2e-14
 Identities = 16/57 (28%), Positives = 32/57 (56%), Gaps = 1/57 (1%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          L  +     +  +F + G V    +PK + TG+ +G+ FVEF ++E+A  A++  ++
Sbjct: 23 LDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIK-IMD 78

>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 = 62.6 bits (153), Expect = 2e-14
 Identities = 20/58 (34%), Positives = 32/58 (55%), Gaps = 2/58 (3%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKS-TGKLKGFAFVEFSTKEEATKALELGLN 76
          L      D+I  +FS YGK+  + +P  +      KG+A+VEF   +EA KAL+  ++
Sbjct: 12 LTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK-HMD 68

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 62.8 bits (153), Expect = 2e-14
 Identities = 13/53 (24%), Positives = 24/53 (45%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L       +++ +  KYG+V  V +     T K  G A V F++   A + ++
Sbjct: 14 LNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVK 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 = 61.8 bits (151), Expect = 3e-14
 Identities = 19/57 (33%), Positives = 29/57 (50%), Gaps = 1/57 (1%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          L        +  VFSKYG +  VS+   + + + +GFAFV F   ++A +A E   N
Sbjct: 23 LSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE-RAN 78

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 61.9 bits (151), Expect = 4e-14
 Identities = 15/57 (26%), Positives = 30/57 (52%), Gaps = 2/57 (3%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          LP     + +E +   +G V  + L   +  GK KG A+VE+  + +A++A+   ++
Sbjct: 25 LPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVM-KMD 79

>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 = 64.1 bits (155), Expect = 5e-14
 Identities = 15/56 (26%), Positives = 24/56 (42%), Gaps = 1/56 (1%)

Query: 18  EKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
           +  P +A  D I+      G+V  + + +       KG  FV F + E A K +E 
Sbjct: 115 KGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVET 169

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 63.9 bits (156), Expect = 6e-14
 Identities = 19/72 (26%), Positives = 39/72 (54%), Gaps = 1/72 (1%)

Query: 1   MAELVENNKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVE 60
           + +L E  + + R+ +   +  +   D I+SVF  +GK+   +L +  +TGK KG+ F+E
Sbjct: 115 IDQLAEEARAFNRIYVAS-VHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIE 173

Query: 61  FSTKEEATKALE 72
           +   + +  A+ 
Sbjct: 174 YEKAQSSQDAVS 185

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 56.6 bits (137), Expect = 3e-11
 Identities = 19/53 (35%), Positives = 26/53 (49%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          +  E   D I   F+ +G +  + +     T K KGFAFVE+   E A  ALE
Sbjct: 36 IYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALE 88

>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 = 61.1 bits (149), Expect = 7e-14
 Identities = 19/57 (33%), Positives = 32/57 (56%), Gaps = 1/57 (1%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          L  +     +E VFSKYG+++ V + K + T + +GF FV F   ++A  A+   +N
Sbjct: 20 LSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMM-AMN 75

>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 = 61.6 bits (150), Expect = 7e-14
 Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 2/57 (3%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          L  E     +++VF K+G ++ V L K + T K +GFAF+ F    +A  A +  +N
Sbjct: 15 LNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAK-DMN 69

>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 = 64.6 bits (158), Expect = 8e-14
 Identities = 18/54 (33%), Positives = 26/54 (48%), Gaps = 2/54 (3%)

Query: 20  LPPEA-EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
           LPP   + D +    S     T+  L      G+LKGFA +E+ T E A +A +
Sbjct: 192 LPPGFNDVDALCRALSAVHSPTFCQLAC-GQDGQLKGFAVLEYETAEMAEEAQQ 244

>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 = 64.2 bits (157), Expect = 8e-14
 Identities = 15/53 (28%), Positives = 24/53 (45%)

Query: 20  LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
           LPP       E +   +G +    L   + TG+ KG+ F E+  K+ A +A  
Sbjct: 103 LPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKS 155

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 45.7 bits (109), Expect = 4e-07
 Identities = 14/53 (26%), Positives = 21/53 (39%), Gaps = 7/53 (13%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          LP +  +  +  + S Y         K+    K KG AFV     E+A  A+ 
Sbjct: 30 LPGDVTNQEVHDLLSDYE-------LKYCFVDKYKGTAFVTLLNGEQAEAAIN 75

>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 = 64.2 bits (157), Expect = 9e-14
 Identities = 13/56 (23%), Positives = 26/56 (46%), Gaps = 2/56 (3%)

Query: 20  LPPEA-EHDYIESVFSKYGKVTYVSLPK-FKSTGKLKGFAFVEFSTKEEATKALEL 73
           L  E  + + +   F  +G +  +++P   K        AF+ F  K+ A +AL++
Sbjct: 218 LSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQM 273

>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 = 57.3 bits (139), Expect = 3e-11
 Identities = 12/54 (22%), Positives = 22/54 (40%), Gaps = 2/54 (3%)

Query: 20  LPPEAEHDYIESVFSKYGKVTY-VSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
            PP      I  +      V   + LP        + FA+++ ++KE+A   +E
Sbjct: 125 FPPSYTQRNIRDLLQDINVVALSIRLPS-LRFNTSRRFAYIDVTSKEDARYCVE 177

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 55.4 bits (134), Expect = 2e-10
 Identities = 13/54 (24%), Positives = 22/54 (40%), Gaps = 2/54 (3%)

Query: 19 KLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
           LP     + +   F   G + +V +    S  K   FA +EF+  + A  A+ 
Sbjct: 48 NLPKSYNQNKVYKYFKHCGPIIHVDVAD--SLKKNFRFARIEFARYDGALAAIT 99

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 61.1 bits (149), Expect = 9e-14
 Identities = 17/54 (31%), Positives = 25/54 (46%), Gaps = 1/54 (1%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
          LP       I+++F     +  V L + K T K KGF +VEF   +   +AL  
Sbjct: 23 LPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTY 75

>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 = 60.6 bits (148), Expect = 1e-13
 Identities = 17/57 (29%), Positives = 25/57 (43%), Gaps = 1/57 (1%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          L P      +  +   YGK+        K+T K KG+ FV+F +   A KA+   L 
Sbjct: 13 LQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT-ALK 68

>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 = 61.7 bits (150), Expect = 1e-13
 Identities = 15/57 (26%), Positives = 26/57 (45%), Gaps = 1/57 (1%)

Query: 20  LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
           L      + I  +FSK G +  + +   K      GF FVE+ ++ +A  A+   +N
Sbjct: 47  LSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR-YIN 102

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 60.5 bits (147), Expect = 2e-13
 Identities = 15/54 (27%), Positives = 23/54 (42%), Gaps = 1/54 (1%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
           P +A  D I+      G+V  + + +       KG  FV F + E A K +E 
Sbjct: 19 FPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVET 71

>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 = 59.8 bits (146), Expect = 2e-13
 Identities = 10/57 (17%), Positives = 26/57 (45%), Gaps = 1/57 (1%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          L    + + + + F  +       +     TG  +G+ FV F+++++A  A++  + 
Sbjct: 9  LNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD-SMQ 64

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 62.4 bits (151), Expect = 2e-13
 Identities = 14/76 (18%), Positives = 26/76 (34%), Gaps = 1/76 (1%)

Query: 20  LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCP 79
            P E   +    +  + G     S+  F    +      +E+ +K +A + L   LN   
Sbjct: 131 APLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGF-LNHYQ 189

Query: 80  TDYQSSILTTTSRLSF 95
               +     T +L F
Sbjct: 190 MKNPNGPYPYTLKLCF 205

>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 = 38.5 bits (89), Expect = 1e-04
 Identities = 16/62 (25%), Positives = 23/62 (37%), Gaps = 6/62 (9%)

Query: 12 GRVVLKEKLPPEA-EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKA 70
            V++   L       D + +VF  YG V  V   K K      G A VE +      +A
Sbjct: 4  SPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDRA 58

Query: 71 LE 72
          + 
Sbjct: 59 IT 60

>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 = 60.0 bits (146), Expect = 2e-13
 Identities = 14/54 (25%), Positives = 25/54 (46%), Gaps = 1/54 (1%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
          L P      ++   S+      +++     TG  + F +V+F + E+  KALEL
Sbjct: 25 LNPNKSVAELKVAISELFAKNDLAVVD-VRTGTNRKFGYVDFESAEDLEKALEL 77

>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 = 61.5 bits (150), Expect = 2e-13
 Identities = 17/57 (29%), Positives = 29/57 (50%), Gaps = 1/57 (1%)

Query: 20  LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
           LP     D ++ + + +G +   +L K  +TG  KG+AF E+       +A+  GLN
Sbjct: 102 LPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA-GLN 157

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 50.3 bits (121), Expect = 5e-09
 Identities = 11/59 (18%), Positives = 25/59 (42%), Gaps = 5/59 (8%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKF-----KSTGKLKGFAFVEFSTKEEATKALEL 73
          +P     + +   F+   ++  ++             + K FAF+EF + +E T+A+  
Sbjct: 12 IPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAF 70

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 61.5 bits (150), Expect = 3e-13
 Identities = 16/53 (30%), Positives = 25/53 (47%), Gaps = 5/53 (9%)

Query: 20  LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
           L      D ++ VF    ++  V        GK KG A++EF ++ +A K LE
Sbjct: 107 LSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLE 154

>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 = 55.3 bits (134), Expect = 6e-11
 Identities = 14/54 (25%), Positives = 25/54 (46%), Gaps = 1/54 (1%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
          L P      ++   S+      +++     TG  + F +V+F + E+  KALEL
Sbjct: 21 LNPNKSVAELKVAISELFAKNDLAVVD-VRTGTNRKFGYVDFESAEDLEKALEL 73

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 61.0 bits (149), Expect = 3e-13
 Identities = 13/54 (24%), Positives = 25/54 (46%)

Query: 20  LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
           + P+      E  FS++G +    L   K TG+ +GF FV + + +   +  + 
Sbjct: 95  IGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQN 148

>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 = 51.8 bits (125), Expect = 1e-09
 Identities = 15/53 (28%), Positives = 26/53 (49%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L  +   D +   F KYG VT + + K  +TG+ +GF F+ F       + ++
Sbjct: 11 LNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK 63

>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 = 60.5 bits (147), Expect = 3e-13
 Identities = 15/57 (26%), Positives = 30/57 (52%), Gaps = 1/57 (1%)

Query: 20  LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
           +P   +   +  +F +YG +  V +   + T + +G+ FV+F +   A +A+  GLN
Sbjct: 50  IPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIA-GLN 105

>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 = 59.7 bits (145), Expect = 4e-13
 Identities = 18/53 (33%), Positives = 32/53 (60%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L PE   + I++ F+ +G+++   + K  +TGK KG+ FV F  K +A  A++
Sbjct: 23 LSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQ 75

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A Length = 106

 Score = 59.6 bits (145), Expect = 4e-13
 Identities = 15/54 (27%), Positives = 31/54 (57%)

Query: 19 KLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          ++P   +   ++ +F ++GK+  +++ K + TG  KG AF+ +  +E A KA  
Sbjct: 20 QIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQS 73

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 58.9 bits (143), Expect = 5e-13
 Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 2/55 (3%)

Query: 20 LPPEAEHDYIESVFSKYGK--VTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          + P    D I +  S Y    V  + L K K T + +GFAFV+ S+  +A++ L+
Sbjct: 17 IAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQ 71

>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 = 61.2 bits (149), Expect = 6e-13
 Identities = 14/53 (26%), Positives = 27/53 (50%)

Query: 20  LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
           +  + E  ++   F +YGK+  + +   + +GK +GFAFV F   +   K + 
Sbjct: 112 IKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 164

>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 = 52.7 bits (127), Expect = 7e-10
 Identities = 15/53 (28%), Positives = 28/53 (52%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L  E   + + S F ++G +T   + +  +T + +GF FV ++T EE   A+ 
Sbjct: 21 LSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73

>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 = 58.8 bits (143), Expect = 7e-13
 Identities = 17/55 (30%), Positives = 26/55 (47%), Gaps = 2/55 (3%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKST-GKLKGFAFVEFSTKEEATKALEL 73
          LP +   + I+  F     ++ V LP+  S   +LKGF + EF   +    AL L
Sbjct: 27 LPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSL 80

>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 = 58.4 bits (142), Expect = 1e-12
 Identities = 14/53 (26%), Positives = 26/53 (49%), Gaps = 1/53 (1%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L  +   + +  +F  +G +   ++ +    G  KG AFV+FS+  EA  A+ 
Sbjct: 23 LNKQQSEEDVLRLFQPFGVIDECTVLR-GPDGSSKGCAFVKFSSHTEAQAAIH 74

>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 = 57.9 bits (141), Expect = 1e-12
 Identities = 20/57 (35%), Positives = 31/57 (54%), Gaps = 2/57 (3%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          L   A  + ++ +FS++GKV  V L   + T K KGF FVE    E  ++A+   L+
Sbjct: 9  LVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIA-KLD 63

>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 = 58.0 bits (141), Expect = 1e-12
 Identities = 18/57 (31%), Positives = 28/57 (49%), Gaps = 2/57 (3%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          L      + +  +F + G +T V++ K +  GK K F FV F   E  + A+ L LN
Sbjct: 24 LEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHPESVSYAIAL-LN 78

>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 = 58.5 bits (142), Expect = 1e-12
 Identities = 15/53 (28%), Positives = 27/53 (50%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L P      + S+F+++ +     +     TG+++G AF+ F  KE A +AL 
Sbjct: 33 LSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 85

>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 = 57.6 bits (140), Expect = 1e-12
 Identities = 18/53 (33%), Positives = 30/53 (56%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L PE     I + F+ +G+++   + K  +TGK KG+ FV F  K +A  A++
Sbjct: 14 LSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQ 66

>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 = 59.5 bits (145), Expect = 1e-12
 Identities = 18/53 (33%), Positives = 33/53 (62%)

Query: 20  LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
           LP     D ++++F KYG +   ++ + K TG+ +G AFV ++ +EEA +A+ 
Sbjct: 97  LPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 149

>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 = 55.7 bits (135), Expect = 4e-11
 Identities = 12/53 (22%), Positives = 29/53 (54%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          LP +     + ++F   G +    + +   TG   G+AFV+F+++ ++ +A++
Sbjct: 11 LPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63

>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 = 57.7 bits (140), Expect = 2e-12
 Identities = 17/55 (30%), Positives = 26/55 (47%), Gaps = 2/55 (3%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKS-TGKLKGFAFVEFSTKEEATKALEL 73
          LP +   + I+  F     ++ V LP+  S   +LKGF + EF   +    AL L
Sbjct: 23 LPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSL 76

>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 = 57.7 bits (140), Expect = 2e-12
 Identities = 21/57 (36%), Positives = 28/57 (49%), Gaps = 4/57 (7%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          LPP+     IE VF KYG +  + L   K+      FAFVEF    +A  A+  G +
Sbjct: 30 LPPDIRTKDIEDVFYKYGAIRDIDL---KNRRGGPPFAFVEFEDPRDAEDAVY-GRD 82

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 57.3 bits (139), Expect = 3e-12
 Identities = 19/76 (25%), Positives = 32/76 (42%), Gaps = 10/76 (13%)

Query: 1  MAELVENNKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVE 60
          M    E      R+ ++   P + +   +  +F  +G +  V +          GFAFVE
Sbjct: 21 MHHRQEGELSNTRLFVR-PFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVE 71

Query: 61 FSTKEEATKALELGLN 76
          F   E A KA+E  ++
Sbjct: 72 FEEAESAAKAIE-EVH 86

>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 = 57.3 bits (139), Expect = 3e-12
 Identities = 18/57 (31%), Positives = 26/57 (45%), Gaps = 7/57 (12%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          LPP+   + +  +F KYGK   V + K       KGF F+   T+  A  A    L+
Sbjct: 23 LPPDITEEEMRKLFEKYGKAGEVFIHK------DKGFGFIRLETRTLAEIAKV-ELD 72

>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 = 57.3 bits (139), Expect = 3e-12
 Identities = 15/62 (24%), Positives = 24/62 (38%), Gaps = 8/62 (12%)

Query: 20 LPPEAEHDYIESVFSKYGKVT--------YVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
          L      + +   F + G +          ++L   + TGKLKG A V F     A  A+
Sbjct: 21 LGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAI 80

Query: 72 EL 73
          + 
Sbjct: 81 DW 82

>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 = 57.0 bits (138), Expect = 4e-12
 Identities = 13/57 (22%), Positives = 28/57 (49%), Gaps = 4/57 (7%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          LP +   + +  +F KYG +  + +     T + +G A+V +    +A  A++  L+
Sbjct: 16 LPYKITAEEMYDIFGKYGPIRQIRVGN---TPETRGTAYVVYEDIFDAKNAVD-HLS 68

>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 = 56.5 bits (137), Expect = 5e-12
 Identities = 16/53 (30%), Positives = 24/53 (45%), Gaps = 1/53 (1%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          +    +   I S F++YG V  V +     TG  KG+ FV F    +  K +E
Sbjct: 17 IDVRMDETEIRSFFARYGSVKEVKIIT-DRTGVSKGYGFVSFYNDVDVQKIVE 68

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 56.7 bits (137), Expect = 5e-12
 Identities = 19/44 (43%), Positives = 28/44 (63%)

Query: 29 IESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          + S+FSK GKV  +  P  ++TGK KGF FVE  +  +A K ++
Sbjct: 29 LTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIK 72

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score = 56.1 bits (136), Expect = 6e-12
 Identities = 16/57 (28%), Positives = 31/57 (54%), Gaps = 3/57 (5%)

Query: 16 LKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L EK+  +     + ++FS++G++  + + +   + K++G AFV F     AT AL 
Sbjct: 16 LNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALR 69

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 56.6 bits (137), Expect = 7e-12
 Identities = 15/62 (24%), Positives = 24/62 (38%), Gaps = 8/62 (12%)

Query: 20 LPPEAEHDYIESVFSKYGKVTY--------VSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
          L      + +   F + G +          ++L   + TGKLKG A V F     A  A+
Sbjct: 15 LGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAI 74

Query: 72 EL 73
          + 
Sbjct: 75 DW 76

>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 = 7e-12
 Identities = 13/53 (24%), Positives = 27/53 (50%), Gaps = 1/53 (1%)

Query: 20  LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
           +  +   + I  +FS +G++    + +    G  +G AFV F+T+  A  A++
Sbjct: 103 ISKKCTENDIRVMFSSFGQIEECRILR-GPDGLSRGCAFVTFTTRAMAQTAIK 154

>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 = 54.9 bits (133), Expect = 9e-11
 Identities = 15/59 (25%), Positives = 28/59 (47%), Gaps = 3/59 (5%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKL--KGFAFVEFSTKEEATKALELGLN 76
          +P       +  +F +YG V  +++ + +S      KG  FV F T++ A +A    L+
Sbjct: 11 VPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN-ALH 68

>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 = 56.6 bits (137), Expect = 7e-12
 Identities = 15/57 (26%), Positives = 23/57 (40%), Gaps = 1/57 (1%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          LP E     +  +F  +G V    +   K T   K F FV +     A  A++  +N
Sbjct: 33 LPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQ-SMN 88

>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 = 57.2 bits (139), Expect = 1e-11
 Identities = 10/53 (18%), Positives = 25/53 (47%)

Query: 20  LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
           L    + + + + F  +       +     TG  +G+ FV F+++++A  A++
Sbjct: 95  LNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 147

>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 = 49.8 bits (120), Expect = 7e-09
 Identities = 13/53 (24%), Positives = 22/53 (41%), Gaps = 1/53 (1%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L      D ++  F   G +  + +   K   K   +AFVE+    +A  AL+
Sbjct: 8  LDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQ 59

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 55.8 bits (135), Expect = 1e-11
 Identities = 17/57 (29%), Positives = 24/57 (42%), Gaps = 1/57 (1%)

Query: 20  LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
           LP E     + S F  +G V    +   K T   K F FV F   + A  A++  +N
Sbjct: 48  LPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIK-AMN 103

>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 = 55.5 bits (134), Expect = 1e-11
 Identities = 16/62 (25%), Positives = 22/62 (35%), Gaps = 8/62 (12%)

Query: 20 LPPEAEHDYIESVFSKYGKVT--------YVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
          L      D +   F + G V          + +   K TGK KG A V +     A  A+
Sbjct: 23 LNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAV 82

Query: 72 EL 73
          E 
Sbjct: 83 EW 84

>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 = 55.3 bits (134), Expect = 2e-11
 Identities = 18/56 (32%), Positives = 29/56 (51%), Gaps = 3/56 (5%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKL---KGFAFVEFSTKEEATKALE 72
          L      + ++ VFSK G +   ++ K K+   +    GF FVE+   E+A KAL+
Sbjct: 13 LNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALK 68

>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 = 54.9 bits (133), Expect = 2e-11
 Identities = 18/57 (31%), Positives = 25/57 (43%), Gaps = 9/57 (15%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          LP EA    I S+F +YGKV    +        +K + FV    K  A  A+   L+
Sbjct: 16 LPREATEQEIRSLFEQYGKVLECDI--------IKNYGFVHIEDKTAAEDAIR-NLH 63

>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 = 54.4 bits (132), Expect = 2e-11
 Identities = 17/53 (32%), Positives = 26/53 (49%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L P+   + I   F  +G+V  + LP    T K +GF F+ F  +E   K +E
Sbjct: 7  LSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 59

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 55.5 bits (134), Expect = 2e-11
 Identities = 12/53 (22%), Positives = 27/53 (50%), Gaps = 1/53 (1%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L        I+ +F+++G +   ++   + +G+  G A V F  + +A KA++
Sbjct: 43 LDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMK 94

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 56.4 bits (136), Expect = 2e-11
 Identities = 12/53 (22%), Positives = 27/53 (50%), Gaps = 1/53 (1%)

Query: 20  LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
           L        I+ +F+++G +   ++  +  +G+  G A V F  + +A KA++
Sbjct: 96  LDFGVSDADIQELFAEFGTLKKAAV-DYDRSGRSLGTADVHFERRADALKAMK 147

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 54.6 bits (132), Expect = 3e-11
 Identities = 19/57 (33%), Positives = 26/57 (45%), Gaps = 6/57 (10%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          L   A    +E  FS YG +  V + +        GFAFVEF    +A  A+  GL+
Sbjct: 8  LGTGAGKGELERAFSYYGPLRTVWIAR-----NPPGFAFVEFEDPRDAEDAVR-GLD 58

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 54.6 bits (132), Expect = 3e-11
 Identities = 15/57 (26%), Positives = 26/57 (45%), Gaps = 3/57 (5%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          +P       +  +F ++GK+  V +   +   K  GF FV F    +A +A E  L+
Sbjct: 23 IPFRFRDPDLRQMFGQFGKILDVEIIFNERGSK--GFGFVTFENSADADRARE-KLH 76

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C Length = 90

 Score = 54.1 bits (131), Expect = 3e-11
 Identities = 9/50 (18%), Positives = 21/50 (42%), Gaps = 3/50 (6%)

Query: 29 IESVFSKYG--KVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          +       G   +  +   + ++ G+ KGFA V   ++  + K ++  L 
Sbjct: 18 LTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD-LLP 66

>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 = 4e-11
 Identities = 16/53 (30%), Positives = 25/53 (47%), Gaps = 5/53 (9%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L      D ++ VF    ++  V        GK KG A++EF ++ +A K LE
Sbjct: 24 LSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLE 71

>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 = 54.2 bits (131), Expect = 4e-11
 Identities = 12/44 (27%), Positives = 26/44 (59%), Gaps = 1/44 (2%)

Query: 29 IESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          I+ +F+++G +   ++   + +G+  G A V F  K +A KA++
Sbjct: 46 IQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMK 88

>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 = 54.2 bits (131), Expect = 4e-11
 Identities = 18/57 (31%), Positives = 28/57 (49%), Gaps = 5/57 (8%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          L   A  + ++ VF K   +           GK KG+AF+EF++ E+A +AL    N
Sbjct: 23 LSYSATEETLQEVFEKATFIKVPQ----NQNGKSKGYAFIEFASFEDAKEALN-SCN 74

>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 = 54.6 bits (132), Expect = 4e-11
 Identities = 15/53 (28%), Positives = 23/53 (43%), Gaps = 1/53 (1%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L  +     ++ VFS  G V    + + K  GK +G   V F    EA +A+ 
Sbjct: 23 LDYKVGWKKLKEVFSMAGVVVRADILEDKD-GKSRGIGTVTFEQSIEAVQAIS 74

>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 = 53.9 bits (130), Expect = 5e-11
 Identities = 18/58 (31%), Positives = 28/58 (48%), Gaps = 2/58 (3%)

Query: 20 LPPEAEHDYIESVFSKYG-KVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          L P  + ++I   F+  G  V  V + + + TG   G+ FVEF+    A K L   +N
Sbjct: 17 LEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLH-KIN 73

>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 = 53.7 bits (130), Expect = 5e-11
 Identities = 12/54 (22%), Positives = 24/54 (44%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
          +P       +   F K+G VT V +       + +GF F+ F  ++   +A+ +
Sbjct: 18 IPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM 71

>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 = 53.8 bits (130), Expect = 5e-11
 Identities = 15/53 (28%), Positives = 22/53 (41%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          +P     D I   F  Y  +      K+   G   G A V F +++EAT A+ 
Sbjct: 23 MPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 75

>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 = 53.8 bits (130), Expect = 6e-11
 Identities = 9/54 (16%), Positives = 20/54 (37%), Gaps = 6/54 (11%)

Query: 19 KLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
           L P      +   F ++G +  +         K   FA++++ + + A  A  
Sbjct: 24 GLGPNTSLAALAREFDRFGSIRTIDHV------KGDSFAYIQYESLDAAQAACA 71

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 53.4 bits (129), Expect = 6e-11
 Identities = 12/57 (21%), Positives = 23/57 (40%), Gaps = 9/57 (15%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          +        + S+F + G+V    +        +K +AFV    + +A  A+   LN
Sbjct: 17 VSAACTSQELRSLFERRGRVIECDV--------VKDYAFVHMEKEADAKAAIA-QLN 64

>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 = 53.4 bits (129), Expect = 7e-11
 Identities = 14/57 (24%), Positives = 25/57 (43%), Gaps = 9/57 (15%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          + P   +  + + F +YG V    + K         +AFV     E+A +A+  GL+
Sbjct: 18 ISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERAEDAVEAIR-GLD 65

>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 = 53.4 bits (129), Expect = 8e-11
 Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 8/53 (15%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L      + +E  FS++GK+  V         KLK +AF+ F  ++ A KA+E
Sbjct: 19 LANTVTEEILEKAFSQFGKLERVK--------KLKDYAFIHFDERDGAVKAME 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 = 53.5 bits (129), Expect = 9e-11
 Identities = 20/59 (33%), Positives = 31/59 (52%), Gaps = 12/59 (20%)

Query: 20 LPPEA--EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          L      + D +E++FSKYG+V   S+ K        G+AFV++S +  A  A+  G N
Sbjct: 35 LNTALVKKSD-VETIFSKYGRVAGCSVHK--------GYAFVQYSNERHARAAVL-GEN 83

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 53.1 bits (128), Expect = 9e-11
 Identities = 15/53 (28%), Positives = 22/53 (41%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          +P     D I   F  Y  +      K+   G   G A V F +++EAT A+ 
Sbjct: 23 MPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 75

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 52.8 bits (127), Expect = 1e-10
 Identities = 18/59 (30%), Positives = 31/59 (52%), Gaps = 4/59 (6%)

Query: 14 VVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
           V  ++L        I  +FSK+GK+T    P+    GK KG+ F+E+++   A  A++
Sbjct: 11 QVGPDRLEKLKN--VIHKIFSKFGKITNDFYPE--EDGKTKGYIFLEYASPAHAVDAVK 65

>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 = 53.0 bits (128), Expect = 1e-10
 Identities = 13/57 (22%), Positives = 22/57 (38%), Gaps = 3/57 (5%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          L  +     I  +FS+ G      +    ++     + FVEF    +A  AL   +N
Sbjct: 23 LSRDVTEVLILQLFSQIGPCKSCKMITEHTSND--PYCFVEFYEHRDAAAALA-AMN 76

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 53.0 bits (128), Expect = 1e-10
 Identities = 19/53 (35%), Positives = 28/53 (52%), Gaps = 2/53 (3%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L    + + +   FS +G +T   +      G+ KGF FV FS+ EEATKA+ 
Sbjct: 23 LDDGIDDERLRKAFSPFGTITSAKV--MMEGGRSKGFGFVCFSSPEEATKAVT 73

>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 = 53.3 bits (128), Expect = 1e-10
 Identities = 18/54 (33%), Positives = 24/54 (44%)

Query: 20  LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
           LP     + I   FS    V           GK+ G AFV+F+++E A KAL  
Sbjct: 50  LPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGK 103

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 52.6 bits (127), Expect = 2e-10
 Identities = 12/59 (20%), Positives = 25/59 (42%), Gaps = 12/59 (20%)

Query: 20 LPPEA--EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          LP +   + D +  +FS YG +  +++           F F++F   +    A+E   +
Sbjct: 18 LPLKNVSKED-LFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAIE-CES 66

>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 = 54.1 bits (131), Expect = 2e-10
 Identities = 15/53 (28%), Positives = 28/53 (52%)

Query: 20  LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
           LP       +E +FS+YG++    +   + TG  +G  F+ F  + EA +A++
Sbjct: 96  LPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 148

>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 = 53.7 bits (130), Expect = 2e-10
 Identities = 15/53 (28%), Positives = 26/53 (49%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          LP     +   S+F   G++    L + K TG+  G+ FV +   ++A KA+ 
Sbjct: 10 LPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62

>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 = 52.6 bits (127), Expect = 2e-10
 Identities = 11/57 (19%), Positives = 24/57 (42%), Gaps = 2/57 (3%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          LP   +   +E++   +G+V    + +  S+G  +G  F    + E+    +    N
Sbjct: 33 LPLSMDEQELENMLKPFGQVISTRILR-DSSGTSRGVGFARMESTEKCEAVIG-HFN 87

>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 = 54.7 bits (131), Expect = 2e-10
 Identities = 9/55 (16%), Positives = 22/55 (40%), Gaps = 2/55 (3%)

Query: 20  LPPEAEHDYIESVFSKYG--KVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
           L      + +       G   +  +   + ++ G+ KGFA V   ++  + K ++
Sbjct: 76  LTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 130

>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 = 52.4 bits (126), Expect = 3e-10
 Identities = 9/54 (16%), Positives = 18/54 (33%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
          +P       +                   + G+  G A V+F  +++A K+  L
Sbjct: 23 IPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL 76

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 52.3 bits (126), Expect = 3e-10
 Identities = 15/57 (26%), Positives = 26/57 (45%), Gaps = 3/57 (5%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          +P       +  +F ++GK+  V +   +   K  GF FV F    +A +A E  L+
Sbjct: 37 IPFRFRDPDLRQMFGQFGKILDVEIIFNERGSK--GFGFVTFENSADADRARE-KLH 90

>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 = 54.2 bits (131), Expect = 3e-10
 Identities = 13/53 (24%), Positives = 25/53 (47%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L P+     +   FS  G +  + + +   T +  G+A+V F    +A +AL+
Sbjct: 23 LHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 75

>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 = 53.1 bits (128), Expect = 8e-10
 Identities = 14/53 (26%), Positives = 24/53 (45%), Gaps = 2/53 (3%)

Query: 20  LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
           L    ++  +   FS +G +    +         KG+ FV F T+E A +A+E
Sbjct: 111 LDKSIDNKALYDTFSAFGNILSCKVVC--DENGSKGYGFVHFETQEAAERAIE 161

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 52.0 bits (125), Expect = 3e-10
 Identities = 18/78 (23%), Positives = 37/78 (47%), Gaps = 8/78 (10%)

Query: 1  MAELVENNKKYGRVVLKEKLP--PEAEHD----YIESVFSKYGKVTYVSLPKFKSTGKLK 54
          + +  +       V++ + +P       +     I  +FSK+GK+T    P+    GK K
Sbjct: 4  LKDRPQEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE--EDGKTK 61

Query: 55 GFAFVEFSTKEEATKALE 72
          G+ F+E+++   A  A++
Sbjct: 62 GYIFLEYASPAHAVDAVK 79

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 51.9 bits (125), Expect = 3e-10
 Identities = 11/57 (19%), Positives = 21/57 (36%), Gaps = 7/57 (12%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          +P  A    +  +F  +G +              KG  F+++ T E+A   +   L 
Sbjct: 35 IPHFATEADLIPLFQNFGFILDFKHYP------EKGCCFIKYDTHEQAAVCIV-ALA 84

>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 = 51.5 bits (124), Expect = 4e-10
 Identities = 12/57 (21%), Positives = 21/57 (36%), Gaps = 7/57 (12%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          L P    D +  +F                     G+AFV++  +  A +A+E  L+
Sbjct: 16 LSPAVTADDLRQLFGDRKLPLAGQ------VLLKSGYAFVDYPDQNWAIRAIE-TLS 65

>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 = 4e-10
 Identities = 16/57 (28%), Positives = 31/57 (54%), Gaps = 3/57 (5%)

Query: 16 LKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L EK+  +     + ++FS++G++  + + +   + K++G AFV F     AT AL 
Sbjct: 17 LNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALR 70

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 46.0 bits (108), Expect = 3e-07
 Identities = 13/53 (24%), Positives = 22/53 (41%), Gaps = 5/53 (9%)

Query: 20  LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
           LP E     +  +F+++     V L   +        AFVEF  + +A  A +
Sbjct: 215 LPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARD 262

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 50.9 bits (123), Expect = 4e-10
 Identities = 15/53 (28%), Positives = 26/53 (49%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L      + ++  F ++GKV    L   K+T + +GF FV F +++   K  E
Sbjct: 7  LSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE 59

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 51.4 bits (124), Expect = 4e-10
 Identities = 16/57 (28%), Positives = 26/57 (45%), Gaps = 3/57 (5%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          LP +     ++  F++ G V Y  +      GK KG   V+F + E A +A    +N
Sbjct: 16 LPFDFTWKMLKDKFNECGHVLYADI--KMENGKSKGCGVVKFESPEVAERACR-MMN 69

>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 = 54.5 bits (130), Expect = 5e-10
 Identities = 11/54 (20%), Positives = 26/54 (48%)

Query: 19  KLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
           ++  +     +   F  YG +  + +   K +GK +G+AF+E+  + +   A +
Sbjct: 109 RVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 52.2 bits (125), Expect = 5e-10
 Identities = 19/54 (35%), Positives = 27/54 (50%), Gaps = 2/54 (3%)

Query: 20  LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
           LP +A  + I + FS    V  V +      G++ G A VEF+T EEA  A+  
Sbjct: 54  LPYKATENDIYNFFSPLNPVR-VHIEI-GPDGRVTGEADVEFATHEEAVAAMSK 105

>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 = 52.1 bits (125), Expect = 5e-10
 Identities = 17/54 (31%), Positives = 23/54 (42%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
          LP EAE+ ++   F K   V       +   GK  G  FVEF  + +   AL  
Sbjct: 33 LPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCR 86

>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 = 51.5 bits (124), Expect = 5e-10
 Identities = 13/53 (24%), Positives = 24/53 (45%), Gaps = 6/53 (11%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L      + IE  F+         + K      ++ +AFV FS +E+A +A++
Sbjct: 23 LMLSTSEEMIEKEFNNIKPGAVERVKK------IRDYAFVHFSNREDAVEAMK 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 = 51.3 bits (123), Expect = 6e-10
 Identities = 17/54 (31%), Positives = 24/54 (44%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
          LP     + I   FS    V           G+  G AFV+F+++E A KAL+ 
Sbjct: 23 LPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK 76

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A Length = 150

 Score = 52.2 bits (125), Expect = 7e-10
 Identities = 16/57 (28%), Positives = 23/57 (40%), Gaps = 6/57 (10%)

Query: 20  LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
           L        +E  F  YG +  V + +        GFAFVEF    +A  A+   L+
Sbjct: 81  LGNNGNKTELERAFGYYGPLRSVWVAR-----NPPGFAFVEFEDPRDAADAVR-ELD 131

>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 = 50.7 bits (122), Expect = 7e-10
 Identities = 17/56 (30%), Positives = 29/56 (51%), Gaps = 5/56 (8%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKF---KSTGKLKGFAFVEFSTKEEATKALE 72
          L PE +   +   FS +G +  +  PK      TG  KG+AF+ F++ + +  A+E
Sbjct: 13 LDPEIDEKLLYDTFSAFGVI--LQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 51.4 bits (123), Expect = 9e-10
 Identities = 11/57 (19%), Positives = 26/57 (45%), Gaps = 3/57 (5%)

Query: 16 LKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          +  ++P E     + ++ S  G +  + +     +    G A++ F+T+E A   +E
Sbjct: 37 INPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAFVE 90

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 51.8 bits (124), Expect = 9e-10
 Identities = 12/50 (24%), Positives = 22/50 (44%), Gaps = 3/50 (6%)

Query: 29  IESVFSKYG--KVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
           +  V    G   V  +   + ++ G+ KG+A V  +++    K LE  L 
Sbjct: 72  LIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLE-LLP 120

>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 = 53.2 bits (128), Expect = 1e-09
 Identities = 19/53 (35%), Positives = 27/53 (50%), Gaps = 1/53 (1%)

Query: 20  LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
           L P   ++ +E  FS++G V    +      G+  G  FVEF+ K  A KALE
Sbjct: 104 LSPVVSNELLEQAFSQFGPVEKAVVVV-DDRGRATGKGFVEFAAKPPARKALE 155

>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 = 46.2 bits (110), Expect = 2e-07
 Identities = 11/53 (20%), Positives = 24/53 (45%), Gaps = 6/53 (11%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          LP +   +  + +F +YG+ + V + + +      GF F+   ++  A  A  
Sbjct: 30 LPTDITEEDFKRLFERYGEPSEVFINRDR------GFGFIRLESRTLAEIAKA 76

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 102

 Score = 50.7 bits (122), Expect = 1e-09
 Identities = 14/57 (24%), Positives = 27/57 (47%), Gaps = 4/57 (7%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          L  +   + ++  F    +     +   + TG  KGF FV+F+++E+A  A E  + 
Sbjct: 23 LSEDTTEETLKESFDGSVRA---RIVTDRETGSSKGFGFVDFNSEEDAKAAKE-AME 75

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 50.4 bits (121), Expect = 1e-09
 Identities = 14/57 (24%), Positives = 25/57 (43%), Gaps = 7/57 (12%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          +        +   FS +G++  + +         KG++FV FST E A  A+   +N
Sbjct: 33 IASGLTDQLMRQTFSPFGQIMEIRVFP------EKGYSFVRFSTHESAAHAIV-SVN 82

>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 = 50.0 bits (120), Expect = 1e-09
 Identities = 12/55 (21%), Positives = 24/55 (43%), Gaps = 11/55 (20%)

Query: 20 LPPEA--EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          LP +   + D +  +FS YG +  +++           F F++F   +    A+E
Sbjct: 30 LPLKNVSKED-LFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAIE 75

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 49.0 bits (117), Expect = 4e-09
 Identities = 15/57 (26%), Positives = 28/57 (49%), Gaps = 4/57 (7%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          +PP  + + ++S+  +YG V         S         V +S+K++A +AL+  LN
Sbjct: 23 IPPHLQWEVLDSLLVQYGVVESCEQVNTDSET---AVVNVTYSSKDQARQALD-KLN 75

>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 = 48.8 bits (117), Expect = 5e-09
 Identities = 10/46 (21%), Positives = 19/46 (41%), Gaps = 6/46 (13%)

Query: 27 DYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
            +   FS +G +  +S+         +  AFV +   E A +A+ 
Sbjct: 28 TLLRGAFSPFGNIIDLSMDP------PRNCAFVTYEKMESADQAVA 67

>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 = 48.5 bits (116), Expect = 5e-09
 Identities = 12/54 (22%), Positives = 23/54 (42%), Gaps = 2/54 (3%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
           P       +    +   K   + + +  + G   G+ FV+FS +EE  +AL+ 
Sbjct: 18 APFNVTEKNVMEFLAPL-KPVAIRIVR-NAHGNKTGYIFVDFSNEEEVKQALKC 69

>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 = 48.5 bits (116), Expect = 6e-09
 Identities = 17/54 (31%), Positives = 25/54 (46%), Gaps = 2/54 (3%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
          LP  A  + I + FS       V +      G++ G A VEF+T E+A  A+  
Sbjct: 23 LPYRATENDIYNFFSPL-NPMRVHIEI-GPDGRVTGEADVEFATHEDAVAAMAK 74

>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 = 48.8 bits (117), Expect = 6e-09
 Identities = 16/57 (28%), Positives = 27/57 (47%), Gaps = 3/57 (5%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          L    ++  +   FS +G +  +S          KG+ FV F T+E A +A+E  +N
Sbjct: 13 LDKSIDNKALYDTFSAFGNI--LSCKVVCDENGSKGYGFVHFETQEAAERAIE-KMN 66

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 48.1 bits (115), Expect = 7e-09
 Identities = 12/55 (21%), Positives = 16/55 (29%), Gaps = 5/55 (9%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELG 74
           P   +   +   F  +G V  V + K K       FA VE          L   
Sbjct: 16 FPRGVDSAQLSEYFLAFGPVASVVMDKDK-----GVFAIVEMGDVGAREAVLSQS 65

>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 = 48.4 bits (116), Expect = 8e-09
 Identities = 18/53 (33%), Positives = 26/53 (49%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          LP +     ++  FS +G+V  V + K   TG  KGF FV F+  E   K + 
Sbjct: 23 LPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS 75

>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 = 48.0 bits (115), Expect = 8e-09
 Identities = 11/57 (19%), Positives = 27/57 (47%), Gaps = 6/57 (10%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          L        + + F ++G++  +++ +       +  AF++F+T++ A  A E   N
Sbjct: 20 LGDTITETDLRNHFYQFGEIRTITVVQ------RQQCAFIQFATRQAAEVAAEKSFN 70

>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 = 1e-08
 Identities = 14/53 (26%), Positives = 21/53 (39%), Gaps = 7/53 (13%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          LPP      ++    + G V Y  + +        G   VEF  KE+ T A+ 
Sbjct: 23 LPPSGSWQDLKDHMREAGDVCYADVYR-------DGTGVVEFVRKEDMTYAVR 68

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 48.3 bits (115), Expect = 1e-08
 Identities = 15/58 (25%), Positives = 25/58 (43%), Gaps = 5/58 (8%)

Query: 20 LPPEAEHDYIESVFSKYGKVTY----VSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
          LP  A  + + + F ++  +T     +        G+  G AFV F+ +E A  AL  
Sbjct: 31 LPFTATAEEVVAFFGQHCPITGGKEGILFVT-YPDGRPTGDAFVLFACEEYAQNALRK 87

>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 = 47.4 bits (113), Expect = 1e-08
 Identities = 11/59 (18%), Positives = 25/59 (42%), Gaps = 5/59 (8%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKF-----KSTGKLKGFAFVEFSTKEEATKALEL 73
          +P     + +   F+   ++  ++             + K FAF+EF + +E T+A+  
Sbjct: 14 IPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAF 72

>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 = 48.1 bits (115), Expect = 1e-08
 Identities = 12/53 (22%), Positives = 23/53 (43%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          LP       +   F  +G +    +   + TGK +G+ FV  + +  A +A +
Sbjct: 25 LPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACK 77

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 47.8 bits (114), Expect = 2e-08
 Identities = 13/54 (24%), Positives = 24/54 (44%), Gaps = 2/54 (3%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
          +P  A  + +   F    +V  V L K    G+  G   V+F + ++  +AL+ 
Sbjct: 24 MPFSAMENDVRDFFHGL-RVDAVHLLK-DHVGRNNGNGLVKFLSPQDTFEALKR 75

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 47.5 bits (113), Expect = 2e-08
 Identities = 14/55 (25%), Positives = 23/55 (41%), Gaps = 2/55 (3%)

Query: 20 LPPEAEHDYIESVFSKYGK-VTYVSLPK-FKSTGKLKGFAFVEFSTKEEATKALE 72
          +P   + + I    +K  + V  V +        K +GFAFVE+ +   A  A  
Sbjct: 16 IPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 70

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 46.3 bits (111), Expect = 2e-08
 Identities = 12/53 (22%), Positives = 23/53 (43%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L  +   + +   F ++G+V    + +   T + +GF FV F  +    K L 
Sbjct: 8  LSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 60

