Citrus Sinensis ID: 030819

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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
MAVLGFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKSRAELRQAFKNNPRQN
Secondary Structure (PSIPRED)
cccccccccccccccccHHHHccccccccccccccccccccccccHHHHHHHcccccccccccccccccccccccccccEEEEcccccccHHHHHHHHHccccEEEEEEEcccccccccccEEEEEccHHHHHHHHHHccccccccEEEEEEccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cEEEEcccccccccccccHHHcccccccccccccHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccEEEEEcccccccHHHHHHHHHHHccEEEEEEEEccccccEEEEEEEEEccHHHHHHHHHHHccccccccEEEEEEcccccccccccccccccc
Coil and Loop (DISEMBL)
mavlgflpvpttyfninqNLLIhnltrhspapatpftikrrdfdslfslrqgrgrgacfplaclppsphslstcqpktrlfvsglsfrtseDSLRNAFQGFGQLVEVNLVMDKianrprgfAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKSRAELRQAFKNNPRQN
Flexible Loop (DISEMBL)
MAVLGFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEgmhgkfldgRVIFVEIAKSRAELrqafknnprqn
Low Complexity Region (SEG)
MAVLGFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKSRAELRQAFKNNPRQN
Disordered region (IsUnstruct)
**VLGFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPS**SLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAK****************
Disordered Region (DISOPRED)
**************N****************************************************************LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIF*********************
Disordered Region (DISEMBL)
MAVLGFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKSRAELRQAFKNNPRQN
Disordered Region (DISPRO)
MAVLGFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGAC*****************PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKS***************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAVLGFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKSRAELRQAFKNNPRQN
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	171	2.2.26 [Sep-21-2011]
Q9LIS2	136	Glycine-rich RNA-binding	no	no	0.614	0.772	0.363	1e-13
Q43472	161	Glycine-rich RNA-binding	N/A	no	0.461	0.490	0.443	1e-13
Q9FNR1	309	Glycine-rich RNA-binding	no	no	0.491	0.271	0.357	4e-13
P10979	157	Glycine-rich RNA-binding,	N/A	no	0.502	0.547	0.395	1e-12
Q99070	168	Glycine-rich RNA-binding	N/A	no	0.502	0.511	0.383	2e-12
P49311	169	Glycine-rich RNA-binding	N/A	no	0.450	0.455	0.454	3e-12
Q03878	157	Glycine-rich RNA-binding	N/A	no	0.485	0.528	0.409	3e-12
Q28IQ9	166	Cold-inducible RNA-bindin	yes	no	0.473	0.487	0.414	8e-12
Q9PTX2	164	Cold-inducible RNA-bindin	N/A	no	0.461	0.481	0.430	9e-12
Q42404	427	U1 small nuclear ribonucl	no	no	0.742	0.297	0.284	1e-11

>sp|Q9LIS2|RBG4_ARATH Glycine-rich RNA-binding protein 4, mitochondrial OS=Arabidopsis thaliana GN=RBG4 PE=2 SV=1

 Score = 76.3 bits (186), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 40/110 (36%), Positives = 64/110 (58%), Gaps = 5/110 (4%)

Query: 49  LRQGRGRGACFPLACLPPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVN 108
           LRQG  + +  P+  +  S   +S+     +LFV GLS+ T + SL+ AF  FG++ E  
Sbjct: 11  LRQGVSQSSNGPVTSMLGSLRYMSS-----KLFVGGLSWGTDDSSLKQAFTSFGEVTEAT 65

Query: 109 LVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKSRA 158
           ++ D+   R RGF F+ ++ E+ +  AI+ M GK L+GR I V +A  R+
Sbjct: 66  VIADRETGRSRGFGFVSFSCEDSANNAIKEMDGKELNGRQIRVNLATERS 115

Possibly has a role in RNA transcription or processing during stress. Binds sequence non-specifically to RNAs and DNAs.
Arabidopsis thaliana (taxid: 3702)

>sp|Q43472|GRP_HORVU Glycine-rich RNA-binding protein blt801 OS=Hordeum vulgare GN=blt801 PE=1 SV=1

 Score = 75.9 bits (185), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 35/79 (44%), Positives = 53/79 (67%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           R FV GL + T + SL+NAF  +G +++  ++ D+   R RGF F+ +A++E  R+AIE 
Sbjct: 7   RCFVGGLRWATDDQSLQNAFSKYGDVIDSKIITDRETGRSRGFGFVTFASDEAMRQAIEA 66

Query: 139 MHGKFLDGRVIFVEIAKSR 157
           M+G+ LDGR I V  A+SR
Sbjct: 67  MNGQDLDGRNITVNEAQSR 85

Binds single-stranded DNA and homoribopolymers of guanine, uracil and adenine, but not cytosine. Also binds RNA, with a preference for RNA containing a high proportion of adenine within an open loop structure. Possibly has a role in RNA transcription or processing during stress.

Hordeum vulgare (taxid: 4513)

>sp|Q9FNR1|RBG3_ARATH Glycine-rich RNA-binding protein 3, mitochondrial OS=Arabidopsis thaliana GN=RBG3 PE=2 SV=1

 Score = 73.9 bits (180), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 30/84 (35%), Positives = 52/84 (61%)

Query: 74  CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESR 133
           C   ++LF+ G+++   EDSLR AF  +G++V+  +++D+   R RGF F+ + + E + 
Sbjct: 36  CMSSSKLFIGGMAYSMDEDSLREAFTKYGEVVDTRVILDRETGRSRGFGFVTFTSSEAAS 95

Query: 134 RAIEGMHGKFLDGRVIFVEIAKSR 157
            AI+ + G+ L GRV+ V  A  R
Sbjct: 96  SAIQALDGRDLHGRVVKVNYANDR 119

Possibly has a role in RNA transcription or processing during stress.

Arabidopsis thaliana (taxid: 3702)

>sp|P10979|GRPA_MAIZE Glycine-rich RNA-binding, abscisic acid-inducible protein OS=Zea mays GN=RAB15 PE=1 SV=1

 Score = 72.8 bits (177), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 34/86 (39%), Positives = 54/86 (62%)

Query: 71  LSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEE 130
           ++    + R FV GL++ TS +SL NAF  +G++++  ++ D+   R RGF F+ +++E 
Sbjct: 1   MAAADVEYRCFVGGLAWATSNESLENAFASYGEILDSKVITDRETGRSRGFGFVTFSSEN 60

Query: 131 ESRRAIEGMHGKFLDGRVIFVEIAKS 156
               AIE M+GK LDGR I V  A+S
Sbjct: 61  SMLDAIENMNGKELDGRNITVNQAQS 86

Possibly has a role in RNA transcription or processing during stress.

Zea mays (taxid: 4577)

>sp|Q99070|GRP2_SORBI Glycine-rich RNA-binding protein 2 OS=Sorghum bicolor GN=GRP2 PE=2 SV=1

 Score = 71.6 bits (174), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 33/86 (38%), Positives = 54/86 (62%)

Query: 71  LSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEE 130
           ++    + R FV GL++ T+ ++L  AF  FGQ+++  ++ D+   R RGF F+ +++E+
Sbjct: 1   MAAADVEYRCFVGGLAWATNNETLEQAFANFGQVIDSKVITDRETGRSRGFGFVTFSSEQ 60

Query: 131 ESRRAIEGMHGKFLDGRVIFVEIAKS 156
               AIE M+GK LDGR I V  A+S
Sbjct: 61  SMLDAIENMNGKELDGRNITVNQAQS 86

Possibly has a role in RNA transcription or processing during stress.

Sorghum bicolor (taxid: 4558)

>sp|P49311|GRP2_SINAL Glycine-rich RNA-binding protein GRP2A OS=Sinapis alba PE=2 SV=1

 Score = 71.6 bits (174), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 35/77 (45%), Positives = 49/77 (63%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           R FV GL++ T E SL  AF  FG+LV+  ++ D+   R RGF F+ +  E+  + AIEG
Sbjct: 9   RCFVGGLAWATDERSLETAFSQFGELVDSKIINDRETGRSRGFGFVTFKDEKSMKDAIEG 68

Query: 139 MHGKFLDGRVIFVEIAK 155
           M+G+ LDGR I V  A+
Sbjct: 69  MNGQDLDGRSITVNEAQ 85

May play a general role in circadian phenomena associated with meristematic tissue.

Sinapis alba (taxid: 3728)

>sp|Q03878|GRP1_DAUCA Glycine-rich RNA-binding protein OS=Daucus carota PE=2 SV=1

 Score = 71.2 bits (173), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 34/83 (40%), Positives = 52/83 (62%)

Query: 74  CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESR 133
            + + R FV GL++ T+++SL  AF  FG + +  ++ D+   R RGF F+ +  E+  R
Sbjct: 2   AEVEYRCFVGGLAWATNDESLEQAFSQFGDITDSKIINDRETGRSRGFGFVTFKDEKSMR 61

Query: 134 RAIEGMHGKFLDGRVIFVEIAKS 156
            AIEGM+G+ LDGR I V  A+S
Sbjct: 62  DAIEGMNGQELDGRNITVNEAQS 84

May play a role in the biosynthesis and processing of heterogeneous nuclear RNA and in the maturation of specific mRNAs in response to wounding.

Daucus carota (taxid: 4039)

>sp|Q28IQ9|CIRBP_XENTR Cold-inducible RNA-binding protein OS=Xenopus tropicalis GN=cirbp PE=2 SV=1

 Score = 69.7 bits (169), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 34/82 (41%), Positives = 54/82 (65%), Gaps = 1/82 (1%)

Query: 73  TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEES 132
           +C  + +LFV GL+F T+E+SL   F  +GQ+ EV +V D+ + R RGF F+ +   E++
Sbjct: 2   SC-DEGKLFVGGLNFETTEESLEQVFSKYGQVAEVVVVKDRESKRSRGFGFVTFENPEDA 60

Query: 133 RRAIEGMHGKFLDGRVIFVEIA 154
           + A+  M+GK +DGR I V+ A
Sbjct: 61  KDAMMAMNGKSVDGRQIRVDQA 82

Cold-inducible mRNA binding protein. Acts cooperatively with elavl1/elrA to stabilize AU-rich element (ARE)-containing mRNAs by binding to themm and inhibiting their deadenylation. Essential for embryonic gastrulation and neural development, acting to maintain the expression of a set of adhesion molecules, and cell movement during embryogenesis. Required for pronephros development.

Xenopus tropicalis (taxid: 8364)

>sp|Q9PTX2|CIRBP_LITCT Cold-inducible RNA-binding protein OS=Lithobates catesbeiana GN=cirbp PE=2 SV=1

 Score = 69.7 bits (169), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 34/79 (43%), Positives = 49/79 (62%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
            + +LFV GLSF T E  L   F  +GQ+ EV +V D+   R RGF F+ +   E+++ A
Sbjct: 4   DEGKLFVGGLSFDTDEQCLETVFSKYGQIQEVVVVKDRETKRSRGFGFVTFENCEDAKDA 63

Query: 136 IEGMHGKFLDGRVIFVEIA 154
           + GM+GK +DGR I V+ A
Sbjct: 64  MAGMNGKTVDGRQIRVDQA 82

Cold-inducible mRNA binding protein. Acts cooperatively with elavl1/elrA to stabilize AU-rich element (ARE)-containing mRNAs by binding to them and inhibiting their deadenylation. Essential for embryonic gastrulation and neural development, acting to maintain the expression of a set of adhesion molecules, and cell movement during embryogenesis. Required for pronephros development (By similarity). May play a role in hibernation.

Lithobates catesbeiana (taxid: 8400)

>sp|Q42404|RU17_ARATH U1 small nuclear ribonucleoprotein 70 kDa OS=Arabidopsis thaliana GN=RNU1 PE=1 SV=1

 Score = 68.9 bits (167), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 37/130 (28%), Positives = 68/130 (52%), Gaps = 3/130 (2%)

Query: 30  PAPATPFTIKRRDFDSLFSLRQGRG-RGACFPLACLPPSPHSLSTCQPKTRLFVSGLSFR 88
           P P      ++R+   +  LR  +G   A   L    P+    +T  P   LFVS L++ 
Sbjct: 91  PKPEVELPSQKRE--RIHKLRLEKGVEKAAEDLKKYDPNNDPNATGDPYKTLFVSRLNYE 148

Query: 89  TSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRV 148
           +SE  ++  F+ +G +  V+LV D++ N+P+G+AF+ Y    + + A +   G+ +DGR 
Sbjct: 149 SSESKIKREFESYGPIKRVHLVTDQLTNKPKGYAFIEYMHTRDMKAAYKQADGQKIDGRR 208

Query: 149 IFVEIAKSRA 158
           + V++ + R 
Sbjct: 209 VLVDVERGRT 218

Mediates the splicing of pre-mRNA by binding to the loop I region of U1-snRNA.

Arabidopsis thaliana (taxid: 3702)

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	171
225464267	170	PREDICTED: cold-inducible RNA-binding pr	0.596	0.6	0.807	1e-40
388505224	187	unknown [Lotus japonicus]	0.690	0.631	0.690	3e-38
351725889	180	uncharacterized protein LOC100305561 [Gl	0.631	0.6	0.701	3e-38
224120444	181	predicted protein [Populus trichocarpa]	0.508	0.480	0.816	2e-35
449507141	175	PREDICTED: 40S ribosomal protein S19, mi	0.508	0.497	0.728	1e-31
15219486	181	RNA recognition motif-containing protein	0.543	0.513	0.656	7e-31
297842099	181	RNA recognition motif-containing protein	0.508	0.480	0.712	1e-30
222629430	149	hypothetical protein OsJ_15917 [Oryza sa	0.485	0.557	0.746	2e-30
218195435	152	hypothetical protein OsI_17125 [Oryza sa	0.485	0.546	0.746	3e-30
226498016	147	RNA binding protein [Zea mays] gi|195649	0.555	0.646	0.683	1e-29

>gi|225464267|ref|XP_002271224.1| PREDICTED: cold-inducible RNA-binding protein [Vitis vinifera] gi|296088019|emb|CBI35302.3| unnamed protein product [Vitis vinifera]

 Score =  171 bits (433), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 84/104 (80%), Positives = 94/104 (90%), Gaps = 2/104 (1%)

Query: 59  FPLACLPPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRP 118
           F +ACLP SP+  S   PKTRL+VSGLSFRT+E+SLRNAF+ FGQLVEVNLVMDKIANRP
Sbjct: 62  FAVACLPSSPNQPSI--PKTRLYVSGLSFRTTEESLRNAFETFGQLVEVNLVMDKIANRP 119

Query: 119 RGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKSRAELRQ 162
           RGFAFLRY+TEEES +AIEGMHGKFLDGRVIFVE+AK R+ELRQ
Sbjct: 120 RGFAFLRYSTEEESEKAIEGMHGKFLDGRVIFVEVAKPRSELRQ 163

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388505224|gb|AFK40678.1| unknown [Lotus japonicus]

 Score =  162 bits (411), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 87/126 (69%), Positives = 102/126 (80%), Gaps = 8/126 (6%)

Query: 53  RGRGACFPLACLPPSPHSLSTCQPK--------TRLFVSGLSFRTSEDSLRNAFQGFGQL 104
           R +G+C+ LACLPPS  S S+            TRL+VSGLSFRT+E+SLRN F+ FGQL
Sbjct: 61  RIQGSCYLLACLPPSSESSSSSPSAKPSSSAPSTRLYVSGLSFRTTEESLRNCFKNFGQL 120

Query: 105 VEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKSRAELRQAF 164
           V+VNLVMDK+ANRPRGFAFLRYATEEES++AIEGMHGKFLDGRVIFVE+AK R+ELRQ F
Sbjct: 121 VDVNLVMDKLANRPRGFAFLRYATEEESQKAIEGMHGKFLDGRVIFVEVAKPRSELRQRF 180

Query: 165 KNNPRQ 170
           + N  Q
Sbjct: 181 QQNTMQ 186

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351725889|ref|NP_001237108.1| uncharacterized protein LOC100305561 [Glycine max] gi|255625921|gb|ACU13305.1| unknown [Glycine max]

 Score =  162 bits (411), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 80/114 (70%), Positives = 94/114 (82%), Gaps = 6/114 (5%)

Query: 53  RGRGACFPLACLPPSPHSL------STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVE 106
           R + +C  LACLPP   +       S   P+T+L+VSGLSFRT+E+SLRNAF+ FGQLVE
Sbjct: 57  RNKASCSVLACLPPESSTSSSTAKPSFPSPQTKLYVSGLSFRTTEESLRNAFKNFGQLVE 116

Query: 107 VNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKSRAEL 160
           V LVMD+IANRPRGFAFLRYATEEES++AIEGMHGKFLDGRVIFVE+AK R+EL
Sbjct: 117 VKLVMDRIANRPRGFAFLRYATEEESQKAIEGMHGKFLDGRVIFVEVAKPRSEL 170

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224120444|ref|XP_002318331.1| predicted protein [Populus trichocarpa] gi|222859004|gb|EEE96551.1| predicted protein [Populus trichocarpa]

 Score =  153 bits (387), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 71/87 (81%), Positives = 83/87 (95%)

Query: 77  KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
           KT+L+VSGLSFRT+E+SLRNAFQ FGQLV+VNLVMDK+A RPRGFAFLRY TEEE+++AI
Sbjct: 89  KTKLYVSGLSFRTTEESLRNAFQNFGQLVDVNLVMDKVAKRPRGFAFLRYETEEEAQKAI 148

Query: 137 EGMHGKFLDGRVIFVEIAKSRAELRQA 163
           EGMHGKFLDGRVIFVE+AK R+ELRQ+
Sbjct: 149 EGMHGKFLDGRVIFVEVAKPRSELRQS 175

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449507141|ref|XP_004162944.1| PREDICTED: 40S ribosomal protein S19, mitochondrial-like [Cucumis sativus]

 Score =  141 bits (355), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 67/92 (72%), Positives = 80/92 (86%), Gaps = 5/92 (5%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
           P TRL++SGLSFRT+E+SLRNAF+ FGQLVEVNLVMD++ANRPRGFAFLRYA+EEES++A
Sbjct: 87  PSTRLYISGLSFRTTEESLRNAFKSFGQLVEVNLVMDRLANRPRGFAFLRYASEEESQKA 146

Query: 136 IEGMHGKFLDGRVIFVEIAKSRAELRQAFKNN 167
           IEGMHGK       FVE+AKSR+ELRQ  + N
Sbjct: 147 IEGMHGK-----GDFVEVAKSRSELRQGLEEN 173

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15219486|ref|NP_177494.1| RNA recognition motif-containing protein [Arabidopsis thaliana] gi|11120799|gb|AAG30979.1|AC012396_15 RNA-binding glycine-rich protein, putative [Arabidopsis thaliana] gi|62867629|gb|AAY17418.1| At1g73530 [Arabidopsis thaliana] gi|114050615|gb|ABI49457.1| At1g73530 [Arabidopsis thaliana] gi|332197351|gb|AEE35472.1| RNA recognition motif-containing protein [Arabidopsis thaliana]

 Score =  138 bits (348), Expect = 7e-31,   Method: Compositional matrix adjust.
 Identities = 63/96 (65%), Positives = 84/96 (87%), Gaps = 3/96 (3%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
           PKT+L+VSGLSFRT+ED+LR+ F+ FG L+ +N+VMDK+ANRP+GFAFLRY TEEE+ +A
Sbjct: 75  PKTKLYVSGLSFRTTEDTLRDTFEQFGNLIHMNMVMDKVANRPKGFAFLRYETEEEAMKA 134

Query: 136 IEGMHGKFLDGRVIFVEIAKSRAELRQAFKNNPRQN 171
           I+GMHGKFLDGRVIFVE AK+R+++ +A    PR++
Sbjct: 135 IQGMHGKFLDGRVIFVEEAKTRSDMSRA---KPRRD 167

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297842099|ref|XP_002888931.1| RNA recognition motif-containing protein [Arabidopsis lyrata subsp. lyrata] gi|297334772|gb|EFH65190.1| RNA recognition motif-containing protein [Arabidopsis lyrata subsp. lyrata]

 Score =  137 bits (345), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 62/87 (71%), Positives = 80/87 (91%)

Query: 77  KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
           KT+L+VSGLSFRT+ED+LR+ F+ FG+L+ +NLVMDK+ANRPRGFAFLRY TEEE+ +AI
Sbjct: 76  KTKLYVSGLSFRTTEDTLRDTFEQFGKLIHMNLVMDKVANRPRGFAFLRYETEEEAMKAI 135

Query: 137 EGMHGKFLDGRVIFVEIAKSRAELRQA 163
           +GMHGKFLDGRVIFVE AK+R+++ +A
Sbjct: 136 QGMHGKFLDGRVIFVEEAKTRSDISRA 162

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|222629430|gb|EEE61562.1| hypothetical protein OsJ_15917 [Oryza sativa Japonica Group]

 Score =  137 bits (344), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 62/83 (74%), Positives = 76/83 (91%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           +RL+VSGLSFRT+E+SLRNAF+ FGQL EVNLVM+++A RPRGFAFL YA+EEES+ A+E
Sbjct: 67  SRLYVSGLSFRTTEESLRNAFERFGQLTEVNLVMERVAKRPRGFAFLSYASEEESKNAME 126

Query: 138 GMHGKFLDGRVIFVEIAKSRAEL 160
           GM GKFLDGRVIFVE+A+ R+EL
Sbjct: 127 GMQGKFLDGRVIFVEVARQRSEL 149

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|218195435|gb|EEC77862.1| hypothetical protein OsI_17125 [Oryza sativa Indica Group]

 Score =  136 bits (343), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 62/83 (74%), Positives = 76/83 (91%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           +RL+VSGLSFRT+E+SLRNAF+ FGQL EVNLVM+++A RPRGFAFL YA+EEES+ A+E
Sbjct: 70  SRLYVSGLSFRTTEESLRNAFERFGQLTEVNLVMERVAKRPRGFAFLSYASEEESKNAME 129

Query: 138 GMHGKFLDGRVIFVEIAKSRAEL 160
           GM GKFLDGRVIFVE+A+ R+EL
Sbjct: 130 GMQGKFLDGRVIFVEVARQRSEL 152

Source: Oryza sativa Indica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|226498016|ref|NP_001151732.1| RNA binding protein [Zea mays] gi|195649405|gb|ACG44170.1| RNA binding protein [Zea mays]

 Score =  134 bits (337), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 67/98 (68%), Positives = 76/98 (77%), Gaps = 3/98 (3%)

Query: 62  ACLPPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGF 121
           ACLPP   S       TRL+VSGLSFRT+E SLR+AF+ FG L EV LVMD++A RPRGF
Sbjct: 52  ACLPPPSTSHGAA---TRLYVSGLSFRTTERSLRDAFEKFGDLTEVCLVMDRVAKRPRGF 108

Query: 122 AFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKSRAE 159
           AFL Y  EEE+R A+EGMHGKFLDGRVIFVE+AK R E
Sbjct: 109 AFLSYTGEEEARGAMEGMHGKFLDGRVIFVEVAKRRVE 146

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

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	171
TAIR|locus:2206850	181	AT1G73530 [Arabidopsis thalian	0.713	0.674	0.561	4.7e-32
TAIR|locus:2172144	156	AT5G54580 [Arabidopsis thalian	0.549	0.602	0.484	3.1e-19
TAIR|locus:2088756	374	AT3G20930 [Arabidopsis thalian	0.473	0.216	0.536	3.4e-19
TAIR|locus:2077137	102	AT3G46020 [Arabidopsis thalian	0.543	0.911	0.419	1.6e-17
TAIR|locus:2049816	142	AT2G37510 [Arabidopsis thalian	0.520	0.626	0.466	6e-16
TAIR|locus:2160752	146	AT5G06210 [Arabidopsis thalian	0.485	0.568	0.421	2.6e-15
TAIR|locus:2039590	116	AT2G27330 [Arabidopsis thalian	0.450	0.663	0.389	2.3e-14
UNIPROTKB|Q43472	161	blt801 "Glycine-rich RNA-bindi	0.461	0.490	0.443	7.9e-14
TAIR|locus:2076096	136	GRP4 "glycine-rich RNA-binding	0.649	0.816	0.358	1e-13
TAIR|locus:2159401	309	GR-RBP3 "glycine-rich RNA-bind	0.538	0.297	0.347	2.7e-13

TAIR|locus:2206850 AT1G73530 [Arabidopsis thaliana (taxid:3702)]

 Score = 351 (128.6 bits), Expect = 4.7e-32, P = 4.7e-32
 Identities = 73/130 (56%), Positives = 98/130 (75%)

Query:    46 LFSLRQGRGRGACFPLACLPP----SPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGF 101
             + S R+ R  G     +CL      SP S S+  PKT+L+VSGLSFRT+ED+LR+ F+ F
Sbjct:    42 VISARRRRDIGGVLISSCLSTDSSSSPPS-SSSGPKTKLYVSGLSFRTTEDTLRDTFEQF 100

Query:   102 GQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKSRAELR 161
             G L+ +N+VMDK+ANRP+GFAFLRY TEEE+ +AI+GMHGKFLDGRVIFVE AK+R+++ 
Sbjct:   101 GNLIHMNMVMDKVANRPKGFAFLRYETEEEAMKAIQGMHGKFLDGRVIFVEEAKTRSDMS 160

Query:   162 QAFKNNPRQN 171
             +A    PR++
Sbjct:   161 RA---KPRRD 167

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0008150 "biological_process" evidence=ND

GO:0009507 "chloroplast" evidence=IDA

TAIR|locus:2172144 AT5G54580 [Arabidopsis thaliana (taxid:3702)]

 Score = 230 (86.0 bits), Expect = 3.1e-19, P = 3.1e-19
 Identities = 47/97 (48%), Positives = 66/97 (68%)

Query:    75 QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
             +P T LFVSGLS RT+ + LR AF  FG++ +  +V D+++   +GF F+RYAT E+S +
Sbjct:    53 EPSTNLFVSGLSKRTTSEGLRTAFAQFGEVADAKVVTDRVSGYSKGFGFVRYATLEDSAK 112

Query:   135 AIEGMHGKFLDGRVIFVEIAKSRAELRQAFKNNPRQN 171
              I GM GKFLDG VIF E A+ R E  Q+++  P+ N
Sbjct:   113 GIAGMDGKFLDGWVIFAEYARPR-EQSQSYQ--PQNN 146

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0008150 "biological_process" evidence=ND

GO:0005739 "mitochondrion" evidence=IDA

TAIR|locus:2088756 AT3G20930 [Arabidopsis thaliana (taxid:3702)]

 Score = 232 (86.7 bits), Expect = 3.4e-19, P = 3.4e-19
 Identities = 44/82 (53%), Positives = 66/82 (80%)

Query:    77 KTR-LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
             KT+ LF++GLSF TSE +LR AF+GFG+LVEV ++MDKI+ R +G+AFL Y TEE +  A
Sbjct:   280 KTKKLFITGLSFYTSEKTLRAAFEGFGELVEVKIIMDKISKRSKGYAFLEYTTEEAAGTA 339

Query:   136 IEGMHGKFLDGRVIFVEIAKSR 157
             ++ M+GK ++G +I V++AK++
Sbjct:   340 LKEMNGKIINGWMIVVDVAKTK 361

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0008150 "biological_process" evidence=ND

GO:0000023 "maltose metabolic process" evidence=RCA

GO:0010027 "thylakoid membrane organization" evidence=RCA

GO:0019252 "starch biosynthetic process" evidence=RCA

TAIR|locus:2077137 AT3G46020 [Arabidopsis thaliana (taxid:3702)]

 Score = 214 (80.4 bits), Expect = 1.6e-17, P = 1.6e-17
 Identities = 39/93 (41%), Positives = 63/93 (67%)

Query:    79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
             +LFVS LS  T++ SLR  F  FGQ+ E  L+ D    RP+GF F+ + +E+++R+A++ 
Sbjct:     8 QLFVSRLSAYTTDQSLRQLFSPFGQIKEARLIRDSETQRPKGFGFITFDSEDDARKALKS 67

Query:   139 MHGKFLDGRVIFVEIAKSRAELRQAFKNNPRQN 171
             + GK +DGR+IFVE+AK+  E+R    +N  ++
Sbjct:    68 LDGKIVDGRLIFVEVAKNAEEVRAGINSNKAED 100

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2049816 AT2G37510 [Arabidopsis thaliana (taxid:3702)]

 Score = 199 (75.1 bits), Expect = 6.0e-16, P = 6.0e-16
 Identities = 42/90 (46%), Positives = 61/90 (67%)

Query:    79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
             RLFVSGLS  T+ + L++AF  FGQLV+  ++ D+ + R +GF F+ YAT E++ +A   
Sbjct:    35 RLFVSGLSRLTTNEKLQDAFASFGQLVDARVITDRDSGRSKGFGFVTYATIEDAEKAKAE 94

Query:   139 MHGKFLDGRVIFVEIAKSRAELRQAFKNNP 168
             M+ KFLDG VIFV+ A+ R E R+  +  P
Sbjct:    95 MNAKFLDGWVIFVDPARPR-EPRRPLQQEP 123

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2160752 AT5G06210 [Arabidopsis thaliana (taxid:3702)]

 Score = 193 (73.0 bits), Expect = 2.6e-15, P = 2.6e-15
 Identities = 35/83 (42%), Positives = 60/83 (72%)

Query:    78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
             ++LF+ GLSF T+E  L  AF   GQ+VE  +VMD++++R +GF F+ +A+ +E+++A+ 
Sbjct:    34 SKLFIGGLSFCTTEQGLSEAFSKCGQVVEAQIVMDRVSDRSKGFGFVTFASADEAQKALM 93

Query:   138 GMHGKFLDGRVIFVEIAKSRAEL 160
               +G+ L+GR IFV+ AK++  L
Sbjct:    94 EFNGQQLNGRTIFVDYAKAKQSL 116

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0008150 "biological_process" evidence=ND

GO:0009507 "chloroplast" evidence=ISM

TAIR|locus:2039590 AT2G27330 [Arabidopsis thaliana (taxid:3702)]

 Score = 184 (69.8 bits), Expect = 2.3e-14, P = 2.3e-14
 Identities = 30/77 (38%), Positives = 60/77 (77%)

Query:    80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
             LFV G+SF ++E++L  AF  +GQ+++V+++MDKI  RP+GFA++ ++++EE+ +A+  +
Sbjct:    23 LFVKGISFSSTEETLTQAFSQYGQVLKVDVIMDKIRCRPKGFAYVTFSSKEEAEKALLEL 82

Query:   140 HGKFLDGRVIFVEIAKS 156
             + + +DGRV+ ++  K+
Sbjct:    83 NAQLVDGRVVILDTTKA 99

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|Q43472 blt801 "Glycine-rich RNA-binding protein blt801" [Hordeum vulgare (taxid:4513)]

 Score = 179 (68.1 bits), Expect = 7.9e-14, P = 7.9e-14
 Identities = 35/79 (44%), Positives = 53/79 (67%)

Query:    79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
             R FV GL + T + SL+NAF  +G +++  ++ D+   R RGF F+ +A++E  R+AIE 
Sbjct:     7 RCFVGGLRWATDDQSLQNAFSKYGDVIDSKIITDRETGRSRGFGFVTFASDEAMRQAIEA 66

Query:   139 MHGKFLDGRVIFVEIAKSR 157
             M+G+ LDGR I V  A+SR
Sbjct:    67 MNGQDLDGRNITVNEAQSR 85

GO:0003697 "single-stranded DNA binding" evidence=IDA

GO:0003723 "RNA binding" evidence=IDA

GO:0009409 "response to cold" evidence=IDA

GO:0009737 "response to abscisic acid stimulus" evidence=IDA

TAIR|locus:2076096 GRP4 "glycine-rich RNA-binding protein 4" [Arabidopsis thaliana (taxid:3702)]

 Score = 178 (67.7 bits), Expect = 1.0e-13, P = 1.0e-13
 Identities = 42/117 (35%), Positives = 67/117 (57%)

Query:    49 LRQGRGRGACFPLACLPPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVN 108
             LRQG  + +  P+  +  S   +S+     +LFV GLS+ T + SL+ AF  FG++ E  
Sbjct:    11 LRQGVSQSSNGPVTSMLGSLRYMSS-----KLFVGGLSWGTDDSSLKQAFTSFGEVTEAT 65

Query:   109 LVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKSRAEL-RQAF 164
             ++ D+   R RGF F+ ++ E+ +  AI+ M GK L+GR I V +A  R+   R +F
Sbjct:    66 VIADRETGRSRGFGFVSFSCEDSANNAIKEMDGKELNGRQIRVNLATERSSAPRSSF 122

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0005739 "mitochondrion" evidence=IDA

GO:0003690 "double-stranded DNA binding" evidence=IDA

GO:0003697 "single-stranded DNA binding" evidence=IDA

GO:0006970 "response to osmotic stress" evidence=IMP

GO:0009409 "response to cold" evidence=IEP

GO:0009414 "response to water deprivation" evidence=IEP

GO:0009651 "response to salt stress" evidence=IMP

GO:0006364 "rRNA processing" evidence=RCA

GO:0009664 "plant-type cell wall organization" evidence=RCA

GO:0042545 "cell wall modification" evidence=RCA

TAIR|locus:2159401 GR-RBP3 "glycine-rich RNA-binding protein 3" [Arabidopsis thaliana (taxid:3702)]

 Score = 177 (67.4 bits), Expect = 2.7e-13, P = 2.7e-13
 Identities = 32/92 (34%), Positives = 54/92 (58%)

Query:    66 PSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLR 125
             PS      C   ++LF+ G+++   EDSLR AF  +G++V+  +++D+   R RGF F+ 
Sbjct:    28 PSLFQAIRCMSSSKLFIGGMAYSMDEDSLREAFTKYGEVVDTRVILDRETGRSRGFGFVT 87

Query:   126 YATEEESRRAIEGMHGKFLDGRVIFVEIAKSR 157
             + + E +  AI+ + G+ L GRV+ V  A  R
Sbjct:    88 FTSSEAASSAIQALDGRDLHGRVVKVNYANDR 119

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005739 "mitochondrion" evidence=IDA

GO:0009409 "response to cold" evidence=IEP

GO:0005524 "ATP binding" evidence=IDA

GO:0005507 "copper ion binding" evidence=IDA

GO:0006626 "protein targeting to mitochondrion" evidence=RCA

GO:0009220 "pyrimidine ribonucleotide biosynthetic process" evidence=RCA

GO:0009909 "regulation of flower development" evidence=RCA

GO:0010228 "vegetative to reproductive phase transition of meristem" evidence=RCA

