Psyllid ID: psy6353

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130------
Protein Sequence
MVYQTLLNKLFTYEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLRR
Secondary Structure (PSIPRED)
cEEEccccccccHHHHHHccccEEEEEEEccccccccEEEEEcccHHHHHHHHHHHcccccccEEEEEEEEccccccccccEEEEccccccccHHHHHHHHcccccEEEEEEEEccccccEEEEEEEccccccccc
Secondary Structure Prediction (SSPRO)
cccHHHHHHHHcHHHHHcccccEEEEEEEEccccEEEEEEEEEccHHHHHHHHHHHcccEEccEEcEEEEcccccHHHcccEEEEEcccccccHHHHHHHHHHHccEEEEEEEEccccccccEEEEEcccHHHHcc
Coil and Loop (DISEMBL)
MVYQTLLNKLFTYEkvhlgfsdAEICVFLISTAQSlgygfvnyhrpedAEKAINTLNGlrlqnktikvsyarpssesikganlyvsglpkhmsqQELESLfspygriitsrilcdnlatengkyysglggrerlrr
Flexible Loop (DISEMBL)
MVYQTLLNKLFTYEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVsyarpssesikGANLYVSGLPKHMSQQELESLFSPYGRIITSrilcdnlatengkyysglggrerlrr
Low Complexity Region (SEG)
MVYQTLLNKLFTYEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLRR
Disordered region (IsUnstruct)
**YQTLLNKLFTYEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY**********ANLYVSGL********LESLFSPYGRIITSRILCDNLATENGKYYSG*********
Disordered Region (DISOPRED)
MVYQTLLNKLFTYEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIK***************LYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRE****
Disordered Region (DISEMBL)
MVYQTLLNKLFTYEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLRR
Disordered Region (DISPRO)
*VYQTLLNKLFTYEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGR*****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MVYQTLLNKLFTYEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLRR
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	136	2.2.26 [Sep-21-2011]
Q28GD4	375	ELAV-like protein 2 OS=Xe	yes	N/A	0.566	0.205	0.813	6e-34
P16914	483	Protein elav OS=Drosophil	no	N/A	0.610	0.171	0.795	6e-34
P23241	519	Protein elav OS=Drosophil	N/A	N/A	0.610	0.159	0.795	7e-34
Q91903	389	ELAV-like protein 2 OS=Xe	N/A	N/A	0.647	0.226	0.795	7e-34
Q60899	360	ELAV-like protein 2 OS=Mu	yes	N/A	0.625	0.236	0.813	7e-34
Q5R9Z6	359	ELAV-like protein 2 OS=Po	yes	N/A	0.625	0.236	0.813	8e-34
Q12926	359	ELAV-like protein 2 OS=Ho	no	N/A	0.625	0.236	0.813	8e-34
Q8CH84	359	ELAV-like protein 2 OS=Ra	yes	N/A	0.625	0.236	0.813	8e-34
P26378	380	ELAV-like protein 4 OS=Ho	yes	N/A	0.639	0.228	0.804	9e-34
Q61701	385	ELAV-like protein 4 OS=Mu	no	N/A	0.632	0.223	0.813	9e-34

>sp|Q28GD4|ELAV2_XENTR ELAV-like protein 2 OS=Xenopus tropicalis GN=elavl2 PE=2 SV=2

 Score =  142 bits (358), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 70/86 (81%), Positives = 75/86 (87%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKH 91
           T QSLGYGFVNY  P+DAEKAINTLNGLRLQ KTIKVSYARPSS SI+ ANLYVSGLPK 
Sbjct: 104 TGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKT 163

Query: 92  MSQQELESLFSPYGRIITSRILCDNL 117
           M+Q+ELE LFS YGRIITSRIL D +
Sbjct: 164 MTQKELEQLFSQYGRIITSRILVDQV 189

Binds to poly-U elements and AU-rich elements (AREs) in the 3'-UTR of target mRNAs. Required for the vegetal localization of vg1 mRNA. Probably required for nervous system development.
Xenopus tropicalis (taxid: 8364)

>sp|P16914|ELAV_DROME Protein elav OS=Drosophila melanogaster GN=elav PE=2 SV=1

 Score =  142 bits (358), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 66/83 (79%), Positives = 77/83 (92%)

Query: 31  STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPK 90
           S  QSLGYGFVNY RP+DAE+A+N LNGLRLQNKTIKVS+ARPSS++IKGANLYVSGLPK
Sbjct: 198 SKGQSLGYGFVNYVRPQDAEQAVNVLNGLRLQNKTIKVSFARPSSDAIKGANLYVSGLPK 257

Query: 91  HMSQQELESLFSPYGRIITSRIL 113
            M+QQELE++F+P+G IITSRIL
Sbjct: 258 TMTQQELEAIFAPFGAIITSRIL 280

Required for the proper development and maintenance of neurons presumably by affecting RNA metabolism.

Drosophila melanogaster (taxid: 7227)

>sp|P23241|ELAV_DROVI Protein elav OS=Drosophila virilis GN=elav PE=3 SV=1

 Score =  142 bits (358), Expect = 7e-34,   Method: Composition-based stats.
 Identities = 66/83 (79%), Positives = 77/83 (92%)

Query: 31  STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPK 90
           S  QSLGYGFVNY RP+DAE+A+N LNGLRLQNKTIKVS+ARPSS++IKGANLYVSGLPK
Sbjct: 234 SKGQSLGYGFVNYVRPQDAEQAVNVLNGLRLQNKTIKVSFARPSSDAIKGANLYVSGLPK 293

Query: 91  HMSQQELESLFSPYGRIITSRIL 113
            M+QQELE++F+P+G IITSRIL
Sbjct: 294 TMTQQELEAIFAPFGAIITSRIL 316

Probably involved in the RNA metabolism of neurons.

Drosophila virilis (taxid: 7244)

>sp|Q91903|ELAV2_XENLA ELAV-like protein 2 OS=Xenopus laevis GN=elavl2 PE=1 SV=2

 Score =  142 bits (357), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 70/88 (79%), Positives = 76/88 (86%)

Query: 30  ISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLP 89
           I+  QSLGYGFVNY  P+DAEKAINTLNGLRLQ KTIKVSYARPSS SI+ ANLYVSGLP
Sbjct: 102 ITEGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSSASIRDANLYVSGLP 161

Query: 90  KHMSQQELESLFSPYGRIITSRILCDNL 117
           K M+Q+ELE LFS YGRIITSRIL D +
Sbjct: 162 KTMTQKELEQLFSQYGRIITSRILVDQV 189

Binds to poly-U elements and AU-rich elements (AREs) in the 3'-UTR of target mRNAs. Required for the vegetal localization of vg1 mRNA. Probably required for nervous system development.

Xenopus laevis (taxid: 8355)

>sp|Q60899|ELAV2_MOUSE ELAV-like protein 2 OS=Mus musculus GN=Elavl2 PE=2 SV=1

 Score =  142 bits (357), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 70/86 (81%), Positives = 75/86 (87%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKH 91
           T QSLGYGFVNY  P+DAEKAINTLNGLRLQ KTIKVSYARPSS SI+ ANLYVSGLPK 
Sbjct: 76  TGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKT 135

Query: 92  MSQQELESLFSPYGRIITSRILCDNL 117
           M+Q+ELE LFS YGRIITSRIL D +
Sbjct: 136 MTQKELEQLFSQYGRIITSRILVDQV 161

Binds RNA. Seems to recognize a GAAA motif. Can bind to its own 3'-UTR, the FOS 3'-UTR and the ID 3'-UTR.

Mus musculus (taxid: 10090)

>sp|Q5R9Z6|ELAV2_PONAB ELAV-like protein 2 OS=Pongo abelii GN=ELAVL2 PE=2 SV=1

 Score =  142 bits (357), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 70/86 (81%), Positives = 75/86 (87%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKH 91
           T QSLGYGFVNY  P+DAEKAINTLNGLRLQ KTIKVSYARPSS SI+ ANLYVSGLPK 
Sbjct: 76  TGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKT 135

Query: 92  MSQQELESLFSPYGRIITSRILCDNL 117
           M+Q+ELE LFS YGRIITSRIL D +
Sbjct: 136 MTQKELEQLFSQYGRIITSRILVDQV 161

Binds RNA. Seems to recognize a GAAA motif. Can bind to its own 3'-UTR, the FOS 3'-UTR and the ID 3'-UTR.

Pongo abelii (taxid: 9601)

>sp|Q12926|ELAV2_HUMAN ELAV-like protein 2 OS=Homo sapiens GN=ELAVL2 PE=1 SV=2

 Score =  142 bits (357), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 70/86 (81%), Positives = 75/86 (87%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKH 91
           T QSLGYGFVNY  P+DAEKAINTLNGLRLQ KTIKVSYARPSS SI+ ANLYVSGLPK 
Sbjct: 76  TGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKT 135

Query: 92  MSQQELESLFSPYGRIITSRILCDNL 117
           M+Q+ELE LFS YGRIITSRIL D +
Sbjct: 136 MTQKELEQLFSQYGRIITSRILVDQV 161

Binds RNA. Seems to recognize a GAAA motif. Can bind to its own 3'-UTR, the FOS 3'-UTR and the ID 3'-UTR.

Homo sapiens (taxid: 9606)

>sp|Q8CH84|ELAV2_RAT ELAV-like protein 2 OS=Rattus norvegicus GN=Elavl2 PE=2 SV=1

 Score =  142 bits (357), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 70/86 (81%), Positives = 75/86 (87%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKH 91
           T QSLGYGFVNY  P+DAEKAINTLNGLRLQ KTIKVSYARPSS SI+ ANLYVSGLPK 
Sbjct: 76  TGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKT 135

Query: 92  MSQQELESLFSPYGRIITSRILCDNL 117
           M+Q+ELE LFS YGRIITSRIL D +
Sbjct: 136 MTQKELEQLFSQYGRIITSRILVDQV 161

Binds RNA. Seems to recognize a GAAA motif. Can bind to its own 3'-UTR, the FOS 3'-UTR and the ID 3'-UTR.

Rattus norvegicus (taxid: 10116)

>sp|P26378|ELAV4_HUMAN ELAV-like protein 4 OS=Homo sapiens GN=ELAVL4 PE=1 SV=2

 Score =  142 bits (357), Expect = 9e-34,   Method: Compositional matrix adjust.
 Identities = 70/87 (80%), Positives = 75/87 (86%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKH 91
           T QSLGYGFVNY  P+DAEKAINTLNGLRLQ KTIKVSYARPSS SI+ ANLYVSGLPK 
Sbjct: 83  TGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKT 142

Query: 92  MSQQELESLFSPYGRIITSRILCDNLA 118
           M+Q+ELE LFS YGRIITSRIL D + 
Sbjct: 143 MTQKELEQLFSQYGRIITSRILVDQVT 169

May play a role in neuron-specific RNA processing. Protects CDKN1A mRNA from decay by binding to its 3'-UTR (By similarity). Binds to AU-rich sequences (AREs) of target mRNAs, including VEGF and FOS mRNA.

Homo sapiens (taxid: 9606)

>sp|Q61701|ELAV4_MOUSE ELAV-like protein 4 OS=Mus musculus GN=Elavl4 PE=1 SV=1

 Score =  141 bits (356), Expect = 9e-34,   Method: Compositional matrix adjust.
 Identities = 70/86 (81%), Positives = 75/86 (87%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKH 91
           T QSLGYGFVNY  P+DAEKAINTLNGLRLQ KTIKVSYARPSS SI+ ANLYVSGLPK 
Sbjct: 88  TGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKT 147

Query: 92  MSQQELESLFSPYGRIITSRILCDNL 117
           M+Q+ELE LFS YGRIITSRIL D +
Sbjct: 148 MTQKELEQLFSQYGRIITSRILVDQV 173

May play a role in neuron-specific RNA processing. Protects CDKN1A mRNA from decay by binding to its 3'-UTR. Binds to AU-rich sequences (AREs) of target mRNAs, including VEGF and FOS mRNA.

Mus musculus (taxid: 10090)

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	136
328700227	383	PREDICTED: ELAV-like protein 4-like isof	0.816	0.289	0.741	2e-41
328700229	392	PREDICTED: ELAV-like protein 4-like isof	0.816	0.283	0.741	2e-41
380027075	362	PREDICTED: ELAV-like protein 2-like [Api	0.713	0.267	0.823	3e-41
345493619	383	PREDICTED: ELAV-like protein 3-like isof	0.816	0.289	0.741	6e-41
345493621	349	PREDICTED: ELAV-like protein 3-like isof	0.816	0.318	0.741	7e-41
270014670	350	hypothetical protein TcasGA2_TC004718 [T	0.632	0.245	0.930	7e-41
189233813	352	PREDICTED: similar to RNA-binding protei	0.632	0.244	0.930	7e-41
350425139	371	PREDICTED: ELAV-like protein 2-like [Bom	0.713	0.261	0.813	9e-41
340709266	533	PREDICTED: ELAV-like protein 2-like [Bom	0.713	0.181	0.813	1e-40
328792242	378	PREDICTED: ELAV-like protein 2-like [Api	0.632	0.227	0.918	2e-40

>gi|328700227|ref|XP_001951393.2| PREDICTED: ELAV-like protein 4-like isoform 1 [Acyrthosiphon pisum]

 Score =  173 bits (438), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 86/116 (74%), Positives = 97/116 (83%), Gaps = 5/116 (4%)

Query: 7   LNKLFTYEKVHLGFS---DAEICVFLIS--TAQSLGYGFVNYHRPEDAEKAINTLNGLRL 61
           L +  T E++   FS   + E C  +    T QSLGYGFVNYHRPEDAEKAINTLNGLRL
Sbjct: 43  LPQTMTQEEIRSLFSSIGEVESCKLIRDKVTGQSLGYGFVNYHRPEDAEKAINTLNGLRL 102

Query: 62  QNKTIKVSYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNL 117
           QNKTIKVS+ARPSSE+IKGANLYVSGLPKHM+QQ+LE+LFSPYGRIITSRILCDN+
Sbjct: 103 QNKTIKVSFARPSSEAIKGANLYVSGLPKHMTQQDLENLFSPYGRIITSRILCDNM 158

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328700229|ref|XP_003241188.1| PREDICTED: ELAV-like protein 4-like isoform 2 [Acyrthosiphon pisum]

 Score =  173 bits (438), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 86/116 (74%), Positives = 97/116 (83%), Gaps = 5/116 (4%)

Query: 7   LNKLFTYEKVHLGFS---DAEICVFLIS--TAQSLGYGFVNYHRPEDAEKAINTLNGLRL 61
           L +  T E++   FS   + E C  +    T QSLGYGFVNYHRPEDAEKAINTLNGLRL
Sbjct: 43  LPQTMTQEEIRSLFSSIGEVESCKLIRDKVTGQSLGYGFVNYHRPEDAEKAINTLNGLRL 102

Query: 62  QNKTIKVSYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNL 117
           QNKTIKVS+ARPSSE+IKGANLYVSGLPKHM+QQ+LE+LFSPYGRIITSRILCDN+
Sbjct: 103 QNKTIKVSFARPSSEAIKGANLYVSGLPKHMTQQDLENLFSPYGRIITSRILCDNM 158

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380027075|ref|XP_003697261.1| PREDICTED: ELAV-like protein 2-like [Apis florea]

 Score =  172 bits (437), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 84/102 (82%), Positives = 90/102 (88%), Gaps = 5/102 (4%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKH 91
           T QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE+IKGANLYVSGLPK+
Sbjct: 65  TGQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSEAIKGANLYVSGLPKN 124

Query: 92  MSQQELESLFSPYGRIITSRILCDNL-----ATENGKYYSGL 128
           M+QQ+LE+LFSPYGRIITSRILCDN+      T  G Y  GL
Sbjct: 125 MTQQDLENLFSPYGRIITSRILCDNITVRQFVTGGGDYLPGL 166

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|345493619|ref|XP_003427110.1| PREDICTED: ELAV-like protein 3-like isoform 2 [Nasonia vitripennis]

 Score =  172 bits (435), Expect = 6e-41,   Method: Compositional matrix adjust.
 Identities = 86/116 (74%), Positives = 97/116 (83%), Gaps = 5/116 (4%)

Query: 7   LNKLFTYEKVHLGFS---DAEICVFLIS--TAQSLGYGFVNYHRPEDAEKAINTLNGLRL 61
           L +  T E++   FS   + E C  +    T QSLGYGFVNYHRPEDAEKAINTLNGLRL
Sbjct: 35  LPQTMTQEEIRSLFSSIGEVESCKLIRDKLTGQSLGYGFVNYHRPEDAEKAINTLNGLRL 94

Query: 62  QNKTIKVSYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNL 117
           QNKTIKVSYARPSSE+IKGANLYVSGLPK+M+QQ+LE+LFSPYGRIITSRILCDN+
Sbjct: 95  QNKTIKVSYARPSSEAIKGANLYVSGLPKNMTQQDLENLFSPYGRIITSRILCDNI 150

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|345493621|ref|XP_003427111.1| PREDICTED: ELAV-like protein 3-like isoform 3 [Nasonia vitripennis] gi|345493623|ref|XP_001603257.2| PREDICTED: ELAV-like protein 3-like isoform 1 [Nasonia vitripennis]

 Score =  171 bits (434), Expect = 7e-41,   Method: Compositional matrix adjust.
 Identities = 86/116 (74%), Positives = 97/116 (83%), Gaps = 5/116 (4%)

Query: 7   LNKLFTYEKVHLGFS---DAEICVFLIS--TAQSLGYGFVNYHRPEDAEKAINTLNGLRL 61
           L +  T E++   FS   + E C  +    T QSLGYGFVNYHRPEDAEKAINTLNGLRL
Sbjct: 35  LPQTMTQEEIRSLFSSIGEVESCKLIRDKLTGQSLGYGFVNYHRPEDAEKAINTLNGLRL 94

Query: 62  QNKTIKVSYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNL 117
           QNKTIKVSYARPSSE+IKGANLYVSGLPK+M+QQ+LE+LFSPYGRIITSRILCDN+
Sbjct: 95  QNKTIKVSYARPSSEAIKGANLYVSGLPKNMTQQDLENLFSPYGRIITSRILCDNI 150

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270014670|gb|EFA11118.1| hypothetical protein TcasGA2_TC004718 [Tribolium castaneum]

 Score =  171 bits (434), Expect = 7e-41,   Method: Compositional matrix adjust.
 Identities = 80/86 (93%), Positives = 85/86 (98%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKH 91
           T QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE+IKGANLYVSGLPK+
Sbjct: 79  TGQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSEAIKGANLYVSGLPKN 138

Query: 92  MSQQELESLFSPYGRIITSRILCDNL 117
           M+QQ+LESLFSPYGRIITSRILCDN+
Sbjct: 139 MTQQDLESLFSPYGRIITSRILCDNI 164

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|189233813|ref|XP_971256.2| PREDICTED: similar to RNA-binding protein, putative [Tribolium castaneum]

 Score =  171 bits (434), Expect = 7e-41,   Method: Compositional matrix adjust.
 Identities = 80/86 (93%), Positives = 85/86 (98%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKH 91
           T QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE+IKGANLYVSGLPK+
Sbjct: 81  TGQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSEAIKGANLYVSGLPKN 140

Query: 92  MSQQELESLFSPYGRIITSRILCDNL 117
           M+QQ+LESLFSPYGRIITSRILCDN+
Sbjct: 141 MTQQDLESLFSPYGRIITSRILCDNI 166

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350425139|ref|XP_003494024.1| PREDICTED: ELAV-like protein 2-like [Bombus impatiens]

 Score =  171 bits (433), Expect = 9e-41,   Method: Compositional matrix adjust.
 Identities = 83/102 (81%), Positives = 90/102 (88%), Gaps = 5/102 (4%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKH 91
           T QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE+IKGANLYVSGLPK+
Sbjct: 65  TGQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSEAIKGANLYVSGLPKN 124

Query: 92  MSQQELESLFSPYGRIITSRILCDNL-----ATENGKYYSGL 128
           M+QQ+LE+LF+PYGRIITSRILCDN+      T  G Y  GL
Sbjct: 125 MTQQDLENLFNPYGRIITSRILCDNITVRQFVTGGGDYLPGL 166

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340709266|ref|XP_003393232.1| PREDICTED: ELAV-like protein 2-like [Bombus terrestris]

 Score =  171 bits (433), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 83/102 (81%), Positives = 90/102 (88%), Gaps = 5/102 (4%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKH 91
           T QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE+IKGANLYVSGLPK+
Sbjct: 65  TGQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSEAIKGANLYVSGLPKN 124

Query: 92  MSQQELESLFSPYGRIITSRILCDNL-----ATENGKYYSGL 128
           M+QQ+LE+LF+PYGRIITSRILCDN+      T  G Y  GL
Sbjct: 125 MTQQDLENLFNPYGRIITSRILCDNITVRQFVTGGGDYLPGL 166

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328792242|ref|XP_394166.4| PREDICTED: ELAV-like protein 2-like [Apis mellifera]

 Score =  170 bits (431), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 79/86 (91%), Positives = 85/86 (98%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKH 91
           T QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE+IKGANLYVSGLPK+
Sbjct: 65  TGQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSEAIKGANLYVSGLPKN 124

Query: 92  MSQQELESLFSPYGRIITSRILCDNL 117
           M+QQ+LE+LFSPYGRIITSRILCDN+
Sbjct: 125 MTQQDLENLFSPYGRIITSRILCDNI 150

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	136
FB|FBgn0010263	444	Rbp9 "RNA-binding protein 9" [	0.823	0.252	0.704	2.1e-36
FB|FBgn0086675	356	fne "found in neurons" [Drosop	0.654	0.25	0.775	2.5e-33
FB|FBgn0260400	483	elav "embryonic lethal abnorma	0.610	0.171	0.795	2.6e-31
UNIPROTKB|E1C240	388	ELAVL2 "Uncharacterized protei	0.632	0.221	0.813	2.6e-31
UNIPROTKB|F1NLH0	371	ELAVL4 "Uncharacterized protei	0.632	0.231	0.813	2.6e-31
UNIPROTKB|A2VDK5	366	ELAVL4 "Uncharacterized protei	0.632	0.234	0.813	2.6e-31
UNIPROTKB|G3N063	388	ELAVL2 "Uncharacterized protei	0.632	0.221	0.813	2.6e-31
UNIPROTKB|E2RI94	388	ELAVL2 "Uncharacterized protei	0.632	0.221	0.813	2.6e-31
UNIPROTKB|F1P856	382	ELAVL4 "Uncharacterized protei	0.632	0.225	0.813	2.6e-31
UNIPROTKB|J9PAL3	366	ELAVL4 "Uncharacterized protei	0.632	0.234	0.813	2.6e-31

FB|FBgn0010263 Rbp9 "RNA-binding protein 9" [Drosophila melanogaster (taxid:7227)]

 Score = 392 (143.0 bits), Expect = 2.1e-36, P = 2.1e-36
 Identities = 81/115 (70%), Positives = 92/115 (80%)

Query:    18 LGFSDAEICVFLIS--TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS 75
             + F + E C  +    T QSLGYGFVNY + EDAEKAIN LNGLRLQNKTIKVS ARPSS
Sbjct:   131 VSFGEVESCKLIRDKVTGQSLGYGFVNYVKQEDAEKAINALNGLRLQNKTIKVSIARPSS 190

Query:    76 ESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYS-GLG 129
             ESIKGANLYVSGLPK+M+Q +LESLFSPYG+IITSRILCDN+  E+    S G+G
Sbjct:   191 ESIKGANLYVSGLPKNMTQSDLESLFSPYGKIITSRILCDNITGEHAAGLSKGVG 245

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

GO:0003730 "mRNA 3'-UTR binding" evidence=TAS

GO:0007293 "germarium-derived egg chamber formation" evidence=TAS

GO:0005634 "nucleus" evidence=TAS

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0048477 "oogenesis" evidence=IMP

GO:0036093 "germ cell proliferation" evidence=IMP

GO:0060856 "establishment of blood-brain barrier" evidence=IMP

FB|FBgn0086675 fne "found in neurons" [Drosophila melanogaster (taxid:7227)]

 Score = 363 (132.8 bits), Expect = 2.5e-33, P = 2.5e-33
 Identities = 69/89 (77%), Positives = 80/89 (89%)

Query:    30 ISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLP 89
             +   QSLGYGFVNY R EDAEKA+NTLNGLRLQNK IKVSYARPSSESIKGANLYVSGLP
Sbjct:    79 LQQGQSLGYGFVNYVRAEDAEKAVNTLNGLRLQNKVIKVSYARPSSESIKGANLYVSGLP 138

Query:    90 KHMSQQELESLFSPYGRIITSRILCDNLA 118
             K++SQ +LE +F+ +G+IITSRILCDN++
Sbjct:   139 KNLSQPDLEGMFASFGKIITSRILCDNIS 167

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

GO:0005737 "cytoplasm" evidence=IDA

GO:0051252 "regulation of RNA metabolic process" evidence=IMP

GO:0008266 "poly(U) RNA binding" evidence=IDA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0008049 "male courtship behavior" evidence=IMP

FB|FBgn0260400 elav "embryonic lethal abnormal vision" [Drosophila melanogaster (taxid:7227)]

 Score = 344 (126.2 bits), Expect = 2.6e-31, P = 2.6e-31
 Identities = 66/83 (79%), Positives = 77/83 (92%)

Query:    31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPK 90
             S  QSLGYGFVNY RP+DAE+A+N LNGLRLQNKTIKVS+ARPSS++IKGANLYVSGLPK
Sbjct:   198 SKGQSLGYGFVNYVRPQDAEQAVNVLNGLRLQNKTIKVSFARPSSDAIKGANLYVSGLPK 257

Query:    91 HMSQQELESLFSPYGRIITSRIL 113
              M+QQELE++F+P+G IITSRIL
Sbjct:   258 TMTQQELEAIFAPFGAIITSRIL 280

GO:0005634 "nucleus" evidence=IDA;TAS

GO:0015030 "Cajal body" evidence=IDA

GO:0007417 "central nervous system development" evidence=IMP

GO:0016070 "RNA metabolic process" evidence=NAS

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

GO:0007399 "nervous system development" evidence=NAS

GO:0008266 "poly(U) RNA binding" evidence=IDA

GO:0031441 "negative regulation of mRNA 3'-end processing" evidence=IDA

GO:0003723 "RNA binding" evidence=IDA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|E1C240 ELAVL2 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 344 (126.2 bits), Expect = 2.6e-31, P = 2.6e-31
 Identities = 70/86 (81%), Positives = 75/86 (87%)

Query:    32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKH 91
             T QSLGYGFVNY  P+DAEKAINTLNGLRLQ KTIKVSYARPSS SI+ ANLYVSGLPK 
Sbjct:   104 TGQSLGYGFVNYVDPKDAEKAINTLNGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKT 163

Query:    92 MSQQELESLFSPYGRIITSRILCDNL 117
             M+Q+ELE LFS YGRIITSRIL D +
Sbjct:   164 MTQKELEQLFSQYGRIITSRILVDQV 189

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|F1NLH0 ELAVL4 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 344 (126.2 bits), Expect = 2.6e-31, P = 2.6e-31
 Identities = 70/86 (81%), Positives = 75/86 (87%)

Query:    32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKH 91
             T QSLGYGFVNY  P+DAEKAINTLNGLRLQ KTIKVSYARPSS SI+ ANLYVSGLPK 
Sbjct:    88 TGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKT 147

Query:    92 MSQQELESLFSPYGRIITSRILCDNL 117
             M+Q+ELE LFS YGRIITSRIL D +
Sbjct:   148 MTQKELEQLFSQYGRIITSRILVDQV 173

GO:0000166 "nucleotide binding" evidence=IEA

GO:0017091 "AU-rich element binding" evidence=IEA

UNIPROTKB|A2VDK5 ELAVL4 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 344 (126.2 bits), Expect = 2.6e-31, P = 2.6e-31
 Identities = 70/86 (81%), Positives = 75/86 (87%)

Query:    32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKH 91
             T QSLGYGFVNY  P+DAEKAINTLNGLRLQ KTIKVSYARPSS SI+ ANLYVSGLPK 
Sbjct:    83 TGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKT 142

Query:    92 MSQQELESLFSPYGRIITSRILCDNL 117
             M+Q+ELE LFS YGRIITSRIL D +
Sbjct:   143 MTQKELEQLFSQYGRIITSRILVDQV 168

GO:0017091 "AU-rich element binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|G3N063 ELAVL2 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 344 (126.2 bits), Expect = 2.6e-31, P = 2.6e-31
 Identities = 70/86 (81%), Positives = 75/86 (87%)

Query:    32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKH 91
             T QSLGYGFVNY  P+DAEKAINTLNGLRLQ KTIKVSYARPSS SI+ ANLYVSGLPK 
Sbjct:   105 TGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKT 164

Query:    92 MSQQELESLFSPYGRIITSRILCDNL 117
             M+Q+ELE LFS YGRIITSRIL D +
Sbjct:   165 MTQKELEQLFSQYGRIITSRILVDQV 190

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|E2RI94 ELAVL2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 344 (126.2 bits), Expect = 2.6e-31, P = 2.6e-31
 Identities = 70/86 (81%), Positives = 75/86 (87%)

Query:    32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKH 91
             T QSLGYGFVNY  P+DAEKAINTLNGLRLQ KTIKVSYARPSS SI+ ANLYVSGLPK 
Sbjct:   105 TGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKT 164

Query:    92 MSQQELESLFSPYGRIITSRILCDNL 117
             M+Q+ELE LFS YGRIITSRIL D +
Sbjct:   165 MTQKELEQLFSQYGRIITSRILVDQV 190

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|F1P856 ELAVL4 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 344 (126.2 bits), Expect = 2.6e-31, P = 2.6e-31
 Identities = 70/86 (81%), Positives = 75/86 (87%)

Query:    32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKH 91
             T QSLGYGFVNY  P+DAEKAINTLNGLRLQ KTIKVSYARPSS SI+ ANLYVSGLPK 
Sbjct:    99 TGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKT 158

Query:    92 MSQQELESLFSPYGRIITSRILCDNL 117
             M+Q+ELE LFS YGRIITSRIL D +
Sbjct:   159 MTQKELEQLFSQYGRIITSRILVDQV 184

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|J9PAL3 ELAVL4 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 344 (126.2 bits), Expect = 2.6e-31, P = 2.6e-31
 Identities = 70/86 (81%), Positives = 75/86 (87%)

Query:    32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKH 91
             T QSLGYGFVNY  P+DAEKAINTLNGLRLQ KTIKVSYARPSS SI+ ANLYVSGLPK 
Sbjct:    83 TGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKT 142

Query:    92 MSQQELESLFSPYGRIITSRILCDNL 117
             M+Q+ELE LFS YGRIITSRIL D +
Sbjct:   143 MTQKELEQLFSQYGRIITSRILVDQV 168

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q5R9Z6	ELAV2_PONAB	No assigned EC number	0.8139	0.625	0.2367	yes	N/A
Q8CH84	ELAV2_RAT	No assigned EC number	0.8139	0.625	0.2367	yes	N/A
Q28GD4	ELAV2_XENTR	No assigned EC number	0.8139	0.5661	0.2053	yes	N/A
P26378	ELAV4_HUMAN	No assigned EC number	0.8045	0.6397	0.2289	yes	N/A
Q60899	ELAV2_MOUSE	No assigned EC number	0.8139	0.625	0.2361	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	136
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	9e-56
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	2e-23
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	2e-23
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	7e-23
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	4e-20
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	7e-20
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	3e-19
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	1e-17
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	6e-17
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	3e-16
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-15
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	1e-14
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	5e-14
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	2e-13
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	2e-13
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	6e-12
cd12773	84	cd12773, RRM2_HuR, RNA recognition motif 2 in vert	7e-12
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-11
cd12244	79	cd12244, RRM2_MSSP, RNA recognition motif 2 in the	4e-11
cd12473	85	cd12473, RRM2_MSSP1, RNA recognition motif 2 found	2e-09
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	2e-09
cd12474	86	cd12474, RRM2_MSSP2, RNA recognition motif 2 found	3e-09
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	3e-09
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	4e-09
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	6e-09
smart00360	73	smart00360, RRM, RNA recognition motif	6e-09
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	6e-09
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	1e-08
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	2e-08
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	4e-08
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	4e-08
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	4e-08
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	1e-07
cd12475	88	cd12475, RRM2_RBMS3, RNA recognition motif 2 found	1e-07
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	1e-07
cd12305	75	cd12305, RRM_NELFE, RNA recognition motif in negat	2e-07
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	2e-07
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	2e-07
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	3e-07
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	3e-07
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	5e-07
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	6e-07
smart00360	73	smart00360, RRM, RNA recognition motif	7e-07
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	7e-07
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	8e-07
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	1e-06
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	2e-06
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	2e-06
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	2e-06
cd12470	86	cd12470, RRM1_MSSP1, RNA recognition motif 1 in ve	3e-06
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	3e-06
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	3e-06
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	4e-06
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	5e-06
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	5e-06
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	7e-06
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	8e-06
cd12253	79	cd12253, RRM_PIN4_like, RNA recognition motif in y	9e-06
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	1e-05
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	1e-05
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	1e-05
cd12409	84	cd12409, RRM1_RRT5, RNA recognition motif 1 in yea	2e-05
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	2e-05
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	2e-05
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	2e-05
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	2e-05
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	2e-05
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	2e-05
cd12339	71	cd12339, RRM2_SRSF1_4_like, RNA recognition motif	3e-05
cd12358	73	cd12358, RRM1_VICKZ, RNA recognition motif 1 in th	3e-05
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	3e-05
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	5e-05
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	6e-05
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	6e-05
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	6e-05
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	8e-05
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	1e-04
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	1e-04
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	1e-04
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	1e-04
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	1e-04
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	1e-04
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	1e-04
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	1e-04
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	1e-04
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	1e-04
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	1e-04
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	2e-04
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	2e-04
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	2e-04
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	2e-04
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	2e-04
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	2e-04
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	2e-04
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	2e-04
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	3e-04
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	3e-04
cd12359	76	cd12359, RRM2_VICKZ, RNA recognition motif 2 in th	3e-04
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	3e-04
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	3e-04
cd12232	89	cd12232, RRM3_U2AF65, RNA recognition motif 3 foun	3e-04
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	3e-04
cd12472	80	cd12472, RRM1_RBMS3, RNA recognition motif 1 found	3e-04
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	4e-04
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	4e-04
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	4e-04
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	5e-04
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	5e-04
cd12595	70	cd12595, RRM1_SRSF5, RNA recognition motif 1 in ve	5e-04
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	6e-04
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	6e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	7e-04
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	8e-04
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	8e-04
cd12319	84	cd12319, RRM4_MRD1, RNA recognition motif 4 in yea	9e-04
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	0.001
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	0.001
cd12277	86	cd12277, RRM3_MEI2_EAR1_like, RNA recognition moti	0.001
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	0.001
cd12497	74	cd12497, RRM3_RBM47, RNA recognition motif 3 in ve	0.001
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	0.001
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	0.001
cd12661	77	cd12661, RRM3_hnRNPM, RNA recognition motif 3 in v	0.001
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	0.002
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	0.002
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	0.002
cd12498	83	cd12498, RRM3_ACF, RNA recognition motif 3 in vert	0.002
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	0.002
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	0.002
cd12438	98	cd12438, RRM_CNOT4, RNA recognition motif in Eukar	0.002
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	0.002
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	0.002
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	0.003
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	0.003
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	0.003
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	0.003
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	0.004
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	0.004
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	0.004
cd12439	79	cd12439, RRM_TRMT2A, RNA recognition motif in tRNA	0.004
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	0.004

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

 Score =  177 bits (449), Expect = 9e-56
 Identities = 73/86 (84%), Positives = 80/86 (93%)

Query: 31  STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPK 90
            T QSLGYGFVNY RPEDAEKA+N+LNGLRLQNKTIKVSYARPSS+SIKGANLYVSGLPK
Sbjct: 40  VTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYARPSSDSIKGANLYVSGLPK 99

Query: 91  HMSQQELESLFSPYGRIITSRILCDN 116
            M+Q ELES+FSP+G+IITSRIL DN
Sbjct: 100 TMTQHELESIFSPFGQIITSRILSDN 125

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

 Score = 92.8 bits (230), Expect = 2e-23
 Identities = 40/86 (46%), Positives = 59/86 (68%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKH 91
           T  S GY FV++    D+++AI  LNG+ ++NK +KVSYARP  ESIK  NLYV+ LP+ 
Sbjct: 145 TGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRT 204

Query: 92  MSQQELESLFSPYGRIITSRILCDNL 117
           ++  +L+++F  YG+I+   IL D L
Sbjct: 205 ITDDQLDTIFGKYGQIVQKNILRDKL 230

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

 Score = 86.3 bits (214), Expect = 2e-23
 Identities = 37/41 (90%), Positives = 37/41 (90%)

Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
           T QSLGYGFVNY  PEDAEKAINTLNGLRLQNKTIKVSYA
Sbjct: 38 VTGQSLGYGFVNYVDPEDAEKAINTLNGLRLQNKTIKVSYA 78

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

 Score = 85.0 bits (211), Expect = 7e-23
 Identities = 33/36 (91%), Positives = 35/36 (97%)

Query: 81  ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDN 116
           ANLYVSGLPK M+QQELE+LFSPYGRIITSRILCDN
Sbjct: 1   ANLYVSGLPKTMTQQELEALFSPYGRIITSRILCDN 36

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|241214 cd12770, RRM1_HuD, RNA recognition motif 1 in vertebrate Hu-antigen D (HuD)

 Score = 78.2 bits (192), Expect = 4e-20
 Identities = 39/44 (88%), Positives = 40/44 (90%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS 75
          T QSLGYGFVNY  P+DAEKAINTLNGLRLQ KTIKVSYARPSS
Sbjct: 40 TGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSS 83

This subgroup corresponds to the RRM1 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells, as well as the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 83

>gnl|CDD|241216 cd12772, RRM1_HuC, RNA recognition motif 1 in vertebrate Hu-antigen C (HuC)

 Score = 77.5 bits (190), Expect = 7e-20
 Identities = 37/44 (84%), Positives = 39/44 (88%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS 75
          T QSLGYGFVNY  P DA+KAINTLNGL+LQ KTIKVSYARPSS
Sbjct: 41 TGQSLGYGFVNYVDPNDADKAINTLNGLKLQTKTIKVSYARPSS 84

This subgroup corresponds to the RRM1 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 = 84

>gnl|CDD|241215 cd12771, RRM1_HuB, RNA recognition motif 1 in vertebrate Hu-antigen B (HuB)

 Score = 75.9 bits (186), Expect = 3e-19
 Identities = 37/42 (88%), Positives = 38/42 (90%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
          T QSLGYGFVNY  P+DAEKAINTLNGLRLQ KTIKVSYARP
Sbjct: 42 TGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP 83

This subgroup corresponds to the RRM1 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads and is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 83

>gnl|CDD|241213 cd12769, RRM1_HuR, RNA recognition motif 1 in vertebrate Hu-antigen R (HuR)

 Score = 71.7 bits (175), Expect = 1e-17
 Identities = 34/42 (80%), Positives = 37/42 (88%)

Query: 33 AQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS 74
            SLGYGFVNY   +DAE+AINTLNGLRLQ+KTIKVSYARPS
Sbjct: 40 GHSLGYGFVNYVNAKDAERAINTLNGLRLQSKTIKVSYARPS 81

This subgroup corresponds to the RRM1 of HuR, also termed ELAV-like protein 1 (ELAV-1), a ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response; it binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. Meanwhile, HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

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

 Score = 69.7 bits (171), Expect = 6e-17
 Identities = 28/45 (62%), Positives = 34/45 (75%)

Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS 75
           T  S G+GFV+Y   EDA++AI TLNGL+LQNK IKV+YARP  
Sbjct: 37 RTGYSYGFGFVDYQSAEDAQRAIRTLNGLQLQNKRIKVAYARPGG 81

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

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

 Score = 68.1 bits (167), Expect = 3e-16
 Identities = 27/40 (67%), Positives = 32/40 (80%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
          T QSLGYGFV+Y    DA+KAINTLNG  ++NK +KVSYA
Sbjct: 38 TGQSLGYGFVDYVDENDAQKAINTLNGFEIRNKRLKVSYA 77

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

 Score = 71.0 bits (174), Expect = 2e-15
 Identities = 36/96 (37%), Positives = 53/96 (55%), Gaps = 6/96 (6%)

Query: 30  ISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKV--SYARPSSESIKGANLYVSG 87
             T +SLGYG+VN+  P DAE+A+ T+N  RL  K I++  S   PS       N++V  
Sbjct: 36  SVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQRDPSLRRSGVGNIFVKN 95

Query: 88  LPKHMSQQELESLFSPYGRIITSRILCDNLATENGK 123
           L K +  + L   FS +G I++ ++  D    ENGK
Sbjct: 96  LDKSVDNKALFDTFSKFGNILSCKVATD----ENGK 127

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|241219 cd12775, RRM2_HuB, RNA recognition motif 2 in vertebrate Hu-antigen B (HuB)

 Score = 64.4 bits (156), Expect = 1e-14
 Identities = 31/41 (75%), Positives = 35/41 (85%)

Query: 77  SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNL 117
           SI+ ANLYVSGLPK M+Q+ELE LFS YGRIITSRIL D +
Sbjct: 2   SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQV 42

This subgroup corresponds to the RRM2 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 = 90

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

 Score = 62.3 bits (151), Expect = 5e-14
 Identities = 29/37 (78%), Positives = 32/37 (86%)

Query: 81  ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNL 117
           ANLYVSGLPK MSQ+E+E LFS YGRIITSRIL D +
Sbjct: 2   ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQV 38

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

>gnl|CDD|241218 cd12774, RRM2_HuD, RNA recognition motif 2 in vertebrate Hu-antigen D (HuD)

 Score = 61.3 bits (148), Expect = 2e-13
 Identities = 29/39 (74%), Positives = 33/39 (84%)

Query: 79  KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNL 117
           + ANLYVSGLPK M+Q+ELE LFS YGRIITSRIL D +
Sbjct: 1   RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQV 39

This subgroup corresponds to the RRM2 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 also regulates the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

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

 Score = 60.7 bits (147), Expect = 2e-13
 Identities = 30/37 (81%), Positives = 32/37 (86%)

Query: 81  ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNL 117
           ANLYVSGLPK M+Q+ELE LFS YGRIITSRIL D L
Sbjct: 1   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQL 37

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

 Score = 61.4 bits (149), Expect = 6e-12
 Identities = 28/90 (31%), Positives = 47/90 (52%), Gaps = 5/90 (5%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESI-----KGANLYVS 86
             +S GYGFV++ + E A+ AI  +NG+ L +K + V       E       K  NLYV 
Sbjct: 125 NGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIKKHEREAAPLKKFTNLYVK 184

Query: 87  GLPKHMSQQELESLFSPYGRIITSRILCDN 116
            L   +++ +L  LF+ +G I ++ ++ D 
Sbjct: 185 NLDPSVNEDKLRELFAKFGEITSAAVMKDG 214

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|241217 cd12773, RRM2_HuR, RNA recognition motif 2 in vertebrate Hu-antigen R (HuR)

 Score = 56.9 bits (137), Expect = 7e-12
 Identities = 21/35 (60%), Positives = 30/35 (85%)

Query: 81  ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
           ANLY+SGLP+ M+Q+++E +FS +GRII SR+L D
Sbjct: 1   ANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVD 35

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

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

 Score = 60.2 bits (146), Expect = 1e-11
 Identities = 29/104 (27%), Positives = 51/104 (49%), Gaps = 22/104 (21%)

Query: 34  QSLGYGFVNYHRPEDAEKAINTLNGLRL----QNKTIKVSYARPSSE------------- 76
           +S G+ FVN+ + EDA KA+  +NG ++    + K + V  A+  +E             
Sbjct: 217 RSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQ 276

Query: 77  -----SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
                  +G NLYV  L   ++ ++L  LFS  G I +++++ D
Sbjct: 277 QERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLD 320

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|240690 cd12244, RRM2_MSSP, RNA recognition motif 2 in the c-myc gene single-strand binding proteins (MSSP) family

 Score = 55.0 bits (133), Expect = 4e-11
 Identities = 20/41 (48%), Positives = 30/41 (73%)

Query: 82  NLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENG 122
           NLY+S LP HM +Q+LE++  PYG++I++RIL D+     G
Sbjct: 2   NLYISNLPLHMDEQDLETMLKPYGQVISTRILRDSKGQSRG 42

This subfamily corresponds to the RRM2 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, they 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 = 79

>gnl|CDD|240917 cd12473, RRM2_MSSP1, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 50.9 bits (121), Expect = 2e-09
 Identities = 21/52 (40%), Positives = 35/52 (67%)

Query: 82  NLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRER 133
           NLY+S LP  M +QELE++  P+G++I++RIL D+  T  G  ++ +   E+
Sbjct: 2   NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEK 53

This subgroup corresponds to the RRM2 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2). MSSP-1 is a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with c-MYC, the product of protooncogene c-myc. MSSP-1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 85

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

 Score = 50.2 bits (121), Expect = 2e-09
 Identities = 19/41 (46%), Positives = 25/41 (60%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR 72
          T QS G+ FV +H  EDAE+AI  LNG    N  + V +A+
Sbjct: 37 TGQSRGFAFVTFHTREDAERAIEKLNGFGYDNLILSVEWAK 77

This subfamily corresponds to the RRM of eIF-3G and similar proteins. eIF-3G, also termed eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or eIF3-p44, is the RNA-binding subunit of eIF3, a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and beta-globin mRNA, and therefore appears to be a nonspecific RNA-binding protein. eIF-3G is one of the cytosolic targets and interacts with mature apoptosis-inducing factor (AIF). eIF-3G contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This family also includes yeast eIF3-p33, a homolog of vertebrate eIF-3G, plays an important role in the initiation phase of protein synthesis in yeast. It binds both, mRNA and rRNA, fragments due to an RRM near its C-terminus. . Length = 77

>gnl|CDD|240918 cd12474, RRM2_MSSP2, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 50.4 bits (120), Expect = 3e-09
 Identities = 22/52 (42%), Positives = 34/52 (65%)

Query: 82  NLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRER 133
           NLY+S LP  M +QELES+  P+G++I++RIL D   T  G  ++ +   E+
Sbjct: 2   NLYISNLPLSMDEQELESMLKPFGQVISTRILRDASGTSRGVGFARMESTEK 53

This subgroup corresponds to the RRM2 of MSSP-2, also termed RNA-binding motif, single-stranded-interacting protein 2 (RBMS2), or suppressor of CDC2 with RNA-binding motif 3 (SCR3). MSSP-2 is a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence T(C/A)TT, and stimulates DNA replication in the system using SV40 DNA. MSSP-2 is identical with Scr3, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-2 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-2 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 86

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

 Score = 49.8 bits (120), Expect = 3e-09
 Identities = 15/28 (53%), Positives = 22/28 (78%)

Query: 30 ISTAQSLGYGFVNYHRPEDAEKAINTLN 57
          + T +SLGY +VN+  P DAE+A++TLN
Sbjct: 35 LITRRSLGYAYVNFQNPADAERALDTLN 62

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

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

 Score = 53.0 bits (126), Expect = 4e-09
 Identities = 32/105 (30%), Positives = 48/105 (45%), Gaps = 24/105 (22%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESI------------- 78
           T +S G+ FV +   E AEKAI  LNG  L+ + ++V  A+P+S+               
Sbjct: 153 TGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAK 212

Query: 79  -----------KGANLYVSGLPKHMSQQELESLFSPYGRIITSRI 112
                      K  NLYV  LP   +++EL  LF   G I+ + +
Sbjct: 213 KLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASL 257

Length = 306

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

 Score = 49.1 bits (118), Expect = 6e-09
 Identities = 15/37 (40%), Positives = 22/37 (59%)

Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIK 67
           T +S G+ FV +   EDAEKA+  LNG  L  + ++
Sbjct: 34 ETGRSKGFAFVEFEDEEDAEKALEALNGKELGGRELR 70

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

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

 Score = 49.1 bits (118), Expect = 6e-09
 Identities = 17/37 (45%), Positives = 23/37 (62%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKV 68
          T +S G+ FV +   EDAEKA+  LNG  L  + +KV
Sbjct: 37 TGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73

Length = 73

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

 Score = 49.2 bits (118), Expect = 6e-09
 Identities = 18/38 (47%), Positives = 24/38 (63%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVS 69
          T +S GYGF+ +   EDA+KA+  LNG  L  + IKV 
Sbjct: 36 TGRSKGYGFIQFADAEDAKKALEQLNGFELAGRPIKVG 73

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

 Score = 48.1 bits (115), Expect = 1e-08
 Identities = 18/46 (39%), Positives = 26/46 (56%)

Query: 24 EICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVS 69
           + +      +S G+ FV +  PEDAEKA+  LNG  L  + +KVS
Sbjct: 27 SVRIVRDKDGKSKGFAFVEFESPEDAEKALEALNGKELDGRKLKVS 72

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

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

 Score = 48.0 bits (115), Expect = 2e-08
 Identities = 17/38 (44%), Positives = 24/38 (63%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVS 69
          T QS  +GFV+Y  PE A+ AI  +NG ++  K +KV 
Sbjct: 36 TGQSKCFGFVSYDNPESAQAAIKAMNGFQVGGKRLKVQ 73

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

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

 Score = 47.2 bits (113), Expect = 4e-08
 Identities = 15/35 (42%), Positives = 22/35 (62%)

Query: 34 QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKV 68
           S GYGFV++   E A +AI  +NG+ L +K + V
Sbjct: 41 GSKGYGFVHFETEEAAVRAIEKVNGMLLNDKKVFV 75

This subfamily corresponds to the RRM2 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is a ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 77

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

 Score = 47.2 bits (112), Expect = 4e-08
 Identities = 18/38 (47%), Positives = 28/38 (73%)

Query: 34 QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
          + + YGFV YH+  DAE A+ TLNG +++N  I+V++A
Sbjct: 37 KGVNYGFVEYHQSHDAEIALQTLNGRQIENNEIRVNWA 74

This subgroup corresponds to the RRM1 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. It is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 74

>gnl|CDD|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 = 46.8 bits (112), Expect = 4e-08
 Identities = 21/49 (42%), Positives = 29/49 (59%), Gaps = 3/49 (6%)

Query: 27 VFLIS---TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR 72
          V L+    T +S G+GFV +   EDA+ AI  LNG  L+ + IKV  A+
Sbjct: 31 VLLMKDPETGESRGFGFVTFESVEDADAAIRDLNGKELEGRVIKVEKAK 79

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

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

 Score = 46.1 bits (110), Expect = 1e-07
 Identities = 16/39 (41%), Positives = 22/39 (56%)

Query: 34 QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR 72
          Q  GY FV +   E+AEKA+ +LNG     K + V +A 
Sbjct: 42 QPRGYCFVTFETKEEAEKALKSLNGKTALGKKLVVRWAH 80

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|240919 cd12475, RRM2_RBMS3, RNA recognition motif 2 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 46.2 bits (109), Expect = 1e-07
 Identities = 20/52 (38%), Positives = 32/52 (61%)

Query: 82  NLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRER 133
           NLY+S LP  M +QELE++  P+G +I++RIL D      G  ++ +   E+
Sbjct: 3   NLYISNLPVSMDEQELENMLKPFGHVISTRILRDANGVSRGVGFARMESTEK 54

This subgroup corresponds to the RRM2 of RBMS3, a new member of the c-myc gene single-strand binding proteins (MSSP) family of DNA regulators. Unlike other MSSP proteins, RBMS3 is not a transcriptional regulator. It binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. RBMS3 contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and its C-terminal region is acidic and enriched in prolines, glutamines and threonines. . Length = 88

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

 Score = 45.7 bits (109), Expect = 1e-07
 Identities = 13/34 (38%), Positives = 25/34 (73%)

Query: 82  NLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
           N+Y+ GLP + + ++LE L  P+G+II+++ + D
Sbjct: 2   NVYIRGLPPNTTDEDLEKLCQPFGKIISTKAILD 35

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|240751 cd12305, RRM_NELFE, RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins

 Score = 45.3 bits (108), Expect = 2e-07
 Identities = 16/34 (47%), Positives = 22/34 (64%)

Query: 39 GFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR 72
          GFV + + E A++AI  LNG  +Q   +KVS AR
Sbjct: 41 GFVTFEKMESADRAIAELNGTTVQGVQLKVSLAR 74

This subfamily corresponds to the RRM of NELF-E, also termed RNA-binding protein RD. NELF-E is the RNA-binding subunit of cellular negative transcription elongation factor NELF (negative elongation factor) involved in transcriptional regulation of HIV-1 by binding to the stem of the viral transactivation-response element (TAR) RNA which is synthesized by cellular RNA polymerase II at the viral long terminal repeat. NELF is a heterotetrameric protein consisting of NELF A, B, C or the splice variant D, and E. NELF-E contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It plays a role in the control of HIV transcription by binding to TAR RNA. In addition, NELF-E is associated with the NELF-B subunit, probably via a leucine zipper motif. . Length = 75

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

 Score = 45.0 bits (107), Expect = 2e-07
 Identities = 17/41 (41%), Positives = 26/41 (63%)

Query: 30 ISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
          ++T +  GYGFV     E+A  AI +LNG RL  + ++VS+
Sbjct: 37 LTTNKCKGYGFVTMTNYEEAYSAIASLNGYRLGGRVLQVSF 77

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

 Score = 45.3 bits (108), Expect = 2e-07
 Identities = 19/48 (39%), Positives = 25/48 (52%)

Query: 27 VFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS 74
          + +    Q  G+ FV Y   EDAE+A   LNG  LQ   I+VS+  P 
Sbjct: 35 LAIAPNGQPRGFAFVEYATAEDAEEAQQALNGHSLQGSPIRVSFGNPG 82

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

 Score = 44.9 bits (107), Expect = 3e-07
 Identities = 18/42 (42%), Positives = 24/42 (57%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
          T +S G+GFV     E+A  AI  LNG     +T+ V+ ARP
Sbjct: 37 TGRSRGFGFVEMETAEEANAAIEKLNGTDFGGRTLTVNEARP 78

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

 Score = 44.5 bits (106), Expect = 3e-07
 Identities = 16/37 (43%), Positives = 22/37 (59%)

Query: 35 SLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
          S G+GFVN+   E A+KA+  LNG  +  K + V  A
Sbjct: 41 SKGFGFVNFENHEAAQKAVEELNGKEVNGKKLYVGRA 77

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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 43.7 bits (104), Expect = 5e-07
 Identities = 13/35 (37%), Positives = 21/35 (60%)

Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
          G+ FV +   E AEKA+  LNG+    + ++V Y+
Sbjct: 22 GFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 56

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

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

 Score = 46.8 bits (111), Expect = 6e-07
 Identities = 20/51 (39%), Positives = 33/51 (64%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGAN 82
           T +S G+GF+ +H  E+A++A+  +NG  L  + IKV YA+ S+  +  AN
Sbjct: 224 TGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQDSTYLLDAAN 274

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|214636 smart00360, RRM, RNA recognition motif

 Score = 43.7 bits (104), Expect = 7e-07
 Identities = 12/34 (35%), Positives = 22/34 (64%)

Query: 82  NLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
            L+V  LP   +++EL  LFS +G++ + R++ D
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRD 34

Length = 73

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

 Score = 43.7 bits (104), Expect = 7e-07
 Identities = 16/38 (42%), Positives = 23/38 (60%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVS 69
          T    GYGFV +   EDA+ AI  +N ++L  K I+V+
Sbjct: 36 TQAHQGYGFVEFLSEEDADYAIKIMNMIKLYGKPIRVN 73

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

 Score = 43.4 bits (103), Expect = 8e-07
 Identities = 19/47 (40%), Positives = 28/47 (59%), Gaps = 3/47 (6%)

Query: 28 FLI---STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
          FL+   ST +S GYGFV Y     A KA N L+G ++  + ++V +A
Sbjct: 30 FLVYSESTGESKGYGFVEYASKASALKAKNQLDGKQIGGRKLQVDWA 76

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

 Score = 43.4 bits (103), Expect = 1e-06
 Identities = 17/41 (41%), Positives = 24/41 (58%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR 72
          T  S G+ F++Y   E ++ AI  +NG  L N+ I VSYA 
Sbjct: 40 TGNSKGFAFISYDSFEASDAAIEAMNGQYLCNRPITVSYAF 80

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

>gnl|CDD|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 = 42.6 bits (101), Expect = 2e-06
 Identities = 15/36 (41%), Positives = 24/36 (66%)

Query: 80  GANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
           G  L+VSGL    +++ELE+LFS +GR+    ++ D
Sbjct: 1   GNKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKD 36

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

 Score = 42.6 bits (101), Expect = 2e-06
 Identities = 10/43 (23%), Positives = 22/43 (51%)

Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
           + +  G+G+V +   EDA++A+      +   + I V +A+ 
Sbjct: 36 GSKKCRGFGYVTFALEEDAKRALEEKKKTKFGGRKIHVEFAKK 78

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

 Score = 42.4 bits (100), Expect = 2e-06
 Identities = 16/40 (40%), Positives = 27/40 (67%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
          T +S G+G+V++  PEDA+KAI  ++G  L  + I V ++
Sbjct: 37 TGRSRGFGYVDFESPEDAKKAIEAMDGKELDGRPINVDFS 76

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

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

 Score = 42.5 bits (99), Expect = 3e-06
 Identities = 15/49 (30%), Positives = 28/49 (57%)

Query: 76  ESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKY 124
           + +   NLY+ GLP + + Q+L  L  PYG+I++++ + D    +   Y
Sbjct: 3   DQLSKTNLYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGY 51

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

>gnl|CDD|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 = 42.2 bits (100), Expect = 3e-06
 Identities = 15/39 (38%), Positives = 22/39 (56%)

Query: 30 ISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKV 68
           +T  S GY F  Y  P   ++AI  LNG++L +K + V
Sbjct: 36 SATGLSKGYAFCEYLDPSVTDQAIAGLNGMQLGDKKLTV 74

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

 Score = 44.7 bits (105), Expect = 3e-06
 Identities = 28/90 (31%), Positives = 46/90 (51%), Gaps = 15/90 (16%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS------------ESIK 79
           T +  G+ FV Y  PE A+ A+  +NG  L  + IKV   RPS+            E  K
Sbjct: 145 TGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVG--RPSNMPQAQPIIDMVQEEAK 202

Query: 80  GAN-LYVSGLPKHMSQQELESLFSPYGRII 108
             N +YV+ +   +S+ +++S+F  +G I+
Sbjct: 203 KFNRIYVASVHPDLSETDIKSVFEAFGEIV 232

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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 41.8 bits (99), Expect = 4e-06
 Identities = 14/40 (35%), Positives = 23/40 (57%)

Query: 83  LYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENG 122
           L+V  LP   ++++L+ LFS +G I + RI+ D      G
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKG 40

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

 Score = 41.7 bits (98), Expect = 5e-06
 Identities = 21/66 (31%), Positives = 37/66 (56%), Gaps = 5/66 (7%)

Query: 5  TLLNKLFTYEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNK 64
          TL      +       SDA + ++ + + +S GYGFV++   +DAE AIN +NG  L ++
Sbjct: 15 TLFAAFSAFP----SCSDARV-MWDMKSGRSRGYGFVSFRSQQDAENAINEMNGKWLGSR 69

Query: 65 TIKVSY 70
           I+ ++
Sbjct: 70 PIRCNW 75

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

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

 Score = 41.6 bits (98), Expect = 5e-06
 Identities = 17/39 (43%), Positives = 27/39 (69%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
          T +S GYGFV++ + EDAE AI ++NG  L  + I+ ++
Sbjct: 37 TGKSKGYGFVSFVKKEDAENAIQSMNGQWLGGRAIRTNW 75

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

 Score = 41.1 bits (97), Expect = 7e-06
 Identities = 16/40 (40%), Positives = 26/40 (65%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
          T +S G+GFV +   EDA++A   LNG+ +  + I+V Y+
Sbjct: 37 TGRSRGFGFVYFESVEDAKEAKERLNGMEIDGRRIRVDYS 76

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

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

 Score = 40.8 bits (96), Expect = 8e-06
 Identities = 14/40 (35%), Positives = 22/40 (55%)

Query: 83  LYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENG 122
           L+V  LP   ++++L  LFS +G I + RI+ D      G
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKG 40

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|240699 cd12253, RRM_PIN4_like, RNA recognition motif in yeast RNA-binding protein PIN4, fission yeast RNA-binding post-transcriptional regulators cip1, cip2 and similar proteins

 Score = 40.9 bits (96), Expect = 9e-06
 Identities = 12/36 (33%), Positives = 20/36 (55%)

Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR 72
          G  F N+  PE+A+  +  LNG  +  + ++V Y R
Sbjct: 44 GLAFANFRSPEEAQTVVEALNGYEISGRRLRVEYKR 79

This subfamily corresponds to the RRM in PIN4, also termed psi inducibility protein 4 or modifier of damage tolerance Mdt1, a novel phosphothreonine (pThr)-containing protein that specifically interacts with the pThr-binding site of the Rad53 FHA1 domain. It is encoded by gene MDT1 (YBL051C) from yeast Saccharomyces cerevisiae. PIN4 is involved in normal G2/M cell cycle progression in the absence of DNA damage and functions as a novel target of checkpoint-dependent cell cycle arrest pathways. It contains an N-terminal RRM, a nuclear localization signal, a coiled coil, and a total of 15 SQ/TQ motifs. cip1 (Csx1-interacting protein 1) and cip2 (Csx1-interacting protein 2) are novel cytoplasmic RRM-containing proteins that counteract Csx1 function during oxidative stress. They are not essential for viability in fission yeast Schizosaccharomyces pombe. Both cip1 and cip2 contain one RRM. Like PIN4, Cip2 also possesses an R3H motif that may function in sequence-specific binding to single-stranded nucleic acids. . Length = 79

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

 Score = 41.0 bits (97), Expect = 1e-05
 Identities = 15/40 (37%), Positives = 21/40 (52%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
          T    GY  + Y   ++A+ AI  LNG  L  +TI V +A
Sbjct: 44 TGFVKGYALIEYETKKEAQAAIEGLNGKELLGQTISVDWA 83

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|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 = 40.6 bits (96), Expect = 1e-05
 Identities = 10/25 (40%), Positives = 17/25 (68%)

Query: 83  LYVSGLPKHMSQQELESLFSPYGRI 107
           L+V  LPK  +++++ +LF  YG I
Sbjct: 2   LFVGQLPKTATEEDVRALFEEYGNI 26

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

 Score = 40.6 bits (95), Expect = 1e-05
 Identities = 14/42 (33%), Positives = 24/42 (57%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
          T +S GYGFV +   EDA++A+  L   +L  + +++  A  
Sbjct: 37 TGESRGYGFVTFAMLEDAQEALAKLKNKKLHGRILRLDIAER 78

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|240855 cd12409, RRM1_RRT5, RNA recognition motif 1 in yeast regulator of rDNA transcription protein 5 (RRT5) and similar proteins

 Score = 40.4 bits (95), Expect = 2e-05
 Identities = 18/70 (25%), Positives = 29/70 (41%)

Query: 4  QTLLNKLFTYEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQN 63
          + L   L  +E V +      +  F     + LG  +  +  PE AEK +  LNG   +N
Sbjct: 14 EDLEEFLKDFEPVSVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQAEKVVKDLNGKVFKN 73

Query: 64 KTIKVSYARP 73
          + + V    P
Sbjct: 74 RKLFVKLHVP 83

This subfamily corresponds to the RRM1 of the lineage specific family containing a group of uncharacterized yeast regulators of rDNA transcription protein 5 (RRT5), which may play roles in the modulation of rDNA transcription. RRT5 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 84

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

 Score = 40.3 bits (95), Expect = 2e-05
 Identities = 15/44 (34%), Positives = 24/44 (54%), Gaps = 4/44 (9%)

Query: 80  GANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGK 123
           G NLYV  L   +  + L   FSP+G I +++++ D    E G+
Sbjct: 1   GVNLYVKNLDDSIDDERLREEFSPFGTITSAKVMTD----EKGR 40

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|240833 cd12387, RRM3_hnRNPM_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 39.9 bits (94), Expect = 2e-05
 Identities = 14/35 (40%), Positives = 23/35 (65%)

Query: 34 QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKV 68
          +S G+G V +  PEDA++AI   NG  L+ + ++V
Sbjct: 37 RSKGFGTVLFESPEDAQRAIEMFNGYDLEGRELEV 71

This subfamily corresponds to the RRM3 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. 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 = 72

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

 Score = 40.3 bits (94), Expect = 2e-05
 Identities = 14/37 (37%), Positives = 22/37 (59%)

Query: 81  ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNL 117
            NLYV+ LP+ +++ EL  +F  YG I+   +L D  
Sbjct: 1   TNLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKS 37

This subfamily corresponds to the RRM2 of the sex-lethal protein (SXL) which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 79

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

 Score = 39.9 bits (94), Expect = 2e-05
 Identities = 13/37 (35%), Positives = 21/37 (56%)

Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
          G+ FV +  P DAE A+  L+G R+    ++V  +R 
Sbjct: 37 GFAFVEFEDPRDAEDAVRALDGRRICGNRVRVELSRG 73

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

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

 Score = 39.8 bits (94), Expect = 2e-05
 Identities = 13/36 (36%), Positives = 21/36 (58%)

Query: 34 QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVS 69
             GY +V +  PEDAEKAI  ++G ++  + + V 
Sbjct: 38 LPRGYAYVEFESPEDAEKAIKHMDGGQIDGQEVTVE 73

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

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

 Score = 39.5 bits (93), Expect = 2e-05
 Identities = 13/35 (37%), Positives = 22/35 (62%)

Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
          G+ FV +    DAEKAI  +NG +++ + + V +A
Sbjct: 41 GFAFVQFTSKADAEKAIKGVNGKKIKGRPVAVDWA 75

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

>gnl|CDD|240785 cd12339, RRM2_SRSF1_4_like, RNA recognition motif 2 in serine/arginine-rich splicing factor SRSF1, SRSF4 and similar proteins

 Score = 39.5 bits (93), Expect = 3e-05
 Identities = 10/32 (31%), Positives = 18/32 (56%)

Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKV 68
          G G V +   ED E+A+  L+G   + + ++V
Sbjct: 38 GEGVVEFTSQEDMERALRKLDGTEFRGRRVRV 69

This subfamily corresponds to the RRM2 of several serine/arginine (SR) proteins that have been classified into two subgroups. The first subgroup consists of serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS) and serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). The second subgroup is composed of 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). These SR proteins are mainly involved in regulating constitutive and alternative pre-mRNA splicing. They also have been implicated in transcription, genomic stability, mRNA export and translation. All SR proteins in this family, except SRSF5, undergo nucleocytoplasmic shuttling, suggesting their widespread roles in gene expression. These SR proteins share a common domain architecture comprising 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. Both domains can directly contact with RNA. The RRMs appear to determine the binding specificity and the SR domain also mediates protein-protein interactions. In addition, this subfamily includes the yeast nucleolar protein 3 (Npl3p), also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. It 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 with two RRMs, separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues. . Length = 71

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

 Score = 39.3 bits (92), Expect = 3e-05
 Identities = 17/39 (43%), Positives = 22/39 (56%)

Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS 75
          GY FV+      A+KAI  LNG  LQ K I+V ++ P  
Sbjct: 35 GYAFVDCPDQSWADKAIEKLNGKILQGKVIEVEHSVPKK 73

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

>gnl|CDD|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 = 39.1 bits (92), Expect = 3e-05
 Identities = 12/32 (37%), Positives = 20/32 (62%)

Query: 81  ANLYVSGLPKHMSQQELESLFSPYGRIITSRI 112
             +YV  LP  ++++EL+  FSP+G I   R+
Sbjct: 1   TTVYVGNLPHGLTEEELQRTFSPFGAIEEVRV 32

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

 Score = 38.7 bits (91), Expect = 5e-05
 Identities = 14/33 (42%), Positives = 21/33 (63%)

Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVS 69
          G+ FV +  PEDA  AI+ +N   L  +TI+V+
Sbjct: 41 GFAFVEFEEPEDAAAAIDNMNESELFGRTIRVN 73

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

 Score = 38.4 bits (90), Expect = 6e-05
 Identities = 16/33 (48%), Positives = 20/33 (60%)

Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQN 63
           T +  GYGFV++  PE A KAI  LNG  +Q 
Sbjct: 37 KTNKCKGYGFVDFDSPEAALKAIEGLNGRGVQA 69

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

 Score = 38.7 bits (91), Expect = 6e-05
 Identities = 13/36 (36%), Positives = 20/36 (55%)

Query: 35 SLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
          S+GYGFV +   E A+KA+  L G  L    +++  
Sbjct: 46 SMGYGFVEFKSKEAAQKALKRLQGTVLDGHALELKL 81

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|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 = 38.4 bits (90), Expect = 6e-05
 Identities = 14/40 (35%), Positives = 20/40 (50%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
          T +  GYGF  +   E A  AI  LNG     + ++V +A
Sbjct: 36 TGKPKGYGFCEFEDIETAASAIRNLNGYEFNGRALRVDFA 75

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

 Score = 38.4 bits (90), Expect = 8e-05
 Identities = 15/36 (41%), Positives = 23/36 (63%)

Query: 38 YGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
          Y FV++   +DA KA+  +NG  L+   I+VS A+P
Sbjct: 37 YAFVHFEERDDAVKAMEEMNGKELEGSPIEVSLAKP 72

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

 Score = 38.0 bits (89), Expect = 1e-04
 Identities = 12/34 (35%), Positives = 25/34 (73%)

Query: 82  NLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
           NLYV  LP ++++++L+ LF  +G + ++R++ D
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITD 34

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

 Score = 37.6 bits (88), Expect = 1e-04
 Identities = 15/38 (39%), Positives = 24/38 (63%)

Query: 34 QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
          +S G+GFV +  PE+A KA+  +NG  +  K + V+ A
Sbjct: 40 RSKGFGFVCFSSPEEATKAVTEMNGRIIGGKPLYVALA 77

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

 Score = 37.8 bits (88), Expect = 1e-04
 Identities = 12/34 (35%), Positives = 17/34 (50%)

Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
           + F+ +   E A+ AI TLNG  +    IKV  
Sbjct: 38 PHAFITFENLEAAQLAIETLNGASVDGNCIKVQR 71

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

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

 Score = 37.9 bits (89), Expect = 1e-04
 Identities = 16/49 (32%), Positives = 26/49 (53%)

Query: 19 GFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIK 67
           +   E    + +  +  G+ FV +  PEDAE A+  LNGL L  +T++
Sbjct: 21 PYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNGLVLDGRTLR 69

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

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

 Score = 38.3 bits (89), Expect = 1e-04
 Identities = 28/75 (37%), Positives = 38/75 (50%), Gaps = 19/75 (25%)

Query: 10 LFTYEKVHL--GFSDAEIC-VFL-----IS--------TAQSLGYGFVNYHRPEDAEKAI 53
          LF Y   HL   F DAE+  +FL     IS        T QS  +GFV++  P  A+ AI
Sbjct: 7  LFIY---HLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAI 63

Query: 54 NTLNGLRLQNKTIKV 68
            +NG ++  K +KV
Sbjct: 64 QAMNGFQIGMKRLKV 78

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

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

 Score = 37.9 bits (88), Expect = 1e-04
 Identities = 15/44 (34%), Positives = 25/44 (56%), Gaps = 1/44 (2%)

Query: 80  GANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGK 123
           G NL++  LP+     EL  +F P+G +I++++  D  AT   K
Sbjct: 4   GCNLFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDR-ATNQSK 46

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

>gnl|CDD|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 = 37.9 bits (88), Expect = 1e-04
 Identities = 16/43 (37%), Positives = 26/43 (60%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS 74
          T +S G+GFV +  P+DA+ A+  +NG  +  + I+V  A  S
Sbjct: 38 TQRSRGFGFVTFENPDDAKDAMMAMNGKSVDGRQIRVDQAGKS 80

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

 Score = 37.8 bits (88), Expect = 1e-04
 Identities = 13/37 (35%), Positives = 23/37 (62%)

Query: 35 SLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
          S G+GFV +    DA++A   L+G  ++ + I+V+ A
Sbjct: 39 SKGFGFVTFANSADADRAREKLHGTVVEGRKIEVNNA 75

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

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

 Score = 37.8 bits (87), Expect = 1e-04
 Identities = 20/51 (39%), Positives = 31/51 (60%), Gaps = 1/51 (1%)

Query: 21 SDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
          SDA + V  ++T +S GYGFV++    DAE AI  + G  L  + I+ ++A
Sbjct: 29 SDARV-VKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA 78

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

 Score = 37.6 bits (88), Expect = 1e-04
 Identities = 13/38 (34%), Positives = 22/38 (57%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVS 69
          + +S G   V + + EDAE+AI   NG+ L  + ++V 
Sbjct: 37 SGRSEGTADVVFEKREDAERAIKQFNGVLLDGQPMQVE 74

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

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

 Score = 37.8 bits (88), Expect = 1e-04
 Identities = 11/37 (29%), Positives = 20/37 (54%)

Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
          G  +V Y     A +A+  ++G  ++ KTI V+ + P
Sbjct: 44 GLAYVEYENESSASQAVLKMDGTEIKEKTISVAISNP 80

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

 Score = 37.3 bits (87), Expect = 2e-04
 Identities = 16/34 (47%), Positives = 23/34 (67%)

Query: 82  NLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
           NL V+ LP+ M+Q+EL SLF   G I + +I+ D
Sbjct: 2   NLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRD 35

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

 Score = 37.2 bits (87), Expect = 2e-04
 Identities = 11/33 (33%), Positives = 22/33 (66%)

Query: 83  LYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
           L++  LP   + Q+L  LF+P+G +I++++  D
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVD 33

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

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

 Score = 39.9 bits (93), Expect = 2e-04
 Identities = 22/89 (24%), Positives = 36/89 (40%), Gaps = 10/89 (11%)

Query: 30  ISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA----RPSSESIKGANLYV 85
           I+T  S GY F  Y  P   + AI  LNG    +  + V  A      ++         V
Sbjct: 331 IATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVGANQATIDTSNGMAPV 390

Query: 86  SGLPKHMSQQELESLFSPYGRIITSRILC 114
           + L K +SQ    S+    G+   ++++ 
Sbjct: 391 TLLAKALSQ----SILQIGGK--PTKVVQ 413

These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi. Length = 509

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

 Score = 37.5 bits (88), Expect = 2e-04
 Identities = 15/43 (34%), Positives = 24/43 (55%), Gaps = 3/43 (6%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLR---LQNKTIKVSYA 71
          T  S G+ FV +   EDA + ++ LN L    +  + ++VSYA
Sbjct: 42 TGTSRGFAFVEFPSLEDATQWMDALNNLDPFVIDGRVVRVSYA 84

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

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

 Score = 37.3 bits (87), Expect = 2e-04
 Identities = 13/34 (38%), Positives = 20/34 (58%)

Query: 38 YGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
          Y FV Y+    A  A+ T+NG  +  + IKV++A
Sbjct: 39 YAFVEYYDHRSAAAALQTMNGRLILGQEIKVNWA 72

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

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

 Score = 37.7 bits (87), Expect = 2e-04
 Identities = 13/40 (32%), Positives = 26/40 (65%)

Query: 76  ESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
           E  +GANL++  LP+    Q+L  +F P+G ++++++  D
Sbjct: 3   EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFID 42

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

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

 Score = 37.3 bits (86), Expect = 2e-04
 Identities = 15/40 (37%), Positives = 24/40 (60%)

Query: 38 YGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES 77
          +GFV+Y  P  A+ AI  +NG ++  K +KV   R  ++S
Sbjct: 51 FGFVSYDNPVSAQAAIQAMNGFQIGMKRLKVQLKRSKNDS 90

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

>gnl|CDD|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 = 36.9 bits (86), Expect = 2e-04
 Identities = 14/38 (36%), Positives = 22/38 (57%)

Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKV 68
           T +S G+ FV++  PE A KA + L+G   Q + + V
Sbjct: 36 ETKRSKGFAFVSFMFPEHAVKAYSELDGSIFQGRLLHV 73

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

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

 Score = 39.1 bits (91), Expect = 3e-04
 Identities = 25/94 (26%), Positives = 39/94 (41%), Gaps = 13/94 (13%)

Query: 34  QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKV-----------SYARPSSESIKGA- 81
           +S G  +V ++  E   KA+  L G  L  + I V             A      I    
Sbjct: 129 RSKGVAYVEFYDVESVIKAL-ALTGQMLLGRPIIVQSSQAEKNRAAKAATHQPGDIPNFL 187

Query: 82  NLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
            LYV  L  ++++QEL  +F P+G I   ++  D
Sbjct: 188 KLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRD 221

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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 36.8 bits (86), Expect = 3e-04
 Identities = 12/33 (36%), Positives = 22/33 (66%)

Query: 83  LYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
           LYV  LP  +++++L   FSPYG++   R++ +
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRN 33

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

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

 Score = 36.9 bits (86), Expect = 3e-04
 Identities = 14/31 (45%), Positives = 19/31 (61%)

Query: 40 FVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
           V Y  PE A++A+N LNG   +   +KVSY
Sbjct: 43 NVTYESPEQAQQAVNKLNGHEYEGSKLKVSY 73

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

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

 Score = 36.9 bits (86), Expect = 3e-04
 Identities = 15/37 (40%), Positives = 22/37 (59%)

Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
          G+GFV +  P DA+ A+  LNG  L  + + V +AR 
Sbjct: 34 GFGFVEFEDPRDADDAVYELNGKELCGERVIVEHARG 70

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

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

 Score = 37.2 bits (87), Expect = 3e-04
 Identities = 12/28 (42%), Positives = 20/28 (71%)

Query: 34 QSLGYGFVNYHRPEDAEKAINTLNGLRL 61
          ++ GY FV +  PE+A++A+  LNG +L
Sbjct: 48 KTKGYAFVEFATPEEAKEAVKALNGYKL 75

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

>gnl|CDD|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 = 37.2 bits (87), Expect = 3e-04
 Identities = 13/38 (34%), Positives = 18/38 (47%), Gaps = 2/38 (5%)

Query: 34 QSLGYG--FVNYHRPEDAEKAINTLNGLRLQNKTIKVS 69
             G G  FV +   EDA+KA   L G +   +T+  S
Sbjct: 52 DVPGVGKVFVEFADVEDAQKAQLALAGRKFDGRTVVAS 89

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

 Score = 37.0 bits (85), Expect = 3e-04
 Identities = 20/51 (39%), Positives = 32/51 (62%), Gaps = 1/51 (1%)

Query: 21 SDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
          SDA + V  ++T +S GYGFV+++   DAE AI  + G  L  + I+ ++A
Sbjct: 29 SDARV-VKDMATGKSKGYGFVSFYNKLDAENAIVHMGGQWLGGRQIRTNWA 78

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

 Score = 36.7 bits (84), Expect = 3e-04
 Identities = 14/34 (41%), Positives = 23/34 (67%)

Query: 82  NLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
           NLY+ GLP   + Q+L  L  PYG+I++++ + D
Sbjct: 6   NLYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILD 39

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

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

 Score = 36.8 bits (86), Expect = 4e-04
 Identities = 16/39 (41%), Positives = 24/39 (61%)

Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVS 69
           T +S GYGFV++  P D  KA+  +NG  + N+ IK+ 
Sbjct: 43 RTGKSKGYGFVSFSDPNDYLKAMKEMNGKYVGNRPIKLR 81

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

 Score = 36.5 bits (84), Expect = 4e-04
 Identities = 11/37 (29%), Positives = 23/37 (62%)

Query: 79  KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
           +G NL++  LP+  +  +L   F P+G +I++++  D
Sbjct: 3   EGCNLFIYHLPQEFTDTDLAQTFLPFGNVISAKVFID 39

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

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

 Score = 36.1 bits (84), Expect = 4e-04
 Identities = 16/31 (51%), Positives = 17/31 (54%)

Query: 38 YGFVNYHRPEDAEKAINTLNGLRLQNKTIKV 68
          YGFV+    EDAE AI  LNG     K I V
Sbjct: 35 YGFVHMEEEEDAEDAIKALNGYEFMGKRINV 65

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

 Score = 36.4 bits (85), Expect = 5e-04
 Identities = 14/42 (33%), Positives = 26/42 (61%), Gaps = 4/42 (9%)

Query: 82  NLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGK 123
           N+YV  L + M  ++L+ LF  YG+I +++++ D    + GK
Sbjct: 3   NVYVKNLGEDMDDEKLKELFGKYGKITSAKVMKD----DEGK 40

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

 Score = 36.2 bits (84), Expect = 5e-04
 Identities = 14/44 (31%), Positives = 26/44 (59%), Gaps = 1/44 (2%)

Query: 82  NLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYY 125
           NL+VSGL       +L+ LFS YG+++ ++I+  N  +   + +
Sbjct: 1   NLWVSGLSSTTKAADLKQLFSKYGKVVGAKIV-TNARSPGARCF 43

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

>gnl|CDD|241039 cd12595, RRM1_SRSF5, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 5 (SRSF5)

 Score = 36.1 bits (83), Expect = 5e-04
 Identities = 14/36 (38%), Positives = 23/36 (63%)

Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR 72
          G+GFV +  P DA+ A+  L+G  L N+ + + +AR
Sbjct: 34 GFGFVEFDDPRDADDAVYELDGKELCNERVTIEHAR 69

This subgroup corresponds to the RRM1 of SRSF5, also termed delayed-early protein HRS, or pre-mRNA-splicing factor SRp40, or splicing factor, arginine/serine-rich 5 (SFRS5). SFSF5 is an essential splicing regulatory serine/arginine (SR) protein that 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 it is necessary for enhancer activation. SRSF5 also functions as a factor required for insulin-regulated splice site selection for protein kinase C (PKC) betaII mRNA. It is involved in the regulation of PKCbetaII exon inclusion by insulin via its increased phosphorylation by a phosphatidylinositol 3-kinase (PI 3-kinase) signaling pathway. Moreover, SRSF5 can regulate alternative splicing in exon 9 of glucocorticoid receptor pre-mRNA in a dose-dependent manner. SRSF5 contains 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. The specific RNA binding by SRSF5 requires the phosphorylation of its SR domain. . Length = 70

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

 Score = 35.7 bits (83), Expect = 6e-04
 Identities = 12/37 (32%), Positives = 23/37 (62%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKV 68
          T +S G+ FV ++   DAE A++ ++G  L  + ++V
Sbjct: 36 TRESRGFAFVRFYDKRDAEDAMDAMDGKELDGRELRV 72

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

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

 Score = 36.1 bits (84), Expect = 6e-04
 Identities = 13/40 (32%), Positives = 26/40 (65%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
          T +S GYGFV +   ++ ++A+  +NG+   ++ ++VS A
Sbjct: 40 TGRSKGYGFVRFGDEDERDRALTEMNGVYCSSRPMRVSPA 79

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

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

 Score = 37.9 bits (88), Expect = 7e-04
 Identities = 16/45 (35%), Positives = 25/45 (55%)

Query: 27  VFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
           V L     S G+GFV +  PE+A +A+  ++G  L  K + V+ A
Sbjct: 317 VMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALA 361

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

 Score = 37.6 bits (87), Expect = 8e-04
 Identities = 17/40 (42%), Positives = 26/40 (65%)

Query: 31  STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
           +T Q  GYGFV+    ++A  AI +LNG  L N+ ++VS+
Sbjct: 306 TTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSF 345

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

 Score = 35.8 bits (82), Expect = 8e-04
 Identities = 17/40 (42%), Positives = 26/40 (65%)

Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
          +T +  G+GFV     E+A  AI +LNG RL +K ++VS+
Sbjct: 38 NTNKCKGFGFVTMTNYEEAAMAIASLNGYRLGDKILQVSF 77

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

>gnl|CDD|240765 cd12319, RRM4_MRD1, RNA recognition motif 4 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 35.6 bits (82), Expect = 9e-04
 Identities = 12/38 (31%), Positives = 22/38 (57%)

Query: 35 SLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR 72
          S+G+GFV +   E A+ A+  ++G  L   T+ V ++ 
Sbjct: 46 SMGFGFVGFKTKEQAQAALKAMDGFVLDGHTLVVKFSH 83

This subfamily corresponds to the RRM4 of MRD1which 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 = 84

>gnl|CDD|241213 cd12769, RRM1_HuR, RNA recognition motif 1 in vertebrate Hu-antigen R (HuR)

 Score = 35.4 bits (81), Expect = 0.001
 Identities = 17/43 (39%), Positives = 29/43 (67%)

Query: 82  NLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKY 124
           NL V+ LP++M+Q EL SLFS  G + +++++ D +A  +  Y
Sbjct: 3   NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGY 45

This subgroup corresponds to the RRM1 of HuR, also termed ELAV-like protein 1 (ELAV-1), a ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response; it binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. Meanwhile, HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

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

 Score = 35.2 bits (82), Expect = 0.001
 Identities = 15/32 (46%), Positives = 22/32 (68%)

Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKV 68
          G+ FV Y+  EDAE A+  LNG +L ++ I+V
Sbjct: 41 GFCFVEYYTREDAENAVKYLNGTKLDDRIIRV 72

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

>gnl|CDD|240723 cd12277, RRM3_MEI2_EAR1_like, RNA recognition motif 3 in Mei2-like proteins and terminal EAR1-like proteins

 Score = 35.3 bits (82), Expect = 0.001
 Identities = 16/41 (39%), Positives = 23/41 (56%), Gaps = 4/41 (9%)

Query: 36 LGYGFVNYHRPEDAEKAINTLNGLRLQN----KTIKVSYAR 72
          +GY F+N+  PE AEK     NG + +N    K   ++YAR
Sbjct: 43 VGYAFINFVNPEYAEKFYKAFNGKKWKNFKSKKVCDITYAR 83

This subfamily corresponds to the RRM3 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding proteins family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins. . Length = 86

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

 Score = 35.2 bits (81), Expect = 0.001
 Identities = 12/25 (48%), Positives = 19/25 (76%)

Query: 83  LYVSGLPKHMSQQELESLFSPYGRI 107
           L+V  L K  +++E+E +FSPYGR+
Sbjct: 2   LFVGCLNKQATEKEVEEVFSPYGRV 26

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

 Score = 35.0 bits (80), Expect = 0.001
 Identities = 16/36 (44%), Positives = 23/36 (63%)

Query: 38 YGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
          Y FV++   EDA  A+N LNG  L+   I+V+ A+P
Sbjct: 39 YAFVHFTSREDAVHAMNNLNGTELEGSCIEVTLAKP 74

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

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

 Score = 34.7 bits (80), Expect = 0.001
 Identities = 10/34 (29%), Positives = 19/34 (55%)

Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
           + FV +   E A +A ++++G  L N  + V+Y
Sbjct: 34 NFAFVEFESLESAIRAKDSVHGKVLNNNPLYVTY 67

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

 Score = 35.0 bits (81), Expect = 0.001
 Identities = 12/34 (35%), Positives = 17/34 (50%)

Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
          G GFV +     AE AI  L G  +    I++S+
Sbjct: 38 GCGFVQFVHRAAAEAAIQQLQGTIIGGSRIRLSW 71

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

>gnl|CDD|241105 cd12661, RRM3_hnRNPM, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 34.9 bits (80), Expect = 0.001
 Identities = 15/39 (38%), Positives = 21/39 (53%)

Query: 34 QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR 72
          +S G G V +  PE AE+A   +NG +L  + I V   R
Sbjct: 37 KSKGCGVVRFESPEVAERACRMMNGYKLNGREIDVRIDR 75

This subgroup corresponds to the RRM3 of hnRNP M, a 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). . Length = 77

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

 Score = 35.1 bits (81), Expect = 0.002
 Identities = 15/34 (44%), Positives = 24/34 (70%)

Query: 82  NLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
           NL V+ LP++M+Q E+ SLFS  G I + +++ D
Sbjct: 3   NLIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRD 36

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

 Score = 34.8 bits (80), Expect = 0.002
 Identities = 13/39 (33%), Positives = 19/39 (48%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
          T  S  YGF+ +  PE A  A  ++N   L  K ++V  
Sbjct: 37 TGNSKHYGFIQFLNPEVAAIAAKSMNNYLLMGKVLQVHV 75

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

>gnl|CDD|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 = 35.1 bits (81), Expect = 0.002
 Identities = 12/43 (27%), Positives = 25/43 (58%), Gaps = 3/43 (6%)

Query: 75  SESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNL 117
            ++IK   L+V  +P+++ +++L  LF  +G+I    +L D  
Sbjct: 3   DDAIK---LFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKY 42

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

 Score = 35.0 bits (80), Expect = 0.002
 Identities = 15/36 (41%), Positives = 22/36 (61%)

Query: 38 YGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
          Y FV++   EDA  A+N LNG  +    I+V+ A+P
Sbjct: 46 YAFVHFSNREDAVDAMNALNGKVIDGSPIEVTLAKP 81

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

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

 Score = 34.9 bits (81), Expect = 0.002
 Identities = 11/39 (28%), Positives = 20/39 (51%)

Query: 84  YVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENG 122
           +V G+P   +++EL   FS +G +   +I+ D      G
Sbjct: 6   FVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVSKG 44

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

 Score = 34.6 bits (79), Expect = 0.002
 Identities = 14/40 (35%), Positives = 26/40 (65%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
          T +S G+ FV + R +D+++A+   NG+ L  + I+V Y+
Sbjct: 37 TGRSRGFAFVYFERIDDSKEAMEHANGMELDGRRIRVDYS 76

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|240884 cd12438, RRM_CNOT4, RNA recognition motif in Eukaryotic CCR4-NOT transcription complex subunit 4 (NOT4) and similar proteins

 Score = 34.8 bits (81), Expect = 0.002
 Identities = 11/32 (34%), Positives = 18/32 (56%)

Query: 40 FVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
          +V Y R EDA + I  ++G  L  + +K S+ 
Sbjct: 57 YVTYSRKEDALRCIQAVDGFYLDGRLLKASFG 88

This subfamily corresponds to the RRM of NOT4, also termed CCR4-associated factor 4, or E3 ubiquitin-protein ligase CNOT4, or potential transcriptional repressor NOT4Hp, a component of the CCR4-NOT complex, a global negative regulator of RNA polymerase II transcription. NOT4 functions as an ubiquitin-protein ligase (E3). It contains an N-terminal C4C4 type RING finger motif, followed by a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The RING fingers may interact with a subset of ubiquitin-conjugating enzymes (E2s), including UbcH5B, and mediate protein-protein interactions. T. Length = 98

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

 Score = 35.8 bits (82), Expect = 0.002
 Identities = 21/58 (36%), Positives = 32/58 (55%), Gaps = 2/58 (3%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA--RPSSESIKGANLYVSG 87
           T +S G+GFVN++    A  AI+ ++G  L  + I+V+ A  RPS+    G     SG
Sbjct: 72  TGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPANDRPSAPRAYGGGGGYSG 129

Length = 144

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

 Score = 34.2 bits (79), Expect = 0.002
 Identities = 12/36 (33%), Positives = 20/36 (55%)

Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR 72
          G  +V     +DA +A+  L  ++L  K IKV++A 
Sbjct: 39 GCAYVCMETRQDAHRALQKLRNVKLAGKKIKVAWAP 74

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

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

 Score = 36.1 bits (82), Expect = 0.003
 Identities = 12/77 (15%), Positives = 25/77 (32%)

Query: 42  NYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKHMSQQELESLF 101
                E  +           +      S         +   L+V  LP  +++++L  LF
Sbjct: 77  EREMEEQNDGERGYTKEFEEELFRSSESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELF 136

Query: 102 SPYGRIITSRILCDNLA 118
             +G +   R++ D   
Sbjct: 137 KKFGPVKRVRLVRDRET 153

Length = 306

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

 Score = 34.2 bits (79), Expect = 0.003
 Identities = 13/46 (28%), Positives = 24/46 (52%)

Query: 80  GANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYY 125
           GANL++  L   + ++ L   FS +G I+ +  +  +  T N K +
Sbjct: 1   GANLFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGF 46

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

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

 Score = 34.1 bits (78), Expect = 0.003
 Identities = 25/74 (33%), Positives = 35/74 (47%), Gaps = 7/74 (9%)

Query: 7  LNKLFTYEKVHLGFSD----AEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGL--- 59
          LNK  T ++V   FS      +I +      QS G  FV Y   E A+ AI  LNG+   
Sbjct: 7  LNKQATEKEVEEVFSPYGRVEDIYMMRDEMKQSRGCAFVKYSSKEMAQAAIKALNGVYTM 66

Query: 60 RLQNKTIKVSYARP 73
          R  ++ + V +A P
Sbjct: 67 RGCDQPLIVRFADP 80

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

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

 Score = 34.2 bits (79), Expect = 0.003
 Identities = 13/47 (27%), Positives = 25/47 (53%), Gaps = 4/47 (8%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESI 78
          T  SL Y F+ +   ED E+A   ++ + + ++ I V +    S+S+
Sbjct: 41 TGDSLQYAFIEFETKEDCEEAYFKMDNVLIDDRRIHVDF----SQSV 83

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

 Score = 33.9 bits (78), Expect = 0.004
 Identities = 15/34 (44%), Positives = 24/34 (70%), Gaps = 5/34 (14%)

Query: 83  LYVSGLPKHMSQQELESLFSPYG-----RIITSR 111
           L+VSGLP  ++++ELE LF  +G     R++T+R
Sbjct: 5   LFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNR 38

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

 Score = 35.7 bits (82), Expect = 0.004
 Identities = 21/67 (31%), Positives = 32/67 (47%)

Query: 38  YGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKHMSQQEL 97
           Y FV++   EDA KA++ LNG  L+   I+V+ A+P  +         +G      Q   
Sbjct: 271 YAFVHFEDREDAVKAMDELNGKELEGSEIEVTLAKPVDKKSYVRYTRGTGGRGKERQAAR 330

Query: 98  ESLFSPY 104
           +SL   Y
Sbjct: 331 QSLGQVY 337

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

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

 Score = 33.9 bits (77), Expect = 0.004
 Identities = 15/40 (37%), Positives = 26/40 (65%)

Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
          +T +  G+GFV     ++A  AI +LNG RL ++ ++VS+
Sbjct: 40 NTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSF 79

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|240885 cd12439, RRM_TRMT2A, RNA recognition motif in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and similar proteins

 Score = 33.8 bits (78), Expect = 0.004
 Identities = 9/36 (25%), Positives = 20/36 (55%)

Query: 38 YGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
          + FV +   E+ +KA+  L+G + + + +    A+P
Sbjct: 44 FAFVTFRSEEERQKALEILDGFKWKGRVLSARLAKP 79

This subfamily corresponds to the RRM of TRMT2A, also known as HpaII tiny fragments locus 9c protein (HTF9C), a novel cell cycle regulated protein. It is an independent biologic factor expressed in tumors associated with clinical outcome in HER2 expressing breast cancer. The function of TRMT2A remains unclear although by sequence homology it has a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), related to RNA methyltransferases. . Length = 79

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

 Score = 33.4 bits (77), Expect = 0.004
 Identities = 10/25 (40%), Positives = 17/25 (68%)

Query: 83  LYVSGLPKHMSQQELESLFSPYGRI 107
           L+V  LP  ++++E + LFS YG +
Sbjct: 4   LFVGNLPNDITEEEFKELFSKYGEV 28

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	136
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	100.0
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.98
KOG0148|consensus	321		99.97
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.97
KOG0145|consensus	360		99.97
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.96
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.95
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.95
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.95
KOG0144|consensus	510		99.95
KOG0131|consensus	203		99.94
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.93
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.93
KOG0145|consensus	360		99.92
KOG0123|consensus	369		99.92
KOG0117|consensus	506		99.92
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.92
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.91
KOG0127|consensus	678		99.91
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.9
KOG0127|consensus	678		99.9
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.89
KOG0124|consensus	544		99.89
KOG0109|consensus	346		99.88
KOG0123|consensus	369		99.86
KOG0110|consensus	725		99.86
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.86
KOG4205|consensus	311		99.85
KOG0105|consensus	241		99.8
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.78
KOG0144|consensus	510		99.77
KOG4206|consensus	221		99.76
KOG0146|consensus	371		99.75
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.75
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.75
KOG0147|consensus	549		99.72
KOG0125|consensus	376		99.68
KOG0122|consensus	270		99.67
KOG0148|consensus	321		99.65
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.65
KOG0147|consensus	549		99.63
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.61
KOG0107|consensus	195		99.59
KOG0149|consensus	247		99.58
KOG1457|consensus	284		99.58
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.57
KOG4211|consensus	510		99.57
KOG0126|consensus	219		99.55
PLN03120	260	nucleic acid binding protein; Provisional	99.55
KOG4212|consensus	608		99.54
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.54
PLN03213	759	repressor of silencing 3; Provisional	99.53
smart00362	72	RRM_2 RNA recognition motif.	99.52
KOG0106|consensus	216		99.51
KOG4207|consensus	256		99.49
smart00360	71	RRM RNA recognition motif.	99.48
PLN03121	243	nucleic acid binding protein; Provisional	99.48
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.45
smart00361	70	RRM_1 RNA recognition motif.	99.45
KOG0111|consensus	298		99.44
KOG1190|consensus	492		99.44
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.43
KOG0121|consensus	153		99.43
KOG0113|consensus	335		99.42
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.41
KOG0114|consensus	124		99.4
KOG0130|consensus	170		99.4
KOG0108|consensus	435		99.38
KOG0117|consensus	506		99.36
KOG0124|consensus	544		99.32
KOG0120|consensus	500		99.32
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.31
KOG1548|consensus	382		99.3
KOG0125|consensus	376		99.29
KOG0149|consensus	247		99.28
KOG0146|consensus	371		99.28
KOG4208|consensus	214		99.26
PLN03120	260	nucleic acid binding protein; Provisional	99.26
PLN03121	243	nucleic acid binding protein; Provisional	99.25
KOG0122|consensus	270		99.24
KOG0110|consensus	725		99.23
KOG0131|consensus	203		99.21
KOG4454|consensus	267		99.15
smart00362	72	RRM_2 RNA recognition motif.	99.1
KOG4212|consensus	608		99.08
KOG0126|consensus	219		99.06
KOG0114|consensus	124		99.05
KOG0121|consensus	153		99.03
KOG0129|consensus	520		99.01
KOG0415|consensus	479		99.0
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	98.98
KOG4661|consensus	940		98.97
PLN03213	759	repressor of silencing 3; Provisional	98.96
KOG0153|consensus	377		98.94
smart00360	71	RRM RNA recognition motif.	98.94
KOG0109|consensus	346		98.93
KOG4205|consensus	311		98.91
KOG0128|consensus	881		98.9
KOG0533|consensus	243		98.9
KOG0132|consensus	894		98.88
KOG1365|consensus	508		98.86
COG0724	306	RNA-binding proteins (RRM domain) [General functio	98.85
KOG0113|consensus	335		98.84
KOG0107|consensus	195		98.84
KOG0226|consensus	290		98.82
KOG1456|consensus	494		98.82
KOG0151|consensus	877		98.74
KOG0105|consensus	241		98.74
KOG0116|consensus	419		98.73
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.72
KOG4211|consensus	510		98.72
KOG1456|consensus	494		98.68
KOG1190|consensus	492		98.64
KOG4209|consensus	231		98.63
KOG0108|consensus	435		98.61
KOG0415|consensus	479		98.61
KOG4660|consensus	549		98.61
KOG2193|consensus	584		98.6
KOG0130|consensus	170		98.59
KOG4210|consensus	285		98.59
KOG4207|consensus	256		98.56
KOG0111|consensus	298		98.54
KOG0153|consensus	377		98.45
KOG0120|consensus	500		98.43
KOG0112|consensus	975		98.42
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.39
KOG0132|consensus	894		98.32
KOG2314|consensus	698		98.31
KOG0226|consensus	290		98.3
KOG4208|consensus	214		98.28
smart00361	70	RRM_1 RNA recognition motif.	98.28
KOG0116|consensus	419		98.24
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	98.23
COG5175	480	MOT2 Transcriptional repressor [Transcription]	98.17
KOG1365|consensus	508		98.17
KOG1548|consensus	382		98.08
KOG4661|consensus	940		98.07
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.01
KOG4206|consensus	221		97.97
KOG3152|consensus	278		97.9
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.85
KOG4454|consensus	267		97.74
KOG0533|consensus	243		97.72
KOG0115|consensus	275		97.72
KOG0106|consensus	216		97.6
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.59
KOG4209|consensus	231		97.53
KOG1995|consensus	351		97.52
KOG0151|consensus	877		97.49
KOG4210|consensus	285		97.43
KOG4307|consensus	944		97.43
KOG0128|consensus	881		97.42
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.42
KOG4676|consensus	479		97.3
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.23
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.22
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	97.15
KOG4660|consensus	549		97.12
KOG1457|consensus	284		97.09
KOG1996|consensus	378		97.09
KOG2202|consensus	260		97.08
KOG1855|consensus	484		96.96
PF07292	88	NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909	96.94
KOG3152|consensus	278		96.84
KOG1855|consensus	484		96.78
KOG4307|consensus	944		96.73
KOG4849|consensus	498		96.65
KOG4676|consensus	479		96.29
KOG2068|consensus	327		96.22
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	96.15
KOG0115|consensus	275		96.04
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	95.76
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	95.75
KOG0129|consensus	520		95.71
COG5175	480	MOT2 Transcriptional repressor [Transcription]	95.71
KOG2135|consensus	526		95.7
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	95.46
KOG2416|consensus	718		95.41
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	95.05
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	94.97
KOG0112|consensus	975		94.52
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	94.07
KOG4574|consensus	1007		94.03
KOG1995|consensus	351		93.92
KOG2314|consensus	698		93.86
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	93.82
KOG4285|consensus	350		93.28
PF14111	153	DUF4283: Domain of unknown function (DUF4283)	93.16
KOG0804|consensus	493		92.51
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	91.85
KOG2591|consensus	684		91.27
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	91.17
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	90.36
KOG2202|consensus	260		89.93
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	89.72
KOG0804|consensus	493		89.07
KOG2068|consensus	327		87.08
PF10567	309	Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IP	84.83
PF15513	62	DUF4651: Domain of unknown function (DUF4651)	84.56
KOG4849|consensus	498		83.81
KOG4019|consensus	193		83.53
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	82.83
KOG1996|consensus	378		82.77
COG5353	161	Uncharacterized protein conserved in bacteria [Fun	81.55
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	80.02

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=100.00  E-value=2.7e-33  Score=200.43  Aligned_cols=134  Identities=34%  Similarity=0.633  Sum_probs=125.8

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..+|   |+++|+.||+|.+|++++  .+++++|||||+|.+.++|+.|+..||+..+.+++|+|.++.+...
T Consensus       110 LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~~a~p~~~  189 (346)
T TIGR01659       110 LIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYARPGGE  189 (346)
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeeeccccccc
Confidence            89999999999   999999999999999988  7899999999999999999999999999999999999999988766


Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      .....+|||.|||..+|+++|+++|++||.|..+++++|..++.. +.+||+|.+.|+|.
T Consensus       190 ~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~  249 (346)
T TIGR01659       190 SIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQ  249 (346)
T ss_pred             ccccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHH
Confidence            667789999999999999999999999999999999999988777 55999999999875

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

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.98  E-value=1.4e-31  Score=193.06  Aligned_cols=134  Identities=59%  Similarity=0.893  Sum_probs=125.8

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||+|.+|++++  .+|+++|||||+|.+.++|+.|+..|||..+.|++|++.++.+...
T Consensus         6 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~~~~~   85 (352)
T TIGR01661         6 LIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYARPSSD   85 (352)
T ss_pred             EEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeeccccc
Confidence            79999999998   999999999999999998  6899999999999999999999999999999999999999998877


Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      .....+|||+|||..+++++|+++|++||.|..+.++.+..++.. +.+||+|.+.|+|.
T Consensus        86 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~  145 (352)
T TIGR01661        86 SIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEAD  145 (352)
T ss_pred             ccccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHH
Confidence            777889999999999999999999999999999999999877655 56999999999875

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

>KOG0148|consensus

Probab=99.97  E-value=9.9e-31  Score=176.23  Aligned_cols=129  Identities=26%  Similarity=0.464  Sum_probs=119.6

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+.|..+++   |++.|.+||+|.++++++  .+++|||||||.|.+.++|+.||..|||..|++|.|+..|+.-+..
T Consensus        65 vfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATRKp~  144 (321)
T KOG0148|consen   65 VFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATRKPS  144 (321)
T ss_pred             EEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeeccccccCcc
Confidence            78999999998   999999999999999999  8999999999999999999999999999999999999999865442


Q ss_pred             ----------------CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          77 ----------------SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        77 ----------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                                      +.+.+++|++|++..+|+++|++.|++||+|..|++.+++     +++||+|++.|.|-
T Consensus       145 e~n~~~ltfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~q-----GYaFVrF~tkEaAa  214 (321)
T KOG0148|consen  145 EMNGKPLTFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKDQ-----GYAFVRFETKEAAA  214 (321)
T ss_pred             ccCCCCccHHHHhccCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEeccc-----ceEEEEecchhhHH
Confidence                            2467899999999999999999999999999999999875     78999999999874

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

Probab=99.97  E-value=3.7e-30  Score=193.58  Aligned_cols=134  Identities=20%  Similarity=0.344  Sum_probs=120.3

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||+|.+|.++.  .+|+++|||||+|.+.++|+.|+..+||..+.|+.|++.+......
T Consensus       110 LfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp~~~p~  189 (612)
T TIGR01645       110 VYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSNMPQ  189 (612)
T ss_pred             EEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeecccccccc
Confidence            79999999998   999999999999999988  7899999999999999999999999999999999999976442211


Q ss_pred             -----------CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          77 -----------SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        77 -----------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                                 .....+|||+|||+++++++|+++|+.||.|.++++.+|+.++.+ |++||+|.+.|++.
T Consensus       190 a~~~~~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~  260 (612)
T TIGR01645       190 AQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQS  260 (612)
T ss_pred             cccccccccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHH
Confidence                       123478999999999999999999999999999999999988866 56999999999874

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.