>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 = 47.9 bits (114), Expect = 2e-08
 Identities = 12/58 (20%), Positives = 26/58 (44%), Gaps = 5/58 (8%)

Query: 20  LPPEAEHDYIESVFSKYGKVTYVSLP-----KFKSTGKLKGFAFVEFSTKEEATKALE 72
           L    +   ++ +F +Y   +  +       +    G++KG AF+    ++ A KAL+
Sbjct: 53  LAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALK 110

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 46.7 bits (111), Expect = 3e-08
 Identities = 13/60 (21%), Positives = 20/60 (33%), Gaps = 6/60 (10%)

Query: 13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
           VV    L        +     ++G ++YV +         K  A VEF     A  A+ 
Sbjct: 22 PVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVLGACNAVN 75

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 48.4 bits (115), Expect = 3e-08
 Identities = 19/81 (23%), Positives = 34/81 (41%), Gaps = 10/81 (12%)

Query: 20  LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCP 79
           +PP    + ++ +FS  G V       FK   K +  A ++  + EEA +AL   L+   
Sbjct: 128 IPPSVSEEDLKVLFSSNGGVV----KGFKFFQKDRKMALIQMGSVEEAVQALI-DLHNHD 182

Query: 80  TDYQSSILTTTSRLSFGITPL 100
                 +     R+SF  + +
Sbjct: 183 LGENHHL-----RVSFSKSTI 198

>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 = 37.6 bits (87), Expect = 2e-04
 Identities = 14/54 (25%), Positives = 20/54 (37%), Gaps = 6/54 (11%)

Query: 20 LPPEA-EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L PE      +  +F  YG V  V     K     K  A V+ +   +A  A+ 
Sbjct: 11 LNPERVTPQSLFILFGVYGDVQRV-----KILFNKKENALVQMADGNQAQLAMS 59

>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 = 46.0 bits (110), Expect = 4e-08
 Identities = 13/53 (24%), Positives = 26/53 (49%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L  +     ++  F+K+G+V   ++    +TG+ +GF F+ F       K L+
Sbjct: 19 LSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD 71

>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 = 46.7 bits (111), Expect = 4e-08
 Identities = 14/53 (26%), Positives = 21/53 (39%), Gaps = 7/53 (13%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          LPP      ++    + G V Y  + +        G   VEF  KE+ T A+ 
Sbjct: 24 LPPSGSWQDLKDHMREAGDVCYADVYR-------DGTGVVEFVRKEDMTYAVR 69

>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 = 46.3 bits (110), Expect = 4e-08
 Identities = 14/60 (23%), Positives = 21/60 (35%), Gaps = 6/60 (10%)

Query: 13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
           VV    L        +     K+G + YV +  F      K  A VEF   + A + + 
Sbjct: 16 PVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVT 69

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score = 46.5 bits (111), Expect = 5e-08
 Identities = 12/53 (22%), Positives = 23/53 (43%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L  +   + +   F ++G+V    + +   T + +GF FV F  +    K L 
Sbjct: 33 LSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 85

>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 = 46.4 bits (110), Expect = 5e-08
 Identities = 11/46 (23%), Positives = 21/46 (45%), Gaps = 3/46 (6%)

Query: 30 ESVFSKYGKVTYVSLPKFKSTGKLK---GFAFVEFSTKEEATKALE 72
             F K+GK+  V +    S    +     A+V +   E+A +A++
Sbjct: 36 PEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQ 81

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 48.1 bits (114), Expect = 6e-08
 Identities = 15/53 (28%), Positives = 25/53 (47%), Gaps = 4/53 (7%)

Query: 20  LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
           +PP    + ++ +FS  G V  V   KF    +    A ++  + EEA +AL 
Sbjct: 159 IPPSVSEEDLKVLFSSNGGV--VKGFKFFQKDR--KMALIQMGSVEEAVQALI 207

>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 = 38.4 bits (89), Expect = 1e-04
 Identities = 16/62 (25%), Positives = 23/62 (37%), Gaps = 6/62 (9%)

Query: 12 GRVVLKEKLPPEA-EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKA 70
            V+L   L PE      +  +F  YG V  V     K     K  A V+ +   +A  A
Sbjct: 34 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRV-----KILFNKKENALVQMADGNQAQLA 88

Query: 71 LE 72
          + 
Sbjct: 89 MS 90

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 45.6 bits (108), Expect = 8e-08
 Identities = 11/57 (19%), Positives = 21/57 (36%), Gaps = 6/57 (10%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          LP +A    ++    + G V     P   +    +  AF+ +     A +A+   L 
Sbjct: 27 LPRDARVSDLKRALRELGSV-----PLRLTWQGPRRRAFLHYPDSAAAQQAVS-CLQ 77

>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 = 46.0 bits (109), Expect = 8e-08
 Identities = 17/53 (32%), Positives = 22/53 (41%), Gaps = 6/53 (11%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          LP       I+  FS++G +  V LP+          A VEF    EA KA  
Sbjct: 18 LPAGTLAAEIQETFSRFGSLGRVLLPEG------GITAIVEFLEPLEARKAFR 64

>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 = 45.3 bits (108), Expect = 1e-07
 Identities = 16/53 (30%), Positives = 25/53 (47%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L      + + S FS+YG+V    + K K+T + +GF FV+F         L 
Sbjct: 24 LDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLA 76

>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 = 45.3 bits (107), Expect = 1e-07
 Identities = 14/59 (23%), Positives = 23/59 (38%), Gaps = 6/59 (10%)

Query: 14 VVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          VV    L      + +  V  K G V  + +P        K ++F  + T EE+ +A  
Sbjct: 29 VVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYV 81

>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 = 44.5 bits (106), Expect = 2e-07
 Identities = 15/53 (28%), Positives = 22/53 (41%), Gaps = 5/53 (9%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
             +   D +   FS+YG V  V +PK       + FAFV F+  + A     
Sbjct: 13 CTGDMTEDELREFFSQYGDVMDVFIPK-----PFRAFAFVTFADDQIAQSLCG 60

>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 = 46.2 bits (109), Expect = 2e-07
 Identities = 11/55 (20%), Positives = 21/55 (38%), Gaps = 4/55 (7%)

Query: 18  EKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
           E L      D +  +FSK+G V  +      +  +    A ++++    A  A  
Sbjct: 52  ENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQ----ALLQYADPVSAQHAKL 102

>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 = 45.3 bits (108), Expect = 2e-07
 Identities = 13/53 (24%), Positives = 28/53 (52%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L  E   + + + + ++GK+T   + +  ++ + +GF FV FS+  E   A+ 
Sbjct: 35 LSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA 87

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 45.4 bits (107), Expect = 2e-07
 Identities = 11/55 (20%), Positives = 21/55 (38%), Gaps = 4/55 (7%)

Query: 18 EKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          E L      D +  +FSK+G V  +      +  +    A ++++    A  A  
Sbjct: 34 ENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQ----ALLQYADPVSAQHAKL 84

>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 = 45.3 bits (107), Expect = 2e-07
 Identities = 18/60 (30%), Positives = 29/60 (48%), Gaps = 6/60 (10%)

Query: 13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          RV+   KLP +     + S+   +GKVT + + K       K  AF+E +T+E A   + 
Sbjct: 32 RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVN 85

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 44.5 bits (105), Expect = 3e-07
 Identities = 18/60 (30%), Positives = 29/60 (48%), Gaps = 6/60 (10%)

Query: 13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          RV+   KLP +     + S+   +GKVT + + K       K  AF+E +T+E A   + 
Sbjct: 17 RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVN 70

>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 = 43.6 bits (103), Expect = 4e-07
 Identities = 11/53 (20%), Positives = 20/53 (37%), Gaps = 7/53 (13%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          LP ++    +  +   Y         K+    + K  AFV     E+A  A++
Sbjct: 13 LPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQNAIQ 58

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 43.8 bits (104), Expect = 5e-07
 Identities = 15/54 (27%), Positives = 25/54 (46%), Gaps = 2/54 (3%)

Query: 20 LPPEAEHDYIESVFSK-YGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L P+ +   +   F K Y       +   + TG  KG+ FV+F+ + E  +AL 
Sbjct: 17 LTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALT 69

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89

 Score = 43.0 bits (102), Expect = 6e-07
 Identities = 13/53 (24%), Positives = 23/53 (43%), Gaps = 5/53 (9%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
             +   + ++  F +YG+V  V +PK       + FAFV F+  + A     
Sbjct: 19 CTEDMTAEELQQFFCQYGEVVDVFIPK-----PFRAFAFVTFADDKVAQSLCG 66

>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 = 43.3 bits (102), Expect = 7e-07
 Identities = 18/61 (29%), Positives = 29/61 (47%), Gaps = 6/61 (9%)

Query: 12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
           RV+   KLP E     + ++   +GKVT + + K       K  AF+E +T+E A   +
Sbjct: 15 SRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMV 68

Query: 72 E 72
           
Sbjct: 69 N 69

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A Length = 136

 Score = 43.8 bits (103), Expect = 8e-07
 Identities = 15/68 (22%), Positives = 25/68 (36%), Gaps = 4/68 (5%)

Query: 9   KKYGRVVLKEKLPPEAEHDYIESVFSKY---GKVTYVSLPKFKSTGKLKGFAFVEFSTKE 65
              G VV    LP     + +++  S          V        G+  G AFVE  +++
Sbjct: 41  GGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIY-TREGRQSGEAFVELGSED 99

Query: 66  EATKALEL 73
           +   AL+ 
Sbjct: 100 DVKMALKK 107

>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 = 42.2 bits (99), Expect = 3e-06
 Identities = 13/57 (22%), Positives = 23/57 (40%), Gaps = 4/57 (7%)

Query: 20 LPPEAEHDYIESVFSKY---GKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
          LP     + +++  S       V  V        G+  G AFVE  ++++   AL+ 
Sbjct: 25 LPWSCSIEDVQNFLSDCTIHDGVAGVHFIY-TREGRQSGEAFVELESEDDVKLALKK 80

>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 = 41.8 bits (98), Expect = 3e-06
 Identities = 14/72 (19%), Positives = 28/72 (38%), Gaps = 4/72 (5%)

Query: 5  VENNKKYGRVVLKEKLPPEAEHDYIESVFSKY---GKVTYVSLPKFKSTGKLKGFAFVEF 61
          +E       ++  + LP     + + + FS          +        GK +G A +E 
Sbjct: 4  LEEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLL-NRDGKRRGDALIEM 62

Query: 62 STKEEATKALEL 73
           ++++  KALE 
Sbjct: 63 ESEQDVQKALEK 74

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 40.5 bits (94), Expect = 7e-06
 Identities = 24/82 (29%), Positives = 36/82 (43%), Gaps = 13/82 (15%)

Query: 6  ENNKKYGRVVLKEKLPPEAE------HDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFV 59
           + +   ++ LK K   E E       D +  +  KYG+V  + L       K  G A V
Sbjct: 5  SSGQGTPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLSS-----KKPGTAVV 59

Query: 60 EFSTKEEATKAL--ELGLNPCP 79
          EF+T + A  A+  E+GL   P
Sbjct: 60 EFATVKAAELAVQNEVGLVDNP 81

>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 Length = 104

 Score = 40.2 bits (94), Expect = 9e-06
 Identities = 15/54 (27%), Positives = 26/54 (48%), Gaps = 2/54 (3%)

Query: 23 EAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          E   +    +  KYG+V  +++        L G  +V+F  +E+A KA+   LN
Sbjct: 38 EFFEEVFTEMEEKYGEVEEMNVCD-NLGDHLVGNVYVKFRREEDAEKAVI-DLN 89

>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 Length = 114

 Score = 40.4 bits (95), Expect = 1e-05
 Identities = 10/63 (15%), Positives = 26/63 (41%), Gaps = 8/63 (12%)

Query: 17 KEKLPPEAEHDYIESVF---SKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
          + +     + +  + V    +K+G V ++ + K  + G      +V+  +   A  A+  
Sbjct: 19 QTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGN----VYVKCPSIAAAIAAVN- 73

Query: 74 GLN 76
           L+
Sbjct: 74 ALH 76

>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 = 39.9 bits (93), Expect = 2e-05
 Identities = 16/69 (23%), Positives = 31/69 (44%), Gaps = 9/69 (13%)

Query: 6  ENNKKYGRVVLKEKLPPEA--EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFST 63
          +  ++ GRV+    LP     +   +  +   YGK+    L       ++K  AF+E  T
Sbjct: 19 DQKQELGRVIHLSNLPHSGYSDSA-VLKLAEPYGKIKNYIL------MRMKSQAFIEMET 71

Query: 64 KEEATKALE 72
          +E+A   ++
Sbjct: 72 REDAMAMVD 80

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 39.0 bits (91), Expect = 3e-05
 Identities = 12/54 (22%), Positives = 24/54 (44%), Gaps = 5/54 (9%)

Query: 20 LPPEAEHDYIESVFSKYG-KVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          LP       ++ +  +   + T+ S+    +T    G   +EF ++E   +ALE
Sbjct: 36 LPEGCSWQDLKDLARENSLETTFSSV----NTRDFDGTGALEFPSEEILVEALE 85

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 39.2 bits (91), Expect = 3e-05
 Identities = 14/55 (25%), Positives = 27/55 (49%), Gaps = 2/55 (3%)

Query: 20 LPPEAEHDYIESVFSKYGKVT--YVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          LPP+ + D I + F ++G +   +    + KS    KG+AF+ F  +      ++
Sbjct: 16 LPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALID 70

>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 Length = 112

 Score = 38.5 bits (90), Expect = 5e-05
 Identities = 14/58 (24%), Positives = 24/58 (41%), Gaps = 8/58 (13%)

Query: 22 PEAEHDYIESVF---SKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          P   ++  E +    SK+G++  + L      G     A V F   EEA   ++  L+
Sbjct: 33 PLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGV----ASVSFRDPEEADYCIQ-TLD 85

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 38.5 bits (89), Expect = 6e-05
 Identities = 12/55 (21%), Positives = 19/55 (34%), Gaps = 5/55 (9%)

Query: 18 EKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          +        D + +V +  GKV      +     +    A VEF +   A KA  
Sbjct: 31 QNPLYPITVDVLYTVCNPVGKV-----QRIVIFKRNGIQAMVEFESVLCAQKAKA 80

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 39.4 bits (91), Expect = 6e-05
 Identities = 14/55 (25%), Positives = 21/55 (38%), Gaps = 6/55 (10%)

Query: 18  EKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
           + L P      I  VFS+ G +  +   + K         FV+F  +  A  A E
Sbjct: 149 KHLKPAQIESRIRFVFSRLGDIDRIRYVESK------NCGFVKFKYQANAEFAKE 197

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster} Length = 89

 Score = 37.7 bits (87), Expect = 8e-05
 Identities = 14/65 (21%), Positives = 31/65 (47%), Gaps = 7/65 (10%)

Query: 15 VLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELG 74
          +L + L  + +   + ++  ++G +        +      G A  +++T+EEA KA ++ 
Sbjct: 10 LLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYLNQ------GIALCKYTTREEANKA-QMA 62

Query: 75 LNPCP 79
          LN C 
Sbjct: 63 LNNCV 67

>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} PDB: 3us5_A 2dny_A Length = 118

 Score = 37.8 bits (88), Expect = 1e-04
 Identities = 15/59 (25%), Positives = 25/59 (42%), Gaps = 7/59 (11%)

Query: 21 PPEAEHDYIESVF---SKYGKVTYVSLPK----FKSTGKLKGFAFVEFSTKEEATKALE 72
          P + + D    V     K+G V  V + +     +   ++    FVEFS   E  KA++
Sbjct: 31 PKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQ 89

>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 Length = 105

 Score = 35.9 bits (83), Expect = 4e-04
 Identities = 15/59 (25%), Positives = 26/59 (44%), Gaps = 2/59 (3%)

Query: 16 LKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFK--STGKLKGFAFVEFSTKEEATKALE 72
          L +    E   + +    SKYG V  + +P+          G  FVEF++  +  KA++
Sbjct: 19 LLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQ 77

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	115
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.89
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.87
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.86
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.86
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.86
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.86
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.86
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.86
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.85
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.85
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.85
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.85
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.85
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.85
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.85
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.85
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.85
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.85
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.85
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.84
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.84
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.84
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.84
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.84
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.84
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.84
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.84
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.84
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.84
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.84
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.84
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.84
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.84
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.84
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.84
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.83
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.83
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.83
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.83
2div_A	99	TRNA selenocysteine associated protein; structural	99.83
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.82
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.82
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.82
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.82
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.82
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.82
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.82
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.82
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.82
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.82
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.82
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.82
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.82
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.82
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.81
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.81
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.81
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.81
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.81
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.81
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.81
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.81
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.81
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.7
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.81
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.81
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.8
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.8
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.8
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.8
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.8
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.8
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.8
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.8
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.8
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.8
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.8
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.8
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.8
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.8
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.8
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.79
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.79
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.79
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.79
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.79
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.79
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.79
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.79
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.79
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.79
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.79
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.79
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.79
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.78
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.78
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.78
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.78
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.78
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.78
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.78
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.77
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.77
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.77
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.77
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.77
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.77
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.77
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.76
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.76
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.76
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.76
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.76
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.76
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.76
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.76
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.76
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.76
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.75
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.75
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.75
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.75
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.75
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.75
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.75
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.75
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.75
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.75
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.75
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.75
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.74
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.74
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.74
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.74
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.74
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.74
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.74
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.74
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.74
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.74
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.73
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.73
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.73
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.73
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.73
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.73
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.73
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.73
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.72
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.72
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.72
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.72
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.72
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.72
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.72
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.71
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.71
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.7
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.7
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.7
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.7
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.7
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.69
1x5p_A	97	Negative elongation factor E; structure genomics,	99.69
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.69
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.69
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.68
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.68
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.67
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.67
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.66
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.66
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.66
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.66
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.65
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.65
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.65
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.63
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.63
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.62
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.61
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.61
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.61
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.61
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.61
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.58
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.57
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.56
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.56
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.55
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.54
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.54
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.54
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.54
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.54
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.5
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.5
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.48
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.46
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.45
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.44
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.44
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.4
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.22
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.17
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.02
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.95
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.86
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.6
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.88
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.71
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.68
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.45
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.45
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.23
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	96.96
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	96.9
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	96.39
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	94.91
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	94.09
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	94.08

>4fxv_A ELAV-like protein 1; RNA recognition motif, putative RNA-binding domain, transcri structural genomics, joint center for structural genomics; 1.90A {Homo sapiens}

Probab=99.89  E-value=1.2e-22  Score=118.42  Aligned_cols=83  Identities=22%  Similarity=0.284  Sum_probs=77.8

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      ..++++|||+|||.++++++|+++|++||.|..+++++++.+|.++|||||+|.+.++|++|++.||+..+.|+.++|..
T Consensus        16 ~~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~   95 (99)
T 4fxv_A           16 YFQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSY   95 (99)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            34568999999999999999999999999999999999998999999999999999999999999999999999999887


Q ss_pred             eee
Q psy3928          89 TTS   91 (115)
Q Consensus        89 ~~~   91 (115)
                      ++|
T Consensus        96 AkP   98 (99)
T 4fxv_A           96 ARP   98 (99)
T ss_dssp             CCB
T ss_pred             eeC
Confidence            764

>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=6.1e-21  Score=109.97  Aligned_cols=86  Identities=26%  Similarity=0.287  Sum_probs=79.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      ...++|||+|||..+++++|+++|.+||.+..+.+..++.++.++|||||+|.+.++|++|+..||+..+.|+.++|..+
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   82 (95)
T 2dnz_A            3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHV   82 (95)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEES
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEc
Confidence            45689999999999999999999999999999999999888999999999999999999999999999999999999888


Q ss_pred             eecccc
Q psy3928          90 TSRLSF   95 (115)
Q Consensus        90 ~~~~~~   95 (115)
                      +++...
T Consensus        83 ~~~~~~   88 (95)
T 2dnz_A           83 TERLDG   88 (95)
T ss_dssp             SCCCCC
T ss_pred             ccccCC
Confidence            775544

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.86  E-value=7.6e-21  Score=111.30  Aligned_cols=94  Identities=17%  Similarity=0.147  Sum_probs=82.2

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhh-cCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCC-CCCceeeE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSK-YGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPC-PTDYQSSI   86 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~-~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~-~~~~~~~v   86 (115)
                      ....++|||+|||.++++++|+++|.. ||.|..+.++.++ ++.++|||||+|.+.++|++|++.|++.. +.|+.+.|
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v   84 (104)
T 2dhg_A            6 SGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRL   84 (104)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEE
Confidence            455689999999999999999999999 9999999999998 99999999999999999999999999999 99999998


Q ss_pred             EEeeeccccCCCCCCCC
Q psy3928          87 LTTTSRLSFGITPLGFE  103 (115)
Q Consensus        87 ~~~~~~~~~~~~~~~~~  103 (115)
                      ..+.++.....+...++
T Consensus        85 ~~a~~~~~~~~~~~~~p  101 (104)
T 2dhg_A           85 SVAIPKASRVKPVESGP  101 (104)
T ss_dssp             CBCCCCCSCCCCCCCCC
T ss_pred             EEccCCCcCCCCCCCCC
Confidence            88876555443333333

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.86  E-value=5.2e-21  Score=113.46  Aligned_cols=82  Identities=17%  Similarity=0.123  Sum_probs=77.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      ...++|||+|||..+++++|+++|++||.|..+.|+.++.+++++|||||+|.+.++|++|++.||+..+.|+.+.|..+
T Consensus         4 ~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a   83 (110)
T 3s8s_A            4 IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLD   83 (110)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            45689999999999999999999999999999999999989999999999999999999999999999999999999877


Q ss_pred             ee
Q psy3928          90 TS   91 (115)
Q Consensus        90 ~~   91 (115)
                      ..
T Consensus        84 ~~   85 (110)
T 3s8s_A           84 IK   85 (110)
T ss_dssp             ST
T ss_pred             CC
Confidence            54

>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=1e-20  Score=110.39  Aligned_cols=86  Identities=22%  Similarity=0.291  Sum_probs=80.0

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      ....++|||+|||.++++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|++|++.||+..+.++.+.|..
T Consensus         9 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   88 (102)
T 1x5s_A            9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQ   88 (102)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            45678999999999999999999999999999999999888899999999999999999999999999999999999998


Q ss_pred             eeeccc
Q psy3928          89 TTSRLS   94 (115)
Q Consensus        89 ~~~~~~   94 (115)
                      ++++..
T Consensus        89 a~~~~~   94 (102)
T 1x5s_A           89 AGKSSD   94 (102)
T ss_dssp             EECCCC
T ss_pred             CCCCCC
Confidence            886544

>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=1.4e-20  Score=109.27  Aligned_cols=87  Identities=16%  Similarity=0.212  Sum_probs=79.6

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      .....++|||+|||..+++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|++|+. +++..+.|+.+.|.
T Consensus         6 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V~   84 (99)
T 2dgs_A            6 SGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVK   84 (99)
T ss_dssp             CCSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEEE
Confidence            34567899999999999999999999999999999999998889999999999999999999999 99999999999998


Q ss_pred             Eeeecccc
Q psy3928          88 TTTSRLSF   95 (115)
Q Consensus        88 ~~~~~~~~   95 (115)
                      .+.++...
T Consensus        85 ~a~~~~~~   92 (99)
T 2dgs_A           85 RAEPRDSK   92 (99)
T ss_dssp             ECCCCCCC
T ss_pred             ECCCCccc
Confidence            88765443

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.86  E-value=1.1e-20  Score=109.66  Aligned_cols=86  Identities=26%  Similarity=0.273  Sum_probs=79.8

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      ....++|||+|||..+++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|++|+..|++..+.|+.+.|..
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   84 (99)
T 1whw_A            5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLP   84 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            35678999999999999999999999999999999999988899999999999999999999999999999999999988


Q ss_pred             eeeccc
Q psy3928          89 TTSRLS   94 (115)
Q Consensus        89 ~~~~~~   94 (115)
                      +.++..
T Consensus        85 a~~~~~   90 (99)
T 1whw_A           85 STIKKE   90 (99)
T ss_dssp             CCCCST
T ss_pred             cCCCcc
Confidence            877544

>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=5.8e-21  Score=111.68  Aligned_cols=87  Identities=22%  Similarity=0.247  Sum_probs=80.3

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      .....++|||+|||..+++++|+++|..||.|..+.+..++.++.++|||||+|.+.++|++|+..||+..+.|+.+.|.
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   88 (103)
T 2dnm_A            9 DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQ   88 (103)
T ss_dssp             CCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            44567899999999999999999999999999999999998889999999999999999999999999999999999998


Q ss_pred             Eeeeccc
Q psy3928          88 TTTSRLS   94 (115)
Q Consensus        88 ~~~~~~~   94 (115)
                      .+++...
T Consensus        89 ~a~~~~~   95 (103)
T 2dnm_A           89 VARYGRR   95 (103)
T ss_dssp             ECSSCCS
T ss_pred             ECCcCCC
Confidence            8876443

>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=1.3e-20  Score=110.65  Aligned_cols=88  Identities=18%  Similarity=0.261  Sum_probs=79.9

Q ss_pred             cccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCC---CCce
Q psy3928           7 NNKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCP---TDYQ   83 (115)
Q Consensus         7 ~~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~---~~~~   83 (115)
                      ......++|||+|||..+++++|+++|.+||.|..+.++.++.++.++|||||+|.+.++|++|++.|++..+   .++.
T Consensus         8 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~   87 (106)
T 2dgp_A            8 MKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRP   87 (106)
T ss_dssp             CCCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCce
Confidence            3456678999999999999999999999999999999999988899999999999999999999999999987   8888


Q ss_pred             eeEEEeeeccc
Q psy3928          84 SSILTTTSRLS   94 (115)
Q Consensus        84 ~~v~~~~~~~~   94 (115)
                      +.|..+.++..
T Consensus        88 l~v~~a~~~~~   98 (106)
T 2dgp_A           88 IQVKPADSESR   98 (106)
T ss_dssp             CEEEECCCCSC
T ss_pred             EEEEECCcccc
Confidence            88888776443

>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=9.8e-21  Score=112.76  Aligned_cols=87  Identities=18%  Similarity=0.138  Sum_probs=80.0

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      .....++|||+|||.++++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|++|++.||+..+.++.++|.
T Consensus        21 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~  100 (115)
T 2cpz_A           21 EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQ  100 (115)
T ss_dssp             CCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34456899999999999999999999999999999999998899999999999999999999999999999999999998


Q ss_pred             Eeeeccc
Q psy3928          88 TTTSRLS   94 (115)
Q Consensus        88 ~~~~~~~   94 (115)
                      .++++..
T Consensus       101 ~a~~~~~  107 (115)
T 2cpz_A          101 LKRSKND  107 (115)
T ss_dssp             CCCCSCC
T ss_pred             EcCCCCc
Confidence            8876544

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.85  E-value=1.7e-20  Score=115.04  Aligned_cols=86  Identities=16%  Similarity=0.243  Sum_probs=79.8

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      ....++|||+|||.++++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|++|+..|++..+.|+.++|..
T Consensus        39 ~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  118 (139)
T 1u6f_A           39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVAL  118 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            44568999999999999999999999999999999999988899999999999999999999999999999999999998


Q ss_pred             eeeccc
Q psy3928          89 TTSRLS   94 (115)
Q Consensus        89 ~~~~~~   94 (115)
                      ++++..
T Consensus       119 a~~~~~  124 (139)
T 1u6f_A          119 AASGHQ  124 (139)
T ss_dssp             SSCCCC
T ss_pred             CCCCCC
Confidence            876544

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C

Probab=99.85  E-value=1.7e-21  Score=111.51  Aligned_cols=82  Identities=12%  Similarity=0.152  Sum_probs=71.7

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhcC--CeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEee
Q psy3928          13 RVVLKEKLPPEAEHDYIESVFSKYG--KVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTT   90 (115)
Q Consensus        13 ~~l~V~~l~~~~~~~~l~~~f~~~g--~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~   90 (115)
                      .+|||+|||.++++++|+++|.+||  .+..+.++.++.+|+++|||||+|.+.++|++|++.||+..+.|+.+.|..+.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            5799999999999999999999999  99999999998899999999999999999999999999999999999988777


Q ss_pred             eccc
Q psy3928          91 SRLS   94 (115)
Q Consensus        91 ~~~~   94 (115)
                      +...
T Consensus        82 ~~~~   85 (90)
T 3p5t_L           82 KLEH   85 (90)
T ss_dssp             ----
T ss_pred             CCcc
Confidence            6433

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens}

Probab=99.85  E-value=1.5e-20  Score=106.66  Aligned_cols=83  Identities=25%  Similarity=0.280  Sum_probs=75.7

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      ...++|||+|||.++++++|+++|++||.+..+.+..++.++.++|||||+|.+.++|++|++.|++..+.|+.+.|..+
T Consensus         4 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   83 (87)
T 3bs9_A            4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA   83 (87)
T ss_dssp             --CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEec
Confidence            45679999999999999999999999999999999999889999999999999999999999999999999999998887


Q ss_pred             eec
Q psy3928          90 TSR   92 (115)
Q Consensus        90 ~~~   92 (115)
                      +++
T Consensus        84 ~~k   86 (87)
T 3bs9_A           84 TRK   86 (87)
T ss_dssp             C--
T ss_pred             CCC
Confidence            754

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.85  E-value=2.6e-20  Score=109.45  Aligned_cols=88  Identities=28%  Similarity=0.424  Sum_probs=80.6

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEecee-CCCCCeeeEEEEEecCHHHHHHHHHhh-CCCCCCCceee
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKF-KSTGKLKGFAFVEFSTKEEATKALELG-LNPCPTDYQSS   85 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~-~~~~~~~g~~fv~f~~~~~a~~al~~l-~~~~~~~~~~~   85 (115)
                      .....++|||+|||..+++++|+++|..||.|..+.++.+ +.++.++|||||+|.+.++|++|+..| |+..+.|+.+.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~   90 (107)
T 2cph_A           11 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLV   90 (107)
T ss_dssp             CSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEE
Confidence            4556789999999999999999999999999999999988 678999999999999999999999999 99999999999


Q ss_pred             EEEeeecccc
Q psy3928          86 ILTTTSRLSF   95 (115)
Q Consensus        86 v~~~~~~~~~   95 (115)
                      |..++++...
T Consensus        91 v~~a~~~~~~  100 (107)
T 2cph_A           91 LEWADSEVTV  100 (107)
T ss_dssp             EEECCCCCCC
T ss_pred             EEeCCCCCCC
Confidence            9988875443

>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=2.1e-20  Score=109.54  Aligned_cols=87  Identities=20%  Similarity=0.260  Sum_probs=80.0

Q ss_pred             cccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeE
Q psy3928           7 NNKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSI   86 (115)
Q Consensus         7 ~~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v   86 (115)
                      ......++|||+|||..+++++|+++|.+||.|..+.+..++.++.++|||||+|.+.++|++|+..|++..+.|+.+.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   89 (105)
T 1x5u_A           10 SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRV   89 (105)
T ss_dssp             CCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            34556789999999999999999999999999999999999889999999999999999999999999999999999998


Q ss_pred             EEeeecc
Q psy3928          87 LTTTSRL   93 (115)
Q Consensus        87 ~~~~~~~   93 (115)
                      ..++++.
T Consensus        90 ~~a~~~~   96 (105)
T 1x5u_A           90 NKASAHN   96 (105)
T ss_dssp             EETTTTS
T ss_pred             EECCCCC
Confidence            8877543

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=1.3e-20  Score=110.15  Aligned_cols=87  Identities=20%  Similarity=0.306  Sum_probs=80.3

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      .....++|||+|||..+++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|++|+..|++..+.|+.+.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   90 (103)
T 2cq0_A           11 RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVE   90 (103)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            45567899999999999999999999999999999999998899999999999999999999999999999999999988


Q ss_pred             Eeeeccc
Q psy3928          88 TTTSRLS   94 (115)
Q Consensus        88 ~~~~~~~   94 (115)
                      .++++..
T Consensus        91 ~a~~~~~   97 (103)
T 2cq0_A           91 WAKPSTN   97 (103)
T ss_dssp             ESSCCCC
T ss_pred             ECCCCCC
Confidence            8776543

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.85  E-value=1.9e-20  Score=110.65  Aligned_cols=88  Identities=24%  Similarity=0.320  Sum_probs=80.5

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhC------CCCCCC
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGL------NPCPTD   81 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~------~~~~~~   81 (115)
                      .....++|||+|||.++++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|++|+..++      +..+.|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g   90 (111)
T 1x4h_A           11 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDG   90 (111)
T ss_dssp             CCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSS
T ss_pred             cCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcC
Confidence            34567899999999999999999999999999999999998889999999999999999999999999      999999


Q ss_pred             ceeeEEEeeecccc
Q psy3928          82 YQSSILTTTSRLSF   95 (115)
Q Consensus        82 ~~~~v~~~~~~~~~   95 (115)
                      +.+.|..+.++...
T Consensus        91 ~~l~v~~a~~~~~~  104 (111)
T 1x4h_A           91 RQLKVDLAVTRDEA  104 (111)
T ss_dssp             CEEEEECCCCCCCC
T ss_pred             EEEEEEECCCCccC
Confidence            99998888775444

>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=2.2e-20  Score=110.36  Aligned_cols=85  Identities=24%  Similarity=0.270  Sum_probs=79.2

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      .....++|||+|||..+++++|+++|++||.+..+.++.++.++.++|||||+|.+.++|++|++.+++..+.|+.++|.
T Consensus        22 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~  101 (108)
T 2jrs_A           22 GSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVG  101 (108)
T ss_dssp             SCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            35567899999999999999999999999999999999998899999999999999999999999999999999999988


Q ss_pred             Eeeec
Q psy3928          88 TTTSR   92 (115)
Q Consensus        88 ~~~~~   92 (115)
                      .++++
T Consensus       102 ~a~~k  106 (108)
T 2jrs_A          102 HVTER  106 (108)
T ss_dssp             CSCSS
T ss_pred             EcccC
Confidence            77654

>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=1.5e-20  Score=108.94  Aligned_cols=86  Identities=21%  Similarity=0.224  Sum_probs=77.7

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCC---CCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeE
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKS---TGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSI   86 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~---~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v   86 (115)
                      .+.++|||+|||.++++++|+++|..||.|..+.+..++.   ++.++|||||+|.+.++|++|+..|++..+.|+.+.|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   82 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEV   82 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEE
Confidence            4568999999999999999999999999999999998875   5589999999999999999999999999999999988


Q ss_pred             EEeeecccc
Q psy3928          87 LTTTSRLSF   95 (115)
Q Consensus        87 ~~~~~~~~~   95 (115)
                      ..++++...
T Consensus        83 ~~a~~~~~~   91 (98)
T 2cpf_A           83 RISERATKP   91 (98)
T ss_dssp             ECSSCSSCC
T ss_pred             EEccCCCCC
Confidence            887765443

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} SCOP: d.58.7.0

Probab=99.84  E-value=2.7e-20  Score=104.69  Aligned_cols=80  Identities=14%  Similarity=0.174  Sum_probs=75.7

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEeeec
Q psy3928          13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTTSR   92 (115)
Q Consensus        13 ~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~~~   92 (115)
                      .+|||+|||.++++++|+++|.+||.+..+.++.++.++.++|||||+|.+.++|++|+..|++..+.|+.+++..++++
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   81 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKL   81 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCcC
Confidence            58999999999999999999999999999999999889999999999999999999999999999999999998877754

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens}

Probab=99.84  E-value=3.7e-20  Score=110.64  Aligned_cols=85  Identities=21%  Similarity=0.224  Sum_probs=78.8

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      ....++|||+|||.++++++|+++|+.||.|..+.+..++ ++.++|||||+|.+.++|++|++.|++..+.|..+.|..
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~   82 (116)
T 2fy1_A            4 ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQ   82 (116)
T ss_dssp             TCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3556899999999999999999999999999999999988 899999999999999999999999999999999999998


Q ss_pred             eeeccc
Q psy3928          89 TTSRLS   94 (115)
Q Consensus        89 ~~~~~~   94 (115)
                      ++++..
T Consensus        83 a~~~~~   88 (116)
T 2fy1_A           83 AKKPSF   88 (116)
T ss_dssp             CCCSSC
T ss_pred             CCCCCC
Confidence            876543

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.84  E-value=4.8e-21  Score=111.71  Aligned_cols=85  Identities=25%  Similarity=0.261  Sum_probs=78.8

Q ss_pred             CCCCEEEEcCCCC------CCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCC-c
Q psy3928          10 KYGRVVLKEKLPP------EAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTD-Y   82 (115)
Q Consensus        10 ~~~~~l~V~~l~~------~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~-~   82 (115)
                      ...++|||+|||.      .+++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|++.||+..+.| +
T Consensus         4 ~~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r   83 (100)
T 3ns6_A            4 GSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKH   83 (100)
T ss_dssp             CGGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSC
T ss_pred             CcCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCe
Confidence            3457999999999      99999999999999999999999999889999999999999999999999999999999 9


Q ss_pred             eeeEEEeeeccc
Q psy3928          83 QSSILTTTSRLS   94 (115)
Q Consensus        83 ~~~v~~~~~~~~   94 (115)
                      .+.|..+.++..
T Consensus        84 ~l~V~~a~~~~~   95 (100)
T 3ns6_A           84 RLFLYTMKDVER   95 (100)
T ss_dssp             BCEEEESHHHHH
T ss_pred             EEEEEECchhhh
Confidence            999988876543

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.84  E-value=5.5e-20  Score=107.47  Aligned_cols=85  Identities=22%  Similarity=0.252  Sum_probs=78.2

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      .....++|||+|||..+++++|+++|..||.|..+.+..+  ++.+++||||+|.+.++|++|+..||+..+.++.+.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   88 (103)
T 2d9p_A           11 TRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVA   88 (103)
T ss_dssp             CCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            4456789999999999999999999999999999999887  88999999999999999999999999999999999999


Q ss_pred             Eeeeccc
Q psy3928          88 TTTSRLS   94 (115)
Q Consensus        88 ~~~~~~~   94 (115)
                      .++++..
T Consensus        89 ~a~~~~~   95 (103)
T 2d9p_A           89 LAQRKEE   95 (103)
T ss_dssp             ECSSCCC
T ss_pred             Eeccccc
Confidence            8876544

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.84  E-value=3.9e-20  Score=108.15  Aligned_cols=85  Identities=22%  Similarity=0.265  Sum_probs=78.0

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      .....++|||+|||..+++++|+++|..|| |..+.++.++.++.++|||||+|.+.++|++|+ .|++..+.|+.+.|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~   88 (103)
T 2dng_A           11 PTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVD   88 (103)
T ss_dssp             CSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEE
Confidence            445678999999999999999999999996 999999999888999999999999999999999 899999999999998


Q ss_pred             Eeeeccc
Q psy3928          88 TTTSRLS   94 (115)
Q Consensus        88 ~~~~~~~   94 (115)
                      .+.++..
T Consensus        89 ~a~~~~~   95 (103)
T 2dng_A           89 IAEGRKQ   95 (103)
T ss_dssp             ECCCCCC
T ss_pred             EecCCCC
Confidence            8876544

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.84  E-value=6.4e-20  Score=109.16  Aligned_cols=86  Identities=24%  Similarity=0.290  Sum_probs=79.8

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      .....++|||+|||..+++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|++|++.|++..+.|+.+.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   90 (115)
T 2dgo_A           11 DTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTN   90 (115)
T ss_dssp             CSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            44567899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             Eeeecc
Q psy3928          88 TTTSRL   93 (115)
Q Consensus        88 ~~~~~~   93 (115)
                      .++++.
T Consensus        91 ~a~~~~   96 (115)
T 2dgo_A           91 WATRKP   96 (115)
T ss_dssp             ESSCCC
T ss_pred             EccCCC
Confidence            887643

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ISO mRNA processing, mRNA splicing, nucleus; 1.85A {Homo sapiens} SCOP: d.58.7.1 PDB: 2kyx_A 3lpy_A*

Probab=99.84  E-value=2.7e-20  Score=105.14  Aligned_cols=81  Identities=25%  Similarity=0.331  Sum_probs=75.7

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      ....++|||+|||.++++++|+++|.+||.+..+.++.++.++.++|||||+|.+.++|++|++.||+..+.|+.+++..
T Consensus         4 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   83 (85)
T 3mdf_A            4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   83 (85)
T ss_dssp             CCCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            35678999999999999999999999999999999999988999999999999999999999999999999999888776


Q ss_pred             e
Q psy3928          89 T   89 (115)
Q Consensus        89 ~   89 (115)
                      +
T Consensus        84 a   84 (85)
T 3mdf_A           84 A   84 (85)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=1.5e-20  Score=111.53  Aligned_cols=90  Identities=18%  Similarity=0.153  Sum_probs=81.1

Q ss_pred             hcccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeE--------EEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCC
Q psy3928           6 ENNKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVT--------YVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNP   77 (115)
Q Consensus         6 ~~~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~--------~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~   77 (115)
                      +......++|||+|||..+++++|+++|..||.+.        .+.+..++.++.++|||||+|.+.++|++|+..||+.
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~   88 (113)
T 2cpe_A            9 PDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGK   88 (113)
T ss_dssp             CCCCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTC
T ss_pred             cccCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCC
Confidence            34556778999999999999999999999999998        6999998889999999999999999999999999999


Q ss_pred             CCCCceeeEEEeeecccc
Q psy3928          78 CPTDYQSSILTTTSRLSF   95 (115)
Q Consensus        78 ~~~~~~~~v~~~~~~~~~   95 (115)
                      .+.|+.+.|..++++...
T Consensus        89 ~~~g~~l~V~~a~~~~~~  106 (113)
T 2cpe_A           89 DFQGSKLKVSLARKKPPM  106 (113)
T ss_dssp             EETTEECEEECSSCCCCS
T ss_pred             ccCCCEEEEEECCCCCCC
Confidence            999999998887765443

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.84  E-value=3.7e-20  Score=107.69  Aligned_cols=85  Identities=19%  Similarity=0.225  Sum_probs=78.5

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      .....++|||+|||..+++++|+++|..||.+..+.+..++ ++.++|||||+|.+.++|++|+..|++..+.|+.+.|.
T Consensus        13 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   91 (100)
T 2do4_A           13 TSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVA   91 (100)
T ss_dssp             SCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999988 89999999999999999999999999999999999988


Q ss_pred             Eeeecc
Q psy3928          88 TTTSRL   93 (115)
Q Consensus        88 ~~~~~~   93 (115)
                      .++++.
T Consensus        92 ~a~~~~   97 (100)
T 2do4_A           92 ISNSGP   97 (100)
T ss_dssp             ECCCCS
T ss_pred             ECCCCC
Confidence            877644

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=5.6e-20  Score=107.91  Aligned_cols=83  Identities=27%  Similarity=0.311  Sum_probs=77.8

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      ...++|||+|||..+++++|+++|..||.|..+.+..++.++.++|||||+|.+.++|++|+..|++..+.|+.+.|..+
T Consensus        21 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a  100 (106)
T 1p27_B           21 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC  100 (106)
T ss_dssp             TTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEee
Confidence            44578999999999999999999999999999999999888999999999999999999999999999999999999887


Q ss_pred             eec
Q psy3928          90 TSR   92 (115)
Q Consensus        90 ~~~   92 (115)
                      .++
T Consensus       101 ~~~  103 (106)
T 1p27_B          101 FVR  103 (106)
T ss_dssp             EES
T ss_pred             cCC
Confidence            764

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.84  E-value=2.1e-21  Score=111.51  Aligned_cols=80  Identities=30%  Similarity=0.408  Sum_probs=72.6

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhcC-CeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhC-CCCCCCceeeEEEee
Q psy3928          13 RVVLKEKLPPEAEHDYIESVFSKYG-KVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGL-NPCPTDYQSSILTTT   90 (115)
Q Consensus        13 ~~l~V~~l~~~~~~~~l~~~f~~~g-~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~-~~~~~~~~~~v~~~~   90 (115)
                      ++|||+|||.++++++|+++|++|| .+..+++++++.++.++|||||+|.+.++|++|++.++ +..+.|+.++|..+.
T Consensus         2 ~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a~   81 (91)
T 2lxi_A            2 NIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYSD   81 (91)
T ss_dssp             CEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEcC
Confidence            6899999999999999999999999 79999999999899999999999999999999999875 456889988887766