GO:0034968 "histone lysine methylation" evidence=RCA

---

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

Fail to connect to STRING server

---

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	171
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	7e-26
smart00360	73	smart00360, RRM, RNA recognition motif	1e-23
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	1e-20
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	3e-20
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	1e-19
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	3e-19
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	1e-18
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	1e-18
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	4e-18
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	7e-18
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	1e-17
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	2e-17
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	5e-17
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	9e-17
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	1e-16
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	2e-16
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	3e-16
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	3e-15
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	8e-15
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	1e-14
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	1e-14
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	2e-14
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	2e-14
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	2e-14
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	9e-14
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	1e-13
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	2e-13
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	2e-13
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	2e-13
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	6e-13
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	8e-13
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	9e-13
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	1e-12
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	2e-12
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	2e-12
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	3e-12
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	3e-12
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	3e-12
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	4e-12
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	4e-12
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	4e-12
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	5e-12
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	5e-12
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	6e-12
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	6e-12
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	1e-11
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	1e-11
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	1e-11
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	1e-11
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	2e-11
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	2e-11
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	2e-11
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	3e-11
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	4e-11
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	4e-11
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	4e-11
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	6e-11
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	6e-11
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	7e-11
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	7e-11
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	8e-11
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	8e-11
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	1e-10
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	1e-10
cd12404	77	cd12404, RRM2_NCL, RNA recognition motif 2 in vert	2e-10
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	2e-10
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	2e-10
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	3e-10
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	3e-10
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	4e-10
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	4e-10
cd12585	75	cd12585, RRM2_hnRPDL, RNA recognition motif 2 in h	5e-10
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	5e-10
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	6e-10
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	6e-10
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	7e-10
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	7e-10
cd12305	75	cd12305, RRM_NELFE, RNA recognition motif in negat	7e-10
cd12583	75	cd12583, RRM2_hnRNPD, RNA recognition motif 2 in h	8e-10
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	8e-10
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	9e-10
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	9e-10
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	1e-09
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	1e-09
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	1e-09
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	2e-09
cd12584	80	cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in	2e-09
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	3e-09
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	3e-09
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	3e-09
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	4e-09
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	4e-09
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	4e-09
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	7e-09
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	7e-09
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	9e-09
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	9e-09
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	1e-08
cd12453	86	cd12453, RRM1_RIM4_like, RNA recognition motif 1 i	1e-08
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	1e-08
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	1e-08
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	2e-08
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	2e-08
cd12679	76	cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in	2e-08
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	2e-08
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	2e-08
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	3e-08
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	3e-08
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	4e-08
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	4e-08
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	4e-08
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	5e-08
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	5e-08
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	5e-08
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	6e-08
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	6e-08
cd12758	76	cd12758, RRM1_hnRPDL, RNA recognition motif 1 in h	6e-08
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	6e-08
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	7e-08
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	9e-08
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	9e-08
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	1e-07
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	1e-07
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	1e-07
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	1e-07
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	2e-07
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	2e-07
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	2e-07
cd12302	110	cd12302, RRM_scSet1p_like, RNA recognition motif i	2e-07
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	2e-07
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	3e-07
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	4e-07
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	4e-07
cd12405	72	cd12405, RRM3_NCL, RNA recognition motif 3 in vert	4e-07
cd12573	79	cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA	5e-07
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	5e-07
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	5e-07
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	6e-07
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	7e-07
cd12409	84	cd12409, RRM1_RRT5, RNA recognition motif 1 in yea	8e-07
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	9e-07
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	1e-06
cd12635	81	cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2	1e-06
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	1e-06
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	1e-06
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	1e-06
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	1e-06
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	2e-06
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	2e-06
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	2e-06
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	2e-06
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	2e-06
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	2e-06
cd12319	84	cd12319, RRM4_MRD1, RNA recognition motif 4 in yea	2e-06
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	2e-06
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	2e-06
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	2e-06
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	2e-06
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	2e-06
cd12621	74	cd12621, RRM3_TIA1, RNA recognition motif 3 in nuc	3e-06
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	3e-06
cd12358	73	cd12358, RRM1_VICKZ, RNA recognition motif 1 in th	4e-06
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	4e-06
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	5e-06
cd12470	86	cd12470, RRM1_MSSP1, RNA recognition motif 1 in ve	6e-06
cd12620	73	cd12620, RRM3_TIAR, RNA recognition motif 3 in nuc	7e-06
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	7e-06
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	8e-06
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	9e-06
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	9e-06
cd12369	68	cd12369, RRM4_RBM45, RNA recognition motif 4 in RN	9e-06
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	1e-05
cd12594	74	cd12594, RRM1_SRSF4, RNA recognition motif 1 in ve	1e-05
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	1e-05
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	1e-05
cd12539	103	cd12539, RRM_U2AF35B, RNA recognition motif in spl	1e-05
cd12401	76	cd12401, RRM_eIF4H, RNA recognition motif in eukar	1e-05
cd12232	89	cd12232, RRM3_U2AF65, RNA recognition motif 3 foun	1e-05
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	2e-05
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	2e-05
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	2e-05
cd12467	78	cd12467, RRM_Srp1p_like, RNA recognition motif 1 i	2e-05
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	2e-05
cd12561	81	cd12561, RRM1_RBM5_like, RNA recognition motif 1 i	2e-05
cd12596	70	cd12596, RRM1_SRSF6, RNA recognition motif 1 in ve	2e-05
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	3e-05
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	3e-05
cd12494	72	cd12494, RRM3_hnRNPR, RNA recognition motif 3 in v	3e-05
cd12471	75	cd12471, RRM1_MSSP2, RNA recognition motif 1 in ve	3e-05
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	4e-05
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	4e-05
cd12285	85	cd12285, RRM3_RBM39_like, RNA recognition motif 3	4e-05
cd12466	70	cd12466, RRM2_AtRSp31_like, RNA recognition motif	5e-05
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	5e-05
cd12250	82	cd12250, RRM2_hnRNPR_like, RNA recognition motif 2	5e-05
cd12342	71	cd12342, RRM_Nab3p, RNA recognition motif in yeast	5e-05
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	5e-05
cd12622	74	cd12622, RRM3_PUB1, RNA recognition motif 3 in yea	6e-05
cd12680	75	cd12680, RRM_THOC4, RNA recognition motif in THO c	6e-05
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	6e-05
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	6e-05
cd12247	72	cd12247, RRM2_U1A_like, RNA recognition motif 2 in	7e-05
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	8e-05
cd12550	76	cd12550, RRM_II_PABPN1, RNA recognition motif in t	8e-05
cd12495	72	cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in v	8e-05
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	8e-05
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	9e-05
cd12534	83	cd12534, RRM_SARFH, RNA recognition motif in Droso	1e-04
cd12472	80	cd12472, RRM1_RBMS3, RNA recognition motif 1 found	1e-04
cd12483	79	cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in v	1e-04
cd12551	77	cd12551, RRM_II_PABPN1L, RNA recognition motif in	1e-04
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	1e-04
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	1e-04
cd12244	79	cd12244, RRM2_MSSP, RNA recognition motif 2 in the	1e-04
cd12582	80	cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in	2e-04
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	2e-04
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	2e-04
cd12282	91	cd12282, RRM2_TatSF1_like, RNA recognition motif 2	2e-04
cd12484	78	cd12484, RRM1_RBM46, RNA recognition motif 1 found	2e-04
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	2e-04
cd12636	81	cd12636, RRM2_Bruno_like, RNA recognition motif 2	2e-04
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	2e-04
cd12485	78	cd12485, RRM1_RBM47, RNA recognition motif 1 found	2e-04
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	3e-04
cd12612	82	cd12612, RRM2_SECp43, RNA recognition motif 2 in t	3e-04
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	3e-04
cd12473	85	cd12473, RRM2_MSSP1, RNA recognition motif 2 found	3e-04
cd12773	84	cd12773, RRM2_HuR, RNA recognition motif 2 in vert	4e-04
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	4e-04
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	4e-04
cd12497	74	cd12497, RRM3_RBM47, RNA recognition motif 3 in ve	4e-04
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	4e-04
cd12603	71	cd12603, RRM_hnRNPC, RNA recognition motif in vert	5e-04
cd12482	79	cd12482, RRM1_hnRNPR, RNA recognition motif 1 in v	5e-04
cd12431	80	cd12431, RRM_ALKBH8, RNA recognition motif in alky	5e-04
cd12607	67	cd12607, RRM2_RBM4, RNA recognition motif 2 in ver	5e-04
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	6e-04
cd12678	74	cd12678, RRM_SLTM, RNA recognition motif in Scaffo	6e-04
cd12631	84	cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif	7e-04
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	8e-04
cd12486	78	cd12486, RRM1_ACF, RNA recognition motif 1 found i	8e-04
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	9e-04
cd12562	86	cd12562, RRM2_RBM5_like, RNA recognition motif 2 i	0.001
cd12657	76	cd12657, RRM1_hnRNPM, RNA recognition motif 1 in v	0.001
cd12634	81	cd12634, RRM2_CELF1_2, RNA recognition motif 2 in	0.001
cd12487	78	cd12487, RRM1_DND1, RNA recognition motif 1 found	0.001
cd12754	87	cd12754, RRM2_RBM10, RNA recognition motif 2 in ve	0.001
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	0.001
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	0.002
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	0.002
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	0.002
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	0.002
cd12556	85	cd12556, RRM2_RBM15B, RNA recognition motif 2 in p	0.002
cd12646	77	cd12646, RRM_SRSF7, RNA recognition motif in verte	0.002
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	0.002
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	0.002
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	0.002
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	0.002
cd12681	69	cd12681, RRM_SKAR, RNA recognition motif in S6K1 A	0.002
cd12498	83	cd12498, RRM3_ACF, RNA recognition motif 3 in vert	0.002
cd12357	89	cd12357, RRM_PPARGC1A_like, RNA recognition motif	0.002
cd12287	102	cd12287, RRM_U2AF35_like, RNA recognition motif in	0.003
cd12496	74	cd12496, RRM3_RBM46, RNA recognition motif 3 in ve	0.003
cd12439	79	cd12439, RRM_TRMT2A, RNA recognition motif in tRNA	0.003
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	0.003
cd12364	81	cd12364, RRM_RDM1, RNA recognition motif of RAD52	0.003
cd12475	88	cd12475, RRM2_RBMS3, RNA recognition motif 2 found	0.004
cd12432	90	cd12432, RRM_ACINU, RNA recognition motif in apopt	0.004
cd12438	98	cd12438, RRM_CNOT4, RNA recognition motif in Eukar	0.004
cd12322	71	cd12322, RRM2_TDP43, RNA recognition motif 2 in TA	0.004
cd12661	77	cd12661, RRM3_hnRNPM, RNA recognition motif 3 in v	0.004
cd12279	74	cd12279, RRM_TUT1, RNA recognition motif in speckl	0.004
cd12462	79	cd12462, RRM_SCAF8, RNA recognition motif in SR-re	0.004

>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 = 93.8 bits (234), Expect = 7e-26
 Identities = 36/78 (46%), Positives = 49/78 (62%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
            +LFVSGLS RT+E  L   F  FG++ EV L+ D      RGF F+ + + E++  AI 
Sbjct: 2   NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR 61

Query: 138 GMHGKFLDGRVIFVEIAK 155
            ++GK L+GRVI VE AK
Sbjct: 62  DLNGKELEGRVIKVEKAK 79

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

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

 Score = 87.6 bits (218), Expect = 1e-23
 Identities = 31/73 (42%), Positives = 47/73 (64%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
            LFV  L   T+E+ LR  F  FG++  V LV DK   + +GFAF+ + +EE++ +A+E 
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 139 MHGKFLDGRVIFV 151
           ++GK LDGR + V
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

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

 Score = 80.4 bits (199), Expect = 1e-20
 Identities = 25/77 (32%), Positives = 42/77 (54%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
            L+V  L +  +E+ L++ F  FG++    ++ D+   R RGF F+   T EE+  AIE 
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 139 MHGKFLDGRVIFVEIAK 155
           ++G    GR + V  A+
Sbjct: 61  LNGTDFGGRTLTVNEAR 77

This subfamily corresponds to the RRM of H. pylori HP0827, a putative ssDNA-binding protein 12rnp2 precursor, containing one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The ssDNA binding may be important in activation of HP0827. . Length = 78

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

 Score = 79.3 bits (196), Expect = 3e-20
 Identities = 29/73 (39%), Positives = 46/73 (63%), Gaps = 1/73 (1%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           LFV  L   T+E+ LR  F  FG++  V +V DK   + +GFAF+ + + E++ +A+E +
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDK-DGKSKGFAFVEFESPEDAEKALEAL 59

Query: 140 HGKFLDGRVIFVE 152
           +GK LDGR + V 
Sbjct: 60  NGKELDGRKLKVS 72

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

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

 Score = 78.4 bits (193), Expect = 1e-19
 Identities = 32/76 (42%), Positives = 49/76 (64%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           +LF+ GLSF T+E SL   F  +GQ+ EV +V D+   R RGF F+ +   ++++ A+  
Sbjct: 2   KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMA 61

Query: 139 MHGKFLDGRVIFVEIA 154
           M+GK +DGR I V+ A
Sbjct: 62  MNGKSVDGRQIRVDQA 77

This subfamily corresponds to the RRM domain of two structurally related heterogenous nuclear ribonucleoproteins, CIRBP (also termed CIRP or A18 hnRNP) and RBM3 (also termed RNPL), both of which belong to a highly conserved cold shock proteins family. The cold shock proteins can be induced after exposure to a moderate cold-shock and other cellular stresses such as UV radiation and hypoxia. CIRBP and RBM3 may function in posttranscriptional regulation of gene expression by binding to different transcripts, thus allowing the cell to response rapidly to environmental signals. However, the kinetics and degree of cold induction are different between CIRBP and RBM3. Tissue distribution of their expression is different. CIRBP and RBM3 may be differentially regulated under physiological and stress conditions and may play distinct roles in cold responses of cells. CIRBP, also termed glycine-rich RNA-binding protein CIRP, is localized in the nucleus and mediates the cold-induced suppression of cell cycle progression. CIRBP also binds DNA and possibly serves as a chaperone that assists in the folding/unfolding, assembly/disassembly and transport of various proteins. RBM3 may enhance global protein synthesis and the formation of active polysomes while reducing the levels of ribonucleoprotein complexes containing microRNAs. RBM3 may also serve to prevent the loss of muscle mass by its ability to decrease cell death. Furthermore, RBM3 may be essential for cell proliferation and mitosis. Both, CIRBP and RBM3, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), that is involved in RNA binding, and C-terminal glycine-rich domain (RGG motif) that probably enhances RNA-binding via protein-protein and/or protein-RNA interactions. Like CIRBP, RBM3 can also bind to both RNA and DNA via its RRM domain. . Length = 80

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

 Score = 76.7 bits (189), Expect = 3e-19
 Identities = 28/76 (36%), Positives = 47/76 (61%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
            LFV  LS+   ++ L+  F+ FG +V   ++ D+   R RGF ++ + + E++++AIE 
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 139 MHGKFLDGRVIFVEIA 154
           M GK LDGR I V+ +
Sbjct: 61  MDGKELDGRPINVDFS 76

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

>gnl|CDD|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 = 75.0 bits (185), Expect = 1e-18
 Identities = 29/73 (39%), Positives = 44/73 (60%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           RLFV  L F T+E+ LR  F+ FG++ EV+L +DK   R +GFAF+ +   E + +A   
Sbjct: 1   RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSE 60

Query: 139 MHGKFLDGRVIFV 151
           + G    GR++ V
Sbjct: 61  LDGSIFQGRLLHV 73

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

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

 Score = 74.9 bits (185), Expect = 1e-18
 Identities = 26/70 (37%), Positives = 44/70 (62%), Gaps = 1/70 (1%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           LFV  L   T+E+ L++ F  FG +  + +V D+   R +GFAF+ +  EE++ +A+E +
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDET-GRSKGFAFVEFEDEEDAEKALEAL 59

Query: 140 HGKFLDGRVI 149
           +GK L GR +
Sbjct: 60  NGKELGGREL 69

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

 Score = 79.2 bits (194), Expect = 4e-18
 Identities = 34/96 (35%), Positives = 55/96 (57%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
               LFV  L +  +E+ LR  F+ FG +  V LV D+   + RGFAF+ + +EE + +A
Sbjct: 114 ENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKA 173

Query: 136 IEGMHGKFLDGRVIFVEIAKSRAELRQAFKNNPRQN 171
           IE ++GK L+GR + V+ A+  ++ R    NN   +
Sbjct: 174 IEELNGKELEGRPLRVQKAQPASQPRSELSNNLDAS 209

Length = 306

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

 Score = 73.1 bits (180), Expect = 7e-18
 Identities = 29/79 (36%), Positives = 46/79 (58%), Gaps = 2/79 (2%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
            LFV  LS+   +D L   F+  G++V+V +  D    R +GF  + +ATEE +++A+E 
Sbjct: 1   TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDD-DGRSKGFGHVEFATEEGAQKALE- 58

Query: 139 MHGKFLDGRVIFVEIAKSR 157
             G+ L GR I V++A  R
Sbjct: 59  KSGEELLGREIRVDLATER 77

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

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

 Score = 73.0 bits (180), Expect = 1e-17
 Identities = 30/81 (37%), Positives = 50/81 (61%), Gaps = 1/81 (1%)

Query: 77  KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
           KT LFV+ L++ T+E  LR  F+ +G +  + LV DK   +PRG+AF+ +  E + + A 
Sbjct: 2   KT-LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAY 60

Query: 137 EGMHGKFLDGRVIFVEIAKSR 157
           +   GK +DGR + V++ + R
Sbjct: 61  KYADGKKIDGRRVLVDVERGR 81

This subfamily corresponds to the RRM of U1-70K, also termed snRNP70, a key component of the U1 snRNP complex, which is one of the key factors facilitating the splicing of pre-mRNA via interaction at the 5' splice site, and is involved in regulation of polyadenylation of some viral and cellular genes, enhancing or inhibiting efficient poly(A) site usage. U1-70K plays an essential role in targeting the U1 snRNP to the 5' splice site through protein-protein interactions with regulatory RNA-binding splicing factors, such as the RS protein ASF/SF2. Moreover, U1-70K protein can specifically bind to stem-loop I of the U1 small nuclear RNA (U1 snRNA) contained in the U1 snRNP complex. It also mediates the binding of U1C, another U1-specific protein, to the U1 snRNP complex. U1-70K contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region at the N-terminal half, and two serine/arginine-rich (SR) domains at the C-terminal half. The RRM is responsible for the binding of stem-loop I of U1 snRNA molecule. Additionally, the most prominent immunodominant region that can be recognized by auto-antibodies from autoimmune patients may be located within the RRM. The SR domains are involved in protein-protein interaction with SR proteins that mediate 5' splice site recognition. For instance, the first SR domain is necessary and sufficient for ASF/SF2 Binding. The family also includes Drosophila U1-70K that is an essential splicing factor required for viability in flies, but its SR domain is dispensable. The yeast U1-70k doesn't contain easily recognizable SR domains and shows low sequence similarity in the RRM region with other U1-70k proteins and therefore not included in this family. The RRM domain is dispensable for yeast U1-70K function. Length = 91

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

 Score = 74.3 bits (182), Expect = 2e-17
 Identities = 41/116 (35%), Positives = 61/116 (52%), Gaps = 5/116 (4%)

Query: 49  LRQGRGRGACFPLACLPPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVN 108
           LRQ        P+  +  S   +ST     +LF+ GLS+ T + SLR+AF  FG +V+  
Sbjct: 11  LRQNISSNGNVPVTSMLGSLRLMST-----KLFIGGLSWGTDDASLRDAFAHFGDVVDAK 65

Query: 109 LVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKSRAELRQAF 164
           +++D+   R RGF F+ +  E  +  AI  M GK L+GR I V  A  R    +A+
Sbjct: 66  VIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPANDRPSAPRAY 121

Length = 144

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

 Score = 71.5 bits (176), Expect = 5e-17
 Identities = 29/82 (35%), Positives = 45/82 (54%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
           P   LFV  LS +T+E++LR  F  +G +  + LV D +    +G+AF+ Y  E ++ RA
Sbjct: 2   PYLTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRA 61

Query: 136 IEGMHGKFLDGRVIFVEIAKSR 157
               H   +DG  IFV+  + R
Sbjct: 62  YRDAHKLVIDGSEIFVDFERER 83

This subfamily corresponds to the RRM of U11/U12-35K, also termed protein HM-1, or U1 snRNP-binding protein homolog, and is one of the components of the U11/U12 snRNP, which is a subunit of the minor (U12-dependent) spliceosome required for splicing U12-type nuclear pre-mRNA introns. U11/U12-35K is highly conserved among bilateria and plants, but lacks in some organisms, such as Saccharomyces cerevisiae and Caenorhabditis elegans. Moreover, U11/U12-35K shows significant sequence homology to U1 snRNP-specific 70 kDa protein (U1-70K or snRNP70). It contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region, and Arg-Asp and Arg-Glu dipeptide repeats rich domain, making U11/U12-35K a possible functional analog of U1-70K. It may facilitate 5' splice site recognition in the minor spliceosome and play a role in exon bridging, interacting with components of the major spliceosome bound to the pyrimidine tract of an upstream U2-type intron. The family corresponds to the RRM of U11/U12-35K that may directly contact the U11 or U12 snRNA through the RRM domain. Length = 93

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

 Score = 70.3 bits (173), Expect = 9e-17
 Identities = 28/75 (37%), Positives = 45/75 (60%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           L V GLS  T+E  LR  F  +G + +V +V D+   R RGF F+ + + E+++ A E +
Sbjct: 2   LGVFGLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERL 61

Query: 140 HGKFLDGRVIFVEIA 154
           +G  +DGR I V+ +
Sbjct: 62  NGMEIDGRRIRVDYS 76

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

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

 Score = 69.6 bits (171), Expect = 1e-16
 Identities = 27/72 (37%), Positives = 45/72 (62%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           L V  L++RT+ D LR  F+ +G++ +V +  D+     RGFAF+R+  + ++  A++ M
Sbjct: 1   LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAM 60

Query: 140 HGKFLDGRVIFV 151
            GK LDGR + V
Sbjct: 61  DGKELDGRELRV 72

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

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

 Score = 69.6 bits (171), Expect = 2e-16
 Identities = 26/77 (33%), Positives = 46/77 (59%), Gaps = 1/77 (1%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           T++FV GL + T++DSLR  F  FG++ E  ++ D+   + RG+ F+ +  +E + RA +
Sbjct: 1   TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 60

Query: 138 GMHGKFLDGRVIFVEIA 154
             +   +DGR   V +A
Sbjct: 61  DPN-PIIDGRKANVNLA 76

This subfamily corresponds to the RRM of RBM24 and RBM38 from vertebrate, SUPpressor family member SUP-12 from Caenorhabditis elegans and similar proteins. Both, RBM24 and RBM38, are preferentially expressed in cardiac and skeletal muscle tissues. They regulate myogenic differentiation by controlling the cell cycle in a p21-dependent or -independent manner. RBM24, also termed RNA-binding region-containing protein 6, interacts with the 3'-untranslated region (UTR) of myogenin mRNA and regulates its stability in C2C12 cells. RBM38, also termed CLL-associated antigen KW-5, or HSRNASEB, or RNA-binding region-containing protein 1(RNPC1), or ssDNA-binding protein SEB4, is a direct target of the p53 family. It is required for maintaining the stability of the basal and stress-induced p21 mRNA by binding to their 3'-UTRs. It also binds the AU-/U-rich elements in p63 3'-UTR and regulates p63 mRNA stability and activity. SUP-12 is a novel tissue-specific splicing factor that controls muscle-specific splicing of the ADF/cofilin pre-mRNA in C. elegans. All family members contain a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 76

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

 Score = 69.2 bits (170), Expect = 3e-16
 Identities = 27/71 (38%), Positives = 41/71 (57%), Gaps = 3/71 (4%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE-G 138
           LF+ GLS+ T+E+SLR  F  +G++V+  ++ D I  R RGF F+ +A      + +   
Sbjct: 1   LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAK 60

Query: 139 MHGKFLDGRVI 149
            H   LDGR I
Sbjct: 61  PH--VLDGREI 69

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

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

 Score = 66.1 bits (162), Expect = 3e-15
 Identities = 25/72 (34%), Positives = 39/72 (54%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           L+V GL+    E  L  AF  FG + ++ + +D    + RGFAF+ +   E++  AI+ M
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 140 HGKFLDGRVIFV 151
           +   L GR I V
Sbjct: 61  NESELFGRTIRV 72

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

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

 Score = 65.7 bits (161), Expect = 8e-15
 Identities = 24/80 (30%), Positives = 44/80 (55%), Gaps = 5/80 (6%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE-- 137
           +F+  L F  +E+ L+  F  FG++    +V DK+    +G AF+++ T+E +++ +E  
Sbjct: 3   VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAA 62

Query: 138 ---GMHGKFLDGRVIFVEIA 154
                 G  LDGR + V +A
Sbjct: 63  DNAEDSGLSLDGRRLIVTLA 82

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

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

 Score = 65.3 bits (160), Expect = 1e-14
 Identities = 27/78 (34%), Positives = 43/78 (55%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           LFV  L + T+++ L   F   G +    +V DK + + RGF ++ +A EE+++RA+E  
Sbjct: 2   LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 140 HGKFLDGRVIFVEIAKSR 157
                 GR I VE AK +
Sbjct: 62  KKTKFGGRKIHVEFAKKK 79

This subfamily corresponds to the RRM1 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 79

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

 Score = 64.6 bits (158), Expect = 1e-14
 Identities = 25/76 (32%), Positives = 46/76 (60%), Gaps = 1/76 (1%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           RL V  L F+ +E  L+  F  FG + EV +       + +GFAF+++ ++ ++ +AI+G
Sbjct: 1   RLIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKP-DGKKKGFAFVQFTSKADAEKAIKG 59

Query: 139 MHGKFLDGRVIFVEIA 154
           ++GK + GR + V+ A
Sbjct: 60  VNGKKIKGRPVAVDWA 75

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

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

 Score = 64.5 bits (158), Expect = 2e-14
 Identities = 31/74 (41%), Positives = 43/74 (58%)

Query: 82  VSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHG 141
           V+ LS    ED LR  F+ FG +  V L  DK   + RGFAF+ + T E++ RAIE ++G
Sbjct: 4   VTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNG 63

Query: 142 KFLDGRVIFVEIAK 155
              D  ++ VE AK
Sbjct: 64  FGYDNLILSVEWAK 77

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

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

 Score = 64.1 bits (157), Expect = 2e-14
 Identities = 24/73 (32%), Positives = 46/73 (63%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           L V  L+   ++D L+  F  +G + +V+L +D+  N PRG+A++ + + E++ +AI+ M
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 140 HGKFLDGRVIFVE 152
            G  +DG+ + VE
Sbjct: 61  DGGQIDGQEVTVE 73

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

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

 Score = 64.1 bits (156), Expect = 2e-14
 Identities = 28/70 (40%), Positives = 42/70 (60%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           T L+V+ L  + +ED LR  F+ +G +V+ NL+ DK    PRG AF+RY   EE++ AI 
Sbjct: 1   TNLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAIS 60

Query: 138 GMHGKFLDGR 147
            ++G    G 
Sbjct: 61  SLNGTIPPGS 70

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

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

 Score = 62.7 bits (153), Expect = 9e-14
 Identities = 27/72 (37%), Positives = 44/72 (61%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           L+V  L F  +ED LR  F+ FG++  V L  D    R +G+ F+++A  E++++A+E +
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60

Query: 140 HGKFLDGRVIFV 151
           +G  L GR I V
Sbjct: 61  NGFELAGRPIKV 72

This subfamily corresponds to the RRM2 of RBM39 (also termed HCC1), a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor. . Length = 73

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

 Score = 62.2 bits (152), Expect = 1e-13
 Identities = 27/70 (38%), Positives = 45/70 (64%), Gaps = 2/70 (2%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           L+V  L    +E+ LR  F  +G++  V LV +K  +RPRGFAF+ +A+ E++  A++ +
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNK--DRPRGFAFVEFASPEDAEAALKKL 58

Query: 140 HGKFLDGRVI 149
           +G  LDGR +
Sbjct: 59  NGLVLDGRTL 68

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

>gnl|CDD|240807 cd12361, RRM1_2_CELF1-6_like, RNA recognition motif 1 and 2 in CELF/Bruno-like family of RNA binding proteins and plant flowering time control protein FCA

 Score = 61.8 bits (151), Expect = 2e-13
 Identities = 23/64 (35%), Positives = 43/64 (67%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           +LFV  L    +E+ +R  F+ +G + EV ++ DK   + +G AF+++++ EE+++AIE 
Sbjct: 1   KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEA 60

Query: 139 MHGK 142
           +HGK
Sbjct: 61  LHGK 64

This subfamily corresponds to the RRM1 and RRM2 domains of the CUGBP1 and ETR-3-like factors (CELF) as well as plant flowering time control protein FCA. CELF, also termed BRUNOL (Bruno-like) proteins, is a family of structurally related RNA-binding proteins involved in regulation of pre-mRNA splicing in the nucleus, and control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both, sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. This subfamily also includes plant flowering time control protein FCA that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RRMs, and a WW protein interaction domain. . Length = 77

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

 Score = 61.7 bits (150), Expect = 2e-13
 Identities = 27/73 (36%), Positives = 44/73 (60%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           R++V  +SF   ED++R AF  FG +  +++  D +  + +GFAF+ Y   E ++ A+E 
Sbjct: 2   RVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQ 61

Query: 139 MHGKFLDGRVIFV 151
           M+G  L GR I V
Sbjct: 62  MNGVMLGGRNIKV 74

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

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

 Score = 61.6 bits (150), Expect = 2e-13
 Identities = 26/73 (35%), Positives = 44/73 (60%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           RLFV  L +   ED L   F  FG+L EV++ +DK + + +GFA++ +   E++ +A + 
Sbjct: 4   RLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKE 63

Query: 139 MHGKFLDGRVIFV 151
           + GK   GR+I +
Sbjct: 64  LDGKVFQGRLIHI 76

This subgroup corresponds to the RRM2 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 79

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

 Score = 60.5 bits (147), Expect = 6e-13
 Identities = 25/73 (34%), Positives = 43/73 (58%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           RLF+  L++  +E+ L   F  +G L EV+L +DK+  +P+GFAF+ Y   E + +A   
Sbjct: 4   RLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAE 63

Query: 139 MHGKFLDGRVIFV 151
           + G    GR++ +
Sbjct: 64  LDGTVFQGRLLHL 76

This subgroup corresponds to the RRM3 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 60.1 bits (146), Expect = 8e-13
 Identities = 27/79 (34%), Positives = 46/79 (58%), Gaps = 1/79 (1%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           +LF+ GLS+ T++DSL+N F  +G++ +  ++ D    R RGF F+ +A+  E   A+  
Sbjct: 1   KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNA 60

Query: 139 MHGKFLDGRVIFVEIAKSR 157
              K +DGR +  + A  R
Sbjct: 61  RPHK-VDGREVEPKRAVPR 78

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

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

 Score = 60.1 bits (146), Expect = 9e-13
 Identities = 23/70 (32%), Positives = 42/70 (60%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           +FV  LS     ++LR AF  FG++ +  +V D    + +G+ F+ +  +E++  AI+ M
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61

Query: 140 HGKFLDGRVI 149
           +G++L GR I
Sbjct: 62  NGQWLGGRAI 71

This subfamily corresponds to the RRM2 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis. TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. Length = 75

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

 Score = 59.7 bits (145), Expect = 1e-12
 Identities = 25/68 (36%), Positives = 42/68 (61%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           LFV  LSF   EDS+  AF  +G++  V L  D  + RP+GF ++ ++++E ++ A++ +
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 140 HGKFLDGR 147
            G  L GR
Sbjct: 61  GGTDLLGR 68

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

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

 Score = 59.6 bits (145), Expect = 2e-12
 Identities = 24/73 (32%), Positives = 44/73 (60%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           +++ GL +  +E  +   F  +G++V++NLV DK   + +GFAFL Y  +  +  A++ +
Sbjct: 12  IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNL 71

Query: 140 HGKFLDGRVIFVE 152
           +G  L GR I V+
Sbjct: 72  NGIKLLGRTIRVD 84

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

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

 Score = 59.3 bits (144), Expect = 2e-12
 Identities = 29/81 (35%), Positives = 47/81 (58%), Gaps = 3/81 (3%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
           P +RLF+       +ED LR AF  FG++ ++ +V DK     +G A++++A    + RA
Sbjct: 2   PNSRLFIV-CGKSVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARA 60

Query: 136 IEGMHGKFL--DGRVIFVEIA 154
           +E M+GK L  D + + V IA
Sbjct: 61  MEEMNGKCLGGDTKPLKVLIA 81

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

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

 Score = 58.8 bits (143), Expect = 3e-12
 Identities = 23/73 (31%), Positives = 38/73 (52%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           ++F+ GL    SED ++   + FG+L   NLV D      +G+AF  Y     + +AI G
Sbjct: 2   KIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAG 61

Query: 139 MHGKFLDGRVIFV 151
           ++G  L  + + V
Sbjct: 62  LNGMQLGDKKLTV 74

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

>gnl|CDD|240772 cd12326, RRM1_hnRNPA0, RNA recognition motif 1 found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 59.0 bits (143), Expect = 3e-12
 Identities = 27/77 (35%), Positives = 46/77 (59%), Gaps = 1/77 (1%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           +LFV GL+ +TS+  LR  F  +G+L E  +++D    R RGF F+ +++ +E+  A+E 
Sbjct: 4   KLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAMEA 63

Query: 139 MHGKFLDGRVIFVEIAK 155
                +DG  I ++ AK
Sbjct: 64  Q-PHSIDGNQIELKRAK 79

This subfamily corresponds to the RRM1 of hnRNP A0 which is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 79

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

 Score = 58.5 bits (142), Expect = 3e-12
 Identities = 24/52 (46%), Positives = 35/52 (67%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEE 130
           ++FV GLS  T+E+ +R  F  FG +VE+ L MDK  N+ RGF F+ + +EE
Sbjct: 1   KIFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEE 52

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

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

 Score = 58.4 bits (141), Expect = 4e-12
 Identities = 31/76 (40%), Positives = 46/76 (60%)

Query: 82  VSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHG 141
           V GLS  T+E  LR  F  +G L  VN+V D+   R RGFAF+ +   ++S+ A+E  +G
Sbjct: 4   VFGLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANG 63

Query: 142 KFLDGRVIFVEIAKSR 157
             LDGR I V+ + ++
Sbjct: 64  MELDGRRIRVDYSITK 79

This subgroup corresponds to the RRM of TRA2-alpha or TRA-2-alpha, also termed transformer-2 protein homolog A, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein (SRp40) that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-alpha contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. . Length = 79

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

 Score = 58.5 bits (141), Expect = 4e-12
 Identities = 30/82 (36%), Positives = 49/82 (59%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
           P   L V GLS  T+E  LR  F  +G + +V++V D+ + R RGFAF+ +   ++++ A
Sbjct: 8   PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 67

Query: 136 IEGMHGKFLDGRVIFVEIAKSR 157
            E  +G  LDGR I V+ + ++
Sbjct: 68  KERANGMELDGRRIRVDFSITK 89

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

>gnl|CDD|240800 cd12354, RRM3_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1

 Score = 58.0 bits (141), Expect = 4e-12
 Identities = 22/72 (30%), Positives = 39/72 (54%), Gaps = 6/72 (8%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           T ++V  L    +E+ L+  F  FG + EV +  DK      G+AF+R+ T E +  AI 
Sbjct: 1   TTVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKDK------GYAFVRFDTHEAAATAIV 54

Query: 138 GMHGKFLDGRVI 149
            ++G  ++G+ +
Sbjct: 55  AVNGTSINGQTV 66

This subfamily corresponds to the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR) are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. They share high sequence similarity and are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both TIA-1 and TIAR bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. This subfamily also includes a yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1, termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein, which has been identified as both a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP). It may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RRMs, and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 73

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

 Score = 58.1 bits (141), Expect = 5e-12
 Identities = 27/76 (35%), Positives = 39/76 (51%), Gaps = 1/76 (1%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVM-DKIANRPRGFAFLRYATEEESRRAIEG 138
           LF+  L     E  L + F  FG +++   +M D      +GFAF+ Y + E S  AIE 
Sbjct: 4   LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEA 63

Query: 139 MHGKFLDGRVIFVEIA 154
           M+G++L  R I V  A
Sbjct: 64  MNGQYLCNRPITVSYA 79

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

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

 Score = 57.6 bits (140), Expect = 5e-12
 Identities = 24/76 (31%), Positives = 42/76 (55%), Gaps = 8/76 (10%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           L+V  L   T+E+ LR  F  +G++  V  + D        +AF+ +   +++ +A+E M
Sbjct: 4   LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD--------YAFVHFEERDDAVKAMEEM 55

Query: 140 HGKFLDGRVIFVEIAK 155
           +GK L+G  I V +AK
Sbjct: 56  NGKELEGSPIEVSLAK 71

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

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

 Score = 58.1 bits (141), Expect = 6e-12
 Identities = 23/78 (29%), Positives = 45/78 (57%)

Query: 77  KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
           K+ ++VS L F  + + L   F  +G++V+V +V DK   + +G AF+ +   E++ + +
Sbjct: 1   KSTVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCV 60

Query: 137 EGMHGKFLDGRVIFVEIA 154
           + ++ K L GR +   IA
Sbjct: 61  KALNNKELFGRTLKCSIA 78

This subfamily corresponds to the RRM of ZCRB1, also termed MADP-1, or U11/U12 small nuclear ribonucleoprotein 31 kDa protein (U11/U12 snRNP 31 or U11/U12-31K), a novel multi-functional nuclear factor, which may be involved in morphine dependence, cold/heat stress, and hepatocarcinoma. It is located in the nucleoplasm, but outside the nucleolus. ZCRB1 is one of the components of U11/U12 snRNPs that bind to U12-type pre-mRNAs and form a di-snRNP complex, simultaneously recognizing the 5' splice site and branchpoint sequence. ZCRB1 is characterized by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCHC-type Zinc finger motif. In addition, it contains core nucleocapsid motifs, and Lys- and Glu-rich domains. . Length = 78

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

 Score = 62.1 bits (151), Expect = 6e-12
 Identities = 33/97 (34%), Positives = 54/97 (55%), Gaps = 9/97 (9%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           T L+V  L    +ED LR  F  FG++    ++ D  + R RGFAF+ +   E++ +A+E
Sbjct: 179 TNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDG-SGRSRGFAFVNFEKHEDAAKAVE 237

Query: 138 GMHGKFLD----GRVIFVEIAKSRAE----LRQAFKN 166
            M+GK +     G+ ++V  A+ RAE    LR+ F+ 
Sbjct: 238 EMNGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEE 274

These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis (GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ), broadly expressed (SP:P11940_PABP1) and of unknown tissue range (SP:Q15097_PABP2). Length = 562

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

 Score = 57.4 bits (139), Expect = 1e-11
 Identities = 26/78 (33%), Positives = 44/78 (56%), Gaps = 2/78 (2%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           L V GL ++T+E  L++ F  FG+L+ V +  D    + +GF F+R+A  E+  + +   
Sbjct: 2   LIVLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVLSQR 61

Query: 140 HGKFLDGRVIFVEIAKSR 157
           H   +DGR   V+I  S+
Sbjct: 62  H--MIDGRWCDVKIPNSK 77

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

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

 Score = 57.2 bits (139), Expect = 1e-11
 Identities = 17/74 (22%), Positives = 42/74 (56%), Gaps = 1/74 (1%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           T ++V  L     ++ L+  F  +G++    ++ D    + +GF F+ +   E +++A+E
Sbjct: 2   TNVYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEG-KSKGFGFVNFENHEAAQKAVE 60

Query: 138 GMHGKFLDGRVIFV 151
            ++GK ++G+ ++V
Sbjct: 61  ELNGKEVNGKKLYV 74

This subfamily corresponds to the RRM3 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 80

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

 Score = 57.0 bits (138), Expect = 1e-11
 Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 3/77 (3%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI-E 137
           ++FV GL    +E+  +  F  FG++V+  L+ D    R RGF F+ + +E    R    
Sbjct: 1   KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSA 60

Query: 138 GMHGKFLDGRVIFVEIA 154
           GM    L G+ + V+ A
Sbjct: 61  GMLE--LGGKQVEVKRA 75

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

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

 Score = 57.0 bits (138), Expect = 1e-11
 Identities = 25/78 (32%), Positives = 44/78 (56%), Gaps = 1/78 (1%)

Query: 77  KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
           K +LFVSGL F  +++ L   F+  G +  V LV ++ + +P+G A++ Y  E  + +A+
Sbjct: 2   KHKLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNR-SGKPKGLAYVEYENESSASQAV 60

Query: 137 EGMHGKFLDGRVIFVEIA 154
             M G  +  + I V I+
Sbjct: 61  LKMDGTEIKEKTISVAIS 78

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

 Score = 56.8 bits (138), Expect = 2e-11
 Identities = 23/84 (27%), Positives = 42/84 (50%), Gaps = 5/84 (5%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFG--QLVEVNLVMDKIANRPRGFAFLRYATEEESR 133
           P   L + GL   T+E+ +  A        + +V L+ DK+    RGFAF+ + + E++ 
Sbjct: 1   PTNTLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDAT 60

Query: 134 RAIE---GMHGKFLDGRVIFVEIA 154
           + ++    +    +DGRV+ V  A
Sbjct: 61  QWMDALNNLDPFVIDGRVVRVSYA 84

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

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

 Score = 56.5 bits (137), Expect = 2e-11
 Identities = 22/80 (27%), Positives = 44/80 (55%), Gaps = 3/80 (3%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKI---ANRPRGFAFLRYATEEESRRA 135
           RL++  L  R +E  L   F  +G++ + + +  K      +PRG+ F+ + T+EE+ +A
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 136 IEGMHGKFLDGRVIFVEIAK 155
           ++ ++GK   G+ + V  A 
Sbjct: 61  LKSLNGKTALGKKLVVRWAH 80

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

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

 Score = 56.1 bits (136), Expect = 2e-11
 Identities = 21/74 (28%), Positives = 37/74 (50%)

Query: 81  FVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMH 140
           FV  + +  +E+ L   F   G +V   LV D+   +P+G+ F  +   E +  AI  ++
Sbjct: 2   FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLN 61

Query: 141 GKFLDGRVIFVEIA 154
           G   +GR + V+ A
Sbjct: 62  GYEFNGRALRVDFA 75

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

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

 Score = 55.9 bits (135), Expect = 3e-11
 Identities = 22/59 (37%), Positives = 36/59 (61%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           ++FV GLS  T+ED ++  F  FG++ +  L+ DK  NR RGF F+ + +E+   +  E
Sbjct: 1   KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCE 59

