Citrus Sinensis ID: 030444

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------
Protein Sequence
MIAISKARAFSGDRLRRAVPGGVTRLPVSDPSVTGRHGATGPDLVQNLRSSSIDDQLPFDAAARPGHETLPLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPRSVFGARGRR
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEccccccccHHHHHHHHcccccEEEEEEEEccccccccccccEEEEEEccHHHHHHHHHHHccccccccccccccEEEEEEccccccccccccccc
Secondary Structure Prediction (SSPRO)
cEEEEEEcccccccccccccccccccccccccHcccccccccccccccccccccccccccccccccccccccccccccEEEEccccccccHHHHHHHHccccccEEEEEEEccccccccccEEEEEEEcccHHHHHHHHHHHcccEEcccccccccEEEEEEccccccccccccccc
Coil and Loop (DISEMBL)
MIAISKARAfsgdrlrravpggvtrlpvsdpsvtgrhgatgpdlvqnlrsssiddqlpfdaaarpghetlplppdasstlyveglpadstkrevahifrpfvgyKEVRLVIKEsklrggdplilcfvdfenpaCAATALSALQgyrmdeddpdskflrlqfsrnpgprsvfgargrr
Flexible Loop (DISEMBL)
miaiskarafsgdrlrravpggvtrlpvsdpsvtgrhgatgpdLVQNLRSSSIDDQLPFDAAARPGHETLPLPPDASSTLYVEGLPADSTKREVAHifrpfvgykeVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFlrlqfsrnpgprsvfgargrr
Low Complexity Region (SEG)
MIAISKARAFSGDRLRRAVPGGVTRLPVSDPSVTGRHGATGPDLVQNLRSSSIDDQLPFDAAARPGHETLPLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPRSVFGARGRR
Disordered region (IsUnstruct)
********************************************************************************YVEGL****TKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGY********************************
Disordered Region (DISOPRED)
******************************************************************************TLYVEGLPADSTKREVAHIFRPFVGYKEVR**************ILCFVDFENPACAATALSALQGYRMDEDDPDSKFL********************
Disordered Region (DISEMBL)
MIAISKARAFSGDRLRRAVPGGVTRLPVSDPSVTGRHGATGPDLVQNLRSSSIDDQLPFDAAARPGHETLPLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFLRLQFSRNPGP**********
Disordered Region (DISPRO)
MIAISKARAFS*******************************************D*LPFDAA*RP*H*TLPLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFLRLQFSRN*************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MIAISKARAFSGDRLRRAVPGGVTRLPVSDPSVTGRHGATGPDLVQNLRSSSIDDQLPFDAAARPGHETLPLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPRSVFGARGRR
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	177	2.2.26 [Sep-21-2011]
Q9YGP5	196	RNA-binding protein with	N/A	no	0.429	0.387	0.435	9e-08
P34761	661	Protein WHI3 OS=Saccharom	yes	no	0.734	0.196	0.314	3e-07
Q9W6I1	200	RNA-binding protein with	yes	no	0.429	0.38	0.423	3e-07
Q8VC52	206	RNA-binding protein with	yes	no	0.497	0.427	0.385	8e-07
Q6ZRY4	209	RNA-binding protein with	yes	no	0.429	0.363	0.423	1e-06
Q93062	196	RNA-binding protein with	no	no	0.429	0.387	0.411	3e-06
O74452	561	Cell wall integrity prote	yes	no	0.446	0.140	0.375	4e-06
Q9WVB0	197	RNA-binding protein with	no	no	0.429	0.385	0.411	4e-06
Q39244	250	U1 small nuclear ribonucl	no	no	0.485	0.344	0.291	1e-05
Q01617	738	Protein couch potato OS=D	no	no	0.463	0.111	0.360	2e-05

>sp|Q9YGP5|RBPMS_XENLA RNA-binding protein with multiple splicing OS=Xenopus laevis GN=rbpms PE=2 SV=1

 Score = 56.6 bits (135), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 37/85 (43%), Positives = 49/85 (57%), Gaps = 9/85 (10%)

Query: 79  TLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATA 138
           TL+V GLP D   RE+  +FRPF GY E  L+   SK   G      FV F+N A A  A
Sbjct: 21  TLFVSGLPIDIKPRELYLLFRPFKGY-EGSLIKLTSKQPVG------FVTFDNRAGAEAA 73

Query: 139 LSALQGYRMDEDDPDSKFLRLQFSR 163
            +AL G R D ++P +  LRL+F++
Sbjct: 74  KNALNGIRFDPENPQT--LRLEFAK 96

Acts as a coactivator of transcriptional activity. Binds RNA.
Xenopus laevis (taxid: 8355)

>sp|P34761|WHI3_YEAST Protein WHI3 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=WHI3 PE=1 SV=1

 Score = 54.7 bits (130), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 44/140 (31%), Positives = 68/140 (48%), Gaps = 10/140 (7%)

Query: 44  LVQNLRSSSIDDQLPFDAAAR---PGHETLPLPPDASSTLYVEGLPADSTKREVAHIFRP 100
           L  N+  S+   Q      AR   P +     PP   +TLYV  LP+D+T++E+  +F  
Sbjct: 503 LSSNITGSASISQADLSLLARIPPPANPADQNPP--CNTLYVGNLPSDATEQELRQLFSG 560

Query: 101 FVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK-FLRL 159
             G++ +    K +   G     +CFV+F++ + A  AL+ L G ++      SK  +RL
Sbjct: 561 QEGFRRLSFRNKNTTSNGHSHGPMCFVEFDDVSFATRALAELYGRQLPRSTVSSKGGIRL 620

Query: 160 QFSRNP----GPRSVFGARG 175
            FS+NP    GP S  G  G
Sbjct: 621 SFSKNPLGVRGPNSRRGGSG 640

Involved in size control and cell cycle.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

>sp|Q9W6I1|RBPMS_CHICK RNA-binding protein with multiple splicing OS=Gallus gallus GN=RBPMS PE=2 SV=1

 Score = 54.7 bits (130), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 36/85 (42%), Positives = 50/85 (58%), Gaps = 9/85 (10%)

Query: 79  TLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATA 138
           TL+V GLP D   RE+  +FRPF GY E  L+    KL    P  + FV F++ A A  A
Sbjct: 23  TLFVSGLPVDIKPRELYLLFRPFKGY-EGSLI----KLTSKQP--VGFVTFDSRAGAEAA 75

Query: 139 LSALQGYRMDEDDPDSKFLRLQFSR 163
            +AL G R D ++P +  LRL+F++
Sbjct: 76  KNALNGIRFDPENPQT--LRLEFAK 98

Acts as a coactivator of transcriptional activity. Binds RNA.

Gallus gallus (taxid: 9031)

>sp|Q8VC52|RBPS2_MOUSE RNA-binding protein with multiple splicing 2 OS=Mus musculus GN=Rbpms2 PE=1 SV=1

 Score = 53.5 bits (127), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 42/109 (38%), Positives = 56/109 (51%), Gaps = 21/109 (19%)

Query: 79  TLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATA 138
           TL+V GLP D   RE+  +FRPF GY E  L+    KL    P  + FV F++ A A  A
Sbjct: 26  TLFVSGLPVDIKPRELYLLFRPFKGY-EGSLI----KLTSRQP--VGFVIFDSRAGAEAA 78

Query: 139 LSALQGYRMDEDDPDSKFLRLQFSR------------NPGPRSVFGARG 175
            +AL G R D ++P +  LRL+F++             P P SV  A G
Sbjct: 79  KNALNGIRFDPENPQT--LRLEFAKANTKMAKSKLIATPNPTSVHPALG 125

Mus musculus (taxid: 10090)

>sp|Q6ZRY4|RBPS2_HUMAN RNA-binding protein with multiple splicing 2 OS=Homo sapiens GN=RBPMS2 PE=2 SV=1

 Score = 53.1 bits (126), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 36/85 (42%), Positives = 50/85 (58%), Gaps = 9/85 (10%)

Query: 79  TLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATA 138
           TL+V GLP D   RE+  +FRPF GY E  L+    KL    P  + FV F++ A A  A
Sbjct: 32  TLFVSGLPVDIKPRELYLLFRPFKGY-EGSLI----KLTARQP--VGFVIFDSRAGAEAA 84

Query: 139 LSALQGYRMDEDDPDSKFLRLQFSR 163
            +AL G R D ++P +  LRL+F++
Sbjct: 85  KNALNGIRFDPENPQT--LRLEFAK 107

Homo sapiens (taxid: 9606)

>sp|Q93062|RBPMS_HUMAN RNA-binding protein with multiple splicing OS=Homo sapiens GN=RBPMS PE=1 SV=1

 Score = 51.2 bits (121), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 35/85 (41%), Positives = 49/85 (57%), Gaps = 9/85 (10%)

Query: 79  TLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATA 138
           TL+V GLP D   RE+  +FRPF GY E  L+    KL    P  + FV F++ + A  A
Sbjct: 25  TLFVSGLPLDIKPRELYLLFRPFKGY-EGSLI----KLTSKQP--VGFVSFDSRSEAEAA 77

Query: 139 LSALQGYRMDEDDPDSKFLRLQFSR 163
            +AL G R D + P +  LRL+F++
Sbjct: 78  KNALNGIRFDPEIPQT--LRLEFAK 100

Acts as a coactivator of transcriptional activity. Required to increase TGFB1/Smad-mediated transactivation. Acts through SMAD2, SMAD3 and SMAD4 to increase transcriptional activity. Increases phosphorylation of SMAD2 and SMAD3 on their C-terminal SSXS motif, possibly through recruitment of TGFBR1. Promotes the nuclear accumulation of SMAD2, SMAD3 and SMAD4 proteins. Binds to poly(A) RNA.

Homo sapiens (taxid: 9606)

>sp|O74452|SCW1_SCHPO Cell wall integrity protein scw1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=scw1 PE=1 SV=1

 Score = 51.2 bits (121), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 33/88 (37%), Positives = 47/88 (53%), Gaps = 9/88 (10%)

Query: 78  STLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAAT 137
           +T+YV  LP  +++ E+  +F   VGYK  RL  +    +G  P  +CFV+FEN   A  
Sbjct: 426 NTIYVGNLPPSTSEEELKVLFSTQVGYK--RLCFRT---KGNGP--MCFVEFENIPYAME 478

Query: 138 ALSALQGYRMDEDDPDSKFLRLQFSRNP 165
           AL  LQG  +         +RL FS+NP
Sbjct: 479 ALKNLQGVCLSSSIKGG--IRLSFSKNP 504

Acts as a negative regulator of cell wall and septum deposition.

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

>sp|Q9WVB0|RBPMS_MOUSE RNA-binding protein with multiple splicing OS=Mus musculus GN=Rbpms PE=2 SV=2

 Score = 51.2 bits (121), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 35/85 (41%), Positives = 49/85 (57%), Gaps = 9/85 (10%)

Query: 79  TLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATA 138
           TL+V GLP D   RE+  +FRPF GY E  L+    KL    P  + FV F++ + A  A
Sbjct: 25  TLFVSGLPLDIKPRELYLLFRPFKGY-EGSLI----KLTSKQP--VGFVSFDSRSEAEAA 77

Query: 139 LSALQGYRMDEDDPDSKFLRLQFSR 163
            +AL G R D + P +  LRL+F++
Sbjct: 78  KNALNGIRFDPEIPQT--LRLEFAK 100

Acts as a coactivator of transcriptional activity. Required to increase TGFB1/Smad-mediated transactivation. Acts through SMAD2, SMAD3 and SMAD4 to increase transcriptional activity. Increases phosphorylation of SMAD2 and SMAD3 on their C-terminal SSXS motif, possibly through recruitment of TGFBR1. Promotes the nuclear accumulation of SMAD2, SMAD3 and SMAD4 proteins. Binds to poly(A) RNA.

Mus musculus (taxid: 10090)

>sp|Q39244|RU1A_ARATH U1 small nuclear ribonucleoprotein A OS=Arabidopsis thaliana GN=U1A PE=1 SV=1

 Score = 49.3 bits (116), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 28/96 (29%), Positives = 53/96 (55%), Gaps = 10/96 (10%)

Query: 56  QLPFDAAARPGHETLPLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESK 115
           Q+P+    +P     P PP+  + L+V+ LP ++T   +  +F  + G+KEVR++  E+K
Sbjct: 157 QVPYPGGMKPNMPEAPAPPN--NILFVQNLPHETTPMVLQMLFCQYQGFKEVRMI--EAK 212

Query: 116 LRGGDPLILCFVDFENPACAATALSALQGYRMDEDD 151
                P I  FV+F +   +  A+  LQG+++ ++ 
Sbjct: 213 -----PGI-AFVEFADEMQSTVAMQGLQGFKIQQNQ 242

Involved in nuclear pre-mRNA splicing (By similarity). Seems to not be involved in polyadenylation.

Arabidopsis thaliana (taxid: 3702)

>sp|Q01617|CPO_DROME Protein couch potato OS=Drosophila melanogaster GN=cpo PE=2 SV=3

 Score = 48.5 bits (114), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 31/86 (36%), Positives = 46/86 (53%), Gaps = 4/86 (4%)

Query: 79  TLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATA 138
           TL+V GLP D+  RE+  +FR + GY+   L +     +   P  + FV F   A A  A
Sbjct: 452 TLFVSGLPMDAKPRELYLLFRAYEGYEGSLLKVTSKNGKTASP--VGFVTFHTRAGAEAA 509

Query: 139 LSALQGYRMDEDDPDSKFLRLQFSRN 164
              LQG R D D P +  +RL+F+++
Sbjct: 510 KQDLQGVRFDPDMPQT--IRLEFAKS 533

May play a role in the development or function of the peripheral nervous system by regulating the processing of nervous system-specific transcripts.

Drosophila melanogaster (taxid: 7227)

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	177
388513795	239	unknown [Lotus japonicus]	0.892	0.661	0.721	1e-58
356576041	252	PREDICTED: uncharacterized protein LOC10	0.960	0.674	0.680	1e-55
356576043	244	PREDICTED: uncharacterized protein LOC10	0.960	0.696	0.680	1e-55
255645608	242	unknown [Glycine max]	0.847	0.619	0.72	5e-55
356535810	243	PREDICTED: uncharacterized protein LOC10	0.841	0.613	0.733	3e-54
356535808	251	PREDICTED: uncharacterized protein LOC10	0.841	0.593	0.733	4e-54
356535806	251	PREDICTED: uncharacterized protein LOC10	0.841	0.593	0.72	2e-53
255637493	251	unknown [Glycine max]	0.841	0.593	0.72	2e-53
356576047	245	PREDICTED: uncharacterized protein LOC10	0.858	0.620	0.712	3e-53
356576045	252	PREDICTED: uncharacterized protein LOC10	0.858	0.603	0.712	3e-53

>gi|388513795|gb|AFK44959.1| unknown [Lotus japonicus]

 Score =  231 bits (588), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 114/158 (72%), Positives = 129/158 (81%)

Query: 20  PGGVTRLPVSDPSVTGRHGATGPDLVQNLRSSSIDDQLPFDAAARPGHETLPLPPDASST 79
           PGG+    ++D +  GRHG  GPD+  N R  +   Q P D+ +RPGHET+PLPPDASST
Sbjct: 82  PGGLPGHSLADHAAMGRHGGGGPDIAPNGRGFNYGGQPPVDSVSRPGHETVPLPPDASST 141

Query: 80  LYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATAL 139
           LYVEGLP+DSTKREVAHIFRPFVGY+EVRLV KESK RGGDPLILCFVDFENPACAATAL
Sbjct: 142 LYVEGLPSDSTKREVAHIFRPFVGYREVRLVTKESKHRGGDPLILCFVDFENPACAATAL 201

Query: 140 SALQGYRMDEDDPDSKFLRLQFSRNPGPRSVFGARGRR 177
           SALQGY++DE DP+S  LRLQFSR PGPRS  G RG+R
Sbjct: 202 SALQGYKVDELDPESGHLRLQFSRYPGPRSGPGFRGKR 239

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356576041|ref|XP_003556143.1| PREDICTED: uncharacterized protein LOC100812551 isoform 1 [Glycine max]

 Score =  220 bits (561), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 117/172 (68%), Positives = 135/172 (78%), Gaps = 2/172 (1%)

Query: 6   KARAFSGDRLRRAVPGGVTRLPVSDPSVTGRHGATGPDLVQNLRSSSIDDQLPFDAAARP 65
           +A A     L R V GG+ R  ++DP+V G H   G DL +  R+ +  DQLP DAA+ P
Sbjct: 83  EASAIGSVGLERGV-GGLPRHSLTDPAVMG-HPGGGHDLARGGRNVNYGDQLPVDAASMP 140

Query: 66  GHETLPLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILC 125
           G ET+PLPPDASSTLYVEGLP+DST+REVAHIFRPFVGY+EVRLV KESK RGGDPLILC
Sbjct: 141 GPETVPLPPDASSTLYVEGLPSDSTRREVAHIFRPFVGYREVRLVSKESKHRGGDPLILC 200

Query: 126 FVDFENPACAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPRSVFGARGRR 177
           FVDF NPACAATALSALQGY++DE +P+S  LRLQFSR PGPRS  G RG+R
Sbjct: 201 FVDFANPACAATALSALQGYKVDELNPESSHLRLQFSRFPGPRSGPGPRGKR 252

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356576043|ref|XP_003556144.1| PREDICTED: uncharacterized protein LOC100812551 isoform 2 [Glycine max]

 Score =  220 bits (561), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 117/172 (68%), Positives = 135/172 (78%), Gaps = 2/172 (1%)

Query: 6   KARAFSGDRLRRAVPGGVTRLPVSDPSVTGRHGATGPDLVQNLRSSSIDDQLPFDAAARP 65
           +A A     L R V GG+ R  ++DP+V G H   G DL +  R+ +  DQLP DAA+ P
Sbjct: 75  EASAIGSVGLERGV-GGLPRHSLTDPAVMG-HPGGGHDLARGGRNVNYGDQLPVDAASMP 132

Query: 66  GHETLPLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILC 125
           G ET+PLPPDASSTLYVEGLP+DST+REVAHIFRPFVGY+EVRLV KESK RGGDPLILC
Sbjct: 133 GPETVPLPPDASSTLYVEGLPSDSTRREVAHIFRPFVGYREVRLVSKESKHRGGDPLILC 192

Query: 126 FVDFENPACAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPRSVFGARGRR 177
           FVDF NPACAATALSALQGY++DE +P+S  LRLQFSR PGPRS  G RG+R
Sbjct: 193 FVDFANPACAATALSALQGYKVDELNPESSHLRLQFSRFPGPRSGPGPRGKR 244

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255645608|gb|ACU23298.1| unknown [Glycine max]

 Score =  218 bits (556), Expect = 5e-55,   Method: Compositional matrix adjust.
 Identities = 108/150 (72%), Positives = 122/150 (81%)

Query: 28  VSDPSVTGRHGATGPDLVQNLRSSSIDDQLPFDAAARPGHETLPLPPDASSTLYVEGLPA 87
           ++DPSV GRHG  GPDL  N R  +   QLP DA +RPG ET+ LPPDASSTLYVEGLP+
Sbjct: 93  LADPSVMGRHGGGGPDLAPNGRGVNYGGQLPVDAVSRPGPETVSLPPDASSTLYVEGLPS 152

Query: 88  DSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRM 147
           DST+REVAHIFRPFVGY+EVRLV KESK RGGDP  LCFVDF NPACAATA+SALQGY++
Sbjct: 153 DSTRREVAHIFRPFVGYREVRLVSKESKHRGGDPHYLCFVDFANPACAATAMSALQGYKV 212

Query: 148 DEDDPDSKFLRLQFSRNPGPRSVFGARGRR 177
           DE +P+S  LRLQFSR PGPRS    RG+R
Sbjct: 213 DELNPESSHLRLQFSRYPGPRSGPAFRGKR 242

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356535810|ref|XP_003536436.1| PREDICTED: uncharacterized protein LOC100816230 isoform 2 [Glycine max]

 Score =  216 bits (549), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 110/150 (73%), Positives = 125/150 (83%), Gaps = 1/150 (0%)

Query: 28  VSDPSVTGRHGATGPDLVQNLRSSSIDDQLPFDAAARPGHETLPLPPDASSTLYVEGLPA 87
           ++DP+VTG H   G DL +N R+ +   QLP DAA+ PG ETLPLPPDASSTLYVEGLP+
Sbjct: 95  LTDPAVTG-HPGGGHDLSRNGRNVNYASQLPVDAASMPGPETLPLPPDASSTLYVEGLPS 153

Query: 88  DSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRM 147
            ST+REVAHIFRPFVGY+EVRLV KESK RGGDPLILCFVDF NPACAATALSALQGY++
Sbjct: 154 GSTRREVAHIFRPFVGYREVRLVSKESKHRGGDPLILCFVDFANPACAATALSALQGYKV 213

Query: 148 DEDDPDSKFLRLQFSRNPGPRSVFGARGRR 177
           DE +P+S  LRLQFSR PGPRS  G RG+R
Sbjct: 214 DELNPESSHLRLQFSRFPGPRSGPGLRGKR 243

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356535808|ref|XP_003536435.1| PREDICTED: uncharacterized protein LOC100816230 isoform 1 [Glycine max]

 Score =  215 bits (548), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 110/150 (73%), Positives = 125/150 (83%), Gaps = 1/150 (0%)

Query: 28  VSDPSVTGRHGATGPDLVQNLRSSSIDDQLPFDAAARPGHETLPLPPDASSTLYVEGLPA 87
           ++DP+VTG H   G DL +N R+ +   QLP DAA+ PG ETLPLPPDASSTLYVEGLP+
Sbjct: 103 LTDPAVTG-HPGGGHDLSRNGRNVNYASQLPVDAASMPGPETLPLPPDASSTLYVEGLPS 161

Query: 88  DSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRM 147
            ST+REVAHIFRPFVGY+EVRLV KESK RGGDPLILCFVDF NPACAATALSALQGY++
Sbjct: 162 GSTRREVAHIFRPFVGYREVRLVSKESKHRGGDPLILCFVDFANPACAATALSALQGYKV 221

Query: 148 DEDDPDSKFLRLQFSRNPGPRSVFGARGRR 177
           DE +P+S  LRLQFSR PGPRS  G RG+R
Sbjct: 222 DELNPESSHLRLQFSRFPGPRSGPGLRGKR 251

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356535806|ref|XP_003536434.1| PREDICTED: uncharacterized protein LOC100815695 [Glycine max]

 Score =  213 bits (542), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 108/150 (72%), Positives = 124/150 (82%), Gaps = 1/150 (0%)

Query: 28  VSDPSVTGRHGATGPDLVQNLRSSSIDDQLPFDAAARPGHETLPLPPDASSTLYVEGLPA 87
           ++DP+V G H   G D  +N R+ +   QLP DAA+ PG ET+PLPPDASSTLYVEGLP+
Sbjct: 103 LTDPAVMG-HPGGGHDHARNGRNVNYGGQLPLDAASMPGPETVPLPPDASSTLYVEGLPS 161

Query: 88  DSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRM 147
           DST+REVAHIFRPFVGY+EVRLV KESK RGGDPLILCFVDF NPACAATALSALQGY++
Sbjct: 162 DSTRREVAHIFRPFVGYREVRLVSKESKHRGGDPLILCFVDFANPACAATALSALQGYKV 221

Query: 148 DEDDPDSKFLRLQFSRNPGPRSVFGARGRR 177
           DE +P+S  LRLQFSR PGPRS  G RG+R
Sbjct: 222 DELNPESSHLRLQFSRFPGPRSGPGPRGKR 251

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255637493|gb|ACU19073.1| unknown [Glycine max]

 Score =  213 bits (542), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 108/150 (72%), Positives = 124/150 (82%), Gaps = 1/150 (0%)

Query: 28  VSDPSVTGRHGATGPDLVQNLRSSSIDDQLPFDAAARPGHETLPLPPDASSTLYVEGLPA 87
           ++DP+V G H   G D  +N R+ +   QLP DAA+ PG ET+PLPPDASSTLYVEGLP+
Sbjct: 103 LTDPAVMG-HPGGGHDHARNGRNVNYGGQLPLDAASMPGPETVPLPPDASSTLYVEGLPS 161

Query: 88  DSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRM 147
           DST+REVAHIFRPFVGY+EVRLV KESK RGGDPLILCFVDF NPACAATALSALQGY++
Sbjct: 162 DSTRREVAHIFRPFVGYREVRLVSKESKHRGGDPLILCFVDFANPACAATALSALQGYKV 221

Query: 148 DEDDPDSKFLRLQFSRNPGPRSVFGARGRR 177
           DE +P+S  LRLQFSR PGPRS  G RG+R
Sbjct: 222 DELNPESSHLRLQFSRFPGPRSGPGPRGKR 251

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356576047|ref|XP_003556146.1| PREDICTED: uncharacterized protein LOC100813445 isoform 2 [Glycine max]

 Score =  213 bits (541), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 109/153 (71%), Positives = 125/153 (81%), Gaps = 1/153 (0%)

Query: 25  RLPVSDPSVTGRHGATGPDLVQNLRSSSIDDQLPFDAAARPGHETLPLPPDASSTLYVEG 84
           R  ++DP+V G H   G DL +N R+ +   QL  DAA+ PG ET+PLPPDASSTLYVEG
Sbjct: 94  RHSLTDPAVMG-HPGGGHDLARNGRNVNYGGQLTVDAASMPGPETVPLPPDASSTLYVEG 152

Query: 85  LPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQG 144
           LP+DST+REVAHIFRPFVGY+EVRLV KESK RGGDPLILCFVDF NPACAATALSALQG
Sbjct: 153 LPSDSTRREVAHIFRPFVGYREVRLVSKESKHRGGDPLILCFVDFANPACAATALSALQG 212

Query: 145 YRMDEDDPDSKFLRLQFSRNPGPRSVFGARGRR 177
           Y++DE +P+S  LRLQFSR PGPRS  G RG+R
Sbjct: 213 YKVDELNPESSHLRLQFSRFPGPRSGPGPRGKR 245

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356576045|ref|XP_003556145.1| PREDICTED: uncharacterized protein LOC100813445 isoform 1 [Glycine max]

 Score =  213 bits (541), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 109/153 (71%), Positives = 125/153 (81%), Gaps = 1/153 (0%)

Query: 25  RLPVSDPSVTGRHGATGPDLVQNLRSSSIDDQLPFDAAARPGHETLPLPPDASSTLYVEG 84
           R  ++DP+V G H   G DL +N R+ +   QL  DAA+ PG ET+PLPPDASSTLYVEG
Sbjct: 101 RHSLTDPAVMG-HPGGGHDLARNGRNVNYGGQLTVDAASMPGPETVPLPPDASSTLYVEG 159

Query: 85  LPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQG 144
           LP+DST+REVAHIFRPFVGY+EVRLV KESK RGGDPLILCFVDF NPACAATALSALQG
Sbjct: 160 LPSDSTRREVAHIFRPFVGYREVRLVSKESKHRGGDPLILCFVDFANPACAATALSALQG 219

Query: 145 YRMDEDDPDSKFLRLQFSRNPGPRSVFGARGRR 177
           Y++DE +P+S  LRLQFSR PGPRS  G RG+R
Sbjct: 220 YKVDELNPESSHLRLQFSRFPGPRSGPGPRGKR 252

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

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	177
TAIR|locus:2014937	421	AT1G21320 [Arabidopsis thalian	0.937	0.394	0.572	6.4e-44
TAIR|locus:2025232	233	AT1G76940 [Arabidopsis thalian	0.587	0.446	0.773	5.3e-40
UNIPROTKB|G5EH29	622	MGCH7_ch7g848 "RNA binding pro	0.542	0.154	0.381	9.1e-10
DICTYBASE|DDB_G0268988	356	DDB_G0268988 "RNA-binding regi	0.604	0.300	0.342	9.1e-10
UNIPROTKB|Q9YGP5	196	rbpms "RNA-binding protein wit	0.429	0.387	0.435	2.9e-09
SGD|S000005141	661	WHI3 "RNA binding protein that	0.734	0.196	0.314	3.5e-09
UNIPROTKB|F1NZ89	180	RBPMS2 "Uncharacterized protei	0.429	0.422	0.423	7.6e-09
UNIPROTKB|F1P2M9	198	RBPMS2 "Uncharacterized protei	0.429	0.383	0.423	7.6e-09
UNIPROTKB|Q9W6I1	200	RBPMS "RNA-binding protein wit	0.429	0.38	0.423	7.6e-09
UNIPROTKB|F1N2U8	203	RBPMS2 "Uncharacterized protei	0.485	0.423	0.406	7.6e-09

TAIR|locus:2014937 AT1G21320 [Arabidopsis thaliana (taxid:3702)]

 Score = 463 (168.0 bits), Expect = 6.4e-44, P = 6.4e-44
 Identities = 99/173 (57%), Positives = 118/173 (68%)

Query:     6 KARAFSGDRLRRAVPGGVTRLPVSDPSVTGRHGATGPDLVQNLRSSSIDDQL-PFDAAAR 64
             +A  F+G  + R   GG   +P   PS+       G  L  + R +  D      D+  R
Sbjct:   254 EAGPFNGVGMVRQ--GGSNMMP--GPSMGELMAGCGGSLPSDFRPNGRDMGFGQLDSVGR 309

Query:    65 PGHETLPLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLIL 124
             PG E  PLPPD S+TLYVEGLP++ ++REV+HIFRPFVGY+EVRLV ++SK R GDP +L
Sbjct:   310 PGREPHPLPPDVSNTLYVEGLPSNCSRREVSHIFRPFVGYREVRLVTQDSKHRSGDPTVL 369

Query:   125 CFVDFENPACAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPRSVFGARGRR 177
             CFVDFEN ACAATALSALQ YRMDED+PDSK LRLQF RNPGPR   G RG R
Sbjct:   370 CFVDFENSACAATALSALQDYRMDEDEPDSKILRLQFFRNPGPRP--GQRGGR 420

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2025232 AT1G76940 [Arabidopsis thaliana (taxid:3702)]

 Score = 426 (155.0 bits), Expect = 5.3e-40, P = 5.3e-40
 Identities = 82/106 (77%), Positives = 93/106 (87%)

Query:    72 LPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFEN 131
             LP DAS+TLYVEGLP++ ++REVAHIFRPFVGY+EVRLV K+SK R GDP++LCFVDF N
Sbjct:   130 LPSDASNTLYVEGLPSNCSRREVAHIFRPFVGYREVRLVTKDSKHRNGDPIVLCFVDFTN 189

Query:   132 PACAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPRSVFGARGRR 177
             PACAATALSALQGYRMDE++ DSKFLRLQFSR PG R   G RGRR
Sbjct:   190 PACAATALSALQGYRMDENESDSKFLRLQFSRKPGSRP--GQRGRR 233

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|G5EH29 MGCH7_ch7g848 "RNA binding protein" [Magnaporthe oryzae 70-15 (taxid:242507)]

 Score = 131 (51.2 bits), Expect = 9.1e-10, Sum P(2) = 9.1e-10
 Identities = 42/110 (38%), Positives = 59/110 (53%)

Query:    65 PGHETLPL-PPDAS---STLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGD 120
             PGH   P+ P D +   +TLYV  LP D+++ E+   F    GYK  RL  + +K  G  
Sbjct:   401 PGHSFPPVNPADQNPPCNTLYVGNLPIDTSEEELKATFSKQRGYK--RLCFR-TKQNG-- 455

Query:   121 PLILCFVDFENPACAATALSALQGYRMDEDDPDSKFLRLQFSRNP-GPRS 169
             P+  CFV+FE+ + A  AL  L G+ +         +RL FS+NP G RS
Sbjct:   456 PM--CFVEFEDVSFATKALHELYGHMLHNSVKGG--IRLSFSKNPLGVRS 501

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

DICTYBASE|DDB_G0268988 DDB_G0268988 "RNA-binding region RNP-1 domain-containing protein" [Dictyostelium discoideum (taxid:44689)]

 Score = 147 (56.8 bits), Expect = 9.1e-10, P = 9.1e-10
 Identities = 39/114 (34%), Positives = 60/114 (52%)

Query:    50 SSSIDDQLPFDAAARPGHETLPLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRL 109
             S+S+        +A P   ++       STL+V  LP D T+RE++ +FR   G+  +RL
Sbjct:   244 STSLSSSHYHGGSALPPQSSISTTGMPCSTLFVSNLPKDVTERELSILFRFMRGFVGIRL 303

Query:   110 VIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFLRLQFSR 163
             + KE KL    P+  CF DF +   +  AL  LQG+RMD  D  S  + ++F +
Sbjct:   304 INKEGKL----PM--CFCDFIDTQSSMFALEFLQGFRMDASDISSS-ISIEFDK 350

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0044351 "macropinocytosis" evidence=RCA

UNIPROTKB|Q9YGP5 rbpms "RNA-binding protein with multiple splicing" [Xenopus laevis (taxid:8355)]

 Score = 136 (52.9 bits), Expect = 2.9e-09, P = 2.9e-09
 Identities = 37/85 (43%), Positives = 50/85 (58%)

Query:    79 TLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATA 138
             TL+V GLP D   RE+  +FRPF GY E  L+    KL    P+   FV F+N A A  A
Sbjct:    21 TLFVSGLPIDIKPRELYLLFRPFKGY-EGSLI----KLTSKQPV--GFVTFDNRAGAEAA 73

Query:   139 LSALQGYRMDEDDPDSKFLRLQFSR 163
              +AL G R D ++P +  LRL+F++
Sbjct:    74 KNALNGIRFDPENPQT--LRLEFAK 96

GO:0003713 "transcription coactivator activity" evidence=ISS

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

GO:0010862 "positive regulation of pathway-restricted SMAD protein phosphorylation" evidence=ISS

GO:0060391 "positive regulation of SMAD protein import into nucleus" evidence=ISS

SGD|S000005141 WHI3 "RNA binding protein that sequesters CLN3 mRNA in cytoplasmic foci" [Saccharomyces cerevisiae (taxid:4932)]

 Score = 146 (56.5 bits), Expect = 3.5e-09, P = 3.5e-09
 Identities = 44/140 (31%), Positives = 68/140 (48%)

Query:    44 LVQNLRSSSIDDQLPFDAAAR---PGHETLPLPPDASSTLYVEGLPADSTKREVAHIFRP 100
             L  N+  S+   Q      AR   P +     PP   +TLYV  LP+D+T++E+  +F  
Sbjct:   503 LSSNITGSASISQADLSLLARIPPPANPADQNPP--CNTLYVGNLPSDATEQELRQLFSG 560

Query:   101 FVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF-LRL 159
               G++ +    K +   G     +CFV+F++ + A  AL+ L G ++      SK  +RL
Sbjct:   561 QEGFRRLSFRNKNTTSNGHSHGPMCFVEFDDVSFATRALAELYGRQLPRSTVSSKGGIRL 620

Query:   160 QFSRNP----GPRSVFGARG 175
              FS+NP    GP S  G  G
Sbjct:   621 SFSKNPLGVRGPNSRRGGSG 640

GO:0003723 "RNA binding" evidence=IEA;ISS;IMP;IDA

GO:0008361 "regulation of cell size" evidence=IGI;IMP

GO:0007124 "pseudohyphal growth" evidence=IMP

GO:0007049 "cell cycle" evidence=IEA

GO:0001403 "invasive growth in response to glucose limitation" evidence=IMP

GO:0051220 "cytoplasmic sequestering of protein" evidence=IMP

GO:0005737 "cytoplasm" evidence=IDA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|F1NZ89 RBPMS2 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 132 (51.5 bits), Expect = 7.6e-09, P = 7.6e-09
 Identities = 36/85 (42%), Positives = 50/85 (58%)

Query:    79 TLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATA 138
             TL+V GLP D   RE+  +FRPF GY E  L+    KL    P+   FV F++ A A  A
Sbjct:     3 TLFVSGLPVDIKPRELYLLFRPFKGY-EGSLI----KLTSKQPV--GFVTFDSRAGAEAA 55

Query:   139 LSALQGYRMDEDDPDSKFLRLQFSR 163
              +AL G R D ++P +  LRL+F++
Sbjct:    56 KNALNGIRFDPENPQT--LRLEFAK 78

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|F1P2M9 RBPMS2 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 132 (51.5 bits), Expect = 7.6e-09, P = 7.6e-09
 Identities = 36/85 (42%), Positives = 50/85 (58%)

Query:    79 TLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATA 138
             TL+V GLP D   RE+  +FRPF GY E  L+    KL    P+   FV F++ A A  A
Sbjct:    21 TLFVSGLPVDIKPRELYLLFRPFKGY-EGSLI----KLTSKQPV--GFVTFDSRAGAEAA 73

Query:   139 LSALQGYRMDEDDPDSKFLRLQFSR 163
              +AL G R D ++P +  LRL+F++
Sbjct:    74 KNALNGIRFDPENPQT--LRLEFAK 96

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|Q9W6I1 RBPMS "RNA-binding protein with multiple splicing" [Gallus gallus (taxid:9031)]

 Score = 132 (51.5 bits), Expect = 7.6e-09, P = 7.6e-09
 Identities = 36/85 (42%), Positives = 50/85 (58%)

Query:    79 TLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATA 138
             TL+V GLP D   RE+  +FRPF GY E  L+    KL    P+   FV F++ A A  A
Sbjct:    23 TLFVSGLPVDIKPRELYLLFRPFKGY-EGSLI----KLTSKQPV--GFVTFDSRAGAEAA 75

Query:   139 LSALQGYRMDEDDPDSKFLRLQFSR 163
              +AL G R D ++P +  LRL+F++
Sbjct:    76 KNALNGIRFDPENPQT--LRLEFAK 98

GO:0000166 "nucleotide binding" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0003713 "transcription coactivator activity" evidence=ISS

GO:0010862 "positive regulation of pathway-restricted SMAD protein phosphorylation" evidence=ISS

GO:0060391 "positive regulation of SMAD protein import into nucleus" evidence=ISS

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

UNIPROTKB|F1N2U8 RBPMS2 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 132 (51.5 bits), Expect = 7.6e-09, P = 7.6e-09
 Identities = 39/96 (40%), Positives = 54/96 (56%)

Query:    68 ETLPLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFV 127
             ET P   +   TL+V GLP D   RE+  +FRPF GY E  L+    KL    P+   FV
Sbjct:    16 ETSPTIQEVR-TLFVSGLPVDIKPRELYLLFRPFKGY-EGSLI----KLTSRQPV--GFV 67

Query:   128 DFENPACAATALSALQGYRMDEDDPDSKFLRLQFSR 163
              F++ A A  A +AL G R D ++P +  LRL+F++
Sbjct:    68 IFDSRAGAEAAKNALNGIRFDPENPQT--LRLEFAK 101

GO:0003676 "nucleic acid 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

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: gw1.II.3487.1 hypothetical protein (243 aa) (Populus trichocarpa)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	177
cd12420	79	cd12420, RRM_RBPMS_like, RNA recognition motif in	4e-32
cd12247	72	cd12247, RRM2_U1A_like, RNA recognition motif 2 in	5e-13
cd12245	79	cd12245, RRM_scw1_like, RNA recognition motif in y	1e-12
smart00360	73	smart00360, RRM, RNA recognition motif	2e-10
cd12684	83	cd12684, RRM_cpo, RNA recognition motif in Drosoph	5e-10
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	5e-10
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	5e-09
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	7e-09
cd12683	76	cd12683, RRM_RBPMS2, RNA recognition motif in vert	4e-08
cd12682	76	cd12682, RRM_RBPMS, RNA recognition motif in verte	3e-07
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	6e-07
cd12481	80	cd12481, RRM2_U2B, RNA recognition motif 2 found i	1e-06
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	2e-06
cd12480	80	cd12480, RRM2_U1A, RNA recognition motif 2 found i	5e-06
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	5e-06
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	6e-06
cd12479	80	cd12479, RRM2_SNF, RNA recognition motif 2 found i	1e-05
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	9e-05
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	2e-04
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	3e-04
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	3e-04
cd12319	84	cd12319, RRM4_MRD1, RNA recognition motif 4 in yea	3e-04
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	3e-04
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	4e-04
cd12470	86	cd12470, RRM1_MSSP1, RNA recognition motif 1 in ve	5e-04
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	7e-04
cd12239	82	cd12239, RRM2_RBM40_like, RNA recognition motif 2	8e-04
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	0.001
cd12615	74	cd12615, RRM1_TIA1, RNA recognition motif 1 in nuc	0.002
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	0.002
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	0.002
cd12404	77	cd12404, RRM2_NCL, RNA recognition motif 2 in vert	0.002
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	0.003
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	0.003

>gnl|CDD|240866 cd12420, RRM_RBPMS_like, RNA recognition motif in RNA-binding protein with multiple splicing (RBP-MS)-like proteins

 Score =  110 bits (276), Expect = 4e-32
 Identities = 44/83 (53%), Positives = 55/83 (66%), Gaps = 4/83 (4%)

Query: 78  STLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAAT 137
            TL+V GLP+D  +RE+AH+FRPF GY+  RLV KE K  GG+   + FVDF +  CAA 
Sbjct: 1   RTLFVSGLPSDVKERELAHLFRPFPGYEASRLVFKEKK--GGEKQPVGFVDFSSAQCAAA 58

Query: 138 ALSALQGYRMDEDDPDSKFLRLQ 160
           A+ ALQGYR   D   S  LRL+
Sbjct: 59  AMDALQGYRF--DPDTSSVLRLE 79

This subfamily corresponds to the RRM of RNA-binding proteins with multiple splicing (RBP-MS)-like proteins, including protein products of RBPMS genes (RBP-MS and its paralogue RBP-MS2), the Drosophila couch potato (cpo), and Caenorhabditis elegans Mec-8 genes. RBP-MS may be involved in regulation of mRNA translation and localization during Xenopus laevis development. It has also been shown to physically interact with Smad2, Smad3 and Smad4, and stimulates Smad-mediated transactivation. Cpo may play an important role in regulating normal function of the nervous system, whereas mutations in Mec-8 affect mechanosensory and chemosensory neuronal function. All members contain a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Some uncharacterized family members contain two RRMs; this subfamily includes their RRM1. Their RRM2 shows high sequence homology to the RRM of yeast proteins scw1, Whi3, and Whi4. Length = 79

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

 Score = 60.7 bits (148), Expect = 5e-13
 Identities = 27/76 (35%), Positives = 41/76 (53%), Gaps = 9/76 (11%)

Query: 77  SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAA 136
           +  L+++ LP ++TK  +  +F  F G+KEVRLV      RG     + FV+FE    A 
Sbjct: 2   NKILFLQNLPEETTKEMLEMLFNQFPGFKEVRLV----PRRG-----IAFVEFETEEQAT 52

Query: 137 TALSALQGYRMDEDDP 152
            AL ALQG+++     
Sbjct: 53  VALQALQGFKITPGHA 68

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

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

 Score = 59.9 bits (146), Expect = 1e-12
 Identities = 25/86 (29%), Positives = 50/86 (58%), Gaps = 9/86 (10%)

Query: 78  STLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAAT 137
           +TL+V  L  ++T+ E+  +F    G++ +++  K     GG P+  CFV+FE+ + A  
Sbjct: 3   NTLFVANLGPNTTEEELRQLFSRQPGFRRLKMHNK-----GGGPV--CFVEFEDVSFATQ 55

Query: 138 ALSALQGYRMDEDDPDSKFLRLQFSR 163
           AL++LQG  +     D   +R+++++
Sbjct: 56  ALNSLQGAVL--SSSDRGGIRIEYAK 79

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

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

 Score = 53.8 bits (130), Expect = 2e-10
 Identities = 27/72 (37%), Positives = 38/72 (52%), Gaps = 7/72 (9%)

Query: 79  TLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKES--KLRGGDPLILCFVDFENPACAA 136
           TL+V  LP D+T+ E+  +F  F   + VRLV  +   K +G       FV+FE+   A 
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKG-----FAFVEFESEEDAE 55

Query: 137 TALSALQGYRMD 148
            AL AL G  +D
Sbjct: 56  KALEALNGKELD 67

Length = 73

>gnl|CDD|241128 cd12684, RRM_cpo, RNA recognition motif in Drosophila couch potato (cpo) coding RNA-binding protein and similar proteins

 Score = 53.2 bits (127), Expect = 5e-10
 Identities = 32/85 (37%), Positives = 46/85 (54%), Gaps = 4/85 (4%)

Query: 79  TLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATA 138
           TL+V GLP D+  RE+  +FR + GY+   L +     +   P  + FV FE  A A  A
Sbjct: 3   TLFVSGLPMDAKPRELYLLFRAYKGYEGSLLKVTSKNGKTTSP--VGFVTFETRAGAEAA 60

Query: 139 LSALQGYRMDEDDPDSKFLRLQFSR 163
              LQG R D D P +  +RL+F++
Sbjct: 61  KQDLQGVRFDPDIPQT--IRLEFAK 83

This subfamily corresponds to the RRM of Cpo, an RNA-binding protein encoded by Drosophila couch potato (cpo) gene. Cpo contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It may control the processing of RNA molecules required for the proper functioning of the peripheral nervous system (PNS). . Length = 83

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

 Score = 52.7 bits (127), Expect = 5e-10
 Identities = 24/69 (34%), Positives = 36/69 (52%), Gaps = 4/69 (5%)

Query: 80  LYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATAL 139
           L+V  LP D+T+ ++  +F  F   + VR+V  +     G      FV+FE+P  A  AL
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKG----FAFVEFESPEDAEKAL 56

Query: 140 SALQGYRMD 148
            AL G  +D
Sbjct: 57  EALNGKELD 65

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

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

 Score = 50.3 bits (121), Expect = 5e-09
 Identities = 22/69 (31%), Positives = 35/69 (50%), Gaps = 4/69 (5%)

Query: 80  LYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATAL 139
           L+V  LP D+T+ ++  +F  F   + +R+V  E+    G      FV+FE+   A  AL
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKG----FAFVEFEDEEDAEKAL 56

Query: 140 SALQGYRMD 148
            AL G  + 
Sbjct: 57  EALNGKELG 65

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

 Score = 50.1 bits (120), Expect = 7e-09
 Identities = 25/71 (35%), Positives = 37/71 (52%), Gaps = 4/71 (5%)

Query: 79  TLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATA 138
            L+V GLP   TK E+  +F+     K VRLV      R G P  L +V++EN + A+ A
Sbjct: 4   KLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTN----RSGKPKGLAYVEYENESSASQA 59

Query: 139 LSALQGYRMDE 149
           +  + G  + E
Sbjct: 60  VLKMDGTEIKE 70

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|241127 cd12683, RRM_RBPMS2, RNA recognition motif in vertebrate RNA-binding protein with multiple splicing 2 (RBP-MS2)

 Score = 48.1 bits (114), Expect = 4e-08
 Identities = 36/83 (43%), Positives = 48/83 (57%), Gaps = 9/83 (10%)

Query: 79  TLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATA 138
           TL+V GLP D   RE+  +FRPF GY E  L+    KL    P  + FV F++ A A  A
Sbjct: 3   TLFVSGLPVDIKPRELYLLFRPFKGY-EGSLI----KLTSKQP--VGFVTFDSRAGAEAA 55

Query: 139 LSALQGYRMDEDDPDSKFLRLQF 161
            +AL G R D ++P +  LRL+F
Sbjct: 56  KNALNGIRFDPENPQT--LRLEF 76

This subfamily corresponds to the RRM of RBP-MS2, encoded by RBPMS2 gene, a paralog of RNA-binding protein with multiple splicing (RBP-MS). The biological function of RBP-MS2 remains unclear. Like RBP-MS, RBP-MS2 contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 76

>gnl|CDD|241126 cd12682, RRM_RBPMS, RNA recognition motif in vertebrate RNA-binding protein with multiple splicing (RBP-MS)

 Score = 45.4 bits (107), Expect = 3e-07
 Identities = 35/83 (42%), Positives = 46/83 (55%), Gaps = 9/83 (10%)

Query: 79  TLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATA 138
           TL+V GLP D   RE+  +FRPF GY E  L+   SK   G      FV F++ + A  A
Sbjct: 3   TLFVSGLPLDIKPRELYLLFRPFKGY-EGSLIKLTSKQPVG------FVSFDSRSEAEAA 55

Query: 139 LSALQGYRMDEDDPDSKFLRLQF 161
            +AL G R D + P +  LRL+F
Sbjct: 56  KNALNGIRFDPEIPQT--LRLEF 76

This subfamily corresponds to the RRM of RBP-MS, also termed heart and RRM expressed sequence (hermes), an RNA-binding proteins found in various vertebrate species. It contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). RBP-MS physically interacts with Smad2, Smad3 and Smad4 and plays a role in regulation of Smad-mediated transcriptional activity. In addition, RBP-MS may be involved in regulation of mRNA translation and localization during Xenopus laevis development. . Length = 76

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

 Score = 44.5 bits (106), Expect = 6e-07
 Identities = 23/65 (35%), Positives = 32/65 (49%), Gaps = 5/65 (7%)

Query: 80  LYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATAL 139
           LYV  LP   T+ ++   F P+   + VRLV  + + RG       FV+F +P  A  AL
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRG-----FAFVEFASPEDAEAAL 55

Query: 140 SALQG 144
             L G
Sbjct: 56  KKLNG 60

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

>gnl|CDD|240925 cd12481, RRM2_U2B, RNA recognition motif 2 found in vertebrate U2 small nuclear ribonucleoprotein B" (U2B")

 Score = 44.2 bits (104), Expect = 1e-06
 Identities = 26/75 (34%), Positives = 41/75 (54%), Gaps = 10/75 (13%)

Query: 73  PPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENP 132
           PP+    L++  LP ++ +  ++ +F  F G+KEVRLV             + FV+FEN 
Sbjct: 3   PPN--YILFLNNLPEETNEMMLSMLFNQFPGFKEVRLVPGRHD--------IAFVEFENE 52

Query: 133 ACAATALSALQGYRM 147
           A A  A  ALQG+++
Sbjct: 53  AQAGAARDALQGFKI 67

This subgroup corresponds to the RRM1 of U2B" (also termed U2 snRNP B"), a unique protein that comprises the U2 snRNP. It was initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. U2B" does not require an auxiliary protein for binding to RNA and its nuclear transport is independent of U2 snRNA binding. U2B" contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It also contains a nuclear localization signal (NLS) in the central domain. However, nuclear import of U2B'' does not depend on this NLS. The N-terminal RRM is sufficient to direct U2B" to the nucleus. . Length = 80

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

 Score = 43.4 bits (103), Expect = 2e-06
 Identities = 21/74 (28%), Positives = 35/74 (47%), Gaps = 2/74 (2%)

Query: 78  STLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLIL--CFVDFENPACA 135
           +TL+V+ L   +T+  +   F    G + V +  K+     G  L +   FV+F++   A
Sbjct: 1   TTLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAA 60

Query: 136 ATALSALQGYRMDE 149
             AL  LQG  +D 
Sbjct: 61  QKALKRLQGTVLDG 74

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|240924 cd12480, RRM2_U1A, RNA recognition motif 2 found in vertebrate U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A)

 Score = 42.8 bits (100), Expect = 5e-06
 Identities = 24/79 (30%), Positives = 42/79 (53%), Gaps = 10/79 (12%)

Query: 73  PPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENP 132
           PP+    L++  LP ++ +  ++ +F  F G+KEVRLV             + FV+F+N 
Sbjct: 3   PPN--HILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHD--------IAFVEFDNE 52

Query: 133 ACAATALSALQGYRMDEDD 151
             A  A  ALQG+++ + +
Sbjct: 53  VQAGAAREALQGFKITQSN 71

This subgroup corresponds to the RRM2 of U1A (also termed U1 snRNP A or U1-A), an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins, including polypyrimidine tract binding protein (PTB), polypyrimidine-tract binding protein-associated factor (PSF), and non-POU-domain-containing, octamer-binding (NONO), DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5). U1A also binds to a flavivirus NS5 protein and plays an important role in virus replication. It contains two RNA recognition motifs (RRMs); the N-terminal RRM (RRM1) binds tightly and specifically to the U1 snRNA SLII and its own 3'-UTR, while in contrast, the C-terminal RRM (RRM2) does not appear to associate with any RNA and it may be free for binding other proteins. U1A also contains a proline-rich region, and a nuclear localization signal (NLS) in the central domain that is responsible for its nuclear import. . Length = 80

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

 Score = 42.2 bits (100), Expect = 5e-06
 Identities = 23/68 (33%), Positives = 34/68 (50%), Gaps = 6/68 (8%)

Query: 78  STLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIK-ESKLRGGDPLILCFVDFENPACAA 136
           + L V  +P ++TK+E+  +F PF   K VRL  K +   RG       FV+F     A 
Sbjct: 1   TKLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFDGSHRG-----FAFVEFVTKQEAQ 55

Query: 137 TALSALQG 144
            A+ AL+ 
Sbjct: 56  NAMEALKS 63

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

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

 Score = 44.9 bits (105), Expect = 6e-06
 Identities = 28/94 (29%), Positives = 47/94 (50%), Gaps = 12/94 (12%)

Query: 73  PPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVI--KESKLRGGDPLILCFVDFE 130
             + ++TL+V  LP D T+ ++  +F+ F   K VRLV   +  K RG       FV+FE
Sbjct: 111 SKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRG-----FAFVEFE 165

Query: 131 NPACAATALSALQGYRMDEDDPDSKFLRLQFSRN 164
           +   A  A+  L G  +     + + LR+Q ++ 
Sbjct: 166 SEESAEKAIEELNGKEL-----EGRPLRVQKAQP 194

Length = 306

>gnl|CDD|240923 cd12479, RRM2_SNF, RNA recognition motif 2 found in Drosophila melanogaster sex determination protein SNF and similar proteins

 Score = 41.6 bits (97), Expect = 1e-05
 Identities = 25/75 (33%), Positives = 41/75 (54%), Gaps = 10/75 (13%)

Query: 73  PPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENP 132
           PP+    L++  LP ++ +  ++ +F  F G+KEVRLV             + FV+FEN 
Sbjct: 3   PPN--QILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPGRHD--------IAFVEFENE 52

Query: 133 ACAATALSALQGYRM 147
             +A A  ALQG+++
Sbjct: 53  VQSAAAKEALQGFKI 67

This subgroup corresponds to the RRM2 of SNF (Sans fille), also termed U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A), an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila. It is essential in Drosophila sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). SNF contains two RNA recognition motifs (RRMs); it can self-associate through RRM1, and each RRM can recognize poly(U) RNA binding independently. . Length = 80

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

 Score = 39.1 bits (92), Expect = 9e-05
 Identities = 24/81 (29%), Positives = 36/81 (44%), Gaps = 14/81 (17%)

Query: 77  SSTLYVEGLP-ADSTKRE-----VAHIFRPFVGYKEVRLVI---KESKLRGGDPLILCFV 127
            + + V+GLP     K E     +  IF  F   K V + +   +  K +G       FV
Sbjct: 1   DNVVVVDGLPVVGEEKLEKLKKVLRKIFSKFGVGKIVGIYMPVDETGKTKG-----YAFV 55

Query: 128 DFENPACAATALSALQGYRMD 148
           +F  P  A  A+ AL GY++D
Sbjct: 56  EFATPEEAKEAVKALNGYKLD 76

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

 Score = 38.4 bits (90), Expect = 2e-04
 Identities = 18/71 (25%), Positives = 29/71 (40%), Gaps = 5/71 (7%)

Query: 79  TLYVEGLPADSTKREVAHIFRPFVGYKEVRLVI-KESKLRGGDPLILCFVDFENPACAAT 137
            LYV  LP + T+ ++  +F  F      R++  +E+    G      FV+ E    A  
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRG----FGFVEMETAEEANA 56

Query: 138 ALSALQGYRMD 148
           A+  L G    
Sbjct: 57  AIEKLNGTDFG 67

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|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 = 37.6 bits (88), Expect = 3e-04
 Identities = 23/71 (32%), Positives = 34/71 (47%), Gaps = 11/71 (15%)

Query: 78  STLYVEGLPADSTKREVAHIFRPFVGYKEVRLVI----KESKLRGGDPLILCFVDFENPA 133
           + L+V GL   +T++E+  +F  F   +EV L+      ES  RG       FV FE+  
Sbjct: 2   NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGES--RG-----FGFVTFESVE 54

Query: 134 CAATALSALQG 144
            A  A+  L G
Sbjct: 55  DADAAIRDLNG 65

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|240700 cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognition motif found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family, epithelial splicing regulatory proteins (ESRPs), Drosophila RNA-binding protein Fusilli, RNA-binding protein 12 (RBM12) and similar proteins

 Score = 37.5 bits (88), Expect = 3e-04
 Identities = 13/68 (19%), Positives = 27/68 (39%), Gaps = 5/68 (7%)

Query: 79  TLYVEGLPADSTKREVAHIFRPFVGYKE-VRLVIKESKLRGGDPLILCFVDFENPACAAT 137
            + + GLP  +T+ ++   F       + + +V  +     G+     +V+F +P  A  
Sbjct: 1   VVRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPTGE----AYVEFASPEDARR 56

Query: 138 ALSALQGY 145
           AL      
Sbjct: 57  ALRKHNNK 64

The family includes RRM domains in the hnRNP H protein family, G-rich sequence factor 1 (GRSF-1), ESRPs (also termed RBM35), Drosophila Fusilli, RBM12 (also termed SWAN), RBM12B, RBM19 (also termed RBD-1) and similar proteins. The hnRNP H protein family includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9), which represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing. GRSF-1 is a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B) are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. Fusilli shows high sequence homology to ESRPs. It can regulate endogenous FGFR2 splicing and functions as a splicing factor. The biological roles of both, RBM12 and RBM12B, remain unclear. RBM19 is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. Members in this family contain 2~6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

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

 Score = 37.5 bits (87), Expect = 3e-04
 Identities = 21/73 (28%), Positives = 35/73 (47%), Gaps = 2/73 (2%)

Query: 78  STLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILC--FVDFENPACA 135
           +TL+V+ L   +T + +   F+   G+   R+  K    R G  L +   FV F+    A
Sbjct: 1   ATLFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQA 60

Query: 136 ATALSALQGYRMD 148
             AL A+ G+ +D
Sbjct: 61  QAALKAMDGFVLD 73

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|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 = 37.3 bits (87), Expect = 3e-04
 Identities = 24/66 (36%), Positives = 31/66 (46%), Gaps = 5/66 (7%)

Query: 80  LYVEGLPADSTKREVAHIFRPFVGYKEVRLVI-KESKLRGGDPLILCFVDFENPACAATA 138
           L+V  LP  +T+ E+  +F  F    EV L + KE+K   G      FV F  P  A  A
Sbjct: 2   LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKG----FAFVSFMFPEHAVKA 57

Query: 139 LSALQG 144
            S L G
Sbjct: 58  YSELDG 63

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

 Score = 37.1 bits (87), Expect = 4e-04
 Identities = 26/89 (29%), Positives = 42/89 (47%), Gaps = 15/89 (16%)

Query: 79  TLYVEGLP----ADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPAC 134
           TLY+  L      D  KR +  +F  F    ++ +  K  K+RG       FV F++   
Sbjct: 1   TLYINNLNEKIKKDELKRSLYALFSQFGPVLDI-VASKTLKMRGQ-----AFVVFKDVES 54

Query: 135 AATALSALQGYRMDEDDPDSKFLRLQFSR 163
           A  AL ALQG+   +     K +R+Q+++
Sbjct: 55  ATNALRALQGFPFYD-----KPMRIQYAK 78

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

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

 Score = 37.1 bits (85), Expect = 5e-04
 Identities = 24/86 (27%), Positives = 45/86 (52%), Gaps = 14/86 (16%)

Query: 76  ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKES--KLRGGDPLILCFVDFENPA 133
           + + LY+ GLP ++T +++  + +P+      + ++ ++  K +G       FVDF++PA
Sbjct: 6   SKTNLYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKG-----YGFVDFDSPA 60

Query: 134 CAATALSAL-------QGYRMDEDDP 152
            A  A+SAL       Q  +  E DP
Sbjct: 61  AAQKAVSALKASGVQAQMAKQQEQDP 86

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

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

 Score = 36.8 bits (86), Expect = 7e-04
 Identities = 18/73 (24%), Positives = 31/73 (42%), Gaps = 11/73 (15%)

Query: 77  SSTLYVEGLPADSTKREVAHIFRPFVG--YKEVRLVIKE---SKLRGGDPLILCFVDFEN 131
           ++TL + GL   +T+ ++            K+VRL I++      RG       FV+F +
Sbjct: 2   TNTLILRGLDLLTTEEDILQALSAIASVPIKDVRL-IRDKLTGTSRG-----FAFVEFPS 55

Query: 132 PACAATALSALQG 144
              A   + AL  
Sbjct: 56  LEDATQWMDALNN 68

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

 Score = 36.4 bits (85), Expect = 8e-04
 Identities = 22/78 (28%), Positives = 36/78 (46%), Gaps = 13/78 (16%)

Query: 77  SSTLYVEGLPADSTKREVAHIFRPFVGYKE-------VRLVIKESKLRGGDPLILCFVDF 129
           S  LYV+ L    T+ ++ +IF  FV           +RL + E +++G       FV F
Sbjct: 1   SKRLYVKNLSKRVTEEDLVYIFGRFVDSSSEEKNMFDIRL-MTEGRMKGQ-----AFVTF 54

Query: 130 ENPACAATALSALQGYRM 147
            +   A  AL+ + GY +
Sbjct: 55  PSEEIATKALNLVNGYVL 72

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

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

 Score = 35.8 bits (83), Expect = 0.001
 Identities = 22/69 (31%), Positives = 29/69 (42%), Gaps = 8/69 (11%)

Query: 78  STLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIK---ESKLRGGDPLILCFVDFENPAC 134
           S + V  +P ++T +E+  +F  F   K VRL  K       RG       FVDF     
Sbjct: 1   SKILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRG-----FGFVDFITKQD 55

Query: 135 AATALSALQ 143
           A  A  AL 
Sbjct: 56  AKRAFKALC 64

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

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

 Score = 35.4 bits (81), Expect = 0.002
 Identities = 21/69 (30%), Positives = 35/69 (50%), Gaps = 5/69 (7%)

Query: 79  TLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATA 138
           TLYV  L  D T+  +  +F      K  ++++  +   G DP   CFV+F     AA +
Sbjct: 1   TLYVGNLSRDVTEALILQLFSQIGPCKSCKMIMDTA---GNDPY--CFVEFFEHRHAAAS 55

Query: 139 LSALQGYRM 147
           L+A+ G ++
Sbjct: 56  LAAMNGRKI 64

This subgroup corresponds to the RRM1 of TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1) and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and functions as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 74

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

 Score = 35.1 bits (81), Expect = 0.002
 Identities = 24/70 (34%), Positives = 33/70 (47%), Gaps = 6/70 (8%)

Query: 79  TLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATA 138
           T+YV  LP D  +REV  +F     YK   +V  + KL    P    F++FE+   A  A
Sbjct: 1   TVYVGNLPGDIREREVEDLF-----YKYGPIVDIDLKL-PPRPPGYAFIEFEDARDAEDA 54

Query: 139 LSALQGYRMD 148
           +    GY  D
Sbjct: 55  IRGRDGYDFD 64

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

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

 Score = 35.1 bits (81), Expect = 0.002
 Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 12/73 (16%)

Query: 80  LYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATAL 139
           LYV   P D+++  +  IF P+   KEV++ I              FV+FE+   A  A 
Sbjct: 2   LYVRPFPPDTSESAIREIFSPYGAVKEVKM-ISNFA----------FVEFESLESAIRAK 50

Query: 140 SALQGYRMDEDDP 152
            ++ G ++  ++P
Sbjct: 51  DSVHG-KVLNNNP 62

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

 Score = 35.2 bits (81), Expect = 0.002
 Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 7/73 (9%)

Query: 76  ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACA 135
            + TL+V+ LP + T  E+  +F   V   ++RL       + G    + +++F+  A A
Sbjct: 2   DARTLFVKNLPYNITVDELKEVFEDAV---DIRLPSG----KDGSSKGIAYIEFKTEAEA 54

Query: 136 ATALSALQGYRMD 148
             AL   QG  +D
Sbjct: 55  EKALEEKQGAEVD 67

This subfamily corresponds to the RRM2 of ubiquitously expressed protein nucleolin, also termed protein C23, a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines.RRM2, together with RRM1, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop. . Length = 77

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

 Score = 34.5 bits (80), Expect = 0.003
 Identities = 20/69 (28%), Positives = 36/69 (52%), Gaps = 9/69 (13%)

Query: 80  LYVEGLPADSTKREVAHIFRPFVGYKEVRLVI--KESKLRG-GDPLILCFVDFENPACAA 136
           +Y+ GLP ++T  ++  + +PF      + ++  K +K +G G      FVDF++P  A 
Sbjct: 3   VYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYG------FVDFDSPEAAL 56

Query: 137 TALSALQGY 145
            A+  L G 
Sbjct: 57  KAIEGLNGR 65

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|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 = 34.8 bits (80), Expect = 0.003
 Identities = 21/78 (26%), Positives = 38/78 (48%), Gaps = 12/78 (15%)

Query: 74  PDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVI----KESKLRGGDPLILCFVDF 129
           P+  + L++  LP +    E+  +F PF      ++ +     +SK  G       FV F
Sbjct: 2   PEGCN-LFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFG-------FVSF 53

Query: 130 ENPACAATALSALQGYRM 147
           +NPA A  A+ A+ G+++
Sbjct: 54  DNPASAQAAIQAMNGFQI 71

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	177
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.85
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.79
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.77
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.75
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.72
KOG0122	270	consensus Translation initiation factor 3, subunit	99.72
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.71
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.71
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.69
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.68
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.65
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.64
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.63
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.63
PLN03120	260	nucleic acid binding protein; Provisional	99.63
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.62
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.62
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.61
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.61
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.6
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.6
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.59
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.59
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.59
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.58
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.57
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.57
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.56
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.56
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.56
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.55
PLN03121	243	nucleic acid binding protein; Provisional	99.55
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.54
PLN03213	759	repressor of silencing 3; Provisional	99.54
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.54
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.54
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.53
smart00362	72	RRM_2 RNA recognition motif.	99.53
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.53
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.53
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.53
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.52
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.52
smart00360	71	RRM RNA recognition motif.	99.5
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.48
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	99.47
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.46
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.45
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.4
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.39
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.38
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.36
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.33
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	99.32
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.32
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.32
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.28
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.27
smart00361	70	RRM_1 RNA recognition motif.	99.26
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.26
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.25
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.25
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	99.23
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.23
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.22
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.15
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.15
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.12
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.1
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	99.07
KOG0533	243	consensus RRM motif-containing protein [RNA proces	99.03
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	99.03
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.02
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	98.96
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.94
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.92
KOG1548	382	consensus Transcription elongation factor TAT-SF1	98.92
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.91
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.89
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.89
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.82
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.82
KOG0151	877	consensus Predicted splicing regulator, contains R	98.78
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.75
KOG0226	290	consensus RNA-binding proteins [General function p	98.71
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.7
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.67
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	98.66
KOG1995	351	consensus Conserved Zn-finger protein [General fun	98.63
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	98.55
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	98.41
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.35
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	98.35
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.3
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	98.16
KOG4210	285	consensus Nuclear localization sequence binding pr	98.13
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	98.0
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	97.99
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.94
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	97.93
KOG2314	698	consensus Translation initiation factor 3, subunit	97.89
KOG1855	484	consensus Predicted RNA-binding protein [General f	97.8
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	97.78
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.76
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	97.68
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.65
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	97.64
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	97.63
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	97.61
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.61
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	97.57
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	97.48
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.45
KOG3152	278	consensus TBP-binding protein, activator of basal	97.39
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	97.3
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	97.18
KOG1548	382	consensus Transcription elongation factor TAT-SF1	97.06
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	97.06
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	97.03
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	96.96
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	96.91
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	96.85
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	96.61
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	96.56
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	96.52
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	96.52
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	96.43
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	96.42
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	96.24
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	96.22
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	96.11
KOG2591	684	consensus c-Mpl binding protein, contains La domai	95.41
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	95.19
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	95.1
KOG1996	378	consensus mRNA splicing factor [RNA processing and	95.0
KOG2068	327	consensus MOT2 transcription factor [Transcription	94.57
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	94.16
KOG4660	549	consensus Protein Mei2, essential for commitment t	92.9
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	92.48
KOG2318	650	consensus Uncharacterized conserved protein [Funct	91.86
KOG4210	285	consensus Nuclear localization sequence binding pr	90.85
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	90.73
KOG2135	526	consensus Proteins containing the RNA recognition	90.54
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	90.43
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	88.7
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	86.28
KOG4410	396	consensus 5-formyltetrahydrofolate cyclo-ligase [C	83.29
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	82.11
KOG4483	528	consensus Uncharacterized conserved protein [Funct	80.41

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

Probab=99.85  E-value=1.9e-20  Score=138.85  Aligned_cols=82  Identities=18%  Similarity=0.416  Sum_probs=76.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      +++|||+|||+++||++|+++|++||.|.+|+|+.++   .+++++|||||+|.+.++|++|++.||+..|.+     +.
T Consensus        34 ~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~---~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~G-----r~  105 (144)
T PLN03134         34 STKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDR---ETGRSRGFGFVNFNDEGAATAAISEMDGKELNG-----RH  105 (144)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecC---CCCCcceEEEEEECCHHHHHHHHHHcCCCEECC-----EE
Confidence            6899999999999999999999999999999999987   678999999999999999999999999999976     58


Q ss_pred             eEEEeecCCC
Q 030444          157 LRLQFSRNPG  166 (177)
Q Consensus       157 l~V~~a~~~~  166 (177)
                      |+|+|++.+.
T Consensus       106 l~V~~a~~~~  115 (144)
T PLN03134        106 IRVNPANDRP  115 (144)
T ss_pred             EEEEeCCcCC
Confidence            9999997653

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.79  E-value=8.1e-19  Score=146.44  Aligned_cols=84  Identities=24%  Similarity=0.387  Sum_probs=77.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      +.+|||+|||+++++++|+++|++||.|.+|+|+.+.   .++.+||||||+|.+.++|.+|++.|||+.|.+     |.
T Consensus       269 ~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~---~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~g-----r~  340 (352)
T TIGR01661       269 GYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDL---TTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGN-----RV  340 (352)
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcC---CCCCccceEEEEECCHHHHHHHHHHhCCCEECC-----eE
Confidence            4579999999999999999999999999999999987   678999999999999999999999999999966     58


Q ss_pred             eEEEeecCCCCC
Q 030444          157 LRLQFSRNPGPR  168 (177)
Q Consensus       157 l~V~~a~~~~~r  168 (177)
                      |+|+|+.++..|
T Consensus       341 i~V~~~~~~~~~  352 (352)
T TIGR01661       341 LQVSFKTNKAYR  352 (352)
T ss_pred             EEEEEccCCCCC
Confidence            999999877654

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

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.77  E-value=9.8e-18  Score=140.33  Aligned_cols=81  Identities=28%  Similarity=0.449  Sum_probs=75.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      ..++|||+|||+++||++|+++|+.||.|++|+|+.+.   .+++++|||||+|.++++|++||+.||+..|.+     +
T Consensus       106 ~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~---~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~g-----r  177 (346)
T TIGR01659       106 SGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDY---KTGYSFGYAFVDFGSEADSQRAIKNLNGITVRN-----K  177 (346)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecC---CCCccCcEEEEEEccHHHHHHHHHHcCCCccCC-----c
Confidence            47899999999999999999999999999999999887   678899999999999999999999999999976     4


Q ss_pred             ceEEEeecC
Q 030444          156 FLRLQFSRN  164 (177)
Q Consensus       156 ~l~V~~a~~  164 (177)
                      +|+|+|++.
T Consensus       178 ~i~V~~a~p  186 (346)
T TIGR01659       178 RLKVSYARP  186 (346)
T ss_pred             eeeeecccc
Confidence            799999865

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=99.75  E-value=5.2e-18  Score=141.57  Aligned_cols=81  Identities=26%  Similarity=0.470  Sum_probs=75.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++||++|+++|++||.|.+|+|+.++   .+++++|||||+|.+.++|++||+.|||..|.+     ++
T Consensus         3 ~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~---~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g-----~~   74 (352)
T TIGR01661         3 KTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDK---VTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQN-----KT   74 (352)
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcC---CCCccceEEEEEECcHHHHHHHHhhcccEEECC-----ee
Confidence            6899999999999999999999999999999999987   678899999999999999999999999999976     47


Q ss_pred             eEEEeecCC
Q 030444          157 LRLQFSRNP  165 (177)
Q Consensus       157 l~V~~a~~~  165 (177)
                      |+|+|++..
T Consensus        75 i~v~~a~~~   83 (352)
T TIGR01661        75 IKVSYARPS   83 (352)
T ss_pred             EEEEeeccc
Confidence            999999754

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

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.72  E-value=3.4e-17  Score=137.13  Aligned_cols=83  Identities=24%  Similarity=0.361  Sum_probs=76.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++||++|+++|++||.|+.|+|+.++   .+++++|||||+|.+.++|++||+.||+..+.+.   .++
T Consensus       193 ~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~---~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~---~~~  266 (346)
T TIGR01659       193 DTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDK---LTGTPRGVAFVRFNKREEAQEAISALNNVIPEGG---SQP  266 (346)
T ss_pred             cceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecC---CCCccceEEEEEECCHHHHHHHHHHhCCCccCCC---cee
Confidence            5689999999999999999999999999999999886   6789999999999999999999999999999763   357


Q ss_pred             eEEEeecCC
Q 030444          157 LRLQFSRNP  165 (177)
Q Consensus       157 l~V~~a~~~  165 (177)
                      |+|.|++..
T Consensus       267 l~V~~a~~~  275 (346)
T TIGR01659       267 LTVRLAEEH  275 (346)
T ss_pred             EEEEECCcc
Confidence            999999764

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

>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]

Probab=99.72  E-value=2.7e-17  Score=128.52  Aligned_cols=83  Identities=31%  Similarity=0.488  Sum_probs=77.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCC
Q 030444           75 DASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDS  154 (177)
Q Consensus        75 ~~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~  154 (177)
                      ++.++|=|.||+.+++|++|++||.+||.|..+.|..++   .+|.+||||||+|.+.++|++||+.|||+-++.-    
T Consensus       187 ~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK---~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~L----  259 (270)
T KOG0122|consen  187 DDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDK---ETGLSKGFAFVTFESRDDAARAIADLNGYGYDNL----  259 (270)
T ss_pred             CccceeEEecCccccChhHHHHHhhccCccceeEEEEcc---ccCcccceEEEEEecHHHHHHHHHHccCcccceE----
Confidence            357999999999999999999999999999999999998   8999999999999999999999999999988654    


Q ss_pred             cceEEEeecCC
Q 030444          155 KFLRLQFSRNP  165 (177)
Q Consensus       155 r~l~V~~a~~~  165 (177)
                       .|+|+|+++.
T Consensus       260 -ILrvEwskP~  269 (270)
T KOG0122|consen  260 -ILRVEWSKPS  269 (270)
T ss_pred             -EEEEEecCCC
Confidence             6999999764

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=99.71  E-value=2.8e-17  Score=117.23  Aligned_cols=79  Identities=23%  Similarity=0.428  Sum_probs=71.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      ++||||+||++.++|++|.+||+.+|.|+.|.+-.++-   +-.+.|||||+|...++|+.|++.++++.|++     |+
T Consensus        36 S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~---kktpCGFCFVeyy~~~dA~~AlryisgtrLdd-----r~  107 (153)
T KOG0121|consen   36 SCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRF---KKTPCGFCFVEYYSRDDAEDALRYISGTRLDD-----RP  107 (153)
T ss_pred             cceEEEeeeeeeecHHHHHHHHHhccchheeEeccccC---CcCccceEEEEEecchhHHHHHHHhccCcccc-----cc
Confidence            79999999999999999999999999999998877773   34477999999999999999999999999987     48


Q ss_pred             eEEEeec
Q 030444          157 LRLQFSR  163 (177)
Q Consensus       157 l~V~~a~  163 (177)
                      |+|+|.-
T Consensus       108 ir~D~D~  114 (153)
T KOG0121|consen  108 IRIDWDA  114 (153)
T ss_pred             eeeeccc
Confidence            9999864

>PF00076 RRM_1: RNA recognition motif

Probab=99.71  E-value=6.4e-17  Score=104.24  Aligned_cols=67  Identities=30%  Similarity=0.527  Sum_probs=62.3

Q ss_pred             EEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCC
Q 030444           80 LYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDED  150 (177)
Q Consensus        80 LfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~  150 (177)
                      |||+|||+++|+++|+++|++||.|..+.+..+.    .+..++||||+|.+.++|++|++.||++.+.+.
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~~----~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~   67 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRNS----SGKSKGYAFVEFESEEDAEKALEELNGKKINGR   67 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEET----TSSEEEEEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhcccccccccc----cccccceEEEEEcCHHHHHHHHHHcCCCEECcc
Confidence            7999999999999999999999999999998863    577889999999999999999999999999763

(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 ....

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.69  E-value=1.2e-16  Score=119.49  Aligned_cols=80  Identities=28%  Similarity=0.425  Sum_probs=70.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+||+..+++.||+.+|..||.|.+|-|...        +.|||||||+|..+|+.|+..|+|..|.+.     .
T Consensus        10 ~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn--------PPGfAFVEFed~RDA~DAvr~LDG~~~cG~-----r   76 (195)
T KOG0107|consen   10 NTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARN--------PPGFAFVEFEDPRDAEDAVRYLDGKDICGS-----R   76 (195)
T ss_pred             CceEEeccCCCCcchHHHHHHHHhcCcceeEEEeec--------CCCceEEeccCcccHHHHHhhcCCccccCc-----e
Confidence            589999999999999999999999999998866554        346999999999999999999999999885     7


Q ss_pred             eEEEeecCCCCCC
Q 030444          157 LRLQFSRNPGPRS  169 (177)
Q Consensus       157 l~V~~a~~~~~r~  169 (177)
                      |+|+++......+
T Consensus        77 ~rVE~S~G~~r~~   89 (195)
T KOG0107|consen   77 IRVELSTGRPRGS   89 (195)
T ss_pred             EEEEeecCCcccc
Confidence            9999998765543

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=99.68  E-value=3.4e-16  Score=125.47  Aligned_cols=86  Identities=21%  Similarity=0.340  Sum_probs=79.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCC
Q 030444           74 PDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPD  153 (177)
Q Consensus        74 ~~~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~  153 (177)
                      .++-+||||+-|+.+++|+.|+..|+.||.|+.|+|+.++   .+|+++|||||+|+++.+...|.+..+|.+|++    
T Consensus        98 gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~---vTgkskGYAFIeye~erdm~~AYK~adG~~Idg----  170 (335)
T KOG0113|consen   98 GDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDK---VTGKSKGYAFIEYEHERDMKAAYKDADGIKIDG----  170 (335)
T ss_pred             CCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeec---ccCCccceEEEEeccHHHHHHHHHhccCceecC----
Confidence            3568999999999999999999999999999999999998   899999999999999999999999999999977    


Q ss_pred             CcceEEEeecCCCC
Q 030444          154 SKFLRLQFSRNPGP  167 (177)
Q Consensus       154 ~r~l~V~~a~~~~~  167 (177)
                       +.|-|++-+....
T Consensus       171 -rri~VDvERgRTv  183 (335)
T KOG0113|consen  171 -RRILVDVERGRTV  183 (335)
T ss_pred             -cEEEEEecccccc
Confidence             4799998765533

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

Probab=99.65  E-value=8.8e-16  Score=135.79  Aligned_cols=83  Identities=16%  Similarity=0.342  Sum_probs=76.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++++++|+++|+.||.|.+|+|..++   .+++++|||||+|++.++|.+|++.||++.|.++     .
T Consensus       204 ~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~---~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr-----~  275 (612)
T TIGR01645       204 FNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAP---TGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQ-----Y  275 (612)
T ss_pred             cceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecC---CCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCe-----E
Confidence            5799999999999999999999999999999999987   5688999999999999999999999999999764     7


Q ss_pred             eEEEeecCCCC
Q 030444          157 LRLQFSRNPGP  167 (177)
Q Consensus       157 l~V~~a~~~~~  167 (177)
                      |+|.++..++.
T Consensus       276 LrV~kAi~pP~  286 (612)
T TIGR01645       276 LRVGKCVTPPD  286 (612)
T ss_pred             EEEEecCCCcc
Confidence            99999987543

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.

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=99.64  E-value=6e-16  Score=116.87  Aligned_cols=78  Identities=33%  Similarity=0.603  Sum_probs=69.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||.++.|.||++||.+||.|.+|.|....     + +..||||+|++..+|+.||..-+|+.+++.     .
T Consensus         6 ~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~-----g-~ppfafVeFEd~RDAeDAiygRdGYdydg~-----r   74 (241)
T KOG0105|consen    6 SRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRP-----G-PPPFAFVEFEDPRDAEDAIYGRDGYDYDGC-----R   74 (241)
T ss_pred             cceEEecCCCcchhhccHHHHHhhhcceEEEEeccCC-----C-CCCeeEEEecCccchhhhhhcccccccCcc-----e
Confidence            6899999999999999999999999999999886543     1 335999999999999999999999999874     7


Q ss_pred             eEEEeecCC
Q 030444          157 LRLQFSRNP  165 (177)
Q Consensus       157 l~V~~a~~~  165 (177)
                      |+|+|++.-
T Consensus        75 LRVEfprgg   83 (241)
T KOG0105|consen   75 LRVEFPRGG   83 (241)
T ss_pred             EEEEeccCC
Confidence            999998754

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.63  E-value=1.3e-15  Score=123.52  Aligned_cols=79  Identities=23%  Similarity=0.347  Sum_probs=71.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCC
Q 030444           75 DASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDS  154 (177)
Q Consensus        75 ~~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~  154 (177)
                      +..+.|||+|||+...|.||+.+|++||.|.+|+|+.++     .-+|||+||+|++.++|++|.+.|||..+.+     
T Consensus        94 ~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNE-----RGSKGFGFVTmen~~dadRARa~LHgt~VEG-----  163 (376)
T KOG0125|consen   94 DTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNE-----RGSKGFGFVTMENPADADRARAELHGTVVEG-----  163 (376)
T ss_pred             CCCceeEeecCCccccCccHHHHHHhhCceeeEEEEecc-----CCCCccceEEecChhhHHHHHHHhhcceeec-----
Confidence            345889999999999999999999999999999999986     3378999999999999999999999999955     


Q ss_pred             cceEEEeec
Q 030444          155 KFLRLQFSR  163 (177)
Q Consensus       155 r~l~V~~a~  163 (177)
                      |+|.|..|.
T Consensus       164 RkIEVn~AT  172 (376)
T KOG0125|consen  164 RKIEVNNAT  172 (376)
T ss_pred             eEEEEeccc
Confidence            689998875

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.63  E-value=2.1e-15  Score=126.46  Aligned_cols=81  Identities=25%  Similarity=0.372  Sum_probs=75.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .+.|||+.||.|+.|++|..||++.|.|.++||+.++   .+|.+||||||+|.+.+.|+.||+.||+++|..    ++.
T Consensus        83 G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~---~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~----GK~  155 (506)
T KOG0117|consen   83 GCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDP---FSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRP----GKL  155 (506)
T ss_pred             CceEEecCCCccccchhhHHHHHhccceeeEEEeecc---cCCCCcceEEEEeecHHHHHHHHHHhhCccccC----CCE
Confidence            8999999999999999999999999999999999997   689999999999999999999999999999974    467


Q ss_pred             eEEEeecC
Q 030444          157 LRLQFSRN  164 (177)
Q Consensus       157 l~V~~a~~  164 (177)
                      |.|+.+..
T Consensus       156 igvc~Sva  163 (506)
T KOG0117|consen  156 LGVCVSVA  163 (506)
T ss_pred             eEEEEeee
Confidence            99987753

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.63  E-value=2e-15  Score=120.48  Aligned_cols=76  Identities=20%  Similarity=0.316  Sum_probs=68.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+.+||++|+++|+.||.|.+|+|+.++      .++|||||+|++.++|+.|+ .|||..|.++     .
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~------~~~GfAFVtF~d~eaAe~Al-lLnG~~l~gr-----~   71 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSEN------ERSQIAYVTFKDPQGAETAL-LLSGATIVDQ-----S   71 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecC------CCCCEEEEEeCcHHHHHHHH-HhcCCeeCCc-----e
Confidence            5899999999999999999999999999999998775      14579999999999999999 5999999774     7


Q ss_pred             eEEEeecC
Q 030444          157 LRLQFSRN  164 (177)
Q Consensus       157 l~V~~a~~  164 (177)
                      |+|+++..
T Consensus        72 V~Vt~a~~   79 (260)
T PLN03120         72 VTITPAED   79 (260)
T ss_pred             EEEEeccC
Confidence            99999864

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

Probab=99.62  E-value=2.2e-15  Score=132.90  Aligned_cols=79  Identities=23%  Similarity=0.342  Sum_probs=70.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      ..++|||+|||++++|++|+++|++||.|.+|+|+.+.    +++++|||||+|.+.++|++||+.||++.|...    +
T Consensus        57 ~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D~----sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~G----r  128 (578)
T TIGR01648        57 RGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDF----SGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPG----R  128 (578)
T ss_pred             CCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEECC----CCCccceEEEEeCCHHHHHHHHHHcCCCeecCC----c
Confidence            36899999999999999999999999999999999884    688999999999999999999999999998632    3


Q ss_pred             ceEEEee
Q 030444          156 FLRLQFS  162 (177)
Q Consensus       156 ~l~V~~a  162 (177)
                      .|.|+++
T Consensus       129 ~l~V~~S  135 (578)
T TIGR01648       129 LLGVCIS  135 (578)
T ss_pred             ccccccc
Confidence            5666654

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.

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

Probab=99.62  E-value=2e-15  Score=133.56  Aligned_cols=80  Identities=20%  Similarity=0.371  Sum_probs=74.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++++++|+++|++||.|.+|+|+.++   .+++++|||||+|.+.++|+.|++.|||..|.+     |.
T Consensus       107 ~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~---~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~G-----R~  178 (612)
T TIGR01645       107 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDP---ATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGG-----RN  178 (612)
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecC---CCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEec-----ce
Confidence            6899999999999999999999999999999999987   678999999999999999999999999999976     47


Q ss_pred             eEEEeecC
Q 030444          157 LRLQFSRN  164 (177)
Q Consensus       157 l~V~~a~~  164 (177)
                      |+|.+..+
T Consensus       179 IkV~rp~~  186 (612)
T TIGR01645       179 IKVGRPSN  186 (612)
T ss_pred             eeeccccc
Confidence            99987543

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.

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

Probab=99.61  E-value=4.3e-15  Score=128.26  Aligned_cols=80  Identities=24%  Similarity=0.463  Sum_probs=74.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|..|+|+.+.   .+|+++|||||+|.+.++|.+|++.|||+.|.+     ++
T Consensus       186 ~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~---~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g-----~~  257 (457)
T TIGR01622       186 FLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDP---ETGRSKGFGFIQFHDAEEAKEALEVMNGFELAG-----RP  257 (457)
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcC---CCCccceEEEEEECCHHHHHHHHHhcCCcEECC-----EE
Confidence            6899999999999999999999999999999999887   567899999999999999999999999999966     58


Q ss_pred             eEEEeecC
Q 030444          157 LRLQFSRN  164 (177)
Q Consensus       157 l~V~~a~~  164 (177)
                      |+|.|+..
T Consensus       258 i~v~~a~~  265 (457)
T TIGR01622       258 IKVGYAQD  265 (457)
T ss_pred             EEEEEccC
Confidence            99999763

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.

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.61  E-value=6.6e-15  Score=95.43  Aligned_cols=67  Identities=28%  Similarity=0.526  Sum_probs=60.3

Q ss_pred             EEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCC
Q 030444           80 LYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDED  150 (177)
Q Consensus        80 LfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~  150 (177)
                      |||+|||+++++++|.++|+.||.|..+++..++   . +..+++|||+|.+.++|.+|++.+++..+.++
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~---~-~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~   67 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNK---D-GQSRGFAFVEFSSEEDAKRALELLNGKEIDGR   67 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEEST---T-SSEEEEEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeee---c-cccCCEEEEEeCCHHHHHHHHHHCCCcEECCE
Confidence            7999999999999999999999999999999876   3 77889999999999999999999999999763

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 ....