Q ss_pred             ec
Q psy3928          91 SR   92 (115)
Q Consensus        91 ~~   92 (115)
                      ++
T Consensus        82 ~~   83 (91)
T 2lxi_A           82 PK   83 (91)
T ss_dssp             SC
T ss_pred             CC
Confidence            54

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=1.8e-20  Score=108.15  Aligned_cols=85  Identities=19%  Similarity=0.290  Sum_probs=78.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEE-EeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYV-SLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~-~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      ...++|||+|||..+++++|+++|..||.+..+ .++.++.++.++|||||+|.+.++|++|+..||+..+.|+.+.|..
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   82 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSY   82 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            456899999999999999999999999999999 9999888999999999999999999999999999999999999888


Q ss_pred             eeeccc
Q psy3928          89 TTSRLS   94 (115)
Q Consensus        89 ~~~~~~   94 (115)
                      +.++..
T Consensus        83 a~~~~~   88 (96)
T 1x5t_A           83 AFKKDS   88 (96)
T ss_dssp             SCCCCC
T ss_pred             ecccCC
Confidence            776443

>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=4e-20  Score=111.64  Aligned_cols=86  Identities=26%  Similarity=0.285  Sum_probs=79.7

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      ....++|||+|||..+++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|++|+..||+..+.|..+.|..
T Consensus        19 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   98 (126)
T 3ex7_B           19 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW   98 (126)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEE
Confidence            44567999999999999999999999999999999999988999999999999999999999999999999999999998


Q ss_pred             eeeccc
Q psy3928          89 TTSRLS   94 (115)
Q Consensus        89 ~~~~~~   94 (115)
                      +.++..
T Consensus        99 a~~~~~  104 (126)
T 3ex7_B           99 CFVRGP  104 (126)
T ss_dssp             SEESSS
T ss_pred             ecCCCC
Confidence            876544

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=1.4e-20  Score=109.84  Aligned_cols=86  Identities=23%  Similarity=0.292  Sum_probs=79.3

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      ....++|||+|||..+++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|++|++.|++..+.|+.+.|..
T Consensus         9 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   88 (102)
T 2cqb_A            9 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   88 (102)
T ss_dssp             CCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEe
Confidence            34678999999999999999999999999999999999988899999999999999999999999999999999999988


Q ss_pred             eeeccc
Q psy3928          89 TTSRLS   94 (115)
Q Consensus        89 ~~~~~~   94 (115)
                      ++++..
T Consensus        89 a~~~~~   94 (102)
T 2cqb_A           89 AKPMRI   94 (102)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            876543

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.84  E-value=7e-21  Score=110.16  Aligned_cols=83  Identities=23%  Similarity=0.282  Sum_probs=74.6

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCC--eEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCC----CCCc
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGK--VTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPC----PTDY   82 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~--i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~----~~~~   82 (115)
                      ...-.+|||+|||+.+++++|+++|++||.  +..+++++++.++.++|||||+|.+.++|++|++.||+..    ++|+
T Consensus         6 ~~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr   85 (95)
T 2lkz_A            6 HHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGK   85 (95)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTE
T ss_pred             CCccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCE
Confidence            445679999999999999999999999995  6789999999899999999999999999999999999974    7888


Q ss_pred             eeeEEEeee
Q psy3928          83 QSSILTTTS   91 (115)
Q Consensus        83 ~~~v~~~~~   91 (115)
                      .+.|..++.
T Consensus        86 ~i~V~~Aks   94 (95)
T 2lkz_A           86 TIGVDFAKS   94 (95)
T ss_dssp             EEEEEECCC
T ss_pred             EEEEEEccC
Confidence            888877653

>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=4.3e-20  Score=108.17  Aligned_cols=86  Identities=20%  Similarity=0.250  Sum_probs=78.3

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCC-CCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeE
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKST-GKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSI   86 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~-~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v   86 (115)
                      .....++|||+|||..+++++|+++|..|| +..+.++.++.+ +.++|||||+|.+.++|++|+ .+++..+.++.+.|
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V   88 (104)
T 1wi8_A           11 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRV   88 (104)
T ss_dssp             CSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEE
T ss_pred             CCCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEE
Confidence            345678999999999999999999999999 999999998877 899999999999999999999 99999999999999


Q ss_pred             EEeeecccc
Q psy3928          87 LTTTSRLSF   95 (115)
Q Consensus        87 ~~~~~~~~~   95 (115)
                      ..+.++...
T Consensus        89 ~~a~~~~~~   97 (104)
T 1wi8_A           89 DVADQAQDK   97 (104)
T ss_dssp             EECCCCCCC
T ss_pred             EEccCCCCC
Confidence            888775443

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.83  E-value=8.7e-20  Score=105.98  Aligned_cols=82  Identities=18%  Similarity=0.197  Sum_probs=76.3

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEE--------EEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCC
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTY--------VSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCP   79 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~--------~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~   79 (115)
                      .....++|||+|||.++++++|+++|++||.+..        +.++.++.++.++|||||+|.+.++|++|++.|++..+
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~   88 (99)
T 2la6_A            9 SHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEF   88 (99)
T ss_dssp             SCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEe
Confidence            3456789999999999999999999999999999        99999988999999999999999999999999999999


Q ss_pred             CCceeeEEEe
Q psy3928          80 TDYQSSILTT   89 (115)
Q Consensus        80 ~~~~~~v~~~   89 (115)
                      .|+.++|..+
T Consensus        89 ~g~~l~V~~A   98 (99)
T 2la6_A           89 SGNPIKVSFA   98 (99)
T ss_dssp             SSSBCEEEEC
T ss_pred             CCcEEEEEec
Confidence            9999888765

>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=99.83  E-value=1.6e-19  Score=105.76  Aligned_cols=84  Identities=18%  Similarity=0.215  Sum_probs=77.1

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCC---ceee
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTD---YQSS   85 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~---~~~~   85 (115)
                      ....++|||+|||..+++++|+++|..||.|..+.+..++ ++.++|||||+|.+.++|++|+..|++..+.+   +.+.
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~   90 (105)
T 2dnh_A           12 GGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLV   90 (105)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEE
Confidence            4467899999999999999999999999999999999988 89999999999999999999999999999998   8888


Q ss_pred             EEEeeecc
Q psy3928          86 ILTTTSRL   93 (115)
Q Consensus        86 v~~~~~~~   93 (115)
                      |..+.++.
T Consensus        91 V~~a~~~~   98 (105)
T 2dnh_A           91 VKFADTDK   98 (105)
T ss_dssp             EEESCSSC
T ss_pred             EEECccCc
Confidence            88777543

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B

Probab=99.83  E-value=5e-20  Score=106.44  Aligned_cols=83  Identities=22%  Similarity=0.193  Sum_probs=77.7

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEeee
Q psy3928          12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTTS   91 (115)
Q Consensus        12 ~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~~   91 (115)
                      .++|||+|||..+++++|+++|++||.+..+.+..++.++.++|||||+|.+.++|++|++.+++..++|+.+.|..+.+
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   81 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSN   81 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcCC
Confidence            57899999999999999999999999999999999988899999999999999999999999999999999999988876


Q ss_pred             ccc
Q psy3928          92 RLS   94 (115)
Q Consensus        92 ~~~   94 (115)
                      +..
T Consensus        82 ~~~   84 (96)
T 2x1f_A           82 SDI   84 (96)
T ss_dssp             SSG
T ss_pred             CCC
Confidence            543

>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=7.4e-20  Score=109.07  Aligned_cols=85  Identities=14%  Similarity=0.201  Sum_probs=78.2

Q ss_pred             cccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeE
Q psy3928           7 NNKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSI   86 (115)
Q Consensus         7 ~~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v   86 (115)
                      ..+...++|||+|||..+++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|++|+..+++ .+.++.+.|
T Consensus        12 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V   90 (116)
T 2cqd_A           12 QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANV   90 (116)
T ss_dssp             CCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEE
Confidence            3456678999999999999999999999999999999999988899999999999999999999999998 899999999


Q ss_pred             EEeeec
Q psy3928          87 LTTTSR   92 (115)
Q Consensus        87 ~~~~~~   92 (115)
                      ..+.+.
T Consensus        91 ~~a~~~   96 (116)
T 2cqd_A           91 NLAYLG   96 (116)
T ss_dssp             EESTTT
T ss_pred             EEcccC
Confidence            887653

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.83  E-value=7e-20  Score=106.26  Aligned_cols=83  Identities=20%  Similarity=0.255  Sum_probs=76.0

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeE-EEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCce----
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVT-YVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQ----   83 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~-~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~----   83 (115)
                      ....++|||+|||.++++++|+++|.+||.+. .+.++.++.++.++|||||+|.+.++|++|++.||+..+.+..    
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~   85 (99)
T 2div_A            6 SGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKR   85 (99)
T ss_dssp             CSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEE
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCccee
Confidence            34678999999999999999999999999999 9999999889999999999999999999999999999999988    


Q ss_pred             eeEEEeee
Q psy3928          84 SSILTTTS   91 (115)
Q Consensus        84 ~~v~~~~~   91 (115)
                      +++..+++
T Consensus        86 l~v~~a~~   93 (99)
T 2div_A           86 FKLNYATY   93 (99)
T ss_dssp             CCEEETTC
T ss_pred             EEEeecCC
Confidence            66666553

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D*

Probab=99.82  E-value=9.2e-20  Score=107.68  Aligned_cols=84  Identities=24%  Similarity=0.285  Sum_probs=78.1

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      ....++|||+|||..+++++|+++|..||.+..+.++.++.++.++|||||+|.+.++|++|+..|++..+.|..+.|..
T Consensus        23 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  102 (110)
T 1oo0_B           23 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW  102 (110)
T ss_dssp             BTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            34567899999999999999999999999999999999888999999999999999999999999999999999999888


Q ss_pred             eeec
Q psy3928          89 TTSR   92 (115)
Q Consensus        89 ~~~~   92 (115)
                      +.++
T Consensus       103 a~~~  106 (110)
T 1oo0_B          103 CFVK  106 (110)
T ss_dssp             SEES
T ss_pred             cccC
Confidence            7764

>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=105.75  Aligned_cols=90  Identities=22%  Similarity=0.247  Sum_probs=78.4

Q ss_pred             cccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeE
Q psy3928           7 NNKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSI   86 (115)
Q Consensus         7 ~~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v   86 (115)
                      ......++|||+|||..+++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|++|+..  +..++|+.+.|
T Consensus        10 ~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g~~l~v   87 (103)
T 2cqg_A           10 RAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWCDC   87 (103)
T ss_dssp             CCCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTEEEEE
T ss_pred             CccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHHc--CCeeCCeEEEE
Confidence            3455678999999999999999999999999999999999988899999999999999999999994  56788888888


Q ss_pred             EEeeeccccCCC
Q psy3928          87 LTTTSRLSFGIT   98 (115)
Q Consensus        87 ~~~~~~~~~~~~   98 (115)
                      ..+.++.....+
T Consensus        88 ~~a~~~~~~~~~   99 (103)
T 2cqg_A           88 KLPNSKQSQDSG   99 (103)
T ss_dssp             ECCCTTCCCCCS
T ss_pred             EecCCCCcCCCC
Confidence            888776554433

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.82  E-value=7.3e-20  Score=114.56  Aligned_cols=81  Identities=17%  Similarity=0.175  Sum_probs=75.9

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcC--CeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYG--KVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g--~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      ..++|||+|||.++++++|+++|..||  .+..+.++.++.+|.++|||||+|.+.++|++|+..||+..+.|+.+.|..
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~  133 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRP  133 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEE
Confidence            457999999999999999999999999  999999999988999999999999999999999999999999999999988


Q ss_pred             eee
Q psy3928          89 TTS   91 (115)
Q Consensus        89 ~~~   91 (115)
                      +.+
T Consensus       134 a~~  136 (156)
T 3n9u_C          134 ATR  136 (156)
T ss_dssp             CCH
T ss_pred             cCC
Confidence            765

>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=99.82  E-value=2e-19  Score=105.05  Aligned_cols=87  Identities=20%  Similarity=0.265  Sum_probs=77.6

Q ss_pred             cccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeE
Q psy3928           7 NNKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSI   86 (115)
Q Consensus         7 ~~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v   86 (115)
                      ......++|||+|||..+++++|+++|..||.|..+.++.++  +.++|||||+|.+.++|++|+..|++..+.|+.+.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~--~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   87 (103)
T 2cq3_A           10 ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEV   87 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT--TTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecC--CCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            345667899999999999999999999999999999998875  337899999999999999999999999999999999


Q ss_pred             EEeeecccc
Q psy3928          87 LTTTSRLSF   95 (115)
Q Consensus        87 ~~~~~~~~~   95 (115)
                      ..+.++...
T Consensus        88 ~~a~~~~~~   96 (103)
T 2cq3_A           88 NNATARVMT   96 (103)
T ss_dssp             EECCSSCCC
T ss_pred             EEcccCCCC
Confidence            888775443

>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=99.82  E-value=1.1e-19  Score=108.43  Aligned_cols=79  Identities=22%  Similarity=0.273  Sum_probs=72.9

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEeee
Q psy3928          12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTTS   91 (115)
Q Consensus        12 ~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~~   91 (115)
                      ..+|||+|||.++++++|+++|..||.|..++|+.++  +.++|||||+|.+.++|++|++.|++..+.|+.+.|..+.+
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~--~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~   82 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   82 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSC
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            4689999999999999999999999999999999885  45899999999999999999999999999999999987765


Q ss_pred             c
Q psy3928          92 R   92 (115)
Q Consensus        92 ~   92 (115)
                      +
T Consensus        83 ~   83 (115)
T 4f25_A           83 R   83 (115)
T ss_dssp             C
T ss_pred             c
Confidence            4

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.82  E-value=6.3e-20  Score=105.63  Aligned_cols=82  Identities=22%  Similarity=0.214  Sum_probs=75.8

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      ....++|||+|||..+++++|+++|..||.+..+.++.++.++.++|||||+|.+.++|++|+..||+..+.|+.+.|..
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   91 (95)
T 2cqc_A           12 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSG   91 (95)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            34567999999999999999999999999999999999988899999999999999999999999999999999888776


Q ss_pred             ee
Q psy3928          89 TT   90 (115)
Q Consensus        89 ~~   90 (115)
                      ++
T Consensus        92 a~   93 (95)
T 2cqc_A           92 PS   93 (95)
T ss_dssp             CS
T ss_pred             cC
Confidence            54

>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=99.82  E-value=1.8e-19  Score=112.44  Aligned_cols=83  Identities=19%  Similarity=0.155  Sum_probs=78.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      ...++|||+|||..+++++|+++|..||.|..+.|+.++.++.+++||||+|.+.++|++|+..|++..+.+..+.|..+
T Consensus        37 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  116 (156)
T 1h2v_Z           37 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD  116 (156)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            45689999999999999999999999999999999999888999999999999999999999999999999999999988


Q ss_pred             eec
Q psy3928          90 TSR   92 (115)
Q Consensus        90 ~~~   92 (115)
                      ++.
T Consensus       117 ~~~  119 (156)
T 1h2v_Z          117 AGF  119 (156)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            763

>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=99.82  E-value=3e-20  Score=108.66  Aligned_cols=84  Identities=25%  Similarity=0.310  Sum_probs=78.1

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      +...++|||+|||..+++++|+++|..||.+..+.+..++.++.++|||||+|.+.++|++|++.+++..+.|+.+.|..
T Consensus         5 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   84 (104)
T 1p1t_A            5 DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDN   84 (104)
T ss_dssp             HHHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEE
T ss_pred             CCCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEe
Confidence            34458899999999999999999999999999999999988999999999999999999999999999999999999988


Q ss_pred             eeec
Q psy3928          89 TTSR   92 (115)
Q Consensus        89 ~~~~   92 (115)
                      +.++
T Consensus        85 a~~~   88 (104)
T 1p1t_A           85 AASE   88 (104)
T ss_dssp             TTCT
T ss_pred             CCCc
Confidence            7764

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.82  E-value=4.4e-20  Score=108.22  Aligned_cols=86  Identities=21%  Similarity=0.193  Sum_probs=78.3

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      .....++|||+|||..+++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|++|+.. ++..+.|+.+.|.
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V~   90 (105)
T 2dh8_A           12 GADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPK   90 (105)
T ss_dssp             CSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEEE
Confidence            456778999999999999999999999999999999999988999999999999999999999999 9999999988887


Q ss_pred             Eeeeccc
Q psy3928          88 TTTSRLS   94 (115)
Q Consensus        88 ~~~~~~~   94 (115)
                      .+.++..
T Consensus        91 ~a~~~~~   97 (105)
T 2dh8_A           91 PCTPRGM   97 (105)
T ss_dssp             CSCCSSC
T ss_pred             EccCCCC
Confidence            7765443

>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=99.82  E-value=1e-19  Score=103.32  Aligned_cols=81  Identities=26%  Similarity=0.342  Sum_probs=75.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCC-eeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGK-LKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~-~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      ..++|||+|||.++++++|+++|.+||.+..+.+..++.++. ++|+|||+|.+.++|++|+..||+..+.|+.+.+..+
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   82 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAV   82 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEEC
Confidence            467999999999999999999999999999999999876665 8999999999999999999999999999999998877


Q ss_pred             ee
Q psy3928          90 TS   91 (115)
Q Consensus        90 ~~   91 (115)
                      .+
T Consensus        83 ~~   84 (88)
T 4a8x_A           83 LA   84 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            65

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.82  E-value=6.8e-20  Score=105.34  Aligned_cols=82  Identities=28%  Similarity=0.248  Sum_probs=76.0

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      .....++|||+|||..+++++|+++|.+||.+..+.+..++.++.++|||||+|.+.++|++|++.||+..+.|+.+.|.
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   91 (94)
T 2e5h_A           12 LAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKAS   91 (94)
T ss_dssp             CCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            34567899999999999999999999999999999999998889999999999999999999999999999999988887


Q ss_pred             Ee
Q psy3928          88 TT   89 (115)
Q Consensus        88 ~~   89 (115)
                      .+
T Consensus        92 ~a   93 (94)
T 2e5h_A           92 IA   93 (94)
T ss_dssp             EC
T ss_pred             ec
Confidence            64

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.82  E-value=4.5e-20  Score=112.31  Aligned_cols=85  Identities=21%  Similarity=0.258  Sum_probs=78.2

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEE--EEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCC----CCCC
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTY--VSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNP----CPTD   81 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~--~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~----~~~~   81 (115)
                      .....++|||+|||.++++++|+++|.+||.+..  ++|+.++.++.++|||||+|.+. +|.+|+..||+.    .++|
T Consensus        19 ~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~g   97 (131)
T 2m2b_A           19 SENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDG   97 (131)
T ss_dssp             CSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGG
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCC
Confidence            3456789999999999999999999999999976  99999998999999999999999 999999999999    9999


Q ss_pred             ceeeEEEeeecc
Q psy3928          82 YQSSILTTTSRL   93 (115)
Q Consensus        82 ~~~~v~~~~~~~   93 (115)
                      +.+.|..++++.
T Consensus        98 r~l~V~~a~~~~  109 (131)
T 2m2b_A           98 KTINVEFAKGSK  109 (131)
T ss_dssp             CCCCCEECCCSC
T ss_pred             EEEEEEECCCCC
Confidence            999998887653

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A

Probab=99.82  E-value=2.4e-19  Score=105.32  Aligned_cols=82  Identities=21%  Similarity=0.213  Sum_probs=76.1

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      .....++|||+|||..+++++|+++|.+||.|..+.++.++ ++.++|||||+|.+.++|++|++.|++..+.|+.+.|.
T Consensus        25 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~  103 (107)
T 3ulh_A           25 GVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQ  103 (107)
T ss_dssp             CCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            34557899999999999999999999999999999999988 99999999999999999999999999999999998887


Q ss_pred             Eee
Q psy3928          88 TTT   90 (115)
Q Consensus        88 ~~~   90 (115)
                      .++
T Consensus       104 ~a~  106 (107)
T 3ulh_A          104 LVT  106 (107)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            764

>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=1.8e-19  Score=102.27  Aligned_cols=81  Identities=17%  Similarity=0.261  Sum_probs=72.5

Q ss_pred             cccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeE
Q psy3928           7 NNKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSI   86 (115)
Q Consensus         7 ~~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v   86 (115)
                      ......++|||+|||..+++++|+++|.+||.+..+.++.++.++.++|||||+|.+.++|++|++. ++..++|+.+.|
T Consensus         6 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~-~~~~~~g~~i~v   84 (87)
T 3s7r_A            6 KNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQ-KEHRLDGRVIDP   84 (87)
T ss_dssp             -CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHHS-SCEEETTEEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHHh-CCCEECCEEEEE
Confidence            3456778999999999999999999999999999999999988899999999999999999999975 667788888776


Q ss_pred             EE
Q psy3928          87 LT   88 (115)
Q Consensus        87 ~~   88 (115)
                      ..
T Consensus        85 ~~   86 (87)
T 3s7r_A           85 KK   86 (87)
T ss_dssp             EE
T ss_pred             Ee
Confidence            54

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.81  E-value=8.4e-20  Score=109.07  Aligned_cols=81  Identities=21%  Similarity=0.175  Sum_probs=75.5

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      ....++|||+|||.++++++|+++|..||.+..+.+..++.++.++|||||+|.+.++|++|++.||+..+.|+.++|..
T Consensus        37 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~  116 (118)
T 2khc_A           37 GPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQL  116 (118)
T ss_dssp             CCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            45568999999999999999999999999999999999888899999999999999999999999999999999888775


Q ss_pred             e
Q psy3928          89 T   89 (115)
Q Consensus        89 ~   89 (115)
                      +
T Consensus       117 a  117 (118)
T 2khc_A          117 K  117 (118)
T ss_dssp             C
T ss_pred             c
Confidence            4

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A

Probab=99.81  E-value=1.2e-19  Score=103.35  Aligned_cols=80  Identities=25%  Similarity=0.298  Sum_probs=74.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEee
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTT   90 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~   90 (115)
                      ..++|||+|||.++++++|+++|.+||.+..+.+..++.++.++|||||+|.+.++|++|+ .+++..+.|+.+.|..++
T Consensus         5 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~   83 (89)
T 3ucg_A            5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKR   83 (89)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETT
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEcc
Confidence            3478999999999999999999999999999999998889999999999999999999999 999999999999888766


Q ss_pred             e
Q psy3928          91 S   91 (115)
Q Consensus        91 ~   91 (115)
                      +
T Consensus        84 ~   84 (89)
T 3ucg_A           84 T   84 (89)
T ss_dssp             T
T ss_pred             C
Confidence            4

>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=99.81  E-value=1.6e-19  Score=103.99  Aligned_cols=82  Identities=22%  Similarity=0.263  Sum_probs=75.2

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      .....++|||+|||..+++++|+++|.+||.|..+.+..++ ++.++|||||+|.+.++|++|++.|++..+.|+.+.|.
T Consensus        12 ~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   90 (95)
T 2ywk_A           12 QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVS   90 (95)
T ss_dssp             CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEE
Confidence            44566899999999999999999999999999999999988 48999999999999999999999999999999988877


Q ss_pred             Eee
Q psy3928          88 TTT   90 (115)
Q Consensus        88 ~~~   90 (115)
                      .++
T Consensus        91 ~a~   93 (95)
T 2ywk_A           91 GPS   93 (95)
T ss_dssp             CCC
T ss_pred             EcC
Confidence            654

>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=99.81  E-value=1.1e-19  Score=110.51  Aligned_cols=84  Identities=21%  Similarity=0.211  Sum_probs=77.4

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      ....++|||+|||..+++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|++|+..|++..++|+.+.|..
T Consensus        43 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~~  122 (129)
T 2kxn_B           43 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDF  122 (129)
T ss_dssp             CCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEESC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            34568999999999999999999999999999999999988899999999999999999999999999999999988877


Q ss_pred             eeec
Q psy3928          89 TTSR   92 (115)
Q Consensus        89 ~~~~   92 (115)
                      ++++
T Consensus       123 a~~~  126 (129)
T 2kxn_B          123 SITK  126 (129)
T ss_dssp             CSSS
T ss_pred             ecCC
Confidence            6653

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=1.5e-19  Score=106.02  Aligned_cols=80  Identities=24%  Similarity=0.258  Sum_probs=73.5

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      +...++|||+|||.++++++|+++|++||.|..+.++.++. +.++|||||+|.+.++|++|+. +++..++|+.+.|..
T Consensus         8 ~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~   85 (103)
T 1s79_A            8 DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILF   85 (103)
T ss_dssp             CSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEE
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEE
Confidence            34568999999999999999999999999999999999885 9999999999999999999999 899999999998876


Q ss_pred             ee
Q psy3928          89 TT   90 (115)
Q Consensus        89 ~~   90 (115)
                      ..
T Consensus        86 ~~   87 (103)
T 1s79_A           86 KD   87 (103)
T ss_dssp             HH
T ss_pred             ch
Confidence            54

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.81  E-value=7e-19  Score=104.42  Aligned_cols=83  Identities=22%  Similarity=0.236  Sum_probs=76.9

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      .....++|||+|||..+++++|+++|..||.|..+.+..++ ++.++|||||+|.+.++|++|+..|++..+.++.+.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   89 (114)
T 2do0_A           11 AGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVK   89 (114)
T ss_dssp             CCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEE
Confidence            34557899999999999999999999999999999999987 69999999999999999999999999999999999998


Q ss_pred             Eeee
Q psy3928          88 TTTS   91 (115)
Q Consensus        88 ~~~~   91 (115)
                      .++.
T Consensus        90 ~a~~   93 (114)
T 2do0_A           90 MDER   93 (114)
T ss_dssp             ECSC
T ss_pred             Eccc
Confidence            7764

>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=99.81  E-value=3.1e-19  Score=104.28  Aligned_cols=85  Identities=16%  Similarity=0.145  Sum_probs=75.9

Q ss_pred             cccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeE
Q psy3928           7 NNKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSI   86 (115)
Q Consensus         7 ~~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v   86 (115)
                      ......++|||+|||..+++++|+++|.+||.|..+.+..++  +.++|||||+|.+.++|++|+..|++..+.|+.+.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~--~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   87 (103)
T 2cqi_A           10 EDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEH--TSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKV   87 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCC--CSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecC--CCCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEE
Confidence            345667899999999999999999999999999999998875  336899999999999999999999999999999998


Q ss_pred             EEeeecc
Q psy3928          87 LTTTSRL   93 (115)
Q Consensus        87 ~~~~~~~   93 (115)
                      ..++++.
T Consensus        88 ~~a~~~~   94 (103)
T 2cqi_A           88 NWATTPS   94 (103)
T ss_dssp             EECCCTT
T ss_pred             EECCCCc
Confidence            8877643

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=99.81  E-value=2.8e-19  Score=111.66  Aligned_cols=84  Identities=24%  Similarity=0.317  Sum_probs=78.5

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      ...++|||+|||..+++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|+.|+..||+..+.|+.+.|..+
T Consensus        68 ~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  147 (158)
T 2kn4_A           68 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA  147 (158)
T ss_dssp             CBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            34689999999999999999999999999999999999889999999999999999999999999999999999999988


Q ss_pred             eecc
Q psy3928          90 TSRL   93 (115)
Q Consensus        90 ~~~~   93 (115)
                      ++..
T Consensus       148 ~~~~  151 (158)
T 2kn4_A          148 RYGR  151 (158)
T ss_dssp             CCSS
T ss_pred             CCCC
Confidence            7643

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.81  E-value=6.5e-19  Score=100.82  Aligned_cols=82  Identities=18%  Similarity=0.244  Sum_probs=75.2

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      ....++|||+|||.++++++|+++|.+||.+..+.+..+  ++.++|||||+|.+.++|++|+..|++..+.|+.+.|..
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~--~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~   82 (92)
T 2dgv_A            5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRI   82 (92)
T ss_dssp             SSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            456789999999999999999999999999999988873  789999999999999999999999999999999988887


Q ss_pred             eeec
Q psy3928          89 TTSR   92 (115)
Q Consensus        89 ~~~~   92 (115)
                      +++.
T Consensus        83 a~~~   86 (92)
T 2dgv_A           83 DRNA   86 (92)
T ss_dssp             CSCC
T ss_pred             cCCC
Confidence            7653

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.70  E-value=1.4e-21  Score=116.60  Aligned_cols=88  Identities=19%  Similarity=0.215  Sum_probs=79.7

Q ss_pred             cccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEE--------EEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCC
Q psy3928           7 NNKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTY--------VSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPC   78 (115)
Q Consensus         7 ~~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~--------~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~   78 (115)
                      +...+.++|||+|||..+++++|+++|..||.+..        +.++.++.++.++|||||+|.+.++|++|+..||+..
T Consensus         2 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~   81 (116)
T 2lcw_A            2 QDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKE   81 (116)
Confidence            34556789999999999999999999999999988        8888888789999999999999999999999999999


Q ss_pred             CCCceeeEEEeeeccc
Q psy3928          79 PTDYQSSILTTTSRLS   94 (115)
Q Consensus        79 ~~~~~~~v~~~~~~~~   94 (115)
                      +.|+.+.|..++++..
T Consensus        82 ~~g~~l~V~~a~~~~~   97 (116)
T 2lcw_A           82 FSGNPIKVSFATRRAD   97 (116)
Confidence            9999999888876543

>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=6.1e-19  Score=104.73  Aligned_cols=75  Identities=12%  Similarity=0.216  Sum_probs=69.2

Q ss_pred             cccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCc
Q psy3928           7 NNKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDY   82 (115)
Q Consensus         7 ~~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~   82 (115)
                      ......++|||+|||.++++++|+++|..||.|..+.++.++ ++.++|||||+|.+.++|++|+..||+..+.+.
T Consensus        20 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~   94 (114)
T 1x5o_A           20 QQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTP   94 (114)
T ss_dssp             CCCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCC
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCC
Confidence            344567899999999999999999999999999999999998 899999999999999999999999999998543

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=1.3e-19  Score=108.00  Aligned_cols=84  Identities=18%  Similarity=0.217  Sum_probs=77.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEee
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTT   90 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~   90 (115)
                      ..++|||+|||..+++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|++|+.. ++..+.|+.+.|..+.
T Consensus        26 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a~  104 (116)
T 1x4b_A           26 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAV  104 (116)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECCS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEECC
Confidence            348999999999999999999999999999999999988899999999999999999999998 9999999999988887


Q ss_pred             ecccc
Q psy3928          91 SRLSF   95 (115)
Q Consensus        91 ~~~~~   95 (115)
                      ++...
T Consensus       105 ~~~~~  109 (116)
T 1x4b_A          105 AREES  109 (116)
T ss_dssp             SCCCC
T ss_pred             CCccC
Confidence            65543

>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=99.80  E-value=1e-19  Score=105.37  Aligned_cols=83  Identities=19%  Similarity=0.184  Sum_probs=75.4

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      ....++|||+|||..+++++|+++|..||.+..+.++.++.++.++|||||+|.+.++|++|++.|++..+.|+.++|..
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~   91 (98)
T 2cqp_A           12 KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVL   91 (98)
T ss_dssp             CCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEE
Confidence            34567999999999999999999999999998777778777999999999999999999999999999999999988887


Q ss_pred             eee
Q psy3928          89 TTS   91 (115)
Q Consensus        89 ~~~   91 (115)
                      +..
T Consensus        92 a~~   94 (98)
T 2cqp_A           92 GSG   94 (98)
T ss_dssp             SSC
T ss_pred             cCC
Confidence            654

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.80  E-value=1.5e-19  Score=106.17  Aligned_cols=85  Identities=22%  Similarity=0.327  Sum_probs=74.8

Q ss_pred             cccCCCCEEEEcCCCCCC------CHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCC
Q psy3928           7 NNKKYGRVVLKEKLPPEA------EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPT   80 (115)
Q Consensus         7 ~~~~~~~~l~V~~l~~~~------~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~   80 (115)
                      ......++|||+|||..+      ++++|+++|++||.|..+.++  +.+|.++|||||+|.+.++|++|+..|||..+.
T Consensus        10 ~~~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~--~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~   87 (105)
T 2nlw_A           10 EADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLD   87 (105)
T ss_dssp             SCCSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC--CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECS
T ss_pred             CCCCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee--CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccC
Confidence            345557899999999999      679999999999999999988  348899999999999999999999999999999


Q ss_pred             Cc-eeeEEEeeecc
Q psy3928          81 DY-QSSILTTTSRL   93 (115)
Q Consensus        81 ~~-~~~v~~~~~~~   93 (115)
                      |+ .+.|..+....
T Consensus        88 g~~~l~V~~a~~~~  101 (105)
T 2nlw_A           88 KQHTFRVNLFTDFD  101 (105)
T ss_dssp             TTCEEEEECSCCCC
T ss_pred             CCceEEEEEcchHh
Confidence            98 88887766443

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.80  E-value=1.7e-19  Score=99.74  Aligned_cols=74  Identities=20%  Similarity=0.235  Sum_probs=69.4

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928          14 VVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus        14 ~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      +|||+|||.++++++|+++|++||.+..+.++.++.++.++|||||+|.+.++|++|++ +++..++|+.+.+..
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~   74 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKK   74 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSSCCCEEEC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECCEEEEEEe
Confidence            48999999999999999999999999999999988889999999999999999999998 999999999887753

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=4.9e-20  Score=104.19  Aligned_cols=76  Identities=21%  Similarity=0.241  Sum_probs=70.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceee
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSS   85 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~   85 (115)
                      ...++|||+|||.++++++|+++|.+||.+..+.++.++.++.++|||||+|.+.++|++|++.||+..+.++.++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~   78 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK   78 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEe
Confidence            4678999999999999999999999999999999999988899999999999999999999999999988887654

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=1e-18  Score=102.39  Aligned_cols=82  Identities=26%  Similarity=0.259  Sum_probs=74.2

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEE-EEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTY-VSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~-~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      ....++|||+|||..+++++|+++|.+||.+.. +.|+.+ .+++++|||||+|.+.++|++|+.. ++..+.++.+.|.
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~   89 (104)
T 1wg5_A           12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIF   89 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEE
Confidence            355789999999999999999999999999987 888887 5899999999999999999999998 9999999999988


Q ss_pred             Eeeec
Q psy3928          88 TTTSR   92 (115)
Q Consensus        88 ~~~~~   92 (115)
                      .+..+
T Consensus        90 ~~~~~   94 (104)
T 1wg5_A           90 KSSRA   94 (104)
T ss_dssp             EECTT
T ss_pred             ECCHH
Confidence            77653

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A

Probab=99.80  E-value=1.1e-19  Score=104.72  Aligned_cols=81  Identities=20%  Similarity=0.164  Sum_probs=73.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      ...++|||+|||.++++++|+++|.+||.+..+.++.++.++.++|||||+|.+.++|++|++.||+..+.|+.++|...
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a   92 (95)
T 2ek1_A           13 PGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGP   92 (95)
T ss_dssp             --CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEec
Confidence            44689999999999999999999999999988888888888999999999999999999999999999999999888765


Q ss_pred             e
Q psy3928          90 T   90 (115)
Q Consensus        90 ~   90 (115)
                      +
T Consensus        93 ~   93 (95)
T 2ek1_A           93 S   93 (95)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.80  E-value=1.6e-19  Score=107.03  Aligned_cols=85  Identities=18%  Similarity=0.164  Sum_probs=75.8

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHH---HHhhhcCCeEEEEeceeCCCC---CeeeEEEEEecCHHHHHHHHHhhCCCCCCCc
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIE---SVFSKYGKVTYVSLPKFKSTG---KLKGFAFVEFSTKEEATKALELGLNPCPTDY   82 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~---~~f~~~g~i~~~~i~~~~~~~---~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~   82 (115)
                      ....++|||+|||..+++++|+   ++|.+||.|..+.+..++.++   .++|||||+|.+.++|++|++.||+..++|+
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr   91 (111)
T 2cpi_A           12 VVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGR   91 (111)
T ss_dssp             CCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             ccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCE
Confidence            3456799999999999999999   999999999999998876543   5669999999999999999999999999999


Q ss_pred             eeeEEEeeecc
Q psy3928          83 QSSILTTTSRL   93 (115)
Q Consensus        83 ~~~v~~~~~~~   93 (115)
                      .++|..++++.
T Consensus        92 ~l~V~~a~~k~  102 (111)
T 2cpi_A           92 TLKASLGTTKY  102 (111)
T ss_dssp             EEEEESCCCCS
T ss_pred             EEEEEeccccc
Confidence            99988877654

>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=99.80  E-value=7.4e-20  Score=104.47  Aligned_cols=80  Identities=25%  Similarity=0.292  Sum_probs=73.1

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEeeec
Q psy3928          13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTTSR   92 (115)
Q Consensus        13 ~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~~~   92 (115)
                      ++|||+|||.++++++|+++|++||.+..+.+..++.++.++|||||+|.+.+ |++|+..+|+..+.|+.+.+..+.+.
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~~   80 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANPK   80 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC---
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCCC
Confidence            57999999999999999999999999999999999888999999999999999 99999999999999999999887764


Q ss_pred             c
Q psy3928          93 L   93 (115)
Q Consensus        93 ~   93 (115)
                      .
T Consensus        81 ~   81 (90)
T 2ki2_A           81 K   81 (90)
T ss_dssp             -
T ss_pred             C
Confidence            3

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A

Probab=99.80  E-value=6.6e-19  Score=110.93  Aligned_cols=85  Identities=24%  Similarity=0.266  Sum_probs=77.7

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      ...++|||+|||..+++.+|+.+|.+||.|..+.|+.++.++.++|||||+|.+.++|+.|+..||+..+.|..+.|..+
T Consensus        70 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  149 (165)
T 1rk8_A           70 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC  149 (165)
T ss_dssp             C-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            34578999999999999999999999999999999999889999999999999999999999999999999999999888


Q ss_pred             eeccc
Q psy3928          90 TSRLS   94 (115)
Q Consensus        90 ~~~~~   94 (115)
                      .++..
T Consensus       150 ~~~~~  154 (165)
T 1rk8_A          150 FVKGP  154 (165)
T ss_dssp             EECC-
T ss_pred             cCCCC
Confidence            76443

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.80  E-value=6.5e-19  Score=100.74  Aligned_cols=82  Identities=17%  Similarity=0.209  Sum_probs=75.3

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      ....++|||+|||.++++++|+++|..| .+..+.++.+ .++.++|+|||+|.+.++|++|+. +++..+.|+.+.|..
T Consensus         7 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~   83 (91)
T 2dgw_A            7 GTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFR   83 (91)
T ss_dssp             CCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEE
T ss_pred             CCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEE
Confidence            4567899999999999999999999999 8999999988 589999999999999999999999 999999999999888


Q ss_pred             eeecc
Q psy3928          89 TTSRL   93 (115)
Q Consensus        89 ~~~~~   93 (115)
                      ++++.
T Consensus        84 a~~~~   88 (91)
T 2dgw_A           84 EKSGP   88 (91)
T ss_dssp             ESSCC
T ss_pred             CCcCC
Confidence            77653

>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=99.80  E-value=2.2e-19  Score=104.59  Aligned_cols=83  Identities=19%  Similarity=0.271  Sum_probs=73.4

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeC-CCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeE
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFK-STGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSI   86 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~-~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v   86 (115)
                      .....++|||+|||.++++++|+++|..|| +..+.+..++ .+++++|||||+|.+.++|++|+ .+++..+.|+.+.|
T Consensus        15 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V   92 (100)
T 2j76_E           15 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRV   92 (100)
T ss_dssp             -----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEEE
Confidence            345678999999999999999999999999 9999999987 58999999999999999999999 89999999999988


Q ss_pred             EEeeec
Q psy3928          87 LTTTSR   92 (115)
Q Consensus        87 ~~~~~~   92 (115)
                      ..++++
T Consensus        93 ~~a~~~   98 (100)
T 2j76_E           93 DVADQA   98 (100)
T ss_dssp             EECCCS
T ss_pred             EeccCC
Confidence            877654

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.80  E-value=3.1e-19  Score=100.16  Aligned_cols=72  Identities=25%  Similarity=0.438  Sum_probs=66.1

Q ss_pred             CEEEEcCCCCCC------CHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCc-eee
Q psy3928          13 RVVLKEKLPPEA------EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDY-QSS   85 (115)
Q Consensus        13 ~~l~V~~l~~~~------~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~-~~~   85 (115)
                      ++|||+|||..+      ++++|+++|++||.+..+.++  +.+|.++|||||+|.+.++|++|+..||+..+.|+ .++
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~--~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~   79 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFR   79 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC--CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCC
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec--CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEE
Confidence            689999999999      679999999999999999887  34889999999999999999999999999999998 765


Q ss_pred             E
Q psy3928          86 I   86 (115)
Q Consensus        86 v   86 (115)
                      |
T Consensus        80 V   80 (81)
T 2krb_A           80 V   80 (81)
T ss_dssp             C
T ss_pred             e
Confidence            4

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.80  E-value=3.3e-19  Score=105.36  Aligned_cols=85  Identities=16%  Similarity=0.171  Sum_probs=74.0

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      .....++|||+|||..+++++|+++|..||.+..+.++.++.++.++|||||+|.+.++|++|+..++ ..++|+.+.+.
T Consensus        21 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~~-~~l~g~~l~V~   99 (109)
T 2rs2_A           21 MGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPK   99 (109)
T ss_dssp             -----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSSC-EEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHCC-CcCCCEEEEEE
Confidence            44567899999999999999999999999999999999998889999999999999999999999875 88899998888


Q ss_pred             Eeeecc
Q psy3928          88 TTTSRL   93 (115)
Q Consensus        88 ~~~~~~   93 (115)
                      .+.++.
T Consensus       100 ~a~~~~  105 (109)
T 2rs2_A          100 VAFPRR  105 (109)
T ss_dssp             ECCCCC
T ss_pred             EccCCC
Confidence            777543

>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=99.80  E-value=1.1e-18  Score=102.06  Aligned_cols=81  Identities=23%  Similarity=0.247  Sum_probs=72.4

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      ....++|||+|||.++++++|+++|.+||. ..+.|+.++ +++++|||||+|.+.++|++|+. +++..+.++.+.|..
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~-~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~   88 (102)
T 1wez_A           12 STTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFL   88 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCc-eEEEEEECC-CCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEE
Confidence            345689999999999999999999999994 489999988 89999999999999999999995 799999999988877


Q ss_pred             eeec
Q psy3928          89 TTSR   92 (115)
Q Consensus        89 ~~~~   92 (115)
                      ..+.
T Consensus        89 ~~~~   92 (102)
T 1wez_A           89 NSTA   92 (102)
T ss_dssp             ECCC
T ss_pred             CCCC
Confidence            6643

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.80  E-value=2.5e-19  Score=109.63  Aligned_cols=84  Identities=24%  Similarity=0.319  Sum_probs=78.0

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      ....++|||+|||..+++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|++|+..|++..+.|+.+.|..
T Consensus        44 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~  123 (135)
T 2lea_A           44 VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQM  123 (135)
T ss_dssp             GGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34567899999999999999999999999999999999888899999999999999999999999999999999999988


Q ss_pred             eeec
Q psy3928          89 TTSR   92 (115)
Q Consensus        89 ~~~~   92 (115)
                      +++.
T Consensus       124 a~~~  127 (135)
T 2lea_A          124 ARYG  127 (135)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7764

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.79  E-value=1.2e-18  Score=104.90  Aligned_cols=83  Identities=19%  Similarity=0.237  Sum_probs=77.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      ...++|||+|||..+++++|+++|..||.|..+.+..++ ++.++|||||+|.+.++|++|+..+++..+.|+.+.|..+
T Consensus        33 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  111 (124)
T 2kt5_A           33 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLV  111 (124)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEe
Confidence            445799999999999999999999999999999999988 8999999999999999999999999999999999999887


Q ss_pred             eecc
Q psy3928          90 TSRL   93 (115)
Q Consensus        90 ~~~~   93 (115)
                      .+..
T Consensus       112 ~~~~  115 (124)
T 2kt5_A          112 ASQI  115 (124)
T ss_dssp             CCTT
T ss_pred             CCCC
Confidence            7643