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

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

 Score = 56.2 bits (135), Expect = 4e-11
 Identities = 31/79 (39%), Positives = 49/79 (62%), Gaps = 1/79 (1%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           +LF+ GLSF T+++SLR+ F+ +G L +  ++ D    R RGF F+ Y++ EE   A+  
Sbjct: 4   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAMNA 63

Query: 139 MHGKFLDGRVIFVEIAKSR 157
              K +DGRV+  + A SR
Sbjct: 64  RPHK-VDGRVVEPKRAVSR 81

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

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

 Score = 55.7 bits (135), Expect = 4e-11
 Identities = 22/77 (28%), Positives = 38/77 (49%), Gaps = 4/77 (5%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNL---VMDKIANRPRGFAFLRYATEEESRRAI 136
           ++V  L F+  ED LR  F  FG++  + +     +K      GFAF+ +     +  A+
Sbjct: 3   IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENAL 62

Query: 137 EGMHGKFLDGRVIFVEI 153
           + ++G  L GR I V +
Sbjct: 63  Q-LNGTELGGRKISVSL 78

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

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

 Score = 55.9 bits (134), Expect = 4e-11
 Identities = 32/79 (40%), Positives = 47/79 (59%), Gaps = 1/79 (1%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           +LF+ GLSF T++DSLR  F+ +G L +  ++ D    R RGF F+ Y+  EE   A+  
Sbjct: 4   KLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAMSA 63

Query: 139 MHGKFLDGRVIFVEIAKSR 157
              K +DGRV+  + A SR
Sbjct: 64  RPHK-VDGRVVEPKRAVSR 81

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

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

 Score = 55.3 bits (134), Expect = 6e-11
 Identities = 19/48 (39%), Positives = 28/48 (58%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRY 126
           +LFV GL    +E+ LR  F  +G +  V +V DK   + RGFAF+ +
Sbjct: 1   KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTF 48

This subfamily corresponds to the RRM2 of hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 73

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

 Score = 59.5 bits (144), Expect = 6e-11
 Identities = 28/73 (38%), Positives = 42/73 (57%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           +L+V  L F  +E  LR  F+ FG + +V L  D    R +GF F+++   EE++ A+E 
Sbjct: 188 KLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEV 247

Query: 139 MHGKFLDGRVIFV 151
           M+G  L GR I V
Sbjct: 248 MNGFELAGRPIKV 260

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

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

 Score = 54.9 bits (133), Expect = 7e-11
 Identities = 25/76 (32%), Positives = 43/76 (56%), Gaps = 1/76 (1%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           TRL VS L +  +E+ L   F   G++ +V +  D+ + R  G A + +   E++ RAI+
Sbjct: 1   TRLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDR-SGRSEGTADVVFEKREDAERAIK 59

Query: 138 GMHGKFLDGRVIFVEI 153
             +G  LDG+ + VE+
Sbjct: 60  QFNGVLLDGQPMQVEL 75

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

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

 Score = 55.1 bits (133), Expect = 7e-11
 Identities = 26/76 (34%), Positives = 44/76 (57%), Gaps = 2/76 (2%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           RL VS + FR  +  LR  F  FG +++V ++ ++  ++  GF F+ +A   ++ RA E 
Sbjct: 2   RLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERGSK--GFGFVTFANSADADRAREK 59

Query: 139 MHGKFLDGRVIFVEIA 154
           +HG  ++GR I V  A
Sbjct: 60  LHGTVVEGRKIEVNNA 75

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

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

 Score = 54.9 bits (132), Expect = 8e-11
 Identities = 19/69 (27%), Positives = 38/69 (55%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
             L+VSGL    ++  L   F  +G+++   ++ D++    RG  F+R+    E+  AI+
Sbjct: 1   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIK 60

Query: 138 GMHGKFLDG 146
           G++G+  +G
Sbjct: 61  GLNGQKPEG 69

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

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

 Score = 59.3 bits (143), Expect = 8e-11
 Identities = 28/73 (38%), Positives = 44/73 (60%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           R++V  +SF   ED++R AF  FG +  +N+  D    + +GFAF+ Y   E ++ A+E 
Sbjct: 109 RVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQ 168

Query: 139 MHGKFLDGRVIFV 151
           M+G+ L GR I V
Sbjct: 169 MNGQMLGGRNIKV 181

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

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

 Score = 54.5 bits (132), Expect = 1e-10
 Identities = 21/75 (28%), Positives = 42/75 (56%), Gaps = 5/75 (6%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPR-----GFAFLRYATEEESRR 134
           LFV  L+F+T+E++L+  F+  G +  V +   K    P      G+ F+ + ++E +++
Sbjct: 3   LFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQK 62

Query: 135 AIEGMHGKFLDGRVI 149
           A++ + G  LDG  +
Sbjct: 63  ALKRLQGTVLDGHAL 77

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

 Score = 54.2 bits (131), Expect = 1e-10
 Identities = 21/72 (29%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           +FV  L F  +   L++ F+  G ++  ++  D    R +GF  + + + E+++RAIE  
Sbjct: 1   IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDN-DGRSKGFGTVLFESPEDAQRAIEMF 59

Query: 140 HGKFLDGRVIFV 151
           +G  L+GR + V
Sbjct: 60  NGYDLEGRELEV 71

This subfamily corresponds to the RRM3 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 72

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

 Score = 54.1 bits (130), Expect = 2e-10
 Identities = 23/73 (31%), Positives = 38/73 (52%), Gaps = 4/73 (5%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           LFV  L +  + D L+  F+     V++ L   K     +G A++ + TE E+ +A+E  
Sbjct: 6   LFVKNLPYNITVDELKEVFE---DAVDIRLPSGK-DGSSKGIAYIEFKTEAEAEKALEEK 61

Query: 140 HGKFLDGRVIFVE 152
            G  +DGR I V+
Sbjct: 62  QGAEVDGRSIVVD 74

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

 Score = 54.1 bits (130), Expect = 2e-10
 Identities = 23/70 (32%), Positives = 40/70 (57%), Gaps = 2/70 (2%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           +F+ GL++ T++DSLR  F  FG++ +  ++ D    R RGF FL +   +     ++  
Sbjct: 1   MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKKE 60

Query: 140 HGKFLDGRVI 149
           H   LDG++I
Sbjct: 61  H--ILDGKII 68

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

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

 Score = 53.8 bits (130), Expect = 2e-10
 Identities = 22/77 (28%), Positives = 45/77 (58%), Gaps = 1/77 (1%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           +R+ V  L    +ED LR  F+  G++ +V ++  +   + R F F+ + +EE++++A++
Sbjct: 1   SRIIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTR-DGKSRRFGFVGFKSEEDAQQAVK 59

Query: 138 GMHGKFLDGRVIFVEIA 154
             +  F+D   I VE+A
Sbjct: 60  YFNKTFIDTSKISVELA 76

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

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

 Score = 53.4 bits (129), Expect = 3e-10
 Identities = 22/72 (30%), Positives = 40/72 (55%), Gaps = 2/72 (2%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           +FVS L +   ED LR  F   G++ +V LV +    + +G+A++ +  EE  + A+  +
Sbjct: 2   VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNY-KGKSKGYAYVEFENEESVQEAL-KL 59

Query: 140 HGKFLDGRVIFV 151
             + + GR +FV
Sbjct: 60  DRELIKGRPMFV 71

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

>gnl|CDD|241200 cd12756, RRM1_hnRNPD, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 53.5 bits (128), Expect = 3e-10
 Identities = 24/70 (34%), Positives = 42/70 (60%), Gaps = 1/70 (1%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           +F+ GLS+ T++  L++ F  FG++V+  L +D I  R RGF F+ +   E   + ++  
Sbjct: 1   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60

Query: 140 HGKFLDGRVI 149
             K L+G+VI
Sbjct: 61  EHK-LNGKVI 69

This subgroup corresponds to the RRM1 of hnRNP D0, also termed AU-rich element RNA-binding protein 1, which is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP D0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), in the middle and an RGG box rich in glycine and arginine residues in the C-terminal part. Each of RRMs can bind solely to the UUAG sequence specifically. . Length = 74

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

 Score = 53.5 bits (129), Expect = 4e-10
 Identities = 23/78 (29%), Positives = 42/78 (53%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           T L+V  ++  T  D LR  F  +G +V+V + +D    RPRGFA++++    ++  A+ 
Sbjct: 1   TSLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALY 60

Query: 138 GMHGKFLDGRVIFVEIAK 155
            +      GR I ++ A+
Sbjct: 61  YLDRTRFLGREIEIQFAQ 78

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

>gnl|CDD|241019 cd12575, RRM1_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

 Score = 53.0 bits (127), Expect = 4e-10
 Identities = 24/70 (34%), Positives = 40/70 (57%), Gaps = 1/70 (1%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           +FV GLS+ T++  L+  F  FG++V+  + +D +  R RGF F+ +       + ++  
Sbjct: 1   MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQK 60

Query: 140 HGKFLDGRVI 149
             K LDGRVI
Sbjct: 61  EHK-LDGRVI 69

This subfamily corresponds to the RRM1 in hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 74

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

 Score = 53.1 bits (127), Expect = 5e-10
 Identities = 23/69 (33%), Positives = 39/69 (56%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           ++FV GLS  T+E+ ++  F  FG++  + L MD   N  RGF F+ Y  EE  ++ +E 
Sbjct: 1   KVFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQKLLES 60

Query: 139 MHGKFLDGR 147
            + +   G+
Sbjct: 61  RYHQIGSGK 69

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

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

 Score = 52.6 bits (126), Expect = 5e-10
 Identities = 28/76 (36%), Positives = 43/76 (56%), Gaps = 8/76 (10%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
            ++FV  +S   + D LR  F+ FG++VE + V D        +AF+    EEE+  AIE
Sbjct: 1   WKIFVGNVSATCTSDELRGLFEEFGRVVECDKVKD--------YAFVHMEREEEALAAIE 52

Query: 138 GMHGKFLDGRVIFVEI 153
            ++GK + GR I VE+
Sbjct: 53  ALNGKEVKGRRINVEL 68

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

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

 Score = 52.6 bits (127), Expect = 6e-10
 Identities = 22/75 (29%), Positives = 41/75 (54%), Gaps = 1/75 (1%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           L+V  L     ++ LR  F  FG +     VM     R +GF F+ +++ EE+ +A+  M
Sbjct: 4   LYVKNLDDSIDDERLREEFSPFGTITSAK-VMTDEKGRSKGFGFVCFSSPEEATKAVTEM 62

Query: 140 HGKFLDGRVIFVEIA 154
           +G+ + G+ ++V +A
Sbjct: 63  NGRIIGGKPLYVALA 77

This subfamily corresponds to the RRM4 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in theThe CD corresponds to the RRM. regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 79

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

 Score = 52.5 bits (126), Expect = 6e-10
 Identities = 21/70 (30%), Positives = 39/70 (55%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           +FV  LS   ++ +L  AF  F    +  ++ D  + R RG+ F+ + +++++  AI  M
Sbjct: 2   IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEM 61

Query: 140 HGKFLDGRVI 149
           +GK+L  R I
Sbjct: 62  NGKWLGSRPI 71

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

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

 Score = 52.7 bits (127), Expect = 7e-10
 Identities = 23/73 (31%), Positives = 41/73 (56%), Gaps = 2/73 (2%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           +FV  LS   +++ L   F   G+++EVNL+  K AN    FAF+++  E+ + RA+E  
Sbjct: 6   IFVGQLSPDVTKEELNERFSRHGKILEVNLI--KRANHTNAFAFIKFEREQAAARAVESE 63

Query: 140 HGKFLDGRVIFVE 152
           +   L  + + V+
Sbjct: 64  NHSMLKNKTMHVQ 76

This subfamily corresponds to the RRM2 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1. . Length = 80

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

 Score = 52.4 bits (126), Expect = 7e-10
 Identities = 24/76 (31%), Positives = 41/76 (53%), Gaps = 1/76 (1%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           ++FV GL    +E  LR  F  FG + EV ++ D    RPRGF F+ + +E+   + +  
Sbjct: 4   KIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVV-N 62

Query: 139 MHGKFLDGRVIFVEIA 154
            H   ++G+ + V+ A
Sbjct: 63  EHFHDINGKKVEVKRA 78

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

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

 Score = 52.3 bits (126), Expect = 7e-10
 Identities = 21/81 (25%), Positives = 42/81 (51%), Gaps = 9/81 (11%)

Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
           +  T L+V G  +  +E+ L+ AF  FG ++ ++  M+K     +   F+ +   E + R
Sbjct: 3   KGNT-LYVHG--YGLTEEILKKAFSPFGNIINIS--MEK----EKNCGFVTFEKMESADR 53

Query: 135 AIEGMHGKFLDGRVIFVEIAK 155
           AI  ++G  + G  + V +A+
Sbjct: 54  AIAELNGTTVQGVQLKVSLAR 74

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

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

 Score = 52.3 bits (125), Expect = 8e-10
 Identities = 22/62 (35%), Positives = 36/62 (58%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           ++FV GLS  T E+ +R  F  FG++  + L MD   N+ RGF F+ +  EE  ++ +E 
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 139 MH 140
            +
Sbjct: 61  KY 62

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

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

 Score = 51.9 bits (125), Expect = 8e-10
 Identities = 22/73 (30%), Positives = 35/73 (47%), Gaps = 6/73 (8%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           RLFV  L    +E+  +  F  +G++ EV L      N+ +GF F+R  T   + +A   
Sbjct: 3   RLFVGNLPNDITEEEFKELFSKYGEVSEVFL------NKEKGFGFIRLDTRTNAEKAKAE 56

Query: 139 MHGKFLDGRVIFV 151
           + G    GR + V
Sbjct: 57  LDGIMRKGRQLRV 69

This subfamily corresponds to the RRM1 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. This subfamily also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior, and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contain a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members. . Length = 71

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

 Score = 52.6 bits (127), Expect = 9e-10
 Identities = 25/79 (31%), Positives = 49/79 (62%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           +FV+G+     E+ + + F  FG++  ++L +D+     +G+A + Y T++E++ AIEG+
Sbjct: 9   IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68

Query: 140 HGKFLDGRVIFVEIAKSRA 158
           +GK L G+ I V+ A  + 
Sbjct: 69  NGKELLGQTISVDWAFVKG 87

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

>gnl|CDD|241206 cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 52.4 bits (125), Expect = 9e-10
 Identities = 28/79 (35%), Positives = 48/79 (60%), Gaps = 1/79 (1%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           +LF+ GLSF T+E+SLRN ++ +G+L +  ++ D  + R RGF F+ ++   E   A+  
Sbjct: 4   KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAM-A 62

Query: 139 MHGKFLDGRVIFVEIAKSR 157
                +DGRV+  + A +R
Sbjct: 63  ARPHTIDGRVVEPKRAVAR 81

This subgroup corresponds to the RRM1 of hnRNP A2/B1 which is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Moreover, the overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 81

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

 Score = 51.7 bits (124), Expect = 1e-09
 Identities = 25/77 (32%), Positives = 40/77 (51%), Gaps = 9/77 (11%)

Query: 80  LFVSGLS-FRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           LFV G     T E+ +   F+ FG LV  ++         + FAF+ +   E++ +A+E 
Sbjct: 2   LFVVGFDPGTTREEDIEKLFEPFGPLVRCDI--------RKTFAFVEFEDSEDATKALEA 53

Query: 139 MHGKFLDGRVIFVEIAK 155
           +HG  +DG V+ VE  K
Sbjct: 54  LHGSRIDGSVLTVEFVK 70

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

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

 Score = 52.1 bits (125), Expect = 1e-09
 Identities = 26/71 (36%), Positives = 42/71 (59%), Gaps = 1/71 (1%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           +LFV GLS+ T++++LR  F  +G++V+  ++ DK  NR RGF F+++         + G
Sbjct: 1   KLFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLAG 60

Query: 139 MHGKFLDGRVI 149
                LDGR I
Sbjct: 61  -GPHTLDGRTI 70

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

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

 Score = 51.9 bits (124), Expect = 1e-09
 Identities = 25/78 (32%), Positives = 46/78 (58%), Gaps = 3/78 (3%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           LFV GLS  T+E++L+ +F G    +   +V D+     +GF F+ +++EE+++ A E M
Sbjct: 3   LFVKGLSEDTTEETLKESFDG---SIAARIVTDRDTGSSKGFGFVDFSSEEDAKAAKEAM 59

Query: 140 HGKFLDGRVIFVEIAKSR 157
               +DG  + ++ AK +
Sbjct: 60  EDGEIDGNKVTLDFAKPK 77

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

>gnl|CDD|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 = 51.5 bits (124), Expect = 2e-09
 Identities = 27/77 (35%), Positives = 42/77 (54%), Gaps = 1/77 (1%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           T+L V  + F  ++  LR  F  FGQ+  V L   K     RGFAF+ + T++E++ A+E
Sbjct: 1   TKLIVRNVPFEATKKELRELFSPFGQVKSVRLPK-KFDGSHRGFAFVEFVTKQEAQNAME 59

Query: 138 GMHGKFLDGRVIFVEIA 154
            +    L GR + +E A
Sbjct: 60  ALKSTHLYGRHLVLEYA 76

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

 Score = 51.1 bits (122), Expect = 2e-09
 Identities = 20/63 (31%), Positives = 36/63 (57%)

Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
            P  ++FV GL+   +E+ +R  F  FG++  + L MD   N+ RGF F+ +  E+  ++
Sbjct: 2   DPVKKIFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEEDPVKK 61

Query: 135 AIE 137
            +E
Sbjct: 62  VLE 64

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

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

 Score = 54.3 bits (130), Expect = 3e-09
 Identities = 24/69 (34%), Positives = 41/69 (59%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           T L+V+ L    ++D L   F  +GQ+V+ N++ DK+   PRG AF+R+   EE++ AI 
Sbjct: 194 TNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAIS 253

Query: 138 GMHGKFLDG 146
            ++    +G
Sbjct: 254 ALNNVIPEG 262

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

>gnl|CDD|241201 cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 50.8 bits (121), Expect = 3e-09
 Identities = 24/71 (33%), Positives = 40/71 (56%), Gaps = 1/71 (1%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           ++FV GLS+ TS+  L++ F  FG++ +  + MD    R RGF F+ +       + +E 
Sbjct: 1   KMFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQ 60

Query: 139 MHGKFLDGRVI 149
              + LDGR+I
Sbjct: 61  KEHR-LDGRLI 70

This subgroup corresponds to the RRM1 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), which is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 75

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

 Score = 50.9 bits (121), Expect = 3e-09
 Identities = 24/79 (30%), Positives = 42/79 (53%)

Query: 77  KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
           +T L V+ L    ++D LR+ F   G++    L+ DK+A    G+ F+ Y   +++ RAI
Sbjct: 1   RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAI 60

Query: 137 EGMHGKFLDGRVIFVEIAK 155
             ++G  L  + I V  A+
Sbjct: 61  NTLNGLRLQSKTIKVSYAR 79

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

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

 Score = 50.4 bits (121), Expect = 4e-09
 Identities = 25/73 (34%), Positives = 38/73 (52%), Gaps = 1/73 (1%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           LFV  L + T+ + L   F+  G    V L+ DK   + +G AF+ + T E   +A++ +
Sbjct: 3   LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALK-L 61

Query: 140 HGKFLDGRVIFVE 152
           H   L GR I VE
Sbjct: 62  HHTLLKGRKINVE 74

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

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

 Score = 50.3 bits (121), Expect = 4e-09
 Identities = 19/78 (24%), Positives = 40/78 (51%), Gaps = 5/78 (6%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           +++V  L  R ++  L + F+ +G L  V      +A  P GFAF+ +    ++  A+  
Sbjct: 1   KVYVGNLGPRATKRELEDEFEKYGPLRSV-----WVARNPPGFAFVEFEDPRDAEDAVRA 55

Query: 139 MHGKFLDGRVIFVEIAKS 156
           + G+ + G  + VE+++ 
Sbjct: 56  LDGRRICGNRVRVELSRG 73

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

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

 Score = 49.9 bits (120), Expect = 4e-09
 Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 8/74 (10%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           +LFV  L   T+ + LR  F+ +G + E ++V        + + F+    EE++  AI+ 
Sbjct: 1   KLFVGNLPDATTSEELRALFEKYGTVTECDVV--------KNYGFVHMEEEEDAEDAIKA 52

Query: 139 MHGKFLDGRVIFVE 152
           ++G    G+ I VE
Sbjct: 53  LNGYEFMGKRINVE 66

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

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

 Score = 49.7 bits (119), Expect = 7e-09
 Identities = 27/73 (36%), Positives = 41/73 (56%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           L+VSGLS  T    L+  F  +G++V   +V +  +   R F F+  A+ EE+ + I+ +
Sbjct: 2   LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQHL 61

Query: 140 HGKFLDGRVIFVE 152
           H   L GRVI VE
Sbjct: 62  HRTELHGRVISVE 74

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

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

 Score = 49.8 bits (119), Expect = 7e-09
 Identities = 22/78 (28%), Positives = 42/78 (53%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           LFV  L+F  +++ L + F     +    +V D      RG+ F+ +A  E+++ A+  +
Sbjct: 2   LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61

Query: 140 HGKFLDGRVIFVEIAKSR 157
             K L GR++ ++IA+ R
Sbjct: 62  KNKKLHGRILRLDIAERR 79

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

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

 Score = 53.3 bits (128), Expect = 9e-09
 Identities = 25/92 (27%), Positives = 50/92 (54%), Gaps = 1/92 (1%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           L+V  L    +++ LR  F   G++    +++D+     RGF F+ ++  EE+ RA+  M
Sbjct: 288 LYVKNLDDTVTDEKLRELFSECGEITSAKVMLDE-KGVSRGFGFVCFSNPEEANRAVTEM 346

Query: 140 HGKFLDGRVIFVEIAKSRAELRQAFKNNPRQN 171
           HG+ L G+ ++V +A+ + + R   ++   Q 
Sbjct: 347 HGRMLGGKPLYVALAQRKEQRRAHLQDQFMQL 378

These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis (GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ), broadly expressed (SP:P11940_PABP1) and of unknown tissue range (SP:Q15097_PABP2). Length = 562

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

 Score = 49.7 bits (119), Expect = 9e-09
 Identities = 20/77 (25%), Positives = 41/77 (53%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           T L V+ L    +++ LR+ F+  G +    +V D+I  +  G+ F+ Y  E ++++AI 
Sbjct: 1   TNLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAIN 60

Query: 138 GMHGKFLDGRVIFVEIA 154
            ++G  +  + + V  A
Sbjct: 61  TLNGFEIRNKRLKVSYA 77

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

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

 Score = 49.2 bits (118), Expect = 1e-08
 Identities = 23/72 (31%), Positives = 36/72 (50%), Gaps = 6/72 (8%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           T +FV GL    +ED LR+ F  FG++V V     KI    +G  F+++     +  AI+
Sbjct: 2   TTVFVGGLDPAVTEDELRSLFGPFGEIVYV-----KIPP-GKGCGFVQFVHRAAAEAAIQ 55

Query: 138 GMHGKFLDGRVI 149
            + G  + G  I
Sbjct: 56  QLQGTIIGGSRI 67

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

>gnl|CDD|240899 cd12453, RRM1_RIM4_like, RNA recognition motif 1 in yeast meiotic activator RIM4 and similar proteins

 Score = 49.3 bits (118), Expect = 1e-08
 Identities = 28/84 (33%), Positives = 44/84 (52%), Gaps = 7/84 (8%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNA----FQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEE 131
           P   +FV+ L    S+D L  A    F  +G LV V ++ D    RP  +AF+++  +++
Sbjct: 1   PSACVFVASLPASKSDDELEAAVTEHFSKYGTLVFVKVLRD-WRQRP--YAFVQFTNDDD 57

Query: 132 SRRAIEGMHGKFLDGRVIFVEIAK 155
           ++ A+    G  LDGR I  E AK
Sbjct: 58  AKNALAKGQGTILDGRHIRCERAK 81

This subfamily corresponds to the RRM1 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1. . Length = 86

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

 Score = 49.3 bits (117), Expect = 1e-08
 Identities = 26/76 (34%), Positives = 44/76 (57%), Gaps = 1/76 (1%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           ++F+ GLS++TS DSLR+ F  FG++ E  ++ D    R RGF F+ +A      + +  
Sbjct: 1   KMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVLAQ 60

Query: 139 MHGKFLDGRVIFVEIA 154
            H + LD + I  ++A
Sbjct: 61  PHHE-LDSKTIDPKVA 75

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

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

 Score = 49.2 bits (118), Expect = 1e-08
 Identities = 16/70 (22%), Positives = 36/70 (51%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           L++  L     E  + +AF   G++  V ++ +K   +  G+ F+ +AT E + +A++ +
Sbjct: 2   LWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSL 61

Query: 140 HGKFLDGRVI 149
           +GK +     
Sbjct: 62  NGKPIPNTQQ 71

This subfamily corresponds to the RRM1 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs. . Length = 81

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

 Score = 48.8 bits (117), Expect = 2e-08
 Identities = 22/76 (28%), Positives = 39/76 (51%), Gaps = 1/76 (1%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVE-VNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           +FV  L+   ++  L+  F+     V    +VMD +  R +G+ F+R+  E+E  RA+  
Sbjct: 4   IFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRALTE 63

Query: 139 MHGKFLDGRVIFVEIA 154
           M+G +   R + V  A
Sbjct: 64  MNGVYCSSRPMRVSPA 79

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

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

 Score = 48.4 bits (116), Expect = 2e-08
 Identities = 19/65 (29%), Positives = 41/65 (63%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           T +++ GL   T+++ L    Q FG+++    ++DK  N+ +G+ F+ + + E + +AIE
Sbjct: 1   TNVYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIE 60

Query: 138 GMHGK 142
           G++G+
Sbjct: 61  GLNGR 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|241123 cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), and similar proteins

 Score = 48.6 bits (115), Expect = 2e-08
 Identities = 26/73 (35%), Positives = 41/73 (56%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           L+VSGLS  T    L+N F  +G++V   +V +  +   R + F+  +T EE+ + I  +
Sbjct: 4   LWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSEEATKCINHL 63

Query: 140 HGKFLDGRVIFVE 152
           H   L GR+I VE
Sbjct: 64  HRTELHGRMISVE 76

This subgroup corresponds to RRM of SAFB1, also termed scaffold attachment factor B (SAF-B), heat-shock protein 27 estrogen response element ERE and TATA-box-binding protein (HET), or heterogeneous nuclear ribonucleoprotein hnRNP A1- associated protein (HAP), a large multi-domain protein with well-described functions in transcriptional repression, RNA splicing and metabolism, and a proposed role in chromatin organization. Based on the numerous functions, SAFB1 has been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. SAFB1 specifically binds to AT-rich scaffold or matrix attachment region DNA elements (S/MAR DNA) by using its N-terminal scaffold attachment factor-box (SAF-box, also known as SAP domain), a homeodomain-like DNA binding motif. The central region of SAFB1 is composed of an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a nuclear localization signal (NLS). The C-terminus of SAFB1 contains Glu/Arg- and Gly-rich regions that might be involved in protein-protein interaction. Additional studies indicate that the C-terminal region contains a potent and transferable transcriptional repression domain. Another family member is SAFB2, a homolog of SAFB1. Both SAFB1 and SAFB2 are ubiquitously coexpressed and share very high sequence similarity, suggesting that they might function in a similar manner. However, unlike SAFB1, exclusively existing in the nucleus, SAFB2 is also present in the cytoplasm. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1. Length = 76

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

 Score = 48.6 bits (116), Expect = 2e-08
 Identities = 23/78 (29%), Positives = 41/78 (52%)

Query: 77  KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
           KT L V+ L    ++D +R+ F   G++    L+ DK+  +  G+ F+ Y   E++ +AI
Sbjct: 1   KTNLIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAI 60

Query: 137 EGMHGKFLDGRVIFVEIA 154
             ++G  L  + I V  A
Sbjct: 61  NTLNGLRLQNKTIKVSYA 78

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

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

 Score = 48.4 bits (116), Expect = 2e-08
 Identities = 19/73 (26%), Positives = 37/73 (50%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           LF+  L    ++  L   F  FG ++   + +DK   + + F F+ Y   E ++ AI+ M
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 140 HGKFLDGRVIFVE 152
           +G  + G+ + V+
Sbjct: 61  NGFQVGGKRLKVQ 73

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

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

 Score = 51.5 bits (123), Expect = 3e-08
 Identities = 24/90 (26%), Positives = 47/90 (52%), Gaps = 1/90 (1%)

Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
           + KT L V+ L    +++ +R+ F   G++    LV DK+  +  G+ F+ Y   E++ +
Sbjct: 1   ESKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEK 60

Query: 135 AIEGMHGKFLDGRVIFVEIAK-SRAELRQA 163
           A+  ++G  L  + I V  A+ S   ++ A
Sbjct: 61  AVNSLNGLRLQNKTIKVSYARPSSDSIKGA 90

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

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

 Score = 48.1 bits (115), Expect = 3e-08
 Identities = 23/72 (31%), Positives = 35/72 (48%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           +FV  L     E  L   F  FG +  V ++ D   N+ +G+ F+     EE+  AI  +
Sbjct: 4   IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIASL 63

Query: 140 HGKFLDGRVIFV 151
           +G  L GRV+ V
Sbjct: 64  NGYRLGGRVLQV 75

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

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

 Score = 47.7 bits (114), Expect = 4e-08
 Identities = 29/77 (37%), Positives = 42/77 (54%), Gaps = 1/77 (1%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           +RL V  L     ED LR  F+ FG + +V L   K   + R F F+ Y TEEE+++A++
Sbjct: 1   SRLIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTK-DGKFRKFGFVGYKTEEEAQKALK 59

Query: 138 GMHGKFLDGRVIFVEIA 154
             +  F+D   I VEI 
Sbjct: 60  HFNNSFIDTSKITVEIC 76

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

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

 Score = 47.8 bits (114), Expect = 4e-08
 Identities = 17/48 (35%), Positives = 30/48 (62%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYA 127
           +F+ GLS++T+ + LR  F  FG++ E  ++ D    R RGF F+ ++
Sbjct: 1   MFIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFS 48

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

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

 Score = 48.0 bits (115), Expect = 4e-08
 Identities = 18/71 (25%), Positives = 38/71 (53%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           R+FV  L    +++ L  AF  +    +  +V DK   + +G+ F+ ++   +  +A++ 
Sbjct: 8   RIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAMKE 67

Query: 139 MHGKFLDGRVI 149
           M+GK++  R I
Sbjct: 68  MNGKYVGNRPI 78

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

>gnl|CDD|241016 cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 47.7 bits (113), Expect = 5e-08
 Identities = 20/59 (33%), Positives = 36/59 (61%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           ++FV GLS  T+ + ++  F+ FG++ +  L+ DK  NR RGF F+ + +E+   +  E
Sbjct: 1   KIFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE 59

This subgroup corresponds to the RRM2 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1) and has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. It represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 74

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

 Score = 47.5 bits (113), Expect = 5e-08
 Identities = 23/74 (31%), Positives = 40/74 (54%), Gaps = 8/74 (10%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           ++FV  +   TS++ LR  F+ +G ++   ++        R FAF+    E  + RAIE 
Sbjct: 2   KIFVGNVDEDTSQEELRALFEAYGAVLSCAVM--------RQFAFVHLRGEAAADRAIEE 53

Query: 139 MHGKFLDGRVIFVE 152
           ++G+ L GR + VE
Sbjct: 54  LNGRELHGRKLVVE 67

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

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

 Score = 47.5 bits (114), Expect = 5e-08
 Identities = 17/54 (31%), Positives = 31/54 (57%), Gaps = 1/54 (1%)

Query: 98  FQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFV 151
           F  FG ++   +  D+     +G+ F+ + TEE + RAIE ++G  L+ + +FV
Sbjct: 23  FSAFGNILSCKVATDE-NGGSKGYGFVHFETEEAAVRAIEKVNGMLLNDKKVFV 75

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

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

 Score = 47.3 bits (113), Expect = 6e-08
 Identities = 21/77 (27%), Positives = 40/77 (51%), Gaps = 8/77 (10%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           R+++  L +R  E  +   F+G+G++ E+NL          GF F+ +    ++  A+  
Sbjct: 1   RVYIGRLPYRARERDVERFFKGYGRIREINL--------KNGFGFVEFEDPRDADDAVYE 52

Query: 139 MHGKFLDGRVIFVEIAK 155
           ++GK L G  + VE A+
Sbjct: 53  LNGKELCGERVIVEHAR 69

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

>gnl|CDD|240717 cd12271, RRM1_PHIP1, RNA recognition motif 1 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 47.3 bits (113), Expect = 6e-08
 Identities = 24/73 (32%), Positives = 46/73 (63%), Gaps = 1/73 (1%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           ++V G+ + ++ED +R+ F   G++ E++L+      R RG AF+ + TEE ++RA+  +
Sbjct: 1   VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRALA-L 59

Query: 140 HGKFLDGRVIFVE 152
            G+ + GR + VE
Sbjct: 60  DGEDMGGRFLKVE 72

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

>gnl|CDD|241202 cd12758, RRM1_hnRPDL, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP DL) and similar proteins

 Score = 47.3 bits (112), Expect = 6e-08
 Identities = 23/77 (29%), Positives = 41/77 (53%), Gaps = 1/77 (1%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           ++F+ GLS+ TS+  L      FG++++  +  D +  R RGF F+ +       + +E 
Sbjct: 1   KMFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLEL 60

Query: 139 MHGKFLDGRVIFVEIAK 155
              K LDG++I  + AK
Sbjct: 61  KEHK-LDGKLIDPKRAK 76

This subgroup corresponds to the RRM1 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), which is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 76

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

 Score = 47.3 bits (112), Expect = 6e-08
 Identities = 20/64 (31%), Positives = 37/64 (57%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           +LFV  +    +E  +R  F+  G ++EV ++ DK     +G  F++Y+T +E+ RAI  
Sbjct: 1   KLFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRA 60

Query: 139 MHGK 142
           +H +
Sbjct: 61  LHNQ 64

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

>gnl|CDD|241004 cd12560, RRM_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor 12 (SRSF12) and similar proteins

 Score = 47.3 bits (112), Expect = 7e-08
 Identities = 24/78 (30%), Positives = 46/78 (58%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           T LFV  ++  T  + LR  F  +G +V+V + +D    RPRGFA++++    ++  A+ 
Sbjct: 1   TSLFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALY 60

Query: 138 GMHGKFLDGRVIFVEIAK 155
            ++ K++ GR I ++ A+
Sbjct: 61  NLNRKWVCGRQIEIQFAQ 78

This subgroup corresponds to the RRM of SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19). SRSF12 is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. SRSF12 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

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

 Score = 46.9 bits (112), Expect = 9e-08
 Identities = 23/81 (28%), Positives = 41/81 (50%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
           P+  LFV  L+  T+++ L   F  FG++    ++ DK       +AF+ + T+E+   A
Sbjct: 2   PENVLFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEA 61

Query: 136 IEGMHGKFLDGRVIFVEIAKS 156
              M    +D R I V+ ++S
Sbjct: 62  YFKMDNVLIDDRRIHVDFSQS 82

This subfamily corresponds to the RRM of PPIase, also termed cyclophilin-like protein PPIL4, or rotamase PPIL4, a novel nuclear RNA-binding protein encoded by cyclophilin-like PPIL4 gene. The precise role of PPIase remains unclear. PPIase contains a conserved N-terminal peptidyl-prolyl cistrans isomerase (PPIase) motif, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a lysine rich domain, and a pair of bipartite nuclear targeting sequences (NLS) at the C-terminus. Length = 83

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

 Score = 47.6 bits (113), Expect = 9e-08
 Identities = 16/61 (26%), Positives = 27/61 (44%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
             LFV  L +  +E+SL   F  FG +     V+DK   R +G  F+ +  +      ++
Sbjct: 2   FTLFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACLK 61

Query: 138 G 138
            
Sbjct: 62  N 62

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

>gnl|CDD|241003 cd12559, RRM_SRSF10, RNA recognition motif in serine/arginine-rich splicing factor 10 (SRSF10) and similar proteins

 Score = 46.9 bits (111), Expect = 1e-07
 Identities = 23/78 (29%), Positives = 45/78 (57%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           + LFV  ++  T  + LR  F  +G +V+V + +D    RPRGFA++++    ++  A+ 
Sbjct: 1   SSLFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALH 60

Query: 138 GMHGKFLDGRVIFVEIAK 155
            +  K++ GR I ++ A+
Sbjct: 61  NLDRKWICGRQIEIQFAQ 78

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

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

 Score = 46.4 bits (111), Expect = 1e-07
 Identities = 24/79 (30%), Positives = 36/79 (45%), Gaps = 10/79 (12%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRP-RGFAFLRYATEEESRRAIEG 138
           L+V GL   TS   L   F  FG +        +I   P R +A++ Y + E ++ A E 
Sbjct: 1   LWVGGLGPWTSLAELEREFDRFGAI-------RRIDYDPGRNYAYIEYESIEAAQAAKEA 53

Query: 139 MHGKFL--DGRVIFVEIAK 155
           + G  L   GR + V+ A 
Sbjct: 54  LRGFPLGGPGRRLRVDFAD 72

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

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

 Score = 46.4 bits (111), Expect = 1e-07
 Identities = 26/78 (33%), Positives = 41/78 (52%), Gaps = 1/78 (1%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLR-YATEEESRRAIE 137
           RLFV GLS   +E  L   F  FG + +V ++  K A   RGFA++    +E + ++   
Sbjct: 1   RLFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKS 60

Query: 138 GMHGKFLDGRVIFVEIAK 155
            ++G    G V+ +E AK
Sbjct: 61  TLNGTKWKGSVLKIEEAK 78

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

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

 Score = 46.3 bits (110), Expect = 1e-07
 Identities = 24/69 (34%), Positives = 38/69 (55%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           LFV  LSF T+ED LR  F   G++  V ++  + + + +GFAF+ +   E +  A++G 
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNALKGK 60

Query: 140 HGKFLDGRV 148
           H      RV
Sbjct: 61  HLNGRALRV 69

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

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

 Score = 46.2 bits (109), Expect = 2e-07
 Identities = 20/70 (28%), Positives = 40/70 (57%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           +FV  LS   + + +++AF  FG++ +  +V D    + +G+ F+ +  + ++  AI  M
Sbjct: 4   VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63