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

Probab=99.60  E-value=6.6e-15  Score=128.59  Aligned_cols=81  Identities=19%  Similarity=0.349  Sum_probs=74.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      ..++|||+|||+.+|+++|+++|+.||.|..+.|+.+.   .+|.++|||||+|.+.+.|+.|++.|||..|.+.     
T Consensus       294 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~---~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~-----  365 (509)
T TIGR01642       294 SKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDI---ATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDN-----  365 (509)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecC---CCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCe-----
Confidence            36899999999999999999999999999999999876   5788999999999999999999999999999764     


Q ss_pred             ceEEEeecC
Q 030444          156 FLRLQFSRN  164 (177)
Q Consensus       156 ~l~V~~a~~  164 (177)
                      .|+|+++..
T Consensus       366 ~l~v~~a~~  374 (509)
T TIGR01642       366 KLHVQRACV  374 (509)
T ss_pred             EEEEEECcc
Confidence            799999854

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

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

Probab=99.60  E-value=3.9e-15  Score=131.79  Aligned_cols=78  Identities=31%  Similarity=0.459  Sum_probs=72.7

Q ss_pred             eEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcceE
Q 030444           79 TLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFLR  158 (177)
Q Consensus        79 tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~l~  158 (177)
                      +|||+|||+++||++|+++|++||.|.+|+|+.+.   .+++++|||||+|.+.++|++|++.||+..|.+     +.|+
T Consensus         2 sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~---~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~g-----k~i~   73 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDS---VTRRSLGYGYVNFQNPADAERALETMNFKRLGG-----KPIR   73 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecC---CCCCcceEEEEEECCHHHHHHHHHHhCCCEECC-----eeEE
Confidence            79999999999999999999999999999999987   668899999999999999999999999999976     4799


Q ss_pred             EEeecC
Q 030444          159 LQFSRN  164 (177)
Q Consensus       159 V~~a~~  164 (177)
                      |.|+..
T Consensus        74 i~~s~~   79 (562)
T TIGR01628        74 IMWSQR   79 (562)
T ss_pred             eecccc
Confidence            999853

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

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.59  E-value=8.4e-15  Score=115.85  Aligned_cols=81  Identities=26%  Similarity=0.466  Sum_probs=75.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .+.|.|..||..+|+|||+.||...|+|++|++++|+   .+|.+-||+||.|.++++|++|+..|||..|..     ++
T Consensus        41 kTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDK---itGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~-----KT  112 (360)
T KOG0145|consen   41 KTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDK---ITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQN-----KT  112 (360)
T ss_pred             cceeeeeecccccCHHHHHHHhhcccceeeeeeeecc---ccccccccceeeecChHHHHHHHhhhcceeecc-----ce
Confidence            4569999999999999999999999999999999998   789999999999999999999999999999955     48


Q ss_pred             eEEEeecCC
Q 030444          157 LRLQFSRNP  165 (177)
Q Consensus       157 l~V~~a~~~  165 (177)
                      |+|+||++.
T Consensus       113 IKVSyARPS  121 (360)
T KOG0145|consen  113 IKVSYARPS  121 (360)
T ss_pred             EEEEeccCC
Confidence            999999764

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

Probab=99.59  E-value=5.2e-15  Score=131.00  Aligned_cols=81  Identities=22%  Similarity=0.349  Sum_probs=74.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      ..+|||+||++++|+++|+++|++||.|.+|+++.+.    ++.++|||||+|.+.++|++|++.||+..|.+     ++
T Consensus       285 ~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d~----~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~g-----k~  355 (562)
T TIGR01628       285 GVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDE----KGVSRGFGFVCFSNPEEANRAVTEMHGRMLGG-----KP  355 (562)
T ss_pred             CCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEECC----CCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCC-----ce
Confidence            6789999999999999999999999999999999884    68899999999999999999999999999966     58


Q ss_pred             eEEEeecCCC
Q 030444          157 LRLQFSRNPG  166 (177)
Q Consensus       157 l~V~~a~~~~  166 (177)
                      |+|.||..+.
T Consensus       356 l~V~~a~~k~  365 (562)
T TIGR01628       356 LYVALAQRKE  365 (562)
T ss_pred             eEEEeccCcH
Confidence            9999997653

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

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=99.59  E-value=3.6e-15  Score=114.30  Aligned_cols=80  Identities=23%  Similarity=0.328  Sum_probs=75.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      ..+|-|-||.+-+|.++|+.+|++||.|-+|.|..++   .+.+++|||||-|.+..+|+.|+++|+|.+|++.     .
T Consensus        13 m~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr---~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgR-----e   84 (256)
T KOG4207|consen   13 MTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDR---YTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGR-----E   84 (256)
T ss_pred             ceeEEecceeccCCHHHHHHHHHHhCcccceeccccc---ccccccceeEEEeeecchHHHHHHhhcceeeccc-----e
Confidence            5789999999999999999999999999999999998   7889999999999999999999999999999875     6


Q ss_pred             eEEEeecC
Q 030444          157 LRLQFSRN  164 (177)
Q Consensus       157 l~V~~a~~  164 (177)
                      |+|++|+.
T Consensus        85 lrVq~ary   92 (256)
T KOG4207|consen   85 LRVQMARY   92 (256)
T ss_pred             eeehhhhc
Confidence            99999875

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=99.58  E-value=2.4e-15  Score=117.12  Aligned_cols=77  Identities=18%  Similarity=0.271  Sum_probs=65.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      -++|||++|+|+++.++|++.|++||+|++..|+.|+   .+|++|||+||+|.|.+.|++|++.-| -.|++     |+
T Consensus        12 ~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~---~t~rskGyGfVTf~d~~aa~rAc~dp~-piIdG-----R~   82 (247)
T KOG0149|consen   12 FTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDK---NTGRSKGYGFVTFRDAEAATRACKDPN-PIIDG-----RK   82 (247)
T ss_pred             EEEEEEcCcccccchHHHHHHHHHhCceEEEEEEecc---CCccccceeeEEeecHHHHHHHhcCCC-Ccccc-----cc
Confidence            4689999999999999999999999999999999998   889999999999999999999985433 34444     45


Q ss_pred             eEEEee
Q 030444          157 LRLQFS  162 (177)
Q Consensus       157 l~V~~a  162 (177)
                      -.+.+|
T Consensus        83 aNcnlA   88 (247)
T KOG0149|consen   83 ANCNLA   88 (247)
T ss_pred             cccchh
Confidence            555554

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.57  E-value=5.3e-16  Score=116.72  Aligned_cols=81  Identities=20%  Similarity=0.434  Sum_probs=75.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      ++.-|||+|||+++||.||--+|++||.|..|.|++++   .||+++||||+.|+|..+..-|+..|||..|.+     |
T Consensus        34 dsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk---~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~g-----R  105 (219)
T KOG0126|consen   34 DSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDK---KTGKSKGFAFLCYEDQRSTILAVDNLNGIKILG-----R  105 (219)
T ss_pred             cceEEEECCCcccccCCcEEEEeeccCceEEEEEEecC---CCCcccceEEEEecCccceEEEEeccCCceecc-----e
Confidence            36889999999999999999999999999999999998   899999999999999999999999999999977     6


Q ss_pred             ceEEEeecC
Q 030444          156 FLRLQFSRN  164 (177)
Q Consensus       156 ~l~V~~a~~  164 (177)
                      .|+|+...+
T Consensus       106 tirVDHv~~  114 (219)
T KOG0126|consen  106 TIRVDHVSN  114 (219)
T ss_pred             eEEeeeccc
Confidence            899986543

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

Probab=99.57  E-value=2e-14  Score=124.14  Aligned_cols=80  Identities=18%  Similarity=0.262  Sum_probs=72.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      +.++|||+|||+++|+++|+++|++||.|.+|+|+.++   .+++++|||||+|.+.++|++||. |+|..|.+     +
T Consensus        88 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~---~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g-----~  158 (457)
T TIGR01622        88 DDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDR---NSRRSKGVAYVEFYDVESVIKALA-LTGQMLLG-----R  158 (457)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecC---CCCCcceEEEEEECCHHHHHHHHH-hCCCEECC-----e
Confidence            47899999999999999999999999999999999887   678899999999999999999995 99999976     4


Q ss_pred             ceEEEeecC
Q 030444          156 FLRLQFSRN  164 (177)
Q Consensus       156 ~l~V~~a~~  164 (177)
                      +|.|++++.
T Consensus       159 ~i~v~~~~~  167 (457)
T TIGR01622       159 PIIVQSSQA  167 (457)
T ss_pred             eeEEeecch
Confidence            799988754

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.

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=99.56  E-value=7.2e-15  Score=125.51  Aligned_cols=82  Identities=23%  Similarity=0.432  Sum_probs=77.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcce
Q 030444           78 STLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFL  157 (177)
Q Consensus        78 ~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~l  157 (177)
                      +.|||+|||++++|++|.++|+..|.|.+++++.|+   .+|+++||+|++|.+.++|+.|++.|||.++.+     |+|
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~---~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~g-----r~l   90 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDR---ETGKPKGFGFCEFTDEETAERAIRNLNGAEFNG-----RKL   90 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccc---cCCCcCceeeEecCchhhHHHHHHhcCCcccCC-----ceE
Confidence            889999999999999999999999999999999998   899999999999999999999999999999955     689


Q ss_pred             EEEeecCCCC
Q 030444          158 RLQFSRNPGP  167 (177)
Q Consensus       158 ~V~~a~~~~~  167 (177)
                      +|.|+.+...
T Consensus        91 ~v~~~~~~~~  100 (435)
T KOG0108|consen   91 RVNYASNRKN  100 (435)
T ss_pred             Eeecccccch
Confidence            9999987644

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.56  E-value=3.7e-14  Score=97.84  Aligned_cols=82  Identities=26%  Similarity=0.489  Sum_probs=72.0

Q ss_pred             CCCCCCCCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCC
Q 030444           70 LPLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDE  149 (177)
Q Consensus        70 ~~~p~~~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~  149 (177)
                      ..+|+.-++.|||.|||+++|.++..+||.+||.|..|+|-..+      ..+|-|||.|++..+|.+|++.|+|+.+..
T Consensus        11 ~rlppevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k------~TrGTAFVVYedi~dAk~A~dhlsg~n~~~   84 (124)
T KOG0114|consen   11 IRLPPEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTK------ETRGTAFVVYEDIFDAKKACDHLSGYNVDN   84 (124)
T ss_pred             CCCChhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCcc------CcCceEEEEehHhhhHHHHHHHhcccccCC
Confidence            45566668999999999999999999999999999999997654      245799999999999999999999999966


Q ss_pred             CCCCCcceEEEee
Q 030444          150 DDPDSKFLRLQFS  162 (177)
Q Consensus       150 ~~~~~r~l~V~~a  162 (177)
                           +.|.|-|-
T Consensus        85 -----ryl~vlyy   92 (124)
T KOG0114|consen   85 -----RYLVVLYY   92 (124)
T ss_pred             -----ceEEEEec
Confidence                 57888775

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.56  E-value=9.3e-15  Score=115.97  Aligned_cols=86  Identities=16%  Similarity=0.305  Sum_probs=78.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .-.+||+.|..+++.++|++.|.+||+|.+++|++|.   .++|+|||+||.|.+.++|+.||..|||..|..     |.
T Consensus        62 hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~---~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~-----R~  133 (321)
T KOG0148|consen   62 HFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDM---NTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGR-----RT  133 (321)
T ss_pred             ceeEEehhcchhcchHHHHHHhccccccccceEeecc---cCCcccceeEEeccchHHHHHHHHHhCCeeecc-----ce
Confidence            4569999999999999999999999999999999998   789999999999999999999999999999954     78


Q ss_pred             eEEEeecCCCCCCC
Q 030444          157 LRLQFSRNPGPRSV  170 (177)
Q Consensus       157 l~V~~a~~~~~r~~  170 (177)
                      |+..||.-++.+.+
T Consensus       134 IRTNWATRKp~e~n  147 (321)
T KOG0148|consen  134 IRTNWATRKPSEMN  147 (321)
T ss_pred             eeccccccCccccC
Confidence            99999976654443

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

Probab=99.55  E-value=3.5e-14  Score=125.29  Aligned_cols=75  Identities=21%  Similarity=0.349  Sum_probs=68.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCC--CCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCC
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPF--VGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDS  154 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~--G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~  154 (177)
                      .++|||+||++++||++|+++|++|  |.|++|+++.           +||||+|++.++|++|++.||+..|.+     
T Consensus       233 ~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~r-----------gfAFVeF~s~e~A~kAi~~lnG~~i~G-----  296 (578)
T TIGR01648       233 VKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIR-----------DYAFVHFEDREDAVKAMDELNGKELEG-----  296 (578)
T ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEeec-----------CeEEEEeCCHHHHHHHHHHhCCCEECC-----
Confidence            5789999999999999999999999  9999987753           399999999999999999999999976     


Q ss_pred             cceEEEeecCCCC
Q 030444          155 KFLRLQFSRNPGP  167 (177)
Q Consensus       155 r~l~V~~a~~~~~  167 (177)
                      +.|+|+|++++..
T Consensus       297 r~I~V~~Akp~~~  309 (578)
T TIGR01648       297 SEIEVTLAKPVDK  309 (578)
T ss_pred             EEEEEEEccCCCc
Confidence            4899999987644

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.

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.55  E-value=3e-14  Score=112.30  Aligned_cols=75  Identities=17%  Similarity=0.224  Sum_probs=66.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      ..||||+||++.+||++|+++|+.||.|.+|+|+.+.      +.++||||+|++++.|+.|+ .|+|..|.++     +
T Consensus         5 g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~------et~gfAfVtF~d~~aaetAl-lLnGa~l~d~-----~   72 (243)
T PLN03121          5 GYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG------EYACTAYVTFKDAYALETAV-LLSGATIVDQ-----R   72 (243)
T ss_pred             ceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC------CcceEEEEEECCHHHHHHHH-hcCCCeeCCc-----e
Confidence            6899999999999999999999999999999998874      34479999999999999999 8999999885     6


Q ss_pred             eEEEeec
Q 030444          157 LRLQFSR  163 (177)
Q Consensus       157 l~V~~a~  163 (177)
                      |.|.-..
T Consensus        73 I~It~~~   79 (243)
T PLN03121         73 VCITRWG   79 (243)
T ss_pred             EEEEeCc
Confidence            7877543

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.54  E-value=3e-14  Score=119.17  Aligned_cols=87  Identities=17%  Similarity=0.364  Sum_probs=76.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .-+|||+.||..++|+||++||++||.|.+|.|++|+   .++.++|||||.|.+.++|.+|+.+||+......  ...+
T Consensus        34 ~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk---~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG--~~~p  108 (510)
T KOG0144|consen   34 AVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDK---STGQSKGCCFVKYYTRKEADEAINALHNQKTLPG--MHHP  108 (510)
T ss_pred             hhhheeccCCccccHHHHHHHHHHhCceeEEEeeccc---ccCcccceEEEEeccHHHHHHHHHHhhcccccCC--CCcc
Confidence            5689999999999999999999999999999999998   7789999999999999999999999998765443  2247


Q ss_pred             eEEEeecCCCCC
Q 030444          157 LRLQFSRNPGPR  168 (177)
Q Consensus       157 l~V~~a~~~~~r  168 (177)
                      |.|.||....+|
T Consensus       109 vqvk~Ad~E~er  120 (510)
T KOG0144|consen  109 VQVKYADGERER  120 (510)
T ss_pred             eeecccchhhhc
Confidence            999999765444

>PLN03213 repressor of silencing 3; Provisional

Probab=99.54  E-value=2.2e-14  Score=121.96  Aligned_cols=76  Identities=22%  Similarity=0.355  Sum_probs=68.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCH--HHHHHHHHHhCCCeeCCCCCCC
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENP--ACAATALSALQGYRMDEDDPDS  154 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~--~~A~~Ai~~l~g~~l~~~~~~~  154 (177)
                      ..+||||||++++|+++|+.+|+.||.|.+|.|++.     +|  ||||||+|.+.  .++.+||+.|||..+.+     
T Consensus        10 gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRE-----TG--RGFAFVEMssdddaEeeKAISaLNGAEWKG-----   77 (759)
T PLN03213         10 GVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRT-----KG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKG-----   77 (759)
T ss_pred             ceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecc-----cC--CceEEEEecCCcHHHHHHHHHHhcCCeecC-----
Confidence            578999999999999999999999999999999833     45  79999999987  78999999999999977     


Q ss_pred             cceEEEeecC
Q 030444          155 KFLRLQFSRN  164 (177)
Q Consensus       155 r~l~V~~a~~  164 (177)
                      |.|+|+-|+.
T Consensus        78 R~LKVNKAKP   87 (759)
T PLN03213         78 GRLRLEKAKE   87 (759)
T ss_pred             ceeEEeeccH
Confidence            5799998864

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=99.54  E-value=1.7e-14  Score=103.93  Aligned_cols=81  Identities=19%  Similarity=0.309  Sum_probs=75.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .-.|||.++..++||++|.+.|..||.|+.+.|..++   ++|..||||+|+|++.+.|++|+..+||..|.++     .
T Consensus        72 GwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDR---RtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q-----~  143 (170)
T KOG0130|consen   72 GWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDR---RTGYVKGYALVEYETLKEAQAAIDALNGAELLGQ-----N  143 (170)
T ss_pred             eEEEEEeccCcchhHHHHHHHHhhcccccceeecccc---ccccccceeeeehHhHHHHHHHHHhccchhhhCC-----c
Confidence            5689999999999999999999999999999999998   8999999999999999999999999999999997     5


Q ss_pred             eEEEeecCC
Q 030444          157 LRLQFSRNP  165 (177)
Q Consensus       157 l~V~~a~~~  165 (177)
                      |.|+|+=.+
T Consensus       144 v~VDw~Fv~  152 (170)
T KOG0130|consen  144 VSVDWCFVK  152 (170)
T ss_pred             eeEEEEEec
Confidence            889886444

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

Probab=99.54  E-value=3.8e-14  Score=123.60  Aligned_cols=77  Identities=21%  Similarity=0.302  Sum_probs=69.7

Q ss_pred             CCCeEEEcCCCC-CCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCC
Q 030444           76 ASSTLYVEGLPA-DSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDS  154 (177)
Q Consensus        76 ~~~tLfV~nLp~-~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~  154 (177)
                      ++++|||+|||+ .+|+++|++||++||.|.+|+|+.++        +|||||+|.+.++|+.|++.||+..|.++    
T Consensus       274 ~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~--------~g~afV~f~~~~~A~~Ai~~lng~~l~g~----  341 (481)
T TIGR01649       274 PGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNK--------KETALIEMADPYQAQLALTHLNGVKLFGK----  341 (481)
T ss_pred             CCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC--------CCEEEEEECCHHHHHHHHHHhCCCEECCc----
Confidence            378999999998 69999999999999999999998763        36999999999999999999999999774    


Q ss_pred             cceEEEeecCC
Q 030444          155 KFLRLQFSRNP  165 (177)
Q Consensus       155 r~l~V~~a~~~  165 (177)
                       +|+|++++..
T Consensus       342 -~l~v~~s~~~  351 (481)
T TIGR01649       342 -PLRVCPSKQQ  351 (481)
T ss_pred             -eEEEEEcccc
Confidence             7999998653

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).

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.53  E-value=7e-15  Score=113.79  Aligned_cols=85  Identities=22%  Similarity=0.383  Sum_probs=78.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCC
Q 030444           75 DASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDS  154 (177)
Q Consensus        75 ~~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~  154 (177)
                      ...+||||+.|..++||.-|...|-+||.|.+|.+..+.   .++++|||+||+|+..++|.+||..||+.+|.+     
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDy---esqkHRgFgFVefe~aEDAaaAiDNMnesEL~G-----   79 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDY---ESQKHRGFGFVEFEEAEDAAAAIDNMNESELFG-----   79 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccccccchhhcccccch---hcccccceeEEEeeccchhHHHhhcCchhhhcc-----
Confidence            347899999999999999999999999999999999887   778999999999999999999999999999987     


Q ss_pred             cceEEEeecCCCC
Q 030444          155 KFLRLQFSRNPGP  167 (177)
Q Consensus       155 r~l~V~~a~~~~~  167 (177)
                      |.|+|.||++..-
T Consensus        80 rtirVN~AkP~ki   92 (298)
T KOG0111|consen   80 RTIRVNLAKPEKI   92 (298)
T ss_pred             eeEEEeecCCccc
Confidence            5899999987643

>smart00362 RRM_2 RNA recognition motif

Probab=99.53  E-value=6.4e-14  Score=89.24  Aligned_cols=71  Identities=31%  Similarity=0.523  Sum_probs=63.4

Q ss_pred             eEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcceE
Q 030444           79 TLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFLR  158 (177)
Q Consensus        79 tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~l~  158 (177)
                      +|||.|||.++++++|+++|++||.+..+++..+.     +.++++|||+|.+.+.|+.|++.+++..+.+.     .|+
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~-----~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~-----~i~   70 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT-----GKSKGFAFVEFESEEDAEKAIEALNGTKLGGR-----PLR   70 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC-----CCCCceEEEEeCCHHHHHHHHHHhCCcEECCE-----EEe
Confidence            58999999999999999999999999999888764     55778999999999999999999999999653     566


Q ss_pred             E
Q 030444          159 L  159 (177)
Q Consensus       159 V  159 (177)
                      |
T Consensus        71 v   71 (72)
T smart00362       71 V   71 (72)
T ss_pred             e
Confidence            5

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.53  E-value=2.3e-14  Score=120.19  Aligned_cols=77  Identities=19%  Similarity=0.342  Sum_probs=70.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .+.|||.||+.++||+.|+.+|++||.|..|+.+.|           ||||+|.+.++|.+|++.+||++|+++     .
T Consensus       259 VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD-----------YaFVHf~eR~davkAm~~~ngkeldG~-----~  322 (506)
T KOG0117|consen  259 VKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD-----------YAFVHFAEREDAVKAMKETNGKELDGS-----P  322 (506)
T ss_pred             eeeeeeeccchhhhHHHHHHHHHhccceEEeecccc-----------eeEEeecchHHHHHHHHHhcCceecCc-----e
Confidence            678999999999999999999999999999987755           999999999999999999999999886     7


Q ss_pred             eEEEeecCCCCCC
Q 030444          157 LRLQFSRNPGPRS  169 (177)
Q Consensus       157 l~V~~a~~~~~r~  169 (177)
                      |.|.+||++.++.
T Consensus       323 iEvtLAKP~~k~k  335 (506)
T KOG0117|consen  323 IEVTLAKPVDKKK  335 (506)
T ss_pred             EEEEecCChhhhc
Confidence            9999999875443

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

Probab=99.53  E-value=5.2e-14  Score=110.72  Aligned_cols=79  Identities=33%  Similarity=0.544  Sum_probs=74.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|.++|.+||.|..+++..++   .+++++|||||+|.+.++|..|++.+++..|.+     ++
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~---~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~-----~~  186 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDR---ETGKSRGFAFVEFESEESAEKAIEELNGKELEG-----RP  186 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeecc---ccCccCceEEEEecCHHHHHHHHHHcCCCeECC-----ce
Confidence            5999999999999999999999999999999999886   678999999999999999999999999999976     58


Q ss_pred             eEEEeec
Q 030444          157 LRLQFSR  163 (177)
Q Consensus       157 l~V~~a~  163 (177)
                      |+|+++.
T Consensus       187 ~~v~~~~  193 (306)
T COG0724         187 LRVQKAQ  193 (306)
T ss_pred             eEeeccc
Confidence            9999965

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

Probab=99.53  E-value=4.6e-14  Score=123.09  Aligned_cols=75  Identities=17%  Similarity=0.244  Sum_probs=67.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHh--CCCeeCCCCCCC
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSAL--QGYRMDEDDPDS  154 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l--~g~~l~~~~~~~  154 (177)
                      +++|||+|||+++||++|+++|++||.|.+|+++.++         +||||+|++.++|++|++.|  ++..|.+     
T Consensus         2 s~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~~k---------~~afVef~~~e~A~~Ai~~~~~~~~~l~g-----   67 (481)
T TIGR01649         2 SPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPGK---------RQALVEFEDEESAKACVNFATSVPIYIRG-----   67 (481)
T ss_pred             ccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEECCC---------CEEEEEeCchHHHHHHHHHhhcCCceEcC-----
Confidence            7899999999999999999999999999999998643         59999999999999999875  6778865     


Q ss_pred             cceEEEeecCC
Q 030444          155 KFLRLQFSRNP  165 (177)
Q Consensus       155 r~l~V~~a~~~  165 (177)
                      ++|+|+|+..+
T Consensus        68 ~~l~v~~s~~~   78 (481)
T TIGR01649        68 QPAFFNYSTSQ   78 (481)
T ss_pred             eEEEEEecCCc
Confidence            58999999654

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).

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.52  E-value=4.9e-14  Score=111.91  Aligned_cols=75  Identities=23%  Similarity=0.427  Sum_probs=70.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      +++|||+||+.-+||++|++.|++||.|.+||+..++         ||+||.|++.+.|.+||..+|+.++.++     .
T Consensus       164 NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~q---------GYaFVrF~tkEaAahAIv~mNntei~G~-----~  229 (321)
T KOG0148|consen  164 NTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKDQ---------GYAFVRFETKEAAAHAIVQMNNTEIGGQ-----L  229 (321)
T ss_pred             CceEEeCCcCccccHHHHHHhcccCCcceEEEEeccc---------ceEEEEecchhhHHHHHHHhcCceeCce-----E
Confidence            8999999999999999999999999999999999886         6999999999999999999999999876     7


Q ss_pred             eEEEeecCC
Q 030444          157 LRLQFSRNP  165 (177)
Q Consensus       157 l~V~~a~~~  165 (177)
                      +++.|-|..
T Consensus       230 VkCsWGKe~  238 (321)
T KOG0148|consen  230 VRCSWGKEG  238 (321)
T ss_pred             EEEeccccC
Confidence            899998753

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.52  E-value=1.4e-14  Score=121.10  Aligned_cols=87  Identities=25%  Similarity=0.330  Sum_probs=77.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+-|+..+||+|++++|++||.|++|.|+++.    .+.+||||||.|...+.|..||+.||+..-...  -.-+
T Consensus       124 e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~----~~~sRGcaFV~fstke~A~~Aika~ng~~tmeG--cs~P  197 (510)
T KOG0144|consen  124 ERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDP----DGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEG--CSQP  197 (510)
T ss_pred             chhhhhhhccccccHHHHHHHHHhhCccchhhheecc----cccccceeEEEEehHHHHHHHHHhhccceeecc--CCCc
Confidence            6899999999999999999999999999999999985    688999999999999999999999999776554  2348


Q ss_pred             eEEEeecCCCCCC
Q 030444          157 LRLQFSRNPGPRS  169 (177)
Q Consensus       157 l~V~~a~~~~~r~  169 (177)
                      |.|.||..+..+.
T Consensus       198 LVVkFADtqkdk~  210 (510)
T KOG0144|consen  198 LVVKFADTQKDKD  210 (510)
T ss_pred             eEEEecccCCCch
Confidence            9999998775554

>smart00360 RRM RNA recognition motif

Probab=99.50  E-value=1.5e-13  Score=87.11  Aligned_cols=70  Identities=36%  Similarity=0.525  Sum_probs=62.6

Q ss_pred             EcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcceEE
Q 030444           82 VEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFLRL  159 (177)
Q Consensus        82 V~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~l~V  159 (177)
                      |+|||.++++++|+++|++||.|..+.+..++   .+++++++|||+|.+.++|..|++.|++..+.++     .|+|
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~---~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~-----~~~v   70 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDK---DTGKSKGFAFVEFESEEDAEKALEALNGKELDGR-----PLKV   70 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCC---CCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCc-----EEEe
Confidence            68999999999999999999999999998775   4577889999999999999999999999999663     5665

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.48  E-value=3.8e-14  Score=113.48  Aligned_cols=72  Identities=24%  Similarity=0.463  Sum_probs=67.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcce
Q 030444           78 STLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFL  157 (177)
Q Consensus        78 ~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~l  157 (177)
                      .+|||+|||.++++.+|+.||++||+|.+|.|+.+           |+||+.++...|+.||..||++.|++.     -|
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN-----------YgFVHiEdktaaedairNLhgYtLhg~-----nI   66 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVKN-----------YGFVHIEDKTAAEDAIRNLHGYTLHGV-----NI   66 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeecc-----------cceEEeecccccHHHHhhcccceecce-----EE
Confidence            57999999999999999999999999999999876           899999999999999999999999885     59


Q ss_pred             EEEeecCC
Q 030444          158 RLQFSRNP  165 (177)
Q Consensus       158 ~V~~a~~~  165 (177)
                      +|+-+|++
T Consensus        67 nVeaSksK   74 (346)
T KOG0109|consen   67 NVEASKSK   74 (346)
T ss_pred             EEEecccc
Confidence            99988877

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.47  E-value=6.9e-14  Score=114.70  Aligned_cols=81  Identities=22%  Similarity=0.411  Sum_probs=76.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .+.|||..|.+-+|+++|+.+|+.||.|.+|.++.++   .+|.+-.||||+|++.+++++|.-.|++..|++     |+
T Consensus       239 eNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~---ktgdsLqyaFiEFen~escE~AyFKMdNvLIDD-----rR  310 (479)
T KOG0415|consen  239 ENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDR---KTGDSLQYAFIEFENKESCEQAYFKMDNVLIDD-----RR  310 (479)
T ss_pred             cceEEEEecCCcccccchhhHHhhcccceeeeEEecc---cccchhheeeeeecchhhHHHHHhhhcceeecc-----ce
Confidence            6999999999999999999999999999999999998   789999999999999999999999999999988     48


Q ss_pred             eEEEeecCC
Q 030444          157 LRLQFSRNP  165 (177)
Q Consensus       157 l~V~~a~~~  165 (177)
                      |+|.|+.+.
T Consensus       311 IHVDFSQSV  319 (479)
T KOG0415|consen  311 IHVDFSQSV  319 (479)
T ss_pred             EEeehhhhh
Confidence            999998764

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.46  E-value=1.2e-13  Score=104.08  Aligned_cols=82  Identities=15%  Similarity=0.156  Sum_probs=75.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCC
Q 030444           74 PDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPD  153 (177)
Q Consensus        74 ~~~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~  153 (177)
                      .+...||||+||+..++++.|.+||-+.|.|..+++..++   .+...+|||||+|.++++|+-|++.||...|.+    
T Consensus         6 rnqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDr---v~~~~qGygF~Ef~~eedadYAikiln~VkLYg----   78 (203)
T KOG0131|consen    6 RNQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDR---VTQKHQGYGFAEFRTEEDADYAIKILNMVKLYG----   78 (203)
T ss_pred             cCCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhh---hcccccceeEEEEechhhhHHHHHHHHHHHhcC----
Confidence            4457899999999999999999999999999999999988   667789999999999999999999999888876    


Q ss_pred             CcceEEEeec
Q 030444          154 SKFLRLQFSR  163 (177)
Q Consensus       154 ~r~l~V~~a~  163 (177)
                       |+|+|..+.
T Consensus        79 -rpIrv~kas   87 (203)
T KOG0131|consen   79 -RPIRVNKAS   87 (203)
T ss_pred             -ceeEEEecc
Confidence             589999875

>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=99.45  E-value=1e-12  Score=84.05  Aligned_cols=74  Identities=34%  Similarity=0.556  Sum_probs=65.3

Q ss_pred             eEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcceE
Q 030444           79 TLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFLR  158 (177)
Q Consensus        79 tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~l~  158 (177)
                      +|||+|||+++++++|+++|+.||.|..+.+..+.    ...++++|||+|.+.++|..|++.+++..+.+     +.|.
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~----~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~-----~~~~   71 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDK----DTKSKGFAFVEFEDEEDAEKALEALNGKELGG-----RPLR   71 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCC----CCCcceEEEEEECCHHHHHHHHHHhCCCeECC-----eEEE
Confidence            58999999999999999999999999999998765    22567899999999999999999999999865     3677


Q ss_pred             EEe
Q 030444          159 LQF  161 (177)
Q Consensus       159 V~~  161 (177)
                      |+|
T Consensus        72 v~~   74 (74)
T cd00590          72 VEF   74 (74)
T ss_pred             EeC
Confidence            764

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).

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=99.40  E-value=8.5e-13  Score=102.43  Aligned_cols=78  Identities=26%  Similarity=0.402  Sum_probs=70.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHH----hhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCC
Q 030444           77 SSTLYVEGLPADSTKREVAH----IFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDP  152 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~----lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~  152 (177)
                      +.||||.||+..+..++|++    ||++||.|.+|....      +.+.+|.|||.|.+.+.|..|+..|+|+.+.++  
T Consensus         9 n~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~k------t~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK--   80 (221)
T KOG4206|consen    9 NGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFK------TPKMRGQAFVVFKETEAASAALRALQGFPFYGK--   80 (221)
T ss_pred             CceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecC------CCCccCceEEEecChhHHHHHHHHhcCCcccCc--
Confidence            56999999999999999988    999999999887643      467889999999999999999999999999885  


Q ss_pred             CCcceEEEeecCC
Q 030444          153 DSKFLRLQFSRNP  165 (177)
Q Consensus       153 ~~r~l~V~~a~~~  165 (177)
                         +++|+||+++
T Consensus        81 ---~mriqyA~s~   90 (221)
T KOG4206|consen   81 ---PMRIQYAKSD   90 (221)
T ss_pred             ---hhheecccCc
Confidence               7999999876

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.39  E-value=4.3e-13  Score=106.59  Aligned_cols=83  Identities=24%  Similarity=0.490  Sum_probs=77.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      +.|.|||-+||.+..+.||...|-.||.|.+.++..|+   -+..+|+|+||.|+++.+|+.||..|||+.|.-+     
T Consensus       284 eGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDR---ATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMK-----  355 (371)
T KOG0146|consen  284 EGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDR---ATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMK-----  355 (371)
T ss_pred             CcceEEEEeCchhhccHHHHHHhccccceeeeeeeehh---ccccccceeeEecCCchhHHHHHHHhcchhhhhh-----
Confidence            37999999999999999999999999999999999998   6788999999999999999999999999999774     


Q ss_pred             ceEEEeecCCC
Q 030444          156 FLRLQFSRNPG  166 (177)
Q Consensus       156 ~l~V~~a~~~~  166 (177)
                      +|+|++-+++.
T Consensus       356 RLKVQLKRPkd  366 (371)
T KOG0146|consen  356 RLKVQLKRPKD  366 (371)
T ss_pred             hhhhhhcCccc
Confidence            79999887664

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.38  E-value=3e-12  Score=101.49  Aligned_cols=81  Identities=25%  Similarity=0.413  Sum_probs=75.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .-+|||-||.++++|.-|+++|.+||.|..|++++|-   .+.+.|||+||.+.+-++|..||..|||+.+.+     |.
T Consensus       278 g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~---ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~-----rv  349 (360)
T KOG0145|consen  278 GWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDF---TTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGD-----RV  349 (360)
T ss_pred             eeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecC---CcccccceeEEEecchHHHHHHHHHhcCccccc-----eE
Confidence            5689999999999999999999999999999999997   668899999999999999999999999999966     58


Q ss_pred             eEEEeecCC
Q 030444          157 LRLQFSRNP  165 (177)
Q Consensus       157 l~V~~a~~~  165 (177)
                      |.|.|-.++
T Consensus       350 LQVsFKtnk  358 (360)
T KOG0145|consen  350 LQVSFKTNK  358 (360)
T ss_pred             EEEEEecCC
Confidence            999997664

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.36  E-value=2.2e-12  Score=110.82  Aligned_cols=80  Identities=21%  Similarity=0.361  Sum_probs=73.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .-.|.|.||||.|.+.+|+.+|+.||.|.+|.|....    .|+.+|||||.|.+..+|..|++.+|+.+|++     |+
T Consensus       117 k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~----dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~g-----R~  187 (678)
T KOG0127|consen  117 KWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKK----DGKLCGFAFVQFKEKKDAEKALEFFNGNKIDG-----RP  187 (678)
T ss_pred             cceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCC----CCCccceEEEEEeeHHHHHHHHHhccCceecC-----ce
Confidence            4579999999999999999999999999999998654    67777999999999999999999999999976     68


Q ss_pred             eEEEeecCC
Q 030444          157 LRLQFSRNP  165 (177)
Q Consensus       157 l~V~~a~~~  165 (177)
                      |-|+||-.+
T Consensus       188 VAVDWAV~K  196 (678)
T KOG0127|consen  188 VAVDWAVDK  196 (678)
T ss_pred             eEEeeeccc
Confidence            999999765

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.33  E-value=4.1e-12  Score=106.79  Aligned_cols=77  Identities=19%  Similarity=0.368  Sum_probs=70.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhC-CCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFR-PFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~-~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      .+.+||.|||+++.+++|++||. +.|.|..|+|+.|.    .||++|||.|||++++.+++|++.||.+.+.+     |
T Consensus        44 ~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~----~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~G-----R  114 (608)
T KOG4212|consen   44 DRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDE----SGKARGCAVVEFKDPENVQKALEKLNKYEVNG-----R  114 (608)
T ss_pred             cceEEEecCcchhhhHhHHHHHHHhcCceEeeeeeccc----CCCcCCceEEEeeCHHHHHHHHHHhhhccccC-----c
Confidence            46699999999999999999996 66999999999996    79999999999999999999999999999955     6


Q ss_pred             ceEEEee
Q 030444          156 FLRLQFS  162 (177)
Q Consensus       156 ~l~V~~a  162 (177)
                      +|+|.-.
T Consensus       115 ~l~vKEd  121 (608)
T KOG4212|consen  115 ELVVKED  121 (608)
T ss_pred             eEEEecc
Confidence            8988754

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=99.32  E-value=3.5e-12  Score=113.11  Aligned_cols=79  Identities=25%  Similarity=0.487  Sum_probs=73.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      ++||||+.|+..++|.||..+|+.||.|.+|.++..+         +||||.+....+|++|+.+|+.+.+..     +.
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~R---------~cAfI~M~~RqdA~kalqkl~n~kv~~-----k~  486 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPPR---------GCAFIKMVRRQDAEKALQKLSNVKVAD-----KT  486 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEeeccCC---------ceeEEEEeehhHHHHHHHHHhcccccc-----ee
Confidence            7899999999999999999999999999999998765         699999999999999999999999966     48


Q ss_pred             eEEEeecCCCCCC
Q 030444          157 LRLQFSRNPGPRS  169 (177)
Q Consensus       157 l~V~~a~~~~~r~  169 (177)
                      |+|.|+..++.+.
T Consensus       487 Iki~Wa~g~G~ks  499 (894)
T KOG0132|consen  487 IKIAWAVGKGPKS  499 (894)
T ss_pred             eEEeeeccCCcch
Confidence            9999999987775

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.32  E-value=5.1e-12  Score=108.57  Aligned_cols=80  Identities=25%  Similarity=0.417  Sum_probs=71.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHh-----CC-CeeCCC
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSAL-----QG-YRMDED  150 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l-----~g-~~l~~~  150 (177)
                      ..||||.|||+++||++|.++|++||.|..+.|+.++   .++.++|.|||.|.+...|..||+.-     .| +.|++ 
T Consensus       292 ~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k---~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~G-  367 (678)
T KOG0127|consen  292 GKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDK---DTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLLDG-  367 (678)
T ss_pred             cceEEEecCCccccHHHHHHHHHhhccceeEEEEecc---CCCCcccceEEEeccHHHHHHHHHhcCccCCCceEEEec-
Confidence            5899999999999999999999999999999999988   78999999999999999999999877     33 55544 


Q ss_pred             CCCCcceEEEeecC
Q 030444          151 DPDSKFLRLQFSRN  164 (177)
Q Consensus       151 ~~~~r~l~V~~a~~  164 (177)
                          |.|+|..|-.
T Consensus       368 ----R~Lkv~~Av~  377 (678)
T KOG0127|consen  368 ----RLLKVTLAVT  377 (678)
T ss_pred             ----cEEeeeeccc
Confidence                6899988754

>PF13893 RRM_5: RNA recognition motif

Probab=99.32  E-value=1.1e-11  Score=77.02  Aligned_cols=56  Identities=21%  Similarity=0.438  Sum_probs=49.1

Q ss_pred             HHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcceEEEee
Q 030444           94 VAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFLRLQFS  162 (177)
Q Consensus        94 L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~l~V~~a  162 (177)
                      |.++|++||.|.++++..++        +++|||+|.+.++|+.|++.||+..+.+     ++|+|+||
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--------RGFAFVEFASVEDAQKAIEQLNGRQFNG-----RPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS--------TTEEEEEESSHHHHHHHHHHHTTSEETT-----EEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC--------CCEEEEEECCHHHHHHHHHHhCCCEECC-----cEEEEEEC
Confidence            67899999999999987653        3599999999999999999999999966     58999997

(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 ....

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.28  E-value=1.1e-11  Score=98.71  Aligned_cols=87  Identities=25%  Similarity=0.391  Sum_probs=77.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+-|...-.|||++.||..||.|.+|.+....    .|.+||||||.|.+..+|..||..|||......  -.-.
T Consensus        19 drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~----dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpG--ASSS   92 (371)
T KOG0146|consen   19 DRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGP----DGNSKGCAFVKFSSHAEAQAAINALHGSQTMPG--ASSS   92 (371)
T ss_pred             chhhhhhhhcccccHHHHHHHhcccCCcceeEEecCC----CCCCCCceEEEeccchHHHHHHHHhcccccCCC--Cccc
Confidence            6899999999999999999999999999999998774    688999999999999999999999999877654  2347


Q ss_pred             eEEEeecCCCCCC
Q 030444          157 LRLQFSRNPGPRS  169 (177)
Q Consensus       157 l~V~~a~~~~~r~  169 (177)
                      |.|.|+...++|.
T Consensus        93 LVVK~ADTdkER~  105 (371)
T KOG0146|consen   93 LVVKFADTDKERT  105 (371)
T ss_pred             eEEEeccchHHHH
Confidence            9999998776654

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.27  E-value=5.9e-12  Score=101.05  Aligned_cols=74  Identities=23%  Similarity=0.335  Sum_probs=69.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      .+.+|+|+||.+.++.+||+..|++||.+.+|+|+++           |+||.|+-.++|..|++.||+.+++++     
T Consensus        77 ~stkl~vgNis~tctn~ElRa~fe~ygpviecdivkd-----------y~fvh~d~~eda~~air~l~~~~~~gk-----  140 (346)
T KOG0109|consen   77 ASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKD-----------YAFVHFDRAEDAVEAIRGLDNTEFQGK-----  140 (346)
T ss_pred             CccccccCCCCccccCHHHhhhhcccCCceeeeeecc-----------eeEEEEeeccchHHHHhcccccccccc-----
Confidence            3789999999999999999999999999999999876           999999999999999999999999775     


Q ss_pred             ceEEEeecCC
Q 030444          156 FLRLQFSRNP  165 (177)
Q Consensus       156 ~l~V~~a~~~  165 (177)
                      +|+|+.+.+.
T Consensus       141 ~m~vq~stsr  150 (346)
T KOG0109|consen  141 RMHVQLSTSR  150 (346)
T ss_pred             eeeeeeeccc
Confidence            8999998664

>smart00361 RRM_1 RNA recognition motif

Probab=99.26  E-value=2.5e-11  Score=79.08  Aligned_cols=63  Identities=17%  Similarity=0.241  Sum_probs=52.1

Q ss_pred             HHHHHHhhC----CCCCEEEEE-EeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcceEE
Q 030444           91 KREVAHIFR----PFVGYKEVR-LVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFLRL  159 (177)
Q Consensus        91 e~~L~~lF~----~~G~i~~v~-l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~l~V  159 (177)
                      +++|+++|+    .||.|.+|. ++.++.. .++.++||+||+|.+.++|.+|++.|||..+.+     |.|++
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~-~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~g-----r~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVG-YENHKRGNVYITFERSEDAARAIVDLNGRYFDG-----RTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCC-CCCCCcEEEEEEECCHHHHHHHHHHhCCCEECC-----EEEEe
Confidence            678999998    999999995 6555411 127899999999999999999999999999976     46665

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=99.26  E-value=1.6e-10  Score=89.95  Aligned_cols=92  Identities=30%  Similarity=0.509  Sum_probs=74.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCC
Q 030444           74 PDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPD  153 (177)
Q Consensus        74 ~~~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~  153 (177)
                      ++.-+||||.+||.|+...||..||..|-..+.+.|.....  ...-.+-+|||+|.+...|.+|++.|||..|+-.  .
T Consensus        31 ~~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk--~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE--~  106 (284)
T KOG1457|consen   31 PGAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSK--GDQVCKPVAFATFTSHQFALAAMNALNGVRFDPE--T  106 (284)
T ss_pred             ccccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccC--CCccccceEEEEecchHHHHHHHHHhcCeeeccc--c
Confidence            34479999999999999999999999998887776644320  1112346999999999999999999999999987  3


Q ss_pred             CcceEEEeecCCCCCC
Q 030444          154 SKFLRLQFSRNPGPRS  169 (177)
Q Consensus       154 ~r~l~V~~a~~~~~r~  169 (177)
                      +..|+|++||+..++.
T Consensus       107 ~stLhiElAKSNtK~k  122 (284)
T KOG1457|consen  107 GSTLHIELAKSNTKRK  122 (284)
T ss_pred             CceeEeeehhcCcccc
Confidence            4689999999865443

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.25  E-value=6.1e-12  Score=103.80  Aligned_cols=77  Identities=19%  Similarity=0.355  Sum_probs=71.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      -|.||||.|.+++.|+.|+..|..||.|++|.+-+|.   .++++||||||||+-++.|+-|++.|||..+.++     -
T Consensus       113 McRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp---~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGR-----N  184 (544)
T KOG0124|consen  113 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDP---ATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGR-----N  184 (544)
T ss_pred             hHheeeeeeEEEechHHHHhhccCCCCcceeeccccc---ccccccceEEEEEeCcHHHHHHHHHhccccccCc-----c
Confidence            4889999999999999999999999999999999998   7899999999999999999999999999999774     5


Q ss_pred             eEEEe
Q 030444          157 LRLQF  161 (177)
Q Consensus       157 l~V~~  161 (177)
                      |+|..
T Consensus       185 iKVgr  189 (544)
T KOG0124|consen  185 IKVGR  189 (544)
T ss_pred             ccccC
Confidence            88764

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.25  E-value=1e-11  Score=106.63  Aligned_cols=77  Identities=26%  Similarity=0.433  Sum_probs=70.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcce
Q 030444           78 STLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFL  157 (177)
Q Consensus        78 ~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~l  157 (177)
                      ..|||+||.+++||++|+.+|+.||.|..|.+..+.   .+|.++||+||+|.+.++|.+|++.|||++|-+     |.|
T Consensus       279 ~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~---~tG~skgfGfi~f~~~~~ar~a~e~lngfelAG-----r~i  350 (549)
T KOG0147|consen  279 RRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDS---ETGRSKGFGFITFVNKEDARKALEQLNGFELAG-----RLI  350 (549)
T ss_pred             hhhhhcccccCchHHHHhhhccCcccceeeeecccc---ccccccCcceEEEecHHHHHHHHHHhccceecC-----ceE
Confidence            349999999999999999999999999999998886   689999999999999999999999999999965     678


Q ss_pred             EEEee
Q 030444          158 RLQFS  162 (177)
Q Consensus       158 ~V~~a  162 (177)
                      +|...
T Consensus       351 kV~~v  355 (549)
T KOG0147|consen  351 KVSVV  355 (549)
T ss_pred             EEEEe
Confidence            88764

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=99.23  E-value=2.8e-11  Score=92.85  Aligned_cols=78  Identities=26%  Similarity=0.428  Sum_probs=69.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCC-CCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPF-VGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~-G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      ...+||..+|.-+.+.+|..+|.+| |.++.+++-+++   +||.+||||||+|++.+.|+-|-+.||+|.|.++     
T Consensus        49 ~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnk---rTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~-----  120 (214)
T KOG4208|consen   49 EGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNK---RTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEH-----  120 (214)
T ss_pred             ccceeecccccchhHHHHhhhhhhcCCeeEEEEeeccc---ccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhh-----
Confidence            4679999999999999999999999 666777776666   7999999999999999999999999999999885     


Q ss_pred             ceEEEee
Q 030444          156 FLRLQFS  162 (177)
Q Consensus       156 ~l~V~~a  162 (177)
                      .|.+.|-
T Consensus       121 lL~c~vm  127 (214)
T KOG4208|consen  121 LLECHVM  127 (214)
T ss_pred             eeeeEEe
Confidence            6888876

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.23  E-value=1.9e-11  Score=92.27  Aligned_cols=85  Identities=12%  Similarity=0.303  Sum_probs=74.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEE-EEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEV-RLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v-~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      +..|||+||.++++|..|.++|+.||.+... +++++.   .+|.+++|+||.|.+.+.+.+|+..+|++.+..     |
T Consensus        96 ganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~---~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~n-----r  167 (203)
T KOG0131|consen   96 GANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDP---DTGNPKGFGFINYASFEASDAAIGSMNGQYLCN-----R  167 (203)
T ss_pred             cccccccccCcchhHHHHHHHHHhccccccCCcccccc---cCCCCCCCeEEechhHHHHHHHHHHhccchhcC-----C
Confidence            5789999999999999999999999988653 677776   678999999999999999999999999999954     6


Q ss_pred             ceEEEeecCCCCCC
Q 030444          156 FLRLQFSRNPGPRS  169 (177)
Q Consensus       156 ~l~V~~a~~~~~r~  169 (177)
                      ++.|+|+..+...+
T Consensus       168 ~itv~ya~k~~~kg  181 (203)
T KOG0131|consen  168 PITVSYAFKKDTKG  181 (203)
T ss_pred             ceEEEEEEecCCCc
Confidence            89999997664443

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.22  E-value=3.5e-11  Score=101.65  Aligned_cols=80  Identities=18%  Similarity=0.321  Sum_probs=70.8

Q ss_pred             eEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcceE
Q 030444           79 TLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFLR  158 (177)
Q Consensus        79 tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~l~  158 (177)
                      .|||.||+++++..+|.++|+.||.|.+|++..+.    .| ++|| ||+|++++.|.+|++.|||..+.++     .|.
T Consensus        78 ~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~----~g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~k-----ki~  146 (369)
T KOG0123|consen   78 LVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDE----NG-SKGY-FVQFESEESAKKAIEKLNGMLLNGK-----KIY  146 (369)
T ss_pred             eeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcC----CC-ceee-EEEeCCHHHHHHHHHHhcCcccCCC-----eeE
Confidence            39999999999999999999999999999999986    34 8999 9999999999999999999999775     688


Q ss_pred             EEeecCCCCCC
Q 030444          159 LQFSRNPGPRS  169 (177)
Q Consensus       159 V~~a~~~~~r~  169 (177)
                      |.....+..|.
T Consensus       147 vg~~~~~~er~  157 (369)
T KOG0123|consen  147 VGLFERKEERE  157 (369)
T ss_pred             Eeeccchhhhc
Confidence            87665554443

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

Probab=99.15  E-value=1.6e-10  Score=101.10  Aligned_cols=83  Identities=10%  Similarity=0.200  Sum_probs=67.6

Q ss_pred             CCCeEEEcCCCCC--C--------CHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCC
Q 030444           76 ASSTLYVEGLPAD--S--------TKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGY  145 (177)
Q Consensus        76 ~~~tLfV~nLp~~--~--------te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~  145 (177)
                      ++++|+|.||...  +        ..++|+++|++||.|..|+|........++..+|++||+|.+.++|++|+..|||.
T Consensus       408 ~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnGr  487 (509)
T TIGR01642       408 PTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGR  487 (509)
T ss_pred             CceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEeeccCcCCCcCCCcceEEEEECCHHHHHHHHHHcCCC
Confidence            3689999999642  1        23579999999999999999875322344566799999999999999999999999


Q ss_pred             eeCCCCCCCcceEEEeec
Q 030444          146 RMDEDDPDSKFLRLQFSR  163 (177)
Q Consensus       146 ~l~~~~~~~r~l~V~~a~  163 (177)
                      .|.+     |.|.|.|..
T Consensus       488 ~~~g-----r~v~~~~~~  500 (509)
T TIGR01642       488 KFND-----RVVVAAFYG  500 (509)
T ss_pred             EECC-----eEEEEEEeC
Confidence            9966     589999863

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

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.15  E-value=3.7e-10  Score=95.17  Aligned_cols=73  Identities=21%  Similarity=0.281  Sum_probs=65.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .|+|||.|||+++|++.|++-|..||.|..+.|+.      .|+++|  .|.|.++++|+.|+..|++..|+++     -
T Consensus       536 a~qIiirNlP~dfTWqmlrDKfre~G~v~yadime------~GkskG--VVrF~s~edAEra~a~Mngs~l~Gr-----~  602 (608)
T KOG4212|consen  536 ACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIME------NGKSKG--VVRFFSPEDAERACALMNGSRLDGR-----N  602 (608)
T ss_pred             ccEEEEecCCccccHHHHHHHHHhccceehhhhhc------cCCccc--eEEecCHHHHHHHHHHhccCcccCc-----e
Confidence            57899999999999999999999999999988853      377776  8999999999999999999999774     6


Q ss_pred             eEEEee
Q 030444          157 LRLQFS  162 (177)
Q Consensus       157 l~V~~a  162 (177)
                      |+|.|.
T Consensus       603 I~V~y~  608 (608)
T KOG4212|consen  603 IKVTYF  608 (608)
T ss_pred             eeeeeC
Confidence            999874

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.12  E-value=2e-10  Score=101.30  Aligned_cols=82  Identities=28%  Similarity=0.385  Sum_probs=70.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcce
Q 030444           78 STLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFL  157 (177)
Q Consensus        78 ~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~l  157 (177)
                      ++|||.||++++|.++|..+|...|.|.++.|...+.....-.+.||+||+|.+.++|+.|++.|+|+.|+++     .|
T Consensus       516 t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH-----~l  590 (725)
T KOG0110|consen  516 TKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGH-----KL  590 (725)
T ss_pred             hhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCc-----eE
Confidence            3499999999999999999999999999998877653322223669999999999999999999999999886     69


Q ss_pred             EEEeecC
Q 030444          158 RLQFSRN  164 (177)
Q Consensus       158 ~V~~a~~  164 (177)
                      .|+++.+
T Consensus       591 ~lk~S~~  597 (725)
T KOG0110|consen  591 ELKISEN  597 (725)
T ss_pred             EEEeccC
Confidence            9999973

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.10  E-value=6.6e-11  Score=104.26  Aligned_cols=81  Identities=32%  Similarity=0.450  Sum_probs=73.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      +++|+|.|||+..+-.+++.||..||.+.+|+|....   ..+.++|||||+|-++.+|..|+++|..+.|.+     |+
T Consensus       613 ~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~---~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyG-----Rr  684 (725)
T KOG0110|consen  613 GTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKI---GKGAHRGFGFVDFLTPREAKNAFDALGSTHLYG-----RR  684 (725)
T ss_pred             cceeeeeccchHHHHHHHHHHHhcccceeeeccchhh---cchhhccceeeeccCcHHHHHHHHhhcccceec-----hh
Confidence            5789999999999999999999999999999998763   346688999999999999999999999999977     58


Q ss_pred             eEEEeecCC
Q 030444          157 LRLQFSRNP  165 (177)
Q Consensus       157 l~V~~a~~~  165 (177)
                      |.++||++.
T Consensus       685 LVLEwA~~d  693 (725)
T KOG0110|consen  685 LVLEWAKSD  693 (725)
T ss_pred             hheehhccc
Confidence            999999764

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.07  E-value=6.5e-10  Score=91.18  Aligned_cols=74  Identities=19%  Similarity=0.366  Sum_probs=64.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHh-CCCeeCCCCCCCc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSAL-QGYRMDEDDPDSK  155 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l-~g~~l~~~~~~~r  155 (177)
                      -+||||++|-..++|.+|++.|.+||+|+++++...+         ++|||+|.+.+.|+.|.+.+ +...|.     ++
T Consensus       228 I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~~---------~CAFv~ftTR~aAE~Aae~~~n~lvI~-----G~  293 (377)
T KOG0153|consen  228 IKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPRK---------GCAFVTFTTREAAEKAAEKSFNKLVIN-----GF  293 (377)
T ss_pred             eeEEEecccccchhHHHHHHHHhhcCCeeeEEeeccc---------ccceeeehhhHHHHHHHHhhcceeeec-----ce
Confidence            5789999999999999999999999999999998765         49999999999999998755 444443     46


Q ss_pred             ceEEEeecC
Q 030444          156 FLRLQFSRN  164 (177)
Q Consensus       156 ~l~V~~a~~  164 (177)
                      +|+|.|.++
T Consensus       294 Rl~i~Wg~~  302 (377)
T KOG0153|consen  294 RLKIKWGRP  302 (377)
T ss_pred             EEEEEeCCC
Confidence            899999976

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=99.03  E-value=9.6e-10  Score=87.54  Aligned_cols=80  Identities=21%  Similarity=0.332  Sum_probs=71.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      ..+|+|.|||..|+++||++||++|+.+..+-+..++    .|.+.|.|-|.|...++|++|++.||+..+++.     +
T Consensus        83 ~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~----~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~-----~  153 (243)
T KOG0533|consen   83 STKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDR----AGRSLGTADVSFNRRDDAERAVKKYNGVALDGR-----P  153 (243)
T ss_pred             cceeeeecCCcCcchHHHHHHHHHhccceEEeeccCC----CCCCCccceeeecchHhHHHHHHHhcCcccCCc-----e
Confidence            4789999999999999999999999988888887775    788999999999999999999999999888764     6


Q ss_pred             eEEEeecCC
Q 030444          157 LRLQFSRNP  165 (177)
Q Consensus       157 l~V~~a~~~  165 (177)
                      |+++...++
T Consensus       154 mk~~~i~~~  162 (243)
T KOG0533|consen  154 MKIEIISSP  162 (243)
T ss_pred             eeeEEecCc
Confidence            888776544

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=99.03  E-value=5.6e-10  Score=96.77  Aligned_cols=81  Identities=16%  Similarity=0.335  Sum_probs=72.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .+.|||..|...+.-.+|+.||++||.|+-.+++++.   ++---++|+||++.+..+|.+||+.||.+.|++     |.
T Consensus       405 gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNa---RsPGaRCYGfVTMSts~eAtkCI~hLHrTELHG-----rm  476 (940)
T KOG4661|consen  405 GRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNA---RSPGARCYGFVTMSTSAEATKCIEHLHRTELHG-----RM  476 (940)
T ss_pred             ccceeeeccccchhhhHHHHHHHHhcceeceeeeecC---CCCCcceeEEEEecchHHHHHHHHHhhhhhhcc-----ee
Confidence            5789999999999999999999999999999999875   333457899999999999999999999999977     58


Q ss_pred             eEEEeecCC
Q 030444          157 LRLQFSRNP  165 (177)
Q Consensus       157 l~V~~a~~~  165 (177)
                      |.|+-+++.
T Consensus       477 ISVEkaKNE  485 (940)
T KOG4661|consen  477 ISVEKAKNE  485 (940)
T ss_pred             eeeeecccC
Confidence            999999875

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.02  E-value=6.3e-10  Score=92.05  Aligned_cols=81  Identities=16%  Similarity=0.359  Sum_probs=72.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      -+.|||..+.++++|+||+.+|+.||.|.+|.+....   .++.+|||+|+||.+......||..||-+.|.++     -
T Consensus       210 fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~p---t~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQ-----y  281 (544)
T KOG0124|consen  210 FNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAP---TGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQ-----Y  281 (544)
T ss_pred             hheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccC---CCCCccceeeEEeccccchHHHhhhcchhhcccc-----e
Confidence            5789999999999999999999999999999998886   5667999999999999999999999999999776     6


Q ss_pred             eEEEeecCC
Q 030444          157 LRLQFSRNP  165 (177)
Q Consensus       157 l~V~~a~~~  165 (177)
                      |+|--+-.|
T Consensus       282 LRVGk~vTP  290 (544)
T KOG0124|consen  282 LRVGKCVTP  290 (544)
T ss_pred             EecccccCC
Confidence            888665544

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=98.96  E-value=2.5e-09  Score=90.45  Aligned_cols=73  Identities=25%  Similarity=0.354  Sum_probs=66.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcce
Q 030444           78 STLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFL  157 (177)
Q Consensus        78 ~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~l  157 (177)
                      ..|||+   +++||..|.++|+++|.+.++++..+.     + +-|||||.|.++.+|++||+.||-..+.++     +|
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~-----t-slgy~yvnf~~~~da~~A~~~~n~~~~~~~-----~~   67 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDA-----T-SLGYAYVNFQQPADAERALDTMNFDVLKGK-----PI   67 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecC-----C-ccceEEEecCCHHHHHHHHHHcCCcccCCc-----EE
Confidence            469999   999999999999999999999999984     3 789999999999999999999999999774     89


Q ss_pred             EEEeecC
Q 030444          158 RLQFSRN  164 (177)
Q Consensus       158 ~V~~a~~  164 (177)
                      +|-|+..
T Consensus        68 rim~s~r   74 (369)
T KOG0123|consen   68 RIMWSQR   74 (369)
T ss_pred             Eeehhcc
Confidence            9999854

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=98.94  E-value=1e-09  Score=85.82  Aligned_cols=72  Identities=24%  Similarity=0.432  Sum_probs=64.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcce
Q 030444           78 STLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFL  157 (177)
Q Consensus        78 ~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~l  157 (177)
                      ..+||++||+.+.+.+|+.||..||.|.++.+..           +|+||+|+|..+|+.|+..||+..|.+.     .+
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk~-----------gf~fv~fed~rda~Dav~~l~~~~l~~e-----~~   65 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMKN-----------GFGFVEFEDPRDADDAVHDLDGKELCGE-----RL   65 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceeec-----------ccceeccCchhhhhcccchhcCceecce-----ee
Confidence            4689999999999999999999999999987744           4899999999999999999999999875     38


Q ss_pred             EEEeecCC
Q 030444          158 RLQFSRNP  165 (177)
Q Consensus       158 ~V~~a~~~  165 (177)
                      .|+|++..
T Consensus        66 vve~~r~~   73 (216)
T KOG0106|consen   66 VVEHARGK   73 (216)
T ss_pred             eeeccccc
Confidence            99999753

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.92  E-value=3.8e-09  Score=83.93  Aligned_cols=80  Identities=16%  Similarity=0.262  Sum_probs=72.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      ...+||+|+.+.+|.++++..|+.||.|..+.+..++   ..+.+|+|+||+|.+.+.++.|+. ||+..|.+.     .
T Consensus       101 ~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~---~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~-----~  171 (231)
T KOG4209|consen  101 APSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDK---FRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGP-----A  171 (231)
T ss_pred             CceEEEeccccccccchhhheeeccCCccceeeeccc---cCCCcceeEEEecccHhhhHHHhh-cCCcccccc-----c
Confidence            6789999999999999999999999999988898887   567799999999999999999997 999999774     7


Q ss_pred             eEEEeecCC
Q 030444          157 LRLQFSRNP  165 (177)
Q Consensus       157 l~V~~a~~~  165 (177)
                      ++|.+.+..
T Consensus       172 i~vt~~r~~  180 (231)
T KOG4209|consen  172 IEVTLKRTN  180 (231)
T ss_pred             ceeeeeeee
Confidence            888887654

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=98.92  E-value=5.9e-09  Score=85.58  Aligned_cols=80  Identities=20%  Similarity=0.230  Sum_probs=71.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEE--------EEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeC
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYK--------EVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMD  148 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~--------~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~  148 (177)
                      +..|||+|||.++|.+++.++|++||.|.        .|+|..+.    .|+.||-|+|.|-..++++-|++.|++..|.
T Consensus       134 Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~----~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~r  209 (382)
T KOG1548|consen  134 NTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDN----QGKLKGDALCCYIKRESVELAIKILDEDELR  209 (382)
T ss_pred             CceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecC----CCCccCceEEEeecccHHHHHHHHhCccccc
Confidence            56799999999999999999999999875        47787775    5999999999999999999999999999997


Q ss_pred             CCCCCCcceEEEeecCC
Q 030444          149 EDDPDSKFLRLQFSRNP  165 (177)
Q Consensus       149 ~~~~~~r~l~V~~a~~~  165 (177)
                      +.     .|+|+-|+..
T Consensus       210 g~-----~~rVerAkfq  221 (382)
T KOG1548|consen  210 GK-----KLRVERAKFQ  221 (382)
T ss_pred             Cc-----EEEEehhhhh
Confidence            64     7999988764

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=98.91  E-value=1.6e-09  Score=89.35  Aligned_cols=70  Identities=21%  Similarity=0.376  Sum_probs=60.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCC
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDE  149 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~  149 (177)
                      +.++|||++|+|+++++.|++.|++||.|.+|.++.++   .+++++||+||+|++.+...+++.. .-+.|++
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~---~t~rsrgFgfv~f~~~~~v~~vl~~-~~h~~dg   74 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDP---STGRSRGFGFVTFATPEGVDAVLNA-RTHKLDG   74 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccC---CCCCcccccceecCCCcchheeecc-cccccCC
Confidence            37899999999999999999999999999999999998   5689999999999998888888743 3344433

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=98.89  E-value=1.4e-09  Score=84.80  Aligned_cols=70  Identities=29%  Similarity=0.538  Sum_probs=60.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCC
Q 030444           75 DASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDD  151 (177)
Q Consensus        75 ~~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~  151 (177)
                      ..+.||||-||.++|||++|+.+|+.|-.+..++|...     +|.  ..|||+|++.+.|..|+..|+|..|...+
T Consensus       208 ~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~-----~g~--~vaf~~~~~~~~at~am~~lqg~~~s~~d  277 (284)
T KOG1457|consen  208 RACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRAR-----GGM--PVAFADFEEIEQATDAMNHLQGNLLSSSD  277 (284)
T ss_pred             hhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecC-----CCc--ceEeecHHHHHHHHHHHHHhhcceecccc
Confidence            34789999999999999999999999988887777543     343  48999999999999999999999997653

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=98.89  E-value=6.1e-09  Score=88.93  Aligned_cols=81  Identities=27%  Similarity=0.464  Sum_probs=64.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCC
Q 030444           75 DASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDS  154 (177)
Q Consensus        75 ~~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~  154 (177)
                      ....+|||.|||+++++++|+++|.+||.|+...|....   ..++..+|+||+|.+.+.++.||++- -..|     ++
T Consensus       286 ~~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~---~~~~~~~fgFV~f~~~~~~~~~i~As-p~~i-----g~  356 (419)
T KOG0116|consen  286 ADGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRS---PGGKNPCFGFVEFENAAAVQNAIEAS-PLEI-----GG  356 (419)
T ss_pred             ecccceEeecCCCCCCHHHHHHHHhhcccccccceEEec---cCCCcCceEEEEEeecchhhhhhhcC-cccc-----CC
Confidence            345679999999999999999999999999998887654   34555589999999999999998654 3334     33


Q ss_pred             cceEEEeecC
Q 030444          155 KFLRLQFSRN  164 (177)
Q Consensus       155 r~l~V~~a~~  164 (177)
                      ++|.|+--+.
T Consensus       357 ~kl~Veek~~  366 (419)
T KOG0116|consen  357 RKLNVEEKRP  366 (419)
T ss_pred             eeEEEEeccc
Confidence            5788875543

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=98.82  E-value=3.9e-09  Score=91.15  Aligned_cols=67  Identities=25%  Similarity=0.329  Sum_probs=59.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCC
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDED  150 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~  150 (177)
                      +..+|+|-|||..|++++|..+|+.||+|+.|+.-..+        ++.+||+|.|..+|++|++.|++.++.++
T Consensus        74 ~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~~--------~~~~~v~FyDvR~A~~Alk~l~~~~~~~~  140 (549)
T KOG4660|consen   74 NQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPNK--------RGIVFVEFYDVRDAERALKALNRREIAGK  140 (549)
T ss_pred             ccceEEEEecCCcCCHHHHHHHHHhhcchhhhhccccc--------CceEEEEEeehHhHHHHHHHHHHHHhhhh
Confidence            46899999999999999999999999999997654432        46999999999999999999999999775

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=98.82  E-value=2e-09  Score=83.64  Aligned_cols=75  Identities=16%  Similarity=0.166  Sum_probs=66.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .+||||+|+-..++|+-|.+||-+-|.|.+|.|...+    .++.| ||||+|+++....-|++.+||..+.+.     .
T Consensus         9 drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~----d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~-----e   78 (267)
T KOG4454|consen    9 DRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQ----DQEQK-FAYVFFPNENSVQLAGQLENGDDLEED-----E   78 (267)
T ss_pred             hhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCc----cCCCc-eeeeecccccchhhhhhhcccchhccc-----h
Confidence            6899999999999999999999999999999887765    46666 999999999999999999999999775     4


Q ss_pred             eEEEe
Q 030444          157 LRLQF  161 (177)
Q Consensus       157 l~V~~  161 (177)
                      |+|++
T Consensus        79 ~q~~~   83 (267)
T KOG4454|consen   79 EQRTL   83 (267)
T ss_pred             hhccc
Confidence            56554

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=98.78  E-value=1.9e-08  Score=89.18  Aligned_cols=83  Identities=24%  Similarity=0.287  Sum_probs=71.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .+.|||+||++.++|+.|...|..||.|..++|++.++.-.....+-|+||-|-+..+|++|++.|+|..+..     +.
T Consensus       174 TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~-----~e  248 (877)
T KOG0151|consen  174 TTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVME-----YE  248 (877)
T ss_pred             ccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeee-----ee
Confidence            5679999999999999999999999999999999876333333455699999999999999999999999966     46


Q ss_pred             eEEEeecC
Q 030444          157 LRLQFSRN  164 (177)
Q Consensus       157 l~V~~a~~  164 (177)
                      +++-|++.
T Consensus       249 ~K~gWgk~  256 (877)
T KOG0151|consen  249 MKLGWGKA  256 (877)
T ss_pred             eeeccccc
Confidence            99999864

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=98.75  E-value=6e-08  Score=75.60  Aligned_cols=75  Identities=27%  Similarity=0.615  Sum_probs=67.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      +.+||+.|||.+++.+.|..+|++|....+++++..+        ++.|||+|.+...|..|...|++..+.-++    .
T Consensus       146 n~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~~--------~~iAfve~~~d~~a~~a~~~lq~~~it~~~----~  213 (221)
T KOG4206|consen  146 NNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPPR--------SGIAFVEFLSDRQASAAQQALQGFKITKKN----T  213 (221)
T ss_pred             ceEEEEecCCcchhHHHHHHHHhhCcccceeEeccCC--------CceeEEecchhhhhHHHhhhhccceeccCc----e
Confidence            7899999999999999999999999999999998865        248999999999999999999999997543    6


Q ss_pred             eEEEeec
Q 030444          157 LRLQFSR  163 (177)
Q Consensus       157 l~V~~a~  163 (177)
                      ++|.|++
T Consensus       214 m~i~~a~  220 (221)
T KOG4206|consen  214 MQITFAK  220 (221)
T ss_pred             EEecccC
Confidence            9999885

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=98.71  E-value=1.4e-08  Score=80.40  Aligned_cols=79  Identities=20%  Similarity=0.389  Sum_probs=71.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      ....||++.|--+++++.|...|.+|-.....++++++   ++|+++||+||.|.+..++..|++.|+|.-+.     .|
T Consensus       189 ~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdk---RTgKSkgygfVSf~~pad~~rAmrem~gkyVg-----sr  260 (290)
T KOG0226|consen  189 DDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDK---RTGKSKGYGFVSFRDPADYVRAMREMNGKYVG-----SR  260 (290)
T ss_pred             ccceeecccccccccHHHHHHHHHhccchhhccccccc---cccccccceeeeecCHHHHHHHHHhhcccccc-----cc
Confidence            35789999999999999999999999999999999988   89999999999999999999999999999984     46


Q ss_pred             ceEEEee
Q 030444          156 FLRLQFS  162 (177)
Q Consensus       156 ~l~V~~a  162 (177)
                      +|++.-+
T Consensus       261 piklRkS  267 (290)
T KOG0226|consen  261 PIKLRKS  267 (290)
T ss_pred             hhHhhhh
Confidence            7776543

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=98.70  E-value=2.3e-08  Score=82.54  Aligned_cols=80  Identities=18%  Similarity=0.306  Sum_probs=68.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      ..+|||+.||.++++++|++.|++||.|..+.++.+.   .+.++++|+||+|++++.+++++ ...-+.|.+     +.
T Consensus        97 tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~---~~~~~rgFgfv~~~~e~sVdkv~-~~~f~~~~g-----k~  167 (311)
T KOG4205|consen   97 TKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDK---TTSRPRGFGFVTFDSEDSVDKVT-LQKFHDFNG-----KK  167 (311)
T ss_pred             eeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecc---cccccccceeeEeccccccceec-ccceeeecC-----ce
Confidence            5689999999999999999999999999999999987   66789999999999999999886 455566654     35


Q ss_pred             eEEEeecCC
Q 030444          157 LRLQFSRNP  165 (177)
Q Consensus       157 l~V~~a~~~  165 (177)
                      +.|.-|.++
T Consensus       168 vevkrA~pk  176 (311)
T KOG4205|consen  168 VEVKRAIPK  176 (311)
T ss_pred             eeEeeccch
Confidence            777777654

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.67  E-value=2.5e-07  Score=63.92  Aligned_cols=85  Identities=21%  Similarity=0.330  Sum_probs=68.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHhhCCC--CCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           78 STLYVEGLPADSTKREVAHIFRPF--VGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        78 ~tLfV~nLp~~~te~~L~~lF~~~--G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      +||-|.|||...|.++|.+++...  |...-+-+..|-   .+.-+.|||||.|.+++.|.+-.+.++|..+..-+ ..+
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf---~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~-s~K   77 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDF---KNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFN-SKK   77 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeec---cCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCC-CCc
Confidence            689999999999999999988643  555556666665   45668899999999999999999999999997543 345


Q ss_pred             ceEEEeecCCC
Q 030444          156 FLRLQFSRNPG  166 (177)
Q Consensus       156 ~l~V~~a~~~~  166 (177)
                      .+.|.||+-.+
T Consensus        78 vc~i~yAriQG   88 (97)
T PF04059_consen   78 VCEISYARIQG   88 (97)
T ss_pred             EEEEehhHhhC
Confidence            78999997543

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=98.66  E-value=3.3e-07  Score=77.02  Aligned_cols=78  Identities=17%  Similarity=0.266  Sum_probs=69.8

Q ss_pred             CCeEEEcCCCC-CCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           77 SSTLYVEGLPA-DSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        77 ~~tLfV~nLp~-~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      +..|.|.||.. .+|.+.|..||.-||.|.+|+|+.++.        --|+|.|.|...|+-|++.|+|.++.++     
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkk--------d~ALIQmsd~~qAqLA~~hL~g~~l~gk-----  363 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKK--------DNALIQMSDGQQAQLAMEHLEGHKLYGK-----  363 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCC--------cceeeeecchhHHHHHHHHhhcceecCc-----
Confidence            68899999966 599999999999999999999998862        2699999999999999999999999884     


Q ss_pred             ceEEEeecCCCC
Q 030444          156 FLRLQFSRNPGP  167 (177)
Q Consensus       156 ~l~V~~a~~~~~  167 (177)
                      +|+|.++|.+..
T Consensus       364 ~lrvt~SKH~~v  375 (492)
T KOG1190|consen  364 KLRVTLSKHTNV  375 (492)
T ss_pred             eEEEeeccCccc
Confidence            799999997643

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=98.63  E-value=2.1e-07  Score=76.94  Aligned_cols=82  Identities=18%  Similarity=0.326  Sum_probs=71.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEE--------EEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeC
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYK--------EVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMD  148 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~--------~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~  148 (177)
                      ..+|||.+||..+++++|.++|.+|+.|.        .|.|.+++   .++++|+-|.|.|+|...|+.|+..+++..+.
T Consensus        66 ~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dk---eT~~~KGeatvS~~D~~~akaai~~~agkdf~  142 (351)
T KOG1995|consen   66 NETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDK---ETGAPKGEATVSYEDPPAAKAAIEWFAGKDFC  142 (351)
T ss_pred             cccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccc---cccCcCCceeeeecChhhhhhhhhhhcccccc
Confidence            68999999999999999999999999874        24455555   78999999999999999999999999999998


Q ss_pred             CCCCCCcceEEEeecCCC
Q 030444          149 EDDPDSKFLRLQFSRNPG  166 (177)
Q Consensus       149 ~~~~~~r~l~V~~a~~~~  166 (177)
                      +.     +|+|.+++...
T Consensus       143 gn-----~ikvs~a~~r~  155 (351)
T KOG1995|consen  143 GN-----TIKVSLAERRT  155 (351)
T ss_pred             CC-----Cchhhhhhhcc
Confidence            74     68888876543

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=98.55  E-value=7.8e-08  Score=83.43  Aligned_cols=82  Identities=26%  Similarity=0.479  Sum_probs=74.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCC
Q 030444           74 PDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPD  153 (177)
Q Consensus        74 ~~~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~  153 (177)
                      ++..+++||++||..+++++++++...||.+...+++.+.   .+|.++||||.+|.+......|+..|||.++.+.   
T Consensus       286 ~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~---~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~---  359 (500)
T KOG0120|consen  286 PDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDS---ATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDK---  359 (500)
T ss_pred             ccccchhhhccCcCccCHHHHHHHHHhcccchhheeeccc---ccccccceeeeeeeCCcchhhhhcccchhhhcCc---
Confidence            3446889999999999999999999999999999999887   6688999999999999999999999999999875   


Q ss_pred             CcceEEEeec
Q 030444          154 SKFLRLQFSR  163 (177)
Q Consensus       154 ~r~l~V~~a~  163 (177)
                        .|.|+.|-
T Consensus       360 --~lvvq~A~  367 (500)
T KOG0120|consen  360 --KLVVQRAI  367 (500)
T ss_pred             --eeEeehhh
Confidence              68888774

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=98.41  E-value=7.1e-07  Score=75.03  Aligned_cols=77  Identities=21%  Similarity=0.332  Sum_probs=65.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      +.+|++.|+|.+++||+|+.+|.+-|...+......+       .+-+|++.+++.+.|..|+-.++.+.+.+.+    -
T Consensus       414 satlHlsnip~svsee~lk~~f~~~g~~vkafkff~k-------d~kmal~q~~sveeA~~ali~~hnh~lgen~----h  482 (492)
T KOG1190|consen  414 SATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFFQK-------DRKMALPQLESVEEAIQALIDLHNHYLGENH----H  482 (492)
T ss_pred             hhheeeccCCcccchhHHHHhhhcCCceEEeeeecCC-------CcceeecccCChhHhhhhccccccccCCCCc----e
Confidence            7899999999999999999999999877655433322       1239999999999999999999999998764    4


Q ss_pred             eEEEeecC
Q 030444          157 LRLQFSRN  164 (177)
Q Consensus       157 l~V~~a~~  164 (177)
                      |+|+|+++
T Consensus       483 lRvSFSks  490 (492)
T KOG1190|consen  483 LRVSFSKS  490 (492)
T ss_pred             EEEEeecc
Confidence            99999976

>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=98.35  E-value=2.9e-06  Score=56.68  Aligned_cols=68  Identities=22%  Similarity=0.285  Sum_probs=47.1

Q ss_pred             CeEEEcCCCCCCCHHH----HHHhhCCCCC-EEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCC
Q 030444           78 STLYVEGLPADSTKRE----VAHIFRPFVG-YKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDP  152 (177)
Q Consensus        78 ~tLfV~nLp~~~te~~----L~~lF~~~G~-i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~  152 (177)
                      +.|||.|||.+.+...    |++|+..||+ |..|  . .          +.|+|.|.+.+.|++|.+.|+|..+.+.  
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v--~-~----------~tAilrF~~~~~A~RA~KRmegEdVfG~--   67 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV--S-G----------GTAILRFPNQEFAERAQKRMEGEDVFGN--   67 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE-----T----------T-EEEEESSHHHHHHHHHHHTT--SSSS--
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE--e-C----------CEEEEEeCCHHHHHHHHHhhcccccccc--
Confidence            4699999999988765    6678889965 3332  1 1          3799999999999999999999999885  


Q ss_pred             CCcceEEEeec
Q 030444          153 DSKFLRLQFSR  163 (177)
Q Consensus       153 ~~r~l~V~~a~  163 (177)
                         .|.|+|..
T Consensus        68 ---kI~v~~~~   75 (90)
T PF11608_consen   68 ---KISVSFSP   75 (90)
T ss_dssp             -----EEESS-
T ss_pred             ---eEEEEEcC
Confidence               69999984

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=98.35  E-value=1.7e-07  Score=80.98  Aligned_cols=80  Identities=19%  Similarity=0.287  Sum_probs=72.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCC
Q 030444           75 DASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDS  154 (177)
Q Consensus        75 ~~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~  154 (177)
                      .+.+|+|+-.|+-.+++.+|.++|+.+|.|.+|+|+.++   .++.++|.+||+|.|.+....|| .|.|..+.+.    
T Consensus       177 Rd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr---~s~rskgi~Yvef~D~~sVp~ai-aLsGqrllg~----  248 (549)
T KOG0147|consen  177 RDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDR---NSRRSKGIAYVEFCDEQSVPLAI-ALSGQRLLGV----  248 (549)
T ss_pred             HhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccc---cchhhcceeEEEEecccchhhHh-hhcCCcccCc----
Confidence            346899999999999999999999999999999999998   67889999999999999999999 8999999886    


Q ss_pred             cceEEEeec
Q 030444          155 KFLRLQFSR  163 (177)
Q Consensus       155 r~l~V~~a~  163 (177)
                       +|.|+...
T Consensus       249 -pv~vq~sE  256 (549)
T KOG0147|consen  249 -PVIVQLSE  256 (549)
T ss_pred             -eeEecccH
Confidence             68887643

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=98.30  E-value=2.3e-06  Score=73.33  Aligned_cols=74  Identities=18%  Similarity=0.327  Sum_probs=57.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      ...|=+..|||++|++||.++|+.|. |..+.+.+.     +|++.|-|||||.+++++++|++ .|...+.     .|-
T Consensus        10 ~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r~-----~Gr~sGeA~Ve~~seedv~~Alk-kdR~~mg-----~RY   77 (510)
T KOG4211|consen   10 AFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPRR-----NGRPSGEAYVEFTSEEDVEKALK-KDRESMG-----HRY   77 (510)
T ss_pred             ceEEEecCCCccccHHHHHHHHhcCc-eeEEEEecc-----CCCcCcceEEEeechHHHHHHHH-hhHHHhC-----Cce
Confidence            45566789999999999999999995 777666543     58888999999999999999995 4544442     245


Q ss_pred             eEEEee
Q 030444          157 LRLQFS  162 (177)
Q Consensus       157 l~V~~a  162 (177)
                      |.|--+
T Consensus        78 IEVf~~   83 (510)
T KOG4211|consen   78 IEVFTA   83 (510)
T ss_pred             EEEEcc
Confidence            666443

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=98.16  E-value=1.7e-06  Score=71.62  Aligned_cols=79  Identities=11%  Similarity=0.208  Sum_probs=65.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCC--CEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCC
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFV--GYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDS  154 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G--~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~  154 (177)
                      ..++||+||-|++|++||.+.+...|  .|.++++..++   ..|.+||||+|...+.....+-++.|--..|+++++  
T Consensus        80 k~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR---~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P--  154 (498)
T KOG4849|consen   80 KYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENR---TNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSP--  154 (498)
T ss_pred             eEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcc---cCCcccceEEEEecchHHHHHHHHhcccceecCCCC--
Confidence            35699999999999999988887654  45667777776   679999999999999999999999999999999864  


Q ss_pred             cceEEEee
Q 030444          155 KFLRLQFS  162 (177)
Q Consensus       155 r~l~V~~a  162 (177)
                        ..+.|.
T Consensus       155 --~V~~~N  160 (498)
T KOG4849|consen  155 --TVLSYN  160 (498)
T ss_pred             --eeeccc
Confidence              555553

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.13  E-value=3.4e-06  Score=69.17  Aligned_cols=83  Identities=25%  Similarity=0.293  Sum_probs=70.9

Q ss_pred             CCeEE-EcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           77 SSTLY-VEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        77 ~~tLf-V~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      ..++| |++|++++++++|+..|..++.|..+++..+.   .++.++||+||+|.+...+..++.. +...+..     +
T Consensus       184 s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~---~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~-----~  254 (285)
T KOG4210|consen  184 SDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDE---ESGDSKGFAYVDFSAGNSKKLALND-QTRSIGG-----R  254 (285)
T ss_pred             cccceeecccccccchHHHhhhccCcCcceeeccCCCC---CccchhhhhhhhhhhchhHHHHhhc-ccCcccC-----c
Confidence            45666 99999999999999999999999999998887   7899999999999999999988876 6666644     5


Q ss_pred             ceEEEeecCCCCC
Q 030444          156 FLRLQFSRNPGPR  168 (177)
Q Consensus       156 ~l~V~~a~~~~~r  168 (177)
                      ++.|.+.+..+.+
T Consensus       255 ~~~~~~~~~~~~~  267 (285)
T KOG4210|consen  255 PLRLEEDEPRPKS  267 (285)
T ss_pred             ccccccCCCCccc
Confidence            7999998765443

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=98.00  E-value=3.9e-05  Score=64.17  Aligned_cols=79  Identities=19%  Similarity=0.249  Sum_probs=65.6

Q ss_pred             CCCeEEEcCCC--CCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCC
Q 030444           76 ASSTLYVEGLP--ADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPD  153 (177)
Q Consensus        76 ~~~tLfV~nLp--~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~  153 (177)
                      +++.|.+.-|.  ..+|-+-|..+...+|.|..|.|..+.     |   ..|.|||++.+.|++|...|||..|...   
T Consensus       119 pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkkn-----g---VQAmVEFdsv~~AqrAk~alNGADIYsG---  187 (494)
T KOG1456|consen  119 PNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKKN-----G---VQAMVEFDSVEVAQRAKAALNGADIYSG---  187 (494)
T ss_pred             CCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEecc-----c---eeeEEeechhHHHHHHHhhccccccccc---
Confidence            36667666554  469999999999999999999887653     3   3799999999999999999999999863   


Q ss_pred             CcceEEEeecCC
Q 030444          154 SKFLRLQFSRNP  165 (177)
Q Consensus       154 ~r~l~V~~a~~~  165 (177)
                      =.+|+|+|||+.
T Consensus       188 CCTLKIeyAkP~  199 (494)
T KOG1456|consen  188 CCTLKIEYAKPT  199 (494)
T ss_pred             ceeEEEEecCcc
Confidence            258999999854

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=97.99  E-value=0.00014  Score=65.18  Aligned_cols=74  Identities=23%  Similarity=0.407  Sum_probs=61.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHhhCCCCCEE-EEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           78 STLYVEGLPADSTKREVAHIFRPFVGYK-EVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        78 ~tLfV~nLp~~~te~~L~~lF~~~G~i~-~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      +.|-+.|+|++++-+||.++|..|-.+. +|++..+.    .|+..|-|.|-|++.++|..|..-|++.+|..     |.
T Consensus       868 ~V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~nd----~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~n-----r~  938 (944)
T KOG4307|consen  868 RVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRND----DGVPTGECMVAFESQEEARRASMDLDGQKIRN-----RV  938 (944)
T ss_pred             eEEEecCCCccccHHHHHHHhcccccCCCceeEeecC----CCCcccceeEeecCHHHHHhhhhccccCcccc-----ee
Confidence            4788999999999999999999996653 45554443    57777899999999999999999999999955     45


Q ss_pred             eEEE
Q 030444          157 LRLQ  160 (177)
Q Consensus       157 l~V~  160 (177)
                      ++|.
T Consensus       939 V~l~  942 (944)
T KOG4307|consen  939 VSLR  942 (944)
T ss_pred             EEEE
Confidence            6665

>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=97.94  E-value=2.8e-05  Score=54.54  Aligned_cols=59  Identities=22%  Similarity=0.342  Sum_probs=39.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCC
Q 030444           78 STLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGY  145 (177)
Q Consensus        78 ~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~  145 (177)
                      +.|+|.+++..++-++|+++|++|+.|..|.+....         --|||-|.+.+.|+.|++.+.-.
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~---------~~g~VRf~~~~~A~~a~~~~~~~   60 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGD---------TEGYVRFKTPEAAQKALEKLKEA   60 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT----------SEEEEEESS---HHHHHHHHHHT
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCC---------CEEEEEECCcchHHHHHHHHHhc
Confidence            578999999999999999999999999988886543         17999999999999999887655

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=97.93  E-value=7e-06  Score=64.38  Aligned_cols=69  Identities=22%  Similarity=0.271  Sum_probs=59.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .+.|+|.|++.++.+++|.+.|.++|.+....+..           .++||+|...++|..|++.|++..+.++     .
T Consensus        99 ~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~~~-----------~~~~v~Fs~~~da~ra~~~l~~~~~~~~-----~  162 (216)
T KOG0106|consen   99 HFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDARR-----------NFAFVEFSEQEDAKRALEKLDGKKLNGR-----R  162 (216)
T ss_pred             cceeeeccchhhhhHHHHhhhhcccCCCchhhhhc-----------cccceeehhhhhhhhcchhccchhhcCc-----e
Confidence            57899999999999999999999999985554422           3899999999999999999999999775     6


Q ss_pred             eEEEe
Q 030444          157 LRLQF  161 (177)
Q Consensus       157 l~V~~  161 (177)
                      |++.+
T Consensus       163 l~~~~  167 (216)
T KOG0106|consen  163 ISVEK  167 (216)
T ss_pred             eeecc
Confidence            77744

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=97.89  E-value=2.9e-05  Score=67.85  Aligned_cols=77  Identities=22%  Similarity=0.339  Sum_probs=62.7

Q ss_pred             CCeEEEcCCCCC------CCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCC
Q 030444           77 SSTLYVEGLPAD------STKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDED  150 (177)
Q Consensus        77 ~~tLfV~nLp~~------~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~  150 (177)
                      .+.|+|.|+|--      .-..-|..+|+++|.|....+..+.    .|..+||.|++|.+..+|+.|++.|||+.|+-+
T Consensus        58 D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e----~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldkn  133 (698)
T KOG2314|consen   58 DSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDE----EGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKN  133 (698)
T ss_pred             ceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCc----cCCeeeEEEEEecChhhHHHHHHhcccceeccc
Confidence            467999999852      2233577899999999998887775    455999999999999999999999999999876


Q ss_pred             CCCCcceEEEe
Q 030444          151 DPDSKFLRLQF  161 (177)
Q Consensus       151 ~~~~r~l~V~~  161 (177)
                      +    ++.|..
T Consensus       134 H----tf~v~~  140 (698)
T KOG2314|consen  134 H----TFFVRL  140 (698)
T ss_pred             c----eEEeeh
Confidence            4    566653

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=97.80  E-value=3.7e-05  Score=65.22  Aligned_cols=71  Identities=24%  Similarity=0.324  Sum_probs=56.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeec---CcccCCCC-------cceEEEEEecCHHHHHHHHHHhCCC
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIK---ESKLRGGD-------PLILCFVDFENPACAATALSALQGY  145 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~---~~~~~~g~-------~kg~afV~f~~~~~A~~Ai~~l~g~  145 (177)
                      +++||.+.|||.+-.-+.|.+||+.+|.|..|+|+.-   ...-....       .+-+|+|+|+..+.|.+|.+.|+..
T Consensus       230 ~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~~e  309 (484)
T KOG1855|consen  230 PSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLNPE  309 (484)
T ss_pred             ccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhchh
Confidence            4799999999999888999999999999999999765   11111111       2458999999999999999988644


Q ss_pred             e
Q 030444          146 R  146 (177)
Q Consensus       146 ~  146 (177)
                      .
T Consensus       310 ~  310 (484)
T KOG1855|consen  310 Q  310 (484)
T ss_pred             h
Confidence            3

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=97.78  E-value=0.00015  Score=62.52  Aligned_cols=66  Identities=23%  Similarity=0.377  Sum_probs=50.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEE-EEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCee
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKE-VRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRM  147 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~-v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l  147 (177)
                      ...|=+..||+.||++||.++|+-.-.+.. |.++.+.    .+++.|=|||.|++.+.|++|+. -|...|
T Consensus       103 d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~----rgR~tGEAfVqF~sqe~ae~Al~-rhre~i  169 (510)
T KOG4211|consen  103 DGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQ----RGRPTGEAFVQFESQESAEIALG-RHRENI  169 (510)
T ss_pred             CceEEecCCCccCcHHHHHHHhcCCcccccceeeeccC----CCCcccceEEEecCHHHHHHHHH-HHHHhh
Confidence            467888999999999999999997654444 4444443    46677889999999999999984 343444

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=97.76  E-value=8e-05  Score=64.46  Aligned_cols=65  Identities=29%  Similarity=0.350  Sum_probs=49.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcce---EEEEEecCHHHHHHHHHHh
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLI---LCFVDFENPACAATALSAL  142 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg---~afV~f~~~~~A~~Ai~~l  142 (177)
                      +++||||.||++++|++|...|..||.+. |....+...+..--++|   |+|+.|+++..+..-+...
T Consensus       259 S~KVFvGGlp~dise~~i~~~F~~FGs~~-VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC  326 (520)
T KOG0129|consen  259 SRKVFVGGLPWDITEAQINASFGQFGSVK-VDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSAC  326 (520)
T ss_pred             ccceeecCCCccccHHHHHhhcccccceE-eecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHH
Confidence            68999999999999999999999999864 44443222212223567   9999999999888766544

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=97.68  E-value=0.0012  Score=50.57  Aligned_cols=63  Identities=13%  Similarity=0.122  Sum_probs=56.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCC
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDE  149 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~  149 (177)
                      ...|.|..||+.-++++|++...+-|.|....+..+          |++.|+|-..++.+-|+..|+...+.-
T Consensus       115 e~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD----------g~GvV~~~r~eDMkYAvr~ld~~~~~s  177 (241)
T KOG0105|consen  115 EYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD----------GVGVVEYLRKEDMKYAVRKLDDQKFRS  177 (241)
T ss_pred             ceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc----------cceeeeeeehhhHHHHHHhhccccccC
Confidence            467999999999999999999999999998888766          389999999999999999999888765

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=97.65  E-value=0.00011  Score=45.06  Aligned_cols=52  Identities=17%  Similarity=0.288  Sum_probs=42.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHH
Q 030444           78 STLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATAL  139 (177)
Q Consensus        78 ~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai  139 (177)
                      ++|-|.+.+++..+.-|+ .|.+||.|.++.+....         -+.||.|.+..+|++|+
T Consensus         2 ~wI~V~Gf~~~~~~~vl~-~F~~fGeI~~~~~~~~~---------~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAEEVLE-HFASFGEIVDIYVPEST---------NWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHHHHHH-HHHhcCCEEEEEcCCCC---------cEEEEEECCHHHHHhhC
Confidence            578889999887766665 78899999998875222         28999999999999985

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=97.64  E-value=7.7e-05  Score=68.24  Aligned_cols=77  Identities=18%  Similarity=0.315  Sum_probs=68.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      ++.+||+.|..++....|...|..||.|..|.+-...         -||||.|++...++.|++.|.+..|.+.   .++
T Consensus       455 ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~hgq---------~yayi~yes~~~aq~a~~~~rgap~G~P---~~r  522 (975)
T KOG0112|consen  455 TTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRHGQ---------PYAYIQYESPPAAQAATHDMRGAPLGGP---PRR  522 (975)
T ss_pred             ceeeccCCCCCCChHHHHHHHhhccCcceeeecccCC---------cceeeecccCccchhhHHHHhcCcCCCC---Ccc
Confidence            6789999999999999999999999999987764332         3999999999999999999999999884   457


Q ss_pred             eEEEeecCC
Q 030444          157 LRLQFSRNP  165 (177)
Q Consensus       157 l~V~~a~~~  165 (177)
                      |+|.|+..+
T Consensus       523 ~rvdla~~~  531 (975)
T KOG0112|consen  523 LRVDLASPP  531 (975)
T ss_pred             cccccccCC
Confidence            999999765

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=97.63  E-value=0.0026  Score=53.50  Aligned_cols=77  Identities=13%  Similarity=0.179  Sum_probs=66.9

Q ss_pred             CCCeEEEcCCCCC-CCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCC
Q 030444           76 ASSTLYVEGLPAD-STKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDS  154 (177)
Q Consensus        76 ~~~tLfV~nLp~~-~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~  154 (177)
                      +.+.+.|-.|... ++-+-|..||-.||.|.+|+++..+    .    |-|.||+.|....++|+..||+..+.+.    
T Consensus       286 ~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk----~----gtamVemgd~~aver~v~hLnn~~lfG~----  353 (494)
T KOG1456|consen  286 PGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK----P----GTAMVEMGDAYAVERAVTHLNNIPLFGG----  353 (494)
T ss_pred             CCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc----c----ceeEEEcCcHHHHHHHHHHhccCccccc----
Confidence            3788999999765 6777899999999999999998876    2    4799999999999999999999999875    


Q ss_pred             cceEEEeecCC
Q 030444          155 KFLRLQFSRNP  165 (177)
Q Consensus       155 r~l~V~~a~~~  165 (177)
                       +|.|++++..
T Consensus       354 -kl~v~~SkQ~  363 (494)
T KOG1456|consen  354 -KLNVCVSKQN  363 (494)
T ss_pred             -eEEEeecccc
Confidence             6888888754

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=97.61  E-value=8.5e-05  Score=65.34  Aligned_cols=79  Identities=19%  Similarity=0.258  Sum_probs=64.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHhhCCC-CCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCC
Q 030444           75 DASSTLYVEGLPADSTKREVAHIFRPF-VGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPD  153 (177)
Q Consensus        75 ~~~~tLfV~nLp~~~te~~L~~lF~~~-G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~  153 (177)
                      ..++.|||.||-.-+|.-+|+.|+..- |.|.+.  +.++.       |..|||.|.+.++|..-+.+|||..+...  +
T Consensus       442 ~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~--WmDkI-------KShCyV~yss~eEA~atr~AlhnV~WP~s--N  510 (718)
T KOG2416|consen  442 EPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEF--WMDKI-------KSHCYVSYSSVEEAAATREALHNVQWPPS--N  510 (718)
T ss_pred             CccceEeeecccccchHHHHHHHHhhccCchHHH--HHHHh-------hcceeEecccHHHHHHHHHHHhccccCCC--C
Confidence            347899999999999999999999954 545444  44442       33799999999999999999999999887  4


Q ss_pred             CcceEEEeecC
Q 030444          154 SKFLRLQFSRN  164 (177)
Q Consensus       154 ~r~l~V~~a~~  164 (177)
                      .+.|.+.|...
T Consensus       511 PK~L~adf~~~  521 (718)
T KOG2416|consen  511 PKHLIADFVRA  521 (718)
T ss_pred             CceeEeeecch
Confidence            47899999753

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.61  E-value=0.00022  Score=59.14  Aligned_cols=82  Identities=18%  Similarity=0.359  Sum_probs=61.4

Q ss_pred             CCeEEEcCCCCCCCHHH----H--HHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCC
Q 030444           77 SSTLYVEGLPADSTKRE----V--AHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDED  150 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~----L--~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~  150 (177)
                      .+-+||-.||+.+-.++    |  .++|.+||.|.+|.+..+.+..++-.+---.||+|...++|..||...+|..+++ 
T Consensus       114 KNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DG-  192 (480)
T COG5175         114 KNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDG-  192 (480)
T ss_pred             cceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccC-
Confidence            46799999998877766    2  4789999999998775543221211111124999999999999999999999977 


Q ss_pred             CCCCcceEEEeec
Q 030444          151 DPDSKFLRLQFSR  163 (177)
Q Consensus       151 ~~~~r~l~V~~a~  163 (177)
                          |.|+..|..
T Consensus       193 ----r~lkatYGT  201 (480)
T COG5175         193 ----RVLKATYGT  201 (480)
T ss_pred             ----ceEeeecCc
Confidence                479988864

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=97.57  E-value=0.00063  Score=45.49  Aligned_cols=56  Identities=18%  Similarity=0.343  Sum_probs=43.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCC
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQG  144 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g  144 (177)
                      ....||. .|.+.-..||.+||+.||.|. |..+.+.          -|||...+.+.|..++..+.-
T Consensus         9 dHVFhlt-FPkeWK~~DI~qlFspfG~I~-VsWi~dT----------SAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen    9 DHVFHLT-FPKEWKTSDIYQLFSPFGQIY-VSWINDT----------SAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             CCEEEEE---TT--HHHHHHHCCCCCCEE-EEEECTT----------EEEEEECCCHHHHHHHHHHTT
T ss_pred             ceEEEEe-CchHhhhhhHHHHhccCCcEE-EEEEcCC----------cEEEEeecHHHHHHHHHHhcc
Confidence            3556665 999999999999999999876 6677664          699999999999999998863

; GO: 0003723 RNA binding, 0004535 poly(A)-specific ribonuclease activity, 0046872 metal ion binding, 0006402 mRNA catabolic process, 0005634 nucleus, 0005737 cytoplasm; PDB: 3CTR_A 2ROK_A 3D45_B 1WHV_A.