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=1.2e-18  Score=102.70  Aligned_cols=83  Identities=25%  Similarity=0.283  Sum_probs=73.6

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      .....++|||+|||.++++++|+++|.+||.|..+.+..   ++.+++||||+|.+.++|++|++.||+..+.++.+.|.
T Consensus        18 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   94 (109)
T 1x4a_A           18 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN---RRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVE   94 (109)
T ss_dssp             CCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECC---SSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEE---CCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            345668999999999999999999999999999998854   45678999999999999999999999999999998888


Q ss_pred             Eeeecc
Q psy3928          88 TTTSRL   93 (115)
Q Consensus        88 ~~~~~~   93 (115)
                      .++++.
T Consensus        95 ~a~~~~  100 (109)
T 1x4a_A           95 FPRSGR  100 (109)
T ss_dssp             CCCCCC
T ss_pred             EcccCC
Confidence            777543

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.79  E-value=8.2e-19  Score=105.57  Aligned_cols=80  Identities=19%  Similarity=0.263  Sum_probs=75.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEee
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTT   90 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~   90 (115)
                      ..++|||+|||.++++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|++|+ .+++..+.|+.+.|..++
T Consensus        35 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~  113 (124)
T 2jwn_A           35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKR  113 (124)
T ss_dssp             HHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECC
Confidence            4589999999999999999999999999999999999889999999999999999999999 899999999999888776


Q ss_pred             e
Q psy3928          91 S   91 (115)
Q Consensus        91 ~   91 (115)
                      +
T Consensus       114 ~  114 (124)
T 2jwn_A          114 T  114 (124)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.79  E-value=4.7e-19  Score=102.44  Aligned_cols=82  Identities=16%  Similarity=0.084  Sum_probs=74.0

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHH----HHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCcee
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIE----SVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQS   84 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~----~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~   84 (115)
                      ....++|||+|||..+++++|+    ++|.+||.|..+.++.++.+   ++||||+|.+.++|++|++.||+..+.|+.+
T Consensus         6 ~~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l   82 (96)
T 2dgx_A            6 SGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSKKI   82 (96)
T ss_dssp             CSSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCeEE
Confidence            3456899999999999999999    99999999999999988744   7899999999999999999999999999999


Q ss_pred             eEEEeeecc
Q psy3928          85 SILTTTSRL   93 (115)
Q Consensus        85 ~v~~~~~~~   93 (115)
                      +|..++++.
T Consensus        83 ~V~~a~~~~   91 (96)
T 2dgx_A           83 LVSLATGAS   91 (96)
T ss_dssp             EEEECCCSS
T ss_pred             EEEEcCCCC
Confidence            988876543

>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=99.79  E-value=1.4e-19  Score=107.52  Aligned_cols=82  Identities=21%  Similarity=0.211  Sum_probs=76.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEee
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTT   90 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~   90 (115)
                      ..++|||+|||..+++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|++|+ .+++..+.|+.+.|..++
T Consensus        24 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~  102 (114)
T 2cq4_A           24 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQ  102 (114)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEecC
Confidence            3479999999999999999999999999999999999888999999999999999999999 999999999999998877


Q ss_pred             ecc
Q psy3928          91 SRL   93 (115)
Q Consensus        91 ~~~   93 (115)
                      ++.
T Consensus       103 ~~~  105 (114)
T 2cq4_A          103 AEK  105 (114)
T ss_dssp             HHH
T ss_pred             CCc
Confidence            654

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.79  E-value=2.5e-19  Score=99.36  Aligned_cols=76  Identities=16%  Similarity=0.181  Sum_probs=70.8

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        13 ~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      ++|||+|||.++++++|+++|++||.+..+.++.++.++.++|+|||+|.+.++|++|+..++ ..++|+.+.+..+
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a   76 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            479999999999999999999999999999999988889999999999999999999999999 8999998887653

>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=2.7e-19  Score=106.46  Aligned_cols=82  Identities=13%  Similarity=0.063  Sum_probs=75.6

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCe-EEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKV-TYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i-~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      ....++|||+|||.++++++|+++|..||.+ ..+.|+.++ ++.++|||||+|.+.++|++|+.. ++..+.|+.+.|.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~   89 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVH   89 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEE
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEE
Confidence            4456899999999999999999999999998 789999988 999999999999999999999997 9999999999998


Q ss_pred             Eeeec
Q psy3928          88 TTTSR   92 (115)
Q Consensus        88 ~~~~~   92 (115)
                      .+.++
T Consensus        90 ~a~~~   94 (114)
T 2cpy_A           90 VVTLE   94 (114)
T ss_dssp             EECHH
T ss_pred             ECCHH
Confidence            88764

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=1.5e-18  Score=101.16  Aligned_cols=84  Identities=17%  Similarity=0.232  Sum_probs=74.5

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      .....++|||+|||.++++++|+++|..|+   .+.++.++.++.++|||||+|.+.++|++|++.|++..+.++.+.|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   87 (102)
T 2fc8_A           11 RSQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLD   87 (102)
T ss_dssp             SSCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            345678999999999999999999999874   56677777789999999999999999999999999999999999998


Q ss_pred             Eeeeccc
Q psy3928          88 TTTSRLS   94 (115)
Q Consensus        88 ~~~~~~~   94 (115)
                      .++++..
T Consensus        88 ~a~~~~~   94 (102)
T 2fc8_A           88 WAKPKGE   94 (102)
T ss_dssp             ECCCCCS
T ss_pred             EecCCCC
Confidence            8876544

>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=99.79  E-value=1.1e-18  Score=102.97  Aligned_cols=84  Identities=17%  Similarity=0.196  Sum_probs=74.7

Q ss_pred             hcccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceee
Q psy3928           6 ENNKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSS   85 (115)
Q Consensus         6 ~~~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~   85 (115)
                      .......++|||+|||..+++++|+++|..||.|..+.+..+      +|||||+|.+.++|++|+..|++..+.|+.+.
T Consensus        19 ~~~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~------~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   92 (109)
T 1x4g_A           19 NQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVK   92 (109)
T ss_dssp             HHSCSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             cCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCCCEECCcEEE
Confidence            345566789999999999999999999999999999988754      68999999999999999999999999999999


Q ss_pred             EEEeeecccc
Q psy3928          86 ILTTTSRLSF   95 (115)
Q Consensus        86 v~~~~~~~~~   95 (115)
                      |..++++...
T Consensus        93 v~~a~~~~~~  102 (109)
T 1x4g_A           93 CYWGKESPDM  102 (109)
T ss_dssp             EECCCCCCSS
T ss_pred             EEecCCCCCC
Confidence            8888775543

>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=99.79  E-value=1.8e-18  Score=101.88  Aligned_cols=85  Identities=18%  Similarity=0.112  Sum_probs=76.7

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCC-eEEEEec-eeCCCCCeeeEEEEEecCHHHHHHHHHhhC--CCCCCCceee
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGK-VTYVSLP-KFKSTGKLKGFAFVEFSTKEEATKALELGL--NPCPTDYQSS   85 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~-i~~~~i~-~~~~~~~~~g~~fv~f~~~~~a~~al~~l~--~~~~~~~~~~   85 (115)
                      ...++|||+|||..+++++|+++|..||. +..+.++ .++.++.++|||||+|.+.++|+.|+..|+  +..+.|+.+.
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~   85 (109)
T 2dis_A            6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIA   85 (109)
T ss_dssp             CCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCE
T ss_pred             cCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEE
Confidence            35679999999999999999999999998 9999988 777788999999999999999999999996  5889999999


Q ss_pred             EEEeeeccc
Q psy3928          86 ILTTTSRLS   94 (115)
Q Consensus        86 v~~~~~~~~   94 (115)
                      |..++++..
T Consensus        86 V~~a~~~~~   94 (109)
T 2dis_A           86 VDWAEPEID   94 (109)
T ss_dssp             EEESCSSCS
T ss_pred             EEEcCCCCC
Confidence            998877544

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=1e-18  Score=101.75  Aligned_cols=82  Identities=23%  Similarity=0.289  Sum_probs=72.7

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      .....++|||+|||..+++++|+++|.+||.|   .++.+ .++.++|||||+|.+.++|++|+..|++..+.++.+.|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   86 (101)
T 2fc9_A           11 WSGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLE   86 (101)
T ss_dssp             CSCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEE
Confidence            44567899999999999999999999999966   55655 488899999999999999999999999999999999988


Q ss_pred             Eeeecc
Q psy3928          88 TTTSRL   93 (115)
Q Consensus        88 ~~~~~~   93 (115)
                      .++++.
T Consensus        87 ~a~~~~   92 (101)
T 2fc9_A           87 LQGPRG   92 (101)
T ss_dssp             ECSSCC
T ss_pred             EcCCCC
Confidence            887653

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=2.7e-18  Score=97.99  Aligned_cols=78  Identities=22%  Similarity=0.257  Sum_probs=70.8

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      ....++|||+|||.++++++|+++|.+||.+..+.+.        ++||||+|.+.++|++|+..+++..+.++.++|..
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   76 (90)
T 2dnq_A            5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEA   76 (90)
T ss_dssp             SSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEC
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEE
Confidence            4567899999999999999999999999999999886        46999999999999999999999999999999888


Q ss_pred             eeeccc
Q psy3928          89 TTSRLS   94 (115)
Q Consensus        89 ~~~~~~   94 (115)
                      ++++..
T Consensus        77 a~~~~~   82 (90)
T 2dnq_A           77 SKNKSK   82 (90)
T ss_dssp             SSCCCC
T ss_pred             CCCCCC
Confidence            776544

>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=99.79  E-value=3.2e-19  Score=106.03  Aligned_cols=86  Identities=21%  Similarity=0.210  Sum_probs=72.7

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      ...++|||+|||..+++++|+++|..||.+..+.+..+..++.++|||||+|.+.++|++|+..|++..+.|+.+.|..+
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a  102 (115)
T 2cpx_A           23 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG  102 (115)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEc
Confidence            34589999999999999999999999998843322222227889999999999999999999999999999999999988


Q ss_pred             eecccc
Q psy3928          90 TSRLSF   95 (115)
Q Consensus        90 ~~~~~~   95 (115)
                      +++...
T Consensus       103 ~~~~~~  108 (115)
T 2cpx_A          103 KNKKQR  108 (115)
T ss_dssp             CCCSCC
T ss_pred             cCCCCC
Confidence            875443

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.78  E-value=8.2e-19  Score=107.36  Aligned_cols=80  Identities=25%  Similarity=0.333  Sum_probs=74.4

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      ....++|||+|||..+++++|+++|.+||.+..+.++.++.++.++|||||+|.+.++|++|++.+++..+.|+.++|..
T Consensus        60 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  139 (140)
T 2ku7_A           60 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL  139 (140)
T ss_dssp             CSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEEC
T ss_pred             CCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            34568999999999999999999999999999999999988999999999999999999999999999999998887754

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=6.5e-19  Score=104.09  Aligned_cols=83  Identities=22%  Similarity=0.294  Sum_probs=75.4

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      .....++|||+|||.++++++|+++|..||.|..+.+..++  +.++|||||+|.+.++|++|+..|++..++|+.+.|.
T Consensus        25 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  102 (109)
T 2err_A           25 NKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN  102 (109)
T ss_dssp             CTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            45567899999999999999999999999999999998875  4588999999999999999999999999999999988


Q ss_pred             Eeeec
Q psy3928          88 TTTSR   92 (115)
Q Consensus        88 ~~~~~   92 (115)
                      .++++
T Consensus       103 ~a~~~  107 (109)
T 2err_A          103 NATAR  107 (109)
T ss_dssp             ECCCS
T ss_pred             ECCCC
Confidence            87754

>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=99.78  E-value=8.6e-19  Score=102.51  Aligned_cols=81  Identities=14%  Similarity=0.087  Sum_probs=70.7

Q ss_pred             cCCCCEEEEcCCCC-CCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCC--CCCceee
Q psy3928           9 KKYGRVVLKEKLPP-EAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPC--PTDYQSS   85 (115)
Q Consensus         9 ~~~~~~l~V~~l~~-~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~--~~~~~~~   85 (115)
                      ..+.++|||+|||. .+++++|+++|.+||.|..+.++.+      +++|||+|.+.++|++|++.|++..  +.|+.+.
T Consensus        12 ~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~   85 (102)
T 1x4d_A           12 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVR   85 (102)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHHcCCCceECCcEEE
Confidence            34568999999999 9999999999999999999998754      3799999999999999999998754  8999999


Q ss_pred             EEEeeecccc
Q psy3928          86 ILTTTSRLSF   95 (115)
Q Consensus        86 v~~~~~~~~~   95 (115)
                      |..++.....
T Consensus        86 V~~a~~~~~~   95 (102)
T 1x4d_A           86 VHLSQKYKRI   95 (102)
T ss_dssp             EEEECCCTTS
T ss_pred             EEECCCCCCC
Confidence            9888764443

>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=9.2e-19  Score=115.61  Aligned_cols=81  Identities=12%  Similarity=0.156  Sum_probs=75.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcC--CeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYG--KVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g--~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      ..++|||+|||..+++++|+++|..||  .|..+.|+.++.+++++|||||+|.+.++|++|++.||+..+.++.|.|..
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~  146 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTP  146 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEE
Confidence            457899999999999999999999999  999999999988999999999999999999999999999999999999987


Q ss_pred             eee
Q psy3928          89 TTS   91 (115)
Q Consensus        89 ~~~   91 (115)
                      +++
T Consensus       147 a~~  149 (229)
T 3q2s_C          147 VNK  149 (229)
T ss_dssp             CCH
T ss_pred             CCC
Confidence            654

>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=99.78  E-value=2.4e-18  Score=101.44  Aligned_cols=78  Identities=22%  Similarity=0.236  Sum_probs=70.1

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCC-----ce
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTD-----YQ   83 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~-----~~   83 (115)
                      ....++|||+|||.++++++|+++|.+||.|..+.++.+       |||||+|.+.++|++|++.||+..+.+     ..
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~   84 (108)
T 1x4c_A           12 RRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAY   84 (108)
T ss_dssp             CSCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceE
Confidence            345689999999999999999999999999999988754       799999999999999999999999998     78


Q ss_pred             eeEEEeeecc
Q psy3928          84 SSILTTTSRL   93 (115)
Q Consensus        84 ~~v~~~~~~~   93 (115)
                      +.|..++++.
T Consensus        85 i~V~~a~~~~   94 (108)
T 1x4c_A           85 IRVKVDGPRS   94 (108)
T ss_dssp             EEEEESSCCS
T ss_pred             EEEEeCCCCC
Confidence            8888777643

>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=99.78  E-value=6.6e-19  Score=107.92  Aligned_cols=82  Identities=18%  Similarity=0.193  Sum_probs=75.0

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCC---eEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceee
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGK---VTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSS   85 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~---i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~   85 (115)
                      ....++|||+|||.++++++|+++|.+||.   +..+.++.++. |+++|||||+|.+.++|++|++ +++..+.++.+.
T Consensus        41 ~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~  118 (136)
T 2hgl_A           41 GGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIE  118 (136)
T ss_dssp             CCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEE
Confidence            445689999999999999999999999998   78899999885 9999999999999999999999 999999999999


Q ss_pred             EEEeeec
Q psy3928          86 ILTTTSR   92 (115)
Q Consensus        86 v~~~~~~   92 (115)
                      |..++++
T Consensus       119 V~~a~~~  125 (136)
T 2hgl_A          119 VFKSHRT  125 (136)
T ss_dssp             EEECCHH
T ss_pred             EEECChH
Confidence            8877543

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*

Probab=99.78  E-value=2.4e-18  Score=122.75  Aligned_cols=85  Identities=14%  Similarity=0.234  Sum_probs=79.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEee
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTT   90 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~   90 (115)
                      ..++|||+|||..+++.+|..+|.+||.|..|.|+.++.++.++|||||+|.+.++|++|+..||+..|.|..|.|..+.
T Consensus       101 ~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a~  180 (437)
T 3pgw_S          101 AFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  180 (437)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            34799999999999999999999999999999999998899999999999999999999999999999999999999888


Q ss_pred             ecccc
Q psy3928          91 SRLSF   95 (115)
Q Consensus        91 ~~~~~   95 (115)
                      ++...
T Consensus       181 ~~~~~  185 (437)
T 3pgw_S          181 GRTVK  185 (437)
T ss_pred             CCCCC
Confidence            65443

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=1.2e-18  Score=102.27  Aligned_cols=79  Identities=25%  Similarity=0.246  Sum_probs=69.4

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCC--CCCCCceeeE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN--PCPTDYQSSI   86 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~--~~~~~~~~~v   86 (115)
                      ....++|||+|||.++++++|+++|.+||.|..+.++.+      +|||||+|.+.++|++|++.+++  ..+.|+.++|
T Consensus        13 ~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V   86 (105)
T 1sjq_A           13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYI   86 (105)
T ss_dssp             CCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCB
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEE
Confidence            456789999999999999999999999999999998753      58999999999999999998875  5688998888


Q ss_pred             EEeeecc
Q psy3928          87 LTTTSRL   93 (115)
Q Consensus        87 ~~~~~~~   93 (115)
                      ..++++.
T Consensus        87 ~~A~~~~   93 (105)
T 1sjq_A           87 QFSNHKE   93 (105)
T ss_dssp             CCCSSSS
T ss_pred             EEcCCCC
Confidence            7776543

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=4e-18  Score=99.55  Aligned_cols=82  Identities=24%  Similarity=0.224  Sum_probs=70.7

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhC--CCCCCCceee
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGL--NPCPTDYQSS   85 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~--~~~~~~~~~~   85 (115)
                      .....++|||+|||..+++++|+++|.+||.|..+.++.+      +|||||+|.+.++|++|++.++  +..+.|+.+.
T Consensus        11 ~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~   84 (101)
T 2cq1_A           11 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIY   84 (101)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCcEEE
Confidence            3456689999999999999999999999999999987643      6899999999999999999875  5568999999


Q ss_pred             EEEeeecccc
Q psy3928          86 ILTTTSRLSF   95 (115)
Q Consensus        86 v~~~~~~~~~   95 (115)
                      |..++++...
T Consensus        85 V~~a~~~~~~   94 (101)
T 2cq1_A           85 IQYSNHKELK   94 (101)
T ss_dssp             EEECSCSSCC
T ss_pred             EEEcCcccCc
Confidence            9888765443

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.77  E-value=1e-18  Score=104.60  Aligned_cols=81  Identities=20%  Similarity=0.210  Sum_probs=74.6

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCC---eEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceee
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGK---VTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSS   85 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~---i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~   85 (115)
                      ....++|||+|||.++++++|+++|..||.   +..+.|+.++. ++++|||||+|.+.++|++|++ +++..+.++.+.
T Consensus        14 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~   91 (118)
T 2db1_A           14 GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALK-KDRESMGHRYIE   91 (118)
T ss_dssp             BCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEE
Confidence            456789999999999999999999999998   88999999885 9999999999999999999999 999999999999


Q ss_pred             EEEeee
Q psy3928          86 ILTTTS   91 (115)
Q Consensus        86 v~~~~~   91 (115)
                      |..+..
T Consensus        92 V~~a~~   97 (118)
T 2db1_A           92 VFKSHR   97 (118)
T ss_dssp             EEEECH
T ss_pred             EEECCH
Confidence            987765

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=6.8e-19  Score=106.11  Aligned_cols=83  Identities=24%  Similarity=0.259  Sum_probs=73.9

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      ....++|||+|||..+++++|+++|..||.+..+.++.+..++.++|||||+|.+.++|++|+. +|+..+.|+.+.|..
T Consensus        22 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~  100 (124)
T 1wel_A           22 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHP  100 (124)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEE
Confidence            3456899999999999999999999999998775555555699999999999999999999999 999999999999988


Q ss_pred             eeec
Q psy3928          89 TTSR   92 (115)
Q Consensus        89 ~~~~   92 (115)
                      ++..
T Consensus       101 a~~~  104 (124)
T 1wel_A          101 ITKK  104 (124)
T ss_dssp             ECHH
T ss_pred             CCHH
Confidence            7653

>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=99.77  E-value=7.3e-19  Score=97.08  Aligned_cols=74  Identities=24%  Similarity=0.393  Sum_probs=68.6

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928          14 VVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus        14 ~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      +|||+|||.++++++|+++|++||.+..+.++.++.++.++|||||+|.+.++|++|++. ++..+.|+.+.+..
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~v~~   74 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIKV   74 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTT-SSCCBTTBCCCEEE
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEE
Confidence            589999999999999999999999999999999888899999999999999999999995 88889999887754

>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=99.77  E-value=4.3e-19  Score=109.09  Aligned_cols=82  Identities=24%  Similarity=0.220  Sum_probs=72.9

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      ....++|||+|||.++++++|+++|.+|| +..+.|+.++. ++++|||||+|.+.++|++|+ .+++..+.++.+.|..
T Consensus        43 ~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~-g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~  119 (139)
T 2hgn_A           43 STTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFL  119 (139)
T ss_dssp             --CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSS-SCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCC-CCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEE
Confidence            34567999999999999999999999999 77999999884 999999999999999999999 7899999999998887


Q ss_pred             eeecc
Q psy3928          89 TTSRL   93 (115)
Q Consensus        89 ~~~~~   93 (115)
                      +.++.
T Consensus       120 a~~~~  124 (139)
T 2hgn_A          120 NSTTG  124 (139)
T ss_dssp             CCCSC
T ss_pred             CCCCC
Confidence            76543

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens}

Probab=99.77  E-value=9e-19  Score=103.12  Aligned_cols=83  Identities=16%  Similarity=0.159  Sum_probs=75.5

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCC---eEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCcee
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGK---VTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQS   84 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~---i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~   84 (115)
                      .....++|||+|||.++++++|+++|..||.   +..+.++.++. |.++|||||+|.+.++|++|+. +++..+.|+.+
T Consensus         7 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i   84 (107)
T 2lmi_A            7 EVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALE-KHRMYMGQRYV   84 (107)
T ss_dssp             CCSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCC
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEE
Confidence            3456789999999999999999999999987   88999999885 9999999999999999999999 99999999999


Q ss_pred             eEEEeeec
Q psy3928          85 SILTTTSR   92 (115)
Q Consensus        85 ~v~~~~~~   92 (115)
                      .|..+.++
T Consensus        85 ~V~~a~~~   92 (107)
T 2lmi_A           85 EVYEINNE   92 (107)
T ss_dssp             CCEECCHH
T ss_pred             EEEECCHH
Confidence            98887653

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.76  E-value=5.1e-18  Score=98.00  Aligned_cols=78  Identities=15%  Similarity=0.286  Sum_probs=69.6

Q ss_pred             cCCCCEEEEcCCCC-CCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928           9 KKYGRVVLKEKLPP-EAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus         9 ~~~~~~l~V~~l~~-~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      ....++|||+|||. .+++++|+++|.+||.|..+.+.        +|||||+|.+.++|+.|+..|++..+.|+.+.|.
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   78 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILE   78 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            45678999999998 99999999999999999998873        5799999999999999999999999999999998


Q ss_pred             Eeeeccc
Q psy3928          88 TTTSRLS   94 (115)
Q Consensus        88 ~~~~~~~   94 (115)
                      .+++...
T Consensus        79 ~a~~~~~   85 (96)
T 2kvi_A           79 VSSSNAR   85 (96)
T ss_dssp             EEECCCC
T ss_pred             EcCcCCC
Confidence            8876433

>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=99.76  E-value=6.8e-18  Score=101.12  Aligned_cols=80  Identities=25%  Similarity=0.234  Sum_probs=70.8

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCC--CCCCCceeeE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN--PCPTDYQSSI   86 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~--~~~~~~~~~v   86 (115)
                      ....++|||+|||.++++++|+++|++||.|..+.++.+      +|||||+|.+.++|++|++.+++  ..+.|+.+.|
T Consensus        28 ~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V  101 (119)
T 2ad9_A           28 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYI  101 (119)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEE
Confidence            445689999999999999999999999999999998764      58999999999999999999874  5789999999


Q ss_pred             EEeeeccc
Q psy3928          87 LTTTSRLS   94 (115)
Q Consensus        87 ~~~~~~~~   94 (115)
                      ..++++..
T Consensus       102 ~~a~~k~~  109 (119)
T 2ad9_A          102 QFSNHKEL  109 (119)
T ss_dssp             EECSSSSC
T ss_pred             EEccCCCC
Confidence            98876543

>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=99.76  E-value=8.3e-18  Score=97.19  Aligned_cols=79  Identities=14%  Similarity=0.136  Sum_probs=70.7

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCC--CceeeE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPT--DYQSSI   86 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~--~~~~~v   86 (115)
                      ....++|||+|||.++++++|+++|.+||.|..+.+..+      ++||||+|.+.++|++|++.||+..+.  ++.+.|
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V   87 (97)
T 1why_A           14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRV   87 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEE
Confidence            345689999999999999999999999999999988643      679999999999999999999999999  899988


Q ss_pred             EEeeecc
Q psy3928          87 LTTTSRL   93 (115)
Q Consensus        87 ~~~~~~~   93 (115)
                      ..++++.
T Consensus        88 ~~a~~~~   94 (97)
T 1why_A           88 DFAKSGP   94 (97)
T ss_dssp             EECCCCC
T ss_pred             EECCCCC
Confidence            8877643

>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=99.76  E-value=7.2e-18  Score=98.92  Aligned_cols=80  Identities=21%  Similarity=0.243  Sum_probs=69.9

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCC--CCCceee
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPC--PTDYQSS   85 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~--~~~~~~~   85 (115)
                      .....++|||+|||..+++++|+++|.+||.|..+.++.+      +|||||+|.+.++|++|++.+++..  +.|+.+.
T Consensus        11 ~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~   84 (104)
T 1wex_A           11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAF   84 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            3456789999999999999999999999999999987642      5899999999999999999987654  8999999


Q ss_pred             EEEeeecc
Q psy3928          86 ILTTTSRL   93 (115)
Q Consensus        86 v~~~~~~~   93 (115)
                      |..++.+.
T Consensus        85 V~~a~~~~   92 (104)
T 1wex_A           85 FNYSTSKR   92 (104)
T ss_dssp             EEECSSSS
T ss_pred             EEEccCcc
Confidence            98887643

>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=99.76  E-value=6.5e-18  Score=98.00  Aligned_cols=80  Identities=24%  Similarity=0.240  Sum_probs=71.7

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      .....++|||+|||..+++++|+++|.+||.+..+.+..+      +|||||+|.+.++|++|++.|++..+.|+.+.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~   84 (99)
T 2cpj_A           11 TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVR   84 (99)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEE
Confidence            3456689999999999999999999999999999988643      5899999999999999999999999999999988


Q ss_pred             Eeeecc
Q psy3928          88 TTTSRL   93 (115)
Q Consensus        88 ~~~~~~   93 (115)
                      .++++.
T Consensus        85 ~a~~~~   90 (99)
T 2cpj_A           85 FACHSA   90 (99)
T ss_dssp             ESSCCS
T ss_pred             EcCCCC
Confidence            877643

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.76  E-value=9.7e-18  Score=101.62  Aligned_cols=82  Identities=18%  Similarity=0.194  Sum_probs=72.2

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHH----HHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCcee
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIE----SVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQS   84 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~----~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~   84 (115)
                      ....++|||+|||..+++++|+    ++|++||.|..+.+..   ++.++|||||+|.+.++|+.|+..|||..+.|+.+
T Consensus        26 ~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~---~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l  102 (127)
T 2a3j_A           26 TEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPL  102 (127)
T ss_dssp             CSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC---CCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc---CCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEE
Confidence            3456899999999999998865    7999999999887742   67889999999999999999999999999999999


Q ss_pred             eEEEeeecc
Q psy3928          85 SILTTTSRL   93 (115)
Q Consensus        85 ~v~~~~~~~   93 (115)
                      .|..++.+.
T Consensus       103 ~V~~a~~~~  111 (127)
T 2a3j_A          103 VITFSETPQ  111 (127)
T ss_dssp             EEEECCCCC
T ss_pred             EEEEccCcc
Confidence            998887643

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.76  E-value=2e-17  Score=107.19  Aligned_cols=85  Identities=19%  Similarity=0.235  Sum_probs=79.5

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      ...++|||+|||..+++++|+++|..||.|..+.+..++.++.++|+|||+|.+.++|.+|+..||+..+.|+.+.|..+
T Consensus       123 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a  202 (216)
T 2qfj_A          123 RAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA  202 (216)
T ss_dssp             TTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEEC
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEe
Confidence            45689999999999999999999999999999999999889999999999999999999999999999999999999988


Q ss_pred             eeccc
Q psy3928          90 TSRLS   94 (115)
Q Consensus        90 ~~~~~   94 (115)
                      .++..
T Consensus       203 ~~~~~  207 (216)
T 2qfj_A          203 VTPPM  207 (216)
T ss_dssp             SSCSS
T ss_pred             cCCCC
Confidence            87543

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.76  E-value=5.6e-18  Score=98.53  Aligned_cols=78  Identities=19%  Similarity=0.174  Sum_probs=69.1

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCC--CCCceeeE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPC--PTDYQSSI   86 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~--~~~~~~~v   86 (115)
                      ..+.++|||+|||..+++++|+++|.+||.+..+.+++      .+|+|||+|.+.++|.+|++.+++..  +.|+.+.|
T Consensus        18 ~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~------~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V   91 (100)
T 3r27_A           18 TPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP------KKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFV   91 (100)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEc------CCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEE
Confidence            44678999999999999999999999999999998864      25799999999999999999999886  77999888


Q ss_pred             EEeeec
Q psy3928          87 LTTTSR   92 (115)
Q Consensus        87 ~~~~~~   92 (115)
                      ..++++
T Consensus        92 ~~S~~k   97 (100)
T 3r27_A           92 NYSTSQ   97 (100)
T ss_dssp             EECSCS
T ss_pred             Eecccc
Confidence            887653

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.76  E-value=5.1e-18  Score=98.70  Aligned_cols=76  Identities=25%  Similarity=0.244  Sum_probs=70.0

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEeeec
Q psy3928          13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTTSR   92 (115)
Q Consensus        13 ~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~~~   92 (115)
                      ++|||+|||.++++++|+++|++||.+..+.+..+     ++|||||+|.+.++|++|+..|++..+.|..+.|..++++
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   75 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGM   75 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS-----SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC-----CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCC
Confidence            47999999999999999999999999999988765     6789999999999999999999999999999999988764


Q ss_pred             c
Q psy3928          93 L   93 (115)
Q Consensus        93 ~   93 (115)
                      .
T Consensus        76 ~   76 (101)
T 2hvz_A           76 P   76 (101)
T ss_dssp             C
T ss_pred             C
Confidence            4

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.76  E-value=9.8e-18  Score=109.27  Aligned_cols=82  Identities=17%  Similarity=0.181  Sum_probs=74.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      ...++|||+|||.++++++|+++|++||.|..++|+.++.+++++|||||+|.+.++|++|++.+++..+.++.+++...
T Consensus        13 ~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~   92 (213)
T 4f02_A           13 YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWS   92 (213)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcccccccc
Confidence            34579999999999999999999999999999999999989999999999999999999999999999999998887665


Q ss_pred             ee
Q psy3928          90 TS   91 (115)
Q Consensus        90 ~~   91 (115)
                      ..
T Consensus        93 ~~   94 (213)
T 4f02_A           93 QR   94 (213)
T ss_dssp             CC
T ss_pred             cc
Confidence            43

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.75  E-value=2e-18  Score=97.72  Aligned_cols=73  Identities=16%  Similarity=0.141  Sum_probs=67.6

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEee
Q psy3928          12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTT   90 (115)
Q Consensus        12 ~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~   90 (115)
                      ...|||+||++.+++++|+++|.+||+|..+.+..      ++|||||+|.++++|++|++.||+..+.|+.|++..++
T Consensus         7 ~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~   79 (89)
T 2wbr_A            7 SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             CCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             cceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            46799999999999999999999999999998854      57999999999999999999999999999999987764

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=1.1e-17  Score=96.99  Aligned_cols=80  Identities=19%  Similarity=0.242  Sum_probs=70.3

Q ss_pred             cccCCCCEEEEcCCCCCCCHHHHHHHhhhc--CCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCcee
Q psy3928           7 NNKKYGRVVLKEKLPPEAEHDYIESVFSKY--GKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQS   84 (115)
Q Consensus         7 ~~~~~~~~l~V~~l~~~~~~~~l~~~f~~~--g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~   84 (115)
                      ......++|||+|||..+++++|+++|.+|  |.+..+.+.        ++||||+|.+.++|++|+..||+..+.|+.+
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   81 (99)
T 2cpd_A           10 DTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKVLDGSPI   81 (99)
T ss_dssp             SCSSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSEEETTEEE
T ss_pred             cccCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEE
Confidence            344567899999999999999999999999  888888764        4699999999999999999999999999999


Q ss_pred             eEEEeeeccc
Q psy3928          85 SILTTTSRLS   94 (115)
Q Consensus        85 ~v~~~~~~~~   94 (115)
                      .|..++++..
T Consensus        82 ~v~~a~~~~~   91 (99)
T 2cpd_A           82 EVTLAKPVDK   91 (99)
T ss_dssp             EEECCCCCCC
T ss_pred             EEEECCCCCC
Confidence            8888776543

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.75  E-value=3.6e-19  Score=103.64  Aligned_cols=81  Identities=17%  Similarity=0.112  Sum_probs=72.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      ...++|||+|||.++++++|+++|..||.+.. .++.++.++.++|||||+|.+.++|++|++ +++..+.|+.+.|..+
T Consensus        15 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~a   92 (101)
T 1fj7_A           15 TTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP   92 (101)
T ss_dssp             SCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEEc
Confidence            35689999999999999999999999998876 566666678899999999999999999999 9999999999988877


Q ss_pred             eec
Q psy3928          90 TSR   92 (115)
Q Consensus        90 ~~~   92 (115)
                      +++
T Consensus        93 ~~~   95 (101)
T 1fj7_A           93 KGR   95 (101)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            654

>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=99.75  E-value=1.8e-17  Score=103.33  Aligned_cols=80  Identities=19%  Similarity=0.264  Sum_probs=75.4

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEeee
Q psy3928          12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTTS   91 (115)
Q Consensus        12 ~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~~   91 (115)
                      .++|||+|||.++++++|+++|..||.+..+.+..++.++.++|+|||+|.+.++|++|++.+++..+.+..+.+....+
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            57899999999999999999999999999999999988999999999999999999999999999999999988877664

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.75  E-value=2.1e-18  Score=100.56  Aligned_cols=83  Identities=22%  Similarity=0.285  Sum_probs=74.4

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      ....++|||+|||.++++++|+++|..||.+..+.++.++ ++.++|||||+|.+.++|++|+.  ++..++|..+.+..
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~   82 (102)
T 2xs2_A            6 KIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGP   82 (102)
T ss_dssp             EEEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEE
Confidence            3456899999999999999999999999999999999998 99999999999999999999999  88888889888877


Q ss_pred             eeeccc
Q psy3928          89 TTSRLS   94 (115)
Q Consensus        89 ~~~~~~   94 (115)
                      +.++..
T Consensus        83 a~~~~~   88 (102)
T 2xs2_A           83 AIRKQN   88 (102)
T ss_dssp             EEECC-
T ss_pred             CCcCcc
Confidence            766543

>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=99.75  E-value=4.7e-18  Score=101.26  Aligned_cols=69  Identities=23%  Similarity=0.269  Sum_probs=61.8

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceee
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSS   85 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~   85 (115)
                      ...++|||+|||.++++++|+++|.+||.|..+.++.+       |||||+|.+.++|++|++.||+..++|..+.
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~   82 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGE   82 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEee
Confidence            45689999999999999999999999999999988653       8999999999999999999999999998833

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.75  E-value=1.6e-17  Score=94.80  Aligned_cols=78  Identities=14%  Similarity=0.188  Sum_probs=70.4

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      .....++|||+|||..+++++|+++|.+||.|..+.+.+        +||||+|.+.++|++|+..|++..+.|+.+.|.
T Consensus         5 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   76 (90)
T 2dnp_A            5 SSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK--------DYAFVHMEKEADAKAAIAQLNGKEVKGKRINVE   76 (90)
T ss_dssp             SSCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECS--------SCEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            345678999999999999999999999999999998863        399999999999999999999999999999988


Q ss_pred             Eeeecc
Q psy3928          88 TTTSRL   93 (115)
Q Consensus        88 ~~~~~~   93 (115)
                      .++++.
T Consensus        77 ~a~~~~   82 (90)
T 2dnp_A           77 LSTKGQ   82 (90)
T ss_dssp             ESCCCC
T ss_pred             ECCCCC
Confidence            887653

>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=99.75  E-value=1.6e-17  Score=98.63  Aligned_cols=82  Identities=16%  Similarity=0.247  Sum_probs=73.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      ...++|||+|||..+++++|+++|..||.+..+.++.+   +.++|||||+|.+.++|++|+..||+..+.|+.+.|..+
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   82 (115)
T 3lqv_A            6 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYY   82 (115)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEe
Confidence            45689999999999999999999999999999988754   455899999999999999999999999999999999988


Q ss_pred             eeccc
Q psy3928          90 TSRLS   94 (115)
Q Consensus        90 ~~~~~   94 (115)
                      .++..
T Consensus        83 ~~~~~   87 (115)
T 3lqv_A           83 NANRA   87 (115)
T ss_dssp             CHHHH
T ss_pred             cCChh
Confidence            76443

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.75  E-value=1.4e-17  Score=106.03  Aligned_cols=82  Identities=20%  Similarity=0.235  Sum_probs=76.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEee
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTT   90 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~   90 (115)
                      ..++|||+|||..+++++|+++|..||.|..+.+..++ ++.++|||||+|.+.++|++|++.+++..+.|..+.|..+.
T Consensus        87 ~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~a~  165 (177)
T 2f3j_A           87 TGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVA  165 (177)
T ss_dssp             TCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEec
Confidence            45799999999999999999999999999999999988 89999999999999999999999999999999999998877


Q ss_pred             ecc
Q psy3928          91 SRL   93 (115)
Q Consensus        91 ~~~   93 (115)
                      ...
T Consensus       166 ~~~  168 (177)
T 2f3j_A          166 SQI  168 (177)
T ss_dssp             SGG
T ss_pred             CCC
Confidence            643

>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=99.75  E-value=1.5e-17  Score=98.49  Aligned_cols=78  Identities=24%  Similarity=0.210  Sum_probs=70.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      ...++|||+|||..+++++|+++|.+||.|..+.++.      +++||||+|.+.++|+.|++.||+..+.|+.+.|..+
T Consensus         8 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   81 (111)
T 1whx_A            8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWA   81 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            3457999999999999999999999999999998863      4579999999999999999999999999999999887


Q ss_pred             eecc
Q psy3928          90 TSRL   93 (115)
Q Consensus        90 ~~~~   93 (115)
                      ....
T Consensus        82 ~~~~   85 (111)
T 1whx_A           82 PIGV   85 (111)
T ss_dssp             ETTT
T ss_pred             CCCc
Confidence            6543

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.75  E-value=4.6e-18  Score=98.92  Aligned_cols=78  Identities=14%  Similarity=0.074  Sum_probs=69.0

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      .....++|||+|||.++++++|+++|..||.|..+.+.      .++|||||+|.+.++|+.|+..|++..++|+.++|.
T Consensus        23 ~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~------~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   96 (101)
T 2la4_A           23 APPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY------PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTG   96 (101)
T ss_dssp             SCSSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE------TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCC
T ss_pred             CCCCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe------cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            34456899999999999999999999999999999886      346899999999999999999999999999988876


Q ss_pred             Eeee
Q psy3928          88 TTTS   91 (115)
Q Consensus        88 ~~~~   91 (115)
                      .+++
T Consensus        97 ~a~~  100 (101)
T 2la4_A           97 WGKE  100 (101)
T ss_dssp             BCCC
T ss_pred             eccC
Confidence            6554

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.75  E-value=1.8e-17  Score=94.92  Aligned_cols=79  Identities=23%  Similarity=0.296  Sum_probs=70.5

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      .....++|||+|||..+++++|+++|.+||.+..+.+.+        +||||+|.+.++|++|+..||+..+.|+.+.|.
T Consensus         6 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   77 (92)
T 2dgt_A            6 SGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQ   77 (92)
T ss_dssp             CCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECS--------SEEEEEESCHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEE
Confidence            345678999999999999999999999999999998863        399999999999999999999999999999888


Q ss_pred             Eeeeccc
Q psy3928          88 TTTSRLS   94 (115)
Q Consensus        88 ~~~~~~~   94 (115)
                      .++++..
T Consensus        78 ~a~~~~~   84 (92)
T 2dgt_A           78 LSTSRLR   84 (92)
T ss_dssp             ESSCCCS
T ss_pred             EccCCCC
Confidence            8876443

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.74  E-value=5.2e-18  Score=100.59  Aligned_cols=78  Identities=15%  Similarity=0.136  Sum_probs=69.7

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcC-CeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYG-KVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g-~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      ....+|||+|||.++++++|+++|.+|| .+..+.+..    ..++|||||+|.+.++|++|++.||+..++|+.++|..
T Consensus        26 ~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~----~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~  101 (111)
T 2jvr_A           26 AKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNT----RDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVER  101 (111)
T ss_dssp             CCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSS----CSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEc----CCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            3457999999999999999999999999 899988753    34789999999999999999999999999999998887


Q ss_pred             eee
Q psy3928          89 TTS   91 (115)
Q Consensus        89 ~~~   91 (115)
                      ++.
T Consensus       102 a~~  104 (111)
T 2jvr_A          102 DDN  104 (111)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            664

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=99.74  E-value=1.8e-17  Score=103.66  Aligned_cols=81  Identities=15%  Similarity=0.259  Sum_probs=76.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEee
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTT   90 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~   90 (115)
                      ..++|||+|||.++++++|+++|+.||.+..+.+..++.++.++|||||+|.+.++|++|++.+++..+.|+.+.+....
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            45789999999999999999999999999999999998899999999999999999999999999999999998888766


Q ss_pred             e
Q psy3928          91 S   91 (115)
Q Consensus        91 ~   91 (115)
                      +
T Consensus        82 ~   82 (168)
T 1b7f_A           82 P   82 (168)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.74  E-value=2.2e-17  Score=96.44  Aligned_cols=78  Identities=22%  Similarity=0.293  Sum_probs=70.3

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      ....++|||+|||.++++++|+++|.+||.|..+.++        ++||||+|.+.++|++|+..|++..+.++.+.|..
T Consensus         8 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   79 (103)
T 2dgu_A            8 MAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVF   79 (103)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEE
Confidence            3456899999999999999999999999999999885        34999999999999999999999999999999998


Q ss_pred             eeeccc
Q psy3928          89 TTSRLS   94 (115)
Q Consensus        89 ~~~~~~   94 (115)
                      ++++..
T Consensus        80 a~~~~~   85 (103)
T 2dgu_A           80 AKPPDQ   85 (103)
T ss_dssp             CCCCCC
T ss_pred             cCCCcc
Confidence            876543

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.74  E-value=1.5e-17  Score=96.13  Aligned_cols=79  Identities=14%  Similarity=0.126  Sum_probs=69.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      ...++|||+|||..+++++|+++|..||.+. +.++.    +.++|||||+|.+.++|++|+..||+..+.|+.+.|..+
T Consensus        17 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~----~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   91 (97)
T 2e5j_A           17 PLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTW----QGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALA   91 (97)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEE----ETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEEC
T ss_pred             CCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEc----CCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            4468999999999999999999999999886 55543    356789999999999999999999999999999999887


Q ss_pred             eecc
Q psy3928          90 TSRL   93 (115)
Q Consensus        90 ~~~~   93 (115)
                      +++.
T Consensus        92 ~~~~   95 (97)
T 2e5j_A           92 RQQR   95 (97)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7643

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.74  E-value=3e-18  Score=98.83  Aligned_cols=80  Identities=25%  Similarity=0.352  Sum_probs=70.4

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      .....++|||+|||..+++++|+++|..||.+..+     ..++.++|||||+|.+.++|++|+..+++..+.|+.+.+.
T Consensus        12 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   86 (96)
T 1fjc_A           12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLY   86 (96)
T ss_dssp             TTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            34557899999999999999999999999977655     2378899999999999999999999999999999998888