Query: 140 HGKFLDGRVI 149
            G++L GR I
Sbjct: 64  GGQWLGGRQI 73

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

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

 Score = 46.3 bits (110), Expect = 2e-07
 Identities = 24/77 (31%), Positives = 40/77 (51%), Gaps = 1/77 (1%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           T++ V  L F  ++  +R  F  +GQL  V  V  K     RGFAF+ ++T +E+  A+ 
Sbjct: 1   TKILVKNLPFEATKKDVRTLFSSYGQLKSVR-VPKKFDQSARGFAFVEFSTAKEALNAMN 59

Query: 138 GMHGKFLDGRVIFVEIA 154
            +    L GR + ++ A
Sbjct: 60  ALKDTHLLGRRLVLQYA 76

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

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

 Score = 46.1 bits (110), Expect = 2e-07
 Identities = 20/77 (25%), Positives = 41/77 (53%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
            R++V+ +    SED +++ F+ FG++   +L  D    + +G+ F+ Y   + ++ AI 
Sbjct: 1   NRIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIA 60

Query: 138 GMHGKFLDGRVIFVEIA 154
            M+   L G+ + V  A
Sbjct: 61  SMNLFDLGGQQLRVGKA 77

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

>gnl|CDD|240748 cd12302, RRM_scSet1p_like, RNA recognition motif in budding yeast Saccharomyces cerevisiae SET domain-containing protein 1 (scSet1p) and similar proteins

 Score = 47.0 bits (112), Expect = 2e-07
 Identities = 21/95 (22%), Positives = 36/95 (37%), Gaps = 8/95 (8%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEES--- 132
           P   + V G    TSED ++N F  FG++ E+    D     P G   ++Y         
Sbjct: 1   PPVEIVVWGFQPSTSEDIIKNYFSSFGEIAEIRNFNDPNTAVPLGIYLIKYYGSPGKPDR 60

Query: 133 -----RRAIEGMHGKFLDGRVIFVEIAKSRAELRQ 162
                 +A+       + G    VE+  +  +L +
Sbjct: 61  AAKAALKAVRKAQDCRIGGAEFKVELNPNERKLEK 95

This subfamily corresponds to the RRM of scSet1p, also termed H3 lysine-4 specific histone-lysine N-methyltransferase, or COMPASS component SET1, or lysine N-methyltransferase 2, which is encoded by SET1 from the yeast S. cerevisiae. It is a nuclear protein that may play a role in both silencing and activating transcription. scSet1p is closely related to the SET domain proteins of multicellular organisms, which are implicated in diverse aspects of cell morphology, growth control, and chromatin-mediated transcriptional silencing. scSet1p contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a conserved SET domain that may play a role in DNA repair and telomere function. . Length = 110

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

 Score = 45.8 bits (109), Expect = 2e-07
 Identities = 18/74 (24%), Positives = 35/74 (47%), Gaps = 3/74 (4%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI-E 137
           +LFV  L +      L+  F  FG++   N+  DK     +G+ F+ +++ +    A+ +
Sbjct: 1   KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQK 60

Query: 138 GMHGKFLDGRVIFV 151
             H   L+G  + V
Sbjct: 61  QKH--ILEGNKLQV 72

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

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

 Score = 45.2 bits (107), Expect = 3e-07
 Identities = 22/75 (29%), Positives = 42/75 (56%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           +FV  + +  +E+ L++ F   G +V   LV D+   +P+G+ F  Y  +E +  A+  +
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 140 HGKFLDGRVIFVEIA 154
           +G  L+GR + V+ A
Sbjct: 61  NGYELNGRQLRVDNA 75

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

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

 Score = 44.8 bits (107), Expect = 4e-07
 Identities = 17/61 (27%), Positives = 34/61 (55%), Gaps = 5/61 (8%)

Query: 94  LRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEI 153
           L   F  FG + ++     K+  +  GFAF+ ++TEE + +A++ ++G    GR + V+ 
Sbjct: 1   LYKLFSPFGNVEKI-----KLLKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDY 55

Query: 154 A 154
           +
Sbjct: 56  S 56

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

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

 Score = 45.4 bits (108), Expect = 4e-07
 Identities = 19/67 (28%), Positives = 35/67 (52%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           L+VSGL    ++  L   F  +G+++   ++ D +    RG  F+R+    E+ RAI+ +
Sbjct: 3   LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL 62

Query: 140 HGKFLDG 146
           +G    G
Sbjct: 63  NGTIPPG 69

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

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

 Score = 44.9 bits (106), Expect = 4e-07
 Identities = 21/73 (28%), Positives = 42/73 (57%), Gaps = 5/73 (6%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           L V+ LS+  SEDSL+  F+        ++ + +   RP+G+AF+ + + E+++ A+   
Sbjct: 4   LVVNNLSYSASEDSLQEVFEK-----ATSIRIPQNNGRPKGYAFVEFESAEDAKEALNSC 58

Query: 140 HGKFLDGRVIFVE 152
           +   ++GR I +E
Sbjct: 59  NNTEIEGRSIRLE 71

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

>gnl|CDD|241017 cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA-binding protein Musashi homolog 2 (Musashi-2) and similar proteins

 Score = 45.1 bits (106), Expect = 5e-07
 Identities = 20/59 (33%), Positives = 34/59 (57%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           ++FV GLS  T  + ++  F+ FG++ +  L+ DK  NR RGF F+ +  E+   +  E
Sbjct: 5   KIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEKVCE 63

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 79

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

 Score = 45.2 bits (107), Expect = 5e-07
 Identities = 22/76 (28%), Positives = 38/76 (50%), Gaps = 1/76 (1%)

Query: 80  LFVSGLSFRTSEDSLRNAFQG-FGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           +FV  LS   +E  L + FQ  F       ++ D +    RG+ F+R++ E + +RA+  
Sbjct: 4   IFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRALIE 63

Query: 139 MHGKFLDGRVIFVEIA 154
           M G +  GR + +  A
Sbjct: 64  MQGVYCGGRPMRISTA 79

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

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

 Score = 44.8 bits (107), Expect = 5e-07
 Identities = 24/73 (32%), Positives = 42/73 (57%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           L+V  LSF T+E+ +   F   G +  + + +D+    P GF F+ Y T E++  A++ +
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYL 60

Query: 140 HGKFLDGRVIFVE 152
           +G  LD R+I V+
Sbjct: 61  NGTKLDDRIIRVD 73

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

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

 Score = 44.8 bits (106), Expect = 6e-07
 Identities = 20/56 (35%), Positives = 38/56 (67%), Gaps = 1/56 (1%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
           R+FV G+ F+T+E+ LR  F  +G + EV +V D+ A   +G+ F+ + T+E++++
Sbjct: 4   RIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDR-AGVSKGYGFVTFETQEDAQK 58

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

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

 Score = 44.7 bits (105), Expect = 7e-07
 Identities = 21/70 (30%), Positives = 40/70 (57%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           +FV  LS   + D ++ AF  FG++ +  +V D    + +G+ F+ +  + ++  AI+ M
Sbjct: 4   VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 63

Query: 140 HGKFLDGRVI 149
            G++L GR I
Sbjct: 64  GGQWLGGRQI 73

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

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

 Score = 44.7 bits (106), Expect = 8e-07
 Identities = 20/79 (25%), Positives = 40/79 (50%), Gaps = 7/79 (8%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLV------MDKIANRPRGFAFLRYATEEES 132
           R+++S LS+ +SE+ L    + F   V V +             RP G A+  +++ E++
Sbjct: 1   RVYISNLSYSSSEEDLEEFLKDFEP-VSVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQA 59

Query: 133 RRAIEGMHGKFLDGRVIFV 151
            + ++ ++GK    R +FV
Sbjct: 60  EKVVKDLNGKVFKNRKLFV 78

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

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

 Score = 44.3 bits (104), Expect = 9e-07
 Identities = 23/79 (29%), Positives = 42/79 (53%)

Query: 77  KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
           KT L V+ L    +++ L++ F   G++    LV DKI  +  G+ F+ Y   +++ +AI
Sbjct: 4   KTNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 63

Query: 137 EGMHGKFLDGRVIFVEIAK 155
             ++G  L  + I V  A+
Sbjct: 64  NTLNGLRLQTKTIKVSYAR 82

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

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

 Score = 44.3 bits (105), Expect = 1e-06
 Identities = 21/80 (26%), Positives = 46/80 (57%), Gaps = 6/80 (7%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           T L++  LS + +E+ L+N F+ +G++  ++++       PRG A++   T +++ RA++
Sbjct: 3   TTLWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIP------PRGCAYVCMETRQDAHRALQ 56

Query: 138 GMHGKFLDGRVIFVEIAKSR 157
            +    L G+ I V  A ++
Sbjct: 57  KLRNVKLAGKKIKVAWAPNK 76

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

>gnl|CDD|241079 cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 44.3 bits (105), Expect = 1e-06
 Identities = 21/63 (33%), Positives = 38/63 (60%), Gaps = 1/63 (1%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           +LFV  LS + +ED +R  F+ FG + E  ++     N  +G AF+++++  E++ AI  
Sbjct: 3   KLFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGPDGNS-KGCAFVKFSSHAEAQAAINA 61

Query: 139 MHG 141
           +HG
Sbjct: 62  LHG 64

This subgroup corresponds to the RRM2 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, being highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, being 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 a 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 = 81

>gnl|CDD|241203 cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 43.8 bits (103), Expect = 1e-06
 Identities = 17/51 (33%), Positives = 33/51 (64%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATE 129
           ++F+ GLS++T+++ LR  F  FG++ E  ++ D +  R RGF F+ +  +
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQ 52

This subgroup corresponds to the RRM1 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells and associated with asymmetric divisions in neural progenitor cells. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). Musashi-1 has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, it represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 77

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

 Score = 43.6 bits (103), Expect = 1e-06
 Identities = 22/73 (30%), Positives = 38/73 (52%), Gaps = 8/73 (10%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           RL+V      TSE ++R  F  +G + EV ++          FAF+ + + E + RA + 
Sbjct: 1   RLYVRPFPPDTSESAIREIFSPYGAVKEVKMI--------SNFAFVEFESLESAIRAKDS 52

Query: 139 MHGKFLDGRVIFV 151
           +HGK L+   ++V
Sbjct: 53  VHGKVLNNNPLYV 65

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

 Score = 43.8 bits (104), Expect = 1e-06
 Identities = 20/71 (28%), Positives = 40/71 (56%), Gaps = 5/71 (7%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           R+FV G+   T+E+ LR+ F  FG + +V ++ D+     +G+ F+ + T+E++ + +  
Sbjct: 4   RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAG-VSKGYGFVTFETQEDAEKILAM 62

Query: 139 ----MHGKFLD 145
                 GK L+
Sbjct: 63  GNLNFRGKKLN 73

This subfamily corresponds to the RRM domain of two Deleted in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE. BOULE is the founder member of the family and DAZL arose from BOULE in an ancestor of vertebrates. The DAZ gene subsequently originated from a duplication transposition of the DAZL gene. Invertebrates contain a single DAZ homolog, BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. The family members encode closely related RNA-binding proteins that are required for fertility in numerous organisms. These proteins contain an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a varying number of copies of a DAZ motif, believed to mediate protein-protein interactions. DAZL and BOULE contain a single copy of the DAZ motif, while DAZ proteins can contain 8-24 copies of this repeat. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 80

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

 Score = 43.8 bits (104), Expect = 1e-06
 Identities = 16/70 (22%), Positives = 35/70 (50%), Gaps = 2/70 (2%)

Query: 80  LFVSGLSFRTSEDSLRNAFQ--GFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           L+V  L++ T+++ L  A    G   +  +     K   + +GFA++ +A+E  +    E
Sbjct: 1   LYVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKE 60

Query: 138 GMHGKFLDGR 147
            + G+  +G+
Sbjct: 61  KLEGREFNGK 70

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

>gnl|CDD|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 43.7 bits (104), Expect = 2e-06
 Identities = 23/78 (29%), Positives = 40/78 (51%), Gaps = 2/78 (2%)

Query: 77  KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
              +FV  +     ED L   F+  G + E+ L+MD      RG+AF+ Y  +E ++RA+
Sbjct: 1   GCEVFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFSGLN-RGYAFVTYTNKEAAQRAV 59

Query: 137 EGMHGKFLD-GRVIFVEI 153
           + +H   +  G+ + V I
Sbjct: 60  KQLHNYEIRPGKRLGVCI 77

This subfamily corresponds to the RRM1 in hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF), and dead end protein homolog 1 (DND1). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. It has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. DND1 is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members in this family, except for DND1, contain three conserved RNA recognition motifs (RRMs); DND1 harbors only two RRMs. . Length = 78

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

 Score = 43.4 bits (103), Expect = 2e-06
 Identities = 17/71 (23%), Positives = 36/71 (50%), Gaps = 1/71 (1%)

Query: 81  FVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMH 140
           FV  + + T+ + L+  F+  G +  + ++ DK   +P+GFA++ +  ++ S      ++
Sbjct: 3   FVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEF-LDKSSVENALLLN 61

Query: 141 GKFLDGRVIFV 151
                GR I V
Sbjct: 62  ESEFRGRQIKV 72

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

>gnl|CDD|240796 cd12350, RRM3_SHARP, RNA recognition motif 3 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 43.5 bits (103), Expect = 2e-06
 Identities = 21/70 (30%), Positives = 38/70 (54%), Gaps = 4/70 (5%)

Query: 78  TR-LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
           TR LF+  L   T+   LR AF+ FG+++++++   K       +AF++YA      +A+
Sbjct: 2   TRTLFIGNLEKTTTYSDLREAFERFGEIIDIDI---KKQGGNPAYAFIQYADIASVVKAM 58

Query: 137 EGMHGKFLDG 146
             M G++L  
Sbjct: 59  RKMDGEYLGN 68

This subfamily corresponds to the RRM3 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins. . Length = 74

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

 Score = 43.5 bits (103), Expect = 2e-06
 Identities = 20/66 (30%), Positives = 33/66 (50%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
            +LFV  +     E  LR  F+ FG++ E+ ++ DK     +G AFL Y   E + +A  
Sbjct: 6   IKLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALKAQS 65

Query: 138 GMHGKF 143
            +H + 
Sbjct: 66  ALHEQK 71

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

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

 Score = 43.4 bits (103), Expect = 2e-06
 Identities = 20/72 (27%), Positives = 40/72 (55%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           ++V  L  + +E+ L   F   G +V V++  D++    +G+ F+ + +EE++  AI+ M
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 140 HGKFLDGRVIFV 151
           +   L G+ I V
Sbjct: 61  NMIKLYGKPIRV 72

This subfamily corresponds to the RRM1 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 a component of the multiprotein complex splicing factor 3b (SF3B), an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA, and is involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B4 functions to tether U2 snRNP with pre-mRNA at the branch site during spliceosome assembly. It is an evolutionarily highly conserved protein with orthologs across diverse species. SF3B4 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It binds directly to pre-mRNA and also interacts directly and highly specifically with another SF3B subunit called SAP 145. . Length = 74

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

 Score = 43.5 bits (102), Expect = 2e-06
 Identities = 18/63 (28%), Positives = 37/63 (58%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           L+VSGL    S+  +   F  +G+++   +++D++    RG  F+R+    E+  AI+G+
Sbjct: 4   LYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIKGL 63

Query: 140 HGK 142
           +G+
Sbjct: 64  NGQ 66

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

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

 Score = 43.7 bits (103), Expect = 2e-06
 Identities = 24/80 (30%), Positives = 40/80 (50%), Gaps = 5/80 (6%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRP-----RGFAFLRYATEEESRR 134
           LFV  L+F T+   L +AF+     V   +       RP      GF F+ + T+E+++ 
Sbjct: 3   LFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQAQA 62

Query: 135 AIEGMHGKFLDGRVIFVEIA 154
           A++ M G  LDG  + V+ +
Sbjct: 63  ALKAMDGFVLDGHTLVVKFS 82

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

 Score = 43.6 bits (102), Expect = 2e-06
 Identities = 24/91 (26%), Positives = 45/91 (49%), Gaps = 9/91 (9%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           L+VSGL    ++  L   F  +G+++   +++D++    RG  F+R+    E+  AI+G+
Sbjct: 8   LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 67

Query: 140 HGKFLDGRVIFVEIAKSRAELRQAFKNNPRQ 170
           +G+   G         +   +   F NNP Q
Sbjct: 68  NGQKPPG---------ATEPITVKFANNPSQ 89

This subgroup corresponds to the RRM2 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 90

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

 Score = 43.6 bits (102), Expect = 2e-06
 Identities = 22/79 (27%), Positives = 40/79 (50%)

Query: 77  KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
           KT L V+ L    +++  ++ F   G++    LV DKI  +  G+ F+ Y    ++ +AI
Sbjct: 3   KTNLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAI 62

Query: 137 EGMHGKFLDGRVIFVEIAK 155
             ++G  L  + I V  A+
Sbjct: 63  NTLNGLKLQTKTIKVSYAR 81

This subgroup corresponds to the RRM1 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 84

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

 Score = 43.2 bits (101), Expect = 2e-06
 Identities = 18/63 (28%), Positives = 37/63 (58%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           L+VSGL    ++  L   F  +G+++   +++D++    RG  F+R+    E+  AI+G+
Sbjct: 5   LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 64

Query: 140 HGK 142
           +G+
Sbjct: 65  NGQ 67

This subgroup corresponds to the RRM2 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells and also regulates the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

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

 Score = 43.0 bits (102), Expect = 2e-06
 Identities = 22/71 (30%), Positives = 37/71 (52%), Gaps = 7/71 (9%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           T L+V GL  R +E  LR+ F  FG++  + +V  +        AF+ + T E + +A E
Sbjct: 2   TTLYVGGLGERVTEKDLRDHFYQFGEIRSITVVPRQ------QCAFVTFTTREAAEKAAE 55

Query: 138 GMHGK-FLDGR 147
            +  K  ++GR
Sbjct: 56  RLFNKLIINGR 66

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

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

 Score = 43.1 bits (101), Expect = 2e-06
 Identities = 15/48 (31%), Positives = 30/48 (62%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRY 126
           +LFV G+   T E  LR+ F+ +G++  + ++ D+ + + RGF F+ +
Sbjct: 2   KLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTF 49

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

>gnl|CDD|241065 cd12621, RRM3_TIA1, RNA recognition motif 3 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 43.1 bits (101), Expect = 3e-06
 Identities = 20/70 (28%), Positives = 40/70 (57%), Gaps = 6/70 (8%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           ++  G++   +E  +R  F  FGQ++EV +  DK      G++F+R+ + E +  AI  +
Sbjct: 3   VYCGGVTSGLTEQLMRQTFSPFGQIMEVRVFPDK------GYSFVRFNSHESAAHAIVSV 56

Query: 140 HGKFLDGRVI 149
           +G  ++G V+
Sbjct: 57  NGTTIEGHVV 66

This subgroup corresponds to the RRM3 of p40-TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1) and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and function as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 74

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

 Score = 43.2 bits (101), Expect = 3e-06
 Identities = 23/79 (29%), Positives = 41/79 (51%)

Query: 77  KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
           KT L V+ L    +++  R+ F   G++    LV DKI  +  G+ F+ Y   +++ +AI
Sbjct: 2   KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61

Query: 137 EGMHGKFLDGRVIFVEIAK 155
             ++G  L  + I V  A+
Sbjct: 62  NTLNGLRLQTKTIKVSYAR 80

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

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

 Score = 42.4 bits (100), Expect = 4e-06
 Identities = 22/78 (28%), Positives = 41/78 (52%), Gaps = 6/78 (7%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           L++  LS   +E  LR  F+    +   ++++ K      G+AF+    +  + +AIE +
Sbjct: 1   LYIGNLSSDVNESDLRQLFEEHK-IPVSSVLVKK-----GGYAFVDCPDQSWADKAIEKL 54

Query: 140 HGKFLDGRVIFVEIAKSR 157
           +GK L G+VI VE +  +
Sbjct: 55  NGKILQGKVIEVEHSVPK 72

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

>gnl|CDD|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 = 42.2 bits (100), Expect = 4e-06
 Identities = 23/73 (31%), Positives = 41/73 (56%), Gaps = 3/73 (4%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVE-VNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           + + GL F  +E+ +R+ F G     + +++V D    RP G A++ +A+ E++RRA+  
Sbjct: 2   VRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDD-DGRPTGEAYVEFASPEDARRALR- 59

Query: 139 MHGKFLDGRVIFV 151
            H   + GR I V
Sbjct: 60  KHNNKMGGRYIEV 72

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

 Score = 42.2 bits (100), Expect = 5e-06
 Identities = 20/60 (33%), Positives = 34/60 (56%), Gaps = 3/60 (5%)

Query: 94  LRNAFQGFGQLVEVNLVM--DKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFV 151
           LR  F  FG    V + M  D+   + +G+AF+ +AT EE++ A++ ++G  LD +  F 
Sbjct: 24  LRKIFSKFGVGKIVGIYMPVDE-TGKTKGYAFVEFATPEEAKEAVKALNGYKLDKKHTFA 82

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

 Score = 42.5 bits (99), Expect = 6e-06
 Identities = 16/63 (25%), Positives = 36/63 (57%)

Query: 77  KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
           KT L++ GL   T++  L    Q +G++V    ++DK  N+ +G+ F+ + +   +++A+
Sbjct: 7   KTNLYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAAQKAV 66

Query: 137 EGM 139
             +
Sbjct: 67  SAL 69

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|241064 cd12620, RRM3_TIAR, RNA recognition motif 3 in nucleolysin TIAR and similar proteins

 Score = 41.9 bits (98), Expect = 7e-06
 Identities = 19/70 (27%), Positives = 41/70 (58%), Gaps = 6/70 (8%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           ++  G++   +E  +R  F  FGQ++E+ +  +K      G++F+R++T E +  AI  +
Sbjct: 3   VYCGGIASGLTEQLMRQTFSPFGQIMEIRVFPEK------GYSFIRFSTHESAAHAIVSV 56

Query: 140 HGKFLDGRVI 149
           +G  ++G V+
Sbjct: 57  NGTTIEGHVV 66

This subgroup corresponds to the RRM3 of nucleolysin TIAR, also termed TIA-1-related protein, a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 73

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

 Score = 41.9 bits (98), Expect = 7e-06
 Identities = 15/48 (31%), Positives = 31/48 (64%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRY 126
           ++FV G+   T E  LR+ F+ +G++  + ++ D+ + + RGFAF+ +
Sbjct: 2   KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 49

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

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

 Score = 41.4 bits (98), Expect = 8e-06
 Identities = 18/72 (25%), Positives = 42/72 (58%), Gaps = 9/72 (12%)

Query: 79  RLFVSGL-SFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           R+FV  L + + S++ L   F  +G+++ ++L         +G+ F+++  EE++R A+ 
Sbjct: 2   RVFVGNLNTDKVSKEDLEEIFSKYGKILGISL--------HKGYGFVQFDNEEDARAAVA 53

Query: 138 GMHGKFLDGRVI 149
           G +G+ + G+ +
Sbjct: 54  GENGREIAGQKL 65

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

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

 Score = 44.4 bits (105), Expect = 9e-06
 Identities = 20/87 (22%), Positives = 41/87 (47%), Gaps = 1/87 (1%)

Query: 77  KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
              +FV  L       +L + F  FG ++   +  D+   + RG+ F+ +  EE ++ AI
Sbjct: 88  VGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDE-NGKSRGYGFVHFEKEESAKAAI 146

Query: 137 EGMHGKFLDGRVIFVEIAKSRAELRQA 163
           + ++G  L+ + ++V     + E   A
Sbjct: 147 QKVNGMLLNDKEVYVGRFIKKHEREAA 173

These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis (GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ), broadly expressed (SP:P11940_PABP1) and of unknown tissue range (SP:Q15097_PABP2). Length = 562

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

 Score = 42.0 bits (98), Expect = 9e-06
 Identities = 24/78 (30%), Positives = 37/78 (47%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           +FV  LS    E  L   F  FG +  V ++ D   N+ +GF F+     +E+  AI  +
Sbjct: 4   IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63

Query: 140 HGKFLDGRVIFVEIAKSR 157
           +G  L  RV+ V    S+
Sbjct: 64  NGYRLGDRVLQVSFKTSK 81

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

>gnl|CDD|240815 cd12369, RRM4_RBM45, RNA recognition motif 4 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 41.1 bits (97), Expect = 9e-06
 Identities = 22/68 (32%), Positives = 34/68 (50%), Gaps = 6/68 (8%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           RLF+        +  L + F  FG L++V LV  K       + + +YA  E + RAI  
Sbjct: 1   RLFIVCNPSPPPDYILEDVFCRFGGLIDVYLVPGK------NYGYAKYADRESAERAITT 54

Query: 139 MHGKFLDG 146
           +HGK ++G
Sbjct: 55  LHGKEVNG 62

This subfamily corresponds to the RRM4 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 68

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

 Score = 43.8 bits (103), Expect = 1e-05
 Identities = 24/79 (30%), Positives = 39/79 (49%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           +FV  LS  T E  L   F  FG +  V ++ D   N+ +G+ F+     +E+  AI  +
Sbjct: 272 IFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSL 331

Query: 140 HGKFLDGRVIFVEIAKSRA 158
           +G  L  RV+ V    ++A
Sbjct: 332 NGYTLGNRVLQVSFKTNKA 350

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

>gnl|CDD|241038 cd12594, RRM1_SRSF4, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 4 (SRSF4)

 Score = 41.5 bits (97), Expect = 1e-05
 Identities = 20/77 (25%), Positives = 42/77 (54%), Gaps = 8/77 (10%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           R+++  LS++  E  +   F+G+G+++EV+L          G+ F+ +    ++  A+  
Sbjct: 1   RVYIGRLSYQARERDVERFFKGYGKILEVDL--------KNGYGFVEFDDLRDADDAVYE 52

Query: 139 MHGKFLDGRVIFVEIAK 155
           ++GK L G  + VE A+
Sbjct: 53  LNGKDLCGERVIVEHAR 69

This subgroup corresponds to the RRM1 of SRSF4, also termed pre-mRNA-splicing factor SRp75, or SRP001LB, or splicing factor, arginine/serine-rich 4 (SFRS4). SRSF4 is a splicing regulatory serine/arginine (SR) protein that plays an important role in both constitutive splicing and alternative splicing of many pre-mRNAs. For instance, it interacts with heterogeneous nuclear ribonucleoproteins, hnRNP G and hnRNP E2, and further regulates the 5' splice site of tau exon 10, whose misregulation causes frontotemporal dementia. SFSF4 also induces production of HIV-1 vpr mRNA through the inhibition of the 5'-splice site of exon 3. In addition, it activates splicing of the cardiac troponin T (cTNT) alternative exon by direct interactions with the cTNT exon 5 enhancer RNA. SRSF4 can shuttle between the nucleus and cytoplasm. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine-rich region, an internal region homologous to the RRM, and a very long, highly phosphorylated C-terminal SR domains rich in serine-arginine dipeptides. . Length = 74

>gnl|CDD|240832 cd12386, RRM2_hnRNPM_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 41.2 bits (97), Expect = 1e-05
 Identities = 18/74 (24%), Positives = 38/74 (51%), Gaps = 1/74 (1%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           +FV+ L ++     L+  F+  G++V  ++  DK     RG   +++    E+ +AI   
Sbjct: 1   IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKEGKS-RGMGVVQFEHPIEAVQAISMF 59

Query: 140 HGKFLDGRVIFVEI 153
           +G+ L  R + V++
Sbjct: 60  NGQMLFDRPMRVKM 73

This subfamily corresponds to the RRM2 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 74

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

 Score = 41.2 bits (97), Expect = 1e-05
 Identities = 17/60 (28%), Positives = 33/60 (55%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           ++V  L    + + L+  F  +G +V V+L   K     +GFAF+ + T EE+++A + +
Sbjct: 2   VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHL 61

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

>gnl|CDD|240983 cd12539, RRM_U2AF35B, RNA recognition motif in splicing factor U2AF 35 kDa subunit B (U2AF35B)

 Score = 41.6 bits (98), Expect = 1e-05
 Identities = 17/52 (32%), Positives = 31/52 (59%), Gaps = 1/52 (1%)

Query: 101 FGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE 152
           FG++  +N V D + +   G  ++++  EE +  A++ + G+F DGR I VE
Sbjct: 50  FGEVEALN-VCDNLGDHMVGNVYVKFRDEEHAAAALKALQGRFYDGRPIIVE 100

This subgroup corresponds to the RRM of U2AF35B, also termed zinc finger CCCH domain-containing protein 60 (C3H60), which is one of the small subunits of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF). It has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. Members in this family are mainly found in plant. They show high sequence homology to vertebrates U2AF35 that directly binds to the 3' splice site of the conserved AG dinucleotide and performs multiple functions in the splicing process in a substrate-specific manner. U2AF35B contains two N-terminal zinc fingers, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal arginine/serine (SR)-rich domain. In contrast to U2AF35, U2AF35B has a plant-specific conserved C-terminal region containing SERE motif(s), which may have an important function specific to higher plants. . Length = 103

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

 Score = 41.2 bits (97), Expect = 1e-05
 Identities = 23/74 (31%), Positives = 36/74 (48%), Gaps = 2/74 (2%)

Query: 81  FVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMH 140
           FV  L F T +  L   F+    +  V LV DK  ++ +GF ++ +   E  + A+E   
Sbjct: 5   FVGNLPFNTVQGDLDAIFKDL-SVKSVRLVRDKETDKFKGFCYVEFEDVESLKEALE-YD 62

Query: 141 GKFLDGRVIFVEIA 154
           G   D R + V+IA
Sbjct: 63  GALFDDRSLRVDIA 76

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

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

 Score = 41.4 bits (98), Expect = 1e-05
 Identities = 11/64 (17%), Positives = 29/64 (45%), Gaps = 3/64 (4%)

Query: 92  DSLRNAFQGFGQLVEVNLVMDKIANRP---RGFAFLRYATEEESRRAIEGMHGKFLDGRV 148
           + ++     +G+++ V +   +         G  F+ +A  E++++A   + G+  DGR 
Sbjct: 26  EDVKEECGKYGKVLSVVIPRPEAEGVDVPGVGKVFVEFADVEDAQKAQLALAGRKFDGRT 85

Query: 149 IFVE 152
           +   
Sbjct: 86  VVAS 89

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

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

 Score = 43.8 bits (103), Expect = 2e-05
 Identities = 24/92 (26%), Positives = 43/92 (46%), Gaps = 9/92 (9%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           L+VSGL    ++  L + F  FGQ++   ++ D +    +G  F+R+   +E+ RAI+ +
Sbjct: 92  LYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTL 151

Query: 140 HGKFLDGRVIFVEIAKSRAELRQAFKNNPRQN 171
           +G    G             +   F NNP  +
Sbjct: 152 NGTTPSG---------CTEPITVKFANNPSSS 174

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

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

 Score = 40.7 bits (96), Expect = 2e-05
 Identities = 19/75 (25%), Positives = 35/75 (46%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           L V  L    +++  R     FG +    LV  +     +G+ F+ YA++  + +A   +
Sbjct: 2   LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQL 61

Query: 140 HGKFLDGRVIFVEIA 154
            GK + GR + V+ A
Sbjct: 62  DGKQIGGRKLQVDWA 76

This subfamily corresponds to the RRM2 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only. . Length = 77

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

 Score = 40.7 bits (96), Expect = 2e-05
 Identities = 23/78 (29%), Positives = 41/78 (52%), Gaps = 2/78 (2%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGF-GQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
           +RL V  L    +E  L+  F    G++ +V L+  +   + R  AF+ Y TEEE+++A 
Sbjct: 1   SRLIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTE-DGKSRRIAFIGYKTEEEAQKAK 59

Query: 137 EGMHGKFLDGRVIFVEIA 154
           +  +  +++   I VE A
Sbjct: 60  DYFNNTYINTSKISVEFA 77

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

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

 Score = 40.6 bits (95), Expect = 2e-05
 Identities = 23/78 (29%), Positives = 38/78 (48%), Gaps = 3/78 (3%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           L+V+G    T    L   F+ +G+LV  ++   +     R FAF+ Y +  ++  A E M
Sbjct: 2   LYVTGFGAETRARDLAYEFERYGRLVRCDIPPPRTFQ-SRPFAFVEYESHRDAEDAYEEM 60

Query: 140 HGK--FLDGRVIFVEIAK 155
           HG+     G  + V+ AK
Sbjct: 61  HGRRFPDTGDTLHVQWAK 78

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

>gnl|CDD|240968 cd12524, RRM1_MEI2_like, RNA recognition motif 1 in plant Mei2-like proteins

 Score = 40.3 bits (95), Expect = 2e-05
 Identities = 19/70 (27%), Positives = 32/70 (45%), Gaps = 5/70 (7%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           LFV  ++    ++ LR  F+ FG   ++  +      + RGF  + Y     +RRA   +
Sbjct: 4   LFVRNINSNVEDEELRALFEQFG---DIRTLYTAC--KHRGFIMVSYYDIRAARRAKRAL 58

Query: 140 HGKFLDGRVI 149
            G  L GR +
Sbjct: 59  QGTELGGRKL 68

This subgroup corresponds to the RRM1 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and it is highly conserved between plants and fungi. Up to date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear. . Length = 77

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

 Score = 40.4 bits (95), Expect = 2e-05
 Identities = 22/74 (29%), Positives = 35/74 (47%), Gaps = 1/74 (1%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFG-QLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
           P   + + GL    +E+ +RNA    G +  +V L+  K     RGFAF+ + + EE+ R
Sbjct: 1   PNNTIMLRGLPLSVTEEDIRNALVSHGVEPKDVRLMRRKTTGASRGFAFVEFMSLEEATR 60

Query: 135 AIEGMHGKFLDGRV 148
            +E   GK      
Sbjct: 61  WMELNQGKLQLQDY 74

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

>gnl|CDD|241040 cd12596, RRM1_SRSF6, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 6 (SRSF6)

 Score = 40.3 bits (94), Expect = 2e-05
 Identities = 20/77 (25%), Positives = 41/77 (53%), Gaps = 8/77 (10%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           R+++  LS+   E  ++  F G+G+L+E++L          G+ F+ +    ++  A+  
Sbjct: 1   RVYIGRLSYHVREKDIQRFFGGYGKLLEIDL--------KNGYGFVEFEDSRDADDAVYE 52

Query: 139 MHGKFLDGRVIFVEIAK 155
           ++GK L G  + VE A+
Sbjct: 53  LNGKDLCGERVIVEHAR 69

This subfamily corresponds to the RRM1 of SRSF6, also termed pre-mRNA-splicing factor SRp55, which is an essential splicing regulatory serine/arginine (SR) protein that preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. For instance, it does not bind to the purine-rich sequence in the calcitonin-specific ESE, but binds to a region adjacent to the purine tract. Moreover, cellular levels of SRSF6 may control tissue-specific alternative splicing of the calcitonin/ calcitonin gene-related peptide (CGRP) pre-mRNA. SRSF6 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal SR domains rich in serine-arginine dipeptides. . Length = 70

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

 Score = 43.1 bits (101), Expect = 3e-05
 Identities = 18/73 (24%), Positives = 36/73 (49%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           R++V+ +    SE  +++ F+ FG++V+  L         +G+ F+ Y   +    AI  
Sbjct: 206 RIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIAS 265

Query: 139 MHGKFLDGRVIFV 151
           M+   L G+ + V
Sbjct: 266 MNLFDLGGQYLRV 278

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

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

 Score = 40.1 bits (94), Expect = 3e-05
 Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 4/75 (5%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           TRLFV      T ED LR  F+ FG +  V++V DK     +GF ++++    ++  A+E
Sbjct: 2   TRLFVVIPKSYTEED-LREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVALE 60

Query: 138 GMHGKFLDGRVIFVE 152
                F   + +  E
Sbjct: 61  NCDKSF---KAVLAE 72

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

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

 Score = 40.0 bits (93), Expect = 3e-05
 Identities = 23/76 (30%), Positives = 41/76 (53%), Gaps = 8/76 (10%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           LFV  L+   +E+ L  +F  FG+L  V  + D        +AF+ +   + + RA++ M
Sbjct: 4   LFVRNLATTVTEEILEKSFSEFGKLERVKKLKD--------YAFVHFEERDAAVRAMDEM 55

Query: 140 HGKFLDGRVIFVEIAK 155
           +GK ++G  I + +AK
Sbjct: 56  NGKEIEGEEIEIVLAK 71

This subgroup corresponds to the RRM3 of hnRNP R. a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP R is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, as well as in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP R binds RNA through its RRM domains. . Length = 72

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

 Score = 40.1 bits (93), Expect = 3e-05
 Identities = 16/63 (25%), Positives = 36/63 (57%)

Query: 77  KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
           KT L++ GL   T++  L    Q +G++V    ++DK  N+ +G+ F+ + +   +++A+
Sbjct: 1   KTNLYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAV 60

Query: 137 EGM 139
             +
Sbjct: 61  TAL 63

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

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

 Score = 40.1 bits (93), Expect = 4e-05
 Identities = 23/79 (29%), Positives = 38/79 (48%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           +FV  LS  + E  L   F  FG +  V ++ D   N+ +GF F+     +E+  AI  +
Sbjct: 6   IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 140 HGKFLDGRVIFVEIAKSRA 158
           +G  L  RV+ V    ++ 
Sbjct: 66  NGYRLGDRVLQVSFKTNKT 84

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

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

 Score = 39.6 bits (93), Expect = 4e-05
 Identities = 23/73 (31%), Positives = 36/73 (49%), Gaps = 1/73 (1%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           LFV  L  R +E+ L   F   G L  V +  D    +P+ FAF+ +  E     AI+ +
Sbjct: 4   LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDP-NGKPKSFAFVTFKHEVSVPYAIQLL 62

Query: 140 HGKFLDGRVIFVE 152
           +G  L GR + ++
Sbjct: 63  NGIRLFGRELRIK 75

This subfamily corresponds to the RRM of RBM7, RBM11 and their eukaryotic homologous. RBM7 is an ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. It interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20, and may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM11 is a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. It is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. Both, RBM7 and RBM11, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization. . Length = 75

>gnl|CDD|240731 cd12285, RRM3_RBM39_like, RNA recognition motif 3 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins

 Score = 39.8 bits (94), Expect = 4e-05
 Identities = 12/38 (31%), Positives = 24/38 (63%)

Query: 116 NRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEI 153
           N P G  ++++ T E +++ I+ ++G++ DGR I  E 
Sbjct: 46  NSPEGVVYVKFKTVEAAQKCIQALNGRWFDGRQITAEY 83

This subfamily corresponds to the RRM3 of RBM39, also termed hepatocellular carcinoma protein 1, or RNA-binding region-containing protein 2, or splicing factor HCC1, ia nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Based on the specific domain composition, RBM39 has been classified into a family of non-snRNP (small nuclear ribonucleoprotein) splicing factors that are usually not complexed to snRNAs. . Length = 85