>KOG0145|consensus

Probab=99.97  E-value=2.3e-30  Score=174.02  Aligned_cols=134  Identities=57%  Similarity=0.830  Sum_probs=127.5

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |.|..||..+|   ++.+|+..|+|++|++++  .+|+|-|||||.|.++++|++|++.+||..+..+.|+|.+++|...
T Consensus        44 LIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSyARPSs~  123 (360)
T KOG0145|consen   44 LIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSYARPSSD  123 (360)
T ss_pred             eeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEeccCChh
Confidence            45678999998   899999999999999999  8999999999999999999999999999999999999999999999


Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccc-eEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGK-YYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~-~fv~f~~~e~~~  135 (136)
                      ...+.+|||++||..+|..+|+++|++||.|..-+|..|.-+|.+++ +|++|+.++||.
T Consensus       124 ~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe  183 (360)
T KOG0145|consen  124 SIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAE  183 (360)
T ss_pred             hhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHH
Confidence            99999999999999999999999999999999999999998888865 999999999875

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

Probab=99.96  E-value=3.7e-29  Score=189.99  Aligned_cols=134  Identities=26%  Similarity=0.421  Sum_probs=121.4

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCC-
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS-   75 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~-   75 (136)
                      |||+|||..+|   |+++|++||+|.+|++++  .+++++|||||+|.+.++|++|+..+|+..+.|++|+|.|+.... 
T Consensus         3 l~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~~~~   82 (562)
T TIGR01628         3 LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQRDPS   82 (562)
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeeccccccc
Confidence            89999999999   999999999999999999  679999999999999999999999999999999999999875332 


Q ss_pred             -CCCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          76 -ESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        76 -~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                       ......+|||+|||.++++++|+++|+.||.|.+|++..+..+..++.+||+|.+.|+|.
T Consensus        83 ~~~~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~~g~skg~afV~F~~~e~A~  143 (562)
T TIGR01628        83 LRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAK  143 (562)
T ss_pred             ccccCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecCCCCcccEEEEEECCHHHHH
Confidence             223456899999999999999999999999999999999976656678999999999875

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=99.95  E-value=1.2e-27  Score=177.91  Aligned_cols=133  Identities=20%  Similarity=0.266  Sum_probs=119.1

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||+|.+|.++.  .++.++|||||+|.+.++|++|+. ++|..+.|++|.+..+.....
T Consensus        92 l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~~~~~~~~  170 (457)
T TIGR01622        92 VFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQSSQAEKN  170 (457)
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEeecchhhh
Confidence            89999999998   999999999999999998  789999999999999999999997 899999999999987543221


Q ss_pred             ------------CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          77 ------------SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        77 ------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                                  .....+|||+|||..+++++|+++|++||.|..|.++.+..+|.. +.|||+|.+.|+|.
T Consensus       171 ~~~~~~~~~~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~  242 (457)
T TIGR01622       171 RAAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAK  242 (457)
T ss_pred             hhhhcccccCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHH
Confidence                        122478999999999999999999999999999999999988666 56999999999875

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

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.95  E-value=3.8e-27  Score=169.97  Aligned_cols=134  Identities=25%  Similarity=0.408  Sum_probs=115.7

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCC--ceEEEEeeCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQN--KTIKVSYARPS   74 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g--~~l~v~~~~~~   74 (136)
                      |||+|||..++   |+++|++||.+..+.++.  .++.++|||||+|.+.++|+.|++.|||..+.|  .++.+.++...
T Consensus        92 l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~~~~i~v~~a~~~  171 (352)
T TIGR01661        92 LYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVKFANNP  171 (352)
T ss_pred             EEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCCC
Confidence            89999999998   999999999999999888  578899999999999999999999999988876  56777765422


Q ss_pred             CC------------------------------------------------------------------------------
Q psy6353          75 SE------------------------------------------------------------------------------   76 (136)
Q Consensus        75 ~~------------------------------------------------------------------------------   76 (136)
                      ..                                                                              
T Consensus       172 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  251 (352)
T TIGR01661       172 SSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQHAVAQQHAAQRASPPATDG  251 (352)
T ss_pred             CcCCchhcCchhhcccCcccCCCCccccccccCCCCccCcccccccCcchhhhhhhhhhhhcccccccccccCCCccccc
Confidence            20                                                                              


Q ss_pred             --------------CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          77 --------------SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        77 --------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                                    ...+.+|||+|||+++++++|+++|++||.|.+++|++|+.++.+ |+|||+|.+.|+|.
T Consensus       252 ~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~  325 (352)
T TIGR01661       252 QTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAA  325 (352)
T ss_pred             cccccccCCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHH
Confidence                          001225999999999999999999999999999999999977777 55999999999874

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

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

Probab=99.95  E-value=8.3e-27  Score=177.17  Aligned_cols=134  Identities=25%  Similarity=0.427  Sum_probs=120.9

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES   77 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~~   77 (136)
                      |||+|||.+++   |+++|++||.|.+|+++. .+|+++|||||+|.+.++|+.|+.++||..+.++.+.+....++.+.
T Consensus        91 vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~~g~skg~afV~F~~~e~A~~Ai~~lng~~~~~~~i~v~~~~~~~~~  170 (562)
T TIGR01628        91 IFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIKKHER  170 (562)
T ss_pred             eEEcCCCccCCHHHHHHHHHhcCCcceeEeeecCCCCcccEEEEEECCHHHHHHHHHHhcccEecCceEEEecccccccc
Confidence            79999999998   999999999999999998 88899999999999999999999999999999999999765544332


Q ss_pred             -----CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          78 -----IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        78 -----~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                           ...++|||+|||.++|+++|+++|++||.|.++.+..+..+...+.+||+|.+.|+|.
T Consensus       171 ~~~~~~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~~~~~g~~~G~afV~F~~~e~A~  233 (562)
T TIGR01628       171 EAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAA  233 (562)
T ss_pred             ccccccCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHH
Confidence                 3457899999999999999999999999999999999986666677999999999875

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

>KOG0144|consensus

Probab=99.95  E-value=7.2e-28  Score=171.14  Aligned_cols=133  Identities=24%  Similarity=0.381  Sum_probs=121.2

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcC-ceeCC--ceEEEEeeCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNG-LRLQN--KTIKVSYARP   73 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~-~~~~g--~~l~v~~~~~   73 (136)
                      +||+-+|...+   |+++|++||.|.+|.+++  .+++++|||||.|.+.++|.+|+.+||. +++.|  .++.+++++.
T Consensus        37 lfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqvk~Ad~  116 (510)
T KOG0144|consen   37 LFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQVKYADG  116 (510)
T ss_pred             heeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceeecccch
Confidence            68999999888   999999999999999999  8999999999999999999999999987 55654  6889999886


Q ss_pred             CCCC-CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCccccc
Q psy6353          74 SSES-IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERL  134 (136)
Q Consensus        74 ~~~~-~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~  134 (136)
                      ..+. ...++|||+-|+..+||.+++++|++||.|++|.|.+|...-.+|++||.|.++|-|
T Consensus       117 E~er~~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fstke~A  178 (510)
T KOG0144|consen  117 ERERIVEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFSTKEMA  178 (510)
T ss_pred             hhhccccchhhhhhhccccccHHHHHHHHHhhCccchhhheecccccccceeEEEEehHHHH
Confidence            6543 347899999999999999999999999999999999999999999999999999754

>KOG0131|consensus

Probab=99.94  E-value=3.6e-27  Score=150.92  Aligned_cols=134  Identities=24%  Similarity=0.327  Sum_probs=121.1

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCC-C
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS-S   75 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~-~   75 (136)
                      ||++|||..++   |.++|-+.|+|.++.+++  .+...+||||++|.++++|+.|++-||...+.|++|++..+... .
T Consensus        12 iyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~kas~~~~   91 (203)
T KOG0131|consen   12 LYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKASAHQK   91 (203)
T ss_pred             EEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEecccccc
Confidence            79999999998   999999999999999999  77789999999999999999999999999999999999877632 2


Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHhhcCCCceEE-EEEEeCCCCCCcc-ceEeecCcccccc
Q psy6353          76 ESIKGANLYVSGLPKHMSQQELESLFSPYGRIIT-SRILCDNLATENG-KYYSGLGGRERLR  135 (136)
Q Consensus        76 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~-~~i~~~~~~~~~~-~~fv~f~~~e~~~  135 (136)
                      +...+.++||+||.+.+++..|.+.|+.||++.. .++++++++|..+ ++|+.|++.|..+
T Consensus        92 nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd  153 (203)
T KOG0131|consen   92 NLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASD  153 (203)
T ss_pred             cccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHH
Confidence            3456789999999999999999999999999876 6999999988885 6999999988754

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

Probab=99.93  E-value=6.3e-25  Score=164.15  Aligned_cols=127  Identities=13%  Similarity=0.163  Sum_probs=110.1

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHH--cCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTL--NGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~--~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||+|.++.+++    +||||||+|.+.++|+.|++.+  ++..+.|++|.|.++.++..
T Consensus         5 v~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~----~k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~s~~~~~   80 (481)
T TIGR01649         5 VHVRNLPQDVVEADLVEALIPFGPVSYVMMLP----GKRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYSTSQEI   80 (481)
T ss_pred             EEEcCCCCCCCHHHHHHHHHhcCCeeEEEEEC----CCCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEecCCccc
Confidence            89999999998   999999999999999885    6789999999999999999864  78999999999999864321


Q ss_pred             C------------CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          77 S------------IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~------------~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      .            ....+|+|.||+..+|+++|+++|++||.|..|.+.++..+   +.|||+|.+.|+|.
T Consensus        81 ~~~~~~~~~~~~~~~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~~~---~~afVef~~~~~A~  148 (481)
T TIGR01649        81 KRDGNSDFDSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKNNV---FQALVEFESVNSAQ  148 (481)
T ss_pred             ccCCCCcccCCCCCceEEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecCCc---eEEEEEECCHHHHH
Confidence            1            11237999999999999999999999999999999886532   46999999999875

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).

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

Probab=99.93  E-value=6.2e-25  Score=164.18  Aligned_cols=130  Identities=17%  Similarity=0.246  Sum_probs=110.9

Q ss_pred             eeecCCCh-hhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC-
Q psy6353           2 VYQTLLNK-LFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE-   76 (136)
Q Consensus         2 v~v~nl~~-~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~-   76 (136)
                      |||+|||. .++   |+++|++||.|.+|++++   ..+|+|||+|.+.++|+.|+..|||..+.|++|+|.+++.... 
T Consensus       278 l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~---~~~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~~~~~~  354 (481)
T TIGR01649       278 LMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMK---NKKETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQNVQ  354 (481)
T ss_pred             EEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEe---CCCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEccccccc
Confidence            89999997 576   999999999999999987   3479999999999999999999999999999999987643210 


Q ss_pred             ------------------------------------CCCCceEEEcCCCCCCCHHHHHHhhcCCCc--eEEEEEEeCCCC
Q psy6353          77 ------------------------------------SIKGANLYVSGLPKHMSQQELESLFSPYGR--IITSRILCDNLA  118 (136)
Q Consensus        77 ------------------------------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~--v~~~~i~~~~~~  118 (136)
                                                          ...+.+|||+|||.++++++|+++|++||.  |..+++..+. +
T Consensus       355 ~~~~~~~~~~~~~~~d~~~~~~~r~~~~~~~~~~~~~~ps~~L~v~NLp~~~tee~L~~lF~~~G~~~i~~ik~~~~~-~  433 (481)
T TIGR01649       355 PPREGQLDDGLTSYKDYSSSRNHRFKKPGSANKNNIQPPSATLHLSNIPLSVSEEDLKELFAENGVHKVKKFKFFPKD-N  433 (481)
T ss_pred             CCCCCcCcCCCcccccccCCccccCCCcccccccccCCCCcEEEEecCCCCCCHHHHHHHHHhcCCccceEEEEecCC-C
Confidence                                                012468999999999999999999999998  7888887544 3


Q ss_pred             CCccceEeecCcccccc
Q psy6353         119 TENGKYYSGLGGRERLR  135 (136)
Q Consensus       119 ~~~~~~fv~f~~~e~~~  135 (136)
                      +.++.|||+|++.|+|.
T Consensus       434 ~~~~~gfVeF~~~e~A~  450 (481)
T TIGR01649       434 ERSKMGLLEWESVEDAV  450 (481)
T ss_pred             CcceeEEEEcCCHHHHH
Confidence            45678999999999875

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).

>KOG0145|consensus

Probab=99.92  E-value=9.3e-25  Score=147.14  Aligned_cols=133  Identities=24%  Similarity=0.383  Sum_probs=117.4

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCC--ceEEEEeeCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQN--KTIKVSYARPS   74 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g--~~l~v~~~~~~   74 (136)
                      |||+.||+.+|   |+++|++||.|..-++..  .+|.++|.|||.|...++|+.|+..+||..-.|  .+|.|+++...
T Consensus       130 LYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~P~g~tepItVKFannP  209 (360)
T KOG0145|consen  130 LYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQKPSGCTEPITVKFANNP  209 (360)
T ss_pred             eEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhccCCCCCCCCCCeEEEecCCc
Confidence            79999999999   899999999987776666  789999999999999999999999999988765  57888876533


Q ss_pred             CC---------------------------------------------------------------CCCCceEEEcCCCCC
Q psy6353          75 SE---------------------------------------------------------------SIKGANLYVSGLPKH   91 (136)
Q Consensus        75 ~~---------------------------------------------------------------~~~~~~l~v~nl~~~   91 (136)
                      ..                                                               ...++.|||-||.++
T Consensus       210 sq~t~~a~ls~ly~sp~rr~~Gp~hh~~~r~r~~~~~~~~~~~~rfsP~~~d~m~~l~~~~lp~~~~~g~ciFvYNLspd  289 (360)
T KOG0145|consen  210 SQKTNQALLSQLYQSPARRYGGPMHHQAQRFRLDNLLNPHAAQARFSPMTIDGMSGLAGVNLPGGPGGGWCIFVYNLSPD  289 (360)
T ss_pred             ccccchhhhHHhhcCccccCCCcccchhhhhccccccchhhhhccCCCccccccceeeeeccCCCCCCeeEEEEEecCCC
Confidence            22                                                               024579999999999


Q ss_pred             CCHHHHHHhhcCCCceEEEEEEeCCCCCCccc-eEeecCccccc
Q psy6353          92 MSQQELESLFSPYGRIITSRILCDNLATENGK-YYSGLGGRERL  134 (136)
Q Consensus        92 ~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~-~fv~f~~~e~~  134 (136)
                      ++|.-|+++|.+||.|..+++++|.+++++++ +||.|.+.+||
T Consensus       290 ~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEA  333 (360)
T KOG0145|consen  290 ADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEA  333 (360)
T ss_pred             chHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHH
Confidence            99999999999999999999999999999955 89999999886

>KOG0123|consensus

Probab=99.92  E-value=1.2e-24  Score=156.97  Aligned_cols=124  Identities=21%  Similarity=0.405  Sum_probs=110.6

Q ss_pred             eeecCCChhhh--HHHHhccCCCeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCCCC
Q psy6353           2 VYQTLLNKLFT--YEKVHLGFSDAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESI   78 (136)
Q Consensus         2 v~v~nl~~~~~--l~~~f~~~G~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~~~   78 (136)
                      |||+  |.-.+  |.+.|+++|++.++++++ . + +-|||||.|.++.+|++|+.++|...+.|+++++.|+...+.  
T Consensus         4 l~vg--~~v~e~~l~~~f~~~~~v~s~rvc~d~-t-slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd~~--   77 (369)
T KOG0123|consen    4 LYVG--PDVTEAMLFDKFSPAGPVLSIRVCRDA-T-SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRDPS--   77 (369)
T ss_pred             eecC--CcCChHHHHHHhcccCCceeEEEeecC-C-ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccCCc--
Confidence            6777  33333  999999999999999999 7 6 999999999999999999999999999999999999875433  


Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCccccccC
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLRR  136 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~~  136 (136)
                         .+||.||+++++..+|.++|+.||+|.+|++.++.++  .+++||+|+++|+|++
T Consensus        78 ---~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g--~kg~FV~f~~e~~a~~  130 (369)
T KOG0123|consen   78 ---LVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENG--SKGYFVQFESEESAKK  130 (369)
T ss_pred             ---eeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCC--ceeeEEEeCCHHHHHH
Confidence               2999999999999999999999999999999999866  4555999999999863

>KOG0117|consensus

Probab=99.92  E-value=1.6e-24  Score=154.72  Aligned_cols=126  Identities=20%  Similarity=0.317  Sum_probs=111.8

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeC-CceEEEEeeCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQ-NKTIKVSYARPSS   75 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~-g~~l~v~~~~~~~   75 (136)
                      |||+.||..+.   |..+|++.|+|-+++++.  .+|.++|||||+|.+.+.|+.|++.||+++|. |+.|.|+.+..+.
T Consensus        86 VfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~Svan~  165 (506)
T KOG0117|consen   86 VFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCVSVANC  165 (506)
T ss_pred             EEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEEeeecc
Confidence            79999999887   999999999999999999  89999999999999999999999999999985 8999987655322


Q ss_pred             C----------C--------------------------------------------------------------------
Q psy6353          76 E----------S--------------------------------------------------------------------   77 (136)
Q Consensus        76 ~----------~--------------------------------------------------------------------   77 (136)
                      +          .                                                                    
T Consensus       166 RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g~~klwgn~~tVdWA  245 (506)
T KOG0117|consen  166 RLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMPGKIKLWGNAITVDWA  245 (506)
T ss_pred             eeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhccCCceeecCCcceeecc
Confidence            1          0                                                                    


Q ss_pred             -----------CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCccccc
Q psy6353          78 -----------IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERL  134 (136)
Q Consensus        78 -----------~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~  134 (136)
                                 ..-..|||+||+.++|++.|+++|++||.|+.|+.++|       +|||.|+++|++
T Consensus       246 ep~~e~ded~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD-------YaFVHf~eR~da  306 (506)
T KOG0117|consen  246 EPEEEPDEDTMSKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD-------YAFVHFAEREDA  306 (506)
T ss_pred             CcccCCChhhhhheeeeeeeccchhhhHHHHHHHHHhccceEEeecccc-------eeEEeecchHHH
Confidence                       11246999999999999999999999999999998865       789999999986

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

Probab=99.92  E-value=2.1e-24  Score=162.33  Aligned_cols=128  Identities=16%  Similarity=0.285  Sum_probs=108.3

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeC-CceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQ-NKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~-g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |.++|++||.|.++++++ .+|+++|||||+|.+.++|+.|++.||+..+. |+.+.+..+.    
T Consensus        61 lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~S~----  136 (578)
T TIGR01648        61 VFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCISV----  136 (578)
T ss_pred             EEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEECCCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCccccccccc----
Confidence            79999999998   999999999999999999 89999999999999999999999999998885 7887776654    


Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCc-eEEEEEE-eCCCCCC-ccceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGR-IITSRIL-CDNLATE-NGKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~-v~~~~i~-~~~~~~~-~~~~fv~f~~~e~~~  135 (136)
                        ..++|||+|||.++++++|.+.|.+++. +..+.+. .+...+. ++.+||+|.+.++|.
T Consensus       137 --~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa  196 (578)
T TIGR01648       137 --DNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAA  196 (578)
T ss_pred             --cCceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHH
Confidence              3578999999999999999999999964 4444333 2233333 366999999998863

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

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

Probab=99.91  E-value=6.3e-24  Score=159.76  Aligned_cols=129  Identities=12%  Similarity=0.219  Sum_probs=105.6

Q ss_pred             eeecCCChhhh---HHHHhccC------------CCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceE
Q psy6353           2 VYQTLLNKLFT---YEKVHLGF------------SDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTI   66 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~------------G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l   66 (136)
                      |||+|||..+|   |.++|.++            +.|..+.    .+.++|||||+|.+.++|..|+. |||..+.|++|
T Consensus       178 lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~----~~~~kg~afVeF~~~e~A~~Al~-l~g~~~~g~~l  252 (509)
T TIGR01642       178 LYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVN----INKEKNFAFLEFRTVEEATFAMA-LDSIIYSNVFL  252 (509)
T ss_pred             EEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEE----ECCCCCEEEEEeCCHHHHhhhhc-CCCeEeeCcee
Confidence            89999999998   88999875            2333332    34678999999999999999995 99999999999


Q ss_pred             EEEeeCCCC-----------------------------CCCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCC
Q psy6353          67 KVSYARPSS-----------------------------ESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNL  117 (136)
Q Consensus        67 ~v~~~~~~~-----------------------------~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~  117 (136)
                      +|.......                             ......+|||+|||..+++++|+++|+.||.|..+.++.+..
T Consensus       253 ~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~  332 (509)
T TIGR01642       253 KIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIA  332 (509)
T ss_pred             EecCccccCCccccCCCCCCCCCcccccccccccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC
Confidence            996422110                             012346899999999999999999999999999999999988


Q ss_pred             CCCc-cceEeecCcccccc
Q psy6353         118 ATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus       118 ~~~~-~~~fv~f~~~e~~~  135 (136)
                      +|.+ |.|||+|.+.+.|.
T Consensus       333 ~g~~~g~afv~f~~~~~a~  351 (509)
T TIGR01642       333 TGLSKGYAFCEYKDPSVTD  351 (509)
T ss_pred             CCCcCeEEEEEECCHHHHH
Confidence            8866 56999999988763

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

>KOG0127|consensus

Probab=99.91  E-value=1.1e-23  Score=153.69  Aligned_cols=133  Identities=20%  Similarity=0.327  Sum_probs=119.6

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC-
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE-   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~-   76 (136)
                      |.|.|||..+.   |+.+|+.||.|.+|.|++ ..|+-.|||||.|....+|..|++.+|+..|.||++.+.|+-++.. 
T Consensus       120 LIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd~y  199 (678)
T KOG0127|consen  120 LIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDKDTY  199 (678)
T ss_pred             EEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeecccccc
Confidence            57899999887   999999999999999999 7777779999999999999999999999999999999999765432 


Q ss_pred             --------------------------------------------------------------------------------
Q psy6353          77 --------------------------------------------------------------------------------   76 (136)
Q Consensus        77 --------------------------------------------------------------------------------   76 (136)
                                                                                                      
T Consensus       200 e~ta~~~~~s~Kk~~~eEed~e~~~d~~~~~~~Ed~e~d~edeEe~D~~se~~ee~~~~Eee~~~vDd~e~S~~~~~~k~  279 (678)
T KOG0127|consen  200 EDTAHEEKQSLKKAVKEEEDKEADEDDGKDFDEEDGEEDSEDEEETDGNSEAFEEGEESEEEEDDVDDEESSGKKESDKK  279 (678)
T ss_pred             cccchhhhhhhhhccchhhhcccccccccccchhcccccccccccccccchhhhccccccccccccccccccccCcccch
Confidence                                                                                            


Q ss_pred             ---------CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccc-eEeecCccccc
Q psy6353          77 ---------SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGK-YYSGLGGRERL  134 (136)
Q Consensus        77 ---------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~-~fv~f~~~e~~  134 (136)
                               ..-+.+|||+|||+++|++.|.+.|++||+|.++.|+.++.++.+.| |||.|.+.+++
T Consensus       280 ~q~k~~~en~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~  347 (678)
T KOG0127|consen  280 AQNKTTRENITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAA  347 (678)
T ss_pred             hccccccccccccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHH
Confidence                     00136899999999999999999999999999999999999999955 99999988764

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

Probab=99.90  E-value=2.9e-23  Score=156.20  Aligned_cols=134  Identities=22%  Similarity=0.283  Sum_probs=111.2

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||.|..+.++.  .+|.++|||||+|.+.++|+.|+..|||..++|+.|.|.++.....
T Consensus       298 l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~~~~  377 (509)
T TIGR01642       298 IYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVGAN  377 (509)
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECccCCC
Confidence            79999999998   999999999999999888  6899999999999999999999999999999999999988643211


Q ss_pred             ----------------------------CCCCceEEEcCCCCCC----------CHHHHHHhhcCCCceEEEEEEeCCCC
Q psy6353          77 ----------------------------SIKGANLYVSGLPKHM----------SQQELESLFSPYGRIITSRILCDNLA  118 (136)
Q Consensus        77 ----------------------------~~~~~~l~v~nl~~~~----------t~~~l~~~f~~~G~v~~~~i~~~~~~  118 (136)
                                                  .....+|++.|+....          ..++|+++|.+||.|..|.|+++...
T Consensus       378 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~~~~~~  457 (509)
T TIGR01642       378 QATIDTSNGMAPVTLLAKALSQSILQIGGKPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGD  457 (509)
T ss_pred             CCCccccccccccccccccchhhhccccCCCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEeeccCcC
Confidence                                        1134678889986421          23689999999999999999986322


Q ss_pred             ---CC-ccceEeecCcccccc
Q psy6353         119 ---TE-NGKYYSGLGGRERLR  135 (136)
Q Consensus       119 ---~~-~~~~fv~f~~~e~~~  135 (136)
                         +. .|.+||+|.+.|+|.
T Consensus       458 ~~~~~~~G~~fV~F~~~e~A~  478 (509)
T TIGR01642       458 RNSTPGVGKVFLEYADVRSAE  478 (509)
T ss_pred             CCcCCCcceEEEEECCHHHHH
Confidence               22 256899999999875

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

>KOG0127|consensus

Probab=99.90  E-value=2.2e-23  Score=152.08  Aligned_cols=134  Identities=17%  Similarity=0.306  Sum_probs=121.3

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||++||...+   |.++|+..|+|..+.++.  .++.++|||||+|...++++.|+...++..++|+.|.+..+.++..
T Consensus         8 lfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A~~R~r   87 (678)
T KOG0127|consen    8 LFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDPAKKRAR   87 (678)
T ss_pred             EEEecCCCccchhHHHHhhhcccCcceeEEecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceeccccccccccc
Confidence            89999999998   999999999999999998  6778999999999999999999999999999999999987665432


Q ss_pred             C--------------------------CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCc
Q psy6353          77 S--------------------------IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGG  130 (136)
Q Consensus        77 ~--------------------------~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~  130 (136)
                      .                          ...++|.|+|||.++.+.+|+.+|+.||.|..+.|++...++.+|+|||.|..
T Consensus        88 ~e~~~~~e~~~veK~~~q~~~~k~~v~~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaFV~fk~  167 (678)
T KOG0127|consen   88 SEEVEKGENKAVEKPIEQKRPTKAKVDLPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAFVQFKE  167 (678)
T ss_pred             chhcccccchhhhcccccCCcchhhccCccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCccceEEEEEee
Confidence            1                          13678999999999999999999999999999999999999999999999987


Q ss_pred             ccccc
Q psy6353         131 RERLR  135 (136)
Q Consensus       131 ~e~~~  135 (136)
                      .-+|+
T Consensus       168 ~~dA~  172 (678)
T KOG0127|consen  168 KKDAE  172 (678)
T ss_pred             HHHHH
Confidence            76553

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

Probab=99.89  E-value=3.1e-22  Score=150.65  Aligned_cols=127  Identities=20%  Similarity=0.269  Sum_probs=106.4

Q ss_pred             eeecCCChhhh---HHHHhccCCC-eeEEEEEc---cCCCceeeEEEEcCCHHHHHHHHHHHcC--ceeCCceEEEEeeC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSD-AEICVFLI---STAQSLGYGFVNYHRPEDAEKAINTLNG--LRLQNKTIKVSYAR   72 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~-v~~~~~~~---~~~~~kg~~fv~f~~~~~a~~a~~~~~~--~~~~g~~l~v~~~~   72 (136)
                      |||+|||..++   |.+.|++++. +.++.+..   ..++++|||||+|.+.++|..|+.+++.  ..+.|+.|.|.|+.
T Consensus       141 LFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~gki~l~Gr~I~VdwA~  220 (578)
T TIGR01648       141 LFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAVDWAE  220 (578)
T ss_pred             eEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhccceEecCceEEEEeec
Confidence            79999999998   7888888863 44444433   4567899999999999999999988763  56889999999998


Q ss_pred             CCCCC-----CCCceEEEcCCCCCCCHHHHHHhhcCC--CceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          73 PSSES-----IKGANLYVSGLPKHMSQQELESLFSPY--GRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        73 ~~~~~-----~~~~~l~v~nl~~~~t~~~l~~~f~~~--G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      +....     ....+|||+|||.++++++|+++|++|  |.|..|.+++       +.+||+|+++|+|.
T Consensus       221 p~~~~d~~~~~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~r-------gfAFVeF~s~e~A~  283 (578)
T TIGR01648       221 PEEEVDEDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIR-------DYAFVHFEDREDAV  283 (578)
T ss_pred             ccccccccccccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEeec-------CeEEEEeCCHHHHH
Confidence            76432     235789999999999999999999999  9999998774       47999999999875

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.

>KOG0124|consensus

Probab=99.89  E-value=8.5e-23  Score=143.40  Aligned_cols=132  Identities=20%  Similarity=0.337  Sum_probs=116.3

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+.+..++.   |+..|..||+|++|.+-.  .+++.||||||+|+-++.|+.|+++|||..++||.|++.....-..
T Consensus       116 vYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPsNmpQ  195 (544)
T KOG0124|consen  116 VYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSNMPQ  195 (544)
T ss_pred             eeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCCCCcc
Confidence            78888887765   999999999999999888  8999999999999999999999999999999999999974432221


Q ss_pred             -----------CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccc-eEeecCcccc
Q psy6353          77 -----------SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGK-YYSGLGGRER  133 (136)
Q Consensus        77 -----------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~-~fv~f~~~e~  133 (136)
                                 ...-.++||..+.++++++||++.|..||+|..|.+.+++.++.+++ +|++|++..+
T Consensus       196 AQpiID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs  264 (544)
T KOG0124|consen  196 AQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQS  264 (544)
T ss_pred             cchHHHHHHHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccc
Confidence                       12457899999999999999999999999999999999998888855 8999988654

>KOG0109|consensus

Probab=99.88  E-value=1.6e-22  Score=138.02  Aligned_cols=118  Identities=24%  Similarity=0.366  Sum_probs=108.9

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESI   78 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~~~   78 (136)
                      |||+|||...+   |+.+|++||+|.+|.|++      .||||..++...++.|+.-|||.+|+|..|.|+-++++  +.
T Consensus         5 LFIGNLp~~~~~~elr~lFe~ygkVlECDIvK------NYgFVHiEdktaaedairNLhgYtLhg~nInVeaSksK--sk   76 (346)
T KOG0109|consen    5 LFIGNLPREATEQELRSLFEQYGKVLECDIVK------NYGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSK--SK   76 (346)
T ss_pred             hhccCCCcccchHHHHHHHHhhCceEeeeeec------ccceEEeecccccHHHHhhcccceecceEEEEEecccc--CC
Confidence            79999999998   999999999999999986      79999999999999999999999999999999988876  34


Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERL  134 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~  134 (136)
                      ...+++|+|+.+.++.++++..|.+||+|+.|.|++       ..+||.|+..|++
T Consensus        77 ~stkl~vgNis~tctn~ElRa~fe~ygpviecdivk-------dy~fvh~d~~eda  125 (346)
T KOG0109|consen   77 ASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVK-------DYAFVHFDRAEDA  125 (346)
T ss_pred             CccccccCCCCccccCHHHhhhhcccCCceeeeeec-------ceeEEEEeeccch
Confidence            778999999999999999999999999999999997       4579999887764

>KOG0123|consensus

Probab=99.86  E-value=4.4e-21  Score=138.50  Aligned_cols=132  Identities=28%  Similarity=0.459  Sum_probs=119.0

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES   77 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~~   77 (136)
                      |||.||++.++   |.++|+.||.|.+|++.. ..| ++|| ||.|.+.+.|++|+..+||..+.++++-|.....+...
T Consensus        79 ~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~er  156 (369)
T KOG0123|consen   79 VFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENG-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERKEER  156 (369)
T ss_pred             eeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCC-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccchhhh
Confidence            79999999999   999999999999999999 666 9999 99999999999999999999999999999766544331


Q ss_pred             --------CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          78 --------IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        78 --------~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                              ..-..+++.|.+.+.+++.|...|+.+|.|.++.++.+..+...+.+||.|.+.|.++
T Consensus       157 ~~~~~~~~~~~t~v~vk~~~~~~~~~~l~~~f~~~g~i~s~~v~~~~~g~~~~~gfv~f~~~e~a~  222 (369)
T KOG0123|consen  157 EAPLGEYKKRFTNVYVKNLEEDSTDEELKDLFSAYGSITSVAVMRDSIGKSKGFGFVNFENPEDAK  222 (369)
T ss_pred             cccccchhhhhhhhheeccccccchHHHHHhhcccCcceEEEEeecCCCCCCCccceeecChhHHH
Confidence                    2346789999999999999999999999999999999998887788999999988764

>KOG0110|consensus

Probab=99.86  E-value=2.2e-21  Score=145.06  Aligned_cols=134  Identities=19%  Similarity=0.329  Sum_probs=114.7

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc-cCC----CceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI-STA----QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP   73 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~-~~~----~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~   73 (136)
                      +|+.||+...|   +..+|.+.|.|.++.|.. ..+    .|.|||||+|.+.++|+.|+.+|+|+.+.|+.|.|+.+..
T Consensus       518 lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~~  597 (725)
T KOG0110|consen  518 LFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISEN  597 (725)
T ss_pred             hhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEeccC
Confidence            68999999888   888999999999998887 333    3669999999999999999999999999999999988872


Q ss_pred             CCC---------CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCC-ccceEeecCcccccc
Q psy6353          74 SSE---------SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATE-NGKYYSGLGGRERLR  135 (136)
Q Consensus        74 ~~~---------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~-~~~~fv~f~~~e~~~  135 (136)
                      ++.         ....++|.|+|||+.++..+++.+|..||++.+|+|+.....+. +|++||+|.+..++.
T Consensus       598 k~~~~~gK~~~~kk~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~  669 (725)
T KOG0110|consen  598 KPASTVGKKKSKKKKGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAK  669 (725)
T ss_pred             ccccccccccccccccceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHH
Confidence            211         12357899999999999999999999999999999998855555 467999999977653

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

Probab=99.86  E-value=1.6e-20  Score=139.86  Aligned_cols=131  Identities=25%  Similarity=0.419  Sum_probs=108.1

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||.|..+.++.  .+|+++|||||+|.+.++|..|+..|||..+.|++|.|.++.....
T Consensus       189 l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~~~~~  268 (457)
T TIGR01622       189 LYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQDSTY  268 (457)
T ss_pred             EEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEccCCCc
Confidence            89999999988   999999999999999988  6779999999999999999999999999999999999998431100


Q ss_pred             --------------------------------------------------------------------------------
Q psy6353          77 --------------------------------------------------------------------------------   76 (136)
Q Consensus        77 --------------------------------------------------------------------------------   76 (136)
                                                                                                      
T Consensus       269 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  348 (457)
T TIGR01622       269 LLDAANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGDGGLLIPGTGSKIALMQKLQRDGIIDPNIPSRYATGALAIMA  348 (457)
T ss_pred             cccchhhhccccccccCCcCCCccchHHHHHhhccCCCCccccCCCccchhhhhcccccccccccccccccccccccccc
Confidence                                                                                            


Q ss_pred             ----------CCCCceEEEcCCCCCCC----------HHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          77 ----------SIKGANLYVSGLPKHMS----------QQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        77 ----------~~~~~~l~v~nl~~~~t----------~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                                ......|++.||....+          .+||++.|++||.|..+.+....   ..|.+||+|.+.|+|.
T Consensus       349 ~~~~~~~~~~~~~~~~l~l~n~~~~~~~~~~~~~~~~~~dv~~e~~k~G~v~~v~v~~~~---~~G~~fV~F~~~e~A~  424 (457)
T TIGR01622       349 RNSFVPSTNNNLATTCLVLSNMFDPATEEEPNFDNEILDDVKEECSKYGGVVHIYVDTKN---SAGKIYLKFSSVDAAL  424 (457)
T ss_pred             CCCCCCcccCCCCCcEEEEecCCCCcccccchHHHHHHHHHHHHHHhcCCeeEEEEeCCC---CceeEEEEECCHHHHH
Confidence                      01234577788754433          36899999999999999987542   3366899999999874

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.

>KOG4205|consensus

Probab=99.85  E-value=7.1e-21  Score=133.75  Aligned_cols=134  Identities=19%  Similarity=0.433  Sum_probs=120.7

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      +||+.|+...+   |++.|++||++.++.+++  .+++++||+||+|++.+.+.+++.. ..+.+.|+.|.+..+.|+..
T Consensus         9 lfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~-~~h~~dgr~ve~k~av~r~~   87 (311)
T KOG4205|consen    9 LFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNA-RTHKLDGRSVEPKRAVSRED   87 (311)
T ss_pred             eeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecc-cccccCCccccceeccCccc
Confidence            68999999888   999999999999999999  8899999999999999999999884 46889999999998887765


Q ss_pred             CC------CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccc-eEeecCccccccC
Q psy6353          77 SI------KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGK-YYSGLGGRERLRR  136 (136)
Q Consensus        77 ~~------~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~-~fv~f~~~e~~~~  136 (136)
                      ..      ...++||++||..++++++++.|.+||.|..+.++.|..+...++ +||.|.++|.+++
T Consensus        88 ~~~~~~~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdk  154 (311)
T KOG4205|consen   88 QTKVGRHLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDK  154 (311)
T ss_pred             ccccccccceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccce
Confidence            43      245899999999999999999999999999999999999998855 9999999998764

>KOG0105|consensus

Probab=99.80  E-value=8.5e-19  Score=113.11  Aligned_cols=127  Identities=20%  Similarity=0.277  Sum_probs=108.7

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC--
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE--   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~--   76 (136)
                      +||+|||..+.   ++++|.+||.|..|.+.. .....+||||+|+++.+|+.|+..-+|..+.|..|+|+++..-..  
T Consensus         9 iyvGNLP~diRekeieDlFyKyg~i~~ieLK~-r~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfprggr~s~   87 (241)
T KOG0105|consen    9 IYVGNLPGDIREKEIEDLFYKYGRIREIELKN-RPGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPRGGRSSS   87 (241)
T ss_pred             EEecCCCcchhhccHHHHHhhhcceEEEEecc-CCCCCCeeEEEecCccchhhhhhcccccccCcceEEEEeccCCCccc
Confidence            79999999987   999999999999988764 333568999999999999999999999999999999987653211  


Q ss_pred             ------------------------CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCccc
Q psy6353          77 ------------------------SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRE  132 (136)
Q Consensus        77 ------------------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e  132 (136)
                                              ......+.|++||++.+++||++...+-|.|....+.+|      +.+-|+|...|
T Consensus        88 ~~~G~y~gggrgGgg~gg~rgppsrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD------g~GvV~~~r~e  161 (241)
T KOG0105|consen   88 DRRGSYSGGGRGGGGGGGRRGPPSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD------GVGVVEYLRKE  161 (241)
T ss_pred             ccccccCCCCCCCCCCCcccCCcccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc------cceeeeeeehh
Confidence                                    124468999999999999999999999999988888877      35679999999


Q ss_pred             ccc
Q psy6353         133 RLR  135 (136)
Q Consensus       133 ~~~  135 (136)
                      +|+
T Consensus       162 DMk  164 (241)
T KOG0105|consen  162 DMK  164 (241)
T ss_pred             hHH
Confidence            885

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

Probab=99.78  E-value=1.7e-18  Score=110.56  Aligned_cols=75  Identities=24%  Similarity=0.367  Sum_probs=70.5

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||+|.++.++.  .+++++|||||+|.+.++|+.|++.+|+..+.|++|+|.++.++..
T Consensus        37 lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~a~~~~~  116 (144)
T PLN03134         37 LFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPANDRPS  116 (144)
T ss_pred             EEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEeCCcCCC
Confidence            89999999998   999999999999999988  6899999999999999999999999999999999999999876543

>KOG0144|consensus

Probab=99.77  E-value=1.3e-18  Score=124.35  Aligned_cols=75  Identities=27%  Similarity=0.442  Sum_probs=68.7

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcC-ceeCC--ceEEEEeeCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNG-LRLQN--KTIKVSYARPS   74 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~-~~~~g--~~l~v~~~~~~   74 (136)
                      |||+-|++..+   ++++|++||.|.+|.+.+ ..+.++|||||.|.+.+.|..|+++||| .++.|  .+|.|+|++++
T Consensus       127 LFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVkFADtq  206 (510)
T KOG0144|consen  127 LFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVKFADTQ  206 (510)
T ss_pred             hhhhhccccccHHHHHHHHHhhCccchhhheecccccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEEecccC
Confidence            68999999886   999999999999999999 9999999999999999999999999999 66765  68999999876


Q ss_pred             CC
Q psy6353          75 SE   76 (136)
Q Consensus        75 ~~   76 (136)
                      ++
T Consensus       207 kd  208 (510)
T KOG0144|consen  207 KD  208 (510)
T ss_pred             CC
Confidence            64

>KOG4206|consensus

Probab=99.76  E-value=8.5e-18  Score=111.43  Aligned_cols=127  Identities=19%  Similarity=0.336  Sum_probs=109.0

Q ss_pred             eeecCCChhhh-------HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCC
Q psy6353           2 VYQTLLNKLFT-------YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS   74 (136)
Q Consensus         2 v~v~nl~~~~~-------l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~   74 (136)
                      +||.||++-+.       |..+|++||.|..|... .+.+.+|.|||.|.+.+.|-.|+.+|+|..+.|+++++.++..+
T Consensus        12 lYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~-kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriqyA~s~   90 (221)
T KOG4206|consen   12 LYINNLNEKIKKDELKRSLYLLFSQFGKILDISAF-KTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQYAKSD   90 (221)
T ss_pred             EeehhccccccHHHHHHHHHHHHHhhCCeEEEEec-CCCCccCceEEEecChhHHHHHHHHhcCCcccCchhheecccCc
Confidence            79999998886       56699999999988766 47788999999999999999999999999999999999987653


Q ss_pred             CC--------------------------------------------------CCCCceEEEcCCCCCCCHHHHHHhhcCC
Q psy6353          75 SE--------------------------------------------------SIKGANLYVSGLPKHMSQQELESLFSPY  104 (136)
Q Consensus        75 ~~--------------------------------------------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~  104 (136)
                      ..                                                  ......+++.|||...+.+.+..+|.+|
T Consensus        91 sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~~~~~~~~~p~p~~~~~~ppn~ilf~~niP~es~~e~l~~lf~qf  170 (221)
T KOG4206|consen   91 SDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHFYNMNRMNLPPPFLAQMAPPNNILFLTNIPSESESEMLSDLFEQF  170 (221)
T ss_pred             cchhhccCceeccccCccccccccccCCcccccccccccccccCCCCccccCCCCceEEEEecCCcchhHHHHHHHHhhC
Confidence            32                                                  1123579999999999999999999999


Q ss_pred             CceEEEEEEeCCCCCCccceEeecCcccc
Q psy6353         105 GRIITSRILCDNLATENGKYYSGLGGRER  133 (136)
Q Consensus       105 G~v~~~~i~~~~~~~~~~~~fv~f~~~e~  133 (136)
                      +....++++.    +.++.+||+|.++-+
T Consensus       171 ~g~keir~i~----~~~~iAfve~~~d~~  195 (221)
T KOG4206|consen  171 PGFKEIRLIP----PRSGIAFVEFLSDRQ  195 (221)
T ss_pred             cccceeEecc----CCCceeEEecchhhh
Confidence            9999999886    455779999998754

>KOG0146|consensus

Probab=99.75  E-value=1.5e-17  Score=112.86  Aligned_cols=75  Identities=27%  Similarity=0.489  Sum_probs=63.3

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcC-ceeCC--ceEEEEeeCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNG-LRLQN--KTIKVSYARPS   74 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~-~~~~g--~~l~v~~~~~~   74 (136)
                      |||+.|.+.-.   ++.+|..||.+.+|.+.+ ..|.+|||+||.|.+.-+|+.||+.||| .++.|  ..|.|++++..
T Consensus        22 lfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK~ADTd  101 (371)
T KOG0146|consen   22 LFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPDGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVKFADTD  101 (371)
T ss_pred             hhhhhhcccccHHHHHHHhcccCCcceeEEecCCCCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEEeccch
Confidence            56777765444   789999999999999999 9999999999999999999999999999 55654  67888887765


Q ss_pred             CC
Q psy6353          75 SE   76 (136)
Q Consensus        75 ~~   76 (136)
                      ++
T Consensus       102 kE  103 (371)
T KOG0146|consen  102 KE  103 (371)
T ss_pred             HH
Confidence            43

>PF00076 RRM_1: RNA recognition motif

Probab=99.75  E-value=1.5e-17  Score=93.52  Aligned_cols=66  Identities=32%  Similarity=0.497  Sum_probs=63.3

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEE
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIK   67 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~   67 (136)
                      |||+|||..++   |+++|++||++..+.+.. .+++++|+|||+|.+.++|+.|+..+||..+.|++|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhcccccccccccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            79999999999   999999999999999999 8999999999999999999999999999999999875

(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 ....

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

Probab=99.75  E-value=4.9e-17  Score=123.18  Aligned_cols=72  Identities=19%  Similarity=0.391  Sum_probs=67.6

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP   73 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~   73 (136)
                      |||+|||..++   |+++|+.||+|.++.+++  .+++++|||||+|.+.++|..|+..||+..++|+.|+|.++.+
T Consensus       207 LfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi~  283 (612)
T TIGR01645       207 IYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVT  283 (612)
T ss_pred             EEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecCC
Confidence            79999999988   999999999999999998  6788999999999999999999999999999999999987653

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.

>KOG0147|consensus

Probab=99.72  E-value=2.6e-18  Score=125.75  Aligned_cols=123  Identities=20%  Similarity=0.307  Sum_probs=107.6

Q ss_pred             HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC--------------
Q psy6353          13 YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE--------------   76 (136)
Q Consensus        13 l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~--------------   76 (136)
                      |.++|+.+|+|..|.++.  .++.+||.|+|+|.+.+++..|+. |.|..+.|.+|.|..+....+              
T Consensus       196 L~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aia-LsGqrllg~pv~vq~sEaeknr~a~~s~a~~~k~~  274 (549)
T KOG0147|consen  196 LEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIA-LSGQRLLGVPVIVQLSEAEKNRAANASPALQGKGF  274 (549)
T ss_pred             HHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhh-hcCCcccCceeEecccHHHHHHHHhcccccccccc
Confidence            899999999999999998  889999999999999999999996 899999999999976543221              


Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCccccccC
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLRR  136 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~~  136 (136)
                      ..+-..|||+||.+++++++++.+|.+||.|..+.++.|..+|.+ +++|++|.+.|.+|+
T Consensus       275 ~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~  335 (549)
T KOG0147|consen  275 TGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARK  335 (549)
T ss_pred             ccchhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHH
Confidence            112233899999999999999999999999999999999977777 559999999998763

>KOG0125|consensus

Probab=99.68  E-value=9.7e-17  Score=111.42  Aligned_cols=73  Identities=22%  Similarity=0.348  Sum_probs=67.9

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS   74 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~   74 (136)
                      |+|+|||..+.   |+.+|++||+|.+|.|+.+...|||||||+|++.+||++|..+|||..+.||+|+|+.+.++
T Consensus        99 LhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~ATar  174 (376)
T KOG0125|consen   99 LHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNATAR  174 (376)
T ss_pred             eEeecCCccccCccHHHHHHhhCceeeEEEEeccCCCCccceEEecChhhHHHHHHHhhcceeeceEEEEeccchh
Confidence            78999999997   99999999999999999966669999999999999999999999999999999999877643

>KOG0122|consensus

Probab=99.67  E-value=2.9e-16  Score=105.18  Aligned_cols=73  Identities=29%  Similarity=0.442  Sum_probs=69.9

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS   74 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~   74 (136)
                      |-|.||+++++   |+++|.+||++..+.+.+  .+|.+||||||+|.+.++|.+|+..|||+-+.+--|+|.|++|+
T Consensus       192 vRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEwskP~  269 (270)
T KOG0122|consen  192 VRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEWSKPS  269 (270)
T ss_pred             eEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEecCCC
Confidence            45889999998   999999999999999999  89999999999999999999999999999999999999999986

>KOG0148|consensus

Probab=99.65  E-value=3.2e-16  Score=106.47  Aligned_cols=102  Identities=15%  Similarity=0.308  Sum_probs=85.2

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeC-----C
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR-----P   73 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~-----~   73 (136)
                      |||+||+..+|   |..||++.|++.+++++..                                 .+++.|+.     +
T Consensus         9 lyvgnld~~vte~~i~~lf~qig~v~~~k~i~~---------------------------------e~~v~wa~~p~nQs   55 (321)
T KOG0148|consen    9 LYVGNLDSTVTEDFIATLFNQIGSVTKTKVIFD---------------------------------ELKVNWATAPGNQS   55 (321)
T ss_pred             EEeeccChhhHHHHHHHHHHhccccccceeehh---------------------------------hhccccccCcccCC
Confidence            89999999999   8999999999999999861                                 22333322     2


Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccc-eEeecCccccccC
Q psy6353          74 SSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGK-YYSGLGGRERLRR  136 (136)
Q Consensus        74 ~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~-~fv~f~~~e~~~~  136 (136)
                      ++.....-.+||+.|.+.++-++|++.|.+||+|.++++++|..++++++ +||.|..+|+|++
T Consensus        56 k~t~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEn  119 (321)
T KOG0148|consen   56 KPTSNQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAEN  119 (321)
T ss_pred             CCccccceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHH
Confidence            22233456799999999999999999999999999999999999999966 8999999999863

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.65  E-value=2.2e-15  Score=84.88  Aligned_cols=66  Identities=27%  Similarity=0.461  Sum_probs=59.8

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEE
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIK   67 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~   67 (136)
                      |||+|||..++   |.++|+.+|.|..+.+.. ..++++|+|||+|.+.++|..|++.+++..+.|+.|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            79999999998   999999999999999998 5589999999999999999999999988999999874

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 ....

>KOG0147|consensus

Probab=99.63  E-value=9.6e-16  Score=112.47  Aligned_cols=69  Identities=33%  Similarity=0.485  Sum_probs=65.4

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEe
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY   70 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~   70 (136)
                      |||+||..+++   ++.+|+.||+|..|.++.  .+|++|||||++|.+.++|..|+.+|||+.+.|+.|+|..
T Consensus       281 l~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~  354 (549)
T KOG0147|consen  281 LYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSV  354 (549)
T ss_pred             hhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEE
Confidence            59999999998   999999999999999999  4999999999999999999999999999999999999864

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

Probab=99.61  E-value=1.8e-14  Score=99.72  Aligned_cols=116  Identities=31%  Similarity=0.472  Sum_probs=100.6

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeC----
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR----   72 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~----   72 (136)
                      |||+|||..++   |.++|.+||.+..+.+..  .++.++|+|||+|.+.++|..|+..++|..+.|+++.+.+..    
T Consensus       118 l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~~~~~  197 (306)
T COG0724         118 LFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQPASQ  197 (306)
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeeccccccc
Confidence            79999999998   999999999999999988  589999999999999999999999999999999999998843    


Q ss_pred             CCCCC--------------------CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCC
Q psy6353          73 PSSES--------------------IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNL  117 (136)
Q Consensus        73 ~~~~~--------------------~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~  117 (136)
                      +....                    .....+++.+++..++..++...|..+|.+....+.....
T Consensus       198 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  262 (306)
T COG0724         198 PRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSKD  262 (306)
T ss_pred             cccccccccchhhhccccccccccccccceeeccccccccchhHHHHhccccccceeeeccCCCC
Confidence            22211                    2346789999999999999999999999996666665443

>KOG0107|consensus

Probab=99.59  E-value=4.5e-15  Score=95.05  Aligned_cols=71  Identities=24%  Similarity=0.371  Sum_probs=65.7

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS   75 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~   75 (136)
                      |||+||+...+   |+..|..||++.+++|.+   .+.|||||+|+++.+|+.|+..|+|..|.|..+.|+.+.-..
T Consensus        13 VYVGnL~~~a~k~eLE~~F~~yG~lrsvWvAr---nPPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G~~   86 (195)
T KOG0107|consen   13 VYVGNLGSRATKRELERAFSKYGPLRSVWVAR---NPPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTGRP   86 (195)
T ss_pred             EEeccCCCCcchHHHHHHHHhcCcceeEEEee---cCCCceEEeccCcccHHHHHhhcCCccccCceEEEEeecCCc
Confidence            89999999998   999999999999999887   778999999999999999999999999999999998776544

>KOG0149|consensus

Probab=99.58  E-value=2.6e-15  Score=100.22  Aligned_cols=70  Identities=20%  Similarity=0.297  Sum_probs=62.6

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR   72 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~   72 (136)
                      |||++|+....   |+++|++||+|.+..++.  .+|+|||||||+|.|.+.|.+|++.- .-.|+||+..|+.+.
T Consensus        15 ifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp-~piIdGR~aNcnlA~   89 (247)
T KOG0149|consen   15 IFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDP-NPIIDGRKANCNLAS   89 (247)
T ss_pred             EEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCC-CCcccccccccchhh
Confidence            79999999887   999999999999998888  89999999999999999999999854 466899998887543

>KOG1457|consensus

Probab=99.58  E-value=2.3e-14  Score=95.26  Aligned_cols=130  Identities=18%  Similarity=0.250  Sum_probs=101.8

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc-cCC--CceeeEEEEcCCHHHHHHHHHHHcCceeC---CceEEEEeeC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI-STA--QSLGYGFVNYHRPEDAEKAINTLNGLRLQ---NKTIKVSYAR   72 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~-~~~--~~kg~~fv~f~~~~~a~~a~~~~~~~~~~---g~~l~v~~~~   72 (136)
                      |||++||..+.   |..+|..|-......+.. ..+  -.+-+||++|.+..+|.+|+++|||..++   ++.|++..++
T Consensus        37 LFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLhiElAK  116 (284)
T KOG1457|consen   37 LFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLHIELAK  116 (284)
T ss_pred             eeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeEeeehh
Confidence            79999999998   888899888777776655 221  23579999999999999999999999987   7788887765


Q ss_pred             CCCCC---------------------------------------------------------------------------
Q psy6353          73 PSSES---------------------------------------------------------------------------   77 (136)
Q Consensus        73 ~~~~~---------------------------------------------------------------------------   77 (136)
                      ...+.                                                                           
T Consensus       117 SNtK~kr~k~sgtP~~s~al~~~~~~~~qr~sa~~qhd~~l~~p~~l~~~~~a~al~~~~~t~~~~l~a~~~~~P~a~a~  196 (284)
T KOG1457|consen  117 SNTKRKRRKGSGTPGSSPALVIDNRNKEQRKSADDQHDEGLSDPDELQEPGNADALKENDTTKSEALSAPDSKAPSANAH  196 (284)
T ss_pred             cCcccccCCCCCCCCCCccccccccChhhcccchhhccccccCccccCCccccccCCCccccchhhhhhhhhcCCcccch
Confidence            43220                                                                           


Q ss_pred             -----------CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCccccc
Q psy6353          78 -----------IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERL  134 (136)
Q Consensus        78 -----------~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~  134 (136)
                                 ..-.+|||-||.++++|++|+.+|+.|......+|-.   .|....+|++|++-|.+
T Consensus       197 l~ks~q~~~~~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~---~~g~~vaf~~~~~~~~a  261 (284)
T KOG1457|consen  197 LEKSSQGGSGARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRA---RGGMPVAFADFEEIEQA  261 (284)
T ss_pred             hhhhhcccccchhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEec---CCCcceEeecHHHHHHH
Confidence                       0124899999999999999999999998776666653   34446789999877654

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.57  E-value=1.5e-14  Score=104.23  Aligned_cols=74  Identities=23%  Similarity=0.345  Sum_probs=67.6

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCC--ceEEEEeeCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQN--KTIKVSYARPS   74 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g--~~l~v~~~~~~   74 (136)
                      |||.|||..++   |+++|++||.|..+.+++  .+++++|||||+|.+.++|++|+++||+..+.+  ++|+|.++...
T Consensus       196 lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~a~~~  275 (346)
T TIGR01659       196 LYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRLAEEH  275 (346)
T ss_pred             eEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCcc
Confidence            79999999998   999999999999999988  689999999999999999999999999998865  78899887754


Q ss_pred             C
Q psy6353          75 S   75 (136)
Q Consensus        75 ~   75 (136)
                      .
T Consensus       276 ~  276 (346)
T TIGR01659       276 G  276 (346)
T ss_pred             c
Confidence            3

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

>KOG4211|consensus

Probab=99.57  E-value=3.7e-14  Score=103.13  Aligned_cols=133  Identities=18%  Similarity=0.191  Sum_probs=104.2

Q ss_pred             eeecCCChhhhHHHHhccCC--CeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC---
Q psy6353           2 VYQTLLNKLFTYEKVHLGFS--DAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE---   76 (136)
Q Consensus         2 v~v~nl~~~~~l~~~f~~~G--~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~---   76 (136)
                      |-+..||.+.|.+++...|+  .|.++.+.+.+|+..|-|||+|.+.++++.|++ .+...+..|.|.|-.+.+...   
T Consensus        13 vr~rGLPwsat~~ei~~Ff~~~~I~~~~~~r~~Gr~sGeA~Ve~~seedv~~Alk-kdR~~mg~RYIEVf~~~~~e~d~~   91 (510)
T KOG4211|consen   13 VRLRGLPWSATEKEILDFFSNCGIENLEIPRRNGRPSGEAYVEFTSEEDVEKALK-KDRESMGHRYIEVFTAGGAEADWV   91 (510)
T ss_pred             EEecCCCccccHHHHHHHHhcCceeEEEEeccCCCcCcceEEEeechHHHHHHHH-hhHHHhCCceEEEEccCCcccccc
Confidence            44578999999555555544  346666666889999999999999999999999 578889999999976543221   


Q ss_pred             --------CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEE-EEEEeCCCCCCccceEeecCcccccc
Q psy6353          77 --------SIKGANLYVSGLPKHMSQQELESLFSPYGRIIT-SRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        77 --------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~-~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                              ......|.+++||..+|++||.++|+..-.|.. +-++.++.....+.|||.|++.|.+.
T Consensus        92 ~~~~g~~s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae  159 (510)
T KOG4211|consen   92 MRPGGPNSSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAE  159 (510)
T ss_pred             ccCCCCCCCCCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHH
Confidence                    125568999999999999999999998876665 45666666666677999999999874

>KOG0126|consensus

Probab=99.55  E-value=5.7e-16  Score=99.78  Aligned_cols=71  Identities=23%  Similarity=0.341  Sum_probs=67.2

Q ss_pred             CeeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEee
Q psy6353           1 MVYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA   71 (136)
Q Consensus         1 ~v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~   71 (136)
                      |+|+++||...|   |-..|++||.+.+|.+++  .||+|+||||+.|.+..+...|+.-+||..|.||.|+|.+.
T Consensus        37 ~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv  112 (219)
T KOG0126|consen   37 YIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHV  112 (219)
T ss_pred             EEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeec
Confidence            689999999999   788899999999999999  89999999999999999999999999999999999999654

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.55  E-value=2.8e-14  Score=97.70  Aligned_cols=70  Identities=17%  Similarity=0.219  Sum_probs=63.7

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP   73 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~   73 (136)
                      |||+|||...+   |+++|++||+|.++.+++. +.++|||||+|.++++|+.|+. |||..+.|++|.|.++..
T Consensus         7 VfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d-~~~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~   79 (260)
T PLN03120          7 VKVSNVSLKATERDIKEFFSFSGDIEYVEMQSE-NERSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAED   79 (260)
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeec-CCCCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccC
Confidence            89999999998   9999999999999999872 2357999999999999999996 999999999999998764

>KOG4212|consensus

Probab=99.54  E-value=1.8e-13  Score=98.74  Aligned_cols=131  Identities=15%  Similarity=0.269  Sum_probs=112.3

Q ss_pred             CeeecCCChhhh---HHHHhc-cCCCeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCC
Q psy6353           1 MVYQTLLNKLFT---YEKVHL-GFSDAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS   75 (136)
Q Consensus         1 ~v~v~nl~~~~~---l~~~f~-~~G~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~   75 (136)
                      |||+.|+|..+.   |++++. +-|+|..|.+.. .+|+++|||.|+|++++.+++|++.||.+.+.||+|.++-....+
T Consensus        46 ~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd~d~q  125 (608)
T KOG4212|consen   46 SVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKEDHDEQ  125 (608)
T ss_pred             eEEEecCcchhhhHhHHHHHHHhcCceEeeeeecccCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEeccCchh
Confidence            689999999987   999995 789999999998 999999999999999999999999999999999999997433211


Q ss_pred             C-------------------------------------------------------------------------------
Q psy6353          76 E-------------------------------------------------------------------------------   76 (136)
Q Consensus        76 ~-------------------------------------------------------------------------------   76 (136)
                      .                                                                               
T Consensus       126 ~~~~~~~~r~g~~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D~Dr~sr~~~t~t~~~~~~~~~~~~lfgl~~~Flr  205 (608)
T KOG4212|consen  126 RDQYGRIVRDGGGGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRDDDRLSRRNNTNTMSNDYNNSSNYNLFGLSASFLR  205 (608)
T ss_pred             hhhhhheeeccCcccccCcceecccccccccCCCCccccCCCCcccccccccccCccccccccccchhhhcccchhhhhh
Confidence            0                                                                               


Q ss_pred             ------CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcc
Q psy6353          77 ------SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGR  131 (136)
Q Consensus        77 ------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~  131 (136)
                            ..-..++||.||...+..+.|.+.|.--|.|..+.+--|+...+.+.+-.++++.
T Consensus       206 ~~h~f~pPl~~k~fvanl~~~vg~~kL~qvfgmAGkv~~vdf~idKeG~s~G~~vi~y~hp  266 (608)
T KOG4212|consen  206 SLHIFSPPLHNKVFVANLDYKVGNKKLKQVFGMAGKVQSVDFSIDKEGNSRGFAVIEYDHP  266 (608)
T ss_pred             hccCCCCCccceeeeeccccccchHHHHHHhccceeeeeeceeeccccccCCeeEEEecch
Confidence                  0112578999999999999999999999999999999999887777777777654

>PF13893 RRM_5: RNA recognition motif

Probab=99.54  E-value=9e-14  Score=74.98  Aligned_cols=56  Identities=34%  Similarity=0.563  Sum_probs=50.0

Q ss_pred             HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEee
Q psy6353          13 YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA   71 (136)
Q Consensus        13 l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~   71 (136)
                      |.++|++||+|.++.+....   +++|||+|.+.++|+.|++.+||..+.|++|+|.++
T Consensus         1 L~~~f~~fG~V~~i~~~~~~---~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK---RGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS---TTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC---CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            57899999999999987611   589999999999999999999999999999999875

(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 ....

>PLN03213 repressor of silencing 3; Provisional

Probab=99.53  E-value=2.6e-14  Score=104.42  Aligned_cols=117  Identities=10%  Similarity=0.181  Sum_probs=85.6

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCH--HHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRP--EDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~--~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+||+..++   |+++|+.||.|.++.|++.+|  +|||||+|.+.  .++.+|+.+|||..+.|+.|+|..++|.--
T Consensus        13 IYVGNLSydVTEDDLravFSeFGsVkdVEIpRETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKAKP~YL   90 (759)
T PLN03213         13 LHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKAKEHYL   90 (759)
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeeccHHHH
Confidence            79999999999   999999999999999998666  89999999987  689999999999999999999998876310


Q ss_pred             -----------CCCCceEEEcCCCCC-CCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEe
Q psy6353          77 -----------SIKGANLYVSGLPKH-MSQQELESLFSPYGRIITSRILCDNLATENGKYYS  126 (136)
Q Consensus        77 -----------~~~~~~l~v~nl~~~-~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv  126 (136)
                                 .....++-   +|.. ....+|+-+|...+++   +-++-..+|++++.|=
T Consensus        91 eRLkrEReea~s~~~~~~k---l~k~~~e~~qLnifFPrLrKv---KslPfsGTGKHkYSFr  146 (759)
T PLN03213         91 ARLKREWEAASSTSDNTIK---APSDSPPATHLNIFFPRLRKV---KAMPLSGTGKHKYSFQ  146 (759)
T ss_pred             HHHHHHHHHhhcccccccc---ccccCCccceeeEeccccccc---cccccCCCccceeeee
Confidence                       01112222   2222 2333455566555544   4344556777766653

>smart00362 RRM_2 RNA recognition motif

Probab=99.52  E-value=1.2e-13  Score=77.19  Aligned_cols=67  Identities=31%  Similarity=0.477  Sum_probs=61.2

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEE
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKV   68 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v   68 (136)
                      ||+.|||...+   |+++|++||++..+.+....+.++|+|||+|.+.++|+.|+..+++..+.|+++.+
T Consensus         2 v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v   71 (72)
T smart00362        2 LFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDTGKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRV   71 (72)
T ss_pred             EEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCCCCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEee
Confidence            79999999888   99999999999999888733778999999999999999999999999999998876

>KOG0106|consensus

Probab=99.51  E-value=2e-14  Score=96.07  Aligned_cols=122  Identities=25%  Similarity=0.371  Sum_probs=102.3

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCC---
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS---   75 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~---   75 (136)
                      ||+++||+...   ++.+|..||.+..+.+..      ||+||+|.+..+|+.|+..+|+..+.+-.+.+.++....   
T Consensus         4 v~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk~------gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~~~~~   77 (216)
T KOG0106|consen    4 VYIGRLPYRARERDVERFFKGYGKIPDADMKN------GFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGKRRGR   77 (216)
T ss_pred             eeecccCCccchhHHHHHHhhccccccceeec------ccceeccCchhhhhcccchhcCceecceeeeeeccccccccc
Confidence            79999999988   999999999999998764      899999999999999999999999998888887776310   


Q ss_pred             ---C--------------CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCccccccC
Q psy6353          76 ---E--------------SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLRR  136 (136)
Q Consensus        76 ---~--------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~~  136 (136)
                         .              ......+.+.+++....+.+|.+.|.++|++....+       ....++|+|+.+|+|++
T Consensus        78 g~~~~g~r~~~~~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~-------~~~~~~v~Fs~~~da~r  148 (216)
T KOG0106|consen   78 GRPRGGDRRSDSRRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA-------RRNFAFVEFSEQEDAKR  148 (216)
T ss_pred             CCCCCCCccchhhccCCcccccceeeeccchhhhhHHHHhhhhcccCCCchhhh-------hccccceeehhhhhhhh
Confidence               0              124467889999999999999999999999855444       22557999999999875

>KOG4207|consensus

Probab=99.49  E-value=3.2e-14  Score=93.53  Aligned_cols=71  Identities=25%  Similarity=0.381  Sum_probs=64.7

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR   72 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~   72 (136)
                      |-|.||-.-.+   |..+|++||.|-+|.|++  .+++++|||||.|.+..+|+.|+.+|+|..+.|+.|.|+.+.
T Consensus        16 LkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~ar   91 (256)
T KOG4207|consen   16 LKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMAR   91 (256)
T ss_pred             EEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehhhh
Confidence            45678877666   999999999999999999  899999999999999999999999999999999999886554

>smart00360 RRM RNA recognition motif

Probab=99.48  E-value=2.4e-13  Score=75.60  Aligned_cols=65  Identities=32%  Similarity=0.471  Sum_probs=59.2

Q ss_pred             ecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEE
Q psy6353           4 QTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKV   68 (136)
Q Consensus         4 v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v   68 (136)
                      ++|||..++   |+++|++||.+..+.+..  .++.++|+|||+|.+.++|..|+..+++..+.|+.+.+
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            478888887   899999999999998888  46889999999999999999999999999999998876

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.48  E-value=2.5e-13  Score=91.82  Aligned_cols=69  Identities=13%  Similarity=0.088  Sum_probs=62.8

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR   72 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~   72 (136)
                      |||+||+...|   |+++|+++|+|.+|.+++ .+..+|+|||+|.+++.++.|+. |||..|.+++|.|..+.
T Consensus         8 V~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~-D~et~gfAfVtF~d~~aaetAll-LnGa~l~d~~I~It~~~   79 (243)
T PLN03121          8 AEVTNLSPKATEKDVYDFFSHCGAIEHVEIIR-SGEYACTAYVTFKDAYALETAVL-LSGATIVDQRVCITRWG   79 (243)
T ss_pred             EEEecCCCCCCHHHHHHHHHhcCCeEEEEEec-CCCcceEEEEEECCHHHHHHHHh-cCCCeeCCceEEEEeCc
Confidence            79999999999   999999999999999987 34556899999999999999997 99999999999997654

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

Probab=99.45  E-value=2.1e-13  Score=87.10  Aligned_cols=58  Identities=14%  Similarity=0.390  Sum_probs=53.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ...++|||+|||..+++++|+++|.+||.|.++.++.|+.++.+ +++||+|.+.|+|.
T Consensus        32 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~   90 (144)
T PLN03134         32 LMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAAT   90 (144)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHH
Confidence            35678999999999999999999999999999999999988877 55999999999875

>smart00361 RRM_1 RNA recognition motif

Probab=99.45  E-value=5.9e-13  Score=75.00  Aligned_cols=56  Identities=27%  Similarity=0.436  Sum_probs=48.5

Q ss_pred             HHHHhc----cCCCeeEEE-EEc--cC--CCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEE
Q psy6353          13 YEKVHL----GFSDAEICV-FLI--ST--AQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKV   68 (136)
Q Consensus        13 l~~~f~----~~G~v~~~~-~~~--~~--~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v   68 (136)
                      |+++|+    +||.|.++. ++.  .+  ++++|+|||+|.+.++|..|+..|||..+.|+.|++
T Consensus         5 l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~   69 (70)
T smart00361        5 FEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKA   69 (70)
T ss_pred             HHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence            456666    999999985 433  44  899999999999999999999999999999999876

>KOG0111|consensus

Probab=99.44  E-value=2e-13  Score=90.70  Aligned_cols=74  Identities=28%  Similarity=0.480  Sum_probs=70.8

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS   75 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~   75 (136)
                      |||+.|-++++   |...|-+||.|..|.++.  .+++.+|||||+|...++|.+|+.-||+.++.||.|+|.++.|..
T Consensus        13 lYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~AkP~k   91 (298)
T KOG0111|consen   13 LYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAKPEK   91 (298)
T ss_pred             EEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeecCCcc
Confidence            79999999999   899999999999999999  889999999999999999999999999999999999999999865

>KOG1190|consensus

Probab=99.44  E-value=3.5e-12  Score=91.30  Aligned_cols=127  Identities=18%  Similarity=0.266  Sum_probs=100.7

Q ss_pred             eeecCCCh-hhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCCC
Q psy6353           2 VYQTLLNK-LFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES   77 (136)
Q Consensus         2 v~v~nl~~-~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~~   77 (136)
                      |-|+||.+ .+|   |..+|+-||.|..|++....   +--|+|.+.+...|+.|++.|+|+.++|++|++.+++...-.
T Consensus       300 llvsnln~~~VT~d~LftlFgvYGdVqRVkil~nk---kd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH~~vq  376 (492)
T KOG1190|consen  300 LLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNK---KDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKHTNVQ  376 (492)
T ss_pred             EEEecCchhccchhHHHHHHhhhcceEEEEeeecC---CcceeeeecchhHHHHHHHHhhcceecCceEEEeeccCcccc
Confidence            34566654 445   88899999999999999822   245999999999999999999999999999999877632210


Q ss_pred             -----------------------------------CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCcc
Q psy6353          78 -----------------------------------IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENG  122 (136)
Q Consensus        78 -----------------------------------~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~  122 (136)
                                                         .+..++..+|+|+++++++++.+|..-|-........   .+.++
T Consensus       377 lp~egq~d~glT~dy~~spLhrfkkpgsKN~~ni~PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkff---~kd~k  453 (492)
T KOG1190|consen  377 LPREGQEDQGLTKDYGNSPLHRFKKPGSKNYQNIFPPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFF---QKDRK  453 (492)
T ss_pred             CCCCCCccccccccCCCCchhhccCcccccccccCCchhheeeccCCcccchhHHHHhhhcCCceEEeeeec---CCCcc
Confidence                                               2346899999999999999999999988765544333   23557


Q ss_pred             ceEeecCccccc
Q psy6353         123 KYYSGLGGRERL  134 (136)
Q Consensus       123 ~~fv~f~~~e~~  134 (136)
                      .+.+.+++.|++
T Consensus       454 mal~q~~sveeA  465 (492)
T KOG1190|consen  454 MALPQLESVEEA  465 (492)
T ss_pred             eeecccCChhHh
Confidence            789999999886

>PF00076 RRM_1: RNA recognition motif

Probab=99.43  E-value=1.6e-13  Score=76.94  Aligned_cols=53  Identities=25%  Similarity=0.553  Sum_probs=48.2

Q ss_pred             EEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          83 LYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        83 l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      |||+|||+++|+++|+++|++||.|..+.+..+......+.|||+|+++|+|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~a~V~F~~~~~a~   53 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEEDAE   53 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHHHH
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhcccccccccccccccceEEEEEcCHHHHH
Confidence            79999999999999999999999999999999855555577999999999875

(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 ....

>KOG0121|consensus

Probab=99.43  E-value=3.6e-13  Score=82.35  Aligned_cols=71  Identities=24%  Similarity=0.392  Sum_probs=64.7

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR   72 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~   72 (136)
                      |||+||+...+   +.++|++.|+|..|.+-.  .+..+.|||||+|.+.++|..|+.-++|..+..++|++.|.-
T Consensus        39 vyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D~  114 (153)
T KOG0121|consen   39 VYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWDA  114 (153)
T ss_pred             EEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeeccc
Confidence            89999999888   899999999999886555  788899999999999999999999999999999999997643

>KOG0113|consensus

Probab=99.42  E-value=7e-13  Score=91.38  Aligned_cols=70  Identities=19%  Similarity=0.349  Sum_probs=65.6

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEee
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA   71 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~   71 (136)
                      |||+-|+...+   |+..|+.||+|..|.+++  .+|+++|||||+|.+.-+...|.+..+|..|.|+.|-|..-
T Consensus       104 LFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDvE  178 (335)
T KOG0113|consen  104 LFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDVE  178 (335)
T ss_pred             eeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEec
Confidence            78999998887   999999999999999999  89999999999999999999999999999999999988653

>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=99.41  E-value=2.8e-12  Score=71.83  Aligned_cols=69  Identities=28%  Similarity=0.477  Sum_probs=62.6

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEe
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY   70 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~   70 (136)
                      |++++||...+   ++++|+.+|.+..+.+.. ..+.++|+|||+|.+.++|..|++.+++..+.|+.+.+.+
T Consensus         2 i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           2 LFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             EEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            68999999887   899999999999999988 5557899999999999999999999999999999988753

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).

>KOG0114|consensus

Probab=99.40  E-value=2e-12  Score=76.35  Aligned_cols=73  Identities=25%  Similarity=0.306  Sum_probs=65.0

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS   75 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~   75 (136)
                      |||.|||..+|   ..++|.+||.|..|++- .+...+|-|||.|++..+|..|+..|+|..+.++.+.+.+.++..
T Consensus        21 LyirNLp~~ITseemydlFGkyg~IrQIRiG-~~k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq~~~   96 (124)
T KOG0114|consen   21 LYIRNLPFKITSEEMYDLFGKYGTIRQIRIG-NTKETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQPED   96 (124)
T ss_pred             EEEecCCccccHHHHHHHhhcccceEEEEec-CccCcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecCHHH
Confidence            89999999999   78899999999877765 466678999999999999999999999999999999998877643

>KOG0130|consensus

Probab=99.40  E-value=9.7e-13  Score=81.22  Aligned_cols=73  Identities=21%  Similarity=0.344  Sum_probs=67.6

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS   74 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~   74 (136)
                      |||.++.++.+   +.+.|.-||+|+++.+-.  .+|-.||||+|+|.+...|++|+.++||..+.|+.+.|.|+..+
T Consensus        75 i~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~Fv~  152 (170)
T KOG0130|consen   75 IFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWCFVK  152 (170)
T ss_pred             EEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEEEec
Confidence            78999998888   899999999999998877  88999999999999999999999999999999999999887544

>KOG0108|consensus

Probab=99.38  E-value=1.2e-12  Score=96.16  Aligned_cols=75  Identities=23%  Similarity=0.394  Sum_probs=70.5

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|+|.+++   |.++|+..|+|.+++++.  .+|+++||||++|.+.++|..|+..|||.++.|++|++.++...+.
T Consensus        21 v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~~~~  100 (435)
T KOG0108|consen   21 VFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASNRKN  100 (435)
T ss_pred             eEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeecccccch
Confidence            79999999998   999999999999999999  8999999999999999999999999999999999999998775543

>KOG0117|consensus

Probab=99.36  E-value=2.3e-12  Score=93.06  Aligned_cols=72  Identities=31%  Similarity=0.403  Sum_probs=66.2

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESI   78 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~~~   78 (136)
                      |||.||+.++|   |+++|++||.|..|+.++      -||||.|.++++|-+|++.+||..|.|..|.|..++|..+..
T Consensus       262 LYVRNL~~~tTeE~lk~~F~~~G~veRVkk~r------DYaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAKP~~k~k  335 (506)
T KOG0117|consen  262 LYVRNLMESTTEETLKKLFNEFGKVERVKKPR------DYAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAKPVDKKK  335 (506)
T ss_pred             eeeeccchhhhHHHHHHHHHhccceEEeeccc------ceeEEeecchHHHHHHHHHhcCceecCceEEEEecCChhhhc
Confidence            89999999999   999999999999998664      599999999999999999999999999999999999876543


Q ss_pred             C
Q psy6353          79 K   79 (136)
Q Consensus        79 ~   79 (136)
                      .
T Consensus       336 ~  336 (506)
T KOG0117|consen  336 K  336 (506)
T ss_pred             c
Confidence            3

>KOG0124|consensus

Probab=99.32  E-value=2.4e-11  Score=86.23  Aligned_cols=71  Identities=20%  Similarity=0.396  Sum_probs=61.8

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR   72 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~   72 (136)
                      +||..+....+   |+..|+-||+|..|.+.+  ..+..|||||++|.+..+.+.|+..||=+.++|+.|++..+.
T Consensus       213 iYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~v  288 (544)
T KOG0124|consen  213 IYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCV  288 (544)
T ss_pred             EEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEeccccc
Confidence            57766665555   999999999999999999  556689999999999999999999999999999999996543

>KOG0120|consensus

Probab=99.32  E-value=2.5e-12  Score=95.28  Aligned_cols=134  Identities=19%  Similarity=0.312  Sum_probs=100.8

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      +|+++||..++   ++++.+.||++....++.  .+|.++||||.+|.++...+.|+..+||..++++++.+..+.+...
T Consensus       292 i~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~g~~  371 (500)
T KOG0120|consen  292 IFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIVGAS  371 (500)
T ss_pred             hhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhccch
Confidence            47889998887   899999999999998888  6789999999999999999999999999999999999876543221


Q ss_pred             C------------------------CCCceEEEcCCC--CCC-C-------HHHHHHhhcCCCceEEEEEEeC-CCCC--
Q psy6353          77 S------------------------IKGANLYVSGLP--KHM-S-------QQELESLFSPYGRIITSRILCD-NLAT--  119 (136)
Q Consensus        77 ~------------------------~~~~~l~v~nl~--~~~-t-------~~~l~~~f~~~G~v~~~~i~~~-~~~~--  119 (136)
                      .                        .....|...|+=  ..+ +       -++++.-+.+||.|..|.++++ ....  
T Consensus       372 ~~~~~~~~~~~~~~~i~~~~~q~~g~~t~Vl~L~n~Vt~deLkdd~EyeeIlEdvr~ec~k~g~v~~v~ipr~~~~~~~~  451 (500)
T KOG0120|consen  372 NANVNFNISQSQVPGIPLLMTQMAGIPTEVLCLTNVVTPDELKDDEEYEEILEDVRTECAKFGAVRSVEIPRPYPDENPV  451 (500)
T ss_pred             hccccCCccccccccchhhhcccCCCcchhhhhhhcCCHHHhcchHHHHHHHHHHHHHhcccCceeEEecCCCCCCCCcC
Confidence            1                        111222222221  111 1       1467788899999999999998 3222  


Q ss_pred             -CccceEeecCcccccc
Q psy6353         120 -ENGKYYSGLGGRERLR  135 (136)
Q Consensus       120 -~~~~~fv~f~~~e~~~  135 (136)
                       ..|.-||+|.+.|++.
T Consensus       452 ~G~GkVFVefas~ed~q  468 (500)
T KOG0120|consen  452 PGTGKVFVEFADTEDSQ  468 (500)
T ss_pred             CCcccEEEEecChHHHH
Confidence             2255799999998764

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.31  E-value=3.4e-12  Score=71.71  Aligned_cols=53  Identities=21%  Similarity=0.497  Sum_probs=45.9

Q ss_pred             EEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          83 LYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        83 l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      |+|+|||+++++++|.++|+.||.|..+.+..++.+...+.|||+|.+.|+|.
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~   53 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKDGQSRGFAFVEFSSEEDAK   53 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTTSSEEEEEEEEESSHHHHH
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeeccccCCEEEEEeCCHHHHH
Confidence            78999999999999999999999999999999987444466999999999875

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 ....

>KOG1548|consensus

Probab=99.30  E-value=2.9e-11  Score=84.96  Aligned_cols=131  Identities=15%  Similarity=0.169  Sum_probs=103.8

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeE--------EEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEE
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEI--------CVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVS   69 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~--------~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~   69 (136)
                      |||+|||..+|   ..++|+++|-|..        |++-+ ..|+.||=|.+.|...+++..|+.-|++..+.|+.|+|.
T Consensus       137 VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~~~rVe  216 (382)
T KOG1548|consen  137 VYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDELRGKKLRVE  216 (382)
T ss_pred             EEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCcccccCcEEEEe
Confidence            89999999999   7788999997643        77777 889999999999999999999999999999999999997


Q ss_pred             eeCCCCC--------------------------------------CCCCceEEEcCCC----CCCC-------HHHHHHh
Q psy6353          70 YARPSSE--------------------------------------SIKGANLYVSGLP----KHMS-------QQELESL  100 (136)
Q Consensus        70 ~~~~~~~--------------------------------------~~~~~~l~v~nl~----~~~t-------~~~l~~~  100 (136)
                      .++-...                                      ....++|.++|+=    ...+       +++|.+-
T Consensus       217 rAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~~dw~pd~~~~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~ee  296 (382)
T KOG1548|consen  217 RAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKLLDWRPDRDDPSKARADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEE  296 (382)
T ss_pred             hhhhhhccCcCcccccccccccHHHHHHHHHhhcccCCCccccccccCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHH
Confidence            6541110                                      1235678888872    1223       4677888


Q ss_pred             hcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353         101 FSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus       101 f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      +.+||.|..+.+.-.+   ..|.+-|.|.+.|+|.
T Consensus       297 c~K~G~v~~vvv~d~h---PdGvvtV~f~n~eeA~  328 (382)
T KOG1548|consen  297 CEKFGQVRKVVVYDRH---PDGVVTVSFRNNEEAD  328 (382)
T ss_pred             HHHhCCcceEEEeccC---CCceeEEEeCChHHHH
Confidence            9999999999888543   3355789999999873

>KOG0125|consensus

Probab=99.29  E-value=3.6e-12  Score=88.95  Aligned_cols=80  Identities=19%  Similarity=0.333  Sum_probs=65.6

Q ss_pred             HcCceeCCceEEEEeeCCCCCCCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          56 LNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        56 ~~~~~~~g~~l~v~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      -++....|..+....+..........+|+|+|||+...+.||+.+|.+||+|.+|.|+.+. .|++|++||.|++.+++.
T Consensus        72 ~~~~~t~g~~~~~~~st~s~s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNE-RGSKGFGFVTmen~~dad  150 (376)
T KOG0125|consen   72 SNGAPTDGQPIQTQPSTNSSSKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNE-RGSKGFGFVTMENPADAD  150 (376)
T ss_pred             cCCCCCCCCccccCCCCcCCCCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEecc-CCCCccceEEecChhhHH
Confidence            3455556666666655555555677899999999999999999999999999999999876 556699999999999886


Q ss_pred             C
Q psy6353         136 R  136 (136)
Q Consensus       136 ~  136 (136)
                      |
T Consensus       151 R  151 (376)
T KOG0125|consen  151 R  151 (376)
T ss_pred             H
Confidence            5

>KOG0149|consensus

Probab=99.28  E-value=4.2e-12  Score=85.02  Aligned_cols=58  Identities=17%  Similarity=0.345  Sum_probs=54.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccc-eEeecCccccccC
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGK-YYSGLGGRERLRR  136 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~-~fv~f~~~e~~~~  136 (136)
                      .-++|||++|+-.++.+.|++.|.+||+|++..++.|+.+|++++ +||.|.+.|++.|
T Consensus        11 ~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~r   69 (247)
T KOG0149|consen   11 TFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATR   69 (247)
T ss_pred             eEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHH
Confidence            457899999999999999999999999999999999999999966 8999999999876

>KOG0146|consensus

Probab=99.28  E-value=5.2e-12  Score=86.25  Aligned_cols=75  Identities=28%  Similarity=0.502  Sum_probs=68.4

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||=.||.++.   |-.+|-.||-|.+.++..  .+++||+||||.|.++.+|+.||.+|||+.|+-++|+|..-+|+..
T Consensus       288 lFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQLKRPkda  367 (371)
T KOG0146|consen  288 LFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQLKRPKDA  367 (371)
T ss_pred             EEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhhhcCcccc
Confidence            68888999987   889999999998887766  8999999999999999999999999999999999999988877754

>KOG4208|consensus

Probab=99.26  E-value=2.1e-11  Score=80.23  Aligned_cols=73  Identities=23%  Similarity=0.285  Sum_probs=62.5

Q ss_pred             eeecCCChhhh---HHHHhccC-CCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGF-SDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS   74 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~-G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~   74 (136)
                      +|+..+|..+-   +..+|.++ |.+...++-|  .||.|||||||+|.+.+.|..|.+.||+..+.++-|.|..-.|.
T Consensus        52 ~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~vmppe  130 (214)
T KOG4208|consen   52 VYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHVMPPE  130 (214)
T ss_pred             eeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEEeCch
Confidence            56667776554   77788887 7888888877  89999999999999999999999999999999999999876654

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.26  E-value=1e-11  Score=85.26  Aligned_cols=55  Identities=15%  Similarity=0.198  Sum_probs=49.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ..++|||+|||+.+|+++|+++|+.||+|.+|.|+++..  .++.+||+|.++++++
T Consensus         3 ~~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~--~~GfAFVtF~d~eaAe   57 (260)
T PLN03120          3 QVRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE--RSQIAYVTFKDPQGAE   57 (260)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC--CCCEEEEEeCcHHHHH
Confidence            357899999999999999999999999999999999874  3578999999998874

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.25  E-value=1.3e-11  Score=83.57  Aligned_cols=55  Identities=18%  Similarity=0.215  Sum_probs=49.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      .+.+|+|+||++.+|+++|+++|+.||+|.+|.|++|..+  .+.+||+|.++++++
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~et--~gfAfVtF~d~~aae   58 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSGEY--ACTAYVTFKDAYALE   58 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCCCc--ceEEEEEECCHHHHH
Confidence            5689999999999999999999999999999999998433  367999999998764

>KOG0122|consensus

Probab=99.24  E-value=1.1e-11  Score=83.49  Aligned_cols=57  Identities=23%  Similarity=0.387  Sum_probs=53.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccc-eEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGK-YYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~-~fv~f~~~e~~~  135 (136)
                      ..++|.|.||+.++++.+|.++|.+||.|..+.|.+|+.+|.++| |||.|.++|+|-
T Consensus       188 D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~  245 (270)
T KOG0122|consen  188 DEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAA  245 (270)
T ss_pred             ccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHH
Confidence            567899999999999999999999999999999999999999955 999999999874

>KOG0110|consensus

Probab=99.23  E-value=2.5e-11  Score=91.91  Aligned_cols=130  Identities=18%  Similarity=0.257  Sum_probs=101.2

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeC------
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR------   72 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~------   72 (136)
                      ++++|||....   +.++|..||+|..+.++. .|.   -+.|.|.++.+|..|...+....+...++.+.|+.      
T Consensus       388 il~kNlpa~t~~~elt~~F~~fG~i~rvllp~-~G~---~aiv~fl~p~eAr~Afrklaysr~k~~plyle~aP~dvf~~  463 (725)
T KOG0110|consen  388 ILVKNLPAGTLSEELTEAFLRFGEIGRVLLPP-GGT---GAIVEFLNPLEARKAFRKLAYSRFKSAPLYLEWAPEDVFTE  463 (725)
T ss_pred             eeeccCccccccHHHHHHhhcccccceeecCc-ccc---eeeeeecCccchHHHHHHhchhhhccCccccccChhhhccC
Confidence            57899998877   899999999999996653 222   28999999999999999998877777776665432      


Q ss_pred             -CCCC-----------------------------C--------------CCCceEEEcCCCCCCCHHHHHHhhcCCCceE
Q psy6353          73 -PSSE-----------------------------S--------------IKGANLYVSGLPKHMSQQELESLFSPYGRII  108 (136)
Q Consensus        73 -~~~~-----------------------------~--------------~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~  108 (136)
                       |+..                             .              ...++||++|++...|.+++...|...|.|.
T Consensus       464 ~pka~~~~~e~~~~~ee~~~Er~s~~d~~v~eD~d~te~ss~a~~a~~~~~~t~lfvkNlnf~Tt~e~l~~~F~k~G~Vl  543 (725)
T KOG0110|consen  464 DPKADDLSAESRSKMEENPSERVSAEDGQVEEDKDPTEESSLARVAEDEETETKLFVKNLNFDTTLEDLEDLFSKQGTVL  543 (725)
T ss_pred             CccccccccccccccccCcceecccccccccccCCccccccchhhhhccccchhhhhhcCCcccchhHHHHHHHhcCeEE
Confidence             1000                             0              1123499999999999999999999999999


Q ss_pred             EEEEEeCCCCC----CccceEeecCcccccc
Q psy6353         109 TSRILCDNLAT----ENGKYYSGLGGRERLR  135 (136)
Q Consensus       109 ~~~i~~~~~~~----~~~~~fv~f~~~e~~~  135 (136)
                      ++.|...++.-    +.|.+||+|.+.|.|+
T Consensus       544 S~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~  574 (725)
T KOG0110|consen  544 SIEISKKKDPANKYLSMGFGFVEFAKPESAQ  574 (725)
T ss_pred             EEEEeccccccccccccceeEEEecCHHHHH
Confidence            99887665432    3377999999999775

>KOG0131|consensus

Probab=99.21  E-value=2.6e-11  Score=78.46  Aligned_cols=74  Identities=27%  Similarity=0.376  Sum_probs=67.0

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEE-EEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEIC-VFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS   75 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~-~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~   75 (136)
                      +|++||+.++.   |.+.|+.||.+... .+++  .+|.++|+||+.|.+.+.+++|+..+||..+.++++.+.++..+.
T Consensus        99 lfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~ya~k~~  178 (203)
T KOG0131|consen   99 LFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPITVSYAFKKD  178 (203)
T ss_pred             ccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCceEEEEEEecC
Confidence            68999999888   99999999998663 7777  789999999999999999999999999999999999999887554

>KOG4454|consensus

Probab=99.15  E-value=1.3e-11  Score=81.96  Aligned_cols=116  Identities=15%  Similarity=0.116  Sum_probs=94.1

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES   77 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~~   77 (136)
                      |||.|+...++   |.++|-+-|+|..+.|+. ..+..| ||||.|.++.++..|++-+||..+.++++++.+-.-..  
T Consensus        12 l~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r~G~s--   88 (267)
T KOG4454|consen   12 LLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLRCGNS--   88 (267)
T ss_pred             HHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCc-eeeeecccccchhhhhhhcccchhccchhhcccccCCC--
Confidence            68899998888   899999999999999988 667777 99999999999999999999999999998876432211  


Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEee
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSG  127 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~  127 (136)
                        ...     +....+++.+...|+.-|.+..+++.++.++..+.+.++.
T Consensus        89 --hap-----ld~r~~~ei~~~v~s~a~p~~~~R~~~~~d~rnrn~~~~~  131 (267)
T KOG4454|consen   89 --HAP-----LDERVTEEILYEVFSQAGPIEGVRIPTDNDGRNRNFGFVT  131 (267)
T ss_pred             --cch-----hhhhcchhhheeeecccCCCCCccccccccCCccCccchh
Confidence              011     4566788888999999999999999998875454555554

>smart00362 RRM_2 RNA recognition motif

Probab=99.10  E-value=1.8e-10  Score=63.98  Aligned_cols=53  Identities=26%  Similarity=0.518  Sum_probs=47.3

Q ss_pred             eEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        82 ~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      +|+|+|||..+++++|+++|.+||++..+.+..++ ....+.+||+|.+.+++.
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~-~~~~~~~~v~f~~~~~a~   53 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT-GKSKGFAFVEFESEEDAE   53 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC-CCCCceEEEEeCCHHHHH
Confidence            58999999999999999999999999999999887 444477999999998874

>KOG4212|consensus

Probab=99.08  E-value=1.1e-09  Score=79.53  Aligned_cols=68  Identities=22%  Similarity=0.326  Sum_probs=56.1

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEE
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVS   69 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~   69 (136)
                      +|+.||...+.   |.+.|.-.|++..+.+-- ..|.++|++.++|..+-.|-.|+..+++.-+..++..+.
T Consensus       218 ~fvanl~~~vg~~kL~qvfgmAGkv~~vdf~idKeG~s~G~~vi~y~hpveavqaIsml~~~g~~~~~~~~R  289 (608)
T KOG4212|consen  218 VFVANLDYKVGNKKLKQVFGMAGKVQSVDFSIDKEGNSRGFAVIEYDHPVEAVQAISMLDRQGLFDRRMTVR  289 (608)
T ss_pred             eeeeccccccchHHHHHHhccceeeeeeceeeccccccCCeeEEEecchHHHHHHHHhhccCCCccccceee
Confidence            67888988776   899999999998887666 778999999999999999999999888755555555443

>KOG0126|consensus

Probab=99.06  E-value=9.3e-11  Score=75.94  Aligned_cols=55  Identities=22%  Similarity=0.504  Sum_probs=50.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRER  133 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~  133 (136)
                      .++-|||+|||..+|+.||--.|++||+|+.+++++|..||.+ |++|+.+++..+
T Consensus        34 dsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRS   89 (219)
T KOG0126|consen   34 DSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRS   89 (219)
T ss_pred             cceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccc
Confidence            5678999999999999999999999999999999999999999 559999988653

>KOG0114|consensus

Probab=99.05  E-value=3.8e-10  Score=66.81  Aligned_cols=56  Identities=23%  Similarity=0.357  Sum_probs=49.4

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCccccccC
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLRR  136 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~~  136 (136)
                      -.+-|||+|||.++|.++..++|.+||.|..++|...+  +.+|-|||.+++-++||+
T Consensus        17 vnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k--~TrGTAFVVYedi~dAk~   72 (124)
T KOG0114|consen   17 VNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTK--ETRGTAFVVYEDIFDAKK   72 (124)
T ss_pred             hheeEEEecCCccccHHHHHHHhhcccceEEEEecCcc--CcCceEEEEehHhhhHHH
Confidence            45789999999999999999999999999999998765  455669999999988864

>KOG0121|consensus

Probab=99.03  E-value=2.6e-10  Score=69.93  Aligned_cols=57  Identities=21%  Similarity=0.296  Sum_probs=51.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      .+++|||+||+..++|++|.++|+.+|+|..+.+-.|..+... |+.||+|-++++|.
T Consensus        35 ~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~   92 (153)
T KOG0121|consen   35 KSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAE   92 (153)
T ss_pred             hcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHH
Confidence            5689999999999999999999999999999999999877766 66899999998864

>KOG0129|consensus

Probab=99.01  E-value=1.1e-08  Score=75.49  Aligned_cols=130  Identities=15%  Similarity=0.199  Sum_probs=93.4

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc-----cCCCcee---eEEEEcCCHHHHHHHHHHHcC----cee-----
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI-----STAQSLG---YGFVNYHRPEDAEKAINTLNG----LRL-----   61 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~-----~~~~~kg---~~fv~f~~~~~a~~a~~~~~~----~~~-----   61 (136)
                      ||++.||..++   |...|..||.+ .+.++.     ..-.++|   |+|+-|+++.+++.-+.+...    ..|     
T Consensus       262 VFvGGlp~dise~~i~~~F~~FGs~-~VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~~~~~~yf~vss~  340 (520)
T KOG0129|consen  262 VFVGGLPWDITEAQINASFGQFGSV-KVDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSEGEGNYYFKVSSP  340 (520)
T ss_pred             eeecCCCccccHHHHHhhcccccce-EeecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHhhcccceEEEEecC
Confidence            79999999999   78889999986 566663     2233567   999999999999887765422    111     


Q ss_pred             --CCceEEEEeeCCCC---------CCCCCceEEEcCCCCCCCHHHHHHhhc-CCCceEEEEEEeCCCCCCc-cceEeec
Q psy6353          62 --QNKTIKVSYARPSS---------ESIKGANLYVSGLPKHMSQQELESLFS-PYGRIITSRILCDNLATEN-GKYYSGL  128 (136)
Q Consensus        62 --~g~~l~v~~~~~~~---------~~~~~~~l~v~nl~~~~t~~~l~~~f~-~~G~v~~~~i~~~~~~~~~-~~~fv~f  128 (136)
                        ..+.++|..+....         .-...+|+||++||.-++.++|..+|. -||.|..+.|-.|+.-+-. |.+=|.|
T Consensus       341 ~~k~k~VQIrPW~laDs~fv~d~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtF  420 (520)
T KOG0129|consen  341 TIKDKEVQIRPWVLADSDFVLDHNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTF  420 (520)
T ss_pred             cccccceeEEeeEeccchhhhccCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeee
Confidence              12234443332211         124678999999999999999999999 8999999999999543333 4467777


Q ss_pred             Cccc
Q psy6353         129 GGRE  132 (136)
Q Consensus       129 ~~~e  132 (136)
                      .+..
T Consensus       421 snqq  424 (520)
T KOG0129|consen  421 SNQQ  424 (520)
T ss_pred             cccH
Confidence            6653

>KOG0415|consensus

Probab=99.00  E-value=7.5e-10  Score=78.43  Aligned_cols=72  Identities=22%  Similarity=0.460  Sum_probs=65.5

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP   73 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~   73 (136)
                      |||=-|..-.+   |+-+|+.||+|.+|.+++  .+|.+..||||+|.+.+++++|.-+|++..|..+.|.|.++++
T Consensus       242 LFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDFSQS  318 (479)
T KOG0415|consen  242 LFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDFSQS  318 (479)
T ss_pred             EEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeehhhh
Confidence            56666766666   899999999999999999  8999999999999999999999999999999999999988764

>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=98.98  E-value=1.1e-09  Score=61.03  Aligned_cols=54  Identities=26%  Similarity=0.538  Sum_probs=49.2

Q ss_pred             eEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        82 ~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      +|+|+|||..+++++|+++|+.+|.|..+.+..++.+...+.+||+|.+.|++.
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~   54 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDEEDAE   54 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCHHHHH
Confidence            489999999999999999999999999999999887766678999999999874

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).