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=97.48  E-value=6.7e-05  Score=63.72  Aligned_cols=79  Identities=22%  Similarity=0.246  Sum_probs=58.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcce
Q 030444           78 STLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFL  157 (177)
Q Consensus        78 ~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~l  157 (177)
                      ++||++||.+.++.++|+.+|....--.+-.++...         ||+||.+.+...|.+|++.+++..=.    .+.++
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~k~---------gyafvd~pdq~wa~kaie~~sgk~el----qGkr~   68 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLVKS---------GYAFVDCPDQQWANKAIETLSGKVEL----QGKRQ   68 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceeeec---------ceeeccCCchhhhhhhHHhhchhhhh----cCcee
Confidence            579999999999999999999754111111222222         59999999999999999999986543    23478


Q ss_pred             EEEeecCCCCCC
Q 030444          158 RLQFSRNPGPRS  169 (177)
Q Consensus       158 ~V~~a~~~~~r~  169 (177)
                      .|+++-.+..|+
T Consensus        69 e~~~sv~kkqrs   80 (584)
T KOG2193|consen   69 EVEHSVPKKQRS   80 (584)
T ss_pred             eccchhhHHHHh
Confidence            998887666555

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=97.45  E-value=0.00039  Score=60.27  Aligned_cols=67  Identities=31%  Similarity=0.320  Sum_probs=57.2

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHhhC-CCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHH
Q 030444           72 LPPDASSTLYVEGLPADSTKREVAHIFR-PFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSA  141 (177)
Q Consensus        72 ~p~~~~~tLfV~nLp~~~te~~L~~lF~-~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~  141 (177)
                      .+-++.+|||||.||.-++-++|..+|+ .||.|..+-|-+|.   +=..++|-+-|+|.+...-.+||++
T Consensus       365 q~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~---k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  365 QPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDP---KLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             cccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCc---ccCCCCCcceeeecccHHHHHHHhh
Confidence            4556689999999999999999999999 79999999887773   2345778899999999999999863

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=97.39  E-value=0.00012  Score=58.43  Aligned_cols=75  Identities=15%  Similarity=0.218  Sum_probs=59.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcc-----cCCCCcce----EEEEEecCHHHHHHHHHHhCCCee
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESK-----LRGGDPLI----LCFVDFENPACAATALSALQGYRM  147 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~-----~~~g~~kg----~afV~f~~~~~A~~Ai~~l~g~~l  147 (177)
                      .-.||+++||+.+...-|+++|++||.|-.|.|......     ...|....    =+.|+|.+...|..+...||+..|
T Consensus        74 ~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~I  153 (278)
T KOG3152|consen   74 TGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTPI  153 (278)
T ss_pred             ceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCcc
Confidence            457999999999999999999999999988877665411     01122221    257999999999999999999999


Q ss_pred             CCCC
Q 030444          148 DEDD  151 (177)
Q Consensus       148 ~~~~  151 (177)
                      .+.+
T Consensus       154 ggkk  157 (278)
T KOG3152|consen  154 GGKK  157 (278)
T ss_pred             CCCC
Confidence            8863

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=97.30  E-value=0.0003  Score=59.24  Aligned_cols=72  Identities=17%  Similarity=0.214  Sum_probs=57.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCC
Q 030444           78 STLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDED  150 (177)
Q Consensus        78 ~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~  150 (177)
                      ..|-|.||.+.+|.++++.||...|.|.+++|+.......--...-.|||.|.|...+..|- .|.++.+-+.
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQ-hLtntvfvdr   79 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQ-HLTNTVFVDR   79 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHh-hhccceeeee
Confidence            47899999999999999999999999999999875322122223458999999999999885 6777777663

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=97.18  E-value=0.0016  Score=57.05  Aligned_cols=81  Identities=15%  Similarity=0.213  Sum_probs=55.0

Q ss_pred             CCeEEEcCC--CCC-CCHHH-------HHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCe
Q 030444           77 SSTLYVEGL--PAD-STKRE-------VAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYR  146 (177)
Q Consensus        77 ~~tLfV~nL--p~~-~te~~-------L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~  146 (177)
                      ...|.+.|+  |.+ ..++|       ++.-+++||.|.+|.+..........-.-|-.||+|.+.+++++|.+.|+|.+
T Consensus       399 t~Vl~L~n~Vt~deLkdd~EyeeIlEdvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrK  478 (500)
T KOG0120|consen  399 TEVLCLTNVVTPDELKDDEEYEEILEDVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRK  478 (500)
T ss_pred             chhhhhhhcCCHHHhcchHHHHHHHHHHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCce
Confidence            566776665  222 22333       33445689999999887762111122234678999999999999999999999


Q ss_pred             eCCCCCCCcceEEEee
Q 030444          147 MDEDDPDSKFLRLQFS  162 (177)
Q Consensus       147 l~~~~~~~r~l~V~~a  162 (177)
                      +.+     |.+...|-
T Consensus       479 F~n-----RtVvtsYy  489 (500)
T KOG0120|consen  479 FAN-----RTVVASYY  489 (500)
T ss_pred             eCC-----cEEEEEec
Confidence            966     56776664

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=97.06  E-value=0.002  Score=53.55  Aligned_cols=74  Identities=16%  Similarity=0.221  Sum_probs=57.4

Q ss_pred             CCeEEEcCCC----CCCC-------HHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCC
Q 030444           77 SSTLYVEGLP----ADST-------KREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGY  145 (177)
Q Consensus        77 ~~tLfV~nLp----~~~t-------e~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~  145 (177)
                      .+||.+.||=    ++.+       +++|.+-.++||.|.+|.|....       +.|.+.|.|.+.+.|+.||+.|+|.
T Consensus       265 ~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d~h-------PdGvvtV~f~n~eeA~~ciq~m~GR  337 (382)
T KOG1548|consen  265 DRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYDRH-------PDGVVTVSFRNNEEADQCIQTMDGR  337 (382)
T ss_pred             CcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEeccC-------CCceeEEEeCChHHHHHHHHHhcCe
Confidence            6899999983    2344       33555667899999998776443       4579999999999999999999999


Q ss_pred             eeCCCCCCCcceEEEee
Q 030444          146 RMDEDDPDSKFLRLQFS  162 (177)
Q Consensus       146 ~l~~~~~~~r~l~V~~a  162 (177)
                      .+.+     |.|..+..
T Consensus       338 ~fdg-----Rql~A~i~  349 (382)
T KOG1548|consen  338 WFDG-----RQLTASIW  349 (382)
T ss_pred             eecc-----eEEEEEEe
Confidence            9976     46776653

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=97.06  E-value=0.00028  Score=64.34  Aligned_cols=77  Identities=22%  Similarity=0.237  Sum_probs=66.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      ...|||.|+|+..|.++|+.++..+|.+++++++..+    .|+++|.|||.|.++.++.+++...+...+...     -
T Consensus       736 K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r----~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~-----~  806 (881)
T KOG0128|consen  736 KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVR----AGKPKGKARVDYNTEADASRKVASVDVAGKREN-----N  806 (881)
T ss_pred             hhhhheeCCCCCCchHHHHhhccccCCccccchhhhh----ccccccceeccCCCcchhhhhcccchhhhhhhc-----C
Confidence            4679999999999999999999999999999988775    789999999999999999999887777777554     3


Q ss_pred             eEEEee
Q 030444          157 LRLQFS  162 (177)
Q Consensus       157 l~V~~a  162 (177)
                      +.|+.+
T Consensus       807 ~~v~vs  812 (881)
T KOG0128|consen  807 GEVQVS  812 (881)
T ss_pred             cccccc
Confidence            555553

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=97.03  E-value=0.0017  Score=58.35  Aligned_cols=83  Identities=22%  Similarity=0.267  Sum_probs=61.6

Q ss_pred             CCCCCCCCCeEEEcCCCCCCCHHHHHHhhCCCCCEEE-EEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeC
Q 030444           70 LPLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKE-VRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMD  148 (177)
Q Consensus        70 ~~~p~~~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~-v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~  148 (177)
                      .+.|......|||-.||..+++.++.++|..--.|++ |.|...    .+++.++.|||+|.+++.+..|...-+.+-+.
T Consensus       427 vp~P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~----P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G  502 (944)
T KOG4307|consen  427 VPFPGGAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRL----PTDLLRPAAFVAFIHPTAPLTASSVKTKFYPG  502 (944)
T ss_pred             CCCCCCccceEEeccCCccccccchhhhhhhhhhhhheeEeccC----CcccccchhhheeccccccchhhhcccccccC
Confidence            3455555889999999999999999999998777776 555443    35666779999999988888887544433332


Q ss_pred             CCCCCCcceEEEe
Q 030444          149 EDDPDSKFLRLQF  161 (177)
Q Consensus       149 ~~~~~~r~l~V~~  161 (177)
                           .|.|+|.-
T Consensus       503 -----~r~irv~s  510 (944)
T KOG4307|consen  503 -----HRIIRVDS  510 (944)
T ss_pred             -----ceEEEeec
Confidence                 25788863

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons

Probab=96.96  E-value=0.0021  Score=49.21  Aligned_cols=87  Identities=11%  Similarity=0.166  Sum_probs=54.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCC-CCCE---EEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCC
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRP-FVGY---KEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDP  152 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~-~G~i---~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~  152 (177)
                      ..+|.|.+||+.+||+++.+.++. ++..   ..+.-.......... .-.-|||.|.+.+++..=...++|+.+.+...
T Consensus         7 ~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~-~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~kg   85 (176)
T PF03467_consen    7 GTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPP-TYSRAYINFKNPEDLLEFRDRFDGHVFVDSKG   85 (176)
T ss_dssp             --EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS---EEEEEEESSCHHHHHHHHHCTTEEEE-TTS
T ss_pred             CceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCC-cceEEEEEeCCHHHHHHHHHhcCCcEEECCCC
Confidence            578999999999999999998877 5655   233311221110111 12359999999999999999999999987642


Q ss_pred             CCcceEEEeecC
Q 030444          153 DSKFLRLQFSRN  164 (177)
Q Consensus       153 ~~r~l~V~~a~~  164 (177)
                      ...+-.|+||-.
T Consensus        86 ~~~~~~VE~Apy   97 (176)
T PF03467_consen   86 NEYPAVVEFAPY   97 (176)
T ss_dssp             -EEEEEEEE-SS
T ss_pred             CCcceeEEEcch
Confidence            224678888865

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.

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=96.91  E-value=0.0074  Score=51.02  Aligned_cols=60  Identities=32%  Similarity=0.378  Sum_probs=46.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHhhCCC----CCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHH
Q 030444           78 STLYVEGLPADSTKREVAHIFRPF----VGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSA  141 (177)
Q Consensus        78 ~tLfV~nLp~~~te~~L~~lF~~~----G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~  141 (177)
                      -.|-+.+||+++|+.|+.++|.+-    +....|-+++..    .|+..|-|||.|..+++|+.|+..
T Consensus       162 vivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rp----dgrpTGdAFvlfa~ee~aq~aL~k  225 (508)
T KOG1365|consen  162 VIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRP----DGRPTGDAFVLFACEEDAQFALRK  225 (508)
T ss_pred             eEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECC----CCCcccceEEEecCHHHHHHHHHH
Confidence            345568999999999999999632    345566666653    567778999999999999999853

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=96.85  E-value=0.0044  Score=39.23  Aligned_cols=54  Identities=22%  Similarity=0.390  Sum_probs=44.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHhhCCC---CCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHh
Q 030444           78 STLYVEGLPADSTKREVAHIFRPF---VGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSAL  142 (177)
Q Consensus        78 ~tLfV~nLp~~~te~~L~~lF~~~---G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l  142 (177)
                      .+|+|.++ .+++.++|+.+|..|   .....|+++.+.          -|-|.|.+.+.|.+|+.+|
T Consensus         6 eavhirGv-d~lsT~dI~~y~~~y~~~~~~~~IEWIdDt----------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    6 EAVHIRGV-DELSTDDIKAYFSEYFDEEGPFRIEWIDDT----------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             ceEEEEcC-CCCCHHHHHHHHHHhcccCCCceEEEecCC----------cEEEEECCHHHHHHHHHcC
Confidence            68999998 458889999999988   234568888886          5899999999999999764

>PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT []

Probab=96.61  E-value=0.011  Score=41.03  Aligned_cols=78  Identities=21%  Similarity=0.279  Sum_probs=48.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCc------ccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCC
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKES------KLRGGDPLILCFVDFENPACAATALSALQGYRMDED  150 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~------~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~  150 (177)
                      .+.|.|-+.|+..+ +.+-+.|++||.|.+..-.....      ....+  ..+-.|.|+++.+|.+|| .-||..|.+.
T Consensus         6 ~~wVtVFGfp~~~~-~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~--~NWi~I~Y~~~~~A~rAL-~~NG~i~~g~   81 (100)
T PF05172_consen    6 ETWVTVFGFPPSAS-NQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSG--GNWIHITYDNPLSAQRAL-QKNGTIFSGS   81 (100)
T ss_dssp             CCEEEEE---GGGH-HHHHHHHHCCS-EECEEGGG----------E-CC--TTEEEEEESSHHHHHHHH-TTTTEEETTC
T ss_pred             CeEEEEEccCHHHH-HHHHHHHHhcceEEEeecccccccccccccCCCC--CCEEEEECCCHHHHHHHH-HhCCeEEcCc
Confidence            56788889998855 45667899999998764110000      00011  139999999999999999 6799999764


Q ss_pred             CCCCcceEEEee
Q 030444          151 DPDSKFLRLQFS  162 (177)
Q Consensus       151 ~~~~r~l~V~~a  162 (177)
                          --+-|.+.
T Consensus        82 ----~mvGV~~~   89 (100)
T PF05172_consen   82 ----LMVGVKPC   89 (100)
T ss_dssp             ----EEEEEEE-
T ss_pred             ----EEEEEEEc
Confidence                13445555

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.

>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []

Probab=96.56  E-value=0.081  Score=37.38  Aligned_cols=78  Identities=12%  Similarity=0.206  Sum_probs=54.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHhhCCC-CCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           78 STLYVEGLPADSTKREVAHIFRPF-VGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        78 ~tLfV~nLp~~~te~~L~~lF~~~-G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      ..+.+...|..++-++|..+.+.+ ..|..++|+++.     ..++-.+++.|.+.+.|..-.+.+||..+..-++  ..
T Consensus        14 ~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~-----~pnrymVLikF~~~~~Ad~Fy~~fNGk~FnslEp--E~   86 (110)
T PF07576_consen   14 TLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDG-----TPNRYMVLIKFRDQESADEFYEEFNGKPFNSLEP--ET   86 (110)
T ss_pred             eEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCC-----CCceEEEEEEECCHHHHHHHHHHhCCCccCCCCC--ce
Confidence            344444555556666777666665 456778888764     2355689999999999999999999999976543  23


Q ss_pred             eEEEee
Q 030444          157 LRLQFS  162 (177)
Q Consensus       157 l~V~~a  162 (177)
                      .+|-|.
T Consensus        87 ChvvfV   92 (110)
T PF07576_consen   87 CHVVFV   92 (110)
T ss_pred             eEEEEE
Confidence            444443

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=96.52  E-value=0.00019  Score=65.43  Aligned_cols=68  Identities=18%  Similarity=0.263  Sum_probs=57.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCee
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRM  147 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l  147 (177)
                      ..++||.||+..+.+++|...|..++.+..+++....   ..++.+|+|||+|.+.+++.+|+...+...+
T Consensus       667 ~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~---n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~  734 (881)
T KOG0128|consen  667 LIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHK---NEKRFRGKAYVEFLKPEHAGAAVAFRDSCFF  734 (881)
T ss_pred             HHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHh---hccccccceeeEeecCCchhhhhhhhhhhhh
Confidence            3579999999999999999999999988877766322   4577889999999999999999976665554

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=96.52  E-value=0.005  Score=55.05  Aligned_cols=62  Identities=13%  Similarity=0.086  Sum_probs=55.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCC
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDED  150 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~  150 (177)
                      ..++||+|+...+.++-++.++..||-|.+++.+  +          |+|++|.+......|+..++-..++++
T Consensus        40 ~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~--~----------fgf~~f~~~~~~~ra~r~~t~~~~~~~  101 (668)
T KOG2253|consen   40 RDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRD--K----------FGFCEFLKHIGDLRASRLLTELNIDDQ  101 (668)
T ss_pred             CceeEecchhhhhhHHHHHHHHhhCCcchhhhhh--h----------hcccchhhHHHHHHHHHHhcccCCCcc
Confidence            6899999999999999999999999988776542  2          899999999999999999998888776

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=96.43  E-value=0.0084  Score=50.70  Aligned_cols=67  Identities=21%  Similarity=0.338  Sum_probs=55.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCC-EEE--EEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCee
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVG-YKE--VRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRM  147 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~-i~~--v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l  147 (177)
                      ..+|-+.+||++.+.++|-++|..|.. |..  |.++.+.    .|++.|-|||+|.+.+.|..|....+.+..
T Consensus       280 kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~----qGrPSGeAFIqm~nae~a~aaaqk~hk~~m  349 (508)
T KOG1365|consen  280 KDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNG----QGRPSGEAFIQMRNAERARAAAQKCHKKLM  349 (508)
T ss_pred             CCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcC----CCCcChhhhhhhhhhHHHHHHHHHHHHhhc
Confidence            567888999999999999999998854 222  6666664    577888999999999999999988877665

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=96.42  E-value=0.0013  Score=52.47  Aligned_cols=61  Identities=16%  Similarity=0.188  Sum_probs=47.7

Q ss_pred             HHHhhC-CCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcceEEEeec
Q 030444           94 VAHIFR-PFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFLRLQFSR  163 (177)
Q Consensus        94 L~~lF~-~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~l~V~~a~  163 (177)
                      +...|+ +||.|+++.+..+.    .-...|-+||.|...++|++|++.||+-.+.+     ++|..++..
T Consensus        85 ~f~E~~~kygEiee~~Vc~Nl----~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G-----~pi~ae~~p  146 (260)
T KOG2202|consen   85 VFTELEDKYGEIEELNVCDNL----GDHLVGNVYVKFRSEEDAEAALEDLNNRWYNG-----RPIHAELSP  146 (260)
T ss_pred             HHHHHHHHhhhhhhhhhhccc----chhhhhhhhhhcccHHHHHHHHHHHcCccccC-----CcceeeecC
Confidence            333344 89999988776654    23355789999999999999999999999965     589988864

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=96.24  E-value=0.023  Score=42.01  Aligned_cols=53  Identities=25%  Similarity=0.412  Sum_probs=43.0

Q ss_pred             HHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcceEEEee
Q 030444           93 EVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFLRLQFS  162 (177)
Q Consensus        93 ~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~l~V~~a  162 (177)
                      +|-+.|.+||.+.-+|++.+           .-+|+|.+.+.|.+|+ .++|.++.+     +.|+|..-
T Consensus        52 ~ll~~~~~~GevvLvRfv~~-----------~mwVTF~dg~sALaal-s~dg~~v~g-----~~l~i~LK  104 (146)
T PF08952_consen   52 ELLQKFAQYGEVVLVRFVGD-----------TMWVTFRDGQSALAAL-SLDGIQVNG-----RTLKIRLK  104 (146)
T ss_dssp             HHHHHHHCCS-ECEEEEETT-----------CEEEEESSCHHHHHHH-HGCCSEETT-----EEEEEEE-
T ss_pred             HHHHHHHhCCceEEEEEeCC-----------eEEEEECccHHHHHHH-ccCCcEECC-----EEEEEEeC
Confidence            67778889999998888765           3789999999999998 799999966     47888754

; PDB: 1UFW_A 2DNR_A.

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=96.22  E-value=0.005  Score=49.30  Aligned_cols=63  Identities=21%  Similarity=0.288  Sum_probs=54.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhC
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQ  143 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~  143 (177)
                      ...|||.||+.-++.+.|.+-|+.||.|....++.|.    .++..+=.+|+|.....|.+|+..+.
T Consensus        31 ~a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~----r~k~t~eg~v~~~~k~~a~~a~rr~~   93 (275)
T KOG0115|consen   31 HAELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDD----RGKPTREGIVEFAKKPNARKAARRCR   93 (275)
T ss_pred             cceEEEEecchhhhhHHHHHhhhhcCccchheeeecc----cccccccchhhhhcchhHHHHHHHhc
Confidence            3689999999999999999999999999877666664    35555678999999999999998884

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=96.11  E-value=0.001  Score=61.07  Aligned_cols=70  Identities=21%  Similarity=0.219  Sum_probs=58.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCC
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDE  149 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~  149 (177)
                      .+.|||++||+..+++.+|+..|..+|.|.+|.|-..+.+  +  -.-|+||.|.+...+-.|+..+.+..|..
T Consensus       371 atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~~--~--esa~~f~~~~n~dmtp~ak~e~s~~~I~~  440 (975)
T KOG0112|consen  371 ATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHIK--T--ESAYAFVSLLNTDMTPSAKFEESGPLIGN  440 (975)
T ss_pred             hhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCCC--c--ccchhhhhhhccccCcccchhhcCCcccc
Confidence            4789999999999999999999999999999988655321  1  12399999999999999998888877754

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=95.41  E-value=0.053  Score=47.97  Aligned_cols=63  Identities=16%  Similarity=0.244  Sum_probs=52.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhC--CCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHh-------CCCee
Q 030444           77 SSTLYVEGLPADSTKREVAHIFR--PFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSAL-------QGYRM  147 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~--~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l-------~g~~l  147 (177)
                      .|.|.+.-||..+-+|+++.||.  .|-.+.+|.+-.+.          -=||+|++..+|++|.+.|       +|+.|
T Consensus       175 RcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~----------nWyITfesd~DAQqAykylreevk~fqgKpI  244 (684)
T KOG2591|consen  175 RCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND----------NWYITFESDTDAQQAYKYLREEVKTFQGKPI  244 (684)
T ss_pred             eeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC----------ceEEEeecchhHHHHHHHHHHHHHhhcCcch
Confidence            46678899999999999999996  57889999987765          3599999999999998655       56666


Q ss_pred             CC
Q 030444          148 DE  149 (177)
Q Consensus       148 ~~  149 (177)
                      ..
T Consensus       245 mA  246 (684)
T KOG2591|consen  245 MA  246 (684)
T ss_pred             hh
Confidence            55

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=95.19  E-value=0.013  Score=54.00  Aligned_cols=74  Identities=19%  Similarity=0.223  Sum_probs=60.9

Q ss_pred             eEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcceE
Q 030444           79 TLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFLR  158 (177)
Q Consensus        79 tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~l~  158 (177)
                      +.++.|.+-..+...|..||++||.+.+...+++-         -.|.|+|...+.|..|+++|+|.++..   .+-+-+
T Consensus       300 ~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~---------N~alvs~~s~~sai~a~dAl~gkevs~---~g~Ps~  367 (1007)
T KOG4574|consen  300 KQSLENNAVNLTSSSLATLCSDYGSVASAWTLRDL---------NMALVSFSSVESAILALDALQGKEVSV---TGAPSR  367 (1007)
T ss_pred             hhhhhcccccchHHHHHHHHHhhcchhhheecccc---------cchhhhhHHHHHHHHhhhhhcCCcccc---cCCcee
Confidence            34455555577888999999999999998776654         179999999999999999999999876   345799


Q ss_pred             EEeecC
Q 030444          159 LQFSRN  164 (177)
Q Consensus       159 V~~a~~  164 (177)
                      |.||+.
T Consensus       368 V~~ak~  373 (1007)
T KOG4574|consen  368 VSFAKT  373 (1007)
T ss_pred             EEeccc
Confidence            999975

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=95.10  E-value=0.12  Score=38.14  Aligned_cols=70  Identities=20%  Similarity=0.233  Sum_probs=51.7

Q ss_pred             CCeEEEcCCCCCCCH-HHH---HHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCC
Q 030444           77 SSTLYVEGLPADSTK-REV---AHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDP  152 (177)
Q Consensus        77 ~~tLfV~nLp~~~te-~~L---~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~  152 (177)
                      -.||.|.-|..++.. +||   ...++.||+|.+|.+.-..          -|.|.|.|..+|=.|+.+++.....    
T Consensus        86 MsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cGrq----------savVvF~d~~SAC~Av~Af~s~~pg----  151 (166)
T PF15023_consen   86 MSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCGRQ----------SAVVVFKDITSACKAVSAFQSRAPG----  151 (166)
T ss_pred             ceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecCCc----------eEEEEehhhHHHHHHHHhhcCCCCC----
Confidence            688999888776542 334   4456789999999875443          6999999999999999999874332    


Q ss_pred             CCcceEEEee
Q 030444          153 DSKFLRLQFS  162 (177)
Q Consensus       153 ~~r~l~V~~a  162 (177)
                        ..+...|-
T Consensus       152 --tm~qCsWq  159 (166)
T PF15023_consen  152 --TMFQCSWQ  159 (166)
T ss_pred             --ceEEeecc
Confidence              24776664

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=95.00  E-value=0.082  Score=43.40  Aligned_cols=65  Identities=18%  Similarity=0.208  Sum_probs=49.0

Q ss_pred             HHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcceEEEee
Q 030444           91 KREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFLRLQFS  162 (177)
Q Consensus        91 e~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~l~V~~a  162 (177)
                      ++++++..++||.|..|.|....+.-..  -..--||+|...++|.+|+--|||.-|.+     |.++.+|-
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~d--eavRiFveF~r~e~aiKA~VdlnGRyFGG-----r~v~A~Fy  364 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPED--EAVRIFVEFERVESAIKAVVDLNGRYFGG-----RVVSACFY  364 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccc--hhheeeeeeccHHHHHHHHHhcCCceecc-----eeeeheec
Confidence            4467788899999998877666422111  11247999999999999999999999966     56777764

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=94.57  E-value=0.02  Score=47.52  Aligned_cols=82  Identities=17%  Similarity=0.321  Sum_probs=58.8

Q ss_pred             CCeEEEcCCCCCCCHHH-HH--HhhCCCCCEEEEEEeecCc-ccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCC
Q 030444           77 SSTLYVEGLPADSTKRE-VA--HIFRPFVGYKEVRLVIKES-KLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDP  152 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~-L~--~lF~~~G~i~~v~l~~~~~-~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~  152 (177)
                      .+-+||-.|+..+.+++ |+  +.|.+||.|.+|.+..+.+ ....+-. .-++|+|...++|..||...+|..++++  
T Consensus        77 knlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~-~s~yITy~~~eda~rci~~v~g~~~dg~--  153 (327)
T KOG2068|consen   77 KNLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGT-CSVYITYEEEEDADRCIDDVDGFVDDGR--  153 (327)
T ss_pred             hhhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCC-CcccccccchHhhhhHHHHhhhHHhhhh--
Confidence            46688989988765554 33  5788999999987766542 1111111 2389999999999999999999999774  


Q ss_pred             CCcceEEEeecC
Q 030444          153 DSKFLRLQFSRN  164 (177)
Q Consensus       153 ~~r~l~V~~a~~  164 (177)
                         .|+..|..+
T Consensus       154 ---~lka~~gtt  162 (327)
T KOG2068|consen  154 ---ALKASLGTT  162 (327)
T ss_pred             ---hhHHhhCCC
Confidence               566666544

>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=94.16  E-value=0.088  Score=40.56  Aligned_cols=62  Identities=21%  Similarity=0.234  Sum_probs=43.9

Q ss_pred             CHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhC--CCeeCCCCCCCcceEEEeecCC
Q 030444           90 TKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQ--GYRMDEDDPDSKFLRLQFSRNP  165 (177)
Q Consensus        90 te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~--g~~l~~~~~~~r~l~V~~a~~~  165 (177)
                      ..+.|+++|..|+.+..+..+..-         +=..|.|.+.+.|..|...|+  ++.+.+.     .|+|.|+...
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~sF---------rRi~v~f~~~~~A~~~r~~l~~~~~~~~g~-----~l~~yf~~~~   71 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKSF---------RRIRVVFESPESAQRARQLLHWDGTSFNGK-----RLRVYFGQPT   71 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETTT---------TEEEEE-SSTTHHHHHHHTST--TSEETTE-----E-EEE----S
T ss_pred             hHHHHHHHHHhcCCceEEEEcCCC---------CEEEEEeCCHHHHHHHHHHhcccccccCCC-----ceEEEEcccc
Confidence            457899999999988877666543         137899999999999999999  8999775     6999998543

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.

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=92.90  E-value=0.17  Score=44.76  Aligned_cols=87  Identities=15%  Similarity=0.278  Sum_probs=58.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCC----------------------------CCCEEEEEEeecCcccCCCCcceEEEEE
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRP----------------------------FVGYKEVRLVIKESKLRGGDPLILCFVD  128 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~----------------------------~G~i~~v~l~~~~~~~~~g~~kg~afV~  128 (177)
                      ..++-|.|||..-+..+|.++...                            .+...-+.+..|-   ..-...|||||.
T Consensus       361 Rtt~~i~ni~n~~~~~dl~~Ildge~~rtt~~iknipNK~T~~ml~~~d~~~~gtYDFlYLPiDF---~nkcNvGYAFIN  437 (549)
T KOG4660|consen  361 RTTVMIKNIPNKYGQLDLLRILDGECPRTTLMIKNIPNKYTSKMLLAADEKNKGTYDFLYLPIDF---KNKCNVGYAFIN  437 (549)
T ss_pred             hhhhhhhccccchhHHHHHHHHhCcCchhhhHhhccCchhhHHhhhhhhccccCccceEEecccc---ccccccceeEEe
Confidence            456778888877777777766642                            1222223333332   223356899999


Q ss_pred             ecCHHHHHHHHHHhCCCeeCCCCCCCcceEEEeecCCCC
Q 030444          129 FENPACAATALSALQGYRMDEDDPDSKFLRLQFSRNPGP  167 (177)
Q Consensus       129 f~~~~~A~~Ai~~l~g~~l~~~~~~~r~l~V~~a~~~~~  167 (177)
                      |-+.+.+....+++||+.+..=+ ..+...+.||+..+.
T Consensus       438 m~sp~ai~~F~kAFnGk~W~~Fn-S~Kia~itYArIQGk  475 (549)
T KOG4660|consen  438 MTSPEAIIRFYKAFNGKKWEKFN-SEKIASITYARIQGK  475 (549)
T ss_pred             ecCHHHHHHHHHHHcCCchhhhc-ceeeeeeehhhhhch
Confidence            99999999999999998775432 234688888876543

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=92.48  E-value=0.95  Score=39.31  Aligned_cols=71  Identities=20%  Similarity=0.331  Sum_probs=59.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCC-CCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCC
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPF-VGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDP  152 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~-G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~  152 (177)
                      +..|+|--+|..+|-.||-.+...+ -.|.+++|+++.     -..+-..+|.|.+..+|..=.+.+||..|..-++
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~-----~pnrymvLIkFr~q~da~~Fy~efNGk~Fn~le~  145 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDG-----MPNRYMVLIKFRDQADADTFYEEFNGKQFNSLEP  145 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecC-----CCceEEEEEEeccchhHHHHHHHcCCCcCCCCCc
Confidence            7889999999999999999888755 567889999864     2234578999999999999999999999976543

>KOG2318 consensus Uncharacterized conserved protein [Function unknown]

Probab=91.86  E-value=0.66  Score=41.44  Aligned_cols=85  Identities=16%  Similarity=0.226  Sum_probs=62.6

Q ss_pred             CCCCeEEEcCCCCC-CCHHHHHHhhCCC----CCEEEEEEeecCcc-------cCCCC----------------------
Q 030444           75 DASSTLYVEGLPAD-STKREVAHIFRPF----VGYKEVRLVIKESK-------LRGGD----------------------  120 (177)
Q Consensus        75 ~~~~tLfV~nLp~~-~te~~L~~lF~~~----G~i~~v~l~~~~~~-------~~~g~----------------------  120 (177)
                      ..++.|-|.||.|+ +.-++|..+|+.|    |.|.+|.|....-.       ...|.                      
T Consensus       172 ~~T~RLAVvNMDWd~v~AkDL~v~~nSFlP~gGsilSV~IYpSeFGkeRM~eEeV~GP~~el~~~~e~~~~s~sD~ee~~  251 (650)
T KOG2318|consen  172 EETKRLAVVNMDWDRVKAKDLFVLFNSFLPKGGSILSVKIYPSEFGKERMKEEEVHGPPKELFKPVEEYKESESDDEEEE  251 (650)
T ss_pred             cccceeeEeccccccccHHHHHHHHHhhcCCCCceeEEEechhhhhHHHhhhhcccCChhhhccccccCcccccchhhhh
Confidence            34788999999997 8888999999877    58888887664300       00011                      


Q ss_pred             --------------cc-eEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcceEEEee
Q 030444          121 --------------PL-ILCFVDFENPACAATALSALQGYRMDEDDPDSKFLRLQFS  162 (177)
Q Consensus       121 --------------~k-g~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~l~V~~a  162 (177)
                                    .+ -||.|+|.+...|....+.++|..+.-.   +-.|-+.|-
T Consensus       252 ~~~~~kLR~Yq~~rLkYYyAVvecDsi~tA~~vYe~CDG~EfEsS---~~~~DLRFI  305 (650)
T KOG2318|consen  252 DVDREKLRQYQLNRLKYYYAVVECDSIETAKAVYEECDGIEFESS---ANKLDLRFI  305 (650)
T ss_pred             hHHHHHHHHHHhhhheeEEEEEEecCchHHHHHHHhcCcceeccc---cceeeeeec
Confidence                          11 3799999999999999999999999763   234555553

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=90.85  E-value=0.14  Score=42.18  Aligned_cols=70  Identities=19%  Similarity=0.023  Sum_probs=57.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCC
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDE  149 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~  149 (177)
                      .+++|++++.+.+.++++..++..+|....+.+....   ....+++++++.|...+.+..|+.....+.+..
T Consensus        88 ~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~---~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~  157 (285)
T KOG4210|consen   88 SSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLE---DSLSSKGGLSVHFAGKSQFFAALEESGSKVLDG  157 (285)
T ss_pred             cccccccccccchhhccccccchhhcCcccchhhhhc---cccccccceeeccccHHHHHHHHHhhhcccccc
Confidence            6789999999999999999999999987777665543   346688999999999999999997665555544

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=90.73  E-value=1.9  Score=35.74  Aligned_cols=62  Identities=19%  Similarity=0.227  Sum_probs=45.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCC
Q 030444           78 STLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDED  150 (177)
Q Consensus        78 ~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~  150 (177)
                      ..|-|-..|+.-.. -|-.+|++||.|.+...- .     +|   -|-+|.|.+..+|++|| ..||..|++.
T Consensus       198 ~WVTVfGFppg~~s-~vL~~F~~cG~Vvkhv~~-~-----ng---NwMhirYssr~~A~KAL-skng~ii~g~  259 (350)
T KOG4285|consen  198 TWVTVFGFPPGQVS-IVLNLFSRCGEVVKHVTP-S-----NG---NWMHIRYSSRTHAQKAL-SKNGTIIDGD  259 (350)
T ss_pred             ceEEEeccCccchh-HHHHHHHhhCeeeeeecC-C-----CC---ceEEEEecchhHHHHhh-hhcCeeeccc
Confidence            45666677765444 455689999999876443 1     12   29999999999999999 5788888774

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=90.54  E-value=0.15  Score=44.40  Aligned_cols=73  Identities=22%  Similarity=0.322  Sum_probs=56.3

Q ss_pred             CCeEEEcCCCCCC-CHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           77 SSTLYVEGLPADS-TKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        77 ~~tLfV~nLp~~~-te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      .+.|-+.-.|+.. |-++|...|.+||.|..|.+-...         --|.|+|.+..+|-.|. ..++..|+.     |
T Consensus       372 hs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~~---------~~a~vTF~t~aeag~a~-~s~~avlnn-----r  436 (526)
T KOG2135|consen  372 HSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYSS---------LHAVVTFKTRAEAGEAY-ASHGAVLNN-----R  436 (526)
T ss_pred             cchhhhhccCCCCchHhhhhhhhhhcCccccccccCch---------hhheeeeeccccccchh-ccccceecC-----c
Confidence            4566666666664 456899999999999999875541         15899999999997775 678888855     6


Q ss_pred             ceEEEeecC
Q 030444          156 FLRLQFSRN  164 (177)
Q Consensus       156 ~l~V~~a~~  164 (177)
                      .|+|-|-+.
T Consensus       437 ~iKl~whnp  445 (526)
T KOG2135|consen  437 FIKLFWHNP  445 (526)
T ss_pred             eeEEEEecC
Confidence            899999754

>PF03880 DbpA: DbpA RNA binding domain ; InterPro: IPR005580 This RNA binding domain is found at the C terminus of a number of DEAD helicase proteins []

Probab=90.43  E-value=1.3  Score=28.68  Aligned_cols=59  Identities=20%  Similarity=0.322  Sum_probs=35.4

Q ss_pred             CCCCHHHHHHhhCCCCCE-----EEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcceEEEe
Q 030444           87 ADSTKREVAHIFRPFVGY-----KEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFLRLQF  161 (177)
Q Consensus        87 ~~~te~~L~~lF~~~G~i-----~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~l~V~~  161 (177)
                      ..++..+|..++.....|     -.|+|..+           |+||+-.. +.|+.+++.|++..+.+     ++++|+.
T Consensus        11 dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~~-----------~S~vev~~-~~a~~v~~~l~~~~~~g-----k~v~ve~   73 (74)
T PF03880_consen   11 DGLTPRDIVGAICNEAGIPGRDIGRIDIFDN-----------FSFVEVPE-EVAEKVLEALNGKKIKG-----KKVRVER   73 (74)
T ss_dssp             GT--HHHHHHHHHTCTTB-GGGEEEEEE-SS------------EEEEE-T-T-HHHHHHHHTT--SSS---------EEE
T ss_pred             cCCCHHHHHHHHHhccCCCHHhEEEEEEeee-----------EEEEEECH-HHHHHHHHHhcCCCCCC-----eeEEEEE
Confidence            458888999888876554     45666543           89999875 58899999999999976     4788876


Q ss_pred             e
Q 030444          162 S  162 (177)
Q Consensus       162 a  162 (177)
                      |
T Consensus        74 A   74 (74)
T PF03880_consen   74 A   74 (74)
T ss_dssp             -
T ss_pred             C
Confidence            4

; PDB: 2G0C_A 3MOJ_B.

>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=88.70  E-value=2.2  Score=27.22  Aligned_cols=50  Identities=14%  Similarity=0.179  Sum_probs=39.4

Q ss_pred             CCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCC
Q 030444           88 DSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDE  149 (177)
Q Consensus        88 ~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~  149 (177)
                      .++-++|+..+..|.- ..  |..++    +|     =||.|.+..+|++|....++..+..
T Consensus        11 ~~~v~d~K~~Lr~y~~-~~--I~~d~----tG-----fYIvF~~~~Ea~rC~~~~~~~~~f~   60 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYRW-DR--IRDDR----TG-----FYIVFNDSKEAERCFRAEDGTLFFT   60 (66)
T ss_pred             CccHHHHHHHHhcCCc-ce--EEecC----CE-----EEEEECChHHHHHHHHhcCCCEEEE
Confidence            4778899999999863 33  44454    32     4899999999999999999988854

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=86.28  E-value=0.027  Score=48.27  Aligned_cols=76  Identities=12%  Similarity=0.250  Sum_probs=61.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      .++++-|.|+|+...++-|..|+.+||.+..|..+...+..      -.--|+|...+.+..||..|++..+...     
T Consensus        79 rsrk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~et------avvnvty~~~~~~~~ai~kl~g~Q~en~-----  147 (584)
T KOG2193|consen   79 RSRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDSET------AVVNVTYSAQQQHRQAIHKLNGPQLENQ-----  147 (584)
T ss_pred             HhhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccchHH------HHHHHHHHHHHHHHHHHHhhcchHhhhh-----
Confidence            36789999999999999999999999999988765433111      1345789999999999999999999765     


Q ss_pred             ceEEEee
Q 030444          156 FLRLQFS  162 (177)
Q Consensus       156 ~l~V~~a  162 (177)
                      .++|.|-
T Consensus       148 ~~k~~Yi  154 (584)
T KOG2193|consen  148 HLKVGYI  154 (584)
T ss_pred             hhhcccC
Confidence            5888773

>KOG4410 consensus 5-formyltetrahydrofolate cyclo-ligase [Coenzyme transport and metabolism]

Probab=83.29  E-value=5  Score=33.14  Aligned_cols=49  Identities=16%  Similarity=0.254  Sum_probs=35.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHH
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPA  133 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~  133 (177)
                      ..-||++||+.++.-.||+..+.+-+.+- .+|-+.-       +.+-||++|.+..
T Consensus       330 ~~di~~~nl~rd~rv~dlk~~lr~~~~~p-m~iswkg-------~~~k~flh~~~~~  378 (396)
T KOG4410|consen  330 KTDIKLTNLSRDIRVKDLKSELRKRECTP-MSISWKG-------HFGKCFLHFGNRK  378 (396)
T ss_pred             ccceeeccCccccchHHHHHHHHhcCCCc-eeEeeec-------CCcceeEecCCcc
Confidence            34599999999999999999998766442 3343332       2356999998854

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=82.11  E-value=0.58  Score=37.08  Aligned_cols=69  Identities=20%  Similarity=0.244  Sum_probs=58.8

Q ss_pred             CCeEEEcC----CCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCC
Q 030444           77 SSTLYVEG----LPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDE  149 (177)
Q Consensus        77 ~~tLfV~n----Lp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~  149 (177)
                      ..+++.|+    |...++++.+.+.|+.-+.+..+++-.+.    .++++-+.|+++......-.++..+++..+.-
T Consensus        80 q~~~r~G~shapld~r~~~ei~~~v~s~a~p~~~~R~~~~~----d~rnrn~~~~~~qr~~~~P~~~~~y~~l~~~~  152 (267)
T KOG4454|consen   80 QRTLRCGNSHAPLDERVTEEILYEVFSQAGPIEGVRIPTDN----DGRNRNFGFVTYQRLCAVPFALDLYQGLELFQ  152 (267)
T ss_pred             hcccccCCCcchhhhhcchhhheeeecccCCCCCccccccc----cCCccCccchhhhhhhcCcHHhhhhcccCcCC
Confidence            46788888    88889999999999999999999987765    46677799999999999999998888877754

>KOG4483 consensus Uncharacterized conserved protein [Function unknown]

Probab=80.41  E-value=4.2  Score=35.01  Aligned_cols=55  Identities=16%  Similarity=0.255  Sum_probs=44.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCE-EEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHH
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGY-KEVRLVIKESKLRGGDPLILCFVDFENPACAATALSA  141 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i-~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~  141 (177)
                      ...|-|-++|...-.+||-.+|+.|+.- -+|+++.+.          .+|-.|.+...|..|+..
T Consensus       391 pHVlEIydfp~efkteDll~~f~~yq~kgfdIkWvDdt----------halaVFss~~~AaeaLt~  446 (528)
T KOG4483|consen  391 PHVLEIYDFPDEFKTEDLLKAFETYQNKGFDIKWVDDT----------HALAVFSSVNRAAEALTL  446 (528)
T ss_pred             cceeEeccCchhhccHHHHHHHHHhhcCCceeEEeecc----------eeEEeecchHHHHHHhhc
Confidence            3678899999999899999999998542 345566554          799999999999999854

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	177
2do4_A	100	Solution Structure Of The Rna Binding Domain Of Squ		2e-05
2u1a_A	88	Rna Binding Domain 2 Of Human U1a Protein, Nmr, 20		2e-05
3pgw_A	282	Crystal Structure Of Human U1 Snrnp Length = 282		2e-05

>pdb|2DO4|A Chain A, Solution Structure Of The Rna Binding Domain Of Squamous Cell Carcinoma Antigen Recognized By T Cells 3 Length = 100

Iteration: 1
 Score = 45.4 bits (106), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 28/90 (31%), Positives = 46/90 (51%), Gaps = 10/90 (11%)
Query: 80  LYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATAL 139
           L++ GLP   TK E+  I +     K++RLV      R G P  L +V++EN + A+ A+
Sbjct: 20  LFISGLPFSCTKEELEEICKAHGTVKDLRLVTN----RAGKPKGLAYVEYENESQASQAV 75
Query: 140 SALQGYRMDEDDPDSKFLRLQFSRNPGPRS 169
             + G  + E+      +++  S N GP S
Sbjct: 76  MKMDGMTIKEN-----IIKVAIS-NSGPSS 99

>pdb|2U1A|A Chain A, Rna Binding Domain 2 Of Human U1a Protein, Nmr, 20 Structures Length = 88

Iteration: 1
 Score = 45.1 bits (105), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 28/91 (30%), Positives = 48/91 (52%), Gaps = 13/91 (14%)
Query: 61  AAARPGHETLPLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGD 120
           A A+P  E    PP+    L++  LP ++ +  ++ +F  F G+KEVRLV          
Sbjct: 2   APAQPLSEN---PPN--HILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHD----- 51
Query: 121 PLILCFVDFENPACAATALSALQGYRMDEDD 151
              + FV+F+N   A  A  ALQG+++ +++
Sbjct: 52  ---IAFVEFDNEVQAGAARDALQGFKITQNN 79

>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp Length = 282

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 24/79 (30%), Positives = 43/79 (54%), Gaps = 10/79 (12%)
Query: 73  PPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENP 132
           PP+    L++  LP ++ +  ++ +F  F G+KEVRLV             + FV+F+N 
Sbjct: 205 PPN--HILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHD--------IAFVEFDNE 254
Query: 133 ACAATALSALQGYRMDEDD 151
             A  A  ALQG+++ +++
Sbjct: 255 VQAGAARDALQGFKITQNN 273

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	177
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	5e-13
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	2e-12
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	1e-05
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	8e-12
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-04
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	1e-11
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	9e-10
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	3e-08
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	2e-09
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	4e-09
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	8e-09
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	1e-08
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	1e-05
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	4e-08
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	4e-08
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	4e-04
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	5e-08
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	6e-08
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	6e-08
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	8e-08
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	9e-08
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	1e-07
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	1e-07
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-07
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	4e-05
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	1e-07
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	1e-07
2dis_A	109	Unnamed protein product; structural genomics, RRM	2e-07
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	2e-07
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-07
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	5e-06
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	4e-05
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	3e-07
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	3e-07
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	3e-07
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	3e-07
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	5e-07
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	5e-07
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	5e-07
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	6e-07
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	6e-07
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	7e-07
2div_A	99	TRNA selenocysteine associated protein; structural	7e-07
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	7e-07
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	8e-07
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	9e-07
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	1e-06
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	1e-06
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	1e-06
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	1e-06
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-06
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	2e-06
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	2e-06
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	2e-06
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	2e-06
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	2e-06
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	2e-06
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	3e-06
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	3e-06
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	3e-06
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	3e-06
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	3e-06
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	4e-06
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	4e-06
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	4e-06
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	4e-06
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	4e-06
1x4e_A	85	RNA binding motif, single-stranded interacting pro	4e-06
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	4e-06
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	5e-06
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	6e-06
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	8e-06
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	8e-06
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	8e-06
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	9e-06
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	9e-06
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	1e-05
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	1e-05
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	1e-05
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	1e-05
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	1e-05
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	1e-05
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	1e-05
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	2e-05
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	2e-05
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-05
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	2e-05
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	3e-05
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	3e-05
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	3e-05
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	3e-05
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	3e-05
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	3e-05
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	3e-05
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	5e-05
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	4e-05
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	4e-05
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	4e-05
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	4e-05
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	4e-05
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	4e-05
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	4e-05
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	5e-05
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	5e-05
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	6e-05
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	6e-05
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	7e-05
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	7e-05
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	7e-05
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	9e-05
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	9e-05
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	1e-04
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	1e-04
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	1e-04
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-04
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	1e-04
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	2e-04
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	2e-04
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	2e-04
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	2e-04
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	2e-04
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	3e-04
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	3e-04
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	3e-04
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	4e-04
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	4e-04
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	4e-04
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	4e-04
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	5e-04
1x5p_A	97	Negative elongation factor E; structure genomics,	7e-04
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	9e-04
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	9e-04

>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 = 61.2 bits (149), Expect = 5e-13
 Identities = 25/99 (25%), Positives = 43/99 (43%), Gaps = 12/99 (12%)

Query: 73  PPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVI--KESKLRGGDPLILCFVDFE 130
           P + +  LY++ L    T+R++  +F  F   K   +       ++RG       F+ F 
Sbjct: 21  PGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRG-----QAFITFP 75

Query: 131 NPACAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPRS 169
           N   A  AL  + GY++       K L ++F +N   RS
Sbjct: 76  NKEIAWQALHLVNGYKL-----YGKILVIEFGKNKKQRS 109

>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 = 61.8 bits (150), Expect = 2e-12
 Identities = 14/89 (15%), Positives = 37/89 (41%), Gaps = 11/89 (12%)

Query: 77  SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAA 136
           S+TL++  +P   ++ ++  +F    G  +     ++ +        +  +   +   A 
Sbjct: 120 SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRK-------MALIQMGSVEEAV 172

Query: 137 TALSALQGYRMDEDDPDSKFLRLQFSRNP 165
            AL  L  + +     ++  LR+ FS++ 
Sbjct: 173 QALIDLHNHDL----GENHHLRVSFSKST 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 = 42.6 bits (100), Expect = 1e-05
 Identities = 18/95 (18%), Positives = 36/95 (37%), Gaps = 14/95 (14%)

Query: 76  ASSTLYVEGL-PADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPAC 134
            +S L V  L P   T + +  +F  +   + V+ ++   K           V   +   
Sbjct: 2   GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVK-ILFNKKENA-------LVQMADGNQ 53

Query: 135 AATALSALQGYRMDEDDPDSKFLRLQFSRNPGPRS 169
           A  A+S L G++        K +R+  S++   + 
Sbjct: 54  AQLAMSHLNGHK-----LHGKPIRITLSKHQNVQL 83

>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 = 60.4 bits (146), Expect = 8e-12
 Identities = 14/89 (15%), Positives = 37/89 (41%), Gaps = 11/89 (12%)

Query: 77  SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAA 136
           S+TL++  +P   ++ ++  +F    G  +     ++ +        +  +   +   A 
Sbjct: 151 SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRK-------MALIQMGSVEEAV 203

Query: 137 TALSALQGYRMDEDDPDSKFLRLQFSRNP 165
            AL  L  + +     ++  LR+ FS++ 
Sbjct: 204 QALIDLHNHDL----GENHHLRVSFSKST 228

>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 = 40.4 bits (94), Expect = 1e-04
 Identities = 20/111 (18%), Positives = 41/111 (36%), Gaps = 15/111 (13%)

Query: 61  AAARPGHETLP-LPPDASSTLYVEGLPADS-TKREVAHIFRPFVGYKEVRLVIKESKLRG 118
             +  G   +P L    +S L V  L  +  T + +  +F  +   + V+ ++   K   
Sbjct: 17  RGSHMGRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVK-ILFNKKENA 75

Query: 119 GDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPRS 169
                   V   +   A  A+S L G++        K +R+  S++   + 
Sbjct: 76  -------LVQMADGNQAQLAMSHLNGHK-----LHGKPIRITLSKHQNVQL 114

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 57.8 bits (140), Expect = 1e-11
 Identities = 21/92 (22%), Positives = 42/92 (45%), Gaps = 11/92 (11%)

Query: 72  LPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFEN 131
           LPP+ +  LY+  LP   T  E+  IF  +   +++R+     + RG       +V +E+
Sbjct: 3   LPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVG-NTPETRG-----TAYVVYED 56

Query: 132 PACAATALSALQGYRMDEDDPDSKFLRLQFSR 163
              A  A+  L G+     +  +++L + +  
Sbjct: 57  IFDAKNAVDHLSGF-----NVSNRYLVVLYYN 83

>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 = 55.3 bits (132), Expect = 9e-10
 Identities = 26/133 (19%), Positives = 53/133 (39%), Gaps = 12/133 (9%)

Query: 31  PSVTGRHGATGPDLVQNLRSSSIDDQLPFDAAARPGHETLPLPPDASSTLYVEGLPADST 90
           P      G   P  +   +              +            +  L++  LP ++ 
Sbjct: 161 PPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETN 220

Query: 91  KREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDED 150
           +  ++ +F  F G+KEVRLV     +         FV+F+N   A  A  ALQG+++ ++
Sbjct: 221 ELMLSMLFNQFPGFKEVRLVPGRHDI--------AFVEFDNEVQAGAARDALQGFKITQN 272

Query: 151 DPDSKFLRLQFSR 163
           +     +++ F++
Sbjct: 273 NA----MKISFAK 281

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 50.6 bits (120), Expect = 3e-08
 Identities = 22/92 (23%), Positives = 41/92 (44%), Gaps = 13/92 (14%)

Query: 77  SSTLYVEGLPADSTKREVAHIFRP-FVGYKEVR--LVIKESKLRGGDPLILCFVDFENPA 133
           + T+Y+  L     K E+       F  + ++   LV +  K+RG       FV F+  +
Sbjct: 9   NHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRG-----QAFVIFKEVS 63

Query: 134 CAATALSALQGYRMDEDDPDSKFLRLQFSRNP 165
            A  AL ++QG+         K +R+Q+++  
Sbjct: 64  SATNALRSMQGFPF-----YDKPMRIQYAKTD 90

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 52.2 bits (125), Expect = 2e-09
 Identities = 16/114 (14%), Positives = 32/114 (28%), Gaps = 15/114 (13%)

Query: 56  QLPFDAAARPGHETLPLPPDASSTLYVEGLPADSTKREVAH----IFRPFVGYKEVRLVI 111
           +        P   + P   + S  + +  +  +  K ++      +        ++  V 
Sbjct: 8   KFERQHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIV-VD 66

Query: 112 KESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFLRLQFSRNP 165
                 G       ++ F     A   + A QGY           L + FS  P
Sbjct: 67  LSDDNSG-----KAYIVFATQESAQAFVEAFQGYPF-----QGNPLVITFSETP 110

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 50.6 bits (121), Expect = 4e-09
 Identities = 22/96 (22%), Positives = 40/96 (41%), Gaps = 13/96 (13%)

Query: 73  PPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENP 132
               ++ +YV  LP D+   ++    R   G   +RL  +  + R        F+ + + 
Sbjct: 15  GAPLAADVYVGNLPRDARVSDLKRALREL-GSVPLRLTWQGPRRR-------AFLHYPDS 66

Query: 133 ACAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPR 168
           A A  A+S LQG R+      +  LR+  +R    +
Sbjct: 67  AAAQQAVSCLQGLRL-----GTDTLRVALARQQRDK 97

>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 = 49.7 bits (119), Expect = 8e-09
 Identities = 22/98 (22%), Positives = 33/98 (33%), Gaps = 20/98 (20%)

Query: 77  SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAA 136
           SS + V+ LP DS  +EV  + + +   K   +     + +        FV   N   A 
Sbjct: 5   SSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYV----DRNKR-----TAFVTLLNGEQAQ 54

Query: 137 TALSALQGYRMDEDDPDSKFLRLQFSRN-----PGPRS 169
            A+     Y         K L +Q          GP S
Sbjct: 55  NAIQMFHQYSFRG-----KDLIVQLQPTDALLCSGPSS 87

>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 = 51.2 bits (122), Expect = 1e-08
 Identities = 15/99 (15%), Positives = 33/99 (33%), Gaps = 4/99 (4%)

Query: 64  RPGHETLPLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLI 123
            P           S+ L+    P + T+     I       +   + +   K    +   
Sbjct: 110 TPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK---SERSS 166

Query: 124 LCFVDFENPACAATALSALQGYRMDEDDPDSKF-LRLQF 161
              +++++ + A   L  L  Y+M   +    + L+L F
Sbjct: 167 SGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKLCF 205

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 42.8 bits (100), Expect = 1e-05
 Identities = 17/89 (19%), Positives = 27/89 (30%), Gaps = 12/89 (13%)

Query: 77  SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAA 136
           S  L V GL       +   +F  F  Y  V  V       G        V+  +     
Sbjct: 4   SPVLMVYGLDQSKMNCD--RVFNVFCLYGNVEKVKFMKSKPG-----AAMVEMADGYAVD 56

Query: 137 TALSALQGYRMDEDDPDSKFLRLQFSRNP 165
            A++ L    M       + + +  S+ P
Sbjct: 57  RAITHLNNNFMFG-----QKMNVCVSKQP 80

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 47.8 bits (114), Expect = 4e-08
 Identities = 11/92 (11%), Positives = 30/92 (32%), Gaps = 11/92 (11%)

Query: 74  PDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPA 133
                 L +  +P       +  +   +   +    V  +S+           V + +  
Sbjct: 12  RQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVV------NVTYSSKD 65

Query: 134 CAATALSALQGYRMDEDDPDSKFLRLQFSRNP 165
            A  AL  L G+++     ++  L++ +  + 
Sbjct: 66  QARQALDKLNGFQL-----ENFTLKVAYIPDE 92

>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 = 49.1 bits (118), Expect = 4e-08
 Identities = 21/90 (23%), Positives = 43/90 (47%), Gaps = 13/90 (14%)

Query: 73  PPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENP 132
              A+ TL  + L  + T+ E+  +F   +   E+RLV ++ K +G     + +++F++ 
Sbjct: 95  KVRAARTLLAKNLSFNITEDELKEVFEDAL---EIRLVSQDGKSKG-----IAYIEFKSE 146

Query: 133 ACAATALSALQGYRMDEDDPDSKFLRLQFS 162
           A A   L   QG      + D + + L ++
Sbjct: 147 ADAEKNLEEKQGA-----EIDGRSVSLYYT 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 = 38.0 bits (89), Expect = 4e-04
 Identities = 14/99 (14%), Positives = 32/99 (32%), Gaps = 12/99 (12%)

Query: 72  LPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKL-RGGDPLILCFVDFE 130
                   L++  L  + +  E+           ++ +V   +   R        +VDFE
Sbjct: 8   SESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRK-----FGYVDFE 62

Query: 131 NPACAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPRS 169
           +      AL  L G ++         ++L+  +    + 
Sbjct: 63  SAEDLEKAL-ELTGLKV-----FGNEIKLEKPKGRDSKK 95

>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 = 47.7 bits (114), Expect = 5e-08
 Identities = 15/76 (19%), Positives = 27/76 (35%), Gaps = 5/76 (6%)

Query: 74  PDASSTLYVEGLPADSTKREVAHIFRPF-VGYKEVRLVIKESKLRGGDPLILCFVDFENP 132
               + + V+ +P   +  E+   F  + V    V L   E  +  G+      V FE+ 
Sbjct: 12  KPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGE----AMVAFESR 67

Query: 133 ACAATALSALQGYRMD 148
             A  A+  L    + 
Sbjct: 68  DEATAAVIDLNDRPIG 83

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 47.3 bits (113), Expect = 6e-08
 Identities = 16/95 (16%), Positives = 34/95 (35%), Gaps = 10/95 (10%)

Query: 73  PPDASSTLYVEGLPADSTKREVAHIFRPF--VGYKEVRLVI-KESKL-RGGDPLILCFVD 128
                 T+ +  +   +    +     P+  +    +RL+  K+++  RG       FV 
Sbjct: 5   HHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRG-----FAFVQ 59

Query: 129 FENPACAATALSALQGYRMDEDDPDSKFLRLQFSR 163
             +   A+  L  LQ         D K + + F++
Sbjct: 60  LSSAMDASQLLQILQS-LHPPLKIDGKTIGVDFAK 93

>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 = 48.6 bits (116), Expect = 6e-08
 Identities = 32/135 (23%), Positives = 58/135 (42%), Gaps = 10/135 (7%)

Query: 44  LVQNLRS-SSIDDQLPFDAAARPGHETLPLPPDASSTLYVEGLPADSTKREVAHIFRPFV 102
           L++ LRS S ++     D   R  +E        S TLYV  L   +T+ ++  +F    
Sbjct: 5   LLKALRSDSYVELSQYRDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSG 64

Query: 103 GYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFLRLQFS 162
             K++ + + + K         CFV++ + A A  A+  + G R+D+     + +R  + 
Sbjct: 65  DIKKIIMGLDKMKKT---ACGFCFVEYYSRADAENAMRYINGTRLDD-----RIIRTDWD 116

Query: 163 RNPGPRSVFGARGRR 177
                   +G RGR 
Sbjct: 117 AGFKEGRQYG-RGRS 130

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 47.3 bits (113), Expect = 8e-08
 Identities = 27/110 (24%), Positives = 48/110 (43%), Gaps = 12/110 (10%)

Query: 61  AAARPGHETLPLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKES-KLRGG 119
            ++                L++ GLP   TK E+  I +     K++RLV   + K +G 
Sbjct: 1   GSSGSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKG- 59

Query: 120 DPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPRS 169
               L +V++EN + A+ A+  + G  + E       +++  S N GP S
Sbjct: 60  ----LAYVEYENESQASQAVMKMDGMTIKE-----NIIKVAIS-NSGPSS 99

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 46.9 bits (112), Expect = 9e-08
 Identities = 18/93 (19%), Positives = 33/93 (35%), Gaps = 10/93 (10%)

Query: 74  PDASSTLYVEGLPADSTKREVAHIFRPF-VGYKEVRLVIKESKLRGGDPLILCFVDFENP 132
               + + V+ +P   +  E+   F  + V    V L   E  +  G+      V FE+ 
Sbjct: 12  KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGE----AMVAFESR 67

Query: 133 ACAATALSALQGYRMDEDDPDSKFLRLQFSRNP 165
             A  A+  L    +      S+ ++L     P
Sbjct: 68  DEATAAVIDLNDRPI-----GSRKVKLVLGSGP 95

>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 = 47.3 bits (113), Expect = 1e-07
 Identities = 21/103 (20%), Positives = 39/103 (37%), Gaps = 11/103 (10%)

Query: 73  PPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENP 132
             +    +YV  LP D   +++  +F  +   +++  +               FV+FE+P
Sbjct: 18  AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDID-LKNRRGGPP-----FAFVEFEDP 71

Query: 133 ACAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPRSVFGARG 175
             A  A+    GY       D   LR++F R+        + G
Sbjct: 72  RDAEDAVYGRDGYDY-----DGYRLRVEFPRSGRGTGSGPSSG 109

>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 = 47.0 bits (112), Expect = 1e-07
 Identities = 19/104 (18%), Positives = 34/104 (32%), Gaps = 17/104 (16%)

Query: 73  PPDASSTLYVEGLPADS-TKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFEN 131
           P   +S +++  L      K +V  IF  + G       +    +  G      FV + N
Sbjct: 23  PKSINSRVFIGNLNTALVKKSDVETIFSKY-GR------VAGCSVHKG----YAFVQYSN 71

Query: 132 PACAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPRSVFGARG 175
              A  A+    G  +       + L +  +  P P     + G
Sbjct: 72  ERHARAAVLGENGRVL-----AGQTLDINMAGEPKPDRSGPSSG 110

>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 = 49.2 bits (118), Expect = 1e-07
 Identities = 14/75 (18%), Positives = 28/75 (37%), Gaps = 3/75 (4%)

Query: 74  PDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPA 133
                TL++   P   T+R +  + +       V L I+   LR        ++D  +  
Sbjct: 114 HLTECTLWMTNFPPSYTQRNIRDLLQDI-N--VVALSIRLPSLRFNTSRRFAYIDVTSKE 170

Query: 134 CAATALSALQGYRMD 148
            A   +  L G +++
Sbjct: 171 DARYCVEKLNGLKIE 185

>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 = 41.9 bits (99), Expect = 4e-05
 Identities = 11/71 (15%), Positives = 22/71 (30%), Gaps = 5/71 (7%)

Query: 78  STLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAAT 137
           +T+ V+ LP    + +V   F+       V +     K           ++F     A  
Sbjct: 42  TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFR-----FARIEFARYDGALA 96

Query: 138 ALSALQGYRMD 148
           A++        
Sbjct: 97  AITKTHKVVGQ 107

>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 = 46.5 bits (111), Expect = 1e-07
 Identities = 23/102 (22%), Positives = 38/102 (37%), Gaps = 14/102 (13%)

Query: 74  PDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPA 133
               S L+V  LP D T+ E+  +F  +    EV +     K +G       F+  E   
Sbjct: 12  FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIH----KDKG-----FGFIRLETRT 62

Query: 134 CAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPRSVFGARG 175
            A  A   L    +       K LR++F+ +    +   + G
Sbjct: 63  LAEIAKVELDNMPL-----RGKQLRVRFACHSASLTSGPSSG 99

>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 = 46.5 bits (111), Expect = 1e-07
 Identities = 24/99 (24%), Positives = 44/99 (44%), Gaps = 17/99 (17%)

Query: 73  PPDA--SSTLYVEGLP----ADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCF 126
            P+   + T+Y+  L      D  K+ +  IF  F    ++  V +  K+RG       F
Sbjct: 2   VPETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDIL-VSRSLKMRGQ-----AF 55

Query: 127 VDFENPACAATALSALQGYRMDEDDPDSKFLRLQFSRNP 165
           V F+  + A  AL ++QG+         K +R+Q+++  
Sbjct: 56  VIFKEVSSATNALRSMQGFPF-----YDKPMRIQYAKTD 89

>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 = 46.3 bits (110), Expect = 2e-07
 Identities = 13/76 (17%), Positives = 27/76 (35%), Gaps = 1/76 (1%)

Query: 76  ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACA 135
            +  L++ G+P    + E+              +V   +  +  +     FV++E+   A
Sbjct: 7   GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGF-AFVEYESHRAA 65

Query: 136 ATALSALQGYRMDEDD 151
           A A   L   R+    
Sbjct: 66  AMARRKLMPGRIQLWG 81

>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 = 46.1 bits (110), Expect = 2e-07
 Identities = 17/106 (16%), Positives = 39/106 (36%), Gaps = 17/106 (16%)

Query: 73  PPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKES-KLRGGDPLILCFVDFEN 131
               S TL +  L   +T+  +  +F        +++   ++ K +G       F++F +
Sbjct: 11  WSGESKTLVLSNLSYSATEETLQEVFEK---ATFIKVPQNQNGKSKG-----YAFIEFAS 62

Query: 132 PACAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPRSVFGARGRR 177
              A  AL++     +     + + +RL+      PR    +    
Sbjct: 63  FEDAKEALNSCNKREI-----EGRAIRLELQG---PRGSPNSGPSS 100

>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 = 48.4 bits (116), Expect = 2e-07
 Identities = 20/96 (20%), Positives = 35/96 (36%), Gaps = 12/96 (12%)

Query: 76  ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKES--KLRGGDPLILCFVDFENPA 133
             + L V  LP   T+++   + RPF   +   LV  E   + +G       F ++    
Sbjct: 94  TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKG-----YGFAEYMKKD 148

Query: 134 CAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPRS 169
            AA A S L G  +       + L + ++       
Sbjct: 149 SAARAKSDLLGKPL-----GPRTLYVHWTDAGQLTP 179

>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 = 44.6 bits (106), Expect = 5e-06
 Identities = 21/92 (22%), Positives = 32/92 (34%), Gaps = 15/92 (16%)

Query: 74  PDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPA 133
                 + + GLP D T +EV  +   +   K    V K    +G       FV   N  
Sbjct: 19  FRNRRKILIRGLPGDVTNQEVHDLLSDY-ELKYCF-VDKY---KG-----TAFVTLLNGE 68

Query: 134 CAATALSALQGYRMDEDDPDSKFLRLQFSRNP 165
            A  A++A    R+ E     + L +Q     
Sbjct: 69  QAEAAINAFHQSRLRE-----RELSVQLQPTD 95

>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 = 41.9 bits (99), Expect = 4e-05
 Identities = 16/95 (16%), Positives = 27/95 (28%), Gaps = 14/95 (14%)

Query: 77  SSTLYVEGLPADSTKRE-VAHIFRPFVGYKEVRLVIKES-KLRG-GDPLILCFVDFENPA 133
           S  L V+ LP      + +             +L   +  +L+G         +++E   
Sbjct: 184 SRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFA------VLEYETAE 237

Query: 134 CAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPR 168
            A  A     G            LR+ F     P 
Sbjct: 238 MAEEAQQQADGL-----SLGGSHLRVSFCAPGPPG 267

>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 = 45.7 bits (109), Expect = 3e-07
 Identities = 20/76 (26%), Positives = 38/76 (50%), Gaps = 8/76 (10%)

Query: 73  PPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENP 132
              A+ TL  + L  + T+ E+  +F   +   E+RLV ++ K +G     + +++F++ 
Sbjct: 12  KVRAARTLLAKNLSFNITEDELKEVFEDAL---EIRLVSQDGKSKG-----IAYIEFKSE 63

Query: 133 ACAATALSALQGYRMD 148
           A A   L   QG  +D
Sbjct: 64  ADAEKNLEEKQGAEID 79

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens} Length = 143

 Score = 46.7 bits (111), Expect = 3e-07
 Identities = 32/144 (22%), Positives = 59/144 (40%), Gaps = 24/144 (16%)

Query: 38  GATGPDLVQNLRSSSIDD-QLPFDAAARPGHETLPL-----PPDASSTLYVEGLPADSTK 91
           G  G D    + S  I   +L     +R   ETL +     P + +  +YV+ L     +
Sbjct: 1   GPLGSD-SDEMPSECISRRELEKGRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQE 59

Query: 92  REVAHIFRPF-----VGYKEVRLVI--KESKLRGGDPLILCFVDFENPACAATALSALQG 144
           +++ +IF  +        + +  +   KE +++G       F+   N   AA AL    G
Sbjct: 60  KDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKG-----QAFIGLPNEKAAAKALKEANG 114

Query: 145 YRMDEDDPDSKFLRLQFSRNPGPR 168
           Y +       K + +QF+R+  P+
Sbjct: 115 YVL-----FGKPMVVQFARSARPK 133

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 45.7 bits (109), Expect = 3e-07
 Identities = 25/116 (21%), Positives = 45/116 (38%), Gaps = 15/116 (12%)

Query: 63  ARPGHETLPLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKES---KLRGG 119
              G     LP     T ++  LP D T+  +   FR       VRL  + S   +L+G 
Sbjct: 1   GSSGSSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNPERLKG- 58

Query: 120 DPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPRSVFGARG 175
                 + +FE+     +ALS      ++E+   +K +R+  +     +    + G
Sbjct: 59  ----FGYAEFEDLDSLLSALS------LNEESLGNKRIRVDVADQAQDKDSGPSSG 104

>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 = 45.3 bits (108), Expect = 3e-07
 Identities = 22/99 (22%), Positives = 42/99 (42%), Gaps = 5/99 (5%)

Query: 77  SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAA 136
           SS L+++ L   +T+  +  +F      K   +  K++K      +   FV+++ P  A 
Sbjct: 5   SSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQ 64

Query: 137 TALSALQGYRMDEDDPDSKFLRLQFSRNPGPRSVFGARG 175
            AL  LQG+ +     D   L ++ S      +   + G
Sbjct: 65  KALKQLQGHTV-----DGHKLEVRISERATKPASGPSSG 98

>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 = 46.4 bits (110), Expect = 5e-07
 Identities = 20/109 (18%), Positives = 42/109 (38%), Gaps = 12/109 (11%)

Query: 71  PLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVI-KES-KLRGGDPLILCFVD 128
           P        L+V  +  ++ + E+   F  +   K + L + + +   +G        V+
Sbjct: 66  PQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKG-----YALVE 120

Query: 129 FENPACAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPRSVFGARGRR 177
           +E    A  A  AL G  +       + +++ +    GP+ V  +  RR
Sbjct: 121 YETHKQALAAKEALNGAEIMG-----QTIQVDWCFVKGPKRVKKSEKRR 164

>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 = 44.9 bits (107), Expect = 5e-07
 Identities = 18/95 (18%), Positives = 41/95 (43%), Gaps = 12/95 (12%)

Query: 74  PDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPA 133
            + ++ L+V GL  +++   +A  F  F G       I+      GD     ++ +E+  
Sbjct: 14  ANPTTRLWVGGLGPNTSLAALAREFDRF-G------SIRTIDHVKGDSF--AYIQYESLD 64

Query: 134 CAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPR 168
            A  A + ++G+ +       + LR+ F+++    
Sbjct: 65  AAQAACAKMRGFPL---GGPDRRLRVDFAKSGPSS 96

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100

 Score = 44.9 bits (107), Expect = 5e-07
 Identities = 21/91 (23%), Positives = 35/91 (38%), Gaps = 10/91 (10%)

Query: 61  AAARPGHETLPLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKES---KLR 117
            +    H    LP     T ++  LP D T+  +   FR       VRL  + S   +L+
Sbjct: 3   GSHHHHHHRSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNPERLK 61

Query: 118 GGDPLILCFVDFENPACAATALSALQGYRMD 148
           G       + +FE+     +AL +L    + 
Sbjct: 62  G-----FGYAEFEDLDSLLSAL-SLNEESLG 86

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 44.9 bits (107), Expect = 6e-07
 Identities = 21/112 (18%), Positives = 45/112 (40%), Gaps = 12/112 (10%)

Query: 58  PFDAAARPGHETLPLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVI-KES-K 115
            +D+  + G E  P        L+V G+  ++T+ ++   F  +   K + L + + +  
Sbjct: 4   DYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGY 63

Query: 116 LRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFLRLQFSRNPGP 167
           L+G        V++E    A  A+  L G  +       + + + +    GP
Sbjct: 64  LKG-----YTLVEYETYKEAQAAMEGLNGQDLMG-----QPISVDWCFVRGP 105

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 45.1 bits (107), Expect = 6e-07
 Identities = 22/109 (20%), Positives = 41/109 (37%), Gaps = 18/109 (16%)

Query: 77  SSTLYVEGLPADSTKREVAHIFRPF--------VGYKEVRLVI-KESKLRGGDPLILCFV 127
           ++T++V+GL  + T   VA  F+           G   + L   +E+    G+      V
Sbjct: 7   NNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGE----ATV 62

Query: 128 DFENPACAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPRSVFGARGR 176
            F++P  A  A+    G            +++ F+      +  G  GR
Sbjct: 63  SFDDPPSAKAAIDWFDGKEF-----SGNPIKVSFATRRADFNRGGGNGR 106

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 45.0 bits (107), Expect = 7e-07
 Identities = 25/92 (27%), Positives = 41/92 (44%), Gaps = 16/92 (17%)

Query: 77  SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAA 136
           ++ L+V   P D  + E+  IF PF   KEV+++       G       FV+FE    AA
Sbjct: 31  NTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL------NG-----FAFVEFEEAESAA 79

Query: 137 TALSALQGYRMDEDDPDSKFLRLQFSRNPGPR 168
            A+  + G         ++ L + +S+ P  R
Sbjct: 80  KAIEEVHGKSF-----ANQPLEVVYSKLPAKR 106

>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 = 44.6 bits (106), Expect = 7e-07
 Identities = 20/97 (20%), Positives = 38/97 (39%), Gaps = 3/97 (3%)

Query: 73  PPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENP 132
               +++L++  L     +  ++  F           +I+      G P   CFV+F + 
Sbjct: 5   SSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRL--TGIPAGYCFVEFADL 62

Query: 133 ACAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPRS 169
           A A   L  + G  +    P +K  +L ++   GP S
Sbjct: 63  ATAEKCLHKINGKPLPGATP-AKRFKLNYATYSGPSS 98

>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 = 44.1 bits (105), Expect = 7e-07
 Identities = 22/94 (23%), Positives = 36/94 (38%), Gaps = 11/94 (11%)

Query: 77  SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVI--KESKLRGGDPLILCFVDFENPAC 134
            + +++  L  + TK  +  IF  +   K + + +      L  G      +V+FENP  
Sbjct: 4   PTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKG----YAYVEFENPDE 59

Query: 135 AATALSALQGYRMDEDDPDSKFLRLQFSRNPGPR 168
           A  AL       MD    D + +       P PR
Sbjct: 60  AEKALKH-----MDGGQIDGQEITATAVLAPWPR 88

>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 = 44.6 bits (106), Expect = 8e-07
 Identities = 21/96 (21%), Positives = 33/96 (34%), Gaps = 19/96 (19%)

Query: 79  TLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATA 138
            LYV  L   +++  +   F         R+     K+R        FV F N   A  A
Sbjct: 17  ILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK----KIRD-----YAFVHFSNREDAVEA 67

Query: 139 LSALQGYRMDEDDPDSKFLRLQFSRNP-----GPRS 169
           + AL G  +     D   + +  ++       GP S
Sbjct: 68  MKALNGKVL-----DGSPIEVTLAKPVDKDSSGPSS 98

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 44.1 bits (105), Expect = 9e-07
 Identities = 21/101 (20%), Positives = 36/101 (35%), Gaps = 18/101 (17%)

Query: 77  SSTLYVEGLPADS-TKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACA 135
            S L++  LP  + +K ++  IF P+    ++ +                F+ F+NP   
Sbjct: 10  KSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK------NA-----FGFIQFDNPQSV 58

Query: 136 ATALSALQGYRMDEDDPDSKFLRLQFSR-NPGPRSVFGARG 175
             A+               K L L+ S  N  P+   G  G
Sbjct: 59  RDAIECESQEMN-----FGKKLILEVSSSNARPQFDHGDHG 94

>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 = 45.3 bits (108), Expect = 1e-06
 Identities = 27/95 (28%), Positives = 43/95 (45%), Gaps = 9/95 (9%)

Query: 76  ASST-LYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPAC 134
           AS+T L V  LP D T RE+  +FR        R ++++ K   G      FVDF +   
Sbjct: 1   ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCR-IMRDYK--TGYSYGYAFVDFTSEMD 57

Query: 135 AATALSALQGYRMDEDDPDSKFLRLQFSRNPGPRS 169
           +  A+  L G  +      +K L++ ++R  G   
Sbjct: 58  SQRAIKVLNGITV-----RNKRLKVSYARPGGESI 87

>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 = 43.8 bits (104), Expect = 1e-06
 Identities = 19/101 (18%), Positives = 34/101 (33%), Gaps = 18/101 (17%)

Query: 69  TLPLPPDASSTLYVEGLPADS-TKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFV 127
            +P      S L++  LP  + +K ++  IF P+    ++ +                F+
Sbjct: 14  LVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK------NA-----FGFI 62

Query: 128 DFENPACAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPR 168
            F+NP     A+               K L L+ S     R
Sbjct: 63  QFDNPQSVRDAIEXESQEMN-----FGKKLILEVSS-SNAR 97

>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 = 43.7 bits (104), Expect = 1e-06
 Identities = 23/78 (29%), Positives = 36/78 (46%), Gaps = 7/78 (8%)

Query: 73  PPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVI-KES-KLRGGDPLILCFVDFE 130
            PD +  L V GL   +T+R++  +F  +    +V +V  ++S + RG       FV FE
Sbjct: 11  NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRG-----FAFVYFE 65

Query: 131 NPACAATALSALQGYRMD 148
           N   A  A     G  +D
Sbjct: 66  NVDDAKEAKERANGMELD 83

>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 = 44.3 bits (105), Expect = 1e-06
 Identities = 24/122 (19%), Positives = 48/122 (39%), Gaps = 12/122 (9%)

Query: 58  PFDAAARPGHETLPLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVI-KES-K 115
            +D+  + G E  P        L+V G+  ++T+ ++   F  +   K + L + + +  
Sbjct: 3   DYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGY 62

Query: 116 LRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPRSVFGARG 175
           L+G        V++E    A  A+  L G  +       + + + +    GP       G
Sbjct: 63  LKG-----YTLVEYETYKEAQAAMEGLNGQDLMG-----QPISVDWCFVRGPPKGKRRGG 112

Query: 176 RR 177
           RR
Sbjct: 113 RR 114

>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 = 44.0 bits (104), Expect = 2e-06
 Identities = 15/72 (20%), Positives = 24/72 (33%), Gaps = 9/72 (12%)

Query: 77  SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAA 136
            + +  + LPA +   E+   F  F     V  ++ E         I   V+F  P  A 
Sbjct: 10  KTVILAKNLPAGTLAAEIQETFSRFGSLGRV--LLPEGG-------ITAIVEFLEPLEAR 60

Query: 137 TALSALQGYRMD 148
            A   L   +  
Sbjct: 61  KAFRHLAYSKFH 72

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 43.5 bits (103), Expect = 2e-06
 Identities = 14/75 (18%), Positives = 27/75 (36%), Gaps = 5/75 (6%)

Query: 66  GHETLPLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILC 125
           G             +++ GLP  +T+ ++ + F P      V + I       G+     
Sbjct: 4   GSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPL-NPMRVHIEIGPDGRVTGE----A 58

Query: 126 FVDFENPACAATALS 140
            V+F     A  A++
Sbjct: 59  DVEFATHEDAVAAMA 73

>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 = 44.4 bits (105), Expect = 2e-06
 Identities = 22/107 (20%), Positives = 46/107 (42%), Gaps = 14/107 (13%)

Query: 74  PDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVI-KES-KLRG-GDPLILCFVDFE 130
           PD    L V  +P    + ++  +F  +   + V++V  +E+ + RG G      FV F+
Sbjct: 39  PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYG------FVKFQ 92

Query: 131 NPACAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPRSVFGARGRR 177
           + + A  A++ L G+ +      +K L++  + +   R         
Sbjct: 93  SGSSAQQAIAGLNGFNI-----LNKRLKVALAASGHQRPGIAGAVGD 134

>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 = 43.4 bits (103), Expect = 2e-06
 Identities = 19/96 (19%), Positives = 33/96 (34%), Gaps = 17/96 (17%)

Query: 62  AARPGHETLPLPPDASSTLYVEGLPADSTKREVAHIF--------RPFVGYKEVRLVI-K 112
                H +       ++T++V+GL  + T   VA  F            G   + L   +
Sbjct: 2   GHHHHHHS----HSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDR 57

Query: 113 ESKLRGGDPLILCFVDFENPACAATALSALQGYRMD 148
           E+    G+      V F++P  A  A+    G    
Sbjct: 58  ETGKLKGE----ATVSFDDPPSAKAAIDWFDGKEFS 89

>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 = 43.0 bits (102), Expect = 2e-06
 Identities = 18/97 (18%), Positives = 34/97 (35%), Gaps = 16/97 (16%)

Query: 73  PPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENP 132
               +  ++V  + A  T +E+  +F       E  +V      +        FV  E  
Sbjct: 5   SSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV------KD-----YAFVHMEKE 53

Query: 133 ACAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPRS 169
           A A  A++ L G  +       K + ++ S     +S
Sbjct: 54  ADAKAAIAQLNGKEV-----KGKRINVELSTKGQKKS 85

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 43.5 bits (103), Expect = 2e-06
 Identities = 21/117 (17%), Positives = 43/117 (36%), Gaps = 16/117 (13%)

Query: 60  DAAARPGHETLPLPPDASSTLYVEGLPADSTKREVAHIFRPFVGY-KEVRLVIKESKLRG 118
           +       + +      + T+Y  G+ +  T + +   F PF G   E+R V  E   +G
Sbjct: 8   NTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPF-GQIMEIR-VFPE---KG 62

Query: 119 GDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPRSVFGARG 175
                  FV F     AA A+ ++ G  +     +   ++  + +     +   + G
Sbjct: 63  -----YSFVRFSTHESAAHAIVSVNGTTI-----EGHVVKCYWGKESPDMTSGPSSG 109

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 43.7 bits (103), Expect = 2e-06
 Identities = 17/80 (21%), Positives = 22/80 (27%)

Query: 61  AAARPGHETLPLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGD 120
                      L  +    + + GLP  +T  EV   F         +  I       G 
Sbjct: 7   GGGTSNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGR 66

Query: 121 PLILCFVDFENPACAATALS 140
           P    FV F     A  AL 
Sbjct: 67  PTGDAFVLFACEEYAQNALR 86

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 43.1 bits (102), Expect = 3e-06
 Identities = 23/98 (23%), Positives = 37/98 (37%), Gaps = 13/98 (13%)

Query: 80  LYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATAL 139
           +YV  L   + K E+   F  +   + V +          +P    FV+FE+P  A  A+
Sbjct: 3   VYVGNLGTGAGKGELERAFSYYGPLRTVWIA--------RNPPGFAFVEFEDPRDAEDAV 54

Query: 140 SALQGYRMDEDDPDSKFLRLQFSRNPGPRSVFGARGRR 177
             L G  +         +R++ S     RS F     R
Sbjct: 55  RGLDGKVI-----CGSRVRVELSTGMPRRSRFDRPPAR 87

>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 = 43.0 bits (102), Expect = 3e-06
 Identities = 13/74 (17%), Positives = 36/74 (48%), Gaps = 7/74 (9%)

Query: 77  SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVI-KES-KLRGGDPLILCFVDFENPAC 134
           S  +Y+  +P D T+ ++  +         ++++   ++ + +G       F++F +   
Sbjct: 2   SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKG-----YAFIEFRDLES 56

Query: 135 AATALSALQGYRMD 148
           +A+A+  L GY++ 
Sbjct: 57  SASAVRNLNGYQLG 70

>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 = 44.1 bits (105), Expect = 3e-06
 Identities = 19/94 (20%), Positives = 42/94 (44%), Gaps = 8/94 (8%)

Query: 76  ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACA 135
           + + L V  LP + T+ E   +F      +  + ++++     G  L   FV++ +P  A
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCK-LVRDKIT--GQSLGYGFVNYIDPKDA 57

Query: 136 ATALSALQGYRMDEDDPDSKFLRLQFSRNPGPRS 169
             A++ L G R+      +K +++ ++R      
Sbjct: 58  EKAINTLNGLRL-----QTKTIKVSYARPSSASI 86

>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 = 43.0 bits (102), Expect = 3e-06
 Identities = 21/93 (22%), Positives = 40/93 (43%), Gaps = 10/93 (10%)

Query: 77  SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAA 136
             TLYV  L  D T+  +  +F      K  +++ + +          CFV+F     AA
Sbjct: 15  PRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP-----YCFVEFYEHRDAA 69

Query: 137 TALSALQGYRMDEDDPDSKFLRLQFSRNPGPRS 169
            AL+A+ G ++       K +++ ++  P  + 
Sbjct: 70  AALAAMNGRKI-----LGKEVKVNWATTPSSQK 97

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108

 Score = 43.1 bits (102), Expect = 3e-06
 Identities = 22/88 (25%), Positives = 37/88 (42%), Gaps = 7/88 (7%)

Query: 63  ARPGHETLPLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVI-KES-KLRGGD 120
           A      L         LYV  L  + T+  +  IF PF   + ++L++  E+ + +G  
Sbjct: 12  AAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKG-- 69

Query: 121 PLILCFVDFENPACAATALSALQGYRMD 148
                F+ F +  CA  AL  L G+ + 
Sbjct: 70  ---YGFITFSDSECAKKALEQLNGFELA 94

>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 = 43.7 bits (103), Expect = 4e-06
 Identities = 20/93 (21%), Positives = 34/93 (36%), Gaps = 13/93 (13%)

Query: 73  PPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENP 132
                  +YV  L  +  K E+   F  +   + V +          +P    FV+FE+P
Sbjct: 69  SCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVA--------RNPPGFAFVEFEDP 120

Query: 133 ACAATALSALQGYRMDEDDPDSKFLRLQFSRNP 165
             AA A+  L G  +         +R++ S   
Sbjct: 121 RDAADAVRELDGRTL-----CGCRVRVELSNGE 148

>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 = 42.7 bits (101), Expect = 4e-06
 Identities = 20/111 (18%), Positives = 41/111 (36%), Gaps = 16/111 (14%)

Query: 60  DAAARPGHETLPLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVI-KES-KLR 117
           D    PG    P        L+V  +  ++ + E+   F  +   K + L + + +   +
Sbjct: 13  DDELEPG----PQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSK 68

Query: 118 GGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPR 168
           G        V++E    A  A  AL G  +       + +++ +    GP+
Sbjct: 69  G-----YALVEYETHKQALAAKEALNGAEIMG-----QTIQVDWCFVKGPK 109