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

 Score = 39.5 bits (92), Expect = 5e-05
 Identities = 28/77 (36%), Positives = 40/77 (51%), Gaps = 11/77 (14%)

Query: 80  LFVSGLS-FRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           LFV       T    L   F+ +G+LV V +         R FAF++Y T+E++ +A+E 
Sbjct: 2   LFVINFDPINTRTRDLERHFEPYGKLVNVRI--------RRNFAFVQYETQEDATKALES 53

Query: 139 MH-GKFLDGRVIFVEIA 154
            +  K LD RVI VE A
Sbjct: 54  TNMSKVLD-RVISVEYA 69

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

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

 Score = 42.2 bits (99), Expect = 5e-05
 Identities = 21/78 (26%), Positives = 35/78 (44%)

Query: 77  KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
           K R+++  L     ED ++   + FG L   NL+ D      +G+AF  Y     +  AI
Sbjct: 295 KDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAI 354

Query: 137 EGMHGKFLDGRVIFVEIA 154
             ++GK      + V+ A
Sbjct: 355 AALNGKDTGDNKLHVQRA 372

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

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

 Score = 39.6 bits (93), Expect = 5e-05
 Identities = 24/78 (30%), Positives = 37/78 (47%), Gaps = 10/78 (12%)

Query: 77  KTRLFVSGLSFRTSEDSLRNAFQGFGQ-LVEVNL---VMDKIANRPRGFAFLRYATEEES 132
             RLFV G+    +++ +   F    + +V+V +     DK  NR  GFAF+ Y    ES
Sbjct: 1   NCRLFVGGIPKTKTKEEILEEFSKVTEGVVDVIVYRSPDDKNKNR--GFAFVEY----ES 54

Query: 133 RRAIEGMHGKFLDGRVIF 150
            RA      K + GR++ 
Sbjct: 55  HRAAAMARRKLVPGRILL 72

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

>gnl|CDD|240788 cd12342, RRM_Nab3p, RNA recognition motif in yeast nuclear polyadenylated RNA-binding protein 3 (Nab3p) and similar proteins

 Score = 39.3 bits (92), Expect = 5e-05
 Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 9/79 (11%)

Query: 79  RLFVSGL-SFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           RLF+  L + R S++ L   F  +G+L ++ L           + F+++ + E    AI 
Sbjct: 1   RLFIGNLPTKRVSKEDLFRIFSTYGELAQIVL--------KNAYGFVQFDSPESCANAIN 52

Query: 138 GMHGKFLDGRVIFVEIAKS 156
              GK + GR + +E++K 
Sbjct: 53  CEQGKMIRGRKLHLEVSKP 71

This subfamily corresponds to the RRM of Nab3p, an acidic nuclear polyadenylated RNA-binding protein encoded by Saccharomyces cerevisiae NAB3 gene that is essential for cell viability. Nab3p is predominantly localized within the nucleoplasm and essential for growth in yeast. It may play an important role in packaging pre-mRNAs into ribonucleoprotein structures amenable to efficient nuclear RNA processing. Nab3p contains an N-terminal aspartic/glutamic acid-rich region, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal region rich in glutamine and proline residues. . Length = 71

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

 Score = 39.4 bits (92), Expect = 5e-05
 Identities = 21/75 (28%), Positives = 39/75 (52%), Gaps = 3/75 (4%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
            ++V  L     E  + + F  +G +V+++L   K+  RP G+AF+ +    ++  AI G
Sbjct: 1   TVYVGNLPGDIREREVEDLFYKYGPIVDIDL---KLPPRPPGYAFIEFEDARDAEDAIRG 57

Query: 139 MHGKFLDGRVIFVEI 153
             G   DG+ + VE+
Sbjct: 58  RDGYDFDGQRLRVEL 72

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

 Score = 39.4 bits (92), Expect = 6e-05
 Identities = 24/80 (30%), Positives = 38/80 (47%), Gaps = 6/80 (7%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           T ++V  +   T++  L   FQ FG ++E     D      RGFAF++  T E++  AI 
Sbjct: 1   TTVYVGNIPPYTTQADLIPLFQNFGYILEFRHQPD------RGFAFVKLDTHEQAAMAIV 54

Query: 138 GMHGKFLDGRVIFVEIAKSR 157
            + G  + GR +     K R
Sbjct: 55  QLQGFPVHGRPLRCGWGKDR 74

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

>gnl|CDD|241124 cd12680, RRM_THOC4, RNA recognition motif in THO complex subunit 4 (THOC4) and similar proteins

 Score = 39.2 bits (92), Expect = 6e-05
 Identities = 22/76 (28%), Positives = 42/76 (55%), Gaps = 1/76 (1%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           T+L VS L F  S+D ++  F  FG L +  +  D+ + R  G A + +    ++ +A++
Sbjct: 1   TKLLVSNLDFGVSDDDIKELFAEFGALKKAAVHYDR-SGRSLGTADVVFERRADALKAMK 59

Query: 138 GMHGKFLDGRVIFVEI 153
             +G  LDGR + +++
Sbjct: 60  QYNGVPLDGRPMKIQL 75

This subgroup corresponds to the RRM of THOC4, also termed transcriptional coactivator Aly/REF, or ally of AML-1 and LEF-1, or bZIP-enhancing factor BEF, an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus. THOC4 was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid. It might be a novel transcription cofactor for erythroid-specific genes. . Length = 75

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

 Score = 39.1 bits (92), Expect = 6e-05
 Identities = 16/62 (25%), Positives = 30/62 (48%)

Query: 91  EDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIF 150
           E  LR  F  FG +  + L   K   + +G+AF+ + + E ++   E M+   L  R++ 
Sbjct: 13  EPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETMNNYLLFERLLK 72

Query: 151 VE 152
            +
Sbjct: 73  CK 74

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

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

 Score = 39.7 bits (92), Expect = 6e-05
 Identities = 22/78 (28%), Positives = 37/78 (47%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           +FV  L+    E  L   F  FG +  V ++ D   N+ +GF F+     +E+  AI  +
Sbjct: 6   IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 140 HGKFLDGRVIFVEIAKSR 157
           +G  L  RV+ V    ++
Sbjct: 66  NGYRLGDRVLQVSFKTNK 83

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

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

 Score = 39.1 bits (92), Expect = 7e-05
 Identities = 21/66 (31%), Positives = 32/66 (48%), Gaps = 6/66 (9%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
           P   LF+  L   T+++ L   F  F    EV LV        RG AF+ + TEE++  A
Sbjct: 1   PNKILFLQNLPEETTKEMLEMLFNQFPGFKEVRLV------PRRGIAFVEFETEEQATVA 54

Query: 136 IEGMHG 141
           ++ + G
Sbjct: 55  LQALQG 60

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

 Score = 38.7 bits (91), Expect = 8e-05
 Identities = 22/71 (30%), Positives = 38/71 (53%), Gaps = 1/71 (1%)

Query: 81  FVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMH 140
           FV  LS +  E  L   F   G++ +V ++ D+ + R +G A++ +  EE    A+ G+ 
Sbjct: 3   FVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLAL-GLT 61

Query: 141 GKFLDGRVIFV 151
           G+ L G+ I V
Sbjct: 62  GQRLLGQPIMV 72

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

>gnl|CDD|240994 cd12550, RRM_II_PABPN1, RNA recognition motif in type II polyadenylate-binding protein 2 (PABP-2) and similar proteins

 Score = 39.0 bits (91), Expect = 8e-05
 Identities = 19/72 (26%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           ++V  + +  + + L   F G G +  V ++ DK +  P+GFA++ ++ ++ES R    +
Sbjct: 2   VYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFS-DKESVRTALAL 60

Query: 140 HGKFLDGRVIFV 151
                 GR I V
Sbjct: 61  DESLFRGRQIKV 72

This subgroup corresponds to the RRM of PABP-2, also termed poly(A)-binding protein 2, or nuclear poly(A)-binding protein 1 (PABPN1), or poly(A)-binding protein II (PABII), which is a ubiquitously expressed type II nuclear poly(A)-binding protein that directs the elongation of mRNA poly(A) tails during pre-mRNA processing. Although PABP-2 binds poly(A) with high affinity and specificity as type I poly(A)-binding proteins, it contains only one highly conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, PABP-2 possesses an acidic N-terminal domain that is essential for the stimulation of PAP, and an arginine-rich C-terminal domain. . Length = 76

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

 Score = 38.8 bits (90), Expect = 8e-05
 Identities = 25/76 (32%), Positives = 40/76 (52%), Gaps = 8/76 (10%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           LFV  L+   +E+ L  AF  FG+L  V  + D        +AF+ +   + + +A+E M
Sbjct: 4   LFVRNLANTVTEEILEKAFGQFGKLERVKKLKD--------YAFIHFDERDGAVKAMEEM 55

Query: 140 HGKFLDGRVIFVEIAK 155
           +GK L+G  I +  AK
Sbjct: 56  NGKELEGENIEIVFAK 71

This subgroup corresponds to the RRM3 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP that is a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains. . Length = 72

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

 Score = 38.9 bits (91), Expect = 8e-05
 Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 2/71 (2%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
            +++  L++  +ED +R  F+G  ++  V L  DK     +GF  + +A EE    A++ 
Sbjct: 1   TVYIGNLAWDITEDDVREFFKG-CEITSVRLATDKETGEFKGFGHVDFADEESLDAALK- 58

Query: 139 MHGKFLDGRVI 149
           + G  L GR I
Sbjct: 59  LDGTVLCGRPI 69

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

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

 Score = 38.7 bits (90), Expect = 9e-05
 Identities = 17/58 (29%), Positives = 28/58 (48%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
           +LFV GL     E  L   F  FG + +  ++ DK   + RGF F+ +   + + +A 
Sbjct: 1   KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAA 58

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

>gnl|CDD|240978 cd12534, RRM_SARFH, RNA recognition motif in Drosophila melanogaster RNA-binding protein cabeza and similar proteins

 Score = 38.9 bits (91), Expect = 1e-04
 Identities = 24/83 (28%), Positives = 34/83 (40%), Gaps = 8/83 (9%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLV--------EVNLVMDKIANRPRGFAFLRYATEEE 131
           +FVS L   T+E  L   F   G +         ++ L  DK    P+G A + Y     
Sbjct: 1   VFVSNLPPNTTEQDLAEHFGSIGIIKIDKKTGKPKIWLYKDKDTGEPKGEATVTYDDPHA 60

Query: 132 SRRAIEGMHGKFLDGRVIFVEIA 154
           +  AIE  + K   G  I V +A
Sbjct: 61  ASAAIEWFNNKDFMGNTIKVSLA 83

This subgroup corresponds to the RRM in cabeza, also termed P19, or sarcoma-associated RNA-binding fly homolog (SARFH). It is a putative homolog of human RNA-binding proteins FUS (also termed TLS or Pigpen or hnRNP P2), EWS (also termed EWSR1), TAF15 (also termed hTAFII68 or TAF2N or RPB56), and belongs to the of the FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA- and DNA-binding proteins whose expression is altered in cancer. It is a nuclear RNA binding protein that may play an important role in the regulation of RNA metabolism during fly development. Cabeza contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 83

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

 Score = 38.7 bits (89), Expect = 1e-04
 Identities = 16/63 (25%), Positives = 36/63 (57%)

Query: 77  KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
           KT L++ GL   T++  L    Q +G++V    ++DK  N+ +G+ F+ + +   +++A+
Sbjct: 4   KTNLYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQKAV 63

Query: 137 EGM 139
             +
Sbjct: 64  ASL 66

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

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

 Score = 38.8 bits (90), Expect = 1e-04
 Identities = 18/60 (30%), Positives = 34/60 (56%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           T +FV  +     ED L   F+  G + ++ L+MD +    RG+AF+ + T+E ++ A++
Sbjct: 2   TEIFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEAVK 61

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

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

 Score = 38.7 bits (90), Expect = 1e-04
 Identities = 19/72 (26%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           ++V  + + ++ + L   F G G +  V ++ DK +  P+G+A++ +AT +    A+  +
Sbjct: 2   VYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFATRDSVEAAVA-L 60

Query: 140 HGKFLDGRVIFV 151
                 GRVI V
Sbjct: 61  DESSFRGRVIKV 72

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

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

 Score = 38.7 bits (90), Expect = 1e-04
 Identities = 17/65 (26%), Positives = 43/65 (66%), Gaps = 1/65 (1%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           +LFV  L+ + +E  +   F  +G++ ++ ++ D++  + RG AF++Y+++E ++ AI+ 
Sbjct: 1   KLFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEM-KQSRGCAFVKYSSKEMAQAAIKA 59

Query: 139 MHGKF 143
           ++G +
Sbjct: 60  LNGVY 64

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

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

 Score = 38.3 bits (89), Expect = 1e-04
 Identities = 21/75 (28%), Positives = 39/75 (52%), Gaps = 1/75 (1%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           L+V  L  R +ED L+  FQ  G +  V ++ DK  N+   + F+ Y    ++  A++ +
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDK-NNKGVNYGFVEYHQSHDAEIALQTL 59

Query: 140 HGKFLDGRVIFVEIA 154
           +G+ ++   I V  A
Sbjct: 60  NGRQIENNEIRVNWA 74

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

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

 Score = 38.5 bits (90), Expect = 1e-04
 Identities = 19/69 (27%), Positives = 31/69 (44%), Gaps = 1/69 (1%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           T L++S L     E  L    + +GQ++   ++ D      RG  F R  + E+    I 
Sbjct: 1   TNLYISNLPLHMDEQDLETMLKPYGQVISTRILRDSKGQS-RGVGFARMESREKCEDIIS 59

Query: 138 GMHGKFLDG 146
             +GK+L G
Sbjct: 60  KFNGKYLKG 68

This subfamily corresponds to the RRM2 of c-myc gene single-strand binding proteins (MSSP) family, including single-stranded DNA-binding protein MSSP-1 (also termed RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3). All MSSP family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity. Both, MSSP-1 and -2, have been identified as protein factors binding to a putative DNA replication origin/transcriptional enhancer sequence present upstream from the human c-myc gene in both single- and double-stranded forms. Thus they have been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. Moreover, they family includes a new member termed RNA-binding motif, single-stranded-interacting protein 3 (RBMS3), which is not a transcriptional regulator. RBMS3 binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. In addition, a putative meiosis-specific RNA-binding protein termed sporulation-specific protein 5 (SPO5, or meiotic RNA-binding protein 1, or meiotically up-regulated gene 12 protein), encoded by Schizosaccharomyces pombe Spo5/Mug12 gene, is also included in this family. SPO5 is a novel meiosis I regulator that may function in the vicinity of the Mei2 dot. . Length = 79

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

 Score = 38.4 bits (89), Expect = 2e-04
 Identities = 15/48 (31%), Positives = 31/48 (64%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRY 126
           ++FV G+   T E  LR+ F+ +G++  + ++ D+ + + RGFAF+ +
Sbjct: 2   KIFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTF 49

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

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

 Score = 37.9 bits (89), Expect = 2e-04
 Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 81  FVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMH 140
           FV  L F   E+ LR  F+  G +  V +V D+     +GF ++ + T++    A++ ++
Sbjct: 3   FVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALK-LN 61

Query: 141 GKFLDGRVIFVE 152
           G  L GR I V+
Sbjct: 62  GIKLKGRKIRVK 73

This subfamily corresponds to the RRM2 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein. . Length = 73

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

 Score = 38.2 bits (89), Expect = 2e-04
 Identities = 22/70 (31%), Positives = 40/70 (57%), Gaps = 6/70 (8%)

Query: 78  TR-LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRG--FAFLRYATEEESRR 134
           TR LFV  L    +E+ LR AF+ +G + +V++   K   R +G  +AF+++   + + R
Sbjct: 2   TRTLFVGNLEITITEEELRRAFERYGVVEDVDI---KRPPRGQGNAYAFVKFLNLDMAHR 58

Query: 135 AIEGMHGKFL 144
           A   M G+++
Sbjct: 59  AKVAMSGQYI 68

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

>gnl|CDD|240728 cd12282, RRM2_TatSF1_like, RNA recognition motif 2 in HIV Tat-specific factor 1 (Tat-SF1) and similar proteins

 Score = 38.4 bits (90), Expect = 2e-04
 Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 4/61 (6%)

Query: 92  DSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFV 151
           D LR   + FGQ+ +V +        P G A +++   EE+ R IE ++G++  GR +  
Sbjct: 27  DDLREECEKFGQVKKVVV----FDRHPDGVASVKFKEPEEADRCIEALNGRWFAGRQLEA 82

Query: 152 E 152
           E
Sbjct: 83  E 83

This subfamily corresponds to the RRM2 of Tat-SF1 and CUS2. Tat-SF1 is the cofactor for stimulation of transcriptional elongation by human immunodeficiency virus-type 1 (HIV-1) Tat. It is a substrate of an associated cellular kinase. Tat-SF1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a highly acidic carboxyl-terminal half. The family also includes CUS2, a yeast homolog of human Tat-SF1. CUS2 interacts with U2 RNA in splicing extracts and functions as a splicing factor that aids assembly of the splicing-competent U2 snRNP in vivo. CUS2 also associates with PRP11 that is a subunit of the conserved splicing factor SF3a. Like Tat-SF1, CUS2 contains two RRMs as well. . Length = 91

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

 Score = 38.0 bits (88), Expect = 2e-04
 Identities = 23/71 (32%), Positives = 39/71 (54%), Gaps = 7/71 (9%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           +FV  +     ED L   F+  G++ E  L+M+  +   RG+AF+ Y T+EE++ AI  +
Sbjct: 4   VFVGKIPRDMYEDELVPLFERAGKIYEFRLMME-FSGENRGYAFVMYTTKEEAQLAIRIL 62

Query: 140 H------GKFL 144
           +      GKF+
Sbjct: 63  NNYEIRPGKFI 73

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

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

 Score = 38.0 bits (89), Expect = 2e-04
 Identities = 22/84 (26%), Positives = 42/84 (50%), Gaps = 1/84 (1%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           T +FV  +    S+D +R   +  G+++    V D    + + F F  +   E + RA+ 
Sbjct: 1   TTVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALR 60

Query: 138 GMHGKFLDGRVIFVEI-AKSRAEL 160
            ++G  L G+ + V++ AK+R  L
Sbjct: 61  LLNGLELGGKKLLVKVDAKTRKLL 84

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

>gnl|CDD|241080 cd12636, RRM2_Bruno_like, RNA recognition motif 2 in Drosophila melanogaster Bruno protein and similar proteins

 Score = 37.9 bits (88), Expect = 2e-04
 Identities = 21/62 (33%), Positives = 37/62 (59%), Gaps = 1/62 (1%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           +LFV  LS + +E+ +R  F  FG + E  ++ D+   + RG AF+ +A+ + +  AI+ 
Sbjct: 3   KLFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQ-NGQSRGCAFVTFASRQCALNAIKA 61

Query: 139 MH 140
           MH
Sbjct: 62  MH 63

This subgroup corresponds to the RRM2 of Bruno, a Drosophila RNA recognition motif (RRM)-containing protein that plays a central role in regulation of Oskar (Osk) expression. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. . Length = 81

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

 Score = 38.0 bits (89), Expect = 2e-04
 Identities = 28/81 (34%), Positives = 39/81 (48%), Gaps = 8/81 (9%)

Query: 75  QPKTRLFVSGL--SFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEES 132
             +  LFV  L  +FR     LR  F   G+     L +     +PRGFAF+ YAT E++
Sbjct: 1   HSRC-LFVDRLPKTFRDV-SILRKLFSQVGKPTFCQLAIAP-NGQPRGFAFVEYATAEDA 57

Query: 133 RRAIEGMHGKFLDG---RVIF 150
             A + ++G  L G   RV F
Sbjct: 58  EEAQQALNGHSLQGSPIRVSF 78

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

>gnl|CDD|240929 cd12485, RRM1_RBM47, RNA recognition motif 1 found in vertebrate RNA-binding protein 47 (RBM47)

 Score = 37.6 bits (87), Expect = 2e-04
 Identities = 19/57 (33%), Positives = 33/57 (57%), Gaps = 1/57 (1%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
           +FV  +     ED L   F+  G++ E+ L+MD    + RG+AF+ Y  + E++RA+
Sbjct: 4   VFVGKIPRDVYEDELVPVFESVGRIYEMRLMMD-FDGKNRGYAFVMYTQKHEAKRAV 59

This subgroup corresponds to the RRM1 of RBM47, a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM47 contains two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 78

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

 Score = 39.9 bits (93), Expect = 3e-04
 Identities = 20/88 (22%), Positives = 42/88 (47%), Gaps = 1/88 (1%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           +FV  L+ +  E  L   F   G++ +V  + D+ + R +G A++ +   E   +A+  +
Sbjct: 92  VFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKAL-AL 150

Query: 140 HGKFLDGRVIFVEIAKSRAELRQAFKNN 167
            G+ L GR I V+ +++          +
Sbjct: 151 TGQMLLGRPIIVQSSQAEKNRAAKAATH 178

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

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

 Score = 37.7 bits (88), Expect = 3e-04
 Identities = 24/80 (30%), Positives = 40/80 (50%), Gaps = 3/80 (3%)

Query: 80  LFVSGLSFRTSEDSLRNAF-QGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           LFV  L+    +  L   F + +       +V+D+  N  RG+ F+R++ E E +RA+  
Sbjct: 4   LFVGDLTPDVDDYQLYEFFSKRYPSCKGAKVVLDQNGNS-RGYGFVRFSDESEQKRALTE 62

Query: 139 MHGKF-LDGRVIFVEIAKSR 157
           M G   L G+ I V +A  +
Sbjct: 63  MQGASGLGGKPIRVSLAIPK 82

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

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

 Score = 37.4 bits (87), Expect = 3e-04
 Identities = 19/73 (26%), Positives = 31/73 (42%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           LFV  L    +ED L+  F+ FG ++EV +       R   F F+ +   E  ++ +   
Sbjct: 6   LFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILANK 65

Query: 140 HGKFLDGRVIFVE 152
              F     + VE
Sbjct: 66  PIYFRGDHRLNVE 78

This subfamily corresponds to the RRM domain in the G3BP family of RNA-binding and SH3 domain-binding proteins. G3BP acts at the level of RNA metabolism in response to cell signaling, possibly as RNA transcript stabilizing factors or an RNase. Members include G3BP1, G3BP2 and similar proteins. These proteins associate directly with the SH3 domain of GTPase-activating protein (GAP), which functions as an inhibitor of Ras. They all contain an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing PXXP motif(s), an RNA recognition motif (RRM), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). Length = 81

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

 Score = 37.8 bits (87), Expect = 3e-04
 Identities = 20/67 (29%), Positives = 32/67 (47%), Gaps = 1/67 (1%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           T L++S L     E  L N  + FGQ++   ++ D  +   RG  F R  + E+    I 
Sbjct: 1   TNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIS 59

Query: 138 GMHGKFL 144
             +GKF+
Sbjct: 60  HFNGKFI 66

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

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

 Score = 37.3 bits (86), Expect = 4e-04
 Identities = 17/62 (27%), Positives = 34/62 (54%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           L++SGL    ++  + + F  FG+++   +++D+     RG AF+R+    E+  AI   
Sbjct: 3   LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITSF 62

Query: 140 HG 141
           +G
Sbjct: 63  NG 64

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

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

 Score = 37.2 bits (87), Expect = 4e-04
 Identities = 15/74 (20%), Positives = 40/74 (54%), Gaps = 1/74 (1%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           L+V+       +  +R+ F+ +G+++ +     +  N+ R F ++++ + E +  A+  +
Sbjct: 3   LWVTNFPPSFDQSDIRDLFEQYGEILSIRFPSLRF-NKTRRFCYVQFTSPESAAAAVALL 61

Query: 140 HGKFLDGRVIFVEI 153
           +GK  +G  + V+I
Sbjct: 62  NGKLGEGYKLVVKI 75

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

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

 Score = 37.0 bits (86), Expect = 4e-04
 Identities = 22/79 (27%), Positives = 39/79 (49%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           T L ++ L    +++  R+ F   G +    +V DK      GF F+ Y + E+++RAI 
Sbjct: 1   TNLIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIR 60

Query: 138 GMHGKFLDGRVIFVEIAKS 156
            ++G  L  + I V  A+ 
Sbjct: 61  TLNGLQLQNKRIKVAYARP 79

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

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

 Score = 36.9 bits (85), Expect = 4e-04
 Identities = 23/76 (30%), Positives = 41/76 (53%), Gaps = 6/76 (7%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           L+V  L   TSED+++   + FGQ    N    +   + R +AF+ + + E++  A+  +
Sbjct: 4   LYVRNLMIETSEDTIK---KTFGQF---NPGCVERVKKIRDYAFVHFTSREDAVHAMNNL 57

Query: 140 HGKFLDGRVIFVEIAK 155
           +G  L+G  I V +AK
Sbjct: 58  NGTELEGSCIEVTLAK 73

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

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

 Score = 37.4 bits (86), Expect = 4e-04
 Identities = 21/79 (26%), Positives = 37/79 (46%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           +F+  L     E  L   F  FG +  V ++ D   N+ +GF F+     EE+  AI  +
Sbjct: 4   IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASL 63

Query: 140 HGKFLDGRVIFVEIAKSRA 158
           +G  L  +++ V    S++
Sbjct: 64  NGYRLGDKILQVSFKTSKS 82

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

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

 Score = 36.5 bits (84), Expect = 5e-04
 Identities = 19/78 (24%), Positives = 41/78 (52%), Gaps = 9/78 (11%)

Query: 78  TRLFVSGL-SFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
           +R+F+  L +    +  +   F  +G++V  ++         +GFAF++Y  E  +R A+
Sbjct: 2   SRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAV 53

Query: 137 EGMHGKFLDGRVIFVEIA 154
            G  G+ + G+V+ + +A
Sbjct: 54  AGEDGRMIAGQVLDINLA 71

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

>gnl|CDD|240926 cd12482, RRM1_hnRNPR, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 36.9 bits (85), Expect = 5e-04
 Identities = 17/60 (28%), Positives = 35/60 (58%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           T +FV  +     ED L   F+  G + ++ L+MD ++ + RG+AF+ +  +E ++ A++
Sbjct: 2   TEVFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEAVK 61

This subgroup corresponds to the RRM1 of hnRNP R, which is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. It is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, and in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; it binds RNA through its RRM domains. . Length = 79

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

 Score = 36.8 bits (86), Expect = 5e-04
 Identities = 19/68 (27%), Positives = 36/68 (52%), Gaps = 8/68 (11%)

Query: 80  LFVS--GLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           L V+  GL    S + L   F+ +G +   +LVM     +P  + F+ Y++ E++  A +
Sbjct: 4   LVVANGGLGNGVSREELLRVFEKYGTVE--DLVM--PPGKP--YCFVSYSSIEDAAAAYD 57

Query: 138 GMHGKFLD 145
            ++GK L+
Sbjct: 58  ALNGKELE 65

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

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

 Score = 36.5 bits (84), Expect = 5e-04
 Identities = 19/75 (25%), Positives = 36/75 (48%), Gaps = 8/75 (10%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           T+L V  +S   +   LR  F+ +G ++E ++V D        +AF+     E++  AI 
Sbjct: 1   TKLHVGNISSSCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEAIR 52

Query: 138 GMHGKFLDGRVIFVE 152
           G+      G+ + V+
Sbjct: 53  GLDNTEFQGKRMHVQ 67

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

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

 Score = 36.4 bits (84), Expect = 6e-04
 Identities = 18/74 (24%), Positives = 36/74 (48%), Gaps = 8/74 (10%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           +LFV  L    +E  +R+ F+ +G+++E +++        + + F+    +  +  AI  
Sbjct: 2   KLFVGNLPPEATEQEIRSLFEQYGKVLECDII--------KNYGFVHMDDKTAADEAIRN 53

Query: 139 MHGKFLDGRVIFVE 152
           +H   L G  I VE
Sbjct: 54  LHHYKLHGVAINVE 67

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

>gnl|CDD|241122 cd12678, RRM_SLTM, RNA recognition motif in Scaffold attachment factor (SAF)-like transcription modulator (SLTM) and similar proteins

 Score = 36.6 bits (84), Expect = 6e-04
 Identities = 21/73 (28%), Positives = 37/73 (50%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           L+VSGLS  T    L+N F  +G+++   +V +  +   + +  +  ++  E  R I  +
Sbjct: 2   LWVSGLSSNTKAADLKNLFGKYGKVLSAKVVTNARSPGAKCYGIVTMSSSAEVARCISHL 61

Query: 140 HGKFLDGRVIFVE 152
           H   L G+ I VE
Sbjct: 62  HRTELHGQQISVE 74

This subgroup corresponds to the RRM domain of SLTM, also termed modulator of estrogen-induced transcription, which shares high sequence similarity with scaffold attachment factor B1 (SAFB1). It contains a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. To a large extent, SLTM co-localizes with SAFB1 in the nucleus, which suggests that they share similar functions, such as the inhibition of an oestrogen reporter gene. However, rather than mediating a specific inhibitory effect on oestrogen action, SLTM is shown to exert a generalized inhibitory effect on gene expression associated with induction of apoptosis in a wide range of cell lines. . Length = 74

>gnl|CDD|241075 cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif 1 in CUGBP Elav-like family member CELF-1, CELF-2, Drosophila melanogaster Bruno protein and similar proteins

 Score = 36.7 bits (85), Expect = 7e-04
 Identities = 20/71 (28%), Positives = 37/71 (52%), Gaps = 3/71 (4%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRP--RGFAFLRYATEEESRRAI 136
           ++FV  +    SE  LR  F+ +G + ++N++ D+  N P  +G  F+ + T + +  A 
Sbjct: 3   KMFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 62

Query: 137 EGMHG-KFLDG 146
             +H  K L G
Sbjct: 63  NALHNMKTLPG 73

This subgroup corresponds to the RRM1 of CELF-1, CELF-2 and Bruno protein. CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR) belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in regulation of pre-mRNA splicing, and control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. The human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It binds specifically to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it binds preferentially to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contains three highly conserved RRMs. It binds to RNA via the first two RRMs, which are also important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. This subgroup also includes Drosophila melanogaster Bruno protein, which plays a central role in regulation of Oskar (Osk) expression in flies. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. . Length = 84

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

 Score = 36.3 bits (84), Expect = 8e-04
 Identities = 14/74 (18%), Positives = 33/74 (44%), Gaps = 4/74 (5%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
            ++            ++  F+  G + +V ++   +    +  AF+ +   E ++ AIE 
Sbjct: 1   TVYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRTV----QPHAFITFENLEAAQLAIET 56

Query: 139 MHGKFLDGRVIFVE 152
           ++G  +DG  I V+
Sbjct: 57  LNGASVDGNCIKVQ 70

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

>gnl|CDD|240930 cd12486, RRM1_ACF, RNA recognition motif 1 found in vertebrate APOBEC-1 complementation factor (ACF)

 Score = 36.1 bits (83), Expect = 8e-04
 Identities = 20/73 (27%), Positives = 43/73 (58%), Gaps = 2/73 (2%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           +F+  L     ED L    +  G++ E+ ++MD   N  RG+AF+ ++ ++E++ AI+ +
Sbjct: 4   IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGNN-RGYAFVTFSNKQEAKNAIKQL 62

Query: 140 HG-KFLDGRVIFV 151
           +  +  +GR++ V
Sbjct: 63  NNYEIRNGRLLGV 75

This subgroup corresponds to the RRM1 of ACF, also termed APOBEC-1-stimulating protein, an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. ACF shuttles between the cytoplasm and nucleus. It contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which display high affinity for an 11 nucleotide AU-rich mooring sequence 3' of the edited cytidine in apoB mRNA. All three RRMs may be required for complementation of editing activity in living cells. RRM2/3 are implicated in ACF interaction with APOBEC-1. . Length = 78

>gnl|CDD|241116 cd12672, RRM_DAZL, RNA recognition motif in vertebrate deleted in azoospermia-like (DAZL) proteins

 Score = 36.3 bits (84), Expect = 9e-04
 Identities = 20/72 (27%), Positives = 38/72 (52%), Gaps = 5/72 (6%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
           P T +FV G+  R  E  +R+ F  +G + EV ++ D+     +G+ F+ +  + + ++ 
Sbjct: 5   PNT-VFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDR-TGVSKGYGFVSFYDDVDVQKI 62

Query: 136 IE---GMHGKFL 144
           +E     HGK L
Sbjct: 63  VESQINFHGKKL 74

This subgroup corresponds to the RRM of DAZL, also termed SPGY-like-autosomal, encoded by the autosomal homolog of DAZ gene, DAZL. It is ancestral to the deleted in azoospermia (DAZ) protein. DAZL is germ-cell-specific RNA-binding protein that contains a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a DAZ motif, a protein-protein interaction domain. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 82

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

 Score = 36.4 bits (84), Expect = 0.001
 Identities = 22/73 (30%), Positives = 39/73 (53%), Gaps = 6/73 (8%)

Query: 89  TSEDSLRNAFQGFGQLVEVN--LVMDKIANRPRGFAFLRYATEEESRR---AIEGMHGKF 143
           T  DS+ +A   +  L   N  L+ DK   + RGFAF++ ++  E+ +    ++ +H   
Sbjct: 14  TVVDSILSALAPYASLSVSNIRLIKDKQTQQNRGFAFVQLSSALEASQLLQILQALHPPL 73

Query: 144 -LDGRVIFVEIAK 155
            +DG+ I V+ AK
Sbjct: 74  KIDGKTIGVDFAK 86

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

>gnl|CDD|241101 cd12657, RRM1_hnRNPM, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 36.2 bits (83), Expect = 0.001
 Identities = 22/75 (29%), Positives = 41/75 (54%), Gaps = 2/75 (2%)

Query: 79  RLFVSGLSFRTSEDSLRNAF-QGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           R F+S + F     SL++   +  G++  V L+MD    + RG A + +  EE  ++A+E
Sbjct: 1   RAFISNIPFDVKWQSLKDLVKEKVGEVTYVELLMDA-EGKSRGCAVVEFKMEESMKKAVE 59

Query: 138 GMHGKFLDGRVIFVE 152
            ++   L+GR + V+
Sbjct: 60  VLNKHVLNGRPLKVK 74

This subgroup corresponds to the RRM1 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). . Length = 76

>gnl|CDD|241078 cd12634, RRM2_CELF1_2, RNA recognition motif 2 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins

 Score = 36.2 bits (83), Expect = 0.001
 Identities = 20/64 (31%), Positives = 37/64 (57%), Gaps = 5/64 (7%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVM--DKIANRPRGFAFLRYATEEESRRAI 136
           +LF+  +S + +E+ +R  F  FGQ+ E  ++   D ++   RG AF+ + T   ++ AI
Sbjct: 3   KLFIGMVSKKCNENDIRVMFSPFGQIEECRILRGPDGLS---RGCAFVTFTTRAMAQTAI 59

Query: 137 EGMH 140
           + MH
Sbjct: 60  KAMH 63

This subgroup corresponds to the RRM2 of CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. Human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It binds specifically to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 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 two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it preferentially binds to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contains three highly conserved RRMs. It binds to RNA via the first two RRMs, which are also important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. . Length = 81

>gnl|CDD|240931 cd12487, RRM1_DND1, RNA recognition motif 1 found in vertebrate dead end protein homolog 1 (DND1)

 Score = 35.9 bits (83), Expect = 0.001
 Identities = 21/73 (28%), Positives = 34/73 (46%), Gaps = 2/73 (2%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           +F+  +     ED L   FQ  G L E  L+M   +   RGFA+ +Y+    +  AI  +
Sbjct: 4   VFIGKIPQDVYEDRLIPLFQSVGTLYEFRLMMT-FSGLNRGFAYAKYSDRRGASAAIATL 62

Query: 140 HG-KFLDGRVIFV 151
           H  +  +G  + V
Sbjct: 63  HNYELPEGCCLLV 75

This subgroup corresponds to the RRM1 of DND1, also termed RNA-binding motif, single-stranded-interacting protein 4, an RNA-binding protein that is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. For instance, DND1 binds cell cycle inhibitor, P27 (p27Kip1, CDKN1B), and cell cycle regulator and tumor suppressor, LATS2 (large tumor suppressor, homolog 2 of Drosophila). It helps maintain their protein expression through blocking the inhibitory function of microRNAs (miRNA) from these transcripts. DND1 may also impose another level of translational regulation to modulate expression of critical factors in embryonic stem (ES) cells. DND1 interacts specifically with apolipoprotein B editing complex 3 (APOBEC3), a multi-functional protein inhibiting retroviral replication. The DND1-APOBEC3 interaction may play a role in maintaining viability of germ cells and for preventing germ cell tumor development. DND1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 78

>gnl|CDD|241198 cd12754, RRM2_RBM10, RNA recognition motif 2 in vertebrate RNA-binding protein 10 (RBM10)

 Score = 36.1 bits (83), Expect = 0.001
 Identities = 23/82 (28%), Positives = 43/82 (52%), Gaps = 6/82 (7%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVN--LVMDKIANRPRGFAFLRYATEEESR---R 134
           + +  L+  ++ DS+ +A   +  L   N  ++ DK     RGFAF++ +T  E+    +
Sbjct: 5   IILRNLNPHSTMDSILSALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTIVEAAQLLQ 64

Query: 135 AIEGMHGKF-LDGRVIFVEIAK 155
            ++ +H    +DG+ I VE AK
Sbjct: 65  ILQALHPPLSIDGKTINVEFAK 86

This subgroup corresponds to the RRM2 of RBM10, also termed G patch domain-containing protein 9, or RNA-binding protein S1-1 (S1-1), a paralog of putative tumor suppressor RNA-binding protein 5 (RBM5 or LUCA15 or H37). It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. RBM10 is structurally related to RBM5 and RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain. . Length = 87

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

 Score = 35.4 bits (82), Expect = 0.001
 Identities = 23/79 (29%), Positives = 40/79 (50%), Gaps = 2/79 (2%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIA-NRPRGFAFLRYATEEESRRAI 136
           +++ V  + F  +   LR  F  FG+L  V L          RGF F+ + T+++++RA 
Sbjct: 1   SKILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAF 60

Query: 137 EGM-HGKFLDGRVIFVEIA 154
           + + H   L GR + +E A
Sbjct: 61  KALCHSTHLYGRRLVLEWA 79

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

 Score = 35.4 bits (82), Expect = 0.002
 Identities = 19/74 (25%), Positives = 33/74 (44%), Gaps = 3/74 (4%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           R++V  L     E  + + F  +G +  ++L   K   R   FAF+ +    ++  A+ G
Sbjct: 1   RIYVGNLPGDIRERDIEDLFYKYGPIKAIDL---KNRRRGPPFAFVEFEDPRDAEDAVRG 57