Q ss_pred             Eeeec
Q psy3928          88 TTTSR   92 (115)
Q Consensus        88 ~~~~~   92 (115)
                      .+.++
T Consensus        87 ~a~~~   91 (96)
T 1fjc_A           87 YTGEK   91 (96)
T ss_dssp             ECSSS
T ss_pred             EcCCC
Confidence            77653

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.74  E-value=5.1e-18  Score=102.31  Aligned_cols=81  Identities=21%  Similarity=0.240  Sum_probs=72.7

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCe----EEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCcee
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKV----TYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQS   84 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i----~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~   84 (115)
                      .....+|||+|||+++++++|+++|.+||.|    ..+.|+.++ +|+++|||||+|.+.++|++|++. ++..+.++.+
T Consensus        20 ~~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~-~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i   97 (123)
T 2dha_A           20 KENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP-DGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYI   97 (123)
T ss_dssp             CCSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECT-TSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECC-CCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEE
Confidence            4567899999999999999999999999875    578888885 899999999999999999999997 8889999988


Q ss_pred             eEEEeee
Q psy3928          85 SILTTTS   91 (115)
Q Consensus        85 ~v~~~~~   91 (115)
                      .|..+++
T Consensus        98 ~V~~a~~  104 (123)
T 2dha_A           98 ELFRSTA  104 (123)
T ss_dssp             CCEEECH
T ss_pred             EEEECCH
Confidence            8877765

>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=99.74  E-value=1.7e-17  Score=97.99  Aligned_cols=74  Identities=26%  Similarity=0.337  Sum_probs=68.0

Q ss_pred             CCCEEEEcCCCCC-CCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          11 YGRVVLKEKLPPE-AEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        11 ~~~~l~V~~l~~~-~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      ..++|||+|||.. +++++|+++|.+||.|..+.+        +++||||+|.+.++|++|+..|++..+.|..+.|..+
T Consensus        26 ~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   97 (110)
T 1wf1_A           26 INSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMA   97 (110)
T ss_dssp             CSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEES
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            3479999999999 999999999999999999887        4689999999999999999999999999999999887


Q ss_pred             eec
Q psy3928          90 TSR   92 (115)
Q Consensus        90 ~~~   92 (115)
                      +++
T Consensus        98 ~~~  100 (110)
T 1wf1_A           98 GEP  100 (110)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            753

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.74  E-value=8.3e-18  Score=99.43  Aligned_cols=78  Identities=21%  Similarity=0.205  Sum_probs=71.3

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEeee
Q psy3928          12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTTS   91 (115)
Q Consensus        12 ~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~~   91 (115)
                      ..+|||+|||.++++++|+++|..| .+..+.|+.++ .|+++|+|||+|.+.++|++|+ .+++..+.++.+.|..+..
T Consensus        16 ~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a~~   92 (109)
T 2dnn_A           16 DLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDH-VGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPATE   92 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCT-TCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECCH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECC-CCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCc
Confidence            4689999999999999999999999 89999999987 5999999999999999999999 6999999999988877665


Q ss_pred             c
Q psy3928          92 R   92 (115)
Q Consensus        92 ~   92 (115)
                      +
T Consensus        93 ~   93 (109)
T 2dnn_A           93 R   93 (109)
T ss_dssp             H
T ss_pred             c
Confidence            3

>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=99.74  E-value=2e-17  Score=102.56  Aligned_cols=79  Identities=20%  Similarity=0.233  Sum_probs=72.0

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      ....++|||+|||..+++++|+++|.+||.|..+.++.+     ++|||||+|.+.++|+.|+..||+..+.|+.++|..
T Consensus        70 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  144 (150)
T 2i2y_A           70 CPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVEL  144 (150)
T ss_dssp             STTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            345689999999999999999999999999999998764     578999999999999999999999999999999888


Q ss_pred             eeec
Q psy3928          89 TTSR   92 (115)
Q Consensus        89 ~~~~   92 (115)
                      ++++
T Consensus       145 a~~~  148 (150)
T 2i2y_A          145 SNGE  148 (150)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            7654

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.74  E-value=2.1e-17  Score=98.24  Aligned_cols=66  Identities=26%  Similarity=0.466  Sum_probs=59.7

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCC---CCeeeEEEEEecCHHHHHHHHHhhC
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKST---GKLKGFAFVEFSTKEEATKALELGL   75 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~---~~~~g~~fv~f~~~~~a~~al~~l~   75 (115)
                      ....++|||+|||.++++++|+++|.+||.+. +.++.++.+   |.++|||||+|.+.++|++|++.++
T Consensus         5 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~   73 (114)
T 2dnl_A            5 SSGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL   73 (114)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh
Confidence            34568999999999999999999999999999 888877666   7899999999999999999999983

>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=99.73  E-value=6.3e-18  Score=97.54  Aligned_cols=81  Identities=21%  Similarity=0.291  Sum_probs=72.6

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHH----HHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCcee
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIE----SVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQS   84 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~----~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~   84 (115)
                      ....++|||+|||.++++++|+    ++|.+||.+..+.+..   ++.++|||||+|.+.++|+.|+..|++..+.|+.+
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   81 (97)
T 1nu4_A            5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPM   81 (97)
T ss_dssp             -CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEE
Confidence            4567899999999999999999    9999999999998863   56778999999999999999999999999999999


Q ss_pred             eEEEeeec
Q psy3928          85 SILTTTSR   92 (115)
Q Consensus        85 ~v~~~~~~   92 (115)
                      .+..+++.
T Consensus        82 ~v~~a~~~   89 (97)
T 1nu4_A           82 RIQYAKTD   89 (97)
T ss_dssp             EEEECSSC
T ss_pred             EEEEccCC
Confidence            98887654

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A

Probab=99.73  E-value=1.3e-17  Score=100.91  Aligned_cols=79  Identities=25%  Similarity=0.302  Sum_probs=70.7

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeE--EEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVT--YVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~--~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      ....+|||+|||+++++++|+++|.+| .+.  .+.|+.++. |+++|||||+|.+.++|++|++. ++..+.|+.+.|.
T Consensus        40 ~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~~-~~~~l~gR~I~V~  116 (126)
T 2hgm_A           40 ANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALGK-HKERIGHRYIEVF  116 (126)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHTT-TTCCBTTBCCCCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHHH-CCCEECCEEEEEE
Confidence            456789999999999999999999999 677  899999885 99999999999999999999985 6688999998887


Q ss_pred             Eeee
Q psy3928          88 TTTS   91 (115)
Q Consensus        88 ~~~~   91 (115)
                      .+..
T Consensus       117 ~a~~  120 (126)
T 2hgm_A          117 KSSQ  120 (126)
T ss_dssp             EECH
T ss_pred             ECCH
Confidence            7654

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.73  E-value=3.2e-17  Score=94.26  Aligned_cols=79  Identities=18%  Similarity=0.168  Sum_probs=68.0

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      ...++|||+|||.++++++|+++|..||.+..+  +.++.++.   ||||+|.+.++|++|+. +++..+.|+.+.|..+
T Consensus         6 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a   79 (94)
T 2e5g_A            6 SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPR   79 (94)
T ss_dssp             TTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECCCBCS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEEC
Confidence            455799999999999999999999999999987  44444555   99999999999999999 9999999999888766


Q ss_pred             eeccc
Q psy3928          90 TSRLS   94 (115)
Q Consensus        90 ~~~~~   94 (115)
                      .++..
T Consensus        80 ~~~~~   84 (94)
T 2e5g_A           80 EQKEF   84 (94)
T ss_dssp             CCSCC
T ss_pred             CcCCC
Confidence            55433

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.73  E-value=4.4e-17  Score=101.48  Aligned_cols=82  Identities=13%  Similarity=0.165  Sum_probs=76.2

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      .....+|||+|||..+++++|+++|++||.+..+.+..++.++.++|+|||+|.+.++|.+|+..||+..+.|+.+.+..
T Consensus        84 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  163 (166)
T 3md3_A           84 SDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINW  163 (166)
T ss_dssp             CTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEe
Confidence            34567999999999999999999999999999999999988999999999999999999999999999999999988876


Q ss_pred             ee
Q psy3928          89 TT   90 (115)
Q Consensus        89 ~~   90 (115)
                      ++
T Consensus       164 a~  165 (166)
T 3md3_A          164 AA  165 (166)
T ss_dssp             SC
T ss_pred             cC
Confidence            54

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=2.4e-17  Score=92.93  Aligned_cols=76  Identities=14%  Similarity=0.180  Sum_probs=68.2

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhh-CCCCCCCceeeE
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELG-LNPCPTDYQSSI   86 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l-~~~~~~~~~~~v   86 (115)
                      .+...++|||+|||..+++++|+++|.+||.+..+.+..+      +|||||+|.+.++|+.|+..| ++..+.|+.+.+
T Consensus         8 ~~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~------kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v   81 (85)
T 2ytc_A            8 EDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNV   81 (85)
T ss_dssp             SCSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTTTCEETTEECCE
T ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC------CCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEE
Confidence            4556789999999999999999999999999999988753      589999999999999999999 999999988887


Q ss_pred             EEe
Q psy3928          87 LTT   89 (115)
Q Consensus        87 ~~~   89 (115)
                      ..+
T Consensus        82 ~~a   84 (85)
T 2ytc_A           82 KWG   84 (85)
T ss_dssp             EEC
T ss_pred             Eec
Confidence            654

>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=99.73  E-value=1.2e-17  Score=95.74  Aligned_cols=79  Identities=16%  Similarity=0.135  Sum_probs=68.4

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCC-eEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCC-CCCCCceeeE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGK-VTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN-PCPTDYQSSI   86 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~-i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~-~~~~~~~~~v   86 (115)
                      ....++|||+|||.++++++|+++|.+||. +..+.+.       ++|||||+|.+.++|++|++.||+ ..+.|+.+.|
T Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v   77 (93)
T 2cqh_A            5 SSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEV   77 (93)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEE
Confidence            345689999999999999999999999998 5555442       468999999999999999999999 8999999999


Q ss_pred             EEeeeccc
Q psy3928          87 LTTTSRLS   94 (115)
Q Consensus        87 ~~~~~~~~   94 (115)
                      ..++++..
T Consensus        78 ~~a~~~~~   85 (93)
T 2cqh_A           78 DYSVSKKL   85 (93)
T ss_dssp             EECCCCCC
T ss_pred             EEccCccc
Confidence            88876543

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.73  E-value=1.7e-17  Score=97.85  Aligned_cols=77  Identities=21%  Similarity=0.350  Sum_probs=69.4

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      .....++|||+|||.++++++|+++|.+||.|..+.+.        +|||||+|.+.++|++|+..|++..+.|+.+.|.
T Consensus        27 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   98 (108)
T 2jvo_A           27 GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVV   98 (108)
T ss_dssp             -CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            34567899999999999999999999999999999886        5799999999999999999999999999998887


Q ss_pred             Eeeec
Q psy3928          88 TTTSR   92 (115)
Q Consensus        88 ~~~~~   92 (115)
                      .++++
T Consensus        99 ~a~~~  103 (108)
T 2jvo_A           99 YSKLP  103 (108)
T ss_dssp             SCSCC
T ss_pred             EecCC
Confidence            77653

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.73  E-value=9.8e-18  Score=100.96  Aligned_cols=77  Identities=9%  Similarity=0.119  Sum_probs=69.0

Q ss_pred             CEEEEcCC----CCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecC----HHH----HHHHHH--hhCCCC
Q psy3928          13 RVVLKEKL----PPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFST----KEE----ATKALE--LGLNPC   78 (115)
Q Consensus        13 ~~l~V~~l----~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~----~~~----a~~al~--~l~~~~   78 (115)
                      ..|||+||    |+.+++..|+.+|++||.|..+.++.|+.||.++|||||+|.+    ++.    |.+|+.  .+++..
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~   82 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCF   82 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCe
Confidence            68999999    9999999999999999999999999999999999999999995    333    788888  789999


Q ss_pred             CCCceeeEEEe
Q psy3928          79 PTDYQSSILTT   89 (115)
Q Consensus        79 ~~~~~~~v~~~   89 (115)
                      ++|+.++|..-
T Consensus        83 I~Gr~irV~ln   93 (136)
T 2j8a_A           83 IMGFKFEVILN   93 (136)
T ss_dssp             ETTEEEEEEEC
T ss_pred             ecCcEEEEEEC
Confidence            99999888753

>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=99.72  E-value=5.3e-17  Score=93.99  Aligned_cols=76  Identities=16%  Similarity=0.332  Sum_probs=68.5

Q ss_pred             ccCCCCEEEEcCCCC-CCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeE
Q psy3928           8 NKKYGRVVLKEKLPP-EAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSI   86 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~-~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v   86 (115)
                      .....++|||+|||. ++++++|+++|..||.+..+.+.        +|||||+|.+.++|++|+..+++..+.|+.+.|
T Consensus        18 ~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V   89 (97)
T 2xnq_A           18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLIL   89 (97)
T ss_dssp             -CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTEECEE
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            345678999999998 99999999999999999999883        679999999999999999999999999999988


Q ss_pred             EEeee
Q psy3928          87 LTTTS   91 (115)
Q Consensus        87 ~~~~~   91 (115)
                      ..+++
T Consensus        90 ~~a~~   94 (97)
T 2xnq_A           90 EVSSS   94 (97)
T ss_dssp             EECCC
T ss_pred             EecCC
Confidence            87664

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.72  E-value=4.8e-17  Score=104.17  Aligned_cols=84  Identities=18%  Similarity=0.217  Sum_probs=78.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      ...++|||+|||..+++++|+++|.+||.+..+.+..++.++.++|+|||+|.+.++|.+|+..|++..++|+.+.+..+
T Consensus       112 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  191 (198)
T 2yh0_A          112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  191 (198)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            45689999999999999999999999999999999998889999999999999999999999999999999999998887


Q ss_pred             eecc
Q psy3928          90 TSRL   93 (115)
Q Consensus        90 ~~~~   93 (115)
                      .++.
T Consensus       192 ~~~~  195 (198)
T 2yh0_A          192 SVGA  195 (198)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7653

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=99.72  E-value=5.4e-17  Score=103.80  Aligned_cols=84  Identities=21%  Similarity=0.252  Sum_probs=75.5

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      .....++|||+|||.++++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|++|+.. ++..+.|+.+.+.
T Consensus         9 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v~   87 (196)
T 1l3k_A            9 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPK   87 (196)
T ss_dssp             CCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeeee
Confidence            344668999999999999999999999999999999999988899999999999999999999987 8888999988887


Q ss_pred             Eeeec
Q psy3928          88 TTTSR   92 (115)
Q Consensus        88 ~~~~~   92 (115)
                      ...+.
T Consensus        88 ~~~~~   92 (196)
T 1l3k_A           88 RAVSR   92 (196)
T ss_dssp             ECCC-
T ss_pred             cccCc
Confidence            76543

>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=99.72  E-value=3.2e-17  Score=97.22  Aligned_cols=79  Identities=22%  Similarity=0.288  Sum_probs=68.8

Q ss_pred             cCCCCEEEEcCCCCC-CCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCC--CCCCCceee
Q psy3928           9 KKYGRVVLKEKLPPE-AEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN--PCPTDYQSS   85 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~-~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~--~~~~~~~~~   85 (115)
                      ....++|||+|||.+ +++++|+++|.+||.|..+.+++      ++|||||+|.+.++|+.|++.|++  ..+.|+.+.
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~------~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~   95 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR------MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVK   95 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCE
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            345689999999998 99999999999999999998863      358999999999999999998864  458999999


Q ss_pred             EEEeeecc
Q psy3928          86 ILTTTSRL   93 (115)
Q Consensus        86 v~~~~~~~   93 (115)
                      |..++.+.
T Consensus        96 V~~a~~~~  103 (112)
T 1x4f_A           96 VDLSEKYK  103 (112)
T ss_dssp             EEEECSCS
T ss_pred             EEECcccc
Confidence            98887543

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.72  E-value=4e-17  Score=94.04  Aligned_cols=79  Identities=18%  Similarity=0.251  Sum_probs=70.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEE-EeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYV-SLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~-~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      ...++|||+|||..+++++|+++|..||.+..+ .++.++.++.    |||+|.+.++|++|+..||+..+.|+.+.|..
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~~----afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~   88 (96)
T 2e44_A           13 QRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAV----VNVTYSSKDQARQALDKLNGFQLENFTLKVAY   88 (96)
T ss_dssp             CSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSEE----EEEEESSHHHHHHHHHHHTTCBCSSCBCEEEE
T ss_pred             CCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCE----EEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            346899999999999999999999999999999 4776653333    99999999999999999999999999999988


Q ss_pred             eeec
Q psy3928          89 TTSR   92 (115)
Q Consensus        89 ~~~~   92 (115)
                      +.++
T Consensus        89 a~~~   92 (96)
T 2e44_A           89 IPDE   92 (96)
T ss_dssp             CCCC
T ss_pred             cCcc
Confidence            8765

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.72  E-value=5e-17  Score=101.21  Aligned_cols=79  Identities=20%  Similarity=0.195  Sum_probs=72.2

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEeeec
Q psy3928          13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTTSR   92 (115)
Q Consensus        13 ~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~~~   92 (115)
                      ++|||+|||.++++++|+++|++||.+..+.++.++ ++.++|+|||+|.+.++|++|+..+++..+.+..+.+....+.
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~   79 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQS   79 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCC-C-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECC-CCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCC
Confidence            589999999999999999999999999999999887 6788999999999999999999999999999999888776543

>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=99.72  E-value=1.3e-16  Score=100.19  Aligned_cols=72  Identities=21%  Similarity=0.238  Sum_probs=66.7

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCC--CeeeEEEEEecCHHHHHHHHHhhCCCCCCCc
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTG--KLKGFAFVEFSTKEEATKALELGLNPCPTDY   82 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~--~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~   82 (115)
                      +.++|||+|||.++++++|+++|.+||.+..+.++.++.++  .++|||||+|.+.++|++|++.+++..+.+.
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~   75 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPG   75 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTT
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccC
Confidence            56899999999999999999999999999999999998776  8999999999999999999999999887643

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=99.71  E-value=8.7e-17  Score=102.83  Aligned_cols=84  Identities=18%  Similarity=0.338  Sum_probs=74.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEee
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTT   90 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~   90 (115)
                      ..++|||+|||..+++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|.+|+.. ++..++|+.+.|..+.
T Consensus       103 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~a~  181 (196)
T 1l3k_A          103 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKAL  181 (196)
T ss_dssp             CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEECC
T ss_pred             CcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEecC
Confidence            457999999999999999999999999999999999988899999999999999999999987 7889999999998887


Q ss_pred             ecccc
Q psy3928          91 SRLSF   95 (115)
Q Consensus        91 ~~~~~   95 (115)
                      ++...
T Consensus       182 ~k~~~  186 (196)
T 1l3k_A          182 SKQEM  186 (196)
T ss_dssp             -----
T ss_pred             ChhHh
Confidence            76543

>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=99.71  E-value=7.3e-17  Score=101.26  Aligned_cols=79  Identities=19%  Similarity=0.227  Sum_probs=74.2

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      ...+|||+|||..+++++|+++|.+||.+..+.+..++.++.++|+|||+|.+.++|.+|+..||+..+.|+.+.|..+
T Consensus        93 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A           93 GAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             TTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeC
Confidence            3588999999999999999999999999999999999889999999999999999999999999999999998887654

>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=99.70  E-value=3.8e-16  Score=97.53  Aligned_cols=79  Identities=27%  Similarity=0.414  Sum_probs=72.8

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCC--ceeeEE
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTD--YQSSIL   87 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~--~~~~v~   87 (115)
                      ....+|||+|||..+++++|+++|.+||.+..+.+..++.++.++|+|||+|.+.++|.+|+..||+..+.|  ..+.|.
T Consensus        87 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V~  166 (168)
T 1b7f_A           87 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR  166 (168)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEEE
Confidence            456899999999999999999999999999999999988889999999999999999999999999999988  777665


Q ss_pred             E
Q psy3928          88 T   88 (115)
Q Consensus        88 ~   88 (115)
                      .
T Consensus       167 ~  167 (168)
T 1b7f_A          167 L  167 (168)
T ss_dssp             E
T ss_pred             e
Confidence            4

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.70  E-value=1.4e-16  Score=103.27  Aligned_cols=80  Identities=25%  Similarity=0.230  Sum_probs=71.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEee
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTT   90 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~   90 (115)
                      ..++|||+|||.++++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|++|+..+++..+.|+.+.+....
T Consensus        27 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~  106 (216)
T 2qfj_A           27 IMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPS  106 (216)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCS
T ss_pred             cCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCC
Confidence            45799999999999999999999999999999999988889999999999999999999999999999999998886544

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=99.70  E-value=5e-17  Score=101.59  Aligned_cols=81  Identities=20%  Similarity=0.303  Sum_probs=75.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEee
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTT   90 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~   90 (115)
                      ...+|||+|||..+++++|+++|++||.+..+.+..++.++.++|+|||+|.+.++|++|++ +++..+.|+.+.|..+.
T Consensus        86 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a~  164 (167)
T 2cjk_A           86 KTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAE  164 (167)
T ss_dssp             HCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEECC
T ss_pred             CCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeecC
Confidence            35689999999999999999999999999999999988789999999999999999999998 89999999999988877


Q ss_pred             ec
Q psy3928          91 SR   92 (115)
Q Consensus        91 ~~   92 (115)
                      ++
T Consensus       165 pk  166 (167)
T 2cjk_A          165 PR  166 (167)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>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=99.70  E-value=6.4e-17  Score=91.94  Aligned_cols=75  Identities=16%  Similarity=0.232  Sum_probs=67.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEee
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTT   90 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~   90 (115)
                      ..++|||+|||..+++++|+++|.+| .+..+.+.      .++|||||+|.+.++|++|++.+|+..+.|+.+++..+.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~   76 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe------CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcC
Confidence            46789999999999999999999999 89888873      567899999999999999999999999999999888765


Q ss_pred             ec
Q psy3928          91 SR   92 (115)
Q Consensus        91 ~~   92 (115)
                      ..
T Consensus        77 ~~   78 (88)
T 1wg1_A           77 TD   78 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.70  E-value=1.6e-16  Score=103.53  Aligned_cols=80  Identities=21%  Similarity=0.238  Sum_probs=73.7

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEee
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTT   90 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~   90 (115)
                      ...+|||+|||..+++++|+++|..||.|..+.++.++  +.++|||||+|.+.++|++|++.||+..++|+.+.|..++
T Consensus       102 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~--~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~  179 (213)
T 4f02_A          102 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK  179 (213)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             ccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccC--CCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            45789999999999999999999999999999999874  5579999999999999999999999999999999998876


Q ss_pred             ec
Q psy3928          91 SR   92 (115)
Q Consensus        91 ~~   92 (115)
                      ++
T Consensus       180 ~~  181 (213)
T 4f02_A          180 SR  181 (213)
T ss_dssp             CH
T ss_pred             CC
Confidence            53

>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=99.69  E-value=1.1e-17  Score=102.98  Aligned_cols=84  Identities=15%  Similarity=0.179  Sum_probs=71.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEE--ecee---CCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCcee
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVS--LPKF---KSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQS   84 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~--i~~~---~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~   84 (115)
                      ...++|||+|||..+++++|+.+|..||.|..+.  ++.+   ..++.++|||||+|.+.++|++|+..||+..+.|+.+
T Consensus        43 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l  122 (143)
T 3egn_A           43 EPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPM  122 (143)
T ss_dssp             SCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcEE
Confidence            4567999999999999999999999999886631  1111   2378899999999999999999999999999999999


Q ss_pred             eEEEeeecc
Q psy3928          85 SILTTTSRL   93 (115)
Q Consensus        85 ~v~~~~~~~   93 (115)
                      .|..+++..
T Consensus       123 ~V~~a~~~~  131 (143)
T 3egn_A          123 VVQFARSAR  131 (143)
T ss_dssp             EEEECCCSC
T ss_pred             EEEECCCCC
Confidence            998887643

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=1.8e-16  Score=91.58  Aligned_cols=78  Identities=15%  Similarity=0.189  Sum_probs=68.3

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      ....++|||+|+  ++++++|+++|.+||.|..+.+.      .++|||||+|.+.++|++|+..|++..+.|+.+.|..
T Consensus        12 ~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~   83 (97)
T 1x5p_A           12 PRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNI   83 (97)
T ss_dssp             CCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEEC
T ss_pred             CCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            345689999996  89999999999999999999883      4567999999999999999999999999999988887


Q ss_pred             eeeccc
Q psy3928          89 TTSRLS   94 (115)
Q Consensus        89 ~~~~~~   94 (115)
                      +.++..
T Consensus        84 a~~~~~   89 (97)
T 1x5p_A           84 ARKQPM   89 (97)
T ss_dssp             CSSCCC
T ss_pred             CCCCCC
Confidence            776543

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=1.2e-16  Score=94.86  Aligned_cols=77  Identities=16%  Similarity=0.142  Sum_probs=65.1

Q ss_pred             cCCCCEEEE--cCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCC-----CC
Q psy3928           9 KKYGRVVLK--EKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCP-----TD   81 (115)
Q Consensus         9 ~~~~~~l~V--~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~-----~~   81 (115)
                      ....++|||  +||+.++++++|+++|.+||.|..+.++.      .+|||||+|.+.++|++|++.|||..+     .+
T Consensus        22 ~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~------~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g   95 (114)
T 2cq2_A           22 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQK   95 (114)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT------TCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCE
T ss_pred             CCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEEccccCCC
Confidence            445678999  88999999999999999999999988753      268999999999999999999999876     45


Q ss_pred             ceeeEEEeee
Q psy3928          82 YQSSILTTTS   91 (115)
Q Consensus        82 ~~~~v~~~~~   91 (115)
                      ..+.+.++..
T Consensus        96 ~~l~v~~a~~  105 (114)
T 2cq2_A           96 ITLYLNFVEK  105 (114)
T ss_dssp             EECEEEEESC
T ss_pred             cEEEEEeccc
Confidence            5666666653

>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=99.69  E-value=6.9e-16  Score=96.11  Aligned_cols=74  Identities=22%  Similarity=0.323  Sum_probs=69.7

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCce
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQ   83 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~   83 (115)
                      ....+|||+|||..+++++|+++|.+||.+..+.+..++.+|.++|+|||+|.+.++|.+|++.||+..+.|+.
T Consensus        86 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~  159 (167)
T 1fxl_A           86 IRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGAT  159 (167)
T ss_dssp             GTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCS
T ss_pred             CCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCc
Confidence            35678999999999999999999999999999999998888999999999999999999999999999999965

>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=99.68  E-value=6.8e-16  Score=96.89  Aligned_cols=78  Identities=18%  Similarity=0.267  Sum_probs=70.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCC---ceeeEE
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTD---YQSSIL   87 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~---~~~~v~   87 (115)
                      ..++|||+|||..+++++|+++|++||.+..+.++.++ +|.++|+|||+|.+.++|.+|++.||+..+.+   +.+.|.
T Consensus        94 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V~  172 (175)
T 3nmr_A           94 EDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVK  172 (175)
T ss_dssp             GGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEEE
T ss_pred             CCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECC-CCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEEE
Confidence            56799999999999999999999999999999998886 68999999999999999999999999987764   666665


Q ss_pred             Ee
Q psy3928          88 TT   89 (115)
Q Consensus        88 ~~   89 (115)
                      .+
T Consensus       173 ~a  174 (175)
T 3nmr_A          173 FA  174 (175)
T ss_dssp             EC
T ss_pred             ec
Confidence            43

>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=99.68  E-value=4.6e-16  Score=97.61  Aligned_cols=77  Identities=16%  Similarity=0.032  Sum_probs=68.2

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCC--ceeeEEEe
Q psy3928          12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTD--YQSSILTT   89 (115)
Q Consensus        12 ~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~--~~~~v~~~   89 (115)
                      ..+|||+||+..+++++|+++|++||.|..+.+...    .++++|||+|.+.++|++|++.|||..+.+  +.++|..+
T Consensus        46 vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k----~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~A  121 (164)
T 1sjr_A           46 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS  121 (164)
T ss_dssp             EEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES----SSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEEC
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC----CCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEe
Confidence            457899999999999999999999999999988532    257899999999999999999999999966  88888887


Q ss_pred             eec
Q psy3928          90 TSR   92 (115)
Q Consensus        90 ~~~   92 (115)
                      +++
T Consensus       122 k~~  124 (164)
T 1sjr_A          122 KLT  124 (164)
T ss_dssp             SSS
T ss_pred             cCC
Confidence            764

>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=99.67  E-value=2.4e-16  Score=89.10  Aligned_cols=71  Identities=23%  Similarity=0.238  Sum_probs=64.0

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhc----C-------CeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCC
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKY----G-------KVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPC   78 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~----g-------~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~   78 (115)
                      ...++|||+|||.++++++|+++|.+|    |       .+..+.+..+      +|||||+|.+.++|++|+ .+|+..
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~-~l~g~~   76 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAM-AFDGII   76 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHG-GGTTCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHH-hcCCCE
Confidence            456899999999999999999999999    8       8888887643      689999999999999999 999999


Q ss_pred             CCCceeeEE
Q psy3928          79 PTDYQSSIL   87 (115)
Q Consensus        79 ~~~~~~~v~   87 (115)
                      +.|+.++|.
T Consensus        77 ~~g~~l~V~   85 (87)
T 2hzc_A           77 FQGQSLKIR   85 (87)
T ss_dssp             ETTEECEEE
T ss_pred             ECCeEEEEe
Confidence            999988765

>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=99.67  E-value=1.9e-16  Score=98.88  Aligned_cols=78  Identities=19%  Similarity=0.269  Sum_probs=68.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEee
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTT   90 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~   90 (115)
                      +.++|||+|||.++++++|+++|+.||.+..+.++.++.+|.++|||||+|.+.++|++|+..  +..++|+.+.+....
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g~~i~v~~~~   79 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT--QHILDGKVIDPKRAI   79 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS--CCEETTEECCCEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc--ccccCCeEccccccc
Confidence            457999999999999999999999999999999999988999999999999999999999995  345667766665543

>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=99.66  E-value=4.6e-16  Score=88.72  Aligned_cols=76  Identities=21%  Similarity=0.343  Sum_probs=59.1

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCC--CCceee
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCP--TDYQSS   85 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~--~~~~~~   85 (115)
                      ......+|||+|||.++++++|+++|++||.|..+.++.+     ++|||||+|.+.++|++    +++..+  .++.+.
T Consensus         7 ~~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~   77 (89)
T 3d2w_A            7 HHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQS----LCGEDLIIKGISVH   77 (89)
T ss_dssp             ----CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHH----HTTCEEEETTEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHH----HcCCCcccCCEEEE
Confidence            3456789999999999999999999999999999998753     68999999999999883    555543  366666


Q ss_pred             EEEeeec
Q psy3928          86 ILTTTSR   92 (115)
Q Consensus        86 v~~~~~~   92 (115)
                      +..+.++
T Consensus        78 v~~a~~k   84 (89)
T 3d2w_A           78 ISNAEPK   84 (89)
T ss_dssp             EEECC--
T ss_pred             EEEcCCC
Confidence            6666554

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.66  E-value=7.3e-16  Score=93.46  Aligned_cols=76  Identities=17%  Similarity=0.103  Sum_probs=66.2

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeE-EEEEecCHHHHHHHHHhhCCCCCCC--ceeeEEE
Q psy3928          12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGF-AFVEFSTKEEATKALELGLNPCPTD--YQSSILT   88 (115)
Q Consensus        12 ~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~-~fv~f~~~~~a~~al~~l~~~~~~~--~~~~v~~   88 (115)
                      .-.|||+||+..+++++|+++|++||.|..+.+....     +|+ |||+|.+.++|+.|++.|||..+.+  ..+++.+
T Consensus        28 VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~-----~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~  102 (130)
T 3zzy_A           28 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN-----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF  102 (130)
T ss_dssp             EEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEET-----TEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEE
T ss_pred             eEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCC-----CCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEe
Confidence            3578899999999999999999999999999876532     466 9999999999999999999999988  6677777


Q ss_pred             eeec
Q psy3928          89 TTSR   92 (115)
Q Consensus        89 ~~~~   92 (115)
                      +++.
T Consensus       103 ak~~  106 (130)
T 3zzy_A          103 SKLT  106 (130)
T ss_dssp             CSCS
T ss_pred             cCCC
Confidence            7653

>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=99.66  E-value=1.1e-16  Score=90.84  Aligned_cols=75  Identities=23%  Similarity=0.305  Sum_probs=60.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCC--CCCceeeEE
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPC--PTDYQSSIL   87 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~--~~~~~~~v~   87 (115)
                      ...++|||+|||.++++++|+++|.+||.|..+.++.+     ++|||||+|.+.++|+++    ++..  +.+..+.+.
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~----~~~~~~~~g~~l~v~   73 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSL----CGEDLIIKGISVHIS   73 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHT----TTCEEEETTEEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHH----hcCCceeCCEEEEEE
Confidence            35689999999999999999999999999999988653     678999999999999753    4433  356666666


Q ss_pred             Eeeecc
Q psy3928          88 TTTSRL   93 (115)
Q Consensus        88 ~~~~~~   93 (115)
                      .+.++.
T Consensus        74 ~a~~~~   79 (88)
T 1wf0_A           74 NAEPKH   79 (88)
T ss_dssp             CCCCCC
T ss_pred             ecCCCC
Confidence            655543

>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=99.66  E-value=5.3e-16  Score=100.82  Aligned_cols=76  Identities=21%  Similarity=0.198  Sum_probs=69.5

Q ss_pred             CCCEEEEcCCC-CCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          11 YGRVVLKEKLP-PEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        11 ~~~~l~V~~l~-~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      +.++|||+||| ..+++++|+++|.+||.|..++++.+     .+|+|||+|.+.++|++|++.|||..+.|+.++|..+
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s   77 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS-----KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVS   77 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTT-----STTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecC-----CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEc
Confidence            56899999999 89999999999999999999998754     3689999999999999999999999999999998876


Q ss_pred             ee
Q psy3928          90 TS   91 (115)
Q Consensus        90 ~~   91 (115)
                      +.
T Consensus        78 ~~   79 (205)
T 3tyt_A           78 KQ   79 (205)
T ss_dssp             SC
T ss_pred             cC
Confidence            53

>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=99.65  E-value=9.2e-16  Score=98.86  Aligned_cols=76  Identities=25%  Similarity=0.271  Sum_probs=68.5

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        12 ~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      .++|||+|||..+++++|+++|.+||.|..+++++++ ++.++|||||+|.+.++|++|+..++. .+.|+.+.|...
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~-~~~~kG~aFVeF~~~e~A~~A~~~~~~-~~~Gr~l~V~~~  184 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETPGQ-KYKETDLLILFK  184 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESSHHHHHHHHHCTTC-EETTEECEEEET
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHhCCC-eECCEEEEEEEh
Confidence            4789999999999999999999999999999999886 688999999999999999999987664 788888877644

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.65  E-value=1.7e-15  Score=91.29  Aligned_cols=73  Identities=21%  Similarity=0.113  Sum_probs=64.2

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeE-EEEEecCHHHHHHHHHhhCCCCCCC--ceeeEEEee
Q psy3928          14 VVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGF-AFVEFSTKEEATKALELGLNPCPTD--YQSSILTTT   90 (115)
Q Consensus        14 ~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~-~fv~f~~~~~a~~al~~l~~~~~~~--~~~~v~~~~   90 (115)
                      .|||+||+..+++++|+++|++||.|..+.+.. +     .|+ |||+|.+.++|+.|++.|||..+.+  ..++|..++
T Consensus        27 ~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~-~-----~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~Ak  100 (124)
T 2e5i_A           27 LLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFK-R-----NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYAR  100 (124)
T ss_dssp             EEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEE-S-----SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCS
T ss_pred             EEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEe-C-----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEec
Confidence            468999999999999999999999999998853 2     275 9999999999999999999999988  477887777


Q ss_pred             ec
Q psy3928          91 SR   92 (115)
Q Consensus        91 ~~   92 (115)
                      ++
T Consensus       101 ~~  102 (124)
T 2e5i_A          101 PT  102 (124)
T ss_dssp             CS
T ss_pred             CC
Confidence            64

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.65  E-value=2.8e-15  Score=85.69  Aligned_cols=74  Identities=18%  Similarity=0.173  Sum_probs=64.9

Q ss_pred             CCE-EEEcCCCCCCCHHH----HHHHhhhcC-CeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceee
Q psy3928          12 GRV-VLKEKLPPEAEHDY----IESVFSKYG-KVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSS   85 (115)
Q Consensus        12 ~~~-l~V~~l~~~~~~~~----l~~~f~~~g-~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~   85 (115)
                      ..+ |||+|||..+++++    |+++|.+|| .|..+       ++   |+|||.|.+.++|++|++.|+|..+.|+.++
T Consensus         8 ~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~i~   77 (96)
T 2diu_A            8 CHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRMENEDVFGNRII   77 (96)
T ss_dssp             SSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSCCE
T ss_pred             cceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcCCccCCceEE
Confidence            445 99999999999987    668999995 99887       33   8999999999999999999999999999999


Q ss_pred             EEEeeecccc
Q psy3928          86 ILTTTSRLSF   95 (115)
Q Consensus        86 v~~~~~~~~~   95 (115)
                      +.+++.+...
T Consensus        78 v~~A~~~sd~   87 (96)
T 2diu_A           78 VSFTPKNREL   87 (96)
T ss_dssp             EESSCCSCCC
T ss_pred             EEecCCCcce
Confidence            9988875543

>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=99.63  E-value=3.2e-15  Score=100.67  Aligned_cols=82  Identities=21%  Similarity=0.286  Sum_probs=73.7

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHH----HHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCce
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIE----SVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQ   83 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~----~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~   83 (115)
                      +....++|||+|||.++++++|+    ++|..||.|..+.+..   +++++|||||+|.+.++|++|++.+|+..+.|+.
T Consensus         5 ~~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   81 (282)
T 3pgw_A            5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKP   81 (282)
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcE
Confidence            34567899999999999999966    8999999999998864   7888999999999999999999999999999999


Q ss_pred             eeEEEeeec
Q psy3928          84 SSILTTTSR   92 (115)
Q Consensus        84 ~~v~~~~~~   92 (115)
                      +.|..++..
T Consensus        82 l~v~~a~~~   90 (282)
T 3pgw_A           82 MRIQYAKTD   90 (282)
T ss_pred             EEEEEeccC
Confidence            998877653

>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=99.63  E-value=6.5e-15  Score=99.22  Aligned_cols=83  Identities=20%  Similarity=0.255  Sum_probs=77.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      ....+|||+|||..+++++|+++|..||.+..+.++.++.+|.++|+|||+|.+.++|.+|+..+++..+.|+.+.+..+
T Consensus        93 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a  172 (284)
T 3smz_A           93 PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWT  172 (284)
T ss_dssp             CCSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEC
Confidence            34679999999999999999999999999999999998889999999999999999999999999999999999998877


Q ss_pred             eec
Q psy3928          90 TSR   92 (115)
Q Consensus        90 ~~~   92 (115)
                      .+.
T Consensus       173 ~~~  175 (284)
T 3smz_A          173 DAG  175 (284)
T ss_dssp             CGG
T ss_pred             CCC
Confidence            654

>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=99.62  E-value=1.2e-15  Score=96.03  Aligned_cols=77  Identities=26%  Similarity=0.358  Sum_probs=69.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEee
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTT   90 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~   90 (115)
                      ..++|||+|||..+++++|+++|.+||.+..+     ..++.++|+|||+|.+.++|.+|+..|++..+.|+.+.+..+.
T Consensus        98 ~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~  172 (175)
T 1fje_B           98 AARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTG  172 (175)
T ss_dssp             GGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-----CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEECS
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-----cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEecC
Confidence            45799999999999999999999999977665     3478899999999999999999999999999999998888776


Q ss_pred             ec
Q psy3928          91 SR   92 (115)
Q Consensus        91 ~~   92 (115)
                      ++
T Consensus       173 ~k  174 (175)
T 1fje_B          173 EK  174 (175)
T ss_dssp             SC
T ss_pred             CC
Confidence            54

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=99.61  E-value=4.5e-15  Score=97.57  Aligned_cols=79  Identities=20%  Similarity=0.153  Sum_probs=71.6

Q ss_pred             ccCCCCEEEEcCCCC-CCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeE
Q psy3928           8 NKKYGRVVLKEKLPP-EAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSI   86 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~-~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v   86 (115)
                      .....++|||+|||. ++++++|+++|..||.|..+.+..++     +|||||+|.+.++|++|++.+++..+.|+.+.+
T Consensus        30 ~~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v  104 (229)
T 2adc_A           30 AGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRI  104 (229)
T ss_dssp             GCCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEE
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            345678999999999 99999999999999999999998754     679999999999999999999999999999998


Q ss_pred             EEeee
Q psy3928          87 LTTTS   91 (115)
Q Consensus        87 ~~~~~   91 (115)
                      ..+..
T Consensus       105 ~~a~~  109 (229)
T 2adc_A          105 TLSKH  109 (229)
T ss_dssp             ECCSC
T ss_pred             EEecC
Confidence            87664

>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=99.61  E-value=2e-15  Score=102.09  Aligned_cols=82  Identities=18%  Similarity=0.297  Sum_probs=74.1

Q ss_pred             CCCCEEEEcCCCCC-CCHHHHHHHhhhcCCeEEEEeceeCC-CCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928          10 KYGRVVLKEKLPPE-AEHDYIESVFSKYGKVTYVSLPKFKS-TGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus        10 ~~~~~l~V~~l~~~-~~~~~l~~~f~~~g~i~~~~i~~~~~-~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      ...++|||+|||.. +++++|+++|..||.|..+.++.++. ++.++|+|||+|.+.++|.+|+ .||+..+.|+.+.|.
T Consensus       208 ~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~~i~V~  286 (292)
T 2ghp_A          208 LEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISVS  286 (292)
T ss_dssp             CTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEEEEE
T ss_pred             CCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-HhcCCEECCcEEEEE
Confidence            45689999999999 99999999999999999999998774 4899999999999999999999 999999999999988


Q ss_pred             Eeeec
Q psy3928          88 TTTSR   92 (115)
Q Consensus        88 ~~~~~   92 (115)
                      .++++
T Consensus       287 ~a~~k  291 (292)
T 2ghp_A          287 LADKK  291 (292)
T ss_dssp             ECCCC
T ss_pred             EecCC
Confidence            87764

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=99.61  E-value=5.2e-15  Score=99.71  Aligned_cols=82  Identities=23%  Similarity=0.269  Sum_probs=75.8

Q ss_pred             CCCCEEEEcCCCCCC-CHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928          10 KYGRVVLKEKLPPEA-EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~-~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      ....+|||+|||..+ ++++|+++|..||.+..+.+..++ +|.++|+|||+|.+.++|.+|+..|++..+.|+.+.+..
T Consensus       182 ~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~  260 (284)
T 3smz_A          182 LHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSF  260 (284)
T ss_dssp             TSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECS-SCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECC-CCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEE
Confidence            456899999999995 999999999999999999998887 899999999999999999999999999999999999888


Q ss_pred             eeec
Q psy3928          89 TTSR   92 (115)
Q Consensus        89 ~~~~   92 (115)
                      +.++
T Consensus       261 a~~~  264 (284)
T 3smz_A          261 CAPG  264 (284)
T ss_dssp             CCSS
T ss_pred             ecCC
Confidence            7764

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.61  E-value=1e-14  Score=85.53  Aligned_cols=84  Identities=20%  Similarity=0.052  Sum_probs=72.2

Q ss_pred             cCCCCEEEEcCCCC-----CCCHHHHHHHhhhcCCeEEEEeceeCCC-CCeeeEEEEEecCHHHHHHHHHhhCCCCCCCc
Q psy3928           9 KKYGRVVLKEKLPP-----EAEHDYIESVFSKYGKVTYVSLPKFKST-GKLKGFAFVEFSTKEEATKALELGLNPCPTDY   82 (115)
Q Consensus         9 ~~~~~~l~V~~l~~-----~~~~~~l~~~f~~~g~i~~~~i~~~~~~-~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~   82 (115)
                      ....++|+|.|+..     +-.+++|++.|++||.|..+.++.++.+ +.++|++||+|.+.++|++|+..|||..+.|+
T Consensus         5 ~~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr   84 (105)
T 2pe8_A            5 KCPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGR   84 (105)
T ss_dssp             GSCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCc
Confidence            35678999999963     2367899999999999999999887643 67899999999999999999999999999999