>KOG4661|consensus

Probab=98.97  E-value=1.5e-09  Score=81.17  Aligned_cols=73  Identities=18%  Similarity=0.276  Sum_probs=64.0

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS   74 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~   74 (136)
                      |+|+.|+....   |+.+|++||+|...+++.  .+...++|+||++.+.++|-+||.-||...++|+.|.|..++..
T Consensus       408 lWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaKNE  485 (940)
T KOG4661|consen  408 LWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAKNE  485 (940)
T ss_pred             eeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeecccC
Confidence            57777776554   999999999999999988  55667999999999999999999999999999999999877643

>PLN03213 repressor of silencing 3; Provisional

Probab=98.96  E-value=1.2e-09  Score=80.54  Aligned_cols=51  Identities=22%  Similarity=0.338  Sum_probs=46.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGR  131 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~  131 (136)
                      ..+.+|||+||+..+++++|+..|++||.|..+.|++.  +| +++|||+|.+.
T Consensus         8 ~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRE--TG-RGFAFVEMssd   58 (759)
T PLN03213          8 GGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRT--KG-RSFAYIDFSPS   58 (759)
T ss_pred             CcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecc--cC-CceEEEEecCC
Confidence            45688999999999999999999999999999999954  56 78999999987

>KOG0153|consensus

Probab=98.94  E-value=4.3e-09  Score=74.29  Aligned_cols=68  Identities=25%  Similarity=0.374  Sum_probs=60.1

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHH-HcCceeCCceEEEEeeCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINT-LNGLRLQNKTIKVSYARP   73 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~-~~~~~~~g~~l~v~~~~~   73 (136)
                      |||++|.+.++   |++.|.+||+|.++.+..    .+++|||+|.+.+.|+.|..+ +|...|.|++|++.|+.+
T Consensus       231 LyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~----~~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg~~  302 (377)
T KOG0153|consen  231 LYIGGLNDEVLEQDIRDHFYQYGEIRSIRILP----RKGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWGRP  302 (377)
T ss_pred             EEecccccchhHHHHHHHHhhcCCeeeEEeec----ccccceeeehhhHHHHHHHHhhcceeeecceEEEEEeCCC
Confidence            79999987777   999999999999998875    456999999999999999875 556778999999999988

>smart00360 RRM RNA recognition motif

Probab=98.94  E-value=1.4e-09  Score=60.14  Aligned_cols=51  Identities=27%  Similarity=0.512  Sum_probs=45.2

Q ss_pred             EcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          85 VSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        85 v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      |+|||..+++++|+++|++||.|..+.+..++.++.. +.+||+|.+.++|.
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~   52 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAE   52 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHH
Confidence            5799999999999999999999999999998865555 56999999998874

>KOG0109|consensus

Probab=98.93  E-value=1.8e-09  Score=74.69  Aligned_cols=68  Identities=22%  Similarity=0.326  Sum_probs=62.4

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS   75 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~   75 (136)
                      ++|+|+....+   +++.|++||++.+|.+++      +|+||.|.-.++|..|+..|++.++.|++++|..+.++-
T Consensus        81 l~vgNis~tctn~ElRa~fe~ygpviecdivk------dy~fvh~d~~eda~~air~l~~~~~~gk~m~vq~stsrl  151 (346)
T KOG0109|consen   81 LHVGNISPTCTNQELRAKFEKYGPVIECDIVK------DYAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLSTSRL  151 (346)
T ss_pred             cccCCCCccccCHHHhhhhcccCCceeeeeec------ceeEEEEeeccchHHHHhcccccccccceeeeeeecccc
Confidence            67899998888   999999999999999986      899999999999999999999999999999998776543

>KOG4205|consensus

Probab=98.91  E-value=1.6e-09  Score=76.76  Aligned_cols=106  Identities=18%  Similarity=0.226  Sum_probs=84.2

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      +|++.||..++   ++++|++||.|..+.++.  .+.+++||+||+|.+.+.++.++. ...+.+.++++.|+.+.|+..
T Consensus       100 iFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~-~~f~~~~gk~vevkrA~pk~~  178 (311)
T KOG4205|consen  100 IFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL-QKFHDFNGKKVEVKRAIPKEV  178 (311)
T ss_pred             EEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecc-cceeeecCceeeEeeccchhh
Confidence            68999999998   999999999999988888  788899999999999999999988 468999999999999998765


Q ss_pred             CCCCc-----eEEEcCCCCCCCHHHHHHhhcCCCceE
Q psy6353          77 SIKGA-----NLYVSGLPKHMSQQELESLFSPYGRII  108 (136)
Q Consensus        77 ~~~~~-----~l~v~nl~~~~t~~~l~~~f~~~G~v~  108 (136)
                      .....     ...-.|++...+.-.|...+..||.+.
T Consensus       179 ~~~~~~~~~~~~~~~~~g~~~~~~~l~~~~~g~~~~~  215 (311)
T KOG4205|consen  179 MQSTKSSVSTRGKGNNLGNGRTGFFLKKYFKGYGPVG  215 (311)
T ss_pred             ccccccccccccccccccccccccccchhccccCccc
Confidence            43221     122224555555556677777777654

>KOG0128|consensus

Probab=98.90  E-value=2.7e-10  Score=87.96  Aligned_cols=116  Identities=17%  Similarity=0.247  Sum_probs=98.0

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEE-c-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFL-I-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~-~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      +|++||+..+.   |...|..+|.+..+.+. . ..++.+|+|++.|..++++.+|+....+. +.|             
T Consensus       670 ~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~-~~g-------------  735 (881)
T KOG0128|consen  670 IFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSC-FFG-------------  735 (881)
T ss_pred             HHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhh-hhh-------------
Confidence            47889998887   88889999988777655 3 88999999999999999999999854333 333             


Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERL  134 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~  134 (136)
                         ...++|+|.|+..|.+.++.+++..|.+.+.+++....+...|.+||.|.++-++
T Consensus       736 ---K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r~gkpkg~a~v~y~~ea~~  790 (881)
T KOG0128|consen  736 ---KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVRAGKPKGKARVDYNTEADA  790 (881)
T ss_pred             ---hhhhheeCCCCCCchHHHHhhccccCCccccchhhhhccccccceeccCCCcchh
Confidence               2458999999999999999999999999999999888877778899999987654

>KOG0533|consensus

Probab=98.90  E-value=6.3e-09  Score=71.27  Aligned_cols=73  Identities=22%  Similarity=0.351  Sum_probs=66.5

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS   74 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~   74 (136)
                      |+|.|||.-++   |+++|..||.+..+-+.. ..|.+.|.|-|.|...++|..|++++||..+.|+++++....+.
T Consensus        86 v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~~~  162 (243)
T KOG0533|consen   86 VNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIISSP  162 (243)
T ss_pred             eeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEecCc
Confidence            68999999988   999999999888888887 89999999999999999999999999999999999998765543

>KOG0132|consensus

Probab=98.88  E-value=5.2e-09  Score=80.44  Aligned_cols=71  Identities=24%  Similarity=0.416  Sum_probs=65.8

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+.|+.+++   |.++|+.||.|.+|.++.    ++|||||.+...++|.+|+.+|+...+.++.|++.|+..+.-
T Consensus       424 LwvG~i~k~v~e~dL~~~feefGeiqSi~li~----~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g~G~  497 (894)
T KOG0132|consen  424 LWVGGIPKNVTEQDLANLFEEFGEIQSIILIP----PRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVGKGP  497 (894)
T ss_pred             eeeccccchhhHHHHHHHHHhcccceeEeecc----CCceeEEEEeehhHHHHHHHHHhcccccceeeEEeeeccCCc
Confidence            79999999998   999999999999998875    889999999999999999999999999999999999876543

>KOG1365|consensus

Probab=98.86  E-value=8.9e-10  Score=78.76  Aligned_cols=132  Identities=17%  Similarity=0.207  Sum_probs=98.0

Q ss_pred             eecCCChhhhHHHHhccCC-------CeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCC-
Q psy6353           3 YQTLLNKLFTYEKVHLGFS-------DAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP-   73 (136)
Q Consensus         3 ~v~nl~~~~~l~~~f~~~G-------~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~-   73 (136)
                      -...||...+-.+....||       ....+..+. ..|+..|=||+.|..+++|+.|+.+ |...++.|.|.+..+.. 
T Consensus       165 RmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~ee~aq~aL~k-hrq~iGqRYIElFRSTaa  243 (508)
T KOG1365|consen  165 RMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACEEDAQFALRK-HRQNIGQRYIELFRSTAA  243 (508)
T ss_pred             EecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCHHHHHHHHHH-HHHHHhHHHHHHHHHhHH
Confidence            3568998888444444443       445566666 7899999999999999999999984 55556666555432110 


Q ss_pred             ------------------------------CCCCCCCceEEEcCCCCCCCHHHHHHhhcCCCc-eEE--EEEEeCCCCCC
Q psy6353          74 ------------------------------SSESIKGANLYVSGLPKHMSQQELESLFSPYGR-IIT--SRILCDNLATE  120 (136)
Q Consensus        74 ------------------------------~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~-v~~--~~i~~~~~~~~  120 (136)
                                                    .........|.+++||..++.+||-++|..|-. |..  +.++.+..+..
T Consensus       244 Evqqvlnr~~s~pLi~~~~sp~~p~~p~~~~p~~~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~qGrP  323 (508)
T KOG1365|consen  244 EVQQVLNREVSEPLIPGLTSPLLPGGPARLVPPTRSKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNGQGRP  323 (508)
T ss_pred             HHHHHHHhhccccccCCCCCCCCCCCccccCCCCCCCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcCCCCc
Confidence                                          001123567999999999999999999999864 333  78888888888


Q ss_pred             ccceEeecCcccccc
Q psy6353         121 NGKYYSGLGGRERLR  135 (136)
Q Consensus       121 ~~~~fv~f~~~e~~~  135 (136)
                      +|.||++|.++|+++
T Consensus       324 SGeAFIqm~nae~a~  338 (508)
T KOG1365|consen  324 SGEAFIQMRNAERAR  338 (508)
T ss_pred             ChhhhhhhhhhHHHH
Confidence            899999999999875

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

Probab=98.85  E-value=4.7e-09  Score=72.49  Aligned_cols=56  Identities=21%  Similarity=0.469  Sum_probs=50.9

Q ss_pred             CceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          80 GANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        80 ~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ..+|||+|||..+++++|.++|.+||.|..+.+..+..++.. +.|||+|.+.+.+.
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~  171 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAE  171 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHH
Confidence            499999999999999999999999999999999999866666 56999999998764

>KOG0113|consensus

Probab=98.84  E-value=6.9e-09  Score=71.98  Aligned_cols=58  Identities=19%  Similarity=0.287  Sum_probs=53.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccc-eEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGK-YYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~-~fv~f~~~e~~~  135 (136)
                      .+-.||||.-|+.+++|..|+..|..||+|..+.|+.|..+|++++ |||+|+++-+|.
T Consensus        99 DPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~  157 (335)
T KOG0113|consen   99 DPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMK  157 (335)
T ss_pred             CccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHH
Confidence            4568999999999999999999999999999999999999999855 899999987764

>KOG0107|consensus

Probab=98.84  E-value=7.2e-09  Score=66.88  Aligned_cols=53  Identities=21%  Similarity=0.361  Sum_probs=46.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ..++|||+||+..+++.+|...|..||++.++-|.++    ..++|||+|++..+|+
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn----PPGfAFVEFed~RDA~   61 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARN----PPGFAFVEFEDPRDAE   61 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeec----CCCceEEeccCcccHH
Confidence            4688999999999999999999999999999888874    4477999999987764

>KOG0226|consensus

Probab=98.82  E-value=1.9e-09  Score=73.20  Aligned_cols=73  Identities=22%  Similarity=0.380  Sum_probs=64.8

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS   74 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~   74 (136)
                      ||.+.|..+++   |-..|.+|-.....++++  .+|+++||+||.|.+..++..|+.+|||..++.++|++..+..+
T Consensus       193 IfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRkS~wk  270 (290)
T KOG0226|consen  193 IFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRKSEWK  270 (290)
T ss_pred             eecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhhhhHH
Confidence            57778876676   788899999998889999  89999999999999999999999999999999999998765544

>KOG1456|consensus

Probab=98.82  E-value=1.5e-07  Score=67.39  Aligned_cols=118  Identities=11%  Similarity=0.127  Sum_probs=95.0

Q ss_pred             HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC----------------
Q psy6353          13 YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE----------------   76 (136)
Q Consensus        13 l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~----------------   76 (136)
                      |-.+|..||.|..|+.++   ...|-|.|++.|....++|+.-||+..+.|.+|.++.++..--                
T Consensus       305 lFNl~ClYGNV~rvkFmk---Tk~gtamVemgd~~aver~v~hLnn~~lfG~kl~v~~SkQ~~v~~~~pflLpDgSpSfK  381 (494)
T KOG1456|consen  305 LFNLFCLYGNVERVKFMK---TKPGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVCVSKQNFVSPVQPFLLPDGSPSFK  381 (494)
T ss_pred             hhhhhhhcCceeeEEEee---cccceeEEEcCcHHHHHHHHHHhccCccccceEEEeeccccccccCCceecCCCCcchh
Confidence            678999999999999998   3345699999999999999999999999999999987653210                


Q ss_pred             ---------------------CCCCceEEEcCCCCCCCHHHHHHhhcCCCc-eEEEEEEeCCCCCCccceEeecCccccc
Q psy6353          77 ---------------------SIKGANLYVSGLPKHMSQQELESLFSPYGR-IITSRILCDNLATENGKYYSGLGGRERL  134 (136)
Q Consensus        77 ---------------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~-v~~~~i~~~~~~~~~~~~fv~f~~~e~~  134 (136)
                                           ..++..|..-|.|..+||+++.++|..-+. ..++++..-+ +-++-.+-.+|++.++|
T Consensus       382 dys~SkNnRFssp~qAsKNrIq~Ps~vLHffNaP~~vtEe~l~~i~nek~v~~~svkvFp~k-serSssGllEfe~~s~A  460 (494)
T KOG1456|consen  382 DYSGSKNNRFSSPEQASKNRIQPPSNVLHFFNAPLGVTEEQLIGICNEKDVPPTSVKVFPLK-SERSSSGLLEFENKSDA  460 (494)
T ss_pred             hcccccccccCChhHhhcccccCCcceeEEecCCCccCHHHHHHHhhhcCCCcceEEeeccc-ccccccceeeeehHHHH
Confidence                                 134578999999999999999999998764 3466776554 44446688999988765

>KOG0151|consensus

Probab=98.74  E-value=2.5e-08  Score=76.24  Aligned_cols=72  Identities=19%  Similarity=0.337  Sum_probs=64.5

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc-----cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI-----STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP   73 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~-----~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~   73 (136)
                      ||++||+..++   |-..|..||++.+++++.     ...+.+-||||.|.+..+|++|+..|+|..+.+.++++.|+++
T Consensus       177 lyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K~gWgk~  256 (877)
T KOG0151|consen  177 LYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMKLGWGKA  256 (877)
T ss_pred             eeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeeeeccccc
Confidence            79999999998   778889999999998887     3355677999999999999999999999999999999999853

>KOG0105|consensus

Probab=98.74  E-value=1.8e-08  Score=65.73  Aligned_cols=55  Identities=22%  Similarity=0.381  Sum_probs=46.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ..++|||+|||.++.+.+|.++|-+||.|..+.+-..  .+...++||+|++..+|.
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r--~g~ppfafVeFEd~RDAe   59 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNR--PGPPPFAFVEFEDPRDAE   59 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhhcceEEEEeccC--CCCCCeeEEEecCccchh
Confidence            5688999999999999999999999999999877543  244578999999987653

>KOG0116|consensus

Probab=98.73  E-value=1.7e-08  Score=74.24  Aligned_cols=71  Identities=21%  Similarity=0.345  Sum_probs=61.6

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc-c-CCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI-S-TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP   73 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~-~-~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~   73 (136)
                      |||.|||...+   |++.|++||+|....|.. . .+...+||||+|.+.+.++.|+.+ +-..++++++.|+--.+
T Consensus       291 i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek~~  366 (419)
T KOG0116|consen  291 IFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEKRP  366 (419)
T ss_pred             eEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEeccc
Confidence            79999999998   999999999999988777 3 455559999999999999999996 48889999999975544

>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=98.72  E-value=5.3e-08  Score=55.65  Aligned_cols=64  Identities=19%  Similarity=0.229  Sum_probs=45.9

Q ss_pred             CeeecCCChhhh-------HHHHhccCC-CeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeC
Q psy6353           1 MVYQTLLNKLFT-------YEKVHLGFS-DAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR   72 (136)
Q Consensus         1 ~v~v~nl~~~~~-------l~~~f~~~G-~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~   72 (136)
                      +|||.|||...+       |+.++.-+| +|.++        +.+-|.|.|.+++.|++|.+.|+|-.+.|++|.+.+..
T Consensus         4 ~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v--------~~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~~~   75 (90)
T PF11608_consen    4 LLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV--------SGGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSFSP   75 (90)
T ss_dssp             EEEEES--TTS-HHHHHHHHHHHHHTTT--EEE----------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEESS-
T ss_pred             EEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE--------eCCEEEEEeCCHHHHHHHHHhhcccccccceEEEEEcC
Confidence            589999998765       888888887 55554        13679999999999999999999999999999998764

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

>KOG4211|consensus

Probab=98.72  E-value=9.8e-08  Score=70.26  Aligned_cols=132  Identities=17%  Similarity=0.199  Sum_probs=99.2

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeE-EEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCC---
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEI-CVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP---   73 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~-~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~---   73 (136)
                      |-...||..+|   |.++|+-.-.+.. +.++. ..+++.|-|||.|.+.+.|+.|+.. |...|+.|.|.|..+.-   
T Consensus       106 VRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al~r-hre~iGhRYIEvF~Ss~~e~  184 (510)
T KOG4211|consen  106 VRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEIALGR-HRENIGHRYIEVFRSSRAEV  184 (510)
T ss_pred             EEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHHHHHH-HHHhhccceEEeehhHHHHH
Confidence            34578999999   6666766655555 54555 7888999999999999999999984 67788888888843210   


Q ss_pred             -----------------------CC---------------C---------------------------------------
Q psy6353          74 -----------------------SS---------------E---------------------------------------   76 (136)
Q Consensus        74 -----------------------~~---------------~---------------------------------------   76 (136)
                                             +.               .                                       
T Consensus       185 ~~~~~~~~~~~~rpGpy~~~~a~Rg~~d~~~~~~~~~~~~r~g~~~~g~~g~~~~~~~~d~~~~gs~~~~~~~~~~~~~g  264 (510)
T KOG4211|consen  185 KRAAGPGDGRVGRPGPYDRPGAPRGGYDYGQGRDPGRNATRYGAGGEGYYGFSRYPSLQDYGNFGSYGGGRDPNYPVSSG  264 (510)
T ss_pred             HhhccccccccCCCCccccccCCccccccccccCCCccccccccccCCccccccCccccccccccccccccccccCCCCC
Confidence                                   00               0                                       


Q ss_pred             -------------CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          77 -------------SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        77 -------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                                   ...+..+..+++|...++.++..+|+..-.+ .+.|--.++....+.++|+|++.|++.
T Consensus       265 ~~~~g~~g~~~~~~~~g~fv~MRGlpy~a~~~di~nfFspl~p~-~v~i~ig~dGr~TGEAdveF~t~edav  335 (510)
T KOG4211|consen  265 PHRQGGAGDYGNGGPGGHFVHMRGLPYDATENDIANFFSPLNPY-RVHIEIGPDGRATGEADVEFATGEDAV  335 (510)
T ss_pred             cccCCCcccccCCCCCCceeeecCCCccCCCcchhhhcCCCCce-eEEEEeCCCCccCCcceeecccchhhH
Confidence                         0112468889999999999999999876544 666666676777788999999999873

>KOG1456|consensus

Probab=98.68  E-value=4.5e-07  Score=65.04  Aligned_cols=117  Identities=22%  Similarity=0.306  Sum_probs=94.1

Q ss_pred             HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCC--ceEEEEeeCCCCC--------------
Q psy6353          13 YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQN--KTIKVSYARPSSE--------------   76 (136)
Q Consensus        13 l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g--~~l~v~~~~~~~~--------------   76 (136)
                      |..++...|+|..|.+.+.   +--.|.|+|.+.+.|++|..+|||..|..  ..|+|.+++|..-              
T Consensus       139 ly~Icnp~GkVlRIvIfkk---ngVQAmVEFdsv~~AqrAk~alNGADIYsGCCTLKIeyAkP~rlnV~knd~DtwDyTl  215 (494)
T KOG1456|consen  139 LYTICNPQGKVLRIVIFKK---NGVQAMVEFDSVEVAQRAKAALNGADIYSGCCTLKIEYAKPTRLNVQKNDKDTWDYTL  215 (494)
T ss_pred             hhhhcCCCCceEEEEEEec---cceeeEEeechhHHHHHHHhhcccccccccceeEEEEecCcceeeeeecCCccccccC
Confidence            8899999999999998872   33469999999999999999999998864  5788888776321              


Q ss_pred             --------------------------------------------------------------------CCCCceEEEcCC
Q psy6353          77 --------------------------------------------------------------------SIKGANLYVSGL   88 (136)
Q Consensus        77 --------------------------------------------------------------------~~~~~~l~v~nl   88 (136)
                                                                                          ...+..+.|.+|
T Consensus       216 p~~~~~~~~g~~~~~r~~~p~~~~~~pss~~G~h~~y~sg~~~~p~~~~P~r~~~~~~~~~g~a~p~g~~~g~VmMVyGL  295 (494)
T KOG1456|consen  216 PDLRGPYDPGRNHYDRQRQPAPLGYHPSSRGGGHSGYYSGDRHGPPHPPPSRYRDGYRDGRGYASPGGGAPGCVMMVYGL  295 (494)
T ss_pred             CCCCCCCCCCCCCCccccCCCccCCChhhcCCCCCCCcccccCCCCCCCCCCCccccccCCCCCCCCCCCCCcEEEEEec
Confidence                                                                                013457888889


Q ss_pred             CCC-CCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCccccccC
Q psy6353          89 PKH-MSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLRR  136 (136)
Q Consensus        89 ~~~-~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~~  136 (136)
                      +.. ++-+.|..+|-.||.|..++.++.+    .+-|.|+|.+.++..|
T Consensus       296 dh~k~N~drlFNl~ClYGNV~rvkFmkTk----~gtamVemgd~~aver  340 (494)
T KOG1456|consen  296 DHGKMNCDRLFNLFCLYGNVERVKFMKTK----PGTAMVEMGDAYAVER  340 (494)
T ss_pred             cccccchhhhhhhhhhcCceeeEEEeecc----cceeEEEcCcHHHHHH
Confidence            865 5788999999999999999999853    2457999999887653

>KOG1190|consensus

Probab=98.64  E-value=3.9e-07  Score=65.92  Aligned_cols=126  Identities=17%  Similarity=0.220  Sum_probs=90.4

Q ss_pred             eecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCC--ceEEEEeeC-----
Q psy6353           3 YQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQN--KTIKVSYAR-----   72 (136)
Q Consensus         3 ~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g--~~l~v~~~~-----   72 (136)
                      .++|+-.-++   |+.+|++||.|..|.-..  ....=.|+|.|.+.+.|+.|..+|+|..|.+  ..|++.++.     
T Consensus       154 iie~m~ypVslDVLHqvFS~fG~VlKIiTF~--Knn~FQALvQy~d~~sAq~AK~aLdGqnIyngcCtLrId~Sklt~Ln  231 (492)
T KOG1190|consen  154 IIENMFYPVSLDVLHQVFSKFGFVLKIITFT--KNNGFQALVQYTDAVSAQAAKLALDGQNIYNGCCTLRIDFSKLTDLN  231 (492)
T ss_pred             EeccceeeeEHHHHHHHHhhcceeEEEEEEe--cccchhhhhhccchhhHHHHHHhccCCcccCceeEEEeehhhcccce
Confidence            4566666666   899999999998764433  2222348999999999999999999988875  345554322     


Q ss_pred             -----CCCCC---------------------------------------------------CC--CceEEEcCCCCC-CC
Q psy6353          73 -----PSSES---------------------------------------------------IK--GANLYVSGLPKH-MS   93 (136)
Q Consensus        73 -----~~~~~---------------------------------------------------~~--~~~l~v~nl~~~-~t   93 (136)
                           .+.++                                                   ..  ...|-|.|+.+. +|
T Consensus       232 vKynndkSRDyTnp~LP~gd~~p~l~~~~~aa~~~~~~~~g~p~aip~~~~~a~~a~~~~~~~~~n~vllvsnln~~~VT  311 (492)
T KOG1190|consen  232 VKYNNDKSRDYTNPDLPVGDGQPSLDQLMAAAFGSVPAVHGAPLAIPSGAAGANAADGKIESPSANVVLLVSNLNEEAVT  311 (492)
T ss_pred             eeccccccccccCCCCCCCccccccchhhhccccccccccCCcccCCccchhhcccccccccCCCceEEEEecCchhccc
Confidence                 11110                                                   01  356778888765 69


Q ss_pred             HHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCccccc
Q psy6353          94 QQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERL  134 (136)
Q Consensus        94 ~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~  134 (136)
                      .+-|..+|+-||.|..++|..++.    --|.+.|.+...+
T Consensus       312 ~d~LftlFgvYGdVqRVkil~nkk----d~ALIQmsd~~qA  348 (492)
T KOG1190|consen  312 PDVLFTLFGVYGDVQRVKILYNKK----DNALIQMSDGQQA  348 (492)
T ss_pred             hhHHHHHHhhhcceEEEEeeecCC----cceeeeecchhHH
Confidence            999999999999999999998754    3357888776543

>KOG4209|consensus

Probab=98.63  E-value=7.8e-08  Score=65.85  Aligned_cols=70  Identities=20%  Similarity=0.260  Sum_probs=63.8

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR   72 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~   72 (136)
                      +|++|++...|   ++..|+.+|.+..+.++.  .++++|||+||+|.+.+.++.++. |||..+.|+.+.+.+..
T Consensus       104 v~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt~~r  178 (231)
T KOG4209|consen  104 VWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVTLKR  178 (231)
T ss_pred             EEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceeeeee
Confidence            68999999888   788899999999888888  788899999999999999999999 99999999999887654

>KOG0108|consensus

Probab=98.61  E-value=4.4e-08  Score=72.40  Aligned_cols=55  Identities=20%  Similarity=0.375  Sum_probs=51.7

Q ss_pred             ceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccc-eEeecCcccccc
Q psy6353          81 ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGK-YYSGLGGRERLR  135 (136)
Q Consensus        81 ~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~-~fv~f~~~e~~~  135 (136)
                      ..+||+|+|+++++++|.++|+..|.|.+++++-|..+|+.++ +|++|.+.|++.
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~   74 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAE   74 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHH
Confidence            7899999999999999999999999999999999999999955 899999988764

>KOG0415|consensus

Probab=98.61  E-value=3e-08  Score=70.46  Aligned_cols=58  Identities=19%  Similarity=0.378  Sum_probs=53.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      .+.+.|||..|.+-++++||.-+|+.||+|.+|.+++|..+|.+ ..|||+|++.|+++
T Consensus       237 PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE  295 (479)
T KOG0415|consen  237 PPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCE  295 (479)
T ss_pred             CCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHH
Confidence            45688999999999999999999999999999999999999988 67999999999865

>KOG4660|consensus

Probab=98.61  E-value=2.1e-08  Score=74.55  Aligned_cols=105  Identities=20%  Similarity=0.176  Sum_probs=77.5

Q ss_pred             CeeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC-
Q psy6353           1 MVYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE-   76 (136)
Q Consensus         1 ~v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~-   76 (136)
                      .|+|-|||..++   |+.+|+.||+|.++.   .+....|.+||+|.|..+|++|+++|++..+.|+.+++........ 
T Consensus        77 ~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir---~t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k~~~~~~~~~~  153 (549)
T KOG4660|consen   77 TLVVFNLPRSVSNDTLLRIFGAYGEIREIR---ETPNKRGIVFVEFYDVRDAERALKALNRREIAGKRIKRPGGARRAMG  153 (549)
T ss_pred             eEEEEecCCcCCHHHHHHHHHhhcchhhhh---cccccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhcCCCcccccch
Confidence            478999999998   999999999999865   4446788999999999999999999999999999888321110000 


Q ss_pred             ---------------------CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEE
Q psy6353          77 ---------------------SIKGANLYVSGLPKHMSQQELESLFSPYGRIIT  109 (136)
Q Consensus        77 ---------------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~  109 (136)
                                           ......++.- |++..+..-++..++-+|.+..
T Consensus       154 ~~~~~~~~~~~~~p~a~s~pgg~~~~~~~g~-l~P~~s~~~~~~~~~~~~~~~~  206 (549)
T KOG4660|consen  154 LQSGTSFLNHFGSPLANSPPGGWPRGQLFGM-LSPTRSSILLEHISSVDGSSPG  206 (549)
T ss_pred             hcccchhhhhccchhhcCCCCCCcCCcceee-eccchhhhhhhcchhccCcccc
Confidence                                 0011223333 7777777666777777776654

>KOG2193|consensus

Probab=98.60  E-value=1e-08  Score=74.28  Aligned_cols=104  Identities=27%  Similarity=0.426  Sum_probs=85.2

Q ss_pred             eeecCCChhhhHHHHhccCCCe----eEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcC-ceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFTYEKVHLGFSDA----EICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNG-LRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~l~~~f~~~G~v----~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~-~~~~g~~l~v~~~~~~~~   76 (136)
                      +|++||.+..+..++-+-||.-    ..-+++     ..||+|+...+..+|.+|+++++| ..+.|+++.+.++.++..
T Consensus         4 lyignL~p~~~psdl~svfg~ak~~~~g~fl~-----k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~kkq   78 (584)
T KOG2193|consen    4 LYIGNLSPQVTPSDLESVFGDAKIPGSGQFLV-----KSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVPKKQ   78 (584)
T ss_pred             ccccccCCCCChHHHHHHhccccCCCCcceee-----ecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhhHHH
Confidence            6899999999944444445532    122232     258999999999999999999998 778999999998887754


Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEE
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRI  112 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i  112 (136)
                        ..+++-|+|+|+...++.+..+..+||.+..|..
T Consensus        79 --rsrk~Qirnippql~wevld~Ll~qyg~ve~~eq  112 (584)
T KOG2193|consen   79 --RSRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQ  112 (584)
T ss_pred             --HhhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhh
Confidence              5677999999999999999999999999998864

>KOG0130|consensus

Probab=98.59  E-value=5.3e-08  Score=60.46  Aligned_cols=58  Identities=16%  Similarity=0.267  Sum_probs=53.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccc-eEeecCccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGK-YYSGLGGRERL  134 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~-~fv~f~~~e~~  134 (136)
                      +..++-|+|.++.+.+++++|.+.|..||+|.++.+-.|..+|..++ +.|++++.++|
T Consensus        69 SVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keA  127 (170)
T KOG0130|consen   69 SVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEA  127 (170)
T ss_pred             ceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHH
Confidence            45778999999999999999999999999999999999999998855 79999998876

>KOG4210|consensus

Probab=98.59  E-value=5.3e-08  Score=68.67  Aligned_cols=131  Identities=13%  Similarity=0.101  Sum_probs=95.1

Q ss_pred             eecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCC--
Q psy6353           3 YQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS--   75 (136)
Q Consensus         3 ~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~--   75 (136)
                      |++++...+.   ...++...|.........  ....++|++.+.|...+.+..|+.......+.+..+.........  
T Consensus        92 f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~~~~~~~  171 (285)
T KOG4210|consen   92 FVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLNTRRGLR  171 (285)
T ss_pred             cccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCccccccccc
Confidence            4555555554   446677788666665555  678899999999999999999998433345555444432211111  


Q ss_pred             --------CCCCCceEE-EcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccc
Q psy6353          76 --------ESIKGANLY-VSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRER  133 (136)
Q Consensus        76 --------~~~~~~~l~-v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~  133 (136)
                              ......+++ +.+++..++.++|+..|..+|.|..++++.++.++.. +.+|++|...+.
T Consensus       172 ~~n~~~~~~~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~  239 (285)
T KOG4210|consen  172 PKNKLSRLSSGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNS  239 (285)
T ss_pred             ccchhcccccCccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchh
Confidence                    112344556 9999999999999999999999999999999999888 458999987654

>KOG4207|consensus

Probab=98.56  E-value=7e-08  Score=63.99  Aligned_cols=57  Identities=21%  Similarity=0.309  Sum_probs=51.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      .-..|.|.||-..++.++|+.+|.+||.|.+|.|++|..+... ++|||.|-...+|.
T Consensus        12 gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~dae   69 (256)
T KOG4207|consen   12 GMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAE   69 (256)
T ss_pred             cceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHH
Confidence            4567999999999999999999999999999999999988888 55999998876653

>KOG0111|consensus

Probab=98.54  E-value=4.8e-08  Score=65.38  Aligned_cols=57  Identities=23%  Similarity=0.368  Sum_probs=52.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccc-eEeecCccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGK-YYSGLGGRERL  134 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~-~fv~f~~~e~~  134 (136)
                      ...++|||++|...+++.-|...|-+||.|..+.++.|-.++++++ +||+|.-.|+|
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDA   65 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDA   65 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchh
Confidence            3568999999999999999999999999999999999999999855 99999998876

>KOG0153|consensus

Probab=98.45  E-value=2.1e-07  Score=65.90  Aligned_cols=54  Identities=28%  Similarity=0.447  Sum_probs=47.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      .....+|||++|...+++.+|+++|-+||+|.++.+...     .++|||.|.++++|.
T Consensus       225 D~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~-----~~CAFv~ftTR~aAE  278 (377)
T KOG0153|consen  225 DTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR-----KGCAFVTFTTREAAE  278 (377)
T ss_pred             ccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc-----cccceeeehhhHHHH
Confidence            345689999999999999999999999999999998863     368999999999875

>KOG0120|consensus

Probab=98.43  E-value=3.1e-07  Score=68.64  Aligned_cols=126  Identities=14%  Similarity=0.285  Sum_probs=91.2

Q ss_pred             CeeecCCChhhhHHHHhccC--------------C-CeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCce
Q psy6353           1 MVYQTLLNKLFTYEKVHLGF--------------S-DAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKT   65 (136)
Q Consensus         1 ~v~v~nl~~~~~l~~~f~~~--------------G-~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~   65 (136)
                      ++|++++|..++-......+              | .+..+    ...+.+.++|++|.+.++|..|+. +++..+.|++
T Consensus       177 r~~v~~~~~~~~e~~~~~f~~~~~~~~gl~~~~~g~~~~s~----~~n~~~nfa~ie~~s~~~at~~~~-~~~~~f~g~~  251 (500)
T KOG0120|consen  177 RLYVGNIPFTSNEESMMSFFNSRMHASGLNQAPDGPSFVSV----QLNLEKNFAFIEFRSISEATEAMA-LDGIIFEGRP  251 (500)
T ss_pred             hhcccccCCccCcHhhhhhhhhhhhhcccccCCCCCceeee----eecccccceeEEecCCCchhhhhc-ccchhhCCCC
Confidence            46888888777622222211              1 12333    334577899999999999999988 6788888888


Q ss_pred             EEEEeeCCCC-----------------------CCCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-
Q psy6353          66 IKVSYARPSS-----------------------ESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-  121 (136)
Q Consensus        66 l~v~~~~~~~-----------------------~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-  121 (136)
                      +++.......                       ......++++++||...++.++.++...||.+...+++.|..+|.+ 
T Consensus       252 ~~~~r~~d~~~~p~~~~~~~~~~~~~~~~~~t~~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~sk  331 (500)
T KOG0120|consen  252 LKIRRPHDYQPVPGITLSPSQLGKVGLLPASTDVPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSK  331 (500)
T ss_pred             ceecccccccCCccchhhhccccccCCcccccCcccccchhhhccCcCccCHHHHHHHHHhcccchhheeeccccccccc
Confidence            7774211100                       0124568999999999999999999999999999999999987666 


Q ss_pred             cceEeecCcc
Q psy6353         122 GKYYSGLGGR  131 (136)
Q Consensus       122 ~~~fv~f~~~  131 (136)
                      +++|.+|-+.
T Consensus       332 g~af~ey~dp  341 (500)
T KOG0120|consen  332 GFAFCEYCDP  341 (500)
T ss_pred             ceeeeeeeCC
Confidence            5578877653

>KOG0112|consensus

Probab=98.42  E-value=2.3e-07  Score=72.59  Aligned_cols=125  Identities=16%  Similarity=0.143  Sum_probs=105.0

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES   77 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~~   77 (136)
                      ||.+||+..++   ++..|..+|.+.+|.+-. .-++...|+|+.|.+.+.+-.|...+.+..|..-.+++.+..+  ..
T Consensus       375 Lf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~glG~~--ks  452 (975)
T KOG0112|consen  375 LFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHIKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGLGQP--KS  452 (975)
T ss_pred             hhhcCcccchhhhhhhhhhhhhccccccccccCCCCcccchhhhhhhccccCcccchhhcCCccccCccccccccc--cc
Confidence            68899999888   899999999999998877 5677778999999999999999988988888877777777765  34


Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRER  133 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~  133 (136)
                      ...+.++++++++-.....+...|..||.|..+.+--    |. ..+|+.+++.+.
T Consensus       453 t~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~h----gq-~yayi~yes~~~  503 (975)
T KOG0112|consen  453 TPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRH----GQ-PYAYIQYESPPA  503 (975)
T ss_pred             ccceeeccCCCCCCChHHHHHHHhhccCcceeeeccc----CC-cceeeecccCcc
Confidence            4778899999999999999999999999998865432    22 567888887654

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

Probab=98.39  E-value=3.8e-06  Score=49.94  Aligned_cols=71  Identities=25%  Similarity=0.400  Sum_probs=53.5

Q ss_pred             eeecCCChhhh---HHHHhcc--CCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeC----CceEEEEe
Q psy6353           2 VYQTLLNKLFT---YEKVHLG--FSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQ----NKTIKVSY   70 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~--~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~----g~~l~v~~   70 (136)
                      |-+.|+|..+|   |.+++..  .|...-+.++-  .++.+.|||||.|.+++.|..-.+.++|..+.    .+...+.+
T Consensus         4 vMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~i~y   83 (97)
T PF04059_consen    4 VMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCEISY   83 (97)
T ss_pred             EEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEEEeh
Confidence            56889999988   4444322  46666677777  67889999999999999999999999998775    23444555


Q ss_pred             eC
Q psy6353          71 AR   72 (136)
Q Consensus        71 ~~   72 (136)
                      |.
T Consensus        84 Ar   85 (97)
T PF04059_consen   84 AR   85 (97)
T ss_pred             hH
Confidence            54

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

>KOG0132|consensus

Probab=98.32  E-value=4.4e-07  Score=70.16  Aligned_cols=52  Identities=25%  Similarity=0.536  Sum_probs=47.2

Q ss_pred             CceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCccccccC
Q psy6353          80 GANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLRR  136 (136)
Q Consensus        80 ~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~~  136 (136)
                      ++||||+.|+.++++.||.++|..||+|.++.++.     .+++|||.|.++.+|.+
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~-----~R~cAfI~M~~RqdA~k  472 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIP-----PRGCAFIKMVRRQDAEK  472 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEeecc-----CCceeEEEEeehhHHHH
Confidence            57999999999999999999999999999998874     55889999999988753

>KOG2314|consensus

Probab=98.31  E-value=2e-06  Score=64.60  Aligned_cols=68  Identities=31%  Similarity=0.318  Sum_probs=56.4

Q ss_pred             eeecCCChhhh---------HHHHhccCCCeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeC-CceEEEE
Q psy6353           2 VYQTLLNKLFT---------YEKVHLGFSDAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQ-NKTIKVS   69 (136)
Q Consensus         2 v~v~nl~~~~~---------l~~~f~~~G~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~-g~~l~v~   69 (136)
                      |+|.|.|.--.         |..+|+++|++....++. ..|..+||.|++|.+..+|+.|++.+||+.+. +..+.+.
T Consensus        61 Vvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHtf~v~  139 (698)
T KOG2314|consen   61 VVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHTFFVR  139 (698)
T ss_pred             EEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceecccceEEee
Confidence            56777774221         789999999999999887 67779999999999999999999999998887 4555554

>KOG0226|consensus

Probab=98.30  E-value=5.3e-07  Score=61.56  Aligned_cols=123  Identities=8%  Similarity=0.139  Sum_probs=97.9

Q ss_pred             HHHHhccCCCeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEE----eeCCCC--CCCCCceEEE
Q psy6353          13 YEKVHLGFSDAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVS----YARPSS--ESIKGANLYV   85 (136)
Q Consensus        13 l~~~f~~~G~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~----~~~~~~--~~~~~~~l~v   85 (136)
                      +...|+.+-.+...++++ ..+.-.+++|+.|.....-..+...-+++.++.++++..    |-+|.-  -..+..+||.
T Consensus       116 ~~~~f~~~p~L~ktk~v~~~p~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~~~~VR~a~gtswedPsl~ew~~~DfRIfc  195 (290)
T KOG0226|consen  116 LPVVFSEYPSLVKTKLVRDRPQPIRPEAFESFKASDALLKAETEKEKKKIGKPPVRLAAGTSWEDPSLAEWDEDDFRIFC  195 (290)
T ss_pred             chhhhccchhhhhhhhhhcCCCccCcccccCcchhhhhhhhccccccccccCcceeeccccccCCcccccCccccceeec
Confidence            355677777777777777 667778999999998888777777667888888877764    222222  1245689999


Q ss_pred             cCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccc-eEeecCcccccc
Q psy6353          86 SGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGK-YYSGLGGRERLR  135 (136)
Q Consensus        86 ~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~-~fv~f~~~e~~~  135 (136)
                      +.|..+++++-|-..|.+|......++++|+.+|++++ +||.|.+.++++
T Consensus       196 gdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~  246 (290)
T KOG0226|consen  196 GDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYV  246 (290)
T ss_pred             ccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHH
Confidence            99999999999999999999999999999999999955 899999988764

>KOG4208|consensus

Probab=98.28  E-value=1.8e-06  Score=57.22  Aligned_cols=61  Identities=15%  Similarity=0.278  Sum_probs=52.2

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHhhcCC-CceEEEEEEeCCCCCCccc-eEeecCcccccc
Q psy6353          75 SESIKGANLYVSGLPKHMSQQELESLFSPY-GRIITSRILCDNLATENGK-YYSGLGGRERLR  135 (136)
Q Consensus        75 ~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~-G~v~~~~i~~~~~~~~~~~-~fv~f~~~e~~~  135 (136)
                      +......-+++..+|....+..+...|.++ |.+...++.|+..||.+++ |||+|++.|.|+
T Consensus        44 p~~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~  106 (214)
T KOG4208|consen   44 PEQEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAK  106 (214)
T ss_pred             CccCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHH
Confidence            344566789999999999999999999999 7778889999999998855 899999998763

>smart00361 RRM_1 RNA recognition motif

Probab=98.28  E-value=8.2e-07  Score=49.78  Aligned_cols=42  Identities=24%  Similarity=0.409  Sum_probs=33.8

Q ss_pred             HHHHHHhhc----CCCceEEEE-EEeCCCC--CCc-cceEeecCcccccc
Q psy6353          94 QQELESLFS----PYGRIITSR-ILCDNLA--TEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        94 ~~~l~~~f~----~~G~v~~~~-i~~~~~~--~~~-~~~fv~f~~~e~~~  135 (136)
                      +++|++.|+    +||.|.++. ++.++.+  +.. +.+||+|.+.|+|.
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~   51 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAA   51 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHH
Confidence            578888888    999999995 7777655  544 55999999999875

>KOG0116|consensus

Probab=98.24  E-value=1.7e-06  Score=63.89  Aligned_cols=56  Identities=21%  Similarity=0.384  Sum_probs=46.8

Q ss_pred             CceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          80 GANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        80 ~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ..+|||.|||+++++.+|++.|.+||.|....|......+.. .++||+|.+.+++.
T Consensus       288 ~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~  344 (419)
T KOG0116|consen  288 GLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQ  344 (419)
T ss_pred             ccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhh
Confidence            456999999999999999999999999999887776533333 66999999988764

>PF13893 RRM_5: RNA recognition motif

Probab=98.23  E-value=1e-06  Score=47.05  Aligned_cols=35  Identities=23%  Similarity=0.399  Sum_probs=29.5

Q ss_pred             HHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          97 LESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        97 l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      |.++|++||+|..+.+..+.    .+.+||+|.+.|+|+
T Consensus         1 L~~~f~~fG~V~~i~~~~~~----~~~a~V~f~~~~~A~   35 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK----RGFAFVEFASVEDAQ   35 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS----TTEEEEEESSHHHHH
T ss_pred             ChHHhCCcccEEEEEEEeCC----CCEEEEEECCHHHHH
Confidence            67899999999999998765    467999999999885

(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 ....

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=98.17  E-value=5.9e-06  Score=58.76  Aligned_cols=71  Identities=17%  Similarity=0.284  Sum_probs=56.1

Q ss_pred             eeecCCChhhh---------HHHHhccCCCeeEEEEEc-c-CCC-ceee--EEEEcCCHHHHHHHHHHHcCceeCCceEE
Q psy6353           2 VYQTLLNKLFT---------YEKVHLGFSDAEICVFLI-S-TAQ-SLGY--GFVNYHRPEDAEKAINTLNGLRLQNKTIK   67 (136)
Q Consensus         2 v~v~nl~~~~~---------l~~~f~~~G~v~~~~~~~-~-~~~-~kg~--~fv~f~~~~~a~~a~~~~~~~~~~g~~l~   67 (136)
                      |||..||..+.         -.++|.|||+|..|.+-+ . +.. ..+.  .+|+|.+.++|.+|+.+.+|..++||.|+
T Consensus       117 vYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr~lk  196 (480)
T COG5175         117 VYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGRVLK  196 (480)
T ss_pred             eEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCceEe
Confidence            67877776554         368999999999998877 2 111 1222  49999999999999999999999999999


Q ss_pred             EEeeC
Q psy6353          68 VSYAR   72 (136)
Q Consensus        68 v~~~~   72 (136)
                      +.+..
T Consensus       197 atYGT  201 (480)
T COG5175         197 ATYGT  201 (480)
T ss_pred             eecCc
Confidence            97643

>KOG1365|consensus

Probab=98.17  E-value=3.6e-05  Score=55.69  Aligned_cols=121  Identities=15%  Similarity=0.187  Sum_probs=85.7

Q ss_pred             HHHHhccCCCeeEE-EEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC--------------
Q psy6353          13 YEKVHLGFSDAEIC-VFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE--------------   76 (136)
Q Consensus        13 l~~~f~~~G~v~~~-~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~--------------   76 (136)
                      +..+|.-..-..-. .++. ..|+-.|.+.|.|.|++.-+.|++ -|.+-++++.+.+-.+....-              
T Consensus        77 ia~ff~gl~ia~gg~aKOG~~qgrRnge~lvrf~d~e~Rdlalk-Rhkhh~g~ryievYka~ge~f~~iagg~s~e~~~f  155 (508)
T KOG1365|consen   77 IARFFKGLNIANGGRALCLNAQGRRNGEALVRFVDPEGRDLALK-RHKHHMGTRYIEVYKATGEEFLKIAGGTSNEAAPF  155 (508)
T ss_pred             HHHHHhhhhccccceeeeehhhhccccceEEEecCchhhhhhhH-hhhhhccCCceeeeccCchhheEecCCccccCCCC
Confidence            55566544332222 2333 667888999999999999999998 467888899988865443210              


Q ss_pred             --CCCCceEEEcCCCCCCCHHHHHHhhcCC----CceEEEEEEeCCCCCCccceEeecCccccc
Q psy6353          77 --SIKGANLYVSGLPKHMSQQELESLFSPY----GRIITSRILCDNLATENGKYYSGLGGRERL  134 (136)
Q Consensus        77 --~~~~~~l~v~nl~~~~t~~~l~~~f~~~----G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~  134 (136)
                        ....--+.+++||.++++.|+.++|.+-    |..+.+-.+..+++...|.|||.|+.+|.+
T Consensus       156 lsk~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~ee~a  219 (508)
T KOG1365|consen  156 LSKENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACEEDA  219 (508)
T ss_pred             CCcccceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCHHHH
Confidence              1123458889999999999999999733    234556666666666667799999999876

>KOG1548|consensus

Probab=98.08  E-value=1.8e-05  Score=56.40  Aligned_cols=60  Identities=17%  Similarity=0.247  Sum_probs=53.1

Q ss_pred             HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCC
Q psy6353          13 YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS   74 (136)
Q Consensus        13 l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~   74 (136)
                      |.+-+++||+|.+|.+.  ..++.|-+.|.|.+.+.|+.|++.|+|..+.||.|....+..+
T Consensus       293 l~eec~K~G~v~~vvv~--d~hPdGvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i~DG~  352 (382)
T KOG1548|consen  293 LTEECEKFGQVRKVVVY--DRHPDGVVTVSFRNNEEADQCIQTMDGRWFDGRQLTASIWDGK  352 (382)
T ss_pred             HHHHHHHhCCcceEEEe--ccCCCceeEEEeCChHHHHHHHHHhcCeeecceEEEEEEeCCc
Confidence            56778999999999885  4567899999999999999999999999999999999877644

>KOG4661|consensus

Probab=98.07  E-value=5.5e-06  Score=62.62  Aligned_cols=56  Identities=23%  Similarity=0.472  Sum_probs=49.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccc-eEeecCccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGK-YYSGLGGRERL  134 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~-~fv~f~~~e~~  134 (136)
                      -+++|||++|...+..-||+.+|++||+|+-.+++++..+...++ +||.|.+.++|
T Consensus       404 ~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eA  460 (940)
T KOG4661|consen  404 LGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEA  460 (940)
T ss_pred             cccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHH
Confidence            457899999999999999999999999999999999976666655 79999998876

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

Probab=98.01  E-value=1.1e-05  Score=47.90  Aligned_cols=55  Identities=13%  Similarity=0.170  Sum_probs=47.5

Q ss_pred             ceEEEcCCCCCCCHHHHHHhhcCC--CceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          81 ANLYVSGLPKHMSQQELESLFSPY--GRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        81 ~~l~v~nl~~~~t~~~l~~~f~~~--G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      +||.|+|||...|.++|.+++...  |...-+.++-|..++.+ |.|||-|.+.+.+.
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~   59 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAI   59 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHH
Confidence            689999999999999999988754  67778999999888887 66999999988763

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

>KOG4206|consensus

Probab=97.97  E-value=3.9e-05  Score=51.67  Aligned_cols=68  Identities=16%  Similarity=0.330  Sum_probs=57.9

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeC-CceEEEEeeC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQ-NKTIKVSYAR   72 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~-g~~l~v~~~~   72 (136)
                      +|+.|||.+.+   +..+|++|....+++++.   .-++.|||+|.+...|..|.+.+++..+- ...+++.+++
T Consensus       149 lf~~niP~es~~e~l~~lf~qf~g~keir~i~---~~~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~~a~  220 (221)
T KOG4206|consen  149 LFLTNIPSESESEMLSDLFEQFPGFKEIRLIP---PRSGIAFVEFLSDRQASAAQQALQGFKITKKNTMQITFAK  220 (221)
T ss_pred             EEEecCCcchhHHHHHHHHhhCcccceeEecc---CCCceeEEecchhhhhHHHhhhhccceeccCceEEecccC
Confidence            68899999998   899999999999998876   34578999999999999999999998776 6677776553

>KOG3152|consensus

Probab=97.90  E-value=5.5e-06  Score=56.70  Aligned_cols=64  Identities=13%  Similarity=0.215  Sum_probs=54.8

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cC--------CCcee----eEEEEcCCHHHHHHHHHHHcCceeCCc
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--ST--------AQSLG----YGFVNYHRPEDAEKAINTLNGLRLQNK   64 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~--------~~~kg----~~fv~f~~~~~a~~a~~~~~~~~~~g~   64 (136)
                      ||++++|..+.   |++++++||.|-.|.+..  .+        |.+++    -|+|+|.+...|..+...||+..|+|+
T Consensus        77 vylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~Iggk  156 (278)
T KOG3152|consen   77 VYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTPIGGK  156 (278)
T ss_pred             EEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCccCCC
Confidence            79999999998   999999999999999877  22        22222    478999999999999999999999987


Q ss_pred             e
Q psy6353          65 T   65 (136)
Q Consensus        65 ~   65 (136)
                      .
T Consensus       157 k  157 (278)
T KOG3152|consen  157 K  157 (278)
T ss_pred             C
Confidence            5

>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=97.85  E-value=1.9e-05  Score=47.81  Aligned_cols=50  Identities=20%  Similarity=0.300  Sum_probs=31.3

Q ss_pred             ceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          81 ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        81 ~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ..|.+.+++..++.++|++.|++||.|..|.+.+..     ..+||+|.+.|.|.
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~-----~~g~VRf~~~~~A~   51 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGD-----TEGYVRFKTPEAAQ   51 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT------SEEEEEESS---HH
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCC-----CEEEEEECCcchHH
Confidence            468899999999999999999999999998777532     56899999998764

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

>KOG4454|consensus

Probab=97.74  E-value=1.6e-05  Score=53.43  Aligned_cols=54  Identities=17%  Similarity=0.148  Sum_probs=48.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRER  133 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~  133 (136)
                      ..++|||.|+...++++-|.++|-+-|+|..+.|+.+..... ++|||.|+++-.
T Consensus         8 ~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~-kFa~v~f~~E~s   61 (267)
T KOG4454|consen    8 MDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQ-KFAYVFFPNENS   61 (267)
T ss_pred             hhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCC-ceeeeecccccc
Confidence            468999999999999999999999999999999998876665 599999998754

>KOG0533|consensus

Probab=97.72  E-value=4.1e-05  Score=52.74  Aligned_cols=57  Identities=19%  Similarity=0.358  Sum_probs=50.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ...+++|.|||..++++||+++|..||.+..+-+-.++.+.+.+.+=|.|+..+++.
T Consensus        82 ~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~  138 (243)
T KOG0533|consen   82 RSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAE  138 (243)
T ss_pred             CcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHH
Confidence            447899999999999999999999999898899998888878788999999887654

>KOG0115|consensus

Probab=97.72  E-value=8.1e-05  Score=51.13  Aligned_cols=80  Identities=24%  Similarity=0.286  Sum_probs=68.7

Q ss_pred             HHHHHHHHHHcCceeCCceEEEEeeCCCCCCCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEe
Q psy6353          47 EDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYS  126 (136)
Q Consensus        47 ~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv  126 (136)
                      .-|..|..+|++...-++.+++.++..       ..|+|.|+++.++-+.+.+.|+.||+|....+..|......+.+.|
T Consensus         5 t~ae~ak~eLd~~~~~~~~lr~rfa~~-------a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r~k~t~eg~v   77 (275)
T KOG0115|consen    5 TLAEIAKRELDGRFPKGRSLRVRFAMH-------AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDRGKPTREGIV   77 (275)
T ss_pred             cHHHHHHHhcCCCCCCCCceEEEeecc-------ceEEEEecchhhhhHHHHHhhhhcCccchheeeecccccccccchh
Confidence            456777778999999999999999863       5699999999999999999999999999888888877777788899


Q ss_pred             ecCcccc
Q psy6353         127 GLGGRER  133 (136)
Q Consensus       127 ~f~~~e~  133 (136)
                      +|..+=.
T Consensus        78 ~~~~k~~   84 (275)
T KOG0115|consen   78 EFAKKPN   84 (275)
T ss_pred             hhhcchh
Confidence            9887543

>KOG0106|consensus

Probab=97.60  E-value=4.3e-05  Score=51.66  Aligned_cols=62  Identities=19%  Similarity=0.318  Sum_probs=52.1

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEE
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVS   69 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~   69 (136)
                      +.+.+++..+.   |++.|+++|.+.....      ..+++||.|...++|..|+..+++..+.++.|.+.
T Consensus       102 ~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~------~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~~  166 (216)
T KOG0106|consen  102 LIVRNLSLRVSWQDLKDHFRPAGEVTYVDA------RRNFAFVEFSEQEDAKRALEKLDGKKLNGRRISVE  166 (216)
T ss_pred             eeeccchhhhhHHHHhhhhcccCCCchhhh------hccccceeehhhhhhhhcchhccchhhcCceeeec
Confidence            35667777774   9999999999854433      35789999999999999999999999999999994

>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=97.59  E-value=0.0002  Score=43.32  Aligned_cols=52  Identities=21%  Similarity=0.336  Sum_probs=31.0

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHc
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLN   57 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~   57 (136)
                      |.+.+++..++   |++.|++||+|..|.+.+  |.  .-|+|.|.+++.|+.|+.++.
T Consensus         4 l~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~--G~--~~g~VRf~~~~~A~~a~~~~~   58 (105)
T PF08777_consen    4 LKFSGLGEPTSREDIKEAFSQFGEVAYVDFSR--GD--TEGYVRFKTPEAAQKALEKLK   58 (105)
T ss_dssp             EEEEE--SS--HHHHHHHT-SS--EEEEE--T--T---SEEEEEESS---HHHHHHHHH
T ss_pred             EEEecCCCCcCHHHHHHHHHhcCCcceEEecC--CC--CEEEEEECCcchHHHHHHHHH
Confidence            45666777776   999999999888877754  33  248999999999999998663

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

>KOG4209|consensus

Probab=97.53  E-value=0.0001  Score=50.64  Aligned_cols=58  Identities=16%  Similarity=0.253  Sum_probs=51.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERL  134 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~  134 (136)
                      ..+...+|++|+....|.+.+...|+.||.+..+.++.|...+.. +.+|++|.+.+..
T Consensus        98 ~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~  156 (231)
T KOG4209|consen   98 EVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELV  156 (231)
T ss_pred             ccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhh
Confidence            456788999999999999999999999999999999999988765 6699999998764

>KOG1995|consensus

Probab=97.52  E-value=8.4e-05  Score=53.21  Aligned_cols=74  Identities=22%  Similarity=0.198  Sum_probs=60.2

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeE--------EEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEE
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEI--------CVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKV   68 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~--------~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v   68 (136)
                      +||.++|+.++   +.++|.+.|.|..        +++-+  .|+.+||-|.|+|.+...|++|+.-+++..+.+..|+|
T Consensus        69 i~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~gn~ikv  148 (351)
T KOG1995|consen   69 IFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFCGNTIKV  148 (351)
T ss_pred             ceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccccCCCchh
Confidence            68999999998   6777777776532        33333  68999999999999999999999999999999998888


Q ss_pred             EeeCCCC
Q psy6353          69 SYARPSS   75 (136)
Q Consensus        69 ~~~~~~~   75 (136)
                      ..+..+.
T Consensus       149 s~a~~r~  155 (351)
T KOG1995|consen  149 SLAERRT  155 (351)
T ss_pred             hhhhhcc
Confidence            7665443

>KOG0151|consensus

Probab=97.49  E-value=0.00011  Score=56.87  Aligned_cols=57  Identities=19%  Similarity=0.320  Sum_probs=47.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCC----CccceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLAT----ENGKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~----~~~~~fv~f~~~e~~~  135 (136)
                      ..+++|++||++++++++|-..|+.||+|.+++|++....-    .+-++||-|.++-++.
T Consensus       173 ~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~e  233 (877)
T KOG0151|consen  173 QTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAE  233 (877)
T ss_pred             cccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHH
Confidence            45789999999999999999999999999999999876322    2245899998876543

>KOG4210|consensus

Probab=97.43  E-value=8.6e-05  Score=52.61  Aligned_cols=72  Identities=11%  Similarity=0.238  Sum_probs=63.4

Q ss_pred             ecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           4 QTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         4 v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      +.+++..++   |++.|..+|.+..++++.  .++.++|+|++.|.+...+..++.. +...+.++++.+....+...
T Consensus       190 ~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~  266 (285)
T KOG4210|consen  190 VGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEEDEPRPK  266 (285)
T ss_pred             ecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCcccccccCCCCcc
Confidence            889999998   556888999999998888  7899999999999999999999886 78899999999988877654

>KOG4307|consensus

Probab=97.43  E-value=0.00039  Score=54.01  Aligned_cols=121  Identities=12%  Similarity=-0.039  Sum_probs=83.1

Q ss_pred             HHHHhcc-CCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCC--------------C-
Q psy6353          13 YEKVHLG-FSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS--------------E-   76 (136)
Q Consensus        13 l~~~f~~-~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~--------------~-   76 (136)
                      ++++|-- +-.-..+...+..+...|-++|.|....+++.|++ -|...+-.|.+.+...-...              . 
T Consensus       328 ~rkfF~g~~~~~~~l~~~~v~~~~tG~~~v~f~~~~~~q~A~~-rn~~~~~~R~~q~~P~g~~~~~~a~~~~~~~~~~~~  406 (944)
T KOG4307|consen  328 GRKFFPGRNAQSTDLSENRVAPPQTGRKTVMFTPQAPFQNAFT-RNPSDDVNRPFQTGPPGNLGRNGAPPFQAGVPPPVI  406 (944)
T ss_pred             hhhhcCcccccccchhhhhcCCCcCCceEEEecCcchHHHHHh-cCchhhhhcceeecCCCccccccCccccccCCCCcc
Confidence            5666532 22333333333233336789999999999999988 35555667777764321100              0 


Q ss_pred             ------------------------CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEE-EEEEeCCCCCCccceEeecCcc
Q psy6353          77 ------------------------SIKGANLYVSGLPKHMSQQELESLFSPYGRIIT-SRILCDNLATENGKYYSGLGGR  131 (136)
Q Consensus        77 ------------------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~-~~i~~~~~~~~~~~~fv~f~~~  131 (136)
                                              ...+..|||..||..+++.++-++|..--.|++ +.|.+.++.-..+.|||.|..+
T Consensus       407 ~~~hg~p~~~pr~~~~~gq~vp~P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~P~~~~~~~afv~F~~~  486 (944)
T KOG4307|consen  407 QNNHGRPIAPPRAMVRPGQNVPFPGGAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRLPTDLLRPAAFVAFIHP  486 (944)
T ss_pred             cccCCCCCCCcccccCCCCCCCCCCCccceEEeccCCccccccchhhhhhhhhhhhheeEeccCCcccccchhhheeccc
Confidence                                    123468999999999999999999998777776 7777777666667799999997


Q ss_pred             ccc
Q psy6353         132 ERL  134 (136)
Q Consensus       132 e~~  134 (136)
                      ++.
T Consensus       487 ~a~  489 (944)
T KOG4307|consen  487 TAP  489 (944)
T ss_pred             ccc
Confidence            654

>KOG0128|consensus

Probab=97.42  E-value=5.6e-06  Score=64.78  Aligned_cols=121  Identities=22%  Similarity=0.194  Sum_probs=92.6

Q ss_pred             HHHHhccCCCeeEEEEEc-c-CCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCCC----------CCC
Q psy6353          13 YEKVHLGFSDAEICVFLI-S-TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES----------IKG   80 (136)
Q Consensus        13 l~~~f~~~G~v~~~~~~~-~-~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~~----------~~~   80 (136)
                      .+..|..+|.+..+..+. . ..+..-++++.+....+++.|.. ..+..+.++...+..+.+....          ...
T Consensus       589 ~~~~~k~~~~vekv~~p~~g~k~h~q~~~~~~~s~~~~~esat~-pa~~~~a~~~~av~~ad~~~~~~~~kvs~n~~R~~  667 (881)
T KOG0128|consen  589 QRRQFKGEGNVEKVNGPKRGFKAHEQPQQQKVQSKHGSAESATV-PAGGALANRSAAVGLADAEEKEENFKVSPNEIRDL  667 (881)
T ss_pred             hHHHhhcccccccccCccccccccccchhhhhhccccchhhccc-ccccccCCccccCCCCCchhhhhccCcCchHHHHH
Confidence            356788899999998887 2 22222278888988888888877 5677888888888776665422          123


Q ss_pred             ceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCccccc
Q psy6353          81 ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERL  134 (136)
Q Consensus        81 ~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~  134 (136)
                      .++|++|++..+.+.+|...|..+|.+..+++.--.+++.. |.+|++|.+.+.+
T Consensus       668 ~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~  722 (881)
T KOG0128|consen  668 IKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHA  722 (881)
T ss_pred             HHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCch
Confidence            57899999999999999999999999888777744445555 4599999998865

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

Probab=97.42  E-value=0.00021  Score=37.78  Aligned_cols=50  Identities=18%  Similarity=0.386  Sum_probs=38.3

Q ss_pred             ceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCccccccC
Q psy6353          81 ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLRR  136 (136)
Q Consensus        81 ~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~~  136 (136)
                      +.|-|.+.|++..+. +...|.+||+|..+.+.     ......|+.|.++.++++
T Consensus         2 ~wI~V~Gf~~~~~~~-vl~~F~~fGeI~~~~~~-----~~~~~~~l~y~~~~~ae~   51 (53)
T PF14605_consen    2 TWISVSGFPPDLAEE-VLEHFASFGEIVDIYVP-----ESTNWMYLKYKSRKDAEK   51 (53)
T ss_pred             cEEEEEeECchHHHH-HHHHHHhcCCEEEEEcC-----CCCcEEEEEECCHHHHHh
Confidence            467888899886544 55588899999998887     233558999999988764

>KOG4676|consensus

Probab=97.30  E-value=0.00028  Score=51.31  Aligned_cols=114  Identities=9%  Similarity=-0.004  Sum_probs=82.7

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc-c----CCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeC-
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI-S----TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR-   72 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~-~----~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~-   72 (136)
                      +-|.||....|   +..+|...|+|.++.+.. .    -.-....|||-|.|...+..|.. |..+.+-++-|.|...- 
T Consensus        10 Iqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQh-Ltntvfvdraliv~p~~~   88 (479)
T KOG4676|consen   10 IQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQH-LTNTVFVDRALIVRPYGD   88 (479)
T ss_pred             eeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhh-hccceeeeeeEEEEecCC
Confidence            45789999998   899999999999998776 1    12345679999999999988877 55555556555553211 


Q ss_pred             CCCC----------------------------------C---------------------CCCceEEEcCCCCCCCHHHH
Q psy6353          73 PSSE----------------------------------S---------------------IKGANLYVSGLPKHMSQQEL   97 (136)
Q Consensus        73 ~~~~----------------------------------~---------------------~~~~~l~v~nl~~~~t~~~l   97 (136)
                      +...                                  +                     ...+++++.+|+..+...++
T Consensus        89 ~~~p~r~af~~l~~~navprll~pdg~Lp~~~~lt~~nh~p~ailktP~Lp~~~~A~kleeirRt~~v~sl~~~~~l~e~  168 (479)
T KOG4676|consen   89 EVIPDRFAFVELADQNAVPRLLPPDGVLPGDRPLTKINHSPNAILKTPELPPQAAAKKLEEIRRTREVQSLISAAILPES  168 (479)
T ss_pred             CCCccHHHHHhcCcccccccccCCCCccCCCCccccccCCccceecCCCCChHhhhhhhHHHHhhhhhhcchhhhcchhh
Confidence            1000                                  0                     01257899999999999999


Q ss_pred             HHhhcCCCceEEEEEEeCC
Q psy6353          98 ESLFSPYGRIITSRILCDN  116 (136)
Q Consensus        98 ~~~f~~~G~v~~~~i~~~~  116 (136)
                      -+.|..+|+|....+....
T Consensus       169 ~e~f~r~Gev~ya~~ask~  187 (479)
T KOG4676|consen  169 GESFERKGEVSYAHTASKS  187 (479)
T ss_pred             hhhhhhcchhhhhhhhccC
Confidence            9999999998776655443

>PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT []

Probab=97.23  E-value=0.0019  Score=38.71  Aligned_cols=70  Identities=13%  Similarity=0.099  Sum_probs=46.4

Q ss_pred             eeecCCChhhh--HHHHhccCCCeeEEEEEc---------cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEE-EE
Q psy6353           2 VYQTLLNKLFT--YEKVHLGFSDAEICVFLI---------STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIK-VS   69 (136)
Q Consensus         2 v~v~nl~~~~~--l~~~f~~~G~v~~~~~~~---------~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~-v~   69 (136)
                      |.|=+.|...+  +-+.|++||.|.+..-..         ........--|+|.++.+|++|+. .||..+.|..+- |.
T Consensus         9 VtVFGfp~~~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~~mvGV~   87 (100)
T PF05172_consen    9 VTVFGFPPSASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGSLMVGVK   87 (100)
T ss_dssp             EEEE---GGGHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTCEEEEEE
T ss_pred             EEEEccCHHHHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCcEEEEEE
Confidence            45556677666  889999999997775110         001234578899999999999999 589999886544 55


Q ss_pred             eeC
Q psy6353          70 YAR   72 (136)
Q Consensus        70 ~~~   72 (136)
                      +.+
T Consensus        88 ~~~   90 (100)
T PF05172_consen   88 PCD   90 (100)
T ss_dssp             E-H
T ss_pred             EcH
Confidence            553

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.

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

Probab=97.22  E-value=0.00083  Score=35.45  Aligned_cols=48  Identities=17%  Similarity=0.199  Sum_probs=36.9

Q ss_pred             eeecCCChhhh--HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHH
Q psy6353           2 VYQTLLNKLFT--YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAI   53 (136)
Q Consensus         2 v~v~nl~~~~~--l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~   53 (136)
                      |-|.+.|....  +...|.+||+|..+.+.    ...-..++.|.++.+|+.|+
T Consensus         4 I~V~Gf~~~~~~~vl~~F~~fGeI~~~~~~----~~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    4 ISVSGFPPDLAEEVLEHFASFGEIVDIYVP----ESTNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             EEEEeECchHHHHHHHHHHhcCCEEEEEcC----CCCcEEEEEECCHHHHHhhC
Confidence            44555555554  77899999999998775    23457999999999999884

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

Probab=97.15  E-value=0.0027  Score=40.43  Aligned_cols=54  Identities=17%  Similarity=0.377  Sum_probs=42.2

Q ss_pred             HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCC
Q psy6353          13 YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP   73 (136)
Q Consensus        13 l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~   73 (136)
                      |.+.|..||.+.=++...      +.-+|+|.+.++|-+|+. ++|..+.|+.++++.-.|
T Consensus        53 ll~~~~~~GevvLvRfv~------~~mwVTF~dg~sALaals-~dg~~v~g~~l~i~LKtp  106 (146)
T PF08952_consen   53 LLQKFAQYGEVVLVRFVG------DTMWVTFRDGQSALAALS-LDGIQVNGRTLKIRLKTP  106 (146)
T ss_dssp             HHHHHHCCS-ECEEEEET------TCEEEEESSCHHHHHHHH-GCCSEETTEEEEEEE---
T ss_pred             HHHHHHhCCceEEEEEeC------CeEEEEECccHHHHHHHc-cCCcEECCEEEEEEeCCc
Confidence            778889999876555443      357899999999999999 899999999999975443

; PDB: 1UFW_A 2DNR_A.

>KOG4660|consensus

Probab=97.12  E-value=0.00026  Score=53.40  Aligned_cols=59  Identities=24%  Similarity=0.381  Sum_probs=45.0

Q ss_pred             CCCCCCCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCccccc
Q psy6353          72 RPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERL  134 (136)
Q Consensus        72 ~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~  134 (136)
                      .|.......++|+|-|||..+++++|..+|+.||+|..++..+..    .+-.||+|=|-..|
T Consensus        67 np~~~~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~~----~~~~~v~FyDvR~A  125 (549)
T KOG4660|consen   67 NPSEKDMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPNK----RGIVFVEFYDVRDA  125 (549)
T ss_pred             CCCcccCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhccccc----CceEEEEEeehHhH
Confidence            344445677899999999999999999999999999997655432    23358887665444

>KOG1457|consensus

Probab=97.09  E-value=0.00073  Score=45.81  Aligned_cols=58  Identities=19%  Similarity=0.260  Sum_probs=47.1

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCcee
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRL   61 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~   61 (136)
                      |||.||..+++   |+.+|+.|.....+++..  ......||++|.+.+.|-.|+..|+|..+
T Consensus       213 lfianl~~~~~ed~l~~~~~~~~gf~~l~~~~--~~g~~vaf~~~~~~~~at~am~~lqg~~~  273 (284)
T KOG1457|consen  213 LFIANLGPNCTEDELKQLLSRYPGFHILKIRA--RGGMPVAFADFEEIEQATDAMNHLQGNLL  273 (284)
T ss_pred             HhhhccCCCCCHHHHHHHHHhCCCceEEEEec--CCCcceEeecHHHHHHHHHHHHHhhccee
Confidence            68999999998   999999999887666643  22346799999999999999988888655

>KOG1996|consensus

Probab=97.09  E-value=0.0021  Score=45.30  Aligned_cols=59  Identities=17%  Similarity=0.220  Sum_probs=47.9

Q ss_pred             HHHHhccCCCeeEEEEEcc---CCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEee
Q psy6353          13 YEKVHLGFSDAEICVFLIS---TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA   71 (136)
Q Consensus        13 l~~~f~~~G~v~~~~~~~~---~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~   71 (136)
                      .++-+++||.|..|.|...   .-.-.---||+|...++|.+|+-.|||..++||.++.++.
T Consensus       303 ~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fy  364 (378)
T KOG1996|consen  303 TKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFY  364 (378)
T ss_pred             HHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheec
Confidence            6788999999999876661   1222334799999999999999999999999999887654

>KOG2202|consensus

Probab=97.08  E-value=0.00025  Score=48.79  Aligned_cols=55  Identities=20%  Similarity=0.252  Sum_probs=48.5

Q ss_pred             ccCCCeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeC
Q psy6353          18 LGFSDAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR   72 (136)
Q Consensus        18 ~~~G~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~   72 (136)
                      .+||.|.++++.. ..-+-.|=++|.|...++|++|+..||+..+.|++|.+..+.
T Consensus        91 ~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~p  146 (260)
T KOG2202|consen   91 DKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSP  146 (260)
T ss_pred             HHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecC
Confidence            4899999998887 555567889999999999999999999999999999997654

>KOG1855|consensus

Probab=96.96  E-value=0.00087  Score=49.32  Aligned_cols=58  Identities=17%  Similarity=0.089  Sum_probs=47.5

Q ss_pred             CeeecCCChhhh---HHHHhccCCCeeEEEEEcc-------CCCc--------eeeEEEEcCCHHHHHHHHHHHcC
Q psy6353           1 MVYQTLLNKLFT---YEKVHLGFSDAEICVFLIS-------TAQS--------LGYGFVNYHRPEDAEKAINTLNG   58 (136)
Q Consensus         1 ~v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~-------~~~~--------kg~~fv~f~~~~~a~~a~~~~~~   58 (136)
                      ||.+.|||..-.   |.++|+.+|.|..|+++..       .+.+        +-+|+|+|...+.|.+|.+.+|.
T Consensus       233 tivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~~  308 (484)
T KOG1855|consen  233 TIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLNP  308 (484)
T ss_pred             eEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhch
Confidence            577889998776   9999999999999999871       1222        45899999999999999987754

>PF07292 NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909 This entry represents a domain of approximately 90 residues that is tandemly repeated within interferon-induced 35 kDa protein (IFP 35) and the homologous N-myc-interactor (Nmi)

Probab=96.94  E-value=0.01  Score=34.67  Aligned_cols=63  Identities=14%  Similarity=0.358  Sum_probs=44.9

Q ss_pred             EEEEcCCHHHHHHHHHH-HcCceeCCceEEEEeeC--CCC-------CCCCCceEEEcCCCCCCCHHHHHHhh
Q psy6353          39 GFVNYHRPEDAEKAINT-LNGLRLQNKTIKVSYAR--PSS-------ESIKGANLYVSGLPKHMSQQELESLF  101 (136)
Q Consensus        39 ~fv~f~~~~~a~~a~~~-~~~~~~~g~~l~v~~~~--~~~-------~~~~~~~l~v~nl~~~~t~~~l~~~f  101 (136)
                      |.|+|.+..-|+..++. -+...+++..+.+.-+.  ...       .....+++-++|||...++++|++..
T Consensus         1 AlITF~e~~VA~~i~~~~~~~v~l~~~~~~V~v~P~~~~~~~k~qv~~~vs~rtVlvsgip~~l~ee~l~D~L   73 (88)
T PF07292_consen    1 ALITFEEEGVAQRILKKKKHPVPLEDCCVRVKVSPVTLGHLQKFQVFSGVSKRTVLVSGIPDVLDEEELRDKL   73 (88)
T ss_pred             CEEEeCcHHHHHHHHhCCEEEEEECCEEEEEEEEeEecCCceEEEEEEcccCCEEEEeCCCCCCChhhheeeE
Confidence            67999999999998873 23355666666553221  111       12467899999999999999999855

This domain mediates Nmi-Nmi protein interactions and subcellular localisation [].

>KOG3152|consensus

Probab=96.84  E-value=0.00032  Score=48.26  Aligned_cols=40  Identities=23%  Similarity=0.396  Sum_probs=36.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCC
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLA  118 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~  118 (136)
                      ....||+++||+.+....|+++++.||+|-.+.+.+...+
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s  112 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDS  112 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhH
Confidence            5578999999999999999999999999999998877654

>KOG1855|consensus

Probab=96.78  E-value=0.0038  Score=46.10  Aligned_cols=58  Identities=19%  Similarity=0.197  Sum_probs=46.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeC---CCCCCc-----------cceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD---NLATEN-----------GKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~---~~~~~~-----------~~~fv~f~~~e~~~  135 (136)
                      ..+++|.+.|||.+-.-+.|.++|+.+|.|..|+|+..   +...+.           -+|+|+|+..|.|+
T Consensus       229 l~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~  300 (484)
T KOG1855|consen  229 LPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAAR  300 (484)
T ss_pred             cccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHH
Confidence            47899999999999988999999999999999999977   332221           23677777777665

>KOG4307|consensus

Probab=96.73  E-value=0.005  Score=48.17  Aligned_cols=68  Identities=16%  Similarity=0.184  Sum_probs=54.4

Q ss_pred             eeecCCChhhhHHHHhccC---CCe-eEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEE
Q psy6353           2 VYQTLLNKLFTYEKVHLGF---SDA-EICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVS   69 (136)
Q Consensus         2 v~v~nl~~~~~l~~~f~~~---G~v-~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~   69 (136)
                      |-+.|+|..++|+++.+.|   -.. .+|.+-+ ..|...|-|.|.|++.++|.+|...+++..|.++.+.+.
T Consensus       870 ~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~nd~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~V~l~  942 (944)
T KOG4307|consen  870 LSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLR  942 (944)
T ss_pred             EEecCCCccccHHHHHHHhcccccCCCceeEeecCCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEE
Confidence            3467999999966665554   433 3455555 889999999999999999999999999999999998875

>KOG4849|consensus

Probab=96.65  E-value=0.0013  Score=47.32  Aligned_cols=67  Identities=16%  Similarity=0.152  Sum_probs=50.5

Q ss_pred             eeecCCChhhh---HHHHhccCC--CeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEE
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFS--DAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKV   68 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G--~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v   68 (136)
                      +||+||-+..|   |.+.....|  .+.+++...  .+|+|||||++...+...+++-++-|...+|+|+.=.|
T Consensus        83 ~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V  156 (498)
T KOG4849|consen   83 CYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTV  156 (498)
T ss_pred             EEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCee
Confidence            68999866666   444444444  455565555  78999999999999988888899988889999875443

>KOG4676|consensus

Probab=96.29  E-value=0.0046  Score=45.21  Aligned_cols=55  Identities=13%  Similarity=0.227  Sum_probs=45.3

Q ss_pred             CceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCC----CccceEeecCccccc
Q psy6353          80 GANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLAT----ENGKYYSGLGGRERL  134 (136)
Q Consensus        80 ~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~----~~~~~fv~f~~~e~~  134 (136)
                      ...|.|.||.+++|.++++.+|...|+|..+.|..+...-    ..+.+||.|.+...+
T Consensus         7 ~~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv   65 (479)
T KOG4676|consen    7 LGVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSV   65 (479)
T ss_pred             CceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcce
Confidence            3479999999999999999999999999999988754333    335699999987643

>KOG2068|consensus

Probab=96.22  E-value=0.0015  Score=46.67  Aligned_cols=73  Identities=16%  Similarity=0.225  Sum_probs=53.5

Q ss_pred             eeecCCChhhh------HHHHhccCCCeeEEEEEc-cC---C-CceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEe
Q psy6353           2 VYQTLLNKLFT------YEKVHLGFSDAEICVFLI-ST---A-QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY   70 (136)
Q Consensus         2 v~v~nl~~~~~------l~~~f~~~G~v~~~~~~~-~~---~-~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~   70 (136)
                      +|+..|+....      -.+.|.+||.+..+..-+ .+   + ....-++|+|...++|..|+...+|..++|+.+++..
T Consensus        80 vyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lka~~  159 (327)
T KOG2068|consen   80 VYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALKASL  159 (327)
T ss_pred             hhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhHHhh
Confidence            45666664333      356799999999887766 31   1 1223489999999999999999999999999888766


Q ss_pred             eCCC
Q psy6353          71 ARPS   74 (136)
Q Consensus        71 ~~~~   74 (136)
                      ..++
T Consensus       160 gttk  163 (327)
T KOG2068|consen  160 GTTK  163 (327)
T ss_pred             CCCc
Confidence            5443

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=96.15  E-value=0.031  Score=35.55  Aligned_cols=55  Identities=13%  Similarity=0.094  Sum_probs=43.9

Q ss_pred             HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCC
Q psy6353          13 YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP   73 (136)
Q Consensus        13 l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~   73 (136)
                      +....+.||+|.++.++-     +--|.|.|.|..+|-.|+.+++. ...|..+.|.|...
T Consensus       107 V~~~Ls~fGpI~SVT~cG-----rqsavVvF~d~~SAC~Av~Af~s-~~pgtm~qCsWqqr  161 (166)
T PF15023_consen  107 VIQRLSVFGPIQSVTLCG-----RQSAVVVFKDITSACKAVSAFQS-RAPGTMFQCSWQQR  161 (166)
T ss_pred             HHHHHHhcCCcceeeecC-----CceEEEEehhhHHHHHHHHhhcC-CCCCceEEeecccc
Confidence            445568899999997642     33589999999999999999855 67788899988653

>KOG0115|consensus

Probab=96.04  E-value=0.0087  Score=41.41  Aligned_cols=55  Identities=20%  Similarity=0.236  Sum_probs=48.6

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHH
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTL   56 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~   56 (136)
                      |||.||+.-++   +++-|++||++....++- ..++..+-++|.|...-.|..|....
T Consensus        34 l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r~k~t~eg~v~~~~k~~a~~a~rr~   92 (275)
T KOG0115|consen   34 LYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDRGKPTREGIVEFAKKPNARKAARRC   92 (275)
T ss_pred             EEEEecchhhhhHHHHHhhhhcCccchheeeecccccccccchhhhhcchhHHHHHHHh
Confidence            79999999888   888999999998776666 88889999999999999999988765

>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=95.76  E-value=0.011  Score=39.12  Aligned_cols=56  Identities=16%  Similarity=0.242  Sum_probs=34.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcC-CCce---EEEE-EEeCCCCCCc--cceEeecCccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSP-YGRI---ITSR-ILCDNLATEN--GKYYSGLGGRERL  134 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~-~G~v---~~~~-i~~~~~~~~~--~~~fv~f~~~e~~  134 (136)
                      ...+|.|++||+++|++++.+.+++ ++.-   ..+. ...+......  .-||+.|.+.|.+
T Consensus         6 ~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~   68 (176)
T PF03467_consen    6 EGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDL   68 (176)
T ss_dssp             ---EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHH
T ss_pred             cCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHH
Confidence            4568999999999999999999988 6765   2333 1222222222  2389999998875

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.

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

Probab=95.75  E-value=0.033  Score=37.13  Aligned_cols=58  Identities=22%  Similarity=0.339  Sum_probs=43.4

Q ss_pred             HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHc--CceeCCceEEEEeeCCC
Q psy6353          13 YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLN--GLRLQNKTIKVSYARPS   74 (136)
Q Consensus        13 l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~--~~~~~g~~l~v~~~~~~   74 (136)
                      |+++|..++.+......+    +-+-..|.|.+.+.|.+|...++  +..+.|..+++.++.+.
T Consensus        12 l~~l~~~~~~~~~~~~L~----sFrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~   71 (184)
T PF04847_consen   12 LEELFSTYDPPVQFSPLK----SFRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPT   71 (184)
T ss_dssp             HHHHHHTT-SS-EEEEET----TTTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----S
T ss_pred             HHHHHHhcCCceEEEEcC----CCCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEcccc
Confidence            899999999988887665    44458899999999999999998  89999999999877543

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.

>KOG0129|consensus

Probab=95.71  E-value=0.014  Score=44.07  Aligned_cols=55  Identities=13%  Similarity=0.309  Sum_probs=40.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCC-------CCCCccceEeecCccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDN-------LATENGKYYSGLGGRERL  134 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~-------~~~~~~~~fv~f~~~e~~  134 (136)
                      ..+++|+++||.+++|+.|...|..||.+ .+.++...       ..|.-++.|.-|+++..+
T Consensus       258 ~S~KVFvGGlp~dise~~i~~~F~~FGs~-~VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV  319 (520)
T KOG0129|consen  258 YSRKVFVGGLPWDITEAQINASFGQFGSV-KVDWPGKANSRGRAPPKGSYGYVFLVFEDERSV  319 (520)
T ss_pred             cccceeecCCCccccHHHHHhhcccccce-EeecCCCccccccCCCCCcccEEEEEecchHHH
Confidence            56899999999999999999999999975 34444211       122223678888887654

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=95.71  E-value=0.011  Score=42.56  Aligned_cols=57  Identities=23%  Similarity=0.411  Sum_probs=41.6

Q ss_pred             CceEEEcCCCCCCCHHH----H--HHhhcCCCceEEEEEEeCC----CCCCccceEeecCccccccC
Q psy6353          80 GANLYVSGLPKHMSQQE----L--ESLFSPYGRIITSRILCDN----LATENGKYYSGLGGRERLRR  136 (136)
Q Consensus        80 ~~~l~v~nl~~~~t~~~----l--~~~f~~~G~v~~~~i~~~~----~~~~~~~~fv~f~~~e~~~~  136 (136)
                      ..-+||-+||+.+..++    |  .+.|++||+|..+.+-+..    .+..+-|.|+.|.+.|+|.|
T Consensus       114 KNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAar  180 (480)
T COG5175         114 KNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAAR  180 (480)
T ss_pred             cceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHH
Confidence            35689999999876555    2  5699999999987776543    12223456999999998864

>KOG2135|consensus

Probab=95.70  E-value=0.0087  Score=44.79  Aligned_cols=58  Identities=22%  Similarity=0.231  Sum_probs=48.5

Q ss_pred             HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCC
Q psy6353          13 YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS   75 (136)
Q Consensus        13 l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~   75 (136)
                      |...|.+||.|..|.+-.    +.-.|.|+|.+..+|-.|.. .++..|.+|.|++.|..+..
T Consensus       390 ln~hfA~fG~i~n~qv~~----~~~~a~vTF~t~aeag~a~~-s~~avlnnr~iKl~whnps~  447 (526)
T KOG2135|consen  390 LNPHFAQFGEIENIQVDY----SSLHAVVTFKTRAEAGEAYA-SHGAVLNNRFIKLFWHNPSP  447 (526)
T ss_pred             hhhhhhhcCccccccccC----chhhheeeeeccccccchhc-cccceecCceeEEEEecCCc
Confidence            888999999999987644    23458999999998877766 68999999999999998754

>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=95.46  E-value=0.0095  Score=34.37  Aligned_cols=47  Identities=23%  Similarity=0.378  Sum_probs=30.2

Q ss_pred             ceEEEcCCCCCCCHHHH----HHhhcCCC-ceEEEEEEeCCCCCCccceEeecCccccccC
Q psy6353          81 ANLYVSGLPKHMSQQEL----ESLFSPYG-RIITSRILCDNLATENGKYYSGLGGRERLRR  136 (136)
Q Consensus        81 ~~l~v~nl~~~~t~~~l----~~~f~~~G-~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~~  136 (136)
                      ..|+|.|||.+.+...+    +.+...|| +|..+  .       .+-|.+.|.+.|.|+|
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v--~-------~~tAilrF~~~~~A~R   54 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV--S-------GGTAILRFPNQEFAER   54 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE-----------TT-EEEEESSHHHHHH
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE--e-------CCEEEEEeCCHHHHHH
Confidence            46899999998877654    56667886 45444  1       2558999999998865

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

>KOG2416|consensus

Probab=95.41  E-value=0.0099  Score=45.73  Aligned_cols=66  Identities=15%  Similarity=0.203  Sum_probs=51.1

Q ss_pred             eeecCCChhhh---HHHHhccCC-CeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeC---CceEEEEee
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFS-DAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQ---NKTIKVSYA   71 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G-~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~---g~~l~v~~~   71 (136)
                      |+|.||=.-||   |++++.+-| .|.+. ||-   +-|..|||.|.+.++|.+...+|||..+.   .+.|.+.+.
T Consensus       447 lhI~nLvRPFTlgQLkelL~rtgg~Vee~-WmD---kIKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~adf~  519 (718)
T KOG2416|consen  447 LHIDNLVRPFTLGQLKELLGRTGGNVEEF-WMD---KIKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLIADFV  519 (718)
T ss_pred             EeeecccccchHHHHHHHHhhccCchHHH-HHH---HhhcceeEecccHHHHHHHHHHHhccccCCCCCceeEeeec
Confidence            78999988888   788888554 45544 544   45677999999999999999999997763   566776654

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

Probab=95.05  E-value=0.081  Score=30.52  Aligned_cols=46  Identities=24%  Similarity=0.503  Sum_probs=31.6

Q ss_pred             eEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCccccc
Q psy6353          82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERL  134 (136)
Q Consensus        82 ~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~  134 (136)
                      .+|--..|..+...||.++|++||.| .|..+-|      ..|||.+..+|.+
T Consensus        10 HVFhltFPkeWK~~DI~qlFspfG~I-~VsWi~d------TSAfV~l~~r~~~   55 (87)
T PF08675_consen   10 HVFHLTFPKEWKTSDIYQLFSPFGQI-YVSWIND------TSAFVALHNRDQA   55 (87)
T ss_dssp             CEEEEE--TT--HHHHHHHCCCCCCE-EEEEECT------TEEEEEECCCHHH
T ss_pred             eEEEEeCchHhhhhhHHHHhccCCcE-EEEEEcC------CcEEEEeecHHHH
Confidence            35544499999999999999999975 4555543      4579998888765

; 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.

>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []

Probab=94.97  E-value=0.16  Score=30.94  Aligned_cols=42  Identities=14%  Similarity=0.215  Sum_probs=33.5

Q ss_pred             CeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCC
Q psy6353          22 DAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQN   63 (136)
Q Consensus        22 ~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g   63 (136)
                      .+..+++++....++-.+.+.|.+.++|+.....+||..+..
T Consensus        40 ~i~~~riird~~pnrymVLikF~~~~~Ad~Fy~~fNGk~Fns   81 (110)
T PF07576_consen   40 DIEHIRIIRDGTPNRYMVLIKFRDQESADEFYEEFNGKPFNS   81 (110)
T ss_pred             cEEEEEEeeCCCCceEEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            455667776333477789999999999999999999987754

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

>KOG0112|consensus

Probab=94.52  E-value=0.014  Score=46.82  Aligned_cols=57  Identities=16%  Similarity=0.278  Sum_probs=49.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRER  133 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~  133 (136)
                      ...+.+|+++|++..+++.+|+..|..+|.|..+.+-+.+.+..+..+||.|.+...
T Consensus       369 ~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~~~esa~~f~~~~n~dm  425 (975)
T KOG0112|consen  369 FRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHIKTESAYAFVSLLNTDM  425 (975)
T ss_pred             hhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCCCcccchhhhhhhcccc
Confidence            456789999999999999999999999999999999888777777889999877653

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

Probab=94.07  E-value=0.29  Score=28.30  Aligned_cols=45  Identities=20%  Similarity=0.290  Sum_probs=32.4

Q ss_pred             CChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHc
Q psy6353           7 LNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLN   57 (136)
Q Consensus         7 l~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~   57 (136)
                      .|.+..   |.++|+.||.| .|.++.     -.-|||...+.+.|..++..+.
T Consensus        16 FPkeWK~~DI~qlFspfG~I-~VsWi~-----dTSAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen   16 FPKEWKTSDIYQLFSPFGQI-YVSWIN-----DTSAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             --TT--HHHHHHHCCCCCCE-EEEEEC-----TTEEEEEECCCHHHHHHHHHHT
T ss_pred             CchHhhhhhHHHHhccCCcE-EEEEEc-----CCcEEEEeecHHHHHHHHHHhc
Confidence            454443   99999999997 454543     1249999999999999988774

; GO: 0003723 RNA binding, 0004535 poly(A)-specific ribonuclease activity, 0046872 metal ion binding, 0006402 mRNA catabolic process, 0005634 nucleus, 0005737 cytoplasm; PDB: 3CTR_A 2ROK_A 3D45_B 1WHV_A.

>KOG4574|consensus

Probab=94.03  E-value=0.038  Score=44.33  Aligned_cols=69  Identities=17%  Similarity=0.200  Sum_probs=54.1

Q ss_pred             eecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeC--CceEEEEeeCCCC
Q psy6353           3 YQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQ--NKTIKVSYARPSS   75 (136)
Q Consensus         3 ~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~--g~~l~v~~~~~~~   75 (136)
                      ++.|.+-..+   |..+|+.||.+.+.+..+    .--.|.|+|.+.+.|..|.++++|+++.  |-+.+|..+++..
T Consensus       302 ~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr----~~N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~~~  375 (1007)
T KOG4574|consen  302 SLENNAVNLTSSSLATLCSDYGSVASAWTLR----DLNMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKTLP  375 (1007)
T ss_pred             hhhcccccchHHHHHHHHHhhcchhhheecc----cccchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEeccccc
Confidence            4455555444   899999999999998776    3346899999999999999999997764  7778887776543

>KOG1995|consensus

Probab=93.92  E-value=0.079  Score=38.42  Aligned_cols=56  Identities=14%  Similarity=0.201  Sum_probs=45.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceEE--------EEEEeCCCCCCccc-eEeecCcccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRIIT--------SRILCDNLATENGK-YYSGLGGRER  133 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~--------~~i~~~~~~~~~~~-~fv~f~~~e~  133 (136)
                      ....++||.++|.+++++++.+.|.++|.|..        +.|-+|..|+..++ +-|.|++.-.
T Consensus        64 s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~  128 (351)
T KOG1995|consen   64 SDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPA  128 (351)
T ss_pred             cccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhh
Confidence            45678999999999999999999999998742        66777888877755 8888877543

>KOG2314|consensus

Probab=93.86  E-value=0.072  Score=41.02  Aligned_cols=58  Identities=17%  Similarity=0.197  Sum_probs=47.4

Q ss_pred             CCCceEEEcCCCCCC------CHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHM------SQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~------t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      .....++|.|+|.--      -..-|..+|+++|++....++.+..+|..|..|+++++...|.
T Consensus        56 g~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~  119 (698)
T KOG2314|consen   56 GFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAK  119 (698)
T ss_pred             CcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHH
Confidence            345778999998532      2346778999999999999999999998888999999987663

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

Probab=93.82  E-value=0.29  Score=26.62  Aligned_cols=49  Identities=18%  Similarity=0.112  Sum_probs=36.6

Q ss_pred             eeecCCChhhh--HHHHhccC----CCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHH
Q psy6353           2 VYQTLLNKLFT--YEKVHLGF----SDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTL   56 (136)
Q Consensus         2 v~v~nl~~~~~--l~~~f~~~----G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~   56 (136)
                      |++.+++..-|  ++.+|..|    ++ ..|.++..+     -|=|-|.+.+.|.+|+.+|
T Consensus         8 vhirGvd~lsT~dI~~y~~~y~~~~~~-~~IEWIdDt-----ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    8 VHIRGVDELSTDDIKAYFSEYFDEEGP-FRIEWIDDT-----SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             EEEEcCCCCCHHHHHHHHHHhcccCCC-ceEEEecCC-----cEEEEECCHHHHHHHHHcC
Confidence            56777877666  88999888    54 467776511     2668999999999998754

>KOG4285|consensus

Probab=93.28  E-value=0.31  Score=34.81  Aligned_cols=53  Identities=15%  Similarity=0.145  Sum_probs=40.6

Q ss_pred             HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEE-EEe
Q psy6353          13 YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIK-VSY   70 (136)
Q Consensus        13 l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~-v~~   70 (136)
                      +..+|+++|.|......    +.--+-.|.|.+..+|++|+. .||..|+|..+. |+.
T Consensus       213 vL~~F~~cG~Vvkhv~~----~ngNwMhirYssr~~A~KALs-kng~ii~g~vmiGVkp  266 (350)
T KOG4285|consen  213 VLNLFSRCGEVVKHVTP----SNGNWMHIRYSSRTHAQKALS-KNGTIIDGDVMIGVKP  266 (350)
T ss_pred             HHHHHHhhCeeeeeecC----CCCceEEEEecchhHHHHhhh-hcCeeeccceEEeeee
Confidence            78899999998766432    333477899999999999999 589888876433 444

>PF14111 DUF4283: Domain of unknown function (DUF4283)

Probab=93.16  E-value=0.074  Score=33.90  Aligned_cols=79  Identities=15%  Similarity=0.154  Sum_probs=58.8

Q ss_pred             ceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCCCC------CCceEEEcCCCCC-CCHHHHHHhhcCCCce
Q psy6353          35 SLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESI------KGANLYVSGLPKH-MSQQELESLFSPYGRI  107 (136)
Q Consensus        35 ~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~~~------~~~~l~v~nl~~~-~t~~~l~~~f~~~G~v  107 (136)
                      ..++..+.|.+.++++.++. .....+.+..+.+....|..+..      ..-=+.+.|||.. ++++-++.+-+.+|++
T Consensus        54 ~~~~fl~~F~~~~d~~~vl~-~~p~~~~~~~~~l~~W~~~~~~~~~~~~~~~vWVri~glP~~~~~~~~~~~i~~~iG~~  132 (153)
T PF14111_consen   54 GDNLFLFQFESEEDRQRVLK-GGPWNFNGHFLILQRWSPDFNPSEVKFEHIPVWVRIYGLPLHLWSEEILKAIGSKIGEP  132 (153)
T ss_pred             CCCeEEEEEEeccceeEEEe-cccccccccchhhhhhcccccccccceeccchhhhhccCCHHHhhhHHHHHHHHhcCCe
Confidence            35789999999999999987 34566778888887666543211      1223667999987 5889999999999999


Q ss_pred             EEEEEEe
Q psy6353         108 ITSRILC  114 (136)
Q Consensus       108 ~~~~i~~  114 (136)
                      ..+....
T Consensus       133 i~vD~~t  139 (153)
T PF14111_consen  133 IEVDENT  139 (153)
T ss_pred             EEEEcCC
Confidence            8885443

>KOG0804|consensus

Probab=92.51  E-value=0.25  Score=37.13  Aligned_cols=63  Identities=10%  Similarity=0.083  Sum_probs=49.9

Q ss_pred             CeeecCCChhhhHHHHhccCC----CeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCC
Q psy6353           1 MVYQTLLNKLFTYEKVHLGFS----DAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQN   63 (136)
Q Consensus         1 ~v~v~nl~~~~~l~~~f~~~G----~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g   63 (136)
                      ||.+--+|..++..++...+|    .|.++++++..-.++=..+|.|.+..+|......+||..+..
T Consensus        76 mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~pnrymvLIkFr~q~da~~Fy~efNGk~Fn~  142 (493)
T KOG0804|consen   76 MLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGMPNRYMVLIKFRDQADADTFYEEFNGKQFNS  142 (493)
T ss_pred             EEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCCCceEEEEEEeccchhHHHHHHHcCCCcCCC
Confidence            678888999999777777666    467788888222244568999999999999999999988764

>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes

Probab=91.85  E-value=1.2  Score=24.49  Aligned_cols=58  Identities=9%  Similarity=0.126  Sum_probs=40.6

Q ss_pred             ecCCChhhh-HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEE
Q psy6353           4 QTLLNKLFT-YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKV   68 (136)
Q Consensus         4 v~nl~~~~~-l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v   68 (136)
                      |.+.+..++ ++..+..|+-. .|..     ...| -||.|.+..+|++|....+|..+.+..+.+
T Consensus         7 vp~~~~~v~d~K~~Lr~y~~~-~I~~-----d~tG-fYIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen    7 VPVHGVTVEDFKKRLRKYRWD-RIRD-----DRTG-FYIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CCCCCccHHHHHHHHhcCCcc-eEEe-----cCCE-EEEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            344444454 77778888753 3332     2235 479999999999999999998888776654

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

>KOG2591|consensus

Probab=91.27  E-value=1.1  Score=34.76  Aligned_cols=74  Identities=12%  Similarity=0.252  Sum_probs=53.9

Q ss_pred             HHHHHHHcCceeCCceEEEEeeCCCCCCCCCceEEEcCCCCCCCHHHHHHhhcC--CCceEEEEEEeCCCCCCccceEee
Q psy6353          50 EKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKHMSQQELESLFSP--YGRIITSRILCDNLATENGKYYSG  127 (136)
Q Consensus        50 ~~a~~~~~~~~~~g~~l~v~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~--~G~v~~~~i~~~~~~~~~~~~fv~  127 (136)
                      -.++....+..++.+-.+|....      ..+.+.++.||...-.++++.+|+.  |.++++|....+      ..-|+.
T Consensus       151 ~Evlresp~VqvDekgekVrp~~------kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N------~nWyIT  218 (684)
T KOG2591|consen  151 VEVLRESPNVQVDEKGEKVRPNH------KRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHN------DNWYIT  218 (684)
T ss_pred             HHHHhcCCCceeccCccccccCc------ceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeec------CceEEE
Confidence            33444455566666666665433      3356778999999999999999985  788888887654      345999


Q ss_pred             cCcccccc
Q psy6353         128 LGGRERLR  135 (136)
Q Consensus       128 f~~~e~~~  135 (136)
                      |+++++|-
T Consensus       219 fesd~DAQ  226 (684)
T KOG2591|consen  219 FESDTDAQ  226 (684)
T ss_pred             eecchhHH
Confidence            99998863

>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=91.17  E-value=0.95  Score=29.97  Aligned_cols=61  Identities=16%  Similarity=0.159  Sum_probs=40.9

Q ss_pred             eeecCCChhhhHHHHhccCCC----e---eEEE--EEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeC
Q psy6353           2 VYQTLLNKLFTYEKVHLGFSD----A---EICV--FLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQ   62 (136)
Q Consensus         2 v~v~nl~~~~~l~~~f~~~G~----v---~~~~--~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~   62 (136)
                      |.|.+||...|..+++++..+    -   ..+.  ...  ......+-|+|.|.+.+++......++|+.+.
T Consensus        10 vVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~   81 (176)
T PF03467_consen   10 VVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFV   81 (176)
T ss_dssp             EEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE
T ss_pred             EEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEE
Confidence            578999999998888885554    2   2222  111  12223456999999999999999999997775

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.

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

Probab=90.36  E-value=0.63  Score=25.30  Aligned_cols=51  Identities=16%  Similarity=0.276  Sum_probs=36.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCC---CceEEEEEEeCCCCCCccceEeecCccccccC
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPY---GRIITSRILCDNLATENGKYYSGLGGRERLRR  136 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~---G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~~  136 (136)
                      ...+|+|.+++. ++.+|++..|..|   .....+.++-|.      .+-|.|.+.+.++|
T Consensus         4 rpeavhirGvd~-lsT~dI~~y~~~y~~~~~~~~IEWIdDt------ScNvvf~d~~~A~~   57 (62)
T PF10309_consen    4 RPEAVHIRGVDE-LSTDDIKAYFSEYFDEEGPFRIEWIDDT------SCNVVFKDEETAAR   57 (62)
T ss_pred             eeceEEEEcCCC-CCHHHHHHHHHHhcccCCCceEEEecCC------cEEEEECCHHHHHH
Confidence            346799999865 7999999999999   234577777552      24577777776653

>KOG2202|consensus

Probab=89.93  E-value=0.031  Score=38.74  Aligned_cols=41  Identities=15%  Similarity=0.170  Sum_probs=33.9

Q ss_pred             HHHHHhhc-CCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          95 QELESLFS-PYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        95 ~~l~~~f~-~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      +++...+. +||+|+.+++..+..-...|..||.|..+|+|.
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae  124 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAE  124 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHH
Confidence            45555555 999999999998887778788999999999874

>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=89.72  E-value=0.57  Score=26.25  Aligned_cols=43  Identities=30%  Similarity=0.455  Sum_probs=24.5

Q ss_pred             CeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEee
Q psy6353          22 DAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA   71 (136)
Q Consensus        22 ~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~   71 (136)
                      .|-.+.+..      .|+||+-.. +.|+.+++++++..+.|++++++.+
T Consensus        32 ~IG~I~I~~------~~S~vev~~-~~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen   32 DIGRIDIFD------NFSFVEVPE-EVAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             GEEEEEE-S------S-EEEEE-T-T-HHHHHHHHTT--SSS----EEE-
T ss_pred             hEEEEEEee------eEEEEEECH-HHHHHHHHHhcCCCCCCeeEEEEEC
Confidence            455666644      578888766 4788899999999999999998754

; PDB: 2G0C_A 3MOJ_B.

>KOG0804|consensus

Probab=89.07  E-value=1  Score=33.97  Aligned_cols=56  Identities=14%  Similarity=0.214  Sum_probs=45.4

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCC-ceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYG-RIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G-~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      .++.|+|-.+|..++..|+-.++..+- .|.++++++|...+. -...++|.+.++|.
T Consensus        73 ~~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~pnr-ymvLIkFr~q~da~  129 (493)
T KOG0804|consen   73 SSTMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGMPNR-YMVLIKFRDQADAD  129 (493)
T ss_pred             CCcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCCCce-EEEEEEeccchhHH
Confidence            478999999999999999999998774 577899999654333 45788999888763

>KOG2068|consensus

Probab=87.08  E-value=0.45  Score=34.39  Aligned_cols=56  Identities=25%  Similarity=0.341  Sum_probs=39.7

Q ss_pred             CceEEEcCCCCCCC-HHHHH--HhhcCCCceEEEEEEeCC--CCCCc--cceEeecCcccccc
Q psy6353          80 GANLYVSGLPKHMS-QQELE--SLFSPYGRIITSRILCDN--LATEN--GKYYSGLGGRERLR  135 (136)
Q Consensus        80 ~~~l~v~nl~~~~t-~~~l~--~~f~~~G~v~~~~i~~~~--~~~~~--~~~fv~f~~~e~~~  135 (136)
                      ..-+|+-+|++... +..|+  +.|.+||.|..+..-+++  ..+..  -.+|+.|+.+|++.
T Consensus        77 knlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~  139 (327)
T KOG2068|consen   77 KNLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDAD  139 (327)
T ss_pred             hhhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhh
Confidence            35678888988764 44444  378999999999888877  22222  22899999977764

>PF10567 Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IPR018885 This conserved domain is found in fungal proteins and appears to be involved in RNA-processing

Probab=84.83  E-value=1.1  Score=31.99  Aligned_cols=55  Identities=15%  Similarity=0.202  Sum_probs=42.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCC--------CCCCccceEeecCcccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDN--------LATENGKYYSGLGGRER  133 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~--------~~~~~~~~fv~f~~~e~  133 (136)
                      .++.|...|+..+++-..+-..|-+||+|+++.++.+.        ..+.....-+.|-+++.
T Consensus        14 rTRSLLfeNv~~sidLh~Fl~~fv~~~pIESiYL~~~~~~~~d~~~~d~~~~SilLSFlsr~~   76 (309)
T PF10567_consen   14 RTRSLLFENVNNSIDLHSFLTKFVKFGPIESIYLIKSNDKPSDDYNDDKNNQSILLSFLSREI   76 (309)
T ss_pred             eeHHHHHhhccccccHHHHHHHhhccCceeEEEEecCCCcccccccccccceEEEEeeechHH
Confidence            45778899999999999999999999999999999876        22223445666666654

It binds to poly-adenylated RNA, interacts genetically with mRNA 3'-end processing factors, co-purifies with the nuclear cap-binding protein Cbp20p, and is found in complexes containing other translation factors, such as EIF4G as in P39935 from SWISSPROT and P39936 from SWISSPROT.

>PF15513 DUF4651: Domain of unknown function (DUF4651)

Probab=84.56  E-value=2  Score=23.33  Aligned_cols=26  Identities=19%  Similarity=0.250  Sum_probs=19.3

Q ss_pred             HHHHHhhcCCCceEEEEEEeCCCCCC
Q psy6353          95 QELESLFSPYGRIITSRILCDNLATE  120 (136)
Q Consensus        95 ~~l~~~f~~~G~v~~~~i~~~~~~~~  120 (136)
                      .+|+++|++.|+|..+.+-.-..+..
T Consensus         9 ~~iR~~fs~lG~I~vLYvn~~eS~~~   34 (62)
T PF15513_consen    9 AEIRQFFSQLGEIAVLYVNPYESDED   34 (62)
T ss_pred             HHHHHHHHhcCcEEEEEEcccccCCC
Confidence            58999999999998776655443333

>KOG4849|consensus

Probab=83.81  E-value=0.33  Score=35.43  Aligned_cols=56  Identities=11%  Similarity=0.104  Sum_probs=44.6

Q ss_pred             CceEEEcCCCCCCCHHHHHHhhcCCC--ceEEEEEEeCCCCCCccc-eEeecCcccccc
Q psy6353          80 GANLYVSGLPKHMSQQELESLFSPYG--RIITSRILCDNLATENGK-YYSGLGGRERLR  135 (136)
Q Consensus        80 ~~~l~v~nl~~~~t~~~l~~~f~~~G--~v~~~~i~~~~~~~~~~~-~fv~f~~~e~~~  135 (136)
                      ...+||+||--.+|++||-+....-|  .+..++...+..+|.+++ |.+...++.+.+
T Consensus        80 k~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~K  138 (498)
T KOG4849|consen   80 KYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVK  138 (498)
T ss_pred             eEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHH
Confidence            35799999999999999999998877  466788888888887755 788887765543

>KOG4019|consensus

Probab=83.53  E-value=1.1  Score=29.76  Aligned_cols=111  Identities=16%  Similarity=0.194  Sum_probs=69.6

Q ss_pred             HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCc-eEEEEeeCCCCCCCCC--------ceE
Q psy6353          13 YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNK-TIKVSYARPSSESIKG--------ANL   83 (136)
Q Consensus        13 l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~-~l~v~~~~~~~~~~~~--------~~l   83 (136)
                      .+.+|.+|.+..-..+.+    +.+..-|.|.+++.|..|.-++++..+.|+ .+++-++++......+        .+-
T Consensus        32 ~~~lFrq~n~~~~fq~lr----sfrrvRi~f~~p~~a~~a~i~~~~~~f~~~~~~k~yfaQ~~~~~~~~q~L~pP~~eKq  107 (193)
T KOG4019|consen   32 FENLFRQINEDATFQLLR----SFRRVRINFSNPEAAADARIKLHSTSFNGKNELKLYFAQPGHPESNSQYLQPPEPEKQ  107 (193)
T ss_pred             HHhHHhhhCcchHHHHHH----hhceeEEeccChhHHHHHHHHhhhcccCCCceEEEEEccCCCccccccccCCCChhhc
Confidence            567788887765555544    566677999999999999998999999887 8888777765432221        111


Q ss_pred             EE--------------cCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeec
Q psy6353          84 YV--------------SGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGL  128 (136)
Q Consensus        84 ~v--------------~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f  128 (136)
                      |+              ...++.. ..+|-...++.|.-....+..+...+.+...-+.-
T Consensus       108 FLISPPaSPPvgWe~~eda~P~~-n~dLl~~iq~~~~~e~~eLhn~~e~~P~ivvh~~~  165 (193)
T KOG4019|consen  108 FLISPPASPPVGWEPIEDAPPVV-NQDLLAAIQKLGPGEKYELHNGTEKTPSIVVHVCE  165 (193)
T ss_pred             eeecCCCCCCCCCcccccCCccc-cHHHHHHHHHhCccccccccCCCCCCCceEEEecc
Confidence            21              1112222 24555556667766666666666555544433333

>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=82.83  E-value=1.1  Score=26.80  Aligned_cols=56  Identities=16%  Similarity=0.231  Sum_probs=32.1

Q ss_pred             CceEEEcCCCCCCCHHHHHHhhcCCCceEEEE-EEeC-------CCCCCccceEeecCccccccC
Q psy6353          80 GANLYVSGLPKHMSQQELESLFSPYGRIITSR-ILCD-------NLATENGKYYSGLGGRERLRR  136 (136)
Q Consensus        80 ~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~-i~~~-------~~~~~~~~~fv~f~~~e~~~~  136 (136)
                      ..-|.|-+.|+. ....+-+.|++||.|.... +.++       +......-..+.|+++.+|.|
T Consensus         6 ~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~r   69 (100)
T PF05172_consen    6 ETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQR   69 (100)
T ss_dssp             CCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHH
T ss_pred             CeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHH
Confidence            455788888888 6677888899999987664 2111       111111226788888877653

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.