Query: 139 MHGKFLDGRVIFVE 152
             G   DG  + VE
Sbjct: 58  RDGYDFDGYRLRVE 71

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

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

 Score = 37.7 bits (87), Expect = 0.002
 Identities = 21/73 (28%), Positives = 37/73 (50%), Gaps = 1/73 (1%)

Query: 65  PPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFL 124
           PP   S         +FV  +     ED L   F+  G + E+ L+MD  + + RG+AF+
Sbjct: 46  PPPGWSGVQPGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFV 104

Query: 125 RYATEEESRRAIE 137
            +  +EE++ A++
Sbjct: 105 TFCGKEEAKEAVK 117

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

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

 Score = 37.7 bits (87), Expect = 0.002
 Identities = 22/78 (28%), Positives = 42/78 (53%), Gaps = 10/78 (12%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGF--GQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           L+V  L   T+E+ +  +F  F  G++  V  + D        +AF+ +   E++ +A++
Sbjct: 236 LYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIRD--------YAFVHFEDREDAVKAMD 287

Query: 138 GMHGKFLDGRVIFVEIAK 155
            ++GK L+G  I V +AK
Sbjct: 288 ELNGKELEGSEIEVTLAK 305

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

>gnl|CDD|241037 cd12593, RRM_RBM11, RNA recognition motif in vertebrate RNA-binding protein 11 (RBM11)

 Score = 35.3 bits (81), Expect = 0.002
 Identities = 25/72 (34%), Positives = 33/72 (45%), Gaps = 1/72 (1%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           LFV  L  R  E+ L   F   G L +V +  DK    P+ F F+ +   E    AI  +
Sbjct: 4   LFVGNLECRVREEILYELFLQAGPLTKVTICKDKEGK-PKSFGFVCFKHSESVPYAIALL 62

Query: 140 HGKFLDGRVIFV 151
           +G  L GR I V
Sbjct: 63  NGIRLYGRPIKV 74

This subfamily corresponds to the RRM or RBM11, a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. RBM11 is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. RBM11 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM of RBM11 is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization. . Length = 75

>gnl|CDD|241000 cd12556, RRM2_RBM15B, RNA recognition motif 2 in putative RNA binding motif protein 15B (RBM15B) from vertebrate

 Score = 35.7 bits (82), Expect = 0.002
 Identities = 28/87 (32%), Positives = 40/87 (45%), Gaps = 12/87 (13%)

Query: 75  QPKTR-LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRP-RG----FAFLRYAT 128
           Q  TR LF+  L    SE  LR AF  +G + EV      +  RP RG    +AFL++  
Sbjct: 5   QRATRNLFIGNLDHNVSEVELRRAFDKYGIIEEV------VIKRPARGQGGAYAFLKFQN 58

Query: 129 EEESRRAIEGMHGKFLDGRVIFVEIAK 155
            + + RA   M G+ +    I +   K
Sbjct: 59  LDMAHRAKVAMSGRVIGRNPIKIGYGK 85

This subgroup corresponds to the RRM2 of RBM15B, also termed one twenty-two 3 (OTT3), a paralog of RNA binding motif protein 15 (RBM15), also known as One-twenty two protein 1 (OTT1). Like RBM15, RBM15B has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. RBM15B belongs to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 85

>gnl|CDD|241090 cd12646, RRM_SRSF7, RNA recognition motif in vertebrate serine/arginine-rich splicing factor 7 (SRSF7)

 Score = 35.4 bits (81), Expect = 0.002
 Identities = 22/76 (28%), Positives = 37/76 (48%), Gaps = 5/76 (6%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           +++V  L     +  L  AF  +G L  V      IA  P GFAF+ +    ++  A+ G
Sbjct: 1   KVYVGNLGTGAGKGELERAFSYYGPLRTV-----WIARNPPGFAFVEFEDPRDAEDAVRG 55

Query: 139 MHGKFLDGRVIFVEIA 154
           + GK + G  + VE++
Sbjct: 56  LDGKVICGSRVRVELS 71

This subgroup corresponds to the RRM of SRSF7, also termed splicing factor 9G8, is a splicing regulatory serine/arginine (SR) protein that plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. SRSF7 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a CCHC-type zinc knuckle motif in its median region, and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions. . Length = 77

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

 Score = 35.2 bits (82), Expect = 0.002
 Identities = 14/60 (23%), Positives = 29/60 (48%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           L+V  L    +E  L   F   G ++ + +  D I  R  G+A++ +    ++ RA++ +
Sbjct: 2   LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTL 61

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

>gnl|CDD|240671 cd12225, RRM1_2_CID8_like, RNA recognition motif 1 and 2 (RRM1, RRM2) in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins

 Score = 35.4 bits (82), Expect = 0.002
 Identities = 22/76 (28%), Positives = 36/76 (47%), Gaps = 3/76 (3%)

Query: 81  FVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMH 140
            V G+    SED L+  F   G++  V L  D+  +    FAF+ +A  E +  A+  + 
Sbjct: 4   HVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHS--ARFAFVEFADAESALSALN-LS 60

Query: 141 GKFLDGRVIFVEIAKS 156
           G  L G  + V  +K+
Sbjct: 61  GTLLGGHPLRVSPSKT 76

This subgroup corresponds to the RRM domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 77

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

 Score = 35.4 bits (82), Expect = 0.002
 Identities = 19/77 (24%), Positives = 38/77 (49%), Gaps = 5/77 (6%)

Query: 80  LFVSGLSFRTSEDSLRNA----FQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
           +FV G      ED +R +    F   G++  V++  D+     +GFA++ + + +   +A
Sbjct: 2   IFVKGFDSSLGEDDIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEKA 61

Query: 136 IEGMHGKFLDGRVIFVE 152
           +E + G  L G  + V+
Sbjct: 62  LE-LDGSDLGGGNLVVD 77

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

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

 Score = 35.4 bits (81), Expect = 0.002
 Identities = 17/68 (25%), Positives = 31/68 (45%)

Query: 74  CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESR 133
                 LF+  L    ++  L   F  FG ++   + +DK  N  + F F+ Y   + ++
Sbjct: 1   GPEGCNLFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQ 60

Query: 134 RAIEGMHG 141
            AI+ M+G
Sbjct: 61  AAIQAMNG 68

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

>gnl|CDD|241125 cd12681, RRM_SKAR, RNA recognition motif in S6K1 Aly/REF-like target (SKAR) and similar proteins

 Score = 34.9 bits (81), Expect = 0.002
 Identities = 23/76 (30%), Positives = 37/76 (48%), Gaps = 7/76 (9%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           TRL VS L    +ED +   F   G L    LV      RP G A + Y  ++++  AI+
Sbjct: 1   TRLVVSNLHPSVTEDDIVELFSAIGALKRARLV------RP-GVAEVVYVRKDDALTAID 53

Query: 138 GMHGKFLDGRVIFVEI 153
             + + LDG+ +  ++
Sbjct: 54  KYNNRELDGQPMKCKL 69

This subgroup corresponds to the RRM of SKAR, also termed polymerase delta-interacting protein 3 (PDIP3), 46 kDa DNA polymerase delta interaction protein (PDIP46), belonging to the Aly/REF family of RNA binding proteins that have been implicated in coupling transcription with pre-mRNA splicing and nucleo-cytoplasmic mRNA transport. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion. SKAR contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Length = 69

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

 Score = 35.4 bits (81), Expect = 0.002
 Identities = 21/78 (26%), Positives = 39/78 (50%), Gaps = 10/78 (12%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGF--GQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           L+V  L   T+E+++   F     G +  V  + D        +AF+ ++  E++  A+ 
Sbjct: 11  LYVRNLMLSTTEETIEKEFNSIKPGAVERVKKIRD--------YAFVHFSNREDAVDAMN 62

Query: 138 GMHGKFLDGRVIFVEIAK 155
            ++GK +DG  I V +AK
Sbjct: 63  ALNGKVIDGSPIEVTLAK 80

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

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

 Score = 35.4 bits (82), Expect = 0.002
 Identities = 18/60 (30%), Positives = 29/60 (48%), Gaps = 7/60 (11%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRG--FAFLRYATEEESRRAIE 137
           ++V  +   T+   LR  FQ FG++ E+ L       R  G  + F+ Y    ++ RAIE
Sbjct: 5   IYVGKIPIDTTRSELRQRFQPFGEIEEITLHF-----RDDGDNYGFVTYRYACDAFRAIE 59

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

>gnl|CDD|240733 cd12287, RRM_U2AF35_like, RNA recognition motif in U2 small nuclear ribonucleoprotein auxiliary factor U2AF 35 kDa subunit (U2AF35) and similar proteins

 Score = 35.3 bits (82), Expect = 0.003
 Identities = 12/55 (21%), Positives = 33/55 (60%), Gaps = 1/55 (1%)

Query: 98  FQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE 152
              FG++ ++ +  D + +   G  ++++ TEE++  A++ ++G++  GR ++ E
Sbjct: 46  LSRFGEIEDLVVC-DNLGDHLLGNVYVKFETEEDAEAALQALNGRYYAGRPLYPE 99

This subfamily corresponds to the RRM in U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF) which has been implicated in the recruitment of U2 snRNP to pre-mRNAs. It is a highly conserved heterodimer composed of large and small subunits; this family includes the small subunit of U2AF (U2AF35 or U2AF1) and U2AF 35 kDa subunit B (U2AF35B or C3H60). U2AF35 directly binds to the 3' splice site of the conserved AG dinucleotide and performs multiple functions in the splicing process in a substrate-specific manner. It promotes U2 snRNP binding to the branch-point sequences of introns through association with the large subunit of U2AF (U2AF65 or U2AF2). Although the biological role of U2AF35B remains unclear, it shows high sequence homolgy to U2AF35, which contains two N-terminal zinc fingers, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal arginine/serine (SR) -rich segment interrupted by glycines. In contrast to U2AF35, U2AF35B has a plant-specific conserved C-terminal region containing SERE motif(s), which may have an important function specific to higher plants. . Length = 102

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

 Score = 34.6 bits (79), Expect = 0.003
 Identities = 22/76 (28%), Positives = 42/76 (55%), Gaps = 6/76 (7%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           L+V  L   T+E++++  F  F   V     ++++  + R +AF+ +   E++  A+  M
Sbjct: 4   LYVRNLMISTTEETIKAEFNKFKPGV-----VERV-KKLRDYAFVHFFNREDAVAAMSVM 57

Query: 140 HGKFLDGRVIFVEIAK 155
           +GK +DG  I V +AK
Sbjct: 58  NGKCIDGASIEVTLAK 73

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

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

 Score = 34.5 bits (80), Expect = 0.003
 Identities = 21/62 (33%), Positives = 31/62 (50%), Gaps = 5/62 (8%)

Query: 100 GFGQ----LVEVNLVMDKIANRPRG-FAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIA 154
           GF Q    L +      KI    R  FAF+ + +EEE ++A+E + G    GRV+   +A
Sbjct: 18  GFKQLKKFLKKQLFKPHKIKLLKRQDFAFVTFRSEEERQKALEILDGFKWKGRVLSARLA 77

Query: 155 KS 156
           K 
Sbjct: 78  KP 79

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

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

 Score = 34.4 bits (79), Expect = 0.003
 Identities = 16/76 (21%), Positives = 33/76 (43%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           +++  L     E  L+  F  FG +  V +   K     + + F+++   E +  A + M
Sbjct: 2   IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61

Query: 140 HGKFLDGRVIFVEIAK 155
           +   L G+V+ V +  
Sbjct: 62  NNYLLMGKVLQVHVLP 77

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

>gnl|CDD|240810 cd12364, RRM_RDM1, RNA recognition motif of RAD52 motif-containing protein 1 (RDM1) and similar proteins

 Score = 34.7 bits (80), Expect = 0.003
 Identities = 22/78 (28%), Positives = 39/78 (50%), Gaps = 5/78 (6%)

Query: 79  RLFVSGLSFRTSED----SLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
            L+V G+S + +E+    SL +AF  FG L  V +  +     P  +AF+++ +   + R
Sbjct: 2   TLYVWGISPKLTEEEIYESLCSAFSQFGLLYSVKVFPNAAVATPGFYAFVKFYSARAASR 61

Query: 135 AIEGMHGK-FLDGRVIFV 151
           A +  +GK    G  + V
Sbjct: 62  AQKACNGKWLFQGSPLKV 79

This subfamily corresponds to the RRM of RDM1, also termed RAD52 homolog B, a novel factor involved in the cellular response to the anti-cancer drug cisplatin in vertebrates. RDM1 contains a small RD motif that shares with the recombination and repair protein RAD52, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The RD motif is responsible for the acidic pH-dependent DNA-binding properties of RDM1. It interacts with ss- and dsDNA, and may act as a DNA-damage recognition factor by recognizing the distortions of the double helix caused by cisplatin-DNA adducts in vitro. In addition, due to the presence of RRM, RDM1 can bind to RNA as well as DNA. . Length = 81

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

 Score = 34.7 bits (79), Expect = 0.004
 Identities = 19/67 (28%), Positives = 31/67 (46%), Gaps = 1/67 (1%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           T L++S L     E  L N  + FG ++   ++ D      RG  F R  + E+    I+
Sbjct: 2   TNLYISNLPVSMDEQELENMLKPFGHVISTRILRDA-NGVSRGVGFARMESTEKCEVVIQ 60

Query: 138 GMHGKFL 144
             +GK+L
Sbjct: 61  HFNGKYL 67

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

>gnl|CDD|240878 cd12432, RRM_ACINU, RNA recognition motif in apoptotic chromatin condensation inducer in the nucleus (acinus) and similar proteins

 Score = 34.5 bits (80), Expect = 0.004
 Identities = 14/49 (28%), Positives = 21/49 (42%), Gaps = 4/49 (8%)

Query: 94  LRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGK 142
           L+      G  V     MDKI +      ++ Y+T EE+    E +HG 
Sbjct: 18  LKELLSETGTGVIEGFWMDKIKSH----CYVTYSTVEEAVATREALHGL 62

This subfamily corresponds to the RRM of Acinus, a caspase-3-activated nuclear factor that induces apoptotic chromatin condensation after cleavage by caspase-3 without inducing DNA fragmentation. It is essential for apoptotic chromatin condensation and may also participate in nuclear structural changes occurring in normal cells. Acinus contains a P-loop motif and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which indicates Acinus might have ATPase and DNA/RNA-binding activity. . Length = 90

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

 Score = 34.8 bits (81), Expect = 0.004
 Identities = 19/75 (25%), Positives = 43/75 (57%), Gaps = 6/75 (8%)

Query: 81  FVSGLSFRTSEDSLRNAFQGFGQLVEV-NLVMDKIAN-----RPRGFAFLRYATEEESRR 134
           +V GL  R +++ +    + FGQ  ++  +V+++  +      P   A++ Y+ +E++ R
Sbjct: 9   YVVGLPPRLADEEVLKKPEYFGQYGKIKKIVINRNTSYNGSQGPSASAYVTYSRKEDALR 68

Query: 135 AIEGMHGKFLDGRVI 149
            I+ + G +LDGR++
Sbjct: 69  CIQAVDGFYLDGRLL 83

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

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

 Score = 34.2 bits (79), Expect = 0.004
 Identities = 21/77 (27%), Positives = 35/77 (45%), Gaps = 7/77 (9%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
            ++FV  L+   +E+ LR  F  FG++ +V      I    R FAF+ +A  E ++    
Sbjct: 1   RKVFVGRLTEDMTEEDLRQYFSQFGEVTDV-----YIPKPFRAFAFVTFADPEVAQSLCG 55

Query: 138 GMHGKFLDGRVIFVEIA 154
             H   + G  + V  A
Sbjct: 56  EDH--IIKGVSVHVSNA 70

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

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

 Score = 34.2 bits (78), Expect = 0.004
 Identities = 21/78 (26%), Positives = 41/78 (52%), Gaps = 2/78 (2%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           ++FV  L F  +   L++ F   G ++  ++ M+    + +G   +R+ + E + RA   
Sbjct: 1   QIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMEN--GKSKGCGVVRFESPEVAERACRM 58

Query: 139 MHGKFLDGRVIFVEIAKS 156
           M+G  L+GR I V I ++
Sbjct: 59  MNGYKLNGREIDVRIDRN 76

This subgroup corresponds to the RRM3 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). . Length = 77

>gnl|CDD|240725 cd12279, RRM_TUT1, RNA recognition motif in speckle targeted PIP5K1A-regulated poly(A) polymerase (Star-PAP) and similar proteins

 Score = 34.3 bits (79), Expect = 0.004
 Identities = 15/34 (44%), Positives = 21/34 (61%), Gaps = 2/34 (5%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDK 113
           +FVSG    TSE+ L + F  FG ++ V  +MDK
Sbjct: 5   VFVSGFKRGTSEEQLMDYFSAFGPVMNV--IMDK 36

This subfamily corresponds to the RRM of Star-PAP, also termed RNA-binding motif protein 21 (RBM21), which is a ubiquitously expressed U6 snRNA-specific terminal uridylyltransferase (U6-TUTase) essential for cell proliferation. Although it belongs to the well-characterized poly(A) polymerase protein superfamily, Star-PAP is highly divergent from both, the poly(A) polymerase (PAP) and the terminal uridylyl transferase (TUTase), identified within the editing complexes of trypanosomes. Star-PAP predominantly localizes at nuclear speckles and catalyzes RNA-modifying nucleotidyl transferase reactions. It functions in mRNA biosynthesis and may be regulated by phosphoinositides. It binds to glutathione S-transferase (GST)-PIPKIalpha. Star-PAP preferentially uses ATP as a nucleotide substrate and possesses PAP activity that is stimulated by PtdIns4,5P2. It contains an N-terminal C2H2-type zinc finger motif followed by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a split PAP domain linked by a proline-rich region, a PAP catalytic and core domain, a PAP-associated domain, an RS repeat, and a nuclear localization signal (NLS). . Length = 74

>gnl|CDD|240908 cd12462, RRM_SCAF8, RNA recognition motif in SR-related and CTD-associated factor 8 (SCAF8) and similar proteins

 Score = 34.2 bits (78), Expect = 0.004
 Identities = 16/62 (25%), Positives = 34/62 (54%), Gaps = 6/62 (9%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           T L+V  +  + ++  L N F+ FGQ+  +N++       PRG A++     +++ RA++
Sbjct: 3   TTLWVGQVDKKATQQDLTNLFEEFGQIESINMI------PPRGCAYVCMVHRQDAYRALQ 56

Query: 138 GM 139
            +
Sbjct: 57  KL 58

This subgroup corresponds to the RRM of SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8), a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II). The pol II CTD plays a role in coupling transcription and pre-mRNA processing. SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing. Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8, together with SCAF4, represents a new class of SCAFs (SR-like CTD-associated factors). They contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and serine/arginine-rich motifs. Length = 79

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	171
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.88
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.88
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.85
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.84
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.84
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.82
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.78
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.78
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.78
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.78
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.77
KOG0122	270	consensus Translation initiation factor 3, subunit	99.77
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.76
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.76
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.76
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.74
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.74
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.73
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.71
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.71
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.69
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.69
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.69
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.67
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.67
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.66
PLN03120	260	nucleic acid binding protein; Provisional	99.66
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.66
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.65
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.65
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.65
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.65
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.64
PLN03213	759	repressor of silencing 3; Provisional	99.64
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.64
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.63
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.63
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.62
smart00362	72	RRM_2 RNA recognition motif.	99.61
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.61
PLN03121	243	nucleic acid binding protein; Provisional	99.61
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.6
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.6
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.59
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.58
smart00360	71	RRM RNA recognition motif.	99.58
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.57
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.55
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.54
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.54
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.53
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.51
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.5
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.47
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.46
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.46
smart00361	70	RRM_1 RNA recognition motif.	99.45
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.44
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.42
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.42
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.41
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.41
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.39
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	99.38
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	99.35
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.33
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.31
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	99.26
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	99.25
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.19
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.15
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.08
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.07
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	99.06
KOG0533	243	consensus RRM motif-containing protein [RNA proces	99.05
KOG0226	290	consensus RNA-binding proteins [General function p	99.05
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.02
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.99
KOG1548	382	consensus Transcription elongation factor TAT-SF1	98.96
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.92
KOG0151	877	consensus Predicted splicing regulator, contains R	98.9
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.87
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.86
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	98.84
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.83
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.77
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	98.6
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	98.58
KOG4210	285	consensus Nuclear localization sequence binding pr	98.47
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	98.45
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.39
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	98.38
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.35
KOG1995	351	consensus Conserved Zn-finger protein [General fun	98.35
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.34
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.32
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.3
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	98.24
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.23
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	98.09
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	98.05
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.02
COG5175	480	MOT2 Transcriptional repressor [Transcription]	98.0
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	97.96
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	97.87
KOG3152	278	consensus TBP-binding protein, activator of basal	97.86
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.79
KOG2314	698	consensus Translation initiation factor 3, subunit	97.76
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	97.74
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	97.62
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.62
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	97.59
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	97.43
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.38
KOG1548	382	consensus Transcription elongation factor TAT-SF1	97.35
KOG1855	484	consensus Predicted RNA-binding protein [General f	97.3
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	97.24
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	97.19
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	97.04
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	97.01
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	96.94
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	96.87
KOG1996	378	consensus mRNA splicing factor [RNA processing and	96.84
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	96.8
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	96.77
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	96.7
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	96.67
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	96.48
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	96.25
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	96.11
KOG2068	327	consensus MOT2 transcription factor [Transcription	95.99
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	95.78
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	95.71
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	95.56
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	95.37
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	95.29
KOG2135	526	consensus Proteins containing the RNA recognition	95.26
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	95.05
KOG4410	396	consensus 5-formyltetrahydrofolate cyclo-ligase [C	95.03
KOG4660	549	consensus Protein Mei2, essential for commitment t	94.67
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	94.63
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	94.63
COG0724	306	RNA-binding proteins (RRM domain) [General functio	94.52
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	94.5
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	94.47
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	94.01
KOG4210	285	consensus Nuclear localization sequence binding pr	93.04
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	92.56
KOG2591	684	consensus c-Mpl binding protein, contains La domai	90.58
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	90.01
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	89.51
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	89.39
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	85.68
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	85.17
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	83.89
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	82.9

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

Probab=99.88  E-value=8.5e-23  Score=169.99  Aligned_cols=147  Identities=18%  Similarity=0.342  Sum_probs=120.2

Q ss_pred             ceeeeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCCCCCC-----------
Q 030819            2 AVLGFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPSPHS-----------   70 (171)
Q Consensus         2 ~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----------   70 (171)
                      .++|.|||+++.++++++.+...|...+++         .+.....+..+++++|++|+.+..+..+..           
T Consensus       105 ~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I---------~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~  175 (612)
T TIGR01645       105 AIMCRVYVGSISFELREDTIRRAFDPFGPI---------KSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLG  175 (612)
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHHHHccCCE---------EEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEe
Confidence            467999999999999999999999998887         344444444455666666665543321100           


Q ss_pred             ----------------------CCCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCC
Q 030819           71 ----------------------LSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYAT  128 (171)
Q Consensus        71 ----------------------~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~  128 (171)
                                            ........+|||+||++++++++|+++|+.||.|.++++..++.+|+++|||||+|.+
T Consensus       176 GR~IkV~rp~~~p~a~~~~~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~  255 (612)
T TIGR01645       176 GRNIKVGRPSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNN  255 (612)
T ss_pred             cceeeecccccccccccccccccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECC
Confidence                                  0111234789999999999999999999999999999999999899999999999999


Q ss_pred             HHHHHHHHHHhCCceeCCeEEEEEEecCc
Q 030819          129 EEESRRAIEGMHGKFLDGRVIFVEIAKSR  157 (171)
Q Consensus       129 ~~~a~~al~~l~g~~i~g~~i~v~~~~~~  157 (171)
                      .++|..|++.||+..++|+.|+|.++...
T Consensus       256 ~e~A~kAI~amNg~elgGr~LrV~kAi~p  284 (612)
T TIGR01645       256 LQSQSEAIASMNLFDLGGQYLRVGKCVTP  284 (612)
T ss_pred             HHHHHHHHHHhCCCeeCCeEEEEEecCCC
Confidence            99999999999999999999999998754

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.

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.88  E-value=8.4e-23  Score=161.57  Aligned_cols=148  Identities=22%  Similarity=0.334  Sum_probs=119.4

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCCCCCC-------------
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPSPHS-------------   70 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------------   70 (171)
                      -+.|||+++.+++++..|.+.|...+++         .+........+.++++++++.+..+..+..             
T Consensus       107 ~~~LfVgnLp~~~te~~L~~lF~~~G~V---------~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr  177 (346)
T TIGR01659       107 GTNLIVNYLPQDMTDRELYALFRTIGPI---------NTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNK  177 (346)
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhcCCE---------EEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCc
Confidence            3679999999999999999999998877         333344444455666666666654432211             


Q ss_pred             ---------CCCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCC
Q 030819           71 ---------LSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHG  141 (171)
Q Consensus        71 ---------~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g  141 (171)
                               .......++|||+|||+.+++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++||+.||+
T Consensus       178 ~i~V~~a~p~~~~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng  257 (346)
T TIGR01659       178 RLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNN  257 (346)
T ss_pred             eeeeecccccccccccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCC
Confidence                     11223467899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ceeCC--eEEEEEEecCcHHH
Q 030819          142 KFLDG--RVIFVEIAKSRAEL  160 (171)
Q Consensus       142 ~~i~g--~~i~v~~~~~~~~~  160 (171)
                      ..+.+  ++|+|.++......
T Consensus       258 ~~~~g~~~~l~V~~a~~~~~~  278 (346)
T TIGR01659       258 VIPEGGSQPLTVRLAEEHGKA  278 (346)
T ss_pred             CccCCCceeEEEEECCccccc
Confidence            98866  68999998865443

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).

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

Probab=99.85  E-value=3.1e-20  Score=130.21  Aligned_cols=87  Identities=39%  Similarity=0.666  Sum_probs=81.4

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ....+++|||+|||+++++++|+++|++||.|.++.++.++.+++++|||||+|.+.++|++|++.|++..|+|+.|+|.
T Consensus        30 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~  109 (144)
T PLN03134         30 LRLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVN  109 (144)
T ss_pred             ccCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34557799999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EecCcHH
Q 030819          153 IAKSRAE  159 (171)
Q Consensus       153 ~~~~~~~  159 (171)
                      ++.++..
T Consensus       110 ~a~~~~~  116 (144)
T PLN03134        110 PANDRPS  116 (144)
T ss_pred             eCCcCCC
Confidence            9976543

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.84  E-value=2.4e-21  Score=154.10  Aligned_cols=82  Identities=29%  Similarity=0.442  Sum_probs=78.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 030819           77 KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKS  156 (171)
Q Consensus        77 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~~  156 (171)
                      +..|||+|||+++++++|+++|++||.|.+++++.|+.+|.++|||||+|.+.++|.+||..|||..++|+.|+|.|+.+
T Consensus       269 ~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~~  348 (352)
T TIGR01661       269 GYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKTN  348 (352)
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEccC
Confidence            44799999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             cH
Q 030819          157 RA  158 (171)
Q Consensus       157 ~~  158 (171)
                      +.
T Consensus       349 ~~  350 (352)
T TIGR01661       349 KA  350 (352)
T ss_pred             CC
Confidence            65

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

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

Probab=99.84  E-value=6.1e-21  Score=141.84  Aligned_cols=139  Identities=21%  Similarity=0.338  Sum_probs=120.4

Q ss_pred             eecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCCCCCCC---------------
Q 030819            7 LPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPSPHSL---------------   71 (171)
Q Consensus         7 ~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------------   71 (171)
                      +||+.+.-.+..+.|...|..++.+         .+...+.+..+.++|+++|+.+.-...+..+               
T Consensus        65 vfvgdls~eI~~e~lr~aF~pFGev---------S~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IR  135 (321)
T KOG0148|consen   65 VFVGDLSPEIDNEKLREAFAPFGEV---------SDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIR  135 (321)
T ss_pred             EEehhcchhcchHHHHHHhcccccc---------ccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceee
Confidence            8999999999999999999999988         5555666777888888888877544322211               


Q ss_pred             -----------------------CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCC
Q 030819           72 -----------------------STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYAT  128 (171)
Q Consensus        72 -----------------------~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~  128 (171)
                                             ...+++++|||||++..++|++|++.|..||+|.+|++..++      ||+||.|.+
T Consensus       136 TNWATRKp~e~n~~~ltfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~q------GYaFVrF~t  209 (321)
T KOG0148|consen  136 TNWATRKPSEMNGKPLTFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKDQ------GYAFVRFET  209 (321)
T ss_pred             ccccccCccccCCCCccHHHHhccCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEeccc------ceEEEEecc
Confidence                                   456788999999999999999999999999999999999887      999999999


Q ss_pred             HHHHHHHHHHhCCceeCCeEEEEEEecCcHHH
Q 030819          129 EEESRRAIEGMHGKFLDGRVIFVEIAKSRAEL  160 (171)
Q Consensus       129 ~~~a~~al~~l~g~~i~g~~i~v~~~~~~~~~  160 (171)
                      +|+|..||..+|+.+|.|+.+++.|.+.....
T Consensus       210 kEaAahAIv~mNntei~G~~VkCsWGKe~~~~  241 (321)
T KOG0148|consen  210 KEAAAHAIVQMNNTEIGGQLVRCSWGKEGDDG  241 (321)
T ss_pred             hhhHHHHHHHhcCceeCceEEEEeccccCCCC
Confidence            99999999999999999999999999866543

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

Probab=99.82  E-value=5.9e-20  Score=150.90  Aligned_cols=142  Identities=26%  Similarity=0.381  Sum_probs=114.9

Q ss_pred             eeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCCCC----------------
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPSP----------------   68 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----------------   68 (171)
                      ..|||+++.+++++..+...|...+++         .+...+.....++.++++|+.+.....+                
T Consensus        90 ~~l~V~nlp~~~~~~~l~~~F~~~G~v---------~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~l~g~~~~g~~i  160 (457)
T TIGR01622        90 RTVFVLQLALKARERDLYEFFSKVGKV---------RDVQCIKDRNSRRSKGVAYVEFYDVESVIKALALTGQMLLGRPI  160 (457)
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCe---------eEEEEeecCCCCCcceEEEEEECCHHHHHHHHHhCCCEECCeee
Confidence            469999999999999999999988766         3333334444455666666655431100                


Q ss_pred             -----------------CCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHH
Q 030819           69 -----------------HSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEE  131 (171)
Q Consensus        69 -----------------~~~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~  131 (171)
                                       ......+...+|||+|||..+++++|+++|..||.|..+.+..++.+|+++|||||+|.+.++
T Consensus       161 ~v~~~~~~~~~~~~~~~~~~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~  240 (457)
T TIGR01622       161 IVQSSQAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEE  240 (457)
T ss_pred             EEeecchhhhhhhhcccccCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHH
Confidence                             001112336899999999999999999999999999999999999889999999999999999


Q ss_pred             HHHHHHHhCCceeCCeEEEEEEec
Q 030819          132 SRRAIEGMHGKFLDGRVIFVEIAK  155 (171)
Q Consensus       132 a~~al~~l~g~~i~g~~i~v~~~~  155 (171)
                      |..|+..|+|..+.|+.|.|.++.
T Consensus       241 A~~A~~~l~g~~i~g~~i~v~~a~  264 (457)
T TIGR01622       241 AKEALEVMNGFELAGRPIKVGYAQ  264 (457)
T ss_pred             HHHHHHhcCCcEECCEEEEEEEcc
Confidence            999999999999999999999975

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

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

Probab=99.78  E-value=3.7e-20  Score=145.23  Aligned_cols=148  Identities=20%  Similarity=0.339  Sum_probs=123.7

Q ss_pred             eeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCCCCCC--------------
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPSPHS--------------   70 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------------   70 (171)
                      .+||||.++-.+++..+..-|++.+.+         .+...+.+..++.+++.||+.+.....+..              
T Consensus        35 vKlfVgqIprt~sE~dlr~lFe~yg~V---------~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~  105 (510)
T KOG0144|consen   35 VKLFVGQIPRTASEKDLRELFEKYGNV---------YEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGM  105 (510)
T ss_pred             hhheeccCCccccHHHHHHHHHHhCce---------eEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCC
Confidence            479999999999999999999998888         666667777788888999887654332111              


Q ss_pred             --------CC----CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHH
Q 030819           71 --------LS----TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG  138 (171)
Q Consensus        71 --------~~----~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~  138 (171)
                              ++    .-...++|||+.|++.++|.+++++|.+||.|++|.|.+|. .+.+||||||.|.+++.|..||+.
T Consensus       106 ~~pvqvk~Ad~E~er~~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~-~~~sRGcaFV~fstke~A~~Aika  184 (510)
T KOG0144|consen  106 HHPVQVKYADGERERIVEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDP-DGLSRGCAFVKFSTKEMAVAAIKA  184 (510)
T ss_pred             CcceeecccchhhhccccchhhhhhhccccccHHHHHHHHHhhCccchhhheecc-cccccceeEEEEehHHHHHHHHHh
Confidence                    11    11236799999999999999999999999999999999998 899999999999999999999999


Q ss_pred             hCCce-eCC--eEEEEEEecCcHHHHH
Q 030819          139 MHGKF-LDG--RVIFVEIAKSRAELRQ  162 (171)
Q Consensus       139 l~g~~-i~g--~~i~v~~~~~~~~~~~  162 (171)
                      |||.. +.|  .+|.|.|+..++++..
T Consensus       185 ~ng~~tmeGcs~PLVVkFADtqkdk~~  211 (510)
T KOG0144|consen  185 LNGTQTMEGCSQPLVVKFADTQKDKDG  211 (510)
T ss_pred             hccceeeccCCCceEEEecccCCCchH
Confidence            99985 444  6899999987765544

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.78  E-value=3.9e-19  Score=141.45  Aligned_cols=144  Identities=22%  Similarity=0.320  Sum_probs=118.1

Q ss_pred             eeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCCCCCC--------------
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPSPHS--------------   70 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------------   70 (171)
                      ..|||+++++++++..+.+.|...+++         .+...+....++++++++++.+..+..+..              
T Consensus         4 ~~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         4 TNLIVNYLPQTMTQEEIRSLFTSIGEI---------ESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKT   74 (352)
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHccCCE---------EEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCee
Confidence            469999999999999999999999988         444444554556677777776654432211              


Q ss_pred             --------CCCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCc
Q 030819           71 --------LSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGK  142 (171)
Q Consensus        71 --------~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~  142 (171)
                              ........+|||+|||+.+++++|+.+|.+||.|..+.+..+..++.++|||||+|.+.++|+.|++.|||.
T Consensus        75 i~v~~a~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~  154 (352)
T TIGR01661        75 IKVSYARPSSDSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGT  154 (352)
T ss_pred             EEEEeecccccccccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCC
Confidence                    112235678999999999999999999999999999999998888999999999999999999999999999


Q ss_pred             eeCC--eEEEEEEecCc
Q 030819          143 FLDG--RVIFVEIAKSR  157 (171)
Q Consensus       143 ~i~g--~~i~v~~~~~~  157 (171)
                      .+.|  .+|.|.++...
T Consensus       155 ~~~g~~~~i~v~~a~~~  171 (352)
T TIGR01661       155 TPSGCTEPITVKFANNP  171 (352)
T ss_pred             ccCCCceeEEEEECCCC
Confidence            9876  57888887644

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

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

Probab=99.78  E-value=6.8e-19  Score=130.99  Aligned_cols=136  Identities=20%  Similarity=0.355  Sum_probs=111.6

Q ss_pred             eeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCeEEEcCC
Q 030819            6 FLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPSPHSLSTCQPKTRLFVSGL   85 (171)
Q Consensus         6 ~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl   85 (171)
                      .|||||+..+.++..|..-|...+++.++....+..........                 ...+.+....-..+||+.|
T Consensus         8 tlyvgnld~~vte~~i~~lf~qig~v~~~k~i~~e~~v~wa~~p-----------------~nQsk~t~~~hfhvfvgdl   70 (321)
T KOG0148|consen    8 TLYVGNLDSTVTEDFIATLFNQIGSVTKTKVIFDELKVNWATAP-----------------GNQSKPTSNQHFHVFVGDL   70 (321)
T ss_pred             eEEeeccChhhHHHHHHHHHHhccccccceeehhhhccccccCc-----------------ccCCCCccccceeEEehhc
Confidence            59999999999999999999999999665543332222111111                 1111122222457999999


Q ss_pred             CCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEecCcH
Q 030819           86 SFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKSRA  158 (171)
Q Consensus        86 ~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~~~~  158 (171)
                      ..+++-++|++.|.+||+|.++++++|..|+++||||||.|...++|++||..|||.=|.++.|+-.|+..+.
T Consensus        71 s~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATRKp  143 (321)
T KOG0148|consen   71 SPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATRKP  143 (321)
T ss_pred             chhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeeccccccCc
Confidence            9999999999999999999999999999999999999999999999999999999999999999999997665

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

Probab=99.78  E-value=1e-18  Score=145.30  Aligned_cols=82  Identities=26%  Similarity=0.467  Sum_probs=77.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 030819           75 QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIA  154 (171)
Q Consensus        75 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~  154 (171)
                      ....+|||+|||..+++++|+++|..||.|..+.++.+..+|.++|||||+|.+.++|..|+..|+|..+.|+.|.|.++
T Consensus       293 ~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a  372 (509)
T TIGR01642       293 DSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRA  372 (509)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            44679999999999999999999999999999999999889999999999999999999999999999999999999998


Q ss_pred             cC
Q 030819          155 KS  156 (171)
Q Consensus       155 ~~  156 (171)
                      ..
T Consensus       373 ~~  374 (509)
T TIGR01642       373 CV  374 (509)
T ss_pred             cc
Confidence            53

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

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

Probab=99.77  E-value=1.5e-19  Score=139.61  Aligned_cols=145  Identities=18%  Similarity=0.345  Sum_probs=126.6

Q ss_pred             ceeeeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCCCCCCC----------
Q 030819            2 AVLGFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPSPHSL----------   71 (171)
Q Consensus         2 ~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----------   71 (171)
                      ||||.+|||+++|++.++.+...|..++|+         .+..-.++.-+.+.++++|+++.-|..+.-+          
T Consensus       111 aiMcRvYVGSIsfEl~EDtiR~AF~PFGPI---------KSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlG  181 (544)
T KOG0124|consen  111 AIMCRVYVGSISFELREDTIRRAFDPFGPI---------KSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLG  181 (544)
T ss_pred             HHhHheeeeeeEEEechHHHHhhccCCCCc---------ceeecccccccccccceEEEEEeCcHHHHHHHHHhcccccc
Confidence            799999999999999999999999999999         7777778888899999999988877643211          


Q ss_pred             --------CCC---------------CCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCC
Q 030819           72 --------STC---------------QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYAT  128 (171)
Q Consensus        72 --------~~~---------------~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~  128 (171)
                              +.+               ..-..|||..+.++++++||+..|+.||+|..|.+.+++..+.++||||++|.+
T Consensus       182 GRNiKVgrPsNmpQAQpiID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n  261 (544)
T KOG0124|consen  182 GRNIKVGRPSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNN  261 (544)
T ss_pred             CccccccCCCCCcccchHHHHHHHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEecc
Confidence                    111               112589999999999999999999999999999999999778899999999999


Q ss_pred             HHHHHHHHHHhCCceeCCeEEEEEEec
Q 030819          129 EEESRRAIEGMHGKFLDGRVIFVEIAK  155 (171)
Q Consensus       129 ~~~a~~al~~l~g~~i~g~~i~v~~~~  155 (171)
                      ..+...|+..+|-..++|.-|+|-...
T Consensus       262 ~qs~~eAiasMNlFDLGGQyLRVGk~v  288 (544)
T KOG0124|consen  262 LQSQSEAIASMNLFDLGGQYLRVGKCV  288 (544)
T ss_pred             ccchHHHhhhcchhhcccceEeccccc
Confidence            999999999999999999999986543

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

Probab=99.77  E-value=4e-18  Score=125.24  Aligned_cols=85  Identities=29%  Similarity=0.471  Sum_probs=81.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ...+..+|-|.||+.++++++|+++|..||.|..+.+.+|+.||.++|||||.|.+.++|.+||..|||.-++...|+|+
T Consensus       185 ~R~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvE  264 (270)
T KOG0122|consen  185 ERDDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVE  264 (270)
T ss_pred             cCCccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEE
Confidence            44567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EecCc
Q 030819          153 IAKSR  157 (171)
Q Consensus       153 ~~~~~  157 (171)
                      |++++
T Consensus       265 wskP~  269 (270)
T KOG0122|consen  265 WSKPS  269 (270)
T ss_pred             ecCCC
Confidence            99986

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.76  E-value=4.1e-18  Score=134.96  Aligned_cols=85  Identities=24%  Similarity=0.385  Sum_probs=80.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      .....++|||+|||+++++++|+++|+.||.|.+|+|+.|+.+++++|||||+|.+.++|++|++.|++..+.+++|+|.
T Consensus       103 ~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~  182 (346)
T TIGR01659       103 TNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVS  182 (346)
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeee
Confidence            44567899999999999999999999999999999999999899999999999999999999999999999999999999


Q ss_pred             EecCc
Q 030819          153 IAKSR  157 (171)
Q Consensus       153 ~~~~~  157 (171)
                      ++++.
T Consensus       183 ~a~p~  187 (346)
T TIGR01659       183 YARPG  187 (346)
T ss_pred             ccccc
Confidence            98764

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).