Q ss_pred             eeeEEEeeec
Q psy3928          83 QSSILTTTSR   92 (115)
Q Consensus        83 ~~~v~~~~~~   92 (115)
                      .+.+..+.+.
T Consensus        85 ~i~v~~a~~~   94 (105)
T 2pe8_A           85 VVKACFYNLD   94 (105)
T ss_dssp             ECEEEECCHH
T ss_pred             EEEEEEcCHH
Confidence            9998887653

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.58  E-value=5.1e-15  Score=94.98  Aligned_cols=76  Identities=21%  Similarity=0.166  Sum_probs=69.6

Q ss_pred             CCCEEEEcCCCC-CCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          11 YGRVVLKEKLPP-EAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        11 ~~~~l~V~~l~~-~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      ..++|||+|||. .+++++|+++|..||.+..+.++.++     +|||||+|.+.++|+.|+..+++..+.|+.+.+..+
T Consensus         2 ~~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a   76 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLS   76 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEEC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEe
Confidence            357999999999 99999999999999999999987654     679999999999999999999999999999998877


Q ss_pred             ee
Q psy3928          90 TS   91 (115)
Q Consensus        90 ~~   91 (115)
                      ..
T Consensus        77 ~~   78 (198)
T 1qm9_A           77 KH   78 (198)
T ss_dssp             CC
T ss_pred             cC
Confidence            64

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.57  E-value=1e-14  Score=96.65  Aligned_cols=79  Identities=18%  Similarity=0.146  Sum_probs=68.4

Q ss_pred             cCCCCEEEEcCCCCCC---------CHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCC
Q psy3928           9 KKYGRVVLKEKLPPEA---------EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCP   79 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~---------~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~   79 (115)
                      +...++|||+||+..+         ++++|+.+|.+||.|..+.++.+      +|||||+|.+.++|+.|++.|++..+
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~------kG~AFV~F~~~~~Ae~A~~am~g~~l  204 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES------KNCGFVKFKYQANAEFAKEAMSNQTL  204 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHHHTTCCC
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECC------CCEEEEEeCCHHHHHHHHHHhCCCEE
Confidence            4456899999999998         69999999999999999998753      68999999999999999999999999


Q ss_pred             ------------CCceeeEEEeeecc
Q psy3928          80 ------------TDYQSSILTTTSRL   93 (115)
Q Consensus        80 ------------~~~~~~v~~~~~~~   93 (115)
                                  .|+.+.|..++...
T Consensus       205 ~~~~~~e~~~~~~gr~L~V~wA~~~p  230 (240)
T 3u1l_A          205 LLPSDKEWDDRREGTGLLVKWANEDP  230 (240)
T ss_dssp             CCTTSTTGGGGGGSCCCEEEECC---
T ss_pred             eccccccccccCCCCEEEEEEccCCC
Confidence                        78888888776543

>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=99.56  E-value=2.6e-14  Score=96.21  Aligned_cols=77  Identities=19%  Similarity=0.210  Sum_probs=68.8

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCC-CceeeEE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPT-DYQSSIL   87 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~-~~~~~v~   87 (115)
                      ....++|||+|||..+++++|+++|..||.|..+.+..++     +|+|||+|.+.++|.+|+..||+..+. |+.++|.
T Consensus       204 ~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~  278 (282)
T 3pgw_A          204 NPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKIS  278 (282)
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC-----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEE
Confidence            3456889999999999999999999999999999887543     579999999999999999999999999 8888887


Q ss_pred             Eee
Q psy3928          88 TTT   90 (115)
Q Consensus        88 ~~~   90 (115)
                      .++
T Consensus       279 ~ak  281 (282)
T 3pgw_A          279 FAK  281 (282)
T ss_pred             Eec
Confidence            654

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.56  E-value=3.5e-14  Score=94.98  Aligned_cols=80  Identities=25%  Similarity=0.318  Sum_probs=70.2

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCC----CceeeE
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPT----DYQSSI   86 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~----~~~~~v   86 (115)
                      ...+|||+|||..+++++|+++|..||.|..+.++.++ +|.++|+|||+|.+.++|.+|+..+++..+.    ++.+.|
T Consensus        95 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v  173 (261)
T 3sde_A           95 HGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDD-RGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIV  173 (261)
T ss_dssp             CSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET-TSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEE
T ss_pred             cCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCC-CCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEE
Confidence            45789999999999999999999999999999999985 8999999999999999999999999654332    677777


Q ss_pred             EEeee
Q psy3928          87 LTTTS   91 (115)
Q Consensus        87 ~~~~~   91 (115)
                      ..+.+
T Consensus       174 ~~~~~  178 (261)
T 3sde_A          174 EPMEQ  178 (261)
T ss_dssp             EECCC
T ss_pred             eeccc
Confidence            76654

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.55  E-value=3.7e-14  Score=90.94  Aligned_cols=77  Identities=18%  Similarity=0.176  Sum_probs=69.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcC-CeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCC-CceeeEEE
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYG-KVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPT-DYQSSILT   88 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g-~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~-~~~~~v~~   88 (115)
                      ..++|||+|||..+++++|+++|..|| .+..+.+..+     .+|+|||+|.+.++|.+|+..|++..+. |+.+.+..
T Consensus       119 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~  193 (198)
T 1qm9_A          119 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSF  193 (198)
T ss_dssp             CCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESST-----TSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeC-----CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEe
Confidence            368899999999999999999999999 9999988653     2689999999999999999999999999 89999888


Q ss_pred             eeec
Q psy3928          89 TTSR   92 (115)
Q Consensus        89 ~~~~   92 (115)
                      ++++
T Consensus       194 a~~~  197 (198)
T 1qm9_A          194 SKST  197 (198)
T ss_dssp             ECCC
T ss_pred             eccc
Confidence            7754

>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=99.54  E-value=1.2e-14  Score=94.46  Aligned_cols=71  Identities=15%  Similarity=0.092  Sum_probs=63.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCe--EEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCce
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKV--TYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQ   83 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i--~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~   83 (115)
                      ..++|||+|||..+++++|+++|++||.+  ..+++..++  +.++|+|||+|.+.++|.+|+..||+..+.+..
T Consensus       122 p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~--~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~  194 (205)
T 3tyt_A          122 PSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK--SERSSSGLLEWDSKSDALETLGFLNHYQMKNPN  194 (205)
T ss_dssp             CCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCC--SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSS
T ss_pred             CcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCC--CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCC
Confidence            35689999999999999999999999998  888887664  555699999999999999999999999888864

>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=99.54  E-value=2.6e-14  Score=96.58  Aligned_cols=83  Identities=14%  Similarity=0.207  Sum_probs=69.8

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcC-CeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYG-KVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g-~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      ...++|||+|||..+++++|+++|..|| .+..+.++.++ .+.++|||||+|.+.++|.+|+..|++..+.|+.+.+..
T Consensus       115 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~-~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  193 (292)
T 2ghp_A          115 LTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLR-FNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKV  193 (292)
T ss_dssp             CCSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC--------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            3568999999999999999999999999 99999998887 478899999999999999999999999999999998887


Q ss_pred             eeecc
Q psy3928          89 TTSRL   93 (115)
Q Consensus        89 ~~~~~   93 (115)
                      +.+..
T Consensus       194 a~~~~  198 (292)
T 2ghp_A          194 SNPLE  198 (292)
T ss_dssp             CCCC-
T ss_pred             CCCCc
Confidence            76543

>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=99.54  E-value=1.1e-15  Score=96.22  Aligned_cols=82  Identities=16%  Similarity=0.112  Sum_probs=69.2

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      .....++|||+|||.++++++|+++|..||.+..+ ++.+..++.++|||||+|.+.++|++|++ +++..+.|+.+.+.
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~-~~~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~v~   86 (175)
T 1fje_B            9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDL-AVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLE   86 (175)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTC-CCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceE-EEEECCCCccccEEEEEECCHHHHHHHHh-cCCCEeCCeEEEEe
Confidence            34567899999999999999999999999876552 33444478889999999999999999994 99999999998887


Q ss_pred             Eeee
Q psy3928          88 TTTS   91 (115)
Q Consensus        88 ~~~~   91 (115)
                      ...+
T Consensus        87 ~~~~   90 (175)
T 1fje_B           87 KPKG   90 (175)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            7664

>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=99.54  E-value=7.1e-14  Score=82.66  Aligned_cols=82  Identities=18%  Similarity=0.175  Sum_probs=68.6

Q ss_pred             CCCCEEEEcCCCCCCC-----------HHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCC
Q psy3928          10 KYGRVVLKEKLPPEAE-----------HDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPC   78 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~-----------~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~   78 (115)
                      ...++|+|.||.....           +++|+++|.+||.|..+.| .++   .++|||||+|.+.++|++|+..||+..
T Consensus        13 ~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~lng~~   88 (112)
T 2dit_A           13 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTLDGRW   88 (112)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHSTTCE
T ss_pred             CCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHcCCCE
Confidence            3567899999954332           5789999999999999966 433   378999999999999999999999999


Q ss_pred             CCCceeeEEEeeecccc
Q psy3928          79 PTDYQSSILTTTSRLSF   95 (115)
Q Consensus        79 ~~~~~~~v~~~~~~~~~   95 (115)
                      ++|+.+.+..+.++..+
T Consensus        89 ~~gr~l~v~~a~~~~~~  105 (112)
T 2dit_A           89 FGGRQITAQAWDGTTDY  105 (112)
T ss_dssp             ETTEECEEEECCSCCCS
T ss_pred             ECCcEEEEEEeCCCCCc
Confidence            99999999988776554

>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=99.54  E-value=6.3e-14  Score=92.10  Aligned_cols=77  Identities=18%  Similarity=0.176  Sum_probs=69.2

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcC-CeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCC-CceeeEEE
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYG-KVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPT-DYQSSILT   88 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g-~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~-~~~~~v~~   88 (115)
                      ..++|||+|||..+++++|+++|..|| .+..+.+...     .+|+|||+|.+.++|.+|+..|++..+. |+.+.+..
T Consensus       150 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~  224 (229)
T 2adc_A          150 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSF  224 (229)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS-----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEE
T ss_pred             CCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC-----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEE
Confidence            358899999999999999999999999 9999988542     2579999999999999999999999999 89999888


Q ss_pred             eeec
Q psy3928          89 TTSR   92 (115)
Q Consensus        89 ~~~~   92 (115)
                      ++++
T Consensus       225 a~~~  228 (229)
T 2adc_A          225 SKST  228 (229)
T ss_dssp             CSSC
T ss_pred             ecCC
Confidence            7754

>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=99.50  E-value=5.7e-14  Score=93.94  Aligned_cols=76  Identities=17%  Similarity=0.230  Sum_probs=68.1

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      ...++|||+|||.++++++|+++|..||.|..+.+..+      +|||||+|.+.++|+.|+..+++..+.|+.+.+..+
T Consensus        20 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~a   93 (261)
T 3sde_A           20 TQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFA   93 (261)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeec
Confidence            34579999999999999999999999999999988532      589999999999999999999999999999888766


Q ss_pred             ee
Q psy3928          90 TS   91 (115)
Q Consensus        90 ~~   91 (115)
                      .+
T Consensus        94 ~~   95 (261)
T 3sde_A           94 TH   95 (261)
T ss_dssp             CC
T ss_pred             cc
Confidence            54

>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=99.50  E-value=1.3e-14  Score=84.98  Aligned_cols=71  Identities=20%  Similarity=0.181  Sum_probs=60.3

Q ss_pred             EcCCCCCCCHHHHHHHh------------hhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCcee
Q psy3928          17 KEKLPPEAEHDYIESVF------------SKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQS   84 (115)
Q Consensus        17 V~~l~~~~~~~~l~~~f------------~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~   84 (115)
                      +.+||..+++.+|++.|            ++||.|..+.++.++ ++.++|++||+|.+.++|++|+..|||..++|+.+
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~-~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i   98 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPI   98 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCC-CCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEE
Confidence            45666666777666665            999999999998876 57899999999999999999999999999999988


Q ss_pred             eEEE
Q psy3928          85 SILT   88 (115)
Q Consensus        85 ~v~~   88 (115)
                      .+..
T Consensus        99 ~v~~  102 (104)
T 1jmt_A           99 HAEL  102 (104)
T ss_dssp             CEEE
T ss_pred             EEEE
Confidence            7754

>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=99.48  E-value=8.5e-14  Score=87.17  Aligned_cols=73  Identities=22%  Similarity=0.237  Sum_probs=63.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhc----C-------CeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCC
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKY----G-------KVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCP   79 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~----g-------~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~   79 (115)
                      +.++|||+|||.++++++|+++|++|    |       .+..+.+.      .++|||||+|.+.++|++|+ .+++..+
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~------~~~g~afV~f~~~~~A~~A~-~~~~~~~   75 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN------QDKNFAFLEFRSVDETTQAM-AFDGIIF   75 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEE------TTTTEEEEEESSHHHHHHHG-GGTTCEE
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEec------CCCCEEEEEeCCHHHHHHHH-HhCCcEe
Confidence            45799999999999999999999999    5       56666553      34789999999999999999 8999999


Q ss_pred             CCceeeEEEee
Q psy3928          80 TDYQSSILTTT   90 (115)
Q Consensus        80 ~~~~~~v~~~~   90 (115)
                      .|+.+.+....
T Consensus        76 ~g~~i~v~~~~   86 (172)
T 2g4b_A           76 QGQSLKIRRPH   86 (172)
T ss_dssp             TTEECEEECCS
T ss_pred             cCceeeecCCc
Confidence            99988877654

>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=99.46  E-value=3.3e-13  Score=79.08  Aligned_cols=82  Identities=20%  Similarity=0.137  Sum_probs=68.5

Q ss_pred             CCCEEEEcCC--CCCCC--------HHHHHHHhhhcCCeEEEEeceeCCC--CCeeeEEEEEecCHHHHHHHHHhhCCCC
Q psy3928          11 YGRVVLKEKL--PPEAE--------HDYIESVFSKYGKVTYVSLPKFKST--GKLKGFAFVEFSTKEEATKALELGLNPC   78 (115)
Q Consensus        11 ~~~~l~V~~l--~~~~~--------~~~l~~~f~~~g~i~~~~i~~~~~~--~~~~g~~fv~f~~~~~a~~al~~l~~~~   78 (115)
                      +.+.|.+.|+  |....        +++|++.|++||.|..+.|++++.+  +.++|++||+|.+.++|++|++.|||..
T Consensus         4 ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~~   83 (105)
T 3v4m_A            4 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   83 (105)
T ss_dssp             CCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCCE
Confidence            4577888887  33333        2579999999999999999888744  3578999999999999999999999999


Q ss_pred             CCCceeeEEEeeec
Q psy3928          79 PTDYQSSILTTTSR   92 (115)
Q Consensus        79 ~~~~~~~v~~~~~~   92 (115)
                      +.|+.+.+......
T Consensus        84 f~GR~i~v~~~~~~   97 (105)
T 3v4m_A           84 FANRVVVTKYCDPD   97 (105)
T ss_dssp             ETTEECEEEEECHH
T ss_pred             eCCCEEEEEEeCHH
Confidence            99999998876543

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.45  E-value=1.3e-13  Score=88.02  Aligned_cols=74  Identities=22%  Similarity=0.250  Sum_probs=63.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhc----C-------CeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCC
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKY----G-------KVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCP   79 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~----g-------~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~   79 (115)
                      ..++|||+|||.++++++|+++|..|    |       .+..+.+      +.++|||||+|.+.++|++|+ .+++..+
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~------~~~~g~afV~F~~~~~A~~Al-~l~g~~~   75 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI------NQDKNFAFLEFRSVDETTQAM-AFDGIIF   75 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEE------ETTTTEEEEEESCSHHHHHHG-GGTTEEE
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEe------cCCCCEEEEEeCCHHHHHHHH-HhcCCEE
Confidence            46899999999999999999999999    4       4555544      345789999999999999999 8999999


Q ss_pred             CCceeeEEEeee
Q psy3928          80 TDYQSSILTTTS   91 (115)
Q Consensus        80 ~~~~~~v~~~~~   91 (115)
                      .|+.+.+.....
T Consensus        76 ~g~~i~v~~~~~   87 (198)
T 2yh0_A           76 QGQSLKIRRPHD   87 (198)
T ss_dssp             TTEEEEEECCCC
T ss_pred             cCceEEEeCCCC
Confidence            999988876654

>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=99.44  E-value=9e-13  Score=78.72  Aligned_cols=81  Identities=17%  Similarity=0.130  Sum_probs=69.3

Q ss_pred             CCCEEEEcCCCC--CC---CHHHHHHHhhhcCCeEEEEeceeCC----CCCeeeEEEEEecCHHHHHHHHHhhCCCCCCC
Q psy3928          11 YGRVVLKEKLPP--EA---EHDYIESVFSKYGKVTYVSLPKFKS----TGKLKGFAFVEFSTKEEATKALELGLNPCPTD   81 (115)
Q Consensus        11 ~~~~l~V~~l~~--~~---~~~~l~~~f~~~g~i~~~~i~~~~~----~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~   81 (115)
                      ..++|++.|+-.  .+   -+++|++.|++||.|..+.|+.++.    ++.++|++||+|.+.++|.+|++.|||..++|
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~G   98 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG   98 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECC
Confidence            568899999842  22   3578999999999999999998864    35678999999999999999999999999999


Q ss_pred             ceeeEEEeee
Q psy3928          82 YQSSILTTTS   91 (115)
Q Consensus        82 ~~~~v~~~~~   91 (115)
                      +.+.+.....
T Consensus        99 R~i~v~~~~~  108 (118)
T 3ue2_A           99 RKVVAEVYDQ  108 (118)
T ss_dssp             EECEEEEECH
T ss_pred             cEEEEEEcCh
Confidence            9999887755

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.44  E-value=3.4e-12  Score=74.10  Aligned_cols=75  Identities=23%  Similarity=0.178  Sum_probs=59.3

Q ss_pred             CCEEEEcCCC-------CCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCcee
Q psy3928          12 GRVVLKEKLP-------PEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQS   84 (115)
Q Consensus        12 ~~~l~V~~l~-------~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~   84 (115)
                      ..++-|.-..       ..+++++|+++|.+||.|..+.|+     +.++|||||+|.+.++|+.|++.+++  +.++.+
T Consensus        10 ~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l   82 (100)
T 2d9o_A           10 TPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNEVG--LVDNPL   82 (100)
T ss_dssp             SCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBC
T ss_pred             cceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeE
Confidence            4455555433       458899999999999999999886     46789999999999999999998655  467777


Q ss_pred             eEEEeeecc
Q psy3928          85 SILTTTSRL   93 (115)
Q Consensus        85 ~v~~~~~~~   93 (115)
                      .|..++++.
T Consensus        83 ~V~~a~~~~   91 (100)
T 2d9o_A           83 KISWLEGQP   91 (100)
T ss_dssp             EEECSSCCC
T ss_pred             EEEEccCCC
Confidence            777666543

>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=99.40  E-value=8.6e-13  Score=91.50  Aligned_cols=67  Identities=18%  Similarity=0.198  Sum_probs=58.6

Q ss_pred             ccCCCCEEEEcC--CCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCC
Q psy3928           8 NKKYGRVVLKEK--LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPT   80 (115)
Q Consensus         8 ~~~~~~~l~V~~--l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~   80 (115)
                      ......+|||+|  |+..+++++|+++|++||.|..+.+..      .+|||||+|.+.++|++|++.|||..+.
T Consensus        14 ~~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~~~~   82 (345)
T 3tht_A           14 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVV   82 (345)
T ss_dssp             CSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTTCEEE
T ss_pred             cCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCccc
Confidence            345668999998  578999999999999999999987743      3689999999999999999999999763

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.22  E-value=1.1e-10  Score=69.65  Aligned_cols=74  Identities=12%  Similarity=0.106  Sum_probs=62.5

Q ss_pred             cCCCCEEEEcCCCCC-CCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecC-HHHHHHHHHhhC--CCCCCCcee
Q psy3928           9 KKYGRVVLKEKLPPE-AEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFST-KEEATKALELGL--NPCPTDYQS   84 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~-~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~-~~~a~~al~~l~--~~~~~~~~~   84 (115)
                      -..+..|||+||+.. ++.++|+++|+.||.|..|.+..+..      .|||.|.+ ..+|..|+..++  +..+.+..+
T Consensus        15 ~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~   88 (121)
T 1owx_A           15 EKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGNLQLRNKEV   88 (121)
T ss_dssp             CCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCBCTTSSSE
T ss_pred             ccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCCcEEeCcEE
Confidence            456789999999999 99999999999999999999876542      49999999 899999999995  556777665


Q ss_pred             eEEE
Q psy3928          85 SILT   88 (115)
Q Consensus        85 ~v~~   88 (115)
                      .+..
T Consensus        89 ~~ev   92 (121)
T 1owx_A           89 TWEV   92 (121)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            5544

>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=99.17  E-value=4.8e-11  Score=70.79  Aligned_cols=76  Identities=12%  Similarity=0.019  Sum_probs=61.6

Q ss_pred             CCEEEEcCCCCCCC----------HHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCC
Q psy3928          12 GRVVLKEKLPPEAE----------HDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTD   81 (115)
Q Consensus        12 ~~~l~V~~l~~~~~----------~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~   81 (115)
                      .+.|.+.|+-..-.          +++|++.|++||.|..+.+..+.    ++|++||+|.+.++|++|++.|||..++|
T Consensus         7 s~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG~~f~G   82 (114)
T 3s6e_A            7 TQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGRWFAG   82 (114)
T ss_dssp             CSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTCEETT
T ss_pred             CcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            45677777643221          24689999999999999886542    47999999999999999999999999999


Q ss_pred             ceeeEEEeee
Q psy3928          82 YQSSILTTTS   91 (115)
Q Consensus        82 ~~~~v~~~~~   91 (115)
                      +.+.+.....
T Consensus        83 R~i~v~~~~~   92 (114)
T 3s6e_A           83 KMITAAYVPL   92 (114)
T ss_dssp             EECEEEEECH
T ss_pred             EEEEEEEEcH
Confidence            9999988754

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.02  E-value=1.1e-09  Score=62.02  Aligned_cols=73  Identities=18%  Similarity=0.191  Sum_probs=60.4

Q ss_pred             CCCCEEEEcCCCC----C-CCH---HHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCC
Q psy3928          10 KYGRVVLKEKLPP----E-AEH---DYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTD   81 (115)
Q Consensus        10 ~~~~~l~V~~l~~----~-~~~---~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~   81 (115)
                      +...+|+|.-.+.    . ..+   .+|...|.+||.+..+++..++        +||+|.+.+.|.+|+. |||..+.|
T Consensus         5 Ppd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~-mnG~~v~G   75 (91)
T 2dnr_A            5 SSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFLEGSSALNVLS-LNGKELLN   75 (91)
T ss_dssp             CSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEESSHHHHHHGGG-GTTCEETT
T ss_pred             CCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEECChHHHHHHHh-cCCeEeCC
Confidence            4567788877652    2 332   5689999999999999998764        8999999999999998 99999999


Q ss_pred             ceeeEEEeee
Q psy3928          82 YQSSILTTTS   91 (115)
Q Consensus        82 ~~~~v~~~~~   91 (115)
                      +.++|..+++
T Consensus        76 r~LkV~lkt~   85 (91)
T 2dnr_A           76 RTITIALKSP   85 (91)
T ss_dssp             EEEEEEECCC
T ss_pred             eEEEEEeCCC
Confidence            9999888775

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=98.95  E-value=5.4e-09  Score=68.13  Aligned_cols=67  Identities=19%  Similarity=0.128  Sum_probs=58.7

Q ss_pred             CHHHHHHHhhhcCCeEEEEeceeCC----CCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEeee
Q psy3928          25 EHDYIESVFSKYGKVTYVSLPKFKS----TGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTTS   91 (115)
Q Consensus        25 ~~~~l~~~f~~~g~i~~~~i~~~~~----~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~~   91 (115)
                      .+++|.+.|.+||.+..+.+..+..    ++.++|++||+|.+.++|++|++.|||..+.|+.+.+.....
T Consensus       142 ~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~~  212 (222)
T 3dxb_A          142 LEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQ  212 (222)
T ss_dssp             HHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECCH
T ss_pred             HHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcCH
Confidence            4467999999999999999986643    448899999999999999999999999999999999887653

>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=98.86  E-value=4e-09  Score=59.99  Aligned_cols=77  Identities=13%  Similarity=0.129  Sum_probs=62.8

Q ss_pred             hhcccCCCCEEEEcCCCCC------CCH---HHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhC
Q psy3928           5 VENNKKYGRVVLKEKLPPE------AEH---DYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGL   75 (115)
Q Consensus         5 ~~~~~~~~~~l~V~~l~~~------~~~---~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~   75 (115)
                      .....+...+|+|.-++..      ..+   .+|.+.|.+||.+..+++..++        +||+|.+.+.|.+|+. |+
T Consensus         8 i~~~GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~-ld   78 (95)
T 1ufw_A            8 SSFQGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLD-VD   78 (95)
T ss_dssp             SCCCCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHH-GG
T ss_pred             ceecCCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHh-cC
Confidence            3445667789999887743      332   4589999999999999987763        9999999999999998 99


Q ss_pred             CCCCCCceeeEEEee
Q psy3928          76 NPCPTDYQSSILTTT   90 (115)
Q Consensus        76 ~~~~~~~~~~v~~~~   90 (115)
                      |..+.|+.++|....
T Consensus        79 G~~v~Gr~L~V~~k~   93 (95)
T 1ufw_A           79 GMKVKGRAVKISGPS   93 (95)
T ss_dssp             GSEETTEEEEEECCC
T ss_pred             CeeeCCeEEEEeccC
Confidence            999999998887654

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.60  E-value=2.2e-07  Score=54.09  Aligned_cols=76  Identities=13%  Similarity=-0.024  Sum_probs=66.3

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhc-----CCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCce
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKY-----GKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQ   83 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~-----g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~   83 (115)
                      +...++|-+-+||..++...|+.++.++     |.+..+.+..+.      +.|+|+|.+...|.+|.-.|+|..+.|+.
T Consensus        18 ~~~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH------~GAivef~d~~~AgKasLaL~G~ef~gr~   91 (117)
T 2l9w_A           18 KELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF------NGAIIIFRDSKFAAKMLMILNGSQFQGKV   91 (117)
T ss_dssp             TTTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTT------TEEEEECSCHHHHHHHHHHHSSEEETTEE
T ss_pred             ccCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCC------CceEEEEccchhhHHHHhhcCCeeecCeE
Confidence            3447888888999999999999999999     889888876654      57999999999999999999999999998


Q ss_pred             eeEEEee
Q psy3928          84 SSILTTT   90 (115)
Q Consensus        84 ~~v~~~~   90 (115)
                      +++..+.
T Consensus        92 Lr~gTv~   98 (117)
T 2l9w_A           92 IRSGTIN   98 (117)
T ss_dssp             EEEECHH
T ss_pred             EEecCHH
Confidence            8876553

>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=97.88  E-value=6e-05  Score=42.95  Aligned_cols=55  Identities=24%  Similarity=0.295  Sum_probs=46.2

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhC
Q psy3928          12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGL   75 (115)
Q Consensus        12 ~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~   75 (115)
                      .+.+++ ++|+.+...+|.++|++||. ..++++.+-       -|||.|.+++.|..|+..+.
T Consensus        16 ~HVf~l-~FP~ewKt~DI~~lFs~fgg-v~I~WidDT-------sAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           16 DHVLHV-TFPKEWKTSDLYQLFSAFGN-IQISWIDDT-------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CSEEEE-ECCTTCCHHHHHHHHTTTCS-CCCEEEETT-------EEEEECSCHHHHHHHHHHHH
T ss_pred             CeEEEE-eCChhhhhHHHHHHhhccCC-EEEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            466777 99999999999999999983 346666553       79999999999999999774

>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=97.71  E-value=7.2e-05  Score=42.71  Aligned_cols=54  Identities=24%  Similarity=0.282  Sum_probs=46.2

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhC
Q psy3928          13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGL   75 (115)
Q Consensus        13 ~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~   75 (115)
                      +.+++ ++|+.+...+|.++|++|| .-.++++.+-       -|||.|.+++.|..|+..+.
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fg-gv~I~WidDT-------sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFG-NIQISWIDDT-------SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSE-EEEEEEEETT-------EEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccC-CEEEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            56667 9999999999999999998 5556676653       79999999999999999875

>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=97.68  E-value=0.00039  Score=39.23  Aligned_cols=72  Identities=13%  Similarity=0.147  Sum_probs=56.3

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCC--eeeEEEEEecCHHHHHHHHHhhCCCCCCCcee
Q psy3928          13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGK--LKGFAFVEFSTKEEATKALELGLNPCPTDYQS   84 (115)
Q Consensus        13 ~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~--~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~   84 (115)
                      .+|.|++||++++++++.+.+..............+.+.+  ...-|++.|.+.+++....+.++|..+.+...
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D~kg   75 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKG   75 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTC
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEcCCC
Confidence            4789999999999999999999887665555544433222  34579999999999999999999997665543

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.45  E-value=0.0036  Score=35.97  Aligned_cols=71  Identities=18%  Similarity=0.123  Sum_probs=53.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhh----c-CCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCcee
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSK----Y-GKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQS   84 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~----~-g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~   84 (115)
                      ....+|.|.|||..+.++.|.-+|++    . |.+..+....        +-|+|+|.+...|++.|+.-. ..+.+..+
T Consensus         6 ~~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~k~~-H~L~~~~L   76 (104)
T 2dhx_A            6 SGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLAQAD-HELHGAQL   76 (104)
T ss_dssp             CCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHTCSC-CBSSSSBC
T ss_pred             cCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhcCCc-ceecCeEE
Confidence            45679999999999999999999987    2 3566654421        468999999999999998623 35566666


Q ss_pred             eEEEe
Q psy3928          85 SILTT   89 (115)
Q Consensus        85 ~v~~~   89 (115)
                      .|...
T Consensus        77 sV~P~   81 (104)
T 2dhx_A           77 SLRPA   81 (104)
T ss_dssp             EEEEC
T ss_pred             EEEcC
Confidence            66543

>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=97.45  E-value=0.00027  Score=40.72  Aligned_cols=75  Identities=15%  Similarity=-0.007  Sum_probs=59.7

Q ss_pred             CCCEEEEcCCCCCC-CH----HHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceee
Q psy3928          11 YGRVVLKEKLPPEA-EH----DYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSS   85 (115)
Q Consensus        11 ~~~~l~V~~l~~~~-~~----~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~   85 (115)
                      -+.+|+|.||+..+ ..    ..++.+|..|+..........      -.-..|.|.+.++|.+|-..|++..+.|..++
T Consensus         4 ~pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkS------FRRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r   77 (104)
T 1wey_A            4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS------FKRVRINFSNPLSAADARLRLHKTEFLGKEMK   77 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT------TTEEEEECSSTTHHHHHHHTSTTSEETTEECE
T ss_pred             CCceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCc------ceEEEEEeCChHHHHHHHHHhccceecCceeE
Confidence            46789999998755 21    467999999997766554432      12468999999999999999999999999999


Q ss_pred             EEEeee
Q psy3928          86 ILTTTS   91 (115)
Q Consensus        86 v~~~~~   91 (115)
                      +....+
T Consensus        78 ~YFgq~   83 (104)
T 1wey_A           78 LYFAQT   83 (104)
T ss_dssp             EECCCC
T ss_pred             EEecCC
Confidence            988764

>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=97.23  E-value=0.0017  Score=38.35  Aligned_cols=67  Identities=18%  Similarity=0.240  Sum_probs=52.1

Q ss_pred             cccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCC
Q psy3928           7 NNKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTD   81 (115)
Q Consensus         7 ~~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~   81 (115)
                      ......+-|.|.+.|... ...+...|.+||.|.+....    .+  ..+-.|.|.++.+|++||.. ||..+.+
T Consensus        19 ~~~~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~----~~--~NWihI~Y~s~~~A~rAL~k-NG~ii~g   85 (119)
T 1wwh_A           19 EDHLDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMS----NT--GNWMHIRYQSKLQARKALSK-DGRIFGE   85 (119)
T ss_dssp             --CGGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEEC----SS--SSEEEEEESSHHHHHHHHTT-TTCEETT
T ss_pred             CCCCCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccC----CC--CCeEEEEeCCHHHHHHHHHh-CCeEecC
Confidence            344456778899999984 57789999999999887651    22  24899999999999999994 8887765

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=96.96  E-value=0.0013  Score=37.49  Aligned_cols=73  Identities=14%  Similarity=0.129  Sum_probs=51.7

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCC--eeeEEEEEecCHHHHHHHHHhhCCCCCCCcee
Q psy3928          12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGK--LKGFAFVEFSTKEEATKALELGLNPCPTDYQS   84 (115)
Q Consensus        12 ~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~--~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~   84 (115)
                      .-+|.|+.||+.++|+++.+.+...-..........+.+.+  .-.-|+|.|.+.++.....+.++|..+.+.+.
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~kg   83 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKG   83 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECTTC
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeCCC
Confidence            45789999999999999888777654433222222221211  23579999999999999999999987655443

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=96.90  E-value=0.0006  Score=49.07  Aligned_cols=56  Identities=23%  Similarity=0.272  Sum_probs=41.0

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHh
Q psy3928          12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL   73 (115)
Q Consensus        12 ~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~   73 (115)
                      .++|+|. .|...++.+|.++|++||.|..+.+..+  .|   .|+.|||.+.++++.++..
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~--~g---~~~~vef~~~~~~~~~~~~  108 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYES--FG---LYAVVEFCQKESIGSLQNG  108 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECS--SS---EEEEEECC---CCHHHHSS
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEcc--CC---eEEEEEeCCHHHHHHHHhc
Confidence            4789997 6999999999999999999998866543  23   5999999999998876654

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=96.39  E-value=0.0036  Score=38.11  Aligned_cols=33  Identities=24%  Similarity=0.073  Sum_probs=27.2

Q ss_pred             EEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCC
Q psy3928          42 VSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN   76 (115)
Q Consensus        42 ~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~   76 (115)
                      +++.++  ....+||+||+|.+.++|++|++.+++
T Consensus         3 ~kl~ln--~~~~~G~~fV~f~~~~~A~~al~~~~~   35 (158)
T 2kn4_A            3 YKLILN--GKTLKGETTTEAVDAATAEKVFKQYAN   35 (158)
T ss_dssp             EEEEEE--CSSCEEEEEEECSSHHHHHHHHHHHHH
T ss_pred             EEEEec--CccccchhHHHHHHHHhHHHHHHhhcc
Confidence            455665  346899999999999999999988775

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=94.91  E-value=0.05  Score=32.58  Aligned_cols=74  Identities=9%  Similarity=0.117  Sum_probs=50.4

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhcCCeEE-EEeceeC------------CCC-CeeeEEEEEecCHHHHHHHHHhhCCCC
Q psy3928          13 RVVLKEKLPPEAEHDYIESVFSKYGKVTY-VSLPKFK------------STG-KLKGFAFVEFSTKEEATKALELGLNPC   78 (115)
Q Consensus        13 ~~l~V~~l~~~~~~~~l~~~f~~~g~i~~-~~i~~~~------------~~~-~~~g~~fv~f~~~~~a~~al~~l~~~~   78 (115)
                      .-|.|-+.|... ...+.+.|++||.|.+ .......            ... ....+-.|.|.+..+|++||. .||..
T Consensus         8 ~~VtVFGFp~~~-~~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG~i   85 (132)
T 3p3d_A            8 LAILVFGYPETM-ANQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENGAV   85 (132)
T ss_dssp             CEEEEECCCGGG-HHHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTTCE
T ss_pred             eEEEEEecCHHH-HHHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCCeE
Confidence            456777998864 4668889999998865 2221100            001 123588999999999999998 68888


Q ss_pred             CCCceeeEEE
Q psy3928          79 PTDYQSSILT   88 (115)
Q Consensus        79 ~~~~~~~v~~   88 (115)
                      +.|.-+-+..
T Consensus        86 i~G~mIGV~P   95 (132)
T 3p3d_A           86 FNGVLLGVIP   95 (132)
T ss_dssp             ETTEECEEEE
T ss_pred             eCcEEEEEEE
Confidence            8886444443

>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease, hydrolase, magnesium, metal nonsense-mediated mRNA decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus}

Probab=94.09  E-value=0.29  Score=35.68  Aligned_cols=57  Identities=23%  Similarity=0.299  Sum_probs=45.3

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCC
Q psy3928          12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNP   77 (115)
Q Consensus        12 ~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~   77 (115)
                      ...++|+ +|..+...+|.+.|+.||.+ .++++.+.       .|||.|.+.+.|..+++.+...
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~v-~V~widdt-------~a~V~~~~~~~a~~~l~~~~~~  496 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVQIAVNTSKYA  496 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCCC-EEEECSSS-------EEEEECSCHHHHHHHHHHHTTC
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCCE-EEEEEcCC-------eEEEEECCHHHHHHHHHHHHhC
Confidence            4566675 88899999999999999943 45554332       6999999999999999998643

>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=94.08  E-value=0.015  Score=35.11  Aligned_cols=41  Identities=17%  Similarity=0.020  Sum_probs=34.7

Q ss_pred             CCCeeeEEEEEecCHHHHHHHHHhh-CCCCCCCceeeEEEeee
Q psy3928          50 TGKLKGFAFVEFSTKEEATKALELG-LNPCPTDYQSSILTTTS   91 (115)
Q Consensus        50 ~~~~~g~~fv~f~~~~~a~~al~~l-~~~~~~~~~~~v~~~~~   91 (115)
                      ...-+|+++++|.+.+.|++|++.+ |+..++| .+.+..+..
T Consensus         9 g~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~   50 (150)
T 2i2y_A            9 GKTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATK   50 (150)
T ss_dssp             CSSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTT
T ss_pred             cccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccC
Confidence            4456899999999999999999999 9999999 777765543

---

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	115
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	9e-11
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	4e-10
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	6e-10
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	1e-09
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	5e-09
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	2e-08
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	4e-08
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-07
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-07
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	2e-07
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-07
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	2e-07
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	2e-07
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	3e-07
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	6e-07
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	4e-07
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	7e-07
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	9e-07
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	1e-06
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	1e-06
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	2e-06
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	3e-06
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	3e-06
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	3e-06
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-06
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	6e-06
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	1e-05
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	2e-05
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	2e-05
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	3e-05
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	4e-05
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	5e-05
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	5e-05
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	5e-05
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	6e-05
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	9e-05
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	1e-04
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	1e-04
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	1e-04
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	3e-04
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	4e-04
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	4e-04
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	5e-04
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	5e-04
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	6e-04
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	6e-04
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	7e-04
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	0.001
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	0.001
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	0.001
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	0.002
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	0.002
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	0.002
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	0.002
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	0.003
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	0.003

>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 = 51.9 bits (124), Expect = 9e-11
 Identities = 22/58 (37%), Positives = 33/58 (56%), Gaps = 1/58 (1%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPK-FKSTGKLKGFAFVEFSTKEEATKALELGLN 76
          +P +A    I  +FS +G++  V LPK    TG  +GF FV+F TK++A KA     +
Sbjct: 16 IPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCH 73

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.9 bits (119), Expect = 4e-10
 Identities = 13/53 (24%), Positives = 25/53 (47%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L P+     +   FS  G +  + + +   T +  G+A+V F    +A +AL+
Sbjct: 8  LHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 60

>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 = 49.6 bits (118), Expect = 6e-10
 Identities = 12/54 (22%), Positives = 23/54 (42%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
          L  +   + +   F ++G+V    + +   T + +GF FV F  +    K L  
Sbjct: 8  LSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 48.8 bits (116), Expect = 1e-09
 Identities = 18/53 (33%), Positives = 33/53 (62%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          LP     D ++++F KYG +   ++ + K TG+ +G AFV ++ +EEA +A+ 
Sbjct: 14 LPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 66

>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 = 46.9 bits (111), Expect = 5e-09
 Identities = 17/54 (31%), Positives = 26/54 (48%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
          L P+   + I   F  +G+V  + LP    T K +GF F+ F  +E   K +E 
Sbjct: 7  LSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

>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 = 46.2 bits (109), Expect = 2e-08
 Identities = 13/54 (24%), Positives = 28/54 (51%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
          L  E   + + + + ++GK+T   + +  ++ + +GF FV FS+  E   A+  
Sbjct: 28 LSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA 81

>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 = 45.0 bits (106), Expect = 4e-08
 Identities = 15/54 (27%), Positives = 28/54 (51%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
          L  E   + + S F ++G +T   + +  +T + +GF FV ++T EE   A+  
Sbjct: 14 LSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.0 bits (103), Expect = 1e-07
 Identities = 11/59 (18%), Positives = 25/59 (42%), Gaps = 5/59 (8%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKS-----TGKLKGFAFVEFSTKEEATKALEL 73
          +P     + +   F+   ++  ++             + K FAF+EF + +E T+A+  
Sbjct: 9  IPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAF 67

>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 = 43.4 bits (102), Expect = 1e-07
 Identities = 16/54 (29%), Positives = 26/54 (48%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
          L  +     ++  FSK+G+V   +L     TG+ +GF FV F   E   K ++ 
Sbjct: 7  LSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ 60

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]} Length = 114

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.9 bits (103), Expect = 2e-07
 Identities = 13/60 (21%), Positives = 28/60 (46%), Gaps = 3/60 (5%)

Query: 13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          R++    LP +   + +  +F KYG +      +  +T + +G A+V +    +A  A +
Sbjct: 8  RILYIRNLPYKITAEEMYDIFGKYGPIRQ---IRVGNTPETRGTAYVVYEDIFDAKNACD 64

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.1 bits (101), Expect = 2e-07
 Identities = 14/53 (26%), Positives = 26/53 (49%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          LP     D ++ + + +G +   +L K  +TG  KG+AF E+       +A+ 
Sbjct: 9  LPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 61

>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 = 43.0 bits (101), Expect = 2e-07
 Identities = 18/53 (33%), Positives = 26/53 (49%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          LP +     ++  FS +G+V  V + K   TG  KGF FV F+  E   K + 
Sbjct: 16 LPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS 68

>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 = 43.1 bits (101), Expect = 2e-07
 Identities = 16/56 (28%), Positives = 23/56 (41%), Gaps = 3/56 (5%)

Query: 20 LPPEAEHDYIESVFSKYGKVT---YVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L      + ++ VFSK G +                  GF FVE+   E+A KAL+
Sbjct: 6  LNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALK 61

>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 = 44.6 bits (104), Expect = 3e-07
 Identities = 15/54 (27%), Positives = 28/54 (51%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
          L  E   + + S F ++G +T   + +  +T + +GF FV ++T EE   A+  
Sbjct: 14 LSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.5 bits (101), Expect = 6e-07
 Identities = 14/54 (25%), Positives = 27/54 (50%)

Query: 20  LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
           +  + E  ++   F +YGK+  + +   + +GK +GFAFV F   +   K +  
Sbjct: 105 IKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 158

>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 = 4e-07
 Identities = 14/53 (26%), Positives = 24/53 (45%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L      + I  +FSK G +  + +   K      GF FVE+ ++ +A  A+ 
Sbjct: 15 LSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 67

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.9 bits (98), Expect = 7e-07
 Identities = 16/54 (29%), Positives = 25/54 (46%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
          L        +E  FS  GKV  V +   +++ + KG A+VEF   +    A+ L
Sbjct: 26 LAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGL 79

>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 = 41.6 bits (97), Expect = 9e-07
 Identities = 15/53 (28%), Positives = 28/53 (52%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          LP       +E +FS+YG++    +   + TG  +G  F+ F  + EA +A++
Sbjct: 14 LPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 66

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.4 bits (97), Expect = 1e-06
 Identities = 13/72 (18%), Positives = 23/72 (31%), Gaps = 9/72 (12%)

Query: 7  NNKKYGRVVL--------KEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAF 58
          +  ++ RVV+          +  P   ++  E +  +  K   +            G A 
Sbjct: 3  SRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLF-DRHPDGVAS 61