>KOG1996|consensus

Probab=82.77  E-value=1.8  Score=31.06  Aligned_cols=41  Identities=15%  Similarity=0.155  Sum_probs=32.1

Q ss_pred             HHHHHHhhcCCCceEEEEEEeCCCCCCccc--eEeecCccccc
Q psy6353          94 QQELESLFSPYGRIITSRILCDNLATENGK--YYSGLGGRERL  134 (136)
Q Consensus        94 ~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~--~fv~f~~~e~~  134 (136)
                      ++++++.+.+||+|..|.|...+.......  .||+|+.-|++
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~a  342 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESA  342 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHH
Confidence            457788999999999998888765554433  79999988765

>COG5353 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=81.55  E-value=7.4  Score=25.06  Aligned_cols=57  Identities=14%  Similarity=0.250  Sum_probs=43.1

Q ss_pred             CceEEEcCCCCCCCHHHHHHhhcCC---CceEEEEEEeCC-----------CCCCccceEeecCccccccC
Q psy6353          80 GANLYVSGLPKHMSQQELESLFSPY---GRIITSRILCDN-----------LATENGKYYSGLGGRERLRR  136 (136)
Q Consensus        80 ~~~l~v~nl~~~~t~~~l~~~f~~~---G~v~~~~i~~~~-----------~~~~~~~~fv~f~~~e~~~~  136 (136)
                      ..++++.-+.+.+++++.++..+.=   +++.++.+.+..           ..|.-..+||.|++.+.++|
T Consensus        87 ~~KI~~k~asqGISe~~a~~~i~kE~~~~e~~~V~Lg~e~~~PiWEV~y~dkeg~~s~~~vdFetG~~lk~  157 (161)
T COG5353          87 DGKIYSKKASQGISEEDARAIISKEKAVKEIKSVTLGREKEKPIWEVTYLDKEGRLSFYYVDFETGKELKR  157 (161)
T ss_pred             CCeEEEEehhcCCCHHHHHHHHhhhccccceeEEEEEeeCCceeEEEeecCccCcceEEEEEeccchhhhh
Confidence            3789999999999999999988754   566677766654           23333468999999887764

>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=80.02  E-value=7.9  Score=23.60  Aligned_cols=56  Identities=18%  Similarity=0.187  Sum_probs=36.2

Q ss_pred             CCceEEEcCCCCCCC-HHHHHHhhcCCC-ceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMS-QQELESLFSPYG-RIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t-~~~l~~~f~~~G-~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      .+..+.+-.+|+.++ .++|..+...+- .|..++|++|...+. -..-++|.+.+.|.
T Consensus        11 ~~~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~pnr-ymVLikF~~~~~Ad   68 (110)
T PF07576_consen   11 RRSTLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGTPNR-YMVLIKFRDQESAD   68 (110)
T ss_pred             CCceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCCCce-EEEEEEECCHHHHH
Confidence            345566656666664 456666655553 566899999864322 44788999888764

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	136
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		2e-35
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		1e-34
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		1e-30
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		1e-30
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		7e-19
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		1e-18
1d8z_A	89	Solution Structure Of The First Rna-Binding Domain		2e-17
4fxv_A	99	Crystal Structure Of An Elav-Like Protein 1 (Elavl1		9e-14
3hi9_A	84	The X-Ray Crystal Structure Of The First Rna Recogn		1e-13
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		6e-12
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		8e-12
1d9a_A	85	Solution Structure Of The Second Rna-Binding Domain		7e-11
1sxl_A	97	Resonance Assignments And Solution Structure Of The		8e-09
2sxl_A	88	Sex-Lethal Rbd1, Nmr, Minimized Average Structure L		1e-08
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		1e-08
1x5o_A	114	Solution Structure Of Rrm Domain In Rna Binding Mot		1e-06
2cq0_A	103	Solution Structure Of Rna Binding Domain In Eukaryo		4e-05
3sde_B	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		5e-05
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		5e-05
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		7e-05
3smz_A	284	Human Raver1 Rrm1-3 Domains (Residues 39-320) Lengt		1e-04
3h2u_B	283	Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Comple		1e-04
3vf0_B	285	Raver1 In Complex With Metavinculin L954 Deletion M		1e-04
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		2e-04
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		2e-04
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		3e-04
3bs9_A	87	X-Ray Structure Of Human Tia-1 Rrm2 Length = 87		6e-04
2cpz_A	115	Solution Structure Of Rna Binding Domain 3 In Cug T		6e-04
1u6f_A	139	Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit		8e-04

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score =  143 bits (361), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 70/87 (80%), Positives = 75/87 (86%)
Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKH 91
           T QSLGYGFVNY  P+DAEKAINTLNGLRLQ KTIKVSYARPSS SI+ ANLYVSGLPK 
Sbjct: 40  TGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKT 99
Query: 92  MSQQELESLFSPYGRIITSRILCDNLA 118
           M+Q+ELE LFS YGRIITSRIL D + 
Sbjct: 100 MTQKELEQLFSQYGRIITSRILVDQVT 126

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score =  141 bits (356), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 71/96 (73%), Positives = 77/96 (80%), Gaps = 2/96 (2%)
Query: 22  DAEICVFLIS--TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIK 79
           D E C  +    T QSLGYGFVNY  P DA+KAINTLNGL+LQ KTIKVSYARPSS SI+
Sbjct: 30  DIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTIKVSYARPSSASIR 89
Query: 80  GANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
            ANLYVSGLPK MSQ+E+E LFS YGRIITSRIL D
Sbjct: 90  DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLD 125

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score =  127 bits (320), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 59/82 (71%), Positives = 71/82 (86%)
Query: 34  QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKHMS 93
            SLGYGFVNY   +DAE+AINTLNGLRLQ+KTIKVSYARPSSE IK ANLY+SGLP+ M+
Sbjct: 42  HSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMT 101
Query: 94  QQELESLFSPYGRIITSRILCD 115
           Q+++E +FS +GRII SR+L D
Sbjct: 102 QKDVEDMFSRFGRIINSRVLVD 123

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score =  127 bits (320), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 59/82 (71%), Positives = 71/82 (86%)
Query: 34  QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKHMS 93
            SLGYGFVNY   +DAE+AINTLNGLRLQ+KTIKVSYARPSSE IK ANLY+SGLP+ M+
Sbjct: 42  HSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMT 101
Query: 94  QQELESLFSPYGRIITSRILCD 115
           Q+++E +FS +GRII SR+L D
Sbjct: 102 QKDVEDMFSRFGRIINSRVLVD 123

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 89.0 bits (219), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 40/87 (45%), Positives = 58/87 (66%)
Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKH 91
           T  S GY FV++    D+++AI  LNG+ ++NK +KVSYARP  ESIK  NLYV+ LP+ 
Sbjct: 52  TGYSFGYAFVDFTSEXDSQRAIKVLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRT 111
Query: 92  MSQQELESLFSPYGRIITSRILCDNLA 118
           ++  +L+++F  YG I+   IL D L 
Sbjct: 112 ITDDQLDTIFGKYGSIVQKNILRDKLT 138

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 88.2 bits (217), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 40/86 (46%), Positives = 58/86 (67%)
Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKH 91
           T  S GY FV++    D+++AI  LNG+ ++NK +KVSYARP  ESIK  NLYV+ LP+ 
Sbjct: 41  TGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRT 100
Query: 92  MSQQELESLFSPYGRIITSRILCDNL 117
           ++  +L+++F  YG I+   IL D L
Sbjct: 101 ITDDQLDTIFGKYGSIVQKNILRDKL 126

>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1) Of Hu Antigen C (Huc) Length = 89

Iteration: 1
 Score = 84.0 bits (206), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 42/60 (70%), Positives = 46/60 (76%), Gaps = 2/60 (3%)
Query: 22 DAEICVFLIS--TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIK 79
          D E C  +    T QSLGYGFVNY  P DA+KAINTLNGL+LQ KTIKVSYARPSS SI+
Sbjct: 30 DIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTIKVSYARPSSASIR 89

>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From Homo Sapiens At 1.90 A Resolution Length = 99

Iteration: 1
 Score = 72.0 bits (175), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 34/42 (80%), Positives = 37/42 (88%)
Query: 33 AQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS 74
            SLGYGFVNY   +DAE+AINTLNGLRLQ+KTIKVSYARPS
Sbjct: 58 GHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARPS 99

>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition Motif (Rrm1) Of The Au-Rich Element (Are) Binding Protein Hur At 2.0 Angstrom Resolution Length = 84

Iteration: 1
 Score = 72.0 bits (175), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 34/42 (80%), Positives = 37/42 (88%)
Query: 33 AQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS 74
            SLGYGFVNY   +DAE+AINTLNGLRLQ+KTIKVSYARPS
Sbjct: 43 GHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARPS 84

>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In Complex With Polyadenylate Rna Length = 190

Iteration: 1
 Score = 66.2 bits (160), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 32/100 (32%), Positives = 61/100 (61%), Gaps = 7/100 (7%)
Query: 25  ICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR--PSSESIKGAN 82
           +C  +I T +SLGY +VN+ +P DAE+A++T+N   ++ K +++ +++  PS       N
Sbjct: 42  VCRDMI-TRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGN 100
Query: 83  LYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENG 122
           +++  L K +  + L   FS +G I++ +++CD    ENG
Sbjct: 101 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD----ENG 136

>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In Complex With Rrm1-2 Of Pabp And Poly(A) Length = 213

Iteration: 1
 Score = 65.5 bits (158), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 32/100 (32%), Positives = 61/100 (61%), Gaps = 7/100 (7%)
Query: 25  ICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR--PSSESIKGAN 82
           +C  +I T +SLGY +VN+ +P DAE+A++T+N   ++ K +++ +++  PS       N
Sbjct: 47  VCRDMI-TRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGN 105
Query: 83  LYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENG 122
           +++  L K +  + L   FS +G I++ +++CD    ENG
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD----ENG 141

>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2) Of Hu Antigen C (Huc) Length = 85

Iteration: 1
 Score = 62.4 bits (150), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 29/35 (82%), Positives = 31/35 (88%)
Query: 81  ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
           ANLYVSGLPK MSQ+E+E LFS YGRIITSRIL D
Sbjct: 2   ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLD 36

>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 = 55.5 bits (132), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 24/50 (48%), Positives = 34/50 (68%)
Query: 68  VSYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNL 117
           +SYARP  ESIK  NLYV+ LP+ ++  +L+++F  YG I+   IL D L
Sbjct: 1   MSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKL 50

>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure Length = 88

Iteration: 1
 Score = 55.1 bits (131), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 25/48 (52%), Positives = 34/48 (70%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIK 79
          T  S GY FV++    D+++AI  LNG+ ++NK +KVSYARP  ESIK
Sbjct: 41 TGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARPGGESIK 88

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score = 55.1 bits (131), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 26/95 (27%), Positives = 51/95 (53%), Gaps = 2/95 (2%)
Query: 23  AEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGA- 81
           A I + +    +++ Y FV YH+  DA  A+ TLNG +++N  +K+++A  S +S     
Sbjct: 28  ANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQQSSSDDT 87
Query: 82  -NLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
            NL+V  L  ++  + L + F  +   ++  ++ D
Sbjct: 88  FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWD 122

>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif, Single-Stranded Interacting Protein 1 Length = 114

Iteration: 1
 Score = 48.5 bits (114), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 21/52 (40%), Positives = 35/52 (67%)
Query: 82  NLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRER 133
           NLY+S LP  M +QELE++  P+G++I++RIL D+  T  G  ++ +   E+
Sbjct: 27  NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEK 78

>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic Translation Initiation Factor 3 Subunit 4 Length = 103

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 18/47 (38%), Positives = 31/47 (65%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES 77
          +T QS G+ F+++HR EDA +AI  ++G    +  + V +A+PS+ S
Sbjct: 52 TTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPSTNS 98

>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 43.1 bits (100), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 27/100 (27%), Positives = 50/100 (50%), Gaps = 6/100 (6%)
Query: 37  GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKHMSQQE 96
           G+GF+       AE A   L+ + L+ K ++V +A         A+L V  LP+++S + 
Sbjct: 59  GFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFA------CHSASLTVRNLPQYVSNEL 112
Query: 97  LESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLRR 136
           LE  FS +G++  + ++ D+    +GK      G+   R+
Sbjct: 113 LEEAFSVFGQVERAVVIVDDRGRPSGKGIVEFSGKPAARK 152

>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 = 43.1 bits (100), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 27/97 (27%), Positives = 50/97 (51%), Gaps = 15/97 (15%)
Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS------------SESIK 79
           T +  G+ FV Y  PE A+ A+  +N + L  + IKV   RPS            +E  +
Sbjct: 66  TMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKV--GRPSNIGQAQPIIDQLAEEAR 123
Query: 80  GAN-LYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
             N +YV+ + + +S  +++S+F  +G+I ++ +  D
Sbjct: 124 AFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARD 160

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 42.4 bits (98), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 27/97 (27%), Positives = 49/97 (50%), Gaps = 15/97 (15%)
Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS------------SESIK 79
           T +  G+ FV Y  PE A+ A+  +N + L  + IKV   RPS            +E  +
Sbjct: 51  TMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKV--GRPSNIGQAQPIIDQLAEEAR 108
Query: 80  GAN-LYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
             N +YV+ + + +S  +++S+F  +G+I +  +  D
Sbjct: 109 AFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARD 145

>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320) Length = 284

Iteration: 1
 Score = 42.0 bits (97), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 30/96 (31%), Positives = 47/96 (48%), Gaps = 8/96 (8%)
Query: 12  TYEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
           T ++VH   SD E+    +   +  G  FV     E AE AIN  +  RL+ + + V   
Sbjct: 35  TNQEVHDLLSDYELKYCFVDKYK--GTAFVTLLNGEQAEAAINAFHQSRLRERELSVQL- 91
Query: 72  RPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRI 107
           +P+      A L V+ LP  ++QQ+ E L  P+G +
Sbjct: 92  QPTD-----ALLCVANLPPSLTQQQFEELVRPFGSL 122

>pdb|3H2U|B Chain B, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With Human Vinculin Tail Domain Vt Length = 283

Iteration: 1
 Score = 42.0 bits (97), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 30/96 (31%), Positives = 47/96 (48%), Gaps = 8/96 (8%)
Query: 12  TYEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
           T ++VH   SD E+    +   +  G  FV     E AE AIN  +  RL+ + + V   
Sbjct: 33  TNQEVHDLLSDYELKYCFVDKYK--GTAFVTLLNGEQAEAAINAFHQSRLRERELSVQL- 89
Query: 72  RPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRI 107
           +P+      A L V+ LP  ++QQ+ E L  P+G +
Sbjct: 90  QPTD-----ALLCVANLPPSLTQQQFEELVRPFGSL 120

>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant Length = 285

Iteration: 1
 Score = 42.0 bits (97), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 30/96 (31%), Positives = 47/96 (48%), Gaps = 8/96 (8%)
Query: 12  TYEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
           T ++VH   SD E+    +   +  G  FV     E AE AIN  +  RL+ + + V   
Sbjct: 35  TNQEVHDLLSDYELKYCFVDKYK--GTAFVTLLNGEQAEAAINAFHQSRLRERELSVQL- 91
Query: 72  RPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRI 107
           +P+      A L V+ LP  ++QQ+ E L  P+G +
Sbjct: 92  QPTD-----ALLCVANLPPSLTQQQFEELVRPFGSL 122

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 41.2 bits (95), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 20/56 (35%), Positives = 32/56 (57%), Gaps = 1/56 (1%)
Query: 23 AEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA-RPSSES 77
          +E+ +    T++S G+ F+ +  P DA+ A   +NG  L  K IKV  A +PS +S
Sbjct: 35 SEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKKPSFQS 90

>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 = 41.2 bits (95), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 27/97 (27%), Positives = 48/97 (49%), Gaps = 15/97 (15%)
Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS------------SESIK 79
           T +  G+ FV Y  PE A+ A+   N + L  + IKV   RPS            +E  +
Sbjct: 50  TXKHKGFAFVEYEVPEAAQLALEQXNSVXLGGRNIKV--GRPSNIGQAQPIIDQLAEEAR 107
Query: 80  GAN-LYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
             N +YV+ + + +S  +++S+F  +G+I +  +  D
Sbjct: 108 AFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARD 144

>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 = 40.8 bits (94), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 30/95 (31%), Positives = 47/95 (49%), Gaps = 10/95 (10%)
Query: 2   VYQTLLNKLFTYEKVHLGF------SDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINT 55
           V+   L+   T E +   F      SDA + V  ++T +S GYGFV++    DAE AI  
Sbjct: 18  VFVGDLSPEITTEDIKAAFAPFGRISDARV-VKDMATGKSKGYGFVSFFNKWDAENAIQQ 76
Query: 56  LNGLRLQNKTIKVSYAR---PSSESIKGANLYVSG 87
           + G  L  + I+ ++A    P+ +S   +N   SG
Sbjct: 77  MGGQWLGGRQIRTNWATRKPPAPKSTYESNTKQSG 111

>pdb|3BS9|A Chain A, X-Ray Structure Of Human Tia-1 Rrm2 Length = 87

Iteration: 1
 Score = 39.7 bits (91), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/51 (39%), Positives = 31/51 (60%), Gaps = 1/51 (1%)
Query: 21 SDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
          SDA + V  ++T +S GYGFV++    DAE AI  + G  L  + I+ ++A
Sbjct: 34 SDARV-VKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA 83

>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet Repeat Rna-Binding Protein 1 Length = 115

Iteration: 1
 Score = 39.3 bits (90), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 14/48 (29%), Positives = 28/48 (58%)
Query: 68  VSYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
           +  A    E  +GANL++  LP+    Q+L  +F P+G ++++++  D
Sbjct: 13  IGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFID 60

>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From Trypanosoma Cruzi Length = 139

Iteration: 1
 Score = 38.9 bits (89), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 19/40 (47%), Positives = 25/40 (62%)
Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
           T QS GYGFV +     A++AI  LNG  + NK +KV+ A
Sbjct: 80  TRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALA 119

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	136
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	1e-42
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-08
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	4e-07
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	3e-41
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	2e-08
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	3e-07
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	2e-34
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	1e-16
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	6e-08
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	3e-34
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	1e-08
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	1e-07
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	9e-30
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-11
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-29
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	3e-08
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-06
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-28
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	8e-28
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-11
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	3e-07
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	7e-24
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	1e-11
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	2e-05
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-22
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	6e-19
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-11
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-08
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	5e-22
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	2e-13
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	5e-22
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	1e-11
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	7e-21
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	7e-11
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	2e-06
1x5o_A	114	RNA binding motif, single-stranded interacting pro	7e-19
1x5o_A	114	RNA binding motif, single-stranded interacting pro	1e-11
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	2e-16
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	2e-12
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	2e-16
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	6e-16
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	5e-07
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	7e-16
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	3e-12
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	2e-15
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	5e-05
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	3e-15
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	5e-12
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	5e-15
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	2e-07
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	2e-14
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	5e-04
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	8e-14
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	7e-07
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	9e-14
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	4e-04
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	1e-13
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	2e-09
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	2e-13
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	6e-09
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	3e-13
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	2e-05
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	4e-13
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	7e-13
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	1e-06
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	7e-13
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	4e-05
1x4e_A	85	RNA binding motif, single-stranded interacting pro	8e-13
1x4e_A	85	RNA binding motif, single-stranded interacting pro	1e-08
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	8e-13
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	5e-05
1x5p_A	97	Negative elongation factor E; structure genomics,	8e-13
1x5p_A	97	Negative elongation factor E; structure genomics,	8e-04
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	9e-13
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	1e-12
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	3e-06
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	2e-05
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	1e-12
2div_A	99	TRNA selenocysteine associated protein; structural	1e-12
2div_A	99	TRNA selenocysteine associated protein; structural	4e-04
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	1e-12
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	6e-07
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-12
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-05
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	2e-12
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	5e-05
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	4e-12
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	4e-06
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	5e-12
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	3e-06
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	7e-12
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	9e-08
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	8e-12
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	8e-07
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	9e-12
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	1e-05
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	9e-12
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-05
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	6e-05
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	1e-11
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	6e-06
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	1e-11
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	3e-07
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	1e-11
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	5e-04
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-11
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-05
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-11
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	8e-08
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	4e-06
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	3e-11
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	1e-05
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	3e-11
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	6e-06
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	3e-11
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	4e-11
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	4e-04
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	4e-11
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	3e-05
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	4e-11
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	4e-06
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	4e-11
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	6e-06
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	4e-11
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	3e-07
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	5e-11
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	1e-06
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	5e-11
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	1e-04
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	6e-11
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	1e-05
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	6e-11
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	3e-04
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	1e-10
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	8e-07
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	1e-10
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	2e-04
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	1e-10
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	9e-05
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	1e-10
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	2e-07
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	1e-10
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	1e-10
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	2e-06
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	2e-10
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	2e-05
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	2e-10
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	4e-07
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	2e-10
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	2e-10
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	2e-06
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	2e-10
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	5e-07
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	2e-10
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	3e-05
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	2e-10
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	3e-10
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	3e-10
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	3e-04
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	3e-10
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	8e-05
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	3e-10
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	3e-07
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	3e-10
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	5e-06
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	3e-10
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	1e-04
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	5e-10
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	5e-07
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	5e-10
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	7e-06
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	5e-10
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	5e-04
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	5e-10
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	4e-06
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	5e-10
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	2e-06
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	6e-10
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	4e-07
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	6e-10
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	2e-06
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	6e-10
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	4e-06
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	7e-10
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	4e-05
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	8e-10
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	4e-06
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	9e-10
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	1e-09
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	1e-09
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	3e-05
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	2e-09
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	2e-06
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	2e-09
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	8e-06
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	2e-09
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	2e-09
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	3e-09
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	1e-05
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	3e-09
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	1e-04
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	4e-09
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	1e-07
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	4e-09
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	5e-04
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	5e-09
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	1e-05
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	1e-08
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	7e-06
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	2e-08
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	2e-08
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	3e-04
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	2e-08
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	5e-05
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	2e-08
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	2e-08
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	2e-04
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	3e-08
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	5e-08
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	7e-04
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	5e-08
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	3e-04
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	6e-08
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	2e-06
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	6e-08
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	3e-05
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	7e-08
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	2e-05
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-07
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	2e-07
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	3e-07
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	3e-07
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	8e-06
2dis_A	109	Unnamed protein product; structural genomics, RRM	3e-07
2dis_A	109	Unnamed protein product; structural genomics, RRM	9e-07
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	3e-07
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	3e-07
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	4e-07
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	6e-07
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	8e-07
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	1e-06
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	4e-05
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	1e-06
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	8e-05
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	2e-06
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	2e-04
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	2e-06
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	2e-06
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	3e-06
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	4e-06
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	1e-05
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	4e-05
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	3e-04
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	5e-05
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	7e-05
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	1e-04
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	1e-04
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	1e-04
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	2e-04
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	2e-04
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	2e-04
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	2e-04
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	3e-04
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	6e-04
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	6e-04
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	7e-04
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	7e-04

>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 =  137 bits (347), Expect = 1e-42
 Identities = 70/86 (81%), Positives = 74/86 (86%)

Query: 31  STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPK 90
            T QSLGYGFVNY  P+DAEKAINTLNGLRLQ KTIKVSYARPSS SI+ ANLYVSGLPK
Sbjct: 39  ITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSSASIRDANLYVSGLPK 98

Query: 91  HMSQQELESLFSPYGRIITSRILCDN 116
            M+Q+ELE LFS YGRIITSRIL D 
Sbjct: 99  TMTQKELEQLFSQYGRIITSRILVDQ 124

>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 = 49.1 bits (118), Expect = 2e-08
 Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 2/42 (4%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNG--LRLQNKTIKVSYA 71
           T  S G GF+ + +  +AE+AI  LNG       + I V +A
Sbjct: 126 TGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA 167

>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 = 45.6 bits (109), Expect = 4e-07
 Identities = 14/35 (40%), Positives = 23/35 (65%)

Query: 81  ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
            NL V+ LP++M+Q+E  SLF   G I + +++ D
Sbjct: 3   TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRD 37

>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 =  133 bits (338), Expect = 3e-41
 Identities = 40/92 (43%), Positives = 59/92 (64%), Gaps = 3/92 (3%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKH 91
           T  S GY FV++    D+++AI  LNG+ ++NK +KVSYARP  ESIK  NLYV+ LP+ 
Sbjct: 41  TGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRT 100

Query: 92  MSQQELESLFSPYGRIITSRILCDNLATENGK 123
           ++  +L+++F  YG I+   IL D      G+
Sbjct: 101 ITDDQLDTIFGKYGSIVQKNILRDK---LTGR 129

>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 = 49.1 bits (118), Expect = 2e-08
 Identities = 13/42 (30%), Positives = 25/42 (59%), Gaps = 2/42 (4%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQ--NKTIKVSYA 71
           T +  G  FV Y++ E+A++AI+ LN +  +  ++ + V  A
Sbjct: 127 TGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 168

>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 = 45.6 bits (109), Expect = 3e-07
 Identities = 16/36 (44%), Positives = 22/36 (61%)

Query: 80  GANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
             NL V+ LP+ M+ +EL +LF   G I T RI+ D
Sbjct: 3   NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRD 38

>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 =  117 bits (296), Expect = 2e-34
 Identities = 27/86 (31%), Positives = 54/86 (62%), Gaps = 2/86 (2%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR--PSSESIKGANLYVSGLP 89
           T +SLGY +VN+ +P DAE+A++T+N   ++ K +++ +++  PS       N+++  L 
Sbjct: 53  TRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLD 112

Query: 90  KHMSQQELESLFSPYGRIITSRILCD 115
           K +  + L   FS +G I++ +++CD
Sbjct: 113 KSIDNKALYDTFSAFGNILSCKVVCD 138

>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 = 71.9 bits (177), Expect = 1e-16
 Identities = 23/78 (29%), Positives = 36/78 (46%), Gaps = 4/78 (5%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKH 91
              S GYGFV++   E AE+AI  +NG+ L ++ + V   +   E  + A L      K 
Sbjct: 139 ENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKE--REAEL--GARAKE 194

Query: 92  MSQQELESLFSPYGRIIT 109
               ++       GRI+T
Sbjct: 195 FYPYDVPDYAGSSGRIVT 212

>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 = 48.4 bits (116), Expect = 6e-08
 Identities = 16/48 (33%), Positives = 25/48 (52%)

Query: 68  VSYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
           +    PS+ S   A+LYV  L   +++  L   FSP G I++ R+  D
Sbjct: 3   LGSMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRD 50

>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 =  116 bits (292), Expect = 3e-34
 Identities = 19/87 (21%), Positives = 42/87 (48%), Gaps = 4/87 (4%)

Query: 34  QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS----ESIKGANLYVSGLP 89
           QS G  FV ++  + A +A N L+ +++          +P+      +++   L++  + 
Sbjct: 45  QSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMIS 104

Query: 90  KHMSQQELESLFSPYGRIITSRILCDN 116
           K  ++ ++  +FS +G+I   RIL   
Sbjct: 105 KKCTENDIRVMFSSFGQIEECRILRGP 131

>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 = 49.5 bits (119), Expect = 1e-08
 Identities = 9/44 (20%), Positives = 17/44 (38%), Gaps = 3/44 (6%)

Query: 31  STAQSLGYGFVNYHRPEDAEKAINTLNG---LRLQNKTIKVSYA 71
               S G  FV +     A+ AI  ++    +   +  + V +A
Sbjct: 131 PDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFA 174

>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 = 47.2 bits (113), Expect = 1e-07
 Identities = 10/34 (29%), Positives = 19/34 (55%)

Query: 82  NLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
            ++V  +P+  S+++L  LF  YG +    +L D
Sbjct: 5   KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRD 38

>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 =  104 bits (262), Expect = 9e-30
 Identities = 25/94 (26%), Positives = 49/94 (52%), Gaps = 5/94 (5%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIK--GANLYVSGLP 89
             +++ Y FV YH+  DA  A+ TLNG +++N  +K+++A  S +S      NL+V  L 
Sbjct: 37  NNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLN 96

Query: 90  KHMSQQELESLFSPYGRIITSRILCDNLATENGK 123
            ++  + L + F  +   ++  ++ D    + G 
Sbjct: 97  VNVDDETLRNAFKDFPSYLSGHVMWD---MQTGS 127

>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 = 56.0 bits (136), Expect = 5e-11
 Identities = 13/40 (32%), Positives = 27/40 (67%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
           T  S GYGFV++   +DA+ A++++ G  L  + +++++A
Sbjct: 125 TGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA 164

>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 =  106 bits (266), Expect = 2e-29
 Identities = 23/89 (25%), Positives = 42/89 (47%), Gaps = 10/89 (11%)

Query: 35  SLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKHMSQ 94
             G+GF+       AE A   L+G  L+++ +++ +A        GA L V  L   +S 
Sbjct: 57  DRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATH------GAALTVKNLSPVVSN 110

Query: 95  QELESLFSPYGRIITSRILCDNLATENGK 123
           + LE  FS +G +  + ++ D    + G+
Sbjct: 111 ELLEQAFSQFGPVEKAVVVVD----DRGR 135

>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 = 49.7 bits (119), Expect = 3e-08
 Identities = 12/80 (15%), Positives = 25/80 (31%), Gaps = 4/80 (5%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNG----LRLQNKTIKVSYARPSSESIKGANLYVSG 87
             ++ G GFV +     A KA+         L    + + V       +        +  
Sbjct: 133 RGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFDDEDGLPEKLMQK 192

Query: 88  LPKHMSQQELESLFSPYGRI 107
             ++  ++E    F+  G  
Sbjct: 193 TQQYHKEREQPPRFAQPGTF 212

>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 = 44.3 bits (105), Expect = 2e-06
 Identities = 13/52 (25%), Positives = 25/52 (48%), Gaps = 2/52 (3%)

Query: 63  NKTIKV-SYARPSSESIKG-ANLYVSGLPKHMSQQELESLFSPYGRIITSRI 112
             TI + S+ +P  ++      L+V  LP  +++++ + LF  YG      I
Sbjct: 3   GFTIDIKSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFI 54

>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 =  104 bits (261), Expect = 2e-28
 Identities = 27/104 (25%), Positives = 42/104 (40%), Gaps = 11/104 (10%)

Query: 20  FSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIK 79
            SD E+        +  G  FV     E AE AIN  +  RL+ + + V           
Sbjct: 43  LSDYELKY--CFVDKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPTD----- 95

Query: 80  GANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGK 123
            A L V+ LP  ++QQ+ E L  P+G +    ++        G+
Sbjct: 96  -ALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSE---RTGQ 135

>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 =  102 bits (257), Expect = 8e-28
 Identities = 23/96 (23%), Positives = 40/96 (41%), Gaps = 8/96 (8%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA---RPSSESIKGANLYVSGL 88
           T QS GYGF  Y + + A +A + L G  L  +T+ V +    + +   +    L V  L
Sbjct: 133 TGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLTPALLHSRCLCVDRL 192

Query: 89  PKHMSQQE-LESLFSPYGRIITSRILCDNLATENGK 123
           P   +  + L    S        ++ C     ++G+
Sbjct: 193 PPGFNDVDALCRALSAVHSPTFCQLACG----QDGQ 224

>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 = 59.2 bits (144), Expect = 1e-11
 Identities = 13/63 (20%), Positives = 25/63 (39%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKH 91
             Q  G+  + Y   E AE+A    +GL L    ++VS+  P           ++     
Sbjct: 222 DGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPPGRSMLAALIAAQATA 281

Query: 92  MSQ 94
           +++
Sbjct: 282 LNR 284

>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 = 46.9 bits (112), Expect = 3e-07
 Identities = 10/55 (18%), Positives = 20/55 (36%), Gaps = 4/55 (7%)

Query: 61  LQNKTIKVSYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYG----RIITSR 111
           L  + I+        +      + + GLP  ++ QE+  L S Y      +   +
Sbjct: 3   LDPEEIRKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYELKYCFVDKYK 57

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 90.8 bits (226), Expect = 7e-24
 Identities = 24/103 (23%), Positives = 47/103 (45%), Gaps = 14/103 (13%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE-----------SIKG 80
           T +  G+ FV Y  PE A+ A+  +N + L  + IKV       +           +   
Sbjct: 66  TMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAF 125

Query: 81  ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGK 123
             +YV+ + + +S  +++S+F  +G+I ++ +  D      GK
Sbjct: 126 NRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDP---TTGK 165

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 58.5 bits (142), Expect = 1e-11
 Identities = 11/42 (26%), Positives = 24/42 (57%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
           T +  GYGF+ Y + + ++ A++++N   L  + ++V  A  
Sbjct: 163 TGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVT 204

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 41.1 bits (97), Expect = 2e-05
 Identities = 8/45 (17%), Positives = 19/45 (42%)

Query: 71  ARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
           A+        + +YV  +   + +  +   F+P+G I +  +  D
Sbjct: 19  AQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWD 63

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 88.1 bits (219), Expect = 2e-22
 Identities = 17/102 (16%), Positives = 35/102 (34%), Gaps = 8/102 (7%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE-------SIKGANLY 84
              S  + +++    EDA   +  LNGL+++  T+    + P  +       +++G  + 
Sbjct: 155 FNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIM 214

Query: 85  VSGLPKHMSQ-QELESLFSPYGRIITSRILCDNLATENGKYY 125
           +  L   +     L   F  +G I    I             
Sbjct: 215 IRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCC 256

>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 = 79.3 bits (196), Expect = 6e-19
 Identities = 19/113 (16%), Positives = 37/113 (32%), Gaps = 11/113 (9%)

Query: 7   LNKLFTYEKVHLGFSDA-EI--CVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQN 63
           L K +   KV+  F     I       S  ++  +  + + R + A  AI   +   +  
Sbjct: 49  LPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKTHK-VVGQ 107

Query: 64  KTIKVSYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDN 116
             I V         +    L+++  P   +Q+ +  L      +  S  L   
Sbjct: 108 NEIIV-------SHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSL 153

>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 = 59.6 bits (145), Expect = 1e-11
 Identities = 16/84 (19%), Positives = 32/84 (38%), Gaps = 9/84 (10%)

Query: 35  SLGYGFVNYHRPEDAEKAINTLNGLRL--QNKTIKVSYARPSSESIKGANLYVSGLPKHM 92
           S+ YG   +H   D+++ ++  +       +K    +  R      +   + V  LPK  
Sbjct: 1   SMEYG---HHARPDSKRPLDEGSPAAAGLTSKKANEALTRNR----ELTTVLVKNLPKSY 53

Query: 93  SQQELESLFSPYGRIITSRILCDN 116
           +Q ++   F   G II   +    
Sbjct: 54  NQNKVYKYFKHCGPIIHVDVADSL 77

>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 = 50.4 bits (121), Expect = 2e-08
 Identities = 11/43 (25%), Positives = 20/43 (46%), Gaps = 1/43 (2%)

Query: 31  STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
             + +    F+ +   + AE+A+  +N   L N+ I VS A  
Sbjct: 249 EHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSLADK 290

>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 = 84.0 bits (208), Expect = 5e-22
 Identities = 21/60 (35%), Positives = 31/60 (51%), Gaps = 6/60 (10%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE------SIKGANLYV 85
           T QS GYGFV +     A++AI  LNG  + NK +KV+ A    +      ++   N Y+
Sbjct: 80  TRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGIAGAVGDGNGYL 139

>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 = 61.7 bits (150), Expect = 2e-13
 Identities = 19/76 (25%), Positives = 32/76 (42%), Gaps = 3/76 (3%)

Query: 41  VNYHRPEDAEKAINTLNGL-RLQNKTIKVSYARPSSESIKGANLYVSGLPKHMSQQELES 99
           +      D       L  L + Q + I  +   P  +     NL V+ +P  + + +L  
Sbjct: 4   IPLVSQYDPYGQTAQLQQLQQQQQQHIPPTQMNPEPDV--LRNLMVNYIPTTVDEVQLRQ 61

Query: 100 LFSPYGRIITSRILCD 115
           LF  YG I + +I+CD
Sbjct: 62  LFERYGPIESVKIVCD 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 = 85.0 bits (211), Expect = 5e-22
 Identities = 14/92 (15%), Positives = 41/92 (44%), Gaps = 4/92 (4%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKH 91
             Q   + F+ +   ++  +A+   +G+  Q +++K+              L++ GLP +
Sbjct: 47  INQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNY 105

Query: 92  MSQQELESLFSPYGRIITSRILCDNLATENGK 123
           ++  +++ L + +G +    ++ D+     G 
Sbjct: 106 LNDDQVKELLTSFGPLKAFNLVKDS---ATGL 134

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 57.6 bits (140), Expect = 1e-11
 Identities = 15/40 (37%), Positives = 21/40 (52%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
           T  S GY F  Y      ++AI  LNG++L +K + V  A
Sbjct: 132 TGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 171

>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 = 81.9 bits (203), Expect = 7e-21
 Identities = 21/82 (25%), Positives = 37/82 (45%), Gaps = 3/82 (3%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA--RPSSESIKGANLYVSGLP 89
           T  +  +G+V++   ED EKA+  L GL++    IK+     R S +      L    L 
Sbjct: 50  TGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLS 108

Query: 90  KHMSQQELESLFSPYGRIITSR 111
            ++++ EL+ +F     I    
Sbjct: 109 FNITEDELKEVFEDALEIRLVS 130

>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 = 55.7 bits (135), Expect = 7e-11
 Identities = 8/42 (19%), Positives = 18/42 (42%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
             +S G  ++ +    DAEK +    G  +  +++ + Y   
Sbjct: 132 DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGE 173

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 43.7 bits (104), Expect = 2e-06
 Identities = 11/48 (22%), Positives = 18/48 (37%)

Query: 69  SYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDN 116
           S+    SES    NL++  L  + S  EL+   S         ++   
Sbjct: 2   SHMVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR 49

>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 = 75.0 bits (185), Expect = 7e-19
 Identities = 20/56 (35%), Positives = 35/56 (62%), Gaps = 2/56 (3%)

Query: 61  LQNKTIKVSYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDN 116
           L+   ++   A+   +     NLY+S LP  M +QELE++  P+G++I++RIL D+
Sbjct: 8   LKASGVQAQMAKQQEQ--DPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS 61

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 56.5 bits (137), Expect = 1e-11
 Identities = 11/43 (25%), Positives = 15/43 (34%)

Query: 31  STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
           S+  S G GF      E  E  I   NG  ++      +   P
Sbjct: 61  SSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEP 103

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A Length = 115

 Score = 69.3 bits (170), Expect = 2e-16
 Identities = 18/49 (36%), Positives = 28/49 (57%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKG 80
           T  S  +GFV+Y  P  A+ AI ++NG ++  K +KV   R  ++S  G
Sbjct: 63  TNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSKSG 111

>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 = 58.5 bits (142), Expect = 2e-12
 Identities = 17/62 (27%), Positives = 34/62 (54%), Gaps = 4/62 (6%)

Query: 54  NTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRIL 113
           +  +GL  Q+    +  A    E  +GANL++  LP+    Q+L  +F P+G ++++++ 
Sbjct: 3   SGSSGLTQQS----IGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVF 58

Query: 114 CD 115
            D
Sbjct: 59  ID 60

>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 = 70.3 bits (173), Expect = 2e-16
 Identities = 24/84 (28%), Positives = 44/84 (52%), Gaps = 2/84 (2%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKH 91
           T +S G+GF+++ +P   ++ + T +   L  K I    A P  E  K   ++V G+   
Sbjct: 41  TGRSRGFGFLSFEKPSSVDEVVKTQH--ILDGKVIDPKRAIPRDEQDKTGKIFVGGIGPD 98

Query: 92  MSQQELESLFSPYGRIITSRILCD 115
           +  +E E  FS +G II ++++ D
Sbjct: 99  VRPKEFEEFFSQWGTIIDAQLMLD 122

>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 = 67.7 bits (166), Expect = 6e-16
 Identities = 18/73 (24%), Positives = 33/73 (45%), Gaps = 8/73 (10%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE--------SIKGANL 83
              S GYGFV++   E AE+AI  +NG+ L ++ + V   +   E        + +  N+
Sbjct: 41  ENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNV 100

Query: 84  YVSGLPKHMSQQE 96
           Y+       ++  
Sbjct: 101 YIKNFGPGSTRAA 113

>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 = 44.5 bits (106), Expect = 5e-07
 Identities = 10/35 (28%), Positives = 21/35 (60%)

Query: 81  ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
            N+++  L K +  + L   FS +G I++ +++CD
Sbjct: 6   GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD 40

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 69.7 bits (171), Expect = 7e-16
 Identities = 14/112 (12%), Positives = 42/112 (37%), Gaps = 24/112 (21%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP------------------ 73
             Q   + F+ +   ++  +A+   +G+  Q +++K+                       
Sbjct: 47  INQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGV 105

Query: 74  --SSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGK 123
             +        L++ GLP +++  +++ L + +G +    ++ D+     G 
Sbjct: 106 VSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDS---ATGL 154

>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 = 60.0 bits (146), Expect = 3e-12
 Identities = 15/46 (32%), Positives = 24/46 (52%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES 77
           T  S GY F  Y      ++AI  LNG++L +K + V  A   +++
Sbjct: 152 TGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAKN 197

>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 = 66.1 bits (162), Expect = 2e-15
 Identities = 18/49 (36%), Positives = 30/49 (61%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKG 80
           T Q  GYGFV +   EDA+ AI  ++ ++L  K I+V+ A   ++++ G
Sbjct: 53  TGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNKNLSG 101

>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 = 38.8 bits (91), Expect = 5e-05
 Identities = 14/45 (31%), Positives = 24/45 (53%)

Query: 71  ARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
           + P SE  + A +YV GL + +S+  L  LF   G ++ + +  D
Sbjct: 6   SGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKD 50

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 65.9 bits (161), Expect = 3e-15
 Identities = 14/41 (34%), Positives = 25/41 (60%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR 72
           T+ S  +GFV++  P+ A+ AI  +NG ++  K +KV   +
Sbjct: 78  TSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLKK 118

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 57.8 bits (140), Expect = 5e-12
 Identities = 17/81 (20%), Positives = 38/81 (46%), Gaps = 10/81 (12%)

Query: 38  YGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESI---KGANLYVSGLPKHMSQ 94
            G   +        + + L+   L +  +  + A  + + I   +G NL++  LP+  + 
Sbjct: 2   AGLPQFG-------SASALSTSPLASVALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTD 54

Query: 95  QELESLFSPYGRIITSRILCD 115
            +L S F P+G +I++++  D
Sbjct: 55  TDLASTFLPFGNVISAKVFID 75

>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 = 64.9 bits (159), Expect = 5e-15
 Identities = 18/46 (39%), Positives = 30/46 (65%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES 77
          T QS G+ F+++HR EDA +AI  ++G    +  + V +A+PS+ S
Sbjct: 53 TGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPSTNS 98

>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 = 45.3 bits (108), Expect = 2e-07
 Identities = 11/44 (25%), Positives = 21/44 (47%)

Query: 72  RPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
            P+  +   A + V+ L +   + +L+ LF P+G I    +  D
Sbjct: 7   GPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKD 50

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 63.4 bits (155), Expect = 2e-14
 Identities = 14/45 (31%), Positives = 23/45 (51%)

Query: 37  GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGA 81
            Y FV ++   DA  A+  +NG ++  K +KV++A   S    G 
Sbjct: 56  PYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPSSQKSGP 100

>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 = 36.1 bits (84), Expect = 5e-04
 Identities = 8/43 (18%), Positives = 20/43 (46%)

Query: 73  PSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
              +  +   LYV  L + +++  +  LFS  G   + +++ +
Sbjct: 8   MMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITE 50

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 61.7 bits (150), Expect = 8e-14
 Identities = 14/51 (27%), Positives = 25/51 (49%)

Query: 27 VFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES 77
             ++T        V Y   + A +A++ LNG +L+N T+KV+Y      +
Sbjct: 45 CEQVNTDSETAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYIPDEMAA 95

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 43.6 bits (103), Expect = 7e-07
 Identities = 8/37 (21%), Positives = 17/37 (45%)

Query: 79  KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
           +   L +  +P H+  + L+SL   YG + +   +  
Sbjct: 14  RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNT 50

>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 = 61.4 bits (150), Expect = 9e-14
 Identities = 16/42 (38%), Positives = 24/42 (57%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
          T +S GYGFV++    DAE AI  + G  L  + I+ ++A  
Sbjct: 44 TGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATR 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 = 36.4 bits (85), Expect = 4e-04
 Identities = 9/35 (25%), Positives = 21/35 (60%)

Query: 81  ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
            +++V  L   ++   + + F+P+GRI  +R++ D
Sbjct: 7   FHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKD 41

>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 = 61.5 bits (150), Expect = 1e-13
 Identities = 12/43 (27%), Positives = 20/43 (46%)

Query: 74  SSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDN 116
            S   +   L+V  L K  S++++  LF P+G I    +L   
Sbjct: 9   ESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP 51

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Length = 105

 Score = 50.7 bits (122), Expect = 2e-09
 Identities = 21/78 (26%), Positives = 32/78 (41%), Gaps = 7/78 (8%)

Query: 7   LNKLFTYEKVHLGFSD----AEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNG---L 59
           LNK  + E V   F       E  V       S G  FV +    +A+ AI+ L+G   +
Sbjct: 23  LNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTM 82

Query: 60  RLQNKTIKVSYARPSSES 77
              + ++ V +A    ES
Sbjct: 83  PGASSSLVVKFADTDKES 100

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A Length = 106

 Score = 60.8 bits (148), Expect = 2e-13
 Identities = 10/47 (21%), Positives = 24/47 (51%)

Query: 69  SYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
           S      +      L++  +P+++ +++L+ LF  +G+I    +L D
Sbjct: 2   SSGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKD 48

>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 = 49.2 bits (118), Expect = 6e-09
 Identities = 15/48 (31%), Positives = 20/48 (41%), Gaps = 3/48 (6%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNG---LRLQNKTIKVSYARPSSE 76
          T    G  F+ Y   E A KA + L+    L   N+ I+V  A   S 
Sbjct: 51 TGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQVKPADSESR 98

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 60.5 bits (147), Expect = 3e-13
 Identities = 11/57 (19%), Positives = 21/57 (36%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGL 88
           T + LG   V +     A++ +  L+   +    I         + +K   L V+G 
Sbjct: 44  TRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLDIKGQQRMKYYELIVNGS 100

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 40.1 bits (94), Expect = 2e-05
 Identities = 6/36 (16%), Positives = 14/36 (38%)

Query: 80  GANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
              +  + L  ++ +  L+ +   YG +    IL  
Sbjct: 6   LKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLH 41

>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 = 62.3 bits (152), Expect = 4e-13
 Identities = 21/90 (23%), Positives = 40/90 (44%), Gaps = 7/90 (7%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGAN------LYV 85
           T +S G+GFV Y   E+ + A+N     ++  + ++   A    +S +         ++V
Sbjct: 51  TKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFV 109

Query: 86  SGLPKHMSQQELESLFSPYGRIITSRILCD 115
            G+ +   +  L   F  YG+I    I+ D
Sbjct: 110 GGIKEDTEEHHLRDYFEQYGKIEVIEIMTD 139

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 59.6 bits (145), Expect = 7e-13
 Identities = 12/40 (30%), Positives = 23/40 (57%)

Query: 37  GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE 76
           G+ FV +   E A KAI  ++G    N+ ++V Y++  ++
Sbjct: 66  GFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPAK 105

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 43.4 bits (103), Expect = 1e-06
 Identities = 9/42 (21%), Positives = 17/42 (40%)

Query: 71  ARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRI 112
                  +    L+V   P  + + EL  +F P+G +   +I
Sbjct: 22  HHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKI 63

>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 = 59.7 bits (145), Expect = 7e-13
 Identities = 13/46 (28%), Positives = 23/46 (50%)

Query: 37  GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGAN 82
           GY FV +   E A  AI ++NG  ++   +K  + + S +   G +
Sbjct: 62  GYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPDMTSGPS 107

>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 = 39.2 bits (92), Expect = 4e-05
 Identities = 11/43 (25%), Positives = 22/43 (51%)

Query: 73  PSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
            +  S K   +Y  G+   ++ Q +   FSP+G+I+  R+  +
Sbjct: 18  VNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE 60

>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 = 58.7 bits (143), Expect = 8e-13
 Identities = 17/44 (38%), Positives = 24/44 (54%), Gaps = 2/44 (4%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS 75
          T +  GYGFV++  P  A+KA+  L    +Q +  K S   PSS
Sbjct: 43 TNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQS--GPSS 84

>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 = 47.9 bits (115), Expect = 1e-08
 Identities = 12/36 (33%), Positives = 22/36 (61%)

Query: 80  GANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
            + LY+ GL    + Q+L  L  PYG+I++++ + D
Sbjct: 5   SSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILD 40

>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 = 59.2 bits (144), Expect = 8e-13
 Identities = 16/44 (36%), Positives = 24/44 (54%)

Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKG 80
           Y FV++   EDA +A+  LNG  L    I+V+ A+P  +   G
Sbjct: 52 DYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDKDSSG 95

>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 = 38.8 bits (91), Expect = 5e-05
 Identities = 8/34 (23%), Positives = 13/34 (38%)

Query: 79  KGANLYVSGLPKHMSQQELESLFSPYGRIITSRI 112
               LYV  L    S++ +E  F+        R+
Sbjct: 14  SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV 47

>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 = 59.2 bits (144), Expect = 8e-13
 Identities = 14/44 (31%), Positives = 24/44 (54%)

Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKG 80
             FV Y + E A++A+  LNG ++++  +KV+ AR       G
Sbjct: 50 NCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQPMLDSG 93

>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 = 35.3 bits (82), Expect = 8e-04
 Identities = 14/34 (41%), Positives = 17/34 (50%), Gaps = 2/34 (5%)

Query: 79  KGANLYVSGLPKHMSQQELESLFSPYGRIITSRI 112
           KG  LYV G    M+   L   FSP+G II   +
Sbjct: 14  KGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSM 45

>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 = 61.1 bits (148), Expect = 1e-12
 Identities = 19/115 (16%), Positives = 40/115 (34%), Gaps = 35/115 (30%)

Query: 37  GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIK----------------- 79
               V       A+ A++ LNG +L  K I+++ ++  +  +                  
Sbjct: 42  ENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSP 101

Query: 80  ------------------GANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDN 116
                              A L++S +P  +S+++L+ LFS  G ++        
Sbjct: 102 LHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK 156

>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 = 43.7 bits (103), Expect = 3e-06
 Identities = 8/39 (20%), Positives = 20/39 (51%), Gaps = 1/39 (2%)

Query: 37  GYGFVNYHRPEDAEKAINTLNGLRL-QNKTIKVSYARPS 74
               +     E+A +A+  L+   L +N  ++VS+++ +
Sbjct: 159 KMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST 197

>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 = 41.4 bits (97), Expect = 2e-05
 Identities = 13/36 (36%), Positives = 20/36 (55%), Gaps = 1/36 (2%)

Query: 81  ANLYVSGL-PKHMSQQELESLFSPYGRIITSRILCD 115
           + L VS L P+ ++ Q L  LF  YG +   +IL +
Sbjct: 4   SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN 39

>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 = 58.7 bits (143), Expect = 1e-12
 Identities = 18/51 (35%), Positives = 26/51 (50%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGAN 82
          T  S GY F+N+   + ++ AI  +NG  L N+ I VSYA        G +
Sbjct: 44 TGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSKGSGPS 94

>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 = 58.5 bits (142), Expect = 1e-12
 Identities = 17/50 (34%), Positives = 23/50 (46%), Gaps = 4/50 (8%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQN----KTIKVSYARPSSES 77
          T    GY FV +     AEK ++ +NG  L      K  K++YA  S  S
Sbjct: 48 TGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKRFKLNYATYSGPS 97

>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 = 36.5 bits (85), Expect = 4e-04
 Identities = 12/53 (22%), Positives = 21/53 (39%)

Query: 73  PSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYY 125
            S  S   A+L++  L  +M +  +   F+  G  + S  +  N  T     Y
Sbjct: 2   SSGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGY 54

>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 = 58.8 bits (143), Expect = 1e-12
 Identities = 16/45 (35%), Positives = 26/45 (57%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE 76
            +S G+GFV +  PE+A KA+  +NG  +  K + V+ A+   E
Sbjct: 51 GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEE 95

>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 = 44.1 bits (105), Expect = 6e-07
 Identities = 11/38 (28%), Positives = 21/38 (55%)

Query: 79  KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDN 116
           +  NLYV  L   +  + L   FSP+G I +++++ + 
Sbjct: 14  QVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEG 51

>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 = 57.9 bits (141), Expect = 2e-12
 Identities = 13/42 (30%), Positives = 27/42 (64%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
          T  S GYGFV++   +DA+ A++++ G  L  + +++++A  
Sbjct: 39 TGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK 80

>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 = 38.6 bits (91), Expect = 5e-05
 Identities = 7/35 (20%), Positives = 17/35 (48%)

Query: 81  ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
            NL+V  L  ++  + L + F  +   ++  ++ D
Sbjct: 2   FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWD 36

>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 = 58.5 bits (142), Expect = 2e-12
 Identities = 16/42 (38%), Positives = 24/42 (57%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
          T +S GYGFV++    DAE AI  + G  L  + I+ ++A  
Sbjct: 53 TGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATR 94

>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 = 39.3 bits (92), Expect = 5e-05
 Identities = 9/45 (20%), Positives = 27/45 (60%)

Query: 71  ARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
           +    ++    +++V  L   ++ +++++ F+P+GRI  +R++ D
Sbjct: 6   SGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKD 50

>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 = 57.3 bits (139), Expect = 4e-12
 Identities = 11/40 (27%), Positives = 24/40 (60%)

Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE 76
           Y F+++   + A KA+  +NG  L+ + I++ +A+P  +
Sbjct: 46 DYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPPDQ 85

>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 = 41.9 bits (99), Expect = 4e-06
 Identities = 13/42 (30%), Positives = 22/42 (52%)

Query: 74  SSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
           SS   K   L+V  L   ++++ LE  FS +G++   + L D
Sbjct: 5   SSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD 46

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 57.8 bits (140), Expect = 5e-12
 Identities = 11/45 (24%), Positives = 21/45 (46%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE 76
           + +SLG   V++ R  DA KA+    G+ L  + + +       +
Sbjct: 72  SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQID 116

>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 = 42.7 bits (101), Expect = 3e-06
 Identities = 11/45 (24%), Positives = 20/45 (44%)

Query: 71  ARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
                    GA L VS L   +S  +++ LF+ +G +  + +  D
Sbjct: 26  CGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD 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 = 59.9 bits (144), Expect = 7e-12
 Identities = 13/80 (16%), Positives = 34/80 (42%)

Query: 27  VFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVS 86
           + +  + +  G  FV +     A  A+ ++ G    +K +++ YA+  S+ I        
Sbjct: 43  ILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFV 102

Query: 87  GLPKHMSQQELESLFSPYGR 106
              +   +++ +S  +P  +
Sbjct: 103 ERDRKREKRKPKSQETPATK 122

>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 = 48.3 bits (114), Expect = 9e-08
 Identities = 11/37 (29%), Positives = 19/37 (51%), Gaps = 1/37 (2%)

Query: 37  GYGFVNYHRPEDAEKAINTLNGLRL-QNKTIKVSYAR 72
              FV +     A  A + L G ++ QN  +K+S+A+
Sbjct: 245 DIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK 281

>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 = 56.9 bits (138), Expect = 8e-12
 Identities = 11/43 (25%), Positives = 21/43 (48%)

Query: 34 QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE 76
          +S G G V + +  +A +AI+  NG  L ++ + V     +  
Sbjct: 54 KSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDERALP 96

>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 = 43.8 bits (104), Expect = 8e-07
 Identities = 12/55 (21%), Positives = 27/55 (49%), Gaps = 4/55 (7%)

Query: 69  SYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGK 123
             +        G+ ++V+ L   +  ++L+ +FS  G ++ + IL D    ++GK
Sbjct: 4   GSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILED----KDGK 54

>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 = 56.5 bits (137), Expect = 9e-12
 Identities = 15/38 (39%), Positives = 20/38 (52%)

Query: 34 QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
          +   +GFV +  PE    AI  LNG+RL  + I VS  
Sbjct: 55 KPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSGP 92

>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 = 40.3 bits (95), Expect = 1e-05
 Identities = 9/47 (19%), Positives = 17/47 (36%)

Query: 69  SYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
           S     ++      ++V  L   + ++ L  LF   G +    I  D
Sbjct: 5   SSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKD 51

>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 = 58.6 bits (141), Expect = 9e-12
 Identities = 11/125 (8%), Positives = 29/125 (23%), Gaps = 37/125 (29%)

Query: 37  GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR------------------------ 72
           G   V        ++AI  LN   +  + + V  ++                        
Sbjct: 43  GAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSE 102

Query: 73  -------------PSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLAT 119
                         +        L+    P  ++++    +    G    + +   +  +
Sbjct: 103 SRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKS 162

Query: 120 ENGKY 124
           E    
Sbjct: 163 ERSSS 167

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 41.6 bits (97), Expect = 2e-05
 Identities = 8/39 (20%), Positives = 15/39 (38%), Gaps = 1/39 (2%)

Query: 79  KGANLYVSGL-PKHMSQQELESLFSPYGRIITSRILCDN 116
               L V GL    M+   + ++F  YG +   + +   
Sbjct: 3   DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK 41

>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 = 40.1 bits (93), Expect = 6e-05
 Identities = 7/39 (17%), Positives = 16/39 (41%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
            ++    G + +    DA + +  LN  +++N      Y
Sbjct: 161 KSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPY 199

>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 = 57.0 bits (138), Expect = 1e-11
 Identities = 17/45 (37%), Positives = 25/45 (55%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE 76
          T++S G+ F+ +  P DA+ A   +NG  L  K IKV  A+  S 
Sbjct: 44 TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKKPSF 88

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Length = 116

 Score = 41.5 bits (98), Expect = 6e-06
 Identities = 9/40 (22%), Positives = 22/40 (55%)

Query: 76  ESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
           E+     L++ GL +  +++ L+++F  +G I    ++ D
Sbjct: 3   EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD 42

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 56.0 bits (136), Expect = 1e-11
 Identities = 17/49 (34%), Positives = 25/49 (51%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKG 80
            +S G G V +  PE AE+A   +NG++L  + I V   R +S    G
Sbjct: 44 NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDRNASGPSSG 92

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 44.5 bits (106), Expect = 3e-07
 Identities = 11/43 (25%), Positives = 21/43 (48%)

Query: 74  SSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDN 116
           SS S     ++V  LP   + + L+  F+  G ++ + I  +N
Sbjct: 2   SSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMEN 44

>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 = 57.5 bits (139), Expect = 1e-11
 Identities = 18/80 (22%), Positives = 37/80 (46%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKH 91
              + G+ FV Y+   DAE A+  +NG RL ++ I+  +     E  +       G  + 
Sbjct: 77  KKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGRQYGRGRSGGQVRD 136

Query: 92  MSQQELESLFSPYGRIITSR 111
             +Q+ ++    YG++  ++
Sbjct: 137 EYRQDYDAGRGGYGKLAQNQ 156

>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 = 37.1 bits (86), Expect = 5e-04
 Identities = 11/49 (22%), Positives = 19/49 (38%)

Query: 67  KVSYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
           +           K   LYV  L  + +++++  LFS  G I    +  D
Sbjct: 26  RGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLD 74

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 56.2 bits (136), Expect = 1e-11
 Identities = 8/37 (21%), Positives = 14/37 (37%)

Query: 37  GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
           G  F+ Y   E A   I  L     Q + ++  + + 
Sbjct: 64  GCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKE 100

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 40.0 bits (94), Expect = 2e-05
 Identities = 7/34 (20%), Positives = 16/34 (47%)

Query: 82  NLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
             Y+  +P   ++ +L  LF  +G I+  +   +
Sbjct: 29  TAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE 62

>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 = 57.7 bits (139), Expect = 3e-11
 Identities = 20/115 (17%), Positives = 42/115 (36%), Gaps = 35/115 (30%)

Query: 37  GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA------------------------- 71
               V       A+ A++ LNG +L  K I+++ +                         
Sbjct: 73  ENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSP 132

Query: 72  -----RPSSESIKGAN-----LYVSGLPKHMSQQELESLFSPYGRIITSRILCDN 116
                +P S++ +        L++S +P  +S+++L+ LFS  G ++        
Sbjct: 133 LHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK 187

>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 = 8e-08
 Identities = 15/46 (32%), Positives = 22/46 (47%), Gaps = 1/46 (2%)

Query: 71  ARPSSESIKGANLYVSGL-PKHMSQQELESLFSPYGRIITSRILCD 115
           A P       + L VS L P+ ++ Q L  LF  YG +   +IL +
Sbjct: 25  AIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN 70

>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 = 43.4 bits (102), Expect = 4e-06
 Identities = 8/39 (20%), Positives = 20/39 (51%), Gaps = 1/39 (2%)

Query: 37  GYGFVNYHRPEDAEKAINTLNGLRL-QNKTIKVSYARPS 74
               +     E+A +A+  L+   L +N  ++VS+++ +
Sbjct: 190 KMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST 228

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 55.3 bits (134), Expect = 3e-11
 Identities = 13/46 (28%), Positives = 23/46 (50%)

Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGAN 82
          G+GF+       AE A   L+ + L+ K ++V +A  S+    G +
Sbjct: 52 GFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSASLTSGPS 97

>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 = 40.3 bits (95), Expect = 1e-05
 Identities = 10/31 (32%), Positives = 17/31 (54%)

Query: 82  NLYVSGLPKHMSQQELESLFSPYGRIITSRI 112
            L+V  LP  ++++E+  LF  YG+     I
Sbjct: 17  RLFVGNLPPDITEEEMRKLFEKYGKAGEVFI 47

>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 = 55.0 bits (133), Expect = 3e-11
 Identities = 14/42 (33%), Positives = 26/42 (61%)

Query: 35 SLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE 76
          S+G+GFV Y +PE A+KA+  L G  +    ++V  +  +++
Sbjct: 49 SMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISERATK 90

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 41.1 bits (97), Expect = 6e-06
 Identities = 9/39 (23%), Positives = 18/39 (46%)

Query: 77  SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
           S   + L++  L    +++ L+ +FS  G I +  I   
Sbjct: 2   SSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKK 40

>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 = 54.9 bits (133), Expect = 3e-11
 Identities = 11/52 (21%), Positives = 25/52 (48%)

Query: 27 VFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESI 78
          + +  + +  G  FV +     A  A+ ++ G    +K +++ YA+  S+ I
Sbjct: 42 ILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDII 93

>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 = 55.0 bits (133), Expect = 4e-11
 Identities = 13/46 (28%), Positives = 24/46 (52%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES 77
          T  S G+GFV+++  EDA+ A   +    +    + + +A+P  E 
Sbjct: 50 TGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGEG 95

>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 = 36.5 bits (85), Expect = 4e-04
 Identities = 12/43 (27%), Positives = 22/43 (51%), Gaps = 2/43 (4%)

Query: 71  ARPSSESIKGANLYVSGLPKHMSQQELESLFSPYG--RIITSR 111
           + P++ S     L+V GL +  +++ L+  F      RI+T R
Sbjct: 6   SGPNARSQPSKTLFVKGLSEDTTEETLKESFDGSVRARIVTDR 48

>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 = 54.9 bits (133), Expect = 4e-11
 Identities = 13/46 (28%), Positives = 22/46 (47%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES 77
          T +  G+ FV +  PE A KA   ++G   Q + + V  +    E+
Sbjct: 46 TKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKEA 91

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 39.1 bits (92), Expect = 3e-05
 Identities = 15/44 (34%), Positives = 21/44 (47%), Gaps = 3/44 (6%)

Query: 72  RPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
             SS S +   L+V  L    S+++LE LFS YG +       D
Sbjct: 3   SGSSGSGR---LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPID 43

>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 = 55.0 bits (133), Expect = 4e-11
 Identities = 16/45 (35%), Positives = 26/45 (57%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE 76
           T +S GYGF+ +   E A+KA+  LNG  L  + +KV +    ++
Sbjct: 64  TGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTERTD 108

>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 = 41.9 bits (99), Expect = 4e-06
 Identities = 12/54 (22%), Positives = 23/54 (42%)

Query: 62  QNKTIKVSYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
            +             S     LYV  L  ++++  L  +F P+GRI + +++ D
Sbjct: 8   HSHMAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMD 61

>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 = 4e-11
 Identities = 11/45 (24%), Positives = 21/45 (46%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE 76
           + +SLG   V++ R  DA KA+    G+ L  + + +       +
Sbjct: 125 SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQID 169

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 42.5 bits (100), Expect = 6e-06
 Identities = 11/45 (24%), Positives = 20/45 (44%)

Query: 71  ARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
                    GA L VS L   +S  +++ LF+ +G +  + +  D
Sbjct: 79  CGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD 123

>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 = 54.9 bits (133), Expect = 4e-11
 Identities = 16/45 (35%), Positives = 25/45 (55%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE 76
          T +  G+ FV +   EDA  AI+ +N   L  +TI+V+ A+P   
Sbjct: 50 TEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPMRI 94

>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 = 44.5 bits (106), Expect = 3e-07
 Identities = 13/45 (28%), Positives = 21/45 (46%)

Query: 71  ARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
           +  S  +     LYV GL + +  + L + F P+G I   +I  D
Sbjct: 3   SGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLD 47

>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 = 54.5 bits (132), Expect = 5e-11
 Identities = 11/42 (26%), Positives = 22/42 (52%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
             S GY +V +  P++AEKA+  ++G ++  + I  +    
Sbjct: 43 PHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAVLA 84

>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 = 42.5 bits (101), Expect = 1e-06
 Identities = 8/43 (18%), Positives = 23/43 (53%)

Query: 77  SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLAT 119
           S+K   +++  L +++++  +  +FS YG+I    +  + +  
Sbjct: 1   SMKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHP 43

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 93

 Score = 54.2 bits (131), Expect = 5e-11
 Identities = 15/46 (32%), Positives = 22/46 (47%), Gaps = 1/46 (2%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNG-LRLQNKTIKVSYARPSSE 76
               GY FV+Y     A +AI TL+G + L  K ++V Y+     
Sbjct: 40 VLLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKL 85

>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 = 37.6 bits (88), Expect = 1e-04
 Identities = 10/40 (25%), Positives = 17/40 (42%)

Query: 74  SSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRIL 113
           SS S     LY+  L   ++  +L  LF      +  ++L
Sbjct: 2   SSGSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL 41

>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 = 54.1 bits (131), Expect = 6e-11
 Identities = 15/41 (36%), Positives = 24/41 (58%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR 72
          T +  G+ FV +   EDA  AI+ +N   L  +TI+V+ A+
Sbjct: 45 TEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK 85

>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 = 39.8 bits (94), Expect = 1e-05
 Identities = 13/41 (31%), Positives = 20/41 (48%)

Query: 75  SESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
           S +     LYV GL + +  + L + F P+G I   +I  D
Sbjct: 2   SMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLD 42

>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 = 54.6 bits (132), Expect = 6e-11
 Identities = 10/45 (22%), Positives = 23/45 (51%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE 76
           T +  G  F+ +   E A +A++ +NG +L  K + + + +   +
Sbjct: 63  TGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKKQ 107

>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 = 37.3 bits (87), Expect = 3e-04
 Identities = 8/34 (23%), Positives = 16/34 (47%)

Query: 82  NLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
            LY+  L   +++++L SLF+ +       I   
Sbjct: 27  VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFR 60

>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 = 53.8 bits (130), Expect = 1e-10
 Identities = 12/40 (30%), Positives = 21/40 (52%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
           + +SLG   V++ R  DA KA+   NG+ L  + + +   
Sbjct: 66  SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLV 105

>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 = 43.8 bits (104), Expect = 8e-07
 Identities = 10/44 (22%), Positives = 20/44 (45%)

Query: 72  RPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
              +    G  L VS L   +S  +++ LF+ +G +  + +  D
Sbjct: 21  GGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD 64

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C Length = 229

 Score = 56.3 bits (135), Expect = 1e-10
 Identities = 12/75 (16%), Positives = 21/75 (28%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKH 91
             QS G+  V       ++K ++ L    L  +   V+       S        +     
Sbjct: 108 NGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTTQSGQ 167

Query: 92  MSQQELESLFSPYGR 106
           MS +          R
Sbjct: 168 MSGEGKAGPPGGSSR 182

>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 = 38.9 bits (90), Expect = 2e-04
 Identities = 9/55 (16%), Positives = 19/55 (34%), Gaps = 5/55 (9%)

Query: 71  ARPSSESIKGANLYVSGLPKHMSQQELESLFSPYG--RIITSRILCDNLATENGK 123
               + + K   LY+  L    + ++L       G   I+  +   +     NG+
Sbjct: 59  NVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFEN---RANGQ 110

>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 = 54.4 bits (131), Expect = 1e-10
 Identities = 16/73 (21%), Positives = 26/73 (35%), Gaps = 1/73 (1%)

Query: 7   LNKLF-TYEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKT 65
           L  +F  Y             + L+   +  G  F+     + A KA+   NG  L  K 
Sbjct: 62  LKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKP 121

Query: 66  IKVSYARPSSESI 78
           + V +AR +    
Sbjct: 122 MVVQFARSARPKQ 134

>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 = 38.7 bits (90), Expect = 9e-05
 Identities = 16/67 (23%), Positives = 30/67 (44%), Gaps = 3/67 (4%)

Query: 60  RLQNKTI-KVSYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRI--ITSRILCDN 116
           R+  + +  +S  R          +YV  L KH+ +++L+ +F  Y      T RI+ D 
Sbjct: 24  RISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDI 83

Query: 117 LATENGK 123
              + G+
Sbjct: 84  RLMKEGR 90

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 53.8 bits (130), Expect = 1e-10
 Identities = 14/46 (30%), Positives = 25/46 (54%)

Query: 35 SLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKG 80
          S G+GFV +    DA++A   L+G  ++ + I+V+ A     +  G
Sbjct: 54 SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARVMTNSG 99

>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 = 45.0 bits (107), Expect = 2e-07
 Identities = 10/43 (23%), Positives = 19/43 (44%)

Query: 73  PSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
            S        L+VS +P      +L  +F  +G+I+   I+ +
Sbjct: 8   NSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN 50

>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 = 53.4 bits (129), Expect = 1e-10
 Identities = 12/42 (28%), Positives = 24/42 (57%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
            +S GY F+ +   EDA++A+N+ N   ++ + I++    P
Sbjct: 49 NGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQGP 90

>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 = 53.4 bits (129), Expect = 1e-10
 Identities = 16/46 (34%), Positives = 28/46 (60%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES 77
          T +S G+GFV +   +DA+ A+  +NG  +  + I+V  A  SS++
Sbjct: 50 TQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDN 95

>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 = 43.0 bits (102), Expect = 2e-06
 Identities = 14/43 (32%), Positives = 22/43 (51%)

Query: 73  PSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
            S  +     L+V GL    ++Q LE +FS YG+I    ++ D
Sbjct: 5   SSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKD 47

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 53.6 bits (129), Expect = 2e-10
 Identities = 17/60 (28%), Positives = 27/60 (45%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKH 91
           T +  G   V++  P  A+ AI+  +G       IKVS+A   ++  +G      GL  H
Sbjct: 53  TGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADFNRGGGNGRGGLEHH 112

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 40.1 bits (94), Expect = 2e-05
 Identities = 6/32 (18%), Positives = 16/32 (50%)

Query: 76  ESIKGANLYVSGLPKHMSQQELESLFSPYGRI 107
           ++     ++V GL ++++ + +   F   G I
Sbjct: 3   DNSDNNTIFVQGLGENVTIESVADYFKQIGII 34

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 54.0 bits (130), Expect = 2e-10
 Identities = 15/40 (37%), Positives = 23/40 (57%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
           T +  G+ FV +   EDA  AI+ +N   L  +TI+V+ A
Sbjct: 101 TEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 140

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 45.2 bits (107), Expect = 4e-07
 Identities = 15/70 (21%), Positives = 23/70 (32%), Gaps = 2/70 (2%)

Query: 46  PEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYG 105
           PE        +N                   +     LYV GL + +  + L + F P+G
Sbjct: 31  PESVAY--TCVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFG 88

Query: 106 RIITSRILCD 115
            I   +I  D
Sbjct: 89  DITDIQIPLD 98

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 53.8 bits (129), Expect = 2e-10
 Identities = 5/53 (9%), Positives = 20/53 (37%)

Query: 27  VFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIK 79
           + +  +  + G  ++ +   E A+  +    G   Q   + ++++      + 
Sbjct: 63  IVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQSQVA 115

>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 = 53.6 bits (129), Expect = 2e-10
 Identities = 12/42 (28%), Positives = 24/42 (57%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
           + +S G+ FV +   +DA++A    NG+ L  + I+V ++  
Sbjct: 84  SRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSIT 125

>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 = 43.2 bits (102), Expect = 2e-06
 Identities = 12/47 (25%), Positives = 21/47 (44%)

Query: 69  SYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
            +    +       L V GL  + ++++L  +FS YG I    I+ D
Sbjct: 35  RHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYD 81

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 53.1 bits (128), Expect = 2e-10
 Identities = 13/39 (33%), Positives = 23/39 (58%)

Query: 35  SLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
           S G+GFV +    DA++A   L+G  ++ + I+V+ A  
Sbjct: 68  SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATA 106

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 44.2 bits (105), Expect = 5e-07
 Identities = 9/43 (20%), Positives = 20/43 (46%)

Query: 73  PSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
            +    +   L+VS +P      +L  +F  +G+I+   I+ +
Sbjct: 22  NTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN 64

>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 = 52.6 bits (127), Expect = 2e-10
 Identities = 15/46 (32%), Positives = 25/46 (54%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES 77
          T +S GY F+ +   E +  A+  LNG +L ++ +K  Y+  S  S
Sbjct: 40 TGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSNSDIS 85

>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 = 39.1 bits (92), Expect = 3e-05
 Identities = 7/35 (20%), Positives = 19/35 (54%)

Query: 81  ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
             +Y+  +P   +++++  L S  G +I  +++ D
Sbjct: 3   RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFD 37

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 53.0 bits (128), Expect = 2e-10
 Identities = 15/50 (30%), Positives = 27/50 (54%), Gaps = 1/50 (2%)

Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNG-LRLQNKTIKVSYARPSSESIK 79
           T  S GYGFV +    + ++A+    G + L +K +++S A P +  +K
Sbjct: 46 QTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLSVAIPKASRVK 95

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 52.7 bits (127), Expect = 3e-10
 Identities = 14/47 (29%), Positives = 23/47 (48%), Gaps = 4/47 (8%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNG----LRLQNKTIKVSYARPS 74
          T Q+ G+ FV      DA + +  L      L++  KTI V +A+ +
Sbjct: 49 TQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGVDFAKSA 95

>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 = 52.6 bits (127), Expect = 3e-10
 Identities = 8/45 (17%), Positives = 16/45 (35%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE 76
            QS G+  V       ++K ++ L    L  +   V+ +     
Sbjct: 41 NGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSNKLEH 85

>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 = 36.4 bits (85), Expect = 3e-04
 Identities = 8/44 (18%), Positives = 16/44 (36%), Gaps = 5/44 (11%)

Query: 82  NLYVSGLPKHMSQQELESLFSPYG--RIITSRILCDNLATENGK 123
            LY+  L    + ++L       G   I+  +   +     NG+
Sbjct: 3   ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENR---ANGQ 43

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 52.7 bits (127), Expect = 3e-10
 Identities = 8/46 (17%), Positives = 19/46 (41%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES 77
            +S G  ++ +    DAEK +    G  +  +++ + Y      +
Sbjct: 49 DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGGT 94

>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 = 38.0 bits (89), Expect = 8e-05
 Identities = 7/40 (17%), Positives = 14/40 (35%)

Query: 72  RPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSR 111
             S +      L    L  ++++ EL+ +F     I    
Sbjct: 8   CTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS 47

>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 = 52.6 bits (127), Expect = 3e-10
 Identities = 13/42 (30%), Positives = 21/42 (50%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
          T    G+ FV +H   DA+ A   ++G  L  + ++V  AR 
Sbjct: 51 TKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVARY 92

>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 = 44.9 bits (107), Expect = 3e-07
 Identities = 11/47 (23%), Positives = 15/47 (31%)

Query: 69  SYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
           S      +      L V  L    S   L  +F  YGR+    I  +
Sbjct: 2   SSGSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPRE 48

>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 = 52.2 bits (126), Expect = 3e-10
 Identities = 14/45 (31%), Positives = 24/45 (53%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE 76
          T +S GYGF+ +   E A +A+  LNG  L  + ++V +     +
Sbjct: 43 TGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHVTERLD 87

>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 = 41.4 bits (98), Expect = 5e-06
 Identities = 11/39 (28%), Positives = 21/39 (53%)

Query: 77  SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
           S   + LYV  L  ++++  L  +F P+G+I    ++ D
Sbjct: 2   SSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKD 40

>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 = 52.8 bits (127), Expect = 3e-10
 Identities = 17/79 (21%), Positives = 36/79 (45%), Gaps = 8/79 (10%)

Query: 27  VFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVS 86
           + + +T ++ G  +V Y    DA+ A++ L+G  + N+ + V Y   +    K       
Sbjct: 38  IRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYNANRAFQK------- 90

Query: 87  GLPKHMSQQELESLFSPYG 105
            +     +++L+ L   YG
Sbjct: 91  -MDTKKKEEQLKLLKEKYG 108

>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 = 38.1 bits (89), Expect = 1e-04
 Identities = 10/34 (29%), Positives = 17/34 (50%)

Query: 82  NLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
            LY+  LP  ++ +E+  +F  YG I   R+   
Sbjct: 10  ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT 43

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 51.9 bits (125), Expect = 5e-10
 Identities = 10/46 (21%), Positives = 21/46 (45%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES 77
            +  G  +V Y     A +A+  ++G+ ++   IKV+ +     S
Sbjct: 54 AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAISNSGPSS 99

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 44.2 bits (105), Expect = 5e-07
 Identities = 12/41 (29%), Positives = 25/41 (60%)

Query: 75  SESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
           S S++   L++SGLP   +++ELE +   +G +   R++ +
Sbjct: 12  STSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTN 52

>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 = 52.3 bits (126), Expect = 5e-10
 Identities = 14/52 (26%), Positives = 24/52 (46%), Gaps = 1/52 (1%)

Query: 31  STAQSLGYGFVNYHRPEDAEKAINTL-NGLRLQNKTIKVSYARPSSESIKGA 81
            T    G+GFV++   +DA+KA N L +   L  + + + +A        G 
Sbjct: 53  GTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQSGP 104

>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 = 41.1 bits (97), Expect = 7e-06
 Identities = 11/50 (22%), Positives = 22/50 (44%)

Query: 74  SSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGK 123
             +    + + V  +P   +Q+E+  LFS +G + T R+      T   +
Sbjct: 9   VPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHR 58

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 53.4 bits (128), Expect = 5e-10
 Identities = 12/46 (26%), Positives = 16/46 (34%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES 77
             QS GY  V         K +  L G  L  + + V  A   + S
Sbjct: 95  NGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQNLS 140

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 36.8 bits (85), Expect = 5e-04
 Identities = 10/64 (15%), Positives = 20/64 (31%), Gaps = 5/64 (7%)

Query: 62  QNKTIKVSYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYG--RIITSRILCDNLAT 119
            N          S    + A +YV       + Q+L  +    G   ++  +   +    
Sbjct: 37  PNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAEN---R 93

Query: 120 ENGK 123
            NG+
Sbjct: 94  ANGQ 97

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 52.8 bits (127), Expect = 5e-10
 Identities = 15/42 (35%), Positives = 25/42 (59%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
           T +S G+ FV +H   DAE A++ ++G  L  + ++V  AR 
Sbjct: 85  TKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARY 126

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 42.4 bits (100), Expect = 4e-06
 Identities = 15/47 (31%), Positives = 19/47 (40%)

Query: 69  SYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
           SY RP  +     +L V  L    S   L  +F  YGR+    I  D
Sbjct: 36  SYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRD 82

>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 = 51.8 bits (125), Expect = 5e-10
 Identities = 13/41 (31%), Positives = 23/41 (56%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR 72
          + +S G+ FV +   +DA++A    NG+ L  + I+VS   
Sbjct: 53 SRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSGPS 93

>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 = 42.2 bits (100), Expect = 2e-06
 Identities = 14/47 (29%), Positives = 23/47 (48%), Gaps = 2/47 (4%)

Query: 69  SYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
           S  R + +      L V GL  + ++++L  +FS YG I    I+ D
Sbjct: 6   SGNRANPDP--NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYD 50

>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 = 53.3 bits (128), Expect = 6e-10
 Identities = 14/42 (33%), Positives = 19/42 (45%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
           T  S GY  V Y   + A  A   LNG  +  +TI+V +   
Sbjct: 110 TGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFV 151

>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 = 45.6 bits (108), Expect = 4e-07
 Identities = 17/82 (20%), Positives = 30/82 (36%), Gaps = 11/82 (13%)

Query: 45  RPEDAEKAINTLNGLRLQNKTIKVSYARPSSE-----------SIKGANLYVSGLPKHMS 93
             E A+       G     +    SY R  +E           S++G  L+V+ + +   
Sbjct: 26  LKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQ 85

Query: 94  QQELESLFSPYGRIITSRILCD 115
           + E++  F  YG I    +  D
Sbjct: 86  EDEIQEKFCDYGEIKNIHLNLD 107

>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 = 53.3 bits (128), Expect = 6e-10
 Identities = 15/42 (35%), Positives = 25/42 (59%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
           T +S G+ FV +H   DAE A++ ++G  L  + ++V  AR 
Sbjct: 108 TKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARY 149

>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 = 43.7 bits (103), Expect = 2e-06
 Identities = 17/86 (19%), Positives = 25/86 (29%), Gaps = 10/86 (11%)

Query: 40  FVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIK----------GANLYVSGLP 89
            V+    E   K     NG+  +      +     +E               +L V  L 
Sbjct: 20  AVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLT 79

Query: 90  KHMSQQELESLFSPYGRIITSRILCD 115
              S   L  +F  YGR+    I  D
Sbjct: 80  YRTSPDTLRRVFEKYGRVGDVYIPRD 105

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 51.9 bits (125), Expect = 6e-10
 Identities = 13/42 (30%), Positives = 19/42 (45%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
           T    GY  V Y   ++A+ A+  LNG  L  + I V +   
Sbjct: 61  TGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFV 102

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 41.9 bits (99), Expect = 4e-06
 Identities = 10/39 (25%), Positives = 23/39 (58%)

Query: 77  SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
           S++G  L+V+G+ +  +++++   F+ YG I    +  D
Sbjct: 20  SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLD 58

>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 = 52.4 bits (126), Expect = 7e-10
 Identities = 13/42 (30%), Positives = 19/42 (45%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
           T    GY  V Y   ++A+ A+  LNG  L  + I V +   
Sbjct: 60  TGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFV 101

>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 = 39.7 bits (93), Expect = 4e-05
 Identities = 10/40 (25%), Positives = 23/40 (57%)

Query: 76  ESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
            S++G  L+V+G+ +  +++++   F+ YG I    +  D
Sbjct: 18  RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLD 57

>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 = 51.6 bits (124), Expect = 8e-10
 Identities = 15/51 (29%), Positives = 22/51 (43%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGAN 82
           T +  G   V+Y  P  A+ A+   +G   Q   +KVS AR       G +
Sbjct: 61  TGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNSGPS 111

>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 = 42.0 bits (99), Expect = 4e-06
 Identities = 8/37 (21%), Positives = 15/37 (40%)

Query: 71  ARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRI 107
           +    E    + +YV GL   ++  +L   F   G +
Sbjct: 6   SGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVV 42

>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 = 51.8 bits (124), Expect = 9e-10
 Identities = 14/50 (28%), Positives = 22/50 (44%)

Query: 31  STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKG 80
            +       +V Y R EDA +AI  +N + +  +T+K S       S  G
Sbjct: 58  GSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKASLGTTKYCSYSG 107

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 51.0 bits (122), Expect = 1e-09
 Identities = 13/37 (35%), Positives = 22/37 (59%)

Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
             F++Y     A++A++ L GLRL   T++V+ AR 
Sbjct: 57 RRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQ 93

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Length = 110

 Score = 51.1 bits (123), Expect = 1e-09
 Identities = 14/42 (33%), Positives = 19/42 (45%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
           T  S GY  V Y   + A  A   LNG  +  +TI+V +   
Sbjct: 64  TGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFV 105

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Length = 110

 Score = 39.6 bits (93), Expect = 3e-05
 Identities = 10/39 (25%), Positives = 20/39 (51%)

Query: 77  SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
           S++G  L+V+ + +   + E++  F  YG I    +  D
Sbjct: 23  SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLD 61

>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 = 50.3 bits (121), Expect = 2e-09
 Identities = 14/44 (31%), Positives = 21/44 (47%)

Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKG 80
           YGFV+      AE AI  L+  +L    I V  ++  S++  G
Sbjct: 43 NYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNKSKASSG 86

>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 = 42.6 bits (101), Expect = 2e-06
 Identities = 14/39 (35%), Positives = 23/39 (58%)

Query: 74  SSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRI 112
           SS S     L++  LP+  ++QE+ SLF  YG+++   I
Sbjct: 2   SSGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDI 40

>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 = 50.3 bits (121), Expect = 2e-09
 Identities = 14/44 (31%), Positives = 20/44 (45%)

Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKG 80
           Y FV+  R EDA +AI  L+    Q K + V  +     +  G
Sbjct: 45 DYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLRTASG 88

>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 = 40.7 bits (96), Expect = 8e-06
 Identities = 11/41 (26%), Positives = 18/41 (43%), Gaps = 2/41 (4%)

Query: 72  RPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRI 112
             S ++     L+V  +    + QEL + F  YG +I   I
Sbjct: 4   GSSGKA--STKLHVGNISPTCTNQELRAKFEEYGPVIECDI 42

>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 = 50.6 bits (121), Expect = 2e-09
 Identities = 10/41 (24%), Positives = 19/41 (46%)

Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES 77
          G G V + R ED   A+  L+  + ++   + +Y R   + 
Sbjct: 51 GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDG 91

>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 = 50.3 bits (121), Expect = 2e-09
 Identities = 13/46 (28%), Positives = 24/46 (52%), Gaps = 1/46 (2%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES 77
          T  +  +G+V++   ED EKA+  L GL++    IK+   +    +
Sbjct: 54 TGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEKPKGRDGT 98

>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 = 49.9 bits (120), Expect = 3e-09
 Identities = 13/40 (32%), Positives = 20/40 (50%)

Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE 76
           Y FV+  +  DA+ AI  LNG  ++ K I V  +    +
Sbjct: 44 DYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTKGQK 83

>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 = 40.3 bits (95), Expect = 1e-05
 Identities = 12/39 (30%), Positives = 18/39 (46%)

Query: 74  SSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRI 112
           S  S     ++V  +    + QEL SLF   GR+I   +
Sbjct: 3   SGSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDV 41

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 50.0 bits (120), Expect = 3e-09
 Identities = 11/48 (22%), Positives = 20/48 (41%)

Query: 27 VFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS 74
          + L +      + FV +  P DAE A+   +G       ++V + R  
Sbjct: 52 IDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSG 99

>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 = 38.1 bits (89), Expect = 1e-04
 Identities = 9/39 (23%), Positives = 17/39 (43%), Gaps = 3/39 (7%)

Query: 69  SYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRI 107
                 +   +   +YV  LP  +  +++E +F  YG I
Sbjct: 14  IRGPAGNNDCR---IYVGNLPPDIRTKDIEDVFYKYGAI 49

>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 = 49.5 bits (119), Expect = 4e-09
 Identities = 11/40 (27%), Positives = 19/40 (47%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
          T +S G  F+ +   + A+     +N  +L  + IK S A
Sbjct: 54 TRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASIA 93

>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 = 45.3 bits (108), Expect = 1e-07
 Identities = 13/47 (27%), Positives = 24/47 (51%)

Query: 69  SYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
           S       +   + +YVS LP  ++  +L  +FS YG+++   I+ D
Sbjct: 5   SSGMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKD 51

>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 = 49.7 bits (119), Expect = 4e-09
 Identities = 13/46 (28%), Positives = 19/46 (41%)

Query: 37  GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGAN 82
           GY FV Y     A  A+   NG  L  +T+ ++ A        G +
Sbjct: 63  GYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEPKPDRSGPS 108

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A Length = 110

 Score = 36.2 bits (84), Expect = 5e-04
 Identities = 9/58 (15%), Positives = 27/58 (46%), Gaps = 2/58 (3%)

Query: 57  NGLRLQNKTIKVSYARPSSE-SIKGANLYVSGLPKH-MSQQELESLFSPYGRIITSRI 112
           +G    +  ++ S     ++     + +++  L    + + ++E++FS YGR+    +
Sbjct: 3   SGSSGMSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV 60

>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 = 49.6 bits (119), Expect = 5e-09
 Identities = 14/42 (33%), Positives = 19/42 (45%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
          T +  GYGF  Y   E A  A+  LNG     + ++V  A  
Sbjct: 46 TGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAAS 87

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 40.7 bits (96), Expect = 1e-05
 Identities = 8/35 (22%), Positives = 23/35 (65%)

Query: 81  ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
            +++V  +P   ++++L+ +FS  G +++ R++ D
Sbjct: 9   RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYD 43

>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 = 48.4 bits (116), Expect = 1e-08
 Identities = 8/37 (21%), Positives = 16/37 (43%), Gaps = 1/37 (2%)

Query: 37 GYGFVNYHRPEDAEKAI-NTLNGLRLQNKTIKVSYAR 72
             F+ +   + AE A   + N L +  + + V + R
Sbjct: 49 QCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWGR 85

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 40.7 bits (96), Expect = 7e-06
 Identities = 10/32 (31%), Positives = 18/32 (56%)

Query: 82  NLYVSGLPKHMSQQELESLFSPYGRIITSRIL 113
            LYV GL   +++ +L + F  +G I T  ++
Sbjct: 14  TLYVGGLGDTITETDLRNHFYQFGEIRTITVV 45

>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 = 48.3 bits (115), Expect = 2e-08
 Identities = 10/40 (25%), Positives = 19/40 (47%)

Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE 76
          G G V + R ED   A+  L+  + ++   + +Y R   +
Sbjct: 52 GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVD 91

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 48.0 bits (115), Expect = 2e-08
 Identities = 6/39 (15%), Positives = 16/39 (41%)

Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS 75
           +GF+ +  P+    AI   +      K + +  +  ++
Sbjct: 46 AFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSNA 84

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 36.8 bits (86), Expect = 3e-04
 Identities = 13/34 (38%), Positives = 23/34 (67%), Gaps = 1/34 (2%)

Query: 80  GANLYVSGLP-KHMSQQELESLFSPYGRIITSRI 112
            + L++  LP K++S+++L  +FSPYG I+   I
Sbjct: 10  KSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI 43

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 48.1 bits (115), Expect = 2e-08
 Identities = 13/40 (32%), Positives = 20/40 (50%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
          T +  G   V++  P  A+ AI+  +G       IKVS+A
Sbjct: 59 TGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFA 98

>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 = 38.8 bits (91), Expect = 5e-05
 Identities = 6/35 (17%), Positives = 14/35 (40%)

Query: 73  PSSESIKGANLYVSGLPKHMSQQELESLFSPYGRI 107
                     ++V GL ++++ + +   F   G I
Sbjct: 6   HHHSHSDNNTIFVQGLGENVTIESVADYFKQIGII 40

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 48.3 bits (115), Expect = 2e-08
 Identities = 11/59 (18%), Positives = 20/59 (33%)

Query: 15  KVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
           K     +  E     ++T    G G + +   E   +A+  LN +  +   I V     
Sbjct: 46  KDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDDN 104

>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 = 47.7 bits (114), Expect = 2e-08
 Identities = 6/39 (15%), Positives = 16/39 (41%)

Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS 75
           +GF+ +  P+    AI   +      K + +  +  ++
Sbjct: 58 AFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSSNA 96

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A Length = 97

 Score = 37.3 bits (87), Expect = 2e-04
 Identities = 15/45 (33%), Positives = 26/45 (57%), Gaps = 2/45 (4%)

Query: 69  SYARPSSESIKGANLYVSGLP-KHMSQQELESLFSPYGRIITSRI 112
           S   P    +  + L++  LP K++S+++L  +FSPYG I+   I
Sbjct: 12  SGLVPRGSHM-KSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI 55

>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 = 47.3 bits (113), Expect = 3e-08
 Identities = 9/58 (15%), Positives = 20/58 (34%)

Query: 18 LGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS 75
                 +C+         G   V +   ++A  A+  LN   + ++ +K+      S
Sbjct: 39 YQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLGSGPS 96

>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 = 48.0 bits (114), Expect = 5e-08
 Identities = 11/37 (29%), Positives = 18/37 (48%)

Query: 37  GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
           G+ FV +  P DA  A+  L+G  L    ++V  +  
Sbjct: 111 GFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNG 147

>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 = 36.4 bits (84), Expect = 7e-04
 Identities = 14/93 (15%), Positives = 24/93 (25%), Gaps = 16/93 (17%)

Query: 36  LGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIK---------------- 79
            G           AEK           +       A  +    +                
Sbjct: 13  KGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHRDSCPL 72

Query: 80  GANLYVSGLPKHMSQQELESLFSPYGRIITSRI 112
              +YV  L  + ++ ELE  F  YG + +  +
Sbjct: 73  DCKVYVGNLGNNGNKTELERAFGYYGPLRSVWV 105

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 46.9 bits (112), Expect = 5e-08
 Identities = 11/37 (29%), Positives = 19/37 (51%)

Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
          G+ FV +  P DAE A+  L+G  +    ++V  +  
Sbjct: 38 GFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTG 74

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 36.9 bits (86), Expect = 3e-04
 Identities = 12/31 (38%), Positives = 15/31 (48%)

Query: 82  NLYVSGLPKHMSQQELESLFSPYGRIITSRI 112
            +YV  L     + ELE  FS YG + T  I
Sbjct: 2   KVYVGNLGTGAGKGELERAFSYYGPLRTVWI 32

>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 = 46.5 bits (111), Expect = 6e-08
 Identities = 8/43 (18%), Positives = 20/43 (46%), Gaps = 2/43 (4%)

Query: 37 GYGFVNYHRPEDAEKAINTLNGLRL--QNKTIKVSYARPSSES 77
           + ++ Y   + A+ A   + G  L   ++ ++V +A+    S
Sbjct: 54 SFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSGPSS 96

>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 = 42.6 bits (101), Expect = 2e-06
 Identities = 12/52 (23%), Positives = 21/52 (40%), Gaps = 4/52 (7%)

Query: 62  QNKTIKVSYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRIL 113
              + K+ Y + +  +     L+V GL  + S   L   F  +G I T   +
Sbjct: 3   SGSSGKIGYGKANPTT----RLWVGGLGPNTSLAALAREFDRFGSIRTIDHV 50

>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 = 47.0 bits (112), Expect = 6e-08
 Identities = 15/57 (26%), Positives = 24/57 (42%), Gaps = 6/57 (10%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLN------GLRLQNKTIKVSYARPSSESIKGAN 82
           T  S G  F  +   E A+K +   +      GL+L  + +KV  A    E+  G +
Sbjct: 53  TEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAASGPS 109

>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 = 39.6 bits (93), Expect = 3e-05
 Identities = 6/45 (13%), Positives = 19/45 (42%)

Query: 71  ARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
           +   S+  +G  +++  L     ++ L  +   +G +   R++  
Sbjct: 6   SGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLH 50

>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 = 46.0 bits (110), Expect = 7e-08
 Identities = 14/42 (33%), Positives = 22/42 (52%), Gaps = 1/42 (2%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
          T +  G+GFV   + E   +AI  L+      +TI+V+ A P
Sbjct: 39 TKKPKGFGFVEM-QEESVSEAIAKLDNTDFMGRTIRVTEANP 79

>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 = 39.8 bits (94), Expect = 2e-05
 Identities = 9/34 (26%), Positives = 21/34 (61%)

Query: 82  NLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
           N+YV  L    + ++++ LFS +G++   +++ D
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYD 36

>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 = 1e-07
 Identities = 7/42 (16%), Positives = 16/42 (38%)

Query: 30 ISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
          +   +      V +  P +A KA   L   +  +  + + +A
Sbjct: 40 VLLPEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWA 81

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100

 Score = 44.9 bits (107), Expect = 2e-07
 Identities = 10/40 (25%), Positives = 20/40 (50%), Gaps = 1/40 (2%)

Query: 37  GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE 76
           G+G+  +   +    A++ LN   L N+ I+V  A  + +
Sbjct: 62  GFGYAEFEDLDSLLSALS-LNEESLGNRRIRVDVADQAQD 100

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 44.3 bits (105), Expect = 3e-07
 Identities = 11/39 (28%), Positives = 19/39 (48%), Gaps = 1/39 (2%)

Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRL-QNKTIKV 68
             ++ GY F+ Y  P  A  A+   +G +L +  T +V
Sbjct: 42 EDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRV 80

>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 = 44.9 bits (107), Expect = 3e-07
 Identities = 12/45 (26%), Positives = 21/45 (46%), Gaps = 2/45 (4%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE 76
          T  S GYGFV+++   D +K +   + +    K +K+  A     
Sbjct: 46 TGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPAIRKQN 88

>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 = 41.1 bits (97), Expect = 8e-06
 Identities = 10/34 (29%), Positives = 19/34 (55%)

Query: 82  NLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
            ++V G+   M + E+ S F+ YG +   +I+ D
Sbjct: 11  TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD 44

>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 = 45.2 bits (107), Expect = 3e-07
 Identities = 12/47 (25%), Positives = 19/47 (40%), Gaps = 2/47 (4%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLN--GLRLQNKTIKVSYARPSSE 76
            ++ G+ FV Y     A  A   L    ++L    I V +A P  +
Sbjct: 48 KMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEID 94

>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 = 43.6 bits (103), Expect = 9e-07
 Identities = 8/40 (20%), Positives = 17/40 (42%)

Query: 75  SESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILC 114
           S S     L++ G+PK   ++E+    +     +   I+ 
Sbjct: 3   SGSSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVY 42

>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 = 44.3 bits (105), Expect = 3e-07
 Identities = 12/69 (17%), Positives = 23/69 (33%), Gaps = 2/69 (2%)

Query: 12 TYEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
            ++VH    D ++        ++    FV     E A+ AI   +    + K + V   
Sbjct: 18 NCQEVHDLLKDYDLKY--CYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQ 75

Query: 72 RPSSESIKG 80
             +    G
Sbjct: 76 PTDALLCSG 84

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 44.6 bits (106), Expect = 3e-07
 Identities = 15/62 (24%), Positives = 25/62 (40%), Gaps = 6/62 (9%)

Query: 20 FSDAEIC-VFLIS----TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS 74
          F    I  V L        +  G+G+  +   +    A++ LN   L NK I+V  A  +
Sbjct: 36 FRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLGNKRIRVDVADQA 94

Query: 75 SE 76
           +
Sbjct: 95 QD 96

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 44.2 bits (105), Expect = 4e-07
 Identities = 13/61 (21%), Positives = 29/61 (47%), Gaps = 5/61 (8%)

Query: 20 FSDAEIC-VFLIS---TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS 75
          F D  I  V L+    T +  G+ +V +   +  ++A+   +G  L +++++V  A    
Sbjct: 36 FKDLSIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT-YDGALLGDRSLRVDIAEGRK 94

Query: 76 E 76
          +
Sbjct: 95 Q 95

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 44.0 bits (104), Expect = 6e-07
 Identities = 5/41 (12%), Positives = 18/41 (43%)

Query: 76  ESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDN 116
             +K  ++Y+ G P   +  +++      G+++  ++    
Sbjct: 7   NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL 47

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 43.4 bits (103), Expect = 8e-07
 Identities = 9/54 (16%), Positives = 20/54 (37%)

Query: 18 LGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
                 +C+         G   V +   ++A  A+  LN   + ++ +K+S  
Sbjct: 39 YQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGP 92

>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 = 42.9 bits (102), Expect = 1e-06
 Identities = 7/42 (16%), Positives = 17/42 (40%), Gaps = 1/42 (2%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
          +    G+ ++ +   E    ++  L+    + + IKV   R 
Sbjct: 44 SGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKRT 84

>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 = 38.6 bits (91), Expect = 4e-05
 Identities = 11/34 (32%), Positives = 18/34 (52%)

Query: 82  NLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
           ++YV  +    + +ELE+ F   G +    ILCD
Sbjct: 8   SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCD 41

>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 = 43.9 bits (104), Expect = 1e-06
 Identities = 9/51 (17%), Positives = 21/51 (41%), Gaps = 1/51 (1%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGAN 82
           +    GY ++ +      + A+  ++    + +TIKV   R +   I   +
Sbjct: 74  SGHPKGYAYIEFAERNSVDAAVA-MDETVFRGRTIKVLPKRTNMPGISSTD 123

>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 = 38.5 bits (90), Expect = 8e-05
 Identities = 14/45 (31%), Positives = 22/45 (48%)

Query: 71  ARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
           +    + I   ++YV  +    + Q+LE+ FS  G I    ILCD
Sbjct: 27  SAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCD 71

>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 = 43.1 bits (102), Expect = 2e-06
 Identities = 12/51 (23%), Positives = 21/51 (41%), Gaps = 1/51 (1%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGAN 82
           + +S G  +V +   +    AI  L G RL    I V  ++     + G +
Sbjct: 63  SRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQAEKNRLSGPS 112

>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 = 37.7 bits (88), Expect = 2e-04
 Identities = 11/43 (25%), Positives = 19/43 (44%)

Query: 73  PSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
            S E      ++   L   +  ++LE  FS  G++   RI+ D
Sbjct: 18  LSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISD 60

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 42.8 bits (101), Expect = 2e-06
 Identities = 11/42 (26%), Positives = 20/42 (47%), Gaps = 1/42 (2%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRL-QNKTIKVSYAR 72
          T ++ G+ FV      DA+K I + +G RL     + +   +
Sbjct: 50 TGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRLFLYTMK 91

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 42.8 bits (101), Expect = 2e-06
 Identities = 11/41 (26%), Positives = 20/41 (48%), Gaps = 1/41 (2%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRL-QNKTIKVSYA 71
            ++ GY F+ Y  P  A  A+   +G +L +  T +V+  
Sbjct: 57 DGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRVNLF 97

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 41.6 bits (98), Expect = 3e-06
 Identities = 9/47 (19%), Positives = 23/47 (48%), Gaps = 3/47 (6%)

Query: 27 VFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
          V  +   Q   + F+ +   ++  +A+   +G+  Q +++K+   RP
Sbjct: 44 VLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIR--RP 87

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 41.8 bits (98), Expect = 4e-06
 Identities = 11/42 (26%), Positives = 20/42 (47%), Gaps = 5/42 (11%)

Query: 37  GYGFVNYHRPEDAEKAINTLNGLRL-----QNKTIKVSYARP 73
            Y F  Y   E++++A  TLNG  +     Q  T+ +++   
Sbjct: 64  PYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVEK 105

>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 = 41.1 bits (97), Expect = 1e-05
 Identities = 17/61 (27%), Positives = 25/61 (40%), Gaps = 4/61 (6%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE---SIKGANLYVSGL 88
           T +S GYGFV       AE+A    N   +  +   V+ A   ++      G  + VSG 
Sbjct: 55  TGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAYLGAKPRSLQTGFAIGVSGP 113

Query: 89  P 89
            
Sbjct: 114 S 114

>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 = 40.1 bits (93), Expect = 4e-05
 Identities = 15/80 (18%), Positives = 34/80 (42%), Gaps = 5/80 (6%)

Query: 42  NYHRPEDAEKAINTLNGLRLQNKTIKVSYA-RPSSESIKGAN----LYVSGLPKHMSQQE 96
           ++H    A+ A+  +N ++  N  +  S A   +  ++ G +    + V  L   ++   
Sbjct: 3   HHHHHGSAQAALQAVNSVQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDV 62

Query: 97  LESLFSPYGRIITSRILCDN 116
           L  +FS +G ++       N
Sbjct: 63  LHQIFSKFGTVLKIITFTKN 82

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A Length = 164

 Score = 37.8 bits (87), Expect = 3e-04
 Identities = 11/48 (22%), Positives = 25/48 (52%), Gaps = 2/48 (4%)

Query: 37  GYGFVNYHRPEDAEKAINTLNGLRLQN--KTIKVSYARPSSESIKGAN 82
               + Y  P  A+ A  +L+G  + N   T+++ +++ +S ++K  N
Sbjct: 85  FQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSLNVKYNN 132

>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 = 39.1 bits (91), Expect = 5e-05
 Identities = 8/33 (24%), Positives = 19/33 (57%)

Query: 83  LYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
           +++  LP  +++ E+ SL  P+G++    +L  
Sbjct: 34  IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG 66

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 38.7 bits (90), Expect = 7e-05
 Identities = 8/31 (25%), Positives = 19/31 (61%)

Query: 83  LYVSGLPKHMSQQELESLFSPYGRIITSRIL 113
           +++  LP  +++ E+ SL  P+G++    +L
Sbjct: 19  IHIRKLPIDVTEGEVISLGLPFGKVTNLLML 49

>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 = 38.2 bits (89), Expect = 1e-04
 Identities = 14/66 (21%), Positives = 27/66 (40%), Gaps = 4/66 (6%)

Query: 20  FSDAEI-CVFLISTAQ--SLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE 76
           F    +  V L+      + G G V +  P+D  +A+   N + +  + ++VS A     
Sbjct: 37  FHGLRVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPATERQW 95

Query: 77  SIKGAN 82
              G +
Sbjct: 96  VAAGGH 101

>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 = 1e-04
 Identities = 9/43 (20%), Positives = 15/43 (34%)

Query: 37  GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIK 79
             GFV +    +AE A   ++   L   + K    R     + 
Sbjct: 180 NCGFVKFKYQANAEFAKEAMSNQTLLLPSDKEWDDRREGTGLL 222

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 38.1 bits (88), Expect = 1e-04
 Identities = 19/77 (24%), Positives = 28/77 (36%), Gaps = 8/77 (10%)

Query: 4  QTLLNKLFTYEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQN 63
          Q L      + KV          V L           V     +DA  A+N+L+  ++ +
Sbjct: 28 QLLQEAFARHGKV--------KSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGS 79

Query: 64 KTIKVSYARPSSESIKG 80
          K I VS A  +S    G
Sbjct: 80 KKILVSLATGASGPSSG 96

>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 = 37.5 bits (87), Expect = 2e-04
 Identities = 6/34 (17%), Positives = 15/34 (44%)

Query: 82  NLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
            ++V GL + + + +L      +G I    ++  
Sbjct: 17  VVHVRGLCESVVEADLVEALEKFGTICYVMMMPF 50

>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 = 37.5 bits (87), Expect = 2e-04
 Identities = 8/31 (25%), Positives = 19/31 (61%)

Query: 83  LYVSGLPKHMSQQELESLFSPYGRIITSRIL 113
           L++  LP  +++ E+ +L  P+G++    +L
Sbjct: 18  LHIRKLPGEVTETEVIALGLPFGKVTNILML 48

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 37.0 bits (86), Expect = 2e-04
 Identities = 5/33 (15%), Positives = 14/33 (42%)

Query: 83  LYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
           +++ GL   + + +L      +G I    ++  
Sbjct: 24  VHIRGLIDGVVEADLVEALQEFGPISYVVVMPK 56

>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 = 37.1 bits (86), Expect = 2e-04
 Identities = 10/34 (29%), Positives = 16/34 (47%)

Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
          G  FV +    D +KA+  L G +  N+ +   Y
Sbjct: 60 GKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKY 93

>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 = 38.3 bits (88), Expect = 3e-04
 Identities = 15/105 (14%), Positives = 29/105 (27%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKH 91
           + +  GY F+ Y    D   A    +G ++  + + V   R  +           GL   
Sbjct: 140 SGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGT 199

Query: 92  MSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLRR 136
                  ++        +        +    +       RER  R
Sbjct: 200 RRGGADVNIRHSGRDDTSRYDERPGPSPLPHRDRDRDRERERRER 244

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 35.8 bits (83), Expect = 6e-04
 Identities = 8/37 (21%), Positives = 18/37 (48%), Gaps = 2/37 (5%)

Query: 71  ARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRI 107
               S  ++  +++VSG P+ +   +L   F  +G +
Sbjct: 1   GSSGSSGLR--SVFVSGFPRGVDSAQLSEYFLAFGPV 35

>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 = 36.3 bits (84), Expect = 6e-04
 Identities = 9/38 (23%), Positives = 15/38 (39%)

Query: 33  AQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
           A+ +   FV +    +  KAI  LNG     + +    
Sbjct: 68  AEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEV 105

>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 = 35.8 bits (83), Expect = 7e-04
 Identities = 10/37 (27%), Positives = 16/37 (43%)

Query: 37  GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
           G   V++  PE+A+  I TL+G     + I       
Sbjct: 65  GVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDG 101

>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 = 35.9 bits (83), Expect = 7e-04
 Identities = 13/58 (22%), Positives = 22/58 (37%), Gaps = 3/58 (5%)

Query: 19 GFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS 74
          G    E  V ++  +  Q LG   V +   +DA K+   L+  +L  +   V      
Sbjct: 38 GIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVVTLE 94

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	136
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	100.0
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	100.0
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	100.0
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	100.0
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	100.0
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.98
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.98
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.98
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.97
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.97
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.97
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.97
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.96
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.96
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.96
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.96
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.96
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.95
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.95
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.95
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.93
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.89
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.85
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.84
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.84
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.84
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.83
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.83
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.83
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.83
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.82
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.82
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.82
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.82
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.81
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.81
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.81
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.81
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.81
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.81
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.81
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.81
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.81
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.81
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.81
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.81
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.81
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.8
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.8
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.8
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.8
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.8
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.8
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.8
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.8
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.8
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.8
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.8
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.8
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.8
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.79
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.79
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.79
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.79
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.79
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.79
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.79
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.79
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.79
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.79
2div_A	99	TRNA selenocysteine associated protein; structural	99.79
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.79
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.78
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.78
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.78
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.78
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.78
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.78
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.78
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.78
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.78
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.78
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.78
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.78
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.78
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.78
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.78
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.77
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.77
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.77
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.77
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.77
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.77
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.77
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.77
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.77
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.77
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.77
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.77
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.77
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.77
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.77
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.76
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.76
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.76
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.76
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.76
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.76
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.76
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.76
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.76
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.75
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.75
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.75
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.75
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.75
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.75
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.75
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.74
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.74
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.74
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.74
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.74
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.74
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.74
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.74
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.74
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.74
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.73
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.73
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.73
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.73
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.73
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.73
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.73
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.73
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.73
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.73
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.73
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.72
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.72
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.72
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.72
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.72
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.72
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.72
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.72
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.71
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.71
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.71
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.71
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.71
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.55
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.71
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.71
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.7
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.7
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.7
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.7
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.7
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.7
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.7
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.7
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.7
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.7
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.69
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.69
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.69
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.69
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.69
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.69
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.69
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.68
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.68
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.68
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.67
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.67
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.67
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.67
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.67
1x5p_A	97	Negative elongation factor E; structure genomics,	99.67
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.66
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.66
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.66
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.65
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.65
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.65
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.65
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.65
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.64
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.64
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.64
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.64
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.63
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.63
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.62
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.62
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.59
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.59
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.58
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.58
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.58
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.58
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.57
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.56
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.54
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.54
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.54
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.54
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.54
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.54
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.53
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.53
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.53
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.53
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.53
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.53
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.53
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.52
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.52
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.52
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.52
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.52
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.52
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.51
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.51
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.51
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.51
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.51
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.51
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.51
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.51
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.5
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.5
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.5
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.5
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.5
2div_A	99	TRNA selenocysteine associated protein; structural	99.5
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.5
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.5
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.5
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.5
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.5
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.49
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.49
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.49
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.49
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.49
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.49
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.49
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.49
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.49
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.49
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.49
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.48
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.48
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.48
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.48
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.48
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.48
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.47
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.47
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.47
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.47
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.47
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.47
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.47
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.47
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.47
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.47
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.47
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.47
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.47
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.46
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.46
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.46
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.46
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.45
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.45
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.45
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.45
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.45
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.44
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.44
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.44
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.44
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.44
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.44
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.43
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.43
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.43
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.43
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.43
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.43
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.42
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.42
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.42
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.42
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.42
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.42
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.41
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.41
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.41
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.41
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.41
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.41
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.4
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.4
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.4
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.4
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.4
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.4
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.39
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.39
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.39
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.39
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.39
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.38
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.38
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.37
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.37
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.37
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.37
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.37
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.36
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.35
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.34
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.34
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.34
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.33
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.33
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.32
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.32
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.32
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.31
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	98.99
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.31
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.31
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.3
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.3
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.29
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.28
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.28
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.26
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.25
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.25
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.25
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.24
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.23
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.22
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.22
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	99.21
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.21
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.2
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.19
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.19
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.18
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.17
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.16
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.15
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.15
1x5p_A	97	Negative elongation factor E; structure genomics,	99.09
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.08
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.07
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.01
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.0
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	98.98
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.97
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.96
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	98.93
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.91
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	98.8
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	98.79
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	98.78
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	98.65
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	98.63
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.47
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	98.26
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	98.15
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	98.08
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	97.9
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	97.74
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.68
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	97.55
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	97.32
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.19
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	97.04
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	96.81
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	96.74
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	96.71
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	96.57
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	96.55
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	96.39
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	96.35
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	95.77
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	95.67
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	94.99
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	90.29
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	88.93
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	86.18

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=100.00  E-value=6.4e-34  Score=184.54  Aligned_cols=134  Identities=34%  Similarity=0.621  Sum_probs=126.3

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||+|.++.+++  .+|+++|||||+|.+.++|+.|+..+||..+.|++|.+.++.+...
T Consensus         6 l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~~   85 (168)
T 1b7f_A            6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARPGGE   85 (168)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCSS
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecCCCcc
Confidence            79999999998   999999999999999988  6899999999999999999999999999999999999999999888


Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      .....+|+|+|||..+++++|+++|++||.|..+.++++..++.. +.|||+|.+.|+|.
T Consensus        86 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~  145 (168)
T 1b7f_A           86 SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQ  145 (168)
T ss_dssp             TTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHH
T ss_pred             cCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHH
Confidence            888999999999999999999999999999999999999866665 56999999999875

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=100.00  E-value=8e-34  Score=183.70  Aligned_cols=134  Identities=57%  Similarity=0.824  Sum_probs=126.4

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||+|.++.+++  .+|+++|||||+|.+.++|+.|+..+||..+.|+++.+.++.+...
T Consensus         5 l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~~   84 (167)
T 1fxl_A            5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSSA   84 (167)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCCG
T ss_pred             EEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecCCCcc
Confidence            79999999998   999999999999999998  5899999999999999999999999999999999999999998887


Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      .....+|+|+|||..+++++|+++|++||.|..+.++.++.+|.+ +.|||+|.+.|+|.
T Consensus        85 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~  144 (167)
T 1fxl_A           85 SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAE  144 (167)
T ss_dssp             GGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHH
T ss_pred             cCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHH
Confidence            778899999999999999999999999999999999999877775 55999999999875

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=100.00  E-value=5.6e-33  Score=179.53  Aligned_cols=134  Identities=22%  Similarity=0.375  Sum_probs=122.7

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC-
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE-   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~-   76 (136)
                      |||+|||..++   |+++|++||+|.++.+++ .+++++|||||+|.+.++|+.|+..+||..+.|+++.+.++.+... 
T Consensus         3 l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~~~~   82 (166)
T 3md3_A            3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQQS   82 (166)
T ss_dssp             EEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCCCC
T ss_pred             EEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCCCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCCCCC
Confidence            79999999998   999999999999999999 7788999999999999999999999999999999999998876543 


Q ss_pred             -CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCcc-ceEeecCcccccc
Q psy6353          77 -SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENG-KYYSGLGGRERLR  135 (136)
Q Consensus        77 -~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~-~~fv~f~~~e~~~  135 (136)
                       .....+|||+|||..+++++|+++|++||.|..+.+++++.++..+ .|||+|.+.|+|.
T Consensus        83 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~  143 (166)
T 3md3_A           83 SSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQ  143 (166)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHH
T ss_pred             CCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHH
Confidence             3467899999999999999999999999999999999998887774 5999999999875

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=100.00  E-value=2e-32  Score=181.57  Aligned_cols=133  Identities=20%  Similarity=0.376  Sum_probs=118.9

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||+|.++.+++  .+|.++|||||+|.+.++|++|+.. ++..+.|+.|.+.++.+...
T Consensus        16 l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v~~~~~~~~   94 (196)
T 1l3k_A           16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAVSRED   94 (196)
T ss_dssp             EEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEECCC---
T ss_pred             EEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeeeecccCccc
Confidence            89999999998   999999999999999998  6799999999999999999999985 89999999999998876543


Q ss_pred             C------CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          77 S------IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~------~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      .      ...++|||+|||.++|+++|+++|++||.|..+.++.+..++.. +.|||+|.+.|+|.
T Consensus        95 ~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~  160 (196)
T 1l3k_A           95 SQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVD  160 (196)
T ss_dssp             --------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHH
T ss_pred             ccccccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHH
Confidence            2      24589999999999999999999999999999999999877776 55999999999875

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=100.00  E-value=7.3e-33  Score=186.54  Aligned_cols=133  Identities=23%  Similarity=0.396  Sum_probs=121.1

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..+|   |+++|++||+|.+|++++  .+++++|||||+|.+.++|+.|+..+|+..+.|+.+++.++.+...
T Consensus        18 lfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~~~~~~   97 (213)
T 4f02_A           18 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPS   97 (213)
T ss_dssp             EEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCTH
T ss_pred             EEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCccccccccccccc
Confidence            89999999998   999999999999999998  7899999999999999999999999999999999999998875542