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

Probab=99.76  E-value=6.9e-19  Score=148.02  Aligned_cols=89  Identities=27%  Similarity=0.612  Sum_probs=82.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 030819           75 QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIA  154 (171)
Q Consensus        75 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~  154 (171)
                      ..+.+|||+||++.+++++|+++|+.||.|.++.++.+. +|.++|||||+|.+.++|.+|+..|||..+.|++|.|.++
T Consensus       283 ~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d~-~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a  361 (562)
T TIGR01628       283 AQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDE-KGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALA  361 (562)
T ss_pred             cCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEECC-CCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEec
Confidence            346789999999999999999999999999999999995 8999999999999999999999999999999999999999


Q ss_pred             cCcHHHHHhh
Q 030819          155 KSRAELRQAF  164 (171)
Q Consensus       155 ~~~~~~~~~~  164 (171)
                      ..+..+....
T Consensus       362 ~~k~~~~~~~  371 (562)
T TIGR01628       362 QRKEQRRAHL  371 (562)
T ss_pred             cCcHHHHHHH
Confidence            9887665543

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

>PF00076 RRM_1: RNA recognition motif

Probab=99.76  E-value=1e-17  Score=103.00  Aligned_cols=70  Identities=30%  Similarity=0.685  Sum_probs=67.1

Q ss_pred             EEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q 030819           80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIF  150 (171)
Q Consensus        80 l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~  150 (171)
                      |||+|||+++++++|+++|.+||.|..+.+..+ .++..+|+|||+|.+.++|+.|++.|+|..+.|+.|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~-~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRN-SSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEE-TTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhccccccccc-ccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            799999999999999999999999999999988 4899999999999999999999999999999999885

(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 ....

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

Probab=99.74  E-value=1.9e-18  Score=145.32  Aligned_cols=145  Identities=18%  Similarity=0.283  Sum_probs=112.5

Q ss_pred             eeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCCCCCC---------------
Q 030819            6 FLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPSPHS---------------   70 (171)
Q Consensus         6 ~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------------   70 (171)
                      -|||+++..++++..+...|...+++         .+.....+..++++++++++.+..+..+..               
T Consensus         2 sl~VgnLp~~vte~~L~~~F~~~G~v---------~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i   72 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPV---------LSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPI   72 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCE---------EEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeE
Confidence            48999999999999999999998876         333333333334445555554443322111               


Q ss_pred             ---------CCCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCC
Q 030819           71 ---------LSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHG  141 (171)
Q Consensus        71 ---------~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g  141 (171)
                               ........+|||+|||.++++++|+++|++||.|.+|.+..+. +|+++|||||+|.+.++|.+|++.++|
T Consensus        73 ~i~~s~~~~~~~~~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~-~g~skg~afV~F~~~e~A~~Ai~~lng  151 (562)
T TIGR01628        73 RIMWSQRDPSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDE-NGKSRGYGFVHFEKEESAKAAIQKVNG  151 (562)
T ss_pred             EeecccccccccccCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecC-CCCcccEEEEEECCHHHHHHHHHHhcc
Confidence                     1112234579999999999999999999999999999999887 899999999999999999999999999


Q ss_pred             ceeCCeEEEEEEecCcHHH
Q 030819          142 KFLDGRVIFVEIAKSRAEL  160 (171)
Q Consensus       142 ~~i~g~~i~v~~~~~~~~~  160 (171)
                      ..+.|+.|.|.....+..+
T Consensus       152 ~~~~~~~i~v~~~~~~~~~  170 (562)
T TIGR01628       152 MLLNDKEVYVGRFIKKHER  170 (562)
T ss_pred             cEecCceEEEecccccccc
Confidence            9999999999876655433

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

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

Probab=99.74  E-value=9.4e-18  Score=112.10  Aligned_cols=89  Identities=26%  Similarity=0.479  Sum_probs=82.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 030819           74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEI  153 (171)
Q Consensus        74 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~  153 (171)
                      ...+++|||+||+..++|++|.++|.++|+|..+.+-.|+.+..+.|||||+|.+.++|+.|+..++|..++.+.|++.|
T Consensus        33 ~r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~  112 (153)
T KOG0121|consen   33 LRKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDW  112 (153)
T ss_pred             HhhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeec
Confidence            34578999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCcHHHHH
Q 030819          154 AKSRAELRQ  162 (171)
Q Consensus       154 ~~~~~~~~~  162 (171)
                      .-.-.+.+|
T Consensus       113 D~GF~eGRQ  121 (153)
T KOG0121|consen  113 DAGFVEGRQ  121 (153)
T ss_pred             cccchhhhh
Confidence            876655554

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

Probab=99.73  E-value=1e-17  Score=122.52  Aligned_cols=78  Identities=32%  Similarity=0.645  Sum_probs=71.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 030819           77 KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAK  155 (171)
Q Consensus        77 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~  155 (171)
                      -++||||+|+|.+..+.|+++|++||+|.+..++.|+.+|++||||||+|.+.++|.+|++. ..-.|+|++..|..+-
T Consensus        12 ~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNcnlA~   89 (247)
T KOG0149|consen   12 FTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKANCNLAS   89 (247)
T ss_pred             EEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC-CCCcccccccccchhh
Confidence            46899999999999999999999999999999999999999999999999999999999984 4467899988887653

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

Probab=99.71  E-value=7.9e-17  Score=127.09  Aligned_cols=92  Identities=26%  Similarity=0.462  Sum_probs=83.6

Q ss_pred             CCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee
Q 030819           65 PPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFL  144 (171)
Q Consensus        65 ~~~~~~~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i  144 (171)
                      |++.......+.++.||||.||.++.|++|..+|++.|+|.+++++.|+.+|.+||||||.|.+.++|+.|++.||+.+|
T Consensus        71 PpP~weg~~p~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Ei  150 (506)
T KOG0117|consen   71 PPPGWEGPPPPRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEI  150 (506)
T ss_pred             CCCcccCCCCCCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccc
Confidence            33445555668899999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             -CCeEEEEEEecC
Q 030819          145 -DGRVIFVEIAKS  156 (171)
Q Consensus       145 -~g~~i~v~~~~~  156 (171)
                       .|+.|.|+.+..
T Consensus       151 r~GK~igvc~Sva  163 (506)
T KOG0117|consen  151 RPGKLLGVCVSVA  163 (506)
T ss_pred             cCCCEeEEEEeee
Confidence             789999987653

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

Probab=99.71  E-value=9.4e-17  Score=121.03  Aligned_cols=91  Identities=32%  Similarity=0.642  Sum_probs=83.7

Q ss_pred             CCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC
Q 030819           67 SPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDG  146 (171)
Q Consensus        67 ~~~~~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g  146 (171)
                      ...+....++-+||||+.|+++++|..|+..|..||+|+.|.|+.|+.||+++|||||+|.++.++..|.+..+|..|+|
T Consensus        91 ~~dp~a~gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idg  170 (335)
T KOG0113|consen   91 NNDPNAIGDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDG  170 (335)
T ss_pred             CCCCcccCCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecC
Confidence            33344456788999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eEEEEEEecCc
Q 030819          147 RVIFVEIAKSR  157 (171)
Q Consensus       147 ~~i~v~~~~~~  157 (171)
                      +.|.|.+.+.+
T Consensus       171 rri~VDvERgR  181 (335)
T KOG0113|consen  171 RRILVDVERGR  181 (335)
T ss_pred             cEEEEEecccc
Confidence            99999987654

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.69  E-value=3.9e-16  Score=96.25  Aligned_cols=70  Identities=40%  Similarity=0.738  Sum_probs=64.9

Q ss_pred             EEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q 030819           80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIF  150 (171)
Q Consensus        80 l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~  150 (171)
                      |||+|||+++++++|+++|..||.|..+.+..+++ +.++|+|||+|.+.++|.+|+..+++..++|+.|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~-~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKD-GQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTT-SSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeec-cccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            79999999999999999999999999999999986 99999999999999999999999999999999874

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 ....

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

Probab=99.69  E-value=7.4e-17  Score=134.36  Aligned_cols=75  Identities=29%  Similarity=0.543  Sum_probs=69.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcC--CCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 030819           76 PKTRLFVSGLSFRTSEDSLRNAFQGF--GQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEI  153 (171)
Q Consensus        76 ~~~~l~V~nl~~~~~~~~l~~~f~~~--G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~  153 (171)
                      ..++|||+||+.++++++|+++|++|  |.|.++.++        ++||||+|.+.++|.+|++.|||..|.|+.|+|.|
T Consensus       232 ~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~--------rgfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~  303 (578)
T TIGR01648       232 KVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI--------RDYAFVHFEDREDAVKAMDELNGKELEGSEIEVTL  303 (578)
T ss_pred             cccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee--------cCeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            45789999999999999999999999  999998765        36999999999999999999999999999999999


Q ss_pred             ecCcH
Q 030819          154 AKSRA  158 (171)
Q Consensus       154 ~~~~~  158 (171)
                      +++..
T Consensus       304 Akp~~  308 (578)
T TIGR01648       304 AKPVD  308 (578)
T ss_pred             ccCCC
Confidence            98753

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

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

Probab=99.69  E-value=9.7e-17  Score=129.35  Aligned_cols=146  Identities=24%  Similarity=0.364  Sum_probs=109.4

Q ss_pred             eeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCC---------------------
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLAC---------------------   63 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------------------   63 (171)
                      ..|||.+++++..+..+...|+..+|+.....-+         .......||++++.|.                     
T Consensus         6 ~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt---------~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~   76 (678)
T KOG0127|consen    6 ATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVT---------NKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRI   76 (678)
T ss_pred             ceEEEecCCCccchhHHHHhhhcccCcceeEEec---------CCCcccccCccceeeehHhHHHHHHHHhhcCccccee
Confidence            5699999999999999999999999986633211         0011111111111110                     


Q ss_pred             ------------------CCC-------C--CCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCC
Q 030819           64 ------------------LPP-------S--PHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIAN  116 (171)
Q Consensus        64 ------------------~~~-------~--~~~~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g  116 (171)
                                        .+.       .  +.......+.+.|.|.|||+.+...+|+.+|+.||.|.++.|++.++.+
T Consensus        77 l~v~~A~~R~r~e~~~~~e~~~veK~~~q~~~~k~~v~~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgk  156 (678)
T KOG0127|consen   77 LNVDPAKKRARSEEVEKGENKAVEKPIEQKRPTKAKVDLPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGK  156 (678)
T ss_pred             cccccccccccchhcccccchhhhcccccCCcchhhccCccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCC
Confidence                              000       0  0011223447899999999999999999999999999999999888545


Q ss_pred             CcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEecCcHHH
Q 030819          117 RPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKSRAEL  160 (171)
Q Consensus       117 ~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~~~~~~  160 (171)
                      .| |||||.|....+|..||+.+||..|.|++|.|.||.++...
T Consensus       157 lc-GFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd~y  199 (678)
T KOG0127|consen  157 LC-GFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDKDTY  199 (678)
T ss_pred             cc-ceEEEEEeeHHHHHHHHHhccCceecCceeEEeeecccccc
Confidence            45 99999999999999999999999999999999999877543

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

Probab=99.67  E-value=2.8e-16  Score=131.29  Aligned_cols=81  Identities=35%  Similarity=0.631  Sum_probs=76.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 030819           75 QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIA  154 (171)
Q Consensus        75 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~  154 (171)
                      ...++|||+||++++++++|+++|.+||.|.++.++.|+.+|+++|||||+|.+.++|++|++.|||..+.|+.|+|.+.
T Consensus       105 ~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp  184 (612)
T TIGR01645       105 AIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRP  184 (612)
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeeccc
Confidence            34679999999999999999999999999999999999999999999999999999999999999999999999999865


Q ss_pred             c
Q 030819          155 K  155 (171)
Q Consensus       155 ~  155 (171)
                      .
T Consensus       185 ~  185 (612)
T TIGR01645       185 S  185 (612)
T ss_pred             c
Confidence            4

In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

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

Probab=99.67  E-value=3.8e-17  Score=115.35  Aligned_cols=145  Identities=24%  Similarity=0.326  Sum_probs=121.2

Q ss_pred             eeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCCCCCC--------------
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPSPHS--------------   70 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------------   70 (171)
                      ..+|||++.-..++.++..-+...+|+         .++......-+...+|++|+++.....+.-              
T Consensus        10 ~tiyvgnld~kvs~~~l~EL~iqagpV---------v~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrp   80 (203)
T KOG0131|consen   10 ATLYVGNLDEKVSEELLYELFIQAGPV---------VNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRP   80 (203)
T ss_pred             ceEEEecCCHHHHHHHHHHHHHhcCce---------eeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCce
Confidence            469999999999999999999998888         555555555556677888877766554322              


Q ss_pred             ---------CCCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEE-EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC
Q 030819           71 ---------LSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVE-VNLVMDKIANRPRGFAFLRYATEEESRRAIEGMH  140 (171)
Q Consensus        71 ---------~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~-~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~  140 (171)
                               ....+.+..+||+||.+.+++..|.++|+.||.+.. -.++++..+|.++|||||.|.+.+.+.+|++.+|
T Consensus        81 Irv~kas~~~~nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~n  160 (203)
T KOG0131|consen   81 IRVNKASAHQKNLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMN  160 (203)
T ss_pred             eEEEecccccccccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhc
Confidence                     134456689999999999999999999999998755 5788999899999999999999999999999999


Q ss_pred             CceeCCeEEEEEEecCcH
Q 030819          141 GKFLDGRVIFVEIAKSRA  158 (171)
Q Consensus       141 g~~i~g~~i~v~~~~~~~  158 (171)
                      |..++.++|.|.++..+.
T Consensus       161 gq~l~nr~itv~ya~k~~  178 (203)
T KOG0131|consen  161 GQYLCNRPITVSYAFKKD  178 (203)
T ss_pred             cchhcCCceEEEEEEecC
Confidence            999999999999987553

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

Probab=99.66  E-value=2.4e-16  Score=117.13  Aligned_cols=84  Identities=27%  Similarity=0.400  Sum_probs=79.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 030819           74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEI  153 (171)
Q Consensus        74 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~  153 (171)
                      ...++.|||-||.+++.|.-|+++|..||.|..+++++|..+.+|+|||||.+.+-++|..||..|||..+.++.|.|.+
T Consensus       275 ~~~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsF  354 (360)
T KOG0145|consen  275 PGGGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSF  354 (360)
T ss_pred             CCCeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccceEEEEEE
Confidence            34578999999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             ecCc
Q 030819          154 AKSR  157 (171)
Q Consensus       154 ~~~~  157 (171)
                      ...+
T Consensus       355 Ktnk  358 (360)
T KOG0145|consen  355 KTNK  358 (360)
T ss_pred             ecCC
Confidence            7654

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.66  E-value=1.1e-15  Score=115.02  Aligned_cols=75  Identities=15%  Similarity=0.267  Sum_probs=70.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 030819           77 KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAK  155 (171)
Q Consensus        77 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~  155 (171)
                      .++|||+|||+.+++++|+++|+.||.|.++.++.++.   .+|||||+|.+.++|+.||. |+|..|.|+.|.|.++.
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~   78 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAE   78 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEecc
Confidence            57999999999999999999999999999999988763   46899999999999999996 99999999999999986

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

Probab=99.66  E-value=1.1e-15  Score=116.71  Aligned_cols=84  Identities=31%  Similarity=0.615  Sum_probs=76.5

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 030819           72 STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFV  151 (171)
Q Consensus        72 ~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v  151 (171)
                      ......++|+|+|||+...+-||+.+|++||.|.+|.|+.+.  .-+||||||+|++.++|++|-++|||..+.|++|.|
T Consensus        91 ~s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNE--RGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEV  168 (376)
T KOG0125|consen   91 SSKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNE--RGSKGFGFVTMENPADADRARAELHGTVVEGRKIEV  168 (376)
T ss_pred             CCCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEecc--CCCCccceEEecChhhHHHHHHHhhcceeeceEEEE
Confidence            344556799999999999999999999999999999999875  447899999999999999999999999999999999


Q ss_pred             EEecCc
Q 030819          152 EIAKSR  157 (171)
Q Consensus       152 ~~~~~~  157 (171)
                      ..+..+
T Consensus       169 n~ATar  174 (376)
T KOG0125|consen  169 NNATAR  174 (376)
T ss_pred             eccchh
Confidence            998765

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

Probab=99.65  E-value=1.5e-17  Score=117.37  Aligned_cols=80  Identities=28%  Similarity=0.601  Sum_probs=76.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 030819           74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEI  153 (171)
Q Consensus        74 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~  153 (171)
                      -.++..|||||||+++||.||...|++||+|..+.+++|+.||+++||||+.|++-.+..-|+..|||..|.|+.|+|.-
T Consensus        32 YkdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDH  111 (219)
T KOG0126|consen   32 YKDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDH  111 (219)
T ss_pred             cccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeee
Confidence            34577999999999999999999999999999999999999999999999999999999999999999999999999974

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

Probab=99.65  E-value=1.1e-15  Score=127.43  Aligned_cols=84  Identities=26%  Similarity=0.413  Sum_probs=75.4

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC-CeEE
Q 030819           71 LSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLD-GRVI  149 (171)
Q Consensus        71 ~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~-g~~i  149 (171)
                      ...+...++|||+|||++++|++|+++|++||.|.+++|+.| .+|+++|||||+|.+.++|++||+.||+..+. |+.|
T Consensus        52 ~~~p~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l  130 (578)
T TIGR01648        52 GVQPGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLL  130 (578)
T ss_pred             CCCCCCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC-CCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCccc
Confidence            334556799999999999999999999999999999999999 59999999999999999999999999999884 7777


Q ss_pred             EEEEec
Q 030819          150 FVEIAK  155 (171)
Q Consensus       150 ~v~~~~  155 (171)
                      .|+++.
T Consensus       131 ~V~~S~  136 (578)
T TIGR01648       131 GVCISV  136 (578)
T ss_pred             cccccc
Confidence            776653

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

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

Probab=99.65  E-value=1e-16  Score=126.47  Aligned_cols=78  Identities=31%  Similarity=0.504  Sum_probs=71.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 030819           77 KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKS  156 (171)
Q Consensus        77 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~~  156 (171)
                      -..|||.||+.++|++.|+.+|.+||.|..|..++        .||||.|.+.++|-+||+.+||..|+|..|.|.+|++
T Consensus       259 VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~r--------DYaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAKP  330 (506)
T KOG0117|consen  259 VKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPR--------DYAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAKP  330 (506)
T ss_pred             eeeeeeeccchhhhHHHHHHHHHhccceEEeeccc--------ceeEEeecchHHHHHHHHHhcCceecCceEEEEecCC
Confidence            35799999999999999999999999999987664        4999999999999999999999999999999999998


Q ss_pred             cHHHHH
Q 030819          157 RAELRQ  162 (171)
Q Consensus       157 ~~~~~~  162 (171)
                      ..+.+.
T Consensus       331 ~~k~k~  336 (506)
T KOG0117|consen  331 VDKKKK  336 (506)
T ss_pred             hhhhcc
Confidence            765543

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

Probab=99.65  E-value=7.5e-16  Score=108.20  Aligned_cols=80  Identities=28%  Similarity=0.498  Sum_probs=72.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 030819           75 QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIA  154 (171)
Q Consensus        75 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~  154 (171)
                      .-.++|||+||+..+++.+|+..|..||.|..+.|...+     .|||||+|++..+|+.|+..|+|..|+|..|+|+++
T Consensus         8 ~~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnP-----PGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S   82 (195)
T KOG0107|consen    8 NGNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNP-----PGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELS   82 (195)
T ss_pred             CCCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecC-----CCceEEeccCcccHHHHHhhcCCccccCceEEEEee
Confidence            347899999999999999999999999999999887655     489999999999999999999999999999999998


Q ss_pred             cCcHH
Q 030819          155 KSRAE  159 (171)
Q Consensus       155 ~~~~~  159 (171)
                      ..+..
T Consensus        83 ~G~~r   87 (195)
T KOG0107|consen   83 TGRPR   87 (195)
T ss_pred             cCCcc
Confidence            76543

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

Probab=99.64  E-value=5.1e-16  Score=104.75  Aligned_cols=82  Identities=23%  Similarity=0.477  Sum_probs=78.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 030819           74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEI  153 (171)
Q Consensus        74 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~  153 (171)
                      .-.++.|||.++...+++++|.+.|..||+|+.+.+..|+.||..+||++|+|.+.+.|++|+..+||..+.|..|.|.|
T Consensus        69 SVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw  148 (170)
T KOG0130|consen   69 SVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDW  148 (170)
T ss_pred             ceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEE
Confidence            34578999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ec
Q 030819          154 AK  155 (171)
Q Consensus       154 ~~  155 (171)
                      .-
T Consensus       149 ~F  150 (170)
T KOG0130|consen  149 CF  150 (170)
T ss_pred             EE
Confidence            74

>PLN03213 repressor of silencing 3; Provisional

Probab=99.64  E-value=2.2e-15  Score=120.61  Aligned_cols=82  Identities=23%  Similarity=0.357  Sum_probs=74.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCH--HHHHHHHHHhCCceeCCeEEEE
Q 030819           74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATE--EESRRAIEGMHGKFLDGRVIFV  151 (171)
Q Consensus        74 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~--~~a~~al~~l~g~~i~g~~i~v  151 (171)
                      ...+.+||||||++.+++++|+.+|..||.|..+.|+  +.+|  ||||||+|.+.  .++.+||..|||..++|+.|+|
T Consensus         7 ~~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIp--RETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKV   82 (759)
T PLN03213          7 GGGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFV--RTKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRL   82 (759)
T ss_pred             CCcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEe--cccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEE
Confidence            3456799999999999999999999999999999998  4477  89999999976  7899999999999999999999


Q ss_pred             EEecCcHH
Q 030819          152 EIAKSRAE  159 (171)
Q Consensus       152 ~~~~~~~~  159 (171)
                      ..|++.--
T Consensus        83 NKAKP~YL   90 (759)
T PLN03213         83 EKAKEHYL   90 (759)
T ss_pred             eeccHHHH
Confidence            99987643

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

Probab=99.64  E-value=5.5e-16  Score=111.59  Aligned_cols=81  Identities=36%  Similarity=0.685  Sum_probs=77.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 030819           75 QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIA  154 (171)
Q Consensus        75 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~  154 (171)
                      ..-.+|-|-||.+.++.++|+.+|++||.|-+|.|.+|+-|+.++|||||.|.+..+|+.|+++|+|..|+|+.|.|+++
T Consensus        11 ~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~a   90 (256)
T KOG4207|consen   11 EGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMA   90 (256)
T ss_pred             ccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehhh
Confidence            34568999999999999999999999999999999999999999999999999999999999999999999999999887


Q ss_pred             c
Q 030819          155 K  155 (171)
Q Consensus       155 ~  155 (171)
                      +
T Consensus        91 r   91 (256)
T KOG4207|consen   91 R   91 (256)
T ss_pred             h
Confidence            5

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

Probab=99.63  E-value=1.7e-16  Score=115.24  Aligned_cols=86  Identities=31%  Similarity=0.533  Sum_probs=81.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 030819           75 QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIA  154 (171)
Q Consensus        75 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~  154 (171)
                      ...++||||+|..++++.-|...|-.||.|.++.+..|..++++||||||+|...|+|.+||..||+.++.|+.|+|.++
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~A   87 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLA   87 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeec
Confidence            35689999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCcHHH
Q 030819          155 KSRAEL  160 (171)
Q Consensus       155 ~~~~~~  160 (171)
                      ++.+-.
T Consensus        88 kP~kik   93 (298)
T KOG0111|consen   88 KPEKIK   93 (298)
T ss_pred             CCcccc
Confidence            987543

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

Probab=99.63  E-value=6.8e-15  Score=121.00  Aligned_cols=84  Identities=24%  Similarity=0.462  Sum_probs=78.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 030819           74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEI  153 (171)
Q Consensus        74 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~  153 (171)
                      ..+.++|||+|||..+++++|+++|.+||.|..+.++.++.+|+++|||||+|.+.++|.+||. |+|..+.|++|.|.+
T Consensus        86 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~~  164 (457)
T TIGR01622        86 ERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQS  164 (457)
T ss_pred             ccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEee
Confidence            3457899999999999999999999999999999999999999999999999999999999997 999999999999998


Q ss_pred             ecCcH
Q 030819          154 AKSRA  158 (171)
Q Consensus       154 ~~~~~  158 (171)
                      +....
T Consensus       165 ~~~~~  169 (457)
T TIGR01622       165 SQAEK  169 (457)
T ss_pred             cchhh
Confidence            76544

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

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

Probab=99.62  E-value=2.2e-15  Score=118.59  Aligned_cols=88  Identities=30%  Similarity=0.499  Sum_probs=80.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCce-e--CCeEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKF-L--DGRVI  149 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~-i--~g~~i  149 (171)
                      .+.+.-++||+-+|+.++|.||+++|++||.|.+|.+++|+.++.++|||||.|.+.++|.+|+.+||+.+ +  +.++|
T Consensus        30 ~d~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pv  109 (510)
T KOG0144|consen   30 PDGSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPV  109 (510)
T ss_pred             CCchhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcce
Confidence            34567799999999999999999999999999999999999999999999999999999999999999886 4  44689


Q ss_pred             EEEEecCcHHH
Q 030819          150 FVEIAKSRAEL  160 (171)
Q Consensus       150 ~v~~~~~~~~~  160 (171)
                      +|.++....++
T Consensus       110 qvk~Ad~E~er  120 (510)
T KOG0144|consen  110 QVKYADGERER  120 (510)
T ss_pred             eecccchhhhc
Confidence            99999877655

>smart00362 RRM_2 RNA recognition motif

Probab=99.61  E-value=1e-14  Score=89.00  Aligned_cols=72  Identities=36%  Similarity=0.692  Sum_probs=67.0

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        79 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      +|||+|||..+++++|+++|..||.+..+.+..++  +.++|+|||+|.+.++|++|+..++|..+.|+.|.|.
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT--GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC--CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            58999999999999999999999999999988776  7788999999999999999999999999999998863

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

Probab=99.61  E-value=2.1e-15  Score=116.93  Aligned_cols=148  Identities=22%  Similarity=0.388  Sum_probs=123.4

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCCCCCCC------------
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPSPHSL------------   71 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------------   71 (171)
                      .|+||+|.+.|+.+++.+...+...+.+         .+.-.+....+.+++++.++.+..+......            
T Consensus         6 ~~KlfiGgisw~ttee~Lr~yf~~~Gev---------~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~~~h~~dgr~   76 (311)
T KOG4205|consen    6 SGKLFIGGLSWETTEESLREYFSQFGEV---------TDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNARTHKLDGRS   76 (311)
T ss_pred             CcceeecCcCccccHHHHHHHhcccCce---------eeEEEeccCCCCCcccccceecCCCcchheeecccccccCCcc
Confidence            5899999999999999999999887777         4444455555688888888888755532221            


Q ss_pred             ---------------CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHH
Q 030819           72 ---------------STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI  136 (171)
Q Consensus        72 ---------------~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al  136 (171)
                                     .......+|||++||.++++.++++.|.+||.|..+.++.|..+.+.+||+||.|.+++++++++
T Consensus        77 ve~k~av~r~~~~~~~~~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~  156 (311)
T KOG4205|consen   77 VEPKRAVSREDQTKVGRHLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVT  156 (311)
T ss_pred             ccceeccCcccccccccccceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceec
Confidence                           01112448999999999999999999999999999999999999999999999999999999998


Q ss_pred             HHhCCceeCCeEEEEEEecCcHHHH
Q 030819          137 EGMHGKFLDGRVIFVEIAKSRAELR  161 (171)
Q Consensus       137 ~~l~g~~i~g~~i~v~~~~~~~~~~  161 (171)
                      . ..-+.|+|+.+.|..|.++..+.
T Consensus       157 ~-~~f~~~~gk~vevkrA~pk~~~~  180 (311)
T KOG4205|consen  157 L-QKFHDFNGKKVEVKRAIPKEVMQ  180 (311)
T ss_pred             c-cceeeecCceeeEeeccchhhcc
Confidence            7 67788999999999999887654

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.61  E-value=8.6e-15  Score=108.66  Aligned_cols=76  Identities=13%  Similarity=0.166  Sum_probs=69.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 030819           75 QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIA  154 (171)
Q Consensus        75 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~  154 (171)
                      +.+.+|||+||++.+++++|+++|+.||.|.+|.++.+.   ..+|+|||+|.++++++.|+. |+|..|.+++|.|...
T Consensus         3 ~~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~---et~gfAfVtF~d~~aaetAll-LnGa~l~d~~I~It~~   78 (243)
T PLN03121          3 PGGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG---EYACTAYVTFKDAYALETAVL-LSGATIVDQRVCITRW   78 (243)
T ss_pred             CCceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC---CcceEEEEEECCHHHHHHHHh-cCCCeeCCceEEEEeC
Confidence            346899999999999999999999999999999999875   344899999999999999996 9999999999999764

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

Probab=99.60  E-value=3.7e-15  Score=120.20  Aligned_cols=86  Identities=30%  Similarity=0.631  Sum_probs=81.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEecCc
Q 030819           78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKSR  157 (171)
Q Consensus        78 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~~~  157 (171)
                      ..+||||+|+++++++|..+|++.|.|..++++.|+++|+++||||++|.+.+.+..|++.|||.++.|++|+|.|+...
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~~   98 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASNR   98 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeeccccc
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999999876


Q ss_pred             HHHHHh
Q 030819          158 AELRQA  163 (171)
Q Consensus       158 ~~~~~~  163 (171)
                      ....+.
T Consensus        99 ~~~~~~  104 (435)
T KOG0108|consen   99 KNAERS  104 (435)
T ss_pred             chhHHH
Confidence            655543

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

Probab=99.60  E-value=2.7e-15  Score=124.14  Aligned_cols=150  Identities=14%  Similarity=0.156  Sum_probs=99.5

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCCCCCCcccc-cc---cccc------cccc---ccCCCCC-CCCCCCCCCCC--
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIK-RR---DFDS------LFSL---RQGRGRG-ACFPLACLPPS--   67 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~---~~~~------~~~~---~~~~~~~-~~~~~~~~~~~--   67 (171)
                      +..|||+++.++++++.+.+.|...+++.....-.. ..   .+..      +...   ......+ .-.+.......  
T Consensus         2 s~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~~k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~s~~~~~~   81 (481)
T TIGR01649         2 SPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPGKRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYSTSQEIK   81 (481)
T ss_pred             ccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEECCCCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEecCCcccc
Confidence            346999999999999999999999998854211100 00   0110      1100   0000001 01111111000  


Q ss_pred             -CC----CCCCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCc
Q 030819           68 -PH----SLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGK  142 (171)
Q Consensus        68 -~~----~~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~  142 (171)
                       ..    ..........|||+||++.+++++|+++|+.||.|.++.+..+..    .|+|||+|.+.++|.+|++.|||.
T Consensus        82 ~~~~~~~~~~~~~~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~~----~~~afVef~~~~~A~~A~~~Lng~  157 (481)
T TIGR01649        82 RDGNSDFDSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKNN----VFQALVEFESVNSAQHAKAALNGA  157 (481)
T ss_pred             cCCCCcccCCCCCceEEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecCC----ceEEEEEECCHHHHHHHHHHhcCC
Confidence             00    001112234799999999999999999999999999999877542    369999999999999999999999


Q ss_pred             eeCC--eEEEEEEecCc
Q 030819          143 FLDG--RVIFVEIAKSR  157 (171)
Q Consensus       143 ~i~g--~~i~v~~~~~~  157 (171)
                      .|.+  ..|+|.|++..
T Consensus       158 ~i~~~~~~l~v~~sk~~  174 (481)
T TIGR01649       158 DIYNGCCTLKIEYAKPT  174 (481)
T ss_pred             cccCCceEEEEEEecCC
Confidence            9965  58999998753

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

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

Probab=99.59  E-value=1.4e-14  Score=107.85  Aligned_cols=89  Identities=29%  Similarity=0.491  Sum_probs=83.2

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ..+..+.|.|.=||.++|+++++.+|...|+|++|++++|+-+|++.|||||.|.++++|++|+..|||..+..+.|+|.
T Consensus        37 t~~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVS  116 (360)
T KOG0145|consen   37 TDESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVS  116 (360)
T ss_pred             cCcccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEE
Confidence            45566789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EecCcHHHH
Q 030819          153 IAKSRAELR  161 (171)
Q Consensus       153 ~~~~~~~~~  161 (171)
                      ++++....-
T Consensus       117 yARPSs~~I  125 (360)
T KOG0145|consen  117 YARPSSDSI  125 (360)
T ss_pred             eccCChhhh
Confidence            999876543

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

Probab=99.58  E-value=2.9e-14  Score=92.15  Aligned_cols=86  Identities=19%  Similarity=0.393  Sum_probs=76.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ++..++.|||.|||+++|.++..++|.+||.|..+++-..++   .+|-|||.|++..+|.+|+++|+|..++++.+.|-
T Consensus        14 ppevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~---TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vl   90 (124)
T KOG0114|consen   14 PPEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKE---TRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVL   90 (124)
T ss_pred             ChhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCccC---cCceEEEEehHhhhHHHHHHHhcccccCCceEEEE
Confidence            445678999999999999999999999999999999976554   46999999999999999999999999999999999


Q ss_pred             EecCcHHHH
Q 030819          153 IAKSRAELR  161 (171)
Q Consensus       153 ~~~~~~~~~  161 (171)
                      +-.+....+
T Consensus        91 yyq~~~~~~   99 (124)
T KOG0114|consen   91 YYQPEDAFK   99 (124)
T ss_pred             ecCHHHHHH
Confidence            887665544

>smart00360 RRM RNA recognition motif

Probab=99.58  E-value=1.8e-14  Score=87.62  Aligned_cols=71  Identities=39%  Similarity=0.709  Sum_probs=66.7

Q ss_pred             EcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           82 VSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        82 V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      |+|||..+++++|+++|..||.|..+.+..++.++.++|+|||+|.+.++|.+|+..+++..+.|+.|+|.
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            57999999999999999999999999999888779999999999999999999999999999999998873

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

Probab=99.57  E-value=5.3e-14  Score=106.70  Aligned_cols=79  Identities=39%  Similarity=0.724  Sum_probs=76.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 030819           77 KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAK  155 (171)
Q Consensus        77 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~  155 (171)
                      ..+|||+|||.++++++|.++|..||.|..+.+..++.+|.++|||||+|.+.+++..|++.++|..+.|+.|.|.++.
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~  193 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQ  193 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeeccc
Confidence            6999999999999999999999999999999999998899999999999999999999999999999999999999965

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

Probab=99.55  E-value=6.9e-14  Score=115.83  Aligned_cols=79  Identities=27%  Similarity=0.357  Sum_probs=72.6

Q ss_pred             CCCCCeEEEcCCCC-CCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           74 CQPKTRLFVSGLSF-RTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        74 ~~~~~~l~V~nl~~-~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      .+++.+|||+||++ .+++++|+++|+.||.|..++++.++     +|+|||+|.+.++|..|+..|||..+.|+.|+|.
T Consensus       272 ~~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~-----~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~  346 (481)
T TIGR01649       272 GGPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNK-----KETALIEMADPYQAQLALTHLNGVKLFGKPLRVC  346 (481)
T ss_pred             CCCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEE
Confidence            45678999999998 69999999999999999999998764     4899999999999999999999999999999999


Q ss_pred             EecCc
Q 030819          153 IAKSR  157 (171)
Q Consensus       153 ~~~~~  157 (171)
                      +++.+
T Consensus       347 ~s~~~  351 (481)
T TIGR01649       347 PSKQQ  351 (481)
T ss_pred             Ecccc
Confidence            98654

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).