Query: 59 VEFSTKEEATKA 70
          V F   EEA   
Sbjct: 62 VSFRDPEEADYC 73

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 41.1 bits (96), Expect = 1e-06
 Identities = 12/53 (22%), Positives = 29/53 (54%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          LP +     + ++F   G +    + +   TG   G+AFV+F+++ ++ +A++
Sbjct: 10 LPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 62

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.5 bits (94), Expect = 2e-06
 Identities = 15/54 (27%), Positives = 28/54 (51%), Gaps = 1/54 (1%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVS-LPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L PE +   +   FS +G +     + +   TG  KG+AF+ F++ + +  A+E
Sbjct: 6  LDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 59

>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 = 39.9 bits (93), Expect = 3e-06
 Identities = 14/61 (22%), Positives = 32/61 (52%), Gaps = 2/61 (3%)

Query: 12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
          G++++   L        I+ +F+++G +   ++   + +G+  G A V F  K +A KA+
Sbjct: 1  GKLLVS-NLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAM 58

Query: 72 E 72
          +
Sbjct: 59 K 59

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.4 bits (94), Expect = 3e-06
 Identities = 12/55 (21%), Positives = 21/55 (38%), Gaps = 2/55 (3%)

Query: 20 LPPEAEHDYIESVFSKYGKVTY--VSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          +P   + + I    +K  +     +         K +GFAFVE+ +   A  A  
Sbjct: 9  IPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 63

>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 = 39.7 bits (92), Expect = 3e-06
 Identities = 15/54 (27%), Positives = 27/54 (50%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
          L      + ++  F ++GKV    L   K+T + +GF FV F +++   K  E+
Sbjct: 7  LSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60

>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 = 40.0 bits (93), Expect = 4e-06
 Identities = 14/71 (19%), Positives = 31/71 (43%), Gaps = 1/71 (1%)

Query: 2  AELVENNKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEF 61
          ++  +  +     V  ++   E   +    +  KYG+V  +++        L G  +V+F
Sbjct: 17 SQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCD-NLGDHLVGNVYVKF 75

Query: 62 STKEEATKALE 72
            +E+A KA+ 
Sbjct: 76 RREEDAEKAVI 86

>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 = 39.5 bits (92), Expect = 6e-06
 Identities = 17/54 (31%), Positives = 27/54 (50%), Gaps = 9/54 (16%)

Query: 20 LPPE-AEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L     +   +E++FSKYGK+   S+ K        GFAFV++  +  A  A+ 
Sbjct: 23 LNTLVVKKSDVEAIFSKYGKIVGCSVHK--------GFAFVQYVNERNARAAVA 68

>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 = 38.5 bits (89), Expect = 1e-05
 Identities = 16/53 (30%), Positives = 30/53 (56%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L  +     +  +F + G V    +PK + TG+ +G+ FVEF ++E+A  A++
Sbjct: 17 LDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIK 69

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 108

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.5 bits (89), Expect = 2e-05
 Identities = 10/53 (18%), Positives = 20/53 (37%), Gaps = 4/53 (7%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L      D +  +FSK+G V  +      +    +  A ++++    A  A  
Sbjct: 15 LFYPVTLDVLHQIFSKFGTVLKIITFTKNN----QFQALLQYADPVSAQHAKL 63

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 38.0 bits (88), Expect = 2e-05
 Identities = 11/54 (20%), Positives = 21/54 (38%), Gaps = 7/54 (12%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
           P  +   YI   F++YG +    +           +  + + +K +A KAL  
Sbjct: 12 FPQASA-SYILLQFAQYGNILKHVMSNTG------NWMHIRYQSKLQARKALSK 58

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.4 bits (86), Expect = 3e-05
 Identities = 15/53 (28%), Positives = 26/53 (49%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          LP     +   S+F   G++    L + K TG+  G+ FV +   ++A KA+ 
Sbjct: 10 LPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62

>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 = 37.3 bits (86), Expect = 4e-05
 Identities = 12/53 (22%), Positives = 22/53 (41%), Gaps = 6/53 (11%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          +        +   FS +G++  + +   K       ++FV FST E A  A+ 
Sbjct: 26 IASGLTDQLMRQTFSPFGQIMEIRVFPEKG------YSFVRFSTHESAAHAIV 72

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 37.5 bits (86), Expect = 5e-05
 Identities = 11/44 (25%), Positives = 13/44 (29%), Gaps = 6/44 (13%)

Query: 29 IESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
           ES+F  Y K T     K            + FS    A  A  
Sbjct: 27 FESLFRTYDKDTTFQYFKSF------KRVRINFSNPLSAADARL 64

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 112

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.6 bits (86), Expect = 5e-05
 Identities = 19/68 (27%), Positives = 28/68 (41%)

Query: 6  ENNKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKE 65
           +  + G  V  + LP EAE+ ++   F K   V       +   GK  G  FVEF  + 
Sbjct: 12 RSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEA 71

Query: 66 EATKALEL 73
          +   AL  
Sbjct: 72 DYKAALCR 79

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.1 bits (85), Expect = 5e-05
 Identities = 9/54 (16%), Positives = 18/54 (33%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
          +P       +                   + G+  G A V+F  +++A K+  L
Sbjct: 16 IPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL 69

>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 = 36.6 bits (84), Expect = 6e-05
 Identities = 18/53 (33%), Positives = 28/53 (52%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L        +  VFSKYG +  VS+   + + + +GFAFV F   ++A +A E
Sbjct: 17 LSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 69

>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 = 36.2 bits (83), Expect = 9e-05
 Identities = 18/53 (33%), Positives = 29/53 (54%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L  E +   + + F  +G +T + +P    T K +GFAFVEF   E+A  A++
Sbjct: 13 LAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 65

>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 = 36.2 bits (83), Expect = 1e-04
 Identities = 15/53 (28%), Positives = 22/53 (41%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          +P     D I   F  Y  +      K+   G   G A V F +++EAT A+ 
Sbjct: 17 MPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 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 = 36.2 bits (83), Expect = 1e-04
 Identities = 17/53 (32%), Positives = 32/53 (60%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L  +     ++ +F  +G ++ + L K K+TG+ KGFAF+ F  +E+A +A+ 
Sbjct: 16 LSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIA 68

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.3 bits (83), Expect = 1e-04
 Identities = 12/53 (22%), Positives = 23/53 (43%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          LP       +   F  +G +    +   + TGK +G+ FV  + +  A +A +
Sbjct: 18 LPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACK 70

>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 = 35.1 bits (80), Expect = 3e-04
 Identities = 20/53 (37%), Positives = 27/53 (50%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L   +  + +E +FS YG ++ +  P    T K KGFAFV F   E A KA  
Sbjct: 16 LSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

>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 = 34.6 bits (79), Expect = 4e-04
 Identities = 13/53 (24%), Positives = 19/53 (35%), Gaps = 5/53 (9%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
             +   D +   FS+YG V  V           + FAFV F+  + A     
Sbjct: 13 CTGDMTEDELREFFSQYGDVMDV-----FIPKPFRAFAFVTFADDQIAQSLCG 60

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.0 bits (80), Expect = 4e-04
 Identities = 15/59 (25%), Positives = 26/59 (44%), Gaps = 2/59 (3%)

Query: 16 LKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTG--KLKGFAFVEFSTKEEATKALE 72
          L +    E   + +    SKYG V  + +P+          G  FVEF++  +  KA++
Sbjct: 18 LLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQ 76

>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 = 34.7 bits (79), Expect = 5e-04
 Identities = 14/60 (23%), Positives = 23/60 (38%), Gaps = 6/60 (10%)

Query: 13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
           VV    L      + +  V  K G V  + +P  K       ++F  + T EE+ +A  
Sbjct: 21 LVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKP------YSFARYRTTEESKRAYV 74

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.2 bits (78), Expect = 5e-04
 Identities = 14/53 (26%), Positives = 26/53 (49%), Gaps = 2/53 (3%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L    ++  +   FS +G +    +   ++    KG+ FV F T+E A +A+E
Sbjct: 16 LDKSIDNKALYDTFSAFGNILSCKVVCDENGS--KGYGFVHFETQEAAERAIE 66

>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 = 33.9 bits (77), Expect = 6e-04
 Identities = 20/61 (32%), Positives = 33/61 (54%)

Query: 12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
          G ++    +  EA+ D I+  F  YG++  + L   + TG  KG+A VE+ T ++A  A 
Sbjct: 7  GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAK 66

Query: 72 E 72
          E
Sbjct: 67 E 67

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 34.2 bits (78), Expect = 6e-04
 Identities = 16/53 (30%), Positives = 23/53 (43%), Gaps = 6/53 (11%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          LPP+   + +  +F KYGK   V + K K       F F+   T+  A  A  
Sbjct: 16 LPPDITEEEMRKLFEKYGKAGEVFIHKDKG------FGFIRLETRTLAEIAKV 62

>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 = 33.9 bits (77), Expect = 7e-04
 Identities = 16/53 (30%), Positives = 25/53 (47%), Gaps = 5/53 (9%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L      D ++ VF    ++  V        GK KG A++EF ++ +A K LE
Sbjct: 24 LSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLE 71

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 33.5 bits (76), Expect = 0.001
 Identities = 13/60 (21%), Positives = 27/60 (45%), Gaps = 6/60 (10%)

Query: 13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          +++    L      + IE  F+             +   K++ +AFV FS +E+A +A++
Sbjct: 9  KILYVRNLMLSTSEEMIEKEFNNIKPG------AVERVKKIRDYAFVHFSNREDAVEAMK 62

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 33.2 bits (75), Expect = 0.001
 Identities = 18/53 (33%), Positives = 30/53 (56%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L  +     +E VFSKYG+++ V + K + T + +GF FV F   ++A  A+ 
Sbjct: 13 LSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMM 65

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 32.8 bits (74), Expect = 0.001
 Identities = 14/54 (25%), Positives = 27/54 (50%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
          +  + E  ++   F +YGK+  + +   + +GK +GFAFV F   +   K +  
Sbjct: 10 IKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 63

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 33.3 bits (75), Expect = 0.002
 Identities = 18/62 (29%), Positives = 25/62 (40%)

Query: 12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
             V    LP     + I   FS    V           G+  G AFV+F+++E A KAL
Sbjct: 15 DGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKAL 74

Query: 72 EL 73
          + 
Sbjct: 75 KK 76

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 32.8 bits (74), Expect = 0.002
 Identities = 15/64 (23%), Positives = 30/64 (46%), Gaps = 2/64 (3%)

Query: 12 GRVVLKEKLPPEA-EHDYIESVFSKYGKVTYVSLPKF-KSTGKLKGFAFVEFSTKEEATK 69
          GR ++   L  E  + + +   F  +G +  +++P   K        AF+ F  K+ A +
Sbjct: 4  GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAER 63

Query: 70 ALEL 73
          AL++
Sbjct: 64 ALQM 67

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 32.5 bits (73), Expect = 0.002
 Identities = 10/53 (18%), Positives = 19/53 (35%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
           PP      I  +      V              + FA+++ ++KE+A   +E
Sbjct: 9  FPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 61

>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 = 32.4 bits (73), Expect = 0.002
 Identities = 11/53 (20%), Positives = 19/53 (35%), Gaps = 6/53 (11%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L P    D +  +F                     G+AFV++  +  A +A+E
Sbjct: 9  LSPAVTADDLRQLFGDRKLPLA------GQVLLKSGYAFVDYPDQNWAIRAIE 55

>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 = 32.3 bits (73), Expect = 0.003
 Identities = 12/53 (22%), Positives = 18/53 (33%), Gaps = 2/53 (3%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
          L  +     I  +FS+ G      +           + FVEF    +A  AL 
Sbjct: 16 LSRDVTEVLILQLFSQIGPCKSCKMITEH--TSNDPYCFVEFYEHRDAAAALA 66

>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 = 32.8 bits (74), Expect = 0.003
 Identities = 16/61 (26%), Positives = 20/61 (32%), Gaps = 8/61 (13%)

Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKF--------KSTGKLKGFAFVEFSTKEEATKAL 71
          L      D +   F + G V                K TGK KG A V +     A  A+
Sbjct: 16 LNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAV 75

Query: 72 E 72
          E
Sbjct: 76 E 76

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	115
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.89
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.89
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.89
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.88
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.88
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.88
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.88
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.87
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.87
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.87
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.87
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.87
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.87
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.87
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.87
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.87
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.86
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.86
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.86
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.86
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.86
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.86
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.85
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.85
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.85
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.85
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.85
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.84
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.84
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.84
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.84
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.84
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.84
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.84
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.84
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.84
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.83
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.82
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.81
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.81
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.81
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.81
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.81
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.8
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.8
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.8
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.8
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.8
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.79
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.79
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.79
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.78
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.78
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.78
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.78
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.77
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.77
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.77
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.77
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.77
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.77
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.77
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.77
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.77
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.76
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.75
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.74
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.74
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.73
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.73
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.72
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.71
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.7
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.7
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.69
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.68
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.66
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.63
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.63
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.57
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	99.56
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.54
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.51
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.51
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.42
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.39
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.31
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.68
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.19
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	96.38
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	94.86

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.89  E-value=5.9e-23  Score=114.56  Aligned_cols=80  Identities=15%  Similarity=0.270  Sum_probs=75.8

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEeee
Q psy3928          12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTTS   91 (115)
Q Consensus        12 ~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~~   91 (115)
                      .++|||+|||.++++++|+++|++||.+..+++.+++.+|.++|||||+|.+.++|++|++.||+..+.|+.+++..++|
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~p   81 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   81 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            46899999999999999999999999999999999988999999999999999999999999999999999999887764

>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=1.2e-22  Score=114.79  Aligned_cols=84  Identities=24%  Similarity=0.285  Sum_probs=77.9

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      ..++++|||+|||..+++++|+++|+.||.+..++++.++.+|.++|||||+|.+.++|++|+..||+..+.|+.++|..
T Consensus         4 s~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~   83 (88)
T d1rk8a_           4 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW   83 (88)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            44678999999999999999999999999999999999988999999999999999999999999999999999999888


Q ss_pred             eeec
Q psy3928          89 TTSR   92 (115)
Q Consensus        89 ~~~~   92 (115)
                      +.++
T Consensus        84 a~~k   87 (88)
T d1rk8a_          84 CFVK   87 (88)
T ss_dssp             SEEC
T ss_pred             ecCC
Confidence            7654

>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=1.8e-22  Score=116.31  Aligned_cols=85  Identities=26%  Similarity=0.275  Sum_probs=79.0

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      ...++|||+|||..+++++|+++|.+||.|..+.++.++.++.++|||||+|.+.++|++|++.||+..+.|+.++|..+
T Consensus         6 ~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a   85 (99)
T d1whwa_           6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS   85 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            45678999999999999999999999999999999999889999999999999999999999999999999999999888


Q ss_pred             eeccc
Q psy3928          90 TSRLS   94 (115)
Q Consensus        90 ~~~~~   94 (115)
                      +++..
T Consensus        86 ~~~~~   90 (99)
T d1whwa_          86 TIKKE   90 (99)
T ss_dssp             CCCST
T ss_pred             CCCCc
Confidence            76543

>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=99.88  E-value=1.5e-22  Score=113.66  Aligned_cols=81  Identities=19%  Similarity=0.229  Sum_probs=76.4

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEeeec
Q psy3928          13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTTSR   92 (115)
Q Consensus        13 ~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~~~   92 (115)
                      ++|||+|||..+++++|+++|++||+|..++++.++.+|.++|||||+|.++++|+.|++.+++..+.|+.+.|..+++.
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~   81 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG   81 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            47999999999999999999999999999999999989999999999999999999999999999999999999888754


Q ss_pred             c
Q psy3928          93 L   93 (115)
Q Consensus        93 ~   93 (115)
                      .
T Consensus        82 ~   82 (85)
T d2u2fa_          82 A   82 (85)
T ss_dssp             C
T ss_pred             C
Confidence            3

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.88  E-value=1.7e-22  Score=114.57  Aligned_cols=85  Identities=20%  Similarity=0.315  Sum_probs=78.9

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      ...+..+|||+|||.++++++|+++|+.||.+..+.++.++.++.++|||||+|.+.++|++|++.|++..+.|+.+.+.
T Consensus         4 ~~~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~   83 (90)
T d2cq0a1           4 RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVE   83 (90)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34556799999999999999999999999999999999998899999999999999999999999999999999999988


Q ss_pred             Eeeec
Q psy3928          88 TTTSR   92 (115)
Q Consensus        88 ~~~~~   92 (115)
                      .++|+
T Consensus        84 ~akp~   88 (90)
T d2cq0a1          84 WAKPS   88 (90)
T ss_dssp             ESSCC
T ss_pred             eeeCC
Confidence            87765

>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=99.88  E-value=2.4e-22  Score=114.59  Aligned_cols=83  Identities=20%  Similarity=0.267  Sum_probs=77.5

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      ...++|||+|||..+++++|+++|++||.+..+.++.++.++.++|||||+|.+.++|++|++.||+..+.|+.++|..+
T Consensus         7 ~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A   86 (93)
T d1x5ua1           7 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKA   86 (93)
T ss_dssp             CTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEET
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            34579999999999999999999999999999999999889999999999999999999999999999999999998877


Q ss_pred             eec
Q psy3928          90 TSR   92 (115)
Q Consensus        90 ~~~   92 (115)
                      +++
T Consensus        87 ~~~   89 (93)
T d1x5ua1          87 SAH   89 (93)
T ss_dssp             TTT
T ss_pred             CCC
Confidence            654

>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=99.88  E-value=3.9e-22  Score=111.14  Aligned_cols=80  Identities=19%  Similarity=0.264  Sum_probs=75.3

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEeee
Q psy3928          12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTTS   91 (115)
Q Consensus        12 ~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~~   91 (115)
                      ..+|||+|||..+++++|+++|++||.+..++++.++.++.++|||||+|.+.++|+.|++.||+..+.|+.+++..++|
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            45799999999999999999999999999999999888899999999999999999999999999999999999887764

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=3.6e-22  Score=110.88  Aligned_cols=77  Identities=18%  Similarity=0.234  Sum_probs=73.1

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEee
Q psy3928          14 VVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTT   90 (115)
Q Consensus        14 ~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~   90 (115)
                      +|||+|||..+++++|+++|++||.+..++|+.++.++.++|||||+|.++++|..|++.|++..+.|+.+++..++
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~   78 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            69999999999999999999999999999999999899999999999999999999999999999999998887653

>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=99.87  E-value=9.6e-22  Score=112.04  Aligned_cols=81  Identities=20%  Similarity=0.170  Sum_probs=76.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      ...++|||+|||.++++++|+++|++||.+..+.++.++.++.++|||||+|.+.++|+.|++.||+..++|+.++|..+
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a   84 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD   84 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            46689999999999999999999999999999999999989999999999999999999999999999999999888775


Q ss_pred             e
Q psy3928          90 T   90 (115)
Q Consensus        90 ~   90 (115)
                      .
T Consensus        85 ~   85 (93)
T d1h2vz_          85 A   85 (93)
T ss_dssp             S
T ss_pred             C
Confidence            4

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.87  E-value=1.5e-21  Score=109.46  Aligned_cols=79  Identities=27%  Similarity=0.414  Sum_probs=72.1

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCC--ceeeEE
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTD--YQSSIL   87 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~--~~~~v~   87 (115)
                      ...++|||+|||.++++++|+++|++||.+..+++++++.+++++|||||+|.+.++|++|++.||+..+.+  +++.|.
T Consensus         4 ~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~   83 (85)
T d1b7fa2           4 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR   83 (85)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEE
Confidence            355789999999999999999999999999999999998899999999999999999999999999999877  556654


Q ss_pred             E
Q psy3928          88 T   88 (115)
Q Consensus        88 ~   88 (115)
                      .
T Consensus        84 ~   84 (85)
T d1b7fa2          84 L   84 (85)
T ss_dssp             E
T ss_pred             E
Confidence            3

>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=1e-21  Score=119.32  Aligned_cols=82  Identities=17%  Similarity=0.259  Sum_probs=77.3

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEeee
Q psy3928          12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTTS   91 (115)
Q Consensus        12 ~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~~   91 (115)
                      .++|||+|||.++++++|+++|+.||.|..+.++.++.++.++|||||+|.+.++|..|++.||+..+.|+.++|..+.+
T Consensus        42 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~~  121 (139)
T d1u6fa1          42 LRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAAS  121 (139)
T ss_dssp             TSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESSC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            46899999999999999999999999999999999998999999999999999999999999999999999999988775


Q ss_pred             cc
Q psy3928          92 RL   93 (115)
Q Consensus        92 ~~   93 (115)
                      +.
T Consensus       122 ~~  123 (139)
T d1u6fa1         122 GH  123 (139)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.87  E-value=1.3e-22  Score=114.75  Aligned_cols=82  Identities=24%  Similarity=0.324  Sum_probs=76.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEee
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTT   90 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~   90 (115)
                      ..++|||+|||.++++++|+++|++||.+..+.++.++.++.++|||||+|.+.++|++|++.+|+..++|+.+.+..++
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~   83 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK   83 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            45789999999999999999999999999999999999899999999999999999999999999999999999888776


Q ss_pred             ec
Q psy3928          91 SR   92 (115)
Q Consensus        91 ~~   92 (115)
                      ++
T Consensus        84 p~   85 (89)
T d2cqba1          84 PM   85 (89)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=8.1e-22  Score=114.27  Aligned_cols=84  Identities=14%  Similarity=0.207  Sum_probs=75.4

Q ss_pred             cccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeE
Q psy3928           7 NNKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSI   86 (115)
Q Consensus         7 ~~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v   86 (115)
                      +.+...++|||+|||..+++++|+++|+.||.|..+.++.++.++.++|||||+|.+.++|++|++.+++ .++|+.+.|
T Consensus         5 ~~d~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V   83 (103)
T d2cqda1           5 QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANV   83 (103)
T ss_dssp             CCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEE
T ss_pred             CCCCCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEE
Confidence            3455567899999999999999999999999999999999988999999999999999999999999886 688988888


Q ss_pred             EEeee
Q psy3928          87 LTTTS   91 (115)
Q Consensus        87 ~~~~~   91 (115)
                      ..+..
T Consensus        84 ~~a~~   88 (103)
T d2cqda1          84 NLAYL   88 (103)
T ss_dssp             EESTT
T ss_pred             EEcCC
Confidence            66554

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=1e-21  Score=111.25  Aligned_cols=84  Identities=23%  Similarity=0.298  Sum_probs=77.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      .+.++|||+|||.++++++|+++|.+||.|..+.+..++.++.++|||||+|.++++|+.|++.|++..+.|+.+.|..+
T Consensus         3 ~~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a   82 (90)
T d1x5sa1           3 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQA   82 (90)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEE
T ss_pred             CCCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            35678999999999999999999999999999998888888999999999999999999999999999999999999887


Q ss_pred             eecc
Q psy3928          90 TSRL   93 (115)
Q Consensus        90 ~~~~   93 (115)
                      .++.
T Consensus        83 ~~~~   86 (90)
T d1x5sa1          83 GKSS   86 (90)
T ss_dssp             ECCC
T ss_pred             CCCC
Confidence            6543

>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=99.87  E-value=4.7e-22  Score=111.08  Aligned_cols=76  Identities=24%  Similarity=0.239  Sum_probs=71.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeE
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSI   86 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v   86 (115)
                      ..++|||+|||..+++++|+++|++||.+..+.++.++.++.++|||||+|.+.++|+.|++.||+..++|+.++|
T Consensus         8 ~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           8 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             GGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            4578999999999999999999999999999999999889999999999999999999999999999999988765

>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=99.87  E-value=2.6e-21  Score=108.52  Aligned_cols=77  Identities=21%  Similarity=0.323  Sum_probs=70.7

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCce--eeEE
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQ--SSIL   87 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~--~~v~   87 (115)
                      ..++|||+|||..+++++|+++|++||.+..++++.++.++.++|||||+|.+.++|++|++.||+..+.|..  +.|.
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~   83 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVK   83 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEE
Confidence            3578999999999999999999999999999999999888999999999999999999999999999998854  5543

>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=99.86  E-value=8.7e-22  Score=113.96  Aligned_cols=85  Identities=19%  Similarity=0.136  Sum_probs=78.3

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      .+++++|||+|||.++++++|+++|..||.+..+.++.++.++.++|||||+|.+.++|+.|++.||+..+.|+.++|..
T Consensus        15 ~p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~   94 (102)
T d2cpza1          15 GPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQL   94 (102)
T ss_dssp             CSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            45567899999999999999999999999999999999988999999999999999999999999999999999998887


Q ss_pred             eeecc
Q psy3928          89 TTSRL   93 (115)
Q Consensus        89 ~~~~~   93 (115)
                      ++++.
T Consensus        95 a~~k~   99 (102)
T d2cpza1          95 KRSKN   99 (102)
T ss_dssp             CCCSC
T ss_pred             eCCCC
Confidence            76543

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.86  E-value=1.4e-21  Score=107.97  Aligned_cols=76  Identities=21%  Similarity=0.214  Sum_probs=72.2

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEee
Q psy3928          14 VVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTT   90 (115)
Q Consensus        14 ~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~   90 (115)
                      +|||+|||+++++++|+++|++||.+..+.+..++ +++++|||||+|.+.++|+.|++.+|+..+.|+.++|..++
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~   77 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEee-ccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            69999999999999999999999999999999887 89999999999999999999999999999999999988765

>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=2.2e-21  Score=108.59  Aligned_cols=79  Identities=20%  Similarity=0.240  Sum_probs=72.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEee
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTT   90 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~   90 (115)
                      ..++|||+|||.++++++|+++|++||.+..+.++.++.+|.++|||||+|.+.+.|++|+. +++..++|+.+.|..+.
T Consensus         5 ~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEeee
Confidence            34789999999999999999999999999999999999899999999999999999999997 58888999998886653

>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=1.6e-21  Score=107.00  Aligned_cols=73  Identities=22%  Similarity=0.278  Sum_probs=68.6

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928          14 VVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus        14 ~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      +|||+|||+++++++|+++|++||.+..+.++.++.+++++|||||+|.+.++|++|++ +++..++|+.+.|.
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~   73 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPK   73 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEEC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEee
Confidence            48999999999999999999999999999999999899999999999999999999997 68888999888764

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.86  E-value=1e-21  Score=109.23  Aligned_cols=79  Identities=14%  Similarity=0.152  Sum_probs=67.8

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEeee
Q psy3928          13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTTS   91 (115)
Q Consensus        13 ~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~~   91 (115)
                      ++|||+|||.++++++|+++|++||.+..+.++.++.+++++|||||+|.+.++|++|++.||+..+.|+.+.+..++|
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            6899999999999999999999999998887777777899999999999999999999999999999999999887765

>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=99.86  E-value=6.9e-22  Score=114.73  Aligned_cols=81  Identities=26%  Similarity=0.307  Sum_probs=76.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEee
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTT   90 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~   90 (115)
                      ..++|||+|||.++++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|+.|++.|++..+.|+.+.|..+.
T Consensus         7 ~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~   86 (104)
T d1p1ta_           7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAA   86 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETT
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            34689999999999999999999999999999999999899999999999999999999999999999999999988765


Q ss_pred             e
Q psy3928          91 S   91 (115)
Q Consensus        91 ~   91 (115)
                      +
T Consensus        87 ~   87 (104)
T d1p1ta_          87 S   87 (104)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.85  E-value=7.2e-22  Score=108.90  Aligned_cols=76  Identities=16%  Similarity=0.184  Sum_probs=71.1

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        13 ~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      ++|||+|||+++++++|+++|++||.+..++++.++.+++++|||||+|.+.++|++|+. +++..++|+.+.|..+
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            579999999999999999999999999999999999899999999999999999999997 6999999998887654

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=2.6e-21  Score=109.58  Aligned_cols=82  Identities=23%  Similarity=0.281  Sum_probs=72.6

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      .....+|||+|||+++++++|+++|+.||.|..+.|+.++.+|.++|||||+|.+.++|++|++..+  .++|+.+.+..
T Consensus         5 ~~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~~~--~l~Gr~i~v~~   82 (90)
T d2cqga1           5 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRH--MIDGRWCDCKL   82 (90)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSCE--EETTEEEEEEC
T ss_pred             CcCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhcCC--ccCCEEeEEEe
Confidence            3456789999999999999999999999999999999999899999999999999999999998543  67888877766


Q ss_pred             eeec
Q psy3928          89 TTSR   92 (115)
Q Consensus        89 ~~~~   92 (115)
                      +.++
T Consensus        83 a~~k   86 (90)
T d2cqga1          83 PNSK   86 (90)
T ss_dssp             CCTT
T ss_pred             CCCC
Confidence            6553

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.85  E-value=7.7e-21  Score=108.41  Aligned_cols=83  Identities=29%  Similarity=0.418  Sum_probs=75.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCC-CCCeeeEEEEEecCHHHHHHHHHhh-CCCCCCCceeeEE
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKS-TGKLKGFAFVEFSTKEEATKALELG-LNPCPTDYQSSIL   87 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~-~~~~~g~~fv~f~~~~~a~~al~~l-~~~~~~~~~~~v~   87 (115)
                      ....+|||+|||.++++++|+++|.+||.+..+.|+.++. +|.++|||||+|.+.++|++|+..| |+..+.|+.+.|.
T Consensus         6 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~   85 (94)
T d2cpha1           6 QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLE   85 (94)
T ss_dssp             SCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEE
Confidence            3457899999999999999999999999999999987753 7899999999999999999999998 8889999999988


Q ss_pred             Eeeec
Q psy3928          88 TTTSR   92 (115)
Q Consensus        88 ~~~~~   92 (115)
                      .+.+.
T Consensus        86 ~A~~~   90 (94)
T d2cpha1          86 WADSE   90 (94)
T ss_dssp             ECCCC
T ss_pred             EcCCC
Confidence            87754

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=2.3e-21  Score=108.22  Aligned_cols=79  Identities=19%  Similarity=0.325  Sum_probs=72.4

Q ss_pred             EEEcCCCCCCCHHHHHHHhhhcCCeEE-EEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEeeecc
Q psy3928          15 VLKEKLPPEAEHDYIESVFSKYGKVTY-VSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTTSRL   93 (115)
Q Consensus        15 l~V~~l~~~~~~~~l~~~f~~~g~i~~-~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~~~~   93 (115)
                      |||+|||.++++++|+++|++||.+.. +.++.++.+++++|||||+|.+.++|+.|++.+++..+.|+.+++..+.++.
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k~   80 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKD   80 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCCC
Confidence            799999999999999999999999865 4788888889999999999999999999999999999999999988877644

>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=99.85  E-value=6.6e-21  Score=107.87  Aligned_cols=82  Identities=17%  Similarity=0.189  Sum_probs=73.5

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      ++.+.++|||+|||.++++++|+++|+.||.+..+.++.++.++  ++||||+|.+.++|+.|+..+++..+.|+.+++.
T Consensus         4 d~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~--~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~   81 (90)
T d2cqia1           4 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVN   81 (90)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSS--CCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCcc--ceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            45567899999999999999999999999999999998876443  6899999999999999999999999999998887


Q ss_pred             Eeee
Q psy3928          88 TTTS   91 (115)
Q Consensus        88 ~~~~   91 (115)
                      .+++
T Consensus        82 ~a~~   85 (90)
T d2cqia1          82 WATT   85 (90)
T ss_dssp             ECCC
T ss_pred             EcCC
Confidence            7664

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.84  E-value=9.5e-21  Score=108.60  Aligned_cols=85  Identities=25%  Similarity=0.342  Sum_probs=74.7

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCC------CCCCC
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN------PCPTD   81 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~------~~~~~   81 (115)
                      +..+.++|||+|||.++++++|+++|.+||.+..+.+..++.++.++|||||+|.+.++|.+|++.+++      ..+.|
T Consensus         4 ~~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~g   83 (98)
T d1x4ha1           4 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDG   83 (98)
T ss_dssp             CCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSS
T ss_pred             CCCCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECC
Confidence            445678999999999999999999999999999999998888899999999999999999999999874      45677


Q ss_pred             ceeeEEEeeec
Q psy3928          82 YQSSILTTTSR   92 (115)
Q Consensus        82 ~~~~v~~~~~~   92 (115)
                      +.+++..+.++
T Consensus        84 r~l~v~~a~~k   94 (98)
T d1x4ha1          84 RQLKVDLAVTR   94 (98)
T ss_dssp             CEEEEECCCCC
T ss_pred             EEEEEEECCCC
Confidence            77777766654

>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=99.84  E-value=8.7e-21  Score=106.27  Aligned_cols=76  Identities=24%  Similarity=0.331  Sum_probs=69.8

Q ss_pred             EEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCC---CeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEee
Q psy3928          15 VLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTG---KLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTT   90 (115)
Q Consensus        15 l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~---~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~   90 (115)
                      |||+|||.++++++|+++|++||.+..+.++.++.++   .++|||||+|.+.++|++|++.+|+..++|+.+.|..+.
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~   79 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISE   79 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSS
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            7999999999999999999999999999998887554   468999999999999999999999999999998887654

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=7e-21  Score=109.91  Aligned_cols=84  Identities=12%  Similarity=0.193  Sum_probs=74.6

Q ss_pred             hcccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceee
Q psy3928           6 ENNKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSS   85 (115)
Q Consensus         6 ~~~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~   85 (115)
                      .+.+.+.++|||+|||.++++++|+++|++||.+..+.+..+. ++.++|||||+|.+.++|++|++.|||..+.|+++.
T Consensus        12 ~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~-~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~   90 (101)
T d1x5oa1          12 KQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGV   90 (101)
T ss_dssp             SCCCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTS
T ss_pred             ccccCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeeccc-ccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCc
Confidence            3455667899999999999999999999999999999888775 889999999999999999999999999999998877


Q ss_pred             EEEee
Q psy3928          86 ILTTT   90 (115)
Q Consensus        86 v~~~~   90 (115)
                      +..++
T Consensus        91 v~~~~   95 (101)
T d1x5oa1          91 SAPTE   95 (101)
T ss_dssp             CCCSS
T ss_pred             cCCCC
Confidence            64443

>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=99.84  E-value=1.5e-20  Score=106.97  Aligned_cols=85  Identities=20%  Similarity=0.285  Sum_probs=76.8

Q ss_pred             cccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeE
Q psy3928           7 NNKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSI   86 (115)
Q Consensus         7 ~~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v   86 (115)
                      +.....++|||+|||..+++++|+++|.+||.|..+.+..++  +.++|||||+|.+.++|.+|+..||+..+.|+.+.|
T Consensus         6 ~~~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~--~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V   83 (93)
T d2cq3a1           6 ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEV   83 (93)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT--TTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccc--cCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            445667899999999999999999999999999999998875  336899999999999999999999999999999999


Q ss_pred             EEeeecc
Q psy3928          87 LTTTSRL   93 (115)
Q Consensus        87 ~~~~~~~   93 (115)
                      ..++++.
T Consensus        84 ~~A~~r~   90 (93)
T d2cq3a1          84 NNATARV   90 (93)
T ss_dssp             EECCSSC
T ss_pred             EecCcCC
Confidence            9888764

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=1.9e-20  Score=103.46  Aligned_cols=77  Identities=18%  Similarity=0.363  Sum_probs=71.3

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        12 ~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      .++|||+|||+++++++|+++|++||.+..+.+..++.++.++|+|||+|.+.+++++|+. +++..++|+.+.|..+
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEEC
Confidence            4789999999999999999999999999999999998899999999999999999999985 8999999998887653

>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=99.84  E-value=2.5e-21  Score=106.14  Aligned_cols=74  Identities=24%  Similarity=0.393  Sum_probs=67.7

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928          14 VVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus        14 ~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      +|||+|||+++++++|+++|++||.|..+.|+.++.+++++|||||+|.+.++|++|++. ++..++|+.+.+..
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~~-~~~~i~g~~i~vk~   74 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIKV   74 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTTC-SSCCBTTBCCEEEC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHhh-CCCEECCEEeEEEE
Confidence            589999999999999999999999999999999998999999999999999999999975 66678888776643

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=4.9e-21  Score=110.93  Aligned_cols=82  Identities=18%  Similarity=0.247  Sum_probs=75.0

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEeee
Q psy3928          12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTTS   91 (115)
Q Consensus        12 ~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~~   91 (115)
                      .++|||+|||.++++++|+++|.+||.|..+.|+.++.++.++|||||+|.+.++|++|++ +++..++|+.+.|..+.+
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~~   98 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVA   98 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCSS
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECcc
Confidence            3789999999999999999999999999999999998889999999999999999999986 688889999998887776


Q ss_pred             ccc
Q psy3928          92 RLS   94 (115)
Q Consensus        92 ~~~   94 (115)
                      +..
T Consensus        99 ke~  101 (103)
T d1x4ba1          99 REE  101 (103)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            543

>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=99.84  E-value=2.1e-21  Score=112.10  Aligned_cols=80  Identities=21%  Similarity=0.251  Sum_probs=74.5

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEeee
Q psy3928          12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTTS   91 (115)
Q Consensus        12 ~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~~   91 (115)
                      .++|||+|||..+++++|+++|..||.|..+.++.++.+|+++|||||+|.+.++|++|+. ||+..+.|+.+.|..+++
T Consensus        18 ~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a~~   96 (101)
T d2cq4a1          18 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQA   96 (101)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECCC
Confidence            4789999999999999999999999999999999998899999999999999999999995 999999999998887654


Q ss_pred             c
Q psy3928          92 R   92 (115)
Q Consensus        92 ~   92 (115)
                      +
T Consensus        97 ~   97 (101)
T d2cq4a1          97 E   97 (101)
T ss_dssp             H
T ss_pred             C
Confidence            3

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=1e-20  Score=109.09  Aligned_cols=88  Identities=18%  Similarity=0.149  Sum_probs=77.2

Q ss_pred             hcccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeE--------EEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCC
Q psy3928           6 ENNKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVT--------YVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNP   77 (115)
Q Consensus         6 ~~~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~--------~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~   77 (115)
                      ++++....+|||+|||..+++++|+++|..||.+.        .+.+..++.++.++|||||+|.+.++|..|++.||+.
T Consensus         2 p~~~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~   81 (101)
T d2cpea1           2 PDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGK   81 (101)
T ss_dssp             CCCCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTC
T ss_pred             CCCCCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCC
Confidence            34556778999999999999999999999999874        4566677778999999999999999999999999999


Q ss_pred             CCCCceeeEEEeeecc
Q psy3928          78 CPTDYQSSILTTTSRL   93 (115)
Q Consensus        78 ~~~~~~~~v~~~~~~~   93 (115)
                      .+.|+.++|..++++.
T Consensus        82 ~~~gr~i~V~~a~~~~   97 (101)
T d2cpea1          82 DFQGSKLKVSLARKKP   97 (101)
T ss_dssp             EETTEECEEECSSCCC
T ss_pred             EECCEEEEEEEcCCCC
Confidence            9999999998887643

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.83  E-value=1.6e-20  Score=102.77  Aligned_cols=75  Identities=20%  Similarity=0.234  Sum_probs=70.2

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          14 VVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        14 ~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      +|||+|||.++++++|+++|+.||.+..+.+..++.++.++++|||+|.+.++|++|++ +|+..++|+.++|..+
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECCeEEEEEEC
Confidence            48999999999999999999999999999998888889999999999999999999997 9999999999988653

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=1.3e-20  Score=106.50  Aligned_cols=81  Identities=21%  Similarity=0.235  Sum_probs=73.5

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      +...+|||+|||.++++++|+++|+.||.+..+.+..++  +.++|||||+|.+.++|++|++.||+..+.|+.+.|..+
T Consensus         6 s~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a   83 (89)
T d1cvja2           6 SGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRF   83 (89)
T ss_dssp             TTTTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBT--TBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeec--CCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            445689999999999999999999999999999998875  446799999999999999999999999999999999887


Q ss_pred             eec
Q psy3928          90 TSR   92 (115)
Q Consensus        90 ~~~   92 (115)
                      +++
T Consensus        84 ~~~   86 (89)
T d1cvja2          84 KSR   86 (89)
T ss_dssp             CCT
T ss_pred             CCC
Confidence            754

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=4.2e-20  Score=103.90  Aligned_cols=80  Identities=21%  Similarity=0.230  Sum_probs=68.2

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEeeec
Q psy3928          13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTTSR   92 (115)
Q Consensus        13 ~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~~~   92 (115)
                      ++|||+|||.++++++|+++|++||.|..+.+..+       |||||+|.+.++|+.|+..||+..+.|+.+.+..++++
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~   73 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   73 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEE
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhccccccccccc-------ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecC
Confidence            36999999999999999999999999999987542       69999999999999999999999999999988877665


Q ss_pred             cccCCCC
Q psy3928          93 LSFGITP   99 (115)
Q Consensus        93 ~~~~~~~   99 (115)
                      .....+|
T Consensus        74 ~~~~r~~   80 (87)
T d3begb1          74 VDGPRSP   80 (87)
T ss_dssp             ECC----
T ss_pred             cCCCCCC
Confidence            5443433

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=1.9e-20  Score=101.84  Aligned_cols=70  Identities=23%  Similarity=0.294  Sum_probs=66.6

Q ss_pred             EEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCcee
Q psy3928          15 VLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQS   84 (115)
Q Consensus        15 l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~   84 (115)
                      |||+|||.++++++|+++|.+||.+..+.+..++.++.++|+|||+|.+.++|++|+..|||..+.|+.+
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~   70 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMA   70 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEC
Confidence            7999999999999999999999999999999988899999999999999999999999999999888764

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.81  E-value=3.5e-20  Score=104.01  Aligned_cols=81  Identities=20%  Similarity=0.308  Sum_probs=69.6

Q ss_pred             CCCEEEEcCCCCCCC-HHHHHHHhhhcCCeEEEEecee-CCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928          11 YGRVVLKEKLPPEAE-HDYIESVFSKYGKVTYVSLPKF-KSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~-~~~l~~~f~~~g~i~~~~i~~~-~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      +.++|||+|||.+++ ++.|+++|++||.|..+.+..+ +.++.++|||||+|.+.++|++|++ +|+..+.|+.++|..
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~~   81 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSL   81 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEEE
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEEE
Confidence            568999999999875 6679999999999999998764 4578899999999999999999995 999999999999988


Q ss_pred             eeec
Q psy3928          89 TTSR   92 (115)
Q Consensus        89 ~~~~   92 (115)
                      ++++
T Consensus        82 a~~k   85 (86)
T d2ghpa3          82 ADKK   85 (86)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            7754

>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=99.81  E-value=2.1e-20  Score=107.90  Aligned_cols=84  Identities=21%  Similarity=0.227  Sum_probs=77.0

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      .+.++|||+|||.++++++|+++|..||.+..+.+..+..+|+++|||||+|.+.++|+.|++.||+..+.|+.++|..+
T Consensus        16 ~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   95 (102)
T d2cpxa1          16 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG   95 (102)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            34679999999999999999999999999988888877778999999999999999999999999999999999999888


Q ss_pred             eecc
Q psy3928          90 TSRL   93 (115)
Q Consensus        90 ~~~~   93 (115)
                      +++.
T Consensus        96 k~k~   99 (102)
T d2cpxa1          96 KNKK   99 (102)
T ss_dssp             CCCS
T ss_pred             CCcc
Confidence            7653

>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=99.81  E-value=4.4e-19  Score=102.69  Aligned_cols=84  Identities=23%  Similarity=0.179  Sum_probs=72.9

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      ......|||+|||.++++++|+++|..+|.+....++..+.++.++|+|||+|.++++|++|++ +++..+.++.+.|..
T Consensus        12 ~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~   90 (104)
T d1wg5a_          12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFK   90 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEE
Confidence            4455679999999999999999999999988775555555688999999999999999999886 899999999999988


Q ss_pred             eeecc
Q psy3928          89 TTSRL   93 (115)
Q Consensus        89 ~~~~~   93 (115)
                      ++++.
T Consensus        91 ~~~~~   95 (104)
T d1wg5a_          91 SSRAE   95 (104)
T ss_dssp             ECTTT
T ss_pred             CCHHH
Confidence            87654

>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=99.80  E-value=2.3e-19  Score=103.83  Aligned_cols=85  Identities=19%  Similarity=0.250  Sum_probs=72.4