Q ss_pred             --CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          77 --SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        77 --~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                        .....+|||+|||..+|+++|+++|++||.|..++|++|..+ .++.|||+|.+.|+|.
T Consensus        98 ~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~~~-~~g~~fV~f~~~~~a~  157 (213)
T 4f02_A           98 LRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAE  157 (213)
T ss_dssp             HHHHCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTE-EEEEEEEEESSHHHHH
T ss_pred             ccccccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccCCC-CceEEEEEeCCHHHHH
Confidence              234578999999999999999999999999999999998754 4577999999999875

>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=99.98  E-value=5.7e-32  Score=176.24  Aligned_cols=134  Identities=18%  Similarity=0.316  Sum_probs=118.5

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCC--CceeeEEEEcCCHHHHHHHHHHHcCceeC---CceEEEEee
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STA--QSLGYGFVNYHRPEDAEKAINTLNGLRLQ---NKTIKVSYA   71 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~--~~kg~~fv~f~~~~~a~~a~~~~~~~~~~---g~~l~v~~~   71 (136)
                      |||+|||..++   |+++|++||+|.++.+++  .++  +++|||||+|.+.++|+.|+..+||..+.   ++++.+.++
T Consensus         6 l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~~~~~   85 (175)
T 3nmr_A            6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMKPA   85 (175)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCEEEEC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceEEccc
Confidence            79999999998   999999999999999998  444  89999999999999999999999998776   678888877


Q ss_pred             CCCCC-CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          72 RPSSE-SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        72 ~~~~~-~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      .+... ....++|||+|||..+|+++|+++|++||.|..+.+++++.+...+.|||+|.+.|+|.
T Consensus        86 ~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~~~~~A~  150 (175)
T 3nmr_A           86 DSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQ  150 (175)
T ss_dssp             GGGCCSCGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSHHHHH
T ss_pred             cccccccCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEECCHHHHH
Confidence            65543 33678999999999999999999999999999999999986444567999999999875

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.98  E-value=5.8e-32  Score=181.70  Aligned_cols=134  Identities=19%  Similarity=0.331  Sum_probs=120.7

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||+|.++.+++  .+++++|||||+|.+.++|+.|+..+||..+.|+.|.+.++.+...
T Consensus        31 l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~~~~  110 (216)
T 2qfj_A           31 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQ  110 (216)
T ss_dssp             EEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCSCCGG
T ss_pred             EEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCCCccc
Confidence            89999999998   999999999999999988  5899999999999999999999999999999999999988776542


Q ss_pred             -----------CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          77 -----------SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        77 -----------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                                 .....+|||+|||..+++++|+++|++||.|..+.+++++.++.. +.+||+|.+.|+|.
T Consensus       111 ~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~  181 (216)
T 2qfj_A          111 AQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQ  181 (216)
T ss_dssp             GHHHHHHHHHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHH
T ss_pred             cchhhhhhhcccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHH
Confidence                       235689999999999999999999999999999999999888776 56999999999875

>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=99.98  E-value=4.8e-33  Score=180.35  Aligned_cols=132  Identities=21%  Similarity=0.375  Sum_probs=121.3

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||+|.++.+++  .+|.++|||||+|.+.++|+.|+..  +..+.|+.+.+.++.+...
T Consensus         6 l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g~~i~v~~~~~~~~   83 (167)
T 2cjk_A            6 MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT--QHILDGKVIDPKRAIPRDE   83 (167)
T ss_dssp             EEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS--CCEETTEECCCEECCCHHH
T ss_pred             EEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc--ccccCCeEcccccccchhh
Confidence            79999999999   999999999999999988  6899999999999999999999994  6789999999999887766


Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      .....+|||+|||.++++++|+++|++||.|..+.++.++.+|.+ +.|||+|.+.|+|.
T Consensus        84 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~  143 (167)
T 2cjk_A           84 QDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVD  143 (167)
T ss_dssp             HHHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHH
T ss_pred             ccCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHH
Confidence            667789999999999999999999999999999999999877776 55999999999875

>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=99.97  E-value=1.1e-31  Score=179.97  Aligned_cols=130  Identities=11%  Similarity=0.128  Sum_probs=113.3

Q ss_pred             eeecCCC-hhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC-
Q psy6353           2 VYQTLLN-KLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE-   76 (136)
Q Consensus         2 v~v~nl~-~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~-   76 (136)
                      |||+||| ..++   |+++|++||.|.++++++   .++|||||+|.+.++|+.|++.|||..+.|++|.|.++..... 
T Consensus         7 l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~---~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s~~~~~~   83 (205)
T 3tyt_A            7 LMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMK---SKPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQPAIM   83 (205)
T ss_dssp             EEEECCCTTTCCHHHHHHHHTTTSCEEEEEECT---TSTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCSCCC
T ss_pred             EEEeCCCcccCCHHHHHHHHHhcCCeEEEEEec---CCCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEccCCccC
Confidence            8999999 7888   999999999999999986   3579999999999999999999999999999999998753210 


Q ss_pred             ------------------------------------CCCCceEEEcCCCCCCCHHHHHHhhcCCCce--EEEEEEeCCCC
Q psy6353          77 ------------------------------------SIKGANLYVSGLPKHMSQQELESLFSPYGRI--ITSRILCDNLA  118 (136)
Q Consensus        77 ------------------------------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v--~~~~i~~~~~~  118 (136)
                                                          ..+..+|||+|||.++|+++|+++|++||.|  ..+++..+. +
T Consensus        84 p~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~-~  162 (205)
T 3tyt_A           84 PGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK-S  162 (205)
T ss_dssp             CCSCCBCTTSCBSEEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCC-S
T ss_pred             CCcccccccCCccccccCCCccccccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCC-C
Confidence                                                0124579999999999999999999999999  899998876 4


Q ss_pred             CCccceEeecCcccccc
Q psy6353         119 TENGKYYSGLGGRERLR  135 (136)
Q Consensus       119 ~~~~~~fv~f~~~e~~~  135 (136)
                      +.++.|||+|.+.|+|.
T Consensus       163 ~~~g~gfV~f~~~~~A~  179 (205)
T 3tyt_A          163 ERSSSGLLEWDSKSDAL  179 (205)
T ss_dssp             SSSEEEEEECSSHHHHH
T ss_pred             CCceEEEEEeCCHHHHH
Confidence            44578999999999874

>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=99.97  E-value=1.1e-30  Score=169.93  Aligned_cols=129  Identities=12%  Similarity=0.259  Sum_probs=116.9

Q ss_pred             eeecCCChhhh---HHHHhccC----C-------CeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEE
Q psy6353           2 VYQTLLNKLFT---YEKVHLGF----S-------DAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIK   67 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~----G-------~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~   67 (136)
                      |||+|||..++   |+++|++|    |       .|.++.+.    .++|||||+|.+.++|++|+ ++||..+.|+++.
T Consensus         7 l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~----~~~g~afV~f~~~~~A~~A~-~~~~~~~~g~~i~   81 (172)
T 2g4b_A            7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN----QDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLK   81 (172)
T ss_dssp             EEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEE----TTTTEEEEEESSHHHHHHHG-GGTTCEETTEECE
T ss_pred             EEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEec----CCCCEEEEEeCCHHHHHHHH-HhCCcEecCceee
Confidence            79999999999   99999999    6       66666554    47899999999999999999 7999999999999


Q ss_pred             EEeeCCCCCCCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          68 VSYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        68 v~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      +.++.+........+|||+|||..+++++|+++|++||.|..+.+++++.+|.+ +.|||+|.+.|+|.
T Consensus        82 v~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~  150 (172)
T 2g4b_A           82 IRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTD  150 (172)
T ss_dssp             EECCSSCCCCTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHH
T ss_pred             ecCCcccCCCCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHH
Confidence            999887776677899999999999999999999999999999999999877776 55999999999875

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=99.97  E-value=5.5e-30  Score=178.74  Aligned_cols=134  Identities=22%  Similarity=0.301  Sum_probs=122.1

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||.|.++.++.  .+|.++|||||+|.+.++|..|+..+||..+.|++|.+.++.+...
T Consensus        98 l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a~~~~~  177 (284)
T 3smz_A           98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQL  177 (284)
T ss_dssp             EEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCGGGC
T ss_pred             EEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCCC
Confidence            79999999998   999999999999999887  6899999999999999999999999999999999999999886553


Q ss_pred             ---CCCCceEEEcCCCCCC-CHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          77 ---SIKGANLYVSGLPKHM-SQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        77 ---~~~~~~l~v~nl~~~~-t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                         .....+|||+|||.++ ++++|+++|++||.|..+.++.++.+...+.|||+|.+.|+|.
T Consensus       178 ~~~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~  240 (284)
T 3smz_A          178 TPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAE  240 (284)
T ss_dssp             CTTTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECSSCCEEEEEEEECSSHHHHH
T ss_pred             CcccCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECCCCCcccEEEEEeCCHHHHH
Confidence               3467899999999995 9999999999999999999999985555577999999999874

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.97  E-value=1.3e-29  Score=175.41  Aligned_cols=124  Identities=22%  Similarity=0.390  Sum_probs=114.1

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESI   78 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~~~   78 (136)
                      |||+|||..+|   |+++|++||.|.++.+.+    ++|||||+|.+.++|+.|+..+||..+.|++|.|.++.+     
T Consensus        25 l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~----~kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~a~~-----   95 (261)
T 3sde_A           25 LFVGNLPTDITEEDFKRLFERYGEPSEVFINR----DRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATH-----   95 (261)
T ss_dssp             EEEESCCTTCCHHHHHHHTGGGCCCSEEEEET----TTTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC-----
T ss_pred             EEEECCCCCCCHHHHHHHHHhcCCEEEEEEeC----CCcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeeccc-----
Confidence            79999999998   999999999999999865    689999999999999999999999999999999999874     


Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                       +.+|||+|||..+|+++|+++|++||.|..+.++.+..+...+.|||+|.+.++|.
T Consensus        96 -~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~  151 (261)
T 3sde_A           96 -GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPAR  151 (261)
T ss_dssp             -SSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHHHH
T ss_pred             -CCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHHHH
Confidence             47899999999999999999999999999999999964444467999999999874

>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=99.96  E-value=5.6e-30  Score=179.33  Aligned_cols=134  Identities=16%  Similarity=0.273  Sum_probs=115.4

Q ss_pred             eeecCCChhhh---HHHHhccCC-CeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFS-DAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G-~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++|| .|.++.++. ..|.++|||||+|.+.++|..|+..+||..+.|++|.|.++.+...
T Consensus       120 l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  199 (292)
T 2ghp_A          120 LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEK  199 (292)
T ss_dssp             EEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCC--
T ss_pred             EEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCcc
Confidence            79999999998   999999999 999999998 6688999999999999999999999999999999999999887654


Q ss_pred             C-------CCCceEEEcCCCCC-CCHHHHHHhhcCCCceEEEEEEeCCC--CCCccceEeecCcccccc
Q psy6353          77 S-------IKGANLYVSGLPKH-MSQQELESLFSPYGRIITSRILCDNL--ATENGKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~-------~~~~~l~v~nl~~~-~t~~~l~~~f~~~G~v~~~~i~~~~~--~~~~~~~fv~f~~~e~~~  135 (136)
                      .       ....+|||+|||.. +++++|+++|++||.|..+.++++..  +...+.|||+|.+.|+|.
T Consensus       200 ~~~~~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~  268 (292)
T 2ghp_A          200 SKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAE  268 (292)
T ss_dssp             -------CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHH
T ss_pred             cccccccCCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHH
Confidence            3       34589999999999 99999999999999999999999887  444466999999999875

>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=99.96  E-value=6.8e-29  Score=173.07  Aligned_cols=129  Identities=16%  Similarity=0.321  Sum_probs=114.4

Q ss_pred             eeecCCChhhh---HH----HHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCC
Q psy6353           2 VYQTLLNKLFT---YE----KVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS   74 (136)
Q Consensus         2 v~v~nl~~~~~---l~----~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~   74 (136)
                      |||+|||..++   |+    ++|++||.|.+|.+++ +++++|||||+|.+.++|+.|+..+||..+.|+.|+|.++.+.
T Consensus        12 l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~-~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~   90 (282)
T 3pgw_A           12 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR-SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTD   90 (282)
T ss_pred             EEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC-CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEEeccC
Confidence            89999999998   55    7999999999998875 7889999999999999999999999999999999999987654


Q ss_pred             CC------------------------------------------------------------------------------
Q psy6353          75 SE------------------------------------------------------------------------------   76 (136)
Q Consensus        75 ~~------------------------------------------------------------------------------   76 (136)
                      ..                                                                              
T Consensus        91 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~p~~~  170 (282)
T 3pgw_A           91 SDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMI  170 (282)
T ss_pred             cchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCcccccccccccCCCCCCCCCCCCCC
Confidence            32                                                                              


Q ss_pred             ---------------------------------CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccc
Q psy6353          77 ---------------------------------SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGK  123 (136)
Q Consensus        77 ---------------------------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~  123 (136)
                                                       ....++|||+|||..+++++|+++|++||.|..++++.+.    ++.
T Consensus       171 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~----~g~  246 (282)
T 3pgw_A          171 PPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR----HDI  246 (282)
T ss_pred             CCCCCCccccCcccCcccccCccccCccCCccCCCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC----CcE
Confidence                                             1134679999999999999999999999999999999654    468


Q ss_pred             eEeecCcccccc
Q psy6353         124 YYSGLGGRERLR  135 (136)
Q Consensus       124 ~fv~f~~~e~~~  135 (136)
                      +||+|.+.|+|.
T Consensus       247 afV~f~~~~~A~  258 (282)
T 3pgw_A          247 AFVEFDNEVQAG  258 (282)
T ss_pred             EEEEeCCHHHHH
Confidence            999999999874

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.96  E-value=7.3e-29  Score=164.58  Aligned_cols=129  Identities=12%  Similarity=0.268  Sum_probs=112.4

Q ss_pred             eeecCCChhhh---HHHHhccCC-----------CeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEE
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFS-----------DAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIK   67 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G-----------~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~   67 (136)
                      |||+|||..++   |+++|++||           .|.++.+    ++++|||||+|.+.++|++|+ ++||..+.|++|.
T Consensus         7 l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~----~~~~g~afV~F~~~~~A~~Al-~l~g~~~~g~~i~   81 (198)
T 2yh0_A            7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI----NQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLK   81 (198)
T ss_dssp             EEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEE----ETTTTEEEEEESCSHHHHHHG-GGTTEEETTEEEE
T ss_pred             EEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEe----cCCCCEEEEEeCCHHHHHHHH-HhcCCEEcCceEE
Confidence            79999999998   999999994           4555544    457899999999999999999 7999999999999


Q ss_pred             EEeeCCCCC--------------------CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEe
Q psy6353          68 VSYARPSSE--------------------SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYS  126 (136)
Q Consensus        68 v~~~~~~~~--------------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv  126 (136)
                      |.++.+...                    ....++|||+|||..+++++|+++|++||.|..+.+++++.++.. +.+||
T Consensus        82 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV  161 (198)
T 2yh0_A           82 IRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFC  161 (198)
T ss_dssp             EECCCCCCCCCCSSSCSSCCCTTSSCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEE
T ss_pred             EeCCCCCCCCCCCcCCCcCCCCCCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEE
Confidence            998765421                    135689999999999999999999999999999999999877765 56999


Q ss_pred             ecCcccccc
Q psy6353         127 GLGGRERLR  135 (136)
Q Consensus       127 ~f~~~e~~~  135 (136)
                      +|.+.|+|.
T Consensus       162 ~f~~~~~a~  170 (198)
T 2yh0_A          162 EYVDINVTD  170 (198)
T ss_dssp             EESSSSHHH
T ss_pred             EECCHHHHH
Confidence            999999875

>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=99.96  E-value=2.6e-28  Score=170.27  Aligned_cols=123  Identities=22%  Similarity=0.346  Sum_probs=113.3

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESI   78 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~~~   78 (136)
                      |||+|||..++   |+++|++|| |.++.+    ++++|||||+|.+.++|+.|+..+||..+.|+++.+.++.      
T Consensus        25 l~V~nLp~~~te~~l~~~F~~~G-i~~~~~----~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~~~------   93 (284)
T 3smz_A           25 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV----DKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQP------   93 (284)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE----ETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC------
T ss_pred             EEEeCCCCCCCHHHHHHHHHHcC-CEEEEE----ecCCCEEEEEeCCHHHHHHHHHHcCCCeeCCeEEEEEecC------
Confidence            89999999998   999999999 888877    4688999999999999999999999999999999999865      


Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ..++|||+|||..+|+++|+++|++||.|..+.++.++.+|.+ +.+||+|.+.|+|.
T Consensus        94 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~  151 (284)
T 3smz_A           94 TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAA  151 (284)
T ss_dssp             CSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHH
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHH
Confidence            4478999999999999999999999999999999999888877 45999999999874

>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=99.96  E-value=1.1e-29  Score=165.78  Aligned_cols=129  Identities=18%  Similarity=0.242  Sum_probs=110.0

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC-
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE-   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~-   76 (136)
                      |||+|||..++   |+++|++||.+..+.+.. .+++++|||||+|.+.++|+.|++ +||..+.|++|.+.++.+... 
T Consensus        16 l~V~nLp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~v~~~~~~~~~   94 (175)
T 1fje_B           16 LFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKGRDSK   94 (175)
T ss_dssp             EEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECCCCSSCS
T ss_pred             EEEeCCCCCCCHHHHHHHHHHhCCcceEEEEECCCCccccEEEEEECCHHHHHHHHh-cCCCEeCCeEEEEecCCCcccc
Confidence            79999999998   888999999876633333 778899999999999999999995 999999999999999886543 


Q ss_pred             -CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          77 -SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        77 -~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                       ....++|||+|||..+++++|+++|++||.|..+    ...+..++.|||+|.+.|+|.
T Consensus        95 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~----~~~~~~~g~afV~f~~~~~A~  150 (175)
T 1fje_B           95 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAE  150 (175)
T ss_dssp             TTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE----CSSSSCCSEEEEECSSHHHHH
T ss_pred             ccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe----cCCCCCceEEEEEECCHHHHH
Confidence             3456899999999999999999999999988766    333344467999999999875

>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=99.95  E-value=4.4e-28  Score=164.75  Aligned_cols=127  Identities=20%  Similarity=0.275  Sum_probs=111.7

Q ss_pred             eeecCCCh-hhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC-
Q psy6353           2 VYQTLLNK-LFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE-   76 (136)
Q Consensus         2 v~v~nl~~-~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~-   76 (136)
                      |||+|||. .++   |+++|++||.|.++.+++   ..+|||||+|.+.++|+.|++.+||..+.|++|.|.++.+... 
T Consensus        37 l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~---~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~~~  113 (229)
T 2adc_A           37 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILF---NKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQ  113 (229)
T ss_dssp             EEEESCCTTTCCHHHHHHHHHHHTCEEEEEECC---TTSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCCCCC
T ss_pred             EEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEE---CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEecCcccc
Confidence            89999999 888   999999999999999987   2279999999999999999999999999999999998875410 


Q ss_pred             ----------------------------------CCCCceEEEcCCCCCCCHHHHHHhhcCCC-ceEEEEEEeCCCCCCc
Q psy6353          77 ----------------------------------SIKGANLYVSGLPKHMSQQELESLFSPYG-RIITSRILCDNLATEN  121 (136)
Q Consensus        77 ----------------------------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G-~v~~~~i~~~~~~~~~  121 (136)
                                                        .....+|||+|||..+++++|+++|++|| .|..+.+..+    .+
T Consensus       114 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~----~~  189 (229)
T 2adc_A          114 LPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK----DR  189 (229)
T ss_dssp             CCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS----ST
T ss_pred             CccccccccccccccccCcccccCCccccccccCCCCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC----CC
Confidence                                              11257899999999999999999999999 9999999753    24


Q ss_pred             cceEeecCcccccc
Q psy6353         122 GKYYSGLGGRERLR  135 (136)
Q Consensus       122 ~~~fv~f~~~e~~~  135 (136)
                      +.+||+|.+.|+|.
T Consensus       190 g~afV~f~~~~~A~  203 (229)
T 2adc_A          190 KMALIQMGSVEEAV  203 (229)
T ss_dssp             TCEEEEESSHHHHH
T ss_pred             cEEEEEECCHHHHH
Confidence            67999999999875

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.95  E-value=2.3e-28  Score=162.49  Aligned_cols=127  Identities=20%  Similarity=0.274  Sum_probs=111.9

Q ss_pred             eeecCCCh-hhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC-
Q psy6353           2 VYQTLLNK-LFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE-   76 (136)
Q Consensus         2 v~v~nl~~-~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~-   76 (136)
                      |||+|||. .++   |+++|++||.|.++.+++   ..+|||||+|.+.++|+.|+..+||..+.|++|.|.++.+... 
T Consensus         6 l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~---~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~~~~~~   82 (198)
T 1qm9_A            6 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILF---NKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQ   82 (198)
T ss_dssp             EEEECCCSSSCCHHHHHHHHHTTCCCSEEECST---TCSSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECCCCSCC
T ss_pred             EEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEe---CCCCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEecCCCcC
Confidence            79999999 888   999999999999999876   2379999999999999999999999999999999998875421 


Q ss_pred             ----------------------------------CCCCceEEEcCCCCCCCHHHHHHhhcCCC-ceEEEEEEeCCCCCCc
Q psy6353          77 ----------------------------------SIKGANLYVSGLPKHMSQQELESLFSPYG-RIITSRILCDNLATEN  121 (136)
Q Consensus        77 ----------------------------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G-~v~~~~i~~~~~~~~~  121 (136)
                                                        ..+..+|||+|||..+++++|+++|++|| .|..+.+.++.    .
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~~----~  158 (198)
T 1qm9_A           83 LPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD----R  158 (198)
T ss_dssp             CSSSSSSSSSCEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESSTT----S
T ss_pred             CCCcCCccccccccccCCchhhccCccccccccCCCCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeCC----C
Confidence                                              12367899999999999999999999999 99999997643    4


Q ss_pred             cceEeecCcccccc
Q psy6353         122 GKYYSGLGGRERLR  135 (136)
Q Consensus       122 ~~~fv~f~~~e~~~  135 (136)
                      +.+||+|.+.|+|.
T Consensus       159 g~afV~f~~~~~A~  172 (198)
T 1qm9_A          159 KMALIQMGSVEEAV  172 (198)
T ss_dssp             SCEEEECSSHHHHH
T ss_pred             cEEEEEeCCHHHHH
Confidence            77999999999875

>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=99.95  E-value=3e-28  Score=170.54  Aligned_cols=125  Identities=16%  Similarity=0.165  Sum_probs=109.6

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES   77 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~~   77 (136)
                      |||+|||..++   |+++|++||+|.++.+++ ..+ ++|||||+|.+.++|+.|++ +||..+.|++|.+.++      
T Consensus        44 l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~-~~g~afV~f~~~~~A~~A~~-~~~~~~~g~~i~v~~~------  115 (292)
T 2ghp_A           44 VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK-NFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL------  115 (292)
T ss_dssp             EEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS-SSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC------
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCC-CcEEEEEEECCHHHHHHHHH-hCCcEeCCcEEEEEEC------
Confidence            89999999998   999999999999999998 433 68999999999999999995 9999999999999886      


Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCC-ceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYG-RIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G-~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                       ..++|||+|||..+++++|+++|++|| .|..+.++.+..+...+.|||+|.+.|+|.
T Consensus       116 -~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~~~~~g~afV~f~~~~~a~  173 (292)
T 2ghp_A          116 -TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDAR  173 (292)
T ss_dssp             -CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHH
T ss_pred             -CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCCCCcceEEEEEECCHHHHH
Confidence             468899999999999999999999999 999999999987656677999999999875

>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=99.93  E-value=1.8e-25  Score=137.10  Aligned_cols=95  Identities=23%  Similarity=0.421  Sum_probs=69.5

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCCC-
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES-   77 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~~-   77 (136)
                      |||+|||..++   |+++|++||+|.++++++..+.++|||||+|.+.++|++|+..|||..+.|++|.|.++.++... 
T Consensus         8 lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~~~~~~   87 (115)
T 4f25_A            8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKERE   87 (115)
T ss_dssp             EEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSCCCC--
T ss_pred             EEECCCCCCCCHHHHHHHHhccCCEEEEEEeecCCCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCccccc
Confidence            79999999998   99999999999999999855568999999999999999999999999999999999998775532 


Q ss_pred             -------CCCceEEEcCCCCCCCHHH
Q psy6353          78 -------IKGANLYVSGLPKHMSQQE   96 (136)
Q Consensus        78 -------~~~~~l~v~nl~~~~t~~~   96 (136)
                             ....+|||+|||+++|++.
T Consensus        88 ~~~~~~~~~~~~lyv~Nl~~~~T~~a  113 (115)
T 4f25_A           88 AELGARAKEFTNVYIKNFGPGSTRAA  113 (115)
T ss_dssp             --------------------------
T ss_pred             cccccccCCCCceEeCCCCCCccccc
Confidence                   2345799999999999874

>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=9.2e-23  Score=121.90  Aligned_cols=73  Identities=51%  Similarity=0.746  Sum_probs=69.9

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS   74 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~   74 (136)
                      |||+|||..+|   |+++|++||+|.++.+++  .+|+++|||||+|.+.++|++|+..|||..+.|++|+|.+++|.
T Consensus        22 lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~AkPS   99 (99)
T 4fxv_A           22 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARPS   99 (99)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCBC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeCC
Confidence            89999999999   999999999999999998  78999999999999999999999999999999999999999873

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.85  E-value=1.1e-20  Score=114.91  Aligned_cols=73  Identities=16%  Similarity=0.209  Sum_probs=69.3

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS   74 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~   74 (136)
                      |||+|||..++   |+++|++||+|.++.+++  .+++++|||||+|.+.++|++|+..|||..+.|+.|+|.++...
T Consensus         9 lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a~~~   86 (110)
T 3s8s_A            9 VTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLDIKG   86 (110)
T ss_dssp             EEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSTT
T ss_pred             EEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCC
Confidence            89999999998   999999999999999998  67999999999999999999999999999999999999998654

>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=1.9e-20  Score=108.15  Aligned_cols=74  Identities=22%  Similarity=0.411  Sum_probs=70.3

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS   75 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~   75 (136)
                      |||+|||..++   |+++|++||+|.++.+++  .+++++|||||+|.+.++|+.|+..+||..+.|++|+|.++.++.
T Consensus         4 l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~~   82 (83)
T 3md1_A            4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKLE   82 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCCCC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCcCC
Confidence            79999999998   999999999999999988  689999999999999999999999999999999999999998764

>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=99.84  E-value=6.4e-21  Score=122.59  Aligned_cols=110  Identities=16%  Similarity=0.157  Sum_probs=83.9

Q ss_pred             EEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeC-------CceEEEEeeCC------CCCCCCCceEEEcCCCCCC
Q psy6353          26 CVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQ-------NKTIKVSYARP------SSESIKGANLYVSGLPKHM   92 (136)
Q Consensus        26 ~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~-------g~~l~v~~~~~------~~~~~~~~~l~v~nl~~~~   92 (136)
                      +.++.....++|||||+|.+.++|++|+..+++....       +..........      ........+|||+|||.++
T Consensus         3 ~kl~ln~~~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~   82 (158)
T 2kn4_A            3 YKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLTYRT   82 (158)
T ss_dssp             EEEEEECSSCEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEEEETTTTEEEEECCCCCSSCCCCCCBCCEEEEESCCTTC
T ss_pred             EEEEecCccccchhHHHHHHHHhHHHHHHhhcccCCCCCcccccCccccccccccccccccccCCCCCCEEEEeCCCCCC
Confidence            4555544579999999999999999999887753222       22222222111      1122346899999999999


Q ss_pred             CHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          93 SQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        93 t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ++++|+++|++||.|..+.+++|+.+|.+ +.|||+|.+.|+|.
T Consensus        83 ~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~  126 (158)
T 2kn4_A           83 SPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAE  126 (158)
T ss_dssp             CHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHH
T ss_pred             CHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHH
Confidence            99999999999999999999999877776 55999999999874

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.84  E-value=1.6e-21  Score=114.80  Aligned_cols=76  Identities=20%  Similarity=0.333  Sum_probs=69.8

Q ss_pred             eeecCCChhhh---HHHHhccCC-CeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHH-cCceeCCceEEEEeeCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFS-DAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTL-NGLRLQNKTIKVSYARPS   74 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G-~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~-~~~~~~g~~l~v~~~~~~   74 (136)
                      |||+|||..+|   |+++|++|| +|.++++++  .+|+++|||||+|.+.++|++|++.+ |+..++|++|+|.++.|+
T Consensus         4 i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a~~~   83 (91)
T 2lxi_A            4 VMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYSDPK   83 (91)
T ss_dssp             EEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECCCSC
T ss_pred             EEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEcCCC
Confidence            79999999999   999999999 899999988  78999999999999999999999977 457899999999999987


Q ss_pred             CCC
Q psy6353          75 SES   77 (136)
Q Consensus        75 ~~~   77 (136)
                      ++.
T Consensus        84 ~~~   86 (91)
T 2lxi_A           84 PKI   86 (91)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=99.83  E-value=1.5e-21  Score=119.46  Aligned_cols=96  Identities=20%  Similarity=0.264  Sum_probs=86.5

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESI   78 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~~~   78 (136)
                      |||+|||..++   |+++|++||.|.++.++. ++.++|||||+|.+.++|+.|+..|||..+.|+.|.|.++.+.... 
T Consensus        11 l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~-   88 (115)
T 3lqv_A           11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN-TPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYNANRAF-   88 (115)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEC-STTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECCHHHHT-
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeEEEEEee-CCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecCChhh-
Confidence            89999999998   999999999999999885 4566999999999999999999999999999999999999865432 


Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGR  106 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~  106 (136)
                             .+++...+++++.++|++||.
T Consensus        89 -------~~~~~~~~~~~l~~~~~~~g~  109 (115)
T 3lqv_A           89 -------QKMDTKKKEEQLKLLKEKYGI  109 (115)
T ss_dssp             -------TTSCHHHHHHHHHHHHHHHCC
T ss_pred             -------hhhhHhHhHHHHHHHHHHhCC
Confidence                   677888899999999999984

>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=99.83  E-value=3.3e-20  Score=108.02  Aligned_cols=73  Identities=27%  Similarity=0.398  Sum_probs=68.4

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS   74 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~   74 (136)
                      |||+|||..++   |+++|++||.|.++.++.  .+++++|||||+|.+.++|+.|+..+||..+.|++|+|.++.++
T Consensus         9 l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~k   86 (87)
T 3bs9_A            9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRK   86 (87)
T ss_dssp             EEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC--
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEecCCC
Confidence            79999999998   999999999999999988  68999999999999999999999999999999999999999875

>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=99.83  E-value=6.9e-21  Score=111.77  Aligned_cols=75  Identities=17%  Similarity=0.174  Sum_probs=66.4

Q ss_pred             eeecCCChhhh---HHHHhccCC--CeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFS--DAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS   74 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G--~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~   74 (136)
                      |||+|||..++   |+++|++||  .|.++.++.  .+|+++|||||+|.+.++|++|++.|||..+.|+.|+|.++.+.
T Consensus         4 l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~~~   83 (90)
T 3p5t_L            4 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSNKL   83 (90)
T ss_dssp             CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC---
T ss_pred             EEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECCCC
Confidence            79999999998   999999999  999999988  68999999999999999999999999999999999999998876


Q ss_pred             CC
Q psy6353          75 SE   76 (136)
Q Consensus        75 ~~   76 (136)
                      ..
T Consensus        84 ~~   85 (90)
T 3p5t_L           84 EH   85 (90)
T ss_dssp             --
T ss_pred             cc
Confidence            43

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.83  E-value=1.3e-20  Score=111.62  Aligned_cols=72  Identities=19%  Similarity=0.309  Sum_probs=66.5

Q ss_pred             eeecCCChhhh---HHHHhccCCC--eeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCc----eeCCceEEEEe
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSD--AEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGL----RLQNKTIKVSY   70 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~--v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~----~~~g~~l~v~~   70 (136)
                      |||+|||..+|   |+++|++||.  +.+|++++  .+|+++|||||+|.+.++|++|++.+||.    .+.||+|.|.+
T Consensus        12 lfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~i~V~~   91 (95)
T 2lkz_A           12 IILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGVDF   91 (95)
T ss_dssp             EEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEEEEEEE
T ss_pred             EEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEEEEEEE
Confidence            79999999999   9999999995  67899888  78999999999999999999999999985    58999999999


Q ss_pred             eCC
Q psy6353          71 ARP   73 (136)
Q Consensus        71 ~~~   73 (136)
                      +++
T Consensus        92 Aks   94 (95)
T 2lkz_A           92 AKS   94 (95)
T ss_dssp             CCC
T ss_pred             ccC
Confidence            875

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.82  E-value=1e-19  Score=108.60  Aligned_cols=75  Identities=16%  Similarity=0.318  Sum_probs=71.2

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||+|.++.++. .+++++|||||+|.+.++|+.|+..|||..+.|++|+|.++.++..
T Consensus        20 l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   98 (100)
T 2do4_A           20 LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAISNSGPS   98 (100)
T ss_dssp             EEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCCCSC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCCC
Confidence            89999999998   999999999999999998 8899999999999999999999999999999999999999988754

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.82  E-value=1.3e-20  Score=112.68  Aligned_cols=73  Identities=18%  Similarity=0.172  Sum_probs=68.7

Q ss_pred             eeecCCCh------hhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCC-ceEEEE
Q psy6353           2 VYQTLLNK------LFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQN-KTIKVS   69 (136)
Q Consensus         2 v~v~nl~~------~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g-~~l~v~   69 (136)
                      |||+|||.      .++   |+++|++||+|.++.+++  .+|+++|||||+|.+.++|++|+..|||..+.| ++|+|.
T Consensus         9 vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~l~V~   88 (100)
T 3ns6_A            9 IVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRLFLY   88 (100)
T ss_dssp             EEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEE
T ss_pred             EEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCeEEEEE
Confidence            89999999      887   999999999999999998  679999999999999999999999999999999 999999


Q ss_pred             eeCCC
Q psy6353          70 YARPS   74 (136)
Q Consensus        70 ~~~~~   74 (136)
                      ++.|.
T Consensus        89 ~a~~~   93 (100)
T 3ns6_A           89 TMKDV   93 (100)
T ss_dssp             ESHHH
T ss_pred             ECchh
Confidence            88754

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.82  E-value=1.2e-19  Score=108.86  Aligned_cols=76  Identities=28%  Similarity=0.464  Sum_probs=71.5

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||+|.++.++.  .+++++|||||+|.+.++|++|+..|||..+.|+.|+|.++.++..
T Consensus        18 l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~   97 (103)
T 2cq0_A           18 IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPSTN   97 (103)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESSCCCC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEECCCCCC
Confidence            89999999998   999999999999999988  6899999999999999999999999999999999999999988765


Q ss_pred             C
Q psy6353          77 S   77 (136)
Q Consensus        77 ~   77 (136)
                      .
T Consensus        98 ~   98 (103)
T 2cq0_A           98 S   98 (103)
T ss_dssp             S
T ss_pred             C
Confidence            3

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.82  E-value=1.6e-19  Score=106.75  Aligned_cols=76  Identities=25%  Similarity=0.447  Sum_probs=71.5

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||+|.++.+++  .+++++|||||+|.+.++|+.|+..+||..+.|++|+|.++.++..
T Consensus         8 l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~   87 (95)
T 2dnz_A            8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHVTERLD   87 (95)
T ss_dssp             EEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEESSCCCC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEcccccC
Confidence            79999999998   999999999999999998  6799999999999999999999999999999999999999988765


Q ss_pred             C
Q psy6353          77 S   77 (136)
Q Consensus        77 ~   77 (136)
                      .
T Consensus        88 ~   88 (95)
T 2dnz_A           88 G   88 (95)
T ss_dssp             C
T ss_pred             C
Confidence            3

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.81  E-value=1.4e-19  Score=107.85  Aligned_cols=75  Identities=23%  Similarity=0.320  Sum_probs=70.9

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||+|.++.++.  .+++++|||||+|.+.++|+.|+..+||..+.|++|.|.++.++..
T Consensus        11 l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~   90 (99)
T 1whw_A           11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKE   90 (99)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECCCCST
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCCcc
Confidence            89999999998   999999999999999988  5899999999999999999999999999999999999999988765

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B

Probab=99.81  E-value=1.1e-19  Score=107.76  Aligned_cols=75  Identities=23%  Similarity=0.332  Sum_probs=70.5

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||.|.++.++.  .+|+++|||||+|.+.++|+.|+..+||..+.|+.|.|.++.++..
T Consensus         5 l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~   84 (96)
T 2x1f_A            5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSNSDI   84 (96)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCSSG
T ss_pred             EEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcCCCCC
Confidence            79999999998   999999999999999988  6799999999999999999999999999999999999999987653

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.81  E-value=3.4e-20  Score=110.93  Aligned_cols=85  Identities=20%  Similarity=0.268  Sum_probs=75.5

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCCC-
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES-   77 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~~-   77 (136)
                      |||+|||..++   |+++|++||+|.++.++..   ++|||||+|.+.++|+.|+..|||..+.|++|+|.++.++... 
T Consensus         3 l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~---~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~~   79 (101)
T 2hvz_A            3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARN---PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMPRRS   79 (101)
T ss_dssp             EEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS---SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSCCCSS
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCCCCcc
Confidence            79999999998   9999999999999998863   7899999999999999999999999999999999998875532 


Q ss_pred             ---------CCCceEEEcCCC
Q psy6353          78 ---------IKGANLYVSGLP   89 (136)
Q Consensus        78 ---------~~~~~l~v~nl~   89 (136)
                               ....++||+||+
T Consensus        80 ~~~~~~~~~~~~~~ifvg~L~  100 (101)
T 2hvz_A           80 RFDRPPARRKLLEVLFNGPLE  100 (101)
T ss_dssp             CCCSCCCSCCCCSCCCSCCCC
T ss_pred             cCCCCCccccCCCceecCCCC
Confidence                     125689999986

>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=99.81  E-value=1.1e-19  Score=110.01  Aligned_cols=74  Identities=28%  Similarity=0.472  Sum_probs=70.1

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS   75 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~   75 (136)
                      |||+|||..++   |+++|++||+|.++.+++  .+|+++|||||+|.+.++|+.|+..+||..+.|++|+|.++.++.
T Consensus        29 l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~k~  107 (108)
T 2jrs_A           29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTERT  107 (108)
T ss_dssp             EEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEECSCSSC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcccCC
Confidence            79999999988   999999999999999988  678999999999999999999999999999999999999998764

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.81  E-value=7.8e-20  Score=105.61  Aligned_cols=66  Identities=20%  Similarity=0.181  Sum_probs=63.1

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEee
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA   71 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~   71 (136)
                      |||+||+..+|   |+++|.+||+|.++.+..    ++|||||+|.+.++|++|++.||+..+.|++|++..+
T Consensus        10 L~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~----~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A   78 (89)
T 2wbr_A           10 LLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL----NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESP   78 (89)
T ss_dssp             EEEECCCTTCCCHHHHHHHHHHSCEEEEEEET----TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECC
T ss_pred             EEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC----CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEEC
Confidence            79999999999   999999999999999875    8999999999999999999999999999999999876

>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=99.81  E-value=2.2e-19  Score=109.79  Aligned_cols=76  Identities=28%  Similarity=0.482  Sum_probs=71.4

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||.|.++.++.  .+++++|||||+|.+.++|+.|+..||+..+.|++|+|.++.++..
T Consensus        28 l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~  107 (115)
T 2cpz_A           28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKND  107 (115)
T ss_dssp             EEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCCCSCC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCCCc
Confidence            89999999998   999999999999999998  5899999999999999999999999999999999999999987754


Q ss_pred             C
Q psy6353          77 S   77 (136)
Q Consensus        77 ~   77 (136)
                      .
T Consensus       108 ~  108 (115)
T 2cpz_A          108 S  108 (115)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.81  E-value=1e-19  Score=105.44  Aligned_cols=71  Identities=27%  Similarity=0.413  Sum_probs=67.3

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR   72 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~   72 (136)
                      |||+|||..++   |+++|++||+|.++.+++  .+++++|||||+|.+.++|+.|+..+||..+.|++|+|.+++
T Consensus        10 l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~ak   85 (85)
T 3mdf_A           10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK   85 (85)
T ss_dssp             EEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             EEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcC
Confidence            79999999998   999999999999999888  788899999999999999999999999999999999999874

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A

Probab=99.81  E-value=4.8e-20  Score=117.67  Aligned_cols=100  Identities=16%  Similarity=0.167  Sum_probs=86.9

Q ss_pred             cCCCceeeEEEEcCCHHHHHHHHHHH-cCceeCCceEEEEeeCCC----------------CCCCCCceEEEcCCCCCCC
Q psy6353          31 STAQSLGYGFVNYHRPEDAEKAINTL-NGLRLQNKTIKVSYARPS----------------SESIKGANLYVSGLPKHMS   93 (136)
Q Consensus        31 ~~~~~kg~~fv~f~~~~~a~~a~~~~-~~~~~~g~~l~v~~~~~~----------------~~~~~~~~l~v~nl~~~~t   93 (136)
                      .....+|+++++|.+.++|++|+.++ ||..+.| .+.+.++.+.                ......++|||+|||.++|
T Consensus         8 ~g~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~t   86 (150)
T 2i2y_A            8 NGKTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGN   86 (150)
T ss_dssp             CCSSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTEEEEECSSSSCCCCSCSSSSTTSCEEEEESCCSCCS
T ss_pred             ccccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCccccccccccccccccccCCCCCCEEEEeCCCCCCC
Confidence            34456899999999999999999999 9999999 9999876541                1234668999999999999


Q ss_pred             HHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          94 QQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        94 ~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      +++|+++|++||.|..+.++++    .++.|||+|.+.|++.
T Consensus        87 ~~~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~  124 (150)
T 2i2y_A           87 KTELERAFGYYGPLRSVWVARN----PPGFAFVEFEDPRDAA  124 (150)
T ss_dssp             CHHHHHHHHHHSCEEEEEECSS----SCSEEEEEESSHHHHH
T ss_pred             HHHHHHHHHhhCCEEEEEEeeC----CCcEEEEEECCHHHHH
Confidence            9999999999999999999987    4578999999999874

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.81  E-value=1.8e-19  Score=105.89  Aligned_cols=75  Identities=25%  Similarity=0.368  Sum_probs=70.5

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||+|..+.+++.+++++|||||+|.+.++|+.|+..|||..+.|++|+|.++.+...
T Consensus        11 l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~~~   88 (92)
T 2dgv_A           11 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDRNASG   88 (92)
T ss_dssp             EEECSCCTTCCHHHHHHHHHTTSCEEEEEEEESSSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEECSCCSS
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEccCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCCCC
Confidence            79999999998   9999999999999998877888999999999999999999999999999999999999987654

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=1.4e-19  Score=109.02  Aligned_cols=74  Identities=20%  Similarity=0.294  Sum_probs=69.9

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS   75 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~   75 (136)
                      |||+|||..++   |+++|++||+|.++.++.  .+|+++|||||+|.+.++|+.|+..+||..+.|++|.|.++.++.
T Consensus        26 l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~  104 (106)
T 1p27_B           26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRG  104 (106)
T ss_dssp             EEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEESEESS
T ss_pred             EEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEeecCCC
Confidence            89999999998   999999999999999988  679999999999999999999999999999999999999987654

>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=99.81  E-value=3.4e-19  Score=107.17  Aligned_cols=76  Identities=25%  Similarity=0.416  Sum_probs=71.2

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCC---ceEEEEeeCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQN---KTIKVSYARPS   74 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g---~~l~v~~~~~~   74 (136)
                      |||+|||..++   |+++|++||.|.++.++. .+++++|||||+|.+.++|+.|+..|||..+.|   ++|.|.++.++
T Consensus        18 l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V~~a~~~   97 (105)
T 2dnh_A           18 LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVVKFADTD   97 (105)
T ss_dssp             EEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEEEESCSS
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEEEECccC
Confidence            89999999998   999999999999999999 789999999999999999999999999999988   99999999877


Q ss_pred             CCC
Q psy6353          75 SES   77 (136)
Q Consensus        75 ~~~   77 (136)
                      ...
T Consensus        98 ~~~  100 (105)
T 2dnh_A           98 KES  100 (105)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            653

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=1.4e-19  Score=108.30  Aligned_cols=76  Identities=26%  Similarity=0.401  Sum_probs=71.2

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||+|.++.++.  .+++++|||||+|.+.++|+.|+..|||..+.|++|+|.++.++..
T Consensus        15 l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~   94 (102)
T 2cqb_A           15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPMRI   94 (102)
T ss_dssp             EEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECCCCCC
T ss_pred             EEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEeCCCCCC
Confidence            89999999988   999999999999999988  7789999999999999999999999999999999999999987764


Q ss_pred             C
Q psy6353          77 S   77 (136)
Q Consensus        77 ~   77 (136)
                      .
T Consensus        95 ~   95 (102)
T 2cqb_A           95 K   95 (102)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.81  E-value=2.9e-19  Score=106.46  Aligned_cols=75  Identities=15%  Similarity=0.327  Sum_probs=70.3

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||+|.++.++.  .+++++|||||+|.+.++|++|+. +|+..+.|++|.|.++.++..
T Consensus        13 l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V~~a~~~~~   91 (99)
T 2dgs_A           13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVKRAEPRDS   91 (99)
T ss_dssp             EEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEEEECCCCCC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEEEECCCCcc
Confidence            79999999998   999999999999999998  679999999999999999999999 999999999999999988765


Q ss_pred             C
Q psy6353          77 S   77 (136)
Q Consensus        77 ~   77 (136)
                      .
T Consensus        92 ~   92 (99)
T 2dgs_A           92 K   92 (99)
T ss_dssp             C
T ss_pred             c
Confidence            3

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.80  E-value=3.9e-19  Score=108.63  Aligned_cols=75  Identities=27%  Similarity=0.392  Sum_probs=70.9

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||.|.++.+++  .+++++|||||+|.+.++|+.|+..|||..+.|+.|.|.++.++..
T Consensus        18 l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~   97 (115)
T 2dgo_A           18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPP   97 (115)
T ss_dssp             EEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESSCCCC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccCCCC
Confidence            89999999998   999999999999999998  5899999999999999999999999999999999999999987654

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.80  E-value=2.4e-19  Score=106.59  Aligned_cols=76  Identities=25%  Similarity=0.464  Sum_probs=70.0

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--c---CCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--S---TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP   73 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~---~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~   73 (136)
                      |||+|||..++   |+++|++||+|.++.++.  .   +++++|||||+|.+.++|+.|+..|||..+.|++|.|.++.+
T Consensus         8 l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~   87 (98)
T 2cpf_A            8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISER   87 (98)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEccC
Confidence            89999999998   999999999999999988  3   458999999999999999999999999999999999999987


Q ss_pred             CCCC
Q psy6353          74 SSES   77 (136)
Q Consensus        74 ~~~~   77 (136)
                      +...
T Consensus        88 ~~~~   91 (98)
T 2cpf_A           88 ATKP   91 (98)
T ss_dssp             SSCC
T ss_pred             CCCC
Confidence            6543

>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=99.80  E-value=2.4e-19  Score=109.86  Aligned_cols=75  Identities=27%  Similarity=0.402  Sum_probs=70.9

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||.|.++.++. .+++++|||||+|.+.++|+.|+..|||..+.|+.|+|.++.+...
T Consensus        10 l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~   88 (116)
T 2fy1_A           10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKKPSF   88 (116)
T ss_dssp             EEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEECCCSSC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCCC
Confidence            79999999998   999999999999999999 8899999999999999999999999999999999999999987653

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=1.4e-19  Score=107.17  Aligned_cols=75  Identities=25%  Similarity=0.367  Sum_probs=70.7

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEE-EEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEIC-VFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS   75 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~-~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~   75 (136)
                      |||+|||..++   |+++|++||+|.++ .+++  .+++++|||||+|.+.++|+.|+..+||..+.|++|+|.++.++.
T Consensus         8 l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~   87 (96)
T 1x5t_A            8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKD   87 (96)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEecccC
Confidence            79999999998   99999999999999 8888  789999999999999999999999999999999999999998765


Q ss_pred             C
Q psy6353          76 E   76 (136)
Q Consensus        76 ~   76 (136)
                      .
T Consensus        88 ~   88 (96)
T 1x5t_A           88 S   88 (96)
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=99.80  E-value=3.3e-19  Score=105.35  Aligned_cols=72  Identities=22%  Similarity=0.306  Sum_probs=68.1

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP   73 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~   73 (136)
                      |||+|||..++   |+++|++||+|..+.++.  .+++++|||||+|.+.++|++|+..|||..+.|++|+|.++++
T Consensus        18 l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~   94 (95)
T 2cqc_A           18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSGPSS   94 (95)
T ss_dssp             EEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCSC
T ss_pred             EEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEecCC
Confidence            89999999988   999999999999999988  6789999999999999999999999999999999999998864

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.80  E-value=4.2e-19  Score=106.47  Aligned_cols=76  Identities=26%  Similarity=0.445  Sum_probs=71.0

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES   77 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~~   77 (136)
                      |||+|||..++   |+++|++||.|.++.++..+++++|||||+|.+.++|+.|+..|||..+.|++|.|.++.++...
T Consensus        18 l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~   96 (103)
T 2d9p_A           18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEER   96 (103)
T ss_dssp             EEEECCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECSSCCCC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcCCCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEecccccC
Confidence            89999999998   99999999999999988777889999999999999999999999999999999999999877653

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=2.1e-19  Score=108.16  Aligned_cols=76  Identities=28%  Similarity=0.365  Sum_probs=71.4

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||+|.++.++.  .++.++|||||+|.+.++|+.|+..||+..+.|++|+|.++.++..
T Consensus        18 l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   97 (105)
T 1x5u_A           18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNK   97 (105)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETTTTSC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCCCCc
Confidence            79999999998   999999999999999988  5899999999999999999999999999999999999999987765


Q ss_pred             C
Q psy6353          77 S   77 (136)
Q Consensus        77 ~   77 (136)
                      .
T Consensus        98 ~   98 (105)
T 1x5u_A           98 N   98 (105)
T ss_dssp             C
T ss_pred             C
Confidence            3

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=1.7e-19  Score=108.01  Aligned_cols=76  Identities=26%  Similarity=0.409  Sum_probs=71.2

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||+|..+.++.  .+++++|||||+|.+.++|+.|+..||+..+.|++|+|.++.++..
T Consensus        15 l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~   94 (102)
T 1x5s_A           15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSD   94 (102)
T ss_dssp             EEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEECCCC
T ss_pred             EEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCC
Confidence            89999999998   999999999999999988  6888999999999999999999999999999999999999987654


Q ss_pred             C
Q psy6353          77 S   77 (136)
Q Consensus        77 ~   77 (136)
                      .
T Consensus        95 ~   95 (102)
T 1x5s_A           95 N   95 (102)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.80  E-value=3.6e-19  Score=105.00  Aligned_cols=71  Identities=21%  Similarity=0.293  Sum_probs=67.2

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR   72 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~   72 (136)
                      |||+|||..++   |+++|++||+|.++.++.  .+++++|||||+|.+.++|+.|+..|||..+.|++|+|.+++
T Consensus        19 l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~ak   94 (94)
T 2e5h_A           19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASIAI   94 (94)
T ss_dssp             EEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEECC
T ss_pred             EEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEecC
Confidence            89999999998   999999999999999988  668999999999999999999999999999999999999874

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.80  E-value=1.9e-19  Score=107.97  Aligned_cols=75  Identities=20%  Similarity=0.298  Sum_probs=70.4

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||.|..+.++.  .+++++|||||+|.+.++|++|+..|||..+.|++|.|.++.+...
T Consensus        16 l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~   95 (103)
T 2dnm_A           16 LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVARYGRR   95 (103)
T ss_dssp             EEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEEECSSCCS
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEECCcCCC
Confidence            89999999998   999999999999999988  6799999999999999999999999999999999999999987644

>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=99.80  E-value=3.2e-19  Score=104.21  Aligned_cols=73  Identities=16%  Similarity=0.290  Sum_probs=68.8

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS   75 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~   75 (136)
                      |||+|||..++   |+++|++||+|.++.++.  .+++++|||||+|.+.++|++|+ .+||..+.|++|+|.++.+..
T Consensus         9 l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~~~~   86 (89)
T 3ucg_A            9 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKRTNR   86 (89)
T ss_dssp             EEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETTTTS
T ss_pred             EEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEccCCC
Confidence            79999999998   999999999999999988  58999999999999999999999 899999999999999988753

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens}

Probab=99.80  E-value=3.5e-19  Score=105.29  Aligned_cols=72  Identities=25%  Similarity=0.352  Sum_probs=68.1

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP   73 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~   73 (136)
                      |||+|||..++   |+++|++||+|.++.++. .+++++|||||+|.+.++|++|+..|||..+.|++|+|.+++.
T Consensus        19 l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~   94 (95)
T 2ywk_A           19 VFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSGPSS   94 (95)
T ss_dssp             EEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             EEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEEcCC
Confidence            79999999998   999999999999999998 6699999999999999999999999999999999999998763

>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=99.80  E-value=5.9e-19  Score=105.83  Aligned_cols=76  Identities=22%  Similarity=0.384  Sum_probs=69.5

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES   77 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~~   77 (136)
                      |||+|||..++   |+++|++||+|.++.+++..+.++|||||+|.+.++|++|+..||+..+.|++|+|.++.++...
T Consensus        18 l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~   96 (103)
T 2cqi_A           18 LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPSSQ   96 (103)
T ss_dssp             EEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCTTCC
T ss_pred             EEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCCCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEECCCCccc
Confidence            89999999998   99999999999999999844447999999999999999999999999999999999999876543

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D*

Probab=99.79  E-value=2.5e-19  Score=108.67  Aligned_cols=74  Identities=20%  Similarity=0.318  Sum_probs=69.9

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS   75 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~   75 (136)
                      |||+|||..++   |+++|++||.|.++.++.  .+|+++|||||+|.+.++|+.|+..|||..+.|++|.|.++.++.
T Consensus        29 l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~  107 (110)
T 1oo0_B           29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKG  107 (110)
T ss_dssp             EEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEESS
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEcccCC
Confidence            89999999988   999999999999999988  689999999999999999999999999999999999999988664

>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=99.79  E-value=1.1e-18  Score=104.62  Aligned_cols=75  Identities=20%  Similarity=0.321  Sum_probs=69.1

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||+|.++.++...+.++|||||+|.+.++|+.|+..|||..+.|++|.|.++.++..
T Consensus        18 l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   95 (103)
T 2cq3_A           18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARVM   95 (103)
T ss_dssp             EEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCSSCC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcccCCC
Confidence            89999999998   9999999999999999983334899999999999999999999999999999999999987654

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.79  E-value=4.4e-19  Score=105.68  Aligned_cols=71  Identities=21%  Similarity=0.278  Sum_probs=67.0

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeE--------EEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEE
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEI--------CVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKV   68 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~--------~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v   68 (136)
                      |||+|||..++   |+++|++||.|.+        +.++.  .+|+++|||||+|.+.++|+.|++.|||..+.|++|+|
T Consensus        16 l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V   95 (99)
T 2la6_A           16 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKV   95 (99)
T ss_dssp             EEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBSSSSBCEE
T ss_pred             EEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCcEEEE
Confidence            79999999998   9999999999999        98888  67999999999999999999999999999999999999


Q ss_pred             EeeC
Q psy6353          69 SYAR   72 (136)
Q Consensus        69 ~~~~   72 (136)
                      .+++
T Consensus        96 ~~A~   99 (99)
T 2la6_A           96 SFAT   99 (99)
T ss_dssp             EECC
T ss_pred             EecC
Confidence            8863

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A

Probab=99.79  E-value=6.5e-19  Score=106.30  Aligned_cols=71  Identities=20%  Similarity=0.319  Sum_probs=68.1

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR   72 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~   72 (136)
                      |||+|||..++   |+++|++||+|.++.++. .+++++|||||+|.+.++|++|+..|||..+.|++|+|.++.
T Consensus        32 l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~  106 (107)
T 3ulh_A           32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT  106 (107)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEeC
Confidence            89999999998   999999999999999998 889999999999999999999999999999999999999875

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.79  E-value=5.8e-19  Score=107.12  Aligned_cols=76  Identities=25%  Similarity=0.371  Sum_probs=71.2

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHc------CceeCCceEEEEe
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLN------GLRLQNKTIKVSY   70 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~------~~~~~g~~l~v~~   70 (136)
                      |||+|||..++   |+++|++||+|.+|.+++  .+++++|||||+|.+.++|+.|+..+|      +..+.|++|.|.+
T Consensus        18 l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g~~l~v~~   97 (111)
T 1x4h_A           18 VFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDL   97 (111)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCEEEEEC
T ss_pred             EEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcCEEEEEEE
Confidence            89999999998   999999999999999998  678999999999999999999999999      9999999999999


Q ss_pred             eCCCCCC
Q psy6353          71 ARPSSES   77 (136)
Q Consensus        71 ~~~~~~~   77 (136)
                      +.++...
T Consensus        98 a~~~~~~  104 (111)
T 1x4h_A           98 AVTRDEA  104 (111)
T ss_dssp             CCCCCCC
T ss_pred             CCCCccC
Confidence            9877543

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=3.1e-19  Score=107.17  Aligned_cols=74  Identities=22%  Similarity=0.347  Sum_probs=70.0

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS   75 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~   75 (136)
                      |||+|||..++   |+++|++||.|.++.++.  .+|+++|||||+|.+.++|+.|+..+||..+.|+.|+|.++.++.
T Consensus        11 l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   89 (104)
T 1p1t_A           11 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASEK   89 (104)
T ss_dssp             EEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTCTT
T ss_pred             EEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeCCCcc
Confidence            89999999998   999999999999999988  689999999999999999999999999999999999999988764

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens}

Probab=99.79  E-value=2.9e-19  Score=104.11  Aligned_cols=74  Identities=19%  Similarity=0.358  Sum_probs=67.9

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCC-ceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQ-SLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS   75 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~-~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~   75 (136)
                      |||+|||..++   |+++|++||.|.++.++.  .++. ++|||||+|.+.++|++|+..+||..+.|+.|+|.++.+..
T Consensus         7 l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   86 (88)
T 4a8x_A            7 VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAVLAPW   86 (88)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEECCCC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEECCCCC
Confidence            79999999998   999999999999999888  3344 89999999999999999999999999999999999998754

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.79  E-value=5.9e-19  Score=106.44  Aligned_cols=76  Identities=18%  Similarity=0.304  Sum_probs=70.9

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc-c--CCCceeeEEEEcCCHHHHHHHHHHH-cCceeCCceEEEEeeCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI-S--TAQSLGYGFVNYHRPEDAEKAINTL-NGLRLQNKTIKVSYARPS   74 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~-~--~~~~kg~~fv~f~~~~~a~~a~~~~-~~~~~~g~~l~v~~~~~~   74 (136)
                      |||+|||..++   |+++|++||+|.++.+++ .  +++++|||||+|.+.++|++|+..+ |+..+.|++|.|.++.++
T Consensus        18 l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~v~~a~~~   97 (107)
T 2cph_A           18 ILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSE   97 (107)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEEECCCC
T ss_pred             EEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEEEEeCCCC
Confidence            89999999998   999999999999999987 3  8899999999999999999999999 999999999999999877


Q ss_pred             CCC
Q psy6353          75 SES   77 (136)
Q Consensus        75 ~~~   77 (136)
                      ...
T Consensus        98 ~~~  100 (107)
T 2cph_A           98 VTV  100 (107)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=2.3e-19  Score=107.77  Aligned_cols=71  Identities=14%  Similarity=0.063  Sum_probs=66.6

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP   73 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~   73 (136)
                      |||+|||..+|   |+++|++||+|.++.+++ ..|+++|||||+|.+.++|+.|+. +||..+.|++|.|.++.+
T Consensus        14 lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~~~~   88 (103)
T 1s79_A           14 VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKDD   88 (103)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEHHH
T ss_pred             EEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEchH
Confidence            89999999998   999999999999999999 559999999999999999999999 899999999999987653

>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=5.9e-19  Score=104.66  Aligned_cols=73  Identities=18%  Similarity=0.151  Sum_probs=67.1

Q ss_pred             eeecCCChhhh---HH----HHhccCCCeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCC
Q psy6353           2 VYQTLLNKLFT---YE----KVHLGFSDAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP   73 (136)
Q Consensus         2 v~v~nl~~~~~---l~----~~f~~~G~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~   73 (136)
                      |||+|||..++   |+    ++|++||+|.++.++. ..+  +|||||+|.+.++|++|+..+||..+.|++|+|.++.+
T Consensus        12 l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~--rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~   89 (96)
T 2dgx_A           12 VQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY--QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATG   89 (96)
T ss_dssp             EEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST--TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             EEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC--CeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcCC
Confidence            79999999988   77    9999999999999987 333  89999999999999999999999999999999999987


Q ss_pred             CCC
Q psy6353          74 SSE   76 (136)
Q Consensus        74 ~~~   76 (136)
                      ...
T Consensus        90 ~~~   92 (96)
T 2dgx_A           90 ASG   92 (96)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            654

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=4.1e-19  Score=105.75  Aligned_cols=74  Identities=23%  Similarity=0.349  Sum_probs=69.8

Q ss_pred             eeecCCChhhh---HHHHhccCCCee-EEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCce----EEEEee
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAE-ICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKT----IKVSYA   71 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~-~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~----l~v~~~   71 (136)
                      |||+|||..++   |+++|++||+|. ++.+++  .+++++|||||+|.+.++|++|+..|||..+.|+.    |+|.++
T Consensus        12 l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~l~v~~a   91 (99)
T 2div_A           12 LWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKRFKLNYA   91 (99)
T ss_dssp             EEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEECCEEET
T ss_pred             EEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcceeEEEeec
Confidence            89999999998   999999999999 999998  68999999999999999999999999999999999    999998


Q ss_pred             CCCC
Q psy6353          72 RPSS   75 (136)
Q Consensus        72 ~~~~   75 (136)
                      .+..
T Consensus        92 ~~~~   95 (99)
T 2div_A           92 TYSG   95 (99)
T ss_dssp             TCCS
T ss_pred             CCCC
Confidence            8764

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.79  E-value=2e-18  Score=105.21  Aligned_cols=74  Identities=20%  Similarity=0.221  Sum_probs=69.6

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS   75 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~   75 (136)
                      |||+|||..++   |+++|++||.|.++.++. .+++++|||||+|.+.++|+.|+..||+..+.|+.|.|.++.+..
T Consensus        18 l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   95 (114)
T 2do0_A           18 VFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDERAL   95 (114)
T ss_dssp             EEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCCC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEcccCC
Confidence            89999999998   999999999999999998 779999999999999999999999999999999999999987543

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A

Probab=99.78  E-value=4.8e-19  Score=110.43  Aligned_cols=74  Identities=20%  Similarity=0.323  Sum_probs=70.0

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS   75 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~   75 (136)
                      |||+|||..++   |+++|++||+|..+.+++  .+++++|||||+|.+.++|++|+..|||..+.|++|.|.++.++.
T Consensus        49 l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~~a~~~~  127 (129)
T 2kxn_B           49 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKR  127 (129)
T ss_dssp             BCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEESCCSSSS
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCCC
Confidence            79999999998   999999999999999998  678999999999999999999999999999999999999998764

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.78  E-value=1.4e-18  Score=104.20  Aligned_cols=74  Identities=16%  Similarity=0.282  Sum_probs=68.8

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++|| |.++.+++  .+++++|||||+|.+.++|+.|+ ++||..+.|++|.|.++.++..
T Consensus        18 l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~~~~   95 (103)
T 2dng_A           18 AYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDIAEGRKQ   95 (103)
T ss_dssp             EEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEEECCCCCC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEEEecCCCC
Confidence            79999999998   999999997 99999998  67999999999999999999999 8999999999999999987754


Q ss_pred             C
Q psy6353          77 S   77 (136)
Q Consensus        77 ~   77 (136)
                      .
T Consensus        96 ~   96 (103)
T 2dng_A           96 D   96 (103)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.78  E-value=2.6e-19  Score=107.88  Aligned_cols=73  Identities=18%  Similarity=0.298  Sum_probs=68.0

Q ss_pred             eeecCCChhh------h---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCc-eEEEEee
Q psy6353           2 VYQTLLNKLF------T---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNK-TIKVSYA   71 (136)
Q Consensus         2 v~v~nl~~~~------~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~-~l~v~~~   71 (136)
                      |||+|||..+      +   |+++|++||+|.++.+++.+|+++|||||+|.+.++|+.|+..|||..+.|+ +|+|.++
T Consensus        18 l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~~l~V~~a   97 (105)
T 2nlw_A           18 IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRVNLF   97 (105)
T ss_dssp             EEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCCBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTCEEEEECS
T ss_pred             EEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeCCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCceEEEEEc
Confidence            8999999988      4   9999999999999988877889999999999999999999999999999999 9999988


Q ss_pred             CCC
Q psy6353          72 RPS   74 (136)
Q Consensus        72 ~~~   74 (136)
                      .+.
T Consensus        98 ~~~  100 (105)
T 2nlw_A           98 TDF  100 (105)
T ss_dssp             CCC
T ss_pred             chH
Confidence            754

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.78  E-value=4.7e-19  Score=113.84  Aligned_cols=73  Identities=23%  Similarity=0.199  Sum_probs=69.2

Q ss_pred             eeecCCChhhh---HHHHhccCC--CeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFS--DAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS   74 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G--~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~   74 (136)
                      |||+|||..++   |+++|++||  .|.++.++.  .+|+++|||||+|.+.++|+.|+..|||..+.|+.|.|.++.++
T Consensus        58 lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~a~~~  137 (156)
T 3n9u_C           58 VYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQ  137 (156)
T ss_dssp             EEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEECCHH
T ss_pred             EEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEEcCCC
Confidence            89999999998   999999999  999999988  78999999999999999999999999999999999999988653

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.78  E-value=1.4e-18  Score=101.95  Aligned_cols=73  Identities=15%  Similarity=0.144  Sum_probs=69.1

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++| .|.++.+++ .+|+++|||||+|.+.++|+.|+. +||..+.|++|.|.++.++.+
T Consensus        13 l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~a~~~~~   89 (91)
T 2dgw_A           13 VKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFREKSGPS   89 (91)
T ss_dssp             EEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEEESSCCC
T ss_pred             EEEECCCCCCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEECCcCCC
Confidence            79999999998   99999999 999999999 899999999999999999999999 999999999999999987654

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A

Probab=99.78  E-value=4.7e-19  Score=106.76  Aligned_cols=76  Identities=21%  Similarity=0.247  Sum_probs=70.6

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCcee---CCceEEEEeeCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRL---QNKTIKVSYARP   73 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~---~g~~l~v~~~~~   73 (136)
                      |||+|||..++   |+++|++||+|.++.++.  .+++++|||||+|.+.++|+.|+..||+..+   .|++|.|.++.+
T Consensus        16 l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l~v~~a~~   95 (106)
T 2dgp_A           16 LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQVKPADS   95 (106)
T ss_dssp             EEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCEEEECCC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceEEEEECCc
Confidence            89999999998   999999999999999988  6799999999999999999999999999887   899999999987


Q ss_pred             CCCC
Q psy6353          74 SSES   77 (136)
Q Consensus        74 ~~~~   77 (136)
                      +...
T Consensus        96 ~~~~   99 (106)
T 2dgp_A           96 ESRG   99 (106)
T ss_dssp             CSCC
T ss_pred             cccc
Confidence            7643

>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=5.9e-19  Score=107.00  Aligned_cols=73  Identities=21%  Similarity=0.344  Sum_probs=68.1

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS   74 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~   74 (136)
                      |||+|||..++   |+++|++||+|.++.++...+.++|||||+|.+.++|++|+..+||..+.|++|.|.++.++
T Consensus        32 l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  107 (109)
T 2err_A           32 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR  107 (109)
T ss_dssp             EEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTTBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEEECCCS
T ss_pred             EEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            89999999998   99999999999999998844568999999999999999999999999999999999998875

>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=99.78  E-value=9.8e-19  Score=106.33  Aligned_cols=76  Identities=22%  Similarity=0.272  Sum_probs=68.9

Q ss_pred             CeeecCCChhhh---HH---HHhccCCCeeEEEEEc--c---CCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEE
Q psy6353           1 MVYQTLLNKLFT---YE---KVHLGFSDAEICVFLI--S---TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVS   69 (136)
Q Consensus         1 ~v~v~nl~~~~~---l~---~~f~~~G~v~~~~~~~--~---~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~   69 (136)
                      .|||+|||..++   |+   ++|++||+|.++.+++  .   +++++|||||+|.+.++|++|+..|||..+.|++|+|.
T Consensus        17 ~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~   96 (111)
T 2cpi_A           17 LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKAS   96 (111)
T ss_dssp             CEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCEEEEEE
Confidence            389999999998   88   9999999999999988  3   34677999999999999999999999999999999999


Q ss_pred             eeCCCCC
Q psy6353          70 YARPSSE   76 (136)
Q Consensus        70 ~~~~~~~   76 (136)
                      ++.++..
T Consensus        97 ~a~~k~~  103 (111)
T 2cpi_A           97 LGTTKYC  103 (111)
T ss_dssp             SCCCCSC
T ss_pred             ecccccc
Confidence            9988753

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.78  E-value=1.8e-19  Score=102.18  Aligned_cols=69  Identities=19%  Similarity=0.323  Sum_probs=65.0

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEee
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA   71 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~   71 (136)
                      |||+|||..++   |+++|++||+|.++.++.  .+++++|||||+|.+.++|++|+. +||..+.|++|.|.++
T Consensus         2 l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A            2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             EEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSSCCCEEECC
T ss_pred             EEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECCEEEEEEeC
Confidence            79999999998   999999999999999988  589999999999999999999998 9999999999999864

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=8.9e-19  Score=106.70  Aligned_cols=76  Identities=24%  Similarity=0.323  Sum_probs=70.4

Q ss_pred             eeecCCChhhh---HHHHhccCCCee--------EEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEE
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAE--------ICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKV   68 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~--------~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v   68 (136)
                      |||+|||..++   |+++|++||.|.        .+.++.  .+++++|||||+|.+.++|+.|+..|||..+.|++|+|
T Consensus        18 l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V   97 (113)
T 2cpe_A           18 IYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKV   97 (113)
T ss_dssp             EEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             EEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCccCCCEEEE
Confidence            89999999998   999999999998        588887  77999999999999999999999999999999999999


Q ss_pred             EeeCCCCCC
Q psy6353          69 SYARPSSES   77 (136)
Q Consensus        69 ~~~~~~~~~   77 (136)
                      .++.++...
T Consensus        98 ~~a~~~~~~  106 (113)
T 2cpe_A           98 SLARKKPPM  106 (113)
T ss_dssp             ECSSCCCCS
T ss_pred             EECCCCCCC
Confidence            999877543

>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=99.78  E-value=1.2e-18  Score=104.62  Aligned_cols=74  Identities=20%  Similarity=0.293  Sum_probs=68.7

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cC-CCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--ST-AQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS   75 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~-~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~   75 (136)
                      |||+|||..++   |+++|++|| |.++.++.  .+ ++++|||||+|.+.++|++|+ .+|+..+.|++|.|.++.++.
T Consensus        18 l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~~~   95 (104)
T 1wi8_A           18 AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVADQAQ   95 (104)
T ss_dssp             EEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEECCCCC
T ss_pred             EEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEEEEccCCC
Confidence            79999999998   999999999 99999988  44 899999999999999999999 899999999999999998876


Q ss_pred             CC
Q psy6353          76 ES   77 (136)
Q Consensus        76 ~~   77 (136)
                      ..
T Consensus        96 ~~   97 (104)
T 1wi8_A           96 DK   97 (104)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.78  E-value=1.4e-19  Score=104.08  Aligned_cols=67  Identities=19%  Similarity=0.350  Sum_probs=62.3

Q ss_pred             eeecCCChhh------h---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCc-eEEE
Q psy6353           2 VYQTLLNKLF------T---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNK-TIKV   68 (136)
Q Consensus         2 v~v~nl~~~~------~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~-~l~v   68 (136)
                      |||+|||..+      +   |+++|++||+|.++.+++.+|+++|||||+|.+.++|+.|+..|||..+.|+ +|+|
T Consensus         4 l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~V   80 (81)
T 2krb_A            4 IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRV   80 (81)
T ss_dssp             EEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCCBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCCC
T ss_pred             EEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecCCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEEe
Confidence            8999999888      4   8999999999999988777889999999999999999999999999999999 8765

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.78  E-value=6.9e-19  Score=105.67  Aligned_cols=75  Identities=20%  Similarity=0.346  Sum_probs=70.7

Q ss_pred             eeecCCChhhh---HHHHhcc-CCCeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCce-eCCceEEEEeeCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLG-FSDAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLR-LQNKTIKVSYARPSS   75 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~-~G~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~-~~g~~l~v~~~~~~~   75 (136)
                      |||+|||..++   |+++|++ ||.|.++.++. .+++++|||||+|.+.++|+.|+..+||.. +.|++|.|.++.++.
T Consensus        12 l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v~~a~~~~   91 (104)
T 2dhg_A           12 LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLSVAIPKA   91 (104)
T ss_dssp             EEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCCCBCCCCC
T ss_pred             EEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEEEEccCCC
Confidence            89999999998   9999999 99999999999 889999999999999999999999999999 999999999987765


Q ss_pred             C
Q psy6353          76 E   76 (136)
Q Consensus        76 ~   76 (136)
                      .
T Consensus        92 ~   92 (104)
T 2dhg_A           92 S   92 (104)
T ss_dssp             S
T ss_pred             c
Confidence            4

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.78  E-value=1.3e-18  Score=109.63  Aligned_cols=75  Identities=27%  Similarity=0.441  Sum_probs=70.8

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||+|.++.+++  .+++++|||||+|.+.++|++|+..+||..+.|+.|+|.++.+...
T Consensus        45 l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  124 (139)
T 1u6f_A           45 LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQ  124 (139)
T ss_dssp             EEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESSCCCC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCC
Confidence            89999999998   999999999999999988  6789999999999999999999999999999999999999987654

>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=99.78  E-value=5.4e-19  Score=105.05  Aligned_cols=73  Identities=14%  Similarity=0.180  Sum_probs=67.8

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS   74 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~   74 (136)
                      |||+|||..++   |+++|++||.|..+.++.  .+++++|||||+|.+.++|++|+..+||..+.|++|+|.++...
T Consensus        18 l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~   95 (98)
T 2cqp_A           18 IKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLGSGP   95 (98)
T ss_dssp             EEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEESSCS
T ss_pred             EEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEcCCC
Confidence            89999999998   999999999998777666  78899999999999999999999999999999999999998754

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*

Probab=99.77  E-value=7.9e-19  Score=108.87  Aligned_cols=75  Identities=20%  Similarity=0.288  Sum_probs=70.3

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||.|.++.++.  .++.++|||||+|.+.++|+.|+..|||..+.|+.|.|.++.++..
T Consensus        25 l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  104 (126)
T 3ex7_B           25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGP  104 (126)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEESEESSS
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEecCCCC
Confidence            89999999998   999999999999999988  5899999999999999999999999999999999999999876544

>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=99.77  E-value=1.9e-18  Score=100.55  Aligned_cols=69  Identities=20%  Similarity=0.355  Sum_probs=64.4

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEee
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA   71 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~   71 (136)
                      |||+|||..++   |+++|++||+|.++.+++  .+|+++|||||+|.+.++|++|+. +++..+.|++|.|.++
T Consensus        14 l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v~~A   87 (87)
T 3s7r_A           14 MFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDPKKA   87 (87)
T ss_dssp             EEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEEEEC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEEEeC
Confidence            79999999998   999999999999999988  679999999999999999999997 5888999999999864

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=7.8e-19  Score=105.64  Aligned_cols=75  Identities=20%  Similarity=0.345  Sum_probs=70.2

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||+|.++.+++  .+++++|||||+|.+.++|++|+.. |+..+.|+.|.|.++.++..
T Consensus        19 l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V~~a~~~~~   97 (105)
T 2dh8_A           19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPKPCTPRGM   97 (105)
T ss_dssp             ECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBCCCSCCSSC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEEccCCCC
Confidence            79999999998   999999999999999998  6899999999999999999999998 99999999999999987764


Q ss_pred             C
Q psy6353          77 S   77 (136)
Q Consensus        77 ~   77 (136)
                      .
T Consensus        98 ~   98 (105)
T 2dh8_A           98 Q   98 (105)
T ss_dssp             C
T ss_pred             C
Confidence            3

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.77  E-value=1.1e-18  Score=103.76  Aligned_cols=69  Identities=14%  Similarity=0.084  Sum_probs=63.6

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCce--eCCceEEEEeeCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLR--LQNKTIKVSYARPS   74 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~--~~g~~l~v~~~~~~   74 (136)
                      |||+|||..+|   |+++|++||+|.++.+++    +||+|||+|.+.++|..|++.+|+..  +.|++|.|.+++++
T Consensus        24 l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~----~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~~S~~k   97 (100)
T 3r27_A           24 VHIRGLIDGVVEADLVEALQEFGPISYVVVMP----KKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTSQ   97 (100)
T ss_dssp             EEEESCCTTCCHHHHHHHHGGGSCEEEEEEET----TTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEEECSCS
T ss_pred             EEEeCCCCCCCHHHHHHHHhccCCEEEEEEEc----CCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEEecccc
Confidence            79999999998   999999999999999875    68999999999999999999998864  78999999999865

>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=99.77  E-value=5.3e-19  Score=105.62  Aligned_cols=72  Identities=18%  Similarity=0.275  Sum_probs=67.5

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc-c--CCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI-S--TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS   75 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~-~--~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~   75 (136)
                      |||+|||..++   |+++|++|| |.++.+++ .  +|+++|||||+|.+.++|+.|+ .+||..+.|+.|.|.++.++.
T Consensus        22 l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V~~a~~~~   99 (100)
T 2j76_E           22 AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRVDVADQAQ   99 (100)
T ss_dssp             EEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCCEECCCSC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEEEEeccCCC
Confidence            79999999998   999999999 99999988 4  7999999999999999999999 899999999999999998764

>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=99.77  E-value=6.1e-19  Score=104.21  Aligned_cols=72  Identities=15%  Similarity=0.186  Sum_probs=66.5

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP   73 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~   73 (136)
                      |||+|||..++   |+++|++||.|..+.++.  .+++++|||||+|.+.++|++|+..+|+..+.|++|+|.++.+
T Consensus        18 l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a~s   94 (95)
T 2ek1_A           18 IKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGPSS   94 (95)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC-
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEeccC
Confidence            89999999998   999999999998887777  7889999999999999999999999999999999999988753

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=2e-18  Score=105.66  Aligned_cols=75  Identities=17%  Similarity=0.285  Sum_probs=70.2

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||.|..+.++.  .+++++|||||+|.+.++|+.|+.. |+..+.|+.|.|.++.++..
T Consensus        30 l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a~~~~~  108 (116)
T 1x4b_A           30 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAVAREE  108 (116)
T ss_dssp             EEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECCSSCCC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEECCCCcc
Confidence            89999999998   999999999999999998  6799999999999999999999997 99999999999999988765


Q ss_pred             C
Q psy6353          77 S   77 (136)
Q Consensus        77 ~   77 (136)
                      .
T Consensus       109 ~  109 (116)
T 1x4b_A          109 S  109 (116)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.77  E-value=2e-18  Score=106.79  Aligned_cols=74  Identities=18%  Similarity=0.263  Sum_probs=69.3

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||.|.++.++.  .+++++|||||+|.+.++|+.|+ .+||..+.|+.|.|.++.+...
T Consensus        39 l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~~~~  117 (124)
T 2jwn_A           39 VYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKRTNMP  117 (124)
T ss_dssp             EEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESSCCCS
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCCCCC
Confidence            79999999998   999999999999999988  68999999999999999999999 7999999999999999886544

>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=8.1e-19  Score=105.28  Aligned_cols=72  Identities=15%  Similarity=0.164  Sum_probs=65.3

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHc--CceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLN--GLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~--~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||+|.++.+++    .||||||+|.+.++|+.|+..++  +..+.|++|.|.++.++..
T Consensus        19 LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~----~kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~A~~~~~   94 (105)
T 1sjq_A           19 IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLK----GKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKEL   94 (105)
T ss_dssp             EEECSCCTTSCHHHHHHHHHHHCCEEEEEEET----TTTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBCCCSSSSC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEc----CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEcCCCCC
Confidence            89999999998   999999999999999986    48999999999999999999886  4789999999999987654


Q ss_pred             C
Q psy6353          77 S   77 (136)
Q Consensus        77 ~   77 (136)
                      .
T Consensus        95 ~   95 (105)
T 1sjq_A           95 K   95 (105)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.77  E-value=2.6e-18  Score=110.23  Aligned_cols=75  Identities=24%  Similarity=0.350  Sum_probs=70.7

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||+|.+|.++.  .++.++|||||+|.+.++|++|+..||+..+.|++|+|.++.+...
T Consensus        42 l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~  121 (156)
T 1h2v_Z           42 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKE  121 (156)
T ss_dssp             EEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEESCCCT
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCC
Confidence            89999999988   999999999999999988  6799999999999999999999999999999999999999987654

>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=99.77  E-value=3.1e-18  Score=103.70  Aligned_cols=74  Identities=19%  Similarity=0.306  Sum_probs=68.1

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||.|..+.++. +++++|||||+|.+.++|+.|+..||+..+.|++|+|.++.+...
T Consensus        25 l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~  101 (109)
T 1x4a_A           25 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN-RRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRG  101 (109)
T ss_dssp             EEEESCCTTCCHHHHHHHHGGGSCEEEEEECC-SSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCCCCC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEE-CCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcccCCC
Confidence            89999999998   999999999999998864 556899999999999999999999999999999999999987654

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.77  E-value=3.6e-18  Score=105.69  Aligned_cols=75  Identities=17%  Similarity=0.282  Sum_probs=70.8

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||+|.++.++. .+|+++|||||+|.+.++|+.|+..+||..+.|++|+|.++.+...
T Consensus        38 l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~  116 (124)
T 2kt5_A           38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQID  116 (124)
T ss_dssp             EEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEECCTTC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEeCCCCC
Confidence            79999999988   999999999999999999 8889999999999999999999999999999999999999987643

>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=99.77  E-value=1.2e-18  Score=111.87  Aligned_cols=75  Identities=23%  Similarity=0.340  Sum_probs=70.8

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||.|.++.+++  .+|+++|||||+|.+.++|+.|+..|||..+.|++|.|.++.+...
T Consensus        73 l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  152 (158)
T 2kn4_A           73 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRP  152 (158)
T ss_dssp             EEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEECCSSC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCC
Confidence            89999999998   999999999999999988  6899999999999999999999999999999999999999987644

>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=99.77  E-value=2.6e-18  Score=104.75  Aligned_cols=73  Identities=23%  Similarity=0.340  Sum_probs=68.4

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCcee--------CCceEEEE
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRL--------QNKTIKVS   69 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~--------~g~~l~v~   69 (136)
                      |||+|||..++   |+++|++||.|.++.++. .++.++|||||+|.+.++|+.|+..|||..+        .+++|.|.
T Consensus        28 l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~~~~l~v~  107 (114)
T 1x5o_A           28 LYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEPLLCK  107 (114)
T ss_dssp             EEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSSCBEEE
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCCCCceeEE
Confidence            89999999998   999999999999999999 8899999999999999999999999999999        57889999


Q ss_pred             eeCCC
Q psy6353          70 YARPS   74 (136)
Q Consensus        70 ~~~~~   74 (136)
                      ++.|+
T Consensus       108 ~a~p~  112 (114)
T 1x5o_A          108 FSGPS  112 (114)
T ss_dssp             ECCCS
T ss_pred             ccCCC
Confidence            98865

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.77  E-value=7.5e-19  Score=107.81  Aligned_cols=71  Identities=28%  Similarity=0.508  Sum_probs=66.8

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR   72 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~   72 (136)
                      |||+|||..++   |+++|++||.|.++.+++  .+++++|||||+|.+.++|+.|+..|||..+.|++|+|.+++
T Consensus        43 l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~ak  118 (118)
T 2khc_A           43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLKK  118 (118)
T ss_dssp             EEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEEEC-
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEecC
Confidence            79999999998   999999999999999988  678999999999999999999999999999999999998863

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.76  E-value=3e-18  Score=103.89  Aligned_cols=74  Identities=23%  Similarity=0.337  Sum_probs=68.6

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||+|.++.+++  .+|+++|||||+|.+.++|+.|+..+ +..+.|+.|.|.++.++..
T Consensus        28 lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V~~a~~~~~  106 (109)
T 2rs2_A           28 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDPKVAFPRRA  106 (109)
T ss_dssp             EEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEEEECCCCCC
T ss_pred             EEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEEEEccCCCC
Confidence            89999999998   999999999999999998  67999999999999999999999975 6999999999999987654

>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=99.76  E-value=2.3e-18  Score=111.55  Aligned_cols=75  Identities=20%  Similarity=0.311  Sum_probs=70.2

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||.|..|.++.  .+|.++|||||+|.+.++|+.|+..|||..+.|++|.|.++.++..
T Consensus        75 l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~  154 (165)
T 1rk8_A           75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGP  154 (165)
T ss_dssp             EEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEECC-
T ss_pred             EEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCCCC
Confidence            89999999998   999999999999999998  6899999999999999999999999999999999999999876543

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=2.6e-19  Score=103.80  Aligned_cols=71  Identities=25%  Similarity=0.350  Sum_probs=66.1

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR   72 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~   72 (136)
                      |||+|||..++   |+++|++||+|.++.++.  .+++++|||||+|.+.++|+.|+..|||..+.|+.+++.++.
T Consensus         8 l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~~   83 (85)
T 1x4e_A            8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGPS   83 (85)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCCC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCCC
Confidence            79999999998   999999999999999998  679999999999999999999999999999999998877654

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=1.8e-18  Score=105.82  Aligned_cols=74  Identities=28%  Similarity=0.361  Sum_probs=68.8

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||+|.++.+++  .+++++|||||+|.+.++|++|+..+|+ .+.|++|.|.++.+...
T Consensus        20 l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V~~a~~~~~   98 (116)
T 2cqd_A           20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAYLGAK   98 (116)
T ss_dssp             EEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEESTTTCC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEEEEcccCCC
Confidence            89999999998   999999999999999998  6799999999999999999999999998 89999999999976543

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.76  E-value=1.3e-18  Score=108.10  Aligned_cols=73  Identities=14%  Similarity=0.209  Sum_probs=65.9

Q ss_pred             eeecCCChhhh---H----HHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCC
Q psy6353           2 VYQTLLNKLFT---Y----EKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS   74 (136)
Q Consensus         2 v~v~nl~~~~~---l----~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~   74 (136)
                      |||+|||..++   |    .++|++||+|.+|.+. .+++++|||||+|.+.++|+.|+..|||..+.|++|+|.++.++
T Consensus        32 LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~-~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~V~~a~~~  110 (127)
T 2a3j_A           32 VLITNINPEVPKEKLQALLYALASSQGDILDIVVD-LSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETP  110 (127)
T ss_dssp             EEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEEC-CCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCEEEECCCC
T ss_pred             EEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEec-cCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEEEEEccCc
Confidence            89999999887   3    3689999999988775 46789999999999999999999999999999999999999876


Q ss_pred             C
Q psy6353          75 S   75 (136)
Q Consensus        75 ~   75 (136)
                      .
T Consensus       111 ~  111 (127)
T 2a3j_A          111 Q  111 (127)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.76  E-value=1.1e-18  Score=106.50  Aligned_cols=72  Identities=19%  Similarity=0.250  Sum_probs=67.7

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS   74 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~   74 (136)
                      |||+|||..++   |+++|++||.|.++.++.  .+++++|||||+|.+.++|+.|+ .+||..+.|+.|.|.++.++
T Consensus        28 l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~~  104 (114)
T 2cq4_A           28 VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQAE  104 (114)
T ss_dssp             EEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEHHHH
T ss_pred             EEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEecCCC
Confidence            89999999998   999999999999999998  66899999999999999999999 89999999999999988654

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.76  E-value=7.8e-19  Score=99.89  Aligned_cols=69  Identities=23%  Similarity=0.349  Sum_probs=65.3

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEee
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA   71 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~   71 (136)
                      |||+|||..++   |+++|++||+|.++.+++  .+|+++|||||+|.+.++|+.|+..++ ..+.|++|.+.++
T Consensus         3 l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a   76 (77)
T 1uaw_A            3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             EEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            79999999998   999999999999999998  579999999999999999999999998 9999999999876

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori}

Probab=99.76  E-value=2e-19  Score=105.40  Aligned_cols=74  Identities=23%  Similarity=0.354  Sum_probs=66.0

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||+|.++.+++  .+|+++|||||+|.+.+ |+.|+..+||..+.|++|+|.++.+...
T Consensus         4 l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~~~~   82 (90)
T 2ki2_A            4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANPKKS   82 (90)
T ss_dssp             EEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC-----
T ss_pred             EEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCCCCC
Confidence            79999999998   899999999999999998  67999999999999999 9999999999999999999999887543

>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=99.76  E-value=2e-18  Score=103.32  Aligned_cols=71  Identities=14%  Similarity=0.137  Sum_probs=64.0

Q ss_pred             eeecCCCh-hhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcC--ceeCCceEEEEeeCCCC
Q psy6353           2 VYQTLLNK-LFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNG--LRLQNKTIKVSYARPSS   75 (136)
Q Consensus         2 v~v~nl~~-~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~--~~~~g~~l~v~~~~~~~   75 (136)
                      |||+|||. .++   |+++|++||.|.++.+++    .+|||||+|.+.++|+.|+..||+  ..+.|++|.|.++.+..
T Consensus        18 l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~----~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~~~   93 (102)
T 1x4d_A           18 VHIMDFQRGKNLRYQLLQLVEPFGVISNHLILN----KINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKYK   93 (102)
T ss_dssp             EEEESCCCSSSHHHHHHTTTGGGSCEEEEEECS----SSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECCCT
T ss_pred             EEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEc----CCCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEEECCCCC
Confidence            89999999 887   999999999999999875    568999999999999999999886  46999999999998654


Q ss_pred             C
Q psy6353          76 E   76 (136)
Q Consensus        76 ~   76 (136)
                      .
T Consensus        94 ~   94 (102)
T 1x4d_A           94 R   94 (102)
T ss_dssp             T
T ss_pred             C
Confidence            3

>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=99.75  E-value=9.9e-18  Score=100.43  Aligned_cols=74  Identities=15%  Similarity=0.175  Sum_probs=68.2

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||+|..+.++.  .+++++|||||+|.+.++|+.|+.  +++.+.|+.|.|.++.++..
T Consensus        18 l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~v~~a~~~~~   95 (103)
T 2cqg_A           18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCKLPNSKQS   95 (103)
T ss_dssp             EEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEECCCTTCC
T ss_pred             EEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEEEEecCCCCc
Confidence            89999999998   999999999999999988  679999999999999999999999  47899999999999987754


Q ss_pred             C
Q psy6353          77 S   77 (136)
Q Consensus        77 ~   77 (136)
                      .
T Consensus        96 ~   96 (103)
T 2cqg_A           96 Q   96 (103)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.75  E-value=1.3e-18  Score=109.21  Aligned_cols=75  Identities=23%  Similarity=0.340  Sum_probs=70.6

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||+|..+.++.  .+++++|||||+|.+.++|+.|+..|||..+.|++|+|.++.+...
T Consensus        50 l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~~~~  129 (135)
T 2lea_A           50 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRP  129 (135)
T ss_dssp             EEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEECCCCCC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCC
Confidence            89999999998   999999999999999988  6899999999999999999999999999999999999999987654

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.75  E-value=5.6e-18  Score=101.17  Aligned_cols=72  Identities=21%  Similarity=0.301  Sum_probs=66.0

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||.|   .++. .+++++|||||+|.+.++|++|+..+|+..+.|++|+|.++.++..
T Consensus        18 l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~   93 (101)
T 2fc9_A           18 LVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQGPRGS   93 (101)
T ss_dssp             EEEESCCTTCCHHHHHHHCSSCSEE---ECCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEECSSCCC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhCCEE---EEEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEcCCCCC
Confidence            89999999998   99999999977   5666 7899999999999999999999999999999999999999987754

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.75  E-value=5.7e-19  Score=110.34  Aligned_cols=74  Identities=20%  Similarity=0.268  Sum_probs=69.1

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeE--EEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCc----eeCCceEEEEe
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEI--CVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGL----RLQNKTIKVSY   70 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~--~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~----~~~g~~l~v~~   70 (136)
                      |||+|||..++   |+++|++||.|..  |++++  .+|+++|||||+|.+. +|..|+..|||.    .+.|++|.|.+
T Consensus        26 lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr~l~V~~  104 (131)
T 2m2b_A           26 IILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGKTINVEF  104 (131)
T ss_dssp             EEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGCCCCCEE
T ss_pred             EEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCEEEEEEE
Confidence            89999999998   9999999999976  99998  5899999999999999 999999999999    99999999999


Q ss_pred             eCCCCC
Q psy6353          71 ARPSSE   76 (136)
Q Consensus        71 ~~~~~~   76 (136)
                      +.+...
T Consensus       105 a~~~~~  110 (131)
T 2m2b_A          105 AKGSKR  110 (131)
T ss_dssp             CCCSCC
T ss_pred             CCCCCC
Confidence            987644

>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=99.75  E-value=3e-18  Score=103.01  Aligned_cols=73  Identities=19%  Similarity=0.171  Sum_probs=67.5

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeE-EEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEI-CVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS   75 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~-~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~   75 (136)
                      |||+|||..++   |+++|++||.|.+ +.++. .+|+++|||||+|.+.++|++|+.. |+..++|+.|.|.++.++.
T Consensus        18 l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~~~~~~~   95 (104)
T 1wg5_A           18 VRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIFKSSRAE   95 (104)
T ss_dssp             EEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEEEECTTT
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEEECCHHH
Confidence            89999999999   9999999999987 77877 8899999999999999999999997 9999999999999887653

>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=99.75  E-value=5.4e-18  Score=103.95  Aligned_cols=71  Identities=15%  Similarity=0.172  Sum_probs=64.9

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcC--ceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNG--LRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~--~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||.|.++.+++    .||||||+|.+.++|++|+..+++  ..+.|++|.|.++.++..
T Consensus        34 LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~----~kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~k~~  109 (119)
T 2ad9_A           34 IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLK----GKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKEL  109 (119)
T ss_dssp             EEEESCCTTCCHHHHHHHHTTTSCCCEEEEEG----GGTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEEECSSSSC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC----CCCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEEEccCCCC
Confidence            89999999998   999999999999999986    489999999999999999998874  689999999999987653

>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=99.75  E-value=5.4e-18  Score=101.61  Aligned_cols=73  Identities=15%  Similarity=0.084  Sum_probs=66.9

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||.+ ++.++. .+++++|||||+|.+.++|++|+. +|+..+.++.|+|..+.+...
T Consensus        18 l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~~~~~~~   94 (102)
T 1wez_A           18 VHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLNSTAGT   94 (102)
T ss_dssp             EEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEECCCCC
T ss_pred             EEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEECCCCCC
Confidence            89999999998   99999999965 999998 889999999999999999999995 799999999999998876543

>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=99.74  E-value=2.3e-18  Score=104.18  Aligned_cols=75  Identities=17%  Similarity=0.256  Sum_probs=68.9

Q ss_pred             eeecCCChhhh---HHHHhccCCC-eeEEEEE-c--cCCCceeeEEEEcCCHHHHHHHHHHHc--CceeCCceEEEEeeC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSD-AEICVFL-I--STAQSLGYGFVNYHRPEDAEKAINTLN--GLRLQNKTIKVSYAR   72 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~-v~~~~~~-~--~~~~~kg~~fv~f~~~~~a~~a~~~~~--~~~~~g~~l~v~~~~   72 (136)
                      |||+|||..++   |+++|++||. |.++.++ .  .+++++|||||+|.+.++|+.|+..+|  +..+.|++|+|.++.
T Consensus        11 l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~V~~a~   90 (109)
T 2dis_A           11 LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAE   90 (109)
T ss_dssp             EEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEESC
T ss_pred             EEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEEEEEcC
Confidence            79999999998   9999999998 9999998 4  678999999999999999999999996  599999999999998


Q ss_pred             CCCC
Q psy6353          73 PSSE   76 (136)
Q Consensus        73 ~~~~   76 (136)
                      ++..
T Consensus        91 ~~~~   94 (109)
T 2dis_A           91 PEID   94 (109)
T ss_dssp             SSCS
T ss_pred             CCCC
Confidence            7654

>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=3e-18  Score=104.08  Aligned_cols=71  Identities=15%  Similarity=0.153  Sum_probs=64.4

Q ss_pred             eeecCCChhhh---HHHHhccCC-CeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFS-DAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS   74 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G-~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~   74 (136)
                      |||+|||..++   |+++|++|| .|..+.++  .++++|||||+|.+.++|+.|+..|||..+.|+.|+|.++...
T Consensus        31 l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~--~~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a~~~  105 (111)
T 2jvr_A           31 ITMKNLPEGCSWQDLKDLARENSLETTFSSVN--TRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDDNP  105 (111)
T ss_dssp             EEEECSSCCCCHHHHHHHHHHHTCCCSEEECS--SCSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEESCC-
T ss_pred             EEEECCCCCCCHHHHHHHHHHhCCeeEEEEEE--cCCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCCC
Confidence            79999999998   999999999 89988874  3468999999999999999999999999999999999988654

>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=99.74  E-value=8.7e-18  Score=100.02  Aligned_cols=71  Identities=23%  Similarity=0.305  Sum_probs=66.3

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||+|.++.+++    ++|||||+|.+.++|++|+..|||..+.|++|+|.++.++..
T Consensus        18 l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~----~kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~~~   91 (99)
T 2cpj_A           18 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHK----DKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSAS   91 (99)
T ss_dssp             EEEESCCTTCCHHHHHHHTSTTCCCSEEEEET----TTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCSC
T ss_pred             EEEeCCCCCCCHHHHHHHHhhcCCeEEEEEec----CCCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEcCCCCC
Confidence            79999999998   999999999999999875    589999999999999999999999999999999999987654

>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=99.74  E-value=6.5e-18  Score=101.54  Aligned_cols=71  Identities=8%  Similarity=0.073  Sum_probs=64.0

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcC--ceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNG--LRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~--~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||.|.++.+++    .||||||+|.+.++|+.|+..+++  ..+.|++|.|.++.++..
T Consensus        18 l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~----~kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~~a~~~~~   93 (104)
T 1wex_A           18 VHVRGLCESVVEADLVEALEKFGTICYVMMMP----FKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRI   93 (104)
T ss_dssp             EEEESCCSSCCHHHHHHHHTTTSCEEEEEEET----TTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSSSSC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEC----CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEccCccc
Confidence            89999999998   999999999999998875    489999999999999999998875  458999999999987654

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=1.2e-17  Score=99.87  Aligned_cols=71  Identities=18%  Similarity=0.166  Sum_probs=64.2

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHH--cCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTL--NGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~--~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||.|.++.+++    .+|||||+|.+.++|+.|+..+  ++..+.|++|.|.++.++..
T Consensus        18 l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~----~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~~~~   93 (101)
T 2cq1_A           18 LHIRKLPGEVTETEVIALGLPFGKVTNILMLK----GKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHKEL   93 (101)
T ss_dssp             EEEESCCTTCCHHHHHHTTTTTSCEEEEEEET----TTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSCSSC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEC----CCCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEEEcCcccC
Confidence            89999999998   999999999999998875    4899999999999999999976  46889999999999987653

>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=99.74  E-value=2.6e-18  Score=101.86  Aligned_cols=74  Identities=19%  Similarity=0.373  Sum_probs=67.5

Q ss_pred             eeecCCChhhh---HH----HHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCC
Q psy6353           2 VYQTLLNKLFT---YE----KVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS   74 (136)
Q Consensus         2 v~v~nl~~~~~---l~----~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~   74 (136)
                      |||+|||..++   |+    ++|++||.|.++.+++ +|.++|||||+|.+.++|+.|+..|||..+.|++|.|.++.+.
T Consensus        11 l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~   89 (97)
T 1nu4_A           11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR-SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTD   89 (97)
T ss_dssp             EEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH-HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSSC
T ss_pred             EEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc-CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEEEEEccCC
Confidence            79999999998   77    9999999999998774 5678899999999999999999999999999999999999876


Q ss_pred             CC
Q psy6353          75 SE   76 (136)
Q Consensus        75 ~~   76 (136)
                      ..
T Consensus        90 ~~   91 (97)
T 1nu4_A           90 SD   91 (97)
T ss_dssp             CT
T ss_pred             Cc
Confidence            43

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.74  E-value=4.7e-18  Score=106.95  Aligned_cols=70  Identities=27%  Similarity=0.406  Sum_probs=65.9

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEee
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA   71 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~   71 (136)
                      |||+|||..++   |+++|++||+|.++.+++  .+++++|||||+|.+.++|++|+..+||..+.|++|+|.++
T Consensus        66 l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~A  140 (140)
T 2ku7_A           66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA  140 (140)
T ss_dssp             EEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEEC-
T ss_pred             EEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            79999999998   999999999999999988  67899999999999999999999999999999999999864

>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=99.74  E-value=3.1e-18  Score=104.54  Aligned_cols=72  Identities=18%  Similarity=0.186  Sum_probs=67.5

Q ss_pred             eeecCCChhhh---HHHHhccCCCe-eEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDA-EICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS   74 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v-~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~   74 (136)
                      |||+|||..++   |+++|++||.| .++.++. .+|+++|||||+|.+.++|++|+.. |+..+.|++|.|.++.++
T Consensus        18 l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~~a~~~   94 (114)
T 2cpy_A           18 AHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVHVVTLE   94 (114)
T ss_dssp             EEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEEEECHH
T ss_pred             EEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEEECCHH
Confidence            89999999998   99999999999 8899998 8899999999999999999999996 999999999999988654

>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=99.74  E-value=1.2e-17  Score=99.09  Aligned_cols=71  Identities=13%  Similarity=0.287  Sum_probs=65.6

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeC--CceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQ--NKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~--g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||+|.++.++.    .+|||||+|.+.++|+.|+..||+..+.  |++|+|.++.++..
T Consensus        20 l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~----~~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~~a~~~~~   95 (97)
T 1why_A           20 LWVGGLGPNTSLAALAREFDRFGSIRTIDHVK----GDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSGPS   95 (97)
T ss_dssp             EEEECCCSSCCHHHHHHHHHTTSCEEEEEECS----SSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCCCC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeC----CCCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEEECCCCCC
Confidence            89999999988   999999999999998864    3899999999999999999999999999  99999999988754

>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=99.74  E-value=4.1e-18  Score=103.43  Aligned_cols=71  Identities=14%  Similarity=0.206  Sum_probs=64.1

Q ss_pred             eeecCCChh-hh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcC--ceeCCceEEEEeeCCCC
Q psy6353           2 VYQTLLNKL-FT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNG--LRLQNKTIKVSYARPSS   75 (136)
Q Consensus         2 v~v~nl~~~-~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~--~~~~g~~l~v~~~~~~~   75 (136)
                      |||+|||.. ++   |+++|++||+|.++.+++    ++|||||+|.+.++|+.|+..+|+  ..+.|++|.|.++.++.
T Consensus        28 l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~----~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~~~  103 (112)
T 1x4f_A           28 IHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR----MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKYK  103 (112)
T ss_dssp             EEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET----TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECSCS
T ss_pred             EEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec----CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEECcccc
Confidence            899999998 87   999999999999999875    689999999999999999998864  66999999999998765


Q ss_pred             C
Q psy6353          76 E   76 (136)
Q Consensus        76 ~   76 (136)
                      .
T Consensus       104 ~  104 (112)
T 1x4f_A          104 K  104 (112)
T ss_dssp             S
T ss_pred             c
Confidence            4

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.73  E-value=7.9e-18  Score=103.38  Aligned_cols=71  Identities=14%  Similarity=0.109  Sum_probs=66.6

Q ss_pred             eeecCCChhhh---HHHHhccCCC---eeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSD---AEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP   73 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~---v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~   73 (136)
                      |||+|||..+|   |+++|++||.   |.++.++. ..|+++|||||+|.+.++|++|+. +|+..+.|+.|+|.++.+
T Consensus        20 l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~a~~   97 (118)
T 2db1_A           20 VKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK-KDRESMGHRYIEVFKSHR   97 (118)
T ss_dssp             EEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEEEEEECH
T ss_pred             EEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEEEEECCH
Confidence            89999999999   9999999999   89999998 669999999999999999999999 999999999999988753

>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=99.73  E-value=3.9e-18  Score=107.08  Aligned_cols=71  Identities=15%  Similarity=0.114  Sum_probs=66.6

Q ss_pred             eeecCCChhhh---HHHHhccCCC---eeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSD---AEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP   73 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~---v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~   73 (136)
                      |||+|||..+|   |+++|++||.   |.+|.+++ ..|+++|||||+|.+.++|++|+. +|+..+.|+.|+|.++.+
T Consensus        47 lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~V~~a~~  124 (136)
T 2hgl_A           47 VKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIEVFKSHR  124 (136)
T ss_dssp             EEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEEEEECCH
T ss_pred             EEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEEEEECCh
Confidence            89999999999   9999999999   88999998 669999999999999999999999 999999999999988753

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.73  E-value=6.2e-18  Score=100.99  Aligned_cols=69  Identities=16%  Similarity=0.235  Sum_probs=64.6

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS   74 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~   74 (136)
                      |||+|||..++   |+++|++||.|.++.+.+    ++|||||+|.+.++|+.|+..+||..+.|+.|+|.+++++
T Consensus        30 l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~----~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  101 (101)
T 2la4_A           30 AYIGNIPHFATEADLIPLFQNFGFILDFKHYP----EKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKER  101 (101)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCCSEEEEET----TTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCCCC
T ss_pred             EEEcCCCcccCHHHHHHHHHhCCCEEEEEEec----CCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEeccCC
Confidence            89999999998   999999999999999874    7899999999999999999999999999999999998763

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=1.1e-17  Score=101.31  Aligned_cols=70  Identities=19%  Similarity=0.235  Sum_probs=65.0

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP   73 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~   73 (136)
                      |||+|||..++   |+++|++| .|.+|.++. ..|+++|||||+|.+.++|++|+ .+|+..++||.|.|..+.+
T Consensus        19 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           19 VSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPATE   92 (109)
T ss_dssp             EEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECCH
T ss_pred             EEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCc
Confidence            89999999998   99999999 889999998 67999999999999999999999 5999999999999987653

>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=99.73  E-value=3.7e-18  Score=115.91  Aligned_cols=72  Identities=18%  Similarity=0.183  Sum_probs=68.7

Q ss_pred             eeecCCChhhh---HHHHhccCC--CeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFS--DAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP   73 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G--~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~   73 (136)
                      |||+|||..+|   |+++|++||  .|.+|.|++  .+++++|||||+|.+.++|++|+..||+..|.|+.|+|.++.+
T Consensus        71 lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~a~~  149 (229)
T 3q2s_C           71 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNK  149 (229)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEECCH
T ss_pred             EEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEECCC
Confidence            89999999998   999999999  999999998  6899999999999999999999999999999999999998764

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.73  E-value=1.9e-17  Score=102.76  Aligned_cols=71  Identities=17%  Similarity=0.296  Sum_probs=64.7

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceee-EEEEcCCHHHHHHHHHHHcCceeCC--ceEEEEeeCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGY-GFVNYHRPEDAEKAINTLNGLRLQN--KTIKVSYARPSS   75 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~-~fv~f~~~~~a~~a~~~~~~~~~~g--~~l~v~~~~~~~   75 (136)
                      |||+||+..+|   |+++|++||+|.+|.++.   +++|+ |||+|.+.++|+.|++.|||..+.|  +.|+|.++++..
T Consensus        31 I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~---~~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~ak~~~  107 (130)
T 3zzy_A           31 IIVENLFYPVTLDVLHQIFSKFGTVLKIITFT---KNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTS  107 (130)
T ss_dssp             EEEESCCSCCCHHHHHHHHTTSSCEEEEEEEE---ETTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEECSCSS
T ss_pred             EEECCCCCCCCHHHHHHHHhCcCCEEEEEEEc---CCCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEecCCCc
Confidence            78999999998   999999999999998876   34677 9999999999999999999999988  899999998754

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=2.6e-17  Score=96.31  Aligned_cols=70  Identities=23%  Similarity=0.362  Sum_probs=65.2

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES   77 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~~   77 (136)
                      |||+|||..++   |+++|++||+|.++.++      +|||||+|.+.++|+.|+..+|+..+.|++|+|.++.++...
T Consensus        11 l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~   83 (90)
T 2dnq_A           11 LFIGNLPREATEQEIRSLFEQYGKVLECDII------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNKSKA   83 (90)
T ss_dssp             EEEESCCSSCCHHHHHHHHHTSSCEEEEEEE------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECSSCCCCC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEECCCCCCC
Confidence            79999999998   99999999999999987      489999999999999999999999999999999999877653

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=3.3e-17  Score=96.25  Aligned_cols=70  Identities=21%  Similarity=0.302  Sum_probs=64.9