>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 = 42.8 bits (101), Expect = 4e-06
 Identities = 17/79 (21%), Positives = 29/79 (36%), Gaps = 6/79 (7%)

Query: 62  AARPGHETLPLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDP 121
           ++    + LP+ PD    + V G+P  + + +V   F        V L+        G+ 
Sbjct: 2   SSGSSGKPLPINPD-DLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGN- 58

Query: 122 LILCFVDFENPACAATALS 140
                V F +P     AL 
Sbjct: 59  ---GLVKFLSPQDTFEALK 74

>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 = 4e-06
 Identities = 25/102 (24%), Positives = 38/102 (37%), Gaps = 7/102 (6%)

Query: 49  RSSSIDDQLPFDAAARPGHETLPLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVR 108
            S                H      PD +  L V GL   +T+R++  +F  +    +V 
Sbjct: 18  GSHMASMTGGQQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVS 77

Query: 109 LVI-KES-KLRGGDPLILCFVDFENPACAATALSALQGYRMD 148
           +V  ++S + RG       FV FEN   A  A     G  +D
Sbjct: 78  IVYDQQSRRSRG-----FAFVYFENVDDAKEAKERANGMELD 114

>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 = 42.6 bits (101), Expect = 4e-06
 Identities = 20/98 (20%), Positives = 42/98 (42%), Gaps = 12/98 (12%)

Query: 74  PDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVI-KES-KLRGGDPLILCFVDFEN 131
            D ++T+ V  L  D+ + ++  +FRPF     + L   K + + +G       F+ F  
Sbjct: 12  ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKG-----FAFISFHR 66

Query: 132 PACAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPRS 169
              AA A++ + G+       D   L +++++      
Sbjct: 67  REDAARAIAGVSGFGY-----DHLILNVEWAKPSTNSG 99

>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 = 42.1 bits (100), Expect = 4e-06
 Identities = 20/78 (25%), Positives = 40/78 (51%), Gaps = 9/78 (11%)

Query: 74  PDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVI-KESKL-RG-GDPLILCFVDFE 130
              SS LY+ GL   +T +++  + +P+      + ++ K +   +G G      FVDF+
Sbjct: 2   SSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYG------FVDFD 55

Query: 131 NPACAATALSALQGYRMD 148
           +P+ A  A++AL+   + 
Sbjct: 56  SPSAAQKAVTALKASGVQ 73

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 124

 Score = 42.9 bits (101), Expect = 4e-06
 Identities = 18/80 (22%), Positives = 30/80 (37%), Gaps = 3/80 (3%)

Query: 61  AAARPGHETLPLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGD 120
           + +         P +A   +Y++GLP ++  + V   F+       V   I  +    G 
Sbjct: 9   SPSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKK---LDIVEDSIYIAYGPNGK 65

Query: 121 PLILCFVDFENPACAATALS 140
                FV+F N A    AL 
Sbjct: 66  ATGEGFVEFRNEADYKAALC 85

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 42.3 bits (100), Expect = 5e-06
 Identities = 26/115 (22%), Positives = 45/115 (39%), Gaps = 14/115 (12%)

Query: 63  ARPGHETLPLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVI-KES-KLRGGD 120
              G     LP +   T YV  LP ++ + ++  IF+     + VRLV  K++ K +G  
Sbjct: 1   GSSGSSGKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKG-- 57

Query: 121 PLILCFVDFENPACAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPRSVFGARG 175
               C+V+F+       AL+       D      + LR+  +          + G
Sbjct: 58  ---FCYVEFDEVDSLKEALT------YDGALLGDRSLRVDIAEGRKQDKSGPSSG 103

>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 = 43.4 bits (103), Expect = 6e-06
 Identities = 13/71 (18%), Positives = 30/71 (42%), Gaps = 1/71 (1%)

Query: 79  TLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATA 138
            ++V  +P   +++++  +F  +    E+  V+++           CFV F     A  A
Sbjct: 5   KMFVGQVPRTWSEKDLRELFEQYGAVYEIN-VLRDRSQNPPQSKGCCFVTFYTRKAALEA 63

Query: 139 LSALQGYRMDE 149
            +AL   ++  
Sbjct: 64  QNALHNMKVLP 74

>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 = 41.9 bits (99), Expect = 8e-06
 Identities = 22/74 (29%), Positives = 31/74 (41%), Gaps = 8/74 (10%)

Query: 73  PPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKES---KLRGGDPLILCFVDF 129
               +S + V  +P  + +RE+  +F  F   K VRL  K +     RG       FVDF
Sbjct: 11  KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRG-----FGFVDF 65

Query: 130 ENPACAATALSALQ 143
                A  A +AL 
Sbjct: 66  ITKQDAKKAFNALC 79

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A Length = 126

 Score = 42.2 bits (99), Expect = 8e-06
 Identities = 18/87 (20%), Positives = 25/87 (28%), Gaps = 3/87 (3%)

Query: 54  DDQLPFDAAARPGHETLPLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKE 113
                     + G  +          + + GLP   TK E+   F    G + V   I  
Sbjct: 19  SHMASMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFS---GLEIVPNGITL 75

Query: 114 SKLRGGDPLILCFVDFENPACAATALS 140
                G      FV F +   A  AL 
Sbjct: 76  PVDPEGKITGEAFVQFASQELAEKALG 102

>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 = 41.4 bits (98), Expect = 8e-06
 Identities = 19/80 (23%), Positives = 35/80 (43%), Gaps = 8/80 (10%)

Query: 71  PLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVI-KES-KLRGGDPLILCFVD 128
            L P   ST+YV  LP   T  ++  IF  +    +V ++  K++ K +G     + F+ 
Sbjct: 11  GLAPS-KSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKG-----VAFIL 64

Query: 129 FENPACAATALSALQGYRMD 148
           F +   A     A+   ++ 
Sbjct: 65  FLDKDSAQNCTRAINNKQLF 84

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 41.5 bits (98), Expect = 9e-06
 Identities = 16/77 (20%), Positives = 34/77 (44%), Gaps = 12/77 (15%)

Query: 73  PPDASSTLYVEGLPADSTKREVAHIFRPFVGY-KEVRLVIKESKLRGGDPLILCFVDFEN 131
           PP   +T Y+  +P  +T+ ++  +F+ F G+  + +        +G      CF+ ++ 
Sbjct: 24  PPR-VTTAYIGNIPHFATEADLIPLFQNF-GFILDFKHY----PEKG-----CCFIKYDT 72

Query: 132 PACAATALSALQGYRMD 148
              AA  + AL  +   
Sbjct: 73  HEQAAVCIVALANFPFQ 89

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 41.6 bits (98), Expect = 9e-06
 Identities = 11/61 (18%), Positives = 24/61 (39%), Gaps = 4/61 (6%)

Query: 79  TLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATA 138
           ++Y++G P D+T  ++            +++     K   G      FV F++   A   
Sbjct: 13  SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKG----SIFVVFDSIESAKKF 68

Query: 139 L 139
           +
Sbjct: 69  V 69

>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 = 41.5 bits (98), Expect = 1e-05
 Identities = 15/76 (19%), Positives = 24/76 (31%), Gaps = 11/76 (14%)

Query: 73  PPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENP 132
              AS+ L+V  +    T +E+   F  +    E  +V      +        FV  E  
Sbjct: 6   SGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV------KD-----YAFVHMERA 54

Query: 133 ACAATALSALQGYRMD 148
             A  A+  L      
Sbjct: 55  EDAVEAIRGLDNTEFQ 70

>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 = 41.5 bits (98), Expect = 1e-05
 Identities = 20/108 (18%), Positives = 45/108 (41%), Gaps = 12/108 (11%)

Query: 71  PLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVI-KES-KLRGGDPLILCFVD 128
           P    +  +++V  +P ++T+ ++  IF         RLV  +E+ K +G       F +
Sbjct: 2   PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKG-----YGFCE 56

Query: 129 FENPACAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPRSVFGARGR 176
           +++   A +A+  L G          + LR+  + +   +    + G 
Sbjct: 57  YQDQETALSAMRNLNGREFSG-----RALRVDNAASEKNKEELKSLGT 99

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 41.3 bits (97), Expect = 1e-05
 Identities = 14/93 (15%), Positives = 32/93 (34%), Gaps = 12/93 (12%)

Query: 71  PLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFE 130
           P    AS  +++ GL     + ++    + F     V ++ K    +         V+FE
Sbjct: 15  PHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK----KR-----QALVEFE 65

Query: 131 NPACAATALSALQGYRMDEDDPDSKFLRLQFSR 163
           +   A  A++     ++           + +S 
Sbjct: 66  DVLGACNAVNYAADNQIYIAG---HPAFVNYST 95

>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 = 41.6 bits (98), Expect = 1e-05
 Identities = 17/117 (14%), Positives = 31/117 (26%), Gaps = 14/117 (11%)

Query: 63  ARPGHETLPLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKE-VRLVIKESKLRGGDP 121
              G         A    ++  +P   TK +V          +  V +++  +    G  
Sbjct: 1   GSSGSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNN----GQG 56

Query: 122 LILCFVDFENPACAATALSA---------LQGYRMDEDDPDSKFLRLQFSRNPGPRS 169
           L    V F+N   A  +               + +  +D              GP S
Sbjct: 57  LGQALVQFKNEDDARKSERLHRKKLNGREAFVHVVTLEDMREIEKNPPAQGKSGPSS 113

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 40.7 bits (96), Expect = 1e-05
 Identities = 16/68 (23%), Positives = 24/68 (35%), Gaps = 5/68 (7%)

Query: 73  PPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENP 132
                 T+ + G P + T++ V     P      +R+V      + G      FVDF N 
Sbjct: 6   SGTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGY----IFVDFSNE 60

Query: 133 ACAATALS 140
                AL 
Sbjct: 61  EEVKQALK 68

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 41.5 bits (97), Expect = 1e-05
 Identities = 15/97 (15%), Positives = 30/97 (30%), Gaps = 11/97 (11%)

Query: 67  HETLPLPPDASSTLYVE--GLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLIL 124
           HE +     A+ +L V   GL    ++ ++  +         + +   +           
Sbjct: 15  HEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKP---------Y 65

Query: 125 CFVDFENPACAATALSALQGYRMDEDDPDSKFLRLQF 161
            F  +     +  A   L G  + +D      L L F
Sbjct: 66  SFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNF 102

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 41.8 bits (98), Expect = 1e-05
 Identities = 18/117 (15%), Positives = 40/117 (34%), Gaps = 12/117 (10%)

Query: 62  AARPGHETLPLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDP 121
               G     +       +++ GLP  +T+ ++ + F P      V + I       G+ 
Sbjct: 31  GRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPL-NPVRVHIEIGPDGRVTGE- 88

Query: 122 LILCFVDFENPACAATALSALQGYRMDEDDPDSKFLRLQFSRNPG-PRSVFGARGRR 177
                V+F     A  A+S       D  +   +++ L  +   G     + ++  +
Sbjct: 89  ---ADVEFATHEEAVAAMS------KDRANMQHRYIELFLNSTTGASNGAYSSQVMQ 136

>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 = 40.6 bits (96), Expect = 2e-05
 Identities = 18/96 (18%), Positives = 39/96 (40%), Gaps = 16/96 (16%)

Query: 80  LYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATAL 139
           L++  LP ++T++E+  +F  +    E  ++      +        FV  E+   A  A+
Sbjct: 11  LFIGNLPREATEQEIRSLFEQYGKVLECDII------KN-----YGFVHIEDKTAAEDAI 59

Query: 140 SALQGYRMDEDDPDSKFLRLQFSRNPGPRSVFGARG 175
             L  Y++         + ++ S+N    S   + G
Sbjct: 60  RNLHHYKL-----HGVNINVEASKNKSKASSGPSSG 90

>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 = 40.7 bits (96), Expect = 2e-05
 Identities = 18/80 (22%), Positives = 34/80 (42%), Gaps = 6/80 (7%)

Query: 70  LPLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVI-KESKLRGGDPLILCFVD 128
            P   +A  T++V  L A   +  +  +F       +V +   +E K +        FV 
Sbjct: 9   FPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKS-----FGFVC 63

Query: 129 FENPACAATALSALQGYRMD 148
           F++P   + A++ L G R+ 
Sbjct: 64  FKHPESVSYAIALLNGIRLY 83

>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 = 42.4 bits (100), Expect = 2e-05
 Identities = 21/86 (24%), Positives = 38/86 (44%), Gaps = 14/86 (16%)

Query: 79  TLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATA 138
            L+V  LP D T+ +   +F  +    EV  + ++   RG       F+  E+   A  A
Sbjct: 24  RLFVGNLPTDITEEDFKRLFERYGEPSEVF-INRD---RG-----FGFIRLESRTLAEIA 74

Query: 139 LSALQGYRMDEDDPDSKFLRLQFSRN 164
            + L G  +      S+ LR++F+ +
Sbjct: 75  KAELDGTIL-----KSRPLRIRFATH 95

>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 = 40.2 bits (95), Expect = 2e-05
 Identities = 19/76 (25%), Positives = 32/76 (42%), Gaps = 7/76 (9%)

Query: 75  DASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVI-KES-KLRGGDPLILCFVDFENP 132
                LYV GL  +   + +   F PF    ++++ +  E+ K RG       FV+FE  
Sbjct: 5   TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRG-----FAFVEFELA 59

Query: 133 ACAATALSALQGYRMD 148
             AA A+  +    + 
Sbjct: 60  EDAAAAIDNMNESELF 75

>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 = 40.3 bits (95), Expect = 3e-05
 Identities = 19/83 (22%), Positives = 30/83 (36%), Gaps = 5/83 (6%)

Query: 66  GHETLPLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILC 125
           G             L+V  +P      ++  +F  F    +V ++  E   +G       
Sbjct: 4   GSSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKG-----FG 58

Query: 126 FVDFENPACAATALSALQGYRMD 148
           FV FEN A A  A   L G  ++
Sbjct: 59  FVTFENSADADRAREKLHGTVVE 81

>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 = 40.3 bits (95), Expect = 3e-05
 Identities = 20/103 (19%), Positives = 35/103 (33%), Gaps = 13/103 (12%)

Query: 73  PPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENP 132
                + LY+  L    T  ++  +F      K         K  G       FVD+ + 
Sbjct: 4   GSSGMNKLYIGNLSPAVTADDLRQLFGD---RKLPLAGQVLLK-SG-----YAFVDYPDQ 54

Query: 133 ACAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPRSVFGARG 175
             A  A+  L G    + +   K + + +S +   RS   + G
Sbjct: 55  NWAIRAIETLSG----KVELHGKIMEVDYSVSKKLRSSGPSSG 93

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 41.8 bits (98), Expect = 3e-05
 Identities = 26/134 (19%), Positives = 41/134 (30%), Gaps = 13/134 (9%)

Query: 16  RRAVPGGVTRLPVSDPSVTGRHGATGPDLVQNLRSSSIDDQLPFDAAARPGHETLPLPPD 75
           RR   GG  R      +  GR+        + L      D          G        +
Sbjct: 34  RRVNRGGGPRRNRPAIARGGRNRPAPYSRPKPLPDKWQHDLFDSGCGGGEG-------VE 86

Query: 76  ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKES-KLRGGDPLILCFVDFENPAC 134
             + L V  L    +  ++  +F  F   K+  +    S +  G        V FE  A 
Sbjct: 87  TGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLG-----TADVHFERRAD 141

Query: 135 AATALSALQGYRMD 148
           A  A+   +G  +D
Sbjct: 142 ALKAMKQYKGVPLD 155

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 40.4 bits (95), Expect = 3e-05
 Identities = 20/87 (22%), Positives = 31/87 (35%), Gaps = 7/87 (8%)

Query: 63  ARPGHETLPLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRG-GDP 121
              G             L+V  +P      ++  +F  F    +V ++  E   +G G  
Sbjct: 15  VPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFG-- 72

Query: 122 LILCFVDFENPACAATALSALQGYRMD 148
               FV FEN A A  A   L G  ++
Sbjct: 73  ----FVTFENSADADRAREKLHGTVVE 95

>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 = 41.9 bits (99), Expect = 3e-05
 Identities = 25/103 (24%), Positives = 41/103 (39%), Gaps = 9/103 (8%)

Query: 73  PPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENP 132
           P    ++LYV  L  D T+  +   F P      +R V ++   R        +V+F+ P
Sbjct: 11  PSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIR-VCRDMITRRSLGY--AYVNFQQP 67

Query: 133 ACAATALSALQGYRMDEDDPDSKFLRLQFS-RNPGPRSVFGAR 174
           A A  AL  +    +       K +R+ +S R+P  R      
Sbjct: 68  ADAERALDTMNFDVI-----KGKPVRIMWSQRDPSLRKSGVGN 105

>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 = 39.8 bits (94), Expect = 3e-05
 Identities = 21/76 (27%), Positives = 34/76 (44%), Gaps = 7/76 (9%)

Query: 75  DASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVI-KES-KLRGGDPLILCFVDFENP 132
             SS LYV  L  + T+  +  IF PF     + L+   ++ + +G       F+ F + 
Sbjct: 3   SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKG-----YGFITFSDS 57

Query: 133 ACAATALSALQGYRMD 148
            CA  AL  L G+ + 
Sbjct: 58  ECARRALEQLNGFELA 73

>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 = 41.6 bits (98), Expect = 3e-05
 Identities = 13/102 (12%), Positives = 31/102 (30%), Gaps = 18/102 (17%)

Query: 75  DASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKE-------SKLRGGDPLILCFV 127
             +  LYV  +P   T+  +   F   +    +             ++ +        F+
Sbjct: 2   AMARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKN-----FAFL 56

Query: 128 DFENPACAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPRS 169
           +F +      A+ A  G          + L+++   +  P  
Sbjct: 57  EFRSVDETTQAM-AFDGIIFQG-----QSLKIRRPHDYQPLP 92

>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 = 41.2 bits (97), Expect = 5e-05
 Identities = 20/111 (18%), Positives = 41/111 (36%), Gaps = 13/111 (11%)

Query: 61  AAARPGHETLPLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLV--IKESKLRG 118
            +         + PD++  L++ GLP      +V  +   F   K   LV        +G
Sbjct: 98  PSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKG 157

Query: 119 GDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPRS 169
                  F ++ +      A++ L G ++       K L +Q + + G ++
Sbjct: 158 -----YAFCEYVDINVTDQAIAGLNGMQL-----GDKKLLVQRA-SVGAKN 197

>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 = 41.0 bits (97), Expect = 4e-05
 Identities = 14/91 (15%), Positives = 35/91 (38%), Gaps = 9/91 (9%)

Query: 79  TLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATA 138
            LYV  L    T+  +   F+       ++ ++ +   +    +   FV++     A  A
Sbjct: 2   VLYVGNLDKAITEDILKQYFQVGGPIANIK-IMID---KNNKNVNYAFVEYHQSHDANIA 57

Query: 139 LSALQGYRMDEDDPDSKFLRLQFSRNPGPRS 169
           L  L G ++     ++  +++ ++      S
Sbjct: 58  LQTLNGKQI-----ENNIVKINWAFQSQQSS 83

>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 = 39.9 bits (94), Expect = 4e-05
 Identities = 25/106 (23%), Positives = 44/106 (41%), Gaps = 18/106 (16%)

Query: 74  PDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVI-KES-KLRGGDPLILCFVDFEN 131
              S TL+V+GL  D+T+  +   F    G    R+V  +E+   +G       FVDF +
Sbjct: 12  SQPSKTLFVKGLSEDTTEETLKESFD---GSVRARIVTDRETGSSKG-----FGFVDFNS 63

Query: 132 PACAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPRSVFGARGRR 177
              A  A  A++   +     D   + L +++   P+   G+    
Sbjct: 64  EEDAKAAKEAMEDGEI-----DGNKVTLDWAK---PKGEGGSGPSS 101

>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 = 40.2 bits (94), Expect = 4e-05
 Identities = 18/100 (18%), Positives = 30/100 (30%), Gaps = 13/100 (13%)

Query: 78  STLYVEGLPADSTKREV---AHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPAC 134
           + ++V GL       EV      F  F    +V +    S      P    +V +     
Sbjct: 16  NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSED 75

Query: 135 AATALSALQGYRMDEDDPDSKFLRLQFSR-----NPGPRS 169
           A  A+  +    +D      + L+            GP S
Sbjct: 76  ALRAIQCVNNVVVDG-----RTLKASLGTTKYCSYSGPSS 110

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 39.3 bits (92), Expect = 4e-05
 Identities = 17/77 (22%), Positives = 32/77 (41%), Gaps = 11/77 (14%)

Query: 78  STLYVEGLPA------DSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFEN 131
           S + V+ +P       +  K  +  IF  F          ++ K +G       F+++ +
Sbjct: 2   SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKG-----YIFLEYAS 56

Query: 132 PACAATALSALQGYRMD 148
           PA A  A+    GY++D
Sbjct: 57  PAHAVDAVKNADGYKLD 73

>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 = 39.9 bits (94), Expect = 4e-05
 Identities = 23/103 (22%), Positives = 39/103 (37%), Gaps = 17/103 (16%)

Query: 74  PDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVI-KES-KLRGGDPLILCFVDFEN 131
            D   TL V+ L   ++   +  +F  +    +V +     +   RG       FV F +
Sbjct: 10  VDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRG-----FAFVRFHD 64

Query: 132 PACAATALSALQGYRMDEDDPDSKFLRLQFS-----RNPGPRS 169
              A  A +A+ G  +     D + LR+Q +        GP S
Sbjct: 65  RRDAQDAEAAMDGAEL-----DGRELRVQVARYGRRDLSGPSS 102

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 39.7 bits (93), Expect = 4e-05
 Identities = 14/69 (20%), Positives = 23/69 (33%), Gaps = 5/69 (7%)

Query: 73  PPDASSTLYVEGLPADSTKREVAHIFRPF-VGYKEVRLVIKESKLRGGDPLILCFVDFEN 131
                  + + GLP   +K E+   F    +    + L +       G+     FV F +
Sbjct: 11  DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGE----AFVQFAS 66

Query: 132 PACAATALS 140
              A  AL 
Sbjct: 67  QEIAEKALK 75

>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 = 39.5 bits (93), Expect = 4e-05
 Identities = 17/70 (24%), Positives = 29/70 (41%), Gaps = 7/70 (10%)

Query: 77  SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVI-KES-KLRGGDPLILCFVDFENPAC 134
           S  L+V  L   S++ ++  +F  +    E+   I   + K +G       FV F  P  
Sbjct: 8   SGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKG-----FAFVTFMFPEH 62

Query: 135 AATALSALQG 144
           A  A + + G
Sbjct: 63  AVKAYAEVDG 72

>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 = 39.5 bits (93), Expect = 5e-05
 Identities = 12/96 (12%), Positives = 28/96 (29%), Gaps = 12/96 (12%)

Query: 69  TLPLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKES-KLRGGDPLILCFV 127
                      L++  L  + +  E+           ++ +V   +   R        +V
Sbjct: 9   VEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRK-----FGYV 63

Query: 128 DFENPACAATALSALQGYRMDEDDPDSKFLRLQFSR 163
           DFE+      AL       +         ++L+  +
Sbjct: 64  DFESAEDLEKALE------LTGLKVFGNEIKLEKPK 93

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 40.1 bits (94), Expect = 5e-05
 Identities = 19/78 (24%), Positives = 32/78 (41%), Gaps = 7/78 (8%)

Query: 73  PPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVI-KES-KLRGGDPLILCFVDFE 130
                  LYV GL  +   + +   F PF    ++++ +  E+ K RG       FV+FE
Sbjct: 59  SATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRG-----FAFVEFE 113

Query: 131 NPACAATALSALQGYRMD 148
               AA A+  +    + 
Sbjct: 114 LAEDAAAAIDNMNESELF 131

>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 = 39.6 bits (93), Expect = 6e-05
 Identities = 25/104 (24%), Positives = 44/104 (42%), Gaps = 11/104 (10%)

Query: 75  DASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVI-KESKLRGGDPLILCFVDFENPA 133
           D    L++ GL  ++ ++ +  +F       EV L+  + SK RG       F+ FENPA
Sbjct: 5   DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRG-----FAFITFENPA 59

Query: 134 CAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPRSVFGARGRR 177
            A  A        M+      K ++++ ++ P  +S    R   
Sbjct: 60  DAKNAAKD-----MNGKSLHGKAIKVEQAKKPSFQSGGRRRPPA 98

>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 = 40.2 bits (94), Expect = 6e-05
 Identities = 21/110 (19%), Positives = 42/110 (38%), Gaps = 12/110 (10%)

Query: 61  AAARPGHETLPLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVI-KES-KLRG 118
                 H    +  +  ++L V+ L   ++   +  +F  +    +V +   + + + RG
Sbjct: 54  VTEGSHHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRG 113

Query: 119 GDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPR 168
                  FV F +   A  A+ A+ G        D + LR+Q +R   P 
Sbjct: 114 -----FAFVRFHDKRDAEDAMDAMDGA-----VLDGRELRVQMARYGRPP 153

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 39.3 bits (92), Expect = 7e-05
 Identities = 11/77 (14%), Positives = 25/77 (32%), Gaps = 7/77 (9%)

Query: 74  PDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVI--KESKLRGGDPLILCFVDFEN 131
                 +    L  +  +  +  + R +   +EV +++  +  K  G     L  V F +
Sbjct: 3   QIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLG-----LARVLFTS 57

Query: 132 PACAATALSALQGYRMD 148
              A   +  L    + 
Sbjct: 58  TRGAKETVKNLHLTSVM 74

>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 = 39.4 bits (92), Expect = 7e-05
 Identities = 13/101 (12%), Positives = 28/101 (27%), Gaps = 12/101 (11%)

Query: 63  ARPGHETLPLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPL 122
              G          S  ++V GL     + ++      F     V ++  + +       
Sbjct: 1   GSSGSSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQ------- 53

Query: 123 ILCFVDFENPACAATALSALQGYRMDEDDPDSKFLRLQFSR 163
               V+FEN   A   ++      +       +     +S 
Sbjct: 54  --ALVEFENIDSAKECVTFAADVPVYIAG---QQAFFNYST 89

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 40.0 bits (93), Expect = 7e-05
 Identities = 21/107 (19%), Positives = 36/107 (33%), Gaps = 12/107 (11%)

Query: 61  AAARPGHETLPLPPDASSTL--YVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRG 118
           AA+    +        S  L   VE L    T   +  IF  F    ++    K ++ + 
Sbjct: 10  AASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQA 69

Query: 119 GDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFLRLQFSRNP 165
                   + + +P  A  A  +L G  +         LR+ FS+  
Sbjct: 70  -------LLQYADPVSAQHAKLSLDGQNI---YNACCTLRIDFSKLT 106

>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 = 39.3 bits (92), Expect = 9e-05
 Identities = 16/75 (21%), Positives = 30/75 (40%), Gaps = 7/75 (9%)

Query: 71  PLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVI-KESKL-RGGDPLILCFVD 128
           P       T+++  L  DS +  +  + + F   K VR+V+  +++  +G       F  
Sbjct: 9   PSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKG-----CAFAQ 63

Query: 129 FENPACAATALSALQ 143
           F     A   L+A  
Sbjct: 64  FMTQEAAQKCLAAAS 78

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens} Length = 107

 Score = 39.1 bits (91), Expect = 9e-05
 Identities = 14/70 (20%), Positives = 24/70 (34%), Gaps = 7/70 (10%)

Query: 74  PDASSTLYVEGLPADSTKREVAHIFRPF---VGYKEVRLVIKESKLRGGDPLILCFVDFE 130
            D    +  +GLP   T  +V + F       G   +  ++     R GD      ++ E
Sbjct: 8   VDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGD----ALIEME 63

Query: 131 NPACAATALS 140
           +      AL 
Sbjct: 64  SEQDVQKALE 73

>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 = 38.4 bits (90), Expect = 1e-04
 Identities = 17/92 (18%), Positives = 33/92 (35%), Gaps = 14/92 (15%)

Query: 73  PPDAS-STLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFEN 131
             D + +TLYV GL    T+ ++ + F  F   + + +V ++            F+ F  
Sbjct: 7   GEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQ---------CAFIQFAT 57

Query: 132 PACAATALSALQGYRMDEDDPDSKFLRLQFSR 163
              A  A        +         L +++ R
Sbjct: 58  RQAAEVAAEKSFNKLIVNGRR----LNVKWGR 85

>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 = 38.7 bits (91), Expect = 1e-04
 Identities = 19/76 (25%), Positives = 32/76 (42%), Gaps = 7/76 (9%)

Query: 75  DASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVI-KES-KLRGGDPLILCFVDFENP 132
                LYV GL  +   + +   F PF    ++++ +  E+ K RG       FV+FE  
Sbjct: 10  TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRG-----FAFVEFELA 64

Query: 133 ACAATALSALQGYRMD 148
             AA A+  +    + 
Sbjct: 65  EDAAAAIDNMNESELF 80

>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 = 1e-04
 Identities = 16/87 (18%), Positives = 32/87 (36%), Gaps = 12/87 (13%)

Query: 77  SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAA 136
           S  +++  LP D T+ EV  +  PF     + ++    K +        F++      A 
Sbjct: 16  SRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLML----KGKNQ-----AFIEMNTEEAAN 66

Query: 137 TALSALQGYRMDEDDPDSKFLRLQFSR 163
              + +  Y         + + +QFS 
Sbjct: 67  ---TMVNYYTSVTPVLRGQPIYIQFSN 90

>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 = 38.7 bits (90), Expect = 1e-04
 Identities = 16/92 (17%), Positives = 33/92 (35%), Gaps = 12/92 (13%)

Query: 73  PPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENP 132
               S  +++  LP D T+ EV  +  PF     + ++    K +        F++    
Sbjct: 27  AGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLML----KGKNQ-----AFIEMNTE 77

Query: 133 ACAATALSALQGYRMDEDDPDSKFLRLQFSRN 164
             A    + +  Y         + + +QFS +
Sbjct: 78  EAAN---TMVNYYTSVTPVLRGQPIYIQFSNH 106

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 38.6 bits (90), Expect = 1e-04
 Identities = 17/78 (21%), Positives = 32/78 (41%), Gaps = 11/78 (14%)

Query: 77  SSTLYVEGLP------ADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFE 130
            S + V+ +P       +  K  +  IF  F          ++ K +G       F+++ 
Sbjct: 15  DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKG-----YIFLEYA 69

Query: 131 NPACAATALSALQGYRMD 148
           +PA A  A+    GY++D
Sbjct: 70  SPAHAVDAVKNADGYKLD 87

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 113

 Score = 38.5 bits (90), Expect = 2e-04
 Identities = 24/114 (21%), Positives = 42/114 (36%), Gaps = 18/114 (15%)

Query: 71  PLPPDASSTLYVEGLPADSTKREVAHIFRPF--------VGYKEVRLVI-KESKLRGGDP 121
           P     +S +YV+GL    T  ++A  F+           G   + + + KE+    GD 
Sbjct: 9   PDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGD- 67

Query: 122 LILCFVDFENPACAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPRSVFGARG 175
                V +E+P  A  A+    G            L++  +R   P +   + G
Sbjct: 68  ---ATVSYEDPPTAKAAVEWFDGKDF-----QGSKLKVSLARKKPPMNSGPSSG 113

>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 = 38.0 bits (89), Expect = 2e-04
 Identities = 22/77 (28%), Positives = 36/77 (46%), Gaps = 7/77 (9%)

Query: 74  PDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVI-KES-KLRGGDPLILCFVDFEN 131
                 L+V GL  D+ ++ +  +F  +    EV +V  +E+ + RG       FV FEN
Sbjct: 9   ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRG-----FGFVTFEN 63

Query: 132 PACAATALSALQGYRMD 148
              A  A+ A+ G  +D
Sbjct: 64  IDDAKDAMMAMNGKSVD 80

>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 = 38.0 bits (89), Expect = 2e-04
 Identities = 16/90 (17%), Positives = 34/90 (37%), Gaps = 16/90 (17%)

Query: 79  TLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATA 138
            L+V  L    T+  +   F  F   + V+      KL+        F+ F+    A  A
Sbjct: 13  VLFVRNLANTVTEEILEKAFSQFGKLERVK------KLKD-----YAFIHFDERDGAVKA 61

Query: 139 LSALQGYRMDEDDPDSKFLRLQFSRNPGPR 168
           +  + G  +     + + + + F++ P  +
Sbjct: 62  MEEMNGKDL-----EGENIEIVFAKPPDQK 86

>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 = 37.9 bits (88), Expect = 2e-04
 Identities = 15/94 (15%), Positives = 37/94 (39%), Gaps = 12/94 (12%)

Query: 71  PLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFE 130
            +    S  L++  LP + T+ EV  +  PF     + ++  +++          F++  
Sbjct: 9   KMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQ---------AFLELA 59

Query: 131 NPACAATALSALQGYRMDEDDPDSKFLRLQFSRN 164
               A T ++    Y        ++ + +Q+S +
Sbjct: 60  TEEAAITMVNY---YSAVTPHLRNQPIYIQYSNH 90

>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 = 38.0 bits (89), Expect = 2e-04
 Identities = 20/93 (21%), Positives = 34/93 (36%), Gaps = 6/93 (6%)

Query: 77  SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAA 136
              L+V  L    ++ +V  +F+PF    E  ++        G      FV F +   A 
Sbjct: 15  DRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKG----CAFVKFSSHTEAQ 70

Query: 137 TALSALQGYRMDEDDPDSKFLRLQFSRNPGPRS 169
            A+ AL G +       S  L ++F+       
Sbjct: 71  AAIHALHGSQTMPG--ASSSLVVKFADTDKESG 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 = 37.6 bits (88), Expect = 3e-04
 Identities = 12/79 (15%), Positives = 28/79 (35%), Gaps = 5/79 (6%)

Query: 71  PLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVI-KESKLRGGDPLILCFVDF 129
               +  +T+YV GL    ++  +  +F          +   + +    G      FV+F
Sbjct: 9   ISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVT----GQHQGYGFVEF 64

Query: 130 ENPACAATALSALQGYRMD 148
            +   A  A+  +   ++ 
Sbjct: 65  LSEEDADYAIKIMDMIKLY 83

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A Length = 164

 Score = 38.5 bits (89), Expect = 3e-04
 Identities = 21/109 (19%), Positives = 36/109 (33%), Gaps = 11/109 (10%)

Query: 57  LPFDAAARPGHETLPLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKL 116
           L   AAA      +         + VE L    T   +  IF  F    ++    K ++ 
Sbjct: 27  LAASAAAVDAGMAMA-GQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQF 85

Query: 117 RGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFLRLQFSRNP 165
           +         + + +P  A  A  +L G  +         LR+ FS+  
Sbjct: 86  QA-------LLQYADPVSAQHAKLSLDGQNI---YNACCTLRIDFSKLT 124

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 37.8 bits (88), Expect = 3e-04
 Identities = 21/110 (19%), Positives = 43/110 (39%), Gaps = 12/110 (10%)

Query: 61  AAARPGHETLPLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVI-KES-KLRG 118
                 +   P   +  ++L V+ L   ++   +  +F  +    +V +   + + + RG
Sbjct: 31  GRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRG 90

Query: 119 GDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPR 168
                  FV F +   A  A+ A+ G  +     D + LR+Q +R   P 
Sbjct: 91  -----FAFVRFHDKRDAEDAMDAMDGAVL-----DGRELRVQMARYGRPP 130

>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 = 37.3 bits (87), Expect = 4e-04
 Identities = 16/79 (20%), Positives = 26/79 (32%), Gaps = 6/79 (7%)

Query: 71  PLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKES-KLRGGDPLILCFVDF 129
               +    L V  L    +  ++  +F  F   K+  +    S +  G        V F
Sbjct: 23  GAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLG-----TADVHF 77

Query: 130 ENPACAATALSALQGYRMD 148
           E  A A  A+    G  +D
Sbjct: 78  ERKADALKAMKQYNGVPLD 96

>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 = 37.7 bits (88), Expect = 4e-04
 Identities = 20/112 (17%), Positives = 37/112 (33%), Gaps = 16/112 (14%)

Query: 59  FDAAARPGHETLPLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKES-KLR 117
           FD+    G        +  + L V  L    +  ++  +F  F   K+  +    S +  
Sbjct: 22  FDSGCGGGE-----GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSL 76

Query: 118 GGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPRS 169
           G        V FE  A A  A+   +G  +     D + + +Q   +     
Sbjct: 77  G-----TADVHFERRADALKAMKQYKGVPL-----DGRPMDIQLVASQIDLE 118

>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 = 37.3 bits (87), Expect = 4e-04
 Identities = 12/83 (14%), Positives = 33/83 (39%), Gaps = 7/83 (8%)

Query: 71  PLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVI-KESKL-RGGDPLILCFVD 128
            +    +  L++  +P +  ++++  +F  F    E+ ++  + + + +G       F+ 
Sbjct: 7   GMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKG-----CAFLT 61

Query: 129 FENPACAATALSALQGYRMDEDD 151
           +     A  A SAL   +     
Sbjct: 62  YCERESALKAQSALHEQKTLPGM 84

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 38.1 bits (89), Expect = 5e-04
 Identities = 21/132 (15%), Positives = 44/132 (33%), Gaps = 13/132 (9%)

Query: 46  QNLRSSSIDDQLPFDAAARPGHETLPLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYK 105
            ++ S +   Q+   +AA+             S +YV  +  +  +  +   F PF   K
Sbjct: 2   SHMASMTGGQQMGRGSAAQRQGAL-----AIMSRVYVGSIYYELGEDTIRQAFAPFGPIK 56

Query: 106 EVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFLRLQFSRNP 165
            +  +  +S           FV++E P  A  AL  +    +       + +++    N 
Sbjct: 57  SID-MSWDSVTMKHKGF--AFVEYEVPEAAQLALEQMNSVML-----GGRNIKVGRPSNI 108

Query: 166 GPRSVFGARGRR 177
           G       +   
Sbjct: 109 GQAQPIIDQLAE 120

>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 = 36.1 bits (84), Expect = 7e-04
 Identities = 24/101 (23%), Positives = 40/101 (39%), Gaps = 21/101 (20%)

Query: 74  PDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPA 133
           P   +TLYV G   D T   +   F PF    ++   +   +          FV +E   
Sbjct: 12  PRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLS--MDPPRNCA-------FVTYEKME 60

Query: 134 CAATALSALQGYRMDEDDPDSKFLRLQFSR-----NPGPRS 169
            A  A++ L G ++     +S  L++  +R     + GP S
Sbjct: 61  SADQAVAELNGTQV-----ESVQLKVNIARKQPMLDSGPSS 96

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 118

 Score = 36.4 bits (84), Expect = 9e-04
 Identities = 12/71 (16%), Positives = 22/71 (30%), Gaps = 7/71 (9%)

Query: 73  PPDASSTLYVEGLPADSTKREVAHIFRPF---VGYKEVRLVIKESKLRGGDPLILCFVDF 129
                  + + GLP   +  +V +         G   V  +      + G+     FV+ 
Sbjct: 13  EGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGE----AFVEL 68

Query: 130 ENPACAATALS 140
           E+      AL 
Sbjct: 69  ESEDDVKLALK 79

>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 = 37.2 bits (87), Expect = 9e-04
 Identities = 15/107 (14%), Positives = 34/107 (31%), Gaps = 22/107 (20%)

Query: 75  DASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILC--------- 125
            ++  LYV  +P   T+  +   F          + +       G+P++           
Sbjct: 2   GSARRLYVGNIPFGITEEAMMDFFNAQ-------MRLGGLTQAPGNPVLAVQINQDKNFA 54

Query: 126 FVDFENPACAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPRSVFG 172
           F++F +      A+ A  G          + L+++   +  P     
Sbjct: 55  FLEFRSVDETTQAM-AFDGIIFQG-----QSLKIRRPHDYQPLPGAH 95

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	177
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.9
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.9
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.89
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.89
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.89
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.89
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.88
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.88
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.88
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.88
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.88
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.88
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.88
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.88
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.88
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.88
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.88
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.88
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.88
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.88
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.88
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.88
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.87
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.87
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.87
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.87
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.87
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.87
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.87
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.87
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.87
2div_A	99	TRNA selenocysteine associated protein; structural	99.87
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.87
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.87
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.87
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.87
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.87
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.87
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.86
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.86
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.86
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.86
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.86
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.86
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.86
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.86
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.86
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.86
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.86
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.85
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.85
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.85
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.85
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.85
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.85
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.85
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.85
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.85
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.85
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.85
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.85
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.85
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.85
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.84
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.84
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.84
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.84
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.84
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.84
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.84
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.84
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.84
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.84
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.84
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.84
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.84
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.84
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.84
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.84
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.84
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.84
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.83
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.83
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.83
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.83
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.83
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.83
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.83
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.83
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.83
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.83
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.83
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.83
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.83
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.82
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.82
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.82
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.82
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.82
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.82
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.71
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.82
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.82
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.81
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.81
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.81
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.81
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.81
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.81
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.81
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.81
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.81
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.81
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.81
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.81
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.81
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.81
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.81
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.81
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.81
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.8
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.8
1x5p_A	97	Negative elongation factor E; structure genomics,	99.8
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.8
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.8
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.8
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.8
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.8
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.79
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.79
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.79
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.79
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.79
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.79
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.79
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.78
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.78
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.78
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.78
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.78
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.78
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.78
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.78
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.77
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.77
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.77
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.77
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.76
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.76
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.76
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.76
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.76
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.76
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.76
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.76
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.76
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.75
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.75
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.75
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.75
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.75
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.74
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.74
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.74
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.74
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.74
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.74
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.73
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.73
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.73
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.73
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.72
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.72
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.72
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.71
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.7
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.69
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.69
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.69
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.69
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.68
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.68
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.68
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.67
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.66
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.66
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.65
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.64
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.64
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.64
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.63
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.63
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.62
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.62
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.6
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.59
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.57
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.57
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.57
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.57
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.55
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.55
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.55
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.44
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.27
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.24
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	99.01
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	99.0
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.67
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	98.23
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	98.16
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	98.02
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.94
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	97.74
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.7
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	96.72
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	96.62
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	96.27
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	95.12
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	94.97
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	93.77
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	80.02

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.90  E-value=5.2e-23  Score=140.14  Aligned_cols=89  Identities=25%  Similarity=0.359  Sum_probs=80.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      ++++|||+|||+++|+++|+++|++||.|.+|+++.++   .+++++|||||+|.+.++|++|++.||+..|.+     +
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~---~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g-----~   75 (95)
T 2dnz_A            4 GSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDS---DTGRSKGYGFITFSDSECARRALEQLNGFELAG-----R   75 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCS---SSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSS-----S
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecC---CCCceeeEEEEEECCHHHHHHHHHHhCCCeeCC-----c
Confidence            37999999999999999999999999999999999886   568899999999999999999999999999976     4


Q ss_pred             ceEEEeecCCCCCCCCC
Q 030444          156 FLRLQFSRNPGPRSVFG  172 (177)
Q Consensus       156 ~l~V~~a~~~~~r~~~g  172 (177)
                      .|+|+|++.+..+..+.
T Consensus        76 ~l~V~~a~~~~~~~~~~   92 (95)
T 2dnz_A           76 PMRVGHVTERLDGGSGP   92 (95)
T ss_dssp             CCEEEESSCCCCCCCCC
T ss_pred             EEEEEEcccccCCCCCC
Confidence            79999998776555443

>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=99.90  E-value=1.7e-23  Score=144.70  Aligned_cols=80  Identities=24%  Similarity=0.445  Sum_probs=75.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|.+|+|+.++   .+++++|||||+|.+.++|++|++.|||..|.+     ++
T Consensus        19 gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~---~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g-----r~   90 (99)
T 4fxv_A           19 GTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDK---VAGHSLGYGFVNYVTAKDAERAINTLNGLRLQS-----KT   90 (99)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECS---SSCCEEEEEEEEESSHHHHHHHHHHHTTCEETT-----EE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecC---CCCcccccEEEEECCHHHHHHHHHHhCCCEECC-----EE
Confidence            6899999999999999999999999999999999987   678999999999999999999999999999966     58


Q ss_pred             eEEEeecC
Q 030444          157 LRLQFSRN  164 (177)
Q Consensus       157 l~V~~a~~  164 (177)
                      |+|+||++
T Consensus        91 l~V~~AkP   98 (99)
T 4fxv_A           91 IKVSYARP   98 (99)
T ss_dssp             CEEEECCB
T ss_pred             EEEEEeeC
Confidence            99999963

>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=99.89  E-value=1.2e-22  Score=143.21  Aligned_cols=89  Identities=20%  Similarity=0.436  Sum_probs=80.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|.+|+|+.++   .+++++|||||+|.+.++|++|++.||+..|.+     +.
T Consensus        25 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~---~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g-----~~   96 (115)
T 2cpz_A           25 GANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDK---QTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGM-----KR   96 (115)
T ss_dssp             TCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECS---SSCSEEEEEEEECSSHHHHHHHHHHHTTCEETT-----EE
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC---CCCCcCccEEEEECCHHHHHHHHHHcCCCEECC-----EE
Confidence            6899999999999999999999999999999999887   578899999999999999999999999999976     58


Q ss_pred             eEEEeecCCCCCCCCCC
Q 030444          157 LRLQFSRNPGPRSVFGA  173 (177)
Q Consensus       157 l~V~~a~~~~~r~~~g~  173 (177)
                      |+|+|++.+..+....+
T Consensus        97 l~V~~a~~~~~~~~~~~  113 (115)
T 2cpz_A           97 LKVQLKRSKNDSKSGPS  113 (115)
T ss_dssp             CEEECCCCSCCCCCCCC
T ss_pred             EEEEEcCCCCcCCCCCC
Confidence            99999988766554433

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.89  E-value=2.5e-22  Score=137.93  Aligned_cols=89  Identities=18%  Similarity=0.291  Sum_probs=80.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|.+|+|+.++   .+++++|||||+|.+.++|++|++ ||+..|.+     +.
T Consensus        10 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~---~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g-----~~   80 (99)
T 2dgs_A           10 SNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDA---EKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMG-----KK   80 (99)
T ss_dssp             CCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCT---TTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSS-----CB
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC---CCCCCCceEEEEECCHHHHHHHHH-hCCCEECC-----eE
Confidence            7999999999999999999999999999999999886   568899999999999999999998 99999976     48


Q ss_pred             eEEEeecCCCCCCCCCCC
Q 030444          157 LRLQFSRNPGPRSVFGAR  174 (177)
Q Consensus       157 l~V~~a~~~~~r~~~g~~  174 (177)
                      |+|+|++.+..+....++
T Consensus        81 l~V~~a~~~~~~~~~~~~   98 (99)
T 2dgs_A           81 VEVKRAEPRDSKSSGPSS   98 (99)
T ss_dssp             CEEEECCCCCCCCCCSSC
T ss_pred             EEEEECCCCcccCCCCCC
Confidence            999999887666654443

>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=99.89  E-value=1.9e-22  Score=139.88  Aligned_cols=91  Identities=15%  Similarity=0.128  Sum_probs=80.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      +.++|||+|||+++|+++|+++|++||.|.+|+|+.++   .+++++|||||+|.+.++|++|++.||+..|.+     +
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~---~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g-----~   85 (105)
T 1x5u_A           14 QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDR---VTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYG-----K   85 (105)
T ss_dssp             TTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCS---SSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSS-----C
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecC---CCCcCCcEEEEEECCHHHHHHHHHHhCCCeECC-----e
Confidence            37999999999999999999999999999999998886   578899999999999999999999999999976     4


Q ss_pred             ceEEEeecCCCCCCCCCCC
Q 030444          156 FLRLQFSRNPGPRSVFGAR  174 (177)
Q Consensus       156 ~l~V~~a~~~~~r~~~g~~  174 (177)
                      .|+|+|++.+..+...+.+
T Consensus        86 ~l~v~~a~~~~~~~~~~~~  104 (105)
T 1x5u_A           86 PIRVNKASAHNKNLSGPSS  104 (105)
T ss_dssp             BCEEEETTTTSCCCCCCCC
T ss_pred             EEEEEECCCCCcCCCCCCC
Confidence            8999999887655544433

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.89  E-value=2.8e-22  Score=138.75  Aligned_cols=94  Identities=23%  Similarity=0.434  Sum_probs=81.4

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCC
Q 030444           72 LPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDD  151 (177)
Q Consensus        72 ~p~~~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~  151 (177)
                      .+..+.++|||+|||+++|+++|+++|++|+ |.+|+|+.++   .+++++|||||+|.+.++|++|+ .||+..|.+  
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~---~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g--   82 (103)
T 2dng_A           10 LPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDK---DTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGD--   82 (103)
T ss_dssp             CCSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECS---SSCSEEEEEEEEESSHHHHHHHG-GGTTCEETT--
T ss_pred             CCCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecC---CCCccceEEEEEECCHHHHHHHH-hhCCCeECC--
Confidence            3344479999999999999999999999996 9999999987   67889999999999999999999 899999966  


Q ss_pred             CCCcceEEEeecCCCCCCCCCCCC
Q 030444          152 PDSKFLRLQFSRNPGPRSVFGARG  175 (177)
Q Consensus       152 ~~~r~l~V~~a~~~~~r~~~g~~g  175 (177)
                         +.|+|+|++.+..+..+.++|
T Consensus        83 ---~~l~V~~a~~~~~~~~~~~~G  103 (103)
T 2dng_A           83 ---RSLRVDIAEGRKQDKSGPSSG  103 (103)
T ss_dssp             ---EECEEEECCCCCCCCSSCCCC
T ss_pred             ---eEEEEEEecCCCCCCCCCCCC
Confidence               589999998876665544443

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.88  E-value=4.9e-22  Score=137.42  Aligned_cols=86  Identities=21%  Similarity=0.441  Sum_probs=78.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      +.++|||+|||+++|+++|+++|++||.|.+|+|+.++   .+++++|||||+|.+.++|++|++.||+..|.+     +
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~---~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g-----~   85 (103)
T 2cq0_A           14 DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDK---TTGQSKGFAFISFHRREDAARAIAGVSGFGYDH-----L   85 (103)
T ss_dssp             SSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECS---SSCSEEEEEEEEESSHHHHHHHHHHTTTCEETT-----E
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecC---CCCceeeEEEEEECCHHHHHHHHHHcCCCeeCC-----c
Confidence            37999999999999999999999999999999999886   578899999999999999999999999999976     5


Q ss_pred             ceEEEeecCCCCCC
Q 030444          156 FLRLQFSRNPGPRS  169 (177)
Q Consensus       156 ~l~V~~a~~~~~r~  169 (177)
                      .|+|+|++.+..+.
T Consensus        86 ~l~v~~a~~~~~~~   99 (103)
T 2cq0_A           86 ILNVEWAKPSTNSG   99 (103)
T ss_dssp             ECEEEESSCCCCSC
T ss_pred             EEEEEECCCCCCCC
Confidence            89999998765554

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.88  E-value=7.3e-22  Score=136.54  Aligned_cols=90  Identities=21%  Similarity=0.331  Sum_probs=79.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCC
Q 030444           75 DASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDS  154 (177)
Q Consensus        75 ~~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~  154 (177)
                      .+.++|||+|||+++|+++|+++|++||.|.+|+|+.+     +++++|||||+|.+.++|++|++.||+..|.+     
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~-----~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g-----   82 (103)
T 2d9p_A           13 YQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-----GGRSKGFGFVCFSSPEEATKAVTEMNGRIVAT-----   82 (103)
T ss_dssp             SSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC-----SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSS-----
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC-----CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCC-----
Confidence            34799999999999999999999999999999999876     47788999999999999999999999999966     


Q ss_pred             cceEEEeecCCCCCCCCCCC
Q 030444          155 KFLRLQFSRNPGPRSVFGAR  174 (177)
Q Consensus       155 r~l~V~~a~~~~~r~~~g~~  174 (177)
                      +.|+|+|++.+..+....+.
T Consensus        83 ~~l~V~~a~~~~~~~~~~~~  102 (103)
T 2d9p_A           83 KPLYVALAQRKEERQSGPSS  102 (103)
T ss_dssp             SBCEEEECSSCCCCCCCCCC
T ss_pred             cEEEEEEecccccCCCCCCC
Confidence            48999999887666654433

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.88  E-value=2.2e-22  Score=139.16  Aligned_cols=87  Identities=22%  Similarity=0.280  Sum_probs=79.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      +.++|||+|||+++|+++|+++|++||.|.+|+|+.++   .+++++|||||+|.+.++|++|++.||+..|.+     +
T Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~---~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g-----~   83 (103)
T 2dnm_A           12 GMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREP---HTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDG-----R   83 (103)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCS---SSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTT-----B
T ss_pred             CCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCC---CCCCCCeEEEEEECCHHHHHHHHHHcCCCEECC-----c
Confidence            37999999999999999999999999999999998886   568899999999999999999999999999976     5


Q ss_pred             ceEEEeecCCCCCCC
Q 030444          156 FLRLQFSRNPGPRSV  170 (177)
Q Consensus       156 ~l~V~~a~~~~~r~~  170 (177)
                      .|+|+|++...++..
T Consensus        84 ~l~V~~a~~~~~~~~   98 (103)
T 2dnm_A           84 ELRVQVARYGRRDLS   98 (103)
T ss_dssp             CCEEEECSSCCSCCC
T ss_pred             EEEEEECCcCCCCCC
Confidence            799999987655544

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.88  E-value=1.7e-22  Score=139.38  Aligned_cols=90  Identities=18%  Similarity=0.291  Sum_probs=81.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|.+|+|+.++   .+++++|||||+|.+.++|++|++.||+..|.+     +.
T Consensus        12 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~---~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g-----~~   83 (102)
T 2cqb_A           12 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDY---ETEKHRGFAFVEFELAEDAAAAIDNMNESELFG-----RT   83 (102)
T ss_dssp             CSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCS---SSCCCSSEEEECCSSHHHHHHHHHHHTTEEETT-----EE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecC---CCCCcceEEEEEECCHHHHHHHHHHhCCCEECC-----cE
Confidence            7999999999999999999999999999999998886   568899999999999999999999999999976     58


Q ss_pred             eEEEeecCCCCCCCCCCC
Q 030444          157 LRLQFSRNPGPRSVFGAR  174 (177)
Q Consensus       157 l~V~~a~~~~~r~~~g~~  174 (177)
                      |+|+|++.+..+....+.
T Consensus        84 l~V~~a~~~~~~~~~~~~  101 (102)
T 2cqb_A           84 IRVNLAKPMRIKESGPSS  101 (102)
T ss_dssp             EEEEECCCCCCCCCCCCC
T ss_pred             EEEEeCCCCCCCCCCCCC
Confidence            999999887666654443

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.88  E-value=2.6e-22  Score=138.51  Aligned_cols=87  Identities=23%  Similarity=0.334  Sum_probs=78.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|.+|+|+.++   .+++++|||||+|.+.++|++|++.||+..|.+     +.
T Consensus        12 ~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~---~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g-----~~   83 (102)
T 1x5s_A           12 EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDR---ETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDG-----RQ   83 (102)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCS---SSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTS-----CC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCC---CCCCcccEEEEEECCHHHHHHHHHHhCCCEECC-----eE
Confidence            7999999999999999999999999999999999876   568899999999999999999999999999976     47


Q ss_pred             eEEEeecCCCCCCCC
Q 030444          157 LRLQFSRNPGPRSVF  171 (177)
Q Consensus       157 l~V~~a~~~~~r~~~  171 (177)
                      |+|+|++.+..+...
T Consensus        84 l~v~~a~~~~~~~~~   98 (102)
T 1x5s_A           84 IRVDQAGKSSDNRSG   98 (102)
T ss_dssp             CEEEEEECCCCCCCC
T ss_pred             EEEEECCCCCCCCCC
Confidence            999999887555433

>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=99.88  E-value=3.2e-22  Score=138.69  Aligned_cols=89  Identities=20%  Similarity=0.304  Sum_probs=78.3

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCC-CCcceEEEEEecCHHHHHHHHHHhCCCeeCCCC
Q 030444           73 PPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRG-GDPLILCFVDFENPACAATALSALQGYRMDEDD  151 (177)
Q Consensus        73 p~~~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~-g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~  151 (177)
                      +..+.++|||+|||+++|+++|+++|++|| |.+|+|+.++   .+ ++++|||||+|.+.++|++|+ .||+..|.+  
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~---~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g--   83 (104)
T 1wi8_A           11 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREP---SNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGN--   83 (104)
T ss_dssp             CSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCS---SCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETT--
T ss_pred             CCCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCC---CCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCC--
Confidence            334479999999999999999999999999 9999998876   44 889999999999999999999 999999966  


Q ss_pred             CCCcceEEEeecCCCCCCCC
Q 030444          152 PDSKFLRLQFSRNPGPRSVF  171 (177)
Q Consensus       152 ~~~r~l~V~~a~~~~~r~~~  171 (177)
                         +.|+|+|++.+..+..+
T Consensus        84 ---~~l~V~~a~~~~~~~~~  100 (104)
T 1wi8_A           84 ---KRIRVDVADQAQDKDSG  100 (104)
T ss_dssp             ---EECEEEECCCCCCCCCC
T ss_pred             ---cEEEEEEccCCCCCCCC
Confidence               58999999887655543

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.88  E-value=1.3e-22  Score=142.77  Aligned_cols=81  Identities=15%  Similarity=0.148  Sum_probs=76.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|.+|+|+.++   .+++++|||||+|++.++|++|++.||+..|.+     +.
T Consensus         6 ~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~---~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~g-----r~   77 (110)
T 3s8s_A            6 LKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHP---RTRKHLGLARVLFTSTRGAKETVKNLHLTSVMG-----NI   77 (110)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT---TTCCEEEEEEEEESSHHHHHHHHHHHTTCEETT-----EE
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECC---CCCceeeEEEEEECCHHHHHHHHHHhCCCEECC-----eE
Confidence            6899999999999999999999999999999999987   678999999999999999999999999999976     58


Q ss_pred             eEEEeecCC
Q 030444          157 LRLQFSRNP  165 (177)
Q Consensus       157 l~V~~a~~~  165 (177)
                      |+|++++..
T Consensus        78 i~V~~a~~~   86 (110)
T 3s8s_A           78 IHAQLDIKG   86 (110)
T ss_dssp             CEEEECSTT
T ss_pred             EEEEECCCC
Confidence            999999654

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.88  E-value=7.3e-22  Score=137.21  Aligned_cols=87  Identities=26%  Similarity=0.359  Sum_probs=78.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeec-CcccCCCCcceEEEEEecCHHHHHHHHHHh-CCCeeCCCCCC
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIK-ESKLRGGDPLILCFVDFENPACAATALSAL-QGYRMDEDDPD  153 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~-~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l-~g~~l~~~~~~  153 (177)
                      +.++|||+|||+++|+++|+++|++||.|..|+|+.+ +   .+++++|||||+|.+.++|++|++.| |+..|.+    
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~---~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g----   86 (107)
T 2cph_A           14 TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMT---GTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYG----   86 (107)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCS---SSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSS----
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCC---CCCCcCceEEEEECCHHHHHHHHHHhccCCeECC----
Confidence            3799999999999999999999999999999999887 4   56889999999999999999999999 9999976    


Q ss_pred             CcceEEEeecCCCCCCC
Q 030444          154 SKFLRLQFSRNPGPRSV  170 (177)
Q Consensus       154 ~r~l~V~~a~~~~~r~~  170 (177)
                       +.|+|+|++.+..+..
T Consensus        87 -~~l~v~~a~~~~~~~~  102 (107)
T 2cph_A           87 -RRLVLEWADSEVTVQS  102 (107)
T ss_dssp             -CBCEEEECCCCCCCCC
T ss_pred             -CEEEEEeCCCCCCCCC
Confidence             4899999988755543

>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=99.88  E-value=1.2e-21  Score=135.81  Aligned_cols=88  Identities=23%  Similarity=0.324  Sum_probs=78.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|.+|+|+.++    +++++|||||+|.+.++|++|++.||+..+.+.  .+++
T Consensus        15 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~----~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg--~~~~   88 (105)
T 2dnh_A           15 DRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP----DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPG--ASSS   88 (105)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS----SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTT--CSSC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC----CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCC--CCcc
Confidence            7999999999999999999999999999999999885    588999999999999999999999999999762  1257


Q ss_pred             eEEEeecCCCCCCC
Q 030444          157 LRLQFSRNPGPRSV  170 (177)
Q Consensus       157 l~V~~a~~~~~r~~  170 (177)
                      |+|+|++.+..+..
T Consensus        89 l~V~~a~~~~~~~~  102 (105)
T 2dnh_A           89 LVVKFADTDKESGP  102 (105)
T ss_dssp             CEEEESCSSCCCSC
T ss_pred             EEEEECccCcccCC
Confidence            99999988765543

>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=99.88  E-value=4.6e-22  Score=136.53  Aligned_cols=89  Identities=22%  Similarity=0.322  Sum_probs=80.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      +++|||+|||+++|+++|+++|++||.|.+|+|+.++   .+++++|||||+|.+.++|++|++.||+..|.+     +.
T Consensus         8 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~---~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g-----~~   79 (99)
T 1whw_A            8 SGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDS---LTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQG-----RM   79 (99)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCT---TTCCCCSEEEEEESSHHHHHHHHHHTTTEESSS-----CE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecC---CCCCcCeEEEEEECCHHHHHHHHHHhCCCEECC-----cE
Confidence            7899999999999999999999999999999998876   578899999999999999999999999999976     48


Q ss_pred             eEEEeecCCCCCCCCCC
Q 030444          157 LRLQFSRNPGPRSVFGA  173 (177)
Q Consensus       157 l~V~~a~~~~~r~~~g~  173 (177)
                      |+|+|++.+..+...++
T Consensus        80 l~V~~a~~~~~~~~~~~   96 (99)
T 1whw_A           80 LHVLPSTIKKEASQSGP   96 (99)
T ss_dssp             EEEEECCCCSTTCCCCC
T ss_pred             EEEEEcCCCcccccCCC
Confidence            99999988766554443

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.88  E-value=4.3e-22  Score=139.92  Aligned_cols=91  Identities=22%  Similarity=0.354  Sum_probs=80.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEE--------EEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCee
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYK--------EVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRM  147 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~--------~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l  147 (177)
                      +.++|||+|||+++|+++|+++|++||.|.        .|+|+.++   .+++++|||||+|.+.++|++|++.||+..|
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~---~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~   90 (113)
T 2cpe_A           14 DNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDK---ETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   90 (113)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCT---TTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeC---CCCCeeeEEEEEECCHHHHHHHHHHcCCCcc
Confidence            379999999999999999999999999998        69998876   5788999999999999999999999999999


Q ss_pred             CCCCCCCcceEEEeecCCCCCCCCCCC
Q 030444          148 DEDDPDSKFLRLQFSRNPGPRSVFGAR  174 (177)
Q Consensus       148 ~~~~~~~r~l~V~~a~~~~~r~~~g~~  174 (177)
                      .+     +.|+|+|++.+..+..+.+.
T Consensus        91 ~g-----~~l~V~~a~~~~~~~~~~~s  112 (113)
T 2cpe_A           91 QG-----SKLKVSLARKKPPMNSGPSS  112 (113)
T ss_dssp             TT-----EECEEECSSCCCCSTTCCCC
T ss_pred             CC-----CEEEEEECCCCCCCCCCCCC
Confidence            66     58999999887666554433

>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=99.88  E-value=2.7e-22  Score=139.29  Aligned_cols=91  Identities=13%  Similarity=0.173  Sum_probs=79.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      +.++|||+|||+++|+++|+++|++||.|.+|+|+.++   .+++++|||||+|.+.++|++|++.||+..+...  .++
T Consensus        12 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~---~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~--~g~   86 (106)
T 2dgp_A           12 DAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDR---FTGMHKGCAFLTYCERESALKAQSALHEQKTLPG--MNR   86 (106)
T ss_dssp             TCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCS---SSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTT--CSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecC---CCCCcceEEEEEECCHHHHHHHHHHhcCCcccCC--CCc
Confidence            37899999999999999999999999999999999887   5788999999999999999999999999887321  235


Q ss_pred             ceEEEeecCCCCCCCC
Q 030444          156 FLRLQFSRNPGPRSVF  171 (177)
Q Consensus       156 ~l~V~~a~~~~~r~~~  171 (177)
                      +|+|+|++.+..+..+
T Consensus        87 ~l~v~~a~~~~~~~~~  102 (106)
T 2dgp_A           87 PIQVKPADSESRGGSG  102 (106)
T ss_dssp             CCEEEECCCCSCCCCC
T ss_pred             eEEEEECCcccccCCC
Confidence            8999999887655543

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.88  E-value=1.9e-22  Score=137.56  Aligned_cols=87  Identities=13%  Similarity=0.265  Sum_probs=79.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEE-EEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEV-RLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v-~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      +++|||+|||+++|+++|+++|++||.|.+| +|+.++   .+++++|||||+|.+.++|++|++.||+..|.+     +
T Consensus         5 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~---~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g-----~   76 (96)
T 1x5t_A            5 SSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDP---DTGNSKGYAFINFASFDASDAAIEAMNGQYLCN-----R   76 (96)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCT---TTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETT-----E
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcC---CCCCcCeEEEEEECCHHHHHHHHHHcCCCEECC-----E
Confidence            7999999999999999999999999999999 998876   578899999999999999999999999999966     5


Q ss_pred             ceEEEeecCCCCCCCC
Q 030444          156 FLRLQFSRNPGPRSVF  171 (177)
Q Consensus       156 ~l~V~~a~~~~~r~~~  171 (177)
                      .|+|+|++.+..+..+
T Consensus        77 ~l~v~~a~~~~~~~~~   92 (96)
T 1x5t_A           77 PITVSYAFKKDSKGSG   92 (96)
T ss_dssp             ECEEEESCCCCCCCCC
T ss_pred             EEEEEEecccCCCCCC
Confidence            8999999877665543

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.88  E-value=6.2e-22  Score=143.90  Aligned_cols=88  Identities=20%  Similarity=0.380  Sum_probs=80.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCC
Q 030444           74 PDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPD  153 (177)
Q Consensus        74 ~~~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~  153 (177)
                      +.+.++|||+|||+++|+++|+++|+.||.|.+|+|+.++   .+++++|||||+|.+.++|++|++.||+..|.+    
T Consensus        39 ~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~---~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g----  111 (139)
T 1u6f_A           39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDR---ETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILN----  111 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEET---TTTEEEEEEEEEESSHHHHHHHHHHTTTEECSS----
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcC---CCCCcceEEEEEECCHHHHHHHHHHhCCCEECC----
Confidence            3447999999999999999999999999999999999887   568899999999999999999999999999976    


Q ss_pred             CcceEEEeecCCCCCC
Q 030444          154 SKFLRLQFSRNPGPRS  169 (177)
Q Consensus       154 ~r~l~V~~a~~~~~r~  169 (177)
                       +.|+|+|++.+..+.
T Consensus       112 -~~l~v~~a~~~~~~~  126 (139)
T 1u6f_A          112 -KRLKVALAASGHQRP  126 (139)
T ss_dssp             -CEEEEEESSCCCCCC
T ss_pred             -eEEEEEECCCCCCCC
Confidence             489999998876555

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.88  E-value=1.6e-21  Score=134.19  Aligned_cols=83  Identities=28%  Similarity=0.521  Sum_probs=76.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|.+|+|+.++    +++++|||||+|.+.++|++|++.||+..|.+     +.
T Consensus        17 ~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~----~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g-----~~   87 (100)
T 2do4_A           17 KHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR----AGKPKGLAYVEYENESQASQAVMKMDGMTIKE-----NI   87 (100)
T ss_dssp             CSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT----TSCEEEEEEEEESSHHHHHHHHHHHTTEESSS-----CE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC----CCCEEeEEEEEECCHHHHHHHHHHhCCCEECC-----EE
Confidence            6899999999999999999999999999999999875    68899999999999999999999999999976     48


Q ss_pred             eEEEeecCCCCC
Q 030444          157 LRLQFSRNPGPR  168 (177)
Q Consensus       157 l~V~~a~~~~~r  168 (177)
                      |+|+|++.+..+
T Consensus        88 l~v~~a~~~~~~   99 (100)
T 2do4_A           88 IKVAISNSGPSS   99 (100)
T ss_dssp             EEEEECCCCSCC
T ss_pred             EEEEECCCCCCC
Confidence            999999776543

>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=99.88  E-value=1.2e-21  Score=137.02  Aligned_cols=87  Identities=20%  Similarity=0.359  Sum_probs=79.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhC------CCeeCC
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQ------GYRMDE  149 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~------g~~l~~  149 (177)
                      +.++|||+|||+++|+++|+++|++||.|.+|+|+.++   .+++++|||||+|.+.++|++|++.||      +..|.+
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~---~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g   90 (111)
T 1x4h_A           14 EGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHP---DTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDG   90 (111)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCS---SSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecC---CCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcC
Confidence            37899999999999999999999999999999999887   578899999999999999999999999      999966


Q ss_pred             CCCCCcceEEEeecCCCCCCC
Q 030444          150 DDPDSKFLRLQFSRNPGPRSV  170 (177)
Q Consensus       150 ~~~~~r~l~V~~a~~~~~r~~  170 (177)
                           +.|+|+|++.+..+..
T Consensus        91 -----~~l~v~~a~~~~~~~~  106 (111)
T 1x4h_A           91 -----RQLKVDLAVTRDEAAS  106 (111)
T ss_dssp             -----CEEEEECCCCCCCCCC
T ss_pred             -----EEEEEEECCCCccCCC
Confidence                 4899999987755543

>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=99.87  E-value=4.4e-22  Score=133.29  Aligned_cols=82  Identities=22%  Similarity=0.319  Sum_probs=74.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      +.++|||+|||+++|+++|+++|++||.|.+|+++.++   .+++++|||||+|.+.++|++|++.||+..+.+     +
T Consensus         5 ~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~---~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g-----~   76 (87)
T 3bs9_A            5 SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDM---ATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGG-----R   76 (87)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT---TTCCEEEEEEEEESSHHHHHHHHHHHTTCEETT-----E
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecC---CCCccceEEEEEECCHHHHHHHHHHcCCCEECC-----e
Confidence            37899999999999999999999999999999999886   578899999999999999999999999999966     5


Q ss_pred             ceEEEeecCC
Q 030444          156 FLRLQFSRNP  165 (177)
Q Consensus       156 ~l~V~~a~~~  165 (177)
                      .|+|+|++.+
T Consensus        77 ~l~v~~a~~k   86 (87)
T 3bs9_A           77 QIRTNWATRK   86 (87)
T ss_dssp             ECEEEEEC--
T ss_pred             EEEEEecCCC
Confidence            8999999764

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.87  E-value=1.1e-21  Score=134.84  Aligned_cols=83  Identities=22%  Similarity=0.356  Sum_probs=75.9

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHhhCCCCCEEE--------EEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCC
Q 030444           73 PPDASSTLYVEGLPADSTKREVAHIFRPFVGYKE--------VRLVIKESKLRGGDPLILCFVDFENPACAATALSALQG  144 (177)
Q Consensus        73 p~~~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~--------v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g  144 (177)
                      ++.+.++|||+|||+++|+++|+++|++||.|.+        |+++.++   .+++++|||||+|.+.++|++|++.||+
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~---~~g~~~G~afV~f~~~~~a~~Ai~~l~g   85 (99)
T 2la6_A            9 SHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDR---ETGKLKGEATVSFDDPPSAKAAIDWFDG   85 (99)
T ss_dssp             SCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECT---TTCSEEEEEEEEBSSHHHHHHHHHHHTT
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecC---CCCCeeeEEEEEECCHHHHHHHHHHhCC
Confidence            3444799999999999999999999999999999        9999886   5789999999999999999999999999


Q ss_pred             CeeCCCCCCCcceEEEeec
Q 030444          145 YRMDEDDPDSKFLRLQFSR  163 (177)
Q Consensus       145 ~~l~~~~~~~r~l~V~~a~  163 (177)
                      ..|.+     +.|+|+||+
T Consensus        86 ~~~~g-----~~l~V~~A~   99 (99)
T 2la6_A           86 KEFSG-----NPIKVSFAT   99 (99)
T ss_dssp             CBSSS-----SBCEEEECC
T ss_pred             CEeCC-----cEEEEEecC
Confidence            99976     589999984

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.87  E-value=5.3e-22  Score=135.96  Aligned_cols=89  Identities=24%  Similarity=0.313  Sum_probs=77.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      +++|||+|||+++|+++|+++|++||.|..|+|+.++....+++++|||||+|.+.++|++|++.||+..|.+     +.
T Consensus         5 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g-----~~   79 (98)
T 2cpf_A            5 SSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDG-----HK   79 (98)
T ss_dssp             CCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETT-----EE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCC-----eE
Confidence            7899999999999999999999999999999999876211144789999999999999999999999999976     58


Q ss_pred             eEEEeecCCCCCCC
Q 030444          157 LRLQFSRNPGPRSV  170 (177)
Q Consensus       157 l~V~~a~~~~~r~~  170 (177)
                      |+|+|++.+..+..
T Consensus        80 l~V~~a~~~~~~~~   93 (98)
T 2cpf_A           80 LEVRISERATKPAS   93 (98)
T ss_dssp             CEEECSSCSSCCCC
T ss_pred             EEEEEccCCCCCCC
Confidence            99999987655443

>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=99.87  E-value=4.5e-22  Score=142.36  Aligned_cols=85  Identities=20%  Similarity=0.341  Sum_probs=77.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|.+|+|+.++   .+++++|||||+|.+.++|++|++.||+..|.+     +.
T Consensus        22 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~---~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g-----~~   93 (126)
T 3ex7_B           22 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDR---RTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMG-----QP   93 (126)
T ss_dssp             SEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCT---TTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSS-----SB
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecC---CCCccceEEEEEECCHHHHHHHHHHhCCCeeCC-----eE
Confidence            7899999999999999999999999999999998886   578899999999999999999999999999966     48


Q ss_pred             eEEEeecCCCCCC
Q 030444          157 LRLQFSRNPGPRS  169 (177)
Q Consensus       157 l~V~~a~~~~~r~  169 (177)
                      |+|+|++.+.++.
T Consensus        94 l~v~~a~~~~~~~  106 (126)
T 3ex7_B           94 ISVDWCFVRGPPK  106 (126)
T ss_dssp             CEEEESEESSSCC
T ss_pred             EEEEEecCCCCCC
Confidence            9999998764433

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.87  E-value=2.3e-21  Score=135.41  Aligned_cols=84  Identities=25%  Similarity=0.471  Sum_probs=74.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      +.++|||+|||+++|+++|+++|++||.|..|+|..+      +.++|||||+|.+.++|++|++.||+..|.+     +
T Consensus        21 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~------~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g-----~   89 (109)
T 1x4a_A           21 NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR------RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDG-----Y   89 (109)
T ss_dssp             CSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS------SSSSCCEEEEESCHHHHHHHHHHHTTCEETT-----E
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC------CCCCcEEEEEECCHHHHHHHHHHcCCCEECC-----e
Confidence            3789999999999999999999999999999998554      3478899999999999999999999999966     5


Q ss_pred             ceEEEeecCCCCCCC
Q 030444          156 FLRLQFSRNPGPRSV  170 (177)
Q Consensus       156 ~l~V~~a~~~~~r~~  170 (177)
                      .|+|+|++.+..+..
T Consensus        90 ~l~V~~a~~~~~~~~  104 (109)
T 1x4a_A           90 RLRVEFPRSGRGTGS  104 (109)
T ss_dssp             ECEEECCCCCCCCCC
T ss_pred             EEEEEEcccCCCCCC
Confidence            899999987655443

>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=99.87  E-value=1.8e-21  Score=134.59  Aligned_cols=86  Identities=24%  Similarity=0.391  Sum_probs=76.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      +.++|||+|||+++|+++|+++|++||.|.+|+|+.++     ..++|||||+|.+.++|++|++.||+..|.+     +
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-----~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g-----~   83 (103)
T 2cqi_A           14 QPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEH-----TSNDPYCFVEFYEHRDAAAALAAMNGRKILG-----K   83 (103)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCC-----CSSCCEEEEEESSHHHHHHHHHHHTTEEETT-----E
T ss_pred             CCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecC-----CCCCCEEEEEECCHHHHHHHHHHhCCCCcCC-----C
Confidence            37999999999999999999999999999999999875     2257899999999999999999999999976     5


Q ss_pred             ceEEEeecCCCCCCCC
Q 030444          156 FLRLQFSRNPGPRSVF  171 (177)
Q Consensus       156 ~l~V~~a~~~~~r~~~  171 (177)
                      .|+|+|++.+..+...
T Consensus        84 ~l~V~~a~~~~~~~~~   99 (103)
T 2cqi_A           84 EVKVNWATTPSSQKSG   99 (103)
T ss_dssp             EEEEEECCCTTCCCCC
T ss_pred             eEEEEECCCCcccccC
Confidence            8999999887655543

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.87  E-value=2.1e-21  Score=133.91  Aligned_cols=88  Identities=26%  Similarity=0.377  Sum_probs=76.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      +.++|||+|||+++|+++|+++|+.|.   .|+++.++   .+++++|||||+|.+.++|++|++.||+..|.+     +
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~---~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g-----~   82 (102)
T 2fc8_A           14 PSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDR---ETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDG-----N   82 (102)
T ss_dssp             CCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECS---SSCSEEEEEEEECSSHHHHHHHHHHHTTCEETT-----E
T ss_pred             CCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecC---CCCCcCcEEEEEECCHHHHHHHHHHhCCCeECC-----e
Confidence            379999999999999999999999874   56777775   568899999999999999999999999999976     5


Q ss_pred             ceEEEeecCCCCCCCCCCC
Q 030444          156 FLRLQFSRNPGPRSVFGAR  174 (177)
Q Consensus       156 ~l~V~~a~~~~~r~~~g~~  174 (177)
                      .|+|+|++.+..++.+++.
T Consensus        83 ~l~V~~a~~~~~~~~~~~~  101 (102)
T 2fc8_A           83 KVTLDWAKPKGEGGSGPSS  101 (102)
T ss_dssp             ECEEEECCCCCSSSCSCCC
T ss_pred             EEEEEEecCCCCCCCCCCC
Confidence            8999999887666654433

>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=99.87  E-value=3.6e-21  Score=133.05  Aligned_cols=85  Identities=20%  Similarity=0.270  Sum_probs=76.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      +.++|||+|||+++|+++|+++|++||.|.+|+|+.++     ..++|||||+|.+.++|++|++.||+..|.+     +
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~-----~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g-----~   83 (103)
T 2cq3_A           14 TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE-----RGSKGFGFVTFENSADADRAREKLHGTVVEG-----R   83 (103)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT-----TTTCCEEEEEESCHHHHHHHHHHHTTCEETT-----E
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecC-----CCCcEEEEEEECCHHHHHHHHHHhCCCEECC-----E
Confidence            37999999999999999999999999999999999875     2378999999999999999999999999966     5


Q ss_pred             ceEEEeecCCCCCCC
Q 030444          156 FLRLQFSRNPGPRSV  170 (177)
Q Consensus       156 ~l~V~~a~~~~~r~~  170 (177)
                      .|+|+|++.+..+..
T Consensus        84 ~l~v~~a~~~~~~~~   98 (103)
T 2cq3_A           84 KIEVNNATARVMTNS   98 (103)
T ss_dssp             ECEEEECCSSCCCCC
T ss_pred             EEEEEEcccCCCCCC
Confidence            899999988755554

>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=99.87  E-value=9.4e-22  Score=142.08  Aligned_cols=86  Identities=27%  Similarity=0.389  Sum_probs=78.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCC
Q 030444           75 DASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDS  154 (177)
Q Consensus        75 ~~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~  154 (177)
                      +++++|||+|||+++|+++|+++|++||.|.+|+|+.++   .+++++|||||+|.+.++|++|++.||+..|.+     
T Consensus        44 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~---~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g-----  115 (129)
T 2kxn_B           44 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQ---QSRRSRGFAFVYFENVDDAKEAKERANGMELDG-----  115 (129)
T ss_dssp             CCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCS---SSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSS-----
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecC---CCCccceEEEEEECCHHHHHHHHHHhCCCEECC-----
Confidence            347999999999999999999999999999999999887   578899999999999999999999999999976     


Q ss_pred             cceEEEeecCCCCC
Q 030444          155 KFLRLQFSRNPGPR  168 (177)
Q Consensus       155 r~l~V~~a~~~~~r  168 (177)
                      +.|+|+|++.+.++
T Consensus       116 ~~l~V~~a~~~~p~  129 (129)
T 2kxn_B          116 RRIRVDFSITKRPH  129 (129)
T ss_dssp             SCCEESCCSSSSCC
T ss_pred             EEEEEEEecCCCCC
Confidence            47999999876543

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.87  E-value=8e-22  Score=135.31  Aligned_cols=87  Identities=21%  Similarity=0.398  Sum_probs=76.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEE-EEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCC
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYK-EVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDS  154 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~-~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~  154 (177)
                      ++++|||+|||+++|+++|+++|++||.|. +|+|+.++   .+++++|||||+|.+.++|++|++.||+..+.+... .
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~---~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~-~   83 (99)
T 2div_A            8 MAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNR---LTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATP-A   83 (99)
T ss_dssp             SSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECS---SSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSS-C
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecC---CCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCc-c
Confidence            379999999999999999999999999999 99999887   678899999999999999999999999999977510 1


Q ss_pred             cceEEEeecCCC
Q 030444          155 KFLRLQFSRNPG  166 (177)
Q Consensus       155 r~l~V~~a~~~~  166 (177)
                      ++|+|+|++...
T Consensus        84 ~~l~v~~a~~~~   95 (99)
T 2div_A           84 KRFKLNYATYSG   95 (99)
T ss_dssp             EECCEEETTCCS
T ss_pred             eeEEEeecCCCC
Confidence            229999997653

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.87  E-value=2.5e-21  Score=137.00  Aligned_cols=81  Identities=26%  Similarity=0.505  Sum_probs=74.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCC
Q 030444           75 DASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDS  154 (177)
Q Consensus        75 ~~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~  154 (177)
                      .+.++|||+|||+++|+++|+++|++||.|.+|+|+.++   .+++++|||||+|.+.++|++|++.||+..|.+     
T Consensus        38 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~---~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g-----  109 (118)
T 2khc_A           38 PEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDK---QTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGT-----  109 (118)
T ss_dssp             CCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCS---SSSCCCCEEEEEEESSHHHHHHHHHCCCCEETT-----
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCC---CCCCcCcEEEEEECCHHHHHHHHHHcCCCEECC-----
Confidence            347899999999999999999999999999999999886   578899999999999999999999999999976     


Q ss_pred             cceEEEeec
Q 030444          155 KFLRLQFSR  163 (177)
Q Consensus       155 r~l~V~~a~  163 (177)
                      +.|+|+|+|
T Consensus       110 ~~l~V~~ak  118 (118)
T 2khc_A          110 KRLKVQLKK  118 (118)
T ss_dssp             EECCEEEC-
T ss_pred             EEEEEEecC
Confidence            589999985

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.87  E-value=1.5e-21  Score=132.69  Aligned_cols=81  Identities=23%  Similarity=0.317  Sum_probs=75.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      ++++|||+|||+++|+++|+++|++||.|.+|+++.++   .+++++|||||+|.+.++|++|++.||+..|.+     +
T Consensus        14 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~---~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g-----~   85 (95)
T 2cqc_A           14 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQ---QSRRSRGFAFVYFENVDDAKEAKERANGMELDG-----R   85 (95)
T ss_dssp             GGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECS---SSSSEEEEEEEEESSHHHHHHHHHHHTTEEETT-----E
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcC---CCCCcccEEEEEECCHHHHHHHHHHhCCCEECC-----E
Confidence            37999999999999999999999999999999999887   568899999999999999999999999999966     5


Q ss_pred             ceEEEeecC
Q 030444          156 FLRLQFSRN  164 (177)
Q Consensus       156 ~l~V~~a~~  164 (177)
                      +|+|+|++.
T Consensus        86 ~l~v~~a~~   94 (95)
T 2cqc_A           86 RIRVSGPSS   94 (95)
T ss_dssp             EEEEECCSC
T ss_pred             EEEEEecCC
Confidence            899999864

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.87  E-value=1.8e-21  Score=132.20  Aligned_cols=79  Identities=18%  Similarity=0.284  Sum_probs=74.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|.+|+++.++   .+++++|||||+|.+.++|++|++.||+..|.+     +.
T Consensus        16 ~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~---~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g-----~~   87 (94)
T 2e5h_A           16 KSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDK---DTRKSKGVAFILFLDKDSAQNCTRAINNKQLFG-----RV   87 (94)
T ss_dssp             TTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCS---SSCCCTTCEEEEESCHHHHHHHHHHTTTEEETT-----EE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCC---CCCCcccEEEEEECCHHHHHHHHHHcCCCeeCC-----cE
Confidence            7899999999999999999999999999999999887   568889999999999999999999999999976     58


Q ss_pred             eEEEeec
Q 030444          157 LRLQFSR  163 (177)
Q Consensus       157 l~V~~a~  163 (177)
                      |+|+||+
T Consensus        88 l~v~~ak   94 (94)
T 2e5h_A           88 IKASIAI   94 (94)
T ss_dssp             EEEEECC
T ss_pred             EEEEecC
Confidence            9999985

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.87  E-value=1.1e-21  Score=136.13  Aligned_cols=84  Identities=20%  Similarity=0.348  Sum_probs=77.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      ++++|||+|||+++|+++|+++|++||.|.+|+|+.++   .+++++|||||+|.+.++|++|++.||+..|.+     +
T Consensus        22 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~---~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g-----~   93 (106)
T 1p27_B           22 EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDR---RTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMG-----Q   93 (106)
T ss_dssp             TBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT---TTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSS-----S
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecC---CCCceeeEEEEEECCHHHHHHHHHHhcCCEECC-----c
Confidence            36899999999999999999999999999999999887   578899999999999999999999999999976     4


Q ss_pred             ceEEEeecCCCC
Q 030444          156 FLRLQFSRNPGP  167 (177)
Q Consensus       156 ~l~V~~a~~~~~  167 (177)
                      .|+|+|++.+++
T Consensus        94 ~l~V~~a~~~~~  105 (106)
T 1p27_B           94 PISVDWCFVRGP  105 (106)
T ss_dssp             BCEEEESEESSC
T ss_pred             EEEEEeecCCCC
Confidence            899999987654

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.87  E-value=3.4e-22  Score=137.32  Aligned_cols=80  Identities=16%  Similarity=0.352  Sum_probs=72.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCC--EEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCe----eCCC
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVG--YKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYR----MDED  150 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~--i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~----l~~~  150 (177)
                      -+||||+|||+++|+++|+++|++||.  +.+|+++.++   .++++||||||+|.+.++|++|++.||+..    |++ 
T Consensus         9 m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~---~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~G-   84 (95)
T 2lkz_A            9 MDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDK---QTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDG-   84 (95)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCS---SSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETT-
T ss_pred             cCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecC---CCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECC-
Confidence            689999999999999999999999995  5689998887   678999999999999999999999999974    654 


Q ss_pred             CCCCcceEEEeecC
Q 030444          151 DPDSKFLRLQFSRN  164 (177)
Q Consensus       151 ~~~~r~l~V~~a~~  164 (177)
                          |+|+|+||++
T Consensus        85 ----r~i~V~~Aks   94 (95)
T 2lkz_A           85 ----KTIGVDFAKS   94 (95)
T ss_dssp             ----EEEEEEECCC
T ss_pred             ----EEEEEEEccC
Confidence                6899999975

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.87  E-value=2.8e-21  Score=136.15  Aligned_cols=86  Identities=21%  Similarity=0.325  Sum_probs=78.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      +.++|||+|||+++|+++|+++|++||.|.+|+|+.++   .+++++|||||+|.+.++|++|++.||+..|.+     +
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~---~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g-----~   85 (115)
T 2dgo_A           14 NHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDM---ATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGG-----R   85 (115)
T ss_dssp             TCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT---TTCCEEEEEEEEESSHHHHHHHHHHTTTCEETT-----E
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcC---CCCCcceEEEEEECCHHHHHHHHHHhCCCEECC-----E
Confidence            37999999999999999999999999999999999886   578899999999999999999999999999976     5


Q ss_pred             ceEEEeecCCCCCC
Q 030444          156 FLRLQFSRNPGPRS  169 (177)
Q Consensus       156 ~l~V~~a~~~~~r~  169 (177)
                      .|+|+|++.+..+.
T Consensus        86 ~l~V~~a~~~~~~~   99 (115)
T 2dgo_A           86 QIRTNWATRKPPAP   99 (115)
T ss_dssp             ECEEEESSCCCCCS
T ss_pred             EEEEEEccCCCCCC
Confidence            89999998765443

>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=99.86  E-value=1.8e-21  Score=137.97  Aligned_cols=86  Identities=23%  Similarity=0.415  Sum_probs=77.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCC
Q 030444           75 DASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDS  154 (177)
Q Consensus        75 ~~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~  154 (177)
                      ++.++|||+|||+++|+++|+++|++||.|.+|+|+.++    +++++|||||+|.+.++|++|++.||+..|.+     
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~----~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g-----   75 (116)
T 2fy1_A            5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR----TSKSRGFAFITFENPADAKNAAKDMNGKSLHG-----   75 (116)
T ss_dssp             CSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST----TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSS-----
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC----CCCcccEEEEEECCHHHHHHHHHHhCCCEECC-----
Confidence            347899999999999999999999999999999999875    68899999999999999999999999999966     


Q ss_pred             cceEEEeecCCCCCC
Q 030444          155 KFLRLQFSRNPGPRS  169 (177)
Q Consensus       155 r~l~V~~a~~~~~r~  169 (177)
                      +.|+|+|++.+..+.
T Consensus        76 ~~l~V~~a~~~~~~~   90 (116)
T 2fy1_A           76 KAIKVEQAKKPSFQS   90 (116)
T ss_dssp             SBCEEEECCCSSCSS
T ss_pred             EEEEEEECCCCCCCC
Confidence            489999998764433

>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=99.86  E-value=1e-21  Score=138.93  Aligned_cols=83  Identities=17%  Similarity=0.305  Sum_probs=74.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      +.+|||+|||+++|+++|+++|++||.|.+|+|+.++     +.++|||||+|.+.++|++|++.||+..|.+     +.
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~-----~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g-----~~   74 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE-----NGSKGYGFVHFETQEAAERAIEKMNGMLLND-----RK   74 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET-----TEEEEEEEEEESCHHHHHHHHHHHTTCEETT-----EE
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC-----CCCCceEEEEECCHHHHHHHHHHcCCCEECC-----EE
Confidence            5789999999999999999999999999999999875     3478999999999999999999999999966     58


Q ss_pred             eEEEeecCCCCCC
Q 030444          157 LRLQFSRNPGPRS  169 (177)
Q Consensus       157 l~V~~a~~~~~r~  169 (177)
                      |+|++++.+..+.
T Consensus        75 i~V~~a~~~~~~~   87 (115)
T 4f25_A           75 VFVGRFKSRKERE   87 (115)
T ss_dssp             CEEEESSCCCC--
T ss_pred             EEEEECCCccccc
Confidence            9999998765443

>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=99.86  E-value=2.5e-21  Score=128.47  Aligned_cols=82  Identities=20%  Similarity=0.353  Sum_probs=75.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      +.+|||+|||+++|+++|+++|++||.|.+++++.++   .+++++|||||+|.+.++|++|++.||+..+.+     +.
T Consensus         1 t~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~---~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g-----~~   72 (83)
T 3md1_A            1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDM---QTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNG-----RP   72 (83)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECT---TTCCEEEEEEEEESCHHHHHHHHHHHTTCEETT-----EE
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcC---CCCCccceEEEEECCHHHHHHHHHHhcCCeeCC-----cE
Confidence            3689999999999999999999999999999999886   578899999999999999999999999999966     58


Q ss_pred             eEEEeecCCC
Q 030444          157 LRLQFSRNPG  166 (177)
Q Consensus       157 l~V~~a~~~~  166 (177)
                      |+|+|++.+.
T Consensus        73 l~v~~a~~~~   82 (83)
T 3md1_A           73 LRINWAAKLE   82 (83)
T ss_dssp             CEEEECCCCC
T ss_pred             EEEEecCcCC
Confidence            9999997653

>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=99.86  E-value=2.8e-21  Score=135.75  Aligned_cols=85  Identities=18%  Similarity=0.221  Sum_probs=75.8