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeC-CCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFK-STGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~-~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      ....++|||+|||.++++++|+++|..|| +..+.++.++ .++.++|||||+|.+.++|++|+ .+|+..+.++.++|.
T Consensus        12 ~~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~~~gr~l~V~   89 (104)
T d1wi8a_          12 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVD   89 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCEECCEEEEEE
Confidence            44568999999999999999999999998 7777776654 46789999999999999998766 599999999999998


Q ss_pred             Eeeecccc
Q psy3928          88 TTTSRLSF   95 (115)
Q Consensus        88 ~~~~~~~~   95 (115)
                      .+.++...
T Consensus        90 ~a~~~~~~   97 (104)
T d1wi8a_          90 VADQAQDK   97 (104)
T ss_dssp             ECCCCCCC
T ss_pred             ECCCCCCC
Confidence            87765443

>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=99.80  E-value=1.5e-19  Score=103.38  Aligned_cols=82  Identities=18%  Similarity=0.216  Sum_probs=72.6

Q ss_pred             hhcccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCcee
Q psy3928           5 VENNKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQS   84 (115)
Q Consensus         5 ~~~~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~   84 (115)
                      ..+..+..++|||+|||..+++++|+++|++||.|..+++..+      +|||||+|.+.++|+.|+..|++..+.|+.+
T Consensus        11 ~~~~~~~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l   84 (96)
T d1x4ga1          11 VNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVV   84 (96)
T ss_dssp             HHHSCSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             ccCCCCCCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            3445566789999999999999999999999999999998754      5799999999999999999999999999998


Q ss_pred             eEEEeeec
Q psy3928          85 SILTTTSR   92 (115)
Q Consensus        85 ~v~~~~~~   92 (115)
                      ++..++++
T Consensus        85 ~v~~ak~~   92 (96)
T d1x4ga1          85 KCYWGKES   92 (96)
T ss_dssp             EEECCCCC
T ss_pred             EEEEcCCC
Confidence            88776653

>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=99.80  E-value=3.4e-19  Score=101.65  Aligned_cols=80  Identities=26%  Similarity=0.308  Sum_probs=71.1

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      ....++|||+|||.++++++|+++|..||.+..+.+..   ++.+++||||+|.+.++|+.|++.||+..+.|+.+.|..
T Consensus        11 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~---~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~   87 (95)
T d1x4aa1          11 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN---RRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEF   87 (95)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECC---SSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEecc---cccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            34567899999999999999999999999999887754   455678999999999999999999999999999998887


Q ss_pred             eee
Q psy3928          89 TTS   91 (115)
Q Consensus        89 ~~~   91 (115)
                      +++
T Consensus        88 a~~   90 (95)
T d1x4aa1          88 PRS   90 (95)
T ss_dssp             CCC
T ss_pred             ccC
Confidence            664

>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=99.80  E-value=1.8e-19  Score=100.86  Aligned_cols=76  Identities=25%  Similarity=0.276  Sum_probs=69.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      ..++|||+|||.++++++|+++|+.||.+..+.+..++ ++.++|+|||+|.+.++|++|++ +++..+.|+.+.+..
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~-~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~   80 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILF   80 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEE
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeec-cCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEE
Confidence            45789999999999999999999999999999988776 88999999999999999999996 699999998887764

>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=99.80  E-value=4.6e-19  Score=98.73  Aligned_cols=79  Identities=20%  Similarity=0.215  Sum_probs=68.5

Q ss_pred             cccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCC-Cceee
Q psy3928           7 NNKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPT-DYQSS   85 (115)
Q Consensus         7 ~~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~-~~~~~   85 (115)
                      .+.++.++|||+|||.++++++|.++|+.||.+..+++..+     .+|+|||+|.+.++|..|++.|+|..+. ++.+.
T Consensus         3 ~~~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~   77 (83)
T d2b0ga1           3 TEQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN-----RHDIAFVEFTTELQSNAAKEALQGFKITPTHAMK   77 (83)
T ss_dssp             CCCSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT-----TCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc-----cceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEE
Confidence            35567789999999999999999999999999999988653     2579999999999999999999999885 56777


Q ss_pred             EEEee
Q psy3928          86 ILTTT   90 (115)
Q Consensus        86 v~~~~   90 (115)
                      +..++
T Consensus        78 v~~ak   82 (83)
T d2b0ga1          78 ITFAK   82 (83)
T ss_dssp             EEECC
T ss_pred             EEEec
Confidence            76654

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=2.7e-19  Score=105.12  Aligned_cols=78  Identities=18%  Similarity=0.255  Sum_probs=71.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEee
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTT   90 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~   90 (115)
                      ..++|||+|||..+++++|+++|++||.|..+++..   ++.++|||||+|.+.++|..|++.|||..+.|+.+.|..+.
T Consensus         6 ~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~---~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~   82 (114)
T d2f9da1           6 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN---TPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYN   82 (114)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEC---STTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccc---cCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            457999999999999999999999999999998864   45678999999999999999999999999999999988765


Q ss_pred             e
Q psy3928          91 S   91 (115)
Q Consensus        91 ~   91 (115)
                      +
T Consensus        83 ~   83 (114)
T d2f9da1          83 A   83 (114)
T ss_dssp             H
T ss_pred             C
Confidence            4

>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=99.79  E-value=5.2e-19  Score=102.09  Aligned_cols=82  Identities=23%  Similarity=0.221  Sum_probs=71.4

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      ....++|||+|||.++++++|+++|..++ +..+.++.+. ++..+|||||+|.+.++|++|++ +|+..+.++.|+|..
T Consensus        12 ~~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~~-~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~   88 (102)
T d1weza_          12 STTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFL   88 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEec-CCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEE
Confidence            44567999999999999999999999997 4567677665 78899999999999999999986 899999999999987


Q ss_pred             eeecc
Q psy3928          89 TTSRL   93 (115)
Q Consensus        89 ~~~~~   93 (115)
                      .+.+.
T Consensus        89 s~~~~   93 (102)
T d1weza_          89 NSTAG   93 (102)
T ss_dssp             ECCCC
T ss_pred             cCCCC
Confidence            77543

>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=99.79  E-value=7.7e-21  Score=107.83  Aligned_cols=82  Identities=17%  Similarity=0.190  Sum_probs=72.7

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      .....+|||+|||.++++++|+++|..||.+..+.++.++ +|+++|||||+|.+.++|++|++ +|+..+.|+.++|..
T Consensus        10 ~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~-~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~   87 (91)
T d1fjeb1          10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEK   87 (91)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEE-EETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEEC
T ss_pred             CCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecC-CCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEe
Confidence            3455789999999999999999999999998888776554 88999999999999999999996 999999999999887


Q ss_pred             eeec
Q psy3928          89 TTSR   92 (115)
Q Consensus        89 ~~~~   92 (115)
                      ++++
T Consensus        88 ak~k   91 (91)
T d1fjeb1          88 PKGR   91 (91)
T ss_dssp             CCCS
T ss_pred             cCCC
Confidence            7653

>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=99.78  E-value=1.7e-19  Score=103.08  Aligned_cols=81  Identities=26%  Similarity=0.331  Sum_probs=71.2

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      ...+.++|||+|||.++++++|+++|.+||.+..+..     ++.+++||||+|.+.++|++|++.||+..+.|+.++|.
T Consensus        12 ~~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~-----~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~   86 (96)
T d1fjca_          12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ-----DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLY   86 (96)
T ss_dssp             TTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE-----TTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee-----cCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            3445689999999999999999999999997765432     78889999999999999999999999999999999998


Q ss_pred             Eeeecc
Q psy3928          88 TTTSRL   93 (115)
Q Consensus        88 ~~~~~~   93 (115)
                      .+.++.
T Consensus        87 ~a~~k~   92 (96)
T d1fjca_          87 YTGEKG   92 (96)
T ss_dssp             ECSSSC
T ss_pred             EeCCCC
Confidence            877644

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.78  E-value=1.3e-19  Score=102.29  Aligned_cols=76  Identities=18%  Similarity=0.198  Sum_probs=67.5

Q ss_pred             CCCEEEEcCCCCCCCHHHH---HHHhhhcCCeEEEEeceeCCCCC---eeeEEEEEecCHHHHHHHHHhhCCCCCCCcee
Q psy3928          11 YGRVVLKEKLPPEAEHDYI---ESVFSKYGKVTYVSLPKFKSTGK---LKGFAFVEFSTKEEATKALELGLNPCPTDYQS   84 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l---~~~f~~~g~i~~~~i~~~~~~~~---~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~   84 (115)
                      ..++|||+|||+++++++|   .++|.+||.|..+.+..++.++.   .+|||||+|.+.++|++|++.|||..+.|+.+
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~l   86 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTL   86 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEE
Confidence            4568999999999999999   66899999999999998875554   45899999999999999999999999999887


Q ss_pred             eE
Q psy3928          85 SI   86 (115)
Q Consensus        85 ~v   86 (115)
                      ++
T Consensus        87 kv   88 (89)
T d2cpia1          87 KA   88 (89)
T ss_dssp             EE
T ss_pred             EE
Confidence            75

>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=99.78  E-value=1.4e-18  Score=97.66  Aligned_cols=79  Identities=19%  Similarity=0.142  Sum_probs=68.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCC-CCceeeEEE
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCP-TDYQSSILT   88 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~-~~~~~~v~~   88 (115)
                      ++.++|||+|||.++++++|+++|+.||.+..+.+..    ++.+++|||+|.+.++|.+|+..|++..+ +|+.+++..
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~----~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~   83 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFF----QKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSF   83 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEEC----SSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEee----ecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEe
Confidence            4567999999999999999999999999988776543    34567999999999999999999999988 578899887


Q ss_pred             eeec
Q psy3928          89 TTSR   92 (115)
Q Consensus        89 ~~~~   92 (115)
                      .+++
T Consensus        84 sk~~   87 (88)
T d2adca2          84 SKST   87 (88)
T ss_dssp             CSSC
T ss_pred             CCCC
Confidence            7654

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.78  E-value=3.5e-19  Score=99.78  Aligned_cols=79  Identities=22%  Similarity=0.183  Sum_probs=68.9

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEE-EEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTY-VSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~-~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      .+...+|||+|||.++++++|+++|..||.+.. +.+..+ .++.++|+|||+|.+.++|++|++.+|+..+.++.++|.
T Consensus         6 ~p~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~-~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~   84 (86)
T d2cqpa1           6 KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYN-EKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLV   84 (86)
T ss_dssp             CCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEEC-SSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeC-CCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEE
Confidence            345678999999999999999999999998765 344444 489999999999999999999999999999999998875


Q ss_pred             E
Q psy3928          88 T   88 (115)
Q Consensus        88 ~   88 (115)
                      .
T Consensus        85 l   85 (86)
T d2cqpa1          85 L   85 (86)
T ss_dssp             E
T ss_pred             E
Confidence            4

>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=99.77  E-value=2.1e-19  Score=101.19  Aligned_cols=82  Identities=20%  Similarity=0.251  Sum_probs=69.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      ...++|||+|||..+++++|+++|.+||.+..+++.     ..+++||||+|.+.+.|++|+.  ++..++|+.+.|..+
T Consensus         3 ~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~-----~~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a   75 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIP-----KPFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNA   75 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECC-----SSCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEe-----eccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeC
Confidence            456899999999999999999999999999998764     4457899999999999999985  677889999998887


Q ss_pred             eeccccCCC
Q psy3928          90 TSRLSFGIT   98 (115)
Q Consensus        90 ~~~~~~~~~   98 (115)
                      +++......
T Consensus        76 ~~k~~~~~~   84 (88)
T d1wf0a_          76 EPKHNSNSG   84 (88)
T ss_dssp             CCCCCCCSC
T ss_pred             CCCCCCCCC
Confidence            766554333

>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=99.77  E-value=7.9e-19  Score=100.64  Aligned_cols=75  Identities=25%  Similarity=0.325  Sum_probs=66.6

Q ss_pred             cCCCCEEEEcCCC-CCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928           9 KKYGRVVLKEKLP-PEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus         9 ~~~~~~l~V~~l~-~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      .....+|||+||| ..+++.+|+++|++||.|..+.+        ++|||||+|.+.++|++|++.||+..+.|+.++|.
T Consensus        12 ~~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i--------~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~   83 (98)
T d1wf2a_          12 RSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDIN   83 (98)
T ss_dssp             SSCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE--------ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEE
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE--------eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            3445789999997 56888899999999999999987        35799999999999999999999999999999988


Q ss_pred             Eeee
Q psy3928          88 TTTS   91 (115)
Q Consensus        88 ~~~~   91 (115)
                      .+++
T Consensus        84 ~a~~   87 (98)
T d1wf2a_          84 LAAE   87 (98)
T ss_dssp             ETTS
T ss_pred             ECCC
Confidence            8764

>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=99.77  E-value=8.8e-19  Score=98.20  Aligned_cols=77  Identities=25%  Similarity=0.266  Sum_probs=69.5

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      ...++|||+|||.++++++|+++|++||.+..+.+..+      ++||||+|.+.++|+.|++.||+..+.|+.++|..+
T Consensus         6 ~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~------k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A   79 (86)
T d2cpja1           6 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFA   79 (86)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEES
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc------cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            34578999999999999999999999999999988654      479999999999999999999999999999998877


Q ss_pred             eec
Q psy3928          90 TSR   92 (115)
Q Consensus        90 ~~~   92 (115)
                      .+.
T Consensus        80 ~~~   82 (86)
T d2cpja1          80 CHS   82 (86)
T ss_dssp             SCC
T ss_pred             CCc
Confidence            653

>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=99.77  E-value=5.6e-19  Score=98.97  Aligned_cols=79  Identities=16%  Similarity=0.223  Sum_probs=68.7

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      .....++|||+|||..+++++|+++|++||.+..+.+.      .++|||||+|.+.++|..|+..||+..+.|+.+.+.
T Consensus         4 ~~~~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~------~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~   77 (86)
T d2cpda1           4 TMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK------KIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVT   77 (86)
T ss_dssp             CSSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEE------ECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEE
T ss_pred             cccCCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEc------cccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34456899999999999999999999999988776653      346799999999999999999999999999998887


Q ss_pred             Eeeec
Q psy3928          88 TTTSR   92 (115)
Q Consensus        88 ~~~~~   92 (115)
                      .++|+
T Consensus        78 ~akP~   82 (86)
T d2cpda1          78 LAKPV   82 (86)
T ss_dssp             CCCCC
T ss_pred             eccCC
Confidence            76654

>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=99.77  E-value=1e-18  Score=95.57  Aligned_cols=74  Identities=19%  Similarity=0.218  Sum_probs=66.0

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        13 ~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      .+|||+|||.++++++|+++|+.||.|..+.+..++.  ..+++|||+|.++++|++|+. +++..++|+.+.|..+
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~--~~~~~afV~F~~~~~a~~Al~-~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK--KNFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTT--SSSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecc--ccceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            4799999999999999999999999999999988863  334699999999999999985 8999999999888764

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=3.8e-18  Score=99.34  Aligned_cols=75  Identities=21%  Similarity=0.186  Sum_probs=68.1

Q ss_pred             CCEEEEcCCCC-CCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEee
Q psy3928          12 GRVVLKEKLPP-EAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTT   90 (115)
Q Consensus        12 ~~~l~V~~l~~-~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~   90 (115)
                      ..+|||+|||+ .+++++|+++|+.||.|..+.++.++     +|+|||+|.+.++|++|++.|++..+.|+.+++...+
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~-----kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~   76 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   76 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCS
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc-----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            47899999965 59999999999999999999997653     6799999999999999999999999999999988875


Q ss_pred             e
Q psy3928          91 S   91 (115)
Q Consensus        91 ~   91 (115)
                      .
T Consensus        77 ~   77 (109)
T d2adca1          77 H   77 (109)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.77  E-value=2.6e-18  Score=98.47  Aligned_cols=81  Identities=20%  Similarity=0.221  Sum_probs=71.9

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      ......+|||+|||..+++++|+++|.+||.+..+.+..       +|+|||+|.+.++|++|++.||+..+.|+.+++.
T Consensus        11 ~~~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~   83 (98)
T d1wg4a_          11 TRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETS   83 (98)
T ss_dssp             CCSCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEE
Confidence            345567899999999999999999999999999988753       3799999999999999999999999999999999


Q ss_pred             Eeeecccc
Q psy3928          88 TTTSRLSF   95 (115)
Q Consensus        88 ~~~~~~~~   95 (115)
                      .++++...
T Consensus        84 ~~~~~~~~   91 (98)
T d1wg4a_          84 YIRVYPER   91 (98)
T ss_dssp             EEEEECCC
T ss_pred             EEecCCCC
Confidence            88875543

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=1.9e-18  Score=98.60  Aligned_cols=81  Identities=19%  Similarity=0.126  Sum_probs=70.3

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhcCC-eEEEEeceeC-CCCCeeeEEEEEecCHHHHHHHHHhhCCCC--CCCceeeEEE
Q psy3928          13 RVVLKEKLPPEAEHDYIESVFSKYGK-VTYVSLPKFK-STGKLKGFAFVEFSTKEEATKALELGLNPC--PTDYQSSILT   88 (115)
Q Consensus        13 ~~l~V~~l~~~~~~~~l~~~f~~~g~-i~~~~i~~~~-~~~~~~g~~fv~f~~~~~a~~al~~l~~~~--~~~~~~~v~~   88 (115)
                      ++|||+|||.++++++|+++|++||. +..+.++.++ .++.++|||||+|.+.++|..|++.|++..  +.|+.+.|..
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~~   81 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDW   81 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEE
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEEE
Confidence            68999999999999999999999995 8999988875 357899999999999999999999997654  4578888888


Q ss_pred             eeecc
Q psy3928          89 TTSRL   93 (115)
Q Consensus        89 ~~~~~   93 (115)
                      +++..
T Consensus        82 A~p~~   86 (96)
T d2disa1          82 AEPEI   86 (96)
T ss_dssp             SCSSC
T ss_pred             cCCCC
Confidence            77643

>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=99.77  E-value=3.1e-18  Score=99.97  Aligned_cols=75  Identities=25%  Similarity=0.202  Sum_probs=67.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEee
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTT   90 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~   90 (115)
                      ..++|||+|||.++++++|+++|..||.|..+.|..      .++||||+|.+.++|++|++.||+..+.|+.+.+..+.
T Consensus         9 ~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~------~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~   82 (111)
T d1whxa_           9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAP   82 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeec------cCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECC
Confidence            447899999999999999999999999999988742      35899999999999999999999999999999887765


Q ss_pred             e
Q psy3928          91 S   91 (115)
Q Consensus        91 ~   91 (115)
                      .
T Consensus        83 ~   83 (111)
T d1whxa_          83 I   83 (111)
T ss_dssp             T
T ss_pred             C
Confidence            4

>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=3.9e-19  Score=102.73  Aligned_cols=81  Identities=11%  Similarity=0.015  Sum_probs=69.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEe
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTT   89 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~   89 (115)
                      .....|||+|||.++++++|+++|..||.+....++....+|.++|+|||+|.+.++|++|++ +|+..++|+.+.|..+
T Consensus         6 ~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~   84 (103)
T d2cpya1           6 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVV   84 (103)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEEC
Confidence            345679999999999999999999999987653333333489999999999999999999996 8999999999999876


Q ss_pred             ee
Q psy3928          90 TS   91 (115)
Q Consensus        90 ~~   91 (115)
                      ..
T Consensus        85 ~~   86 (103)
T d2cpya1          85 TL   86 (103)
T ss_dssp             CH
T ss_pred             CH
Confidence            54

>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=99.75  E-value=1.3e-18  Score=97.84  Aligned_cols=77  Identities=16%  Similarity=0.214  Sum_probs=65.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEee
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTT   90 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~   90 (115)
                      ...+|||+|||.++++++|+++|.+|| +..+.+      +..++||||+|.+.++|++|++.||+..+.|+.++|..++
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~------~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~   76 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV------DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE------EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcC-ceeeee------eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            457899999999999999999999999 322322      3456899999999999999999999999999999998876


Q ss_pred             eccc
Q psy3928          91 SRLS   94 (115)
Q Consensus        91 ~~~~   94 (115)
                      ....
T Consensus        77 ~~~~   80 (88)
T d1wg1a_          77 TDAL   80 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            5433

>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=99.74  E-value=2.3e-18  Score=97.41  Aligned_cols=79  Identities=22%  Similarity=0.286  Sum_probs=69.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHH----HHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeE
Q psy3928          11 YGRVVLKEKLPPEAEHDYIE----SVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSI   86 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~----~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v   86 (115)
                      +.++|||+|||..+++++|+    .+|++||.+..+.+..   ++.++|||||+|.+.++|..|++.+|+..+.|+.+++
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~---~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v   78 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI   78 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee---eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            35799999999999998875    4678999999988743   5677899999999999999999999999999999998


Q ss_pred             EEeeec
Q psy3928          87 LTTTSR   92 (115)
Q Consensus        87 ~~~~~~   92 (115)
                      ..+++.
T Consensus        79 ~~ak~~   84 (91)
T d1nu4a_          79 QYAKTD   84 (91)
T ss_dssp             EECSSC
T ss_pred             EEeCCC
Confidence            887653

>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=99.74  E-value=2.8e-18  Score=94.87  Aligned_cols=75  Identities=16%  Similarity=0.151  Sum_probs=65.1

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCC-CCCCceeeEEEeee
Q psy3928          13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNP-CPTDYQSSILTTTS   91 (115)
Q Consensus        13 ~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~-~~~~~~~~v~~~~~   91 (115)
                      .+|||+|||.++++++|+++|.+||.+....+.      .++|||||+|.+.++|+.|++.|||. .+.|+.++|..+.+
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~------~~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~   75 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL------LKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVS   75 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEE------EETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEe------cccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCC
Confidence            469999999999999999999999987655443      34689999999999999999999986 58999999988776


Q ss_pred             cc
Q psy3928          92 RL   93 (115)
Q Consensus        92 ~~   93 (115)
                      +.
T Consensus        76 k~   77 (80)
T d2cqha1          76 KK   77 (80)
T ss_dssp             CC
T ss_pred             cC
Confidence            43

>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=99.73  E-value=2.5e-17  Score=94.10  Aligned_cols=76  Identities=13%  Similarity=0.132  Sum_probs=66.5

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCc--eeeEE
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDY--QSSIL   87 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~--~~~v~   87 (115)
                      .+.++|||+|||.++++++|+++|++||.|..+.+.++      +++|||+|.+.++|+.|++.||+..+.+.  .+++.
T Consensus        15 ~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~   88 (97)
T d1whya_          15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVD   88 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEE
Confidence            34589999999999999999999999999999988643      46999999999999999999999999874  56666


Q ss_pred             Eeee
Q psy3928          88 TTTS   91 (115)
Q Consensus        88 ~~~~   91 (115)
                      .+++
T Consensus        89 ~ak~   92 (97)
T d1whya_          89 FAKS   92 (97)
T ss_dssp             ECCC
T ss_pred             eCCC
Confidence            6654

>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=99.73  E-value=1.1e-17  Score=92.16  Aligned_cols=74  Identities=16%  Similarity=0.184  Sum_probs=66.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEee
Q psy3928          11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTT   90 (115)
Q Consensus        11 ~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~   90 (115)
                      ..++|||+|++  +++++|+++|++||.|..+.+..+      ++||||+|.+.++|..|+..||+..+.|+.++|..++
T Consensus         4 ~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~   75 (79)
T d2bz2a1           4 KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIAR   75 (79)
T ss_dssp             CCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT------TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECC
T ss_pred             CCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC------CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEec
Confidence            45799999996  799999999999999999887543      4699999999999999999999999999999998876


Q ss_pred             ec
Q psy3928          91 SR   92 (115)
Q Consensus        91 ~~   92 (115)
                      ++
T Consensus        76 ~~   77 (79)
T d2bz2a1          76 KQ   77 (79)
T ss_dssp             SS
T ss_pred             CC
Confidence            53

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=6.8e-18  Score=98.81  Aligned_cols=82  Identities=24%  Similarity=0.251  Sum_probs=70.8

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      ....++|||+|||..+++++|.++|..+|.+..+.++....+|.++|+|||+|.+.++|++|+. +|+..+.|+.|.|..
T Consensus        15 ~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~   93 (112)
T d1wela1          15 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHP   93 (112)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEE
T ss_pred             CCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEE
Confidence            3456799999999999999999999999987654444445589999999999999999999996 899999999999987


Q ss_pred             eee
Q psy3928          89 TTS   91 (115)
Q Consensus        89 ~~~   91 (115)
                      +..
T Consensus        94 ~~~   96 (112)
T d1wela1          94 ITK   96 (112)
T ss_dssp             ECH
T ss_pred             cCh
Confidence            654

>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=99.71  E-value=3.2e-17  Score=89.52  Aligned_cols=70  Identities=23%  Similarity=0.341  Sum_probs=61.7

Q ss_pred             EEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEeee
Q psy3928          15 VLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTTS   91 (115)
Q Consensus        15 l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~~   91 (115)
                      |||+|||.++++++|+++|++|| +..+.+      ++++|+|||+|.+.++|++|+..||+..+.|+.+.|..++.
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~------~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~   70 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPT   70 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCS
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee------cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCC
Confidence            79999999999999999999998 444433      34578999999999999999999999999999999887753

>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=99.70  E-value=2.1e-16  Score=91.18  Aligned_cols=78  Identities=22%  Similarity=0.253  Sum_probs=67.5

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhC--CCCCCCceeeE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGL--NPCPTDYQSSI   86 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~--~~~~~~~~~~v   86 (115)
                      .....+|||+|||..+++++|.++|.+||.|..+.+.+.      +++|||+|.+.++|+.|+..++  ...+.|+++.+
T Consensus        12 ~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v   85 (104)
T d1wexa_          12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFF   85 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec------ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEE
Confidence            445789999999999999999999999999999988643      4699999999999999999884  45678899999


Q ss_pred             EEeeec
Q psy3928          87 LTTTSR   92 (115)
Q Consensus        87 ~~~~~~   92 (115)
                      ...+..
T Consensus        86 ~~s~~~   91 (104)
T d1wexa_          86 NYSTSK   91 (104)
T ss_dssp             EECSSS
T ss_pred             EEcCCC
Confidence            887653

>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=99.70  E-value=1.1e-16  Score=93.06  Aligned_cols=78  Identities=15%  Similarity=-0.003  Sum_probs=67.1

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCC--CceeeEE
Q psy3928          10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPT--DYQSSIL   87 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~--~~~~~v~   87 (115)
                      .....|||+|||..+++++|+++|.+||.|..+.+..++    .+|+|||+|.+.++|+.|+..||+..+.  +..+++.
T Consensus         5 s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~   80 (108)
T d2adba1           5 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID   80 (108)
T ss_dssp             CCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEE
T ss_pred             CCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEE
Confidence            345689999999999999999999999999999887653    4789999999999999999999999884  5566666


Q ss_pred             Eeee
Q psy3928          88 TTTS   91 (115)
Q Consensus        88 ~~~~   91 (115)
                      ..++
T Consensus        81 ~s~~   84 (108)
T d2adba1          81 FSKL   84 (108)
T ss_dssp             ECSS
T ss_pred             ecCC
Confidence            6544

>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=99.69  E-value=9.7e-17  Score=90.01  Aligned_cols=79  Identities=25%  Similarity=0.284  Sum_probs=68.0

Q ss_pred             ccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhh--CCCCCCCceee
Q psy3928           8 NKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELG--LNPCPTDYQSS   85 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l--~~~~~~~~~~~   85 (115)
                      +..+.++|||+|||.++++++|+++|++||.+..+.+..+      +++|||+|.+.++|++|+..+  ++..+.|+.++
T Consensus         4 ~~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~   77 (88)
T d2cq1a1           4 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIY   77 (88)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc------ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEE
Confidence            4567789999999999999999999999999999987644      369999999999999999876  45678889888


Q ss_pred             EEEeeec
Q psy3928          86 ILTTTSR   92 (115)
Q Consensus        86 v~~~~~~   92 (115)
                      +...+.+
T Consensus        78 v~~sk~~   84 (88)
T d2cq1a1          78 IQYSNHK   84 (88)
T ss_dssp             EEECSCS
T ss_pred             EEECCCC
Confidence            8876643

>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=99.68  E-value=1.9e-16  Score=99.25  Aligned_cols=83  Identities=18%  Similarity=0.338  Sum_probs=75.1

Q ss_pred             cCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928           9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      ....++|||+|||..+++++|+++|..||.+..+.+..++.++.++|+|||+|.+.++|++|+. +++..++|+.+.|..
T Consensus        94 ~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~~  172 (183)
T d1u1qa_          94 HLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRK  172 (183)
T ss_dssp             TCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEEEE
T ss_pred             ccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEe
Confidence            4456899999999999999999999999999999999988889999999999999999999997 688889999988877


Q ss_pred             eeec
Q psy3928          89 TTSR   92 (115)
Q Consensus        89 ~~~~   92 (115)
                      +.++
T Consensus       173 A~~k  176 (183)
T d1u1qa_         173 ALSK  176 (183)
T ss_dssp             CCCH
T ss_pred             cCCc
Confidence            6654

>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=99.66  E-value=2.9e-16  Score=89.87  Aligned_cols=77  Identities=22%  Similarity=0.305  Sum_probs=66.9

Q ss_pred             cCCCCEEEEcCCCCC-CCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHH--hhCCCCCCCceee
Q psy3928           9 KKYGRVVLKEKLPPE-AEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE--LGLNPCPTDYQSS   85 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~-~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~--~l~~~~~~~~~~~   85 (115)
                      ....++|||+|||.. +++++|.++|++||.|..+.+..+      +++|||+|.+.++|..|++  .+++..+.|+.++
T Consensus        15 ~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~   88 (99)
T d1x4fa1          15 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVK   88 (99)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCE
T ss_pred             CCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCCceECCEEEE
Confidence            345689999999975 899999999999999999988654      4799999999999999998  5778889999999


Q ss_pred             EEEeee
Q psy3928          86 ILTTTS   91 (115)
Q Consensus        86 v~~~~~   91 (115)
                      |..++.
T Consensus        89 V~~s~~   94 (99)
T d1x4fa1          89 VDLSEK   94 (99)
T ss_dssp             EEEECS
T ss_pred             EEEcCC
Confidence            987754

>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=99.63  E-value=5.2e-18  Score=95.69  Aligned_cols=74  Identities=18%  Similarity=0.160  Sum_probs=63.5

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEec-----eeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEE
Q psy3928          13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLP-----KFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSIL   87 (115)
Q Consensus        13 ~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~-----~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~   87 (115)
                      ++|||+|||.++++++|+++|+.+|.+..+.+.     .+..++.++|||||+|.+.++|++|+. ||+..+.|+.++|.
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~Gr~l~V~   80 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIR   80 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSSSSCCCCB
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEECCEEEEEC
Confidence            679999999999999999999999877655443     233466788999999999999999985 99999999998875

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.63  E-value=8.8e-16  Score=86.23  Aligned_cols=77  Identities=14%  Similarity=0.098  Sum_probs=66.6

Q ss_pred             cCCCCEEEEcCCCCC-CCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhh--CCCCCCCceee
Q psy3928           9 KKYGRVVLKEKLPPE-AEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELG--LNPCPTDYQSS   85 (115)
Q Consensus         9 ~~~~~~l~V~~l~~~-~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l--~~~~~~~~~~~   85 (115)
                      .+..++|||+|||.. +++++|.++|++||.|..+.+..++      ++|||+|.+.++|..|++.+  ++..+.|++++
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~k------~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~   78 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI------NEAFIEMATTEDAQAAVDYYTTTPALVFGKPVR   78 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS------SCEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeeccc------eEEEEEEcchhhHHHHHHHHhhCCCccCCceEE
Confidence            456789999999986 7899999999999999999887543      58999999999999999976  56668999999


Q ss_pred             EEEeee
Q psy3928          86 ILTTTS   91 (115)
Q Consensus        86 v~~~~~   91 (115)
                      |..++.
T Consensus        79 V~~s~~   84 (89)
T d1x4da1          79 VHLSQK   84 (89)
T ss_dssp             EEEECC
T ss_pred             EEECCC
Confidence            888764

>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=99.57  E-value=2.4e-14  Score=89.45  Aligned_cols=75  Identities=21%  Similarity=0.278  Sum_probs=65.1

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928          13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus        13 ~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      ++|||+|||+.+++++|+++|++||.|..+.++.++.++.++|+|||+|.+.++|++|+..++. .+....+.+..
T Consensus         7 r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~~~~-~~~~~~~~~~~   81 (183)
T d1u1qa_           7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPH-KVDGRVVEPKR   81 (183)
T ss_dssp             HEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSC-EETTEECEEEE
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHhcCC-cccccchhhhh
Confidence            6899999999999999999999999999999999888999999999999999999999986553 44455444443

>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=99.56  E-value=2.7e-16  Score=90.74  Aligned_cols=74  Identities=20%  Similarity=0.104  Sum_probs=66.1

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEE
Q psy3928          14 VVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus        14 ~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      .++|.+++..+.++.|+++|++||.|..+.|+.+. ++.++|++||+|.+.++|.+|+..|||..++|+.+.+..
T Consensus        29 ~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~-~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~  102 (104)
T d1jmta_          29 DVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAEL  102 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEE
T ss_pred             hHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCC-CCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEE
Confidence            35566677778888999999999999999998775 899999999999999999999999999999999988764

>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=99.54  E-value=2.3e-15  Score=86.82  Aligned_cols=77  Identities=14%  Similarity=-0.013  Sum_probs=66.7

Q ss_pred             CCCCEEEEcCCCCCC-CH----HHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCcee
Q psy3928          10 KYGRVVLKEKLPPEA-EH----DYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQS   84 (115)
Q Consensus        10 ~~~~~l~V~~l~~~~-~~----~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~   84 (115)
                      ....+|||+||+.++ ++    ++|+.+|++||.+..+++..      +++||||+|.+.++|.+|+..||+..+.|+.+
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k------~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l   76 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK------SFKRVRINFSNPLSAADARLRLHKTEFLGKEM   76 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET------TTTEEEEECSSTTHHHHHHHTSTTSEETTEEC
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEec------CCCEEEEEECCHHHHHHHHHHhcccccCCCEe
Confidence            456789999999876 33    56999999999999998863      35699999999999999999999999999999


Q ss_pred             eEEEeeec
Q psy3928          85 SILTTTSR   92 (115)
Q Consensus        85 ~v~~~~~~   92 (115)
                      .+..++++
T Consensus        77 ~v~~a~~~   84 (104)
T d1weya_          77 KLYFAQTL   84 (104)
T ss_dssp             EEECCCCS
T ss_pred             EEeecccC
Confidence            99887654

>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=99.51  E-value=6e-14  Score=81.84  Aligned_cols=70  Identities=13%  Similarity=0.124  Sum_probs=60.3

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCH-HHHHHHHHhhCCCCCCCceeeEEE
Q psy3928          13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK-EEATKALELGLNPCPTDYQSSILT   88 (115)
Q Consensus        13 ~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~-~~a~~al~~l~~~~~~~~~~~v~~   88 (115)
                      ..+||||||..+++++|+.+|.+||.|..+.++.+      +++|||.|.++ ++|..|+..+++..+.+..+.+..
T Consensus        12 ~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~   82 (113)
T d1owxa_          12 LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTW   82 (113)
T ss_dssp             EEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEE
T ss_pred             eEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEE
Confidence            35699999999999999999999999999999743      57999999885 678999999999987776665543

>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=99.51  E-value=2e-14  Score=82.35  Aligned_cols=66  Identities=18%  Similarity=0.198  Sum_probs=57.7

Q ss_pred             cCCCCEEEE--cCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCC
Q psy3928           9 KKYGRVVLK--EKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPT   80 (115)
Q Consensus         9 ~~~~~~l~V--~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~   80 (115)
                      ..+..+++|  ||||.++++++|+++|++||.+..+.+..+      ++||||+|.+.++|..|+..|||..+.
T Consensus        15 ~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i~   82 (101)
T d2cq2a1          15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEVV   82 (101)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEEE
T ss_pred             CCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCCC
Confidence            445678888  559999999999999999999999987654      469999999999999999999998763

>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=99.42  E-value=2.4e-13  Score=74.75  Aligned_cols=69  Identities=16%  Similarity=0.173  Sum_probs=56.5

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCce-eeEEE
Q psy3928          12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQ-SSILT   88 (115)
Q Consensus        12 ~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~-~~v~~   88 (115)
                      .+.|+|+|+|++.++. +++.|.+||.|..+.+.      ..++|+||+|.++++|++|++ +||..++|+. +.|..
T Consensus         4 ~~wV~V~G~p~~~~~~-il~~F~~~G~I~~~~~~------~~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~   73 (81)
T d1wwha1           4 DTWVTVFGFPQASASY-ILLQFAQYGNILKHVMS------NTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKP   73 (81)
T ss_dssp             GGEEEEECCCGGGHHH-HHHHHHTTSCEEEEEEC------SSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEE
T ss_pred             ccEEEEECCChHHHHH-HHHHHHhhhhhheEEec------CCCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEe
Confidence            4569999999998865 55689999999998764      335899999999999999996 8999998874 34443

>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=99.39  E-value=5.5e-13  Score=75.95  Aligned_cols=83  Identities=20%  Similarity=0.201  Sum_probs=67.7

Q ss_pred             ccCCCCEEEEcCC--CCCCC---------HHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCC
Q psy3928           8 NKKYGRVVLKEKL--PPEAE---------HDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN   76 (115)
Q Consensus         8 ~~~~~~~l~V~~l--~~~~~---------~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~   76 (115)
                      .....++|+|.|+  |.++.         +++|++.|.+||.|..+.+..    ..++|++||+|.+.++|.+|+..|||
T Consensus         4 ~~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~----~~~~G~~fV~f~~~e~A~~A~~~lng   79 (99)
T d2dita1           4 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFD----RHPDGVASVSFRDPEEADYCIQTLDG   79 (99)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEET----TCTTCEEEEECSCHHHHHHHHHHSTT
T ss_pred             CCCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccC----CCCccEEEEEECCHHHHHHHHHHhCC
Confidence            3456789999998  54321         246889999999999988754    34568999999999999999999999


Q ss_pred             CCCCCceeeEEEeeeccc
Q psy3928          77 PCPTDYQSSILTTTSRLS   94 (115)
Q Consensus        77 ~~~~~~~~~v~~~~~~~~   94 (115)
                      ..++|+.+.+....++..
T Consensus        80 ~~~~gr~i~v~~~~g~~~   97 (99)
T d2dita1          80 RWFGGRQITAQAWDGTTD   97 (99)
T ss_dssp             CEETTEECEEEECCSCCC
T ss_pred             cEECCEEEEEEEeCCcCC
Confidence            999999999988765543

>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=99.31  E-value=2e-11  Score=69.88  Aligned_cols=81  Identities=20%  Similarity=0.150  Sum_probs=66.7

Q ss_pred             CCCEEEEcCC--CCCCCH--------HHHHHHhhhcCCeEEEEeceeCCCC--CeeeEEEEEecCHHHHHHHHHhhCCCC
Q psy3928          11 YGRVVLKEKL--PPEAEH--------DYIESVFSKYGKVTYVSLPKFKSTG--KLKGFAFVEFSTKEEATKALELGLNPC   78 (115)
Q Consensus        11 ~~~~l~V~~l--~~~~~~--------~~l~~~f~~~g~i~~~~i~~~~~~~--~~~g~~fv~f~~~~~a~~al~~l~~~~   78 (115)
                      +.+.|.+.|+  |.....        ++|++.|.+||.|..+.|++++.+.  ...|++||+|.+.++|.+|+..|||..
T Consensus         3 Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~   82 (104)
T d1o0pa_           3 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   82 (104)
T ss_dssp             CCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCC
T ss_pred             CCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCE
Confidence            4678889998  444322        3588999999999999998765443  346899999999999999999999999


Q ss_pred             CCCceeeEEEeee
Q psy3928          79 PTDYQSSILTTTS   91 (115)
Q Consensus        79 ~~~~~~~v~~~~~   91 (115)
                      ++|+.+.+.+..+
T Consensus        83 f~gR~v~v~f~~~   95 (104)
T d1o0pa_          83 FANRVVVTKYCDP   95 (104)
T ss_dssp             SSSSCCEEEEECH
T ss_pred             ECCeEEEEEEcCH
Confidence            9999999887754

>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=97.68  E-value=0.00019  Score=39.15  Aligned_cols=72  Identities=13%  Similarity=0.147  Sum_probs=57.2

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCC--eeeEEEEEecCHHHHHHHHHhhCCCCCCCcee
Q psy3928          13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGK--LKGFAFVEFSTKEEATKALELGLNPCPTDYQS   84 (115)
Q Consensus        13 ~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~--~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~   84 (115)
                      .+|.|+.||++++++++.+.+...+..........+.+.+  .-.-|+|.|.+.++.....+.++|..+.+...
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D~~g   75 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKG   75 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTC
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEcCCC
Confidence            5789999999999999999999888777665554443322  23589999999999999999999987655443

>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=97.19  E-value=0.0012  Score=34.03  Aligned_cols=60  Identities=20%  Similarity=0.166  Sum_probs=49.5

Q ss_pred             HHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCCCCCceeeEEEee
Q psy3928          28 YIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTDYQSSILTTT   90 (115)
Q Consensus        28 ~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~~~~~~~~v~~~~   90 (115)
                      .|.+.|..++.+..+.+.... .+..  .|-|...+..+|..++..|+...+.++++.|..++
T Consensus        12 ~L~~~f~~h~~V~sv~l~~~~-dg~~--~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          12 LLQEAFARHGKVKSVELSPHT-DYQL--KAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHSCEEEEEECSCC-STTC--CEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHhheeEEEEEEEecc-CCcE--EEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            467788889999998875432 3333  79999999999999999999999999998887665

>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=96.38  E-value=0.0023  Score=34.53  Aligned_cols=71  Identities=14%  Similarity=0.142  Sum_probs=51.9

Q ss_pred             ccCCCCEEEEcCCCCCC------CH---HHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhCCCC
Q psy3928           8 NKKYGRVVLKEKLPPEA------EH---DYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPC   78 (115)
Q Consensus         8 ~~~~~~~l~V~~l~~~~------~~---~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~~~~   78 (115)
                      +.+...+|.|.-..++.      ++   .+|.+.|..||++.-+++..+        --.|+|.+-+.|.+|+. +++..
T Consensus        11 qGPpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al~-l~g~~   81 (95)
T d1ufwa_          11 QGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVLD-VDGMK   81 (95)
T ss_dssp             CCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHHH-GGGSE
T ss_pred             cCCCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHhc-cCCeE
Confidence            34455677775444322      33   247888889999888887654        57999999999999998 78888


Q ss_pred             CCCceeeEE
Q psy3928          79 PTDYQSSIL   87 (115)
Q Consensus        79 ~~~~~~~v~   87 (115)
                      +.|+.+.+.
T Consensus        82 v~G~~l~It   90 (95)
T d1ufwa_          82 VKGRAVKIS   90 (95)
T ss_dssp             ETTEEEEEE
T ss_pred             EcceEEEEe
Confidence            888876654

>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=94.86  E-value=0.063  Score=29.13  Aligned_cols=61  Identities=25%  Similarity=0.280  Sum_probs=46.5

Q ss_pred             cccCCCCEEEEcCCCCCCCHHHHHHHhhhcCCeEEEEeceeCCCCCeeeEEEEEecCHHHHHHHHHhhC
Q psy3928           7 NNKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGL   75 (115)
Q Consensus         7 ~~~~~~~~l~V~~l~~~~~~~~l~~~f~~~g~i~~~~i~~~~~~~~~~g~~fv~f~~~~~a~~al~~l~   75 (115)
                      +......-||.-..|..+...+|.++|++||.|.- .++.+  +     =|||.....++|+.++..+.
T Consensus        10 d~~p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~V-swIdd--T-----Sa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          10 DLQPKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQI-SWIDD--T-----SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCCCCCSEEEEECCTTCCHHHHHHHHTTTCSCCC-EEEET--T-----EEEEECSCHHHHHHHHHHHH
T ss_pred             CCCCCcceeEEEeCCcccchhHHHHHhcCCCceEE-EEecC--c-----eEEEEecCHHHHHHHHHHhc
Confidence            33444445777799999999999999999997653 33332  2     58999999999999988765