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES   77 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~~   77 (136)
                      |||+|||..++   |+++|++||.|.++.+++      +||||+|.+.++|++|+..|||..+.|+.|+|.++.++...
T Consensus        13 l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~   85 (92)
T 2dgt_A           13 LHVGNISPTCTNQELRAKFEEYGPVIECDIVK------DYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLRT   85 (92)
T ss_dssp             EEEESCCSSCCHHHHHHHHHTTSCCCEEEECS------SEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEESSCCCSC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEC------CEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEccCCCCC
Confidence            79999999998   999999999999999864      59999999999999999999999999999999999877543

>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=99.73  E-value=1.1e-17  Score=101.74  Aligned_cols=69  Identities=13%  Similarity=0.105  Sum_probs=64.2

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS   74 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~   74 (136)
                      |||+|||..++   |+++|++||.|..+.++.    ++|||||+|.+.++|+.|+..|||..+.|++|.|.++...
T Consensus        13 l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~----~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~   84 (111)
T 1whx_A           13 ILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE----GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIG   84 (111)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEECCS----SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETT
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC----CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCCC
Confidence            79999999998   999999999999998764    7899999999999999999999999999999999998754

>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=1.5e-17  Score=96.20  Aligned_cols=67  Identities=18%  Similarity=0.297  Sum_probs=62.9

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHH-cCceeCCceEEEEeeC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTL-NGLRLQNKTIKVSYAR   72 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~-~~~~~~g~~l~v~~~~   72 (136)
                      |||+|||..++   |+++|++||+|.++.+++    ++|||||+|.+.++|+.|+..| ||..+.|++|+|.+++
T Consensus        15 l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~----~kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~ak   85 (85)
T 2ytc_A           15 LYVGGLGDTITETDLRNHFYQFGEIRTITVVQ----RQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWGR   85 (85)
T ss_dssp             EEEECCTTTSCHHHHHHHHHTTSCEEEEEEEG----GGTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEECC
T ss_pred             EEEcCCCCCCCHHHHHHHHHhCCCEeEEEEEC----CCCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEecC
Confidence            89999999998   999999999999999886    6899999999999999999998 9999999999999874

>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=99.73  E-value=1.5e-18  Score=98.29  Aligned_cols=69  Identities=14%  Similarity=0.232  Sum_probs=64.1

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEee
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA   71 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~   71 (136)
                      |||+|||..++   |+++|++||+|.++.++.  .++.++|||||+|.+.++|+.|+.. ++..+.|+++.+.++
T Consensus         2 l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A            2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTT-SSCCBTTBCCCEEEC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEEC
Confidence            79999999998   999999999999999888  6789999999999999999999994 899999999998764

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.72  E-value=7.9e-18  Score=99.88  Aligned_cols=71  Identities=23%  Similarity=0.313  Sum_probs=64.3

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS   75 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~   75 (136)
                      |||+|||..++   |+++|++||.|. +.++  +++++|||||+|.+.++|+.|+..|||..+.|++|.|.++.++.
T Consensus        22 l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~--~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   95 (97)
T 2e5j_A           22 VYVGNLPRDARVSDLKRALRELGSVP-LRLT--WQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQR   95 (97)
T ss_dssp             EEEECCCTTCCHHHHHHHHHHTTCCC-SEEE--EETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEECCCCC
T ss_pred             EEEeCCCCcCcHHHHHHHHHhcCCEE-EEEE--cCCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCCC
Confidence            79999999998   999999999986 5554  35788999999999999999999999999999999999998764

>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=99.72  E-value=1.9e-17  Score=100.19  Aligned_cols=71  Identities=23%  Similarity=0.357  Sum_probs=66.3

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||.|.++.+++    .+|||||+|.+.++|+.|+..|||..+.|++|+|.++.++..
T Consensus        28 l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  101 (109)
T 1x4g_A           28 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFP----EKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPD  101 (109)
T ss_dssp             EEEECCSSCCCHHHHHHHHHHHSCEEEEEEET----TTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCCCS
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeC----CCCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEecCCCCC
Confidence            89999999998   999999999999999886    389999999999999999999999999999999999987654

>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=99.72  E-value=2e-18  Score=105.39  Aligned_cols=76  Identities=18%  Similarity=0.294  Sum_probs=66.6

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||.|..+.+..  .+++++|||||+|.+.++|+.|+..|||..+.|++|.|.++.++..
T Consensus        28 l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~~~~  107 (115)
T 2cpx_A           28 LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKKQ  107 (115)
T ss_dssp             EEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEECCCCSC
T ss_pred             EEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEccCCCC
Confidence            89999999998   999999999984432222  5789999999999999999999999999999999999999987765


Q ss_pred             C
Q psy6353          77 S   77 (136)
Q Consensus        77 ~   77 (136)
                      .
T Consensus       108 ~  108 (115)
T 2cpx_A          108 R  108 (115)
T ss_dssp             C
T ss_pred             C
Confidence            3

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.72  E-value=8.7e-18  Score=99.42  Aligned_cols=72  Identities=15%  Similarity=0.303  Sum_probs=65.9

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||.|..+   ..+++++|||||+|.+.++|+.|+..+||..+.|++|.|.++.++..
T Consensus        19 l~V~nL~~~~t~~~l~~~F~~~g~v~~~---~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   93 (96)
T 1fjc_A           19 LLAKNLSFNITEDELKEVFEDALEIRLV---SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGG   93 (96)
T ss_dssp             EEEESCCSSCCHHHHHHHHCSEEEECCE---EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSSCC
T ss_pred             EEEeCCCCCCCHHHHHHHHhhCCcEEEe---CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcCCCCC
Confidence            89999999998   99999999988766   46788999999999999999999999999999999999999987654

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.72  E-value=3.2e-17  Score=99.15  Aligned_cols=69  Identities=20%  Similarity=0.394  Sum_probs=64.2

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||.|.++.++      +|||||+|.+.++|+.|+..|||..+.|+.|.|.++.+...
T Consensus        34 l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~  105 (108)
T 2jvo_A           34 LFVRPFPLDVQESELNEIFGPFGPMKEVKIL------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPAK  105 (108)
T ss_dssp             EEECSSCTTCCHHHHHHHHTTTSCCCEEEEE------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEESCSCCC-
T ss_pred             EEEECCCCCCCHHHHHHHHHhcCCEEEEEEE------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecCCCC
Confidence            79999999998   99999999999999986      69999999999999999999999999999999999987643

>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=99.72  E-value=2.7e-18  Score=106.25  Aligned_cols=71  Identities=18%  Similarity=0.149  Sum_probs=65.0

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEE-EEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEIC-VFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP   73 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~-~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~   73 (136)
                      |||+|||..++   |+++|++||.|.++ .+.. .+|+++|||||+|.+.++|++|+. +||..+.|+.|.|.++.+
T Consensus        28 l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~a~~  103 (124)
T 1wel_A           28 VYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPITK  103 (124)
T ss_dssp             EEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEECH
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEECCH
Confidence            89999999998   99999999999884 4444 889999999999999999999999 999999999999998864

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.72  E-value=3.7e-17  Score=98.83  Aligned_cols=70  Identities=21%  Similarity=0.222  Sum_probs=65.3

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCC-----ceEEEEeeCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQN-----KTIKVSYARP   73 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g-----~~l~v~~~~~   73 (136)
                      |||+|||..++   |+++|++||+|..+.++..     |||||+|.+.++|+.|+..|||..+.|     ++|+|.++.+
T Consensus        18 l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-----g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i~V~~a~~   92 (108)
T 1x4c_A           18 VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-----GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGP   92 (108)
T ss_dssp             EEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-----TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEEEEEESSC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-----CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEEEEEeCCC
Confidence            89999999998   9999999999999999862     999999999999999999999999999     9999999987


Q ss_pred             CCC
Q psy6353          74 SSE   76 (136)
Q Consensus        74 ~~~   76 (136)
                      +..
T Consensus        93 ~~~   95 (108)
T 1x4c_A           93 RSP   95 (108)
T ss_dssp             CSC
T ss_pred             CCC
Confidence            654

>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=5.1e-17  Score=104.34  Aligned_cols=72  Identities=22%  Similarity=0.431  Sum_probs=68.2

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP   73 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~   73 (136)
                      |||+|||..++   |+++|++||.|.++.++.  .+|.++|||||+|.+.++|.+|+..+||..+.|++|+|.++++
T Consensus        90 l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~  166 (166)
T 3md3_A           90 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK  166 (166)
T ss_dssp             EEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCC
T ss_pred             EEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEecCC
Confidence            79999999998   999999999999999988  7899999999999999999999999999999999999999863

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.71  E-value=2.3e-17  Score=110.69  Aligned_cols=74  Identities=26%  Similarity=0.473  Sum_probs=68.9

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS   75 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~   75 (136)
                      |||+|||..++   |+++|++||.|.++.+++..+.++|||||+|.+.++|++|+.+|||..++|++|.|.++.++.
T Consensus       106 l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~~~~  182 (213)
T 4f02_A          106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK  182 (213)
T ss_dssp             EEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCHH
T ss_pred             ceECCcccccHHHHHHHHHhhcCCeEEEEeeccCCCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcCCCc
Confidence            79999999998   999999999999999988555689999999999999999999999999999999999988754

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=3.9e-17  Score=95.55  Aligned_cols=69  Identities=22%  Similarity=0.340  Sum_probs=64.4

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||.|.++.+++      +||||+|.+.++|+.|+..|||..+.|++|+|.++.+...
T Consensus        12 l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   83 (90)
T 2dnp_A           12 IFVGNVSAACTSQELRSLFERRGRVIECDVVK------DYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTKGQK   83 (90)
T ss_dssp             EEEESCCTTCCHHHHHHHHHHHSCEEEEEECS------SCEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCCCCC
T ss_pred             EEEeCCCCCCCHHHHHHHHHcCCCEEEEEEEC------CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEECCCCCC
Confidence            89999999998   999999999999999864      5999999999999999999999999999999999987654

>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=99.71  E-value=1.7e-17  Score=105.81  Aligned_cols=71  Identities=21%  Similarity=0.306  Sum_probs=66.5

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS   75 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~   75 (136)
                      |||+|||..++   |+++|++||.|.++.+++   .++|||||+|.+.++|+.|+..|||..+.|++|+|.++.++.
T Consensus        76 l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~---~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  149 (150)
T 2i2y_A           76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVAR---NPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGEK  149 (150)
T ss_dssp             EEEESCCSCCSCHHHHHHHHHHSCEEEEEECS---SSCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECCCCC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhhCCEEEEEEee---CCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcCCCC
Confidence            89999999998   999999999999999876   378999999999999999999999999999999999998764

>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=99.71  E-value=4.6e-17  Score=97.55  Aligned_cols=70  Identities=26%  Similarity=0.476  Sum_probs=64.8

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES   77 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~~   77 (136)
                      |||+|||..++   |+++|++||.|.++.+++      |||||+|.+.++|++|+..||+..+.|++|.|.++.++...
T Consensus        14 l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~~------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~   86 (103)
T 2dgu_A           14 LFVRNLANTVTEEILEKAFSQFGKLERVKKLK------DYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPPDQK   86 (103)
T ss_dssp             EEEECCCTTCCHHHHHHHHHHHSCEEEEEECS------SCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCCCCC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEC------CEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEcCCCccc
Confidence            89999999998   999999999999998864      79999999999999999999999999999999999876543

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.71  E-value=1.2e-18  Score=104.11  Aligned_cols=73  Identities=21%  Similarity=0.332  Sum_probs=66.5

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||.|.. .++.  .+++++|||||+|.+.++|++|+. +||..+.|+.|.|.++.++..
T Consensus        20 l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~a~~~~~   97 (101)
T 1fj7_A           20 LFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKGRDG   97 (101)
T ss_dssp             EEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEECCSCCCC
T ss_pred             EEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEEcCCCCC
Confidence            79999999999   9999999999887 4444  678999999999999999999998 999999999999999987654

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.55  E-value=6.7e-19  Score=107.79  Aligned_cols=76  Identities=20%  Similarity=0.260  Sum_probs=70.0

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeE--------EEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEE
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEI--------CVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKV   68 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~--------~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v   68 (136)
                      |||+|||..++   |+++|++||.|..        +.++.  .+++++|||||+|.+.++|+.|+..|||..+.|++|.|
T Consensus        10 l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V   89 (116)
T 2lcw_A           10 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKV   89 (116)
Confidence            79999999998   9999999999988        87877  67899999999999999999999999999999999999


Q ss_pred             EeeCCCCCC
Q psy6353          69 SYARPSSES   77 (136)
Q Consensus        69 ~~~~~~~~~   77 (136)
                      .++.++...
T Consensus        90 ~~a~~~~~~   98 (116)
T 2lcw_A           90 SFATRRADF   98 (116)
Confidence            999876543

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=1.3e-16  Score=95.30  Aligned_cols=73  Identities=22%  Similarity=0.398  Sum_probs=64.7

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|+.|+   .+.++.  .+++++|||||+|.+.++|+.|+..|||..+.|+.|.|.++.++..
T Consensus        18 l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~   94 (102)
T 2fc8_A           18 LFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGE   94 (102)
T ss_dssp             EEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCCCS
T ss_pred             EEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEecCCCC
Confidence            89999999998   777777663   666666  6899999999999999999999999999999999999999998765


Q ss_pred             C
Q psy6353          77 S   77 (136)
Q Consensus        77 ~   77 (136)
                      .
T Consensus        95 ~   95 (102)
T 2fc8_A           95 G   95 (102)
T ss_dssp             S
T ss_pred             C
Confidence            3

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.71  E-value=1.2e-17  Score=99.90  Aligned_cols=72  Identities=18%  Similarity=0.323  Sum_probs=67.4

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS   75 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~   75 (136)
                      |||+|||..++   |+++|++||.|.++.++. .+|+++|||||+|.+.++|+.|+.  ++..++|+.|.|.++.++.
T Consensus        12 l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~a~~~~   87 (102)
T 2xs2_A           12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPAIRKQ   87 (102)
T ss_dssp             EEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEEEEECC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEECCcCc
Confidence            79999999998   999999999999999999 889999999999999999999999  8999999999998887654

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=1.3e-16  Score=94.90  Aligned_cols=69  Identities=29%  Similarity=0.393  Sum_probs=63.8

Q ss_pred             eeecCCChhhh---HHHHhccC--CCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGF--SDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~--G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++|  |.|..+.++      +|||||+|.+.++|+.|+..|||..+.|++|+|.++.++..
T Consensus        18 l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~   91 (99)
T 2cpd_A           18 LYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI------RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDK   91 (99)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC------SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCCCC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEECCCCCC
Confidence            89999999998   99999999  899888764      58999999999999999999999999999999999988754

>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=99.70  E-value=2e-17  Score=104.68  Aligned_cols=74  Identities=22%  Similarity=0.293  Sum_probs=65.9

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEE------EEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEee
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEIC------VFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA   71 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~------~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~   71 (136)
                      |||+|||..++   |+++|++||.|..+      .+.. .+|+++|||||+|.+.++|..|+..|||..+.|++|.|.++
T Consensus        48 l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a  127 (143)
T 3egn_A           48 IYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFA  127 (143)
T ss_dssp             EEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEECEEEEC
T ss_pred             EEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEEC
Confidence            89999999998   99999999998764      1222 67899999999999999999999999999999999999999


Q ss_pred             CCCC
Q psy6353          72 RPSS   75 (136)
Q Consensus        72 ~~~~   75 (136)
                      .+..
T Consensus       128 ~~~~  131 (143)
T 3egn_A          128 RSAR  131 (143)
T ss_dssp             CCSC
T ss_pred             CCCC
Confidence            7654

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.70  E-value=2.7e-17  Score=107.64  Aligned_cols=74  Identities=18%  Similarity=0.274  Sum_probs=69.9

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS   75 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~   75 (136)
                      |||+|||..++   |+++|++||+|.+|.++. .++.++|||||+|.+.++|+.|+..+||..+.|++|+|.++.+..
T Consensus        91 l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~a~~~~  168 (177)
T 2f3j_A           91 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQI  168 (177)
T ss_dssp             EEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEEESSGG
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEecCCC
Confidence            89999999988   999999999999999998 889999999999999999999999999999999999999987653

>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=99.70  E-value=7.9e-17  Score=95.63  Aligned_cols=68  Identities=10%  Similarity=0.155  Sum_probs=63.0

Q ss_pred             eeecCCCh-hhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCC
Q psy6353           2 VYQTLLNK-LFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS   75 (136)
Q Consensus         2 v~v~nl~~-~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~   75 (136)
                      |||+|||. .++   |+++|++||.|.++.+.      +|||||+|.+.++|+.|+..+||..+.|++|+|.++.++.
T Consensus        25 l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~   96 (97)
T 2xnq_A           25 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSSNA   96 (97)
T ss_dssp             EEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC------SSEEEEEESSHHHHHHHHHHHTTSEETTEECEEEECCCCC
T ss_pred             EEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCCCC
Confidence            79999997 888   99999999999999873      6999999999999999999999999999999999987653

>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=99.70  E-value=3e-17  Score=105.51  Aligned_cols=72  Identities=17%  Similarity=0.242  Sum_probs=65.3

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCC--ceEEEEeeCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQN--KTIKVSYARPSS   75 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g--~~l~v~~~~~~~   75 (136)
                      |||+||+..++   |+++|++||+|.+|.+..  +.++|||||+|.+.++|+.|+..|||..|.|  ++|+|.+++++.
T Consensus        49 l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~--k~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~Ak~~~  125 (164)
T 1sjr_A           49 IIVENLFYPVTLDVLHQIFSKFGTVLKIITFT--KNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTS  125 (164)
T ss_dssp             EEECSCCSCCCHHHHHHHHHHHSCEEEEEEEE--SSSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEECSSSS
T ss_pred             EEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEe--CCCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEecCCc
Confidence            79999999988   999999999999999864  3367999999999999999999999999965  999999998764

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=1.4e-17  Score=102.93  Aligned_cols=71  Identities=18%  Similarity=0.099  Sum_probs=65.0

Q ss_pred             eeecCCChhhh---HHHHhccCCCe----eEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDA----EICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP   73 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v----~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~   73 (136)
                      |||+|||..+|   |+++|++||+|    ..|.++. .+|+++|||||+|.+.++|++|+.. |+..++|+.|.|..+.+
T Consensus        26 v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~V~~a~~  104 (123)
T 2dha_A           26 VRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIELFRSTA  104 (123)
T ss_dssp             EEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEECCEEECH
T ss_pred             EEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEEEEECCH
Confidence            89999999998   99999999975    6899988 8899999999999999999999996 99999999999887643

>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=99.70  E-value=6.4e-18  Score=102.06  Aligned_cols=71  Identities=13%  Similarity=0.114  Sum_probs=66.2

Q ss_pred             eeecCCChhhh---HHHHhccCCC---eeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSD---AEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP   73 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~---v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~   73 (136)
                      |||+|||..+|   |+++|++||.   |.++.++. ..|+++|||||+|.+.++|++|+. +|+..++|+.|.|.++.+
T Consensus        14 l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~a~~   91 (107)
T 2lmi_A           14 IRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVEVYEINN   91 (107)
T ss_dssp             EEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCCCEECCH
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEEEEECCH
Confidence            89999999999   9999999998   89999998 569999999999999999999999 999999999999988764

>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=1.1e-16  Score=107.01  Aligned_cols=75  Identities=19%  Similarity=0.413  Sum_probs=70.6

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||.|..+.+++  .+|+++|||||+|.+.++|.+|+..|||..++|++|.|.++.++..
T Consensus       128 l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a~~~~~  207 (216)
T 2qfj_A          128 IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPM  207 (216)
T ss_dssp             EEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEECSSCSS
T ss_pred             EEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEecCCCC
Confidence            79999999998   999999999999999998  6899999999999999999999999999999999999999987653

>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=99.70  E-value=4.6e-17  Score=95.79  Aligned_cols=71  Identities=28%  Similarity=0.360  Sum_probs=63.8

Q ss_pred             eeecCCChhhh---HHHHhccCCC-eeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcC-ceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSD-AEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNG-LRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~-v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~-~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||. +..+.+.     ++|||||+|.+.++|+.|+..+|| ..+.|++|+|.++.++..
T Consensus        11 l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~~~   85 (93)
T 2cqh_A           11 LYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-----KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKL   85 (93)
T ss_dssp             EEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-----ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCCC
T ss_pred             EEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-----CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEEEccCccc
Confidence            89999999998   9999999999 6666553     589999999999999999999999 999999999999988754


Q ss_pred             C
Q psy6353          77 S   77 (136)
Q Consensus        77 ~   77 (136)
                      .
T Consensus        86 ~   86 (93)
T 2cqh_A           86 R   86 (93)
T ss_dssp             C
T ss_pred             c
Confidence            3

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.70  E-value=1.1e-16  Score=98.89  Aligned_cols=70  Identities=24%  Similarity=0.240  Sum_probs=63.1

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceee-EEEEcCCHHHHHHHHHHHcCceeCC--ceEEEEeeCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGY-GFVNYHRPEDAEKAINTLNGLRLQN--KTIKVSYARPSS   75 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~-~fv~f~~~~~a~~a~~~~~~~~~~g--~~l~v~~~~~~~   75 (136)
                      |||+||+..++   |+++|++||.|.+|.+..   + .|+ |||+|.+.++|+.|+..|||..|.|  ++|+|.+++++.
T Consensus        28 l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~---~-~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~Ak~~~  103 (124)
T 2e5i_A           28 LSIQNPLYPITVDVLYTVCNPVGKVQRIVIFK---R-NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPTR  103 (124)
T ss_dssp             EEEESCCSCCCHHHHHHHHTTTSCEEEEEEEE---S-SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCSCSC
T ss_pred             EEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEe---C-CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEecCCc
Confidence            78999999988   999999999999999865   2 386 9999999999999999999999987  689999998764

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A

Probab=99.69  E-value=7.6e-17  Score=104.31  Aligned_cols=71  Identities=24%  Similarity=0.371  Sum_probs=67.4

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR   72 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~   72 (136)
                      |||+|||..++   |+++|++||+|.++.+++  .+|.++|||||+|.+.++|++|+..|||..++|++|.|.++.
T Consensus        97 l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~As  172 (172)
T 2g4b_A           97 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS  172 (172)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             EEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeCC
Confidence            89999999998   999999999999999988  589999999999999999999999999999999999999863

>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=99.69  E-value=5.7e-17  Score=119.17  Aligned_cols=74  Identities=15%  Similarity=0.302  Sum_probs=70.3

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS   75 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~   75 (136)
                      |||+|||..+|   |.++|++||.|..|.|+.  .+++++|||||+|.+.++|.+|+..|||..|.|+.|.|.++.+..
T Consensus       105 lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a~~~~  183 (437)
T 3pgw_S          105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERGRT  183 (437)
T ss_pred             EEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEeCCCC
Confidence            89999999998   999999999999999988  689999999999999999999999999999999999999998654

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.69  E-value=6.8e-17  Score=95.66  Aligned_cols=69  Identities=10%  Similarity=0.170  Sum_probs=63.7

Q ss_pred             eeecCCCh-hhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNK-LFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~-~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||. .++   |+++|++||+|.++.+.      +|||||+|.+.++|+.|+..|||..+.|++|.|.++.+...
T Consensus        13 l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~   85 (96)
T 2kvi_A           13 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSNAR   85 (96)
T ss_dssp             EEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEEEECCCC
T ss_pred             EEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEcCcCCC
Confidence            79999998 888   99999999999999884      59999999999999999999999999999999999876644

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.69  E-value=5.7e-17  Score=94.52  Aligned_cols=67  Identities=15%  Similarity=0.157  Sum_probs=60.8

Q ss_pred             eeecCCChhhh-------HHHHhccCC-CeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCC
Q psy6353           2 VYQTLLNKLFT-------YEKVHLGFS-DAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP   73 (136)
Q Consensus         2 v~v~nl~~~~~-------l~~~f~~~G-~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~   73 (136)
                      |||.|||..++       |+++|++|| +|.+|     ++   |+|||.|.+.++|++|++.|||..+.||+|+|.+++.
T Consensus        12 lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-----tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v~~A~~   83 (96)
T 2diu_A           12 LYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-----TG---CSAILRFINQDSAERAQKRMENEDVFGNRIIVSFTPK   83 (96)
T ss_dssp             EEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-----CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSCCEEESSCC
T ss_pred             EEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-----ec---CEEEEEECCHHHHHHHHHHhcCCccCCceEEEEecCC
Confidence            79999999998       668999995 99888     23   9999999999999999999999999999999999987


Q ss_pred             CCC
Q psy6353          74 SSE   76 (136)
Q Consensus        74 ~~~   76 (136)
                      +.+
T Consensus        84 ~sd   86 (96)
T 2diu_A           84 NRE   86 (96)
T ss_dssp             SCC
T ss_pred             Ccc
Confidence            654

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=99.69  E-value=3.3e-17  Score=105.56  Aligned_cols=72  Identities=17%  Similarity=0.379  Sum_probs=68.3

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS   74 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~   74 (136)
                      |||+|||..++   |+++|++||.|.++.++.  .+|.++|||||+|.+.++|++|+. +||..+.|++|.|.++.|+
T Consensus        90 l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a~pk  166 (167)
T 2cjk_A           90 IFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAEPR  166 (167)
T ss_dssp             EEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEECCCC
T ss_pred             EEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeecCCC
Confidence            79999999998   999999999999999988  679999999999999999999998 8999999999999999876

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.69  E-value=5e-17  Score=99.93  Aligned_cols=72  Identities=11%  Similarity=0.077  Sum_probs=63.3

Q ss_pred             eeecCC----Chhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCC----HHH----HHHHHH--HHcCceeC
Q psy6353           2 VYQTLL----NKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHR----PED----AEKAIN--TLNGLRLQ   62 (136)
Q Consensus         2 v~v~nl----~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~----~~~----a~~a~~--~~~~~~~~   62 (136)
                      |||+||    |..++   |+++|++||+|.++.++.  .||.++|||||+|.+    +++    |..|+.  .+||..+.
T Consensus         5 I~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~I~   84 (136)
T 2j8a_A            5 IVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCFIM   84 (136)
T ss_dssp             EEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEEET
T ss_pred             EEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCeec
Confidence            799999    99888   999999999999999999  899999999999996    433    778877  78999999


Q ss_pred             CceEEEEeeCC
Q psy6353          63 NKTIKVSYARP   73 (136)
Q Consensus        63 g~~l~v~~~~~   73 (136)
                      |++|+|...+.
T Consensus        85 Gr~irV~ln~~   95 (136)
T 2j8a_A           85 GFKFEVILNKH   95 (136)
T ss_dssp             TEEEEEEECCT
T ss_pred             CcEEEEEECcc
Confidence            99999987653

>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=99.69  E-value=7.6e-17  Score=97.68  Aligned_cols=68  Identities=25%  Similarity=0.388  Sum_probs=63.3

Q ss_pred             eeecCCChh-hh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCC
Q psy6353           2 VYQTLLNKL-FT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS   75 (136)
Q Consensus         2 v~v~nl~~~-~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~   75 (136)
                      |||+|||.. ++   |+++|++||+|.++.+      ++|||||+|.+.++|+.|+..|||..+.|++|+|.++.+..
T Consensus        30 l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~  101 (110)
T 1wf1_A           30 VFIGNLNTALVKKSDVETIFSKYGRVAGCSV------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEPK  101 (110)
T ss_dssp             EEECSCCCSSCCHHHHHHHHGGGSCCSEEEE------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEESCCCC
T ss_pred             EEEeCCCcccCCHHHHHHHHHhCCCeEEEEE------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCCCC
Confidence            799999998 87   9999999999999988      56999999999999999999999999999999999998544

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.68  E-value=1.2e-16  Score=105.52  Aligned_cols=75  Identities=23%  Similarity=0.356  Sum_probs=70.6

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||.|.++.+++  .+|.++|||||+|.+.++|+.|+..|||..+.|++|.|.++.++..
T Consensus       117 l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  196 (198)
T 2yh0_A          117 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAK  196 (198)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEESCCCCC
T ss_pred             EEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCC
Confidence            79999999988   999999999999999988  5899999999999999999999999999999999999999988654

>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=99.68  E-value=1.4e-17  Score=104.97  Aligned_cols=72  Identities=15%  Similarity=0.090  Sum_probs=66.2

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS   75 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~   75 (136)
                      |||+|||..+|   |+++|++|| +.+|.++. .+++++|||||+|.+.++|++|+ ++|+..+.|+.|.|..+.+..
T Consensus        49 lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~a~~~~  124 (139)
T 2hgn_A           49 VHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLNSTTG  124 (139)
T ss_dssp             EECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSSSCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEECCCSC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCCCCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEECCCCC
Confidence            89999999999   999999999 66999988 66999999999999999999999 689999999999998887654

>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=99.68  E-value=1.6e-16  Score=92.56  Aligned_cols=68  Identities=16%  Similarity=0.221  Sum_probs=63.3

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS   74 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~   74 (136)
                      |||+|||..++   |+++|++| +|.++.+.    +++|||||+|.+.++|+.|+..+||..+.|++|+|.++...
T Consensus         8 l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~----~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~   78 (88)
T 1wg1_A            8 ILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD----RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTD   78 (88)
T ss_dssp             EEEESCCSSCCHHHHHHHTCSS-CCCCEEEE----GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCC
T ss_pred             EEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe----CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcCCC
Confidence            89999999998   99999999 99999885    68999999999999999999999999999999999998654

>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=99.67  E-value=2.3e-16  Score=104.03  Aligned_cols=75  Identities=11%  Similarity=0.217  Sum_probs=66.6

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||.|..+.++.  .+|.++|||||+|.+.++|.+|+.. +|..+.|+.|.|.++.++.+
T Consensus       107 l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~a~~k~~  185 (196)
T 1l3k_A          107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKALSKQE  185 (196)
T ss_dssp             EEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEECC----
T ss_pred             EEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEecCChhH
Confidence            79999999998   999999999999999998  5899999999999999999999986 89999999999999988765


Q ss_pred             C
Q psy6353          77 S   77 (136)
Q Consensus        77 ~   77 (136)
                      .
T Consensus       186 ~  186 (196)
T 1l3k_A          186 M  186 (196)
T ss_dssp             -
T ss_pred             h
Confidence            3

>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=99.67  E-value=1.1e-16  Score=97.20  Aligned_cols=70  Identities=19%  Similarity=0.217  Sum_probs=62.0

Q ss_pred             eee--cCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCcee-----CCceEEEEee
Q psy6353           2 VYQ--TLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRL-----QNKTIKVSYA   71 (136)
Q Consensus         2 v~v--~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~-----~g~~l~v~~~   71 (136)
                      |||  +||+..++   |+++|++||.|.++.++.    ++|||||+|.+.++|++|+.+|||..+     .|++|.+.++
T Consensus        28 L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~----~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~l~v~~a  103 (114)
T 2cq2_A           28 LVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP----NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFV  103 (114)
T ss_dssp             EEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT----TCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEEEE
T ss_pred             EEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC----CCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcEEEEEec
Confidence            799  67999888   999999999999987753    489999999999999999999999988     6889999887


Q ss_pred             CCCC
Q psy6353          72 RPSS   75 (136)
Q Consensus        72 ~~~~   75 (136)
                      ...+
T Consensus       104 ~~~p  107 (114)
T 2cq2_A          104 EKVQ  107 (114)
T ss_dssp             SCCC
T ss_pred             ccCc
Confidence            7544

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.67  E-value=9.8e-18  Score=105.26  Aligned_cols=98  Identities=18%  Similarity=0.241  Sum_probs=58.9

Q ss_pred             eeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCCCCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCC
Q psy6353          37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDN  116 (136)
Q Consensus        37 g~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~  116 (136)
                      -++|.++.+...+..|+..++|-...|+. ...+..+.......++|||+|||..+|+++|+++|++||.|..+.++.++
T Consensus         5 ~~~~~~~~~~~~~~~a~~~~~g~~~~g~~-~~~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~   83 (135)
T 2lea_A            5 HHHHHHSSGLVPRGSHMASMTGGQQMGRG-SMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDR   83 (135)
T ss_dssp             -------------------------------CCSCCSCSSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCS
T ss_pred             ccccccccCCCchhhhhhhccCCCCCCCC-CCCcCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecC
Confidence            35778888888888899888876655543 33455666666678899999999999999999999999999999999998


Q ss_pred             CCCCc-cceEeecCcccccc
Q psy6353         117 LATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus       117 ~~~~~-~~~fv~f~~~e~~~  135 (136)
                      .++.. +.+||+|.+.|+|.
T Consensus        84 ~~g~~~G~afV~F~~~~~A~  103 (135)
T 2lea_A           84 YTKESRGFAFVRFHDKRDAE  103 (135)
T ss_dssp             SSSSCCSCCEEECSCHHHHH
T ss_pred             CCCccceEEEEEECCHHHHH
Confidence            77776 55999999999875

>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=99.67  E-value=2.4e-16  Score=92.12  Aligned_cols=68  Identities=15%  Similarity=0.248  Sum_probs=56.8

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCce--eCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLR--LQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~--~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||+|.++.+++   .++|||||+|.+.++|++    +++..  +.|+.+.+.++.++..
T Consensus        14 l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~---~srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v~~a~~k~~   86 (89)
T 3d2w_A           14 VFVGRCTEDMTAEELQQFFCQYGEVVDVFIPK---PFRAFAFVTFADDKVAQS----LCGEDLIIKGISVHISNAEPKHN   86 (89)
T ss_dssp             EEEESCCTTCCHHHHHHHHTTTSCEEEEECCS---SCCSEEEEEESCHHHHHH----HTTCEEEETTEEEEEEECC----
T ss_pred             EEEeCCCCCCCHHHHHHHHhccCCEEEEEEee---CCCCEEEEEECCHHHHHH----HcCCCcccCCEEEEEEEcCCCCc
Confidence            79999999999   999999999999999876   589999999999999883    55544  5699999999987654

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=99.67  E-value=2.7e-16  Score=101.78  Aligned_cols=71  Identities=21%  Similarity=0.352  Sum_probs=65.9

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeC---CceEEEEeeC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQ---NKTIKVSYAR   72 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~---g~~l~v~~~~   72 (136)
                      |||+|||..++   |+++|++||.|.++.+++ .+|+++|||||+|.+.++|.+|+..|||..+.   +++|.|.++.
T Consensus        98 l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V~~ad  175 (175)
T 3nmr_A           98 LFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFAD  175 (175)
T ss_dssp             EEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEEEECC
T ss_pred             EEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEEEecC
Confidence            79999999998   999999999999999999 78999999999999999999999999998776   4999998863

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=6.5e-16  Score=91.55  Aligned_cols=71  Identities=23%  Similarity=0.264  Sum_probs=62.5

Q ss_pred             eeecCCChhhh-HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT-YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~-l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+||+-.-. |+++|++||+|.++.+.    +++|||||+|.+.++|++|+..|||..+.|++|+|.++.++..
T Consensus        18 l~V~n~~~t~~~l~~~F~~~G~i~~v~i~----~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~~~~   89 (97)
T 1x5p_A           18 LYVYGEDMTPTLLRGAFSPFGNIIDLSMD----PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQPM   89 (97)
T ss_dssp             EEEECSSCCHHHHHHHHTTTSCEEEEEEE----TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECCSSCCC
T ss_pred             EEEcCCCCCHHHHHHHHhhCCCEEEEEec----CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCCCCC
Confidence            79999732222 99999999999999885    5789999999999999999999999999999999999987654

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.66  E-value=4.9e-16  Score=93.46  Aligned_cols=72  Identities=18%  Similarity=0.227  Sum_probs=62.0

Q ss_pred             eeecCCCh------hhh--HHHHhccCCCeeEEEEEc-c--CCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEe
Q psy6353           2 VYQTLLNK------LFT--YEKVHLGFSDAEICVFLI-S--TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY   70 (136)
Q Consensus         2 v~v~nl~~------~~~--l~~~f~~~G~v~~~~~~~-~--~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~   70 (136)
                      |++.|+..      ...  |++.|++||+|.++.+++ .  +++++|+|||+|.+.++|++|+..|||..+.||+|.+.+
T Consensus        11 l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~i~v~~   90 (105)
T 2pe8_A           11 VLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVVKACF   90 (105)
T ss_dssp             EEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             EEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcEEEEEE
Confidence            56677752      122  899999999999999988 2  368999999999999999999999999999999999998


Q ss_pred             eCC
Q psy6353          71 ARP   73 (136)
Q Consensus        71 ~~~   73 (136)
                      +.+
T Consensus        91 a~~   93 (105)
T 2pe8_A           91 YNL   93 (105)
T ss_dssp             CCH
T ss_pred             cCH
Confidence            764

>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=99.66  E-value=3.6e-16  Score=103.56  Aligned_cols=71  Identities=15%  Similarity=0.075  Sum_probs=65.5

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP   73 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~   73 (136)
                      |||+|||..++   |+++|++||+|.++.+++ .+++++|||||+|.+.++|+.|+..+ +..+.|++|.|.+...
T Consensus       112 l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~Gr~l~V~~~~~  186 (193)
T 2voo_A          112 VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKDD  186 (193)
T ss_dssp             EEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESSHHHHHHHHHCT-TCEETTEECEEEETTT
T ss_pred             EEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHhC-CCeECCEEEEEEEhHH
Confidence            79999999998   999999999999999998 77999999999999999999999865 5699999999998764

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.66  E-value=3.7e-16  Score=92.11  Aligned_cols=70  Identities=10%  Similarity=0.126  Sum_probs=61.9

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||+|.+| +.. .+++   ||||+|.+.++|++|+. +||..+.|+.|.|.++.++..
T Consensus        11 l~V~nl~~~~t~~~l~~~F~~~G~v~~v-~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a~~~~~   84 (94)
T 2e5g_A           11 VFVSGFPRGVDSAQLSEYFLAFGPVASV-VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPREQKEF   84 (94)
T ss_dssp             EEEECCCTTCCHHHHHHHGGGTSCEEEE-EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECCCBCSCCSCC
T ss_pred             EEEECCCCCCCHHHHHHHHHhcCCeEEE-EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEECCcCCC
Confidence            89999999998   99999999999988 433 4554   99999999999999999 999999999999998876543

>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=99.65  E-value=6.2e-16  Score=99.53  Aligned_cols=70  Identities=26%  Similarity=0.382  Sum_probs=65.7

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCC--ceEEEEee
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQN--KTIKVSYA   71 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g--~~l~v~~~   71 (136)
                      |||+|||..++   |+++|++||.|..+.+++  .+++++|||||+|.+.++|..|+..+||..+.|  ++|+|.++
T Consensus        92 l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A           92 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA  168 (168)
T ss_dssp             EEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             EEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEEEeC
Confidence            79999999998   999999999999999988  589999999999999999999999999999987  99999875

>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=99.65  E-value=1.9e-16  Score=94.38  Aligned_cols=58  Identities=29%  Similarity=0.455  Sum_probs=53.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCcc-ceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENG-KYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~-~~fv~f~~~e~~~  135 (136)
                      ..+++|||+|||+++|+++|+++|++||+|.++++++|+.+|.++ .|||+|.+.|+|.
T Consensus        17 ~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~   75 (99)
T 4fxv_A           17 FQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAE   75 (99)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHH
Confidence            357899999999999999999999999999999999999888875 5999999999875

>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=99.65  E-value=3.5e-16  Score=95.56  Aligned_cols=69  Identities=22%  Similarity=0.241  Sum_probs=60.7

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCce-----EEEEeeCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKT-----IKVSYARP   73 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~-----l~v~~~~~   73 (136)
                      |||+|||..++   |+++|++||+|..+.++..     |||||+|.+.++|+.|++.|||..+.|+.     +++..+.+
T Consensus        19 l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-----g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~v~~~~~   93 (115)
T 3beg_B           19 VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-----GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGP   93 (115)
T ss_dssp             EEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-----SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEECC-
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-----CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEEeccCCC
Confidence            89999999998   9999999999999998752     99999999999999999999999999988     77776665


Q ss_pred             CC
Q psy6353          74 SS   75 (136)
Q Consensus        74 ~~   75 (136)
                      ..
T Consensus        94 ~~   95 (115)
T 3beg_B           94 RS   95 (115)
T ss_dssp             --
T ss_pred             CC
Confidence            43

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.65  E-value=5.7e-16  Score=100.56  Aligned_cols=70  Identities=16%  Similarity=0.313  Sum_probs=65.1

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS   74 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~   74 (136)
                      |||+|||..++   |+++|++||.|..+   ..++.++|||||+|.+.++|.+|+..|||..+.|++|.|.++.|+
T Consensus       102 l~v~nlp~~~t~~~l~~~F~~~g~v~~~---~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~k  174 (175)
T 1fje_B          102 LLAKNLSFNITEDELKEVFEDALEIRLV---SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK  174 (175)
T ss_dssp             EEEESCCSSCCHHHHHHHCTTCSEEEEE---CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEECSSC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCeEEEe---cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEecCCC
Confidence            79999999998   99999999988766   577889999999999999999999999999999999999999876

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.65  E-value=3.2e-16  Score=95.58  Aligned_cols=67  Identities=12%  Similarity=0.097  Sum_probs=56.9

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cC---CCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEee
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--ST---AQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA   71 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~---~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~   71 (136)
                      |||+|||..++   |+++|++||+|. +.++.  .+   |+++|||||+|.+.++|++|+..++  .++|+.+.+..+
T Consensus        11 lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~~~~~   85 (114)
T 2dnl_A           11 VFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYLCVSS   85 (114)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEEEECC
T ss_pred             EEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEEeccC
Confidence            89999999998   999999999998 76666  34   7999999999999999999999883  366766666543

>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=99.64  E-value=1e-16  Score=99.32  Aligned_cols=70  Identities=21%  Similarity=0.185  Sum_probs=63.4

Q ss_pred             eeecCCChhhh---HHHHhccCCCee--EEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAE--ICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP   73 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~--~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~   73 (136)
                      |||+|||..+|   |+++|++| .|.  +|.++. ..|+++|||||+|.+.++|++|+.. ++..+.||.|.|..+.+
T Consensus        45 lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~~-~~~~l~gR~I~V~~a~~  120 (126)
T 2hgm_A           45 VRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGK-HKERIGHRYIEVFKSSQ  120 (126)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHTT-TTCCBTTBCCCCEEECH
T ss_pred             EEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHHH-CCCEECCEEEEEEECCH
Confidence            89999999999   99999999 566  899888 6699999999999999999999994 78999999999987754

>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=99.64  E-value=3.1e-16  Score=94.20  Aligned_cols=59  Identities=22%  Similarity=0.243  Sum_probs=54.2

Q ss_pred             HHHHh-ccCCCeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEee
Q psy6353          13 YEKVH-LGFSDAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA   71 (136)
Q Consensus        13 l~~~f-~~~G~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~   71 (136)
                      |++.| ++||+|.++.+++ .+++++|||||+|.+.++|++|+..|||..+.||+|.+.++
T Consensus        43 l~~~f~~~~G~V~~v~i~~~~~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i~v~~s  103 (104)
T 1jmt_A           43 VFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             HHHHhhccCCceEEEEEEeCCCCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEEEEEEc
Confidence            44555 9999999999999 67899999999999999999999999999999999999875

>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=99.64  E-value=9.4e-16  Score=98.45  Aligned_cols=70  Identities=31%  Similarity=0.477  Sum_probs=64.5

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCce--EEEEee
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKT--IKVSYA   71 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~--l~v~~~   71 (136)
                      |||+|||..++   |+++|++||.|..+.++.  .+|.++|||||+|.+.++|.+|+..|||..+.|+.  |+|.++
T Consensus        91 l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v~~A  167 (167)
T 1fxl_A           91 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA  167 (167)
T ss_dssp             EEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             EEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEEEeC
Confidence            79999999988   999999999999999988  58999999999999999999999999999999965  777764

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.64  E-value=3.3e-16  Score=92.54  Aligned_cols=72  Identities=21%  Similarity=0.334  Sum_probs=63.3

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEE-EEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICV-FLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS   75 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~-~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~   75 (136)
                      |||+|||..++   |+++|++||+|.++. ++...  ..|.|||+|.+.++|+.|+..|||..+.|++|.|.++.++.
T Consensus        18 l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~--~~~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~~   93 (96)
T 2e44_A           18 LQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDS--ETAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYIPDEM   93 (96)
T ss_dssp             EEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSS--SSEEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEECCCCC
T ss_pred             EEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCC--CCCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCccc
Confidence            89999999998   999999999999994 66521  22339999999999999999999999999999999998873

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.63  E-value=8.1e-16  Score=104.62  Aligned_cols=70  Identities=19%  Similarity=0.278  Sum_probs=63.1

Q ss_pred             eeecCCChhh---------h---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCcee--------
Q psy6353           2 VYQTLLNKLF---------T---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRL--------   61 (136)
Q Consensus         2 v~v~nl~~~~---------~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~--------   61 (136)
                      |||+||+..+         +   |+++|++||+|.+|.++.    ++|||||+|.+.++|+.|+.+|||..+        
T Consensus       137 LfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~----~kG~AFV~F~~~~~Ae~A~~am~g~~l~~~~~~e~  212 (240)
T 3u1l_A          137 LYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE----SKNCGFVKFKYQANAEFAKEAMSNQTLLLPSDKEW  212 (240)
T ss_dssp             EEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEG----GGTEEEEEESSHHHHHHHHHHHTTCCCCCTTSTTG
T ss_pred             eecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEEC----CCCEEEEEeCCHHHHHHHHHHhCCCEEeccccccc
Confidence            7999999886         4   999999999999999985    789999999999999999999999999        


Q ss_pred             ----CCceEEEEeeCCCC
Q psy6353          62 ----QNKTIKVSYARPSS   75 (136)
Q Consensus        62 ----~g~~l~v~~~~~~~   75 (136)
                          .|+.|.|.|+.+.+
T Consensus       213 ~~~~~gr~L~V~wA~~~p  230 (240)
T 3u1l_A          213 DDRREGTGLLVKWANEDP  230 (240)
T ss_dssp             GGGGGSCCCEEEECC---
T ss_pred             cccCCCCEEEEEEccCCC
Confidence                89999999998654

>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=99.62  E-value=5.2e-16  Score=90.37  Aligned_cols=71  Identities=15%  Similarity=0.206  Sum_probs=60.4

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES   77 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~~   77 (136)
                      |||+|||..++   |+++|++||+|.++.++.   .++|||||+|.+.++|+++...  ...+.|++|.+.++.++...
T Consensus         8 l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~---~~~g~afV~f~~~~~a~~~~~~--~~~~~g~~l~v~~a~~~~~~   81 (88)
T 1wf0_A            8 VFVGRCTGDMTEDELREFFSQYGDVMDVFIPK---PFRAFAFVTFADDQIAQSLCGE--DLIIKGISVHISNAEPKHNS   81 (88)
T ss_dssp             EEEESCCSSSCHHHHHHHSTTTSCCCEEECCS---SCCSCCEEECSCHHHHHHTTTC--EEEETTEEEEEECCCCCCCC
T ss_pred             EEEeCCCCCCCHHHHHHHHHHcCCeeEEEEec---CCCCEEEEEECCHHHHHHHhcC--CceeCCEEEEEEecCCCCCC
Confidence            89999999998   999999999999999875   4899999999999999865332  35568999999999877653

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A

Probab=99.62  E-value=9.1e-16  Score=88.98  Aligned_cols=64  Identities=11%  Similarity=0.225  Sum_probs=59.0

Q ss_pred             eeecCCChhhh---HHHHhccC----C-------CeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEE
Q psy6353           2 VYQTLLNKLFT---YEKVHLGF----S-------DAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIK   67 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~----G-------~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~   67 (136)
                      |||+|||..++   |+++|++|    |       +|.++.+.+    ++|||||+|.+.++|++|+ .+||..+.|++|+
T Consensus         9 l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~----~kg~afV~f~~~~~a~~A~-~l~g~~~~g~~l~   83 (87)
T 2hzc_A            9 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQ----DKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLK   83 (87)
T ss_dssp             EEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECS----SSSEEEEEESSHHHHHHHG-GGTTCEETTEECE
T ss_pred             EEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecC----CCcEEEEEcCCHHHHHHHH-hcCCCEECCeEEE
Confidence            79999999998   99999999    8       899888764    5899999999999999999 8999999999999


Q ss_pred             EEe
Q psy6353          68 VSY   70 (136)
Q Consensus        68 v~~   70 (136)
                      |+.
T Consensus        84 V~r   86 (87)
T 2hzc_A           84 IRR   86 (87)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            874

>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=99.59  E-value=3e-15  Score=86.82  Aligned_cols=60  Identities=17%  Similarity=0.349  Sum_probs=54.2

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          76 ESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        76 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      .....++|||+|||..+++++|+++|++||.|..+.+++++.++.+ +.|||+|.+.|+|.
T Consensus         7 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~   67 (87)
T 3s7r_A            7 NEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVE   67 (87)
T ss_dssp             CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHH
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHH
Confidence            3457789999999999999999999999999999999999888877 45999999999875

>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=99.59  E-value=7.3e-15  Score=89.99  Aligned_cols=60  Identities=17%  Similarity=0.208  Sum_probs=55.7

Q ss_pred             HHHHhccCCCeeEEEEEc-c-----CCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeC
Q psy6353          13 YEKVHLGFSDAEICVFLI-S-----TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR   72 (136)
Q Consensus        13 l~~~f~~~G~v~~~~~~~-~-----~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~   72 (136)
                      |++.|++||+|.++.+++ .     +++++|++||+|.+.++|.+|+..|||..+.||.|.+.++.
T Consensus        42 l~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~GR~i~v~~~~  107 (118)
T 3ue2_A           42 VTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYD  107 (118)
T ss_dssp             HHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             HHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECCcEEEEEEcC
Confidence            899999999999999998 2     35788999999999999999999999999999999998875

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.58  E-value=1.5e-16  Score=93.32  Aligned_cols=56  Identities=9%  Similarity=0.218  Sum_probs=51.2

Q ss_pred             CceEEEcCCCCCCCHHHHHHhhcCCC-ceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          80 GANLYVSGLPKHMSQQELESLFSPYG-RIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        80 ~~~l~v~nl~~~~t~~~l~~~f~~~G-~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      +++|||+|||+++|+++|+++|++|| +|.+|++++|+.+|.+ ++|||+|.+.|+|.
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~   58 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDAT   58 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHH
Confidence            36899999999999999999999999 8999999999988877 45999999999875

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.58  E-value=2.3e-15  Score=90.20  Aligned_cols=58  Identities=12%  Similarity=0.338  Sum_probs=52.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ...++|||+|||.++|+++|+++|++||+|.+|.+++++.+..+|.|||+|.+.|+|.
T Consensus         9 ~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~g~~rG~aFV~F~~~e~a~   66 (103)
T 1s79_A            9 VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAK   66 (103)
T ss_dssp             SGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHH
Confidence            4568999999999999999999999999999999999988444466999999999874

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.58  E-value=3.1e-15  Score=90.70  Aligned_cols=57  Identities=12%  Similarity=0.146  Sum_probs=52.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      +.++|||+|||..+++++|+++|++||.|.++.|++|+.++.+ +.|||+|.+.|+|.
T Consensus         5 p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~   62 (110)
T 3s8s_A            5 PLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAK   62 (110)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHH
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHH
Confidence            5689999999999999999999999999999999999998877 55999999999875

>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=99.58  E-value=1.5e-14  Score=87.81  Aligned_cols=62  Identities=18%  Similarity=0.263  Sum_probs=55.7

Q ss_pred             HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353          13 YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus        13 l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |+++|++||+|.++.+..  ..++|||||+|.+.++|++|+..|||..+.|++|.|.++.++.+
T Consensus        43 l~~~f~~~G~v~~v~i~~--~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~l~v~~a~~~~~  104 (112)
T 2dit_A           43 LRVECSKFGQIRKLLLFD--RHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGTTD  104 (112)
T ss_dssp             HHHHGGGTSCCSEEEEET--TCTTCEEEEECSCHHHHHHHHHHSTTCEETTEECEEEECCSCCC
T ss_pred             HHHHHHccCCEeEEEEec--CCCCEEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEeCCCCC
Confidence            899999999999996643  34899999999999999999999999999999999999987643

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.57  E-value=8.8e-16  Score=90.75  Aligned_cols=57  Identities=14%  Similarity=0.250  Sum_probs=50.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCc--eEEEEEEeCCCCCCcc-ceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGR--IITSRILCDNLATENG-KYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~--v~~~~i~~~~~~~~~~-~~fv~f~~~e~~~  135 (136)
                      .=.+|||+|||+.+|+++|+++|++||.  +.+|++++|+.+|.++ +|||+|.+.|+|.
T Consensus         8 ~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~   67 (95)
T 2lkz_A            8 HMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDAS   67 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHH
T ss_pred             ccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHH
Confidence            3468999999999999999999999995  5689999999988874 5999999999875

>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=99.56  E-value=1.1e-14  Score=87.50  Aligned_cols=61  Identities=18%  Similarity=0.260  Sum_probs=55.9

Q ss_pred             HHHHhccCCCeeEEEEEc-cC---CCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCC
Q psy6353          13 YEKVHLGFSDAEICVFLI-ST---AQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP   73 (136)
Q Consensus        13 l~~~f~~~G~v~~~~~~~-~~---~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~   73 (136)
                      |++.|++||+|.++.+++ ..   ++++|+|||+|.+.++|++|+.+|||..+.||+|++.++.+
T Consensus        32 l~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~~f~GR~i~v~~~~~   96 (105)
T 3v4m_A           32 VRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDP   96 (105)
T ss_dssp             HHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEECH
T ss_pred             HHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEeCH
Confidence            899999999999999998 32   46899999999999999999999999999999999998753

>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=1.8e-14  Score=97.55  Aligned_cols=70  Identities=13%  Similarity=0.178  Sum_probs=64.8

Q ss_pred             eeecCCChhhh---HHHHhccCC-CeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeC-CceEEEEeeCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFS-DAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQ-NKTIKVSYARPS   74 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G-~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~-g~~l~v~~~~~~   74 (136)
                      |||+|||..++   |+++|++|| .|..+.++.   .++|||||+|.+.++|.+|+..|||..+. |++|+|.++.++
T Consensus       154 l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~---~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~~  228 (229)
T 2adc_A          154 LHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ---KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  228 (229)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS---SSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             EEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEE---CCCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecCC
Confidence            89999999988   999999999 999999865   45799999999999999999999999999 999999999864

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.54  E-value=1.2e-14  Score=96.16  Aligned_cols=70  Identities=13%  Similarity=0.178  Sum_probs=64.7

Q ss_pred             eeecCCChhhh---HHHHhccCC-CeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeC-CceEEEEeeCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFS-DAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQ-NKTIKVSYARPS   74 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G-~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~-g~~l~v~~~~~~   74 (136)
                      |||+|||..++   |+++|++|| .|.++.++.   .++|+|||+|.+.++|..|+..+||..+. |++|+|.++.++
T Consensus       123 l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~---~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~  197 (198)
T 1qm9_A          123 LHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ---KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  197 (198)
T ss_dssp             EEECCCCTTCCHHHHHHHHHHTTSCCCEEEESS---TTSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECCC
T ss_pred             EEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEe---CCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeeccc
Confidence            79999999988   999999999 999999865   34799999999999999999999999999 999999999865

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.54  E-value=1.5e-14  Score=86.46  Aligned_cols=63  Identities=19%  Similarity=0.225  Sum_probs=55.5

Q ss_pred             CCCCCCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          73 PSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        73 ~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      +.......++|||+|||..+++++|+++|++||.|..+.++.++.++.+ +.|||+|.+.|+|.
T Consensus         6 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~   69 (103)
T 2dnm_A            6 SGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQ   69 (103)
T ss_dssp             CSSCCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHH
T ss_pred             CCCCCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHH
Confidence            3344557799999999999999999999999999999999999887776 56999999999875

>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=99.54  E-value=2.6e-14  Score=99.24  Aligned_cols=68  Identities=19%  Similarity=0.323  Sum_probs=63.2

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeC-CceEEEEeeC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQ-NKTIKVSYAR   72 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~-g~~l~v~~~~   72 (136)
                      |||+|||..++   |+++|++||.|.++.++.   ..+|||||+|.+.++|..|+..|||..+. |+.|+|.|++
T Consensus       210 l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~---~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          210 LFLTNLPEETNELMLSMLFNQFPGFKEVRLVP---GRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             EEEeCCCCcCCHHHHHHHHHhcCCeEEEEEec---CCCcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence            89999999998   999999999999999886   22689999999999999999999999999 9999999975

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.54  E-value=1.6e-14  Score=85.73  Aligned_cols=59  Identities=17%  Similarity=0.396  Sum_probs=53.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ....++|||+|||..+++++|+++|++||.|..+.+++++.++.. +.|||+|.+.|+|.
T Consensus         7 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~   66 (99)
T 2dgs_A            7 GSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVD   66 (99)
T ss_dssp             CSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHH
Confidence            456789999999999999999999999999999999999887776 56999999999875

>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=99.54  E-value=5e-15  Score=90.39  Aligned_cols=55  Identities=22%  Similarity=0.536  Sum_probs=49.9

Q ss_pred             CceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          80 GANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        80 ~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ..+|||+|||.++|+++|+++|++||.|.+|+|++|..+ .+++|||+|.+.|+|.
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~-~kg~afV~f~~~~~A~   59 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAE   59 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTE-EEEEEEEEESCHHHHH
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecCCC-CCceEEEEECCHHHHH
Confidence            468999999999999999999999999999999999754 4577999999999875

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.53  E-value=1.4e-14  Score=83.60  Aligned_cols=57  Identities=23%  Similarity=0.501  Sum_probs=52.4

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ..++|||+|||..+++++|+++|++||.|..+.++.++.++.. +.|||+|.+.|+|.
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~   61 (85)
T 1x4e_A            4 GSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQ   61 (85)
T ss_dssp             CCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHH
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHH
Confidence            5689999999999999999999999999999999999887776 55999999999875

>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=99.53  E-value=3.4e-14  Score=97.96  Aligned_cols=74  Identities=20%  Similarity=0.293  Sum_probs=67.1

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHc-CceeC---CceEEEEeeCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLN-GLRLQ---NKTIKVSYARP   73 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~-~~~~~---g~~l~v~~~~~   73 (136)
                      |||+|||..++   |+++|++||.|.++.++. .+|.++|||||+|.+.++|.+|+..+| +..+.   ++++.|.++.+
T Consensus        99 l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v~~~~~  178 (261)
T 3sde_A           99 LTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQ  178 (261)
T ss_dssp             EEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEEEECCC
T ss_pred             ccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEEeeccc
Confidence            79999999998   999999999999999999 899999999999999999999999995 55554   89999998876


Q ss_pred             CC
Q psy6353          74 SS   75 (136)
Q Consensus        74 ~~   75 (136)
                      ..
T Consensus       179 ~~  180 (261)
T 3sde_A          179 FD  180 (261)
T ss_dssp             EE
T ss_pred             cC
Confidence            54

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.53  E-value=1.6e-14  Score=86.33  Aligned_cols=62  Identities=21%  Similarity=0.367  Sum_probs=54.9

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          74 SSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        74 ~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ..+....++|||+|||..+++++|+++|++||.|..|.+++++.++.. +.|||+|.+.|+|.
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~   71 (103)
T 2cq0_A            9 NRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAA   71 (103)
T ss_dssp             CCCCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHH
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHH
Confidence            334557799999999999999999999999999999999999877776 45999999999874

>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=99.53  E-value=1.8e-14  Score=86.31  Aligned_cols=59  Identities=20%  Similarity=0.352  Sum_probs=52.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ....++|||+|||..+++++|+++|++||.|..+.++.++.+...+.|||+|.+.|+|.
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~   70 (105)
T 2dnh_A           12 GGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQ   70 (105)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHH
Confidence            34679999999999999999999999999999999999985444467999999999874

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.53  E-value=5.6e-15  Score=83.70  Aligned_cols=55  Identities=16%  Similarity=0.395  Sum_probs=50.4

Q ss_pred             ceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          81 ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        81 ~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ++|||+|||.++++++|+++|++||+|..+.+++++.++.+ +.|||+|.+.|+|.
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~   56 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVD   56 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHH
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHH
Confidence            47999999999999999999999999999999999887776 56999999999875

>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=99.53  E-value=1.4e-14  Score=96.74  Aligned_cols=70  Identities=10%  Similarity=0.105  Sum_probs=61.4

Q ss_pred             eeecCCChhhh---HHHHhccCCCe--eEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCc----eEEEEee
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDA--EICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNK----TIKVSYA   71 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v--~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~----~l~v~~~   71 (136)
                      |||+|||..++   |+++|++||.|  .+++++...+.++|+|||+|.+.++|..|+..|||..+.|+    ++.++++
T Consensus       126 l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~vk~~  204 (205)
T 3tyt_A          126 LHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKLC  204 (205)
T ss_dssp             EEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCCSSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEECEEE
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCCCCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceEEEec
Confidence            89999999998   99999999999  88988874466679999999999999999999999999876    5666553

>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=99.53  E-value=1.5e-14  Score=83.00  Aligned_cols=55  Identities=15%  Similarity=0.347  Sum_probs=50.8

Q ss_pred             ceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          81 ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        81 ~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      .+|||+|||.++++++|+++|++||.|..+.+++++.++.+ +.|||+|.+.|+|.
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~   57 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQ   57 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHH
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHH
Confidence            68999999999999999999999999999999999887776 55999999999875

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.52  E-value=1.2e-14  Score=87.83  Aligned_cols=59  Identities=17%  Similarity=0.398  Sum_probs=51.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ....++|||+|||.++++++|+++|++||.|..|.+++++.+|.+ +.|||+|.+.|+|.
T Consensus        22 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~   81 (109)
T 2rs2_A           22 GSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVD   81 (109)
T ss_dssp             ----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHH
Confidence            346789999999999999999999999999999999999887776 56999999999875

>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=99.52  E-value=1.6e-14  Score=86.52  Aligned_cols=61  Identities=25%  Similarity=0.364  Sum_probs=54.5

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          75 SESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        75 ~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ......++|||+|||..+++++|+++|++||.|..+.++.++.++.. +.|||+|.+.|+|.
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~   71 (105)
T 1x5u_A           10 SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDAD   71 (105)
T ss_dssp             CCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHH
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHH
Confidence            34457789999999999999999999999999999999999877776 56999999999875

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.52  E-value=2.4e-14  Score=84.12  Aligned_cols=59  Identities=22%  Similarity=0.446  Sum_probs=53.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ....++|||+|||..+++++|+++|++||+|..+.++.++.++.. +.+||+|.+.|+|.
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~   72 (94)
T 2e5h_A           13 APSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQ   72 (94)
T ss_dssp             CCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHH
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHH
Confidence            346789999999999999999999999999999999999887776 56999999999875

>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=99.52  E-value=2e-14  Score=85.87  Aligned_cols=59  Identities=24%  Similarity=0.352  Sum_probs=53.5

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ....++|||+|||..+++++|+++|++||.|..|.++.++.++.. +.|||+|.+.|+|.
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~   71 (103)
T 2cqg_A           12 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQV   71 (103)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHH
T ss_pred             cCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHH
Confidence            446789999999999999999999999999999999999887777 45999999999874

>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=99.52  E-value=1.4e-14  Score=93.64  Aligned_cols=95  Identities=17%  Similarity=0.271  Sum_probs=52.7

Q ss_pred             EEcCCHHHHHHHHHHHcCceeC--CceEEEEee-------------------CC-CCCCCCCceEEEcCCCCCCCHHHHH
Q psy6353          41 VNYHRPEDAEKAINTLNGLRLQ--NKTIKVSYA-------------------RP-SSESIKGANLYVSGLPKHMSQQELE   98 (136)
Q Consensus        41 v~f~~~~~a~~a~~~~~~~~~~--g~~l~v~~~-------------------~~-~~~~~~~~~l~v~nl~~~~t~~~l~   98 (136)
                      .+|.+.++|+.++..+++....  |+.....++                   .+ .......++|||+|||..+++++|+
T Consensus        11 ee~e~~~d~e~~~~~~~~~~~~~kgr~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~L~   90 (165)
T 1rk8_A           11 EEFEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQ   90 (165)
T ss_dssp             -------------------------------------------------------CCCCC-CEEEEEESCCTTCCHHHHH
T ss_pred             hhhhccccccccchhhccccccccCCCCCCCccccccccCccccccCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHH
Confidence            5678888888888777764443  433333221                   01 1122356789999999999999999


Q ss_pred             HhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          99 SLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        99 ~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ++|++||.|..|.++.+..+|.+ ++|||+|.+.++|.
T Consensus        91 ~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~  128 (165)
T 1rk8_A           91 EKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQAL  128 (165)
T ss_dssp             HHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHH
T ss_pred             HHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHH
Confidence            99999999999999999888876 56999999998874

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.52  E-value=7.2e-15  Score=88.04  Aligned_cols=53  Identities=17%  Similarity=0.315  Sum_probs=48.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ...++|||+|||.++|+++|+++|++||+|.+|.++++     +++|||+|++.|+|.
T Consensus        14 ~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~-----kGfaFVeF~~~~~A~   66 (105)
T 1sjq_A           14 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAAN   66 (105)
T ss_dssp             CCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT-----TTEEEEEESSHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC-----CCEEEEEECCHHHHH
Confidence            36789999999999999999999999999999999975     478999999999874

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.51  E-value=2.1e-14  Score=84.47  Aligned_cols=59  Identities=22%  Similarity=0.316  Sum_probs=53.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ....++|||+|||..+++++|+++|++||.|..+.+++++.++.. +.|||+|.+.|+|.
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~   71 (95)
T 2cqc_A           12 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAK   71 (95)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHH
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHH
Confidence            346789999999999999999999999999999999999988776 46999999999875

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.51  E-value=2.5e-14  Score=85.73  Aligned_cols=59  Identities=24%  Similarity=0.386  Sum_probs=53.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ....++|||+|||..+++++|+++|++||+|..|.+++++.++.. +.|||+|.+.|+|.
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~   72 (105)
T 2dh8_A           13 ADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVG   72 (105)
T ss_dssp             SSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHH
Confidence            456789999999999999999999999999999999999888777 45999999999875

>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=99.51  E-value=2.4e-15  Score=110.61  Aligned_cols=58  Identities=14%  Similarity=0.214  Sum_probs=52.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ....+|||+|||..+|+++|.++|++||.|..|.|+.+..++.. ++|||+|.+.|+|.
T Consensus       100 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~  158 (437)
T 3pgw_S          100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMH  158 (437)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHH
Confidence            35679999999999999999999999999999999999877776 66999999999874

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.51  E-value=3.6e-14  Score=83.47  Aligned_cols=57  Identities=23%  Similarity=0.416  Sum_probs=52.4

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ..++|||+|||..+++++|+++|++||.|..+.+++++.++.. +.|||+|.+.|+|.
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~   61 (95)
T 2dnz_A            4 GSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECAR   61 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHH
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHH
Confidence            5689999999999999999999999999999999999887776 56999999999875

>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=99.51  E-value=1.9e-14  Score=83.36  Aligned_cols=57  Identities=18%  Similarity=0.374  Sum_probs=51.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ..++|||+|||.++++++|+++|++||.|.++.+++++.++.. +.|||+|.+.|+|.
T Consensus         5 ~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~   62 (87)
T 3bs9_A            5 SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAE   62 (87)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHH
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHH
Confidence            5689999999999999999999999999999999999877776 56999999999875

>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=99.51  E-value=2e-14  Score=83.92  Aligned_cols=54  Identities=17%  Similarity=0.333  Sum_probs=48.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ....+|||+|||.++|+++|+++|++||.|.+|.++++    .+|+|||+|.+.|+|.
T Consensus         9 ~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~----srGfaFV~F~~~~~A~   62 (89)
T 3d2w_A            9 HHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP----FRAFAFVTFADDKVAQ   62 (89)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS----CCSEEEEEESCHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC----CCCEEEEEECCHHHHH
Confidence            36689999999999999999999999999999999985    5578999999999874

>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=99.51  E-value=1.3e-14  Score=83.62  Aligned_cols=58  Identities=24%  Similarity=0.367  Sum_probs=52.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ...++|||+|||..+++++|+++|++||.|..+.+++++.++.. +.|||+|.+.|+|.
T Consensus         5 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~   63 (85)
T 3mdf_A            5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA   63 (85)
T ss_dssp             CCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHH
Confidence            36789999999999999999999999999999999999877766 55999999999875

>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=99.51  E-value=3.1e-14  Score=82.78  Aligned_cols=57  Identities=26%  Similarity=0.494  Sum_probs=51.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ..++|||+|||.++++++|+++|++||.|..+.++.++.++.+ +.|||+|.+.|+|.
T Consensus         5 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~   62 (89)
T 3ucg_A            5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR   62 (89)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHH
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHH
Confidence            3578999999999999999999999999999999999877776 56999999999875

>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=99.50  E-value=3.1e-14  Score=85.96  Aligned_cols=59  Identities=24%  Similarity=0.437  Sum_probs=53.5

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ....++|||+|||..+++++|+++|++||.|..+.+++++.++.. +.|||+|.+.|+|.
T Consensus        23 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~   82 (108)
T 2jrs_A           23 SAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAK   82 (108)
T ss_dssp             CSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHH
Confidence            346789999999999999999999999999999999999887776 56999999999875

>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=99.50  E-value=2.2e-14  Score=84.39  Aligned_cols=58  Identities=16%  Similarity=0.176  Sum_probs=52.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ...++|||+|||..+++++|+++|++||+|..+.+++++....++.+||+|.+.|+|.
T Consensus        14 ~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~   71 (95)
T 2ywk_A           14 EADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVS   71 (95)
T ss_dssp             TGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHH
Confidence            4668999999999999999999999999999999999987444467999999999875

>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=99.50  E-value=9.9e-14  Score=91.82  Aligned_cols=91  Identities=12%  Similarity=0.269  Sum_probs=71.1

Q ss_pred             CHHHHHHHHHHH--cCceeCCceEEEEeeC--CCCC-------CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEE
Q psy6353          45 RPEDAEKAINTL--NGLRLQNKTIKVSYAR--PSSE-------SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRIL  113 (136)
Q Consensus        45 ~~~~a~~a~~~~--~~~~~~g~~l~v~~~~--~~~~-------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~  113 (136)
                      +.+.+..|+...  ....+.+....+....  |.+.       ....++|||+|||.++|+++|+++|++||.|..|+++
T Consensus        63 d~~~I~~Al~~S~~~~lev~ed~~~vrR~~~~p~p~~~~~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~  142 (193)
T 2voo_A           63 DFNVIVEALSKSKAELMEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMR  142 (193)
T ss_dssp             CHHHHHHHHHTCSSCCEEECTTSSEEEECTTSCCCCCCHHHHHHHHHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEE
T ss_pred             CHHHHHHHHhhcccceEEEecccceEEecccCCCcccchhhhhccccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEE
Confidence            667788888876  5566766655665542  2221       1135799999999999999999999999999999999


Q ss_pred             eCCCCCCccceEeecCcccccc
Q psy6353         114 CDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus       114 ~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ++..+..+|.|||+|.+.|+|.
T Consensus       143 ~~~~~~~kG~aFVeF~~~e~A~  164 (193)
T 2voo_A          143 RTLHKAFKGSIFVVFDSIESAK  164 (193)
T ss_dssp             ECTTCCEEEEEEEEESSHHHHH
T ss_pred             ECCCCCcccEEEEEECCHHHHH
Confidence            9987555577999999999875

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.50  E-value=3.4e-14  Score=86.63  Aligned_cols=59  Identities=20%  Similarity=0.420  Sum_probs=53.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ....++|||+|||..+++++|+++|++||.|..|.+++++.++.. +.|||+|.+.|+|.
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~   73 (116)
T 2cqd_A           14 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAE   73 (116)
T ss_dssp             SCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHH
Confidence            456789999999999999999999999999999999999887777 46999999999875

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.50  E-value=3.5e-14  Score=86.42  Aligned_cols=60  Identities=17%  Similarity=0.405  Sum_probs=54.0

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          76 ESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        76 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      .....++|||+|||..+++++|+++|++||.|..|.+++++.++.. +.|||+|.+.|+|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~   71 (115)
T 2dgo_A           11 DTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAE   71 (115)
T ss_dssp             CSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHH
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHH
Confidence            3457789999999999999999999999999999999999877776 56999999999875

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.50  E-value=2.5e-14  Score=84.80  Aligned_cols=58  Identities=16%  Similarity=0.278  Sum_probs=53.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceE-EEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRII-TSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~-~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ...++|||+|||..+++++|+++|++||.|. .+.+++++.++.. +.|||+|.+.|+|.
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~   66 (99)
T 2div_A            7 GMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAE   66 (99)
T ss_dssp             SSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHH
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHH
Confidence            4678999999999999999999999999999 9999999988777 55999999999874

>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=99.50  E-value=5.4e-14  Score=83.98  Aligned_cols=58  Identities=17%  Similarity=0.360  Sum_probs=52.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ....++|||+|||..+++++|+++|++||.|..|.++.+..+ ..+.|||+|.+.|+|.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~-~~g~afV~f~~~~~a~   69 (103)
T 2cq3_A           12 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADAD   69 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTT-TCCEEEEEESCHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCC-CcEEEEEEECCHHHHH
Confidence            456789999999999999999999999999999999998765 5578999999999875

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.50  E-value=9.7e-15  Score=82.37  Aligned_cols=54  Identities=13%  Similarity=0.422  Sum_probs=49.5

Q ss_pred             eEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        82 ~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      +|||+|||.++++++|+++|++||+|..+.++.++.++.+ +.|||+|.+.|+|.
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~   55 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVE   55 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHH
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHH
Confidence            5899999999999999999999999999999999877776 55999999999875

>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=99.50  E-value=2.7e-14  Score=84.71  Aligned_cols=58  Identities=26%  Similarity=0.335  Sum_probs=52.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ...++|||+|||..+++++|+++|++||.|..+.++.++.++.. +.|||+|.+.|+|.
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~   64 (99)
T 1whw_A            6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAV   64 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHH
Confidence            46789999999999999999999999999999999999877776 56999999999875

>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=99.50  E-value=3.3e-14  Score=85.96  Aligned_cols=58  Identities=12%  Similarity=0.300  Sum_probs=53.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ...++|||+|||..+++++|+++|++||.|..|.+++++.++.. +.|||+|.+.|+|.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~   71 (111)
T 1x4h_A           13 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQ   71 (111)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHH
Confidence            46789999999999999999999999999999999999888766 56999999999874

>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=99.50  E-value=1e-14  Score=91.78  Aligned_cols=97  Identities=13%  Similarity=0.179  Sum_probs=50.2

Q ss_pred             eeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEe--eCCCCCCCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEe
Q psy6353          37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY--ARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILC  114 (136)
Q Consensus        37 g~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~--~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~  114 (136)
                      |+|+.++.-++.+..+...+... ..+...--..  ...........+|||+|||.++|+++|+++|++|| |..|.|+.
T Consensus         2 ~~~~~~~~~~~~~~~~~~~~~~~-~gg~~~g~~~g~~~~~~~~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~   79 (139)
T 2hgn_A            2 GSSHHHHHHSSGLVPRGSHMASM-TGGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEI   79 (139)
T ss_dssp             --------------------------------------------CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCC
T ss_pred             CcccccccCccccchhcccchhc-cCCCCCCCCCCCcccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEE
Confidence            56777777666665555433222 2222211111  11112234668999999999999999999999999 67999999


Q ss_pred             CCCCCCccceEeecCcccccc
Q psy6353         115 DNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus       115 ~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      |+....++.+||+|.+.|+|.
T Consensus        80 d~~g~srGfaFV~F~~~e~A~  100 (139)
T 2hgn_A           80 GPDGRVTGEADVEFATHEEAV  100 (139)
T ss_dssp             SSSSCSSCCCEEECSHHHHHH
T ss_pred             CCCCCCceEEEEEeCCHHHHH
Confidence            987444567999999999875

>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=99.49  E-value=3.5e-14  Score=86.93  Aligned_cols=54  Identities=17%  Similarity=0.312  Sum_probs=49.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ..+.++|||+|||.++|+++|+++|++||.|.++.++++     ++.|||+|++.|+|.
T Consensus        28 ~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~-----kG~AFVeF~~~e~A~   81 (119)
T 2ad9_A           28 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAAN   81 (119)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG-----GTEEEEECSCHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC-----CCEEEEEECCHHHHH
Confidence            346789999999999999999999999999999999975     478999999999874

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.49  E-value=5.2e-14  Score=83.50  Aligned_cols=59  Identities=15%  Similarity=0.273  Sum_probs=53.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEE--------EEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIIT--------SRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~--------~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      .....+|||+|||..+++++|+++|++||.|..        +.++.++.+|.. +.|||+|.+.|+|.
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~   77 (99)
T 2la6_A           10 HSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAK   77 (99)
T ss_dssp             CCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHH
Confidence            346789999999999999999999999999999        999999887776 55999999999874

>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=99.49  E-value=3.4e-14  Score=86.51  Aligned_cols=60  Identities=22%  Similarity=0.490  Sum_probs=53.7

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCcc-ceEeecCcccccc
Q psy6353          76 ESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENG-KYYSGLGGRERLR  135 (136)
Q Consensus        76 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~-~~fv~f~~~e~~~  135 (136)
                      .....++|||+|||..+++++|+++|++||.|..+.+++++.++..+ .+||+|.+.|+|.
T Consensus        21 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~   81 (115)
T 2cpz_A           21 EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQ   81 (115)
T ss_dssp             CCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHH
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHH
Confidence            34466899999999999999999999999999999999999777774 5999999999875

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.49  E-value=3.8e-14  Score=85.05  Aligned_cols=59  Identities=19%  Similarity=0.316  Sum_probs=53.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ...+++|||+|||..+++++|+++|++||.|..+.++.++.++.+ +.|||+|.+.|+|.
T Consensus        20 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~   79 (106)
T 1p27_B           20 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ   79 (106)
T ss_dssp             BTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHH
Confidence            346689999999999999999999999999999999999988776 55999999999874

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.49  E-value=3.5e-14  Score=85.27  Aligned_cols=60  Identities=18%  Similarity=0.330  Sum_probs=53.3

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeC-CCCCCc-cceEeecCcccccc
Q psy6353          76 ESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD-NLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        76 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~-~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      .....++|||+|||..+++++|+++|++||.|..|.++++ ..++.. +.|||+|.+.|+|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~   72 (107)
T 2cph_A           11 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAK   72 (107)
T ss_dssp             CSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHH
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHH
Confidence            3457789999999999999999999999999999999999 666665 56999999999875

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.49  E-value=5.6e-14  Score=83.47  Aligned_cols=58  Identities=21%  Similarity=0.417  Sum_probs=51.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ...++|||+|||..+++++|+++|++||.|..+.++.+.....++.|||+|.+.|+|.
T Consensus        15 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~   72 (100)
T 2do4_A           15 LEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQAS   72 (100)
T ss_dssp             CCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHH
Confidence            4678999999999999999999999999999999999983333466999999999875

>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=99.49  E-value=2.8e-14  Score=84.24  Aligned_cols=56  Identities=16%  Similarity=0.322  Sum_probs=51.4

Q ss_pred             CceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          80 GANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        80 ~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      +++|||+|||..+++++|+++|++||.|..+.++.++.+|.. +.|||+|.+.|+|.
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~   58 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSA   58 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHH
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHH
Confidence            578999999999999999999999999999999999887776 56999999999874

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.49  E-value=4.3e-14  Score=86.39  Aligned_cols=59  Identities=20%  Similarity=0.501  Sum_probs=53.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ....++|||+|||.++++++|+++|++||.|..+.+++++.++.. +.+||+|.+.|++.
T Consensus        37 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~   96 (118)
T 2khc_A           37 GPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQ   96 (118)
T ss_dssp             CCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHH
Confidence            345689999999999999999999999999999999999877776 56999999999875

>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=99.49  E-value=5.6e-14  Score=83.81  Aligned_cols=54  Identities=19%  Similarity=0.292  Sum_probs=48.5

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ..+.++|||+|||..+++++|+++|++||.|..+.++++     ++.|||+|++.|+|.
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~-----kg~aFVef~~~~~A~   65 (101)
T 2cq1_A           12 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAI   65 (101)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT-----TTEEEEEESSHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC-----CCEEEEEECCHHHHH
Confidence            346789999999999999999999999999999999875     578999999999874

>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=99.49  E-value=1.5e-14  Score=86.85  Aligned_cols=60  Identities=20%  Similarity=0.460  Sum_probs=53.9

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          76 ESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        76 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      .....++|||+|||..+++++|+++|++||.|..+.++.++.++.. +.|||+|.+.|+|.
T Consensus         9 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~   69 (106)
T 2dgp_A            9 KDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESAL   69 (106)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHH
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHH
Confidence            3456789999999999999999999999999999999999887776 55999999999874

>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=99.49  E-value=1.2e-14  Score=84.96  Aligned_cols=55  Identities=15%  Similarity=0.297  Sum_probs=48.3

Q ss_pred             ceEEEcCCCCCCCHHHHHHhhcCCC--ceEEEEEEeCCCCCCcc-ceEeecCcccccc
Q psy6353          81 ANLYVSGLPKHMSQQELESLFSPYG--RIITSRILCDNLATENG-KYYSGLGGRERLR  135 (136)
Q Consensus        81 ~~l~v~nl~~~~t~~~l~~~f~~~G--~v~~~~i~~~~~~~~~~-~~fv~f~~~e~~~  135 (136)
                      .+|||+|||.++|+++|+++|++||  .|.+++++.|+.+|.++ .|||+|.+.|+|.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~   59 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSK   59 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHH
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHH
Confidence            4799999999999999999999999  99999999999888874 5999999999875

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.48  E-value=3.6e-14  Score=85.77  Aligned_cols=64  Identities=16%  Similarity=0.330  Sum_probs=54.3

Q ss_pred             eCCCCCCCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          71 ARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        71 ~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      +.+.......++|||+|||..+++++|+++|++||.|..+.++++... .++.|||+|.+.|+|.
T Consensus        20 S~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~-~kg~afV~f~~~~~A~   83 (109)
T 2err_A           20 HMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADAD   83 (109)
T ss_dssp             --CCSCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTTB-CTTEEEEECCCSHHHH
T ss_pred             CCCccCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCCC-CceEEEEEECCHHHHH
Confidence            344445567899999999999999999999999999999999998654 5578999999999875

>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=99.48  E-value=7.9e-15  Score=82.70  Aligned_cols=54  Identities=17%  Similarity=0.438  Sum_probs=49.7

Q ss_pred             eEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        82 ~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      +|||+|||.++++++|+++|++||+|..+.+++++.++.+ +.|||+|.+.|+|.
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~   55 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVK   55 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHH
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHH
Confidence            5899999999999999999999999999999999887776 56999999999875

>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=99.48  E-value=4.6e-14  Score=84.27  Aligned_cols=59  Identities=14%  Similarity=0.276  Sum_probs=52.7

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          76 ESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        76 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      .....++|||+|||..+++++|+++|++||.|..|.++++..+ .++.|||+|.+.|+|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~-~~g~afV~f~~~~~a~   69 (103)
T 2cqi_A           11 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS-NDPYCFVEFYEHRDAA   69 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS-SCCEEEEEESSHHHHH
T ss_pred             CCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCC-CCCEEEEEECCHHHHH
Confidence            3456789999999999999999999999999999999999765 4578999999999875

>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=99.48  E-value=5.9e-14  Score=84.11  Aligned_cols=58  Identities=17%  Similarity=0.247  Sum_probs=50.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceEE-EEEEeCCCCCCccceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRIIT-SRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~-~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ....+|||+|||..+|+++|+++|++||.|.. +.++.+..+..++.|||+|.+.|+|.
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~   71 (104)
T 1wg5_A           13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAE   71 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHH
Confidence            46789999999999999999999999999987 88998844444467999999999875

>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=99.48  E-value=6.3e-14  Score=83.76  Aligned_cols=57  Identities=19%  Similarity=0.292  Sum_probs=49.8

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      .....+|||+|||.++|+++|+++|++||. ..|.++.|+ ++.+ +.|||+|.+.|+|.
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~-~~v~i~~d~-~g~~~G~afV~F~~~~~a~   69 (102)
T 1wez_A           12 STTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGP-DGRVTGEADVEFATHEDAV   69 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESS-SSCEEEEEEEECSSSHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCc-eEEEEEECC-CCCEeeEEEEEECCHHHHH
Confidence            346689999999999999999999999995 599999998 5554 66999999999875

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.48  E-value=7.4e-14  Score=83.38  Aligned_cols=58  Identities=22%  Similarity=0.438  Sum_probs=51.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ....++|||+|||..+|+++|+++|++||.|..+.++.+ .....+.|||+|.+.|+|.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~-~g~~~g~afV~f~~~~~A~   69 (103)
T 2d9p_A           12 RYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEAT   69 (103)
T ss_dssp             CSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC-SSSEEEEEEEEESSHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC-CCCcCEEEEEEECCHHHHH
Confidence            446789999999999999999999999999999999998 3334467999999999875

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.47  E-value=8.8e-14  Score=84.48  Aligned_cols=59  Identities=19%  Similarity=0.236  Sum_probs=52.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ....++|||+|||..+++++|+++|.+||.|..+.++.++.....+.+||+|.+.|+|.
T Consensus        12 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~   70 (114)
T 2do0_A           12 GRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAV   70 (114)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHH
Confidence            34678999999999999999999999999999999999986444467999999998874

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.47  E-value=2.5e-14  Score=84.32  Aligned_cols=57  Identities=16%  Similarity=0.357  Sum_probs=52.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEE-EEEeCCCCCCc-cceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITS-RILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~-~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ..++|||+|||..+++++|+++|++||.|..+ .+++++.++.. +.|||+|.+.|+|.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~   62 (96)
T 1x5t_A            4 GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASD   62 (96)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHH
Confidence            56899999999999999999999999999999 99999777776 56999999999875

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.47  E-value=3.8e-14  Score=84.49  Aligned_cols=56  Identities=20%  Similarity=0.424  Sum_probs=50.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ..++|||+|||..+++++|+++|++||.|..+.++++. ++.. +.|||+|.+.|+|.
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~   64 (102)
T 2xs2_A            8 MPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQ   64 (102)
T ss_dssp             EEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHH
Confidence            56899999999999999999999999999999999998 5554 66999999999875

>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=99.47  E-value=6e-14  Score=87.27  Aligned_cols=59  Identities=22%  Similarity=0.316  Sum_probs=53.5

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ....++|||+|||..+++++|+++|++||+|..|.+++++.++.. +.|||+|.+.|+|.
T Consensus        43 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~  102 (129)
T 2kxn_B           43 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAK  102 (129)
T ss_dssp             CCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHH
Confidence            346789999999999999999999999999999999999888776 56999999999875

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.47  E-value=3.5e-14  Score=84.62  Aligned_cols=58  Identities=24%  Similarity=0.367  Sum_probs=52.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ...++|||+|||..+++++|+++|++||.|..+.++.++.++.. +.|||+|.+.|+|.
T Consensus        10 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~   68 (102)
T 2cqb_A           10 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA   68 (102)
T ss_dssp             CCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHH
Confidence            46789999999999999999999999999999999999887776 56999999999875

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.47  E-value=6.2e-14  Score=83.83  Aligned_cols=58  Identities=16%  Similarity=0.210  Sum_probs=52.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcC-CCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSP-YGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~-~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ....++|||+|||..+|+++|+++|++ ||.|..+.++.+. ++.+ +.|||+|.+.|+|.
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~   65 (104)
T 2dhg_A            6 SGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQK   65 (104)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHH
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHH
Confidence            346789999999999999999999999 9999999999999 5554 66999999999874

>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=99.47  E-value=9.1e-14  Score=84.48  Aligned_cols=57  Identities=19%  Similarity=0.393  Sum_probs=52.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ..++|||+|||..+++++|+++|++||.|..|.++.++.++.. +.|||+|.+.|+|.
T Consensus        24 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~   81 (114)
T 2cq4_A           24 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVP   81 (114)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHH
Confidence            3479999999999999999999999999999999999987776 56999999999875

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.47  E-value=9.4e-15  Score=87.02  Aligned_cols=57  Identities=21%  Similarity=0.378  Sum_probs=52.1

Q ss_pred             CCceEEEcCCCC------CCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          79 KGANLYVSGLPK------HMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~------~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      .+++|||+|||.      ++++++|+++|++||.|.++.+++++.+|.+ +.|||+|.+.|+|.
T Consensus         5 ~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~   68 (100)
T 3ns6_A            5 SDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAK   68 (100)
T ss_dssp             GGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHH
T ss_pred             cCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHH
Confidence            467899999999      9999999999999999999999999997777 55999999998875

>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=99.47  E-value=6.7e-14  Score=85.48  Aligned_cols=58  Identities=16%  Similarity=0.312  Sum_probs=51.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ...++|||+|||.++++++|+++|++||.|..|.++.+..+...+.|||+|.+.|+|.
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~F~~~~~A~   62 (116)
T 2fy1_A            5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAK   62 (116)
T ss_dssp             CSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHH
Confidence            3568999999999999999999999999999999999984444467999999999875

>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=99.47  E-value=8.3e-14  Score=83.32  Aligned_cols=58  Identities=14%  Similarity=0.241  Sum_probs=51.8

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCC-CCc-cceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLA-TEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~-~~~-~~~fv~f~~~e~~~  135 (136)
                      ....++|||+|||..+++++|+++|++|| |..|.++.++.+ +.. +.|||+|.+.|+|.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~   71 (104)
T 1wi8_A           12 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLL   71 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHH
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHH
Confidence            34668999999999999999999999999 999999999876 555 56999999999875

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.47  E-value=4.5e-14  Score=84.16  Aligned_cols=59  Identities=24%  Similarity=0.402  Sum_probs=53.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ....++|||+|||..+++++|+++|++||.|..+.+++++.++.. +.|||+|.+.|+|.
T Consensus         9 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~   68 (102)
T 1x5s_A            9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAK   68 (102)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHH
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHH
Confidence            346789999999999999999999999999999999999887776 56999999999875

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.47  E-value=1.3e-13  Score=82.31  Aligned_cols=58  Identities=21%  Similarity=0.351  Sum_probs=52.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ....++|||+|||..+++++|+++|++|| |..|.+++++.++.. +.|||+|.+.|+|.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~   70 (103)
T 2dng_A           12 TEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLK   70 (103)
T ss_dssp             SSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHH
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHH
Confidence            34678999999999999999999999997 999999999988877 45999999999875

>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=99.47  E-value=6.4e-14  Score=83.65  Aligned_cols=53  Identities=15%  Similarity=0.203  Sum_probs=48.1

Q ss_pred             CCCceEEEcCCCC-CCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPK-HMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~-~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      .+.++|||+|||. .+|+++|+++|++||.|.++.+++++     +.|||+|++.|+|.
T Consensus        13 ~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~k-----g~aFVef~~~~~A~   66 (102)
T 1x4d_A           13 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI-----NEAFIEMATTEDAQ   66 (102)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS-----SCEEEEESSHHHHH
T ss_pred             CCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcCC-----CEEEEEECCHHHHH
Confidence            4678999999999 99999999999999999999998753     67999999999874

>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=99.46  E-value=5.7e-14  Score=85.48  Aligned_cols=59  Identities=10%  Similarity=0.135  Sum_probs=51.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCce-EEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRI-ITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v-~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ....++|||+|||..+|+++|+++|++||.| ..|.++.|+....++.|||+|.+.|+|.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~   71 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDAR   71 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHH
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHH
Confidence            3467899999999999999999999999999 8899999994334577999999999875

>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=99.46  E-value=4.3e-14  Score=81.91  Aligned_cols=57  Identities=16%  Similarity=0.388  Sum_probs=51.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCC--ccceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATE--NGKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~--~~~~fv~f~~~e~~~  135 (136)
                      ..++|||+|||.++++++|+++|++||.|..+.++.+..++.  .+.|||+|.+.|+|.
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~   61 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAE   61 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHH
Confidence            468999999999999999999999999999999999987654  467999999999875

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.46  E-value=1.1e-13  Score=82.17  Aligned_cols=54  Identities=9%  Similarity=0.095  Sum_probs=48.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ..++++|||+|||.++|+++|+++|++||+|.++.++++     ++.|||+|++.|+|.
T Consensus        18 ~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~-----kg~AFVef~~~~~A~   71 (100)
T 3r27_A           18 TPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK-----KRQALVEFEDVLGAC   71 (100)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETT-----TTEEEEEESSHHHHH
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcC-----CCEEEEEECCHHHHH
Confidence            346789999999999999999999999999999999853     478999999999875

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.46  E-value=8.4e-14  Score=84.88  Aligned_cols=57  Identities=12%  Similarity=0.352  Sum_probs=52.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ..++|||+|||..+++++|+++|++||.|..|.+++++.++.. +.|||+|.+.++|.
T Consensus        26 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~   83 (116)
T 1x4b_A           26 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVD   83 (116)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHH
Confidence            4579999999999999999999999999999999999887776 56999999999874

>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=99.45  E-value=1.4e-13  Score=83.56  Aligned_cols=58  Identities=34%  Similarity=0.666  Sum_probs=51.8

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ....++|||+|||..+++++|+++|++||.|..+.+++++ ++.. +.+||+|.+.|+|.
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~   80 (114)
T 1x5o_A           22 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCE   80 (114)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHH
Confidence            3467899999999999999999999999999999999998 5554 66999999999874

>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=99.45  E-value=7.4e-14  Score=84.34  Aligned_cols=59  Identities=19%  Similarity=0.291  Sum_probs=53.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ....++|||+|||..+++++|+++|++||.|..+.++.+..+|.. +.|||+|.+.|+|.
T Consensus        23 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~   82 (110)
T 1oo0_B           23 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQAL   82 (110)
T ss_dssp             BTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHH
Confidence            346789999999999999999999999999999999999877776 56999999999874

>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=99.45  E-value=2.4e-13  Score=82.69  Aligned_cols=58  Identities=17%  Similarity=0.111  Sum_probs=53.3

Q ss_pred             HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeC
Q psy6353          13 YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR   72 (136)
Q Consensus        13 l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~   72 (136)
                      |++.|++||.|.++.+++.  .++|++||+|.+.++|++|+..|||..++||.|.+.++.
T Consensus        34 l~~~f~kfG~V~~v~i~~~--~~~G~~fV~f~~~e~A~~Ai~~lnG~~f~GR~i~v~~~~   91 (114)
T 3s6e_A           34 VIEECNKHGGVIHIYVDKN--SAQGNVYVKCPSIAAAIAAVNALHGRWFAGKMITAAYVP   91 (114)
T ss_dssp             HHHHHTTTTCCSEEEECTT--CTTCCEEEECSSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             HHHHHhccCCEEEEEEecC--CCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEEc
Confidence            8999999999999998763  258999999999999999999999999999999999875

>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=99.45  E-value=1.6e-13  Score=82.24  Aligned_cols=53  Identities=11%  Similarity=0.139  Sum_probs=47.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      .+.++|||+|||..+++++|+++|++||.|..+.++++     ++.|||+|++.|+|.
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~-----kg~aFVef~~~~~A~   65 (104)
T 1wex_A           13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAK   65 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT-----TTEEEEEESSHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC-----CCEEEEEECCHHHHH
Confidence            35689999999999999999999999999999998864     478999999999874

>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=99.45  E-value=1.3e-13  Score=82.86  Aligned_cols=58  Identities=19%  Similarity=0.294  Sum_probs=52.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCC-ccceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATE-NGKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~-~~~~fv~f~~~e~~~  135 (136)
                      ....++|||+|||..+++++|+++|++||.|..+.++.+. ++. .+.|||+|.+.|+|.
T Consensus        26 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~   84 (107)
T 3ulh_A           26 VETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADAL   84 (107)
T ss_dssp             CCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHH
Confidence            3467899999999999999999999999999999999999 555 467999999999875

>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=99.44  E-value=7.3e-14  Score=82.49  Aligned_cols=56  Identities=18%  Similarity=0.188  Sum_probs=51.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHH----HhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELE----SLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~----~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ....+|||+|||..+++++|+    ++|++||.|.+|.++.++.+  ++.|||+|.+.|+|.
T Consensus         7 ~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~--rg~afV~f~~~~~A~   66 (96)
T 2dgx_A            7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY--QLKAVVQMENLQDAI   66 (96)
T ss_dssp             SSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST--TCCEEEEESSHHHHH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC--CeEEEEEECCHHHHH
Confidence            356899999999999999999    99999999999999999877  678999999999875

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.44  E-value=7e-14  Score=82.73  Aligned_cols=57  Identities=18%  Similarity=0.240  Sum_probs=50.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCC---CCCc-cceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNL---ATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~---~~~~-~~~fv~f~~~e~~~  135 (136)
                      ..++|||+|||..+++++|+++|++||.|..+.++.++.   ++.. +.|||+|.+.|+|.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~   64 (98)
T 2cpf_A            4 GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQ   64 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHH
Confidence            568999999999999999999999999999999999876   3344 66999999999875

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.44  E-value=9.5e-14  Score=89.01  Aligned_cols=57  Identities=12%  Similarity=0.233  Sum_probs=51.4

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCC--ceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYG--RIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G--~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ..++|||+|||..+|+++|+++|++||  .|..++++.|+.+|.+ |+|||+|.+.|+|.
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~  113 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVH  113 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHH
Confidence            457999999999999999999999999  9999999999988887 55999999999875

>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=99.44  E-value=1.1e-13  Score=80.38  Aligned_cols=53  Identities=17%  Similarity=0.291  Sum_probs=48.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ..++|||+|||.++++++|+++|++||.|..+.++.+    .++.|||+|.+.|+|.
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~   56 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP----FRAFAFVTFADDQIAQ   56 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS----CCSCCEEECSCHHHHH
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC----CCCEEEEEECCHHHHH
Confidence            5689999999999999999999999999999999875    4578999999999874

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.44  E-value=6.5e-14  Score=84.66  Aligned_cols=56  Identities=16%  Similarity=0.262  Sum_probs=50.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ...+|||+|||.++|+++|+++|++| .|..|.|+.|+.+..+|.|||+|.+.|+|.
T Consensus        15 ~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~g~~~G~afV~F~~~~~a~   70 (109)
T 2dnn_A           15 DDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTF   70 (109)
T ss_dssp             HHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHH
Confidence            45789999999999999999999999 899999999987555577999999999875

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.44  E-value=5.8e-13  Score=79.20  Aligned_cols=59  Identities=17%  Similarity=0.256  Sum_probs=52.6

Q ss_pred             HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353          13 YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus        13 l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |+++|++||.|.++.++.   +++|||||+|.+.++|+.|+..+++  +.+++|+|.++.++..
T Consensus        34 L~~~F~~~G~V~~v~i~~---~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~V~~a~~~~~   92 (100)
T 2d9o_A           34 LLRLLQKYGEVLNLVLSS---KKPGTAVVEFATVKAAELAVQNEVG--LVDNPLKISWLEGQPQ   92 (100)
T ss_dssp             HHHHHHTTSCEEEEEEES---SSSSEEEEEESCHHHHHHHHHTCCB--CSSSBCEEECSSCCCC
T ss_pred             HHHHHHhcCCEEEEEEcc---CCCCEEEEEECCHHHHHHHHHhcCC--CCCCeEEEEEccCCCC
Confidence            999999999999999874   7899999999999999999997444  6799999999887654

>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=99.43  E-value=9.7e-14  Score=87.01  Aligned_cols=58  Identities=16%  Similarity=0.303  Sum_probs=51.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCc---eEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGR---IITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~---v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ....+|||+|||.++|+++|+++|++||.   |..|.+++|+.+..++.|||+|.+.|+|.
T Consensus        42 ~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~  102 (136)
T 2hgl_A           42 GEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVK  102 (136)
T ss_dssp             CTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHH
Confidence            46789999999999999999999999999   88999999988444467999999999875

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.43  E-value=1.2e-13  Score=84.53  Aligned_cols=58  Identities=14%  Similarity=0.281  Sum_probs=51.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCc---eEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGR---IITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~---v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ...++|||+|||.++|+++|+++|++||.   |..|+++.+..+..++.|||+|.+.|+|.
T Consensus        15 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~   75 (118)
T 2db1_A           15 GEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVK   75 (118)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHH
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHH
Confidence            46789999999999999999999999999   89999999988444567999999999875

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.43  E-value=1.4e-13  Score=83.48  Aligned_cols=60  Identities=18%  Similarity=0.316  Sum_probs=53.3

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHhhcCCCceE--------EEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          76 ESIKGANLYVSGLPKHMSQQELESLFSPYGRII--------TSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        76 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~--------~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      +....++|||+|||..+++++|+++|++||.|.        .+.++.++.++.. +.|||+|.+.|+|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~   79 (113)
T 2cpe_A           11 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAK   79 (113)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHH
T ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHH
Confidence            345778999999999999999999999999999        6999999777776 56999999999875

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.43  E-value=1.7e-13  Score=85.90  Aligned_cols=58  Identities=24%  Similarity=0.367  Sum_probs=52.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ...++|||+|||..+++++|+++|++||.|..+.+++++.++.. +.|||+|.+.|+|.
T Consensus        61 ~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~  119 (140)
T 2ku7_A           61 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA  119 (140)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHH
T ss_pred             CCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHH
Confidence            46789999999999999999999999999999999999877776 55999999999875

>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=99.43  E-value=2.6e-13  Score=83.91  Aligned_cols=57  Identities=18%  Similarity=0.286  Sum_probs=50.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceE--EEEEEeCCCCCCccceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRII--TSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~--~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ....+|||+|||.++|+++|+++|++| .|.  .|.|+.|+.+..+|.|||+|.+.|+|.
T Consensus        40 ~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~   98 (126)
T 2hgm_A           40 ANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITGEAFVQFASQELAE   98 (126)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHH
Confidence            456889999999999999999999999 566  899999988444577999999999875

>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=99.43  E-value=8.9e-14  Score=83.09  Aligned_cols=57  Identities=18%  Similarity=0.380  Sum_probs=52.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ..++|||+|||..+++++|+++|++||.|..+.+++++.+|.+ +.|||+|.+.|+|.
T Consensus         7 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~   64 (104)
T 1p1t_A            7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETAL   64 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHH
T ss_pred             CccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHH
Confidence            4578999999999999999999999999999999999877776 56999999999875

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.42  E-value=2.9e-13  Score=79.01  Aligned_cols=58  Identities=12%  Similarity=0.360  Sum_probs=50.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      .....+|||+|||.++++++|+++|++| .|..+.++++..+..++.|||+|.+.|+|.
T Consensus         7 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~   64 (91)
T 2dgw_A            7 GTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVK   64 (91)
T ss_dssp             CCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHH
T ss_pred             CCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHH
Confidence            4467899999999999999999999999 899999999944444467999999999875

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.42  E-value=1.2e-13  Score=86.78  Aligned_cols=58  Identities=24%  Similarity=0.410  Sum_probs=53.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ...++|||+|||.++++++|+++|++||.|..|.+++++.++.. +.|||+|.+.|+|.
T Consensus        40 ~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~   98 (139)
T 1u6f_A           40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQ   98 (139)
T ss_dssp             TTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHH
Confidence            45689999999999999999999999999999999999988876 55999999999875

>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=99.42  E-value=1.9e-13  Score=84.43  Aligned_cols=59  Identities=19%  Similarity=0.316  Sum_probs=53.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ....++|||+|||..+|+++|+++|++||.|..|.++.++.++.. +.|||+|.+.|+|.
T Consensus        19 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~   78 (126)
T 3ex7_B           19 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ   78 (126)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHH
Confidence            346789999999999999999999999999999999999877775 66999999999874

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.42  E-value=3.3e-13  Score=78.82  Aligned_cols=56  Identities=16%  Similarity=0.262  Sum_probs=49.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCC-ccceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATE-NGKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~-~~~~fv~f~~~e~~~  135 (136)
                      ...++|||+|||..+++++|+++|++||.|..+.++++  ++. ++.+||+|.+.|+|.
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~--~g~~~g~afV~f~~~~~a~   62 (92)
T 2dgv_A            6 SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAE   62 (92)
T ss_dssp             SSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHH
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHH
Confidence            46789999999999999999999999999999999985  444 466999999999875

>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=99.42  E-value=1.8e-13  Score=82.93  Aligned_cols=59  Identities=17%  Similarity=0.250  Sum_probs=51.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHH---HhhcCCCceEEEEEEeCCCCCCc----cceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELE---SLFSPYGRIITSRILCDNLATEN----GKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~---~~f~~~G~v~~~~i~~~~~~~~~----~~~fv~f~~~e~~~  135 (136)
                      ....++|||+|||..+++++|+   ++|++||+|..+.++++..++..    +.|||+|.+.|+|.
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~   77 (111)
T 2cpi_A           12 VVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL   77 (111)
T ss_dssp             CCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHH
T ss_pred             ccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHH
Confidence            3467899999999999999999   99999999999999999875433    47999999999875

>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=99.42  E-value=9e-14  Score=82.68  Aligned_cols=58  Identities=14%  Similarity=0.239  Sum_probs=49.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCC-CCCCc-cceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDN-LATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~-~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ....++|||+|||.++++++|+++|++|| |..+.++++. .+|.+ +.|||+|.+.|+|.
T Consensus        16 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~   75 (100)
T 2j76_E           16 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLL   75 (100)
T ss_dssp             ----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHH
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHH
Confidence            34678999999999999999999999999 9999999998 45655 66999999999875

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.41  E-value=2.8e-13  Score=83.53  Aligned_cols=57  Identities=23%  Similarity=0.315  Sum_probs=51.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCC-ccceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATE-NGKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~-~~~~fv~f~~~e~~~  135 (136)
                      ..+++|||+|||..+++++|+++|++||.|..+.++.+. +|. ++.|||+|.+.|+|.
T Consensus        33 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~   90 (124)
T 2kt5_A           33 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADAL   90 (124)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHH
Confidence            456899999999999999999999999999999999998 554 467999999999875

>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=99.41  E-value=1e-13  Score=83.49  Aligned_cols=59  Identities=12%  Similarity=0.108  Sum_probs=52.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCc---eEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGR---IITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~---v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      .....+|||+|||.++|+++|+++|++||.   |..+.++.++.+..+|.|||+|.+.|+|.
T Consensus         8 ~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~   69 (107)
T 2lmi_A            8 VDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQ   69 (107)
T ss_dssp             CSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHH
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHH
Confidence            346789999999999999999999999998   89999999988444567999999999875

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.41  E-value=1.4e-13  Score=84.73  Aligned_cols=57  Identities=28%  Similarity=0.471  Sum_probs=51.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ..++|||+|||..+|+++|+++|++||.|..+.+++++.++.. +.|||+|.+.|++.
T Consensus        35 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~   92 (124)
T 2jwn_A           35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVD   92 (124)
T ss_dssp             HHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHH
Confidence            3579999999999999999999999999999999999877776 56999999999874

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.41  E-value=1.2e-13  Score=79.07  Aligned_cols=54  Identities=13%  Similarity=0.210  Sum_probs=46.3

Q ss_pred             CceEEEcCCCCCC------CHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          80 GANLYVSGLPKHM------SQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        80 ~~~l~v~nl~~~~------t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      +++|||+|||..+      ++++|+++|++||+|..+.+++  .+|.+ +.|||+|.+.++|.
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~~--~~g~~~g~afV~f~~~~~A~   61 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE--EDGKTKGYIFLEYASPAHAV   61 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCC--BTTBCCCEEEEEESSHHHHH
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecC--CCCcEeEEEEEEECCHHHHH
Confidence            3689999999999      7799999999999999999883  34444 67999999999874

>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=99.41  E-value=3.4e-13  Score=86.25  Aligned_cols=59  Identities=22%  Similarity=0.265  Sum_probs=53.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ....++|||+|||..+|+++|+++|++||+|..|.++.++.++.. +.|||+|.+.|+|.
T Consensus        36 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~   95 (156)
T 1h2v_Z           36 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAE   95 (156)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHH
Confidence            346789999999999999999999999999999999999988876 56999999999874

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.41  E-value=1.6e-13  Score=83.52  Aligned_cols=57  Identities=14%  Similarity=0.311  Sum_probs=50.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCC---CCc-cceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLA---TEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~---~~~-~~~fv~f~~~e~~~  135 (136)
                      ...++|||+|||.++++++|+++|++||+|. +.++.+..+   |.+ ++|||+|.+.|+|.
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~   66 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQ   66 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHH
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHH
Confidence            3568999999999999999999999999999 888888776   444 66999999999874

>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=99.40  E-value=1e-13  Score=82.06  Aligned_cols=58  Identities=21%  Similarity=0.166  Sum_probs=51.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ...++|||+|||..+++++|+++|++||.|..+.++.+..++.. +.|||+|.+.|+|.
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~   71 (98)
T 2cqp_A           13 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEAT   71 (98)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHH
Confidence            35688999999999999999999999999998888888877776 56999999999875

>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=99.40  E-value=7.4e-14  Score=82.13  Aligned_cols=57  Identities=21%  Similarity=0.187  Sum_probs=51.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ..++|||+|||..+++++|+++|++||.|..+.++.++.++.. +.+||+|.+.|+|.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~   71 (95)
T 2ek1_A           14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEAT   71 (95)
T ss_dssp             -CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHH
Confidence            4589999999999999999999999999999999998888766 56999999999875