Q ss_pred             CCeEEEcCCCCCCCHHHHH---HhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCC
Q 030444           77 SSTLYVEGLPADSTKREVA---HIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPD  153 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~---~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~  153 (177)
                      .++|||+|||+++++++|+   ++|++||.|.+|+|+.++.....++++|||||+|.+.++|++|++.||+..|.+    
T Consensus        15 ~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~g----   90 (111)
T 2cpi_A           15 KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDG----   90 (111)
T ss_dssp             SSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETT----
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECC----
Confidence            6899999999999999999   999999999999998876332334677999999999999999999999999966    


Q ss_pred             CcceEEEeecCCC
Q 030444          154 SKFLRLQFSRNPG  166 (177)
Q Consensus       154 ~r~l~V~~a~~~~  166 (177)
                       ++|+|+||+++.
T Consensus        91 -r~l~V~~a~~k~  102 (111)
T 2cpi_A           91 -RTLKASLGTTKY  102 (111)
T ss_dssp             -EEEEEESCCCCS
T ss_pred             -EEEEEEeccccc
Confidence             589999998764

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.86  E-value=1e-22  Score=138.48  Aligned_cols=83  Identities=19%  Similarity=0.269  Sum_probs=74.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCC-CEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhC-CCeeCCCCCCC
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFV-GYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQ-GYRMDEDDPDS  154 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G-~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~-g~~l~~~~~~~  154 (177)
                      +++|||+|||+++||++|+++|++|| .|.+|+|+.++   .+++++|||||+|.+.++|++|++.++ +..+.+     
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~---~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~g-----   72 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNK---SSGQSRGFAFVEFSHLQDATRWMEANQHSLNILG-----   72 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCS---SSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETT-----
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecC---CCCCcCceEEEEecCHHHHHHHHHhcCCCeEECC-----
Confidence            47999999999999999999999999 79999999887   678999999999999999999999874 567855     


Q ss_pred             cceEEEeecCCCC
Q 030444          155 KFLRLQFSRNPGP  167 (177)
Q Consensus       155 r~l~V~~a~~~~~  167 (177)
                      |+|+|+||++++.
T Consensus        73 r~i~V~~a~~~~~   85 (91)
T 2lxi_A           73 QKVSMHYSDPKPK   85 (91)
T ss_dssp             EEEEEECCCSCCC
T ss_pred             EEEEEEEcCCCCC
Confidence            5899999976544

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.86  E-value=9.9e-21  Score=132.98  Aligned_cols=84  Identities=17%  Similarity=0.234  Sum_probs=76.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      +++|||+|||+++|+++|+++|++||.|.+|+|+.++    +++++|||||+|.+.++|++|++.||+..|.+     +.
T Consensus        15 ~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~----~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g-----~~   85 (114)
T 2do0_A           15 GSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK----DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFD-----RP   85 (114)
T ss_dssp             CSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT----TCSEEEEEEEEESSHHHHHHHHHHHTTCEETT-----EE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC----CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCC-----CE
Confidence            7899999999999999999999999999999999886    48899999999999999999999999999966     58


Q ss_pred             eEEEeecCCCCCC
Q 030444          157 LRLQFSRNPGPRS  169 (177)
Q Consensus       157 l~V~~a~~~~~r~  169 (177)
                      |+|+|++...++.
T Consensus        86 l~v~~a~~~~~~~   98 (114)
T 2do0_A           86 MHVKMDERALPKG   98 (114)
T ss_dssp             CEEEECSCCCCCS
T ss_pred             EEEEEcccCCCCC
Confidence            9999997654443

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ISO mRNA processing, mRNA splicing, nucleus; 1.85A {Homo sapiens} SCOP: d.58.7.1 PDB: 2kyx_A 3lpy_A*

Probab=99.86  E-value=1.5e-21  Score=130.19  Aligned_cols=80  Identities=20%  Similarity=0.375  Sum_probs=74.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      +.++|||+|||+++|+++|+++|++||.|.+|+++.++   .+++++|||||+|.+.++|++|++.||+..+.+     +
T Consensus         6 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~---~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g-----~   77 (85)
T 3mdf_A            6 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDY---ETEKHRGFAFVEFELAEDAAAAIDNMNESELFG-----R   77 (85)
T ss_dssp             CSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEET---TTTEECSEEEEEESSHHHHHHHHHHHTTCEETT-----E
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECC---CCCccccEEEEEECCHHHHHHHHHHhCCCEECC-----c
Confidence            37999999999999999999999999999999998876   568889999999999999999999999999966     5


Q ss_pred             ceEEEeec
Q 030444          156 FLRLQFSR  163 (177)
Q Consensus       156 ~l~V~~a~  163 (177)
                      .|+|+||+
T Consensus        78 ~l~v~~ak   85 (85)
T 3mdf_A           78 TIRVNLAK   85 (85)
T ss_dssp             ECEEEECC
T ss_pred             EEEEEEcC
Confidence            89999985

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B

Probab=99.86  E-value=2.2e-21  Score=132.58  Aligned_cols=82  Identities=21%  Similarity=0.476  Sum_probs=76.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      +++|||+|||+++++++|+++|++||.|.+|+++.++   .+++++|||||+|.+.++|++|++.||+..+.+     +.
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~---~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g-----~~   73 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDP---QTGRSKGYAFIEFRDLESSASAVRNLNGYQLGS-----RF   73 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCT---TTCCBCSEEEEEESSHHHHHHHHHHHTTCEETT-----EE
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCC---CCCccceEEEEEECCHHHHHHHHHHhCCCeECC-----eE
Confidence            6899999999999999999999999999999998886   568899999999999999999999999999976     58


Q ss_pred             eEEEeecCCC
Q 030444          157 LRLQFSRNPG  166 (177)
Q Consensus       157 l~V~~a~~~~  166 (177)
                      |+|+|++.+.
T Consensus        74 l~V~~a~~~~   83 (96)
T 2x1f_A           74 LKCGYSSNSD   83 (96)
T ss_dssp             CEEEECSCSS
T ss_pred             EEEEEcCCCC
Confidence            9999997653

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.86  E-value=4.1e-21  Score=129.96  Aligned_cols=82  Identities=20%  Similarity=0.312  Sum_probs=74.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      +.++|||+|||+++|+++|+++|++||.|..|+|+.+     +++++|||||+|.+.++|++|++.||+..|.+     +
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~-----~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g-----~   76 (92)
T 2dgv_A            7 GACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-----NGKSKGCGVVKFESPEVAERACRMMNGMKLSG-----R   76 (92)
T ss_dssp             SCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES-----SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTT-----B
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc-----CCCcceEEEEEECCHHHHHHHHHHhCCCEECC-----c
Confidence            3799999999999999999999999999999999874     47889999999999999999999999999976     4


Q ss_pred             ceEEEeecCCCC
Q 030444          156 FLRLQFSRNPGP  167 (177)
Q Consensus       156 ~l~V~~a~~~~~  167 (177)
                      .|+|+|++.+..
T Consensus        77 ~l~v~~a~~~~~   88 (92)
T 2dgv_A           77 EIDVRIDRNASG   88 (92)
T ss_dssp             CCCCEECSCCSS
T ss_pred             EEEEEEcCCCCC
Confidence            799999977543

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.86  E-value=1.6e-21  Score=137.67  Aligned_cols=88  Identities=13%  Similarity=0.169  Sum_probs=78.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      +.++|||+|||+++|+++|+++|++||.|..|+|+.++   .+++++|||||+|.+.++|++|++. ++..|.+     +
T Consensus        26 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~---~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g-----~   96 (116)
T 1x4b_A           26 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDP---ASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDG-----R   96 (116)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCT---TTSSCCSEEEEECSSHHHHHHHHTS-CSEEETT-----E
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC---CCCCcCceEEEEeCCHHHHHHHHHh-CCcEECC-----E
Confidence            36899999999999999999999999999999999886   5788999999999999999999988 9999966     5


Q ss_pred             ceEEEeecCCCCCCCCC
Q 030444          156 FLRLQFSRNPGPRSVFG  172 (177)
Q Consensus       156 ~l~V~~a~~~~~r~~~g  172 (177)
                      .|+|+|++.+..+...+
T Consensus        97 ~l~V~~a~~~~~~~~~~  113 (116)
T 1x4b_A           97 VVEPKRAVAREESGSGP  113 (116)
T ss_dssp             EEEEECCSSCCCCCCSC
T ss_pred             EEEEEECCCCccCCCCC
Confidence            89999998876655443

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.86  E-value=2.2e-21  Score=134.52  Aligned_cols=87  Identities=17%  Similarity=0.292  Sum_probs=78.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      +.++|||+|||+++|+++|+++|++||.|.+|+|+.++   .+++++|||||+|.+.++|++|++. |+..|.+     +
T Consensus        15 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~---~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g-----~   85 (105)
T 2dh8_A           15 EIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDK---TTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDG-----R   85 (105)
T ss_dssp             SSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECS---SSCCEEEEEEEEESSTTHHHHHHHH-CSEEETT-----E
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCC---CCCCcceEEEEEECCHHHHHHHHHh-CCCeECC-----E
Confidence            37999999999999999999999999999999999986   5788999999999999999999998 9999976     5


Q ss_pred             ceEEEeecCCCCCCCC
Q 030444          156 FLRLQFSRNPGPRSVF  171 (177)
Q Consensus       156 ~l~V~~a~~~~~r~~~  171 (177)
                      .|+|+|++.+..+..+
T Consensus        86 ~l~V~~a~~~~~~~~~  101 (105)
T 2dh8_A           86 NIDPKPCTPRGMQPSG  101 (105)
T ss_dssp             EEBCCCSCCSSCCTTC
T ss_pred             EEEEEEccCCCCCCCC
Confidence            8999999877555543

>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=99.85  E-value=4.8e-21  Score=141.96  Aligned_cols=85  Identities=22%  Similarity=0.371  Sum_probs=78.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      +.++|||+|||+++|+++|+++|++||.|.+|+|+.++   .+++++|||||+|.+.++|++||+.||+..|.+     +
T Consensus        38 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~---~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g-----~  109 (156)
T 1h2v_Z           38 KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDK---MKKTACGFCFVEYYSRADAENAMRYINGTRLDD-----R  109 (156)
T ss_dssp             TCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT---TTCCEEEEEEEEESSHHHHHHHHHHTTTSEETT-----E
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecC---CCCccceEEEEEECCHHHHHHHHHHhCCCEECC-----e
Confidence            37999999999999999999999999999999999987   578899999999999999999999999999966     5


Q ss_pred             ceEEEeecCCCCC
Q 030444          156 FLRLQFSRNPGPR  168 (177)
Q Consensus       156 ~l~V~~a~~~~~r  168 (177)
                      .|+|+|++.+.++
T Consensus       110 ~l~V~~a~~~~~~  122 (156)
T 1h2v_Z          110 IIRTDWDAGFKEG  122 (156)
T ss_dssp             ECEEEEESCCCTT
T ss_pred             EEEEEECCCCCCc
Confidence            8999999876443

>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=99.85  E-value=2.1e-21  Score=135.69  Aligned_cols=85  Identities=20%  Similarity=0.336  Sum_probs=77.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      ++++|||+|||+++|+++|+++|++||.|.+|+|+.++   .+++++|||||+|.+.++|++|++.||+..|.+     +
T Consensus        25 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~---~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g-----~   96 (110)
T 1oo0_B           25 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDR---RTGFSKGYALVEYETHKQALAAKEALNGAEIMG-----Q   96 (110)
T ss_dssp             TBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCT---TTSSBCSEEEEEESSHHHHHHHHHHHTTCEETT-----E
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecC---CCCCcceEEEEEECCHHHHHHHHHHcCCCEECC-----c
Confidence            36899999999999999999999999999999998876   578899999999999999999999999999966     5


Q ss_pred             ceEEEeecCCCCC
Q 030444          156 FLRLQFSRNPGPR  168 (177)
Q Consensus       156 ~l~V~~a~~~~~r  168 (177)
                      .|+|+|++.+.++
T Consensus        97 ~l~V~~a~~~~~~  109 (110)
T 1oo0_B           97 TIQVDWCFVKGPK  109 (110)
T ss_dssp             ECEEEESEESSCC
T ss_pred             EEEEEEcccCCCC
Confidence            8999999876544

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens}

Probab=99.85  E-value=8.2e-21  Score=132.94  Aligned_cols=82  Identities=23%  Similarity=0.455  Sum_probs=76.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      +.++|||+|||+++|+++|+++|++||.|.+|+++.++   .+++++|||||+|.+.++|++|++.||+..|.+     +
T Consensus        25 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~---~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g-----~   96 (108)
T 2jrs_A           25 GPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDS---ETGRSKGYGFITFSDSECAKKALEQLNGFELAG-----R   96 (108)
T ss_dssp             SCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEET---TTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSS-----S
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcC---CCCccceEEEEEECCHHHHHHHHHHcCCCEECC-----E
Confidence            37899999999999999999999999999999999886   578899999999999999999999999999976     4


Q ss_pred             ceEEEeecCC
Q 030444          156 FLRLQFSRNP  165 (177)
Q Consensus       156 ~l~V~~a~~~  165 (177)
                      .|+|+|++.+
T Consensus        97 ~l~V~~a~~k  106 (108)
T 2jrs_A           97 PMKVGHVTER  106 (108)
T ss_dssp             CCEEECSCSS
T ss_pred             EEEEEEcccC
Confidence            7999999765

>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=99.85  E-value=1.5e-21  Score=137.36  Aligned_cols=89  Identities=26%  Similarity=0.402  Sum_probs=73.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCC
Q 030444           75 DASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDS  154 (177)
Q Consensus        75 ~~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~  154 (177)
                      .++++|||+|||+++|+++|+++|++||.|..+.+..+.   .+++++|||||+|.+.++|++|++.||+..|.+     
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~---~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g-----   94 (115)
T 2cpx_A           23 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRM---MTGRMRGQAFITFPNKEIAWQALHLVNGYKLYG-----   94 (115)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEE---ECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSS-----
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEc---CCCccceEEEEEECCHHHHHHHHHHhCCCEeCC-----
Confidence            347999999999999999999999999998433222221   246788999999999999999999999999966     


Q ss_pred             cceEEEeecCCCCCCCC
Q 030444          155 KFLRLQFSRNPGPRSVF  171 (177)
Q Consensus       155 r~l~V~~a~~~~~r~~~  171 (177)
                      +.|+|+|++.+..+...
T Consensus        95 ~~l~v~~a~~~~~~~~~  111 (115)
T 2cpx_A           95 KILVIEFGKNKKQRSSG  111 (115)
T ss_dssp             CBCEEEECCCCSCCCCC
T ss_pred             cEEEEEEccCCCCCCCC
Confidence            48999999887665543

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C

Probab=99.85  E-value=6.9e-22  Score=133.76  Aligned_cols=83  Identities=12%  Similarity=0.138  Sum_probs=70.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHhhCCCC--CEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           78 STLYVEGLPADSTKREVAHIFRPFV--GYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        78 ~tLfV~nLp~~~te~~L~~lF~~~G--~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      .+|||+|||+++|+++|+++|++||  .|.+++++.++   .+|+++|||||+|.+.++|++|++.||+..|.+     +
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~---~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~g-----r   73 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENR---ANGQSKGFALVGVGSEASSKKLMDLLPKRELHG-----Q   73 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECT---TTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSS-----C
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecC---CCCccCcEEEEEECCHHHHHHHHHHcCCCeeCC-----E
Confidence            5799999999999999999999999  99999999987   678999999999999999999999999999976     5


Q ss_pred             ceEEEeecCCCCC
Q 030444          156 FLRLQFSRNPGPR  168 (177)
Q Consensus       156 ~l~V~~a~~~~~r  168 (177)
                      .|+|++++.+.+.
T Consensus        74 ~i~V~~~~~~~~~   86 (90)
T 3p5t_L           74 NPVVTPSNKLEHH   86 (90)
T ss_dssp             CCEECCC------
T ss_pred             EEEEEECCCCccc
Confidence            7999999876443

>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=99.85  E-value=2.8e-21  Score=129.50  Aligned_cols=84  Identities=23%  Similarity=0.334  Sum_probs=75.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCC-CcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGG-DPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g-~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      .++|||+|||+++|+++|+++|++||.|.+|+++.++   .++ +++|||||+|.+.++|++|++.||+..+.+     +
T Consensus         4 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~---~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g-----~   75 (88)
T 4a8x_A            4 PTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVER---MHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDG-----Q   75 (88)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEET---TEEEEECSEEEEEESSHHHHHHHHHHHTTCEETT-----E
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCC---CCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECC-----e
Confidence            5899999999999999999999999999999998876   233 378999999999999999999999999976     5


Q ss_pred             ceEEEeecCCCCC
Q 030444          156 FLRLQFSRNPGPR  168 (177)
Q Consensus       156 ~l~V~~a~~~~~r  168 (177)
                      .|+|++++.+.+|
T Consensus        76 ~l~v~~a~~~~~R   88 (88)
T 4a8x_A           76 EITATAVLAPWPR   88 (88)
T ss_dssp             ECEEEEECCCCCC
T ss_pred             EEEEEECCCCCCC
Confidence            8999999876554

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.85  E-value=5e-21  Score=133.09  Aligned_cols=77  Identities=12%  Similarity=0.151  Sum_probs=68.7

Q ss_pred             CCCCeEEEcCCCC-CCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCC--eeCCCC
Q 030444           75 DASSTLYVEGLPA-DSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGY--RMDEDD  151 (177)
Q Consensus        75 ~~~~tLfV~nLp~-~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~--~l~~~~  151 (177)
                      +++++|||+|||+ ++|+++|+++|++||.|.+|+|+.++         +||||+|++.++|++|++.||+.  .|.+  
T Consensus        13 ~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~k---------g~aFVef~~~~~A~~Ai~~l~~~~~~~~G--   81 (102)
T 1x4d_A           13 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI---------NEAFIEMATTEDAQAAVDYYTTTPALVFG--   81 (102)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS---------SCEEEEESSHHHHHHHHHHHHHSCCEETT--
T ss_pred             CCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcCC---------CEEEEEECCHHHHHHHHHHHcCCCceECC--
Confidence            3479999999999 99999999999999999999998654         59999999999999999999865  4755  


Q ss_pred             CCCcceEEEeecCC
Q 030444          152 PDSKFLRLQFSRNP  165 (177)
Q Consensus       152 ~~~r~l~V~~a~~~  165 (177)
                         |+|+|+||+..
T Consensus        82 ---r~l~V~~a~~~   92 (102)
T 1x4d_A           82 ---KPVRVHLSQKY   92 (102)
T ss_dssp             ---EECEEEEECCC
T ss_pred             ---cEEEEEECCCC
Confidence               68999999854

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.85  E-value=9.9e-21  Score=127.84  Aligned_cols=82  Identities=21%  Similarity=0.367  Sum_probs=73.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      +.++|||+|||+++|+++|+++|++||.|.+|+++           ++||||+|.+.++|++|++.||+..|.+     +
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~-----------~g~afV~f~~~~~A~~A~~~l~g~~~~g-----~   70 (90)
T 2dnq_A            7 GMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII-----------KNYGFVHIEDKTAAEDAIRNLHHYKLHG-----V   70 (90)
T ss_dssp             CCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE-----------TTEEEEEESSHHHHHHHHHHHTTCBCSS-----C
T ss_pred             CCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE-----------CCEEEEEECCHHHHHHHHHHhcCCccCC-----c
Confidence            37999999999999999999999999999999987           2499999999999999999999999976     4


Q ss_pred             ceEEEeecCCCCCCCCCC
Q 030444          156 FLRLQFSRNPGPRSVFGA  173 (177)
Q Consensus       156 ~l~V~~a~~~~~r~~~g~  173 (177)
                      .|+|+|++.+..+..+.+
T Consensus        71 ~l~v~~a~~~~~~~~~~~   88 (90)
T 2dnq_A           71 NINVEASKNKSKASSGPS   88 (90)
T ss_dssp             BCEEECSSCCCCCCSSCC
T ss_pred             EEEEEECCCCCCCCCCCC
Confidence            899999988766654433

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.85  E-value=9.3e-21  Score=130.49  Aligned_cols=83  Identities=18%  Similarity=0.285  Sum_probs=71.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      +.++|||+|||+++|+++|+++|++||.|   +++.+    .+++++|||||+|.+.++|++|++.||+..|.+     +
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~----~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g-----~   81 (101)
T 2fc9_A           14 ESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN----QNGKSKGYAFIEFASFEDAKEALNSCNKREIEG-----R   81 (101)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC----SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETT-----E
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC----CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCC-----e
Confidence            37999999999999999999999999976   45544    357889999999999999999999999999976     5


Q ss_pred             ceEEEeecCCCCCCC
Q 030444          156 FLRLQFSRNPGPRSV  170 (177)
Q Consensus       156 ~l~V~~a~~~~~r~~  170 (177)
                      .|+|+|++.+..+..
T Consensus        82 ~l~v~~a~~~~~~~~   96 (101)
T 2fc9_A           82 AIRLELQGPRGSPNS   96 (101)
T ss_dssp             EEEEEECSSCCCCCC
T ss_pred             EEEEEEcCCCCCCCC
Confidence            899999987654443

>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=99.85  E-value=3.2e-21  Score=131.24  Aligned_cols=80  Identities=21%  Similarity=0.326  Sum_probs=74.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      +.++|||+|||+++++++|+++|++||.|.+|+|+.++    .++++|||||+|.+.++|++|++.||+..|.+     +
T Consensus        15 ~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~----~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g-----~   85 (95)
T 2ywk_A           15 ADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR----EGKPKSFGFVCFKHPESVSYAIALLNGIRLYG-----R   85 (95)
T ss_dssp             GGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT----TSCEEEEEEEEESSTHHHHHHHHHHTTCEETT-----E
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECC----CCCCceEEEEEECCHHHHHHHHHHhCCCEECC-----C
Confidence            37899999999999999999999999999999999886    38899999999999999999999999999976     5


Q ss_pred             ceEEEeecC
Q 030444          156 FLRLQFSRN  164 (177)
Q Consensus       156 ~l~V~~a~~  164 (177)
                      .|+|+|+++
T Consensus        86 ~l~V~~a~~   94 (95)
T 2ywk_A           86 PINVSGPSS   94 (95)
T ss_dssp             ECEEECCCC
T ss_pred             EEEEEEcCC
Confidence            899999864

>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=99.85  E-value=1.8e-20  Score=129.51  Aligned_cols=85  Identities=20%  Similarity=0.284  Sum_probs=75.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      +.++|||+|||+++|+++|+++|++||.|.+|+|+.++   .+++++|||||+|.+.++|++|++  ++..|.+     +
T Consensus        14 ~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~---~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g-----~   83 (103)
T 2cqg_A           14 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDL---KTGHSKGFGFVRFTEYETQVKVMS--QRHMIDG-----R   83 (103)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECS---SSCSEEEEEEEEESSHHHHHHHHH--SCEEETT-----E
T ss_pred             CCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecC---CCCCccceEEEEECCHHHHHHHHH--cCCeeCC-----e
Confidence            36899999999999999999999999999999999987   578999999999999999999998  5677855     5


Q ss_pred             ceEEEeecCCCCCCC
Q 030444          156 FLRLQFSRNPGPRSV  170 (177)
Q Consensus       156 ~l~V~~a~~~~~r~~  170 (177)
                      .|+|+|++.+.....
T Consensus        84 ~l~v~~a~~~~~~~~   98 (103)
T 2cqg_A           84 WCDCKLPNSKQSQDS   98 (103)
T ss_dssp             EEEEECCCTTCCCCC
T ss_pred             EEEEEecCCCCcCCC
Confidence            899999987655443

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=2.4e-20  Score=129.37  Aligned_cols=80  Identities=18%  Similarity=0.262  Sum_probs=70.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhC--CCeeCCCCCC
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQ--GYRMDEDDPD  153 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~--g~~l~~~~~~  153 (177)
                      ++++|||+|||+++|+++|+++|++||.|.+|+++.+         ||||||+|++.++|++|++.|+  +..|.+    
T Consensus        14 p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~---------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~G----   80 (101)
T 2cq1_A           14 PSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG---------KNQAFLELATEEAAITMVNYYSAVTPHLRN----   80 (101)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT---------TTEEEEEESSHHHHHHHHHHHHHSCCEETT----
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC---------CCEEEEEECCHHHHHHHHHHhccCCceECC----
Confidence            3799999999999999999999999999999988765         3699999999999999999874  677855    


Q ss_pred             CcceEEEeecCCCCCC
Q 030444          154 SKFLRLQFSRNPGPRS  169 (177)
Q Consensus       154 ~r~l~V~~a~~~~~r~  169 (177)
                       ++|+|+|++.+....
T Consensus        81 -r~l~V~~a~~~~~~~   95 (101)
T 2cq1_A           81 -QPIYIQYSNHKELKT   95 (101)
T ss_dssp             -EECEEEECSCSSCCC
T ss_pred             -cEEEEEEcCcccCcC
Confidence             689999998765443

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.85  E-value=6.9e-21  Score=131.70  Aligned_cols=85  Identities=21%  Similarity=0.288  Sum_probs=76.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCC-CCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCe-eCCCCCC
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRP-FVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYR-MDEDDPD  153 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~-~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~-l~~~~~~  153 (177)
                      +.++|||+|||+++|+++|+++|++ ||.|.+|+|+.++    +++++|||||+|.+.++|++|++.||+.. |.+    
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~----~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g----   79 (104)
T 2dhg_A            8 PEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ----TGVSKGYGFVKFTDELEQKRALTECQGAVGLGS----   79 (104)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT----TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSS----
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC----CCCccceEEEEECCHHHHHHHHHHccCCcccCC----
Confidence            3789999999999999999999999 9999999999885    67899999999999999999999999999 866    


Q ss_pred             CcceEEEeecCCCCCC
Q 030444          154 SKFLRLQFSRNPGPRS  169 (177)
Q Consensus       154 ~r~l~V~~a~~~~~r~  169 (177)
                       +.|+|+|++.+..+.
T Consensus        80 -~~l~v~~a~~~~~~~   94 (104)
T 2dhg_A           80 -KPVRLSVAIPKASRV   94 (104)
T ss_dssp             -SCCCCCBCCCCCSCC
T ss_pred             -EeEEEEEccCCCcCC
Confidence             479999997765443

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=1.8e-20  Score=132.18  Aligned_cols=80  Identities=19%  Similarity=0.271  Sum_probs=73.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|.+|+|+.++   .+++++|||||+|.+.++|++|++.|++ .|.+     +.
T Consensus        17 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~---~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g-----~~   87 (116)
T 2cqd_A           17 FTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDR---QTGKSRGYGFVTMADRAAAERACKDPNP-IIDG-----RK   87 (116)
T ss_dssp             SSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCS---SSCCCCSEEEEEESSHHHHHHHHTCSSC-EETT-----EE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcC---CCCccceEEEEEECCHHHHHHHHHhCCC-cCCC-----EE
Confidence            7999999999999999999999999999999999886   5788999999999999999999999998 7865     58


Q ss_pred             eEEEeecCC
Q 030444          157 LRLQFSRNP  165 (177)
Q Consensus       157 l~V~~a~~~  165 (177)
                      |+|+|++..
T Consensus        88 l~V~~a~~~   96 (116)
T 2cqd_A           88 ANVNLAYLG   96 (116)
T ss_dssp             CEEEESTTT
T ss_pred             EEEEEcccC
Confidence            999999653

>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=99.84  E-value=1.1e-21  Score=138.15  Aligned_cols=84  Identities=19%  Similarity=0.282  Sum_probs=76.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      ..++|||+|||+++|+++|+++|++||.|.+|+|+.++   .+++++|||||+|.+.++|++|+ .||++.|.+     +
T Consensus        24 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~---~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g-----~   94 (114)
T 2cq4_A           24 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDR---NSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLG-----V   94 (114)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSC---CSSSCCCCEEEEESCGGGHHHHH-HHTTEEETT-----E
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecC---CCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCC-----e
Confidence            36899999999999999999999999999999999887   56889999999999999999999 999999966     5


Q ss_pred             ceEEEeecCCCCC
Q 030444          156 FLRLQFSRNPGPR  168 (177)
Q Consensus       156 ~l~V~~a~~~~~r  168 (177)
                      .|+|+|++.+..+
T Consensus        95 ~l~V~~a~~~~~~  107 (114)
T 2cq4_A           95 PIIVQASQAEKNR  107 (114)
T ss_dssp             EEEEEEHHHHHHH
T ss_pred             EEEEEecCCCccC
Confidence            8999999765443

>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=99.84  E-value=7.3e-20  Score=128.60  Aligned_cols=85  Identities=18%  Similarity=0.334  Sum_probs=76.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCC---C
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDP---D  153 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~---~  153 (177)
                      .++|||+|||+++|+++|+++|++||.|.+|+|+.++    +++++|||||+|.+.++|++|++.||+..|.+...   .
T Consensus        25 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~----~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~  100 (114)
T 1x5o_A           25 PTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS----SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAP  100 (114)
T ss_dssp             TTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS----SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC----CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCC
Confidence            6899999999999999999999999999999999885    57899999999999999999999999999965421   2


Q ss_pred             CcceEEEeecCC
Q 030444          154 SKFLRLQFSRNP  165 (177)
Q Consensus       154 ~r~l~V~~a~~~  165 (177)
                      +++|+|.|++++
T Consensus       101 ~~~l~v~~a~p~  112 (114)
T 1x5o_A          101 TEPLLCKFSGPS  112 (114)
T ss_dssp             SSCBEEEECCCS
T ss_pred             CCceeEEccCCC
Confidence            468999999743

>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=99.84  E-value=5.4e-21  Score=130.92  Aligned_cols=81  Identities=17%  Similarity=0.240  Sum_probs=74.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|..++++.++   .+++++|||||+|.+.++|++|++.||+..|.+     +.
T Consensus        15 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~---~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g-----~~   86 (98)
T 2cqp_A           15 PTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYN---EKGMPTGEAMVAFESRDEATAAVIDLNDRPIGS-----RK   86 (98)
T ss_dssp             SEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEEC---SSSCEEEEEEEEESCHHHHHHHHHHTTTCEETT-----EE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEEC---CCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCC-----eE
Confidence            6899999999999999999999999999888777776   578899999999999999999999999999966     58


Q ss_pred             eEEEeecCC
Q 030444          157 LRLQFSRNP  165 (177)
Q Consensus       157 l~V~~a~~~  165 (177)
                      |+|+|++.+
T Consensus        87 l~V~~a~~~   95 (98)
T 2cqp_A           87 VKLVLGSGP   95 (98)
T ss_dssp             CEEEESSCS
T ss_pred             EEEEEcCCC
Confidence            999999754

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=1.9e-21  Score=129.82  Aligned_cols=80  Identities=21%  Similarity=0.404  Sum_probs=72.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      ++++|||+|||+++|+++|+++|++||.|.+|+++.++   .+++++|||||+|.+.++|++|++.||+..|.+     +
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~---~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g-----~   75 (85)
T 1x4e_A            4 GSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDK---TTNKCKGYGFVDFDSPSAAQKAVTALKASGVQA-----Q   75 (85)
T ss_dssp             CCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCS---SSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCE-----E
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecC---CCCCcCcEEEEEECCHHHHHHHHHHhcCCeEee-----E
Confidence            47999999999999999999999999999999999886   578899999999999999999999999999966     4


Q ss_pred             ceEEEeec
Q 030444          156 FLRLQFSR  163 (177)
Q Consensus       156 ~l~V~~a~  163 (177)
                      .|+|++++
T Consensus        76 ~~~~~~~~   83 (85)
T 1x4e_A           76 MAKQSGPS   83 (85)
T ss_dssp             SCCSSCCC
T ss_pred             EEeecCCC
Confidence            67776653

>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=99.84  E-value=2e-20  Score=129.81  Aligned_cols=80  Identities=20%  Similarity=0.331  Sum_probs=71.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++|| +.+|+|+.++    +++++|||||+|.+.++|++||+ +|+..|.+     |.
T Consensus        15 ~~~l~V~nLp~~~te~~l~~~F~~~G-~~~v~i~~d~----~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~g-----r~   83 (102)
T 1wez_A           15 GHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP----DGRVTGEADVEFATHEDAVAAMA-KDKANMQH-----RY   83 (102)
T ss_dssp             SCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESS----SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSS-----SC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHcC-ceEEEEEECC----CCCEeeEEEEEECCHHHHHHHHH-hCCCeECC-----cE
Confidence            68999999999999999999999999 4589999885    68899999999999999999994 79999866     57


Q ss_pred             eEEEeecCCCC
Q 030444          157 LRLQFSRNPGP  167 (177)
Q Consensus       157 l~V~~a~~~~~  167 (177)
                      |+|.++..+..
T Consensus        84 i~V~~~~~~~~   94 (102)
T 1wez_A           84 VELFLNSTAGT   94 (102)
T ss_dssp             CEEEEECCCCC
T ss_pred             EEEEECCCCCC
Confidence            99999966543

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.84  E-value=3.2e-20  Score=126.99  Aligned_cols=80  Identities=19%  Similarity=0.395  Sum_probs=70.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      +++|||+|||+++|+++|+++|++||.|.+|++..+         +|||||+|.+.++|++|++.||+..|.+   .++.
T Consensus        17 ~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~---------~g~afV~f~~~~~A~~A~~~l~g~~~~~---~g~~   84 (97)
T 1why_A           17 TTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG---------DSFAYIQYESLDAAQAACAKMRGFPLGG---PDRR   84 (97)
T ss_dssp             CSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS---------SCCEEEEESSHHHHHHHHHHHTTCBCSS---SSCB
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC---------CCEEEEEECCHHHHHHHHHHHCCCEeCC---CCcE
Confidence            689999999999999999999999999999988754         3699999999999999999999999972   1358


Q ss_pred             eEEEeecCCCCC
Q 030444          157 LRLQFSRNPGPR  168 (177)
Q Consensus       157 l~V~~a~~~~~r  168 (177)
                      |+|+|++.+..+
T Consensus        85 l~V~~a~~~~~~   96 (97)
T 1why_A           85 LRVDFAKSGPSS   96 (97)
T ss_dssp             CEEEECCCCCCC
T ss_pred             EEEEECCCCCCC
Confidence            999999876543

>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=99.84  E-value=1.5e-20  Score=130.67  Aligned_cols=79  Identities=22%  Similarity=0.312  Sum_probs=73.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      +.++|||+|||+++|+++|+++|++||.|.+|+|+.++    +++++|||||+|.+.++|++|++.||+..|.+     +
T Consensus        28 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~----~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g-----~   98 (107)
T 3ulh_A           28 TGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR----SGRSLGTADVHFERKADALKAMKQYNGVPLDG-----R   98 (107)
T ss_dssp             CSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT----TSCEEEEEEEEESSHHHHHHHHHHHTTCEETT-----E
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC----CCCcceEEEEEECCHHHHHHHHHHhCCCEeCC-----c
Confidence            37999999999999999999999999999999999885    68899999999999999999999999999966     5


Q ss_pred             ceEEEeec
Q 030444          156 FLRLQFSR  163 (177)
Q Consensus       156 ~l~V~~a~  163 (177)
                      .|+|+|+.
T Consensus        99 ~l~V~~a~  106 (107)
T 3ulh_A           99 PMNIQLVT  106 (107)
T ss_dssp             ECEEEEEC
T ss_pred             EEEEEEeC
Confidence            89999985

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.84  E-value=5.6e-21  Score=137.95  Aligned_cols=84  Identities=20%  Similarity=0.308  Sum_probs=75.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEE--EEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCC----eeCC
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKE--VRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGY----RMDE  149 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~--v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~----~l~~  149 (177)
                      ++++|||+|||+++|+++|+++|++||.|..  |+|+.++   .+++++|||||+|.+. +|++|++.||+.    .|.+
T Consensus        22 ~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~---~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~g   97 (131)
T 2m2b_A           22 ANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDK---QTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDG   97 (131)
T ss_dssp             CCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCS---SSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGG
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcC---CCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCC
Confidence            3789999999999999999999999999976  9999887   6789999999999999 999999999999    8866


Q ss_pred             CCCCCcceEEEeecCCCCC
Q 030444          150 DDPDSKFLRLQFSRNPGPR  168 (177)
Q Consensus       150 ~~~~~r~l~V~~a~~~~~r  168 (177)
                           |.|+|+|++...++
T Consensus        98 -----r~l~V~~a~~~~~~  111 (131)
T 2m2b_A           98 -----KTINVEFAKGSKRD  111 (131)
T ss_dssp             -----CCCCCEECCCSCCC
T ss_pred             -----EEEEEEECCCCCCC
Confidence                 58999999775443

>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=99.84  E-value=9.5e-21  Score=141.81  Aligned_cols=87  Identities=21%  Similarity=0.341  Sum_probs=76.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      ++++|||+|||+++|+++|+++|++||.|..|+|+.++   .+++++|||||+|.+.++|++||+.||+..|.+     +
T Consensus        71 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~---~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g-----~  142 (165)
T 1rk8_A           71 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDR---RTGFSKGYALVEYETHKQALAAKEALNGAEIMG-----Q  142 (165)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT---TTSSEEEEEEEEESSHHHHHHHHHHHTTCEETT-----E
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecC---CCCcEeeEEEEEECCHHHHHHHHHHhCCCEECC-----E
Confidence            37899999999999999999999999999999999886   678899999999999999999999999999966     5


Q ss_pred             ceEEEeecCCCCCCC
Q 030444          156 FLRLQFSRNPGPRSV  170 (177)
Q Consensus       156 ~l~V~~a~~~~~r~~  170 (177)
                      .|+|+|++.+.++..
T Consensus       143 ~l~V~~a~~~~~~~~  157 (165)
T 1rk8_A          143 TIQVDWCFVKGPKRV  157 (165)
T ss_dssp             ECEEEESEECC----
T ss_pred             EEEEEEecCCCCCCC
Confidence            899999987655543

>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=99.84  E-value=2.3e-20  Score=130.62  Aligned_cols=83  Identities=18%  Similarity=0.279  Sum_probs=71.9

Q ss_pred             CCCeEEEcCCCCC-CCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCC
Q 030444           76 ASSTLYVEGLPAD-STKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDS  154 (177)
Q Consensus        76 ~~~tLfV~nLp~~-~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~  154 (177)
                      ..++|||+|||++ +|+++|+++|++||.|.+|++  .         ++||||+|.+.++|++|++.||+..|.+     
T Consensus        26 ~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--~---------~g~afV~f~~~~~A~~A~~~l~g~~~~g-----   89 (110)
T 1wf1_A           26 INSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--H---------KGYAFVQYSNERHARAAVLGENGRVLAG-----   89 (110)
T ss_dssp             CSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--E---------TTEEEEECSSSHHHHHHHHHHTTCEETT-----
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--e---------CCEEEEEECCHHHHHHHHHHcCCCEECC-----
Confidence            3689999999999 999999999999999999988  1         3599999999999999999999999976     


Q ss_pred             cceEEEeecCCCCCCCCCCC
Q 030444          155 KFLRLQFSRNPGPRSVFGAR  174 (177)
Q Consensus       155 r~l~V~~a~~~~~r~~~g~~  174 (177)
                      +.|+|+|++.+.++..+..+
T Consensus        90 ~~l~V~~a~~~~~~~~~~~~  109 (110)
T 1wf1_A           90 QTLDINMAGEPKPDRSGPSS  109 (110)
T ss_dssp             EECCEEESCCCCSCCCCCCC
T ss_pred             eEEEEEECCCCCCCCCCCCC
Confidence            58999999866554444434

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.84  E-value=2.7e-20  Score=125.83  Aligned_cols=80  Identities=21%  Similarity=0.332  Sum_probs=73.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      ..++|||+|||+++|+++|+++|++| .|.+|+|+.+.    +++++|||||+|.+.++|++|++ ||+..|.+     +
T Consensus         9 ~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~----~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~g-----r   77 (91)
T 2dgw_A            9 TCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNA----HGNKTGYIFVDFSNEEEVKQALK-CNREYMGG-----R   77 (91)
T ss_dssp             CCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECT----TSCEEEEEEEECSSHHHHHHHHH-SCSEEETT-----E
T ss_pred             CccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECC----CCCCceEEEEEECCHHHHHHHHH-hCCceeCC-----c
Confidence            37899999999999999999999999 99999999874    68899999999999999999999 99999966     5


Q ss_pred             ceEEEeecCCC
Q 030444          156 FLRLQFSRNPG  166 (177)
Q Consensus       156 ~l~V~~a~~~~  166 (177)
                      .|+|.+++.++
T Consensus        78 ~i~v~~a~~~~   88 (91)
T 2dgw_A           78 YIEVFREKSGP   88 (91)
T ss_dssp             EEEEEEESSCC
T ss_pred             EEEEEECCcCC
Confidence            89999997653

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.84  E-value=3.4e-20  Score=127.33  Aligned_cols=80  Identities=25%  Similarity=0.342  Sum_probs=72.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|.+|++..+         +|||||+|.+.++|++|++.||+..|.+     ++
T Consensus        15 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~---------kg~afV~f~~~~~a~~a~~~l~g~~~~g-----~~   80 (99)
T 2cpj_A           15 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD---------KGFGFIRLETRTLAEIAKVELDNMPLRG-----KQ   80 (99)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT---------TTEEEEECSSSHHHHHHHHHHTTCCBTT-----BC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC---------CCEEEEEECCHHHHHHHHHHhCCCEeCC-----ce
Confidence            789999999999999999999999999999998754         3699999999999999999999999976     57


Q ss_pred             eEEEeecCCCCCCC
Q 030444          157 LRLQFSRNPGPRSV  170 (177)
Q Consensus       157 l~V~~a~~~~~r~~  170 (177)
                      |+|+|++.+.....
T Consensus        81 l~v~~a~~~~~~~~   94 (99)
T 2cpj_A           81 LRVRFACHSASLTS   94 (99)
T ss_dssp             CEEEESSCCSCCCC
T ss_pred             EEEEEcCCCCCCCC
Confidence            99999987655443

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.84  E-value=3.2e-21  Score=133.10  Aligned_cols=81  Identities=20%  Similarity=0.266  Sum_probs=75.2

Q ss_pred             CCeEEEcCCCC------CCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCC
Q 030444           77 SSTLYVEGLPA------DSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDED  150 (177)
Q Consensus        77 ~~tLfV~nLp~------~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~  150 (177)
                      +++|||+|||+      ++++++|+++|++||.|.+|+|+.++   .+++++|||||+|.+.++|++|++.|||..|.+.
T Consensus         6 ~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~---~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~   82 (100)
T 3ns6_A            6 DQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDE---ATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLK   82 (100)
T ss_dssp             GGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEET---TTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSS
T ss_pred             CcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcC---CCCccceEEEEEECCHHHHHHHHHHhCCcccCCC
Confidence            68999999999      99999999999999999999999987   6789999999999999999999999999999762


Q ss_pred             CCCCcceEEEeecC
Q 030444          151 DPDSKFLRLQFSRN  164 (177)
Q Consensus       151 ~~~~r~l~V~~a~~  164 (177)
                          +.|+|+++++
T Consensus        83 ----r~l~V~~a~~   92 (100)
T 3ns6_A           83 ----HRLFLYTMKD   92 (100)
T ss_dssp             ----CBCEEEESHH
T ss_pred             ----eEEEEEECch
Confidence                4799999864

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=6.3e-21  Score=133.16  Aligned_cols=80  Identities=19%  Similarity=0.272  Sum_probs=70.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCC--CeeCCCCCC
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQG--YRMDEDDPD  153 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g--~~l~~~~~~  153 (177)
                      +.++|||+|||+++||++|+++|++||.|.+|+|+.++         |||||+|++.++|++|++.|++  ..|.+    
T Consensus        15 ~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~k---------GfaFVeF~~~~~A~~Ai~~l~~~~~~l~G----   81 (105)
T 1sjq_A           15 PSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK---------NQAFIEMNTEEAANTMVNYYTSVTPVLRG----   81 (105)
T ss_dssp             CCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETTT---------TEEEEEESSHHHHHHHHHHHTTSCCEETT----
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcCC---------CEEEEEECCHHHHHHHHHHhccCCceECC----
Confidence            37999999999999999999999999999999998753         6999999999999999998874  67855    


Q ss_pred             CcceEEEeecCCCCCC
Q 030444          154 SKFLRLQFSRNPGPRS  169 (177)
Q Consensus       154 ~r~l~V~~a~~~~~r~  169 (177)
                       |+|+|+||+.+....
T Consensus        82 -r~l~V~~A~~~~~~~   96 (105)
T 1sjq_A           82 -QPIYIQFSNHKELKT   96 (105)
T ss_dssp             -EECCBCCCSSSSCCC
T ss_pred             -EEEEEEEcCCCCCCc
Confidence             689999998764443

>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=99.84  E-value=4.1e-20  Score=129.09  Aligned_cols=82  Identities=13%  Similarity=0.229  Sum_probs=71.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      ..++|||+|||+++|+++|+++|++||.|..|+|+.+          |||||+|.+.++|++||+.||+..|.++....+
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~----------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~   83 (108)
T 1x4c_A           14 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD----------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETA   83 (108)
T ss_dssp             CCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT----------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC----------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcce
Confidence            3789999999999999999999999999999999765          499999999999999999999999977322225


Q ss_pred             ceEEEeecCCCC
Q 030444          156 FLRLQFSRNPGP  167 (177)
Q Consensus       156 ~l~V~~a~~~~~  167 (177)
                      .|+|++++.+.+
T Consensus        84 ~i~V~~a~~~~~   95 (108)
T 1x4c_A           84 YIRVKVDGPRSP   95 (108)
T ss_dssp             EEEEEESSCCSC
T ss_pred             EEEEEeCCCCCC
Confidence            899999987643

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.84  E-value=2.5e-20  Score=126.35  Aligned_cols=82  Identities=22%  Similarity=0.233  Sum_probs=72.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      +.++|||+|||+++|+++|+++|++||.|.+|+++.           +||||+|.+.++|++|++.||+..|.+     +
T Consensus         9 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~-----------~~afV~f~~~~~a~~A~~~l~g~~~~g-----~   72 (92)
T 2dgt_A            9 ASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK-----------DYAFVHMERAEDAVEAIRGLDNTEFQG-----K   72 (92)
T ss_dssp             SSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECS-----------SEEEEEESCHHHHHHHHHHHTTEEETT-----E
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEC-----------CEEEEEECCHHHHHHHHHHhCCCeeCC-----c
Confidence            378999999999999999999999999999999863           299999999999999999999999976     5


Q ss_pred             ceEEEeecCCCCCCCCCC
Q 030444          156 FLRLQFSRNPGPRSVFGA  173 (177)
Q Consensus       156 ~l~V~~a~~~~~r~~~g~  173 (177)
                      .|+|+|++.+..+..+.+
T Consensus        73 ~l~V~~a~~~~~~~~~~~   90 (92)
T 2dgt_A           73 RMHVQLSTSRLRTASGPS   90 (92)
T ss_dssp             EEEEEESSCCCSCCCCCC
T ss_pred             EEEEEEccCCCCCCCCCC
Confidence            899999987755554433

>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=99.84  E-value=1.3e-20  Score=129.01  Aligned_cols=81  Identities=17%  Similarity=0.224  Sum_probs=73.0

Q ss_pred             CCeEEEcCCCCCCCHHHHH----HhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCC
Q 030444           77 SSTLYVEGLPADSTKREVA----HIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDP  152 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~----~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~  152 (177)
                      .++|||+|||+++++++|+    ++|++||.|.+|+|+.++   .+   ++||||+|.+.++|++|++.||+..|.+   
T Consensus         9 ~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~---~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~g---   79 (96)
T 2dgx_A            9 GADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHT---DY---QLKAVVQMENLQDAIGAVNSLHRYKIGS---   79 (96)
T ss_dssp             CEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCC---ST---TCCEEEEESSHHHHHHHHHHHTTEEETT---
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCC---CC---CeEEEEEECCHHHHHHHHHHhCCCEECC---
Confidence            6899999999999999999    999999999999999876   22   6899999999999999999999999966   


Q ss_pred             CCcceEEEeecCCCCC
Q 030444          153 DSKFLRLQFSRNPGPR  168 (177)
Q Consensus       153 ~~r~l~V~~a~~~~~r  168 (177)
                        +.|+|+|++.....
T Consensus        80 --r~l~V~~a~~~~~~   93 (96)
T 2dgx_A           80 --KKILVSLATGASGP   93 (96)
T ss_dssp             --EEEEEEECCCSSCC
T ss_pred             --eEEEEEEcCCCCCC
Confidence              58999999765433

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.84  E-value=1.1e-20  Score=130.72  Aligned_cols=76  Identities=17%  Similarity=0.205  Sum_probs=68.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCe--eCCCCCC
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYR--MDEDDPD  153 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~--l~~~~~~  153 (177)
                      ++++|||+|||+++|+++|+++|++||.|.+|+++..         ||||||+|++.++|.+|++.|++..  +.+    
T Consensus        20 ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~---------kg~AFVef~~~~~A~~Av~~ln~~~~~i~G----   86 (100)
T 3r27_A           20 ASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK---------KRQALVEFEDVLGACNAVNYAADNQIYIAG----   86 (100)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETT---------TTEEEEEESSHHHHHHHHHHHHHSCEEETT----
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcC---------CCEEEEEECCHHHHHHHHHHhcCCCceeCC----
Confidence            3899999999999999999999999999999998754         3699999999999999999999886  544    


Q ss_pred             CcceEEEeecCC
Q 030444          154 SKFLRLQFSRNP  165 (177)
Q Consensus       154 ~r~l~V~~a~~~  165 (177)
                       |+|+|+||+++
T Consensus        87 -r~i~V~~S~~k   97 (100)
T 3r27_A           87 -HPAFVNYSTSQ   97 (100)
T ss_dssp             -EEEEEEECSCS
T ss_pred             -cEEEEEecccc
Confidence             68999999765

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=99.83  E-value=2.6e-20  Score=137.93  Aligned_cols=85  Identities=21%  Similarity=0.330  Sum_probs=78.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|.+|+|+.++   .+++++|||||+|.+.++|++|++.||+..|.+     ++
T Consensus        70 ~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~---~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g-----~~  141 (158)
T 2kn4_A           70 MTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDR---YTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDG-----RE  141 (158)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCS---SCTTSCCEEEEEESBHHHHHHHHHHSTTEESSS-----SE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecC---CCCccceEEEEEECCHHHHHHHHHHhCCCEECC-----eE
Confidence            6899999999999999999999999999999999886   578899999999999999999999999999966     58


Q ss_pred             eEEEeecCCCCCC
Q 030444          157 LRLQFSRNPGPRS  169 (177)
Q Consensus       157 l~V~~a~~~~~r~  169 (177)
                      |+|+|++.+.++.
T Consensus       142 l~v~~a~~~~~~~  154 (158)
T 2kn4_A          142 LRVQMARYGRPPD  154 (158)
T ss_dssp             EEEEEECCSSCCC
T ss_pred             EEEEECCCCCCCC
Confidence            9999998765544

>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=99.83  E-value=4.8e-20  Score=128.49  Aligned_cols=77  Identities=16%  Similarity=0.144  Sum_probs=68.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCe--eCCCCCCC
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYR--MDEDDPDS  154 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~--l~~~~~~~  154 (177)
                      +++|||+|||+++|+++|+++|++||.|.+|+|+.+         ||||||+|++.++|++|++.|++..  |.+     
T Consensus        15 ~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~---------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~G-----   80 (104)
T 1wex_A           15 SPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF---------KRQALVEFENIDSAKECVTFAADVPVYIAG-----   80 (104)
T ss_dssp             CSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT---------TTEEEEEESSHHHHHHHHHHHHHSCCBSSS-----
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC---------CCEEEEEECCHHHHHHHHHHhccCCceECC-----
Confidence            799999999999999999999999999999998764         3699999999999999999997654  644     


Q ss_pred             cceEEEeecCCCC
Q 030444          155 KFLRLQFSRNPGP  167 (177)
Q Consensus       155 r~l~V~~a~~~~~  167 (177)
                      ++|+|+|++.+..
T Consensus        81 r~l~V~~a~~~~~   93 (104)
T 1wex_A           81 QQAFFNYSTSKRI   93 (104)
T ss_dssp             SBCEEEECSSSSC
T ss_pred             EEEEEEEccCccc
Confidence            5899999987643

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.83  E-value=1.8e-20  Score=133.67  Aligned_cols=83  Identities=14%  Similarity=0.292  Sum_probs=75.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|.+|+|+.++   .+++++|||||+|.+.++|++|+ .||+..|.+     +.
T Consensus        36 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~---~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g-----~~  106 (124)
T 2jwn_A           36 KRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDK---FSGHPKGYAYIEFAERNSVDAAV-AMDETVFRG-----RT  106 (124)
T ss_dssp             HTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEEC---TTSSCEEEEEEEESSHHHHHHHH-TTTTCEETT-----EE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecC---CCCCcccEEEEEECCHHHHHHHH-hcCCCeECC-----eE
Confidence            6899999999999999999999999999999999886   57889999999999999999999 899999966     58


Q ss_pred             eEEEeecCCCCC
Q 030444          157 LRLQFSRNPGPR  168 (177)
Q Consensus       157 l~V~~a~~~~~r  168 (177)
                      |+|+|++.+.+.
T Consensus       107 l~V~~a~~~~~~  118 (124)
T 2jwn_A          107 IKVLPKRTNMPG  118 (124)
T ss_dssp             CEEEESSCCCSS
T ss_pred             EEEEECCCCCCC
Confidence            999999765443

>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=99.83  E-value=1.7e-20  Score=126.04  Aligned_cols=80  Identities=18%  Similarity=0.316  Sum_probs=74.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|.+++++.++   .+++++|||||+|.+.++|++|+ .||+..+.+     +.
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~---~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g-----~~   76 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDK---FSGHPKGFAYIEFSDKESVRTSL-ALDESLFRG-----RQ   76 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESC---SSSSCCEEEEEEESSTHHHHHHG-GGTTCEETT-----EE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecC---CCCCcceEEEEEECCHHHHHHHH-hcCCCEECC-----cE
Confidence            5899999999999999999999999999999999886   57889999999999999999999 999999966     58


Q ss_pred             eEEEeecCC
Q 030444          157 LRLQFSRNP  165 (177)
Q Consensus       157 l~V~~a~~~  165 (177)
                      |+|++++++
T Consensus        77 l~V~~a~~~   85 (89)
T 3ucg_A           77 IKVIPKRTN   85 (89)
T ss_dssp             CEEEETTTT
T ss_pred             EEEEEccCC
Confidence            999999764

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.83  E-value=1.6e-20  Score=131.65  Aligned_cols=86  Identities=16%  Similarity=0.215  Sum_probs=73.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCC
Q 030444           74 PDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPD  153 (177)
Q Consensus        74 ~~~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~  153 (177)
                      ..+.++|||+|||+++|+++|+++|++||.|.+|+|+.++   .+++++|||||+|.+.++|++|++.++ ..|.+    
T Consensus        22 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~---~tg~~kg~afV~f~~~~~A~~Ai~~~~-~~l~g----   93 (109)
T 2rs2_A           22 GSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDP---LTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDS----   93 (109)
T ss_dssp             ----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCT---TTCCCTTCEEEEESSHHHHHHHHHSSC-EEETT----
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECC---CCCCcCcEEEEEECCHHHHHHHHHHCC-CcCCC----
Confidence            3447899999999999999999999999999999999886   578899999999999999999998764 88865    


Q ss_pred             CcceEEEeecCCCCC
Q 030444          154 SKFLRLQFSRNPGPR  168 (177)
Q Consensus       154 ~r~l~V~~a~~~~~r  168 (177)
                       +.|+|+++..+..+
T Consensus        94 -~~l~V~~a~~~~~~  107 (109)
T 2rs2_A           94 -KTIDPKVAFPRRAQ  107 (109)
T ss_dssp             -EEEEEEECCCCCCC
T ss_pred             -EEEEEEEccCCCCC
Confidence             58999999766443

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.83  E-value=5.9e-21  Score=131.96  Aligned_cols=83  Identities=20%  Similarity=0.377  Sum_probs=76.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|.+|+++.++   .+++++|||||+|.+.++|++|++.||+..|.+     +.
T Consensus         8 ~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~---~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g-----~~   79 (104)
T 1p1t_A            8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDR---ETGKPKGYGFCEYQDQETALSAMRNLNGREFSG-----RA   79 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEET---TTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSS-----SC
T ss_pred             ccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCC---CCCccceEEEEEECCHHHHHHHHHHhCCCeeCC-----cE
Confidence            6899999999999999999999999999999999886   578899999999999999999999999999966     47


Q ss_pred             eEEEeecCCCC
Q 030444          157 LRLQFSRNPGP  167 (177)
Q Consensus       157 l~V~~a~~~~~  167 (177)
                      |+|+|++.+..
T Consensus        80 l~v~~a~~~~~   90 (104)
T 1p1t_A           80 LRVDNAASEKN   90 (104)
T ss_dssp             BEEEETTCTTH
T ss_pred             EEEEeCCCccc
Confidence            99999977543

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.83  E-value=1.5e-20  Score=131.66  Aligned_cols=80  Identities=21%  Similarity=0.308  Sum_probs=73.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      +.++|||+|||+++|+++|+++|++||.|.+|+++.++     +.++|||||+|.+.++|++|++.||+..|.+     +
T Consensus        28 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~-----~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g-----~   97 (109)
T 2err_A           28 QPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE-----RGSKGFGFVTFENSADADRAREKLHGTVVEG-----R   97 (109)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT-----TBCTTEEEEECCCSHHHHHHHHHHTTCEETT-----E
T ss_pred             CCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC-----CCCceEEEEEECCHHHHHHHHHHcCCCEECC-----E
Confidence            47899999999999999999999999999999998875     3478999999999999999999999999966     5


Q ss_pred             ceEEEeecCC
Q 030444          156 FLRLQFSRNP  165 (177)
Q Consensus       156 ~l~V~~a~~~  165 (177)
                      .|+|+|++.+
T Consensus        98 ~l~V~~a~~~  107 (109)
T 2err_A           98 KIEVNNATAR  107 (109)
T ss_dssp             ECEEEECCCS
T ss_pred             EEEEEECCCC
Confidence            8999999764

>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=99.83  E-value=7.9e-21  Score=130.99  Aligned_cols=83  Identities=20%  Similarity=0.315  Sum_probs=71.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCC
Q 030444           74 PDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPD  153 (177)
Q Consensus        74 ~~~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~  153 (177)
                      ....++|||+|||+++|+++|+++|++|| |.+|+|+.++.  .+++++|||||+|.+.++|++|+ .||+..|.+    
T Consensus        16 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~--~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g----   87 (100)
T 2j76_E           16 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPS--NPERLKGFGYAEFEDLDSLLSAL-SLNEESLGN----   87 (100)
T ss_dssp             ----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTT--TTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTT----
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCC--cCCccCeEEEEEECCHHHHHHHH-hcCCCEECC----
Confidence            34479999999999999999999999999 99999987641  25889999999999999999999 999999966    


Q ss_pred             CcceEEEeecCC
Q 030444          154 SKFLRLQFSRNP  165 (177)
Q Consensus       154 ~r~l~V~~a~~~  165 (177)
                       +.|+|++++..
T Consensus        88 -~~l~V~~a~~~   98 (100)
T 2j76_E           88 -RRIRVDVADQA   98 (100)
T ss_dssp             -BCCCCEECCCS
T ss_pred             -eEEEEEeccCC
Confidence             57999999764

>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=99.83  E-value=7.8e-20  Score=126.91  Aligned_cols=83  Identities=20%  Similarity=0.306  Sum_probs=72.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEE-EEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCC
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKE-VRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDS  154 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~-v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~  154 (177)
                      ..++|||+|||+++|+++|+++|++||.|.+ |+|+.+.    +++++|||||+|.+.++|++|++. |+..|.+     
T Consensus        14 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~----~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~g-----   83 (104)
T 1wg5_A           14 NDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDF----QGRSTGEAFVQFASQEIAEKALKK-HKERIGH-----   83 (104)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCS----SSCBCSEEEEEESSHHHHHHHHTT-TTCCSSS-----
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECC----CCCcceEEEEEECCHHHHHHHHHh-CcchhCC-----
Confidence            3689999999999999999999999999987 7777763    688999999999999999999987 9998865     


Q ss_pred             cceEEEeecCCCCC
Q 030444          155 KFLRLQFSRNPGPR  168 (177)
Q Consensus       155 r~l~V~~a~~~~~r  168 (177)
                      |.|+|.++.....+
T Consensus        84 r~i~v~~~~~~~~~   97 (104)
T 1wg5_A           84 RYIEIFKSSRAEVR   97 (104)
T ss_dssp             SCCEEEEECTTTSC
T ss_pred             cEEEEEECCHHHHH
Confidence            57999999665433

>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=99.83  E-value=5.3e-20  Score=131.22  Aligned_cols=79  Identities=19%  Similarity=0.274  Sum_probs=70.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCC--CeeCCCCCCC
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQG--YRMDEDDPDS  154 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g--~~l~~~~~~~  154 (177)
                      +++|||+|||+++||++|+++|++||.|.+|+|+.++         |||||+|++.++|++|++.|++  ..|.+     
T Consensus        31 s~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~k---------G~AFVeF~~~e~A~~Ai~~l~~~~~~l~G-----   96 (119)
T 2ad9_A           31 SRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK---------NQAFIEMNTEEAANTMVNYYTSVTPVLRG-----   96 (119)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGGG---------TEEEEECSCHHHHHHHHHHHHHHCCCBTT-----
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCCC---------CEEEEEECCHHHHHHHHHHhccCCceECC-----
Confidence            7999999999999999999999999999999998753         6999999999999999999984  57755     


Q ss_pred             cceEEEeecCCCCCC
Q 030444          155 KFLRLQFSRNPGPRS  169 (177)
Q Consensus       155 r~l~V~~a~~~~~r~  169 (177)
                      ++|+|+||+.+....
T Consensus        97 r~l~V~~a~~k~~~~  111 (119)
T 2ad9_A           97 QPIYIQFSNHKELKT  111 (119)
T ss_dssp             BCCEEEECSSSSCCC
T ss_pred             eEEEEEEccCCCCCc
Confidence            589999998765544

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.83  E-value=1.9e-20  Score=139.41  Aligned_cols=80  Identities=13%  Similarity=0.172  Sum_probs=74.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCC--CEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCC
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFV--GYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDS  154 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G--~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~  154 (177)
                      .++|||+|||+++|+++|+++|++||  .|.+|+|+.++   .+|+++|||||+|.+.++|++||+.||+..|.+     
T Consensus        55 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~---~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~G-----  126 (156)
T 3n9u_C           55 RAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENR---ANGQSKGYAEVVVASENSVHKLLELLPGKVLNG-----  126 (156)
T ss_dssp             -CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECT---TTCCEEEEEEEEESCHHHHHHHHHHSTTCEETT-----
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecC---CCCccceEEEEEECCHHHHHHHHHHcCCCEECC-----
Confidence            68999999999999999999999999  99999999987   679999999999999999999999999999966     


Q ss_pred             cceEEEeecC
Q 030444          155 KFLRLQFSRN  164 (177)
Q Consensus       155 r~l~V~~a~~  164 (177)
                      +.|+|+++..
T Consensus       127 r~l~V~~a~~  136 (156)
T 3n9u_C          127 EKVDVRPATR  136 (156)
T ss_dssp             EECEEEECCH
T ss_pred             eEeEEEEcCC
Confidence            5899999854

>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=99.83  E-value=8.4e-21  Score=129.13  Aligned_cols=80  Identities=16%  Similarity=0.194  Sum_probs=73.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|..++++.++   .+++++|||||+|.+.++|++|++.||+..|.+     +.
T Consensus        15 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~---~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g-----r~   86 (95)
T 2ek1_A           15 PTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYN---EKGMPTGEAMVAFESRDEATAAVIDLNDRPIGS-----RK   86 (95)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEEC---TTSCEEEEEEEEESSHHHHHHHHHHHTTCEETT-----EE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeC---CCCCEeeEEEEEECCHHHHHHHHHHhCCCeECC-----cE
Confidence            5899999999999999999999999999888888776   578899999999999999999999999999966     58


Q ss_pred             eEEEeecC
Q 030444          157 LRLQFSRN  164 (177)
Q Consensus       157 l~V~~a~~  164 (177)
                      |+|+++.+
T Consensus        87 l~v~~a~s   94 (95)
T 2ek1_A           87 VKLSGPSS   94 (95)
T ss_dssp             CEEECCC-
T ss_pred             EEEEeccC
Confidence            99999853

>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=99.83  E-value=4.6e-20  Score=123.59  Aligned_cols=78  Identities=18%  Similarity=0.356  Sum_probs=70.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      +.++|||+|||+++|+++|+++|++||.|.+|+++.++   .+++++|||||+|.+.++|++|++ +++..|.+     +
T Consensus        10 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~---~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g-----~   80 (87)
T 3s7r_A           10 DAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDP---NTGRSRGFGFILFKDAASVEKVLD-QKEHRLDG-----R   80 (87)
T ss_dssp             CTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECT---TTCCEEEEEEEEESSTHHHHHHHH-SSCEEETT-----E
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecC---CCCccccEEEEEECCHHHHHHHHH-hCCCEECC-----E
Confidence            37899999999999999999999999999999999886   578899999999999999999995 58888865     5


Q ss_pred             ceEEEee
Q 030444          156 FLRLQFS  162 (177)
Q Consensus       156 ~l~V~~a  162 (177)
                      .|+|++|
T Consensus        81 ~i~v~~A   87 (87)
T 3s7r_A           81 VIDPKKA   87 (87)
T ss_dssp             EEEEEEC
T ss_pred             EEEEEeC
Confidence            8999876

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.82  E-value=5.6e-20  Score=125.86  Aligned_cols=79  Identities=27%  Similarity=0.473  Sum_probs=69.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      ..++|||+|||+++|+++|+++|++||.|. ++++.+       +++|||||+|.+.++|++|++.||+..|.+     +
T Consensus        18 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~-------~~~g~afV~f~~~~~a~~A~~~l~g~~~~g-----~   84 (97)
T 2e5j_A           18 LAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ-------GPRRRAFLHYPDSAAAQQAVSCLQGLRLGT-----D   84 (97)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE-------TTTTEEEEECSSHHHHHHHHHHHTTCCSSS-----S
T ss_pred             CCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC-------CCCcEEEEEECCHHHHHHHHHHhCCCEECC-----c
Confidence            378999999999999999999999999996 666654       356799999999999999999999999976     4


Q ss_pred             ceEEEeecCCCC
Q 030444          156 FLRLQFSRNPGP  167 (177)
Q Consensus       156 ~l~V~~a~~~~~  167 (177)
                      .|+|+|++.+.+
T Consensus        85 ~l~V~~a~~~~~   96 (97)
T 2e5j_A           85 TLRVALARQQRD   96 (97)
T ss_dssp             CCEEEECCCCCC
T ss_pred             EEEEEEcCCCCC
Confidence            799999977543

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.82  E-value=1e-20  Score=137.55  Aligned_cols=86  Identities=21%  Similarity=0.328  Sum_probs=77.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      +.++|||+|||+++|+++|+++|++||.|..|+|+.++   .+++++|||||+|.+.++|++|++.||+..|.+     +
T Consensus        46 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~---~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g-----~  117 (135)
T 2lea_A           46 GMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDR---YTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDG-----R  117 (135)
T ss_dssp             GCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCS---SSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSS-----S
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecC---CCCccceEEEEEECCHHHHHHHHHHcCCCEECC-----E
Confidence            37899999999999999999999999999999998876   578899999999999999999999999999976     4


Q ss_pred             ceEEEeecCCCCCC
Q 030444          156 FLRLQFSRNPGPRS  169 (177)
Q Consensus       156 ~l~V~~a~~~~~r~  169 (177)
                      +|+|+|++.+.++.
T Consensus       118 ~l~V~~a~~~~~~~  131 (135)
T 2lea_A          118 ELRVQMARYGRPPD  131 (135)
T ss_dssp             CCEEEECCCCCCCT
T ss_pred             EEEEEECCCCCCCc
Confidence            79999998764443

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.82  E-value=9e-20  Score=130.15  Aligned_cols=83  Identities=20%  Similarity=0.289  Sum_probs=75.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCC
Q 030444           75 DASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDS  154 (177)
Q Consensus        75 ~~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~  154 (177)
                      .++++|||+|||+++++++|+++|++||.|.+|+|+.++    +++++|||||+|.+.++|++|++.||+..|.+     
T Consensus        33 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~----~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g-----  103 (124)
T 2kt5_A           33 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR----SGRSLGTADVHFERRADALKAMKQYKGVPLDG-----  103 (124)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS----SSSCCSEEEEEESSHHHHHHHHHHHTTEESSS-----
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC----CCCEeeEEEEEECCHHHHHHHHHHcCCCEECC-----
Confidence            347899999999999999999999999999999998875    57889999999999999999999999999966     


Q ss_pred             cceEEEeecCCC
Q 030444          155 KFLRLQFSRNPG  166 (177)
Q Consensus       155 r~l~V~~a~~~~  166 (177)
                      +.|+|+||..+.
T Consensus       104 ~~l~V~~a~~~~  115 (124)
T 2kt5_A          104 RPMDIQLVASQI  115 (124)
T ss_dssp             CEEEEEEECCTT
T ss_pred             cEEEEEEeCCCC
Confidence            489999997653

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.82  E-value=1.9e-19  Score=123.51  Aligned_cols=78  Identities=22%  Similarity=0.319  Sum_probs=69.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCC--CCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCC
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPF--VGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPD  153 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~--G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~  153 (177)
                      +.++|||+|||+++|+++|+++|++|  |.|.+|++.           ++||||+|.+.++|++|++.||+..|.+    
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~-----------~g~afV~f~~~~~A~~A~~~l~g~~~~g----   78 (99)
T 2cpd_A           14 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI-----------RDYAFVHFSNREDAVEAMKALNGKVLDG----   78 (99)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC-----------SSEEEEEESSHHHHHHHHHHHSSEEETT----
T ss_pred             CcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe-----------CCeEEEEeCCHHHHHHHHHHhCCCEeCC----
Confidence            37999999999999999999999999  999988764           2599999999999999999999999976    


Q ss_pred             CcceEEEeecCCCCCC
Q 030444          154 SKFLRLQFSRNPGPRS  169 (177)
Q Consensus       154 ~r~l~V~~a~~~~~r~  169 (177)
                       +.|+|+|++.+..+.
T Consensus        79 -~~l~v~~a~~~~~~~   93 (99)
T 2cpd_A           79 -SPIEVTLAKPVDKDS   93 (99)
T ss_dssp             -EEEEEECCCCCCCCC
T ss_pred             -cEEEEEECCCCCCCC
Confidence             589999998765443

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.82  E-value=1e-19  Score=128.41  Aligned_cols=77  Identities=13%  Similarity=0.199  Sum_probs=67.5

Q ss_pred             CCCeEEEcCCCCC-CCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCC--CeeCCCCC
Q 030444           76 ASSTLYVEGLPAD-STKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQG--YRMDEDDP  152 (177)
Q Consensus        76 ~~~tLfV~nLp~~-~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g--~~l~~~~~  152 (177)
                      ++++|||+|||++ +|+++|+++|++||.|.+|+|+..         ||||||+|++.++|++|++.||+  ..|.+   
T Consensus        24 p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~~---------kg~aFVef~~~~~A~~Ai~~l~~~~~~l~G---   91 (112)
T 1x4f_A           24 LGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM---------KSQAFIEMETREDAMAMVDHCLKKALWFQG---   91 (112)
T ss_dssp             CCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT---------TTEEEEECSSHHHHHHHHHHHHHSCCCSSS---
T ss_pred             CCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEecC---------CCEEEEEECCHHHHHHHHHHhccCCceECC---
Confidence            3799999999998 999999999999999999999753         36999999999999999998865  45755   


Q ss_pred             CCcceEEEeecCCC
Q 030444          153 DSKFLRLQFSRNPG  166 (177)
Q Consensus       153 ~~r~l~V~~a~~~~  166 (177)
                        |+|+|+||+.+.
T Consensus        92 --r~l~V~~a~~~~  103 (112)
T 1x4f_A           92 --RCVKVDLSEKYK  103 (112)
T ss_dssp             --SCCEEEEECSCS
T ss_pred             --EEEEEEECcccc
Confidence              589999997653

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.82  E-value=3e-20  Score=129.21  Aligned_cols=78  Identities=17%  Similarity=0.239  Sum_probs=71.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|.+|+|+.++   . ++++|||||+|.+.++|++|++ +++..|.+     +.
T Consensus        11 ~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~---~-g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~g-----r~   80 (103)
T 1s79_A           11 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL---H-KAFKGSIFVVFDSIESAKKFVE-TPGQKYKE-----TD   80 (103)
T ss_dssp             GGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCC---T-TSCCCEEEEEESSHHHHHHHHT-SSCCCCTT-----TT
T ss_pred             CCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECC---C-CCCccEEEEEECCHHHHHHHHH-cCCCEECC-----EE
Confidence            6899999999999999999999999999999999886   3 8899999999999999999998 89999966     47


Q ss_pred             eEEEeecC
Q 030444          157 LRLQFSRN  164 (177)
Q Consensus       157 l~V~~a~~  164 (177)
                      |+|.+++.
T Consensus        81 l~V~~~~~   88 (103)
T 1s79_A           81 LLILFKDD   88 (103)
T ss_dssp             CEEEEHHH
T ss_pred             EEEEEchH
Confidence            99998754

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.71  E-value=6.9e-22  Score=139.66  Aligned_cols=87  Identities=21%  Similarity=0.302  Sum_probs=78.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEE--------EEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeC
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKE--------VRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMD  148 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~--------v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~  148 (177)
                      .++|||+|||+++|+++|+++|++||.|..        |+|+.++   .+++++|||||+|.+.++|++|++.||+..|.
T Consensus         7 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~---~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~   83 (116)
T 2lcw_A            7 NNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDR---ETGKLKGEATVSFDDPPSAKAAIDWFDGKEFS   83 (116)
Confidence            789999999999999999999999999998        8888876   56889999999999999999999999999997


Q ss_pred             CCCCCCcceEEEeecCCCCCCCC
Q 030444          149 EDDPDSKFLRLQFSRNPGPRSVF  171 (177)
Q Consensus       149 ~~~~~~r~l~V~~a~~~~~r~~~  171 (177)
                      +     +.|+|+|++.+..+..+
T Consensus        84 g-----~~l~V~~a~~~~~~~~g  101 (116)
T 2lcw_A           84 G-----NPIKVSFATRRADFNRG  101 (116)
Confidence            6     47999999887655533

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.82  E-value=1.3e-20  Score=132.82  Aligned_cols=79  Identities=14%  Similarity=0.171  Sum_probs=69.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCC-CEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFV-GYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G-~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      .++|||+|||+++|+++|+++|++|| .|..+++..+       +++|||||+|.+.++|++|++.|||..|.+     |
T Consensus        28 ~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~-------~~rGfaFV~F~~~e~A~~Ai~~lng~~l~G-----r   95 (111)
T 2jvr_A           28 RYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR-------DFDGTGALEFPSEEILVEALERLNNIEFRG-----S   95 (111)
T ss_dssp             CEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSC-------SSSCCEEEEESSHHHHHHHHHHTTTEEETT-----E
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcC-------CCCCEEEEEECCHHHHHHHHHHcCCCEECC-----e
Confidence            68999999999999999999999999 8999888543       266899999999999999999999999966     5


Q ss_pred             ceEEEeecCCCC
Q 030444          156 FLRLQFSRNPGP  167 (177)
Q Consensus       156 ~l~V~~a~~~~~  167 (177)
                      .|+|++++.+++
T Consensus        96 ~i~V~~a~~~p~  107 (111)
T 2jvr_A           96 VITVERDDNPPP  107 (111)
T ss_dssp             EEEEEESCC---
T ss_pred             EEEEEECCCCCC
Confidence            899999987644

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.82  E-value=8.8e-20  Score=132.15  Aligned_cols=78  Identities=21%  Similarity=0.371  Sum_probs=72.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|.+++|+.++   .+++++|||||+|.+.++|++|++.||+..|.+     +.
T Consensus        63 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~---~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g-----~~  134 (140)
T 2ku7_A           63 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDY---ETEKHRGFAFVEFELAEDAAAAIDNMNESELFG-----RT  134 (140)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCT---TTCCCCSEEEEEESCHHHHHHHHHHSTEEEETT-----EE
T ss_pred             CcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecC---CCCCcCcEEEEEECCHHHHHHHHHHhCCCEECC-----EE
Confidence            7999999999999999999999999999999998886   578899999999999999999999999999966     58


Q ss_pred             eEEEee
Q 030444          157 LRLQFS  162 (177)
Q Consensus       157 l~V~~a  162 (177)
                      |+|+||
T Consensus       135 l~v~~A  140 (140)
T 2ku7_A          135 IRVNLA  140 (140)
T ss_dssp             EEEEC-
T ss_pred             EEEEeC
Confidence            999986

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.81  E-value=5.3e-21  Score=131.71  Aligned_cols=84  Identities=18%  Similarity=0.283  Sum_probs=73.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      +.++|||+|||+++|+++|+++|++||.|.. .++.+.   .+++++|||||+|.+.++|++|++ ||+..|.+     +
T Consensus        16 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~---~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g-----~   85 (101)
T 1fj7_A           16 TPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDV---RTGTNRKFGYVDFESAEDLEKALE-LTGLKVFG-----N   85 (101)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEE---EEETTTTEEEEEESSHHHHHHHHH-GGGCCBTT-----B
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecC---CCCCcCcEEEEEECCHHHHHHHHh-cCCcEECC-----c
Confidence            3689999999999999999999999999877 555554   457889999999999999999998 99999976     5


Q ss_pred             ceEEEeecCCCCCC
Q 030444          156 FLRLQFSRNPGPRS  169 (177)
Q Consensus       156 ~l~V~~a~~~~~r~  169 (177)
                      .|+|+|++.+..+.
T Consensus        86 ~l~V~~a~~~~~~~   99 (101)
T 1fj7_A           86 EIKLEKPKGRDGTR   99 (101)
T ss_dssp             CCEEECCSCCCCSS
T ss_pred             EEEEEEcCCCCCCC
Confidence            79999998765554

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.81  E-value=2.1e-19  Score=136.37  Aligned_cols=82  Identities=21%  Similarity=0.311  Sum_probs=75.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCC
Q 030444           75 DASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDS  154 (177)
Q Consensus        75 ~~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~  154 (177)
                      .++++|||+|||+++|+++|+++|++||.|.+|+|+.++    +++++|||||+|.+.++|++|++.||+..|.+     
T Consensus        86 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~----~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~G-----  156 (177)
T 2f3j_A           86 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR----SGRSLGTADVHFERRADALKAMKQYKGVPLDG-----  156 (177)
T ss_dssp             TTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT----TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSS-----
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC----CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECC-----
Confidence            447899999999999999999999999999999998875    57889999999999999999999999999976     


Q ss_pred             cceEEEeecCC
Q 030444          155 KFLRLQFSRNP  165 (177)
Q Consensus       155 r~l~V~~a~~~  165 (177)
                      +.|+|+||...
T Consensus       157 r~l~V~~a~~~  167 (177)
T 2f3j_A          157 RPMDIQLVASQ  167 (177)
T ss_dssp             SBCEEEEESSG
T ss_pred             EEEEEEEecCC
Confidence            48999999654

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.81  E-value=6.9e-20  Score=132.08  Aligned_cols=80  Identities=16%  Similarity=0.282  Sum_probs=70.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHH----HhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCC
Q 030444           76 ASSTLYVEGLPADSTKREVA----HIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDD  151 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~----~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~  151 (177)
                      ++++|||+|||+++++++|+    ++|++||.|.+|.+..      +++++|||||+|.+.++|+.|++.|||..|.+  
T Consensus        28 p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~------~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~g--   99 (127)
T 2a3j_A           28 PSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL------SDDNSGKAYIVFATQESAQAFVEAFQGYPFQG--   99 (127)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC------CCSSCCCEEEEESSHHHHHHHHHHSTTCCCTT--
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc------CCCcCCEEEEEECCHHHHHHHHHHHCCCEeCC--
Confidence            37899999999999999876    6999999999987742      46788999999999999999999999999976  


Q ss_pred             CCCcceEEEeecCCC
Q 030444          152 PDSKFLRLQFSRNPG  166 (177)
Q Consensus       152 ~~~r~l~V~~a~~~~  166 (177)
                         ++|+|+||+.+.
T Consensus       100 ---r~l~V~~a~~~~  111 (127)
T 2a3j_A          100 ---NPLVITFSETPQ  111 (127)
T ss_dssp             ---SCCEEEECCCCC
T ss_pred             ---CEEEEEEccCcc
Confidence               489999998653

>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=99.81  E-value=9.8e-20  Score=127.18  Aligned_cols=79  Identities=20%  Similarity=0.396  Sum_probs=71.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|.+|+|+.++         |||||+|.+.++|++|++.||+..|.+     +.
T Consensus        25 ~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~---------g~afV~f~~~~~a~~A~~~l~g~~~~g-----~~   90 (109)
T 1x4g_A           25 NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK---------GYSFVRFSTHESAAHAIVSVNGTTIEG-----HV   90 (109)
T ss_dssp             CCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETTT---------TEEEEEESSHHHHHHHHHHHTTCEETT-----EE
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCCC---------CEEEEEECCHHHHHHHHHHcCCCEECC-----cE
Confidence            7899999999999999999999999999999998763         699999999999999999999999976     58


Q ss_pred             eEEEeecCCCCCC
Q 030444          157 LRLQFSRNPGPRS  169 (177)
Q Consensus       157 l~V~~a~~~~~r~  169 (177)
                      |+|+|++.+....
T Consensus        91 l~v~~a~~~~~~~  103 (109)
T 1x4g_A           91 VKCYWGKESPDMT  103 (109)
T ss_dssp             CEEECCCCCCSSC
T ss_pred             EEEEecCCCCCCC
Confidence            9999998765444

>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=99.81  E-value=4e-20  Score=128.90  Aligned_cols=83  Identities=14%  Similarity=0.191  Sum_probs=73.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCC-EEEEEEe-ecCcccCCCCcceEEEEEecCHHHHHHHHHHhC--CCeeCCCCC
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVG-YKEVRLV-IKESKLRGGDPLILCFVDFENPACAATALSALQ--GYRMDEDDP  152 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~-i~~v~l~-~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~--g~~l~~~~~  152 (177)
                      .++|||+|||+++|+++|+++|++||. |.+|+++ .++   .+++++|||||+|.+.++|++|++.||  +..+.+   
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~---~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g---   81 (109)
T 2dis_A            8 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAA---DKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWG---   81 (109)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSC---TTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTT---
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCC---CCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecC---
Confidence            689999999999999999999999998 9999987 554   567899999999999999999999996  588866   


Q ss_pred             CCcceEEEeecCCCC
Q 030444          153 DSKFLRLQFSRNPGP  167 (177)
Q Consensus       153 ~~r~l~V~~a~~~~~  167 (177)
                        +.|+|+|++.+..
T Consensus        82 --~~l~V~~a~~~~~   94 (109)
T 2dis_A           82 --HQIAVDWAEPEID   94 (109)
T ss_dssp             --BCCEEEESCSSCS
T ss_pred             --CeEEEEEcCCCCC
Confidence              5799999986543

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.81  E-value=1.1e-19  Score=122.66  Aligned_cols=78  Identities=23%  Similarity=0.296  Sum_probs=70.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|.+|+++.           +||||+|.+.++|++|++.||+..|.+     +.
T Consensus         9 ~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~-----------~~afV~f~~~~~a~~A~~~l~g~~~~g-----~~   72 (90)
T 2dnp_A            9 TWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK-----------DYAFVHMEKEADAKAAIAQLNGKEVKG-----KR   72 (90)
T ss_dssp             SCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECS-----------SCEEEEESCHHHHHHHHHHHTTCEETT-----EE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEEC-----------CEEEEEECCHHHHHHHHHHhCCCEECC-----cE
Confidence            78999999999999999999999999999999863           299999999999999999999999966     58


Q ss_pred             eEEEeecCCCCCCC
Q 030444          157 LRLQFSRNPGPRSV  170 (177)
Q Consensus       157 l~V~~a~~~~~r~~  170 (177)
                      |+|+|++.+.++.+
T Consensus        73 l~v~~a~~~~~~~~   86 (90)
T 2dnp_A           73 INVELSTKGQKKSG   86 (90)
T ss_dssp             CEEEESCCCCCCCS
T ss_pred             EEEEECCCCCCCCC
Confidence            99999987655543

>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=99.81  E-value=5.7e-20  Score=131.34  Aligned_cols=81  Identities=21%  Similarity=0.332  Sum_probs=71.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCC
Q 030444           75 DASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDS  154 (177)
Q Consensus        75 ~~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~  154 (177)
                      .+.++|||+|||+++|+++|+++|++||.|.++.++.++   .+++++|||||+|.+.++|++||+ ||+..|.+     
T Consensus        23 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~---~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~g-----   93 (124)
T 1wel_A           23 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYG---PNGKATGEGFVEFRNEADYKAALC-RHKQYMGN-----   93 (124)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEEC---TTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTT-----
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEEC---CCCCCCeEEEEEECCHHHHHHHHH-hCCCeECC-----
Confidence            347899999999999999999999999999885555554   578899999999999999999999 99999966     


Q ss_pred             cceEEEeecC
Q 030444          155 KFLRLQFSRN  164 (177)
Q Consensus       155 r~l~V~~a~~  164 (177)
                      |.|+|+++..
T Consensus        94 r~i~V~~a~~  103 (124)
T 1wel_A           94 RFIQVHPITK  103 (124)
T ss_dssp             SCBEEEEECH
T ss_pred             cEEEEEECCH
Confidence            5899999864

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.81  E-value=5.9e-20  Score=127.75  Aligned_cols=80  Identities=21%  Similarity=0.365  Sum_probs=71.8

Q ss_pred             CCeEEEcCCCCCC------CHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCC
Q 030444           77 SSTLYVEGLPADS------TKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDED  150 (177)
Q Consensus        77 ~~tLfV~nLp~~~------te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~  150 (177)
                      .++|||+|||+++      |+++|+++|++||.|.+|+|+.     .+|+++|||||+|.+.++|++|++.|||..|.++
T Consensus        15 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~-----~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~   89 (105)
T 2nlw_A           15 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE-----EDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ   89 (105)
T ss_dssp             CSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCC-----BTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTT
T ss_pred             CCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeC-----CCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCC
Confidence            6899999999999      7899999999999999998872     3688999999999999999999999999999763


Q ss_pred             CCCCcceEEEeecCC
Q 030444          151 DPDSKFLRLQFSRNP  165 (177)
Q Consensus       151 ~~~~r~l~V~~a~~~  165 (177)
                      +    +|+|+++...
T Consensus        90 ~----~l~V~~a~~~  100 (105)
T 2nlw_A           90 H----TFRVNLFTDF  100 (105)
T ss_dssp             C----EEEEECSCCC
T ss_pred             c----eEEEEEcchH
Confidence            1    7999999643

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.81  E-value=4.5e-20  Score=127.05  Aligned_cols=79  Identities=27%  Similarity=0.383  Sum_probs=71.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcce
Q 030444           78 STLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFL  157 (177)
Q Consensus        78 ~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~l  157 (177)
                      ++|||+|||+++|+++|+++|++||.|.+|+++.+        ++|||||+|.+.++|++|++.||+..+.+     +.|
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~--------~~g~afV~f~~~~~a~~A~~~l~g~~~~g-----~~l   67 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN--------PPGFAFVEFEDPRDAEDAVRGLDGKVICG-----SRV   67 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS--------SSSEEEEECSSHHHHHHHHHHHHHSCSSS-----CCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC--------CCCEEEEEECCHHHHHHHHHHHCCCeECC-----cEE
Confidence            58999999999999999999999999999999875        35799999999999999999999999976     479


Q ss_pred             EEEeecCCCCCC
Q 030444          158 RLQFSRNPGPRS  169 (177)
Q Consensus       158 ~V~~a~~~~~r~  169 (177)
                      +|+|++.+..+.
T Consensus        68 ~V~~a~~~~~~~   79 (101)
T 2hvz_A           68 RVELSTGMPRRS   79 (101)
T ss_dssp             EEEESSSCCCSS
T ss_pred             EEEEccCCCCcc
Confidence            999998765443

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} SCOP: d.58.7.1 PDB: 2f9d_A 2f9j_A 2fho_B

Probab=99.81  E-value=1.3e-19  Score=127.44  Aligned_cols=82  Identities=22%  Similarity=0.427  Sum_probs=72.9

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCC
Q 030444           73 PPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDP  152 (177)
Q Consensus        73 p~~~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~  152 (177)
                      |+.++++|||+|||+++|+++|+++|++||.|.+|+++.+      +.++|||||+|.+.++|++|++.|||..+.+   
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~------~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g---   74 (115)
T 3lqv_A            4 PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT------PETRGTAYVVYEDIFDAKNAVDHLSGFNVSN---   74 (115)
T ss_dssp             CTTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS------TTTTTCEEEEESSHHHHHHHHHHHTTCBSSS---
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC------CCCCcEEEEEECCHHHHHHHHHHcCCCEECC---
Confidence            3445799999999999999999999999999999999865      3457899999999999999999999999966   


Q ss_pred             CCcceEEEeecCC
Q 030444          153 DSKFLRLQFSRNP  165 (177)
Q Consensus       153 ~~r~l~V~~a~~~  165 (177)
                        +.|+|+|++.+
T Consensus        75 --~~l~v~~a~~~   85 (115)
T 3lqv_A           75 --RYLVVLYYNAN   85 (115)
T ss_dssp             --CBCEEEECCHH
T ss_pred             --eEEEEEEecCC
Confidence              48999999753

>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=99.81  E-value=5.6e-20  Score=129.64  Aligned_cols=80  Identities=15%  Similarity=0.174  Sum_probs=72.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCE-EEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCC
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGY-KEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDS  154 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i-~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~  154 (177)
                      +.++|||+|||+++|+++|+++|++||.| ..|+|+.++    +++++|||||+|.+.++|++||+. |+..|.+     
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~----~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~g-----   83 (114)
T 2cpy_A           14 AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN----NGQGLGQALVQFKNEDDARKSERL-HRKKLNG-----   83 (114)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT----TSSCSSCEEEECSSHHHHHHHGGG-CSEEETT-----
T ss_pred             CccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC----CCCcceEEEEEECCHHHHHHHHHh-CCCccCC-----
Confidence            37899999999999999999999999999 889998875    688999999999999999999987 9999966     


Q ss_pred             cceEEEeecCC
Q 030444          155 KFLRLQFSRNP  165 (177)
Q Consensus       155 r~l~V~~a~~~  165 (177)
                      +.|+|+++..+
T Consensus        84 r~i~v~~a~~~   94 (114)
T 2cpy_A           84 REAFVHVVTLE   94 (114)
T ss_dssp             EEEEEEEECHH
T ss_pred             eEEEEEECCHH
Confidence            58999998644

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=6.9e-20  Score=124.28  Aligned_cols=84  Identities=20%  Similarity=0.276  Sum_probs=71.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCC-EEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCC-CeeCCCCCC
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVG-YKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQG-YRMDEDDPD  153 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~-i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g-~~l~~~~~~  153 (177)
                      +.++|||+|||+++|+++|+++|++||. |..+.+..          +|||||+|.+.++|++|++.||+ ..|.+    
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~~----------~g~afV~f~~~~~A~~A~~~l~g~~~~~g----   72 (93)
T 2cqh_A            7 GMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK----------SGYAFVDYPDQNWAIRAIETLSGKVELHG----   72 (93)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEE----------TTEEEECCSCHHHHHHHHHHHTTTCEETT----
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEcC----------CCEEEEEECCHHHHHHHHHHccCCeeECC----
Confidence            3789999999999999999999999999 55555532          36999999999999999999999 99966    


Q ss_pred             CcceEEEeecCCCCCCCCCCC
Q 030444          154 SKFLRLQFSRNPGPRSVFGAR  174 (177)
Q Consensus       154 ~r~l~V~~a~~~~~r~~~g~~  174 (177)
                       +.|+|+|++.+..+....+.
T Consensus        73 -~~l~v~~a~~~~~~~~~~~~   92 (93)
T 2cqh_A           73 -KIMEVDYSVSKKLRSSGPSS   92 (93)
T ss_dssp             -EECEEEECCCCCCCCCSCCC
T ss_pred             -EEEEEEEccCccccCCCCCC
Confidence             58999999887666654433