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.40  E-value=1.5e-13  Score=84.76  Aligned_cols=57  Identities=14%  Similarity=0.135  Sum_probs=49.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCce----EEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRI----ITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v----~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ...+|||+|||.++|+++|+++|++||.|    ..|.|+.+..+..++.|||+|.+.|+|.
T Consensus        22 ~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~   82 (123)
T 2dha_A           22 NQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQ   82 (123)
T ss_dssp             SCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHH
Confidence            56899999999999999999999999975    6899999964444467999999999875

>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=99.40  E-value=4.4e-13  Score=77.18  Aligned_cols=54  Identities=20%  Similarity=0.349  Sum_probs=48.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ....++|||+|||..+++++|+++|++||.|..+.++++     ++.|||+|.+.|+|.
T Consensus         9 ~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~-----kg~afV~f~~~~~A~   62 (85)
T 2ytc_A            9 DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR-----QQCAFIQFATRQAAE   62 (85)
T ss_dssp             CSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG-----GTEEEEEESSHHHHH
T ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC-----CCEEEEEECCHHHHH
Confidence            456789999999999999999999999999999999974     477999999999874

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.40  E-value=1.2e-13  Score=85.96  Aligned_cols=57  Identities=16%  Similarity=0.260  Sum_probs=50.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceEE--EEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRIIT--SRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~--~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ...++|||+|||..+|+++|+++|++||.|..  |+|++|+.+|.+ |++||+|.+. ++.
T Consensus        21 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~   80 (131)
T 2m2b_A           21 NANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAA   80 (131)
T ss_dssp             CCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHH
Confidence            46789999999999999999999999999977  999999977776 5599999998 553

>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=99.40  E-value=3.5e-13  Score=81.66  Aligned_cols=54  Identities=22%  Similarity=0.325  Sum_probs=47.9

Q ss_pred             CCCCceEEEcCCCCC-CCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKH-MSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~-~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ...+++|||+|||.+ +++++|+++|++||.|.++.+++.     ++.|||+|++.|+|.
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~~-----kg~aFVef~~~~~A~   76 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM-----KSQAFIEMETREDAM   76 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT-----TTEEEEECSSHHHHH
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEecC-----CCEEEEEECCHHHHH
Confidence            346789999999998 999999999999999999999853     477999999999874

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.39  E-value=3e-13  Score=81.09  Aligned_cols=60  Identities=12%  Similarity=0.158  Sum_probs=49.9

Q ss_pred             CCCCCCCceEEEcCCCCCC------CHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          74 SSESIKGANLYVSGLPKHM------SQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        74 ~~~~~~~~~l~v~nl~~~~------t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      .......++|||+|||..+      |+++|+++|++||.|..+.+++  .+|.+ +.|||+|.+.|+|.
T Consensus         9 ~~~~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~--~~g~~~G~afV~f~~~~~A~   75 (105)
T 2nlw_A            9 QEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE--EDGKTKGYIFLEYASPAHAV   75 (105)
T ss_dssp             CSCCSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCC--BTTBSCCEEEEEECSSSHHH
T ss_pred             CCCCCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeC--CCCCeeeEEEEEECCHHHHH
Confidence            3344567899999999999      7899999999999999999983  34444 67999999999874

>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=99.39  E-value=5.2e-14  Score=82.05  Aligned_cols=54  Identities=19%  Similarity=0.453  Sum_probs=49.4

Q ss_pred             ceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          81 ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        81 ~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ++|||+|||.++++++|+++|++||.|..+.+++++.++.+ +.|||+|.+.| |.
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~   56 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VS   56 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HH
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HH
Confidence            57999999999999999999999999999999999987776 55999999998 64

>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=99.39  E-value=1.6e-13  Score=84.66  Aligned_cols=58  Identities=14%  Similarity=0.249  Sum_probs=50.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ....+|||+|||..+|+++|+++|++||.|..+.++.+..+|.. +.|||+|.+.|+|.
T Consensus        23 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~   81 (124)
T 1wel_A           23 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYK   81 (124)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHH
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHH
Confidence            45689999999999999999999999999998666666666665 66999999999875

>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=99.39  E-value=6.2e-13  Score=80.12  Aligned_cols=57  Identities=16%  Similarity=0.297  Sum_probs=49.5

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ....++|||+|||..+++++|+++|++||.|..|.+..+.  ..++.|||+|.+.|+|.
T Consensus        19 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~--~~~g~afV~f~~~~~A~   75 (109)
T 1x4a_A           19 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR--GGPPFAFVEFEDPRDAE   75 (109)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSS--SSSCCEEEEESCHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC--CCCcEEEEEECCHHHHH
Confidence            3467899999999999999999999999999999997653  34577999999999875

>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=99.39  E-value=4.7e-13  Score=80.60  Aligned_cols=52  Identities=23%  Similarity=0.280  Sum_probs=48.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ...++|||+|||.++++++|+++|++||.|..|.++.+      +.|||+|.+.|+|.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~------g~afV~f~~~~~a~   64 (108)
T 1x4c_A           13 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMT   64 (108)
T ss_dssp             SCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT------TEEEEEESSHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC------CEEEEEECCHHHHH
Confidence            46789999999999999999999999999999999987      78999999998874

>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=99.38  E-value=7.9e-13  Score=80.36  Aligned_cols=55  Identities=22%  Similarity=0.329  Sum_probs=49.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      .+++|||+|||..+++++|+++|++||.|..+.++.+..+  .+.|||+|.+.++|.
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~--~g~afV~f~~~~~A~   61 (115)
T 3lqv_A            7 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET--RGTAYVVYEDIFDAK   61 (115)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTT--TTCEEEEESSHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCC--CcEEEEEECCHHHHH
Confidence            5689999999999999999999999999999999976433  578999999999874

>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=99.38  E-value=2.3e-13  Score=81.95  Aligned_cols=57  Identities=12%  Similarity=0.247  Sum_probs=51.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCc-eEEEEEE-eCCCCCCc-cceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGR-IITSRIL-CDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~-v~~~~i~-~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ..++|||+|||..+++++|+++|.+||. |..+.++ .+..++.. +.|||+|.+.|+|.
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~   66 (109)
T 2dis_A            7 GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAA   66 (109)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHH
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHH
Confidence            5689999999999999999999999998 9999998 77777665 56999999999874

>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=99.37  E-value=3.9e-13  Score=79.40  Aligned_cols=52  Identities=21%  Similarity=0.261  Sum_probs=47.4

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ..++|||+|||..+++++|+++|++||.|..+.+.++     ++.|||+|.+.|+|.
T Consensus        16 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~-----~g~afV~f~~~~~A~   67 (97)
T 1why_A           16 PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-----DSFAYIQYESLDAAQ   67 (97)
T ss_dssp             CCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS-----SCCEEEEESSHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC-----CCEEEEEECCHHHHH
Confidence            5689999999999999999999999999999999864     468999999999875

>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=99.37  E-value=6e-13  Score=90.22  Aligned_cols=57  Identities=18%  Similarity=0.345  Sum_probs=51.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCC--ceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYG--RIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G--~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ..++|||+|||..+|+++|+++|++||  .|..|+|++|+.++.+ +++||+|.+.|+|.
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~  126 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSK  126 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHH
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHH
Confidence            457899999999999999999999999  9999999999888877 55999999999875

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.37  E-value=2.2e-13  Score=78.62  Aligned_cols=52  Identities=15%  Similarity=0.196  Sum_probs=47.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      .+.-|+|+||++.+|+++|+++|.+||+|.++++..     .+|+|||+|.++|+|.
T Consensus         6 ~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~-----~kGfaFVey~~~~eA~   57 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL-----NQGIALCKYTTREEAN   57 (89)
T ss_dssp             CCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET-----TTTEEEEEESSHHHHH
T ss_pred             ccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC-----CCcEEEEEECCHHHHH
Confidence            356799999999999999999999999999999976     4688999999999875

>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=99.37  E-value=9.8e-13  Score=77.93  Aligned_cols=53  Identities=26%  Similarity=0.432  Sum_probs=48.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ...++|||+|||..+++++|+++|++||.|..+.+.++     ++.|||+|.+.|+|.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~-----kg~afV~f~~~~~a~   65 (99)
T 2cpj_A           13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAE   65 (99)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT-----TTEEEEECSSSHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC-----CCEEEEEECCHHHHH
Confidence            46689999999999999999999999999999999864     478999999999875

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.37  E-value=1.4e-12  Score=76.59  Aligned_cols=53  Identities=17%  Similarity=0.298  Sum_probs=47.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ..++|||+|||..+++++|+++|++||.|..|  +.+..++.  .|||+|.+.|+|.
T Consensus         7 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~--~afV~f~~~~~a~   59 (94)
T 2e5g_A            7 GLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV--FAIVEMGDVGARE   59 (94)
T ss_dssp             TCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC--EEEEEESSHHHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc--EEEEEECCHHHHH
Confidence            55799999999999999999999999999987  66776666  9999999998874

>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=99.36  E-value=1.5e-12  Score=92.88  Aligned_cols=67  Identities=16%  Similarity=0.203  Sum_probs=55.7

Q ss_pred             eeecCC--Chhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeC---Cc--eEEEEee
Q psy6353           2 VYQTLL--NKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQ---NK--TIKVSYA   71 (136)
Q Consensus         2 v~v~nl--~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~---g~--~l~v~~~   71 (136)
                      |||+|+  +..+|   |+++|++||.|.++.+..    +||||||+|.+.++|++|+++|||..+.   |+  ++.+.++
T Consensus        21 l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~----~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~~ly~~~~   96 (345)
T 3tht_A           21 LVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP----NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFV   96 (345)
T ss_dssp             EEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT----TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEEEC
T ss_pred             EEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC----CCCEEEEEECCHHHHHHHHHHhCCCccccccCCceEEEEEEe
Confidence            799995  56666   999999999999887653    6899999999999999999999998873   45  5666665


Q ss_pred             C
Q psy6353          72 R   72 (136)
Q Consensus        72 ~   72 (136)
                      .
T Consensus        97 ~   97 (345)
T 3tht_A           97 E   97 (345)
T ss_dssp             S
T ss_pred             e
Confidence            3

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.35  E-value=1.3e-12  Score=76.06  Aligned_cols=51  Identities=22%  Similarity=0.511  Sum_probs=46.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ...++|||+|||.++++++|+++|++||.|..+.++       ++.|||+|.+.|+|.
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~-------~g~afV~f~~~~~A~   56 (90)
T 2dnq_A            6 SGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII-------KNYGFVHIEDKTAAE   56 (90)
T ss_dssp             SCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE-------TTEEEEEESSHHHHH
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE-------CCEEEEEECCHHHHH
Confidence            467899999999999999999999999999999998       368999999999875

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.34  E-value=9.1e-13  Score=77.05  Aligned_cols=52  Identities=23%  Similarity=0.339  Sum_probs=47.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ....++|||+|||..+++++|+++|++||.|..+.++++       .|||+|.+.|+|.
T Consensus         7 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~~-------~afV~f~~~~~a~   58 (92)
T 2dgt_A            7 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD-------YAFVHMERAEDAV   58 (92)
T ss_dssp             CCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECSS-------EEEEEESCHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEECC-------EEEEEECCHHHHH
Confidence            446789999999999999999999999999999999853       8999999998874

>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=99.34  E-value=7.3e-13  Score=79.97  Aligned_cols=67  Identities=15%  Similarity=0.404  Sum_probs=53.1

Q ss_pred             CCceEEEEeeCCCCC---CCCCceEEEcCCCCC-CCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          62 QNKTIKVSYARPSSE---SIKGANLYVSGLPKH-MSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        62 ~g~~l~v~~~~~~~~---~~~~~~l~v~nl~~~-~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      .|.++.+..+.+...   ....++|||+|||.. +++++|+++|++||.|..|.+       .++.|||+|.+.|+|.
T Consensus         6 ~g~~~~~~~s~~~~~~~~~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i-------~~g~afV~f~~~~~A~   76 (110)
T 1wf1_A            6 SGMSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV-------HKGYAFVQYSNERHAR   76 (110)
T ss_dssp             CSCCCCCCCCCSCCSCCCTTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE-------ETTEEEEECSSSHHHH
T ss_pred             CCcccccccCCCCCCCCCCCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE-------eCCEEEEEECCHHHHH
Confidence            355566655443322   234589999999999 999999999999999999998       3478999999999874

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.34  E-value=4.8e-13  Score=79.54  Aligned_cols=51  Identities=25%  Similarity=0.331  Sum_probs=47.1

Q ss_pred             ceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          81 ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        81 ~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ++|||+|||.++|+++|+++|++||+|..+.++.+    .++.|||+|.+.|+|.
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~   51 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN----PPGFAFVEFEDPRDAE   51 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS----SSSEEEEECSSHHHHH
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC----CCCEEEEEECCHHHHH
Confidence            47999999999999999999999999999999987    5578999999999874

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.33  E-value=1.1e-12  Score=80.61  Aligned_cols=50  Identities=14%  Similarity=0.213  Sum_probs=46.8

Q ss_pred             ceEEEcCC----CCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCc
Q psy6353          81 ANLYVSGL----PKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGG  130 (136)
Q Consensus        81 ~~l~v~nl----~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~  130 (136)
                      .+|||+||    |+.+++.+|+++|++||+|.+|.++.|+.||.+ |.|||+|.+
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d   57 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYAS   57 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC-
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECC
Confidence            67999999    999999999999999999999999999999998 459999996

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.33  E-value=9.5e-13  Score=76.67  Aligned_cols=52  Identities=23%  Similarity=0.358  Sum_probs=47.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ....++|||+|||..+|+++|+++|++||.|..+.++++       .+||+|.+.|+|.
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~~-------~afV~f~~~~~a~   57 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD-------YAFVHMEKEADAK   57 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECSS-------CEEEEESCHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEECC-------EEEEEECCHHHHH
Confidence            346789999999999999999999999999999999853       8999999999874

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.32  E-value=1.8e-12  Score=78.08  Aligned_cols=52  Identities=25%  Similarity=0.537  Sum_probs=47.5

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ....++|||+|||..+++++|+++|++||.|..+.++       ++.|||+|.+.|+|.
T Consensus        28 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~-------kg~afV~f~~~~~A~   79 (108)
T 2jvo_A           28 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-------NGFAFVEFEEAESAA   79 (108)
T ss_dssp             CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE-------TTEEEEECSSHHHHH
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE-------CCEEEEEECCHHHHH
Confidence            3467899999999999999999999999999999998       478999999999874

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.32  E-value=2.2e-12  Score=76.65  Aligned_cols=56  Identities=16%  Similarity=0.220  Sum_probs=47.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ....++|||+|||..+++++|+++|++||.|   .++.+.....++.|||+|.+.|+|.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~~~g~~~g~afV~f~~~~~A~   67 (101)
T 2fc9_A           12 SGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFEDAK   67 (101)
T ss_dssp             SCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBCSSSCBCSEEEEECSSHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEECCCCCEeeEEEEEECCHHHHH
Confidence            3467899999999999999999999999987   6677744444577999999999875

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.32  E-value=5.1e-13  Score=80.94  Aligned_cols=66  Identities=17%  Similarity=0.091  Sum_probs=48.1

Q ss_pred             ceEEEEeeCCCCCCCCCceEEEcCCCCCCCHHHHHHhhcCCC-ceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          64 KTIKVSYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYG-RIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        64 ~~l~v~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G-~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      .++.+.++.+.   ....+|||+|||.++++++|+++|++|| +|..+.+..+   ..++.|||+|.+.|+|.
T Consensus        15 ~~~~~~~~~~p---~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~---~~rGfaFV~F~~~e~A~   81 (111)
T 2jvr_A           15 VPRGSHMSKLP---AKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR---DFDGTGALEFPSEEILV   81 (111)
T ss_dssp             ----------C---CCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSC---SSSCCEEEEESSHHHHH
T ss_pred             eecchhcCCCC---CCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcC---CCCCEEEEEECCHHHHH
Confidence            34555555433   2568999999999999999999999999 8999988643   24578999999999875

>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=99.31  E-value=1.2e-12  Score=78.90  Aligned_cols=53  Identities=23%  Similarity=0.514  Sum_probs=48.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ...++|||+|||..+++++|+++|++||.|..|.++++     ++.|||+|.+.|+|.
T Consensus        23 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~g~afV~f~~~~~a~   75 (109)
T 1x4g_A           23 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAA   75 (109)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT-----TTEEEEEESSHHHHH
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC-----CCEEEEEECCHHHHH
Confidence            35689999999999999999999999999999999986     578999999999874

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=98.99  E-value=1.7e-13  Score=83.60  Aligned_cols=59  Identities=15%  Similarity=0.271  Sum_probs=52.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceEE--------EEEEeCCCCCCc-cceEeecCccccccC
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRIIT--------SRILCDNLATEN-GKYYSGLGGRERLRR  136 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~--------~~i~~~~~~~~~-~~~fv~f~~~e~~~~  136 (136)
                      ...++|||+|||..+++++|+++|++||.|..        +.++.++.++.. +.|||+|.+.|+|.+
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~   72 (116)
T 2lcw_A            5 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKA   72 (116)
Confidence            35688999999999999999999999999998        999999877776 569999999998863

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.31  E-value=7.5e-13  Score=77.94  Aligned_cols=55  Identities=18%  Similarity=0.340  Sum_probs=49.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEE-EEEeCCCCCCccceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRIITS-RILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~-~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ...++|||+|||..+++++|+++|++||.|..+ .++.++.++.   |||+|.+.++|.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~~---afV~f~~~~~a~   68 (96)
T 2e44_A           13 QRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAV---VNVTYSSKDQAR   68 (96)
T ss_dssp             CSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSEE---EEEEESSHHHHH
T ss_pred             CCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCE---EEEEECCHHHHH
Confidence            356899999999999999999999999999999 5888876665   999999999774

>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=99.31  E-value=6.3e-13  Score=81.00  Aligned_cols=51  Identities=24%  Similarity=0.301  Sum_probs=46.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ...+|||+|||.++++++|+++|++||+|..|.++.+      +.|||+|.+.|+|.
T Consensus        15 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~------g~afV~f~~~~~a~   65 (115)
T 3beg_B           15 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMT   65 (115)
T ss_dssp             --CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT------SEEEEEESSHHHHH
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC------CEEEEEECCHHHHH
Confidence            5689999999999999999999999999999999876      78999999999874

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.30  E-value=3.2e-12  Score=75.92  Aligned_cols=52  Identities=19%  Similarity=0.396  Sum_probs=46.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ..++|||+|||..+++++|+++|++||.|.++.+.+     .++.|||+|.+.|+|.
T Consensus        26 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~-----~~g~afV~f~~~~~A~   77 (101)
T 2la4_A           26 RVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYP-----EKGCCFIKYDTHEQAA   77 (101)
T ss_dssp             SCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEET-----TTTEEEEECSSHHHHH
T ss_pred             CCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEec-----CCCEEEEEECCHHHHH
Confidence            468999999999999999999999999999999983     3477999999998774

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.30  E-value=2.7e-12  Score=75.63  Aligned_cols=52  Identities=27%  Similarity=0.507  Sum_probs=46.0

Q ss_pred             CCCCceEEEcCCCC-CCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPK-HMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~-~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ....++|||+|||. .+++++|+++|++||.|..+.+.       ++.|||+|.+.|+|.
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~-------~g~afV~f~~~~~A~   59 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVR   59 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE-------TTEEEEEESCHHHHH
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe-------CCEEEEEECCHHHHH
Confidence            34678999999998 99999999999999999999985       478999999999874

>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=99.29  E-value=2.2e-12  Score=76.95  Aligned_cols=51  Identities=22%  Similarity=0.332  Sum_probs=46.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ...++|||+|||..+|+++|+++|++||.|..+.+++       +.+||+|.+.|+|.
T Consensus         9 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~~-------~~afV~f~~~~~a~   59 (103)
T 2dgu_A            9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLK-------DYAFIHFDERDGAV   59 (103)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEECS-------SCEEEEESSHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEC-------CEEEEEeCCHHHHH
Confidence            4568999999999999999999999999999999884       48999999999875

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.28  E-value=2.9e-12  Score=83.65  Aligned_cols=57  Identities=23%  Similarity=0.319  Sum_probs=50.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      .+++|||+|||..+++++|+++|++||.|..|.++.+......+.|||+|.+.|+|.
T Consensus        87 ~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~g~~kG~afV~F~~~~~A~  143 (177)
T 2f3j_A           87 TGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADAL  143 (177)
T ss_dssp             TCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHH
Confidence            468999999999999999999999999999999999983334467999999999874

>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=99.28  E-value=2.3e-12  Score=78.02  Aligned_cols=52  Identities=13%  Similarity=0.093  Sum_probs=46.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ..++|||+|||..+++++|+++|++||.|..|.++.     .++.|||+|.+.|+|.
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~-----~~g~afV~f~~~~~A~   60 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE-----GGITAIVEFLEPLEAR   60 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS-----SSSCEEEEESCHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC-----CCCEEEEEeCCHHHHH
Confidence            457999999999999999999999999999999874     3467999999999875

>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=99.26  E-value=6e-12  Score=74.37  Aligned_cols=52  Identities=29%  Similarity=0.530  Sum_probs=46.7

Q ss_pred             CCCCceEEEcCCCC-CCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPK-HMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~-~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ....++|||+|||. .+++++|+++|++||.|..+.+.       ++.|||+|.+.|+|.
T Consensus        19 ~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~-------~g~afV~f~~~~~A~   71 (97)
T 2xnq_A           19 SHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVR   71 (97)
T ss_dssp             CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC-------SSEEEEEESSHHHHH
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe-------CCEEEEEECCHHHHH
Confidence            34678999999998 99999999999999999999983       578999999999874

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.25  E-value=5.6e-12  Score=78.10  Aligned_cols=57  Identities=16%  Similarity=0.272  Sum_probs=47.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHH----HhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELE----SLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~----~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ....++|||+|||..+++++|+    ++|++||.|..|.+..+  ...+|.|||+|.+.|+|.
T Consensus        26 ~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~~--~~~rG~aFV~F~~~~~A~   86 (127)
T 2a3j_A           26 TEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLS--DDNSGKAYIVFATQESAQ   86 (127)
T ss_dssp             CSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECCC--CSSCCCEEEEESSHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEeccC--CCcCCEEEEEECCHHHHH
Confidence            3467899999999999999876    69999999999887642  334577999999998874

>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=99.25  E-value=2.2e-12  Score=78.23  Aligned_cols=53  Identities=15%  Similarity=0.177  Sum_probs=46.4

Q ss_pred             CCCceEEE--cCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          78 IKGANLYV--SGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v--~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      .+..+|||  +|||.++++++|+++|++||+|..+.++.+     +++|||+|.+.|+|.
T Consensus        23 ~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~-----rgfaFV~f~~~~~A~   77 (114)
T 2cq2_A           23 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-----KPYSFARYRTTEESK   77 (114)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT-----CSCEEEEESSHHHHH
T ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC-----CCEEEEEECCHHHHH
Confidence            35688999  669999999999999999999999988642     478999999999875

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.25  E-value=5.4e-12  Score=74.43  Aligned_cols=54  Identities=15%  Similarity=0.268  Sum_probs=46.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ...++|||+|||..+++++|+++|++||.|. +.++.+   ..++.|||+|.+.++|.
T Consensus        17 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~---~~~g~afV~f~~~~~a~   70 (97)
T 2e5j_A           17 PLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ---GPRRRAFLHYPDSAAAQ   70 (97)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE---TTTTEEEEECSSHHHHH
T ss_pred             CCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC---CCCcEEEEEECCHHHHH
Confidence            3568999999999999999999999999997 677764   34477999999998874

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.24  E-value=1.2e-11  Score=73.45  Aligned_cols=59  Identities=20%  Similarity=0.347  Sum_probs=49.6

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          74 SSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        74 ~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      .......++|||+|||..+++++|+++|++|+   .+.++.+..++.. +.|||+|.+.|+|.
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~   68 (102)
T 2fc8_A            9 NARSQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAK   68 (102)
T ss_dssp             SSSSCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHH
T ss_pred             CCCCCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHH
Confidence            33445778999999999999999999999874   6788888877776 56999999999874

>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=99.23  E-value=1.8e-12  Score=76.37  Aligned_cols=56  Identities=16%  Similarity=0.345  Sum_probs=47.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHH----HhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELE----SLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~----~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ...++|||+|||..+++++|+    ++|++||.|..+.++.+  +..++.|||+|.+.|+|.
T Consensus         6 ~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~~--~~~~g~afV~f~~~~~A~   65 (97)
T 1nu4_A            6 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRS--LKMRGQAFVIFKEVSSAT   65 (97)
T ss_dssp             CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHH--HHHTTCEEEEESSHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEcC--CCcCcEEEEEeCCHHHHH
Confidence            467899999999999999999    99999999999988742  223367999999999874

>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=99.22  E-value=5.1e-12  Score=72.92  Aligned_cols=52  Identities=15%  Similarity=0.348  Sum_probs=47.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCC----C-------ceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPY----G-------RIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~----G-------~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ..++|||+|||.++++++|+++|++|    |       .|.++.+.++     ++.|||+|.+.|+|.
T Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~-----kg~afV~f~~~~~a~   67 (87)
T 2hzc_A            5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD-----KNFAFLEFRSVDETT   67 (87)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS-----SSEEEEEESSHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC-----CcEEEEEcCCHHHHH
Confidence            56899999999999999999999999    8       8999999865     478999999999874

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.22  E-value=3.2e-13  Score=80.28  Aligned_cols=57  Identities=21%  Similarity=0.138  Sum_probs=49.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ...++|||+|||.++|+++|+++|++||.|.. .++.+..++.+ +.|||+|.+.|+|.
T Consensus        15 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~   72 (101)
T 1fj7_A           15 TTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLE   72 (101)
T ss_dssp             SCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHH
Confidence            36789999999999999999999999999888 66667666655 56999999999875

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=99.21  E-value=5.3e-11  Score=80.08  Aligned_cols=60  Identities=17%  Similarity=0.209  Sum_probs=55.4

Q ss_pred             HHHHhccCCCeeEEEEEc------cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeC
Q psy6353          13 YEKVHLGFSDAEICVFLI------STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR   72 (136)
Q Consensus        13 l~~~f~~~G~v~~~~~~~------~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~   72 (136)
                      +.+.|++||.|.++.+++      .+++++|++||+|.+.++|++|+..|||..+.||.|.+.++.
T Consensus       146 l~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~  211 (222)
T 3dxb_A          146 VTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYD  211 (222)
T ss_dssp             HHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECC
T ss_pred             HHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcC
Confidence            889999999999999986      245899999999999999999999999999999999998764

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.21  E-value=2.6e-11  Score=71.74  Aligned_cols=51  Identities=20%  Similarity=0.227  Sum_probs=45.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCC--CceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPY--GRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~--G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ...++|||+|||..+++++|+++|++|  |.|..+.+.       ++.|||+|.+.|+|.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~-------~g~afV~f~~~~~A~   65 (99)
T 2cpd_A           13 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI-------RDYAFVHFSNREDAV   65 (99)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC-------SSEEEEEESSHHHHH
T ss_pred             CCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe-------CCeEEEEeCCHHHHH
Confidence            467899999999999999999999999  999999876       358999999999874

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.20  E-value=1.8e-11  Score=75.85  Aligned_cols=52  Identities=15%  Similarity=0.169  Sum_probs=45.5

Q ss_pred             CceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccc-eEeecCcccccc
Q psy6353          80 GANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGK-YYSGLGGRERLR  135 (136)
Q Consensus        80 ~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~-~fv~f~~~e~~~  135 (136)
                      --.|||+||+..+|+++|+++|++||+|..|.+..+.    +++ |||+|.+.++|.
T Consensus        28 VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~----~gfqAFVef~~~~~A~   80 (130)
T 3zzy_A           28 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQ   80 (130)
T ss_dssp             EEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEET----TEEEEEEEESCHHHHH
T ss_pred             eEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCC----CCcEEEEEECCHHHHH
Confidence            3568899999999999999999999999999988643    356 999999998874

>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=99.19  E-value=1.3e-11  Score=71.49  Aligned_cols=51  Identities=18%  Similarity=0.276  Sum_probs=45.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ..++|||+|||..+++++|+++|++| .|..+.+.     ..++.|||+|.+.|+|.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~-----~~~g~afV~f~~~~~a~   54 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD-----RNKRTAFVTLLNGEQAQ   54 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE-----GGGTEEEECCSCHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe-----CCCcEEEEEECCHHHHH
Confidence            56889999999999999999999999 99999885     34477999999998874

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.19  E-value=4.9e-11  Score=68.87  Aligned_cols=55  Identities=24%  Similarity=0.366  Sum_probs=50.1

Q ss_pred             HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCC
Q psy6353          13 YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS   74 (136)
Q Consensus        13 l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~   74 (136)
                      |.+.|++||.|..++++.      +.+||+|.+.++|.+|++ |||..+.||.|+|..+.|.
T Consensus        32 L~~~F~~~G~Vi~vr~~~------d~~fVtF~d~~sAlaAi~-mnG~~v~Gr~LkV~lkt~d   86 (91)
T 2dnr_A           32 LLQQFASFGEVILIRFVE------DKMWVTFLEGSSALNVLS-LNGKELLNRTITIALKSPS   86 (91)
T ss_dssp             HHHHHHTTCCEEEEEECS------SSEEEEESSHHHHHHGGG-GTTCEETTEEEEEEECCCS
T ss_pred             HHHHHHhCCCeEEEEEec------CCEEEEECChHHHHHHHh-cCCeEeCCeEEEEEeCCCC
Confidence            899999999999999876      238999999999999999 9999999999999987754

>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=99.18  E-value=1.4e-11  Score=74.72  Aligned_cols=54  Identities=20%  Similarity=0.380  Sum_probs=45.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCce----EEEEEEeCCCCCC-ccceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRI----ITSRILCDNLATE-NGKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v----~~~~i~~~~~~~~-~~~~fv~f~~~e~~~  135 (136)
                      ...++|||+|||..+|+++|+++|++||.|    ..+.+.    ++. ++.|||+|.+.|+|.
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~----~g~~~g~afV~f~~~~~a~   81 (115)
T 2cpx_A           23 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMM----TGRMRGQAFITFPNKEIAW   81 (115)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEE----CSSSCSEEEEECSSHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcC----CCccceEEEEEECCHHHHH
Confidence            356899999999999999999999999998    455544    444 467999999999874

>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=99.17  E-value=1.8e-11  Score=78.65  Aligned_cols=54  Identities=13%  Similarity=0.149  Sum_probs=46.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ...+|||+|||..+|+++|+++|++||+|..+.+..+.   .++.|||+|.+.|+|.
T Consensus        45 ~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~---~rgfAFVeF~d~~~A~   98 (164)
T 1sjr_A           45 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN---NQFQALLQYADPVSAQ   98 (164)
T ss_dssp             CEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESS---SCEEEEEEESCHHHHH
T ss_pred             ceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCC---CCCEEEEEECCHHHHH
Confidence            44679999999999999999999999999999997543   3356999999998874

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.16  E-value=6.1e-12  Score=73.99  Aligned_cols=55  Identities=15%  Similarity=0.168  Sum_probs=44.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ....++|||+|||..+++++|+++|++||.|..+    ......++.|||+|.+.|+|.
T Consensus        13 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~----~~~~~~~g~afV~f~~~~~a~   67 (96)
T 1fjc_A           13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAE   67 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE----EETTEEEEEEEEEESSHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe----CCCCCcceEEEEEECCHHHHH
Confidence            3467899999999999999999999999988766    222333467999999999875

>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=99.15  E-value=1.8e-11  Score=71.56  Aligned_cols=52  Identities=15%  Similarity=0.256  Sum_probs=44.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCc-eEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGR-IITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~-v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ...++|||+|||.++|+++|+++|++||. |..+.+.      ..+.|||+|.+.|+|.
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~------~~g~afV~f~~~~~A~   58 (93)
T 2cqh_A            6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAI   58 (93)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE------ETTEEEECCSCHHHHH
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc------CCCEEEEEECCHHHHH
Confidence            35689999999999999999999999999 5556553      2477999999999874

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.15  E-value=8.1e-11  Score=72.47  Aligned_cols=50  Identities=14%  Similarity=0.101  Sum_probs=43.5

Q ss_pred             ceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccc-eEeecCcccccc
Q psy6353          81 ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGK-YYSGLGGRERLR  135 (136)
Q Consensus        81 ~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~-~fv~f~~~e~~~  135 (136)
                      ..|||+|||..+|+++|+++|++||.|..|.+...     .+. |||+|.+.++|.
T Consensus        26 l~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~-----~Gf~aFVef~~~~~A~   76 (124)
T 2e5i_A           26 LLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR-----NGIQAMVEFESVLCAQ   76 (124)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES-----SSEEEEEEESSHHHHH
T ss_pred             EEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC-----CCCEEEEEECCHHHHH
Confidence            34689999999999999999999999999999753     265 999999998764

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.09  E-value=2.6e-10  Score=67.14  Aligned_cols=51  Identities=29%  Similarity=0.401  Sum_probs=44.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ...++|||+|+  .+|+++|+++|++||+|..|.+.     ..++.|||+|.+.|+|.
T Consensus        13 ~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~-----~~~g~afV~f~~~~~a~   63 (97)
T 1x5p_A           13 RKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD-----PPRNCAFVTYEKMESAD   63 (97)
T ss_dssp             CCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE-----TTTTEEEEEESSHHHHH
T ss_pred             CCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec-----CCCCEEEEEECCHHHHH
Confidence            46689999995  89999999999999999999985     24467999999998874

>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=99.08  E-value=2.4e-11  Score=76.49  Aligned_cols=57  Identities=21%  Similarity=0.430  Sum_probs=45.5

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEE--------EEEeCCCCCCccceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITS--------RILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~--------~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ....++|||+|||..+|+++|+++|++||.|..+        .+..  .+..++.|||+|.+.++|.
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~--~g~~~g~afV~f~~~~~A~  106 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMK--EGRMKGQAFIGLPNEKAAA  106 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEE--ETTTEEEEEEECSSHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEecc--CCCcccEEEEEeCCHHHHH
Confidence            3466899999999999999999999999998764        3332  2333467999999998874

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.07  E-value=1.7e-10  Score=67.19  Aligned_cols=47  Identities=17%  Similarity=0.255  Sum_probs=40.1

Q ss_pred             Cce-EEEcCCCCCCCHHH----HHHhhcCC-CceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          80 GAN-LYVSGLPKHMSQQE----LESLFSPY-GRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        80 ~~~-l~v~nl~~~~t~~~----l~~~f~~~-G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ..+ |||+|||..+++++    |+++|++| |+|.++       ++  |.|||+|.+.|+|.
T Consensus         8 ~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg--G~AfV~F~~~esA~   60 (96)
T 2diu_A            8 CHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG--CSAILRFINQDSAE   60 (96)
T ss_dssp             SSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT--TCEEEEESSHHHHH
T ss_pred             cceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec--CEEEEEECCHHHHH
Confidence            444 99999999999988    55899999 599988       23  77999999999885

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.01  E-value=5e-10  Score=67.03  Aligned_cols=57  Identities=12%  Similarity=0.043  Sum_probs=46.9

Q ss_pred             CCceEEEcCCCC-----CCCHHHHHHhhcCCCceEEEEEEeCCCC-C-CccceEeecCcccccc
Q psy6353          79 KGANLYVSGLPK-----HMSQQELESLFSPYGRIITSRILCDNLA-T-ENGKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~-----~~t~~~l~~~f~~~G~v~~~~i~~~~~~-~-~~~~~fv~f~~~e~~~  135 (136)
                      .+++|++.|+..     +-++++|++.|++||+|.++.|++++.+ + .+|.+||+|.+.|+|.
T Consensus         7 ~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~   70 (105)
T 2pe8_A            7 PTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAI   70 (105)
T ss_dssp             CCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHH
T ss_pred             CCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHH
Confidence            568899999963     2378999999999999999999998754 3 3466999999999874

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.00  E-value=2.1e-10  Score=78.03  Aligned_cols=53  Identities=19%  Similarity=0.259  Sum_probs=47.4

Q ss_pred             CCCceEEEcCCCCCC---------CHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHM---------SQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~---------t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ...++|||+|||..+         ++++|+++|++||+|.+|+++.+     +++|||+|.++++|.
T Consensus       132 ~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~-----kG~AFV~F~~~~~Ae  193 (240)
T 3u1l_A          132 KKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES-----KNCGFVKFKYQANAE  193 (240)
T ss_dssp             CCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGG-----GTEEEEEESSHHHHH
T ss_pred             cCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECC-----CCEEEEEeCCHHHHH
Confidence            467899999999998         79999999999999999999963     478999999998874

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.97  E-value=1.6e-09  Score=66.12  Aligned_cols=65  Identities=12%  Similarity=0.093  Sum_probs=55.4

Q ss_pred             eeecCCChh-hh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCC-HHHHHHHHHHHc--CceeCCceEEEEe
Q psy6353           2 VYQTLLNKL-FT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHR-PEDAEKAINTLN--GLRLQNKTIKVSY   70 (136)
Q Consensus         2 v~v~nl~~~-~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~-~~~a~~a~~~~~--~~~~~g~~l~v~~   70 (136)
                      |||+||+.. ++   |+++|++||+|..|.+.+  +..  .|||.|.+ .++|..|+.++|  +..|.|..+++..
T Consensus        21 l~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~--g~~--tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~~ev   92 (121)
T 1owx_A           21 LKFSGDLDDQTCREDLHILFSNHGEIKWIDFVR--GAK--EGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEV   92 (121)
T ss_dssp             EEEEESCCSSCCHHHHHHHTCSSCCEEEEECCT--TCS--EEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEE
T ss_pred             EEEecCCCCcCCHHHHHHHHHhcCCEEEEEEec--CCC--EEEEEECCChHHHHHHHHHhhcCCcEEeCcEEEEEE
Confidence            789999999 76   999999999999999876  221  49999999 899999999885  6888888877754

>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=98.96  E-value=9.3e-10  Score=63.86  Aligned_cols=53  Identities=11%  Similarity=0.263  Sum_probs=47.9

Q ss_pred             HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeC
Q psy6353          13 YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR   72 (136)
Q Consensus        13 l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~   72 (136)
                      |.+.|++||.+..++++.      .-+||+|.+.++|.+|++ |||..+.||.|+|..-.
T Consensus        41 L~~~F~~~G~Vilvr~v~------d~~fVtF~d~~sAl~AI~-ldG~~v~Gr~L~V~~k~   93 (95)
T 1ufw_A           41 LMQTLGSYGTIVLVRINQ------GQMLVTFADSHSALSVLD-VDGMKVKGRAVKISGPS   93 (95)
T ss_dssp             HHHHHHHHSCCSEEEEET------TEEEEECSCSHHHHHHHH-GGGSEETTEEEEEECCC
T ss_pred             HHHHHHHCCCEEEEEEec------CcEEEEEcChHHHHHHHh-cCCeeeCCeEEEEeccC
Confidence            899999999999999876      119999999999999999 99999999999998643

>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=98.93  E-value=5.3e-10  Score=79.74  Aligned_cols=53  Identities=13%  Similarity=0.134  Sum_probs=45.9

Q ss_pred             CCCceEEEcC--CCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          78 IKGANLYVSG--LPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~n--l~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      .++.+|||+|  |+..+|+++|+++|++||+|.++.+.+     .++++||+|.+.|+|+
T Consensus        16 ~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~-----~kgfaFV~f~~~~~A~   70 (345)
T 3tht_A           16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-----NKPYSFARYRTTEESK   70 (345)
T ss_dssp             SCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT-----TCSEEEEEESSHHHHH
T ss_pred             CCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC-----CCCEEEEEECCHHHHH
Confidence            4678999999  578899999999999999999987764     2478999999999875

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.91  E-value=1.5e-09  Score=66.30  Aligned_cols=53  Identities=19%  Similarity=0.092  Sum_probs=47.2

Q ss_pred             CCCCceEEEcCCCCC-CCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCc-cccc
Q psy6353          77 SIKGANLYVSGLPKH-MSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGG-RERL  134 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~-~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~-~e~~  134 (136)
                      -..+..|+|+|++.. ++.++|+++|++||+|..|.+.++..+     |||+|.+ +++|
T Consensus        15 ~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~t-----gfVrf~~~~~~A   69 (121)
T 1owx_A           15 EKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKE-----GIILFKEKAKEA   69 (121)
T ss_dssp             CCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCSE-----EEEEESSCHHHH
T ss_pred             ccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCCE-----EEEEECCChHHH
Confidence            457889999999999 999999999999999999999988764     8999999 5554

>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=98.80  E-value=7.8e-09  Score=62.35  Aligned_cols=55  Identities=15%  Similarity=0.171  Sum_probs=44.0

Q ss_pred             CCCceEEEcCCCCCC-----------CHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHM-----------SQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~-----------t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ..+++|++.||....           ++++|+++|++||.|..|.| .+..  .++.+||+|.+.|+|.
T Consensus        13 ~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~~--~~G~afV~f~~~~~A~   78 (112)
T 2dit_A           13 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDRH--PDGVASVSFRDPEEAD   78 (112)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETTC--TTCEEEEECSCHHHHH
T ss_pred             CCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecCC--CCEEEEEEECCHHHHH
Confidence            467899999994433           26899999999999999966 5543  5678999999999874

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.79  E-value=1.8e-08  Score=59.68  Aligned_cols=43  Identities=14%  Similarity=0.196  Sum_probs=37.2

Q ss_pred             CCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          89 PKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        89 ~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      +..+++++|+++|++||+|..|.++.    ..+++|||+|.+.|+|.
T Consensus        26 ~~~~te~~L~~~F~~~G~V~~v~i~~----~~rGfaFVeF~~~~~A~   68 (100)
T 2d9o_A           26 KGGYSKDVLLRLLQKYGEVLNLVLSS----KKPGTAVVEFATVKAAE   68 (100)
T ss_dssp             CCSCCHHHHHHHHHTTSCEEEEEEES----SSSSEEEEEESCHHHHH
T ss_pred             CCCCCHHHHHHHHHhcCCEEEEEEcc----CCCCEEEEEECCHHHHH
Confidence            36789999999999999999999983    44578999999998874

>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=98.78  E-value=3e-09  Score=63.62  Aligned_cols=57  Identities=14%  Similarity=0.167  Sum_probs=46.0

Q ss_pred             CCceEEEcCC--CCCC--------CHHHHHHhhcCCCceEEEEEEeCCCCC---CccceEeecCcccccc
Q psy6353          79 KGANLYVSGL--PKHM--------SQQELESLFSPYGRIITSRILCDNLAT---ENGKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl--~~~~--------t~~~l~~~f~~~G~v~~~~i~~~~~~~---~~~~~fv~f~~~e~~~  135 (136)
                      +++.|.+.|+  |..+        .+++|++.|++||+|.++.|+++..++   ..|.+||+|.+.|+|.
T Consensus         4 ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~   73 (105)
T 3v4m_A            4 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQ   73 (105)
T ss_dssp             CCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHH
T ss_pred             CCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHH
Confidence            5678899998  3333        347999999999999999999988653   3467999999999875

>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=98.65  E-value=1.1e-09  Score=65.39  Aligned_cols=51  Identities=18%  Similarity=0.266  Sum_probs=40.7

Q ss_pred             EcCCCCCCCHHHHHHhh------------cCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          85 VSGLPKHMSQQELESLF------------SPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        85 v~nl~~~~t~~~l~~~f------------~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      +.|||..+++++|++.|            ++||+|.+|.++++..+..+|.+||+|.+.|+|.
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~~~~~G~~fV~f~~~~~A~   82 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAE   82 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHH
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCCCCccEEEEEEECCHHHHH
Confidence            45666677777776666            9999999999999887555677999999999875

>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=98.63  E-value=2.1e-08  Score=61.10  Aligned_cols=57  Identities=9%  Similarity=0.095  Sum_probs=45.4

Q ss_pred             CCceEEEcCCCC--C---CCHHHHHHhhcCCCceEEEEEEeCCCC----CC-ccceEeecCcccccc
Q psy6353          79 KGANLYVSGLPK--H---MSQQELESLFSPYGRIITSRILCDNLA----TE-NGKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~--~---~t~~~l~~~f~~~G~v~~~~i~~~~~~----~~-~~~~fv~f~~~e~~~  135 (136)
                      ++++|++.|+-.  +   -.+++|++.|++||+|.++.|+++..+    +. .|.+||+|.+.|+|.
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~   85 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETH   85 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHH
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHH
Confidence            467889998832  2   247899999999999999999998753    33 366999999999875

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.47  E-value=7.9e-07  Score=52.78  Aligned_cols=65  Identities=15%  Similarity=0.136  Sum_probs=55.4

Q ss_pred             eeecCCChhhh---HHHHhccC-----CCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEe
Q psy6353           2 VYQTLLNKLFT---YEKVHLGF-----SDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY   70 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~-----G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~   70 (136)
                      +=+-|||+.++   ++.+.+++     |.+..+.+..   .. +=|+|+|.|...|-+|.-+++|.++.|++|+|..
T Consensus        24 iaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~p---DH-~GAivef~d~~~AgKasLaL~G~ef~gr~Lr~gT   96 (117)
T 2l9w_A           24 ICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVS---DF-NGAIIIFRDSKFAAKMLMILNGSQFQGKVIRSGT   96 (117)
T ss_dssp             EEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEET---TT-TEEEEECSCHHHHHHHHHHHSSEEETTEEEEEEC
T ss_pred             EEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEec---CC-CceEEEEccchhhHHHHhhcCCeeecCeEEEecC
Confidence            34568999888   89999999     9999998876   22 2399999999999999888999999999999963

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A

Probab=98.26  E-value=3.8e-07  Score=55.17  Aligned_cols=54  Identities=9%  Similarity=0.049  Sum_probs=41.9

Q ss_pred             CCceEEEcCCCCCC----------CHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHM----------SQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~----------t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      .++.|.+.|+=...          .++||++.|++||.|.++.+.++.   ..|.+||+|.+.|+|.
T Consensus         6 ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~---~~G~~fV~f~~~e~A~   69 (114)
T 3s6e_A            6 ATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS---AQGNVYVKCPSIAAAI   69 (114)
T ss_dssp             CCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC---TTCCEEEECSSHHHHH
T ss_pred             CCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC---CcEEEEEEECCHHHHH
Confidence            45678888873221          346899999999999999997764   3577999999999875

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.15  E-value=2.1e-05  Score=46.19  Aligned_cols=81  Identities=21%  Similarity=0.187  Sum_probs=64.8

Q ss_pred             eeecCCChhhh---HHHHhcc-----CCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLG-----FSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP   73 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~-----~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~   73 (136)
                      |.|.|||....   |+-+|+.     =|+|.++....      +-|+|+|.+...|++.+++ ..+.+++.+|.|....+
T Consensus        11 I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~------~~AvItF~d~~va~rVL~k-~~H~L~~~~LsV~P~~~   83 (104)
T 2dhx_A           11 VEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG------CGGVLTFREPADAERVLAQ-ADHELHGAQLSLRPAPP   83 (104)
T ss_dssp             EEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET------TEEEEEESSHHHHHHHHTC-SCCBSSSSBCEEEECCC
T ss_pred             EEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC------CcEEEEEcChHHHHHHhcC-CcceecCeEEEEEcCCC
Confidence            56889998877   7778876     24777776542      4589999999999999884 36889999999987665


Q ss_pred             CCCCCCCceEEEcCCCCCCC
Q psy6353          74 SSESIKGANLYVSGLPKHMS   93 (136)
Q Consensus        74 ~~~~~~~~~l~v~nl~~~~t   93 (136)
                      .    ..+++.+++||+.++
T Consensus        84 ~----~~~r~ll~gl~~~t~   99 (104)
T 2dhx_A           84 R----APARLLLQGLPPGTS   99 (104)
T ss_dssp             C----CCCCCCCCSCCCCCC
T ss_pred             C----CcceEeeecCCCCCC
Confidence            5    568899999999875

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.08  E-value=1.7e-05  Score=46.71  Aligned_cols=69  Identities=16%  Similarity=0.236  Sum_probs=57.2

Q ss_pred             eeecCCChhh-------h-HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCC
Q psy6353           2 VYQTLLNKLF-------T-YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP   73 (136)
Q Consensus         2 v~v~nl~~~~-------~-l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~   73 (136)
                      |++.||+.++       + ++++|.+|+++......+    |-.-.-|.|.++++|.+|...||+..+.|+.++|.++++
T Consensus         8 Liitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lk----SFRRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~YFgq~   83 (104)
T 1wey_A            8 LIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK----SFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQT   83 (104)
T ss_dssp             EEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET----TTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCCC
T ss_pred             EEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecC----cceEEEEEeCChHHHHHHHHHhccceecCceeEEEecCC
Confidence            5677887755       1 799999999998876665    323468999999999999999999999999999999875


Q ss_pred             C
Q psy6353          74 S   74 (136)
Q Consensus        74 ~   74 (136)
                      .
T Consensus        84 ~   84 (104)
T 1wey_A           84 L   84 (104)
T ss_dssp             S
T ss_pred             C
Confidence            4

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.90  E-value=1.3e-05  Score=46.23  Aligned_cols=50  Identities=20%  Similarity=0.296  Sum_probs=40.0

Q ss_pred             CCCceEEEcCCC----CCCCH----HHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCccccc
Q psy6353          78 IKGANLYVSGLP----KHMSQ----QELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERL  134 (136)
Q Consensus        78 ~~~~~l~v~nl~----~~~t~----~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~  134 (136)
                      .+..|+.|.-.|    .++.+    .+|.+.|++||.|..++++.|.       +||+|.+.|+|
T Consensus         5 Ppd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~-------~fVtF~d~~sA   62 (91)
T 2dnr_A            5 SSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK-------MWVTFLEGSSA   62 (91)
T ss_dssp             CSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS-------EEEEESSHHHH
T ss_pred             CCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC-------EEEEECChHHH
Confidence            356788887766    23444    6789999999999999999865       79999998876

>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=97.74  E-value=1.5e-05  Score=53.33  Aligned_cols=45  Identities=9%  Similarity=0.029  Sum_probs=37.2

Q ss_pred             CCCHHHHHHhhcCCCceEEEEEEeCCCC-----CCccceEeecCcccccc
Q psy6353          91 HMSQQELESLFSPYGRIITSRILCDNLA-----TENGKYYSGLGGRERLR  135 (136)
Q Consensus        91 ~~t~~~l~~~f~~~G~v~~~~i~~~~~~-----~~~~~~fv~f~~~e~~~  135 (136)
                      .-.+++|++.|++||.|.++.++++..+     ...|.+||+|.+.|+|.
T Consensus       140 ~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~  189 (222)
T 3dxb_A          140 DDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETH  189 (222)
T ss_dssp             TTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHH
T ss_pred             HHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHH
Confidence            3467899999999999999999977655     33466999999999875

>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=0.00017  Score=41.57  Aligned_cols=54  Identities=11%  Similarity=0.293  Sum_probs=43.0

Q ss_pred             ceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCC-c--cceEeecCccccc
Q psy6353          81 ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATE-N--GKYYSGLGGRERL  134 (136)
Q Consensus        81 ~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~-~--~~~fv~f~~~e~~  134 (136)
                      .+|.|++||+.+|++++.+.++..+.+.....+..+.+.. .  .-||+.|.+.|++
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v   58 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDI   58 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHH
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHH
Confidence            4789999999999999999999999887766665553322 2  2389999998875

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=97.55  E-value=3.5e-05  Score=44.62  Aligned_cols=52  Identities=17%  Similarity=0.127  Sum_probs=42.1

Q ss_pred             CCCCceEEEcCCCCC-----CCH----HHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKH-----MSQ----QELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~-----~t~----~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ..+..|+.|.-++..     +.+    .+|.+.|.+||+|..+++..|.       +||+|.+.|+|.
T Consensus        12 GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~-------~fVtF~d~~sAl   72 (95)
T 1ufw_A           12 GPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ-------MLVTFADSHSAL   72 (95)
T ss_dssp             CCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE-------EEEECSCSHHHH
T ss_pred             CCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc-------EEEEEcChHHHH
Confidence            346789999987743     333    5688999999999999999876       899999998863

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=97.32  E-value=0.00035  Score=41.49  Aligned_cols=51  Identities=8%  Similarity=-0.048  Sum_probs=46.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCC-----CceEEEEEEeCCCCCCccceEeecCccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPY-----GRIITSRILCDNLATENGKYYSGLGGRERL  134 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~-----G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~  134 (136)
                      ..+++-+-|||..+++..|+.+..++     |.+..+.+..|.     +||.|+|.|...|
T Consensus        20 ~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH-----~GAivef~d~~~A   75 (117)
T 2l9w_A           20 LETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF-----NGAIIIFRDSKFA   75 (117)
T ss_dssp             TTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTT-----TEEEEECSCHHHH
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCC-----CceEEEEccchhh
Confidence            57899999999999999999999999     999999999764     8899999998765

>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=97.19  E-value=0.0019  Score=38.91  Aligned_cols=65  Identities=14%  Similarity=0.066  Sum_probs=49.6

Q ss_pred             eeecCCChhhh--HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCC-ceEEEEee
Q psy6353           2 VYQTLLNKLFT--YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQN-KTIKVSYA   71 (136)
Q Consensus         2 v~v~nl~~~~~--l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g-~~l~v~~~   71 (136)
                      |.|-..|....  +...|++||.|.+....    ....+-.|.|.++.+|++|+. .||..+.| -.|=|.+.
T Consensus        27 VtVFGFp~~~~~~VL~~F~~~G~Iv~~~~~----~~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~p~   94 (119)
T 1wwh_A           27 VTVFGFPQASASYILLQFAQYGNILKHVMS----NTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPC   94 (119)
T ss_dssp             EEEECCCGGGHHHHHHHHHTTSCEEEEEEC----SSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEEC
T ss_pred             EEEECCCHHHHHHHHHHHHhhCcEEEeccC----CCCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEEC
Confidence            45556666665  88999999999887752    234578899999999999999 59999985 44556553

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=97.04  E-value=0.00051  Score=39.95  Aligned_cols=56  Identities=13%  Similarity=0.272  Sum_probs=40.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCC-Cc--cceEeecCccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLAT-EN--GKYYSGLGGRERL  134 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~-~~--~~~fv~f~~~e~~  134 (136)
                      .+-+|.|+.||+.+|++++.+.+++.-++.....+....+. ..  .-||+.|.+.|++
T Consensus         8 ~~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv   66 (97)
T 2l08_A            8 HSHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDI   66 (97)
T ss_dssp             CCCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHH
T ss_pred             cceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHH
Confidence            34679999999999999999999988765443333332222 22  2389999998875

>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=96.81  E-value=0.0026  Score=36.93  Aligned_cols=49  Identities=20%  Similarity=0.320  Sum_probs=38.0

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHH
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTL   56 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~   56 (136)
                      ||+-+.|.+..   |.++|+.||.+ .|.++..     -.|||.|.+++.|..|++.+
T Consensus        18 Vf~l~FP~ewKt~DI~~lFs~fggv-~I~WidD-----TsAlvvf~~~~~a~~al~~i   69 (100)
T 1whv_A           18 VLHVTFPKEWKTSDLYQLFSAFGNI-QISWIDD-----TSAFVSLSQPEQVQIAVNTS   69 (100)
T ss_dssp             EEEEECCTTCCHHHHHHHHTTTCSC-CCEEEET-----TEEEEECSCHHHHHHHHHHH
T ss_pred             EEEEeCChhhhhHHHHHHhhccCCE-EEEEEcC-----CeEEEEecCHHHHHHHHHhc
Confidence            34448888876   99999999965 4555541     24999999999999999866

>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=96.74  E-value=0.0025  Score=37.09  Aligned_cols=46  Identities=24%  Similarity=0.398  Sum_probs=36.8

Q ss_pred             EEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          83 LYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        83 l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ++.-+.|+.+...||.++|++|| -..|+.+-|      .-|||.|.+++.++
T Consensus         8 V~~l~FP~ewKt~Di~~lFs~fg-gv~I~WidD------TsAlvvf~~~~~a~   53 (101)
T 3ctr_A            8 VLHVTFPKEWKTSDLYQLFSAFG-NIQISWIDD------TSAFVSLSQPEQVK   53 (101)
T ss_dssp             EEEEECCTTCCHHHHHHHTTTSE-EEEEEEEET------TEEEEEEEEECHHH
T ss_pred             EEEEeCChhhhhHHHHHHHhccC-CEEEEEEcC------CeEEEEecCHHHHH
Confidence            44449999999999999999999 456777754      45799999888764

>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=96.71  E-value=0.0036  Score=36.34  Aligned_cols=47  Identities=28%  Similarity=0.427  Sum_probs=37.5

Q ss_pred             ceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          81 ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        81 ~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ..+++ +.|+.+...||.++|++||. ..|+.+-|      .-|||.|.+++.++
T Consensus        17 HVf~l-~FP~ewKt~DI~~lFs~fgg-v~I~WidD------TsAlvvf~~~~~a~   63 (100)
T 1whv_A           17 HVLHV-TFPKEWKTSDLYQLFSAFGN-IQISWIDD------TSAFVSLSQPEQVQ   63 (100)
T ss_dssp             SEEEE-ECCTTCCHHHHHHHHTTTCS-CCCEEEET------TEEEEECSCHHHHH
T ss_pred             eEEEE-eCChhhhhHHHHHHhhccCC-EEEEEEcC------CeEEEEecCHHHHH
Confidence            44555 99999999999999999994 45666654      45799999988764

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=96.57  E-value=0.0063  Score=37.26  Aligned_cols=70  Identities=13%  Similarity=0.039  Sum_probs=49.9

Q ss_pred             eeecCCChhhh--HHHHhccCCCeeEE-EEEc--------------cCC-CceeeEEEEcCCHHHHHHHHHHHcCceeCC
Q psy6353           2 VYQTLLNKLFT--YEKVHLGFSDAEIC-VFLI--------------STA-QSLGYGFVNYHRPEDAEKAINTLNGLRLQN   63 (136)
Q Consensus         2 v~v~nl~~~~~--l~~~f~~~G~v~~~-~~~~--------------~~~-~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g   63 (136)
                      |.|=..|...+  +-+.|++||.|.+- ...+              ... ....+--|+|.++.+|++|+. .||..+.|
T Consensus        10 VtVFGFp~~~~~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG~ii~G   88 (132)
T 3p3d_A           10 ILVFGYPETMANQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENGAVFNG   88 (132)
T ss_dssp             EEEECCCGGGHHHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTTCEETT
T ss_pred             EEEEecCHHHHHHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCCeEeCc
Confidence            44555677766  88999999998662 1110              000 134567899999999999999 58999999


Q ss_pred             ceEEEEeeC
Q psy6353          64 KTIKVSYAR   72 (136)
Q Consensus        64 ~~l~v~~~~   72 (136)
                      ..|=|.+..
T Consensus        89 ~mIGV~Py~   97 (132)
T 3p3d_A           89 VLLGVIPYT   97 (132)
T ss_dssp             EECEEEECC
T ss_pred             EEEEEEECC
Confidence            877776654

>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=96.55  E-value=0.0035  Score=36.07  Aligned_cols=62  Identities=13%  Similarity=0.166  Sum_probs=45.2

Q ss_pred             eeecCCChhhhHHHHhccCCCeeEEEEEc-cC------CCceeeEEEEcCCHHHHHHHHHHHcCceeCC
Q psy6353           2 VYQTLLNKLFTYEKVHLGFSDAEICVFLI-ST------AQSLGYGFVNYHRPEDAEKAINTLNGLRLQN   63 (136)
Q Consensus         2 v~v~nl~~~~~l~~~f~~~G~v~~~~~~~-~~------~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g   63 (136)
                      |.|.+||..+|.++++++.++.-++.+.. ..      ...-+-|+|.|.+.+++....+.++|+.+.+
T Consensus         4 vVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D   72 (91)
T 1uw4_A            4 VVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLD   72 (91)
T ss_dssp             EEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEEC
T ss_pred             EEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEc
Confidence            56889999999777766666554443333 11      1234679999999999999999999987753

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=96.39  E-value=0.0065  Score=35.63  Aligned_cols=50  Identities=18%  Similarity=0.189  Sum_probs=40.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcC-----CCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSP-----YGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~-----~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ...+|.|.|||+.++++.|.-.|+.     -|+|..+....       ..|.|+|.+.+.+.
T Consensus         7 ~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~-------~~AvItF~d~~va~   61 (104)
T 2dhx_A            7 GGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG-------CGGVLTFREPADAE   61 (104)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET-------TEEEEEESSHHHHH
T ss_pred             CccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC-------CcEEEEEcChHHHH
Confidence            5678999999999999999999986     25777776643       56799999987764

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=96.35  E-value=0.0079  Score=34.92  Aligned_cols=61  Identities=15%  Similarity=0.178  Sum_probs=49.0

Q ss_pred             eeecCCChhhhHHHHhccCCCeeEEEEEc-cCCC------ceeeEEEEcCCHHHHHHHHHHHcCceeC
Q psy6353           2 VYQTLLNKLFTYEKVHLGFSDAEICVFLI-STAQ------SLGYGFVNYHRPEDAEKAINTLNGLRLQ   62 (136)
Q Consensus         2 v~v~nl~~~~~l~~~f~~~G~v~~~~~~~-~~~~------~kg~~fv~f~~~~~a~~a~~~~~~~~~~   62 (136)
                      |.|..||..+|.++++++.+++....... ..|+      .-+.|+|.|.+.++.....+..+|..+.
T Consensus        12 vVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~   79 (97)
T 2l08_A           12 VVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFL   79 (97)
T ss_dssp             EEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEE
T ss_pred             EEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEE
Confidence            67899999999999999999876665554 2222      2356899999999999999999997764

>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=95.77  E-value=0.0078  Score=35.03  Aligned_cols=49  Identities=18%  Similarity=0.299  Sum_probs=37.7

Q ss_pred             eecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHc
Q psy6353           3 YQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLN   57 (136)
Q Consensus         3 ~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~   57 (136)
                      |.-+.|.+..   |.++|+.||.+ .|.++..     ..|||.|.+++.|..|++.+.
T Consensus         9 ~~l~FP~ewKt~Di~~lFs~fggv-~I~WidD-----TsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            9 LHVTFPKEWKTSDLYQLFSAFGNI-QISWIDD-----TSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEECCTTCCHHHHHHHTTTSEEE-EEEEEET-----TEEEEEEEEECHHHHHHHHHT
T ss_pred             EEEeCChhhhhHHHHHHHhccCCE-EEEEEcC-----CeEEEEecCHHHHHHHHHhcc
Confidence            4448888876   99999999943 5555531     249999999999999998764

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=95.67  E-value=0.0074  Score=44.68  Aligned_cols=51  Identities=12%  Similarity=0.144  Sum_probs=37.0

Q ss_pred             CceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          80 GANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        80 ~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      .+.|+|. .|...++.+|.+.|++||+|.++..-.+.  |  -.+-|+|.++|++.
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~--g--~~~~vef~~~~~~~  103 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF--G--LYAVVEFCQKESIG  103 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS--S--EEEEEECC---CCH
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC--C--eEEEEEeCCHHHHH
Confidence            4789998 79999999999999999999988777532  2  45899999998863

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=94.99  E-value=0.014  Score=43.19  Aligned_cols=49  Identities=18%  Similarity=0.130  Sum_probs=34.1

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHH
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAIN   54 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~   54 (136)
                      |+|. .|..++   |.++|++||+|.++..-...   .-|+.|+|.+.++++.++.
T Consensus        56 v~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~---g~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           56 VLIH-CPEKISENKFLKYLSQFGPINNHFFYESF---GLYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             EEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS---SEEEEEECC---CCHHHHS
T ss_pred             EEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC---CeEEEEEeCCHHHHHHHHh
Confidence            4565 455555   99999999999998776522   2699999999999987765

>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=90.29  E-value=0.32  Score=28.46  Aligned_cols=51  Identities=16%  Similarity=0.153  Sum_probs=38.4

Q ss_pred             CCceEEEcCCCCCC-C----HHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCccccc
Q psy6353          79 KGANLYVSGLPKHM-S----QQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERL  134 (136)
Q Consensus        79 ~~~~l~v~nl~~~~-t----~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~  134 (136)
                      -.++|.|.||+..+ .    .+.++++|..|+++......+.     .+-.-|.|.+.|+|
T Consensus         4 ~pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkS-----FRRirv~F~~~~~A   59 (104)
T 1wey_A            4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS-----FKRVRINFSNPLSA   59 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT-----TTEEEEECSSTTHH
T ss_pred             CCceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCc-----ceEEEEEeCChHHH
Confidence            35789999998765 2    2578999999999888777653     34557888888776

>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=88.93  E-value=0.56  Score=28.14  Aligned_cols=52  Identities=17%  Similarity=0.234  Sum_probs=39.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCccccccC
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLRR  136 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~~  136 (136)
                      ...-|.|-+.|+.. ...+-..|++||.|......    .+ ..-..+.|.++.+|+|
T Consensus        23 ~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~----~~-~NWihI~Y~s~~~A~r   74 (119)
T 1wwh_A           23 DDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMS----NT-GNWMHIRYQSKLQARK   74 (119)
T ss_dssp             GGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEEC----SS-SSEEEEEESSHHHHHH
T ss_pred             CCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccC----CC-CCeEEEEeCCHHHHHH
Confidence            46779999999984 67778889999999987751    11 1336899998887754

>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=86.18  E-value=1.3  Score=33.29  Aligned_cols=48  Identities=27%  Similarity=0.436  Sum_probs=36.1

Q ss_pred             CceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          80 GANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        80 ~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ...++++ .|+.+...+|.+.|+.||. ..++++-+      ..+||.|.+.|.++
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~-v~V~widd------t~a~V~~~~~~~a~  487 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGN-IQISWIDD------TSAFVSLSQPEQVQ  487 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCC-CEEEECSS------SEEEEECSCHHHHH
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCC-EEEEEEcC------CeEEEEECCHHHHH
Confidence            3445555 9999999999999999995 45555533      45899999888764

---

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	136
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	2e-13
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	9e-11
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	1e-10
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-10
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-04
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	2e-10
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	2e-10
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	0.001
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	3e-10
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	2e-06
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	3e-10
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	5e-10
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	2e-06
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	6e-10
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	7e-10
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	6e-05
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	8e-10
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	3e-04
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	1e-09
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	5e-04
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	1e-09
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	4e-05
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	1e-09
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	1e-09
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	1e-05
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	2e-09
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	2e-09
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	3e-09
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	4e-09
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	3e-08
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	6e-09
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	0.001
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	1e-08
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	8e-05
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	1e-08
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	1e-05
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	1e-08
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	1e-08
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	2e-08
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	5e-04
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	2e-08
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-08
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	2e-08
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	2e-04
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	4e-08
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	7e-04
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	4e-08
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	4e-08
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	6e-08
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	3e-05
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	8e-08
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	1e-07
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	2e-04
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	1e-07
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	3e-06
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	1e-07
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	1e-04
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	1e-07
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	2e-07
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	3e-07
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	0.001
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	4e-07
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	4e-07
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	5e-07
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	8e-04
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	5e-07
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	3e-04
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	9e-07
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	2e-06
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	2e-06
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	2e-06
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	7e-04
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	2e-06
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-06
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	3e-06
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	4e-06
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	5e-06
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	2e-04
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	6e-06
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	3e-04
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	7e-06
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	7e-06
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	8e-06
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	1e-05
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	2e-05
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	3e-05
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	0.001
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	4e-05
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	5e-05
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	6e-05
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	6e-05
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	0.004
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	6e-05
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	8e-05
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	8e-05
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	5e-04
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	9e-05
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	9e-05
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:) 1e-04
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	1e-04
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	4e-04
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	8e-04
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	0.001
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	0.002
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	0.003

>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 = 60.0 bits (145), Expect = 2e-13
 Identities = 16/69 (23%), Positives = 29/69 (42%), Gaps = 8/69 (11%)

Query: 37  GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKHMSQQE 96
           G  +V Y    DA+ A + L+G  + N+ + V Y   +    K        +     +++
Sbjct: 47  GTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNANRAFQK--------MDTKKKEEQ 98

Query: 97  LESLFSPYG 105
           L+ L   YG
Sbjct: 99  LKLLKEKYG 107

>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 = 52.3 bits (125), Expect = 9e-11
 Identities = 15/46 (32%), Positives = 24/46 (52%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES 77
          T  S GY F  Y      ++AI  LNG++L +K + V  A   +++
Sbjct: 39 TGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAKN 84

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 52.4 bits (125), Expect = 1e-10
 Identities = 13/67 (19%), Positives = 28/67 (41%)

Query: 7  LNKLFTYEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTI 66
          L+   T +++   F DA     +    +S G  ++ +    DAEK +    G  +  +++
Sbjct: 24 LSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSV 83

Query: 67 KVSYARP 73
           + Y   
Sbjct: 84 SLYYTGE 90

>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 = 51.8 bits (124), Expect = 2e-10
 Identities = 9/46 (19%), Positives = 20/46 (43%)

Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGAN 82
          G+ FV Y    +A  A+   +G  +  + + ++ A     +  G +
Sbjct: 51 GFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEPKVNRSGPS 96

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.0 bits (83), Expect = 2e-04
 Identities = 7/36 (19%), Positives = 20/36 (55%), Gaps = 1/36 (2%)

Query: 80  GANLYVSGLPKH-MSQQELESLFSPYGRIITSRILC 114
            + +++  L    + + ++E++FS YG+I+   +  
Sbjct: 15  NSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHK 50

>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 = 51.6 bits (123), Expect = 2e-10
 Identities = 18/67 (26%), Positives = 30/67 (44%), Gaps = 1/67 (1%)

Query: 7  LNKLFTYEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTI 66
          L    + E +   F+       +    +   Y FV++   EDA +A+  LNG  L    I
Sbjct: 16 LMLSTSEEMIEKEFN-NIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPI 74

Query: 67 KVSYARP 73
          +V+ A+P
Sbjct: 75 EVTLAKP 81

>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 = 51.3 bits (122), Expect = 2e-10
 Identities = 40/58 (68%), Positives = 44/58 (75%)

Query: 17 HLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS 74
           +G  ++   V    T QSLGYGFVNY  P+DAEKAINTLNGLRLQ KTIKVSYARPS
Sbjct: 25 SIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPS 82

>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 = 33.5 bits (76), Expect = 0.001
 Identities = 12/25 (48%), Positives = 17/25 (68%)

Query: 82  NLYVSGLPKHMSQQELESLFSPYGR 106
           NL V+ LP++M+Q+E  SLF   G 
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGE 28

>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 = 51.6 bits (123), Expect = 3e-10
 Identities = 18/60 (30%), Positives = 30/60 (50%)

Query: 19 GFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESI 78
          G            T Q  GYGFV +   EDA+ AI  ++ ++L  K I+V+ A   ++++
Sbjct: 34 GPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNKNL 93

>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 = 41.6 bits (97), Expect = 2e-06
 Identities = 14/44 (31%), Positives = 23/44 (52%)

Query: 73  PSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDN 116
           P SE  + A +YV GL + +S+  L  LF   G ++ + +  D 
Sbjct: 2   PISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDR 45

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.6 bits (123), Expect = 3e-10
 Identities = 11/45 (24%), Positives = 22/45 (48%)

Query: 34 QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESI 78
          +  G  FV +     A  A+ ++ G    +K +++ YA+  S+ I
Sbjct: 44 KMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDII 88

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.3 bits (120), Expect = 5e-10
 Identities = 15/41 (36%), Positives = 31/41 (75%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR 72
          T +SLGY +VN+ +P DAE+A++T+N   ++ K +++ +++
Sbjct: 38 TRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ 78

>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 = 40.7 bits (95), Expect = 2e-06
 Identities = 13/36 (36%), Positives = 20/36 (55%)

Query: 81  ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDN 116
           A+LYV  L   +++  L   FSP G I++ R+  D 
Sbjct: 1   ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDM 36

>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 = 50.7 bits (121), Expect = 6e-10
 Identities = 10/39 (25%), Positives = 18/39 (46%)

Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS 75
          G   V++  PE+A+  I TL+G     + I       ++
Sbjct: 58 GVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGTT 96

>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 = 50.4 bits (120), Expect = 7e-10
 Identities = 17/44 (38%), Positives = 29/44 (65%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS 75
          T QS G+ F+++HR EDA +AI  ++G    +  + V +A+PS+
Sbjct: 46 TGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPST 89

>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 = 37.3 bits (86), Expect = 6e-05
 Identities = 8/32 (25%), Positives = 17/32 (53%)

Query: 73  PSSESIKGANLYVSGLPKHMSQQELESLFSPY 104
           P+  +   A + V+ L +   + +L+ LF P+
Sbjct: 1   PNRRADDNATIRVTNLSEDTRETDLQELFRPF 32

>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 = 50.3 bits (120), Expect = 8e-10
 Identities = 13/39 (33%), Positives = 21/39 (53%)

Query: 38 YGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE 76
          + FV Y+   DAE A+  +NG RL ++ I+  +     E
Sbjct: 51 FCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKE 89

>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 = 35.3 bits (81), Expect = 3e-04
 Identities = 11/47 (23%), Positives = 20/47 (42%)

Query: 79  KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYY 125
           K   LYV  L  + +++++  LFS  G I    +  D +      + 
Sbjct: 6   KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFC 52

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.1 bits (119), Expect = 1e-09
 Identities = 16/44 (36%), Positives = 26/44 (59%)

Query: 34  QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES 77
            S  +GFV+Y  P  A+ AI ++NG ++  K +KV   R  ++S
Sbjct: 58  LSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDS 101

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.1 bits (80), Expect = 5e-04
 Identities = 12/38 (31%), Positives = 20/38 (52%)

Query: 67  KVSYARPSSESIKGANLYVSGLPKHMSQQELESLFSPY 104
            +  A    E  +GANL++  LP+    Q+L  +F P+
Sbjct: 5   SIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPF 42

>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 = 49.9 bits (119), Expect = 1e-09
 Identities = 13/43 (30%), Positives = 23/43 (53%), Gaps = 1/43 (2%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTL-NGLRLQNKTIKVSYARP 73
          T    G+GFV++   +DA+KA N L +   L  + + + +A  
Sbjct: 47 TGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADS 89

>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 = 37.6 bits (87), Expect = 4e-05
 Identities = 11/47 (23%), Positives = 22/47 (46%)

Query: 79  KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYY 125
             + + V  +P   +Q+E+  LFS +G + T R+      T   + +
Sbjct: 7   TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGF 53

>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 = 49.7 bits (118), Expect = 1e-09
 Identities = 16/66 (24%), Positives = 24/66 (36%), Gaps = 2/66 (3%)

Query: 13 YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNG--LRLQNKTIKVSY 70
            KV  G  D  +        ++ G+ FV Y     A  A   L    ++L    I V +
Sbjct: 22 IAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDW 81

Query: 71 ARPSSE 76
          A P  +
Sbjct: 82 AEPEID 87

>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 = 49.3 bits (117), Expect = 1e-09
 Identities = 32/51 (62%), Positives = 37/51 (72%)

Query: 75  SESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYY 125
           S SI+ ANLYVSGLPK M+Q+ELE LFS YGRIITSRIL D +   +    
Sbjct: 1   SASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVG 51

>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 = 39.3 bits (91), Expect = 1e-05
 Identities = 15/40 (37%), Positives = 22/40 (55%), Gaps = 2/40 (5%)

Query: 34 QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKT--IKVSYA 71
           S G GF+ + +  +AE+AI  LNG +    T  I V +A
Sbjct: 46 VSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA 85

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 108

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.6 bits (118), Expect = 2e-09
 Identities = 14/79 (17%), Positives = 34/79 (43%), Gaps = 3/79 (3%)

Query: 7  LNKLFTYEKVH-LGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNG--LRLQN 63
          L    T + +H +      +   +  T  +     + Y  P  A+ A  +L+G  +    
Sbjct: 15 LFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNAC 74

Query: 64 KTIKVSYARPSSESIKGAN 82
           T+++ +++ +S ++K  N
Sbjct: 75 CTLRIDFSKLTSLNVKYNN 93

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.3 bits (117), Expect = 2e-09
 Identities = 14/57 (24%), Positives = 26/57 (45%)

Query: 20 FSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE 76
              + C  +     +  Y FV ++   DA  A+  +NG ++  K +KV++A   S 
Sbjct: 32 IGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPSS 88

>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 = 48.6 bits (115), Expect = 3e-09
 Identities = 17/53 (32%), Positives = 30/53 (56%)

Query: 25 ICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES 77
          + V    T +S G+GFV +   +DA+ A+  +NG  +  + I+V  A  SS++
Sbjct: 36 VVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDN 88

>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 = 48.0 bits (114), Expect = 4e-09
 Identities = 19/49 (38%), Positives = 28/49 (57%)

Query: 76  ESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKY 124
           ESIK  NLYV+ LP+ ++  +L+++F  YG I+   IL D L       
Sbjct: 2   ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGV 50

>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 = 45.7 bits (108), Expect = 3e-08
 Identities = 13/48 (27%), Positives = 26/48 (54%), Gaps = 2/48 (4%)

Query: 26 CVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQ--NKTIKVSYA 71
           +    T +  G  FV Y++ E+A++AI+ LN +  +  ++ + V  A
Sbjct: 38 ILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 85

>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 = 47.7 bits (113), Expect = 6e-09
 Identities = 16/42 (38%), Positives = 25/42 (59%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
          T +  G+ FV +   EDA  AI+ +N   L  +TI+V+ A+P
Sbjct: 43 TEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKP 84

>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 = 33.9 bits (77), Expect = 0.001
 Identities = 12/34 (35%), Positives = 18/34 (52%)

Query: 83  LYVSGLPKHMSQQELESLFSPYGRIITSRILCDN 116
           LYV GL + +  + L + F P+G I   +I  D 
Sbjct: 8   LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDY 41

>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 = 46.9 bits (111), Expect = 1e-08
 Identities = 12/38 (31%), Positives = 22/38 (57%)

Query: 38 YGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS 75
          +GFV Y +PE A+KA+  L G  +    ++V  +  ++
Sbjct: 45 FGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISERAT 82

>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 = 36.9 bits (85), Expect = 8e-05
 Identities = 8/43 (18%), Positives = 16/43 (37%)

Query: 83  LYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYY 125
           L++  L    +++ L+ +FS  G I +  I             
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSM 43

>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 = 46.9 bits (111), Expect = 1e-08
 Identities = 21/48 (43%), Positives = 31/48 (64%)

Query: 26 CVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
           +    T  S GY FV++    D+++AI  LNG+ ++NK +KVSYARP
Sbjct: 34 IMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP 81

>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 = 39.2 bits (91), Expect = 1e-05
 Identities = 16/35 (45%), Positives = 22/35 (62%)

Query: 82  NLYVSGLPKHMSQQELESLFSPYGRIITSRILCDN 116
           NL V+ LP+ M+ +EL +LF   G I T RI+ D 
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDY 38

>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 = 46.9 bits (111), Expect = 1e-08
 Identities = 11/38 (28%), Positives = 20/38 (52%)

Query: 38 YGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS 75
          +GF+       AE A   L+ + L+ K ++V +A  S+
Sbjct: 46 FGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSA 83

>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 = 47.1 bits (111), Expect = 1e-08
 Identities = 9/51 (17%), Positives = 17/51 (33%)

Query: 27 VFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES 77
                 +S     +N+  P  A  A   L+      K +K+ +A+     
Sbjct: 37 DTTFQYFKSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQTLHIG 87

>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 = 46.5 bits (110), Expect = 2e-08
 Identities = 13/48 (27%), Positives = 23/48 (47%)

Query: 24 EICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
          +  V    + +SLG   V++ R  DA KA+   NG+ L  + + +   
Sbjct: 29 KAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLV 76

>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 = 34.5 bits (79), Expect = 5e-04
 Identities = 10/43 (23%), Positives = 19/43 (44%)

Query: 83  LYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYY 125
           L VS L   +S  +++ LF+ +G +  + +  D      G   
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTAD 45

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

 Score = 47.6 bits (112), Expect = 2e-08
 Identities = 17/54 (31%), Positives = 27/54 (50%), Gaps = 6/54 (11%)

Query: 38  YGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE------SIKGANLYV 85
           YGFV +     A++AI  LNG  + NK +KV+ A    +      ++   N Y+
Sbjct: 86  YGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGIAGAVGDGNGYL 139

>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 = 46.9 bits (111), Expect = 2e-08
 Identities = 11/43 (25%), Positives = 17/43 (39%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS 74
               G  FV +    D +KA+  L G +  N+ +   Y  P 
Sbjct: 54 EVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPD 96

>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 = 46.5 bits (110), Expect = 2e-08
 Identities = 8/45 (17%), Positives = 15/45 (33%), Gaps = 2/45 (4%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE 76
          T  S G+GFV +   E   K ++  +   +  +            
Sbjct: 46 TGHSKGFGFVRFTEYETQVKVMSQRHM--IDGRWCDCKLPNSKQS 88

>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 = 35.7 bits (82), Expect = 2e-04
 Identities = 12/37 (32%), Positives = 23/37 (62%)

Query: 79  KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
           K ++L V GLP   ++Q+L+  FS +G ++  ++  D
Sbjct: 7   KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKD 43

>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 = 45.9 bits (108), Expect = 4e-08
 Identities = 14/42 (33%), Positives = 20/42 (47%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
          T +  G   V+Y  P  A+ A+   +G   Q   +KVS AR 
Sbjct: 54 TGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARK 95

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.8 bits (79), Expect = 7e-04
 Identities = 8/41 (19%), Positives = 16/41 (39%)

Query: 75  SESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
            E    + +YV GL   ++  +L   F   G +  ++    
Sbjct: 3   DEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQ 43

>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 = 45.9 bits (108), Expect = 4e-08
 Identities = 12/48 (25%), Positives = 22/48 (45%)

Query: 34 QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGA 81
          +  G+ FV +  PE A KA   ++G   Q + + V  +    E+ +  
Sbjct: 48 KPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKEASQSG 95

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.9 bits (108), Expect = 4e-08
 Identities = 13/41 (31%), Positives = 17/41 (41%)

Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES 77
          GYGF  Y   E A  A+  LNG     + ++V  A      
Sbjct: 51 GYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASEKNK 91

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.3 bits (107), Expect = 6e-08
 Identities = 11/37 (29%), Positives = 19/37 (51%)

Query: 38 YGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS 74
          Y FV +   E A  AI ++NG  ++   +K  + + S
Sbjct: 56 YSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKES 92

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.0 bits (88), Expect = 3e-05
 Identities = 11/43 (25%), Positives = 22/43 (51%)

Query: 74  SSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDN 116
           +  S K   +Y  G+   ++ Q +   FSP+G+I+  R+  + 
Sbjct: 12  NQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK 54

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.6 bits (105), Expect = 8e-08
 Identities = 19/72 (26%), Positives = 33/72 (45%), Gaps = 7/72 (9%)

Query: 8  NKLF------TYEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRL 61
          N L+      T   +   FS     +  +S        FV Y + E A++A+  LNG ++
Sbjct: 6  NTLYVYGEDMTPTLLRGAFSPFGNIID-LSMDPPRNCAFVTYEKMESADQAVAELNGTQV 64

Query: 62 QNKTIKVSYARP 73
          ++  +KV+ AR 
Sbjct: 65 ESVQLKVNIARK 76

>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 = 44.7 bits (105), Expect = 1e-07
 Identities = 13/40 (32%), Positives = 18/40 (45%)

Query: 34 QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
           S GY  V Y   + A  A   LNG  +  +TI+V +   
Sbjct: 47 FSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFV 86

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 35.9 bits (82), Expect = 2e-04
 Identities = 8/30 (26%), Positives = 17/30 (56%)

Query: 76  ESIKGANLYVSGLPKHMSQQELESLFSPYG 105
            S++G  L+V+ + +   + E++  F  YG
Sbjct: 3   RSVEGWILFVTSIHEEAQEDEIQEKFCDYG 32

>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 = 44.6 bits (105), Expect = 1e-07
 Identities = 17/51 (33%), Positives = 27/51 (52%)

Query: 26 CVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE 76
          C  +     S GYGFV++   E AE+AI  +NG+ L ++ + V   +   E
Sbjct: 38 CKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKE 88

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.8 bits (95), Expect = 3e-06
 Identities = 12/44 (27%), Positives = 23/44 (52%)

Query: 73  PSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDN 116
           PS       N+++  L K +  + L   FS +G I++ +++CD 
Sbjct: 1   PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE 44

>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 = 44.4 bits (104), Expect = 1e-07
 Identities = 17/45 (37%), Positives = 24/45 (53%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE 76
          T  S GY F+N+   + ++ AI  +NG  L N+ I VSYA     
Sbjct: 37 TGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDS 81

>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 = 36.3 bits (83), Expect = 1e-04
 Identities = 7/37 (18%), Positives = 18/37 (48%)

Query: 83  LYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLAT 119
           +++  L   + ++ L   FS +G I+ +  +  +  T
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDT 37

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 44.4 bits (104), Expect = 1e-07
 Identities = 14/43 (32%), Positives = 20/43 (46%)

Query: 38 YGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKG 80
           G V Y R ED E A+  L+  + ++   + SY R   E   G
Sbjct: 52 MGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRVYPERSSG 94

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 109

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.4 bits (104), Expect = 2e-07
 Identities = 14/66 (21%), Positives = 25/66 (37%)

Query: 38  YGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKHMSQQEL 97
              V       A+ A++ LNG +L  K I+++ ++  +  +        GL K      L
Sbjct: 42  NALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPL 101

Query: 98  ESLFSP 103
                P
Sbjct: 102 HRFKKP 107

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.5 bits (102), Expect = 3e-07
 Identities = 13/40 (32%), Positives = 23/40 (57%)

Query: 34 QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
           S G+GFV +    DA++A   L+G  ++ + I+V+ A  
Sbjct: 49 GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATA 88

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 33.9 bits (77), Expect = 0.001
 Identities = 10/42 (23%), Positives = 19/42 (45%)

Query: 74  SSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
           S        L+VS +P      +L  +F  +G+I+   I+ +
Sbjct: 5   SESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN 46

>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 = 43.1 bits (101), Expect = 4e-07
 Identities = 12/74 (16%), Positives = 26/74 (35%), Gaps = 2/74 (2%)

Query: 7  LNKLFTYEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTI 66
               T +++   FS     + +        + FV +   + A+        L ++  ++
Sbjct: 13 CTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG--EDLIIKGISV 70

Query: 67 KVSYARPSSESIKG 80
           +S A P   S  G
Sbjct: 71 HISNAEPKHNSNSG 84

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.1 bits (101), Expect = 4e-07
 Identities = 11/48 (22%), Positives = 20/48 (41%)

Query: 26 CVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
           + L +      + FV +  P DAE A+   +G       ++V + R 
Sbjct: 43 DIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRS 90

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 42.7 bits (100), Expect = 5e-07
 Identities = 13/53 (24%), Positives = 22/53 (41%), Gaps = 1/53 (1%)

Query: 19 GFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
          G     + +    T +S G+GFV +      +K +   +   L +KTI    A
Sbjct: 25 GEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA 76

>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 = 33.8 bits (77), Expect = 8e-04
 Identities = 6/32 (18%), Positives = 15/32 (46%)

Query: 83  LYVSGLPKHMSQQELESLFSPYGRIITSRILC 114
           +++ GL    +Q+ L   F  +G +    ++ 
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMR 34

>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 = 43.1 bits (101), Expect = 5e-07
 Identities = 10/61 (16%), Positives = 24/61 (39%), Gaps = 1/61 (1%)

Query: 17  HLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE 76
             G     + +   ++ +S G+GFV +    + + A+       +  + ++   A    E
Sbjct: 43  QWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVAREE 101

Query: 77  S 77
           S
Sbjct: 102 S 102

>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 = 35.4 bits (81), Expect = 3e-04
 Identities = 10/52 (19%), Positives = 25/52 (48%), Gaps = 1/52 (1%)

Query: 64  KTIK-VSYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILC 114
           KT++ V   R   E  +   L++ GL    +++ L + +  +G++    ++ 
Sbjct: 3   KTLETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMR 54

>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 = 42.4 bits (99), Expect = 9e-07
 Identities = 12/42 (28%), Positives = 19/42 (45%), Gaps = 1/42 (2%)

Query: 34 QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS 75
          +S GYGFV       AE+A    N + +  +   V+ A   +
Sbjct: 50 KSRGYGFVTMADRAAAERACKDPNPI-IDGRKANVNLAYLGA 90

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.7 bits (97), Expect = 2e-06
 Identities = 13/50 (26%), Positives = 21/50 (42%), Gaps = 6/50 (12%)

Query: 34 QSLGYGFVNYHRPEDAEKAINTLN------GLRLQNKTIKVSYARPSSES 77
           S G  F  +   E A+K +   +      GL+L  + +KV  A    E+
Sbjct: 48 HSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEA 97

>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 = 41.2 bits (96), Expect = 2e-06
 Identities = 7/40 (17%), Positives = 16/40 (40%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
               G   V +   ++A  A+  LN   + ++ +K+   
Sbjct: 47 KGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG 86

>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 = 41.3 bits (96), Expect = 2e-06
 Identities = 11/55 (20%), Positives = 23/55 (41%)

Query: 19 GFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
                I +  +    S  + +++    EDA   +  LNGL+++  T+    + P
Sbjct: 26 NVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP 80

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 34.4 bits (78), Expect = 7e-04
 Identities = 4/26 (15%), Positives = 11/26 (42%)

Query: 83  LYVSGLPKHMSQQELESLFSPYGRII 108
           L+++  P   +Q+ +  L      + 
Sbjct: 4   LWMTNFPPSYTQRNIRDLLQDINVVA 29

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 41.4 bits (96), Expect = 2e-06
 Identities = 9/67 (13%), Positives = 23/67 (34%), Gaps = 1/67 (1%)

Query: 7  LNKLFTYEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRL-QNKT 65
          L +      + + F+       +          FV +     +  A   L G ++     
Sbjct: 16 LPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKEALQGFKITPTHA 75

Query: 66 IKVSYAR 72
          +K+++A+
Sbjct: 76 MKITFAK 82

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.7 bits (95), Expect = 2e-06
 Identities = 12/40 (30%), Positives = 19/40 (47%), Gaps = 1/40 (2%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
          T +S G+GFV +   E  +K ++     +L  K I    A
Sbjct: 37 TGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKRA 75

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.5 bits (94), Expect = 3e-06
 Identities = 13/55 (23%), Positives = 25/55 (45%), Gaps = 1/55 (1%)

Query: 17 HLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
            G  D  + +F  +T +  G+GFV +   +  EK    ++   + NK ++   A
Sbjct: 22 QFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA 75

>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 = 40.5 bits (94), Expect = 4e-06
 Identities = 11/43 (25%), Positives = 20/43 (46%), Gaps = 1/43 (2%)

Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
            + +    F+ +   + AE+A+  +N   L N+ I VS A  
Sbjct: 43 EHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSLADK 84

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.9 bits (97), Expect = 5e-06
 Identities = 7/40 (17%), Positives = 14/40 (35%), Gaps = 1/40 (2%)

Query: 37  GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE 76
           G+ FV +   +  +K +       +     +V  A    E
Sbjct: 140 GFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKALSKQE 178

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.9 bits (84), Expect = 2e-04
 Identities = 8/34 (23%), Positives = 16/34 (47%)

Query: 83  LYVSGLPKHMSQQELESLFSPYGRIITSRILCDN 116
           L++ GL    + + L S F  +G +    ++ D 
Sbjct: 9   LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDP 42

>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 = 39.7 bits (92), Expect = 6e-06
 Identities = 14/52 (26%), Positives = 25/52 (48%)

Query: 17 HLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKV 68
            G       V+   + +S G+ FV +   +DA++A    NG+ L  + I+V
Sbjct: 32 KYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 83

>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 = 35.4 bits (81), Expect = 3e-04
 Identities = 12/37 (32%), Positives = 19/37 (51%)

Query: 80  GANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDN 116
              L V GL  + ++++L  +FS YG I    I+ D 
Sbjct: 9   NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQ 45

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.7 bits (92), Expect = 7e-06
 Identities = 9/49 (18%), Positives = 17/49 (34%)

Query: 34 QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGAN 82
          ++    FV     E A+ AI   +    + K + V      +    G +
Sbjct: 38 RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDALLCSGPS 86

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.0 bits (93), Expect = 7e-06
 Identities = 8/42 (19%), Positives = 20/42 (47%), Gaps = 2/42 (4%)

Query: 38 YGFVNYHRPEDAEKAINTLNGLRL--QNKTIKVSYARPSSES 77
          + ++ Y   + A+ A   + G  L   ++ ++V +A+    S
Sbjct: 55 FAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSGPSS 96

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.8 bits (92), Expect = 8e-06
 Identities = 10/40 (25%), Positives = 13/40 (32%)

Query: 34 QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
           S G GF      E  E  I   NG  ++      +   P
Sbjct: 57 TSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEP 96

>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 = 39.3 bits (91), Expect = 1e-05
 Identities = 12/70 (17%), Positives = 27/70 (38%), Gaps = 6/70 (8%)

Query: 7  LNKLFTYEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRL----- 61
          L    +  ++        +    +    +  Y F  Y   E++++A  TLNG  +     
Sbjct: 28 LGNGVSRNQLLPVLEKCGLVDA-LLMPPNKPYSFARYRTTEESKRAYVTLNGKEVVDDLG 86

Query: 62 QNKTIKVSYA 71
          Q  T+ +++ 
Sbjct: 87 QKITLYLNFV 96

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.0 bits (90), Expect = 2e-05
 Identities = 10/45 (22%), Positives = 23/45 (51%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE 76
           T +  G  F+ +   E A +A++ +NG +L  K + + + +   +
Sbjct: 56  TGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKKQ 100

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.6 bits (87), Expect = 3e-05
 Identities = 7/53 (13%), Positives = 18/53 (33%), Gaps = 1/53 (1%)

Query: 19 GFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
          G  ++        T +  G+ F+ +   E  +K +       +     ++  A
Sbjct: 24 GEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA 75

>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 = 33.8 bits (77), Expect = 0.001
 Identities = 7/42 (16%), Positives = 19/42 (45%)

Query: 83  LYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKY 124
           ++V GL     ++++   F  +G + +  +  DN   +   +
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGF 43

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.8 bits (87), Expect = 4e-05
 Identities = 12/49 (24%), Positives = 22/49 (44%), Gaps = 1/49 (2%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKG 80
             +  G+G+  +   +    A++ LN   L NK I+V  A  + +   G
Sbjct: 53  PERLKGFGYAEFEDLDSLLSALS-LNEESLGNKRIRVDVADQAQDKDSG 100

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.1 bits (85), Expect = 5e-05
 Identities = 11/30 (36%), Positives = 17/30 (56%)

Query: 38 YGFVNYHRPEDAEKAINTLNGLRLQNKTIK 67
          YGFV++  P  A+KA+  L    +Q +  K
Sbjct: 42 YGFVDFDSPSAAQKAVTALKASGVQAQMAK 71

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.3 bits (86), Expect = 6e-05
 Identities = 15/70 (21%), Positives = 28/70 (40%), Gaps = 6/70 (8%)

Query: 7  LNKLFTYEKVHLGFSDAEICVFLIS-----TAQSLGYGFVNYHRPEDAEKAINTLNGLRL 61
          L+   T E +   F         +      T +S G+GFV Y   E+ + A+N     ++
Sbjct: 14 LSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKV 72

Query: 62 QNKTIKVSYA 71
            + ++   A
Sbjct: 73 DGRVVEPKRA 82

>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 = 37.0 bits (85), Expect = 6e-05
 Identities = 15/41 (36%), Positives = 22/41 (53%), Gaps = 1/41 (2%)

Query: 37 GYGFVNYHRPEDAEKAINTLNG-LRLQNKTIKVSYARPSSE 76
          GY FV+Y     A +AI TL+G + L  K ++V Y+     
Sbjct: 38 GYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKL 78

>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 = 32.0 bits (72), Expect = 0.004
 Identities = 7/32 (21%), Positives = 14/32 (43%)

Query: 83  LYVSGLPKHMSQQELESLFSPYGRIITSRILC 114
           LY+  L   ++  +L  LF      +  ++L 
Sbjct: 4   LYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL 35

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 37.5 bits (86), Expect = 6e-05
 Identities = 6/52 (11%), Positives = 18/52 (34%), Gaps = 2/52 (3%)

Query: 38  YGFVNYHRPEDAEKAINTL--NGLRLQNKTIKVSYARPSSESIKGANLYVSG 87
              V +   + A++ +       + +  +    +Y+     +  G +   SG
Sbjct: 53  QALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRITRPGNSGPSSG 104

>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 = 37.0 bits (85), Expect = 8e-05
 Identities = 7/47 (14%), Positives = 21/47 (44%), Gaps = 1/47 (2%)

Query: 26 CVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR 72
           V  +   Q   + F+ +   ++  +A+   +G+  Q +++K+    
Sbjct: 38 PVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIRRPH 83

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.3 bits (86), Expect = 8e-05
 Identities = 11/42 (26%), Positives = 18/42 (42%), Gaps = 1/42 (2%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
          + +S G  +V +   +    AI  L G RL    I V  ++ 
Sbjct: 56 SRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQA 96

>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 = 35.0 bits (80), Expect = 5e-04
 Identities = 11/44 (25%), Positives = 19/44 (43%)

Query: 73  PSSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDN 116
            S E      ++   L   +  ++LE  FS  G++   RI+ D 
Sbjct: 11  LSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDR 54

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 111

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 37.2 bits (85), Expect = 9e-05
 Identities = 7/41 (17%), Positives = 14/41 (34%)

Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES 77
              V +  P +A KA   L   +  +  + + +A      
Sbjct: 47 ITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGVFG 87

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.7 bits (84), Expect = 9e-05
 Identities = 8/38 (21%), Positives = 15/38 (39%), Gaps = 2/38 (5%)

Query: 38 YGFVNYHRPEDAEKAIN--TLNGLRLQNKTIKVSYARP 73
            F+     E A   +N  +     L+N+ I + Y+  
Sbjct: 46 QAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNH 83

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.9 bits (85), Expect = 1e-04
 Identities = 14/47 (29%), Positives = 20/47 (42%)

Query: 24  EICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
           E+ V        +G  +V + R EDAEKA+  LN      + I    
Sbjct: 56  EMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAEL 102

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.3 bits (83), Expect = 1e-04
 Identities = 10/62 (16%), Positives = 26/62 (41%), Gaps = 1/62 (1%)

Query: 14 EKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRL-QNKTIKVSYAR 72
          +   L  S+  +        +      +     E+A +A+  L+   L +N  ++VS+++
Sbjct: 26 DLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSK 85

Query: 73 PS 74
           +
Sbjct: 86 ST 87

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 34.8 bits (79), Expect = 4e-04
 Identities = 12/36 (33%), Positives = 19/36 (52%)

Query: 34 QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVS 69
                +V Y R EDA +AI  +N + +  +T+K S
Sbjct: 54 GPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKAS 89

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 34.5 bits (78), Expect = 8e-04
 Identities = 13/42 (30%), Positives = 23/42 (54%), Gaps = 1/42 (2%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
          T  +  +G+V++   ED EKA+  L GL++    IK+   + 
Sbjct: 50 TGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKG 90

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.1 bits (77), Expect = 0.001
 Identities = 9/39 (23%), Positives = 18/39 (46%)

Query: 38 YGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE 76
           G V + R ED   A+  L+  + ++   + +Y R   +
Sbjct: 37 TGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVD 75

>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 = 33.7 bits (76), Expect = 0.002
 Identities = 11/51 (21%), Positives = 17/51 (33%), Gaps = 1/51 (1%)

Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGAN 82
            Q LG   V +   +DA K+   L+  +L  +   V             N
Sbjct: 46 NGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVVTLEDMREIEKN 95

>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 = 32.9 bits (74), Expect = 0.003
 Identities = 12/51 (23%), Positives = 24/51 (47%), Gaps = 1/51 (1%)

Query: 32  TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGAN 82
             +S G  FV +   E AEKA+   +  R+ ++ I++  +  +     G +
Sbjct: 53  QGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFKSSRAEVRTSGPS 102

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	136
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.97
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.88
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.88
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.88
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.87
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.87
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.87
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.87
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.87
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.86
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.86
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.86
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.86
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.85
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.85
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.85
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.85
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.85
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.85
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.85
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.84
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.84
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.84
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.84
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.84
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.84
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.84
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.84
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.83
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.83
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.83
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.83
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.82
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.82
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.82
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.82
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.81
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.81
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.81
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.81
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.81
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.8
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.8
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.8
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.8
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.8
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.79
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.79
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.79
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.78
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.78
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.78
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.78
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.77
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.77
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.77
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.77
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.77
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.76
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.76
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.76
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.76
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.75
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.75
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.75
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.75
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.75
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.74
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.73
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.73
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	99.73
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.72
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.72
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.72
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.71
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.71
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.7
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.68
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.67
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.66
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.66
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.65
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.65
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.65
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.64
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.64
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.64
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.64
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.64
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.63
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.63
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.63
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.63
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.63
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.62
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.62
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.61
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.61
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.6
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.6
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.6
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.59
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.59
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.59
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.58
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.58
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.58
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.57
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.57
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.57
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.56
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.56
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.56
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.55
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.55
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.55
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.55
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.54
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.54
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.54
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.53
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.52
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.52
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.52
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.49
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.49
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.49
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.48
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.46
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.45
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.45
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.44
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.43
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.43
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.43
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.43
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.43
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.42
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.42
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.41
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.4
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.39
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.39
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.39
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.39
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.39
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.38
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.38
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.37
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.36
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.36
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.35
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.35
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.34
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.31
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.3
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.28
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.27
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.27
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.26
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.23
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.22
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.21
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.19
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.19
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.16
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.14
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	98.91
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	98.87
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	98.86
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.59
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	98.51
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	98.12
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.87
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.69
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	96.08
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	94.15
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	93.32

>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=99.97  E-value=7.2e-30  Score=166.52  Aligned_cols=133  Identities=19%  Similarity=0.366  Sum_probs=118.5

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..+|   |+++|++||.|.++.+++  .++.++|||||+|.+.++|++|+. .++..+.++.+.+.+..+...
T Consensus         9 lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~-~~~~~~~~~~~~~~~~~~~~~   87 (183)
T d1u1qa_           9 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAVSRED   87 (183)
T ss_dssp             EEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECCCTTG
T ss_pred             EEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHH-hcCCcccccchhhhhhhhccc
Confidence            79999999998   999999999999999988  789999999999999999999998 467788888888876654432


Q ss_pred             ------CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          77 ------SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        77 ------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                            ....++|||+|||..+|+++|+++|+.||.|..+.++.+..++.. +.+||+|.++|+|.
T Consensus        88 ~~~~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~  153 (183)
T d1u1qa_          88 SQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVD  153 (183)
T ss_dssp             GGSTTTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHH
T ss_pred             ccccccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHH
Confidence                  245689999999999999999999999999999999999887776 45999999999875

>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=1.1e-22  Score=116.14  Aligned_cols=73  Identities=58%  Similarity=0.844  Sum_probs=69.7

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS   74 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~   74 (136)
                      |||+|||..++   |+++|++||+|.++.+++  .+++++|||||+|.+.++|+.|+..|||..+.|++|+|.+++|.
T Consensus         5 l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkPs   82 (82)
T d1fxla1           5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPS   82 (82)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             EEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeCc
Confidence            89999999999   999999999999999987  77899999999999999999999999999999999999999873

>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=1.1e-22  Score=118.18  Aligned_cols=74  Identities=27%  Similarity=0.462  Sum_probs=70.9

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS   75 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~   75 (136)
                      |||+|||..++   |+++|++||+|.++.++.  .+|+++|||||+|.+.++|++|+..|||..+.|++|+|.+++|+.
T Consensus        11 i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~akp~~   89 (90)
T d2cq0a1          11 IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPST   89 (90)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESSCCC
T ss_pred             EEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEeeeCCC
Confidence            79999999999   999999999999999998  689999999999999999999999999999999999999999875

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.88  E-value=7.3e-23  Score=116.96  Aligned_cols=72  Identities=33%  Similarity=0.577  Sum_probs=69.2

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP   73 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~   73 (136)
                      |||+|||..++   |+++|++||+|.++.+++  .+|+++|||||+|.+.++|+.|++.|||..+.|++|+|.+++|
T Consensus         5 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           5 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   81 (82)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             EEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            79999999999   999999999999999988  7899999999999999999999999999999999999999986

>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=1.6e-22  Score=117.24  Aligned_cols=74  Identities=27%  Similarity=0.424  Sum_probs=70.5

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS   75 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~   75 (136)
                      |||+|||..++   |+++|++||+|.++.+++  .+|+++|||||+|.+.++|+.|+..+||..++|++|.|.++.|+.
T Consensus         8 lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~p~~   86 (89)
T d2cqba1           8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPMR   86 (89)
T ss_dssp             EEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECCCCC
T ss_pred             EEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCCCC
Confidence            89999999999   999999999999999988  779999999999999999999999999999999999999998764

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=2.1e-22  Score=115.76  Aligned_cols=75  Identities=23%  Similarity=0.356  Sum_probs=71.2

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..+|   |+++|++||+|.++++++  .+|+++|||||+|.++++|+.|+..+||..+.|++|.|.++.+..+
T Consensus         4 lfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~~~   83 (85)
T d2u2fa_           4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAK   83 (85)
T ss_dssp             EEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCCCC
T ss_pred             EEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCCC
Confidence            79999999998   999999999999999998  7899999999999999999999999999999999999999987654

>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=2.5e-22  Score=114.15  Aligned_cols=71  Identities=25%  Similarity=0.356  Sum_probs=68.2

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR   72 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~   72 (136)
                      |||+|||..+|   |+++|++||+|.++++++  .+|+++|||||+|.++++|..|++.|||..+.|++|+|.+++
T Consensus         3 lfV~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           3 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             EEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             EEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            79999999999   999999999999999998  779999999999999999999999999999999999999985

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.87  E-value=4e-22  Score=115.28  Aligned_cols=73  Identities=21%  Similarity=0.320  Sum_probs=69.6

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS   74 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~   74 (136)
                      |||+|||..++   |+++|++||+|.++++++  .+|+++|||||+|.+.++|+.|+..+||..+.|++|+|.|+.++
T Consensus        10 l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~a~~k   87 (88)
T d1rk8a_          10 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVK   87 (88)
T ss_dssp             EEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEEC
T ss_pred             EEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEecCC
Confidence            89999999998   999999999999999988  78999999999999999999999999999999999999998765

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=2.5e-22  Score=117.26  Aligned_cols=75  Identities=28%  Similarity=0.366  Sum_probs=71.3

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..+|   |+++|++||+|.++.+++  .+|.++|||||+|.+.++|+.|+.+|||..+.|++|+|.++.++.+
T Consensus        12 lfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A~~~~~   91 (93)
T d1x5ua1          12 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNK   91 (93)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETTTTSC
T ss_pred             EEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCCCC
Confidence            79999999999   999999999999999988  7899999999999999999999999999999999999999988754

>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=5e-22  Score=112.40  Aligned_cols=71  Identities=20%  Similarity=0.319  Sum_probs=68.4

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR   72 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~   72 (136)
                      |||+|||..++   |+++|++||+|.++.++. .+|+++|||||+|.+.++|+.|++.+||..+.|++|+|.++.
T Consensus         3 l~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~   77 (78)
T d1no8a_           3 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            79999999998   999999999999999999 899999999999999999999999999999999999999875

>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=8e-22  Score=116.95  Aligned_cols=75  Identities=27%  Similarity=0.478  Sum_probs=71.3

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||.+.++.++.  .+|+++|||||+|.+.++|+.|+.+|||..++|++|+|.++.++.+
T Consensus        21 l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a~~k~~  100 (102)
T d2cpza1          21 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKND  100 (102)
T ss_dssp             EEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCCCSCC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEeCCCCC
Confidence            89999999999   999999999999999888  7899999999999999999999999999999999999999998764

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=1.5e-21  Score=113.90  Aligned_cols=74  Identities=23%  Similarity=0.339  Sum_probs=70.0

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS   75 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~   75 (136)
                      |||+|||..+|   |+++|++||+|.++.+++  .+++++|||||+|.+.++|+.|+..|||..+.|++|+|.|+.+..
T Consensus        10 lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a~~~~   88 (93)
T d1h2vz_          10 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFK   88 (93)
T ss_dssp             EEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEESCCC
T ss_pred             EEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            79999999999   999999999999999988  789999999999999999999999999999999999999987654

>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=99.86  E-value=5.3e-22  Score=113.58  Aligned_cols=75  Identities=25%  Similarity=0.367  Sum_probs=68.9

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEE-EEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEIC-VFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS   75 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~-~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~   75 (136)
                      |||+|||..++   |+++|++||.|.++ .+++  .+|+++|||||+|.+.++|+.|++.+||..+.|++|+|.++.++.
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            79999999999   99999999998664 6676  789999999999999999999999999999999999999998765


Q ss_pred             C
Q psy6353          76 E   76 (136)
Q Consensus        76 ~   76 (136)
                      .
T Consensus        81 ~   81 (83)
T d1x5ta1          81 S   81 (83)
T ss_dssp             C
T ss_pred             c
Confidence            3

>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=99.85  E-value=7.7e-22  Score=114.51  Aligned_cols=75  Identities=27%  Similarity=0.410  Sum_probs=70.8

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||+|..+.++.  .++.++|||||+|.+.++|+.|+..|||..++|++|+|.++.++.+
T Consensus         8 ifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a~~~~~   87 (90)
T d1x5sa1           8 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSD   87 (90)
T ss_dssp             EEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEECCCC
T ss_pred             EEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCCCC
Confidence            79999999998   999999999999998887  7899999999999999999999999999999999999999987754

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.85  E-value=1.4e-21  Score=114.27  Aligned_cols=74  Identities=19%  Similarity=0.325  Sum_probs=69.5

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc---cCCCceeeEEEEcCCHHHHHHHHHHH-cCceeCCceEEEEeeCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI---STAQSLGYGFVNYHRPEDAEKAINTL-NGLRLQNKTIKVSYARPS   74 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~---~~~~~kg~~fv~f~~~~~a~~a~~~~-~~~~~~g~~l~v~~~~~~   74 (136)
                      |||+|||..++   |+++|++||+|.++.+++   .+|+++|||||+|.+.++|+.|++.| ||..+.|++|.|.++.+.
T Consensus        11 l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~~A~~~   90 (94)
T d2cpha1          11 ILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSE   90 (94)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEEECCCC
T ss_pred             EEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEEEcCCC
Confidence            89999999998   999999999999999987   47999999999999999999999998 899999999999999876


Q ss_pred             C
Q psy6353          75 S   75 (136)
Q Consensus        75 ~   75 (136)
                      .
T Consensus        91 ~   91 (94)
T d2cpha1          91 V   91 (94)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.85  E-value=2.3e-21  Score=114.41  Aligned_cols=75  Identities=23%  Similarity=0.320  Sum_probs=70.9

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||+|.++.++.  .+++++|||||+|.+.++|+.|+.+|||..+.|++|+|.++.++.+
T Consensus        11 lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a~~~~~   90 (99)
T d1whwa_          11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKE   90 (99)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECCCCST
T ss_pred             EEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCc
Confidence            79999999998   999999999999999988  7899999999999999999999999999999999999999987654

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.85  E-value=2.2e-21  Score=111.45  Aligned_cols=74  Identities=27%  Similarity=0.486  Sum_probs=67.4

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCC---CceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STA---QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP   73 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~---~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~   73 (136)
                      |||+|||..+|   |+++|++||+|.++.+++  .++   .++|||||+|.+.++|+.|++.+||..++|++|.|.++.+
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~~   80 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISER   80 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSC
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            79999999999   999999999999999988  333   4799999999999999999999999999999999999865


Q ss_pred             CC
Q psy6353          74 SS   75 (136)
Q Consensus        74 ~~   75 (136)
                      ..
T Consensus        81 ~~   82 (85)
T d2cpfa1          81 AT   82 (85)
T ss_dssp             SS
T ss_pred             CC
Confidence            43

>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=99.85  E-value=1.3e-21  Score=113.31  Aligned_cols=75  Identities=27%  Similarity=0.483  Sum_probs=69.6

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||.|.++.++...+.++|||||+|.+.++|+.|+++|||..++|++|.|.++.++.+
T Consensus        11 l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~~~~   88 (89)
T d1cvja2          11 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKE   88 (89)
T ss_dssp             EEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTTBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCCTTT
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecCCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCC
Confidence            89999999999   9999999999999999885556899999999999999999999999999999999999987653

>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=99.85  E-value=6.5e-21  Score=111.17  Aligned_cols=75  Identities=20%  Similarity=0.321  Sum_probs=69.3

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||+|.++.++...+.++|||||+|.+.++|+.|+..|||..+.|++|+|.++.++..
T Consensus        14 l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A~~r~~   91 (93)
T d2cq3a1          14 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARVM   91 (93)
T ss_dssp             EEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCSSCC
T ss_pred             EEEECCCCCCCHHHHHHHHhhcceeeeccccccccCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCcCCC
Confidence            79999999998   9999999999999999884445799999999999999999999999999999999999988643

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.85  E-value=1.7e-21  Score=110.95  Aligned_cols=72  Identities=18%  Similarity=0.332  Sum_probs=63.8

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP   73 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~   73 (136)
                      |||+|||..+|   |+++|++||+|..+.++.  .+|+++|||||+|.+.++|++|++.|||..+.|++|.|.+++|
T Consensus         4 l~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           4 LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             EEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             EEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            79999999999   999999999998887776  7889999999999999999999999999999999999999987

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=4.4e-21  Score=110.12  Aligned_cols=70  Identities=30%  Similarity=0.473  Sum_probs=65.3

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCC--ceEEEEee
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQN--KTIKVSYA   71 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g--~~l~v~~~   71 (136)
                      |||+|||..+|   |+++|++||+|.++.+++  .+|+++|||||+|.+.++|+.|++.|||..+.|  ++|+|.|+
T Consensus         9 lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~A   85 (85)
T d1fxla2           9 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA   85 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             EEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEeC
Confidence            79999999999   999999999999999998  679999999999999999999999999999987  56888875

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.84  E-value=5.7e-21  Score=109.66  Aligned_cols=70  Identities=26%  Similarity=0.382  Sum_probs=65.9

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCC--ceEEEEee
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQN--KTIKVSYA   71 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g--~~l~v~~~   71 (136)
                      |||+|||..++   |+++|++||+|.++++++  .+|+++|||||+|.+.++|+.|++.+||..+.|  ++|+|.++
T Consensus         9 lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~~A   85 (85)
T d1b7fa2           9 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA   85 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEEEC
Confidence            79999999998   999999999999999998  789999999999999999999999999998876  88999875

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.84  E-value=2.1e-21  Score=111.77  Aligned_cols=73  Identities=21%  Similarity=0.250  Sum_probs=64.8

Q ss_pred             eeecCCChhhh----HHHHhccCCCeeEEEEEc---cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCC
Q psy6353           2 VYQTLLNKLFT----YEKVHLGFSDAEICVFLI---STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS   74 (136)
Q Consensus         2 v~v~nl~~~~~----l~~~f~~~G~v~~~~~~~---~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~   74 (136)
                      |||+|||..++    |+++|++||+|.++.++.   .+++++|||||+|.+.++|++|++ +||..++|++|+|.++.++
T Consensus         7 l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~~a~~k   85 (86)
T d2ghpa3           7 IMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSLADKK   85 (86)
T ss_dssp             EEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEEECCCC
T ss_pred             EEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEEEcCCC
Confidence            79999998775    889999999999999876   578999999999999999999996 9999999999999999876


Q ss_pred             C
Q psy6353          75 S   75 (136)
Q Consensus        75 ~   75 (136)
                      +
T Consensus        86 P   86 (86)
T d2ghpa3          86 P   86 (86)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.84  E-value=6.7e-21  Score=110.48  Aligned_cols=75  Identities=23%  Similarity=0.388  Sum_probs=68.3

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||+|.++.+++.....+|||||+|.+.++|+.|+..+||..+.|++|+|.++.++..
T Consensus        11 l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~~~~   88 (90)
T d2cqia1          11 LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPSS   88 (90)
T ss_dssp             EEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCTTC
T ss_pred             EEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCccceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCCCC
Confidence            79999999999   9999999999999999883334589999999999999999999999999999999999987643

>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=99.84  E-value=3.2e-21  Score=114.68  Aligned_cols=74  Identities=22%  Similarity=0.347  Sum_probs=69.8

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS   75 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~   75 (136)
                      |||+|||..++   |+++|++||+|.++.+++  .+|+++|||||+|.+.++|+.|++.|||..+.|++|+|.++.+..
T Consensus        11 l~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~~~~   89 (104)
T d1p1ta_          11 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASEK   89 (104)
T ss_dssp             EEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTCTT
T ss_pred             EEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            89999999998   999999999999999988  689999999999999999999999999999999999999987653

>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=4.7e-21  Score=113.67  Aligned_cols=74  Identities=16%  Similarity=0.271  Sum_probs=69.6

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||.|..+.+++  .+++++|||||+|.+.++|++|+. ++++.|.|++|.|.++.|+.+
T Consensus        23 lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~~ke~  101 (103)
T d1x4ba1          23 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVAREE  101 (103)
T ss_dssp             EEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCSSCCC
T ss_pred             EEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECcccCC
Confidence            89999999999   999999999999999998  778999999999999999999997 799999999999999988754

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=9.4e-21  Score=108.27  Aligned_cols=67  Identities=22%  Similarity=0.335  Sum_probs=64.1

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEE
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKV   68 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v   68 (136)
                      |||+|||..+|   |+++|++||+|.++.+++  .+++++|||||+|.+.++|+.|+.+|||..+.|++|+|
T Consensus        12 l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1          12 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             EEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             EEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            79999999998   999999999999999988  67999999999999999999999999999999999986

>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=99.84  E-value=7.4e-21  Score=118.60  Aligned_cols=75  Identities=27%  Similarity=0.441  Sum_probs=70.7

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||+|.++.+++  .+|+++|||||+|.+.++|..|+..|||..+.|++|+|.++.+...
T Consensus        45 l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~~~~~  124 (139)
T d1u6fa1          45 LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQ  124 (139)
T ss_dssp             EEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESSCCCC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCCC
Confidence            89999999998   999999999999999988  7899999999999999999999999999999999999999876554

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=1.4e-20  Score=108.95  Aligned_cols=73  Identities=15%  Similarity=0.173  Sum_probs=67.5

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..+|   |+++|++||+|.++.+++  .+|+++|||||+|.+.++|++|++.  +..++|+.|.|+++.++..
T Consensus        11 lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~--~~~l~Gr~i~v~~a~~k~~   88 (90)
T d2cqga1          11 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWCDCKLPNSKQS   88 (90)
T ss_dssp             EEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTEEEEEECCCTTCC
T ss_pred             EEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhc--CCccCCEEeEEEeCCCCCC
Confidence            79999999999   999999999999999998  7899999999999999999999984  4589999999999988654

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.83  E-value=2.1e-21  Score=109.47  Aligned_cols=69  Identities=23%  Similarity=0.349  Sum_probs=65.4

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEee
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA   71 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~   71 (136)
                      |||+|||..++   |+++|++||+|.++.+++  .+|+++|||||+|.+.++|++|++ +|++.++|++|.|+.+
T Consensus         3 lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             EEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             EEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            79999999999   999999999999999998  779999999999999999999998 7999999999999865

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=3.7e-21  Score=107.93  Aligned_cols=68  Identities=22%  Similarity=0.351  Sum_probs=64.2

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEe
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY   70 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~   70 (136)
                      |||+|||..++   |+++|++||+|.++.+++  .+++++|||||+|.+.++|++|++ +++..+.|++|.|+.
T Consensus         2 lfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~r   74 (75)
T d1hd0a_           2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKR   74 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECC
T ss_pred             EEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeE
Confidence            79999999998   999999999999999998  789999999999999999999998 789999999999864

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=1.3e-20  Score=107.81  Aligned_cols=70  Identities=21%  Similarity=0.329  Sum_probs=66.1

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR   72 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~   72 (136)
                      |||+|||..++   |+++|++||+|.++.+++  .+|+++|||||+|.+.++|++|++ ++++.+.|+.|+|+.+.
T Consensus         9 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           9 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             EEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             EEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEeee
Confidence            79999999999   999999999999999988  789999999999999999999998 68999999999998764

>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=99.82  E-value=1.7e-20  Score=111.30  Aligned_cols=73  Identities=29%  Similarity=0.360  Sum_probs=67.5

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS   75 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~   75 (136)
                      |||+|||..++   |+++|++||+|.++.++.  .+|+++|||||+|.+.++|++|++.+|+ .+.|++|.|.++.+..
T Consensus        13 lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a~~~~   90 (103)
T d2cqda1          13 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAYLGA   90 (103)
T ss_dssp             EEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEESTTTC
T ss_pred             EEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEEcCCCC
Confidence            89999999998   999999999999999998  7799999999999999999999998876 7999999999887543

>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=99.82  E-value=8.6e-21  Score=112.16  Aligned_cols=72  Identities=19%  Similarity=0.257  Sum_probs=67.7

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS   74 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~   74 (136)
                      |||+|||..++   |+++|++||+|.++.+++  .+|+++|||||+|.+.++|++|+. +||..+.|++|.|.++.++
T Consensus        21 ifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a~~~   97 (101)
T d2cq4a1          21 VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQAE   97 (101)
T ss_dssp             EEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHHHH
T ss_pred             EEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECCCC
Confidence            89999999999   999999999999999999  689999999999999999999995 9999999999999987643

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=7.9e-21  Score=112.41  Aligned_cols=72  Identities=22%  Similarity=0.269  Sum_probs=67.9

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP   73 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~   73 (136)
                      |||+|||..++   |+++|++||+|..+.+.. .+++++|||||+|.+.++|++|+++|||..+.|+++.+.++.|
T Consensus        21 lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~~P   96 (101)
T d1x5oa1          21 LYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEP   96 (101)
T ss_dssp             EEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSSC
T ss_pred             EEEeCCCCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCCCC
Confidence            89999999999   999999999999999888 8899999999999999999999999999999999998877665

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=4.3e-20  Score=104.51  Aligned_cols=69  Identities=10%  Similarity=0.224  Sum_probs=64.9

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEee
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA   71 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~   71 (136)
                      |||+|||..+|   |+++|++||++..+.++.  .+++++|||||+|.++++|++|+. +||..+.|++|+|+.|
T Consensus         5 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           5 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             EEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             EEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEEC
Confidence            79999999999   999999999999999888  789999999999999999999996 8999999999999865

>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=99.81  E-value=6.9e-20  Score=105.01  Aligned_cols=70  Identities=14%  Similarity=0.068  Sum_probs=66.2

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR   72 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~   72 (136)
                      |||+|||..+|   |+++|+.||+|.++.+++ .+|+++|||||+|.+.++|++|++ ++|..+.|++|.|.+..
T Consensus         9 vfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           9 VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             EEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             EEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            79999999999   999999999999999988 889999999999999999999997 79999999999998754

>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=99.81  E-value=5.5e-20  Score=110.95  Aligned_cols=96  Identities=20%  Similarity=0.233  Sum_probs=78.0

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESI   78 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~~~   78 (136)
                      |||+|||..++   |+++|++||+|.+|.+.. ++.++|||||+|.+.++|..|+..|||..+.|++|.|.++.+.....
T Consensus        10 l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~-~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~~~~~~   88 (114)
T d2f9da1          10 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN-TPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNANRAFQ   88 (114)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEC-STTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCHHHHTT
T ss_pred             EEEECCCCCCCHHHHHHHHhhcCCeEeecccc-cCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCchhh
Confidence            89999999998   999999999999998875 56779999999999999999999999999999999999886532111


Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGR  106 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~  106 (136)
                              .......++++..+..++|.
T Consensus        89 --------~~~~~~~~~~~~~~~~~~g~  108 (114)
T d2f9da1          89 --------KMDTKKKEEQLKLLKEKYGI  108 (114)
T ss_dssp             --------TSCHHHHHHHHHHHHHHHCC
T ss_pred             --------hhHHHHHHHHHHHHHHHhCC
Confidence                    12222355667777766663

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.81  E-value=2.3e-20  Score=104.61  Aligned_cols=69  Identities=19%  Similarity=0.323  Sum_probs=65.0

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEee
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA   71 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~   71 (136)
                      |||+|||..+|   |+++|++||.+..+.++.  .+++++|||||+|.+.++|++|++ +||+.+.|++|+|++|
T Consensus         2 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             EEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             EEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECCeEEEEEEC
Confidence            79999999999   999999999999998888  678999999999999999999997 9999999999999864

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=5.8e-21  Score=107.03  Aligned_cols=69  Identities=14%  Similarity=0.222  Sum_probs=64.0

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEee
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA   71 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~   71 (136)
                      |||+|||..+|   |+++|++||+|.++.++.  .+++++|||||+|.+.++|++|++ .+++.++|+.+.|+.+
T Consensus         2 lfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~-~~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1           2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTT-CSSCCBTTBCCEEECC
T ss_pred             EEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHh-hCCCEECCEEeEEEEC
Confidence            79999999999   999999999999999998  789999999999999999999997 4788999999988753

>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=99.81  E-value=9e-20  Score=107.16  Aligned_cols=75  Identities=25%  Similarity=0.371  Sum_probs=69.1

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHc------CceeCCceEEEEe
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLN------GLRLQNKTIKVSY   70 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~------~~~~~g~~l~v~~   70 (136)
                      |||+|||..+|   |+++|++||++.++.++.  .+++++|||||+|.+.++|..|++.+|      |..+.|++|+|.+
T Consensus        11 lfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr~l~v~~   90 (98)
T d1x4ha1          11 VFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDL   90 (98)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCEEEEEC
T ss_pred             EEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCEEEEEEE
Confidence            79999999999   999999999999998888  678899999999999999999999886      6788999999999


Q ss_pred             eCCCCC
Q psy6353          71 ARPSSE   76 (136)
Q Consensus        71 ~~~~~~   76 (136)
                      +.++.+
T Consensus        91 a~~k~~   96 (98)
T d1x4ha1          91 AVTRDE   96 (98)
T ss_dssp             CCCCCC
T ss_pred             CCCCCc
Confidence            988754

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=1.4e-20  Score=104.79  Aligned_cols=66  Identities=26%  Similarity=0.393  Sum_probs=62.3

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEE
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIK   67 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~   67 (136)
                      |||+|||..+|   |+++|++||+|..+++++  .++.++|||||+|.+.++|++|++.|||..+.|+.++
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEECc
Confidence            79999999999   999999999999999888  7899999999999999999999999999999998763

>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=6.8e-20  Score=107.33  Aligned_cols=70  Identities=23%  Similarity=0.349  Sum_probs=65.9

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS   75 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~   75 (136)
                      |||+|||..++   |+++|++||+|.++++++    .+|||||+|.+.++|+.|+..|||..+.|++|+|.|+++++
T Consensus        21 l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~----~kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak~~p   93 (96)
T d1x4ga1          21 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFP----EKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESP   93 (96)
T ss_dssp             EEEECCSSCCCHHHHHHHHHHHSCEEEEEEET----TTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCCC
T ss_pred             EEEcCCCCCCCHHHHHHHHHHhCCceEEEEEe----cceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            89999999998   999999999999999986    58999999999999999999999999999999999998764

>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=99.80  E-value=4.2e-20  Score=104.82  Aligned_cols=71  Identities=27%  Similarity=0.337  Sum_probs=64.2

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCc-eeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGL-RLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~-~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||.+.++.+..    ++|||||+|.+.++|+.|++.|||. .++|++|+|.++.|+.+
T Consensus         4 l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~----~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k~~   78 (80)
T d2cqha1           4 LYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL----KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKL   78 (80)
T ss_dssp             EEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE----ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCCC
T ss_pred             EEEECCCCCCCHHHHHHHHHHhCcEEEeEEec----ccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCcCc
Confidence            89999999999   999999999987765554    6899999999999999999999985 79999999999998754

>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=99.80  E-value=1.2e-19  Score=104.26  Aligned_cols=70  Identities=23%  Similarity=0.309  Sum_probs=65.7

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS   75 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~   75 (136)
                      |||+|||..++   |+++|++||+|.++.+.+    ++|||||+|.+.++|+.|+..|||..+.|++|+|.++.+..
T Consensus        11 l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~----~k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~~~   83 (86)
T d2cpja1          11 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHK----DKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSA   83 (86)
T ss_dssp             EEEESCCTTCCHHHHHHHTSTTCCCSEEEEET----TTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCS
T ss_pred             EEEECCCCCCCHHHHHHHHHHhCCceEeeeec----ccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCcC
Confidence            79999999998   999999999999999875    57899999999999999999999999999999999998764

>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=99.80  E-value=1.6e-19  Score=106.66  Aligned_cols=75  Identities=24%  Similarity=0.333  Sum_probs=66.7

Q ss_pred             eeecCCChhhh---HHHHhccCCCee--------EEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEE
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAE--------ICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKV   68 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~--------~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v   68 (136)
                      |||+|||..+|   |+++|++||+|.        .+.+..  .+|+++|||||+|.+.++|+.|+..+||..+.|++|+|
T Consensus        11 i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V   90 (101)
T d2cpea1          11 IYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKV   90 (101)
T ss_dssp             EEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             EEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEECCEEEEE
Confidence            79999999999   999999999874        344444  56899999999999999999999999999999999999


Q ss_pred             EeeCCCCC
Q psy6353          69 SYARPSSE   76 (136)
Q Consensus        69 ~~~~~~~~   76 (136)
                      .++.++..
T Consensus        91 ~~a~~~~p   98 (101)
T d2cpea1          91 SLARKKPP   98 (101)
T ss_dssp             ECSSCCCC
T ss_pred             EEcCCCCC
Confidence            99987654

>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=99.79  E-value=2.8e-19  Score=102.68  Aligned_cols=71  Identities=27%  Similarity=0.366  Sum_probs=65.4

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||.+..+.+.    +++|||||+|.+.++|..|+..|||..+.|++|.|.+++|..+
T Consensus        11 l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~----~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP~~~   84 (86)
T d2cpda1          11 LYVRNLMLSTSEEMIEKEFNNIKPGAVERVK----KIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDK   84 (86)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSTTCEEEEE----ECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCCCC
T ss_pred             EEEcCCCCCCCHHHHHHhhcccceeeeEEEc----cccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccCCCC
Confidence            89999999999   99999999998877664    4789999999999999999999999999999999999998764

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.79  E-value=1.6e-19  Score=104.31  Aligned_cols=69  Identities=26%  Similarity=0.327  Sum_probs=61.1

Q ss_pred             CeeecCCChhhh---H---HHHhccCCCeeEEEEEc--cCC---CceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEE
Q psy6353           1 MVYQTLLNKLFT---Y---EKVHLGFSDAEICVFLI--STA---QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVS   69 (136)
Q Consensus         1 ~v~v~nl~~~~~---l---~~~f~~~G~v~~~~~~~--~~~---~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~   69 (136)
                      .|||+|||..++   |   .++|++||+|.++.+++  .++   .++|||||+|.+.++|+.|+..|||..++|++|++.
T Consensus        10 ~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~lkvS   89 (89)
T d2cpia1          10 LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKAS   89 (89)
T ss_dssp             CEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             EEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEEEEC
Confidence            389999999998   5   56799999999999998  333   345999999999999999999999999999999874

>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=6.4e-21  Score=110.73  Aligned_cols=72  Identities=21%  Similarity=0.302  Sum_probs=67.4

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS   74 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~   74 (136)
                      |||+|||..++   |+++|++||.|.++.++. .+|+++|||||+|.+.++|++|++ +||..++|++|+|.+++++
T Consensus        16 ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~ak~k   91 (91)
T d1fjeb1          16 LFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKGR   91 (91)
T ss_dssp             EEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECCCCS
T ss_pred             EEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEecCCC
Confidence            89999999999   999999999999888877 889999999999999999999996 9999999999999998753

>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=99.78  E-value=2e-20  Score=110.77  Aligned_cols=75  Identities=19%  Similarity=0.298  Sum_probs=70.2

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||.+..+.++.  .+|+++|||||+|.+.++|+.|+..|||..+.|++|+|.+++++.+
T Consensus        21 l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~ak~k~~  100 (102)
T d2cpxa1          21 LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKKQ  100 (102)
T ss_dssp             EEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEECCCCSC
T ss_pred             EEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeCCCccc
Confidence            89999999998   999999999998887777  7899999999999999999999999999999999999999998754

>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=99.78  E-value=4.6e-19  Score=103.58  Aligned_cols=72  Identities=19%  Similarity=0.319  Sum_probs=66.0

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS   74 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~   74 (136)
                      |||+|||..++   |+++|++||.|..+.+.. ++.++|||||+|.+.++|+.|+..|||..+.|++|+|.++++.
T Consensus        17 l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~-~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a~~~   91 (95)
T d1x4aa1          17 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN-RRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSG   91 (95)
T ss_dssp             EEEESCCTTCCHHHHHHHHGGGSCEEEEEECC-SSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCCC
T ss_pred             EEEECCCCCCCHHHHHHHHhcCCceEEEEecc-cccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeccCC
Confidence            89999999999   999999999998887654 4557899999999999999999999999999999999998764

>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=99.78  E-value=1.1e-19  Score=105.41  Aligned_cols=73  Identities=19%  Similarity=0.362  Sum_probs=65.2

Q ss_pred             eeecCCChhhh---H----HHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCC
Q psy6353           2 VYQTLLNKLFT---Y----EKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS   74 (136)
Q Consensus         2 v~v~nl~~~~~---l----~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~   74 (136)
                      |||+|||..++   |    .++|++||+|.+|.+.+ +++++|||||+|.+.++|+.|++++||..+.|++|.|.+++++
T Consensus         6 l~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~-~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~~ak~~   84 (91)
T d1nu4a_           6 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR-SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTD   84 (91)
T ss_dssp             EEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH-HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSSC
T ss_pred             EEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee-eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeCCC
Confidence            89999999998   3    45689999999987654 5668999999999999999999999999999999999999876


Q ss_pred             C
Q psy6353          75 S   75 (136)
Q Consensus        75 ~   75 (136)
                      .
T Consensus        85 ~   85 (91)
T d1nu4a_          85 S   85 (91)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.78  E-value=2e-19  Score=105.29  Aligned_cols=75  Identities=17%  Similarity=0.258  Sum_probs=67.3

Q ss_pred             eeecCCChhhh---HHHHhccCCC-eeEEEEEc---cCCCceeeEEEEcCCHHHHHHHHHHHcC--ceeCCceEEEEeeC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSD-AEICVFLI---STAQSLGYGFVNYHRPEDAEKAINTLNG--LRLQNKTIKVSYAR   72 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~-v~~~~~~~---~~~~~kg~~fv~f~~~~~a~~a~~~~~~--~~~~g~~l~v~~~~   72 (136)
                      |||+|||..++   |+++|++||+ +.++.+++   .+++++|||||+|.+.++|..|+++|++  ..++|++|.|.|+.
T Consensus         4 LyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~~A~   83 (96)
T d2disa1           4 LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAE   83 (96)
T ss_dssp             EEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEESC
T ss_pred             EEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEEEcC
Confidence            89999999999   9999999996 88998887   4688999999999999999999998864  56689999999998


Q ss_pred             CCCC
Q psy6353          73 PSSE   76 (136)
Q Consensus        73 ~~~~   76 (136)
                      |+.+
T Consensus        84 p~~~   87 (96)
T d2disa1          84 PEID   87 (96)
T ss_dssp             SSCS
T ss_pred             CCCC
Confidence            8654

>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=99.77  E-value=1.3e-18  Score=97.36  Aligned_cols=68  Identities=24%  Similarity=0.315  Sum_probs=60.4

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS   74 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~   74 (136)
                      |||+|||..++   |+++|++|| +..+.+    ++++|||||+|.+.++|++|+..|||..+.|++|+|+++.+.
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~----~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d   71 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV----DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE----ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee----cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            79999999999   999999999 444443    458899999999999999999999999999999999998654

>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=99.77  E-value=1e-18  Score=103.70  Aligned_cols=74  Identities=19%  Similarity=0.282  Sum_probs=65.5

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc---cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI---STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS   75 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~---~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~   75 (136)
                      |||+|||..++   |+++|++|| +.++.++.   .+++++|||||+|.+.++|++|+. +|+..+.|+.|+|.++.++.
T Consensus        18 v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~-~~~~~~~gr~l~V~~a~~~~   95 (104)
T d1wi8a_          18 AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLGNKRIRVDVADQAQ   95 (104)
T ss_dssp             EEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHG-GGTCEETTEECEEEECCCCC
T ss_pred             EEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHH-cCCCEECCEEEEEEECCCCC
Confidence            89999999999   999999999 66777666   578899999999999999987775 99999999999999998765


Q ss_pred             CC
Q psy6353          76 ES   77 (136)
Q Consensus        76 ~~   77 (136)
                      ..
T Consensus        96 ~~   97 (104)
T d1wi8a_          96 DK   97 (104)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.77  E-value=3.9e-19  Score=104.09  Aligned_cols=72  Identities=15%  Similarity=0.307  Sum_probs=65.7

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+|||..++   |+++|++||.+..+.   .+++++|||||+|.+.++|+.|+..|||..+.|++|+|.++.++..
T Consensus        19 l~V~nL~~~~te~~l~~~F~~~g~v~~~~---~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a~~k~~   93 (96)
T d1fjca_          19 LLAKNLSFNITEDELKEVFEDALEIRLVS---QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGG   93 (96)
T ss_dssp             EEEESCCSSCCHHHHHHHHCSEEEECCEE---ETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSSCC
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcccceeee---ecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEeCCCCC
Confidence            89999999998   999999999876554   5778999999999999999999999999999999999999998754

>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=7.1e-19  Score=105.16  Aligned_cols=70  Identities=20%  Similarity=0.277  Sum_probs=63.4

Q ss_pred             eeecCCC-hhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCC
Q psy6353           2 VYQTLLN-KLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS   74 (136)
Q Consensus         2 v~v~nl~-~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~   74 (136)
                      |||+||| ..++   |+++|++||+|.++.+++   ..+|||||+|.+.++|++|++.+||..+.|+.|+|.++...
T Consensus         5 l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~---~~kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~~~   78 (109)
T d2adca1           5 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILF---NKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQ   78 (109)
T ss_dssp             EEEESCCTTTCCHHHHHHHHHHHTCEEEEEECC---TTSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCC
T ss_pred             EEEeCCCcccCCHHHHHHHHhhccccceEEEEe---cccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            8999995 4566   999999999999999987   34799999999999999999999999999999999998644

>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=7.6e-19  Score=98.31  Aligned_cols=69  Identities=17%  Similarity=0.066  Sum_probs=62.3

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEee
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA   71 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~   71 (136)
                      |||+|||..++   |+++|++||+|..+.+++..+..+|||||+|.+.++|++|+. +|+..++|++|.|..+
T Consensus         3 v~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~~~~~afV~F~~~~~a~~Al~-~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           3 VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             EEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             EEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccccceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            89999999999   999999999999999988334456899999999999999996 8999999999999754

>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=99.76  E-value=1.1e-18  Score=99.51  Aligned_cols=68  Identities=15%  Similarity=0.298  Sum_probs=62.6

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeC-CceEEEEeeC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQ-NKTIKVSYAR   72 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~-g~~l~v~~~~   72 (136)
                      |||+|||..++   |+++|++||+|.++++++   ..+|||||+|.+.++|..|+..|||..+. |++|+|.|++
T Consensus        11 l~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~---~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~ak   82 (83)
T d2b0ga1          11 LFLTNLPEETNEMMLSMLFNQFPGFKEVRLVP---NRHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFAK   82 (83)
T ss_dssp             EEEESCCTTCCHHHHHHHHTTSTTEEEEEECT---TTCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEECC
T ss_pred             EEEECCCCCCCHHHHHhhhccCccEEEeeeec---ccceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEec
Confidence            89999999999   999999999999999876   45789999999999999999999998885 6899999986

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.76  E-value=8.9e-19  Score=105.03  Aligned_cols=69  Identities=13%  Similarity=0.126  Sum_probs=63.9

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS   74 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~   74 (136)
                      |||+|||..++   |+++|++||+|..|.+.    .++|||||+|.+.++|+.|++.|||..+.|++|.|.++...
T Consensus        13 l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~----~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~~   84 (111)
T d1whxa_          13 ILAKNLPAGTLAAEIQETFSRFGSLGRVLLP----EGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIG   84 (111)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEECC----SSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETT
T ss_pred             EEEECCCCCCCHHHHHhhhhccCCccEEEee----ccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCCC
Confidence            89999999998   99999999999998774    46899999999999999999999999999999999988654

>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=99.76  E-value=1.6e-18  Score=101.70  Aligned_cols=69  Identities=19%  Similarity=0.336  Sum_probs=62.0

Q ss_pred             eeecCCC-hhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCC
Q psy6353           2 VYQTLLN-KLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE   76 (136)
Q Consensus         2 v~v~nl~-~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~   76 (136)
                      |||+||| ..++   |+++|++||+|.++.+.      +|||||+|.+.++|++|+..|||..+.|++|+|.++.++..
T Consensus        18 lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~------rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~~~   90 (98)
T d1wf2a_          18 VFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH------KGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEPKV   90 (98)
T ss_dssp             EEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE------TEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEETTSCCC
T ss_pred             EEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe------CCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCC
Confidence            8999997 4554   89999999999999884      59999999999999999999999999999999999976543

>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=99.76  E-value=1.5e-18  Score=98.06  Aligned_cols=70  Identities=23%  Similarity=0.265  Sum_probs=62.5

Q ss_pred             eeecCCChhhh-HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCC
Q psy6353           2 VYQTLLNKLFT-YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS   75 (136)
Q Consensus         2 v~v~nl~~~~~-l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~   75 (136)
                      |||+|+|-.-. |+++|++||.|.++.+.+    .+|||||+|.+.++|..|+.+|||..+.|++|+|.++++++
T Consensus         8 i~V~~~~~te~~L~~~F~~~G~I~~v~~~~----~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~P   78 (79)
T d2bz2a1           8 LYVYGEDMTPTLLRGAFSPFGNIIDLSMDP----PRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQP   78 (79)
T ss_dssp             EEEECSSCCHHHHHHHHSTTCCCSCEEEET----TTTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECCSSC
T ss_pred             EEEECCCCCHHHHHHHHhccCccceeeecc----CCCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEecCCC
Confidence            79999973222 999999999999998875    67899999999999999999999999999999999998753

>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=99.75  E-value=1.8e-18  Score=103.22  Aligned_cols=72  Identities=15%  Similarity=0.217  Sum_probs=64.5

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeC--CceEEEEeeCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQ--NKTIKVSYARPSS   75 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~--g~~l~v~~~~~~~   75 (136)
                      |||+|||..+|   |+++|++||.|.++.++.  .+++|||||+|.+.++|+.|+..+||..+.  +++|++.+++++.
T Consensus        10 v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~--~~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s~~~~   86 (108)
T d2adba1          10 IIVENLFYPVTLDVLHQIFSKFGTVLKIITFT--KNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTS   86 (108)
T ss_dssp             EESCSCCSTTHHHHHHHHHTTTSCEEEEEEEE--ETTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEECSSCS
T ss_pred             EEEeCcCCCCCHHHHHHHHccCCcEEEEEEEe--eCCCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEecCCcc
Confidence            79999999999   999999999999998876  235899999999999999999999999884  7889999887654

>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=99.75  E-value=2e-18  Score=99.41  Aligned_cols=71  Identities=11%  Similarity=0.166  Sum_probs=63.3

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCcee-CCceEEEEeeCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRL-QNKTIKVSYARPS   74 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~-~g~~l~v~~~~~~   74 (136)
                      |||+|||..++   |+++|++||.+..+....  ++++|||||+|.+.++|..|+..|||..+ .|++|+|.++++.
T Consensus        13 L~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~--~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~sk~~   87 (88)
T d2adca2          13 LHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFF--QKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST   87 (88)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCCEEEEEEC--SSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             EEEECCCCCCCHHHHHHHhhccCCEEEEEEee--ecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeCCCC
Confidence            79999999999   999999999998776543  45689999999999999999999999988 5899999998764

>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=99.75  E-value=8.5e-19  Score=100.62  Aligned_cols=70  Identities=11%  Similarity=0.169  Sum_probs=63.9

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeE-EEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEee
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEI-CVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA   71 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~-~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~   71 (136)
                      |||+|||..++   |+++|+.||.+.. +.+.. .+++++|+|||+|.+.++|+.|+.++|+..+.|++|+|..+
T Consensus        12 l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1          12 IKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             EEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             EEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            89999999999   9999999999866 45555 88999999999999999999999999999999999999753

>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=99.75  E-value=6.1e-19  Score=101.65  Aligned_cols=71  Identities=15%  Similarity=0.210  Sum_probs=64.0

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES   77 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~~   77 (136)
                      |||+|||..+|   |+++|++||+|.+++++.   .++|||||+|.+.++|+.|+.  +++.+.|++|.|.++.|+.+.
T Consensus         8 lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~---~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~~k~~~   81 (88)
T d1wf0a_           8 VFVGRCTGDMTEDELREFFSQYGDVMDVFIPK---PFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAEPKHNS   81 (88)
T ss_dssp             EEEESCCSSSCHHHHHHHSTTTSCCCEEECCS---SCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCCCCCCC
T ss_pred             EEEeCCCCCCCHHHHHHHHHHcCCceEEEEee---ccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCCCCCCC
Confidence            89999999998   999999999999987654   678999999999999999986  788999999999999877654

>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=3.8e-18  Score=98.25  Aligned_cols=69  Identities=14%  Similarity=0.207  Sum_probs=60.5

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS   75 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~   75 (136)
                      |||+|||..++   |+++|++||. ..+.+    +.++|||||+|.+.++|++|++.||+..+.|++|+|.++.++.
T Consensus         8 i~V~nLp~~~t~~~l~~lF~~~G~-~~~~~----~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~~~   79 (88)
T d1wg1a_           8 ILVKNLPQDSNCQEVHDLLKDYDL-KYCYV----DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDA   79 (88)
T ss_dssp             EEEESCCSSCCHHHHHHHTCSSCC-CCEEE----EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCCC
T ss_pred             EEEeCCCCccChHHHHHHHHhcCc-eeeee----eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            79999999998   9999999992 22333    3578999999999999999999999999999999999987654

>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=99.74  E-value=4.6e-19  Score=101.95  Aligned_cols=67  Identities=19%  Similarity=0.177  Sum_probs=61.1

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP   73 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~   73 (136)
                      |||+|||..++   |+++|++||+|.++.+++     +|||||+|.+.++|+.|+.+|||..+.|+.+++.+..+
T Consensus         3 vfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~-----~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~   72 (87)
T d3begb1           3 VVVSGLPPSGSWQDLKDHMREAGDVCYADVYR-----DGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRV   72 (87)
T ss_dssp             EEEEECCSSCCTTHHHHHHGGGSCEEEEEECT-----TSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEE
T ss_pred             EEEECCCCcCCHHHHHHHHhhhcccccccccc-----cceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEec
Confidence            79999999998   999999999999998754     48999999999999999999999999999988766543

>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=99.73  E-value=3.8e-18  Score=100.81  Aligned_cols=74  Identities=16%  Similarity=0.092  Sum_probs=66.4

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES   77 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~~~   77 (136)
                      |||.|||..+|   |+++|+.+|.+ .+.++. .+++++|||||+|.+.++|++|++ +|+..|+||.|+|.++.+....
T Consensus        18 v~v~nLp~~~te~dl~~~F~~~~~~-~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~s~~~~~~   95 (102)
T d1weza_          18 VHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLNSTAGTS   95 (102)
T ss_dssp             EEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEECCCCCC
T ss_pred             EEEeCCCCcCCHHHHHHHHhccCcc-eeeeEEecCCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEcCCCCCC
Confidence            89999999999   99999999854 677777 889999999999999999999986 8999999999999998876543

>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=99.73  E-value=6.1e-18  Score=100.26  Aligned_cols=75  Identities=20%  Similarity=0.142  Sum_probs=67.0

Q ss_pred             CeeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCC
Q psy6353           1 MVYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS   75 (136)
Q Consensus         1 ~v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~   75 (136)
                      +|||+|||..+|   |+++|+++|.+....++.  .+++++|||||+|.++++|++|++ +|+..|+||.|.|.++.+..
T Consensus        17 ~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~~~~~~   95 (104)
T d1wg5a_          17 FVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFKSSRAE   95 (104)
T ss_dssp             EEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEEECTTT
T ss_pred             EEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEECCHHH
Confidence            489999999998   999999999988755555  789999999999999999999996 89999999999999988764


Q ss_pred             C
Q psy6353          76 E   76 (136)
Q Consensus        76 ~   76 (136)
                      .
T Consensus        96 ~   96 (104)
T d1wg5a_          96 V   96 (104)
T ss_dssp             S
T ss_pred             h
Confidence            3

>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=99.73  E-value=1.6e-18  Score=102.71  Aligned_cols=69  Identities=20%  Similarity=0.251  Sum_probs=61.9

Q ss_pred             eecCCChhhh---HHHHhccCCCeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEee
Q psy6353           3 YQTLLNKLFT---YEKVHLGFSDAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA   71 (136)
Q Consensus         3 ~v~nl~~~~~---l~~~f~~~G~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~   71 (136)
                      ++.+++..++   ++++|++||+|.++.+++ .+++++|+|||+|.+.++|.+|+..|||..+.|++|.|.++
T Consensus        31 ~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          31 EMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             HhhhhhhhhhHHHHHHHhccCCCEEEEEeecCCCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            3445555555   889999999999999999 89999999999999999999999999999999999999875

>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=99.72  E-value=7.7e-18  Score=99.72  Aligned_cols=71  Identities=15%  Similarity=0.203  Sum_probs=65.1

Q ss_pred             eeecCCChhhh--------HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCC
Q psy6353           2 VYQTLLNKLFT--------YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP   73 (136)
Q Consensus         2 v~v~nl~~~~~--------l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~   73 (136)
                      |||.||+..+.        |+++|++||.|.++.+.+    ++|||||+|.+.++|.+|+.+|||..+.|++|+|.++++
T Consensus         8 L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k----~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~   83 (104)
T d1weya_           8 LIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK----SFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQT   83 (104)
T ss_dssp             EEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET----TTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCCC
T ss_pred             EEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEec----CCCEEEEEECCHHHHHHHHHHhcccccCCCEeEEeeccc
Confidence            89999999863        888999999999998875    788999999999999999999999999999999999987


Q ss_pred             CCC
Q psy6353          74 SSE   76 (136)
Q Consensus        74 ~~~   76 (136)
                      ...
T Consensus        84 ~~~   86 (104)
T d1weya_          84 LHI   86 (104)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            654

>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=99.72  E-value=5.5e-18  Score=99.40  Aligned_cols=69  Identities=23%  Similarity=0.213  Sum_probs=63.6

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS   75 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~   75 (136)
                      |||+|||..++   |+++|++||+|..+.+.+     +|||||+|.+.++|+.|+++|||..+.|+.|++.+.++..
T Consensus        18 i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-----~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~~~~   89 (98)
T d1wg4a_          18 VLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-----DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRVYP   89 (98)
T ss_dssp             EEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-----TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEEEEC
T ss_pred             EEEECCCCCCCHHHHHHHHHhhcccccccccc-----cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEecCC
Confidence            89999999998   999999999999998864     6899999999999999999999999999999998876544

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.72  E-value=1.5e-17  Score=97.40  Aligned_cols=70  Identities=13%  Similarity=0.282  Sum_probs=63.9

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCC--ceEEEEeeCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQN--KTIKVSYARPSS   75 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g--~~l~v~~~~~~~   75 (136)
                      |||+|||..++   |+++|++||+|..+.+.+    +++||||+|.+.++|+.|++.||+..+.|  ++|+|.++++.+
T Consensus        20 l~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~----~~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~ak~~~   94 (97)
T d1whya_          20 LWVGGLGPNTSLAALAREFDRFGSIRTIDHVK----GDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSGP   94 (97)
T ss_dssp             EEEECCCSSCCHHHHHHHHHTTSCEEEEEECS----SSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCCC
T ss_pred             EEEcCCCCCCCHHHHHHHHHhhcccceEeeec----cccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEeCCCCC
Confidence            89999999998   999999999999998865    57899999999999999999999999976  589999998754

>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=99.71  E-value=7.2e-18  Score=99.78  Aligned_cols=70  Identities=21%  Similarity=0.229  Sum_probs=63.5

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeE-EEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEI-CVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR   72 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~-~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~   72 (136)
                      |||+|||..+|   |+++|+.||.+.. +.++. .+|+++|+|||+|.+.++|+.|+. +|+..|.|++|.|.++.
T Consensus        11 v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~~   85 (103)
T d2cpya1          11 AHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVVT   85 (103)
T ss_dssp             EEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEEC
T ss_pred             EEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEECC
Confidence            89999999999   9999999999876 44545 889999999999999999999996 89999999999998764

>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=99.71  E-value=3.9e-17  Score=93.90  Aligned_cols=70  Identities=19%  Similarity=0.181  Sum_probs=62.9

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHH--cCceeCCceEEEEeeCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTL--NGLRLQNKTIKVSYARPSS   75 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~--~~~~~~g~~l~v~~~~~~~   75 (136)
                      |||+|||..++   |+++|++||.|.++.+.+    ++|||||+|.+.++|++|++.+  ++..+.|++|+|.+++.+.
T Consensus        11 l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~----~~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~~sk~~~   85 (88)
T d2cq1a1          11 LHIRKLPGEVTETEVIALGLPFGKVTNILMLK----GKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHKE   85 (88)
T ss_dssp             EEEESCCTTCCHHHHHHTTTTTSCEEEEEEET----TTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSCSS
T ss_pred             EEEeCCCCCCCHHHHHHHHhcccccccccccc----cceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEEECCCCC
Confidence            79999999998   999999999999998875    5689999999999999999865  5789999999999997653

>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=99.70  E-value=2.7e-17  Score=96.57  Aligned_cols=70  Identities=14%  Similarity=0.221  Sum_probs=62.7

Q ss_pred             eeecCCChh-hh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHH--HHcCceeCCceEEEEeeCCCC
Q psy6353           2 VYQTLLNKL-FT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAIN--TLNGLRLQNKTIKVSYARPSS   75 (136)
Q Consensus         2 v~v~nl~~~-~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~--~~~~~~~~g~~l~v~~~~~~~   75 (136)
                      |||+|||.. +|   |.++|++||.|.++.+++    ++|+|||+|.+.++|..|++  .+++..++|++|+|.++..+.
T Consensus        21 l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~----~k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V~~s~~~~   96 (99)
T d1x4fa1          21 IHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR----MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKYK   96 (99)
T ss_dssp             EEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET----TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECSCS
T ss_pred             EEEeCCcCCccCHHHHHhhhccccceeEEEEee----cCCcEEEEecchHHHHHHHHHHhcCCceECCEEEEEEEcCCcc
Confidence            899999975 66   999999999999999875    57899999999999999997  578899999999999997654

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.68  E-value=1.4e-16  Score=94.24  Aligned_cols=71  Identities=8%  Similarity=0.076  Sum_probs=63.4

Q ss_pred             CeeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHH--cCceeCCceEEEEeeCCCC
Q psy6353           1 MVYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTL--NGLRLQNKTIKVSYARPSS   75 (136)
Q Consensus         1 ~v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~--~~~~~~g~~l~v~~~~~~~   75 (136)
                      .|||+|||..++   |.++|++||+|..+.+.+    .||+|||+|.+.++|+.|+..+  ++..++|++|+|.+++.+.
T Consensus        17 ~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~----~k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~~s~~~~   92 (104)
T d1wexa_          17 VVHVRGLCESVVEADLVEALEKFGTICYVMMMP----FKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKR   92 (104)
T ss_dssp             EEEEESCCSSCCHHHHHHHHTTTSCEEEEEEET----TTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSSSS
T ss_pred             EEEEeCCCCCCCHHHHHHhhhhcccceEEEEEe----cceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEEEcCCCc
Confidence            389999999998   999999999999998875    6789999999999999999877  5677899999999987643

>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=99.67  E-value=1.2e-16  Score=92.04  Aligned_cols=70  Identities=14%  Similarity=0.124  Sum_probs=61.9

Q ss_pred             eeecCCChh-hh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHH--cCceeCCceEEEEeeCCCC
Q psy6353           2 VYQTLLNKL-FT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTL--NGLRLQNKTIKVSYARPSS   75 (136)
Q Consensus         2 v~v~nl~~~-~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~--~~~~~~g~~l~v~~~~~~~   75 (136)
                      |||+|||.. +|   |.++|++||+|.++.+++    .+++|||+|.+.++|..|++.+  ++..+.|++|+|.++.+..
T Consensus        11 v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~----~k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V~~s~~~~   86 (89)
T d1x4da1          11 VHIMDFQRGKNLRYQLLQLVEPFGVISNHLILN----KINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKYK   86 (89)
T ss_dssp             EEEESCCCSSSHHHHHHTTTGGGSCEEEEEECS----SSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECCCT
T ss_pred             EEEECCCCCcCCHHHHHHHHHhhCCeEEEEeec----cceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEEEECCCcc
Confidence            799999986 55   999999999999998875    5679999999999999999855  6789999999999997643

>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=99.66  E-value=5.7e-17  Score=93.54  Aligned_cols=57  Identities=23%  Similarity=0.336  Sum_probs=52.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCcc-ceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENG-KYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~-~~fv~f~~~e~~~  135 (136)
                      ..++|||+|||.++|+++|+++|++||.|..|++++|+.+|.++ .|||+|.+.|+|.
T Consensus         7 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~   64 (90)
T d2cqga1           7 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQV   64 (90)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHH
T ss_pred             CCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHH
Confidence            56889999999999999999999999999999999999888875 5899999999875

>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=99.66  E-value=2.5e-17  Score=92.43  Aligned_cols=55  Identities=15%  Similarity=0.349  Sum_probs=51.0

Q ss_pred             ceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCcc-ceEeecCcccccc
Q psy6353          81 ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENG-KYYSGLGGRERLR  135 (136)
Q Consensus        81 ~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~-~~fv~f~~~e~~~  135 (136)
                      ++|||+|||.++|+++|+++|++||+|..+++++|+.+|.++ .|||+|.++|++.
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~   56 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVD   56 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHH
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHH
Confidence            479999999999999999999999999999999999988775 5999999999875

>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=99.65  E-value=2.8e-17  Score=98.62  Aligned_cols=71  Identities=18%  Similarity=0.149  Sum_probs=63.3

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEE-EEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEIC-VFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP   73 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~-~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~   73 (136)
                      |||+|||..+|   |+++|+.+|.+..+ .+.. .+|.++|+|||+|.+.++|++|+. +||..|+|+.|.|..+.+
T Consensus        21 i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~~~~   96 (112)
T d1wela1          21 VYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPITK   96 (112)
T ss_dssp             EEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEECH
T ss_pred             EEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEEcCh
Confidence            79999999999   99999999998664 3444 889999999999999999999997 899999999999987653

>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=99.65  E-value=7.8e-17  Score=92.06  Aligned_cols=57  Identities=53%  Similarity=0.762  Sum_probs=52.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCcc-ceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENG-KYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~-~~fv~f~~~e~~~  135 (136)
                      .+++|||+|||+.+|+++|+++|++||+|.++++++|+.+|.++ .|||+|.+.|+|.
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~   62 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAE   62 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHH
Confidence            56789999999999999999999999999999999999887774 5899999999875

>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=99.65  E-value=2.9e-17  Score=91.68  Aligned_cols=54  Identities=15%  Similarity=0.391  Sum_probs=50.3

Q ss_pred             eEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCcc-ceEeecCcccccc
Q psy6353          82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENG-KYYSGLGGRERLR  135 (136)
Q Consensus        82 ~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~-~~fv~f~~~e~~~  135 (136)
                      +|||+|||.++|+++|+++|++||+|..+++++|+.++.++ +|||+|.+.|+|.
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~   55 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVK   55 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHH
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHH
Confidence            58999999999999999999999999999999999888875 5999999999875

>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=99.64  E-value=5.8e-17  Score=90.50  Aligned_cols=54  Identities=17%  Similarity=0.431  Sum_probs=50.4

Q ss_pred             eEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        82 ~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      +|||+|||+++|+++|+++|++||+|..+.+++|+.++.+ +.+||+|.+.|+|+
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~   55 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVD   55 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHH
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHH
Confidence            5899999999999999999999999999999999998887 55999999999875

>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=99.64  E-value=3e-16  Score=101.27  Aligned_cols=73  Identities=10%  Similarity=0.206  Sum_probs=67.9

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc--cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI--STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS   75 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~--~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~   75 (136)
                      |||+|||..++   |+++|+.||.|..+.++.  .+|+++|||||+|.+.++|++|+. +++..+.|++|+|.++.|+.
T Consensus       100 i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~~A~~k~  177 (183)
T d1u1qa_         100 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKALSKQ  177 (183)
T ss_dssp             EEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEEEECCCHH
T ss_pred             eEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEecCCcc
Confidence            79999999998   999999999999998888  679999999999999999999997 78999999999999987753

>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=99.64  E-value=1.7e-16  Score=91.53  Aligned_cols=61  Identities=20%  Similarity=0.326  Sum_probs=54.5

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCcc-ceEeecCcccccc
Q psy6353          75 SESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENG-KYYSGLGGRERLR  135 (136)
Q Consensus        75 ~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~-~~fv~f~~~e~~~  135 (136)
                      .......+|||+|||.++++++|+++|++||+|..+.++.|+.+|.++ .|||+|.+.|+|.
T Consensus         3 ~~~~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~   64 (90)
T d2cq0a1           3 RRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAA   64 (90)
T ss_dssp             CCCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHH
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHH
Confidence            344567899999999999999999999999999999999999888775 5899999999875

>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=99.64  E-value=2.2e-16  Score=90.14  Aligned_cols=58  Identities=33%  Similarity=0.636  Sum_probs=52.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCcc-ceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENG-KYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~-~~fv~f~~~e~~~  135 (136)
                      ...++|||+|||..+++++|+++|++||+|..+++++|+.+|.++ .|||+|.+.|+|.
T Consensus         4 ~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~   62 (85)
T d1b7fa2           4 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQ   62 (85)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHH
Confidence            356789999999999999999999999999999999998888875 5899999999875

>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=99.64  E-value=1.6e-16  Score=91.25  Aligned_cols=59  Identities=17%  Similarity=0.247  Sum_probs=53.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCcc-ceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENG-KYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~-~~fv~f~~~e~~~  135 (136)
                      +..+++|||+|||..+|+++|+++|++||+|.++++++|+.+|.++ .|||+|.+.|+|+
T Consensus         4 s~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~   63 (88)
T d1rk8a_           4 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQAL   63 (88)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHH
Confidence            3467899999999999999999999999999999999999888875 4899999999875

>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=99.63  E-value=8.3e-17  Score=91.31  Aligned_cols=56  Identities=29%  Similarity=0.352  Sum_probs=51.7

Q ss_pred             CceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCcc-ceEeecCcccccc
Q psy6353          80 GANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENG-KYYSGLGGRERLR  135 (136)
Q Consensus        80 ~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~-~~fv~f~~~e~~~  135 (136)
                      +++|||+|||+++|+++|+++|++||+|.++++++++.+|..+ .|||+|.+.|+|.
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~   58 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQ   58 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHH
Confidence            4689999999999999999999999999999999998888775 5999999999885

>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=99.63  E-value=1.9e-16  Score=91.89  Aligned_cols=60  Identities=22%  Similarity=0.316  Sum_probs=53.9

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCcc-ceEeecCcccccc
Q psy6353          76 ESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENG-KYYSGLGGRERLR  135 (136)
Q Consensus        76 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~-~~fv~f~~~e~~~  135 (136)
                      +....++|||+|||..+|+++|+++|++||+|.++.+++|+.+|.++ .|||+|.+.|+|.
T Consensus         5 ~~~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~   65 (93)
T d1x5ua1           5 ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDAD   65 (93)
T ss_dssp             CCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHH
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHH
Confidence            34456899999999999999999999999999999999999888775 5999999999875

>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=99.63  E-value=1.5e-16  Score=89.84  Aligned_cols=55  Identities=27%  Similarity=0.420  Sum_probs=51.0

Q ss_pred             ceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          81 ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        81 ~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      +.|||+|||+.+|+++|+++|++||+|.+++|++|+.+|.+ +.|||+|.+.|++.
T Consensus         1 aslfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~   56 (80)
T d1cvja1           1 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAE   56 (80)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHH
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHH
Confidence            36999999999999999999999999999999999998887 56999999999875

>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=99.63  E-value=1.8e-16  Score=90.08  Aligned_cols=57  Identities=21%  Similarity=0.303  Sum_probs=52.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCcc-ceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENG-KYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~-~~fv~f~~~e~~~  135 (136)
                      +.++|||+|||..+|+++|+++|++||.|.++.+++++.++..+ .|||+|.+.|+|+
T Consensus         8 ~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~   65 (83)
T d2cqca1           8 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAK   65 (83)
T ss_dssp             GGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHH
Confidence            56789999999999999999999999999999999999888775 5999999999875

>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=99.63  E-value=1.8e-16  Score=90.29  Aligned_cols=57  Identities=16%  Similarity=0.284  Sum_probs=52.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCcc-ceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENG-KYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~-~~fv~f~~~e~~~  135 (136)
                      ..++|||+|||.++|+++|+++|++||+|..+++++|+.+|.++ .|||+|.+.++++
T Consensus         5 ~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~   62 (84)
T d1l3ka1           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD   62 (84)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHH
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHH
Confidence            34789999999999999999999999999999999999988875 5999999998875

>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=99.62  E-value=3.5e-16  Score=92.35  Aligned_cols=58  Identities=21%  Similarity=0.425  Sum_probs=52.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ...++|||+|||..+++++|+++|++||+|.++++++|+.+|.+ +.|||+|.+.|+|.
T Consensus         8 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~   66 (103)
T d2cqda1           8 TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAE   66 (103)
T ss_dssp             CSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHH
T ss_pred             CCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHH
Confidence            35578999999999999999999999999999999999988877 55999999999875

>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=99.62  E-value=3.2e-16  Score=88.83  Aligned_cols=56  Identities=25%  Similarity=0.387  Sum_probs=51.1

Q ss_pred             CceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCcc-ceEeecCcccccc
Q psy6353          80 GANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENG-KYYSGLGGRERLR  135 (136)
Q Consensus        80 ~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~-~~fv~f~~~e~~~  135 (136)
                      .++|||+|||.++++++|+++|++||+|..++++++..++..+ .|||+|.+.|+|.
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~   58 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAE   58 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHH
Confidence            3579999999999999999999999999999999998887774 5999999999875

>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=99.61  E-value=1.5e-16  Score=91.57  Aligned_cols=57  Identities=23%  Similarity=0.332  Sum_probs=52.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCcc-ceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENG-KYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~-~~fv~f~~~e~~~  135 (136)
                      ..++|||+|||.++|+++|+++|++||+|.++.+++|+.+|.++ .|||+|.+.++|.
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~   61 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA   61 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHH
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHH
Confidence            45799999999999999999999999999999999999888775 5999999999875

>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=99.61  E-value=3.8e-16  Score=89.14  Aligned_cols=55  Identities=15%  Similarity=0.362  Sum_probs=50.8

Q ss_pred             ceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          81 ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        81 ~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      .+|||+|||..+|+++|+++|++||+|..+++++|+.+|.+ +.|||+|.+.|+|.
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~   57 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTD   57 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHH
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHH
Confidence            47999999999999999999999999999999999988887 45899999999875

>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=99.60  E-value=5e-16  Score=90.08  Aligned_cols=57  Identities=21%  Similarity=0.249  Sum_probs=52.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCcc-ceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENG-KYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~-~~fv~f~~~e~~~  135 (136)
                      .+++|||+|||.++|+++|+++|++||+|.++.+++++.++.++ .|||+|.+.|+|.
T Consensus         6 ~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~   63 (93)
T d1h2vz_           6 KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAE   63 (93)
T ss_dssp             TCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHH
Confidence            56899999999999999999999999999999999999888775 5999999999875

>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=99.60  E-value=6.5e-16  Score=88.13  Aligned_cols=57  Identities=12%  Similarity=0.325  Sum_probs=51.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ..++|||+|||.++|+++|+++|+.||+|..+.++.+..+..+|.|||+|.+.|+|.
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~   61 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAK   61 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHH
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHH
Confidence            357899999999999999999999999999999998875555567999999999875

>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=99.60  E-value=9e-16  Score=90.23  Aligned_cols=56  Identities=20%  Similarity=0.397  Sum_probs=51.6

Q ss_pred             CceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          80 GANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        80 ~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      .++|||+|||.++++++|+++|++||+|.++++++|..+|.+ |+|||+|.+.|++.
T Consensus        18 ~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~   74 (101)
T d2cq4a1          18 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVP   74 (101)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHH
Confidence            468999999999999999999999999999999999988877 55999999999874

>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=99.59  E-value=1e-15  Score=86.09  Aligned_cols=56  Identities=16%  Similarity=0.377  Sum_probs=51.4

Q ss_pred             CceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCcc-ceEeecCcccccc
Q psy6353          80 GANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENG-KYYSGLGGRERLR  135 (136)
Q Consensus        80 ~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~-~~fv~f~~~e~~~  135 (136)
                      .++|||+|||+++|+++|+++|++||.|..+.++.++.++.++ .|||+|.+.|++.
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~   58 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVD   58 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHH
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHH
Confidence            4789999999999999999999999999999999999998875 5999999998764

>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=99.59  E-value=3.2e-18  Score=98.95  Aligned_cols=70  Identities=11%  Similarity=0.182  Sum_probs=61.1

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEc-------cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEee
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLI-------STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA   71 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~-------~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~   71 (136)
                      |||+|||..+|   |+++|++||.+..+.+..       .+++++|||||+|.+.++|+.|++ |||..+.|++|+|+.+
T Consensus         4 lyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~Gr~l~V~r~   82 (90)
T d1u2fa_           4 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIRRP   82 (90)
T ss_dssp             EEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSSSSCCCCBCT
T ss_pred             EEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEECCEEEEECCC
Confidence            89999999999   999999999877665432       457889999999999999999985 9999999999999754


Q ss_pred             C
Q psy6353          72 R   72 (136)
Q Consensus        72 ~   72 (136)
                      +
T Consensus        83 k   83 (90)
T d1u2fa_          83 H   83 (90)
T ss_dssp             T
T ss_pred             C
Confidence            3

>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=99.59  E-value=9.4e-16  Score=90.34  Aligned_cols=59  Identities=20%  Similarity=0.478  Sum_probs=53.8

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCcc-ceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENG-KYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~-~~fv~f~~~e~~~  135 (136)
                      ...+++|||+|||.++++++|+++|++||.|.++.++.++.+|.++ .|||+|.+.|+|.
T Consensus        15 ~p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~   74 (102)
T d2cpza1          15 GPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQ   74 (102)
T ss_dssp             CSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHH
Confidence            3466889999999999999999999999999999999999988875 5999999999875

>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=99.58  E-value=8.8e-16  Score=90.57  Aligned_cols=56  Identities=13%  Similarity=0.349  Sum_probs=51.5

Q ss_pred             CceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          80 GANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        80 ~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      .++|||+|||.++++++|+++|++||+|..+.|++|+.++.+ ++|||+|.+.++|.
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~   76 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVD   76 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHH
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHH
Confidence            478999999999999999999999999999999999988766 66999999999874

>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=99.58  E-value=8.3e-16  Score=88.60  Aligned_cols=57  Identities=14%  Similarity=0.265  Sum_probs=51.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ...++|||+|||+++|+++|+++|++||+|..+.++++..++ .+.|||+|.+.|+|.
T Consensus         6 ~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~-~~~afV~f~~~~~A~   62 (90)
T d2cqia1           6 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN-DPYCFVEFYEHRDAA   62 (90)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSS-CCEEEEEESSHHHHH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCcc-ceeeEEEECCHHHHH
Confidence            356799999999999999999999999999999999998776 478999999999875

>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=99.58  E-value=4.4e-16  Score=87.46  Aligned_cols=54  Identities=19%  Similarity=0.281  Sum_probs=49.8

Q ss_pred             eEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        82 ~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      +|||+|||+++++++|+++|++||+|.+++++.++++..++.|||+|.+.|+|.
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~afV~f~~~~~A~   55 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADAL   55 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHH
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHH
Confidence            699999999999999999999999999999999986666678999999999875

>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=99.57  E-value=2.7e-15  Score=86.90  Aligned_cols=59  Identities=17%  Similarity=0.356  Sum_probs=52.5

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          76 ESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        76 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      .....++|||+|||.++++++|+++|++||+|..|.++.+..+ .++.|||+|.+.|+|+
T Consensus         7 ~~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~-~kg~afV~f~~~~~a~   65 (93)
T d2cq3a1           7 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADAD   65 (93)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTT-TCCEEEEEESCHHHHH
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccC-CcceeEEEECCHHHHH
Confidence            3446788999999999999999999999999999999998755 4578999999999885

>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=99.57  E-value=1.5e-15  Score=88.15  Aligned_cols=58  Identities=19%  Similarity=0.336  Sum_probs=51.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCC-CCCc-cceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNL-ATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~-~~~~-~~~fv~f~~~e~~~  135 (136)
                      ....+|||+|||..+++++|+++|++||.|.+++++++.. +|.+ |+|||+|.+.|+|.
T Consensus         6 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~   65 (94)
T d2cpha1           6 QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAK   65 (94)
T ss_dssp             SCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHH
Confidence            3668899999999999999999999999999999998854 5555 56999999999875

>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=99.57  E-value=1.1e-15  Score=85.25  Aligned_cols=54  Identities=17%  Similarity=0.131  Sum_probs=49.7

Q ss_pred             ceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          81 ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        81 ~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ++|||+|||+++++++|+++|++||+|..++++.++.++. +.|||+|.++|+|.
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~~~-~~afV~F~~~~~a~   54 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNF-RFARIEFARYDGAL   54 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSS-EEEEEEESSHHHHH
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccccc-eEEEEEEcchHHhH
Confidence            4799999999999999999999999999999999987654 78999999999875

>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=99.56  E-value=1.8e-15  Score=83.61  Aligned_cols=53  Identities=23%  Similarity=0.486  Sum_probs=49.4

Q ss_pred             EEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCcc-ceEeecCcccccc
Q psy6353          83 LYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENG-KYYSGLGGRERLR  135 (136)
Q Consensus        83 l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~-~~fv~f~~~e~~~  135 (136)
                      |||+|||.++|+++|+++|++||.|..+++.+++.++..+ .|||+|.+.|+|.
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~   54 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQ   54 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHH
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHH
Confidence            7999999999999999999999999999999999888874 5899999999875

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.56  E-value=1.5e-14  Score=84.55  Aligned_cols=61  Identities=18%  Similarity=0.253  Sum_probs=55.1

Q ss_pred             HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCCCC
Q psy6353          13 YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS   75 (136)
Q Consensus        13 l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~~~   75 (136)
                      +++.|++||+|..+.++.  +.++|+|||.|.+.++|..|+..|||..+.||+|.|.+..++.
T Consensus        36 v~~~~~~~G~V~~v~~~~--~~~~G~~fV~f~~~e~A~~A~~~lng~~~~gr~i~v~~~~g~~   96 (99)
T d2dita1          36 LRVECSKFGQIRKLLLFD--RHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGTT   96 (99)
T ss_dssp             HHHHGGGTSCCSEEEEET--TCTTCEEEEECSCHHHHHHHHHHSTTCEETTEECEEEECCSCC
T ss_pred             HHHHhcCcccEEEEeccC--CCCccEEEEEECCHHHHHHHHHHhCCcEECCEEEEEEEeCCcC
Confidence            778899999999998865  4567999999999999999999999999999999999987664

>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=99.56  E-value=3.7e-15  Score=87.59  Aligned_cols=59  Identities=36%  Similarity=0.658  Sum_probs=52.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ....++|||+|||.++++++|+++|++||.|..+.+..+......+.+||+|.+.|+|.
T Consensus        15 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~   73 (101)
T d1x5oa1          15 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCE   73 (101)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHH
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHH
Confidence            34568999999999999999999999999999999999876555577999999999875

>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=99.55  E-value=2.2e-15  Score=88.21  Aligned_cols=57  Identities=25%  Similarity=0.306  Sum_probs=52.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCcc-ceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENG-KYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~-~~fv~f~~~e~~~  135 (136)
                      ..++|||+|||..+++++|+++|++||+|..+.++.|+.++..+ .|||+|.+.|+|.
T Consensus         7 ~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~   64 (99)
T d1whwa_           7 GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAV   64 (99)
T ss_dssp             SCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHH
T ss_pred             CCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHH
Confidence            56789999999999999999999999999999999998888774 5899999999874

>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=99.55  E-value=9.8e-16  Score=88.12  Aligned_cols=56  Identities=21%  Similarity=0.498  Sum_probs=50.4

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ...+|||+|||+++++++|+++|++||.|..+.++.+..+ .++.|||+|.+.|+|.
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~-~kg~afV~f~~~~~A~   62 (89)
T d1cvja2           7 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAE   62 (89)
T ss_dssp             TTTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTTB-CCSCEEEEESCHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecCC-CcceeEEEECCHHHHH
Confidence            3467999999999999999999999999999999998755 4478999999999875

>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=99.55  E-value=1.3e-15  Score=90.04  Aligned_cols=56  Identities=16%  Similarity=0.340  Sum_probs=51.5

Q ss_pred             CceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCcc-ceEeecCcccccc
Q psy6353          80 GANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENG-KYYSGLGGRERLR  135 (136)
Q Consensus        80 ~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~-~~fv~f~~~e~~~  135 (136)
                      .++|||+|||.++++++|+++|++||+|.++.+++++.+|.++ .|||+|.+.|+|.
T Consensus         8 ~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~   64 (104)
T d1p1ta_           8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETAL   64 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHH
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHH
Confidence            4689999999999999999999999999999999999888774 5999999999875

>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=99.55  E-value=1.3e-15  Score=87.69  Aligned_cols=57  Identities=25%  Similarity=0.420  Sum_probs=51.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ...+|||+|||+++++++|+++|++||.|..+.++++..++.. +.|||+|.+.|+|.
T Consensus         4 ~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~   61 (90)
T d1x5sa1           4 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAK   61 (90)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHH
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHH
Confidence            5678999999999999999999999999999999998888876 55899999999875

>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=99.54  E-value=3.9e-15  Score=86.91  Aligned_cols=58  Identities=12%  Similarity=0.300  Sum_probs=52.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ..+++|||+|||..+|+++|+++|++||+|..+.++.+..++.+ |.|||+|.+.|+|.
T Consensus         6 ~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~   64 (98)
T d1x4ha1           6 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQ   64 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHH
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHH
Confidence            35689999999999999999999999999999999999888876 56999999999875

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.54  E-value=1.2e-14  Score=81.91  Aligned_cols=68  Identities=13%  Similarity=0.054  Sum_probs=58.7

Q ss_pred             CeeecCCChhhh--HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCce-EEEEeeCC
Q psy6353           1 MVYQTLLNKLFT--YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKT-IKVSYARP   73 (136)
Q Consensus         1 ~v~v~nl~~~~~--l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~-l~v~~~~~   73 (136)
                      +|+|.++|...+  +.+.|++||+|.++.+.    +++|||||+|.++++|++|++ +||..++|+. +.|.+...
T Consensus         6 wV~V~G~p~~~~~~il~~F~~~G~I~~~~~~----~~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~~   76 (81)
T d1wwha1           6 WVTVFGFPQASASYILLQFAQYGNILKHVMS----NTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCID   76 (81)
T ss_dssp             EEEEECCCGGGHHHHHHHHHTTSCEEEEEEC----SSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECCC
T ss_pred             EEEEECCChHHHHHHHHHHHhhhhhheEEec----CCCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCCC
Confidence            489999999988  66789999999999764    468999999999999999996 8999999985 56777654

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.54  E-value=4.2e-15  Score=89.05  Aligned_cols=68  Identities=12%  Similarity=0.117  Sum_probs=59.4

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCH-HHHHHHHHHHcCceeCCceEEEEeeCC
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRP-EDAEKAINTLNGLRLQNKTIKVSYARP   73 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~-~~a~~a~~~~~~~~~~g~~l~v~~~~~   73 (136)
                      +||+|||..+|   |+++|++||+|.+|.+++    ++|||||.|.++ ++|..|+..+|+..+.++.+.+.+...
T Consensus        14 ~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~----~kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~~   85 (113)
T d1owxa_          14 KFSGDLDDQTCREDLHILFSNHGEIKWIDFVR----GAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVL   85 (113)
T ss_dssp             EEEESCCSSCCHHHHHHHTCSSCCEEEEECCT----TCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEEC
T ss_pred             EEECCCCCCCCHHHHHHHHHhcCChheEEEec----CCceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEeec
Confidence            69999999998   999999999999999975    689999999985 788999999999888877777766543

>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=99.53  E-value=2.6e-15  Score=85.56  Aligned_cols=53  Identities=19%  Similarity=0.254  Sum_probs=48.0

Q ss_pred             EEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCC----ccceEeecCcccccc
Q psy6353          83 LYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATE----NGKYYSGLGGRERLR  135 (136)
Q Consensus        83 l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~----~~~~fv~f~~~e~~~  135 (136)
                      |||+|||.++|+++|+++|++||+|.++.+++++.++.    +|.|||+|.+.|+|.
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~   57 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQ   57 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHH
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHH
Confidence            79999999999999999999999999999999887764    356999999999875

>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=99.52  E-value=3.6e-15  Score=92.38  Aligned_cols=57  Identities=23%  Similarity=0.395  Sum_probs=52.4

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCcc-ceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENG-KYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~-~~fv~f~~~e~~~  135 (136)
                      ..++|||+|||.++|+++|+++|++||.|.++.+++|+.++.++ .|||+|.+.|+|.
T Consensus        41 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~   98 (139)
T d1u6fa1          41 VLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQ   98 (139)
T ss_dssp             TTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHH
Confidence            45689999999999999999999999999999999999888875 5999999999875

>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=99.52  E-value=3.3e-15  Score=83.14  Aligned_cols=54  Identities=13%  Similarity=0.422  Sum_probs=49.5

Q ss_pred             eEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        82 ~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      +|||+|||+++|+++|+++|++||.+..+.++.++.++.. +.|||+|.+.|+|.
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~   55 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVE   55 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHH
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHH
Confidence            5899999999999999999999999999999999887766 55999999999875

>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=99.52  E-value=2.2e-15  Score=85.07  Aligned_cols=55  Identities=16%  Similarity=0.235  Sum_probs=44.4

Q ss_pred             ceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          81 ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        81 ~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ++|||+|||+++|+++|+++|++||.|..+.++.+..+|.+ +.|||+|.+.|+|.
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~   57 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDAR   57 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHH
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHH
Confidence            68999999999999999999999999998888877777666 55999999999875

>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=99.49  E-value=2e-14  Score=84.33  Aligned_cols=56  Identities=20%  Similarity=0.203  Sum_probs=50.3

Q ss_pred             eee--cCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCcee
Q psy6353           2 VYQ--TLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRL   61 (136)
Q Consensus         2 v~v--~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~   61 (136)
                      |||  ++||..+|   |+++|++||.|.++.++.    ++|||||+|.+.++|..|+.+|||..+
T Consensus        21 l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~----~k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          21 LVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP----NKPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             EEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT----TCSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             EEEECCCCCCCCCHHHHHHHHHhhCcccEEeecc----CccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            456  55999999   999999999999998764    578999999999999999999999887

>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=99.49  E-value=5.3e-15  Score=84.97  Aligned_cols=57  Identities=18%  Similarity=0.260  Sum_probs=50.1

Q ss_pred             CCceEEEcCCCCCCCHHHH---HHhhcCCCceEEEEEEeCCCCCCc----cceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQEL---ESLFSPYGRIITSRILCDNLATEN----GKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l---~~~f~~~G~v~~~~i~~~~~~~~~----~~~fv~f~~~e~~~  135 (136)
                      ..++|||+|||+++++++|   +++|++||+|..|.+++++.++..    +.|||+|.+.|+|.
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~   70 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL   70 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHH
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHH
Confidence            4567999999999999999   778999999999999999876654    45899999999875

>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=99.49  E-value=5e-15  Score=83.97  Aligned_cols=53  Identities=17%  Similarity=0.372  Sum_probs=47.8

Q ss_pred             EEEcCCCCCCCHHHHHHhhcCCCceEE-EEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          83 LYVSGLPKHMSQQELESLFSPYGRIIT-SRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        83 l~v~nl~~~~t~~~l~~~f~~~G~v~~-~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      |||+|||+++|+++|+++|++||.|.. +.+++++.+|.+ +.|||+|.+.|+|+
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~   55 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASD   55 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHH
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHH
Confidence            799999999999999999999999976 578999888876 56999999999875

>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=99.48  E-value=3.3e-14  Score=80.54  Aligned_cols=55  Identities=13%  Similarity=0.247  Sum_probs=48.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ..++++|||+|||.++|+++|+++|++||.|..++++++    .++.|||+|.+.|+|.
T Consensus         5 ~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~----~~g~afV~f~~~~~A~   59 (83)
T d2b0ga1           5 QPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN----RHDIAFVEFTTELQSN   59 (83)
T ss_dssp             CSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT----TCSCEEEEESSHHHHH
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc----cceeEEEecCCHHHHH
Confidence            446789999999999999999999999999999999864    3467999999999874

>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=99.46  E-value=1e-14  Score=83.23  Aligned_cols=57  Identities=14%  Similarity=0.230  Sum_probs=46.3

Q ss_pred             CCceEEEcCCCCCCC-HHHHHHhhcCCCceEEEEEEeC-CCCCCc-cceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMS-QQELESLFSPYGRIITSRILCD-NLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t-~~~l~~~f~~~G~v~~~~i~~~-~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      .+++|||+|||++++ +++|+++|++||.|.+++++.+ ..++.+ +.|||+|.+.|+|.
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~   62 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAE   62 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHH
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHH
Confidence            568999999999986 5569999999999999999875 455665 45999999999874

>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=99.45  E-value=8.7e-14  Score=83.24  Aligned_cols=55  Identities=22%  Similarity=0.325  Sum_probs=48.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      .+++|||+|||..+|+++|+++|++||.|.+|.+..+..  ..|.|||+|.+.++|.
T Consensus         6 ~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~~~--~kG~afV~f~~~~~A~   60 (114)
T d2f9da1           6 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPE--TRGTAYVVYEDIFDAK   60 (114)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTT--TTTEEEEEESSHHHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccccCC--cCCeEEEEECCHHHHH
Confidence            467999999999999999999999999999999987643  3477999999999875

>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=99.45  E-value=1.3e-13  Score=81.25  Aligned_cols=61  Identities=18%  Similarity=0.260  Sum_probs=54.7

Q ss_pred             HHHHhccCCCeeEEEEEc-c---CCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeCC
Q psy6353          13 YEKVHLGFSDAEICVFLI-S---TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP   73 (136)
Q Consensus        13 l~~~f~~~G~v~~~~~~~-~---~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~~   73 (136)
                      +++.|++||.|.++.+++ .   .....|++||+|.+.++|.+|+..|||..+.||+|.+.++.+
T Consensus        31 i~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~f~gR~v~v~f~~~   95 (104)
T d1o0pa_          31 VRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDP   95 (104)
T ss_dssp             HHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCCSSSSCCEEEEECH
T ss_pred             HHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCEECCeEEEEEEcCH
Confidence            788899999999999987 2   344579999999999999999999999999999999998753

>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=99.44  E-value=1.1e-13  Score=79.08  Aligned_cols=55  Identities=18%  Similarity=0.303  Sum_probs=49.0

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          76 ESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        76 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      +..++++|||+|||.++++++|+++|++||.|.++++.+++     +.|||+|.+.|+|.
T Consensus         4 ~~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~~-----~~afV~f~~~e~A~   58 (88)
T d2cq1a1           4 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGK-----NQAFLELATEEAAI   58 (88)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETTT-----TEEEEEESSHHHHH
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcccccccccccccc-----eEEEEEeCCHHHHH
Confidence            34578899999999999999999999999999999988643     67999999999875

>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=99.43  E-value=1.4e-13  Score=81.05  Aligned_cols=58  Identities=17%  Similarity=0.249  Sum_probs=48.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      .....|||+|||.++|+++|+++|.++|.+....++.+..++.. +.|||+|.++|+|+
T Consensus        13 ~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~   71 (104)
T d1wg5a_          13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAE   71 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHH
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHH
Confidence            35567999999999999999999999999887655555555555 56999999999875

>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=99.43  E-value=4e-14  Score=81.04  Aligned_cols=53  Identities=17%  Similarity=0.291  Sum_probs=46.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ..++|||+|||.++|+++|+++|++||+|..++++.+    ..++|||+|.+.|+|+
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~~----~~gfafV~f~~~~~a~   56 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP----FRAFAFVTFADDQIAQ   56 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS----CCSCCEEECSCHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEeec----cCceEEEEECCHHHHH
Confidence            5689999999999999999999999999999987643    3467999999998875

>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=99.43  E-value=2.1e-15  Score=87.01  Aligned_cols=58  Identities=19%  Similarity=0.119  Sum_probs=49.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ...++|||+|||.++|+++|+++|++||.|..+.++.+..+..++.|||+|.+.|++.
T Consensus        11 ~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~   68 (91)
T d1fjeb1          11 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLE   68 (91)
T ss_dssp             SSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHH
T ss_pred             CCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHH
Confidence            4567999999999999999999999999999888876654444467999999999875

>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=99.43  E-value=2e-14  Score=82.16  Aligned_cols=49  Identities=24%  Similarity=0.318  Sum_probs=44.8

Q ss_pred             ceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          81 ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        81 ~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      .+|||+|||+++++++|+++|++||+|.++.+.++      +.|||+|.+.|+|.
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~------g~afV~f~~~~~a~   49 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMT   49 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT------SEEEEEESSHHHHH
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhccccccccccc------ceeeEEeCCHHHHH
Confidence            36999999999999999999999999999998764      67999999999875

>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=99.43  E-value=1.1e-13  Score=81.30  Aligned_cols=58  Identities=19%  Similarity=0.267  Sum_probs=50.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ...+.+|||+|||.++|+++|+++|..|| +..+.++.+..+...+.|||+|.+.|+|.
T Consensus        12 ~~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~~~g~~~G~afVeF~~~~~a~   69 (102)
T d1weza_          12 STTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVTGEADVEFATHEDAV   69 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESSSSCEEEEEEEECSSSHHHH
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEecCCcceEEEEEEECCHHHHH
Confidence            44668999999999999999999999998 55788888887766677999999999875

>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=99.42  E-value=5.1e-14  Score=81.84  Aligned_cols=52  Identities=23%  Similarity=0.540  Sum_probs=47.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ..++|||+|||+.+++++|+++|++||+|.+++++++     ++.|||+|.+.|+|+
T Consensus        17 ~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~-----kg~afV~f~~~~~A~   68 (96)
T d1x4ga1          17 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAA   68 (96)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT-----TTEEEEEESSHHHHH
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec-----ceEEEEEECCHHHHH
Confidence            4578999999999999999999999999999999976     478999999999875

>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=99.42  E-value=1.2e-13  Score=78.60  Aligned_cols=52  Identities=27%  Similarity=0.444  Sum_probs=46.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ..++|||+|||.++++++|+++|++||+|.++++.++     ++.|||+|.+.|+|.
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~-----k~~afV~f~~~~~A~   58 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAE   58 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT-----TTEEEEECSSSHHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc-----cceEEEEECCHHHHH
Confidence            3467999999999999999999999999999999865     367999999999875

>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=99.41  E-value=3.9e-14  Score=82.34  Aligned_cols=55  Identities=13%  Similarity=0.284  Sum_probs=48.1

Q ss_pred             ceEEEcCCCCCCCHHHHHHhhcCCCc-eEEEEEEeCCC-CCCc-cceEeecCcccccc
Q psy6353          81 ANLYVSGLPKHMSQQELESLFSPYGR-IITSRILCDNL-ATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        81 ~~l~v~nl~~~~t~~~l~~~f~~~G~-v~~~~i~~~~~-~~~~-~~~fv~f~~~e~~~  135 (136)
                      ++|||+|||..+++++|+++|++||+ |..+.++++.. ++.+ +.|||+|.+.++|.
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~   59 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAA   59 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHH
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHH
Confidence            57999999999999999999999996 88999998864 4444 66999999998875

>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=99.40  E-value=2.1e-13  Score=79.05  Aligned_cols=56  Identities=16%  Similarity=0.300  Sum_probs=48.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ...++|||+|||+++|+++|+++|++||.|..+.+..+.  ..++.|||+|.+.|+|.
T Consensus        12 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~--~~~g~afV~f~~~e~a~   67 (95)
T d1x4aa1          12 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR--GGPPFAFVEFEDPRDAE   67 (95)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSS--SSSCCEEEEESCHHHHH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEecccc--cccceEEEEECCHHHHH
Confidence            456789999999999999999999999999998876553  33477999999999875

>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=99.39  E-value=1.7e-13  Score=79.74  Aligned_cols=52  Identities=21%  Similarity=0.261  Sum_probs=47.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      +.++|||+|||+++++++|+++|++||+|..+++.++     ++.|||+|.+.|+|.
T Consensus        16 Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~-----~~~afV~f~~~~~A~   67 (97)
T d1whya_          16 PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-----DSFAYIQYESLDAAQ   67 (97)
T ss_dssp             CCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS-----SCCEEEEESSHHHHH
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc-----ccEEEeccCCHHHHH
Confidence            5689999999999999999999999999999998864     367999999999875

>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=99.39  E-value=2.2e-13  Score=77.85  Aligned_cols=54  Identities=22%  Similarity=0.364  Sum_probs=46.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ++++|||+|||.++++++|+++|++||.|..+.+..+.   .++.|||+|++.|+|.
T Consensus         9 Ps~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~~---~~~~afV~f~~~~~A~   62 (88)
T d2adca2           9 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK---DRKMALIQMGSVEEAV   62 (88)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS---STTCEEEEESSHHHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeeec---ccceeEEEECCHHHHH
Confidence            46789999999999999999999999999888776543   2467999999999875

>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=99.39  E-value=1.7e-13  Score=80.22  Aligned_cols=59  Identities=17%  Similarity=0.301  Sum_probs=50.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceE--------EEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRII--------TSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~--------~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ....++|||+|||..+|+++|+++|++||+|.        .+.+..+..+|.. +.|||+|.++|+|.
T Consensus         5 ~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~   72 (101)
T d2cpea1           5 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAK   72 (101)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHH
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHH
Confidence            34678999999999999999999999999874        5677788777776 55999999999875

>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=99.39  E-value=3.5e-13  Score=78.53  Aligned_cols=52  Identities=23%  Similarity=0.246  Sum_probs=47.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ....+|||+|||..+++++|+++|++||+|..+.+.++      +.+||+|.+.|+|.
T Consensus        13 ~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~~------g~afV~f~~~~~a~   64 (98)
T d1wg4a_          13 RSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKD------GMGMVEYLRKEDME   64 (98)
T ss_dssp             SCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEETT------TEEEEEESSHHHHH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhhccccccccccc------ceEEEEECCHHHHH
Confidence            35678999999999999999999999999999998743      68999999999875

>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=99.39  E-value=1.2e-13  Score=78.65  Aligned_cols=57  Identities=16%  Similarity=0.206  Sum_probs=47.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEE-EEEEeCCCCCCccceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIIT-SRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~-~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ...+|||+|||.++++++|+++|+.||.+.. +.+..+..+...+.|||+|.++|+|+
T Consensus         8 ~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~   65 (86)
T d2cqpa1           8 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEAT   65 (86)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHH
Confidence            4567999999999999999999999999876 45555554444467999999999885

>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=99.38  E-value=9.7e-14  Score=82.36  Aligned_cols=52  Identities=23%  Similarity=0.353  Sum_probs=46.2

Q ss_pred             CceEEEcCCCC-CCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          80 GANLYVSGLPK-HMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        80 ~~~l~v~nl~~-~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      +.+|||+|||+ .+|+++|+++|++||+|.++.+++++    ++.|||+|.+.|+|.
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~----kg~afV~f~~~~~A~   54 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQ   54 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT----SCCEEEEESCHHHHH
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc----cceEEEEECCHHHHH
Confidence            47899999966 58999999999999999999999874    467999999999875

>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=99.38  E-value=4.8e-13  Score=78.69  Aligned_cols=56  Identities=14%  Similarity=0.263  Sum_probs=47.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCC-CCCc-cceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNL-ATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~-~~~~-~~~fv~f~~~e~~~  135 (136)
                      +..+|||+|||.++|+++|+++|++|| +..+.++.+.. ++.. +.|||+|.+.|+|+
T Consensus        14 p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~   71 (104)
T d1wi8a_          14 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLL   71 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHH
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHH
Confidence            568999999999999999999999999 77888777653 4544 57999999999874

>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=99.37  E-value=6e-13  Score=78.29  Aligned_cols=54  Identities=11%  Similarity=0.130  Sum_probs=48.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ...+.+|||+|||+.+|+++|.++|++||.|..+.+.++     ++.|||+|.+.|+|.
T Consensus        12 ~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~-----k~~AfV~f~~~e~A~   65 (104)
T d1wexa_          12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAK   65 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT-----TTEEEEEESSHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec-----ceeEEEEeCCHHHHH
Confidence            346789999999999999999999999999999999864     367999999999875

>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=99.36  E-value=2.4e-13  Score=80.54  Aligned_cols=54  Identities=13%  Similarity=0.149  Sum_probs=48.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ...+|||+|||..+|+++|+++|++||.|..+.+.+++   .++.|||+|.+.|+|.
T Consensus         6 ~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~---~~g~aFV~f~~~e~A~   59 (108)
T d2adba1           6 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN---NQFQALLQYADPVSAQ   59 (108)
T ss_dssp             CEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET---TEEEEEEEESCHHHHH
T ss_pred             CeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC---CCCeEEEEECCHHHHH
Confidence            45679999999999999999999999999999999874   3466999999999874

>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=99.36  E-value=2.8e-14  Score=83.79  Aligned_cols=58  Identities=17%  Similarity=0.265  Sum_probs=51.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      .++++|||+|||.++++++|+++|++||.|..+.+..+..+|.. +.|||+|.+.|+|.
T Consensus        16 ~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~   74 (102)
T d2cpxa1          16 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAW   74 (102)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHH
Confidence            35689999999999999999999999999999998888766666 55999999999885

>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=99.35  E-value=2.2e-13  Score=80.09  Aligned_cols=57  Identities=5%  Similarity=0.039  Sum_probs=46.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCC-ccceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATE-NGKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~-~~~~fv~f~~~e~~~  135 (136)
                      ...+|||+|||.++|+++|+++|..||.+..+.++.+..+|. .|.|||+|.+.|+|.
T Consensus         7 ~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~   64 (103)
T d2cpya1           7 AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDAR   64 (103)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHH
T ss_pred             CceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHH
Confidence            457799999999999999999999999988754444444444 567999999999875

>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=99.35  E-value=2e-13  Score=81.39  Aligned_cols=58  Identities=14%  Similarity=0.249  Sum_probs=48.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-cceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-GKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~~~fv~f~~~e~~~  135 (136)
                      ....+|||+|||.++|+++|+++|+.||.+..+.++.+..+|.. |.|||+|.+.|+|+
T Consensus        16 ~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~   74 (112)
T d1wela1          16 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYK   74 (112)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHH
T ss_pred             CCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHH
Confidence            45679999999999999999999999999877555555445555 66999999999875

>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=99.34  E-value=3.6e-13  Score=80.06  Aligned_cols=52  Identities=13%  Similarity=0.093  Sum_probs=46.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ..++|||+|||+.+++++|+++|++||+|..|.|..     .++.|||+|.+.++|.
T Consensus         9 ~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~-----~kg~afV~f~~~~~A~   60 (111)
T d1whxa_           9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE-----GGITAIVEFLEPLEAR   60 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS-----SSSCEEEEESCHHHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeec-----cCceEEEEEcCHHHHH
Confidence            457899999999999999999999999999998853     3477999999999875

>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=99.31  E-value=8.1e-13  Score=77.06  Aligned_cols=53  Identities=23%  Similarity=0.330  Sum_probs=46.8

Q ss_pred             CCCceEEEcCCCCC-CCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPKH-MSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~~-~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ..+++|||+|||.+ +|+++|.++|++||.|..+.+.++     ++.|||+|.+.|+|.
T Consensus        16 ~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~-----k~~afV~f~~~~~A~   69 (99)
T d1x4fa1          16 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM-----KSQAFIEMETREDAM   69 (99)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT-----TTEEEEECSSHHHHH
T ss_pred             CCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec-----CCcEEEEecchHHHH
Confidence            45689999999985 899999999999999999999865     367999999999874

>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=99.30  E-value=1.8e-13  Score=76.87  Aligned_cols=50  Identities=16%  Similarity=0.320  Sum_probs=44.2

Q ss_pred             ceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          81 ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        81 ~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      .+|||+|||.++|+++|+++|++||.|.++.+...     ++.|||+|.+.|+|.
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~-----rg~aFV~f~~~~~A~   51 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK-----SGYAFVDYPDQNWAI   51 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEE-----TTEEEECCSCHHHHH
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEecc-----cceEEEEECCHHHHH
Confidence            36999999999999999999999999988777653     467999999999875

>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=99.28  E-value=1.4e-12  Score=72.91  Aligned_cols=50  Identities=30%  Similarity=0.395  Sum_probs=44.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      .+++|||+|+|  +|+++|+++|++||.|.++.+.++     ++.|||+|.+.|+|.
T Consensus         4 ~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~-----~~~afV~f~~~~~A~   53 (79)
T d2bz2a1           4 KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP-----RNCAFVTYEKMESAD   53 (79)
T ss_dssp             CCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT-----TTEEEEECSSHHHHH
T ss_pred             CCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC-----CCEEEEEEcccHHHH
Confidence            56899999986  899999999999999999999864     367999999999874

>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=99.27  E-value=2.3e-12  Score=73.70  Aligned_cols=54  Identities=15%  Similarity=0.181  Sum_probs=47.5

Q ss_pred             CCCCceEEEcCCCCC-CCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKH-MSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~-~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ...+++|||+|||.. +|++||.++|++||.|.++.+..++     +.|||+|++.|+|.
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~k-----~~afV~f~~~~~A~   59 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI-----NEAFIEMATTEDAQ   59 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS-----SCEEEEESSHHHHH
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeeccc-----eEEEEEEcchhhHH
Confidence            346789999999986 7899999999999999999998754     46999999999874

>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=99.27  E-value=1.7e-12  Score=75.51  Aligned_cols=51  Identities=18%  Similarity=0.429  Sum_probs=44.4

Q ss_pred             CCCceEEEcCCCC-CCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          78 IKGANLYVSGLPK-HMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl~~-~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ....+|||+|||+ .+++++|+++|++||+|..+.+.       +++|||+|.+.|+|.
T Consensus        13 ~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~-------rg~aFV~f~~~~~A~   64 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH-------KGFAFVQYVNERNAR   64 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE-------TEEEEEEESSHHHHH
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe-------CCeEEEEECCHHHHH
Confidence            3567899999975 67889999999999999999984       368999999999875

>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=99.26  E-value=5.9e-13  Score=76.50  Aligned_cols=55  Identities=16%  Similarity=0.359  Sum_probs=45.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHH----hhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELES----LFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~----~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      +.++|||+|||+.+++++|++    +|++||+|.+|.+..+  ...++.|||+|.+.|+|.
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~~--~~~~g~afV~F~~~~~A~   60 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRS--LKMRGQAFVIFKEVSSAT   60 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHH--HHHTTCEEEEESSHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEeee--ccCCCceEEEECCHHHHH
Confidence            457899999999999999864    6899999999887653  223467999999999874

>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=99.23  E-value=7.5e-12  Score=70.97  Aligned_cols=52  Identities=19%  Similarity=0.135  Sum_probs=45.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ..++|||+|||.++++++|+++|++||.|..+.+..     .++.|||+|.+.++|.
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~-----~rg~afV~f~~~~~A~   58 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK-----IRDYAFVHFSNREDAV   58 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE-----CSSEEEEEESSHHHHH
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcc-----ccEEEEEEeCCHHHHH
Confidence            457899999999999999999999999998887754     2468999999999875

>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=99.22  E-value=4.2e-13  Score=76.97  Aligned_cols=56  Identities=11%  Similarity=0.176  Sum_probs=45.5

Q ss_pred             ceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEE-----eCCCCCCc-cceEeecCccccccC
Q psy6353          81 ANLYVSGLPKHMSQQELESLFSPYGRIITSRIL-----CDNLATEN-GKYYSGLGGRERLRR  136 (136)
Q Consensus        81 ~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~-----~~~~~~~~-~~~fv~f~~~e~~~~  136 (136)
                      ++|||+|||.++|+++|+++|++||.+..+.+.     .+..++.. +.|||+|.++|++.+
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~   63 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ   63 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTT
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHH
Confidence            689999999999999999999999988765543     23344444 669999999999863

>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=99.21  E-value=2e-12  Score=74.89  Aligned_cols=55  Identities=15%  Similarity=0.148  Sum_probs=44.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        77 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ....++|||+|||.++|+++|+++|++||.|..+..    .+...+.+||+|.+.|+|.
T Consensus        13 ~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~----~~~~~~~afV~f~~~~~A~   67 (96)
T d1fjca_          13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ----DGKSKGIAYIEFKSEADAE   67 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE----TTEEEEEEEEEESSHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee----cCccccEEEEEeCCHHHHH
Confidence            345789999999999999999999999998866542    1233366999999999875

>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=99.19  E-value=9.8e-12  Score=74.03  Aligned_cols=46  Identities=15%  Similarity=0.126  Sum_probs=41.4

Q ss_pred             ceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcc
Q psy6353          81 ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGR  131 (136)
Q Consensus        81 ~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~  131 (136)
                      ..+||+|||..+|+++|+++|++||+|.+|.++++     .++|||+|.++
T Consensus        12 ~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~-----kg~gfV~F~~~   57 (113)
T d1owxa_          12 LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG-----AKEGIILFKEK   57 (113)
T ss_dssp             EEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT-----CSEEEEEESSC
T ss_pred             eEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC-----CceEEEEecCc
Confidence            45699999999999999999999999999999864     37899999986

>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=99.19  E-value=6.3e-12  Score=71.63  Aligned_cols=51  Identities=18%  Similarity=0.266  Sum_probs=41.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ..++|||+|||+++++++|+++|++|| +..+.+.+     .++.|||+|.+.|+|.
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~~~-----~kg~afV~f~~~~~A~   54 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVDR-----NKRTAFVTLLNGEQAQ   54 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEEEG-----GGTEEEECCSCHHHHH
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcC-ceeeeeec-----cCCceEEEECCHHHHH
Confidence            457899999999999999999999999 33344432     3367999999999875

>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=99.16  E-value=2e-11  Score=67.46  Aligned_cols=47  Identities=23%  Similarity=0.366  Sum_probs=39.7

Q ss_pred             EEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          83 LYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        83 l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      |||+|||+++++++|+++|++|| +..+.+.+     .++.|||+|.+.++|.
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~~~-----~~g~afv~f~~~~~A~   47 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDK-----YKGTAFVTLLNGEQAE   47 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEEET-----TTTEEEEEESSHHHHH
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceeecc-----cceeEEEEECCHHHHH
Confidence            79999999999999999999999 55555432     3467999999999875

>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=99.14  E-value=6.8e-12  Score=73.29  Aligned_cols=53  Identities=13%  Similarity=0.142  Sum_probs=46.1

Q ss_pred             CCCceEEEcC--CCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          78 IKGANLYVSG--LPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~n--l~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      .+..+++|.|  ||.++|+++|+++|++||.|..+.+.++     ++.|||+|.+.|+|.
T Consensus        16 ~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~-----k~~aFV~f~~~e~A~   70 (101)
T d2cq2a1          16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-----KPYSFARYRTTEESK   70 (101)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT-----CSCEEEEESSHHHHH
T ss_pred             CCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC-----ccEEEEEECCHHHHH
Confidence            3567888855  9999999999999999999999988865     368999999999875

>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=98.91  E-value=7.8e-12  Score=73.38  Aligned_cols=55  Identities=9%  Similarity=0.103  Sum_probs=48.2

Q ss_pred             ceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          81 ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        81 ~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ..+++.+++..+++++|+++|++||+|.+|+|+++..+..+|.+||+|.+.|+|.
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~~~~~~G~~fV~f~~~~~A~   82 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAE   82 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHH
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCCCCCEeeEEEEEEechhHHH
Confidence            3578888888999999999999999999999998876555577999999999885

>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=98.87  E-value=4.1e-10  Score=65.87  Aligned_cols=52  Identities=15%  Similarity=0.144  Sum_probs=43.9

Q ss_pred             CCceEEEcCCCCCC-C----HHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          79 KGANLYVSGLPKHM-S----QQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl~~~~-t----~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ...+|||+||+.++ +    +++|+++|++||.|.++.+.+     .++.|||+|.+.|+|.
T Consensus         4 ~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k-----~~~~afV~f~~~~~A~   60 (104)
T d1weya_           4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK-----SFKRVRINFSNPLSAA   60 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET-----TTTEEEEECSSTTHHH
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEec-----CCCEEEEEECCHHHHH
Confidence            56789999999875 3    357999999999999999985     3467999999999875

>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=98.86  E-value=4.3e-10  Score=62.81  Aligned_cols=52  Identities=17%  Similarity=0.231  Sum_probs=42.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCccccccC
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLRR  136 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~~  136 (136)
                      ..+.|+|.++|++.+++.| +.|++||+|.++++.++     .+.+||+|.++|+|.+
T Consensus         3 ~~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~~-----~~~~fV~f~~~~~A~~   54 (81)
T d1wwha1           3 DDTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSNT-----GNWMHIRYQSKLQARK   54 (81)
T ss_dssp             GGGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECSS-----SSEEEEEESSHHHHHH
T ss_pred             cccEEEEECCChHHHHHHH-HHHHhhhhhheEEecCC-----CCEEEEEEcccHHHHH
Confidence            4567999999999987655 57999999999987643     3679999999998853

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.59  E-value=6.5e-09  Score=60.59  Aligned_cols=57  Identities=16%  Similarity=0.191  Sum_probs=45.8

Q ss_pred             CCceEEEcCC--CCCC--------CHHHHHHhhcCCCceEEEEEEeCCCCCCc---cceEeecCcccccc
Q psy6353          79 KGANLYVSGL--PKHM--------SQQELESLFSPYGRIITSRILCDNLATEN---GKYYSGLGGRERLR  135 (136)
Q Consensus        79 ~~~~l~v~nl--~~~~--------t~~~l~~~f~~~G~v~~~~i~~~~~~~~~---~~~fv~f~~~e~~~  135 (136)
                      +++.|.+.|+  |..+        ..+||++.|++||.|.++.|++++.+...   +.+||+|.+.|+|.
T Consensus         3 Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~   72 (104)
T d1o0pa_           3 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQ   72 (104)
T ss_dssp             CCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHH
T ss_pred             CCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHH
Confidence            5678999999  5443        23579999999999999999987765433   56999999999875

>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=98.51  E-value=2.9e-08  Score=57.24  Aligned_cols=55  Identities=13%  Similarity=0.205  Sum_probs=44.3

Q ss_pred             CCCceEEEcCC--CCCC---------CHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCcccccc
Q psy6353          78 IKGANLYVSGL--PKHM---------SQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERLR  135 (136)
Q Consensus        78 ~~~~~l~v~nl--~~~~---------t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~~  135 (136)
                      ..+++|+|.||  |.++         .+++|++.|++||.|..+.+..+.   ..|.+||+|.+.|+|.
T Consensus         6 ~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~---~~G~~fV~f~~~e~A~   71 (99)
T d2dita1           6 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRH---PDGVASVSFRDPEEAD   71 (99)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTC---TTCEEEEECSCHHHHH
T ss_pred             CCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCC---CccEEEEEECCHHHHH
Confidence            46789999998  5432         236899999999999999988764   3467999999999875

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.12  E-value=8.5e-06  Score=42.99  Aligned_cols=58  Identities=21%  Similarity=0.206  Sum_probs=51.7

Q ss_pred             HHHHhccCCCeeEEEEEc-cCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEeeC
Q psy6353          13 YEKVHLGFSDAEICVFLI-STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR   72 (136)
Q Consensus        13 l~~~f~~~G~v~~~~~~~-~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~~   72 (136)
                      |.+.|+++|+|.++.+.. ..|..  .|-|...+.++|..|+..+|...+++++|.|.++.
T Consensus        13 L~~~f~~h~~V~sv~l~~~~dg~~--~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          13 LQEAFARHGKVKSVELSPHTDYQL--KAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHSCEEEEEECSCCSTTC--CEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHhheeEEEEEEEeccCCcE--EEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            789999999999998877 66665  48899999999999999999999999999998764

>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=97.87  E-value=2.7e-05  Score=43.53  Aligned_cols=54  Identities=11%  Similarity=0.256  Sum_probs=44.3

Q ss_pred             ceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCc-c--ceEeecCccccc
Q psy6353          81 ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATEN-G--KYYSGLGGRERL  134 (136)
Q Consensus        81 ~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~-~--~~fv~f~~~e~~  134 (136)
                      ++|.|+.||+.+|++++.+.++..|++........+.+... .  -||+.|.+.|++
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v   58 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDI   58 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHH
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHH
Confidence            57999999999999999999999999988776666544332 2  289999999875

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.69  E-value=6.2e-05  Score=41.63  Aligned_cols=52  Identities=12%  Similarity=0.269  Sum_probs=45.6

Q ss_pred             HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHHcCceeCCceEEEEee
Q psy6353          13 YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA   71 (136)
Q Consensus        13 l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g~~l~v~~~   71 (136)
                      |.+.|+.||+|.-++.+.      +--+|+|.+-++|-+|++ ++|.++.|+.|++...
T Consensus        41 Llq~l~~~GeViLvRFv~------d~mwVTF~dG~SAL~al~-l~g~~v~G~~l~It~~   92 (95)
T d1ufwa_          41 LMQTLGSYGTIVLVRINQ------GQMLVTFADSHSALSVLD-VDGMKVKGRAVKISGP   92 (95)
T ss_dssp             HHHHHHHHSCCSEEEEET------TEEEEECSCSHHHHHHHH-GGGSEETTEEEEEECC
T ss_pred             HHHHHhhCCeEEEEEEeC------CeEEEEECCcHHHHHHhc-cCCeEEcceEEEEecC
Confidence            788899999998887765      458999999999999999 8999999999998643

>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=96.08  E-value=0.017  Score=31.78  Aligned_cols=62  Identities=16%  Similarity=0.215  Sum_probs=43.8

Q ss_pred             eeecCCChhhhHHHHhccCCC---eeEEEEEc---cCC-CceeeEEEEcCCHHHHHHHHHHHcCceeCC
Q psy6353           2 VYQTLLNKLFTYEKVHLGFSD---AEICVFLI---STA-QSLGYGFVNYHRPEDAEKAINTLNGLRLQN   63 (136)
Q Consensus         2 v~v~nl~~~~~l~~~f~~~G~---v~~~~~~~---~~~-~~kg~~fv~f~~~~~a~~a~~~~~~~~~~g   63 (136)
                      |.|..||...|..+++++.|+   +.......   ..+ ..-+.|+|.|.+.++.....+..+|+.+.+
T Consensus         4 vVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D   72 (91)
T d1uw4a_           4 VVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLD   72 (91)
T ss_dssp             EEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEEC
T ss_pred             EEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEc
Confidence            568899999996666655554   44333333   112 234679999999999999999999987743

>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=94.15  E-value=0.049  Score=30.18  Aligned_cols=49  Identities=24%  Similarity=0.384  Sum_probs=38.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHhhcCCCceEEEEEEeCCCCCCccceEeecCccccc
Q psy6353          79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRERL  134 (136)
Q Consensus        79 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~v~~~~i~~~~~~~~~~~~fv~f~~~e~~  134 (136)
                      ....+|.-..|..+...||.++|++||.|. +..+-|      ..+||...++|.+
T Consensus        14 ~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~-VswIdd------TSa~V~L~~~e~~   62 (100)
T d1whva_          14 KRDHVLHVTFPKEWKTSDLYQLFSAFGNIQ-ISWIDD------TSAFVSLSQPEQV   62 (100)
T ss_dssp             CCCSEEEEECCTTCCHHHHHHHHTTTCSCC-CEEEET------TEEEEECSCHHHH
T ss_pred             CcceeEEEeCCcccchhHHHHHhcCCCceE-EEEecC------ceEEEEecCHHHH
Confidence            446789999999999999999999999864 333322      3579998888875

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=93.32  E-value=0.13  Score=28.33  Aligned_cols=49  Identities=22%  Similarity=0.369  Sum_probs=36.5

Q ss_pred             eeecCCChhhh---HHHHhccCCCeeEEEEEccCCCceeeEEEEcCCHHHHHHHHHHH
Q psy6353           2 VYQTLLNKLFT---YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTL   56 (136)
Q Consensus         2 v~v~nl~~~~~---l~~~f~~~G~v~~~~~~~~~~~~kg~~fv~f~~~~~a~~a~~~~   56 (136)
                      ||.-..|....   |.++|+.||.|. |..+..+     -|||...+.++|+.++..+
T Consensus        18 Vf~~tFP~~Wk~~dI~~lFSpfG~V~-VswIddT-----Sa~V~L~~~e~~~~v~~~~   69 (100)
T d1whva_          18 VLHVTFPKEWKTSDLYQLFSAFGNIQ-ISWIDDT-----SAFVSLSQPEQVQIAVNTS   69 (100)
T ss_dssp             EEEEECCTTCCHHHHHHHHTTTCSCC-CEEEETT-----EEEEECSCHHHHHHHHHHH
T ss_pred             eEEEeCCcccchhHHHHHhcCCCceE-EEEecCc-----eEEEEecCHHHHHHHHHHh
Confidence            56666676665   999999999974 3333312     4999999999999988754