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.81  E-value=8.3e-20  Score=129.71  Aligned_cols=79  Identities=16%  Similarity=0.223  Sum_probs=72.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCC---EEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCC
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVG---YKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDP  152 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~---i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~  152 (177)
                      +.++|||+|||+++|+++|+++|+.||.   |..|+|+.++    .++++|||||+|.+.++|++||+ +|+..|.+   
T Consensus        16 ~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~----~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~g---   87 (118)
T 2db1_A           16 EGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTR----EGRQSGEAFVELESEDDVKLALK-KDRESMGH---   87 (118)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECS----SSCEEEEEEEEBSSHHHHHHHGG-GTTEEETT---
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECC----CCCCCeEEEEEECCHHHHHHHHh-cCCCeECC---
Confidence            3789999999999999999999999998   8999999886    38899999999999999999999 99999965   


Q ss_pred             CCcceEEEeecC
Q 030444          153 DSKFLRLQFSRN  164 (177)
Q Consensus       153 ~~r~l~V~~a~~  164 (177)
                        |.|+|.++..
T Consensus        88 --r~i~V~~a~~   97 (118)
T 2db1_A           88 --RYIEVFKSHR   97 (118)
T ss_dssp             --EEEEEEEECH
T ss_pred             --eEEEEEECCH
Confidence              5899999853

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.81  E-value=3.3e-20  Score=120.95  Aligned_cols=75  Identities=19%  Similarity=0.329  Sum_probs=69.2

Q ss_pred             eEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcceE
Q 030444           79 TLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFLR  158 (177)
Q Consensus        79 tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~l~  158 (177)
                      +|||+|||+++|+++|+++|++||.|.+|+++.++   .+++++|||||+|.+.++|++|++ ||+..+.+     ++|+
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~---~~~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g-----~~l~   71 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDK---TTNRHRGFGFVTFESEDIVEKVCE-IHFHEINN-----KMVE   71 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCS---SSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSS-----CCCE
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecC---CCCCcCcEEEEEECCHHHHHHHHH-CCCCEECC-----EEEE
Confidence            59999999999999999999999999999998876   578899999999999999999997 99999976     4799


Q ss_pred             EEee
Q 030444          159 LQFS  162 (177)
Q Consensus       159 V~~a  162 (177)
                      |++|
T Consensus        72 v~~A   75 (75)
T 2mss_A           72 CKKA   75 (75)
T ss_dssp             EECC
T ss_pred             EEeC
Confidence            9886

>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=99.81  E-value=1.3e-19  Score=120.69  Aligned_cols=73  Identities=22%  Similarity=0.378  Sum_probs=67.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHh-CCCeeCCCCCCCc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSAL-QGYRMDEDDPDSK  155 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l-~g~~l~~~~~~~r  155 (177)
                      .++|||+|||+++|+++|+++|++||.|.+|+++.++         |||||+|.+.++|++|++.| ++..+.+     +
T Consensus        12 ~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~k---------g~afV~f~~~~~A~~a~~~l~~~~~~~g-----~   77 (85)
T 2ytc_A           12 ITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQ---------QCAFIQFATRQAAEVAAEKSFNKLIVNG-----R   77 (85)
T ss_dssp             CCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGGG---------TEEEEEESSHHHHHHHHHTTTTTCEETT-----E
T ss_pred             ccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECCC---------CEEEEEECCHHHHHHHHHHhcCCeeECC-----C
Confidence            6899999999999999999999999999999998643         69999999999999999988 9999976     5


Q ss_pred             ceEEEeec
Q 030444          156 FLRLQFSR  163 (177)
Q Consensus       156 ~l~V~~a~  163 (177)
                      +|+|+||+
T Consensus        78 ~l~v~~ak   85 (85)
T 2ytc_A           78 RLNVKWGR   85 (85)
T ss_dssp             ECCEEECC
T ss_pred             EEEEEecC
Confidence            89999985

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.81  E-value=1.3e-19  Score=126.94  Aligned_cols=77  Identities=31%  Similarity=0.570  Sum_probs=69.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      +.++|||+|||+++|+++|+++|++||.|.+|+++           +|||||+|.+.++|++|++.||+..|.+     +
T Consensus        30 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~-----------kg~afV~f~~~~~A~~Ai~~l~g~~~~g-----~   93 (108)
T 2jvo_A           30 SNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-----------NGFAFVEFEEAESAAKAIEEVHGKSFAN-----Q   93 (108)
T ss_dssp             SCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE-----------TTEEEEECSSHHHHHHHHHHHTTCEETT-----E
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE-----------CCEEEEEECCHHHHHHHHHHcCCCEECC-----e
Confidence            37999999999999999999999999999999987           2599999999999999999999999966     5


Q ss_pred             ceEEEeecCCCCC
Q 030444          156 FLRLQFSRNPGPR  168 (177)
Q Consensus       156 ~l~V~~a~~~~~r  168 (177)
                      .|+|+|++.+..+
T Consensus        94 ~l~V~~a~~~~~r  106 (108)
T 2jvo_A           94 PLEVVYSKLPAKR  106 (108)
T ss_dssp             ECEEESCSCCC--
T ss_pred             EEEEEEecCCCCC
Confidence            8999999876554

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A

Probab=99.81  E-value=2e-19  Score=123.45  Aligned_cols=76  Identities=22%  Similarity=0.364  Sum_probs=68.7

Q ss_pred             CCCCCeEEEcCCCC-CCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCC
Q 030444           74 PDASSTLYVEGLPA-DSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDP  152 (177)
Q Consensus        74 ~~~~~tLfV~nLp~-~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~  152 (177)
                      ..++++|||+|||+ ++++++|+++|++||.|.+|++.           +|||||+|.+.++|++|++.||+..+.+   
T Consensus        19 ~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~-----------~g~afV~f~~~~~A~~Ai~~l~g~~~~g---   84 (97)
T 2xnq_A           19 SHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-----------NAFGFIQFDNPQSVRDAIEXESQEMNFG---   84 (97)
T ss_dssp             CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC-----------SSEEEEEESSHHHHHHHHHHHTTSEETT---
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe-----------CCEEEEEECCHHHHHHHHHHcCCCEECC---
Confidence            33489999999998 99999999999999999999883           3699999999999999999999999966   


Q ss_pred             CCcceEEEeecCC
Q 030444          153 DSKFLRLQFSRNP  165 (177)
Q Consensus       153 ~~r~l~V~~a~~~  165 (177)
                        +.|+|+|++.+
T Consensus        85 --~~l~V~~a~~~   95 (97)
T 2xnq_A           85 --KKLILEVSSSN   95 (97)
T ss_dssp             --EECEEEECCCC
T ss_pred             --EEEEEEecCCC
Confidence              58999999764

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.80  E-value=4e-20  Score=120.94  Aligned_cols=76  Identities=18%  Similarity=0.260  Sum_probs=70.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcce
Q 030444           78 STLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFL  157 (177)
Q Consensus        78 ~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~l  157 (177)
                      ++|||+|||+++|+++|+++|++||.|.+|+++.++   .+++++|||||+|.+.++|++|++.++ ..+.+     +.|
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~---~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g-----~~l   71 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDP---LTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDS-----KTI   71 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCC---CSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSS-----CCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCC---CCCCcCceEEEEEcCHHHHHHHHHhCC-CccCC-----EEE
Confidence            479999999999999999999999999999999886   568899999999999999999999999 88866     479


Q ss_pred             EEEee
Q 030444          158 RLQFS  162 (177)
Q Consensus       158 ~V~~a  162 (177)
                      +|++|
T Consensus        72 ~v~~a   76 (77)
T 1uaw_A           72 DPKVA   76 (77)
T ss_dssp             EEEEC
T ss_pred             EEEec
Confidence            99987

>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=99.80  E-value=3e-19  Score=123.48  Aligned_cols=75  Identities=19%  Similarity=0.392  Sum_probs=68.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|.+|+++.           +||||+|.+.++|++|++.||+..|.+     +.
T Consensus        11 ~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~~-----------~~afV~f~~~~~a~~A~~~l~g~~~~g-----~~   74 (103)
T 2dgu_A           11 VKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLK-----------DYAFIHFDERDGAVKAMEEMNGKDLEG-----EN   74 (103)
T ss_dssp             CCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEECS-----------SCEEEEESSHHHHHHHHHHHTTEEETT-----EE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEC-----------CEEEEEeCCHHHHHHHHHHHCCCccCC-----CE
Confidence            68999999999999999999999999999998863           399999999999999999999999976     58


Q ss_pred             eEEEeecCCCC
Q 030444          157 LRLQFSRNPGP  167 (177)
Q Consensus       157 l~V~~a~~~~~  167 (177)
                      |+|+|++.+..
T Consensus        75 l~v~~a~~~~~   85 (103)
T 2dgu_A           75 IEIVFAKPPDQ   85 (103)
T ss_dssp             EEEEECCCCCC
T ss_pred             EEEEEcCCCcc
Confidence            99999987644

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=8.4e-19  Score=119.93  Aligned_cols=80  Identities=25%  Similarity=0.337  Sum_probs=70.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      +.++|||+||  ++|+++|+++|++||.|.+|+|..         ++|||||+|.+.++|++|++.||+..|.+     +
T Consensus        14 ~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~~---------~~g~afV~f~~~~~a~~Ai~~l~g~~~~g-----~   77 (97)
T 1x5p_A           14 KGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDP---------PRNCAFVTYEKMESADQAVAELNGTQVES-----V   77 (97)
T ss_dssp             CCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEET---------TTTEEEEEESSHHHHHHHHHHTTTEEETT-----E
T ss_pred             CCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEecC---------CCCEEEEEECCHHHHHHHHHHhCCCeECC-----e
Confidence            3789999996  899999999999999999999843         34799999999999999999999999966     5


Q ss_pred             ceEEEeecCCCCCCCC
Q 030444          156 FLRLQFSRNPGPRSVF  171 (177)
Q Consensus       156 ~l~V~~a~~~~~r~~~  171 (177)
                      +|+|+|++.+..+...
T Consensus        78 ~l~v~~a~~~~~~~~~   93 (97)
T 1x5p_A           78 QLKVNIARKQPMLDSG   93 (97)
T ss_dssp             EEEEECCSSCCCCCSS
T ss_pred             EEEEEECCCCCCCCCC
Confidence            8999999887665543

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori}

Probab=99.80  E-value=1.5e-20  Score=126.78  Aligned_cols=80  Identities=19%  Similarity=0.317  Sum_probs=71.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcce
Q 030444           78 STLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFL  157 (177)
Q Consensus        78 ~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~l  157 (177)
                      ++|||+|||+++++++|+++|++||.|.+|+++.++   .+++++|||||+|.+.+ |++|++.||+..+.+     +.|
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~---~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g-----~~l   72 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDR---ETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMG-----RTI   72 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCS---SSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSS-----SSC
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcC---CCCCcceEEEEEECCHH-HHHHHHHhCCCEECC-----eEE
Confidence            589999999999999999999999999999999886   56889999999999999 999999999999976     479


Q ss_pred             EEEeecCCC
Q 030444          158 RLQFSRNPG  166 (177)
Q Consensus       158 ~V~~a~~~~  166 (177)
                      +|++|..+.
T Consensus        73 ~V~~a~~~~   81 (90)
T 2ki2_A           73 RVTEANPKK   81 (90)
T ss_dssp             SEEEC----
T ss_pred             EEEEcCCCC
Confidence            999997653

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.80  E-value=2e-19  Score=139.38  Aligned_cols=83  Identities=24%  Similarity=0.290  Sum_probs=75.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCC
Q 030444           75 DASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDS  154 (177)
Q Consensus        75 ~~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~  154 (177)
                      .+.+||||+|||+++||++|+++|++||.|.+|+|+.++   .+++++|||||+|.+.++|++|++.+|+..+.+     
T Consensus        13 ~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~---~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g-----   84 (213)
T 4f02_A           13 YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDM---ITRRSLGYAYVNFQQPADAERALDTMNFDVIKG-----   84 (213)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT---TTCCEEEEEEEEESSHHHHHHHHHHHTTCEETT-----
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeccc---CCCCccccccceeCCHHHHHHHHHHhhhhhcCC-----
Confidence            347899999999999999999999999999999999987   678899999999999999999999999999966     


Q ss_pred             cceEEEeecCC
Q 030444          155 KFLRLQFSRNP  165 (177)
Q Consensus       155 r~l~V~~a~~~  165 (177)
                      +.|+|.++...
T Consensus        85 ~~i~~~~~~~~   95 (213)
T 4f02_A           85 KPVRIMWSQRD   95 (213)
T ss_dssp             EECEEEECCCC
T ss_pred             ccccccccccc
Confidence            57999988654

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C

Probab=99.80  E-value=8.8e-20  Score=143.69  Aligned_cols=80  Identities=11%  Similarity=0.139  Sum_probs=73.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCC--CEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCC
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFV--GYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPD  153 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G--~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~  153 (177)
                      ..++|||+|||+++|+++|+++|++||  .|.+|+|+.++   .++++||||||+|.+.++|++||+.||++.|.+    
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~---~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~G----  139 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENR---ANGQSKGFALVGVGSEASSKKLMDLLPKRELHG----  139 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECT---TTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTT----
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecC---CCCccceEEEEEECCHHHHHHHHHHcCCCeECC----
Confidence            367899999999999999999999999  99999999987   679999999999999999999999999999976    


Q ss_pred             CcceEEEeec
Q 030444          154 SKFLRLQFSR  163 (177)
Q Consensus       154 ~r~l~V~~a~  163 (177)
                       +.|+|+|++
T Consensus       140 -r~l~V~~a~  148 (229)
T 3q2s_C          140 -QNPVVTPVN  148 (229)
T ss_dssp             -BCCEEEECC
T ss_pred             -EEeEEEECC
Confidence             579999985

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.80  E-value=1e-19  Score=124.06  Aligned_cols=80  Identities=23%  Similarity=0.381  Sum_probs=70.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      +.++|||+|||+++|+++|+++|++||.|..+    .    .+++++|||||+|.+.++|++|++.||+..|.+     +
T Consensus        15 ~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~----~----~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g-----~   81 (96)
T 1fjc_A           15 AARTLLAKNLSFNITEDELKEVFEDALEIRLV----S----QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDG-----R   81 (96)
T ss_dssp             GGGEEEEESCCSSCCHHHHHHHHCSEEEECCE----E----ETTEEEEEEEEEESSHHHHHHHHHHTTEEEETT-----E
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe----C----CCCCcceEEEEEECCHHHHHHHHHHhCCCEECC-----e
Confidence            37899999999999999999999999887655    2    357789999999999999999999999999966     5


Q ss_pred             ceEEEeecCCCCC
Q 030444          156 FLRLQFSRNPGPR  168 (177)
Q Consensus       156 ~l~V~~a~~~~~r  168 (177)
                      .|+|+|++.+..+
T Consensus        82 ~l~v~~a~~~~~~   94 (96)
T 1fjc_A           82 SVSLYYTGEKGGT   94 (96)
T ss_dssp             EEEEEECSSSCCC
T ss_pred             EEEEEEcCCCCCC
Confidence            8999999765443

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ...

Probab=99.80  E-value=9.1e-20  Score=124.40  Aligned_cols=80  Identities=24%  Similarity=0.380  Sum_probs=71.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHH----HhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCC
Q 030444           76 ASSTLYVEGLPADSTKREVA----HIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDD  151 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~----~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~  151 (177)
                      ++++|||+|||+++|+++|+    ++|++||.|.+|++..      +++++|||||+|.+.++|++|++.||+..+.+  
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~------~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g--   78 (97)
T 1nu4_A            7 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR------SLKMRGQAFVIFKEVSSATNALRSMQGFPFYD--   78 (97)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH------HHHHTTCEEEEESSHHHHHHHHHHHTTCEETT--
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc------CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECC--
Confidence            37999999999999999999    9999999999998863      25567899999999999999999999999966  


Q ss_pred             CCCcceEEEeecCCC
Q 030444          152 PDSKFLRLQFSRNPG  166 (177)
Q Consensus       152 ~~~r~l~V~~a~~~~  166 (177)
                         +.|+|+|++.+.
T Consensus        79 ---~~l~v~~a~~~~   90 (97)
T 1nu4_A           79 ---KPMRIQYAKTDS   90 (97)
T ss_dssp             ---EECEEEECSSCC
T ss_pred             ---cEEEEEEccCCC
Confidence               589999998754

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A

Probab=99.79  E-value=2.5e-19  Score=134.10  Aligned_cols=79  Identities=22%  Similarity=0.263  Sum_probs=70.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      ..+|||+||++++|+++|+++|++||.|.+|+|..++       ++|||||+|++.++|++|++.|||..|.+   .++.
T Consensus        46 vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~-------~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g---~g~~  115 (164)
T 1sjr_A           46 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN-------NQFQALLQYADPVSAQHAKLSLDGQNIYN---ACCT  115 (164)
T ss_dssp             EEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESS-------SCEEEEEEESCHHHHHHHHHHSTTBCSSS---SCSC
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCC-------CCCEEEEEECCHHHHHHHHHHhCCCEecC---CCcE
Confidence            4679999999999999999999999999999986543       45899999999999999999999999976   2358


Q ss_pred             eEEEeecCC
Q 030444          157 LRLQFSRNP  165 (177)
Q Consensus       157 l~V~~a~~~  165 (177)
                      |+|+|++.+
T Consensus       116 L~V~~Ak~~  124 (164)
T 1sjr_A          116 LRIDFSKLT  124 (164)
T ss_dssp             EEEEECSSS
T ss_pred             EEEEEecCC
Confidence            999999865

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A

Probab=99.79  E-value=1.4e-19  Score=131.91  Aligned_cols=78  Identities=15%  Similarity=0.209  Sum_probs=72.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCC---EEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCC
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVG---YKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPD  153 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~---i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~  153 (177)
                      .++|||+|||+++|+++|+++|++||.   |.+|+|+.++   . |+++|||||+|.+.++|++|++ ||+..|.+    
T Consensus        44 ~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~---~-g~srG~aFV~F~~~e~a~~Al~-~~g~~l~g----  114 (136)
T 2hgl_A           44 GFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTR---E-GRQSGEAFVELGSEDDVKMALK-KDRESMGH----  114 (136)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECS---S-SCEEEEEEEECSSHHHHHHHHT-TTEEESSS----
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECC---C-CCCCeEEEEEECCHHHHHHHHh-cCCCEECC----
Confidence            689999999999999999999999999   8899999886   4 8899999999999999999999 99999965    


Q ss_pred             CcceEEEeecC
Q 030444          154 SKFLRLQFSRN  164 (177)
Q Consensus       154 ~r~l~V~~a~~  164 (177)
                       |.|+|.++..
T Consensus       115 -r~i~V~~a~~  124 (136)
T 2hgl_A          115 -RYIEVFKSHR  124 (136)
T ss_dssp             -SEEEEEECCH
T ss_pred             -EEEEEEECCh
Confidence             5899999853

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.79  E-value=9.8e-19  Score=125.52  Aligned_cols=75  Identities=19%  Similarity=0.286  Sum_probs=66.3

Q ss_pred             eEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceE-EEEEecCHHHHHHHHHHhCCCeeCCCCCCCcce
Q 030444           79 TLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLIL-CFVDFENPACAATALSALQGYRMDEDDPDSKFL  157 (177)
Q Consensus        79 tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~-afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~l  157 (177)
                      .|||+||++.+|+++|+++|++||.|.+|+|+..     .    || |||+|.+.++|++|++.|||..|.+.   .+.|
T Consensus        27 ~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~-----~----Gf~aFVef~~~~~A~~A~~~LnG~~i~g~---~~~l   94 (124)
T 2e5i_A           27 LLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR-----N----GIQAMVEFESVLCAQKAKAALNGADIYAG---CCTL   94 (124)
T ss_dssp             EEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES-----S----SEEEEEEESSHHHHHHHHHHHTTCCCBTT---BSEE
T ss_pred             EEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC-----C----CCEEEEEECCHHHHHHHHHHhCCCEecCC---CeEE
Confidence            4689999999999999999999999999998642     1    56 99999999999999999999999762   2479


Q ss_pred             EEEeecCC
Q 030444          158 RLQFSRNP  165 (177)
Q Consensus       158 ~V~~a~~~  165 (177)
                      +|+||+.+
T Consensus        95 ~V~~Ak~~  102 (124)
T 2e5i_A           95 KIEYARPT  102 (124)
T ss_dssp             EEECCSCS
T ss_pred             EEEEecCC
Confidence            99999865

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.79  E-value=1.6e-19  Score=121.70  Aligned_cols=73  Identities=12%  Similarity=0.058  Sum_probs=67.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      +..|||+||++.+||++|+++|.+||+|.+++++.         +||||||+|.+.++|++|++.||+..|.+     |+
T Consensus         7 ~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~---------~kGfaFVey~~~~eA~~Ai~~Ln~~~l~g-----r~   72 (89)
T 2wbr_A            7 SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL---------NQGIALCKYTTREEANKAQMALNNCVLAN-----TT   72 (89)
T ss_dssp             CCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET---------TTTEEEEEESSHHHHHHHHHHHTTEEETT-----EE
T ss_pred             cceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC---------CCcEEEEEECCHHHHHHHHHHhcCCEECC-----cE
Confidence            67899999999999999999999999999999865         34899999999999999999999999976     58


Q ss_pred             eEEEeec
Q 030444          157 LRLQFSR  163 (177)
Q Consensus       157 l~V~~a~  163 (177)
                      |+|++|.
T Consensus        73 I~V~~A~   79 (89)
T 2wbr_A           73 IFAESPS   79 (89)
T ss_dssp             EEEECCC
T ss_pred             EEEEECC
Confidence            9999983

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.79  E-value=1.1e-19  Score=120.40  Aligned_cols=74  Identities=23%  Similarity=0.402  Sum_probs=65.7

Q ss_pred             CCeEEEcCCCCCC------CHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCC
Q 030444           77 SSTLYVEGLPADS------TKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDED  150 (177)
Q Consensus        77 ~~tLfV~nLp~~~------te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~  150 (177)
                      +++|||+|||+++      |+++|+++|++||.|.+|+++.     .+|+++|||||+|.+.++|++|++.|||..|.++
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~~-----~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~   75 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE-----EDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ   75 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCC-----BTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSS
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecC-----CCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCc
Confidence            3789999999999      7899999999999999999872     3688999999999999999999999999999763


Q ss_pred             CCCCcceEE
Q 030444          151 DPDSKFLRL  159 (177)
Q Consensus       151 ~~~~r~l~V  159 (177)
                      +    +|+|
T Consensus        76 ~----~l~V   80 (81)
T 2krb_A           76 H----TFRV   80 (81)
T ss_dssp             S----CCCC
T ss_pred             e----eEEe
Confidence            1    5765

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.79  E-value=5.3e-19  Score=120.80  Aligned_cols=75  Identities=23%  Similarity=0.371  Sum_probs=68.4

Q ss_pred             CCeEEEcCCCC-CCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           77 SSTLYVEGLPA-DSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        77 ~~tLfV~nLp~-~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      +++|||+|||+ ++|+++|+++|++||.|.+|++.           +|||||+|.+.++|++|++.||+..+.+     +
T Consensus        10 ~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~-----------~g~afV~f~~~~~A~~A~~~l~g~~~~g-----~   73 (96)
T 2kvi_A           10 KSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-----------NAFGFIQFDNPQSVRDAIECESQEMNFG-----K   73 (96)
T ss_dssp             CEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE-----------TTEEEEEESCHHHHHHHHHHHTCSSCBT-----T
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe-----------CCEEEEEECCHHHHHHHHHHcCCCeeCC-----c
Confidence            79999999998 99999999999999999999883           2599999999999999999999999976     4


Q ss_pred             ceEEEeecCCCC
Q 030444          156 FLRLQFSRNPGP  167 (177)
Q Consensus       156 ~l~V~~a~~~~~  167 (177)
                      +|+|+|++.+..
T Consensus        74 ~l~V~~a~~~~~   85 (96)
T 2kvi_A           74 KLILEVSSSNAR   85 (96)
T ss_dssp             TBCEEEEECCCC
T ss_pred             EEEEEEcCcCCC
Confidence            799999987543

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.79  E-value=2e-19  Score=123.75  Aligned_cols=74  Identities=19%  Similarity=0.377  Sum_probs=68.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|.+|++...         +|||||+|.+.++|++|++.||+..|.+     +.
T Consensus        27 ~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~---------~g~afV~f~~~~~A~~Ai~~l~g~~~~g-----~~   92 (101)
T 2la4_A           27 VTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE---------KGCCFIKYDTHEQAAVCIVALANFPFQG-----RN   92 (101)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEETT---------TTEEEEECSSHHHHHHHHHHHTTCEETT-----EE
T ss_pred             CCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEecC---------CCEEEEEECCHHHHHHHHHHhCCCeECC-----eE
Confidence            689999999999999999999999999999998733         4799999999999999999999999976     58


Q ss_pred             eEEEeecC
Q 030444          157 LRLQFSRN  164 (177)
Q Consensus       157 l~V~~a~~  164 (177)
                      |+|+|+++
T Consensus        93 l~V~~a~~  100 (101)
T 2la4_A           93 LRTGWGKE  100 (101)
T ss_dssp             CCCCBCCC
T ss_pred             EEEEeccC
Confidence            99999975

>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=99.78  E-value=1.4e-19  Score=126.26  Aligned_cols=80  Identities=16%  Similarity=0.237  Sum_probs=72.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHhhCCCCC---EEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCC
Q 030444           75 DASSTLYVEGLPADSTKREVAHIFRPFVG---YKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDD  151 (177)
Q Consensus        75 ~~~~tLfV~nLp~~~te~~L~~lF~~~G~---i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~  151 (177)
                      +..++|||+|||+++|+++|+++|+.||.   |..|+|+.++   . |+++|||||+|.+.++|++|++ +|+..|.+  
T Consensus         9 ~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~---~-g~~~G~afV~F~~~~~a~~Al~-~~~~~~~g--   81 (107)
T 2lmi_A            9 DDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNR---D-GKRRGDALIEMESEQDVQKALE-KHRMYMGQ--   81 (107)
T ss_dssp             SSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCT---T-STTCSEEEEEBSSHHHHHHHHT-TTTCCSSS--
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECC---C-CCEeeEEEEEECCHHHHHHHHH-hCcceeCC--
Confidence            34789999999999999999999999988   8999998886   3 8899999999999999999999 99999865  


Q ss_pred             CCCcceEEEeecC
Q 030444          152 PDSKFLRLQFSRN  164 (177)
Q Consensus       152 ~~~r~l~V~~a~~  164 (177)
                         |.|+|.++..
T Consensus        82 ---r~i~V~~a~~   91 (107)
T 2lmi_A           82 ---RYVEVYEINN   91 (107)
T ss_dssp             ---SCCCCEECCH
T ss_pred             ---eEEEEEECCH
Confidence               5799999864

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*

Probab=99.78  E-value=9.9e-19  Score=149.45  Aligned_cols=85  Identities=22%  Similarity=0.380  Sum_probs=77.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCC
Q 030444           75 DASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDS  154 (177)
Q Consensus        75 ~~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~  154 (177)
                      .+.++|||+|||++||+++|+++|++||.|..|+|+.++   .+++++|||||+|.+.++|++||+.||++.|.+     
T Consensus       100 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~---~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~g-----  171 (437)
T 3pgw_S          100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSK---RSGKPRGYAFIEYEHERDMHSAYKHADGKKIDG-----  171 (437)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccC---CCCCccceEEEeeccHHHHHHHHHHcCCCEECC-----
Confidence            346899999999999999999999999999999999886   578899999999999999999999999999966     


Q ss_pred             cceEEEeecCCCC
Q 030444          155 KFLRLQFSRNPGP  167 (177)
Q Consensus       155 r~l~V~~a~~~~~  167 (177)
                      +.|+|+|++....
T Consensus       172 r~i~V~~a~~~~~  184 (437)
T 3pgw_S          172 RRVLVDVERGRTV  184 (437)
T ss_pred             EEEEEEEeCCCCC
Confidence            4899999986533

>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=99.78  E-value=5e-19  Score=124.38  Aligned_cols=75  Identities=23%  Similarity=0.264  Sum_probs=68.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|.+|+|+..         ++||||+|.+.++|++|++.||++.|.+     ++
T Consensus        10 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~---------~g~afV~f~~~~~A~~Ai~~l~g~~~~g-----~~   75 (111)
T 1whx_A           10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEG---------GITAIVEFLEPLEARKAFRHLAYSKFHH-----VP   75 (111)
T ss_dssp             EEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCSS---------SSCEEEEESCHHHHHHHHHHHTTCBSSS-----SB
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC---------CCEEEEEeCCHHHHHHHHHHhCCCEECC-----eE
Confidence            579999999999999999999999999999988643         3699999999999999999999999976     58


Q ss_pred             eEEEeecCC
Q 030444          157 LRLQFSRNP  165 (177)
Q Consensus       157 l~V~~a~~~  165 (177)
                      |+|+|++..
T Consensus        76 l~V~~a~~~   84 (111)
T 1whx_A           76 LYLEWAPIG   84 (111)
T ss_dssp             CEEEEEETT
T ss_pred             EEEEECCCC
Confidence            999999754

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A

Probab=99.78  E-value=8.7e-20  Score=133.50  Aligned_cols=80  Identities=20%  Similarity=0.338  Sum_probs=71.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++||++|+++|++|| |.+|+|+.++    .++++|||||+|++.++|++|| .+|+..|.+     |.
T Consensus        46 ~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~----~g~srGfaFV~F~~~e~A~~Al-~~~g~~l~g-----R~  114 (139)
T 2hgn_A           46 GHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGP----DGRVTGEADVEFATHEEAVAAM-SKDRANMQH-----RY  114 (139)
T ss_dssp             CCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSS----SSCSSCCCEEECSHHHHHHHHT-TCCSCSSSS-----CC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECC----CCCCceEEEEEeCCHHHHHHHH-hhCCCEECC-----EE
Confidence            68999999999999999999999999 7799998886    3889999999999999999999 789999966     57


Q ss_pred             eEEEeecCCCC
Q 030444          157 LRLQFSRNPGP  167 (177)
Q Consensus       157 l~V~~a~~~~~  167 (177)
                      |+|.++..+..
T Consensus       115 i~V~~a~~~~~  125 (139)
T 2hgn_A          115 IELFLNSTTGA  125 (139)
T ss_dssp             CCCEECCCSCC
T ss_pred             EEEEECCCCCC
Confidence            99999876544

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.78  E-value=5.9e-19  Score=123.97  Aligned_cols=76  Identities=18%  Similarity=0.242  Sum_probs=69.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      ..+|||+|||+++|+++|+++|++| .|.+|+|+.++    .|+++|||||+|.+.++|++|| .+|+..|.+     |.
T Consensus        16 ~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~----~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~g-----r~   84 (109)
T 2dnn_A           16 DLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDH----VGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQ-----RY   84 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCT----TCCCCSEEEEECSSHHHHHHHH-HTTTEEETT-----EE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECC----CCCCCeEEEEEECCHHHHHHHH-hcCCCeECC-----eE
Confidence            5799999999999999999999999 89999999886    4889999999999999999999 799999965     58


Q ss_pred             eEEEeec
Q 030444          157 LRLQFSR  163 (177)
Q Consensus       157 l~V~~a~  163 (177)
                      |+|..+.
T Consensus        85 i~V~~a~   91 (109)
T 2dnn_A           85 VEVSPAT   91 (109)
T ss_dssp             EEEEECC
T ss_pred             EEEEECC
Confidence            9998774

>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=99.78  E-value=9e-19  Score=128.83  Aligned_cols=77  Identities=26%  Similarity=0.400  Sum_probs=70.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      +.++|||+|||+++|+++|+++|++||.|.+|+|+.+        ++|||||+|.+.++|++|++.||+..|.+     +
T Consensus        72 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~--------~~g~afV~f~~~~~a~~A~~~l~g~~~~g-----~  138 (150)
T 2i2y_A           72 LDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN--------PPGFAFVEFEDPRDAADAVRELDGRTLCG-----C  138 (150)
T ss_dssp             TSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS--------SCSEEEEEESSHHHHHHHHHHHSSSCSSS-----S
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC--------CCcEEEEEECCHHHHHHHHHHcCCCEECC-----e
Confidence            3799999999999999999999999999999999765        35799999999999999999999999966     5


Q ss_pred             ceEEEeecCC
Q 030444          156 FLRLQFSRNP  165 (177)
Q Consensus       156 ~l~V~~a~~~  165 (177)
                      +|+|+|++.+
T Consensus       139 ~l~v~~a~~~  148 (150)
T 2i2y_A          139 RVRVELSNGE  148 (150)
T ss_dssp             CCEEEECCCC
T ss_pred             EEEEEEcCCC
Confidence            8999999764

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.78  E-value=1.2e-18  Score=125.90  Aligned_cols=78  Identities=22%  Similarity=0.267  Sum_probs=68.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceE-EEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLIL-CFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~-afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      --.|||+||++.+|+++|+++|++||.|.+|++..+.        +|| |||+|.+.++|++|++.|||..|.+.   .+
T Consensus        28 VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~--------~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~---~~   96 (130)
T 3zzy_A           28 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN--------NQFQALLQYADPVSAQHAKLSLDGQNIYNA---CC   96 (130)
T ss_dssp             EEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEET--------TEEEEEEEESCHHHHHHHHHHHTTCEEETT---EE
T ss_pred             eEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCC--------CCcEEEEEECCHHHHHHHHHHcCCCeecCC---Cc
Confidence            3457899999999999999999999999999887642        467 99999999999999999999999772   25


Q ss_pred             ceEEEeecCC
Q 030444          156 FLRLQFSRNP  165 (177)
Q Consensus       156 ~l~V~~a~~~  165 (177)
                      +|+|+||+.+
T Consensus        97 ~LrI~~ak~~  106 (130)
T 3zzy_A           97 TLRIDFSKLT  106 (130)
T ss_dssp             EEEEEECSCS
T ss_pred             EEEEEecCCC
Confidence            8999999865

>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=99.78  E-value=7.4e-20  Score=133.65  Aligned_cols=86  Identities=23%  Similarity=0.442  Sum_probs=71.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEE------EEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeC
Q 030444           75 DASSTLYVEGLPADSTKREVAHIFRPFVGYKEV------RLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMD  148 (177)
Q Consensus        75 ~~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v------~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~  148 (177)
                      .++++|||+|||+++|+++|+++|++||.|..+      .+...    .+++++|||||+|.+.++|++|++.||++.|.
T Consensus        43 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~----~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~  118 (143)
T 3egn_A           43 EPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLM----KEGRMKGQAFIGLPNEKAAAKALKEANGYVLF  118 (143)
T ss_dssp             SCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEE----EETTTEEEEEEECSSHHHHHHHHHHHTTBEET
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEec----cCCCcccEEEEEeCCHHHHHHHHHHhCCCEeC
Confidence            347999999999999999999999999998764      11111    25778999999999999999999999999996


Q ss_pred             CCCCCCcceEEEeecCCCCCC
Q 030444          149 EDDPDSKFLRLQFSRNPGPRS  169 (177)
Q Consensus       149 ~~~~~~r~l~V~~a~~~~~r~  169 (177)
                      +     +.|+|+||++..++.
T Consensus       119 g-----~~l~V~~a~~~~~~~  134 (143)
T 3egn_A          119 G-----KPMVVQFARSARPKQ  134 (143)
T ss_dssp             T-----EECEEEECCCSCC--
T ss_pred             C-----cEEEEEECCCCCCcc
Confidence            6     589999998765544

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.77  E-value=4.6e-18  Score=125.11  Aligned_cols=80  Identities=20%  Similarity=0.370  Sum_probs=74.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      +.++|||+|||+++|+++|+++|++||.|.+++++.+.   .++.++|||||+|.+.++|++|++.|||..+.+     +
T Consensus        86 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~---~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g-----~  157 (166)
T 3md3_A           86 DTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDM---QTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNG-----R  157 (166)
T ss_dssp             TCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECT---TTCCEEEEEEEEESCHHHHHHHHHHHTTCEETT-----E
T ss_pred             CCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecC---CCCCcceEEEEEeCCHHHHHHHHHHhCCCccCC-----c
Confidence            37899999999999999999999999999999999886   578899999999999999999999999999965     5


Q ss_pred             ceEEEeec
Q 030444          156 FLRLQFSR  163 (177)
Q Consensus       156 ~l~V~~a~  163 (177)
                      +|+|+||+
T Consensus       158 ~i~v~~a~  165 (166)
T 3md3_A          158 PLRINWAA  165 (166)
T ss_dssp             ECEEEESC
T ss_pred             EEEEEecC
Confidence            89999985

>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=99.77  E-value=2.2e-18  Score=121.75  Aligned_cols=79  Identities=13%  Similarity=0.200  Sum_probs=66.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|.+|+|+.+          |||||+|.+.++|++||+.||++.|.++......
T Consensus        16 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~----------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~   85 (115)
T 3beg_B           16 ENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD----------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAY   85 (115)
T ss_dssp             -CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT----------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCB
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC----------CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEE
Confidence            689999999999999999999999999999998754          5999999999999999999999999875211123


Q ss_pred             eEEEeecCC
Q 030444          157 LRLQFSRNP  165 (177)
Q Consensus       157 l~V~~a~~~  165 (177)
                      |+|+.++..
T Consensus        86 i~v~~~~~~   94 (115)
T 3beg_B           86 IRVKVDGPR   94 (115)
T ss_dssp             CEEEECC--
T ss_pred             EEeccCCCC
Confidence            788877654

>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=99.77  E-value=3.1e-18  Score=126.15  Aligned_cols=81  Identities=26%  Similarity=0.463  Sum_probs=75.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      +++|||+|||+++|+++|+++|++||.|.+++++.++   .+++++|||||+|.+.++|++|++.||+..+.+     +.
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~---~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g-----~~   73 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDK---ITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQT-----KT   73 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT---TTCCEEEEEEEEESSHHHHHHHHHHHTTCEETT-----EE
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC---CCCcceeEEEEEECCHHHHHHHHHHcCCCccCC-----ce
Confidence            6899999999999999999999999999999999886   578899999999999999999999999999966     58


Q ss_pred             eEEEeecCC
Q 030444          157 LRLQFSRNP  165 (177)
Q Consensus       157 l~V~~a~~~  165 (177)
                      |+|+|++..
T Consensus        74 l~v~~~~~~   82 (167)
T 1fxl_A           74 IKVSYARPS   82 (167)
T ss_dssp             CEEEECCCC
T ss_pred             EEEEecCCC
Confidence            999999754

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.77  E-value=4e-18  Score=130.96  Aligned_cols=83  Identities=18%  Similarity=0.359  Sum_probs=76.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|..|+++.++   .+++++|||||+|.+.++|.+|++.||+..|.+     +.
T Consensus       125 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~---~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g-----~~  196 (216)
T 2qfj_A          125 FNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDP---TTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGG-----QY  196 (216)
T ss_dssp             SCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECT---TTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSS-----SB
T ss_pred             CcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecC---CCCCcCceEEEEecCHHHHHHHHHHccCCEeCC-----cE
Confidence            6899999999999999999999999999999999886   578899999999999999999999999999966     58


Q ss_pred             eEEEeecCCCC
Q 030444          157 LRLQFSRNPGP  167 (177)
Q Consensus       157 l~V~~a~~~~~  167 (177)
                      |+|+|++.+..
T Consensus       197 i~V~~a~~~~~  207 (216)
T 2qfj_A          197 LRVGKAVTPPM  207 (216)
T ss_dssp             CEEEECSSCSS
T ss_pred             EEEEEecCCCC
Confidence            99999987633

>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=99.76  E-value=1.7e-18  Score=127.96  Aligned_cols=82  Identities=28%  Similarity=0.446  Sum_probs=75.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      +++|||+|||+++|+++|+++|++||.|.+|+++.++   .+++++|||||+|.+.++|++|++.|++..+.+     ++
T Consensus         3 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~---~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g-----~~   74 (168)
T 1b7f_A            3 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDY---KTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRN-----KR   74 (168)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEET---TTTEECSEEEEEESSHHHHHHHHHHHTTCEETT-----EE
T ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeC---CCCccceEEEEEECCHHHHHHHHHhcCCCEeCC-----cE
Confidence            6899999999999999999999999999999998876   578899999999999999999999999999966     58


Q ss_pred             eEEEeecCCC
Q 030444          157 LRLQFSRNPG  166 (177)
Q Consensus       157 l~V~~a~~~~  166 (177)
                      |+|+|++...
T Consensus        75 l~v~~~~~~~   84 (168)
T 1b7f_A           75 LKVSYARPGG   84 (168)
T ss_dssp             CEEEECCCCS
T ss_pred             EEEEecCCCc
Confidence            9999997653

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=1.1e-18  Score=123.47  Aligned_cols=81  Identities=16%  Similarity=0.206  Sum_probs=69.0

Q ss_pred             CCCeEEE--cCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCee-CCCCC
Q 030444           76 ASSTLYV--EGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRM-DEDDP  152 (177)
Q Consensus        76 ~~~tLfV--~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l-~~~~~  152 (177)
                      ++++|||  +||++++|+++|+++|++||.|.+|.|+.+         ||||||+|.+.++|++|++.|||..| ..-. 
T Consensus        24 pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~---------rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg-   93 (114)
T 2cq2_A           24 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN---------KPYSFARYRTTEESKRAYVTLNGKEVVDDLG-   93 (114)
T ss_dssp             CCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT---------CSCEEEEESSHHHHHHHHHHTTTCEEECTTS-
T ss_pred             CCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC---------CCEEEEEECCHHHHHHHHHHhCCCEEccccC-
Confidence            4789999  779999999999999999999999887543         47999999999999999999999988 2111 


Q ss_pred             CCcceEEEeecCCC
Q 030444          153 DSKFLRLQFSRNPG  166 (177)
Q Consensus       153 ~~r~l~V~~a~~~~  166 (177)
                      .+++|.|.|++..+
T Consensus        94 ~g~~l~v~~a~~~p  107 (114)
T 2cq2_A           94 QKITLYLNFVEKVQ  107 (114)
T ss_dssp             CEEECEEEEESCCC
T ss_pred             CCcEEEEEecccCc
Confidence            24689999998653

>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=99.76  E-value=1.8e-18  Score=116.96  Aligned_cols=75  Identities=17%  Similarity=0.193  Sum_probs=62.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++||++|+++|++||.|.+|+|+.+        +||||||+|++.++|+    .+++..+..   .++.
T Consensus        11 ~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~--------srGfaFV~F~~~~~A~----~~~~~~~~~---~g~~   75 (89)
T 3d2w_A           11 GSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP--------FRAFAFVTFADDKVAQ----SLCGEDLII---KGIS   75 (89)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS--------CCSEEEEEESCHHHHH----HHTTCEEEE---TTEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC--------CCCEEEEEECCHHHHH----HHcCCCccc---CCEE
Confidence            689999999999999999999999999999998764        5689999999999988    367776654   3468


Q ss_pred             eEEEeecCCC
Q 030444          157 LRLQFSRNPG  166 (177)
Q Consensus       157 l~V~~a~~~~  166 (177)
                      |+|.+++++.
T Consensus        76 v~v~~a~~k~   85 (89)
T 3d2w_A           76 VHISNAEPKH   85 (89)
T ss_dssp             EEEEECC---
T ss_pred             EEEEEcCCCC
Confidence            9999997654

>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=99.76  E-value=1.8e-19  Score=117.32  Aligned_cols=75  Identities=13%  Similarity=0.320  Sum_probs=68.0

Q ss_pred             eEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcceE
Q 030444           79 TLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFLR  158 (177)
Q Consensus        79 tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~l~  158 (177)
                      +|||+|||+++|+++|+++|++||.|.+|+++.++   .+++++|||||+|.+.++|++|++. ++..+.+     +.|+
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~---~~~~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g-----~~l~   71 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDN---KTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGL-----SKCE   71 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSC---CCSSSCCCEEEECSSSHHHHHHHTT-SSCCBTT-----BCCC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecC---CCCCcCCEEEEEECCHHHHHHHHHh-CCCeECC-----EEEE
Confidence            69999999999999999999999999999998876   5688999999999999999999984 8888866     4788


Q ss_pred             EEee
Q 030444          159 LQFS  162 (177)
Q Consensus       159 V~~a  162 (177)
                      |++|
T Consensus        72 v~~a   75 (75)
T 1iqt_A           72 IKVA   75 (75)
T ss_dssp             EEEC
T ss_pred             EEEC
Confidence            8875

>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=99.76  E-value=1.3e-18  Score=125.19  Aligned_cols=77  Identities=22%  Similarity=0.354  Sum_probs=68.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEE--EEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCC
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYK--EVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDS  154 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~--~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~  154 (177)
                      .++|||+|||+++|+++|+++|++| .|.  +|+|+.++   . |+++|||||+|.+.++|++||+. ++..|.+     
T Consensus        42 ~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~---~-GrsrGfaFV~F~~~e~A~~Al~~-~~~~l~g-----  110 (126)
T 2hgm_A           42 DGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDP---E-GKITGEAFVQFASQELAEKALGK-HKERIGH-----  110 (126)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCS---S-SSSCSEEEEEESSTTHHHHHHTT-TTCCBTT-----
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECC---C-CCCceEEEEEECCHHHHHHHHHH-CCCEECC-----
Confidence            6899999999999999999999999 677  89998886   3 88999999999999999999975 7788855     


Q ss_pred             cceEEEeecC
Q 030444          155 KFLRLQFSRN  164 (177)
Q Consensus       155 r~l~V~~a~~  164 (177)
                      |.|+|.++..
T Consensus       111 R~I~V~~a~~  120 (126)
T 2hgm_A          111 RYIEVFKSSQ  120 (126)
T ss_dssp             BCCCCEEECH
T ss_pred             EEEEEEECCH
Confidence            5799988743

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.76  E-value=6.1e-18  Score=128.29  Aligned_cols=86  Identities=21%  Similarity=0.337  Sum_probs=78.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCC
Q 030444           75 DASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDS  154 (177)
Q Consensus        75 ~~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~  154 (177)
                      .+.++|||+|||+++|+++|+++|++||.|.+|++..++   .++.++|||||+|.+.++|++|++.||+..|.+     
T Consensus       112 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~---~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g-----  183 (198)
T 2yh0_A          112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDS---ATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGD-----  183 (198)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECT---TTCSEEEEEEEEESSSSHHHHHHHHHTTCEETT-----
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecC---CCCCcceEEEEEECCHHHHHHHHHHcCCCEECC-----
Confidence            347999999999999999999999999999999999886   578899999999999999999999999999966     


Q ss_pred             cceEEEeecCCCCC
Q 030444          155 KFLRLQFSRNPGPR  168 (177)
Q Consensus       155 r~l~V~~a~~~~~r  168 (177)
                      +.|+|+|++.+.++
T Consensus       184 ~~l~v~~a~~~~~~  197 (198)
T 2yh0_A          184 KKLLVQRASVGAKN  197 (198)
T ss_dssp             EECEEEESCCCCCC
T ss_pred             EEEEEEECCCCCCC
Confidence            58999999776543

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.76  E-value=2.6e-18  Score=116.95  Aligned_cols=77  Identities=12%  Similarity=0.236  Sum_probs=68.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEE-EeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVR-LVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~-l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      +++|||+|||+++|+++|+++|++||.|.+|+ ++.++   .+    +.|||+|.+.++|++|++.||+..|.+     +
T Consensus        15 ~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~---~~----~~afV~f~~~~~a~~Ai~~l~g~~~~g-----~   82 (96)
T 2e44_A           15 IRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDS---ET----AVVNVTYSSKDQARQALDKLNGFQLEN-----F   82 (96)
T ss_dssp             CCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSS---SS----EEEEEEESSHHHHHHHHHHHTTCBCSS-----C
T ss_pred             CCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CC----CEEEEEECCHHHHHHHHHHhCCCEECC-----c
Confidence            68999999999999999999999999999995 77665   22    349999999999999999999999976     5


Q ss_pred             ceEEEeecCC
Q 030444          156 FLRLQFSRNP  165 (177)
Q Consensus       156 ~l~V~~a~~~  165 (177)
                      +|+|+|++.+
T Consensus        83 ~l~V~~a~~~   92 (96)
T 2e44_A           83 TLKVAYIPDE   92 (96)
T ss_dssp             BCEEEECCCC
T ss_pred             EEEEEEcCcc
Confidence            8999999765

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.76  E-value=5.8e-19  Score=121.64  Aligned_cols=78  Identities=21%  Similarity=0.296  Sum_probs=71.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|.+|+|+.++    +++++|||||+|.+.++|++|++  ++..+.+     +.
T Consensus         9 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~----~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g-----~~   77 (102)
T 2xs2_A            9 PNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR----TGVSKGYGFVSFYNDVDVQKIVE--SQINFHG-----KK   77 (102)
T ss_dssp             EEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT----TSCEEEEEEEEESSCCCHHHHTT--CCCEETT-----EE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC----CCCccceEEEEECCHHHHHHHHh--CCCeECC-----EE
Confidence            6899999999999999999999999999999999885    68899999999999999999998  9999966     57


Q ss_pred             eEEEeecCC
Q 030444          157 LRLQFSRNP  165 (177)
Q Consensus       157 l~V~~a~~~  165 (177)
                      |.|.++..+
T Consensus        78 l~v~~a~~~   86 (102)
T 2xs2_A           78 LKLGPAIRK   86 (102)
T ss_dssp             CEEEEEEEC
T ss_pred             EEEEECCcC
Confidence            999998754

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.76  E-value=5.2e-18  Score=115.34  Aligned_cols=78  Identities=17%  Similarity=0.282  Sum_probs=67.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|.+|  +.++   .+++   ||||+|.+.++|++|++ ||+..|.+     +.
T Consensus         8 ~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~---~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g-----~~   73 (94)
T 2e5g_A            8 LRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDK---DKGV---FAIVEMGDVGAREAVLS-QSQHSLGG-----HR   73 (94)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECS---SSCC---EEEEEESSHHHHHHHHT-CSCCEETT-----EE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcC---CCCc---EEEEEECCHHHHHHHHh-cCCeEECC-----EE
Confidence            6899999999999999999999999999987  3343   2343   99999999999999999 99999976     58


Q ss_pred             eEEEeecCCCCC
Q 030444          157 LRLQFSRNPGPR  168 (177)
Q Consensus       157 l~V~~a~~~~~r  168 (177)
                      |+|+++..+...
T Consensus        74 l~V~~a~~~~~~   85 (94)
T 2e5g_A           74 LRVRPREQKEFQ   85 (94)
T ss_dssp             CCCBCSCCSCCC
T ss_pred             EEEEECCcCCCC
Confidence            999998765433

>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=99.75  E-value=5.8e-18  Score=113.81  Aligned_cols=74  Identities=26%  Similarity=0.323  Sum_probs=67.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      +++|||+|||+++|+++|+++|++| .|.++++.         +++|||||+|.+.++|++|++.||+..+.+     ++
T Consensus         5 ~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~---------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g-----~~   69 (88)
T 1wg1_A            5 SSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD---------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRG-----KD   69 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE---------GGGTEEEECCSCHHHHHHHHHHHTTEEETT-----EE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe---------CCCcEEEEEECCHHHHHHHHHHhCCCeECC-----cE
Confidence            6899999999999999999999999 99999884         245799999999999999999999999966     58


Q ss_pred             eEEEeecCC
Q 030444          157 LRLQFSRNP  165 (177)
Q Consensus       157 l~V~~a~~~  165 (177)
                      |+|+|++..
T Consensus        70 l~V~~a~~~   78 (88)
T 1wg1_A           70 LIVQLQPTD   78 (88)
T ss_dssp             EEEEECCCC
T ss_pred             EEEEEcCCC
Confidence            999999654

>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=99.75  E-value=1.5e-17  Score=122.92  Aligned_cols=80  Identities=24%  Similarity=0.370  Sum_probs=74.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|..++++.++   .+++++|||||+|.+.++|.+|++.||+..+.+   ..++
T Consensus        89 ~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~---~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g---~~~~  162 (168)
T 1b7f_A           89 DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDK---LTGRPRGVAFVRYNKREEAQEAISALNNVIPEG---GSQP  162 (168)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECT---TTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTT---CSSC
T ss_pred             CCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcC---CCCCcceEEEEEECCHHHHHHHHHHhcCCEecC---CCeE
Confidence            6899999999999999999999999999999999886   578899999999999999999999999999977   2368


Q ss_pred             eEEEee
Q 030444          157 LRLQFS  162 (177)
Q Consensus       157 l~V~~a  162 (177)
                      |+|+||
T Consensus       163 l~V~~A  168 (168)
T 1b7f_A          163 LSVRLA  168 (168)
T ss_dssp             CEEEEC
T ss_pred             EEEEeC
Confidence            999986

>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=99.75  E-value=2.8e-18  Score=115.23  Aligned_cols=79  Identities=18%  Similarity=0.193  Sum_probs=65.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      +++|||+|||+++|+++|+++|++||.|.+|+|+.+        ++|||||+|.+.++|++    +++..+..   .+++
T Consensus         5 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~--------~~g~afV~f~~~~~a~~----~~~~~~~~---~g~~   69 (88)
T 1wf0_A            5 SSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP--------FRAFAFVTFADDQIAQS----LCGEDLII---KGIS   69 (88)
T ss_dssp             CCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS--------CCSCCEEECSCHHHHHH----TTTCEEEE---TTEE
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC--------CCCEEEEEECCHHHHHH----HhcCCcee---CCEE
Confidence            699999999999999999999999999999998754        45799999999999975    45555533   3468


Q ss_pred             eEEEeecCCCCCCC
Q 030444          157 LRLQFSRNPGPRSV  170 (177)
Q Consensus       157 l~V~~a~~~~~r~~  170 (177)
                      |+|++++++..+..
T Consensus        70 l~v~~a~~~~~~~~   83 (88)
T 1wf0_A           70 VHISNAEPKHNSNS   83 (88)
T ss_dssp             EEEECCCCCCCCCS
T ss_pred             EEEEecCCCCCCCC
Confidence            99999987655543

>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=99.75  E-value=6.1e-18  Score=128.10  Aligned_cols=84  Identities=10%  Similarity=0.222  Sum_probs=72.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|..|+++.++   .+++++|||||+|.+.++|++|++. ++..|.+     +.
T Consensus       104 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~---~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G-----~~  174 (196)
T 1l3k_A          104 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR---GSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNG-----HN  174 (196)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECT---TTCCEEEEEEEEESSHHHHHHHHHC-SCCEETT-----EE
T ss_pred             cceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecC---CCCCccceEEEEECCHHHHHHHHHh-CCcEECC-----EE
Confidence            6899999999999999999999999999999999886   5788999999999999999999976 7999966     58


Q ss_pred             eEEEeecCCCCCC
Q 030444          157 LRLQFSRNPGPRS  169 (177)
Q Consensus       157 l~V~~a~~~~~r~  169 (177)
                      |+|.|+.++....
T Consensus       175 i~v~~a~~k~~~~  187 (196)
T 1l3k_A          175 CEVRKALSKQEMA  187 (196)
T ss_dssp             CEEEECC------
T ss_pred             EEEEecCChhHhc
Confidence            9999998764444

>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=99.75  E-value=6.9e-18  Score=125.33  Aligned_cols=81  Identities=22%  Similarity=0.316  Sum_probs=73.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|.+++++.+.    +++++|||||+|.+.++|++|++.|||..+.+.  .+++
T Consensus        95 ~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~----~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g--~~~~  168 (175)
T 3nmr_A           95 DRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP----DGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEG--CSSP  168 (175)
T ss_dssp             GSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT----TSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTT--CSSC
T ss_pred             CCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECC----CCCEEEEEEEEECCHHHHHHHHHHhcCCcccCC--CCCC
Confidence            6899999999999999999999999999999998885    588999999999999999999999999988753  2468


Q ss_pred             eEEEeec
Q 030444          157 LRLQFSR  163 (177)
Q Consensus       157 l~V~~a~  163 (177)
                      |+|+||.
T Consensus       169 l~V~~ad  175 (175)
T 3nmr_A          169 MVVKFAD  175 (175)
T ss_dssp             CEEEECC
T ss_pred             eEEEecC
Confidence            9999983

>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=99.74  E-value=9.3e-18  Score=124.63  Aligned_cols=85  Identities=14%  Similarity=0.274  Sum_probs=75.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCC--CcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCC
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGG--DPLILCFVDFENPACAATALSALQGYRMDEDDPDS  154 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g--~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~  154 (177)
                      +++|||+|||+++|+++|+++|++||.|.+|+++.++   .++  +++|||||+|.+.++|++|++.||+..+...  ..
T Consensus         3 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~---~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~--~~   77 (175)
T 3nmr_A            3 AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDR---SQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPG--MH   77 (175)
T ss_dssp             CEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEC---SSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTT--CS
T ss_pred             ceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecC---CCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccC--Cc
Confidence            6899999999999999999999999999999999886   444  7899999999999999999999999988754  34


Q ss_pred             cceEEEeecCCC
Q 030444          155 KFLRLQFSRNPG  166 (177)
Q Consensus       155 r~l~V~~a~~~~  166 (177)
                      +.+.+.++....
T Consensus        78 ~~~~~~~~~~~~   89 (175)
T 3nmr_A           78 HPIQMKPADSEK   89 (175)
T ss_dssp             SCCEEEECGGGC
T ss_pred             cceEEccccccc
Confidence            679998886543

>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=99.74  E-value=8.5e-18  Score=124.82  Aligned_cols=78  Identities=22%  Similarity=0.363  Sum_probs=73.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|..++++.++   .+++++|||||+|.+.++|++|++.||+..+.+     ++
T Consensus        94 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~---~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g-----~~  165 (172)
T 2g4b_A           94 AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDS---ATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGD-----KK  165 (172)
T ss_dssp             TTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECT---TTCSEEEEEEEEESSTTHHHHHHHHHTTCEETT-----EE
T ss_pred             CCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecC---CCCCcceEEEEEeCCHHHHHHHHHHcCCCEECC-----eE
Confidence            6899999999999999999999999999999999886   578899999999999999999999999999966     58


Q ss_pred             eEEEee
Q 030444          157 LRLQFS  162 (177)
Q Consensus       157 l~V~~a  162 (177)
                      |+|+||
T Consensus       166 l~V~~A  171 (172)
T 2g4b_A          166 LLVQRA  171 (172)
T ss_dssp             CEEEEC
T ss_pred             EEEEeC
Confidence            999997

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.74  E-value=1.4e-18  Score=124.49  Aligned_cols=78  Identities=23%  Similarity=0.293  Sum_probs=69.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCE----EEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCC
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGY----KEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDD  151 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i----~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~  151 (177)
                      +..+|||+|||+++|+++|+++|++||.|    ..|+|+.++    +|+++|||||+|.+.++|++||+. |+..|.+  
T Consensus        22 ~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~----~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~g--   94 (123)
T 2dha_A           22 NQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP----DGRPTGDAFVLFACEEYAQNALRK-HKDLLGK--   94 (123)
T ss_dssp             SCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECT----TSCEEEEEEECCSSHHHHHHHHTT-TTEESSS--
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECC----CCCEeeEEEEEECCHHHHHHHHHh-CCCeeCC--
Confidence            36899999999999999999999999875    688888874    688999999999999999999986 9888855  


Q ss_pred             CCCcceEEEeec
Q 030444          152 PDSKFLRLQFSR  163 (177)
Q Consensus       152 ~~~r~l~V~~a~  163 (177)
                         |.|+|..+.
T Consensus        95 ---R~i~V~~a~  103 (123)
T 2dha_A           95 ---RYIELFRST  103 (123)
T ss_dssp             ---CEECCEEEC
T ss_pred             ---eEEEEEECC
Confidence               578988874

>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=99.74  E-value=5.9e-18  Score=131.02  Aligned_cols=76  Identities=18%  Similarity=0.243  Sum_probs=69.8

Q ss_pred             CCeEEEcCCC-CCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           77 SSTLYVEGLP-ADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        77 ~~tLfV~nLp-~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      +++|||+||| +++|+++|+++|++||.|.+|+|+.++        +|||||+|.+.++|+.|++.|||..|.+     +
T Consensus         4 ~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~~--------~g~afV~f~~~~~A~~Ai~~lng~~~~g-----~   70 (205)
T 3tyt_A            4 SPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK--------PGAAMVEMADGYAVDRAITHLNNNFMFG-----Q   70 (205)
T ss_dssp             CSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTS--------TTCEEEEESSHHHHHHHHHHHTTCEETT-----E
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCC--------CCEEEEEECCHHHHHHHHHHhCCCEECC-----c
Confidence            7899999999 899999999999999999999997653        4799999999999999999999999976     5


Q ss_pred             ceEEEeecCC
Q 030444          156 FLRLQFSRNP  165 (177)
Q Consensus       156 ~l~V~~a~~~  165 (177)
                      +|+|+|++.+
T Consensus        71 ~l~v~~s~~~   80 (205)
T 3tyt_A           71 KMNVCVSKQP   80 (205)
T ss_dssp             ECEEEECSCS
T ss_pred             eEEEEEccCC
Confidence            8999999754

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.74  E-value=2.7e-18  Score=133.04  Aligned_cols=79  Identities=15%  Similarity=0.293  Sum_probs=72.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|.+|+|+.++     +.++|||||+|.+.++|++|++.|||..|.+     ++
T Consensus       103 ~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~-----~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g-----~~  172 (213)
T 4f02_A          103 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE-----NGSKGYGFVHFETQEAAERAIEKMNGMLLND-----RK  172 (213)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET-----TEEEEEEEEEESSHHHHHHHHHHHTTCEETT-----EE
T ss_pred             cccceECCcccccHHHHHHHHHhhcCCeEEEEeeccC-----CCCceEEEEEeCCHHHHHHHHHHhCCCEECC-----EE
Confidence            5789999999999999999999999999999999875     3478999999999999999999999999966     58


Q ss_pred             eEEEeecCC
Q 030444          157 LRLQFSRNP  165 (177)
Q Consensus       157 l~V~~a~~~  165 (177)
                      |+|+||+.+
T Consensus       173 i~V~~a~~~  181 (213)
T 4f02_A          173 VFVGRFKSR  181 (213)
T ss_dssp             CEEEECCCH
T ss_pred             EEEEEcCCC
Confidence            999999754

>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=99.74  E-value=6.4e-18  Score=127.99  Aligned_cols=82  Identities=12%  Similarity=0.216  Sum_probs=73.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCC
Q 030444           75 DASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDS  154 (177)
Q Consensus        75 ~~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~  154 (177)
                      .+.++|||+|||+++|+++|+++|++||.|.+|+|+.++   .+++++|||||+|.+.++|++|++. ++..+.+     
T Consensus        11 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~---~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g-----   81 (196)
T 1l3k_A           11 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDP---NTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDG-----   81 (196)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT---TTCCEEEEEEEEESSHHHHHHHHHT-CSCEETT-----
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcC---CCCCccceEEEEeCCHHHHHHHHhc-CCCEECC-----
Confidence            347899999999999999999999999999999999886   5788999999999999999999976 8889866     


Q ss_pred             cceEEEeecCC
Q 030444          155 KFLRLQFSRNP  165 (177)
Q Consensus       155 r~l~V~~a~~~  165 (177)
                      +.|+|.++...
T Consensus        82 ~~l~v~~~~~~   92 (196)
T 1l3k_A           82 RVVEPKRAVSR   92 (196)
T ss_dssp             EECEEEECCC-
T ss_pred             EEeeeecccCc
Confidence            58999998654

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.73  E-value=1.1e-17  Score=122.98  Aligned_cols=80  Identities=18%  Similarity=0.346  Sum_probs=72.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcce
Q 030444           78 STLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFL  157 (177)
Q Consensus        78 ~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~l  157 (177)
                      ++|||+|||+++|+++|+++|++||.|.+|+++.++    .++++|||||+|.+.++|++|++.||+..+.+     +.|
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~----~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g-----~~i   71 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK----NNKNVNYAFVEYHQSHDANIALQTLNGKQIEN-----NIV   71 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCC----C-CCEEEEEEEESSHHHHHHHHHHHTTCEETT-----EEC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECC----CCCCCCEEEEEeCCHHHHHHHHHHcCCCccCC-----Cee
Confidence            589999999999999999999999999999999886    47789999999999999999999999999966     589


Q ss_pred             EEEeecCCC
Q 030444          158 RLQFSRNPG  166 (177)
Q Consensus       158 ~V~~a~~~~  166 (177)
                      +|+++....
T Consensus        72 ~v~~~~~~~   80 (166)
T 3md3_A           72 KINWAFQSQ   80 (166)
T ss_dssp             EEEECCCCC
T ss_pred             EEEEcCCCC
Confidence            999997653

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=99.73  E-value=2.5e-17  Score=121.28  Aligned_cols=80  Identities=23%  Similarity=0.445  Sum_probs=73.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|.+++++.++   .++.++|||||+|.+.++|++|++.|||..+.+..   .+
T Consensus        88 ~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~---~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~---~~  161 (167)
T 1fxl_A           88 DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQ---VTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGAT---EP  161 (167)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT---TTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCS---SC
T ss_pred             CCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecC---CCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCc---cc
Confidence            6899999999999999999999999999999998876   56889999999999999999999999999998742   36


Q ss_pred             eEEEee
Q 030444          157 LRLQFS  162 (177)
Q Consensus       157 l~V~~a  162 (177)
                      |+|+||
T Consensus       162 i~v~~A  167 (167)
T 1fxl_A          162 ITVKFA  167 (167)
T ss_dssp             CEEEEC
T ss_pred             eEEEeC
Confidence            999986

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=1.6e-17  Score=113.07  Aligned_cols=71  Identities=18%  Similarity=0.237  Sum_probs=62.9

Q ss_pred             CCe-EEEcCCCCCCCHHH----HHHhhCCC-CCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCC
Q 030444           77 SST-LYVEGLPADSTKRE----VAHIFRPF-VGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDED  150 (177)
Q Consensus        77 ~~t-LfV~nLp~~~te~~----L~~lF~~~-G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~  150 (177)
                      +.| |||+|||+.+++++    |+++|++| |.|.+|          ++   |||||+|.+.++|++|++.|||..|.+ 
T Consensus         8 ~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V----------tg---G~AfV~F~~~esA~~A~~~l~G~~l~g-   73 (96)
T 2diu_A            8 CHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI----------TG---CSAILRFINQDSAERAQKRMENEDVFG-   73 (96)
T ss_dssp             SSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC----------CT---TCEEEEESSHHHHHHHHHHHTTCCSSS-
T ss_pred             cceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE----------ec---CEEEEEECCHHHHHHHHHHhcCCccCC-
Confidence            666 99999999999998    55899999 599887          12   699999999999999999999999977 


Q ss_pred             CCCCcceEEEeecCC
Q 030444          151 DPDSKFLRLQFSRNP  165 (177)
Q Consensus       151 ~~~~r~l~V~~a~~~  165 (177)
                          |+|+|+||+..
T Consensus        74 ----r~i~v~~A~~~   84 (96)
T 2diu_A           74 ----NRIIVSFTPKN   84 (96)
T ss_dssp             ----SCCEEESSCCS
T ss_pred             ----ceEEEEecCCC
Confidence                58999999765

>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=99.72  E-value=8.2e-18  Score=124.35  Aligned_cols=80  Identities=11%  Similarity=0.281  Sum_probs=73.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|.+++++.++   .++.++|||||+|.+.++|++|++ +++..+.+     ++
T Consensus        87 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~---~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g-----~~  157 (167)
T 2cjk_A           87 TGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDK---DTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKD-----RK  157 (167)
T ss_dssp             CEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSS---SSSTTSEEEEEEESSHHHHHHHHH-CSEECSSS-----SC
T ss_pred             CCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcC---CCCccceEEEEEECCHHHHHHHHh-CCCEEeCC-----eE
Confidence            6799999999999999999999999999999998886   578899999999999999999997 89999966     58


Q ss_pred             eEEEeecCC
Q 030444          157 LRLQFSRNP  165 (177)
Q Consensus       157 l~V~~a~~~  165 (177)
                      |+|+||+++
T Consensus       158 i~V~~a~pk  166 (167)
T 2cjk_A          158 IEIKRAEPR  166 (167)
T ss_dssp             EEEEECCCC
T ss_pred             EEEeecCCC
Confidence            999999754

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.72  E-value=2.4e-17  Score=126.58  Aligned_cols=81  Identities=19%  Similarity=0.278  Sum_probs=72.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|.+|+|+.++   .+++++|||||+|.+.++|++|++.||+..|.+     +.
T Consensus        28 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~---~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g-----~~   99 (216)
T 2qfj_A           28 MSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDS---VTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGG-----RN   99 (216)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC----CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC------CC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecC---CCCccCceEEEEeCCHHHHHHHHHHccCCeeCC-----ee
Confidence            6899999999999999999999999999999998876   568899999999999999999999999999976     47


Q ss_pred             eEEEeecCC
Q 030444          157 LRLQFSRNP  165 (177)
Q Consensus       157 l~V~~a~~~  165 (177)
                      |+|.++...
T Consensus       100 l~v~~~~~~  108 (216)
T 2qfj_A          100 IKVGRPSNI  108 (216)
T ss_dssp             CEEECCSCC
T ss_pred             EEEecCCCc
Confidence            999988654

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.72  E-value=9.1e-18  Score=118.22  Aligned_cols=70  Identities=24%  Similarity=0.300  Sum_probs=60.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHh---CCCee
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSAL---QGYRM  147 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l---~g~~l  147 (177)
                      .++|||+|||+++|+++|+++|++||.|. +.++.++....+|+++|||||+|.+.++|++|++.|   +|..|
T Consensus         8 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~~~~G~~~   80 (114)
T 2dnl_A            8 SRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACLEEDGKLY   80 (114)
T ss_dssp             CCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSEEETTEEE
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhhhcCCcEE
Confidence            68999999999999999999999999999 877777632223789999999999999999999998   55543

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.71  E-value=1.1e-17  Score=120.06  Aligned_cols=79  Identities=9%  Similarity=0.128  Sum_probs=70.4

Q ss_pred             CeEEEcCC----CCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecC----HHH----HHHHHH--HhC
Q 030444           78 STLYVEGL----PADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFEN----PAC----AATALS--ALQ  143 (177)
Q Consensus        78 ~tLfV~nL----p~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~----~~~----A~~Ai~--~l~  143 (177)
                      ++|||+||    |+.+++++|+++|++||.|.+|+++.|+   .+|.++|||||+|.|    +++    |.+|++  .||
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp---~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~ln   79 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDP---NSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESS   79 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECT---TTCCEEEEEEEECC------CCHHHHHHHHHHHTTTT
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecC---CCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhc
Confidence            68999999    9999999999999999999999999999   889999999999996    433    788888  789


Q ss_pred             CCeeCCCCCCCcceEEEeecC
Q 030444          144 GYRMDEDDPDSKFLRLQFSRN  164 (177)
Q Consensus       144 g~~l~~~~~~~r~l~V~~a~~  164 (177)
                      +..|.+     |+|+|++.++
T Consensus        80 g~~I~G-----r~irV~ln~~   95 (136)
T 2j8a_A           80 GCFIMG-----FKFEVILNKH   95 (136)
T ss_dssp             CEEETT-----EEEEEEECCT
T ss_pred             CCeecC-----cEEEEEECcc
Confidence            999966     6899998754

>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=99.70  E-value=1.7e-17  Score=110.70  Aligned_cols=69  Identities=19%  Similarity=0.331  Sum_probs=63.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCC----C-------CEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCC
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPF----V-------GYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGY  145 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~----G-------~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~  145 (177)
                      .++|||+|||+++|+++|+++|++|    |       .|.++++..+         +|||||+|.+.++|++|+ .||+.
T Consensus         6 ~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~---------kg~afV~f~~~~~a~~A~-~l~g~   75 (87)
T 2hzc_A            6 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD---------KNFAFLEFRSVDETTQAM-AFDGI   75 (87)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS---------SSEEEEEESSHHHHHHHG-GGTTC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC---------CcEEEEEcCCHHHHHHHH-hcCCC
Confidence            6899999999999999999999999    8       8999988754         379999999999999999 99999


Q ss_pred             eeCCCCCCCcceEEE
Q 030444          146 RMDEDDPDSKFLRLQ  160 (177)
Q Consensus       146 ~l~~~~~~~r~l~V~  160 (177)
                      .+.+     +.|+|+
T Consensus        76 ~~~g-----~~l~V~   85 (87)
T 2hzc_A           76 IFQG-----QSLKIR   85 (87)
T ss_dssp             EETT-----EECEEE
T ss_pred             EECC-----eEEEEe
Confidence            9976     478887

>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=99.69  E-value=1.3e-16  Score=127.71  Aligned_cols=79  Identities=24%  Similarity=0.386  Sum_probs=71.7

Q ss_pred             CCeEEEcCCCCCCCHHHHH----HhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCC
Q 030444           77 SSTLYVEGLPADSTKREVA----HIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDP  152 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~----~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~  152 (177)
                      +++|||+|||+++|+++|+    ++|++||.|.+|+++.      +++++|||||+|.+.++|++|++.||+..|.+   
T Consensus         9 ~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~------~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g---   79 (282)
T 3pgw_A            9 NHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR------SLKMRGQAFVIFKEVSSATNALRSMQGFPFYD---   79 (282)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC------CCCcceEEEEEECCHHHHHHHHHHhcCCeeCC---
Confidence            7999999999999999977    8999999999998864      36788999999999999999999999999976   


Q ss_pred             CCcceEEEeecCCC
Q 030444          153 DSKFLRLQFSRNPG  166 (177)
Q Consensus       153 ~~r~l~V~~a~~~~  166 (177)
                        +.|+|+|++...
T Consensus        80 --~~l~v~~a~~~~   91 (282)
T 3pgw_A           80 --KPMRIQYAKTDS   91 (282)
T ss_pred             --cEEEEEEeccCc
Confidence              489999997653

>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=99.69  E-value=6.4e-16  Score=123.75  Aligned_cols=76  Identities=30%  Similarity=0.633  Sum_probs=69.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      ++++|||+|||+++|+++|+++|++||.|.+|+|+.++        +|||||+|.+.++|++|++.|||..|..    ++
T Consensus       206 ~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~~----g~  273 (282)
T 3pgw_A          206 PNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR--------HDIAFVEFDNEVQAGAARDALQGFKITQ----NN  273 (282)
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC--------CcEEEEEeCCHHHHHHHHHHcCCcEeCC----CC
Confidence            37899999999999999999999999999999998654        3699999999999999999999999972    25


Q ss_pred             ceEEEeec
Q 030444          156 FLRLQFSR  163 (177)
Q Consensus       156 ~l~V~~a~  163 (177)
                      .|+|+|++
T Consensus       274 ~l~v~~ak  281 (282)
T 3pgw_A          274 AMKISFAK  281 (282)
T ss_pred             EEEEEEec
Confidence            89999996

>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=99.69  E-value=4.1e-17  Score=126.25  Aligned_cols=80  Identities=15%  Similarity=0.188  Sum_probs=70.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCE--EEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCC
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGY--KEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDS  154 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i--~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~  154 (177)
                      +++|||+|||+++|+++|+++|++||.|  .+++++.++     +..+|||||+|.+.++|.+||..||++.|.+.. ..
T Consensus       123 ~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~-----~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~-~~  196 (205)
T 3tyt_A          123 SNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK-----SERSSSGLLEWDSKSDALETLGFLNHYQMKNPN-GP  196 (205)
T ss_dssp             CSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCC-----SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSS-SS
T ss_pred             cceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCC-----CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCC-CC
Confidence            7899999999999999999999999999  889988764     445689999999999999999999999998863 33


Q ss_pred             cceEEEee
Q 030444          155 KFLRLQFS  162 (177)
Q Consensus       155 r~l~V~~a  162 (177)
                      .++.|.|+
T Consensus       197 ~p~~vk~~  204 (205)
T 3tyt_A          197 YPYTLKLC  204 (205)
T ss_dssp             SCEECEEE
T ss_pred             cceEEEec
Confidence            57888775

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.69  E-value=2.5e-16  Score=109.78  Aligned_cols=81  Identities=12%  Similarity=0.200  Sum_probs=69.9

Q ss_pred             CCCeEEEcCCCC-----CCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCC
Q 030444           76 ASSTLYVEGLPA-----DSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDED  150 (177)
Q Consensus        76 ~~~tLfV~nLp~-----~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~  150 (177)
                      ++++|+|.||..     +-++++|+++|++||.|.+|+|+.++.  .+++++||+||+|.+.++|++|++.|||..+.+ 
T Consensus         7 ~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~--~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~G-   83 (105)
T 2pe8_A            7 PTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPG--APDDEAVRIFLEFERVESAIKAVVDLNGRYFGG-   83 (105)
T ss_dssp             CCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSS--CCTTTSEEEEEEESSHHHHHHHHHHHTTCEETT-
T ss_pred             CCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCC--CCCCCcEEEEEEECCHHHHHHHHHHHCCCEECC-
Confidence            479999999963     347899999999999999999988751  236789999999999999999999999999965 


Q ss_pred             CCCCcceEEEeec
Q 030444          151 DPDSKFLRLQFSR  163 (177)
Q Consensus       151 ~~~~r~l~V~~a~  163 (177)
                          |.|+|+|+.
T Consensus        84 ----r~i~v~~a~   92 (105)
T 2pe8_A           84 ----RVVKACFYN   92 (105)
T ss_dssp             ----EECEEEECC
T ss_pred             ----cEEEEEEcC
Confidence                689999985

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.68  E-value=1.1e-16  Score=119.27  Aligned_cols=77  Identities=22%  Similarity=0.375  Sum_probs=68.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      +.++|||+|||+++|+++|+++|++||.|..+    .    .++.++|||||+|.+.++|.+|++.|||..|.+     +
T Consensus        98 ~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~----~----~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g-----~  164 (175)
T 1fje_B           98 AARTLLAKNLSFNITEDELKEVFEDALEIRLV----S----QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDG-----R  164 (175)
T ss_dssp             GGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE----C----SSSSCCSEEEEECSSHHHHHHHHHHHTEEEETT-----E
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe----c----CCCCCceEEEEEECCHHHHHHHHHHhCCCEECC-----e
Confidence            36899999999999999999999999987755    2    357889999999999999999999999999966     5


Q ss_pred             ceEEEeecCC
Q 030444          156 FLRLQFSRNP  165 (177)
Q Consensus       156 ~l~V~~a~~~  165 (177)
                      .|+|+|++.+
T Consensus       165 ~i~v~~a~~k  174 (175)
T 1fje_B          165 SVSLYYTGEK  174 (175)
T ss_dssp             EEEEEECSSC
T ss_pred             EEEEEecCCC
Confidence            8999999754

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=99.68  E-value=8.1e-17  Score=125.95  Aligned_cols=77  Identities=21%  Similarity=0.330  Sum_probs=70.6

Q ss_pred             CCCeEEEcCCCC-CCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCC
Q 030444           76 ASSTLYVEGLPA-DSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDS  154 (177)
Q Consensus        76 ~~~tLfV~nLp~-~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~  154 (177)
                      ++++|||+|||+ ++|+++|+++|++||.|.+|+|+.++        +|||||+|.+.++|++|++.||+..|.+     
T Consensus        33 ~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~--------~g~afV~F~~~~~A~~Ai~~l~g~~~~g-----   99 (229)
T 2adc_A           33 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK--------KENALVQMADGNQAQLAMSHLNGHKLHG-----   99 (229)
T ss_dssp             CCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT--------SCCEEEEESCHHHHHHHHHHHTTCBCSS-----
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC--------CCEEEEEECCHHHHHHHHHHhCCCeECC-----
Confidence            379999999999 99999999999999999999998764        4699999999999999999999999966     


Q ss_pred             cceEEEeecCC
Q 030444          155 KFLRLQFSRNP  165 (177)
Q Consensus       155 r~l~V~~a~~~  165 (177)
                      +.|+|+|++..
T Consensus       100 ~~l~v~~a~~~  110 (229)
T 2adc_A          100 KPIRITLSKHQ  110 (229)
T ss_dssp             SBCEEECCSCC
T ss_pred             eEEEEEEecCc
Confidence            48999999754

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.68  E-value=8.6e-17  Score=127.29  Aligned_cols=80  Identities=20%  Similarity=0.274  Sum_probs=67.9

Q ss_pred             CCeEEEcCCCCCC---------CHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCee
Q 030444           77 SSTLYVEGLPADS---------TKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRM  147 (177)
Q Consensus        77 ~~tLfV~nLp~~~---------te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l  147 (177)
                      +++|||+||++++         +|++|+++|++||.|.+|+|+..+         |||||+|.+.++|+.|++.|++..|
T Consensus       134 ~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~k---------G~AFV~F~~~~~Ae~A~~am~g~~l  204 (240)
T 3u1l_A          134 NKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESK---------NCGFVKFKYQANAEFAKEAMSNQTL  204 (240)
T ss_dssp             CCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGGG---------TEEEEEESSHHHHHHHHHHHTTCCC
T ss_pred             CceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECCC---------CEEEEEeCCHHHHHHHHHHhCCCEE
Confidence            7999999999998         799999999999999999998653         7999999999999999999999999


Q ss_pred             CCC--C-----CCCcceEEEeecCC
Q 030444          148 DED--D-----PDSKFLRLQFSRNP  165 (177)
Q Consensus       148 ~~~--~-----~~~r~l~V~~a~~~  165 (177)
                      ...  +     ..++.|.|.||+..
T Consensus       205 ~~~~~~e~~~~~~gr~L~V~wA~~~  229 (240)
T 3u1l_A          205 LLPSDKEWDDRREGTGLLVKWANED  229 (240)
T ss_dssp             CCTTSTTGGGGGGSCCCEEEECC--
T ss_pred             eccccccccccCCCCEEEEEEccCC
Confidence            210  0     02358999999764

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=99.67  E-value=8.6e-17  Score=118.80  Aligned_cols=78  Identities=17%  Similarity=0.324  Sum_probs=68.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      +++|||+|||+++|+++|+++|++||.|.+|+++.++   .+++++|||||+|.+.++|++|++.  +..+.+     +.
T Consensus         3 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~---~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g-----~~   72 (167)
T 2cjk_A            3 SCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDP---ATGRSRGFGFLSFEKPSSVDEVVKT--QHILDG-----KV   72 (167)
T ss_dssp             GGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCT---TTSSCCSCEEEEESSTHHHHHHHHS--CCEETT-----EE
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECC---CCCCccceEEEEEccHHHHHHHHhc--ccccCC-----eE
Confidence            6899999999999999999999999999999998886   5788999999999999999999984  556754     46


Q ss_pred             eEEEeecC
Q 030444          157 LRLQFSRN  164 (177)
Q Consensus       157 l~V~~a~~  164 (177)
                      |.|.++..
T Consensus        73 i~v~~~~~   80 (167)
T 2cjk_A           73 IDPKRAIP   80 (167)
T ss_dssp             CCCEECCC
T ss_pred             cccccccc
Confidence            88887753

>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=2.9e-16  Score=120.46  Aligned_cols=79  Identities=15%  Similarity=0.182  Sum_probs=70.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|.+|+|+.+.    +++++|||||+|++.++|++|++.++ ..+.+     +.
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~----~~~~kG~aFVeF~~~e~A~~A~~~~~-~~~~G-----r~  178 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL----HKAFKGSIFVVFDSIESAKKFVETPG-QKYKE-----TD  178 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT----TCCEEEEEEEEESSHHHHHHHHHCTT-CEETT-----EE
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECC----CCCcccEEEEEECCHHHHHHHHHhCC-CeECC-----EE
Confidence            5899999999999999999999999999999999875    47899999999999999999997665 57855     58


Q ss_pred             eEEEeecCC
Q 030444          157 LRLQFSRNP  165 (177)
Q Consensus       157 l~V~~a~~~  165 (177)
                      |+|.+++..
T Consensus       179 l~V~~~~~y  187 (193)
T 2voo_A          179 LLILFKDDY  187 (193)
T ss_dssp             CEEEETTTC
T ss_pred             EEEEEhHHH
Confidence            999998654

>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=99.66  E-value=3e-16  Score=125.76  Aligned_cols=82  Identities=18%  Similarity=0.264  Sum_probs=75.3

Q ss_pred             CCeEEEcCCCCCC-CHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           77 SSTLYVEGLPADS-TKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        77 ~~tLfV~nLp~~~-te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      .++|||+|||+++ |+++|+++|+.||.|.+++|+.+.    +|+++|||||+|.+.++|.+|++.|||..|.+     +
T Consensus       184 ~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~----~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g-----~  254 (284)
T 3smz_A          184 SRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ----DGQLKGFAVLEYETAEMAEEAQQQADGLSLGG-----S  254 (284)
T ss_dssp             CSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECS----SCCEEEEEEEECSSHHHHHHHHHHHTTCEETT-----E
T ss_pred             ccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECC----CCCcccEEEEEeCCHHHHHHHHHHhCCCccCC-----e
Confidence            7899999999995 999999999999999999998875    68899999999999999999999999999966     5


Q ss_pred             ceEEEeecCCCC
Q 030444          156 FLRLQFSRNPGP  167 (177)
Q Consensus       156 ~l~V~~a~~~~~  167 (177)
                      +|+|+|++.+..
T Consensus       255 ~l~v~~a~~~~~  266 (284)
T 3smz_A          255 HLRVSFCAPGPP  266 (284)
T ss_dssp             ECEEEECCSSSC
T ss_pred             EEEEEEecCCCc
Confidence            899999977644

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=1.5e-15  Score=106.53  Aligned_cols=79  Identities=13%  Similarity=0.174  Sum_probs=66.4

Q ss_pred             CCCeEEEcCCCCCC-----------CHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCC
Q 030444           76 ASSTLYVEGLPADS-----------TKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQG  144 (177)
Q Consensus        76 ~~~tLfV~nLp~~~-----------te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g  144 (177)
                      ++++|+|.||....           ++++|+++|++||.|.+|.| .++      .++|||||+|.+.++|++|++.|||
T Consensus        14 ~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~------~~~G~afV~f~~~~~A~~Ai~~lng   86 (112)
T 2dit_A           14 HERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR------HPDGVASVSFRDPEEADYCIQTLDG   86 (112)
T ss_dssp             SCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT------CTTCEEEEECSCHHHHHHHHHHSTT
T ss_pred             CceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC------CCCEEEEEEECCHHHHHHHHHHcCC
Confidence            37999999994432           26899999999999999965 443      2678999999999999999999999


Q ss_pred             CeeCCCCCCCcceEEEeecCCC
Q 030444          145 YRMDEDDPDSKFLRLQFSRNPG  166 (177)
Q Consensus       145 ~~l~~~~~~~r~l~V~~a~~~~  166 (177)
                      ..|.+     |+|+|+|+..+.
T Consensus        87 ~~~~g-----r~l~v~~a~~~~  103 (112)
T 2dit_A           87 RWFGG-----RQITAQAWDGTT  103 (112)
T ss_dssp             CEETT-----EECEEEECCSCC
T ss_pred             CEECC-----cEEEEEEeCCCC
Confidence            99965     589999997643

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.64  E-value=9.7e-16  Score=116.58  Aligned_cols=77  Identities=21%  Similarity=0.344  Sum_probs=69.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCC-CEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFV-GYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G-~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      +++|||+|||+++|+++|+++|++|| .|.+|+++.+.        +|||||+|.+.++|++|++.|||..+.+    ++
T Consensus       120 ~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~~----g~  187 (198)
T 1qm9_A          120 SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD--------RKMALIQMGSVEEAVQALIDLHNHDLGE----NH  187 (198)
T ss_dssp             CCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESSTT--------SSCEEEECSSHHHHHHHHHHHTSSCCSS----CC
T ss_pred             ccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeCC--------CcEEEEEeCCHHHHHHHHHHhcCCccCC----CC
Confidence            79999999999999999999999999 99999987642        4699999999999999999999999961    35


Q ss_pred             ceEEEeecCC
Q 030444          156 FLRLQFSRNP  165 (177)
Q Consensus       156 ~l~V~~a~~~  165 (177)
                      +|+|+|++++
T Consensus       188 ~l~v~~a~~~  197 (198)
T 1qm9_A          188 HLRVSFSKST  197 (198)
T ss_dssp             SCCEEEECCC
T ss_pred             eEEEEeeccc
Confidence            8999999764

>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=99.64  E-value=3.1e-16  Score=126.19  Aligned_cols=82  Identities=12%  Similarity=0.212  Sum_probs=72.8

Q ss_pred             CCCeEEEcCCCCC-CCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCC
Q 030444           76 ASSTLYVEGLPAD-STKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDS  154 (177)
Q Consensus        76 ~~~tLfV~nLp~~-~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~  154 (177)
                      +.++|||+|||++ +|+++|+++|++||.|..|+|+.+..  .++.++|||||+|.+.++|.+|+ .|||..|.+     
T Consensus       209 ~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~--~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~g-----  280 (292)
T 2ghp_A          209 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQK--EHSFNNCCAFMVFENKDSAERAL-QMNRSLLGN-----  280 (292)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC-----CCCEEEEEEESSHHHHHHHG-GGTTEEETT-----
T ss_pred             CCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCC--cCCCCceEEEEEeCCHHHHHHHH-HhcCCEECC-----
Confidence            3789999999999 99999999999999999999988751  13889999999999999999999 999999966     


Q ss_pred             cceEEEeecCC
Q 030444          155 KFLRLQFSRNP  165 (177)
Q Consensus       155 r~l~V~~a~~~  165 (177)
                      ++|+|+|++++
T Consensus       281 ~~i~V~~a~~k  291 (292)
T 2ghp_A          281 REISVSLADKK  291 (292)
T ss_dssp             EEEEEEECCCC
T ss_pred             cEEEEEEecCC
Confidence            58999999765

>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=99.64  E-value=8.5e-16  Score=120.11  Aligned_cols=77  Identities=21%  Similarity=0.344  Sum_probs=69.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCC-CEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFV-GYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G-~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      +++|||+|||+++|+++|+++|++|| .|.+|+++.+.        +|||||+|.+.++|++|++.|||..+..    ++
T Consensus       151 ~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~~----g~  218 (229)
T 2adc_A          151 SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD--------RKMALIQMGSVEEAVQALIDLHNHDLGE----NH  218 (229)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSS--------TTCEEEEESSHHHHHHHHHHHTTCBSSS----SC
T ss_pred             CCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEECC--------CcEEEEEECCHHHHHHHHHHHCCCccCC----CC
Confidence            79999999999999999999999999 99999996632        3699999999999999999999999961    35


Q ss_pred             ceEEEeecCC
Q 030444          156 FLRLQFSRNP  165 (177)
Q Consensus       156 ~l~V~~a~~~  165 (177)
                      +|+|+|++++
T Consensus       219 ~l~v~~a~~~  228 (229)
T 2adc_A          219 HLRVSFSKST  228 (229)
T ss_dssp             BCEEEECSSC
T ss_pred             eEEEEEecCC
Confidence            8999999764

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=99.63  E-value=1.2e-15  Score=122.32  Aligned_cols=82  Identities=26%  Similarity=0.376  Sum_probs=75.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|..++++.++   .++.++|||||+|.+.++|.+|++.||+..+.+     +.
T Consensus        95 ~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~---~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g-----~~  166 (284)
T 3smz_A           95 DALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSE---RTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGP-----RT  166 (284)
T ss_dssp             SCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT---TTCCEEEEEEEEESSHHHHHHHHHHHTTCEETT-----EE
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeC---CCCccceEEEEEECCHHHHHHHHHHhCCCEeCC-----cE
Confidence            5899999999999999999999999999999998876   578899999999999999999999999999966     58


Q ss_pred             eEEEeecCCC
Q 030444          157 LRLQFSRNPG  166 (177)
Q Consensus       157 l~V~~a~~~~  166 (177)
                      |+|+|+..+.
T Consensus       167 i~v~~a~~~~  176 (284)
T 3smz_A          167 LYVHWTDAGQ  176 (284)
T ss_dssp             CEEEECCGGG
T ss_pred             EEEEECCCCC
Confidence            9999997653

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.63  E-value=3.6e-16  Score=118.94  Aligned_cols=76  Identities=21%  Similarity=0.332  Sum_probs=69.6

Q ss_pred             CCeEEEcCCCC-CCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           77 SSTLYVEGLPA-DSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        77 ~~tLfV~nLp~-~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      +++|||+|||+ ++|+++|+++|++||.|.+|+++.++        +|||||+|.+.++|++|++.||+..+.+     +
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~--------~g~afV~f~~~~~a~~A~~~l~~~~~~g-----~   69 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK--------KENALVQMADGNQAQLAMSHLNGHKLHG-----K   69 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC--------SSCCEEECTTTHHHHHHHHHHTTCCCSS-----C
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC--------CCEEEEEECCHHHHHHHHHHhCCCeecC-----e
Confidence            68999999999 99999999999999999999998764        4699999999999999999999999966     4


Q ss_pred             ceEEEeecCC
Q 030444          156 FLRLQFSRNP  165 (177)
Q Consensus       156 ~l~V~~a~~~  165 (177)
                      .|+|+|++.+
T Consensus        70 ~l~v~~a~~~   79 (198)
T 1qm9_A           70 PIRITLSKHQ   79 (198)
T ss_dssp             CCEEEECCCC
T ss_pred             EEEEEEecCC
Confidence            7999999754

>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=99.62  E-value=1.7e-15  Score=120.69  Aligned_cols=83  Identities=17%  Similarity=0.176  Sum_probs=73.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhC-CCeeCCCCCCCc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQ-GYRMDEDDPDSK  155 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~-g~~l~~~~~~~r  155 (177)
                      .++|||+|||+++|+++|+++|+.||.|.+|+|+.+.    +|+++|||||+|.+.++|.+|++.|| +..+...  .+|
T Consensus        96 ~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~----~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~--~~r  169 (261)
T 3sde_A           96 GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDD----RGRATGKGFVEFAAKPPARKALERCGDGAFLLTT--TPR  169 (261)
T ss_dssp             SSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET----TSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSS--SCC
T ss_pred             CCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCC----CCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecC--CCc
Confidence            6899999999999999999999999999999999884    68899999999999999999999995 5554433  357


Q ss_pred             ceEEEeecCC
Q 030444          156 FLRLQFSRNP  165 (177)
Q Consensus       156 ~l~V~~a~~~  165 (177)
                      +|.|+++...
T Consensus       170 ~i~v~~~~~~  179 (261)
T 3sde_A          170 PVIVEPMEQF  179 (261)
T ss_dssp             BCEEEECCCE
T ss_pred             eEEEeecccc
Confidence            8999998764

>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=99.62  E-value=1.3e-15  Score=121.29  Aligned_cols=74  Identities=24%  Similarity=0.391  Sum_probs=67.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|+.||.|.+|++..+         +|||||+|.+.++|++|+..||+..|.+     +.
T Consensus        22 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~---------kg~afV~f~~~~~A~~A~~~l~g~~i~g-----~~   87 (261)
T 3sde_A           22 RCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD---------RGFGFIRLESRTLAEIAKAELDGTILKS-----RP   87 (261)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT---------TTEEEEECSSHHHHHHHHHHHTTCEETT-----EE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC---------CcEEEEEECCHHHHHHHHHHcCCcEECC-----ce
Confidence            689999999999999999999999999999998654         3799999999999999999999999966     58


Q ss_pred             eEEEeecC
Q 030444          157 LRLQFSRN  164 (177)
Q Consensus       157 l~V~~a~~  164 (177)
                      |+|+|+..
T Consensus        88 l~v~~a~~   95 (261)
T 3sde_A           88 LRIRFATH   95 (261)
T ss_dssp             CEEEECCC
T ss_pred             eEeeeccc
Confidence            99999854

>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=99.60  E-value=1.2e-16  Score=119.11  Aligned_cols=82  Identities=17%  Similarity=0.310  Sum_probs=68.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCC
Q 030444           75 DASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDS  154 (177)
Q Consensus        75 ~~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~  154 (177)
                      .+.++|||+|||+++|+++|+++|++||.+..+.+ .+.   .+++++|||||+|.+.++|++|+ .||+..+.+     
T Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~~~-~~~---~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g-----   80 (175)
T 1fje_B           11 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAV-VDV---RTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFG-----   80 (175)
T ss_dssp             SSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCC-CEE---EEETTTTEEEEEESSHHHHHHHH-HGGGEEETT-----
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceEEE-EEC---CCCccccEEEEEECCHHHHHHHH-hcCCCEeCC-----
Confidence            34799999999999999999999999987765322 222   35778899999999999999999 599999976     


Q ss_pred             cceEEEeecCCC
Q 030444          155 KFLRLQFSRNPG  166 (177)
Q Consensus       155 r~l~V~~a~~~~  166 (177)
                      +.|+|++++.+.
T Consensus        81 ~~l~v~~~~~~~   92 (175)
T 1fje_B           81 NEIKLEKPKGRD   92 (175)
T ss_dssp             EEEEEECCCCSS
T ss_pred             eEEEEecCCCcc
Confidence            589999997653

>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=99.59  E-value=2.8e-15  Score=124.34  Aligned_cols=81  Identities=15%  Similarity=0.163  Sum_probs=67.9

Q ss_pred             CCCCCCCeEEEcC--CCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCC
Q 030444           72 LPPDASSTLYVEG--LPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDE  149 (177)
Q Consensus        72 ~p~~~~~tLfV~n--Lp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~  149 (177)
                      .+..++++|||+|  |++.+||++|+++|++||.|.+|.+..         +||||||+|.+.++|++|++.|||..+.+
T Consensus        13 ~~~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~---------~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~   83 (345)
T 3tht_A           13 TVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP---------NKPYSFARYRTTEESKRAYVTLNGKEVVD   83 (345)
T ss_dssp             CCSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT---------TCSEEEEEESSHHHHHHHHHHTTTCEEEC
T ss_pred             ecCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC---------CCCEEEEEECCHHHHHHHHHHhCCCcccc
Confidence            3344589999999  588999999999999999999887743         24799999999999999999999999954


Q ss_pred             CCCCCc--ceEEEeec
Q 030444          150 DDPDSK--FLRLQFSR  163 (177)
Q Consensus       150 ~~~~~r--~l~V~~a~  163 (177)
                      .  .++  +|.|.|++
T Consensus        84 ~--~g~~~~ly~~~~~   97 (345)
T 3tht_A           84 D--LGQKITLYLNFVE   97 (345)
T ss_dssp             T--TSCEEECEEEECS
T ss_pred             c--cCCceEEEEEEee
Confidence            3  233  58888884

>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=99.57  E-value=7.7e-15  Score=102.13  Aligned_cols=81  Identities=12%  Similarity=0.158  Sum_probs=68.2

Q ss_pred             CCeEEEcCC--CCCCC--------HHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCe
Q 030444           77 SSTLYVEGL--PADST--------KREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYR  146 (177)
Q Consensus        77 ~~tLfV~nL--p~~~t--------e~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~  146 (177)
                      +++|.|.|+  |.++.        +++|+++|++||.|.+|+|+.++.. ..++++||+||+|.+.++|++|++.|||..
T Consensus         5 s~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~-~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~~   83 (105)
T 3v4m_A            5 TEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDG-VEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   83 (105)
T ss_dssp             CSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTT-BCCTTTTEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCC-CCcCCcEEEEEEECCHHHHHHHHHHhCCCE
Confidence            789999998  44443        3689999999999999999877522 124678999999999999999999999999


Q ss_pred             eCCCCCCCcceEEEeec
Q 030444          147 MDEDDPDSKFLRLQFSR  163 (177)
Q Consensus       147 l~~~~~~~r~l~V~~a~  163 (177)
                      +.+     |+|+|+|+.
T Consensus        84 f~G-----R~i~v~~~~   95 (105)
T 3v4m_A           84 FAN-----RVVVTKYCD   95 (105)
T ss_dssp             ETT-----EECEEEEEC
T ss_pred             eCC-----CEEEEEEeC
Confidence            965     689999974

>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=99.57  E-value=3.7e-15  Score=119.81  Aligned_cols=80  Identities=16%  Similarity=0.245  Sum_probs=68.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCC-CEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFV-GYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G-~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      .++|||+|||+++|+++|+++|++|| .|..|+++.++    .+.++|||||+|.+.++|++|++.||+..+.+     +
T Consensus       117 ~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~----~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g-----~  187 (292)
T 2ghp_A          117 ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLR----FNTSRRFAYIDVTSKEDARYCVEKLNGLKIEG-----Y  187 (292)
T ss_dssp             SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-----------CCEEEEECSSHHHHHHHHHHHTTCEETT-----E
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCC----CCCcceEEEEEECCHHHHHHHHHHhCCCEeCC-----c
Confidence            78999999999999999999999999 99999998875    37788999999999999999999999999966     5


Q ss_pred             ceEEEeecCC
Q 030444          156 FLRLQFSRNP  165 (177)
Q Consensus       156 ~l~V~~a~~~  165 (177)
                      .|+|+|+...
T Consensus       188 ~l~v~~a~~~  197 (292)
T 2ghp_A          188 TLVTKVSNPL  197 (292)
T ss_dssp             ECEEEECCCC
T ss_pred             EEEEEECCCC
Confidence            8999999754

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.57  E-value=2.6e-14  Score=98.73  Aligned_cols=78  Identities=12%  Similarity=0.120  Sum_probs=62.4

Q ss_pred             CCeEEEcCCC-------CCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCC
Q 030444           77 SSTLYVEGLP-------ADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDE  149 (177)
Q Consensus        77 ~~tLfV~nLp-------~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~  149 (177)
                      .++|-|....       .++|+++|+++|++||.|.+|+|+.        +++|||||+|++.++|+.|++.+++  +.+
T Consensus        10 ~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~~--------~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g   79 (100)
T 2d9o_A           10 TPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLSS--------KKPGTAVVEFATVKAAELAVQNEVG--LVD   79 (100)
T ss_dssp             SCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEES--------SSSSEEEEEESCHHHHHHHHHTCCB--CSS
T ss_pred             cceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEcc--------CCCCEEEEEECCHHHHHHHHHhcCC--CCC
Confidence            4566665544       4689999999999999999999872        3568999999999999999988655  333


Q ss_pred             CCCCCcceEEEeecCCCCCC
Q 030444          150 DDPDSKFLRLQFSRNPGPRS  169 (177)
Q Consensus       150 ~~~~~r~l~V~~a~~~~~r~  169 (177)
                           ++|+|+|++.+..+.
T Consensus        80 -----~~l~V~~a~~~~~~~   94 (100)
T 2d9o_A           80 -----NPLKISWLEGQPQDA   94 (100)
T ss_dssp             -----SBCEEECSSCCCCCC
T ss_pred             -----CeEEEEEccCCCCCC
Confidence                 579999998765544

>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=99.57  E-value=4.3e-15  Score=110.09  Aligned_cols=74  Identities=18%  Similarity=0.295  Sum_probs=65.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCC----C-------CEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCC
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPF----V-------GYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGY  145 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~----G-------~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~  145 (177)
                      .++|||+|||+++|+++|+++|++|    |       .|.++++..+         +|||||+|.+.++|++|+ .||+.
T Consensus         4 ~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~~---------~g~afV~f~~~~~A~~A~-~~~~~   73 (172)
T 2g4b_A            4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD---------KNFAFLEFRSVDETTQAM-AFDGI   73 (172)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEETT---------TTEEEEEESSHHHHHHHG-GGTTC
T ss_pred             ccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecCC---------CCEEEEEeCCHHHHHHHH-HhCCc
Confidence            6899999999999999999999999    6       6777766443         479999999999999999 89999


Q ss_pred             eeCCCCCCCcceEEEeecCC
Q 030444          146 RMDEDDPDSKFLRLQFSRNP  165 (177)
Q Consensus       146 ~l~~~~~~~r~l~V~~a~~~  165 (177)
                      .+.+     ++|+|++++..
T Consensus        74 ~~~g-----~~i~v~~~~~~   88 (172)
T 2g4b_A           74 IFQG-----QSLKIRRPHDY   88 (172)
T ss_dssp             EETT-----EECEEECCSSC
T ss_pred             EecC-----ceeeecCCccc
Confidence            9966     58999998654

>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=99.55  E-value=2.3e-14  Score=101.84  Aligned_cols=82  Identities=16%  Similarity=0.207  Sum_probs=69.3

Q ss_pred             CCeEEEcCCC--CCC---CHHHHHHhhCCCCCEEEEEEeecCcc-cCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCC
Q 030444           77 SSTLYVEGLP--ADS---TKREVAHIFRPFVGYKEVRLVIKESK-LRGGDPLILCFVDFENPACAATALSALQGYRMDED  150 (177)
Q Consensus        77 ~~tLfV~nLp--~~~---te~~L~~lF~~~G~i~~v~l~~~~~~-~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~  150 (177)
                      +++|+|.|+-  .++   .++||+++|++||.|.+|+|+.++.. ..+++++||+||+|.+.++|.+|++.|||..+.+ 
T Consensus        20 s~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~G-   98 (118)
T 3ue2_A           20 STVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG-   98 (118)
T ss_dssp             CCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETT-
T ss_pred             CCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECC-
Confidence            7999999983  222   47899999999999999999987621 1245678999999999999999999999999965 


Q ss_pred             CCCCcceEEEeec
Q 030444          151 DPDSKFLRLQFSR  163 (177)
Q Consensus       151 ~~~~r~l~V~~a~  163 (177)
                          |.|+|+|+.
T Consensus        99 ----R~i~v~~~~  107 (118)
T 3ue2_A           99 ----RKVVAEVYD  107 (118)
T ss_dssp             ----EECEEEEEC
T ss_pred             ----cEEEEEEcC
Confidence                689999974

>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=99.55  E-value=1.8e-15  Score=105.16  Aligned_cols=73  Identities=15%  Similarity=0.222  Sum_probs=63.1

Q ss_pred             EEcCCCCCCCHHHHHHhh------------CCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeC
Q 030444           81 YVEGLPADSTKREVAHIF------------RPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMD  148 (177)
Q Consensus        81 fV~nLp~~~te~~L~~lF------------~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~  148 (177)
                      ++.+||+++++++|+++|            ++||.|.+|+|+.++    .++++|||||+|.+.++|++|++.|||..+.
T Consensus        19 ~~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~----~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~   94 (104)
T 1jmt_A           19 SADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL----GDHLVGNVYVKFRREEDAEKAVIDLNNRWFN   94 (104)
T ss_dssp             --CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS----SSSSEEEEEEEESCHHHHHHHHHHHTTCEET
T ss_pred             ccCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCC----CCCccEEEEEEECCHHHHHHHHHHHCCCEEC
Confidence            356778888888887766            999999999998765    4789999999999999999999999999996


Q ss_pred             CCCCCCcceEEEee
Q 030444          149 EDDPDSKFLRLQFS  162 (177)
Q Consensus       149 ~~~~~~r~l~V~~a  162 (177)
                      +     |+|+|+|+
T Consensus        95 G-----r~i~v~~s  103 (104)
T 1jmt_A           95 G-----QPIHAELS  103 (104)
T ss_dssp             T-----EECCEEEC
T ss_pred             C-----EEEEEEEc
Confidence            6     68999987

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.55  E-value=7.4e-15  Score=111.16  Aligned_cols=74  Identities=18%  Similarity=0.289  Sum_probs=64.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCC----C-------CEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCC
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPF----V-------GYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGY  145 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~----G-------~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~  145 (177)
                      +++|||+|||+++|+++|+++|++|    |       .|.++++..         ++|||||+|.+.++|++|+ .||+.
T Consensus         4 ~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~~~---------~~g~afV~F~~~~~A~~Al-~l~g~   73 (198)
T 2yh0_A            4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQ---------DKNFAFLEFRSVDETTQAM-AFDGI   73 (198)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEEET---------TTTEEEEEESCSHHHHHHG-GGTTE
T ss_pred             eeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEecC---------CCCEEEEEeCCHHHHHHHH-HhcCC
Confidence            6899999999999999999999999    5       566665533         4579999999999999999 89999


Q ss_pred             eeCCCCCCCcceEEEeecCC
Q 030444          146 RMDEDDPDSKFLRLQFSRNP  165 (177)
Q Consensus       146 ~l~~~~~~~r~l~V~~a~~~  165 (177)
                      .|.+     +.|+|++++..
T Consensus        74 ~~~g-----~~i~v~~~~~~   88 (198)
T 2yh0_A           74 IFQG-----QSLKIRRPHDY   88 (198)
T ss_dssp             EETT-----EEEEEECCCCC
T ss_pred             EEcC-----ceEEEeCCCCC
Confidence            9966     58999998764

>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=99.44  E-value=5.3e-13  Score=94.17  Aligned_cols=77  Identities=16%  Similarity=0.144  Sum_probs=63.8

Q ss_pred             CCCCeEEEcCCCC--CC--------CHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCC
Q 030444           75 DASSTLYVEGLPA--DS--------TKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQG  144 (177)
Q Consensus        75 ~~~~tLfV~nLp~--~~--------te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g  144 (177)
                      .++++|.+.|+=.  +.        .+++|+++|++||.|.+|.|..+.       ++||+||+|.+.++|++|++.|||
T Consensus         5 ~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~-------~~G~~fV~f~~~e~A~~Ai~~lnG   77 (114)
T 3s6e_A            5 LATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS-------AQGNVYVKCPSIAAAIAAVNALHG   77 (114)
T ss_dssp             CCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC-------TTCCEEEECSSHHHHHHHHHHHTT
T ss_pred             CCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC-------CcEEEEEEECCHHHHHHHHHHhCC
Confidence            3478999999832  21        245889999999999999885542       478999999999999999999999


Q ss_pred             CeeCCCCCCCcceEEEeec
Q 030444          145 YRMDEDDPDSKFLRLQFSR  163 (177)
Q Consensus       145 ~~l~~~~~~~r~l~V~~a~  163 (177)
                      ..+.+     |.|+|+|+.
T Consensus        78 ~~f~G-----R~i~v~~~~   91 (114)
T 3s6e_A           78 RWFAG-----KMITAAYVP   91 (114)
T ss_dssp             CEETT-----EECEEEEEC
T ss_pred             CEECC-----EEEEEEEEc
Confidence            99966     689999974

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.27  E-value=3.8e-11  Score=85.32  Aligned_cols=72  Identities=11%  Similarity=0.111  Sum_probs=62.2

Q ss_pred             CCeEEEcCCCCC-CCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecC-HHHHHHHHHHhC--CCeeCCCCC
Q 030444           77 SSTLYVEGLPAD-STKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFEN-PACAATALSALQ--GYRMDEDDP  152 (177)
Q Consensus        77 ~~tLfV~nLp~~-~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~-~~~A~~Ai~~l~--g~~l~~~~~  152 (177)
                      ++.|||+||+++ +++++|+++|++||.|..|.++.+.   .      .|||.|.+ ..+|..|++.||  +..|.+.  
T Consensus        18 G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~---~------tgfVrf~~~~~~A~~av~~ln~~~~~i~g~--   86 (121)
T 1owx_A           18 GCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGA---K------EGIILFKEKAKEALGKAKDANNGNLQLRNK--   86 (121)
T ss_dssp             CCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTC---S------EEEEEESSCHHHHHHHHHHTTTSCBCTTSS--
T ss_pred             CeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCC---C------EEEEEECCChHHHHHHHHHhhcCCcEEeCc--
Confidence            899999999999 9999999999999999999998775   1      69999999 899999999995  6666553  


Q ss_pred             CCcceEEEee
Q 030444          153 DSKFLRLQFS  162 (177)
Q Consensus       153 ~~r~l~V~~a  162 (177)
                         .++++..
T Consensus        87 ---~~~~evL   93 (121)
T 1owx_A           87 ---EVTWEVL   93 (121)
T ss_dssp             ---SEEEEEC
T ss_pred             ---EEEEEEC
Confidence               5676653

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.24  E-value=1.9e-11  Score=82.34  Aligned_cols=72  Identities=19%  Similarity=0.259  Sum_probs=60.6

Q ss_pred             CCeEEEcCCCC----CCCH----HHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeC
Q 030444           77 SSTLYVEGLPA----DSTK----REVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMD  148 (177)
Q Consensus        77 ~~tLfV~nLp~----~~te----~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~  148 (177)
                      ..||+|..++.    +..+    .+|.+.|++||.|..++++.++           +||+|.+.++|.+|++ |||+.+.
T Consensus         7 d~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~-----------~fVtF~d~~sAlaAi~-mnG~~v~   74 (91)
T 2dnr_A            7 GGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK-----------MWVTFLEGSSALNVLS-LNGKELL   74 (91)
T ss_dssp             SCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS-----------EEEEESSHHHHHHGGG-GTTCEET
T ss_pred             CCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC-----------EEEEECChHHHHHHHh-cCCeEeC
Confidence            47888887762    3333    5799999999999999998874           8999999999999998 9999996


Q ss_pred             CCCCCCcceEEEeecCC
Q 030444          149 EDDPDSKFLRLQFSRNP  165 (177)
Q Consensus       149 ~~~~~~r~l~V~~a~~~  165 (177)
                      +     |.|+|+++++.
T Consensus        75 G-----r~LkV~lkt~d   86 (91)
T 2dnr_A           75 N-----RTITIALKSPS   86 (91)
T ss_dssp             T-----EEEEEEECCCS
T ss_pred             C-----eEEEEEeCCCC
Confidence            6     68999998653

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.01  E-value=2.4e-10  Score=77.36  Aligned_cols=69  Identities=14%  Similarity=0.231  Sum_probs=58.5

Q ss_pred             CCeEEEcCCCCC-----CCH----HHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCee
Q 030444           77 SSTLYVEGLPAD-----STK----REVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRM  147 (177)
Q Consensus        77 ~~tLfV~nLp~~-----~te----~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l  147 (177)
                      ..||+|..++.+     ..+    .+|.+.|++||.|..++++.++           +||+|.+.+.|.+||+ |||+++
T Consensus        15 D~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~-----------~fVtF~d~~sAl~AI~-ldG~~v   82 (95)
T 1ufw_A           15 DATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ-----------MLVTFADSHSALSVLD-VDGMKV   82 (95)
T ss_dssp             TCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE-----------EEEECSCSHHHHHHHH-GGGSEE
T ss_pred             CCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc-----------EEEEEcChHHHHHHHh-cCCeee
Confidence            578999888743     222    4688999999999999999874           9999999999999998 999999


Q ss_pred             CCCCCCCcceEEEee
Q 030444          148 DEDDPDSKFLRLQFS  162 (177)
Q Consensus       148 ~~~~~~~r~l~V~~a  162 (177)
                      .+     |.|+|++-
T Consensus        83 ~G-----r~L~V~~k   92 (95)
T 1ufw_A           83 KG-----RAVKISGP   92 (95)
T ss_dssp             TT-----EEEEEECC
T ss_pred             CC-----eEEEEecc
Confidence            66     68999864

>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=99.00  E-value=1.5e-09  Score=83.97  Aligned_cols=70  Identities=16%  Similarity=0.201  Sum_probs=59.9

Q ss_pred             CCHHHHHHhhCCCCCEEEEEEeecCc-ccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcceEEEeec
Q 030444           89 STKREVAHIFRPFVGYKEVRLVIKES-KLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFLRLQFSR  163 (177)
Q Consensus        89 ~te~~L~~lF~~~G~i~~v~l~~~~~-~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~l~V~~a~  163 (177)
                      -.+++|++.|++||.|.++.|..+.. ...++.++|++||+|.+.++|.+|++.|||..+.+     |.|+|+|+.
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~g-----r~i~~~~~~  211 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG-----RKVVAEVYD  211 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSS-----SBCEEEECC
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECC-----eEEEEEEcC
Confidence            45778999999999999999986542 12456899999999999999999999999999966     689999973

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.67  E-value=5.8e-08  Score=67.16  Aligned_cols=70  Identities=16%  Similarity=0.187  Sum_probs=63.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCC-----CCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCC
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPF-----VGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDD  151 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~-----G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~  151 (177)
                      .++|-+-|||..+++..|+.|++++     |.|+++.++++.         +-|+|+|.|...|.+|.-.|+|++|.+  
T Consensus        21 ~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH---------~GAivef~d~~~AgKasLaL~G~ef~g--   89 (117)
T 2l9w_A           21 ETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF---------NGAIIIFRDSKFAAKMLMILNGSQFQG--   89 (117)
T ss_dssp             TSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTT---------TEEEEECSCHHHHHHHHHHHSSEEETT--
T ss_pred             CcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCC---------CceEEEEccchhhHHHHhhcCCeeecC--
Confidence            5899999999999999999999999     999999999886         259999999999999999999999965  


Q ss_pred             CCCcceEEE
Q 030444          152 PDSKFLRLQ  160 (177)
Q Consensus       152 ~~~r~l~V~  160 (177)
                         |+|++.
T Consensus        90 ---r~Lr~g   95 (117)
T 2l9w_A           90 ---KVIRSG   95 (117)
T ss_dssp             ---EEEEEE
T ss_pred             ---eEEEec
Confidence               578875

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=98.23  E-value=6.7e-06  Score=55.63  Aligned_cols=55  Identities=16%  Similarity=0.335  Sum_probs=48.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhC
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQ  143 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~  143 (177)
                      ...++| ..|+++...||.++|+.||.|. |+.+.+.          -|||.|.+++.|..|+..+.
T Consensus        16 ~HVf~l-~FP~ewKt~DI~~lFs~fggv~-I~WidDT----------sAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           16 DHVLHV-TFPKEWKTSDLYQLFSAFGNIQ-ISWIDDT----------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CSEEEE-ECCTTCCHHHHHHHHTTTCSCC-CEEEETT----------EEEEECSCHHHHHHHHHHHH
T ss_pred             CeEEEE-eCChhhhhHHHHHHhhccCCEE-EEEEcCC----------eEEEEecCHHHHHHHHHhcc
Confidence            466777 9999999999999999999665 7788775          79999999999999998774

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=98.16  E-value=2.6e-05  Score=52.33  Aligned_cols=87  Identities=14%  Similarity=0.223  Sum_probs=67.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcce
Q 030444           78 STLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFL  157 (177)
Q Consensus        78 ~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~l  157 (177)
                      ++|.|.+||+.+||+++.+.++....+.....+..+.... -..-.-|||.|.+.+++..-.+.++|+.+.+.+-+..+-
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~-~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D~kg~~~~a   80 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLY-PHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPA   80 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSST-TCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEEC
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCC-CCcceEEEEEeCCHHHHHHHHHHhCCcEEEcCCCCEeee
Confidence            5789999999999999999999988777666666542211 112246999999999999999999999998874323356


Q ss_pred             EEEeecCC
Q 030444          158 RLQFSRNP  165 (177)
Q Consensus       158 ~V~~a~~~  165 (177)
                      .|+||-.+
T Consensus        81 ~VE~AP~q   88 (91)
T 1uw4_A           81 IVEFAPFQ   88 (91)
T ss_dssp             EEEECSSC
T ss_pred             EEEEcCCC
Confidence            78888543

>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=98.02  E-value=8.1e-06  Score=55.95  Aligned_cols=75  Identities=20%  Similarity=0.208  Sum_probs=61.5

Q ss_pred             CCeEEEcCCCCCC-C----HHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCC
Q 030444           77 SSTLYVEGLPADS-T----KREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDD  151 (177)
Q Consensus        77 ~~tLfV~nLp~~~-t----e~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~  151 (177)
                      .++|+|.||+.++ +    .++++++|..|+.+........-.         =..|.|.+.++|.+|...||++.+.++ 
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSFR---------Rirv~F~~~~~A~~AR~~Lh~~~f~g~-   74 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFK---------RVRINFSNPLSAADARLRLHKTEFLGK-   74 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTTT---------EEEEECSSTTHHHHHHHTSTTSEETTE-
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcce---------EEEEEeCChHHHHHHHHHhccceecCc-
Confidence            4789999998865 2    257799999999888776665431         368999999999999999999999774 


Q ss_pred             CCCcceEEEeecCC
Q 030444          152 PDSKFLRLQFSRNP  165 (177)
Q Consensus       152 ~~~r~l~V~~a~~~  165 (177)
                          .|+|-|+...
T Consensus        75 ----~~r~YFgq~~   84 (104)
T 1wey_A           75 ----EMKLYFAQTL   84 (104)
T ss_dssp             ----ECEEECCCCS
T ss_pred             ----eeEEEecCCC
Confidence                7999999744

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=97.94  E-value=1.4e-05  Score=54.23  Aligned_cols=54  Identities=17%  Similarity=0.338  Sum_probs=46.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhC
Q 030444           78 STLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQ  143 (177)
Q Consensus        78 ~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~  143 (177)
                      ..++| ..|+++...||.++|+.||.| .|+.+.+.          -|||.|.+++.|..|+..+.
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fggv-~I~WidDT----------sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDDT----------SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSEEE-EEEEEETT----------EEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccCCE-EEEEEcCC----------eEEEEecCHHHHHHHHHhcc
Confidence            45666 999999999999999999954 47888775          79999999999999999875

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=97.74  E-value=0.00011  Score=49.81  Aligned_cols=87  Identities=16%  Similarity=0.222  Sum_probs=62.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      +-+|.|..||+.+||+++.+.++..-.+.....+..+.... -..-.-|||.|.+.++...-.+.++|+.+.+.+-+.-+
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~-~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~kg~~~~   87 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLY-PHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKGLEYP   87 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSC-CSCCCCCEEEESCHHHHHHHHHHSTTEEEECTTCCEEE
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCC-CCcceEEEEEeCCHHHHHHHHHHcCCcEEEeCCCCEee
Confidence            56899999999999999999888765543333333221110 01113589999999999999999999999887433346


Q ss_pred             eEEEeecC
Q 030444          157 LRLQFSRN  164 (177)
Q Consensus       157 l~V~~a~~  164 (177)
                      -.|+||-.
T Consensus        88 a~VE~APy   95 (97)
T 2l08_A           88 AVVEFAPF   95 (97)
T ss_dssp             EEEEECCC
T ss_pred             eEEEecCC
Confidence            77888854

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.70  E-value=0.00014  Score=49.68  Aligned_cols=67  Identities=18%  Similarity=0.147  Sum_probs=51.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCC-----CCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCC
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPF-----VGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDD  151 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~-----G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~  151 (177)
                      .++|.|.|||+++.++.|+-+|++-     |.|.+++... .          -|+|+|.+...|+..++. ..+.|.+. 
T Consensus         8 ~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~-~----------~AvItF~d~~va~rVL~k-~~H~L~~~-   74 (104)
T 2dhx_A            8 GVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG-C----------GGVLTFREPADAERVLAQ-ADHELHGA-   74 (104)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET-T----------EEEEEESSHHHHHHHHTC-SCCBSSSS-
T ss_pred             ccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC-C----------cEEEEEcChHHHHHHhcC-CcceecCe-
Confidence            6899999999999999999999872     5677776644 2          599999999999988753 23455443 


Q ss_pred             CCCcceEEE
Q 030444          152 PDSKFLRLQ  160 (177)
Q Consensus       152 ~~~r~l~V~  160 (177)
                          +|.|.
T Consensus        75 ----~LsV~   79 (104)
T 2dhx_A           75 ----QLSLR   79 (104)
T ss_dssp             ----BCEEE
T ss_pred             ----EEEEE
Confidence                56664

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=96.72  E-value=0.0064  Score=42.52  Aligned_cols=62  Identities=18%  Similarity=0.205  Sum_probs=49.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCC
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDE  149 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~  149 (177)
                      .+.|.|-..|+... +.+-+.|++||.|.+......      +   -+-+|.|+++.+|++|| ..||..|.+
T Consensus        24 ~~wVtVFGFp~~~~-~~VL~~F~~~G~Iv~~~~~~~------~---NWihI~Y~s~~~A~rAL-~kNG~ii~g   85 (119)
T 1wwh_A           24 DTWVTVFGFPQASA-SYILLQFAQYGNILKHVMSNT------G---NWMHIRYQSKLQARKAL-SKDGRIFGE   85 (119)
T ss_dssp             GGEEEEECCCGGGH-HHHHHHHHTTSCEEEEEECSS------S---SEEEEEESSHHHHHHHH-TTTTCEETT
T ss_pred             CCEEEEECCCHHHH-HHHHHHHHhhCcEEEeccCCC------C---CeEEEEeCCHHHHHHHH-HhCCeEecC
Confidence            57899999999864 455578999999998776211      1   29999999999999999 569999975

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=96.62  E-value=0.00081  Score=57.54  Aligned_cols=54  Identities=11%  Similarity=0.176  Sum_probs=41.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHH
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATAL  139 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai  139 (177)
                      .++|||. .|..+++.+|.+.|++||.|.++.+..++     |   -||.|||.+.+++..++
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~-----g---~~~~vef~~~~~~~~~~  106 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF-----G---LYAVVEFCQKESIGSLQ  106 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS-----S---EEEEEECC---CCHHHH
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC-----C---eEEEEEeCCHHHHHHHH
Confidence            5899997 79999999999999999999998776554     2   49999999999988664

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=96.27  E-value=0.0033  Score=45.22  Aligned_cols=35  Identities=9%  Similarity=0.026  Sum_probs=28.2

Q ss_pred             EEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCC
Q 030444          106 EVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGY  145 (177)
Q Consensus       106 ~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~  145 (177)
                      .++|+.+.     .+++||+||+|.+.++|++|++.+++.
T Consensus         2 ~~kl~ln~-----~~~~G~~fV~f~~~~~A~~al~~~~~~   36 (158)
T 2kn4_A            2 QYKLILNG-----KTLKGETTTEAVDAATAEKVFKQYAND   36 (158)
T ss_dssp             EEEEEEEC-----SSCEEEEEEECSSHHHHHHHHHHHHHH
T ss_pred             cEEEEecC-----ccccchhHHHHHHHHhHHHHHHhhccc
Confidence            35566654     468899999999999999999888753

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A

Probab=95.12  E-value=0.0077  Score=43.02  Aligned_cols=41  Identities=10%  Similarity=-0.032  Sum_probs=35.8

Q ss_pred             CCCcceEEEEEecCHHHHHHHHHHh-CCCeeCCCCCCCcceEEEeecC
Q 030444          118 GGDPLILCFVDFENPACAATALSAL-QGYRMDEDDPDSKFLRLQFSRN  164 (177)
Q Consensus       118 ~g~~kg~afV~f~~~~~A~~Ai~~l-~g~~l~~~~~~~r~l~V~~a~~  164 (177)
                      +.+.+|+++|+|.+.++|++|++.+ |+..+++      .|+++++..
T Consensus         9 g~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G------~~~~~~a~~   50 (150)
T 2i2y_A            9 GKTLKGETTTEAVDAATAEKVFKQYANDNGVDG------EWTYDDATK   50 (150)
T ss_dssp             CSSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC------EEEEETTTT
T ss_pred             cccccccceeeecCHHHHHHHHHHHhcCCCCCC------ceecccccC
Confidence            3567899999999999999999999 9999976      499998764

>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease, hydrolase, magnesium, metal nonsense-mediated mRNA decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus}

Probab=94.97  E-value=0.064  Score=46.30  Aligned_cols=55  Identities=16%  Similarity=0.342  Sum_probs=46.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhC
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQ  143 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~  143 (177)
                      ...++|+ +|..+...+|.++|+.||.+ +|+.+.+.          .|||.|.+.+.|..+++.++
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~v-~V~widdt----------~a~V~~~~~~~a~~~l~~~~  494 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGNI-QISWIDDT----------SAFVSLSQPEQVQIAVNTSK  494 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCCC-EEEECSSS----------EEEEECSCHHHHHHHHHHHT
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCCE-EEEEEcCC----------eEEEEECCHHHHHHHHHHHH
Confidence            4567776 88899999999999999954 46666654          79999999999999999886

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=93.77  E-value=0.048  Score=38.65  Aligned_cols=71  Identities=18%  Similarity=0.257  Sum_probs=46.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEE-EEEee---------cCcccCCC-CcceEEEEEecCHHHHHHHHHHhCCC
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKE-VRLVI---------KESKLRGG-DPLILCFVDFENPACAATALSALQGY  145 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~-v~l~~---------~~~~~~~g-~~kg~afV~f~~~~~A~~Ai~~l~g~  145 (177)
                      ...|.|-..|++.+..-| +.|++||.|.+ +....         .+.+.-.. ....|-.|+|++..+|.+|| ..||.
T Consensus         7 e~~VtVFGFp~~~~~~VI-~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL-~~NG~   84 (132)
T 3p3d_A            7 ELAILVFGYPETMANQVI-AYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDAL-LENGA   84 (132)
T ss_dssp             -CEEEEECCCGGGHHHHH-HHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHH-TTTTC
T ss_pred             ceEEEEEecCHHHHHHHH-HHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHH-HhCCe
Confidence            466788888887776655 68999999876 21110         00000000 01248899999999999999 68999


Q ss_pred             eeCC
Q 030444          146 RMDE  149 (177)
Q Consensus       146 ~l~~  149 (177)
                      .|.+
T Consensus        85 ii~G   88 (132)
T 3p3d_A           85 VFNG   88 (132)
T ss_dssp             EETT
T ss_pred             EeCc
Confidence            9866

>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=80.02  E-value=0.35  Score=32.62  Aligned_cols=17  Identities=18%  Similarity=0.415  Sum_probs=0.0

Q ss_pred             CCeEEEcCCCCCCCHHH
Q 030444           77 SSTLYVEGLPADSTKRE   93 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~   93 (177)
                      .++|||+|||+++|++.
T Consensus        97 ~~~lyv~Nl~~~~T~~a  113 (115)
T 4f25_A           97 FTNVYIKNFGPGSTRAA  113 (115)
T ss_dssp             -----------------
T ss_pred             CCceEeCCCCCCccccc
Confidence            56799999999999874

---

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	177
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	1e-10
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	3e-10
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	3e-10
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	1e-09
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	1e-09
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	2e-09
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	5e-09
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	8e-09
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	1e-08
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	1e-08
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	1e-08
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	2e-08
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	2e-08
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	5e-08
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	6e-08
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	6e-08
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	6e-08
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	2e-07
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-07
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	5e-07
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	6e-07
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	6e-07
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	8e-07
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	1e-06
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	1e-06
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	1e-06
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	2e-06
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	2e-06
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-06
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	2e-06
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	3e-06
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	4e-06
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	6e-06
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	6e-06
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	6e-06
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	6e-06
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	1e-05
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	1e-05
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	2e-05
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	2e-05
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	3e-05
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	3e-05
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	3e-05
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	3e-05
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	3e-05
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	5e-05
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	6e-05
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	8e-05
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	1e-04
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	1e-04
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	1e-04
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	1e-04
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	3e-04
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	3e-04
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	3e-04
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	5e-04
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	5e-04
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 6e-04
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	6e-04
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	6e-04
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	8e-04
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	0.001
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	0.001
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	0.001
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	0.002
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	0.002

>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 = 54.3 bits (130), Expect = 1e-10
 Identities = 21/92 (22%), Positives = 40/92 (43%), Gaps = 11/92 (11%)

Query: 72  LPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFEN 131
           LPP+ +  LY+  LP   T  E+  IF  +   +++R+       RG       +V +E+
Sbjct: 2   LPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET-RG-----TAYVVYED 55

Query: 132 PACAATALSALQGYRMDEDDPDSKFLRLQFSR 163
              A  A   L G+ +      +++L + +  
Sbjct: 56  IFDAKNACDHLSGFNV-----CNRYLVVLYYN 82

>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 = 52.3 bits (125), Expect = 3e-10
 Identities = 20/92 (21%), Positives = 40/92 (43%), Gaps = 8/92 (8%)

Query: 77  SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAA 136
           S TLYV  L   +T+ ++  +F      K++ + + + K         CFV++ + A A 
Sbjct: 7   SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKT---ACGFCFVEYYSRADAE 63

Query: 137 TALSALQGYRMDEDDPDSKFLRLQFSRNPGPR 168
            A+  + G R+D+     + +R  +       
Sbjct: 64  NAMRYINGTRLDD-----RIIRTDWDAGFKEG 90

>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 = 52.1 bits (124), Expect = 3e-10
 Identities = 16/94 (17%), Positives = 37/94 (39%), Gaps = 13/94 (13%)

Query: 72  LPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFEN 131
            PP  S+TL++  +P   ++ ++  +F    G       + +          +  +   +
Sbjct: 7   FPP--SATLHLSNIPPSVSEEDLKVLFSSNGG-------VVKGFKFFQKDRKMALIQMGS 57

Query: 132 PACAATALSALQGYRMDEDDPDSKFLRLQFSRNP 165
              A  AL  L  + +     ++  LR+ FS++ 
Sbjct: 58  VEEAVQALIDLHNHDLG----ENHHLRVSFSKST 87

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 51.1 bits (122), Expect = 1e-09
 Identities = 23/92 (25%), Positives = 37/92 (40%), Gaps = 8/92 (8%)

Query: 74  PDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPA 133
              +S + V  +P  + +RE+  +F  F   K VRL  K      G      FVDF    
Sbjct: 5   KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKK--MTGTGAHRGFGFVDFITKQ 62

Query: 134 CAATALSAL-QGYRMDEDDPDSKFLRLQFSRN 164
            A  A +AL     +       + L L+++ +
Sbjct: 63  DAKKAFNALCHSTHL-----YGRRLVLEWADS 89

>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 = 50.8 bits (121), Expect = 1e-09
 Identities = 24/91 (26%), Positives = 40/91 (43%), Gaps = 9/91 (9%)

Query: 76  ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACA 135
           +++ L V  LP D T RE+  +FR        R++        G      FVDF +   +
Sbjct: 1   SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKT---GYSYGYAFVDFTSEMDS 57

Query: 136 ATALSALQGYRMDEDDPDSKFLRLQFSRNPG 166
             A+  L G  +      +K L++ ++R PG
Sbjct: 58  QRAIKVLNGITV-----RNKRLKVSYAR-PG 82

>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 = 49.7 bits (118), Expect = 2e-09
 Identities = 20/75 (26%), Positives = 32/75 (42%), Gaps = 3/75 (4%)

Query: 74  PDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPA 133
           PD +  L V GL   +T+R++  +F  +    +V +V  +   +        FV FEN  
Sbjct: 6   PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQ---QSRRSRGFAFVYFENVD 62

Query: 134 CAATALSALQGYRMD 148
            A  A     G  +D
Sbjct: 63  DAKEAKERANGMELD 77

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.8 bits (116), Expect = 5e-09
 Identities = 20/85 (23%), Positives = 34/85 (40%), Gaps = 8/85 (9%)

Query: 79  TLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATA 138
           +LYV  L  D T+  +   F P      +R+            L   +V+F+ PA A  A
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMIT---RRSLGYAYVNFQQPADAERA 58

Query: 139 LSALQGYRMDEDDPDSKFLRLQFSR 163
           L  +    +       K +R+ +S+
Sbjct: 59  LDTMNFDVI-----KGKPVRIMWSQ 78

>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 = 48.5 bits (115), Expect = 8e-09
 Identities = 21/90 (23%), Positives = 39/90 (43%), Gaps = 10/90 (11%)

Query: 79  TLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATA 138
           TLYV  L  D T+  +  +F      K  +++ +            CFV+F     AA A
Sbjct: 10  TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEH-----TSNDPYCFVEFYEHRDAAAA 64

Query: 139 LSALQGYRMDEDDPDSKFLRLQFSRNPGPR 168
           L+A+ G ++       K +++ ++  P  +
Sbjct: 65  LAAMNGRKI-----LGKEVKVNWATTPSSQ 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 = 48.1 bits (114), Expect = 1e-08
 Identities = 20/95 (21%), Positives = 42/95 (44%), Gaps = 11/95 (11%)

Query: 75  DASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPAC 134
           D ++T+ V  L  D+ + ++  +FRPF     + L   ++    G      F+ F     
Sbjct: 6   DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTT---GQSKGFAFISFHRRED 62

Query: 135 AATALSALQGYRMDEDDPDSKFLRLQFSRNPGPRS 169
           AA A++ + G+       D   L +++++   P +
Sbjct: 63  AARAIAGVSGFGY-----DHLILNVEWAK---PST 89

>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 = 47.7 bits (113), Expect = 1e-08
 Identities = 19/86 (22%), Positives = 37/86 (43%), Gaps = 5/86 (5%)

Query: 80  LYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATAL 139
           L+++ L   +T+  +  +F      K   +  K++K      +   FV+++ P  A  AL
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 140 SALQGYRMDEDDPDSKFLRLQFSRNP 165
             LQG+ +     D   L ++ S   
Sbjct: 61  KQLQGHTV-----DGHKLEVRISERA 81

>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 = 47.6 bits (113), Expect = 1e-08
 Identities = 17/83 (20%), Positives = 28/83 (33%), Gaps = 9/83 (10%)

Query: 80  LYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATAL 139
           L V  L    +  ++  +F  F   K+  +    S       L    V FE  A A  A+
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSG----RSLGTADVHFERKADALKAM 58

Query: 140 SALQGYRMDEDDPDSKFLRLQFS 162
               G  +     D + + +Q  
Sbjct: 59  KQYNGVPL-----DGRPMNIQLV 76

>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 = 48.0 bits (114), Expect = 2e-08
 Identities = 19/114 (16%), Positives = 42/114 (36%), Gaps = 21/114 (18%)

Query: 56  QLPFDAAARPGHETLPLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESK 115
           QL F+       + +      + T+Y  G+ +  T + +   F PF    E+R+  ++  
Sbjct: 4   QLRFE-------DVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGY 56

Query: 116 LRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPRS 169
                     FV F     AA A+ ++ G  +     +   ++  + +     +
Sbjct: 57  ---------SFVRFSTHESAAHAIVSVNGTTI-----EGHVVKCYWGKESPDMT 96

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 47.3 bits (112), Expect = 2e-08
 Identities = 17/72 (23%), Positives = 26/72 (36%), Gaps = 3/72 (4%)

Query: 77  SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAA 136
            + LYV  LP   T  ++  IF  +     +           G P  + FV +     A 
Sbjct: 6   DTNLYVTNLPRTITDDQLDTIFGKY---GSIVQKNILRDKLTGRPRGVAFVRYNKREEAQ 62

Query: 137 TALSALQGYRMD 148
            A+SAL     +
Sbjct: 63  EAISALNNVIPE 74

>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 = 46.4 bits (109), Expect = 5e-08
 Identities = 21/91 (23%), Positives = 44/91 (48%), Gaps = 14/91 (15%)

Query: 73  PPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENP 132
           PP  +  L++  LP ++ +  ++ +F  F G+KEVR           +   + FV+F   
Sbjct: 6   PP--NQILFLTNLPEETNEMMLSMLFNQFPGFKEVR--------LVPNRHDIAFVEFTTE 55

Query: 133 ACAATALSALQGYRMDEDDPDSKFLRLQFSR 163
             +  A  ALQG+++      +  +++ F++
Sbjct: 56  LQSNAAKEALQGFKIT----PTHAMKITFAK 82

>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 = 46.2 bits (109), Expect = 6e-08
 Identities = 17/93 (18%), Positives = 35/93 (37%), Gaps = 9/93 (9%)

Query: 77  SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAA 136
           +  L++ GLP      +V  +   F   K   LV   +           F ++ +     
Sbjct: 1   AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGL---SKGYAFCEYVDINVTD 57

Query: 137 TALSALQGYRMDEDDPDSKFLRLQFSRNPGPRS 169
            A++ L G ++       K L +Q + + G ++
Sbjct: 58  QAIAGLNGMQL-----GDKKLLVQRA-SVGAKN 84

>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 = 46.3 bits (109), Expect = 6e-08
 Identities = 24/97 (24%), Positives = 42/97 (43%), Gaps = 8/97 (8%)

Query: 73  PPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENP 132
           P + +  LY++ L    T+R++  +F  F   K   +     ++  G      F+ F N 
Sbjct: 14  PGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQF---RMMTGRMRGQAFITFPNK 70

Query: 133 ACAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPRS 169
             A  AL  + GY++       K L ++F +N   RS
Sbjct: 71  EIAWQALHLVNGYKL-----YGKILVIEFGKNKKQRS 102

>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 = 45.8 bits (108), Expect = 6e-08
 Identities = 18/85 (21%), Positives = 39/85 (45%), Gaps = 6/85 (7%)

Query: 78  STLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAAT 137
           + LYV GLP   T++E+  +F  +      R+++ +     G    + F+ F+    A  
Sbjct: 7   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVT---GVSRGVGFIRFDKRIEAEE 63

Query: 138 ALSALQGYRMDEDDPDSKFLRLQFS 162
           A+  L G +       ++ + ++F+
Sbjct: 64  AIKGLNGQKPSG---ATEPITVKFA 85

>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 = 44.6 bits (105), Expect = 2e-07
 Identities = 12/75 (16%), Positives = 26/75 (34%), Gaps = 3/75 (4%)

Query: 74  PDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPA 133
            +  +T+YV GL    ++  +  +F          +         G      FV+F +  
Sbjct: 6   RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVT---GQHQGYGFVEFLSEE 62

Query: 134 CAATALSALQGYRMD 148
            A  A+  +   ++ 
Sbjct: 63  DADYAIKIMDMIKLY 77

>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 = 44.5 bits (105), Expect = 3e-07
 Identities = 15/97 (15%), Positives = 29/97 (29%), Gaps = 17/97 (17%)

Query: 73  PPDASSTLYVEGLPADST-KREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFEN 131
           P   +S +++  L      K +V  IF  +       +                FV + N
Sbjct: 11  PRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKG-----------FAFVQYVN 59

Query: 132 PACAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPR 168
              A  A++   G  +       + L +  +  P   
Sbjct: 60  ERNARAAVAGEDGRMI-----AGQVLDINLAAEPKVN 91

>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 = 43.9 bits (103), Expect = 5e-07
 Identities = 18/96 (18%), Positives = 38/96 (39%), Gaps = 13/96 (13%)

Query: 74  PDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPA 133
             A+ TL  + L  + T+ E+  +F   +  + V         + G    + +++F++ A
Sbjct: 13  VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS--------QDGKSKGIAYIEFKSEA 64

Query: 134 CAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPRS 169
            A   L   QG  +     D + + L ++   G   
Sbjct: 65  DAEKNLEEKQGAEI-----DGRSVSLYYTGEKGGTR 95

>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 = 43.2 bits (101), Expect = 6e-07
 Identities = 20/86 (23%), Positives = 37/86 (43%), Gaps = 8/86 (9%)

Query: 78  STLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAAT 137
           + L V  LP + T+ E   +F       E+           G  L   FV++ +P  A  
Sbjct: 3   TNLIVNYLPQNMTQEEFRSLFGSI---GEIESCKLVRDKITGQSLGYGFVNYIDPKDAEK 59

Query: 138 ALSALQGYRMDEDDPDSKFLRLQFSR 163
           A++ L G R+      +K +++ ++R
Sbjct: 60  AINTLNGLRL-----QTKTIKVSYAR 80

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.4 bits (102), Expect = 6e-07
 Identities = 20/89 (22%), Positives = 33/89 (37%), Gaps = 14/89 (15%)

Query: 77  SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAA 136
            S L+V  LP D T+ E+  +F  +    EV +   +            F+  E    A 
Sbjct: 8   RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGF---------GFIRLETRTLAE 58

Query: 137 TALSALQGYRMDEDDPDSKFLRLQFSRNP 165
            A   L    +       K LR++F+ + 
Sbjct: 59  IAKVELDNMPL-----RGKQLRVRFACHS 82

>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 = 43.2 bits (101), Expect = 8e-07
 Identities = 21/104 (20%), Positives = 36/104 (34%), Gaps = 10/104 (9%)

Query: 71  PLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGD-----PLILC 125
           P     +S +YV+GL    T  ++A  F+     K  +   +       D     P    
Sbjct: 2   PDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDA 61

Query: 126 FVDFENPACAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPRS 169
            V +E+P  A  A+    G            L++  +R   P +
Sbjct: 62  TVSYEDPPTAKAAVEWFDGKDF-----QGSKLKVSLARKKPPMN 100

>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 = 42.8 bits (100), Expect = 1e-06
 Identities = 18/87 (20%), Positives = 40/87 (45%), Gaps = 8/87 (9%)

Query: 77  SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAA 136
            + L++  LP +   +++  +F PF      ++ I +   +        FV ++NP  A 
Sbjct: 18  GANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDK---QTNLSKCFGFVSYDNPVSAQ 74

Query: 137 TALSALQGYRMDEDDPDSKFLRLQFSR 163
            A+ ++ G+++       K L++Q  R
Sbjct: 75  AAIQSMNGFQI-----GMKRLKVQLKR 96

>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 = 42.8 bits (100), Expect = 1e-06
 Identities = 19/96 (19%), Positives = 31/96 (32%), Gaps = 8/96 (8%)

Query: 74  PDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPA 133
              S  L+V  L   S++ ++  +F  +    E+   I         P    FV F  P 
Sbjct: 5   SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDS---LTKKPKGFAFVTFMFPE 61

Query: 134 CAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPRS 169
            A  A + + G          + L +  S      S
Sbjct: 62  HAVKAYAEVDGQVF-----QGRMLHVLPSTIKKEAS 92

>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 = 42.3 bits (99), Expect = 1e-06
 Identities = 19/93 (20%), Positives = 36/93 (38%), Gaps = 15/93 (16%)

Query: 77  SSTLYVEGLPADSTKREVAH----IFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENP 132
           + T+Y+  L     K E+      IF  F    ++ +                FV F+  
Sbjct: 3   NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL------KMRGQAFVIFKEV 56

Query: 133 ACAATALSALQGYRMDEDDPDSKFLRLQFSRNP 165
           + A  AL ++QG+         K +R+Q+++  
Sbjct: 57  SSATNALRSMQGFPF-----YDKPMRIQYAKTD 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 = 42.3 bits (99), Expect = 2e-06
 Identities = 16/90 (17%), Positives = 32/90 (35%), Gaps = 8/90 (8%)

Query: 79  TLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATA 138
            LYV GL  +   + +   F PF    ++  +               FV+FE    AA A
Sbjct: 7   VLYVGGLAEEVDDKVLHAAFIPF---GDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 63

Query: 139 LSALQGYRMDEDDPDSKFLRLQFSRNPGPR 168
           +  +    +       + +R+  ++    +
Sbjct: 64  IDNMNESEL-----FGRTIRVNLAKPMRIK 88

>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 = 42.4 bits (99), Expect = 2e-06
 Identities = 22/99 (22%), Positives = 32/99 (32%), Gaps = 20/99 (20%)

Query: 76  ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACA 135
            SS + V+ LP DS  +EV  + + +   K   +   +            FV   N   A
Sbjct: 4   GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVDRNKRT---------AFVTLLNGEQA 53

Query: 136 ATALSALQGYRMDEDDPDSKFLRLQFSRN-----PGPRS 169
             A+     Y         K L +Q          GP S
Sbjct: 54  QNAIQMFHQYSF-----RGKDLIVQLQPTDALLCSGPSS 87

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 42.1 bits (98), Expect = 2e-06
 Identities = 12/92 (13%), Positives = 28/92 (30%), Gaps = 12/92 (13%)

Query: 73  PPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENP 132
               S  ++V GL     + ++      F     V ++  + +           V+FEN 
Sbjct: 11  KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQ---------ALVEFENI 61

Query: 133 ACAATALSALQGYRMDEDDPDSKFLRLQFSRN 164
             A   ++      +       +     +S +
Sbjct: 62  DSAKECVTFAADVPVYIAG---QQAFFNYSTS 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 = 42.1 bits (98), Expect = 2e-06
 Identities = 18/101 (17%), Positives = 33/101 (32%), Gaps = 4/101 (3%)

Query: 70  LPLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDF 129
           LP       T+++  L  DS +  +  + + F   K VR+V+              F  F
Sbjct: 1   LPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHP---DTEHSKGCAFAQF 57

Query: 130 ENPACAATALSALQGYR-MDEDDPDSKFLRLQFSRNPGPRS 169
                A   L+A            D + L++  +      +
Sbjct: 58  MTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAA 98

>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 = 41.2 bits (96), Expect = 3e-06
 Identities = 13/92 (14%), Positives = 31/92 (33%), Gaps = 10/92 (10%)

Query: 77  SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAA 136
              ++++ L      + +   F  F      ++V  E+           FV FE    A 
Sbjct: 8   VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-----SKGYGFVHFETQEAAE 62

Query: 137 TALSALQGYRMDEDDPDSKFLRLQFSRNPGPR 168
            A+  + G  +     + + + +   ++   R
Sbjct: 63  RAIEKMNGMLL-----NDRKVFVGRFKSRKER 89

>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 = 41.2 bits (96), Expect = 4e-06
 Identities = 10/75 (13%), Positives = 26/75 (34%), Gaps = 4/75 (5%)

Query: 74  PDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPA 133
           P+    L++ GL  ++T   +   F  +    +  ++               FV +    
Sbjct: 3   PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDP---NTKRSRGFGFVTYATVE 59

Query: 134 CAATALSALQGYRMD 148
               A+   + +++D
Sbjct: 60  EVDAAM-NARPHKVD 73

>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 = 41.8 bits (97), Expect = 6e-06
 Identities = 21/106 (19%), Positives = 44/106 (41%), Gaps = 9/106 (8%)

Query: 73  PPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENP 132
            PD    L V  +P    + ++  +F  +   + V++V      +        FV F++ 
Sbjct: 38  EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGY---GFVKFQSG 94

Query: 133 ACAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPR-SVFGARGRR 177
           + A  A++ L G+ +      +K L++  + +   R  + GA G  
Sbjct: 95  SSAQQAIAGLNGFNI-----LNKRLKVALAASGHQRPGIAGAVGDG 135

>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 = 40.9 bits (95), Expect = 6e-06
 Identities = 17/96 (17%), Positives = 34/96 (35%), Gaps = 8/96 (8%)

Query: 71  PLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFE 130
           P        L+V  +  ++ + E+   F     Y E++ +      R G       V++E
Sbjct: 1   PQRSVEGWILFVTSIHEEAQEDEIQEKFCD---YGEIKNIHLNLDRRTGFSKGYALVEYE 57

Query: 131 NPACAATALSALQGYRMDEDDPDSKFLRLQFSRNPG 166
               A  A  AL G  +       + +++ +    G
Sbjct: 58  THKQALAAKEALNGAEI-----MGQTIQVDWCFVKG 88

>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 = 40.8 bits (95), Expect = 6e-06
 Identities = 20/93 (21%), Positives = 43/93 (46%), Gaps = 13/93 (13%)

Query: 77  SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAA 136
           ++ L+V GL  +++   +A  F  F   + +  V  +S           ++ +E+   A 
Sbjct: 17  TTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSF---------AYIQYESLDAAQ 67

Query: 137 TALSALQGYRMDEDDPDSKFLRLQFSRNPGPRS 169
            A + ++G+ +   D   + LR+ F++  GP S
Sbjct: 68  AACAKMRGFPLGGPD---RRLRVDFAK-SGPSS 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 = 40.7 bits (95), Expect = 6e-06
 Identities = 16/87 (18%), Positives = 28/87 (32%), Gaps = 10/87 (11%)

Query: 77  SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAA 136
           +S L V GLP  +T++++   F  F     V++         G      FV F       
Sbjct: 8   TSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKT---GHSKGFGFVRFTEYETQV 64

Query: 137 TALSALQGYRMDEDDPDSKFLRLQFSR 163
             +S            D ++   +   
Sbjct: 65  KVMSQRHMI-------DGRWCDCKLPN 84

>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 = 40.1 bits (93), Expect = 1e-05
 Identities = 15/97 (15%), Positives = 30/97 (30%), Gaps = 11/97 (11%)

Query: 67  HETLPLPPDASSTLYV--EGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLIL 124
           HE +     A+ +L V   GL    ++ ++  +         + +   +           
Sbjct: 8   HEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPY--------- 58

Query: 125 CFVDFENPACAATALSALQGYRMDEDDPDSKFLRLQF 161
            F  +     +  A   L G  + +D      L L F
Sbjct: 59  SFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNF 95

>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 = 39.6 bits (92), Expect = 1e-05
 Identities = 18/91 (19%), Positives = 32/91 (35%), Gaps = 15/91 (16%)

Query: 79  TLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATA 138
            LYV  L   +++  +   F         R  +K+ +          FV F N   A  A
Sbjct: 10  ILYVRNLMLSTSEEMIEKEFNNIKPGAVER--VKKIR-------DYAFVHFSNREDAVEA 60

Query: 139 LSALQGYRMDEDDPDSKFLRLQFSRNPGPRS 169
           + AL G  +     D   + +  ++ P  + 
Sbjct: 61  MKALNGKVL-----DGSPIEVTLAK-PVDKD 85

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.7 bits (92), Expect = 2e-05
 Identities = 10/93 (10%), Positives = 27/93 (29%), Gaps = 13/93 (13%)

Query: 74  PDASSTLYVEGLPADS-TKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENP 132
            +    +++         + ++  +  PF       ++ K +           F++    
Sbjct: 5   VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKIN---------EAFIEMATT 55

Query: 133 ACAATALSALQGYRMDEDDPDSKFLRLQFSRNP 165
             A  A+     Y         K +R+  S+  
Sbjct: 56  EDAQAAVDY---YTTTPALVFGKPVRVHLSQKY 85

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.3 bits (91), Expect = 2e-05
 Identities = 21/96 (21%), Positives = 37/96 (38%), Gaps = 11/96 (11%)

Query: 73  PPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENP 132
             +    +YV  LP D   +++  +F  +   +++ L                FV+FE+P
Sbjct: 10  AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLK------NRRGGPPFAFVEFEDP 63

Query: 133 ACAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPR 168
             A  A+    GY       D   LR++F R+    
Sbjct: 64  RDAEDAVYGRDGYDY-----DGYRLRVEFPRSGRGT 94

>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 = 39.3 bits (91), Expect = 3e-05
 Identities = 13/86 (15%), Positives = 30/86 (34%), Gaps = 4/86 (4%)

Query: 78  STLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAAT 137
             L++ G+P    + E+            + +++  S           FV++E+   AA 
Sbjct: 2   CRLFIGGIPKMKKREEILEEIAKV-TEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAM 60

Query: 138 ALSALQGYRMDEDDPDSKFLRLQFSR 163
           A   L   R+         + + ++ 
Sbjct: 61  ARRKLMPGRI---QLWGHQIAVDWAE 83

>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 = 38.4 bits (89), Expect = 3e-05
 Identities = 14/69 (20%), Positives = 25/69 (36%), Gaps = 4/69 (5%)

Query: 80  LYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATAL 139
           +++ GL   +T+  +   F  F   KE  ++               FV F + A     L
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDP---LTKRSRGFGFVTFMDQAGVDKVL 59

Query: 140 SALQGYRMD 148
            A   + +D
Sbjct: 60  -AQSRHELD 67

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 38.6 bits (89), Expect = 3e-05
 Identities = 16/85 (18%), Positives = 31/85 (36%), Gaps = 8/85 (9%)

Query: 79  TLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATA 138
           TL++   P   T+R +  + +       V L I+   LR        ++D  +   A   
Sbjct: 3   TLWMTNFPPSYTQRNIRDLLQD---INVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYC 59

Query: 139 LSALQGYRMDEDDPDSKFLRLQFSR 163
           +  L G ++     +   L  + S 
Sbjct: 60  VEKLNGLKI-----EGYTLVTKVSN 79

>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 = 38.6 bits (89), Expect = 3e-05
 Identities = 9/89 (10%), Positives = 36/89 (40%), Gaps = 7/89 (7%)

Query: 80  LYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATAL 139
           +++  L  +  ++ +   F  F    +   ++++     G+     F++F +   +  A+
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDP--DTGNSKGYAFINFASFDASDAAI 58

Query: 140 SALQGYRMDEDDPDSKFLRLQFSRNPGPR 168
            A+ G  +      ++ + + ++     +
Sbjct: 59  EAMNGQYL-----CNRPITVSYAFKKDSK 82

>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 = 38.5 bits (89), Expect = 3e-05
 Identities = 13/72 (18%), Positives = 24/72 (33%), Gaps = 3/72 (4%)

Query: 77  SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAA 136
            + + V+ +P   +  E+   F  +        +    K   G P     V FE+   A 
Sbjct: 9   PTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEK---GMPTGEAMVAFESRDEAT 65

Query: 137 TALSALQGYRMD 148
            A+  L    + 
Sbjct: 66  AAVIDLNDRPIG 77

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.5 bits (89), Expect = 5e-05
 Identities = 17/75 (22%), Positives = 27/75 (36%), Gaps = 5/75 (6%)

Query: 74  PDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPA 133
                 L+V  +P      ++  +F  F    +V ++  E            FV FEN A
Sbjct: 8   KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER-----GSKGFGFVTFENSA 62

Query: 134 CAATALSALQGYRMD 148
            A  A   L G  ++
Sbjct: 63  DADRAREKLHGTVVE 77

>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 = 38.1 bits (88), Expect = 6e-05
 Identities = 13/102 (12%), Positives = 28/102 (27%), Gaps = 15/102 (14%)

Query: 74  PDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPA 133
              SS ++V     D T+ E+   F  +    +V                  FV F +  
Sbjct: 2   SSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVF--------IPKPFRAFAFVTFADDQ 53

Query: 134 CAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPRSVFGARG 175
            A +     +   +         + +  +      +   + G
Sbjct: 54  IAQSLCG--EDLIIKG-----ISVHISNAEPKHNSNSGPSSG 88

>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 = 8e-05
 Identities = 15/69 (21%), Positives = 36/69 (52%), Gaps = 3/69 (4%)

Query: 80  LYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATAL 139
           LY+ GL   +T +++  + +P+      + ++ ++  +        FVDF++P+ A  A+
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGY---GFVDFDSPSAAQKAV 57

Query: 140 SALQGYRMD 148
           +AL+   + 
Sbjct: 58  TALKASGVQ 66

>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 = 37.8 bits (87), Expect = 1e-04
 Identities = 17/106 (16%), Positives = 40/106 (37%), Gaps = 8/106 (7%)

Query: 71  PLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFE 130
           P    +  +++V  +P ++T+ ++  IF         RLV      +        F +++
Sbjct: 2   PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGY---GFCEYQ 58

Query: 131 NPACAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPRSVFGARGR 176
           +   A +A+  L G          + LR+  + +   +    + G 
Sbjct: 59  DQETALSAMRNLNGREF-----SGRALRVDNAASEKNKEELKSLGT 99

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.4 bits (88), Expect = 1e-04
 Identities = 10/74 (13%), Positives = 22/74 (29%), Gaps = 3/74 (4%)

Query: 74  PDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPA 133
           P+    L++ GL  ++T   +   F  +     +   +              FV +    
Sbjct: 3   PEQLRKLFIGGLSFETTDESLRSHFEQW---GTLTDCVVMRDPNTKRSRGFGFVTYATVE 59

Query: 134 CAATALSALQGYRM 147
               A++A      
Sbjct: 60  EVDAAMNARPHKVD 73

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.4 bits (86), Expect = 1e-04
 Identities = 19/104 (18%), Positives = 35/104 (33%), Gaps = 14/104 (13%)

Query: 71  PLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFE 130
            LP     T ++  LP D T+  +   FR                          + +FE
Sbjct: 9   RLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPS---NPERLKGFGYAEFE 65

Query: 131 NPACAATALSALQGYRMDEDDPDSKFLRLQFS-----RNPGPRS 169
           +     +AL +L    +      +K +R+  +     ++ GP S
Sbjct: 66  DLDSLLSAL-SLNEESL-----GNKRIRVDVADQAQDKDSGPSS 103

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.6 bits (84), Expect = 1e-04
 Identities = 11/88 (12%), Positives = 27/88 (30%), Gaps = 10/88 (11%)

Query: 77  SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAA 136
           + ++Y++G P D+T  ++            +++                FV F++   A 
Sbjct: 6   NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT----LHKAFKGSIFVVFDSIESAK 61

Query: 137 TALSALQGYRMDEDDPDSKFLRLQFSRN 164
             +                 L + F  +
Sbjct: 62  KFV------ETPGQKYKETDLLILFKDD 83

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 35.9 bits (82), Expect = 3e-04
 Identities = 13/69 (18%), Positives = 27/69 (39%), Gaps = 4/69 (5%)

Query: 80  LYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATAL 139
           ++V GL  ++T  +V H F  F    +  L+  ++           FV FE+        
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTT---NRHRGFGFVTFESEDIVEKVC 58

Query: 140 SALQGYRMD 148
             +  + ++
Sbjct: 59  -EIHFHEIN 66

>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 = 36.3 bits (83), Expect = 3e-04
 Identities = 15/99 (15%), Positives = 32/99 (32%), Gaps = 10/99 (10%)

Query: 71  PLPPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFE 130
           P    +   + V GLP   + +++    R         +                 V++ 
Sbjct: 9   PPTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKDGM----------GMVEYL 58

Query: 131 NPACAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPRS 169
                  AL  L   +    + ++ ++R+   R+ GP S
Sbjct: 59  RKEDMEYALRKLDDTKFRSHEGETSYIRVYPERSSGPSS 97

>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 = 36.0 bits (82), Expect = 3e-04
 Identities = 15/97 (15%), Positives = 38/97 (39%), Gaps = 14/97 (14%)

Query: 73  PPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENP 132
            P  S  L++  LP + T+ EV  +  PF     + ++  +++          F++    
Sbjct: 6   AP--SRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQ---------AFLELATE 54

Query: 133 ACAATALSALQGYRMDEDDPDSKFLRLQFSRNPGPRS 169
             A T ++          +   + + +Q+S +   ++
Sbjct: 55  EAAITMVNYYSAVTPHLRN---QPIYIQYSNHKELKT 88

>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 = 35.0 bits (80), Expect = 5e-04
 Identities = 20/90 (22%), Positives = 35/90 (38%), Gaps = 16/90 (17%)

Query: 74  PDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPA 133
           P   +TLYV G     T   +   F PF    ++ +    +           FV +E   
Sbjct: 2   PRKGNTLYVYGEDM--TPTLLRGAFSPFGNIIDLSMDPPRNC---------AFVTYEKME 50

Query: 134 CAATALSALQGYRMDEDDPDSKFLRLQFSR 163
            A  A++ L G ++     +S  L++  +R
Sbjct: 51  SADQAVAELNGTQV-----ESVQLKVNIAR 75

>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 = 35.0 bits (80), Expect = 5e-04
 Identities = 12/69 (17%), Positives = 28/69 (40%), Gaps = 4/69 (5%)

Query: 80  LYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATAL 139
           +++ GL  D+TK+++   F  F    +  L +       G      FV F+        +
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDP---ITGRSRGFGFVLFKESESVDKVM 58

Query: 140 SALQGYRMD 148
              + ++++
Sbjct: 59  -DQKEHKLN 66

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.4 bits (81), Expect = 6e-04
 Identities = 8/85 (9%), Positives = 25/85 (29%), Gaps = 9/85 (10%)

Query: 78  STLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAAT 137
           S + ++    +  +     +   +   +E+ +            +   +V F     A  
Sbjct: 28  SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLG----DHLVGNVYVKFRREEDAEK 83

Query: 138 ALSALQGYRMDEDDPDSKFLRLQFS 162
           A+  L          + + +  + S
Sbjct: 84  AVIDLNNRWF-----NGQPIHAELS 103

>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 = 35.0 bits (80), Expect = 6e-04
 Identities = 18/92 (19%), Positives = 34/92 (36%), Gaps = 13/92 (14%)

Query: 78  STLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAAT 137
           + LY+  L    T  ++  +F           V+ +    G       FVD+ +   A  
Sbjct: 2   NKLYIGNLSPAVTADDLRQLFGDR-KLPLAGQVLLK---SG-----YAFVDYPDQNWAIR 52

Query: 138 ALSALQGYRMDEDDPDSKFLRLQFSRNPGPRS 169
           A+  L G    + +   K + + +S +   RS
Sbjct: 53  AIETLSG----KVELHGKIMEVDYSVSKKLRS 80

>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 = 35.5 bits (81), Expect = 6e-04
 Identities = 16/93 (17%), Positives = 37/93 (39%), Gaps = 14/93 (15%)

Query: 77  SSTLYVEGLPADS-TKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACA 135
           +S L V  L  +  T + +  +F  +   + V+++         +      V   +   A
Sbjct: 2   NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILF--------NKKENALVQMADGNQA 53

Query: 136 ATALSALQGYRMDEDDPDSKFLRLQFSRNPGPR 168
             A+S L G+++       K +R+  S++   +
Sbjct: 54  QLAMSHLNGHKL-----HGKPIRITLSKHQNVQ 81

>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 = 35.2 bits (80), Expect = 8e-04
 Identities = 16/107 (14%), Positives = 30/107 (28%), Gaps = 11/107 (10%)

Query: 73  PPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENP 132
              A    ++  +P   TK +V                +       G  L    V F+N 
Sbjct: 4   VNSAKVCAHITNIPFSITKMDVLQFLEGIPV---DENAVHVLVDNNGQGLGQALVQFKNE 60

Query: 133 ACAATALSALQGYRMD----EDDPDSKFLRLQFSRNPGPRSVFGARG 175
             A  +   L   +++         +     +  +NP  +   G  G
Sbjct: 61  DDARKSE-RLHRKKLNGREAFVHVVTLEDMREIEKNPPAQ---GKSG 103

>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 = 34.9 bits (79), Expect = 0.001
 Identities = 14/71 (19%), Positives = 21/71 (29%), Gaps = 9/71 (12%)

Query: 77  SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAA 136
            + +  + LPA +   E+   F  F     V L                 V+F  P  A 
Sbjct: 10  KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGIT---------AIVEFLEPLEAR 60

Query: 137 TALSALQGYRM 147
            A   L   + 
Sbjct: 61  KAFRHLAYSKF 71

>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 = 34.6 bits (79), Expect = 0.001
 Identities = 16/92 (17%), Positives = 34/92 (36%), Gaps = 9/92 (9%)

Query: 77  SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAA 136
           + T++   L A    R++   F      ++VR++   +  R      + +V+F     + 
Sbjct: 18  ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRR---SKGIAYVEFCEIQ-SV 73

Query: 137 TALSALQGYRMDEDDPDSKFLRLQFSRNPGPR 168
                L G R+         + +Q S+    R
Sbjct: 74  PLAIGLTGQRL-----LGVPIIVQASQAEKNR 100

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.3 bits (78), Expect = 0.001
 Identities = 21/92 (22%), Positives = 36/92 (39%), Gaps = 8/92 (8%)

Query: 77  SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAA 136
              L+V GL  D+ ++ +  +F  +    EV +V      R        FV FEN   A 
Sbjct: 5   EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGF---GFVTFENIDDAK 61

Query: 137 TALSALQGYRMDEDDPDSKFLRLQFSRNPGPR 168
            A+ A+ G  +     D + +R+  +      
Sbjct: 62  DAMMAMNGKSV-----DGRQIRVDQAGKSSDN 88

>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 = 34.3 bits (78), Expect = 0.002
 Identities = 11/75 (14%), Positives = 29/75 (38%), Gaps = 4/75 (5%)

Query: 74  PDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPA 133
            +    L++ GL  ++T+  + + +  +    +  ++               FV F + A
Sbjct: 17  KEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDP---ASKRSRGFGFVTFSSMA 73

Query: 134 CAATALSALQGYRMD 148
               A+ A + + +D
Sbjct: 74  EVDAAM-AARPHSID 87

>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 = 0.002
 Identities = 10/62 (16%), Positives = 22/62 (35%), Gaps = 3/62 (4%)

Query: 80  LYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATAL 139
           ++V GL  D+ + ++   F  F   + + L +             CF+ F+        +
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKT---NKRRGFCFITFKEEEPVKKIM 58

Query: 140 SA 141
             
Sbjct: 59  EK 60

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	177
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.9
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.9
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.9
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.9
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.89
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.89
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.89
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.89
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.89
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.89
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.89
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.89
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.88
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.88
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.88
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.87
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.87
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.87
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.87
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.87
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.87
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.87
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.87
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.86
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.86
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.86
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.86
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.86
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.86
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.86
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.86
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.86
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.86
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.86
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.85
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.85
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.85
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.85
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.85
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.85
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.85
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.84
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.84
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.84
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.84
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.83
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.83
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.83
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.83
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.83
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.83
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.83
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.83
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.83
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.83
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.82
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.82
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.82
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.82
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.82
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.82
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.82
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.81
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.81
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.81
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.81
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.81
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.8
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.8
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.8
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.8
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.78
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.78
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.76
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.76
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.75
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.75
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.7
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.69
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.69
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.68
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	U2	99.63
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.59
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.54
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.51
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.43
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.42
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	98.13
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.3
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.23
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	97.05

>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=99.90  E-value=1.9e-23  Score=142.73  Aligned_cols=89  Identities=22%  Similarity=0.322  Sum_probs=79.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      +++|||+|||+++|+++|+++|++||.|.+|+|+.++   .+++++|||||+|.+.++|++|++.||++.|.+     |.
T Consensus         8 ~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~---~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~g-----r~   79 (99)
T d1whwa_           8 SGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDS---LTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQG-----RM   79 (99)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCT---TTCCCCSEEEEEESSHHHHHHHHHHTTTEESSS-----CE
T ss_pred             CCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccc---cccccCcceEEEECCHHHHHHHHHHcCCCEECC-----EE
Confidence            6789999999999999999999999999999998876   678899999999999999999999999999976     58


Q ss_pred             eEEEeecCCCCCCCCCC
Q 030444          157 LRLQFSRNPGPRSVFGA  173 (177)
Q Consensus       157 l~V~~a~~~~~r~~~g~  173 (177)
                      |+|++++.+......++
T Consensus        80 i~V~~a~~~~~~~~~gp   96 (99)
T d1whwa_          80 LHVLPSTIKKEASQSGP   96 (99)
T ss_dssp             EEEEECCCCSTTCCCCC
T ss_pred             EEEEECCCCCccCCCCC
Confidence            99999988755544333

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.90  E-value=2.3e-23  Score=140.05  Aligned_cols=83  Identities=23%  Similarity=0.483  Sum_probs=76.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCC
Q 030444           75 DASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDS  154 (177)
Q Consensus        75 ~~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~  154 (177)
                      ++.++|||+|||+++|+++|+++|++||.|.+|+|+.++   .+++++|||||+|.+.++|++|++.||++.|.+     
T Consensus         6 ~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~---~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g-----   77 (90)
T d2cq0a1           6 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDK---TTGQSKGFAFISFHRREDAARAIAGVSGFGYDH-----   77 (90)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECS---SSCSEEEEEEEEESSHHHHHHHHHHTTTCEETT-----
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccc---cccccccceeEEECCHHHHHHHHHHhCCCEECC-----
Confidence            346899999999999999999999999999999999887   678999999999999999999999999999966     


Q ss_pred             cceEEEeecCC
Q 030444          155 KFLRLQFSRNP  165 (177)
Q Consensus       155 r~l~V~~a~~~  165 (177)
                      +.|+|+||+++
T Consensus        78 ~~i~v~~akp~   88 (90)
T d2cq0a1          78 LILNVEWAKPS   88 (90)
T ss_dssp             EECEEEESSCC
T ss_pred             EEEEEEeeeCC
Confidence            58999999754

>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=99.90  E-value=1.5e-23  Score=140.42  Aligned_cols=81  Identities=19%  Similarity=0.283  Sum_probs=76.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|.+|+++.++   .+|+++|||||+|.+.++|++|++.|||..|.+     +.
T Consensus         7 ~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~---~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g-----~~   78 (88)
T d1rk8a_           7 GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDR---RTGFSKGYALVEYETHKQALAAKEALNGAEIMG-----QT   78 (88)
T ss_dssp             CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT---TTSSEEEEEEEEESSHHHHHHHHHHHTTCEETT-----EE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccc---cccccccceeEEECCHHHHHHHHHHcCCCEECC-----EE
Confidence            6899999999999999999999999999999999886   678999999999999999999999999999966     58


Q ss_pred             eEEEeecCC
Q 030444          157 LRLQFSRNP  165 (177)
Q Consensus       157 l~V~~a~~~  165 (177)
                      |+|+||.++
T Consensus        79 l~V~~a~~k   87 (88)
T d1rk8a_          79 IQVDWCFVK   87 (88)
T ss_dssp             CEEEESEEC
T ss_pred             EEEEEecCC
Confidence            999999765

>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=99.90  E-value=9e-24  Score=139.44  Aligned_cols=79  Identities=28%  Similarity=0.445  Sum_probs=74.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      +++|||+|||+++|+++|+++|++||.|.+++|+.++   .+++++|||||+|.+.++|++|++.||++.+.+     +.
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~---~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g-----~~   73 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDY---KTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRN-----KR   73 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEET---TTTEECSEEEEEESSHHHHHHHHHHHTTCEETT-----EE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeec---ccCCccccceEEECCHHHHHHHHHHhCCCEECC-----EE
Confidence            5789999999999999999999999999999999876   578899999999999999999999999999966     58


Q ss_pred             eEEEeec
Q 030444          157 LRLQFSR  163 (177)
Q Consensus       157 l~V~~a~  163 (177)
                      |+|+||+
T Consensus        74 l~v~~a~   80 (82)
T d1b7fa1          74 LKVSYAR   80 (82)
T ss_dssp             CEEEECC
T ss_pred             EEEEEcC
Confidence            9999995

>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=99.89  E-value=9.5e-24  Score=141.62  Aligned_cols=83  Identities=19%  Similarity=0.332  Sum_probs=76.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .+||||+|||+++|+++|+++|++||.|.+|+|+.++   .+++++|||||+|.+.++|++|++.||+..|.+     +.
T Consensus         5 ~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~---~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g-----~~   76 (89)
T d2cqba1           5 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDY---ETEKHRGFAFVEFELAEDAAAAIDNMNESELFG-----RT   76 (89)
T ss_dssp             CSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCS---SSCCCSSEEEECCSSHHHHHHHHHHHTTEEETT-----EE
T ss_pred             CcEEEEeCCCCcCCHHHHHHHHhhCCeEEeccccccc---ccccccceeEEEECCHHHHHHHHHHcCCCEECC-----EE
Confidence            6899999999999999999999999999999999887   678999999999999999999999999999976     58


Q ss_pred             eEEEeecCCCC
Q 030444          157 LRLQFSRNPGP  167 (177)
Q Consensus       157 l~V~~a~~~~~  167 (177)
                      |+|+||+++..
T Consensus        77 l~v~~a~p~~~   87 (89)
T d2cqba1          77 IRVNLAKPMRI   87 (89)
T ss_dssp             EEEEECCCCCC
T ss_pred             EEEEEeCCCCC
Confidence            99999976543

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.89  E-value=3.3e-23  Score=140.12  Aligned_cols=81  Identities=23%  Similarity=0.401  Sum_probs=75.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      ++||||+|||+++|+++|+++|++||.|.+|+++.++   .++.++|||||+|.+.++|+.|++.||+..|++     ++
T Consensus         7 s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~---~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g-----r~   78 (93)
T d1h2vz_           7 SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDK---MKKTACGFCFVEYYSRADAENAMRYINGTRLDD-----RI   78 (93)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT---TTCCEEEEEEEEESSHHHHHHHHHHTTTSEETT-----EE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHCCcceecccccc---ccccccceEEEEECCHHHHHHHHHHhCCCEECC-----EE
Confidence            7899999999999999999999999999999999987   678899999999999999999999999999966     58


Q ss_pred             eEEEeecCC
Q 030444          157 LRLQFSRNP  165 (177)
Q Consensus       157 l~V~~a~~~  165 (177)
                      |+|+|+...
T Consensus        79 i~V~~a~~~   87 (93)
T d1h2vz_          79 IRTDWDAGF   87 (93)
T ss_dssp             CEEEEESCC
T ss_pred             EEEEEcCCC
Confidence            999999643

>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=99.89  E-value=4.1e-23  Score=137.28  Aligned_cols=80  Identities=24%  Similarity=0.370  Sum_probs=74.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      +++|||+|||+++||++|+++|++||.|.+++|+.++   .+++++|||||+|.+.++|++|++.||+..+.+.   .++
T Consensus         6 ~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~---~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~---~~~   79 (85)
T d1b7fa2           6 DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDK---LTGRPRGVAFVRYNKREEAQEAISALNNVIPEGG---SQP   79 (85)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECT---TTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTC---SSC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeeccc---ccccCceeEEEEECCHHHHHHHHHHHCCCEeCCC---CeE
Confidence            5789999999999999999999999999999999887   6789999999999999999999999999999873   368


Q ss_pred             eEEEee
Q 030444          157 LRLQFS  162 (177)
Q Consensus       157 l~V~~a  162 (177)
                      |+|+||
T Consensus        80 l~V~~A   85 (85)
T d1b7fa2          80 LSVRLA   85 (85)
T ss_dssp             CEEEEC
T ss_pred             EEEEEC
Confidence            999997

>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=99.89  E-value=3.2e-23  Score=137.94  Aligned_cols=80  Identities=23%  Similarity=0.451  Sum_probs=74.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      +++|||+|||+++|+++|+++|++||.|.+++|+.++   .+++++|||||+|.+.++|++|++.|||..+.+.   .++
T Consensus         6 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~---~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~---~~~   79 (85)
T d1fxla2           6 DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQ---VTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGA---TEP   79 (85)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT---TTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTC---SSC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccccc---ccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCC---CEE
Confidence            5789999999999999999999999999999999986   5788999999999999999999999999999874   357


Q ss_pred             eEEEee
Q 030444          157 LRLQFS  162 (177)
Q Consensus       157 l~V~~a  162 (177)
                      |+|+||
T Consensus        80 i~V~~A   85 (85)
T d1fxla2          80 ITVKFA   85 (85)
T ss_dssp             CEEEEC
T ss_pred             EEEEeC
Confidence            999997

>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=99.89  E-value=3.1e-23  Score=140.24  Aligned_cols=82  Identities=17%  Similarity=0.180  Sum_probs=76.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|.+|+|+.++   .++.++|||||+|.+.++|++|++.||++.|.+     +.
T Consensus         9 ~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~---~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g-----~~   80 (93)
T d1x5ua1           9 DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDR---VTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYG-----KP   80 (93)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCS---SSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSS-----CB
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecc---cccccccceEEEECCHHHHHHHHHHcCCCEECC-----EE
Confidence            6899999999999999999999999999999999887   678999999999999999999999999999976     47


Q ss_pred             eEEEeecCCC
Q 030444          157 LRLQFSRNPG  166 (177)
Q Consensus       157 l~V~~a~~~~  166 (177)
                      |+|+||+...
T Consensus        81 l~V~~A~~~~   90 (93)
T d1x5ua1          81 IRVNKASAHN   90 (93)
T ss_dssp             CEEEETTTTS
T ss_pred             EEEEEcCCCC
Confidence            9999997653

>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=99.89  E-value=5.8e-23  Score=148.31  Aligned_cols=86  Identities=19%  Similarity=0.341  Sum_probs=79.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      ..++|||+|||+++|+++|+++|++||.|.+|+|+.++   .+++++|||||+|.+.++|+.||+.||++.|.+     |
T Consensus        41 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~---~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~g-----r  112 (139)
T d1u6fa1          41 VLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDR---ETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILN-----K  112 (139)
T ss_dssp             TTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEET---TTTEEEEEEEEEESSHHHHHHHHHHTTTEECSS-----C
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhcccccccccccc---ccccccceeeEEECCHHHHHHHHHHhCCCEECC-----E
Confidence            36789999999999999999999999999999999887   678899999999999999999999999999976     5


Q ss_pred             ceEEEeecCCCCCC
Q 030444          156 FLRLQFSRNPGPRS  169 (177)
Q Consensus       156 ~l~V~~a~~~~~r~  169 (177)
                      .|+|+||+...+|.
T Consensus       113 ~l~V~~a~~~~~~p  126 (139)
T d1u6fa1         113 RLKVALAASGHQRP  126 (139)
T ss_dssp             EEEEEESSCCCCCC
T ss_pred             EEEEEEcCCCCCCC
Confidence            89999998776664

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.89  E-value=4.2e-23  Score=141.87  Aligned_cols=84  Identities=21%  Similarity=0.488  Sum_probs=77.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      +++|||+|||+++|+++|+++|++||.|.+++++.++   .++.++|||||+|.+.++|+.||+.||++.|.+     ++
T Consensus        18 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~---~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g-----~~   89 (102)
T d2cpza1          18 GANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDK---QTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGM-----KR   89 (102)
T ss_dssp             TCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECS---SSCSEEEEEEEECSSHHHHHHHHHHHTTCEETT-----EE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeec---ccCCCccceEEEeCCHHHHHHHHHHhCCCEECC-----EE
Confidence            5789999999999999999999999999999999887   678999999999999999999999999999966     58


Q ss_pred             eEEEeecCCCCC
Q 030444          157 LRLQFSRNPGPR  168 (177)
Q Consensus       157 l~V~~a~~~~~r  168 (177)
                      |+|+|++++..+
T Consensus        90 i~V~~a~~k~~~  101 (102)
T d2cpza1          90 LKVQLKRSKNDS  101 (102)
T ss_dssp             CEEECCCCSCCC
T ss_pred             EEEEEeCCCCCC
Confidence            999999876543

>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=99.89  E-value=4.3e-23  Score=136.05  Aligned_cols=80  Identities=26%  Similarity=0.467  Sum_probs=74.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|.+|+++.+.   .+++++|||||+|.+.++|++|++.||+..+.+     ++
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~---~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g-----~~   73 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDK---ITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQT-----KT   73 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT---TTCCEEEEEEEEESSHHHHHHHHHHHTTCEETT-----EE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeec---cCCCceeeEEEEECCHHHHHHHHHHhCCCEECC-----EE
Confidence            3679999999999999999999999999999999876   568899999999999999999999999999976     58


Q ss_pred             eEEEeecC
Q 030444          157 LRLQFSRN  164 (177)
Q Consensus       157 l~V~~a~~  164 (177)
                      |+|+||++
T Consensus        74 l~v~~AkP   81 (82)
T d1fxla1          74 IKVSYARP   81 (82)
T ss_dssp             CEEEECCC
T ss_pred             EEEEEeeC
Confidence            99999964

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.88  E-value=8e-23  Score=136.00  Aligned_cols=80  Identities=21%  Similarity=0.333  Sum_probs=74.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcce
Q 030444           78 STLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFL  157 (177)
Q Consensus        78 ~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~l  157 (177)
                      .+|||+|||+++||++|+++|++||.|.+|+|+.++   .+|+++|||||+|.+.++|+.|++.||++.|.+     ++|
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~---~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g-----~~l   73 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDS---ATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGD-----KKL   73 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCC---SSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSS-----SCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccc---cccccceeEEEEECCHHHHHHHHHHhCCCEECC-----EEE
Confidence            479999999999999999999999999999999987   678999999999999999999999999999976     479


Q ss_pred             EEEeecCC
Q 030444          158 RLQFSRNP  165 (177)
Q Consensus       158 ~V~~a~~~  165 (177)
                      +|+||+..
T Consensus        74 ~V~~A~~~   81 (85)
T d2u2fa_          74 LVQRASVG   81 (85)
T ss_dssp             EEEECCCC
T ss_pred             EEEECCCC
Confidence            99999654

>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=99.88  E-value=1.1e-22  Score=134.54  Aligned_cols=76  Identities=25%  Similarity=0.355  Sum_probs=70.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      ++++|||+|||+++|+++|+++|++||.|.+|+|+.++   .+++++|||||+|.+.++|++|++.||+..|.+     |
T Consensus         8 ~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~---~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g-----r   79 (83)
T d2cqca1           8 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQ---QSRRSRGFAFVYFENVDDAKEAKERANGMELDG-----R   79 (83)
T ss_dssp             GGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECS---SSSSEEEEEEEEESSHHHHHHHHHHHTTEEETT-----E
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccc---cccccccceEEEECCHHHHHHHHHHcCCCEECC-----E
Confidence            37899999999999999999999999999999999887   678999999999999999999999999999976     4


Q ss_pred             ceEE
Q 030444          156 FLRL  159 (177)
Q Consensus       156 ~l~V  159 (177)
                      .|+|
T Consensus        80 ~i~V   83 (83)
T d2cqca1          80 RIRV   83 (83)
T ss_dssp             EEEE
T ss_pred             EeEC
Confidence            7876

>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=99.88  E-value=5.9e-23  Score=135.06  Aligned_cols=77  Identities=26%  Similarity=0.326  Sum_probs=72.9

Q ss_pred             eEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcceE
Q 030444           79 TLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFLR  158 (177)
Q Consensus        79 tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~l~  158 (177)
                      +|||+|||+++||++|+++|++||.|.+|+|+.++   .+++++|||||+|.+.++|+.|++.|||..+.+     |+|+
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~---~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~g-----r~i~   73 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDM---ITRRSLGYAYVNFQQPADAERALDTMNFDVIKG-----KPVR   73 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT---TTCCEEEEEEEEESSHHHHHHHHTTSTTCEETT-----EECE
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecc---cccCCCCceEEEECCHHHHHHHHHHcCCCEECC-----EEEE
Confidence            69999999999999999999999999999999987   678999999999999999999999999999966     5899


Q ss_pred             EEeec
Q 030444          159 LQFSR  163 (177)
Q Consensus       159 V~~a~  163 (177)
                      |+||+
T Consensus        74 v~~a~   78 (80)
T d1cvja1          74 IMWSQ   78 (80)
T ss_dssp             EEECC
T ss_pred             EEEeC
Confidence            99995

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.87  E-value=1e-22  Score=135.19  Aligned_cols=81  Identities=23%  Similarity=0.340  Sum_probs=72.6

Q ss_pred             EEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcceEE
Q 030444           80 LYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFLRL  159 (177)
Q Consensus        80 LfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~l~V  159 (177)
                      |||+|||+++|+++|+++|++||.|.+|+|+.++.+...+.++|||||+|.+.++|++|++.||++.|.+     +.|+|
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g-----~~i~V   75 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDG-----HKLEV   75 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETT-----EECEE
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECC-----EEEEE
Confidence            8999999999999999999999999999999887443344679999999999999999999999999976     58999


Q ss_pred             EeecCC
Q 030444          160 QFSRNP  165 (177)
Q Consensus       160 ~~a~~~  165 (177)
                      +||+..
T Consensus        76 ~~a~~~   81 (85)
T d2cpfa1          76 RISERA   81 (85)
T ss_dssp             ECSSCS
T ss_pred             EECCCC
Confidence            999643

>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=99.87  E-value=3.7e-22  Score=135.12  Aligned_cols=82  Identities=28%  Similarity=0.401  Sum_probs=74.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHh-CCCeeCCCCCCCc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSAL-QGYRMDEDDPDSK  155 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l-~g~~l~~~~~~~r  155 (177)
                      +++|||+|||+++++++|+++|++||.|.+|+|+.+..  .+|+++|||||+|.+.++|++|++.| |+..|.+     +
T Consensus         8 ~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~--~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~G-----r   80 (94)
T d2cpha1           8 TSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMT--GTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYG-----R   80 (94)
T ss_dssp             CCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCS--SSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSS-----C
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccc--cCCCcccEEEEEECCHHHHHHHHHHccCCcEECC-----E
Confidence            68899999999999999999999999999999987641  36889999999999999999999998 8999966     5


Q ss_pred             ceEEEeecCC
Q 030444          156 FLRLQFSRNP  165 (177)
Q Consensus       156 ~l~V~~a~~~  165 (177)
                      +|+|+||+..
T Consensus        81 ~l~V~~A~~~   90 (94)
T d2cpha1          81 RLVLEWADSE   90 (94)
T ss_dssp             BCEEEECCCC
T ss_pred             EEEEEEcCCC
Confidence            8999999765

>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=99.87  E-value=5.6e-22  Score=136.35  Aligned_cols=88  Identities=19%  Similarity=0.285  Sum_probs=74.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCC
Q 030444           74 PDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPD  153 (177)
Q Consensus        74 ~~~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~  153 (177)
                      ..+.++|||+|||+++|+++|+++|++|| +.+++++.++  ..+++++|||||+|.+.++|++|+ .||++.|.+    
T Consensus        12 ~~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~--~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~~~g----   83 (104)
T d1wi8a_          12 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREP--SNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGN----   83 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCS--SCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETT----
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeee--ccCCCcceeeeEEECCHHHHHHHH-HcCCCEECC----
Confidence            33468999999999999999999999998 7788777654  246789999999999999998776 599999966    


Q ss_pred             CcceEEEeecCCCCCCC
Q 030444          154 SKFLRLQFSRNPGPRSV  170 (177)
Q Consensus       154 ~r~l~V~~a~~~~~r~~  170 (177)
                       |.|+|+||+.+..+..
T Consensus        84 -r~l~V~~a~~~~~~~~   99 (104)
T d1wi8a_          84 -KRIRVDVADQAQDKDS   99 (104)
T ss_dssp             -EECEEEECCCCCCCCC
T ss_pred             -EEEEEEECCCCCCCCC
Confidence             5899999987655543

>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=99.87  E-value=2.5e-22  Score=134.86  Aligned_cols=82  Identities=26%  Similarity=0.439  Sum_probs=73.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .+||||+|||+++|+++|+++|++||.|.+|+|+.++   .+  .++||||+|.+.++|+.|++.||+..|.+     +.
T Consensus         8 ~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~---~~--~~~~afV~f~~~~~A~~A~~~l~~~~~~g-----~~   77 (90)
T d2cqia1           8 PRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEH---TS--NDPYCFVEFYEHRDAAAALAAMNGRKILG-----KE   77 (90)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCC---CS--SCCEEEEEESSHHHHHHHHHHHTTEEETT-----EE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeeccc---Cc--cceeeEEEECCHHHHHHHHHHcCCCEECC-----EE
Confidence            5899999999999999999999999999999998876   22  36899999999999999999999999976     58


Q ss_pred             eEEEeecCCCCC
Q 030444          157 LRLQFSRNPGPR  168 (177)
Q Consensus       157 l~V~~a~~~~~r  168 (177)
                      |+|+||+++..+
T Consensus        78 i~v~~a~~~~~~   89 (90)
T d2cqia1          78 VKVNWATTPSSQ   89 (90)
T ss_dssp             EEEEECCCTTCC
T ss_pred             EEEEEcCCCCCC
Confidence            999999876544

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=2.2e-22  Score=134.98  Aligned_cols=82  Identities=24%  Similarity=0.381  Sum_probs=75.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|..+.++.++   .++.++|||||+|.+.++|+.|++.||++.|.+     ++
T Consensus         5 ~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~---~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g-----~~   76 (90)
T d1x5sa1           5 EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDR---ETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDG-----RQ   76 (90)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCS---SSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTS-----CC
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccceeecccc---ccccccceEEEEECCHHHHHHHHHHcCCCEECC-----EE
Confidence            6889999999999999999999999999999988876   578899999999999999999999999999976     47


Q ss_pred             eEEEeecCCC
Q 030444          157 LRLQFSRNPG  166 (177)
Q Consensus       157 l~V~~a~~~~  166 (177)
                      |+|+||..+.
T Consensus        77 l~V~~a~~~~   86 (90)
T d1x5sa1          77 IRVDQAGKSS   86 (90)
T ss_dssp             CEEEEEECCC
T ss_pred             EEEEEcCCCC
Confidence            9999997653

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=9.9e-23  Score=136.57  Aligned_cols=82  Identities=16%  Similarity=0.295  Sum_probs=74.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      ..+|||+|||+++|+++|+++|++||.|.+++|+.++     +.++|||||+|++.++|++|++.|||..|.+     +.
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~-----~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g-----~~   77 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE-----NGSKGYGFVHFETQEAAERAIEKMNGMLLND-----RK   77 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBT-----TBCCSCEEEEESCHHHHHHHTTSSSEEEETT-----EE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeec-----CCCcceeEEEECCHHHHHHHHHHcCCCEECC-----EE
Confidence            4689999999999999999999999999999998875     3467899999999999999999999999966     58


Q ss_pred             eEEEeecCCCCC
Q 030444          157 LRLQFSRNPGPR  168 (177)
Q Consensus       157 l~V~~a~~~~~r  168 (177)
                      |+|++++++.+|
T Consensus        78 i~V~~a~~~~~R   89 (89)
T d1cvja2          78 VFVGRFKSRKER   89 (89)
T ss_dssp             EEEEECCCTTTC
T ss_pred             EEEEECCCCCCC
Confidence            999999876554

>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=99.87  E-value=1.1e-22  Score=134.50  Aligned_cols=81  Identities=11%  Similarity=0.294  Sum_probs=72.6

Q ss_pred             EEEcCCCCCCCHHHHHHhhCCCCCEEEE-EEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcceE
Q 030444           80 LYVEGLPADSTKREVAHIFRPFVGYKEV-RLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFLR  158 (177)
Q Consensus        80 LfV~nLp~~~te~~L~~lF~~~G~i~~v-~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~l~  158 (177)
                      |||+|||+++|+++|+++|++||.|.++ +++.++   .+++++|||||+|.+.++|++|++.||+..+.+     ++|+
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~---~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~g-----r~l~   72 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDP---DTGNSKGYAFINFASFDASDAAIEAMNGQYLCN-----RPIT   72 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCT---TTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETT-----EECE
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeec---cccccCceEEEEECCHHHHHHHHHhCCCcEECC-----EEEE
Confidence            8999999999999999999999998664 677665   578899999999999999999999999999966     5899


Q ss_pred             EEeecCCCCC
Q 030444          159 LQFSRNPGPR  168 (177)
Q Consensus       159 V~~a~~~~~r  168 (177)
                      |+||.++..+
T Consensus        73 v~~a~~k~~k   82 (83)
T d1x5ta1          73 VSYAFKKDSK   82 (83)
T ss_dssp             EEESCCCCCC
T ss_pred             EEEecCCCcC
Confidence            9999876554

>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=99.87  E-value=2.8e-22  Score=131.21  Aligned_cols=77  Identities=22%  Similarity=0.317  Sum_probs=71.8

Q ss_pred             eEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcceE
Q 030444           79 TLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFLR  158 (177)
Q Consensus        79 tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~l~  158 (177)
                      +|||+|||+++|+++|+++|++||.|.+++|..++    +++++|||||+|.+.++|++|++.|||..+.+     ++|+
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~----~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g-----~~l~   72 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR----SGRSLGTADVHFERKADALKAMKQYNGVPLDG-----RPMN   72 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSS----CCCSCCEEEEEESCHHHHHHHHHHHTTCEETT-----EECE
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEee----ccccceeEEEEECCHHHHHHHHHHhCCCEECC-----EEEE
Confidence            69999999999999999999999999999998875    68899999999999999999999999999966     5899


Q ss_pred             EEeecC
Q 030444          159 LQFSRN  164 (177)
Q Consensus       159 V~~a~~  164 (177)
                      |+|+.+
T Consensus        73 V~~a~S   78 (78)
T d1no8a_          73 IQLVTS   78 (78)
T ss_dssp             EEEECC
T ss_pred             EEEeeC
Confidence            999853

>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=99.86  E-value=1.4e-21  Score=131.96  Aligned_cols=79  Identities=22%  Similarity=0.313  Sum_probs=72.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|.+|+++.++     ..++|||||+|.+.++|++|++.||+..|.+     +.
T Consensus        11 ~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~-----~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g-----~~   80 (93)
T d2cq3a1          11 PKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE-----RGSKGFGFVTFENSADADRAREKLHGTVVEG-----RK   80 (93)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT-----TTTCCEEEEEESCHHHHHHHHHHHTTCEETT-----EE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccc-----cCCcceeEEEECCHHHHHHHHHHcCCCEECC-----EE
Confidence            5789999999999999999999999999999998875     3367999999999999999999999999976     58


Q ss_pred             eEEEeecCC
Q 030444          157 LRLQFSRNP  165 (177)
Q Consensus       157 l~V~~a~~~  165 (177)
                      |+|+||+++
T Consensus        81 l~V~~A~~r   89 (93)
T d2cq3a1          81 IEVNNATAR   89 (93)
T ss_dssp             CEEEECCSS
T ss_pred             EEEEecCcC
Confidence            999999765

>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=99.86  E-value=8.8e-23  Score=139.85  Aligned_cols=87  Identities=26%  Similarity=0.435  Sum_probs=78.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCC
Q 030444           75 DASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDS  154 (177)
Q Consensus        75 ~~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~  154 (177)
                      +++++|||+|||.++|+++|+++|++||.|..+.++.+.   .+++++|||||+|.+.++|+.|++.||+..|.+     
T Consensus        16 ~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~---~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g-----   87 (102)
T d2cpxa1          16 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRM---MTGRMRGQAFITFPNKEIAWQALHLVNGYKLYG-----   87 (102)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEE---ECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSS-----
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeeccc---ccccccccceEEeccHHHHHHHHHHhCCCEECC-----
Confidence            347999999999999999999999999999988887765   568899999999999999999999999999966     


Q ss_pred             cceEEEeecCCCCCC
Q 030444          155 KFLRLQFSRNPGPRS  169 (177)
Q Consensus       155 r~l~V~~a~~~~~r~  169 (177)
                      ++|+|+||+++..|+
T Consensus        88 ~~l~V~~ak~k~~rs  102 (102)
T d2cpxa1          88 KILVIEFGKNKKQRS  102 (102)
T ss_dssp             CBCEEEECCCCSCCC
T ss_pred             EEEEEEeCCCcccCC
Confidence            589999998876653

>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=99.86  E-value=5.7e-22  Score=138.38  Aligned_cols=81  Identities=22%  Similarity=0.407  Sum_probs=72.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCC
Q 030444           73 PPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDP  152 (177)
Q Consensus        73 p~~~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~  152 (177)
                      |+..+++|||+|||+++|+++|+++|++||.|.+|++..+      +.++|||||+|.+.++|..|++.|||+.|.+   
T Consensus         3 pp~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~------~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~g---   73 (114)
T d2f9da1           3 PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT------PETRGTAYVVYEDIFDAKNACDHLSGFNVCN---   73 (114)
T ss_dssp             CTTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS------TTTTTEEEEEESSHHHHHHHHHHHTTCEETT---
T ss_pred             ccCCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc------CCcCCeEEEEECCHHHHHHHHHHhCCCEECC---
Confidence            4455899999999999999999999999999999998654      4567999999999999999999999999976   


Q ss_pred             CCcceEEEeecC
Q 030444          153 DSKFLRLQFSRN  164 (177)
Q Consensus       153 ~~r~l~V~~a~~  164 (177)
                        +.|+|+|+..
T Consensus        74 --r~l~V~~a~~   83 (114)
T d2f9da1          74 --RYLVVLYYNA   83 (114)
T ss_dssp             --EECEEEECCH
T ss_pred             --EEEEEEEcCC
Confidence              5899999854

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.86  E-value=1.9e-22  Score=132.70  Aligned_cols=79  Identities=15%  Similarity=0.211  Sum_probs=67.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcce
Q 030444           78 STLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFL  157 (177)
Q Consensus        78 ~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~l  157 (177)
                      +||||+|||+++|+++|+++|++||.|..+.++.++   ..++++|||||+|.+.++|++|++.||+..+.+     ++|
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~---~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g-----~~i   73 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSL---RFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEG-----YTL   73 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC----------CCEEEEECSSHHHHHHHHHHHTTCEETT-----EEC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeeccc---ccccccceeEEEECCHHHHHHHHHHhCCCEECC-----EEE
Confidence            799999999999999999999999999888877765   568899999999999999999999999999966     589


Q ss_pred             EEEeecC
Q 030444          158 RLQFSRN  164 (177)
Q Consensus       158 ~V~~a~~  164 (177)
                      +|+||++
T Consensus        74 ~V~~a~P   80 (81)
T d2ghpa1          74 VTKVSNP   80 (81)
T ss_dssp             EEEECCC
T ss_pred             EEEEccC
Confidence            9999964

>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=99.86  E-value=1.2e-21  Score=133.07  Aligned_cols=88  Identities=18%  Similarity=0.272  Sum_probs=73.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCC-CCCC
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDED-DPDS  154 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~-~~~~  154 (177)
                      +.++|||+|||+++|+++|+++|++||.|.+++++.++   .+++++|||||+|.+.++|++|++.||+...... ...+
T Consensus         7 ~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~---~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~g   83 (98)
T d1x4ha1           7 EGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHP---DTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDG   83 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCS---SSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSS
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHhccccceeeeecccc---ccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECC
Confidence            37899999999999999999999999999999998876   5678899999999999999999999974332211 1134


Q ss_pred             cceEEEeecCCC
Q 030444          155 KFLRLQFSRNPG  166 (177)
Q Consensus       155 r~l~V~~a~~~~  166 (177)
                      |.|+|+||+++.
T Consensus        84 r~l~v~~a~~k~   95 (98)
T d1x4ha1          84 RQLKVDLAVTRD   95 (98)
T ss_dssp             CEEEEECCCCCC
T ss_pred             EEEEEEECCCCC
Confidence            689999997654

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=3e-22  Score=137.79  Aligned_cols=81  Identities=21%  Similarity=0.395  Sum_probs=75.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|.+|+|+.++   .+++++|||||+|.+.++|++|++.||+..|.+     +.
T Consensus         8 ~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~---~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g-----~~   79 (104)
T d1p1ta_           8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDR---ETGKPKGYGFCEYQDQETALSAMRNLNGREFSG-----RA   79 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEET---TTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSS-----SC
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhcccccccccccccc---ceeccCCceEEEECCHHHHHHHHHHcCCCEECC-----EE
Confidence            5789999999999999999999999999999999887   678899999999999999999999999999976     47


Q ss_pred             eEEEeecCC
Q 030444          157 LRLQFSRNP  165 (177)
Q Consensus       157 l~V~~a~~~  165 (177)
                      |+|+||..+
T Consensus        80 i~V~~a~~~   88 (104)
T d1p1ta_          80 LRVDNAASE   88 (104)
T ss_dssp             BEEEETTCT
T ss_pred             EEEEECCCC
Confidence            999999765

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=8.5e-22  Score=134.54  Aligned_cols=84  Identities=24%  Similarity=0.409  Sum_probs=73.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEE--------EEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeC
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKE--------VRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMD  148 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~--------v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~  148 (177)
                      .++|||+|||+++|+++|+++|++||.|..        +.+..++   .+++++|||||+|.+.++|++|++.||++.|.
T Consensus         8 ~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~---~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~   84 (101)
T d2cpea1           8 NSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDK---ETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQ   84 (101)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCT---TTCSBCSEEEEEBSSHHHHHHHHHHHTTCEET
T ss_pred             CCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeecc---ccccccceeeEEecCHHHHHHHHHHhCCCEEC
Confidence            689999999999999999999999998753        3444443   56889999999999999999999999999996


Q ss_pred             CCCCCCcceEEEeecCCCCC
Q 030444          149 EDDPDSKFLRLQFSRNPGPR  168 (177)
Q Consensus       149 ~~~~~~r~l~V~~a~~~~~r  168 (177)
                      +     |.|+|+||+.++++
T Consensus        85 g-----r~i~V~~a~~~~p~   99 (101)
T d2cpea1          85 G-----SKLKVSLARKKPPM   99 (101)
T ss_dssp             T-----EECEEECSSCCCCS
T ss_pred             C-----EEEEEEEcCCCCCC
Confidence            6     58999999887655

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.86  E-value=1.5e-21  Score=129.06  Aligned_cols=75  Identities=28%  Similarity=0.594  Sum_probs=68.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      ++||||+|||+++|+++|+++|++||.|.+|+++.++        +|||||+|.+.++|+.|++.|||+.|.+.    ++
T Consensus         8 ~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~~~----~~   75 (83)
T d2b0ga1           8 NQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR--------HDIAFVEFTTELQSNAAKEALQGFKITPT----HA   75 (83)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTT--------CSCEEEEESSHHHHHHHHHHHTTCBSSTT----CB
T ss_pred             CCEEEEECCCCCCCHHHHHhhhccCccEEEeeeeccc--------ceeEEEecCCHHHHHHHHHHhCCcEeCCC----cE
Confidence            7999999999999999999999999999999997653        36999999999999999999999999643    47


Q ss_pred             eEEEeec
Q 030444          157 LRLQFSR  163 (177)
Q Consensus       157 l~V~~a~  163 (177)
                      |+|+||+
T Consensus        76 i~v~~ak   82 (83)
T d2b0ga1          76 MKITFAK   82 (83)
T ss_dssp             CEEEECC
T ss_pred             EEEEEec
Confidence            9999996

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=1.6e-21  Score=134.11  Aligned_cols=80  Identities=19%  Similarity=0.271  Sum_probs=72.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++||++|+++|++||.|.+|+|+.++   .+++++|||||+|.+.++|++|++.+|+ .|.+     |.
T Consensus        10 ~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~---~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~G-----r~   80 (103)
T d2cqda1          10 FTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDR---QTGKSRGYGFVTMADRAAAERACKDPNP-IIDG-----RK   80 (103)
T ss_dssp             SSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCS---SSCCCCSEEEEEESSHHHHHHHHTCSSC-EETT-----EE
T ss_pred             CcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccc---cccccCCeEEEEECCHHHHHHHHHHCCC-cCCC-----EE
Confidence            4679999999999999999999999999999999987   6789999999999999999999998876 6755     58


Q ss_pred             eEEEeecCC
Q 030444          157 LRLQFSRNP  165 (177)
Q Consensus       157 l~V~~a~~~  165 (177)
                      |+|++|..+
T Consensus        81 l~V~~a~~~   89 (103)
T d2cqda1          81 ANVNLAYLG   89 (103)
T ss_dssp             CEEEESTTT
T ss_pred             EEEEEcCCC
Confidence            999998654

>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=99.86  E-value=1.7e-21  Score=130.94  Aligned_cols=81  Identities=20%  Similarity=0.283  Sum_probs=72.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|.+|+|+.++   .+++++|||||+|.+.++|++||+.  .+.|++     +.
T Consensus         8 ~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~---~tg~srG~aFV~f~~~~~a~~al~~--~~~l~G-----r~   77 (90)
T d2cqga1           8 TSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDL---KTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDG-----RW   77 (90)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECS---SSCSEEEEEEEEESSHHHHHHHHHS--CEEETT-----EE
T ss_pred             CCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCC---CCcccCCEEEEEECCHHHHHHHHhc--CCccCC-----EE
Confidence            6889999999999999999999999999999999987   6799999999999999999999984  447755     58


Q ss_pred             eEEEeecCCCC
Q 030444          157 LRLQFSRNPGP  167 (177)
Q Consensus       157 l~V~~a~~~~~  167 (177)
                      |+|+++.++..
T Consensus        78 i~v~~a~~k~~   88 (90)
T d2cqga1          78 CDCKLPNSKQS   88 (90)
T ss_dssp             EEEECCCTTCC
T ss_pred             eEEEeCCCCCC
Confidence            99999976543

>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=99.86  E-value=1.4e-21  Score=132.31  Aligned_cols=78  Identities=27%  Similarity=0.522  Sum_probs=70.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      +++|||+|||+++|+++|+++|++||.|..+++..+      ..+++||||+|++.++|+.||+.||++.|.+     ++
T Consensus        14 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~------~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g-----~~   82 (95)
T d1x4aa1          14 DCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR------RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDG-----YR   82 (95)
T ss_dssp             SSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS------SSSSCCEEEEESCHHHHHHHHHHHTTCEETT-----EE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc------ccccceEEEEECCHHHHHHHHHHhCCCEECC-----EE
Confidence            689999999999999999999999999999887543      3457899999999999999999999999966     58


Q ss_pred             eEEEeecCC
Q 030444          157 LRLQFSRNP  165 (177)
Q Consensus       157 l~V~~a~~~  165 (177)
                      |+|+||++.
T Consensus        83 l~V~~a~~~   91 (95)
T d1x4aa1          83 LRVEFPRSG   91 (95)
T ss_dssp             CEEECCCCC
T ss_pred             EEEEeccCC
Confidence            999999753

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=1.6e-21  Score=130.22  Aligned_cols=78  Identities=19%  Similarity=0.308  Sum_probs=69.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      +++|||+|||+++|+++|+++|++||.|.++++...+       .++||||+|++.++|.+|+..||++.|.+    ++.
T Consensus        10 s~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~~-------~~~~afV~f~~~~~A~~A~~~l~~~~i~~----g~~   78 (88)
T d2adca2          10 SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-------DRKMALIQMGSVEEAVQALIDLHNHDLGE----NHH   78 (88)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS-------STTCEEEEESSHHHHHHHHHHHTTCBSSS----SCB
T ss_pred             CCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeeec-------ccceeEEEECCHHHHHHHHHhccCCEecC----CCE
Confidence            7899999999999999999999999999888776543       35699999999999999999999999853    257


Q ss_pred             eEEEeecCC
Q 030444          157 LRLQFSRNP  165 (177)
Q Consensus       157 l~V~~a~~~  165 (177)
                      |+|+|+|+.
T Consensus        79 l~v~~sk~~   87 (88)
T d2adca2          79 LRVSFSKST   87 (88)
T ss_dssp             CEEEECSSC
T ss_pred             EEEEeCCCC
Confidence            999999763

>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=99.85  E-value=1.1e-21  Score=134.91  Aligned_cols=83  Identities=12%  Similarity=0.195  Sum_probs=75.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|..+.|+.++   .++.++|||||+|.+.++|++|++ ++++.|.+     +.
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~---~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G-----~~   90 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDP---ASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDG-----RV   90 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCT---TTSSCCSEEEEECSSHHHHHHHHT-SCSEEETT-----EE
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccc---cCCCccCeEEEEECCHHHHHHHHH-hCCCeECC-----EE
Confidence            4799999999999999999999999999999999887   567899999999999999999995 79999965     58


Q ss_pred             eEEEeecCCCCC
Q 030444          157 LRLQFSRNPGPR  168 (177)
Q Consensus       157 l~V~~a~~~~~r  168 (177)
                      |+|++|+++..+
T Consensus        91 i~V~~a~~ke~~  102 (103)
T d1x4ba1          91 VEPKRAVAREES  102 (103)
T ss_dssp             EEEECCSSCCCC
T ss_pred             EEEEECcccCCC
Confidence            999999876554

>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=99.85  E-value=6.4e-22  Score=135.72  Aligned_cols=79  Identities=19%  Similarity=0.291  Sum_probs=73.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .+||||+|||+++|+++|+++|++||.|.+|+|+.++   .+|+++|||||+|.+.++|++|++ ||+..|.+     +.
T Consensus        18 ~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~---~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G-----~~   88 (101)
T d2cq4a1          18 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDR---NSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLG-----VP   88 (101)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSC---CSSSCCCCEEEEESCGGGHHHHHH-HTTEEETT-----EE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecC---CCccccceEEEEECCHHHHHHHHH-HCCCEECC-----EE
Confidence            5799999999999999999999999999999999887   678999999999999999999995 99999966     58


Q ss_pred             eEEEeecC
Q 030444          157 LRLQFSRN  164 (177)
Q Consensus       157 l~V~~a~~  164 (177)
                      |+|++++.
T Consensus        89 l~V~~a~~   96 (101)
T d2cq4a1          89 IIVQASQA   96 (101)
T ss_dssp             EEEEEHHH
T ss_pred             EEEEECCC
Confidence            99999864

>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=99.85  E-value=1.8e-21  Score=129.11  Aligned_cols=78  Identities=12%  Similarity=0.201  Sum_probs=72.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|.+++|+.++   .+++++|||||+|.+.+.|++|++ ++++.|.+     |.
T Consensus         6 ~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~---~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~G-----r~   76 (84)
T d1l3ka1           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDP---NTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDG-----RV   76 (84)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT---TTCCEEEEEEEEESSHHHHHHHHH-TCSCEETT-----EE
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhhccccceeecccc---cCCCcccEEEEEEcCHHHHHHHHH-hCCCEECC-----EE
Confidence            5799999999999999999999999999999999887   679999999999999999999996 69999966     58


Q ss_pred             eEEEeec
Q 030444          157 LRLQFSR  163 (177)
Q Consensus       157 l~V~~a~  163 (177)
                      |+|..|.
T Consensus        77 i~V~~A~   83 (84)
T d1l3ka1          77 VEPKRAV   83 (84)
T ss_dssp             CEEEECC
T ss_pred             EEEEeee
Confidence            9998875

>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=99.85  E-value=7.3e-21  Score=129.31  Aligned_cols=77  Identities=19%  Similarity=0.446  Sum_probs=70.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      +++|||+|||+++|+++|+++|++||.|..+++..++         +||||+|.+.++|++|++.||+..|.+.   .++
T Consensus        17 s~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~---------~~afV~f~~~~~A~~A~~~l~~~~i~g~---~~~   84 (97)
T d1whya_          17 TTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGD---------SFAYIQYESLDAAQAACAKMRGFPLGGP---DRR   84 (97)
T ss_dssp             CSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSSS---------CCEEEEESSHHHHHHHHHHHTTCBCSSS---SCB
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeeccc---------cEEEeccCCHHHHHHHHHHhCCCEeCCC---ceE
Confidence            6899999999999999999999999999999987654         5999999999999999999999999874   358


Q ss_pred             eEEEeecCC
Q 030444          157 LRLQFSRNP  165 (177)
Q Consensus       157 l~V~~a~~~  165 (177)
                      |+|+||+..
T Consensus        85 l~v~~ak~~   93 (97)
T d1whya_          85 LRVDFAKSG   93 (97)
T ss_dssp             CEEEECCCC
T ss_pred             EEEEeCCCC
Confidence            999999764

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.85  E-value=6.4e-22  Score=129.26  Aligned_cols=76  Identities=18%  Similarity=0.253  Sum_probs=70.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcce
Q 030444           78 STLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFL  157 (177)
Q Consensus        78 ~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~l  157 (177)
                      |+|||+|||+++|+++|+++|++||.|.+++|+.++   .+++++|||||+|.+.++|++|++ ++++.+++     |.|
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~---~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~G-----r~i   71 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDP---LTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDS-----KTI   71 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCC---CSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSS-----CCC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeeccc---CCCCccceEEEEECCHHHHHHHHH-cCCCEECC-----eEE
Confidence            689999999999999999999999999999999887   678999999999999999999996 79999966     479


Q ss_pred             EEEee
Q 030444          158 RLQFS  162 (177)
Q Consensus       158 ~V~~a  162 (177)
                      +|++|
T Consensus        72 ~V~~A   76 (77)
T d1uawa_          72 DPKVA   76 (77)
T ss_dssp             EEEEC
T ss_pred             EEEEC
Confidence            99876

>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=99.85  E-value=4.8e-21  Score=130.60  Aligned_cols=76  Identities=18%  Similarity=0.284  Sum_probs=67.1

Q ss_pred             CCCeEEEcCCC-CCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCC
Q 030444           76 ASSTLYVEGLP-ADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDS  154 (177)
Q Consensus        76 ~~~tLfV~nLp-~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~  154 (177)
                      ..++|||+||| ..+++++|+++|++||.|.+|+|.           +|||||+|++.++|++||+.|||+.|.+     
T Consensus        14 ~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~-----------rg~aFV~f~~~~~A~~Ai~~lng~~~~g-----   77 (98)
T d1wf2a_          14 MNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH-----------KGFAFVQYVNERNARAAVAGEDGRMIAG-----   77 (98)
T ss_dssp             CCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE-----------TEEEEEEESSHHHHHHHHHTTTTCEETT-----
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe-----------CCeEEEEECCHHHHHHHHHHcCCCEECC-----
Confidence            36789999997 578899999999999999999882           3699999999999999999999999976     


Q ss_pred             cceEEEeecCCCC
Q 030444          155 KFLRLQFSRNPGP  167 (177)
Q Consensus       155 r~l~V~~a~~~~~  167 (177)
                      ++|+|+|++.+..
T Consensus        78 ~~l~V~~a~~~~~   90 (98)
T d1wf2a_          78 QVLDINLAAEPKV   90 (98)
T ss_dssp             EECEEEETTSCCC
T ss_pred             EEEEEEECCCCCC
Confidence            5899999976533

>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=1.3e-21  Score=130.28  Aligned_cols=81  Identities=12%  Similarity=0.202  Sum_probs=69.2

Q ss_pred             CCeEEEcCCCCCCC-HHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           77 SSTLYVEGLPADST-KREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        77 ~~tLfV~nLp~~~t-e~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      .++|||+|||+++| |++|+++|++||.|.+|+|..+.  ..+++++|||||+|.+.++|++|++ ||++.|.+     +
T Consensus         4 ~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~--~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~g-----r   75 (86)
T d2ghpa3           4 GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQ--KEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGN-----R   75 (86)
T ss_dssp             TTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCC--C---CCCEEEEEEESSHHHHHHHGG-GTTEEETT-----E
T ss_pred             CCEEEEECCCCCcccHHHHHHHHHhhhhccceeeeccc--CCccccceeeeEEECCHHHHHHHHh-cCCCEECC-----E
Confidence            68999999999976 56699999999999999987643  1468899999999999999999996 99999966     5


Q ss_pred             ceEEEeecCC
Q 030444          156 FLRLQFSRNP  165 (177)
Q Consensus       156 ~l~V~~a~~~  165 (177)
                      .|+|+||+.+
T Consensus        76 ~l~V~~a~~k   85 (86)
T d2ghpa3          76 EISVSLADKK   85 (86)
T ss_dssp             EEEEEECCCC
T ss_pred             EEEEEEcCCC
Confidence            8999999764

>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=99.84  E-value=1.2e-20  Score=128.60  Aligned_cols=83  Identities=14%  Similarity=0.090  Sum_probs=72.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      ..+|||+|||+++++++|+++|++||.|.+++|..+          |||||+|.+.++|++||+.||+..|.+     +.
T Consensus        15 ~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~~----------g~afV~f~~~~~a~~Ai~~lng~~~~g-----~~   79 (98)
T d1wg4a_          15 DFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKD----------GMGMVEYLRKEDMEYALRKLDDTKFRS-----HE   79 (98)
T ss_dssp             SCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEETT----------TEEEEEESSHHHHHHHHHHHSSEEEEC-----TT
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhhccccccccccc----------ceEEEEECCHHHHHHHHHHhCCCEeCC-----eE
Confidence            578999999999999999999999999999998643          599999999999999999999999976     47


Q ss_pred             eEEEeecCCCCCCCCCCC
Q 030444          157 LRLQFSRNPGPRSVFGAR  174 (177)
Q Consensus       157 l~V~~a~~~~~r~~~g~~  174 (177)
                      |+|.|++....+..+.+.
T Consensus        80 i~v~~~~~~~~~~~~p~~   97 (98)
T d1wg4a_          80 GETSYIRVYPERSSGPSS   97 (98)
T ss_dssp             SCEEEEEEECCCSSCCSC
T ss_pred             EEEEEEecCCCCCCCCcC
Confidence            999999876666544433

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=8.4e-21  Score=124.08  Aligned_cols=77  Identities=10%  Similarity=0.258  Sum_probs=70.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|..+++..++   .+++++|||||+|.+.++|++|+ .+|++.|.+     |.
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~---~~~~~~g~afV~f~~~e~~~~al-~~~~~~l~G-----r~   72 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR---GSGKKRGFAFVTFDDHDSVDKIV-IQKYHTVNG-----HN   72 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECT---TTCCEEEEEEEEESSHHHHHHHH-HCSCCEETT-----EE
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCC---CCcccccEEEEEEcCHHHHHHHH-HhCCCEECC-----EE
Confidence            4799999999999999999999999999999999887   67889999999999999999998 589999966     58


Q ss_pred             eEEEee
Q 030444          157 LRLQFS  162 (177)
Q Consensus       157 l~V~~a  162 (177)
                      |+|+.|
T Consensus        73 i~V~~A   78 (79)
T d1l3ka2          73 CEVRKA   78 (79)
T ss_dssp             CEEEEC
T ss_pred             EEEEEC
Confidence            999876

>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=99.84  E-value=4.3e-21  Score=130.31  Aligned_cols=75  Identities=21%  Similarity=0.428  Sum_probs=69.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||.++|+++|+++|++||.|.+|+|+.++         |||||+|.+.++|+.|++.||+..|.+     ++
T Consensus        18 ~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~k---------g~afV~f~~~~~A~~Ai~~l~~~~i~g-----~~   83 (96)
T d1x4ga1          18 NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK---------GYSFVRFSTHESAAHAIVSVNGTTIEG-----HV   83 (96)
T ss_dssp             CCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETTT---------TEEEEEESSHHHHHHHHHHHTTCEETT-----EE
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEecc---------eEEEEEECCHHHHHHHHHHhCCCEECC-----EE
Confidence            5789999999999999999999999999999998764         699999999999999999999999966     58


Q ss_pred             eEEEeecCC
Q 030444          157 LRLQFSRNP  165 (177)
Q Consensus       157 l~V~~a~~~  165 (177)
                      |+|+|++..
T Consensus        84 l~v~~ak~~   92 (96)
T d1x4ga1          84 VKCYWGKES   92 (96)
T ss_dssp             CEEECCCCC
T ss_pred             EEEEEcCCC
Confidence            999999764

>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=4.1e-21  Score=124.65  Aligned_cols=75  Identities=17%  Similarity=0.324  Sum_probs=68.0

Q ss_pred             eEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcceE
Q 030444           79 TLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFLR  158 (177)
Q Consensus        79 tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~l~  158 (177)
                      +|||+|||+++||++|+++|++||.|.+++|+.++   .+++++|||||+|.+.++|++|++ +++..|.+     +.|+
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~---~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~G-----r~i~   71 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDP---ITGRSRGFGFVLFKESESVDKVMD-QKEHKLNG-----KVID   71 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBT---TTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTT-----BCCE
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCC---CCCCcCceEEEEECCHHHHHHHHh-cCCCEECC-----CEEE
Confidence            59999999999999999999999999999999887   678999999999999999999996 79999966     4788


Q ss_pred             EEee
Q 030444          159 LQFS  162 (177)
Q Consensus       159 V~~a  162 (177)
                      |..|
T Consensus        72 V~rA   75 (75)
T d1hd0a_          72 PKRA   75 (75)
T ss_dssp             ECCC
T ss_pred             eeEC
Confidence            8643

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=1.5e-20  Score=128.56  Aligned_cols=78  Identities=15%  Similarity=0.279  Sum_probs=69.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|..+++..+.    ++.++|||||+|.+.++|++|++.|||..|.++     +
T Consensus        18 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~----~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr-----~   88 (101)
T d1x5oa1          18 PTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS----SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTP-----P   88 (101)
T ss_dssp             TTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS----SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCC-----T
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhcccccceeeeccc----ccccccceeEEeCCHHHHHHHHHHhCCCEECCc-----C
Confidence            5789999999999999999999999999999988774    578899999999999999999999999999774     5


Q ss_pred             eEEEeec
Q 030444          157 LRLQFSR  163 (177)
Q Consensus       157 l~V~~a~  163 (177)
                      +.|.+++
T Consensus        89 ~~v~~~~   95 (101)
T d1x5oa1          89 GVSAPTE   95 (101)
T ss_dssp             TSCCCSS
T ss_pred             CccCCCC
Confidence            6665553

>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=99.83  E-value=4.1e-20  Score=127.00  Aligned_cols=86  Identities=19%  Similarity=0.223  Sum_probs=73.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      ..+|||+|||+++||+||+++|+.|+.+..+.++.++   .+++++|||||+|.+.++|++|++ +|+..|.+     |.
T Consensus        15 ~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~---~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~g-----R~   85 (104)
T d1wg5a_          15 DGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD---FQGRSTGEAFVQFASQEIAEKALK-KHKERIGH-----RY   85 (104)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC---SSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSS-----SC
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeC---CCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcc-----eE
Confidence            5789999999999999999999999998876555554   467899999999999999999995 89999965     58


Q ss_pred             eEEEeecCCCCCCCC
Q 030444          157 LRLQFSRNPGPRSVF  171 (177)
Q Consensus       157 l~V~~a~~~~~r~~~  171 (177)
                      |+|.++.....+..+
T Consensus        86 i~V~~~~~~~~~~sg  100 (104)
T d1wg5a_          86 IEIFKSSRAEVRTSG  100 (104)
T ss_dssp             CEEEEECTTTSCCSS
T ss_pred             EEEEECCHHHhccCC
Confidence            999999776555533

>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=99.83  E-value=1.5e-20  Score=124.94  Aligned_cols=78  Identities=21%  Similarity=0.238  Sum_probs=69.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|..+++...         +|||||+|.+.++|..|++.||+..|.+     +.
T Consensus         8 ~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~~---------rg~afV~f~~~~~A~~Ai~~l~~~~i~g-----~~   73 (86)
T d2cpda1           8 VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI---------RDYAFVHFSNREDAVEAMKALNGKVLDG-----SP   73 (86)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC---------SSEEEEEESSHHHHHHHHHHHSSEEETT-----EE
T ss_pred             CCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEccc---------cEEEEEEeCCHHHHHHHHHHcCCCEECC-----EE
Confidence            689999999999999999999999999887776443         4699999999999999999999999966     58


Q ss_pred             eEEEeecCCCCC
Q 030444          157 LRLQFSRNPGPR  168 (177)
Q Consensus       157 l~V~~a~~~~~r  168 (177)
                      |+|+||+++.+.
T Consensus        74 i~V~~akP~~~~   85 (86)
T d2cpda1          74 IEVTLAKPVDKD   85 (86)
T ss_dssp             EEEECCCCCCCC
T ss_pred             EEEEeccCCCCC
Confidence            999999866443

>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=99.83  E-value=2.1e-21  Score=127.62  Aligned_cols=78  Identities=22%  Similarity=0.341  Sum_probs=68.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCC-eeCCCCCCCcc
Q 030444           78 STLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGY-RMDEDDPDSKF  156 (177)
Q Consensus        78 ~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~-~l~~~~~~~r~  156 (177)
                      ++|||+|||+++|+++|+++|++||.|.++++...         +|||||+|.+.++|++|++.|||. .+.+     ++
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~---------rg~aFV~f~~~~~A~~Ai~~lng~~~~~G-----~~   67 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK---------SGYAFVDYPDQNWAIRAIETLSGKVELHG-----KI   67 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEE---------TTEEEECCSCHHHHHHHHHHHTTTCEETT-----EE
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEecc---------cceEEEEECCHHHHHHHHHHhCCCeEECC-----EE
Confidence            57999999999999999999999999887776654         369999999999999999999995 6865     58


Q ss_pred             eEEEeecCCCCCC
Q 030444          157 LRLQFSRNPGPRS  169 (177)
Q Consensus       157 l~V~~a~~~~~r~  169 (177)
                      |+|+||.++.+|+
T Consensus        68 i~V~~a~~k~~rs   80 (80)
T d2cqha1          68 MEVDYSVSKKLRS   80 (80)
T ss_dssp             CEEEECCCCCCCC
T ss_pred             EEEEEcCCcCcCC
Confidence            9999998776653

>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=99.83  E-value=1e-20  Score=125.95  Aligned_cols=75  Identities=27%  Similarity=0.383  Sum_probs=69.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++++++|+++|++||.|.+|++..++         +||||+|++.++|++|++.||+..|.+     +.
T Consensus         8 ~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~k---------~~afV~f~~~~~A~~A~~~l~g~~i~g-----~~   73 (86)
T d2cpja1           8 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK---------GFGFIRLETRTLAEIAKVELDNMPLRG-----KQ   73 (86)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETTT---------TEEEEECSSSHHHHHHHHHHTTCCBTT-----BC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeeccc---------ceEEEEECCHHHHHHHHHHhCCCEECC-----EE
Confidence            5789999999999999999999999999999997654         599999999999999999999999976     58


Q ss_pred             eEEEeecCC
Q 030444          157 LRLQFSRNP  165 (177)
Q Consensus       157 l~V~~a~~~  165 (177)
                      |+|+||.++
T Consensus        74 l~V~~A~~~   82 (86)
T d2cpja1          74 LRVRFACHS   82 (86)
T ss_dssp             CEEEESSCC
T ss_pred             EEEEECCCc
Confidence            999999765

>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=99.83  E-value=3e-20  Score=127.32  Aligned_cols=81  Identities=20%  Similarity=0.326  Sum_probs=70.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      ..+|||.|||+++||+||+++|+.|+ +..++++.+.    .++.+|||||+|.+.++|++|++ +|+..|.+     |.
T Consensus        15 ~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~~----~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~g-----R~   83 (102)
T d1weza_          15 GHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP----DGRVTGEADVEFATHEDAVAAMA-KDKANMQH-----RY   83 (102)
T ss_dssp             SCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESS----SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSS-----SC
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEec----CCcceEEEEEEECCHHHHHHHHH-cCCCEECC-----EE
Confidence            68999999999999999999999997 5567777764    57889999999999999999986 89999966     58


Q ss_pred             eEEEeecCCCCC
Q 030444          157 LRLQFSRNPGPR  168 (177)
Q Consensus       157 l~V~~a~~~~~r  168 (177)
                      |+|.++..++..
T Consensus        84 I~V~~s~~~~~~   95 (102)
T d1weza_          84 VELFLNSTAGTS   95 (102)
T ss_dssp             CEEEEECCCCCC
T ss_pred             EEEEEcCCCCCC
Confidence            999999766433

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.83  E-value=7.4e-21  Score=129.00  Aligned_cols=78  Identities=22%  Similarity=0.367  Sum_probs=68.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|..++.        ++++++||||+|.+.++|++|++.||+..|.+     +.
T Consensus        16 ~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~--------~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~g-----r~   82 (96)
T d1fjca_          16 ARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ--------DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDG-----RS   82 (96)
T ss_dssp             GGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE--------TTEEEEEEEEEESSHHHHHHHHHHTTEEEETT-----EE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcccceeeee--------cCccccEEEEEeCCHHHHHHHHHHcCCCEECC-----EE
Confidence            689999999999999999999999998765532        46678999999999999999999999999976     58


Q ss_pred             eEEEeecCCCC
Q 030444          157 LRLQFSRNPGP  167 (177)
Q Consensus       157 l~V~~a~~~~~  167 (177)
                      |+|+|++.+..
T Consensus        83 i~V~~a~~k~~   93 (96)
T d1fjca_          83 VSLYYTGEKGG   93 (96)
T ss_dssp             EEEEECSSSCC
T ss_pred             EEEEEeCCCCC
Confidence            99999976543

>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=99.83  E-value=5.6e-21  Score=129.54  Aligned_cols=85  Identities=15%  Similarity=0.184  Sum_probs=71.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCC-EEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVG-YKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~-i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      +++|||+|||.++|+++|+++|++||. |.+++++.+.  ..+++++|||||+|.+.++|..|++.|++..+.-   .++
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~--~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~---~g~   75 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASA--ADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQL---WGH   75 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSS--CTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCB---TTB
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeec--cccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEE---CCE
Confidence            468999999999999999999999995 8999888764  1357899999999999999999999997655532   235


Q ss_pred             ceEEEeecCCC
Q 030444          156 FLRLQFSRNPG  166 (177)
Q Consensus       156 ~l~V~~a~~~~  166 (177)
                      +|+|+||+++.
T Consensus        76 ~i~V~~A~p~~   86 (96)
T d2disa1          76 QIAVDWAEPEI   86 (96)
T ss_dssp             CCEEEESCSSC
T ss_pred             EEEEEEcCCCC
Confidence            89999997653

>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=99.83  E-value=1.5e-20  Score=130.04  Aligned_cols=79  Identities=22%  Similarity=0.263  Sum_probs=71.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      ..+|||+|||+++|+++|+++|++||.|.+|+++.++       .+|||||+|.+.++|+.|++.||+..|.+   .++.
T Consensus         7 ~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~-------~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~---~~~~   76 (108)
T d2adba1           7 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN-------NQFQALLQYADPVSAQHAKLSLDGQNIYN---ACCT   76 (108)
T ss_dssp             EEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET-------TEEEEEEEESCHHHHHHHHHHHHSCCSST---TCCC
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC-------CCCeEEEEECCHHHHHHHHHHHCCCEecc---CCcE
Confidence            6789999999999999999999999999999998764       36899999999999999999999999976   3458


Q ss_pred             eEEEeecCC
Q 030444          157 LRLQFSRNP  165 (177)
Q Consensus       157 l~V~~a~~~  165 (177)
                      |+|+|++..
T Consensus        77 l~v~~s~~~   85 (108)
T d2adba1          77 LRIDFSKLT   85 (108)
T ss_dssp             CEEEECSSC
T ss_pred             EEEEecCCc
Confidence            999999764

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=1.8e-20  Score=125.21  Aligned_cols=78  Identities=24%  Similarity=0.268  Sum_probs=65.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      +++|||+|||+++|++||+++|++|| +..+.+..         .++||||+|.+.++|++|++.||++.|.+     ++
T Consensus         5 s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~~~---------~kg~afV~f~~~~~A~~Ai~~ln~~~~~G-----~~   69 (88)
T d1wg1a_           5 SSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVDR---------NKRTAFVTLLNGEQAQNAIQMFHQYSFRG-----KD   69 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEEEG---------GGTEEEECCSCHHHHHHHHHHHTTEEETT-----EE
T ss_pred             CCEEEEeCCCCccChHHHHHHHHhcC-ceeeeeec---------cCCceEEEECCHHHHHHHHHHhCCCEECC-----EE
Confidence            68999999999999999999999999 33344322         34799999999999999999999999966     58


Q ss_pred             eEEEeecCCCCCC
Q 030444          157 LRLQFSRNPGPRS  169 (177)
Q Consensus       157 l~V~~a~~~~~r~  169 (177)
                      |+|+|+++.....
T Consensus        70 l~V~~a~~~~~~~   82 (88)
T d1wg1a_          70 LIVQLQPTDALLC   82 (88)
T ss_dssp             EEEEECCCCCCCS
T ss_pred             EEEEEcCCCCCCC
Confidence            9999997764433

>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=99.82  E-value=5.9e-22  Score=133.40  Aligned_cols=79  Identities=19%  Similarity=0.303  Sum_probs=71.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      ..+|||+|||+++|+++|+++|++||.|..++|+.+    .+|+++|||||+|.+.++|++|++ ||+..|.+     +.
T Consensus        13 ~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~----~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g-----~~   82 (91)
T d1fjeb1          13 PFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV----RTGTNRKFGYVDFESAEDLEKALE-LTGLKVFG-----NE   82 (91)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE----EEETTTTEEEEEESSHHHHHHHHH-GGGEEETT-----EE
T ss_pred             CcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec----CCCCccEEeEEeeCCHHHHHHHHh-cCCcEECC-----EE
Confidence            579999999999999999999999999998888655    368899999999999999999996 99999976     58


Q ss_pred             eEEEeecCC
Q 030444          157 LRLQFSRNP  165 (177)
Q Consensus       157 l~V~~a~~~  165 (177)
                      |+|++|+.+
T Consensus        83 i~V~~ak~k   91 (91)
T d1fjeb1          83 IKLEKPKGR   91 (91)
T ss_dssp             EEEECCCCS
T ss_pred             EEEEecCCC
Confidence            999999753

>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=99.82  E-value=1.9e-20  Score=122.58  Aligned_cols=75  Identities=24%  Similarity=0.356  Sum_probs=67.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      .++||||+||+  +|+++|+++|++||.|.+|++..++         +||||+|.+.++|+.|++.||+..+.+     +
T Consensus         4 ~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~~---------~~afV~f~~~~~A~~Ai~~lng~~~~g-----~   67 (79)
T d2bz2a1           4 KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPR---------NCAFVTYEKMESADQAVAELNGTQVES-----V   67 (79)
T ss_dssp             CCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETTT---------TEEEEECSSHHHHHHHHHHHTTCBCSS-----C
T ss_pred             CCCEEEEECCC--CCHHHHHHHHhccCccceeeeccCC---------CEEEEEEcccHHHHHHHHHhCCCEECC-----E
Confidence            37899999995  9999999999999999999987543         599999999999999999999999976     4


Q ss_pred             ceEEEeecCCC
Q 030444          156 FLRLQFSRNPG  166 (177)
Q Consensus       156 ~l~V~~a~~~~  166 (177)
                      +|+|+|++.++
T Consensus        68 ~l~V~~a~~~P   78 (79)
T d2bz2a1          68 QLKVNIARKQP   78 (79)
T ss_dssp             BCEEEECCSSC
T ss_pred             EEEEEEecCCC
Confidence            89999997643

>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=99.82  E-value=1.5e-20  Score=125.86  Aligned_cols=79  Identities=19%  Similarity=0.252  Sum_probs=69.8

Q ss_pred             CCeEEEcCCCCCCCHHHH---HHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCC
Q 030444           77 SSTLYVEGLPADSTKREV---AHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPD  153 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L---~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~  153 (177)
                      .++|||+|||+++++++|   +++|++||.|.+|+++.++........+|||||+|.+.++|++|++.|||+.|.+    
T Consensus         8 ~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~g----   83 (89)
T d2cpia1           8 KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDG----   83 (89)
T ss_dssp             SSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETT----
T ss_pred             cCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECC----
Confidence            578999999999999999   7789999999999999887444444566999999999999999999999999976    


Q ss_pred             CcceEEE
Q 030444          154 SKFLRLQ  160 (177)
Q Consensus       154 ~r~l~V~  160 (177)
                       |+|+|+
T Consensus        84 -r~lkvS   89 (89)
T d2cpia1          84 -RTLKAS   89 (89)
T ss_dssp             -EEEEEE
T ss_pred             -EEEEEC
Confidence             579875

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.82  E-value=8.9e-21  Score=122.64  Aligned_cols=75  Identities=19%  Similarity=0.329  Sum_probs=68.9

Q ss_pred             eEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcceE
Q 030444           79 TLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFLR  158 (177)
Q Consensus        79 tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~l~  158 (177)
                      +|||+|||+++||++|+++|++||.|..+.++.++   .++.+++||||+|.+.++|++|++ +|++.|.+     |.|+
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~---~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~g-----r~i~   71 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDK---TTNRHRGFGFVTFESEDIVEKVCE-IHFHEINN-----KMVE   71 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCT---TCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTT-----BCCE
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeec---cccccCceeEEEECCHHHHHHHHh-cCCCEECC-----eEEE
Confidence            59999999999999999999999999999988876   568899999999999999999996 99999966     5799


Q ss_pred             EEee
Q 030444          159 LQFS  162 (177)
Q Consensus       159 V~~a  162 (177)
                      |++|
T Consensus        72 V~~A   75 (75)
T d2msta_          72 CKKA   75 (75)
T ss_dssp             EEEC
T ss_pred             EEEC
Confidence            9876

>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=99.82  E-value=1.4e-20  Score=130.07  Aligned_cols=76  Identities=21%  Similarity=0.332  Sum_probs=69.0

Q ss_pred             CCeEEEcCCCC-CCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           77 SSTLYVEGLPA-DSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        77 ~~tLfV~nLp~-~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      +++|||+|||+ .+|+++|+++|++||.|.+|+|+.++        +|||||+|++.++|++|++.||+..|.+     +
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~--------kg~afV~f~~~~~A~~ai~~lng~~l~g-----~   68 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK--------KENALVQMADGNQAQLAMSHLNGHKLHG-----K   68 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT--------SCCEEEEESCHHHHHHHHHHHTTCBCSS-----S
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc--------cceEEEEECCHHHHHHHHHHhCCCEECC-----E
Confidence            68999999965 59999999999999999999998764        4699999999999999999999999976     4


Q ss_pred             ceEEEeecCC
Q 030444          156 FLRLQFSRNP  165 (177)
Q Consensus       156 ~l~V~~a~~~  165 (177)
                      .|+|+|++.+
T Consensus        69 ~l~v~~s~~~   78 (109)
T d2adca1          69 PIRITLSKHQ   78 (109)
T ss_dssp             BCEEECCSCC
T ss_pred             EEEEEECCCC
Confidence            8999999754

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=4e-21  Score=128.11  Aligned_cols=73  Identities=14%  Similarity=0.111  Sum_probs=65.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcce
Q 030444           78 STLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFL  157 (177)
Q Consensus        78 ~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~l  157 (177)
                      ++|||+|||+++|+++|+++|++||.|.++++..+          |||||+|.+.++|++||+.||+..|.++     .|
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~----------g~afV~f~~~~~a~~Ai~~l~g~~~~g~-----~i   65 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD----------GTGVVEFVRKEDMTYAVRKLDNTKFRSH-----EG   65 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT----------SEEEEEESSHHHHHHHHHHHTTCBCCCT-----TS
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhccccccccccc----------ceeeEEeCCHHHHHHHHHHhCCCEECCc-----Ee
Confidence            47999999999999999999999999999998654          4999999999999999999999999774     68


Q ss_pred             EEEeecCC
Q 030444          158 RLQFSRNP  165 (177)
Q Consensus       158 ~V~~a~~~  165 (177)
                      +|.|++..
T Consensus        66 ~v~~~~~~   73 (87)
T d3begb1          66 ETAYIRVK   73 (87)
T ss_dssp             CCCBCEEE
T ss_pred             EEeEEecC
Confidence            88776544

>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=99.81  E-value=2.3e-20  Score=129.27  Aligned_cols=75  Identities=23%  Similarity=0.262  Sum_probs=68.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      +++|||+|||+++|+++|+++|++||.|..|.|..         +++||||+|.+.++|++|++.|||..|.+     ++
T Consensus        10 ~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~---------~kg~afV~f~~~~~A~~A~~~lng~~~~g-----r~   75 (111)
T d1whxa_          10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE---------GGITAIVEFLEPLEARKAFRHLAYSKFHH-----VP   75 (111)
T ss_dssp             EEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS---------SSSCEEEEESCHHHHHHHHHHHTTCBSSS-----SB
T ss_pred             CCEEEEECCCCCCCHHHHHhhhhccCCccEEEeec---------cCceEEEEEcCHHHHHHHHHHHcCCccCC-----Ce
Confidence            57899999999999999999999999999998743         34799999999999999999999999976     58


Q ss_pred             eEEEeecCC
Q 030444          157 LRLQFSRNP  165 (177)
Q Consensus       157 l~V~~a~~~  165 (177)
                      |+|+|+...
T Consensus        76 l~v~~a~~~   84 (111)
T d1whxa_          76 LYLEWAPIG   84 (111)
T ss_dssp             CEEEEEETT
T ss_pred             EEEEECCCC
Confidence            999999754

>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=99.81  E-value=1e-20  Score=126.41  Aligned_cols=80  Identities=15%  Similarity=0.156  Sum_probs=68.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      +++|||+|||+++||++|+++|++||.|.+|++..+        +++||||+|++.++|++|+.  +++.|.+     ++
T Consensus         5 s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~~--------~~gfafV~f~~~~~a~~a~~--~~~~i~g-----~~   69 (88)
T d1wf0a_           5 SSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP--------FRAFAFVTFADDQIAQSLCG--EDLIIKG-----IS   69 (88)
T ss_dssp             CCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS--------CCSCCEEECSCHHHHHHTTT--CEEEETT-----EE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEeec--------cCceEEEEECCHHHHHHHHh--CCCEECC-----EE
Confidence            789999999999999999999999999999876433        45799999999999999985  7888865     58


Q ss_pred             eEEEeecCCCCCCCC
Q 030444          157 LRLQFSRNPGPRSVF  171 (177)
Q Consensus       157 l~V~~a~~~~~r~~~  171 (177)
                      |+|+||+++..+..+
T Consensus        70 l~v~~a~~k~~~~~~   84 (88)
T d1wf0a_          70 VHISNAEPKHNSNSG   84 (88)
T ss_dssp             EEEECCCCCCCCCSC
T ss_pred             eEEEeCCCCCCCCCC
Confidence            999999876555433

>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=5e-21  Score=124.38  Aligned_cols=75  Identities=13%  Similarity=0.320  Sum_probs=67.2

Q ss_pred             eEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcceE
Q 030444           79 TLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFLR  158 (177)
Q Consensus        79 tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~l~  158 (177)
                      +|||+|||+++|+++|+++|++||.|.+|+|+.++   .+++++|||||+|.+.++|++||+. +++.|.+     +.|+
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~---~t~~~rG~~FV~f~~~~~a~~al~~-~~~~i~g-----~~i~   71 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDN---KTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGL-----SKCE   71 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCT---TTCCTTCCEEEEESSSHHHHHHTTC-SSCCBTT-----BCCE
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccc---cccccccEEEEEECCHHHHHHHHhh-CCCEECC-----EEeE
Confidence            59999999999999999999999999999999887   6789999999999999999999964 6677765     4688


Q ss_pred             EEee
Q 030444          159 LQFS  162 (177)
Q Consensus       159 V~~a  162 (177)
                      |..|
T Consensus        72 vk~A   75 (75)
T d1x0fa1          72 IKVA   75 (75)
T ss_dssp             EECC
T ss_pred             EEEC
Confidence            8765

>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=6.1e-20  Score=121.81  Aligned_cols=77  Identities=17%  Similarity=0.224  Sum_probs=70.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|+.||.|..|+|..++    +++++|||||+|.+.++|++|++ +++..+.+     +.
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~----~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g-----~~   75 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL----HKAFKGSIFVVFDSIESAKKFVE-TPGQKYKE-----TD   75 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT----TCCEEEEEEEEESCHHHHHHHHT-CCCCEETT-----EE
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeec----cCCcceEEEEEEcCHHHHHHHHH-HCCCEECC-----EE
Confidence            5899999999999999999999999999999998764    68899999999999999999995 79999966     58


Q ss_pred             eEEEeec
Q 030444          157 LRLQFSR  163 (177)
Q Consensus       157 l~V~~a~  163 (177)
                      |+|.|++
T Consensus        76 l~v~~~~   82 (85)
T d1zh5a2          76 LLILFKD   82 (85)
T ss_dssp             CEEEEGG
T ss_pred             EEEEEcC
Confidence            9999874

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=1.5e-20  Score=126.18  Aligned_cols=80  Identities=24%  Similarity=0.385  Sum_probs=69.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHH----hhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCC
Q 030444           76 ASSTLYVEGLPADSTKREVAH----IFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDD  151 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~----lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~  151 (177)
                      |++||||+|||+++|++||++    +|++||.|.+|++..      +++++|||||+|.+.++|++|++.||+..+.+  
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~------~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g--   73 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR------SLKMRGQAFVIFKEVSSATNALRSMQGFPFYD--   73 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH------HHHHTTCEEEEESSHHHHHHHHHHHTTCEETT--
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee------eccCCCceEEEECCHHHHHHHHHHhCCCEECC--
Confidence            379999999999999999864    689999999988743      34567899999999999999999999999976  


Q ss_pred             CCCcceEEEeecCCC
Q 030444          152 PDSKFLRLQFSRNPG  166 (177)
Q Consensus       152 ~~~r~l~V~~a~~~~  166 (177)
                         +.|+|+||+.+.
T Consensus        74 ---~~l~v~~ak~~~   85 (91)
T d1nu4a_          74 ---KPMRIQYAKTDS   85 (91)
T ss_dssp             ---EECEEEECSSCC
T ss_pred             ---EEEEEEEeCCCc
Confidence               589999998753

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=2.4e-19  Score=119.51  Aligned_cols=77  Identities=18%  Similarity=0.270  Sum_probs=68.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHh--CCCeeCCCCCC
Q 030444           76 ASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSAL--QGYRMDEDDPD  153 (177)
Q Consensus        76 ~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l--~g~~l~~~~~~  153 (177)
                      |+++|||+|||+++|+++|+++|++||.|.++++..++         +||||+|.+.++|++|++.+  ++..+.+    
T Consensus         7 Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~~---------~~afV~f~~~e~A~~a~~~~~~~~~~~~g----   73 (88)
T d2cq1a1           7 PSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGK---------NQAFLELATEEAAITMVNYYSAVTPHLRN----   73 (88)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETTT---------TEEEEEESSHHHHHHHHHHHHHSCCEETT----
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcccccccccccccc---------eEEEEEeCCHHHHHHHHHHHccCCCccCC----
Confidence            38999999999999999999999999999999987654         59999999999999999876  5667755    


Q ss_pred             CcceEEEeecCCC
Q 030444          154 SKFLRLQFSRNPG  166 (177)
Q Consensus       154 ~r~l~V~~a~~~~  166 (177)
                       ++|+|+|++.+.
T Consensus        74 -~~l~v~~sk~~~   85 (88)
T d2cq1a1          74 -QPIYIQYSNHKE   85 (88)
T ss_dssp             -EECEEEECSCSS
T ss_pred             -CEEEEEECCCCC
Confidence             589999998754

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=3.5e-20  Score=119.03  Aligned_cols=68  Identities=22%  Similarity=0.470  Sum_probs=64.2

Q ss_pred             EEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCC
Q 030444           80 LYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDED  150 (177)
Q Consensus        80 LfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~  150 (177)
                      |||+|||+++|+++|+++|++||.|..+++..++   .++.++|||||+|.+.++|++|++.|||..|.++
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~---~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr   68 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDK---TTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQ   68 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCS---SSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEE
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhcccccccccccc---ccccccceeEEEECCHHHHHHHHHHhCCCEECCE
Confidence            7999999999999999999999999999998887   6788999999999999999999999999999764

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.80  E-value=6.5e-20  Score=121.68  Aligned_cols=77  Identities=18%  Similarity=0.242  Sum_probs=67.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEE-EEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEV-RLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v-~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      .++|||+|||++++++||+++|+.|+.+... .+..+    .+++++|||||+|.+.++|++|++.||++.|.+     |
T Consensus         9 ~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~----~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~g-----r   79 (86)
T d2cqpa1           9 PTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYN----EKGMPTGEAMVAFESRDEATAAVIDLNDRPIGS-----R   79 (86)
T ss_dssp             SEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEEC----SSSCEEEEEEEEESCHHHHHHHHHHTTTCEETT-----E
T ss_pred             CCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeC----CCCCcceEEEEEEcCcHHHHHHHHHcCCCEECC-----E
Confidence            4679999999999999999999999998764 44444    468899999999999999999999999999965     6


Q ss_pred             ceEEEee
Q 030444          156 FLRLQFS  162 (177)
Q Consensus       156 ~l~V~~a  162 (177)
                      +|+|+++
T Consensus        80 ~i~v~l~   86 (86)
T d2cqpa1          80 KVKLVLG   86 (86)
T ss_dssp             ECEEEES
T ss_pred             EEEEEEC
Confidence            8999875

>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=99.80  E-value=3e-19  Score=122.64  Aligned_cols=77  Identities=16%  Similarity=0.151  Sum_probs=66.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      +++|||+|||+++||++|.++|++||.|.++++...+         +||||+|++.++|+.|++.|+...+..   .+++
T Consensus        15 s~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~k---------~~AfV~f~~~e~A~~ai~~~~~~~~~~---~g~~   82 (104)
T d1wexa_          15 SPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFK---------RQALVEFENIDSAKECVTFAADVPVYI---AGQQ   82 (104)
T ss_dssp             CSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETTT---------TEEEEEESSHHHHHHHHHHHHHSCCBS---SSSB
T ss_pred             CCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEecc---------eeEEEEeCCHHHHHHHHHHHcCCCcEE---eeEE
Confidence            7999999999999999999999999999999987543         599999999999999999885443322   3358


Q ss_pred             eEEEeecCC
Q 030444          157 LRLQFSRNP  165 (177)
Q Consensus       157 l~V~~a~~~  165 (177)
                      |+|+|++.+
T Consensus        83 l~v~~s~~~   91 (104)
T d1wexa_          83 AFFNYSTSK   91 (104)
T ss_dssp             CEEEECSSS
T ss_pred             EEEEEcCCC
Confidence            999999765

>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=99.78  E-value=5.9e-19  Score=114.33  Aligned_cols=71  Identities=24%  Similarity=0.326  Sum_probs=62.3

Q ss_pred             EEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcceEE
Q 030444           80 LYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFLRL  159 (177)
Q Consensus        80 LfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~l~V  159 (177)
                      |||+|||+++|+++|+++|++|| +..+++..         ++|||||+|.+.++|++|++.||++.+.+     ++|+|
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~~~---------~~g~afv~f~~~~~A~~Ai~~ln~~~~~g-----~~l~V   65 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDK---------YKGTAFVTLLNGEQAEAAINTFHQSRLRE-----RELSV   65 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEEET---------TTTEEEEEESSHHHHHHHHHHHTTEESSS-----CEEEE
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceeecc---------cceeEEEEECCHHHHHHHHHHhCCccCCC-----CEEEE
Confidence            79999999999999999999998 55555432         45799999999999999999999999976     58999


Q ss_pred             EeecCC
Q 030444          160 QFSRNP  165 (177)
Q Consensus       160 ~~a~~~  165 (177)
                      +|++..
T Consensus        66 ~~a~~d   71 (75)
T d1wi6a1          66 QLQPTD   71 (75)
T ss_dssp             EECCST
T ss_pred             EEeCCC
Confidence            999654

>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=99.78  E-value=3.6e-19  Score=115.36  Aligned_cols=74  Identities=14%  Similarity=0.136  Sum_probs=65.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcce
Q 030444           78 STLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFL  157 (177)
Q Consensus        78 ~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~l  157 (177)
                      +||||+|||+++++++|+++|++||.|..+++..++     ...++||||+|++.++|++|+ .+|+..|++     ++|
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~-----~~~~~~afV~F~~~~~a~~Al-~~~~~~i~g-----~~i   69 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSL-----KKNFRFARIEFARYDGALAAI-TKTHKVVGQ-----NEI   69 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECT-----TSSSEEEEEEESSHHHHHHHH-TTTTCEETT-----EEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeec-----cccceEEEEEEcchHHhHHHH-HhcCcEECC-----EEE
Confidence            489999999999999999999999999999998876     223579999999999999999 589999966     479


Q ss_pred             EEEee
Q 030444          158 RLQFS  162 (177)
Q Consensus       158 ~V~~a  162 (177)
                      .|+.+
T Consensus        70 ~V~~~   74 (75)
T d2ghpa2          70 IVSHL   74 (75)
T ss_dssp             EEEEC
T ss_pred             EEEEC
Confidence            88764

>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=99.76  E-value=1.2e-18  Score=116.46  Aligned_cols=76  Identities=12%  Similarity=0.136  Sum_probs=67.2

Q ss_pred             CCCeEEEcCCCCC-CCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHh--CCCeeCCCCC
Q 030444           76 ASSTLYVEGLPAD-STKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSAL--QGYRMDEDDP  152 (177)
Q Consensus        76 ~~~tLfV~nLp~~-~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l--~g~~l~~~~~  152 (177)
                      ++++|||+|||.. +|++||.++|++||.|.+|+++.++         ++|||+|++.++|+.|++.|  ++..+.+   
T Consensus         7 ~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~k---------~~afV~f~~~~~A~~A~~~l~~~~~~~~g---   74 (89)
T d1x4da1           7 TRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI---------NEAFIEMATTEDAQAAVDYYTTTPALVFG---   74 (89)
T ss_dssp             CCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS---------SCEEEEESSHHHHHHHHHHHHHSCCEETT---
T ss_pred             CCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeeccc---------eEEEEEEcchhhHHHHHHHHhhCCCccCC---
Confidence            3799999999986 8899999999999999999998764         48999999999999999976  6777855   


Q ss_pred             CCcceEEEeecCC
Q 030444          153 DSKFLRLQFSRNP  165 (177)
Q Consensus       153 ~~r~l~V~~a~~~  165 (177)
                        ++|+|+||++.
T Consensus        75 --r~l~V~~s~~~   85 (89)
T d1x4da1          75 --KPVRVHLSQKY   85 (89)
T ss_dssp             --EECEEEEECCC
T ss_pred             --ceEEEEECCCc
Confidence              68999999764

>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=99.76  E-value=3e-18  Score=116.66  Aligned_cols=76  Identities=13%  Similarity=0.237  Sum_probs=66.8

Q ss_pred             CCCeEEEcCCCCC-CCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHH--HhCCCeeCCCCC
Q 030444           76 ASSTLYVEGLPAD-STKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALS--ALQGYRMDEDDP  152 (177)
Q Consensus        76 ~~~tLfV~nLp~~-~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~--~l~g~~l~~~~~  152 (177)
                      ++++|||+|||.+ +|+++|.++|++||.|.+++++.++         +||||+|.+.++|..|++  .+++..+.+   
T Consensus        17 ~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~k---------~~afV~f~~~~~A~~Ai~~~~~~~~~~~g---   84 (99)
T d1x4fa1          17 LGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMK---------SQAFIEMETREDAMAMVDHCLKKALWFQG---   84 (99)
T ss_dssp             CCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETTT---------TEEEEECSSHHHHHHHHHHHHHSCCCSSS---
T ss_pred             CCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeecC---------CcEEEEecchHHHHHHHHHHhcCCceECC---
Confidence            4789999999985 8999999999999999999997654         599999999999999998  467778866   


Q ss_pred             CCcceEEEeecCC
Q 030444          153 DSKFLRLQFSRNP  165 (177)
Q Consensus       153 ~~r~l~V~~a~~~  165 (177)
                        ++|+|+||+.+
T Consensus        85 --r~l~V~~s~~~   95 (99)
T d1x4fa1          85 --RCVKVDLSEKY   95 (99)
T ss_dssp             --SCCEEEEECSC
T ss_pred             --EEEEEEEcCCc
Confidence              58999999654

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=7.7e-19  Score=120.23  Aligned_cols=78  Identities=15%  Similarity=0.175  Sum_probs=67.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      ..+|||+|||+++|+++|+++|+.||.+..+.++...   .+|+++|||||+|.+.++|++|++ ||+..|.+     |.
T Consensus         8 ~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~---~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~g-----r~   78 (103)
T d2cpya1           8 KVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVD---NNGQGLGQALVQFKNEDDARKSER-LHRKKLNG-----RE   78 (103)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCC---TTSSCSSCEEEECSSHHHHHHHGG-GCSEEETT-----EE
T ss_pred             ceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeC---CCCCcCccEEEEECCHHHHHHHHh-cCCCeECC-----cE
Confidence            5689999999999999999999999988764444333   478899999999999999999996 99999966     58


Q ss_pred             eEEEeec
Q 030444          157 LRLQFSR  163 (177)
Q Consensus       157 l~V~~a~  163 (177)
                      |.|.++.
T Consensus        79 i~V~~~~   85 (103)
T d2cpya1          79 AFVHVVT   85 (103)
T ss_dssp             EEEEEEC
T ss_pred             EEEEECC
Confidence            9999874

>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=99.75  E-value=1.5e-18  Score=120.58  Aligned_cols=82  Identities=22%  Similarity=0.351  Sum_probs=69.4

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCC
Q 030444           73 PPDASSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDP  152 (177)
Q Consensus        73 p~~~~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~  152 (177)
                      |..+.++|||+|||+++|+++|+++|+.||.+..+.++.+.   ..|.++|||||+|.+.++|++|++ ||+..|.+   
T Consensus        14 ~~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~---~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~g---   86 (112)
T d1wela1          14 PHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYG---PNGKATGEGFVEFRNEADYKAALC-RHKQYMGN---   86 (112)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEEC---TTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTT---
T ss_pred             CCCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecC---cccceeeEEEEEECCHHHHHHHHH-cCCCcCCC---
Confidence            34447899999999999999999999999988765444443   468899999999999999999995 89999966   


Q ss_pred             CCcceEEEeec
Q 030444          153 DSKFLRLQFSR  163 (177)
Q Consensus       153 ~~r~l~V~~a~  163 (177)
                        |.|.|..+.
T Consensus        87 --R~i~V~~~~   95 (112)
T d1wela1          87 --RFIQVHPIT   95 (112)
T ss_dssp             --SCBEEEEEC
T ss_pred             --EEEEEEEcC
Confidence              589998773

>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=99.70  E-value=4.2e-18  Score=116.97  Aligned_cols=76  Identities=21%  Similarity=0.202  Sum_probs=66.7

Q ss_pred             CCeEEEcCCCCCC-C----HHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCC
Q 030444           77 SSTLYVEGLPADS-T----KREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDD  151 (177)
Q Consensus        77 ~~tLfV~nLp~~~-t----e~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~  151 (177)
                      +++|||+||+.++ +    +++|+++|++||.|.+++++..+         +||||+|.+.++|++|++.|||+.|.+  
T Consensus         5 ~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~~---------~~afV~f~~~~~A~~Ai~~lng~~~~g--   73 (104)
T d1weya_           5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF---------KRVRINFSNPLSAADARLRLHKTEFLG--   73 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTT---------TEEEEECSSTTHHHHHHHTSTTSEETT--
T ss_pred             CceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecCC---------CEEEEEECCHHHHHHHHHHhcccccCC--
Confidence            6899999999876 3    35799999999999999987543         599999999999999999999999976  


Q ss_pred             CCCcceEEEeecCCC
Q 030444          152 PDSKFLRLQFSRNPG  166 (177)
Q Consensus       152 ~~~r~l~V~~a~~~~  166 (177)
                         ++|+|+|++...
T Consensus        74 ---~~l~v~~a~~~~   85 (104)
T d1weya_          74 ---KEMKLYFAQTLH   85 (104)
T ss_dssp             ---EECEEECCCCSS
T ss_pred             ---CEeEEeecccCC
Confidence               589999997653

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=1.5e-17  Score=113.64  Aligned_cols=80  Identities=15%  Similarity=0.178  Sum_probs=65.2

Q ss_pred             CCCCeEEEcC--CCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCC
Q 030444           75 DASSTLYVEG--LPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDP  152 (177)
Q Consensus        75 ~~~~tLfV~n--Lp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~  152 (177)
                      .++++|||.|  ||+++|+++|+++|++||.|.+|+++.++         +||||+|.+.++|++|++.|||+.+.+...
T Consensus        16 ~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~k---------~~aFV~f~~~e~A~~A~~~lng~~i~~~~~   86 (101)
T d2cq2a1          16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK---------PYSFARYRTTEESKRAYVTLNGKEVVDDLG   86 (101)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTTC---------SCEEEEESSHHHHHHHHHHTTTCEEECTTS
T ss_pred             CCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccCc---------cEEEEEECCHHHHHHHHHHhCCCCCCCCCC
Confidence            3478999955  99999999999999999999999887654         599999999999999999999999866421


Q ss_pred             CCcceEEEeec
Q 030444          153 DSKFLRLQFSR  163 (177)
Q Consensus       153 ~~r~l~V~~a~  163 (177)
                      ..-++.+.|.+
T Consensus        87 ~~i~~~~~~~~   97 (101)
T d2cq2a1          87 QKITLYLNFVE   97 (101)
T ss_dssp             CEEECEEEEES
T ss_pred             cEEEEEEEeee
Confidence            11145556654

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=1.7e-17  Score=123.39  Aligned_cols=81  Identities=10%  Similarity=0.229  Sum_probs=73.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|+.||.|..+.++.++   .+++++|||||+|.+.++|++|++ +++..+.+     +.
T Consensus        97 ~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~---~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G-----~~  167 (183)
T d1u1qa_          97 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR---GSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNG-----HN  167 (183)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT---TTCCEEEEEEEEESCHHHHHHHHT-SSCEEETT-----EE
T ss_pred             cceeEEccCCCcCCHHHHhhhhccCCceeeeeeeccc---ccCccceeEEEEECCHHHHHHHHH-hCCCeECC-----EE
Confidence            6899999999999999999999999999999999887   678899999999999999999996 78888866     58


Q ss_pred             eEEEeecCCC
Q 030444          157 LRLQFSRNPG  166 (177)
Q Consensus       157 l~V~~a~~~~  166 (177)
                      |+|.+|.++.
T Consensus       168 i~V~~A~~k~  177 (183)
T d1u1qa_         168 CEVRKALSKQ  177 (183)
T ss_dssp             EEEEECCCHH
T ss_pred             EEEEecCCcc
Confidence            9999997653

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=1.6e-19  Score=120.74  Aligned_cols=81  Identities=14%  Similarity=0.260  Sum_probs=65.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecC--cccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCc
Q 030444           78 STLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKE--SKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSK  155 (177)
Q Consensus        78 ~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~--~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r  155 (177)
                      ++|||+|||+++||++|+++|++||.+..+.+....  ....+++++|||||+|.+.++|++|++ |||+.+.+     +
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~G-----r   75 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQG-----Q   75 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSSS-----S
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEECC-----E
Confidence            689999999999999999999999987766554322  011346788999999999999999985 99999976     4


Q ss_pred             ceEEEeecC
Q 030444          156 FLRLQFSRN  164 (177)
Q Consensus       156 ~l~V~~a~~  164 (177)
                      .|+|+.++.
T Consensus        76 ~l~V~r~k~   84 (90)
T d1u2fa_          76 SLKIRRPHD   84 (90)
T ss_dssp             CCCCBCTTC
T ss_pred             EEEECCCCC
Confidence            799976543

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.63  E-value=1.9e-17  Score=113.63  Aligned_cols=76  Identities=12%  Similarity=0.113  Sum_probs=69.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcce
Q 030444           78 STLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFL  157 (177)
Q Consensus        78 ~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~l  157 (177)
                      +.++|.+++.+++|++|+++|++||.|.+|+|+.+.    +++++|||||+|.+.++|.+|++.|||..+.+     |+|
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~----~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~g-----r~i   98 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL----GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNG-----QPI   98 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS----SSSSEEEEEEEESCHHHHHHHHHHHTTCEETT-----EEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCC----CCCEeeEEEEEEechhHHHHHHHHHCCCEECC-----EEE
Confidence            458899999999999999999999999999997664    68899999999999999999999999999966     589


Q ss_pred             EEEee
Q 030444          158 RLQFS  162 (177)
Q Consensus       158 ~V~~a  162 (177)
                      +|+|+
T Consensus        99 ~v~~s  103 (104)
T d1jmta_          99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEC
Confidence            99987

>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=99.59  E-value=1.4e-15  Score=105.54  Aligned_cols=65  Identities=9%  Similarity=0.045  Sum_probs=58.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCH-HHHHHHHHHhCCCeeCCC
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENP-ACAATALSALQGYRMDED  150 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~-~~A~~Ai~~l~g~~l~~~  150 (177)
                      +-.+||+|||+++|+++|+++|++||.|.+|+|+.++         +||||.|.+. ++|..|+..|++..+...
T Consensus        11 ~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~k---------g~gfV~F~~~~~~A~~a~~~~~~~~l~~~   76 (113)
T d1owxa_          11 CLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGA---------KEGIILFKEKAKEALGKAKDANNGNLQLR   76 (113)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTC---------SEEEEEESSCHHHHHHHHHHTTTSCBCTT
T ss_pred             CeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecCC---------ceEEEEecCcHHHHHHHHHHhcCCceecC
Confidence            4556999999999999999999999999999997653         6999999985 789999999999999774

>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=99.54  E-value=6.7e-15  Score=109.07  Aligned_cols=78  Identities=13%  Similarity=0.201  Sum_probs=65.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .++|||+|||+++|+++|+++|++||.|.++.++.+.   .++.++|||||+|.+.++|++|+..+ +..+..     +.
T Consensus         6 ~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~---~~~~~~g~afv~f~~~~~a~~a~~~~-~~~~~~-----~~   76 (183)
T d1u1qa_           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDP---NTKRSRGFGFVTYATVEEVDAAMNAR-PHKVDG-----RV   76 (183)
T ss_dssp             HHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT---TTCCEEEEEEEEESSHHHHHHHHHTC-SCEETT-----EE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecc---cCCCccCceecccCCHHHHHHHHHhc-CCcccc-----cc
Confidence            4799999999999999999999999999999999876   57889999999999999999999654 444533     34


Q ss_pred             eEEEeec
Q 030444          157 LRLQFSR  163 (177)
Q Consensus       157 l~V~~a~  163 (177)
                      +.+....
T Consensus        77 ~~~~~~~   83 (183)
T d1u1qa_          77 VEPKRAV   83 (183)
T ss_dssp             CEEEECC
T ss_pred             hhhhhhh
Confidence            6665543

>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=99.51  E-value=2.2e-14  Score=97.21  Aligned_cols=78  Identities=15%  Similarity=0.236  Sum_probs=66.0

Q ss_pred             CCCeEEEcCC--CCCCC---------HHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCC
Q 030444           76 ASSTLYVEGL--PADST---------KREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQG  144 (177)
Q Consensus        76 ~~~tLfV~nL--p~~~t---------e~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g  144 (177)
                      .+++|+|.||  |.++.         +++|++.|++||.|..|++..++       ++||+||+|.+.++|.+|++.|||
T Consensus         7 ~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~-------~~G~~fV~f~~~e~A~~A~~~lng   79 (99)
T d2dita1           7 HERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRH-------PDGVASVSFRDPEEADYCIQTLDG   79 (99)
T ss_dssp             SCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTC-------TTCEEEEECSCHHHHHHHHHHSTT
T ss_pred             CccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCC-------CccEEEEEECCHHHHHHHHHHhCC
Confidence            3799999999  65432         36899999999999999886653       458999999999999999999999


Q ss_pred             CeeCCCCCCCcceEEEeecCC
Q 030444          145 YRMDEDDPDSKFLRLQFSRNP  165 (177)
Q Consensus       145 ~~l~~~~~~~r~l~V~~a~~~  165 (177)
                      ..+.+     |+|+|+|+..+
T Consensus        80 ~~~~g-----r~i~v~~~~g~   95 (99)
T d2dita1          80 RWFGG-----RQITAQAWDGT   95 (99)
T ss_dssp             CEETT-----EECEEEECCSC
T ss_pred             cEECC-----EEEEEEEeCCc
Confidence            99966     68999998543

>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=99.43  E-value=9.6e-14  Score=90.65  Aligned_cols=71  Identities=15%  Similarity=0.135  Sum_probs=58.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcc
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKF  156 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~  156 (177)
                      .+.|||+++|++++++.|+ +|++||.|.++++..+         ++||||+|.++++|++|++ +||..|.++    ..
T Consensus         4 ~~wV~V~G~p~~~~~~il~-~F~~~G~I~~~~~~~~---------~~~~fV~f~~~~~A~~Al~-~nG~~~~g~----~~   68 (81)
T d1wwha1           4 DTWVTVFGFPQASASYILL-QFAQYGNILKHVMSNT---------GNWMHIRYQSKLQARKALS-KDGRIFGES----IM   68 (81)
T ss_dssp             GGEEEEECCCGGGHHHHHH-HHHTTSCEEEEEECSS---------SSEEEEEESSHHHHHHHHT-TTTCEETTT----EE
T ss_pred             ccEEEEECCChHHHHHHHH-HHHhhhhhheEEecCC---------CCEEEEEEcccHHHHHHHh-cCCCeECCc----EE
Confidence            4789999999999976665 7999999999987543         3699999999999999995 999999763    12


Q ss_pred             eEEEee
Q 030444          157 LRLQFS  162 (177)
Q Consensus       157 l~V~~a  162 (177)
                      |.|.-.
T Consensus        69 vgV~~~   74 (81)
T d1wwha1          69 IGVKPC   74 (81)
T ss_dssp             CEEEEC
T ss_pred             EEEEeC
Confidence            456544

>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=99.42  E-value=2.1e-13  Score=92.96  Aligned_cols=81  Identities=12%  Similarity=0.158  Sum_probs=66.2

Q ss_pred             CCeEEEcCC--CCCCC--------HHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCe
Q 030444           77 SSTLYVEGL--PADST--------KREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYR  146 (177)
Q Consensus        77 ~~tLfV~nL--p~~~t--------e~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~  146 (177)
                      +++|+|.||  |.++.        .+||++.|++||.|.+|.|..+... ......|++||+|.+.++|.+|++.|||..
T Consensus         4 s~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~-~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~   82 (104)
T d1o0pa_           4 TEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDG-VEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   82 (104)
T ss_dssp             CSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTS-SSCTTCCEEEEEESCHHHHHHHHHHHSSCC
T ss_pred             CcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCC-CccCCceEEEEEECCHHHHHHHHHHHCCCE
Confidence            799999999  55543        3578999999999999998765421 123356899999999999999999999999


Q ss_pred             eCCCCCCCcceEEEeec
Q 030444          147 MDEDDPDSKFLRLQFSR  163 (177)
Q Consensus       147 l~~~~~~~r~l~V~~a~  163 (177)
                      +.+     |.|+|.|..
T Consensus        83 f~g-----R~v~v~f~~   94 (104)
T d1o0pa_          83 FAN-----RVVVTKYCD   94 (104)
T ss_dssp             SSS-----SCCEEEEEC
T ss_pred             ECC-----eEEEEEEcC
Confidence            966     689999984

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.13  E-value=1.5e-05  Score=51.89  Aligned_cols=87  Identities=14%  Similarity=0.223  Sum_probs=67.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcce
Q 030444           78 STLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFL  157 (177)
Q Consensus        78 ~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~l  157 (177)
                      ++|.|.+||+.+||+++.+.+...+.+.....+..+.... -..-.-|||.|.+.++...-.+.++|+.+.+.+-+..+-
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~-~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D~~g~~~~a   80 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLY-PHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPA   80 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSST-TCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEEC
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCC-CCcceEEEEEeCCHHHHHHHHHHcCCcEEEcCCCCEeee
Confidence            5789999999999999999999999888777766542211 112246999999999999999999999998874223356


Q ss_pred             EEEeecCC
Q 030444          158 RLQFSRNP  165 (177)
Q Consensus       158 ~V~~a~~~  165 (177)
                      .|+||-.+
T Consensus        81 ~VE~AP~q   88 (91)
T d1uw4a_          81 IVEFAPFQ   88 (91)
T ss_dssp             EEEECSSC
T ss_pred             EEEEcCcc
Confidence            78888543

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.30  E-value=0.00034  Score=42.82  Aligned_cols=60  Identities=20%  Similarity=0.206  Sum_probs=49.4

Q ss_pred             HHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCeeCCCCCCCcceEEEeec
Q 030444           93 EVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRMDEDDPDSKFLRLQFSR  163 (177)
Q Consensus        93 ~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l~~~~~~~r~l~V~~a~  163 (177)
                      -|...|.+++.|.++.|....    .+..  .|-|...+.++|..|+..||.++|..     ++|.|.|+.
T Consensus        12 ~L~~~f~~h~~V~sv~l~~~~----dg~~--~A~V~v~~~q~A~~~v~~LhR~KiG~-----KRI~Vs~~~   71 (73)
T d2dgxa1          12 LLQEAFARHGKVKSVELSPHT----DYQL--KAVVQMENLQDAIGAVNSLHRYKIGS-----KKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHSCEEEEEECSCC----STTC--CEEEEESSHHHHHHHHHHHTTEEETT-----EEEEEEECC
T ss_pred             HHHHHHHhheeEEEEEEEecc----CCcE--EEEEEcCCHHHHHHHHHHHHHHhcCC-----eEEEEEEec
Confidence            455678899999999987653    2332  69999999999999999999999965     589999873

>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=97.23  E-value=0.00013  Score=46.91  Aligned_cols=68  Identities=15%  Similarity=0.237  Sum_probs=52.6

Q ss_pred             CCeEEEcCCCCCC------CH---HHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhCCCee
Q 030444           77 SSTLYVEGLPADS------TK---REVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQGYRM  147 (177)
Q Consensus        77 ~~tLfV~nLp~~~------te---~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~g~~l  147 (177)
                      .-||.|.-..++.      +|   ++|-+.|.+||+|.-+|++.++           -.|+|.+-+.|.+|+ .+++.++
T Consensus        15 DgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d~-----------mwVTF~dG~SAL~al-~l~g~~v   82 (95)
T d1ufwa_          15 DATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ-----------MLVTFADSHSALSVL-DVDGMKV   82 (95)
T ss_dssp             TCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE-----------EEEECSCSHHHHHHH-HGGGSEE
T ss_pred             CcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCCe-----------EEEEECCcHHHHHHh-ccCCeEE
Confidence            3677775444332      22   3677888999999999998874           899999999999998 6999999


Q ss_pred             CCCCCCCcceEEEe
Q 030444          148 DEDDPDSKFLRLQF  161 (177)
Q Consensus       148 ~~~~~~~r~l~V~~  161 (177)
                      .+     +.|+|..
T Consensus        83 ~G-----~~l~It~   91 (95)
T d1ufwa_          83 KG-----RAVKISG   91 (95)
T ss_dssp             TT-----EEEEEEC
T ss_pred             cc-----eEEEEec
Confidence            76     4788773

>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=97.05  E-value=0.002  Score=41.82  Aligned_cols=56  Identities=13%  Similarity=0.284  Sum_probs=47.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHhhCCCCCEEEEEEeecCcccCCCCcceEEEEEecCHHHHHHHHHHhC
Q 030444           77 SSTLYVEGLPADSTKREVAHIFRPFVGYKEVRLVIKESKLRGGDPLILCFVDFENPACAATALSALQ  143 (177)
Q Consensus        77 ~~tLfV~nLp~~~te~~L~~lF~~~G~i~~v~l~~~~~~~~~g~~kg~afV~f~~~~~A~~Ai~~l~  143 (177)
                      ...||.-..|......||.+||+.||.|. |..+.+.          -|||...+.++|+.++..+.
T Consensus        15 RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~-VswIddT----------Sa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          15 RDHVLHVTFPKEWKTSDLYQLFSAFGNIQ-ISWIDDT----------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCSEEEEECCTTCCHHHHHHHHTTTCSCC-CEEEETT----------EEEEECSCHHHHHHHHHHHH
T ss_pred             cceeEEEeCCcccchhHHHHHhcCCCceE-EEEecCc----------eEEEEecCHHHHHHHHHHhc
Confidence            56788889999999999999999999876 5555553          69999999999999987765