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

Probab=99.54  E-value=6.5e-15  Score=118.93  Aligned_cols=80  Identities=38%  Similarity=0.719  Sum_probs=75.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEecCc
Q 030819           78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKSR  157 (171)
Q Consensus        78 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~~~  157 (171)
                      ..||||||++++++++|+.+|+.||.|..+.+..|.++|.++|||||+|.+.++|.+|++.|||..|.|+.|+|.....+
T Consensus       279 ~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r  358 (549)
T KOG0147|consen  279 RRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTER  358 (549)
T ss_pred             hhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeeee
Confidence            34899999999999999999999999999999999999999999999999999999999999999999999999876543

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

Probab=99.54  E-value=1.4e-14  Score=102.43  Aligned_cols=82  Identities=28%  Similarity=0.428  Sum_probs=78.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 030819           74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEI  153 (171)
Q Consensus        74 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~  153 (171)
                      .....+|||+||+..++++.|.++|-+.|+|..+.+.+|+.+...+||||++|.++|+|+-|+..||..++.|++|+|..
T Consensus         6 rnqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~k   85 (203)
T KOG0131|consen    6 RNQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNK   85 (203)
T ss_pred             cCCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEe
Confidence            34567999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             ec
Q 030819          154 AK  155 (171)
Q Consensus       154 ~~  155 (171)
                      +.
T Consensus        86 as   87 (203)
T KOG0131|consen   86 AS   87 (203)
T ss_pred             cc
Confidence            76

>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=99.53  E-value=1.8e-13  Score=83.88  Aligned_cols=74  Identities=39%  Similarity=0.722  Sum_probs=68.4

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 030819           79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEI  153 (171)
Q Consensus        79 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~  153 (171)
                      +|+|+|||..+++++|+++|+.+|.|..+.+..++ .+..+|+|||+|.+.++|..|+..+++..+.|+.+.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~-~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDK-DTKSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            48999999999999999999999999999999877 347789999999999999999999999999999998864

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).

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

Probab=99.51  E-value=4.1e-14  Score=112.97  Aligned_cols=140  Identities=19%  Similarity=0.399  Sum_probs=110.5

Q ss_pred             eeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCCCCCCC-------------
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPSPHSL-------------   71 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------------   71 (171)
                      +-+|||   .+.++..+.+.|+..++.         .+...-.+. +  +=+++++.+..+..+..+             
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v---------~s~rvc~d~-t--slgy~yvnf~~~~da~~A~~~~n~~~~~~~~   66 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPV---------LSIRVCRDA-T--SLGYAYVNFQQPADAERALDTMNFDVLKGKP   66 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCc---------eeEEEeecC-C--ccceEEEecCCHHHHHHHHHHcCCcccCCcE
Confidence            458899   889999999999998888         333333333 2  445666666555432221             


Q ss_pred             ----CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCe
Q 030819           72 ----STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGR  147 (171)
Q Consensus        72 ----~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~  147 (171)
                          ....+...+||-||+++++..+|.++|+.||.|.+|++..+. .| ++|| ||+|.++++|++|++.+||..+.|+
T Consensus        67 ~rim~s~rd~~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~-~g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~k  143 (369)
T KOG0123|consen   67 IRIMWSQRDPSLVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDE-NG-SKGY-FVQFESEESAKKAIEKLNGMLLNGK  143 (369)
T ss_pred             EEeehhccCCceeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcC-CC-ceee-EEEeCCHHHHHHHHHHhcCcccCCC
Confidence                122333449999999999999999999999999999999998 66 8999 9999999999999999999999999


Q ss_pred             EEEEEEecCcHHHHH
Q 030819          148 VIFVEIAKSRAELRQ  162 (171)
Q Consensus       148 ~i~v~~~~~~~~~~~  162 (171)
                      +|-|.....+.++..
T Consensus       144 ki~vg~~~~~~er~~  158 (369)
T KOG0123|consen  144 KIYVGLFERKEEREA  158 (369)
T ss_pred             eeEEeeccchhhhcc
Confidence            999998877766543

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

Probab=99.50  E-value=3.6e-14  Score=118.13  Aligned_cols=83  Identities=20%  Similarity=0.410  Sum_probs=68.9

Q ss_pred             CCCCeEEEcCCCCCC----------CHHHHHHHHhcCCCeEEEEEeecC---CCCCcceEEEEEeCCHHHHHHHHHHhCC
Q 030819           75 QPKTRLFVSGLSFRT----------SEDSLRNAFQGFGQLVEVNLVMDK---IANRPRGFAFLRYATEEESRRAIEGMHG  141 (171)
Q Consensus        75 ~~~~~l~V~nl~~~~----------~~~~l~~~f~~~G~i~~~~~~~~~---~~g~~~g~~fv~f~~~~~a~~al~~l~g  141 (171)
                      .+..+|+|.|+...-          ..++|++.|++||.|..|.|..+.   .++..+|++||+|.+.++|++|+..|||
T Consensus       407 ~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnG  486 (509)
T TIGR01642       407 KPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNG  486 (509)
T ss_pred             CCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEeeccCcCCCcCCCcceEEEEECCHHHHHHHHHHcCC
Confidence            356789999986421          125789999999999999998652   3456789999999999999999999999


Q ss_pred             ceeCCeEEEEEEecCc
Q 030819          142 KFLDGRVIFVEIAKSR  157 (171)
Q Consensus       142 ~~i~g~~i~v~~~~~~  157 (171)
                      ..++|+.|.|.|....
T Consensus       487 r~~~gr~v~~~~~~~~  502 (509)
T TIGR01642       487 RKFNDRVVVAAFYGED  502 (509)
T ss_pred             CEECCeEEEEEEeCHH
Confidence            9999999999987643

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

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

Probab=99.47  E-value=1.4e-13  Score=97.71  Aligned_cols=80  Identities=25%  Similarity=0.445  Sum_probs=71.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 030819           75 QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIA  154 (171)
Q Consensus        75 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~  154 (171)
                      ...++|||+|||.++.+.+|+++|.+||.|.+|.+...+   ..-+||||+|++..+|+.|+..-+|..++|..|+|+++
T Consensus         4 r~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~---g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfp   80 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRP---GPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFP   80 (241)
T ss_pred             cccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCC---CCCCeeEEEecCccchhhhhhcccccccCcceEEEEec
Confidence            346899999999999999999999999999999886543   23479999999999999999999999999999999998


Q ss_pred             cCc
Q 030819          155 KSR  157 (171)
Q Consensus       155 ~~~  157 (171)
                      +.-
T Consensus        81 rgg   83 (241)
T KOG0105|consen   81 RGG   83 (241)
T ss_pred             cCC
Confidence            754

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

Probab=99.46  E-value=4.8e-14  Score=109.34  Aligned_cols=77  Identities=36%  Similarity=0.682  Sum_probs=74.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 030819           78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIA  154 (171)
Q Consensus        78 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~  154 (171)
                      +.||||.+++++.|+.|+..|..||+|+++.+-+|+-|++++||+||+|+-+|.|+-|++.+||..++|+.|+|...
T Consensus       114 cRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrP  190 (544)
T KOG0124|consen  114 CRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRP  190 (544)
T ss_pred             HheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCC
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999743

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

Probab=99.46  E-value=6e-13  Score=105.34  Aligned_cols=82  Identities=18%  Similarity=0.419  Sum_probs=75.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHh-cCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           74 CQPKTRLFVSGLSFRTSEDSLRNAFQ-GFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        74 ~~~~~~l~V~nl~~~~~~~~l~~~f~-~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ....+.+||+|||++..|.+|+++|. +.|+|..|.+..|. +|+++|||.|+|+++|.+++|++.||-..+.|++|.|.
T Consensus        41 ~~r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~-~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vK  119 (608)
T KOG4212|consen   41 AARDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDE-SGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVK  119 (608)
T ss_pred             ccccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeeccc-CCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEe
Confidence            34456799999999999999999997 68999999999998 99999999999999999999999999999999999998


Q ss_pred             EecC
Q 030819          153 IAKS  156 (171)
Q Consensus       153 ~~~~  156 (171)
                      ....
T Consensus       120 Ed~d  123 (608)
T KOG4212|consen  120 EDHD  123 (608)
T ss_pred             ccCc
Confidence            7764

>smart00361 RRM_1 RNA recognition motif

Probab=99.45  E-value=6.4e-13  Score=82.00  Aligned_cols=61  Identities=26%  Similarity=0.679  Sum_probs=55.5

Q ss_pred             HHHHHHHHh----cCCCeEEEE-EeecCCC--CCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 030819           91 EDSLRNAFQ----GFGQLVEVN-LVMDKIA--NRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFV  151 (171)
Q Consensus        91 ~~~l~~~f~----~~G~i~~~~-~~~~~~~--g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v  151 (171)
                      +++|+++|.    +||.|.++. +..++.+  +.++|+|||.|.+.++|.+|+..|||..+.|+.|++
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence            578899998    999999995 7777666  899999999999999999999999999999999876

>PF13893 RRM_5: RNA recognition motif

Probab=99.44  E-value=1.2e-12  Score=77.09  Aligned_cols=56  Identities=36%  Similarity=0.717  Sum_probs=50.5

Q ss_pred             HHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 030819           94 LRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIA  154 (171)
Q Consensus        94 l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~  154 (171)
                      |.++|++||.|.++.+..+.     +++|||+|.+.++|..|+..|||..+.|++|+|.|+
T Consensus         1 L~~~f~~fG~V~~i~~~~~~-----~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK-----RGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS-----TTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            67899999999999886543     589999999999999999999999999999999986

(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 ....

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

Probab=99.42  E-value=3.4e-13  Score=109.19  Aligned_cols=85  Identities=32%  Similarity=0.525  Sum_probs=80.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 030819           76 PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAK  155 (171)
Q Consensus        76 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~  155 (171)
                      .+.||||++||+.++.++|.++|+.+|+|..+.++.++.++.++|||||.|...+++++|+..+.+..+.|+.|.|..++
T Consensus         4 ~g~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A~   83 (678)
T KOG0127|consen    4 SGATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDPAK   83 (678)
T ss_pred             CCceEEEecCCCccchhHHHHhhhcccCcceeEEecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceeccccccc
Confidence            34899999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CcHHH
Q 030819          156 SRAEL  160 (171)
Q Consensus       156 ~~~~~  160 (171)
                      .+...
T Consensus        84 ~R~r~   88 (678)
T KOG0127|consen   84 KRARS   88 (678)
T ss_pred             ccccc
Confidence            66543

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

Probab=99.42  E-value=1.5e-13  Score=103.67  Aligned_cols=142  Identities=18%  Similarity=0.264  Sum_probs=99.9

Q ss_pred             eeeeeecCceeecccchhhcccCCcCCCCCCCCcc-------ccccccc--cccccccCCCCCCCCCCCCCCCCCCCCCC
Q 030819            3 VLGFLPVPTTYFNINQNLLIHNLTRHSPAPATPFT-------IKRRDFD--SLFSLRQGRGRGACFPLACLPPSPHSLST   73 (171)
Q Consensus         3 ~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   73 (171)
                      |..+|||||+.-+.+.+.+..-|+..+.+-..-.-       ++.....  .+.+.  ..-+--+......    .+...
T Consensus         1 ~~~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKNYgFVHiEdktaaedairNL--hgYtLhg~nInVe----aSksK   74 (346)
T KOG0109|consen    1 MPVKLFIGNLPREATEQELRSLFEQYGKVLECDIVKNYGFVHIEDKTAAEDAIRNL--HGYTLHGVNINVE----ASKSK   74 (346)
T ss_pred             CccchhccCCCcccchHHHHHHHHhhCceEeeeeecccceEEeecccccHHHHhhc--ccceecceEEEEE----ecccc
Confidence            45689999999999999998888887777221110       0000000  00000  0000000000000    00112


Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 030819           74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEI  153 (171)
Q Consensus        74 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~  153 (171)
                      ....++++|+||.+.++..+|+..|++||.+.+|++++        +|+||.|.-.++|..|+..|++..+.|++++|..
T Consensus        75 sk~stkl~vgNis~tctn~ElRa~fe~ygpviecdivk--------dy~fvh~d~~eda~~air~l~~~~~~gk~m~vq~  146 (346)
T KOG0109|consen   75 SKASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVK--------DYAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQL  146 (346)
T ss_pred             CCCccccccCCCCccccCHHHhhhhcccCCceeeeeec--------ceeEEEEeeccchHHHHhcccccccccceeeeee
Confidence            44678999999999999999999999999999999986        5999999999999999999999999999999999


Q ss_pred             ecCcH
Q 030819          154 AKSRA  158 (171)
Q Consensus       154 ~~~~~  158 (171)
                      +.++.
T Consensus       147 stsrl  151 (346)
T KOG0109|consen  147 STSRL  151 (346)
T ss_pred             ecccc
Confidence            87664

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

Probab=99.41  E-value=1.7e-13  Score=102.47  Aligned_cols=89  Identities=19%  Similarity=0.382  Sum_probs=84.3

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 030819           72 STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFV  151 (171)
Q Consensus        72 ~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v  151 (171)
                      ...++++.|||-.||.+..+.+|..+|-.||.|.+.++..|+.|..+|.||||.|.+..+++.||..|||..|.-++|+|
T Consensus       280 reGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKV  359 (371)
T KOG0146|consen  280 REGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKV  359 (371)
T ss_pred             hcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhh
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEecCcHHH
Q 030819          152 EIAKSRAEL  160 (171)
Q Consensus       152 ~~~~~~~~~  160 (171)
                      ...+++...
T Consensus       360 QLKRPkdan  368 (371)
T KOG0146|consen  360 QLKRPKDAN  368 (371)
T ss_pred             hhcCccccC
Confidence            999888653

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

Probab=99.41  E-value=3.7e-13  Score=101.52  Aligned_cols=72  Identities=31%  Similarity=0.601  Sum_probs=68.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEecCc
Q 030819           78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKSR  157 (171)
Q Consensus        78 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~~~  157 (171)
                      .+|||||||.++++.+|+.+|++||.|.+|+|+++        ||||..++...++.|+..|||.+|+|..|.|+-++++
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN--------YgFVHiEdktaaedairNLhgYtLhg~nInVeaSksK   74 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVKN--------YGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSK   74 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeecc--------cceEEeecccccHHHHhhcccceecceEEEEEecccc
Confidence            47999999999999999999999999999999875        8999999999999999999999999999999998877

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

Probab=99.39  E-value=1.3e-12  Score=97.71  Aligned_cols=90  Identities=27%  Similarity=0.452  Sum_probs=79.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee-C--CeEEE
Q 030819           74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFL-D--GRVIF  150 (171)
Q Consensus        74 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i-~--g~~i~  150 (171)
                      ..+.++||||-|.+.-+|+|++.+|..||.|.+|.+.+.. .|.+|||+||.|.+..+|+.||..|||... -  ...|.
T Consensus        16 g~~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~-dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLV   94 (371)
T KOG0146|consen   16 GGDDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGP-DGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLV   94 (371)
T ss_pred             CccchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCC-CCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceE
Confidence            3467899999999999999999999999999999999988 799999999999999999999999999864 3  35799


Q ss_pred             EEEecCcHHHHHhh
Q 030819          151 VEIAKSRAELRQAF  164 (171)
Q Consensus       151 v~~~~~~~~~~~~~  164 (171)
                      |.++...+++.-++
T Consensus        95 VK~ADTdkER~lRR  108 (371)
T KOG0146|consen   95 VKFADTDKERTLRR  108 (371)
T ss_pred             EEeccchHHHHHHH
Confidence            99998776665433

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

Probab=99.38  E-value=1.1e-12  Score=101.48  Aligned_cols=88  Identities=25%  Similarity=0.462  Sum_probs=82.2

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 030819           72 STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFV  151 (171)
Q Consensus        72 ~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v  151 (171)
                      ...++...|||-.|.+.+++++|.-+|+.||.|..|.+++|..||.+..||||+|.+.+++++|.-.|.+..|+.++|+|
T Consensus       234 d~~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHV  313 (479)
T KOG0415|consen  234 DVKPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHV  313 (479)
T ss_pred             ccCCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEe
Confidence            45677889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEecCcHH
Q 030819          152 EIAKSRAE  159 (171)
Q Consensus       152 ~~~~~~~~  159 (171)
                      .++.+-..
T Consensus       314 DFSQSVsk  321 (479)
T KOG0415|consen  314 DFSQSVSK  321 (479)
T ss_pred             ehhhhhhh
Confidence            99875443

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

Probab=99.35  E-value=6.4e-12  Score=105.29  Aligned_cols=79  Identities=20%  Similarity=0.424  Sum_probs=73.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 030819           76 PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAK  155 (171)
Q Consensus        76 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~  155 (171)
                      -++|||||+|+.++++.+|..+|+.||+|.+|.++..+      |||||.+....+|++|+.+|....+.++.|+|.|+.
T Consensus       420 ~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~R------~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~  493 (894)
T KOG0132|consen  420 CSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPPR------GCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAV  493 (894)
T ss_pred             eeeeeeeccccchhhHHHHHHHHHhcccceeEeeccCC------ceeEEEEeehhHHHHHHHHHhcccccceeeEEeeec
Confidence            36799999999999999999999999999999998765      899999999999999999999999999999999998


Q ss_pred             CcHHH
Q 030819          156 SRAEL  160 (171)
Q Consensus       156 ~~~~~  160 (171)
                      .+.-+
T Consensus       494 g~G~k  498 (894)
T KOG0132|consen  494 GKGPK  498 (894)
T ss_pred             cCCcc
Confidence            76543

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

Probab=99.33  E-value=5.7e-12  Score=92.14  Aligned_cols=85  Identities=22%  Similarity=0.487  Sum_probs=76.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHH----HHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q 030819           75 QPKTRLFVSGLSFRTSEDSLRN----AFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIF  150 (171)
Q Consensus        75 ~~~~~l~V~nl~~~~~~~~l~~----~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~  150 (171)
                      .+..||||.||+..+..++|++    +|++||.|.+|....   +.+.+|-|||.|.+.+.|-.|+..|+|..+.|+.++
T Consensus         7 ~pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~k---t~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mr   83 (221)
T KOG4206|consen    7 NPNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFK---TPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMR   83 (221)
T ss_pred             CCCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecC---CCCccCceEEEecChhHHHHHHHHhcCCcccCchhh
Confidence            3445999999999999999988    999999999987753   788999999999999999999999999999999999


Q ss_pred             EEEecCcHHHHH
Q 030819          151 VEIAKSRAELRQ  162 (171)
Q Consensus       151 v~~~~~~~~~~~  162 (171)
                      |++|+.....-.
T Consensus        84 iqyA~s~sdii~   95 (221)
T KOG4206|consen   84 IQYAKSDSDIIA   95 (221)
T ss_pred             eecccCccchhh
Confidence            999997765543

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

Probab=99.31  E-value=7.7e-13  Score=109.79  Aligned_cols=151  Identities=23%  Similarity=0.326  Sum_probs=108.6

Q ss_pred             eeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCCCC-----------------
Q 030819            6 FLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPSP-----------------   68 (171)
Q Consensus         6 ~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----------------   68 (171)
                      .+||-|+.|+-++..+...|...+.+-.......+....      ...+.|++++.+..+.++                 
T Consensus       517 ~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~------k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l  590 (725)
T KOG0110|consen  517 KLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPAN------KYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKL  590 (725)
T ss_pred             hhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccc------cccccceeEEEecCHHHHHHHHHHhcCceecCceE
Confidence            388889999988888888877755542111110000000      112224444444333310                 


Q ss_pred             --------------CCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHH
Q 030819           69 --------------HSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR  134 (171)
Q Consensus        69 --------------~~~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~  134 (171)
                                    .........+.|+|.|||+..+-.+++.+|..||.+.+++++.....+.++|||||+|-++.+|.+
T Consensus       591 ~lk~S~~k~~~~~gK~~~~kk~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~n  670 (725)
T KOG0110|consen  591 ELKISENKPASTVGKKKSKKKKGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKN  670 (725)
T ss_pred             EEEeccCccccccccccccccccceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHH
Confidence                          111222335799999999999999999999999999999998876678889999999999999999


Q ss_pred             HHHHhCCceeCCeEEEEEEecCcHHHHH
Q 030819          135 AIEGMHGKFLDGRVIFVEIAKSRAELRQ  162 (171)
Q Consensus       135 al~~l~g~~i~g~~i~v~~~~~~~~~~~  162 (171)
                      |+.+|.+..+.|+.|.++|++.-..+..
T Consensus       671 A~~al~STHlyGRrLVLEwA~~d~~~e~  698 (725)
T KOG0110|consen  671 AFDALGSTHLYGRRLVLEWAKSDNTMEA  698 (725)
T ss_pred             HHHhhcccceechhhheehhccchHHHH
Confidence            9999998999999999999987655443

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

Probab=99.26  E-value=3.6e-11  Score=86.85  Aligned_cols=86  Identities=20%  Similarity=0.354  Sum_probs=78.2

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcC-CCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q 030819           72 STCQPKTRLFVSGLSFRTSEDSLRNAFQGF-GQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIF  150 (171)
Q Consensus        72 ~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~-G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~  150 (171)
                      +......-+||..+|..+.+.++..+|.+| |.+..+++-+++.||.++|||||+|.+.+.|.-|.+.||+..++++-|.
T Consensus        44 p~~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~  123 (214)
T KOG4208|consen   44 PEQEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLE  123 (214)
T ss_pred             CccCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheee
Confidence            344556789999999999999999999988 7788889989999999999999999999999999999999999999999


Q ss_pred             EEEecCc
Q 030819          151 VEIAKSR  157 (171)
Q Consensus       151 v~~~~~~  157 (171)
                      |.+-.+.
T Consensus       124 c~vmppe  130 (214)
T KOG4208|consen  124 CHVMPPE  130 (214)
T ss_pred             eEEeCch
Confidence            9887765

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

Probab=99.25  E-value=4.8e-11  Score=92.11  Aligned_cols=79  Identities=22%  Similarity=0.447  Sum_probs=70.2

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCc-eeCCeEEE
Q 030819           72 STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGK-FLDGRVIF  150 (171)
Q Consensus        72 ~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~-~i~g~~i~  150 (171)
                      +.+....+|||++|...+++.+|+++|.+||+|.++++...+      ++|||+|.+.++|+.|.+.+-.. .|+|.+|+
T Consensus       223 PeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~~------~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~  296 (377)
T KOG0153|consen  223 PEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPRK------GCAFVTFTTREAAEKAAEKSFNKLVINGFRLK  296 (377)
T ss_pred             CcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeeccc------ccceeeehhhHHHHHHHHhhcceeeecceEEE
Confidence            445567899999999999999999999999999999988765      79999999999999998876554 57999999


Q ss_pred             EEEecC
Q 030819          151 VEIAKS  156 (171)
Q Consensus       151 v~~~~~  156 (171)
                      |.|+++
T Consensus       297 i~Wg~~  302 (377)
T KOG0153|consen  297 IKWGRP  302 (377)
T ss_pred             EEeCCC
Confidence            999998

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

Probab=99.19  E-value=1.9e-11  Score=95.04  Aligned_cols=85  Identities=34%  Similarity=0.584  Sum_probs=77.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 030819           76 PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAK  155 (171)
Q Consensus        76 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~  155 (171)
                      +.+++||++|+++++++.|++.|.+||+|.+|.+++|+.++.++||+||+|.+.+.+.++|.. .-+.|.|+.|.+..+.
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~-~~h~~dgr~ve~k~av   83 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNA-RTHKLDGRSVEPKRAV   83 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecc-cccccCCccccceecc
Confidence            678999999999999999999999999999999999999999999999999999999998873 4477899999999888


Q ss_pred             CcHHHH
Q 030819          156 SRAELR  161 (171)
Q Consensus       156 ~~~~~~  161 (171)
                      ++....
T Consensus        84 ~r~~~~   89 (311)
T KOG4205|consen   84 SREDQT   89 (311)
T ss_pred             Cccccc
Confidence            876553

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

Probab=99.15  E-value=1.6e-10  Score=92.55  Aligned_cols=74  Identities=20%  Similarity=0.415  Sum_probs=69.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEecCc
Q 030819           78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKSR  157 (171)
Q Consensus        78 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~~~  157 (171)
                      ..||||   +++++.+|.+.|+.+|++.++++.+|. +  +.|||||.|.++++|++||..+|...+.|++|++.|+...
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~-t--slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd   75 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDA-T--SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRD   75 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecC-C--ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccC
Confidence            468999   899999999999999999999999998 6  9999999999999999999999999999999999998643

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

Probab=99.08  E-value=3.2e-10  Score=90.12  Aligned_cols=77  Identities=25%  Similarity=0.469  Sum_probs=69.3

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      .....++|||.|||.+.||..|++-|..||.|....++.   .|+++|  .|.|.++++|++|+..|+|..++|+.|+|.
T Consensus       532 aarKa~qIiirNlP~dfTWqmlrDKfre~G~v~yadime---~GkskG--VVrF~s~edAEra~a~Mngs~l~Gr~I~V~  606 (608)
T KOG4212|consen  532 AARKACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIME---NGKSKG--VVRFFSPEDAERACALMNGSRLDGRNIKVT  606 (608)
T ss_pred             ccccccEEEEecCCccccHHHHHHHHHhccceehhhhhc---cCCccc--eEEecCHHHHHHHHHHhccCcccCceeeee
Confidence            345568899999999999999999999999999988842   688877  899999999999999999999999999998


Q ss_pred             Ee
Q 030819          153 IA  154 (171)
Q Consensus       153 ~~  154 (171)
                      +.
T Consensus       607 y~  608 (608)
T KOG4212|consen  607 YF  608 (608)
T ss_pred             eC
Confidence            73

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

Probab=99.07  E-value=1.5e-09  Score=79.51  Aligned_cols=91  Identities=22%  Similarity=0.299  Sum_probs=73.3

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEee-cCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee---CCe
Q 030819           72 STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVM-DKIANRPRGFAFLRYATEEESRRAIEGMHGKFL---DGR  147 (171)
Q Consensus        72 ~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~-~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i---~g~  147 (171)
                      ...+.-+||||.+||-++...+|..+|..|-.-+.+.+.. ++...-++-+||+.|.+...|.+|+..|||..+   .+.
T Consensus        29 ~~~~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~s  108 (284)
T KOG1457|consen   29 DEPGAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGS  108 (284)
T ss_pred             ccccccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCc
Confidence            3455578999999999999999999999986666555543 222223567999999999999999999999998   477


Q ss_pred             EEEEEEecCcHHHHH
Q 030819          148 VIFVEIAKSRAELRQ  162 (171)
Q Consensus       148 ~i~v~~~~~~~~~~~  162 (171)
                      .|+++++++..++.+
T Consensus       109 tLhiElAKSNtK~kr  123 (284)
T KOG1457|consen  109 TLHIELAKSNTKRKR  123 (284)
T ss_pred             eeEeeehhcCccccc
Confidence            899999998776543

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

Probab=99.06  E-value=5.2e-10  Score=91.56  Aligned_cols=82  Identities=34%  Similarity=0.523  Sum_probs=76.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 030819           76 PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAK  155 (171)
Q Consensus        76 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~  155 (171)
                      -++.|||.+|+..+...+|+.+|.+||.|.-..++.+..+.-.+.||||++.+.++|.+||+.||...|.|+.|.|+.++
T Consensus       404 ~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaK  483 (940)
T KOG4661|consen  404 LGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAK  483 (940)
T ss_pred             cccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeecc
Confidence            35789999999999999999999999999999999988888888999999999999999999999999999999999887


Q ss_pred             Cc
Q 030819          156 SR  157 (171)
Q Consensus       156 ~~  157 (171)
                      ..
T Consensus       484 NE  485 (940)
T KOG4661|consen  484 NE  485 (940)
T ss_pred             cC
Confidence            54

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

Probab=99.05  E-value=1.3e-09  Score=81.99  Aligned_cols=83  Identities=30%  Similarity=0.500  Sum_probs=75.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 030819           75 QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIA  154 (171)
Q Consensus        75 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~  154 (171)
                      ....+|+|.|||+.+.++||+++|..||.+..+.+-.++ .|.+.|.|-|.|...++|.+|++.+||..++|..|++...
T Consensus        81 ~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~-~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i  159 (243)
T KOG0533|consen   81 TRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDR-AGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEII  159 (243)
T ss_pred             CCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCC-CCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEe
Confidence            344789999999999999999999999999999998888 9999999999999999999999999999999999999876


Q ss_pred             cCcH
Q 030819          155 KSRA  158 (171)
Q Consensus       155 ~~~~  158 (171)
                      .+..
T Consensus       160 ~~~~  163 (243)
T KOG0533|consen  160 SSPS  163 (243)
T ss_pred             cCcc
Confidence            5443

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

Probab=99.05  E-value=1.8e-10  Score=85.64  Aligned_cols=86  Identities=22%  Similarity=0.431  Sum_probs=78.4

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q 030819           71 LSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIF  150 (171)
Q Consensus        71 ~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~  150 (171)
                      .........||+|.|.-+++++.|...|.+|-.....++++|+.+|+++||+||.|.+..++.+|+..++|..++.++|+
T Consensus       184 ~ew~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpik  263 (290)
T KOG0226|consen  184 AEWDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIK  263 (290)
T ss_pred             ccCccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhH
Confidence            34566788999999999999999999999998888889999999999999999999999999999999999999999998


Q ss_pred             EEEecC
Q 030819          151 VEIAKS  156 (171)
Q Consensus       151 v~~~~~  156 (171)
                      ++-+..
T Consensus       264 lRkS~w  269 (290)
T KOG0226|consen  264 LRKSEW  269 (290)
T ss_pred             hhhhhH
Confidence            865443

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

Probab=99.02  E-value=1.2e-09  Score=91.25  Aligned_cols=77  Identities=27%  Similarity=0.563  Sum_probs=69.6

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCC---CcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 030819           79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIAN---RPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAK  155 (171)
Q Consensus        79 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g---~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~  155 (171)
                      +|||.||+++++.++|...|...|.|..+.|...++..   .+.|||||+|.+.++|++|+..|+|..|.|+.|.|.++.
T Consensus       517 ~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~  596 (725)
T KOG0110|consen  517 KLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISE  596 (725)
T ss_pred             hhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEecc
Confidence            49999999999999999999999999999887665321   245999999999999999999999999999999999987

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

Probab=98.99  E-value=5.3e-10  Score=91.00  Aligned_cols=75  Identities=21%  Similarity=0.378  Sum_probs=67.2

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q 030819           71 LSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIF  150 (171)
Q Consensus        71 ~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~  150 (171)
                      .....+..+|+|.|||..+++++|.++|+.||+|..++..     -..+|..||+|.|..+|++|+++|++..+.|+.|+
T Consensus        69 ~~~~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t-----~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   69 SEKDMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRET-----PNKRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             CcccCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcc-----cccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            3445678899999999999999999999999999997664     34468999999999999999999999999999888

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

Probab=98.96  E-value=7.5e-09  Score=80.13  Aligned_cols=82  Identities=27%  Similarity=0.364  Sum_probs=74.2

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEE--------EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVE--------VNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFL  144 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~--------~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i  144 (171)
                      ....++.|||.|||.++|-+++.++|+++|-|..        |.+.++. .|+.+|=|++.|.-.+++.-|+..|++..+
T Consensus       130 ~~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~-~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~  208 (382)
T KOG1548|consen  130 EPKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDN-QGKLKGDALCCYIKRESVELAIKILDEDEL  208 (382)
T ss_pred             ccccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecC-CCCccCceEEEeecccHHHHHHHHhCcccc
Confidence            3455678999999999999999999999998753        6788887 699999999999999999999999999999


Q ss_pred             CCeEEEEEEec
Q 030819          145 DGRVIFVEIAK  155 (171)
Q Consensus       145 ~g~~i~v~~~~  155 (171)
                      .|+.|+|+.|+
T Consensus       209 rg~~~rVerAk  219 (382)
T KOG1548|consen  209 RGKKLRVERAK  219 (382)
T ss_pred             cCcEEEEehhh
Confidence            99999998875

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

Probab=98.92  E-value=3.8e-09  Score=85.25  Aligned_cols=82  Identities=21%  Similarity=0.331  Sum_probs=69.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 030819           76 PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAK  155 (171)
Q Consensus        76 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~  155 (171)
                      ...+|||.|||.+++.++|+++|..||.|+...|....-.++..+||||+|.+.++++.||.+ +-..+++++|.|+..+
T Consensus       287 ~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek~  365 (419)
T KOG0116|consen  287 DGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEKR  365 (419)
T ss_pred             cccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEecc
Confidence            345699999999999999999999999999987765442345448999999999999999995 4567899999999887


Q ss_pred             CcH
Q 030819          156 SRA  158 (171)
Q Consensus       156 ~~~  158 (171)
                      +..
T Consensus       366 ~~~  368 (419)
T KOG0116|consen  366 PGF  368 (419)
T ss_pred             ccc
Confidence            643

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

Probab=98.90  E-value=8.9e-09  Score=86.13  Aligned_cols=84  Identities=21%  Similarity=0.373  Sum_probs=74.1

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCC---CCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeE
Q 030819           72 STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKI---ANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRV  148 (171)
Q Consensus        72 ~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~---~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~  148 (171)
                      ...+..+.+||+||++.+++++|...|..||+|..+++++.+.   ....+-||||.|-+..++++|+..|+|..+.+..
T Consensus       169 dgDP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e  248 (877)
T KOG0151|consen  169 DGDPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYE  248 (877)
T ss_pred             CCCCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeee
Confidence            3456678999999999999999999999999999999987652   2334569999999999999999999999999999


Q ss_pred             EEEEEec
Q 030819          149 IFVEIAK  155 (171)
Q Consensus       149 i~v~~~~  155 (171)
                      +++-|++
T Consensus       249 ~K~gWgk  255 (877)
T KOG0151|consen  249 MKLGWGK  255 (877)
T ss_pred             eeecccc
Confidence            9999985

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

Probab=98.87  E-value=4.9e-09  Score=78.77  Aligned_cols=84  Identities=20%  Similarity=0.407  Sum_probs=77.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ...+...+||+|+.+.++.+++...|+.||.|..+.+..|+..|.++||+||+|.+.+.++.|+. |+|..+.|..+.|.
T Consensus        97 ~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt  175 (231)
T KOG4209|consen   97 KEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVT  175 (231)
T ss_pred             hccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceee
Confidence            44567899999999999999999999999999999999999889999999999999999999999 99999999999998


Q ss_pred             EecCc
Q 030819          153 IAKSR  157 (171)
Q Consensus       153 ~~~~~  157 (171)
                      +.+-+
T Consensus       176 ~~r~~  180 (231)
T KOG4209|consen  176 LKRTN  180 (231)
T ss_pred             eeeee
Confidence            87643

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

Probab=98.86  E-value=2.6e-09  Score=78.78  Aligned_cols=71  Identities=25%  Similarity=0.618  Sum_probs=65.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 030819           78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKS  156 (171)
Q Consensus        78 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~~  156 (171)
                      ..+||++||+.+.+.+|..+|..||.+-++.+..        ||+||+|.+..+|..|+..||+..+.|..+.|++++.
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk~--------gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~   72 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMKN--------GFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARG   72 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceeec--------ccceeccCchhhhhcccchhcCceecceeeeeecccc
Confidence            3689999999999999999999999999988743        7999999999999999999999999999999999884

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

Probab=98.84  E-value=1.5e-08  Score=72.37  Aligned_cols=64  Identities=20%  Similarity=0.359  Sum_probs=57.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC
Q 030819           75 QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLD  145 (171)
Q Consensus        75 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~  145 (171)
                      .....|.|.+||++.+|.+|+++..+-|.|+...+.+|       |++.|+|...|+++-|+..|....+.
T Consensus       113 rSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD-------g~GvV~~~r~eDMkYAvr~ld~~~~~  176 (241)
T KOG0105|consen  113 RSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD-------GVGVVEYLRKEDMKYAVRKLDDQKFR  176 (241)
T ss_pred             ccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc-------cceeeeeeehhhHHHHHHhhcccccc
Confidence            34568999999999999999999999999999998876       69999999999999999999887653

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

Probab=98.83  E-value=6e-08  Score=63.11  Aligned_cols=81  Identities=16%  Similarity=0.263  Sum_probs=70.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhc--CCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC----CeEEEE
Q 030819           78 TRLFVSGLSFRTSEDSLRNAFQG--FGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLD----GRVIFV  151 (171)
Q Consensus        78 ~~l~V~nl~~~~~~~~l~~~f~~--~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~----g~~i~v  151 (171)
                      +||.|.|||...+.++|.+++..  .|....+-++.|..++.+.|||||.|.+++.|.+-.+.++|..+.    .+...|
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~i   81 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCEI   81 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEEE
Confidence            68999999999999999998864  467788889999989999999999999999999999999999874    456788


Q ss_pred             EEecCcH
Q 030819          152 EIAKSRA  158 (171)
Q Consensus       152 ~~~~~~~  158 (171)
                      .+|+-++
T Consensus        82 ~yAriQG   88 (97)
T PF04059_consen   82 SYARIQG   88 (97)
T ss_pred             ehhHhhC
Confidence            8887554

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

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

Probab=98.77  E-value=3.5e-09  Score=77.35  Aligned_cols=82  Identities=17%  Similarity=0.208  Sum_probs=73.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 030819           74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEI  153 (171)
Q Consensus        74 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~  153 (171)
                      .+..++|||+|+...++|+-|.++|-+.|+|.++.|..++ .++.+ ||||.|.++.++.-|++.+||..+.+..+++.+
T Consensus         6 ae~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~-d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~   83 (267)
T KOG4454|consen    6 AEMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQ-DQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTL   83 (267)
T ss_pred             cchhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCc-cCCCc-eeeeecccccchhhhhhhcccchhccchhhccc
Confidence            3456899999999999999999999999999999998887 56666 999999999999999999999999999888877


Q ss_pred             ecCc
Q 030819          154 AKSR  157 (171)
Q Consensus       154 ~~~~  157 (171)
                      ....
T Consensus        84 r~G~   87 (267)
T KOG4454|consen   84 RCGN   87 (267)
T ss_pred             ccCC
Confidence            5543

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

Probab=98.60  E-value=6.4e-08  Score=79.36  Aligned_cols=88  Identities=28%  Similarity=0.506  Sum_probs=80.4

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q 030819           71 LSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIF  150 (171)
Q Consensus        71 ~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~  150 (171)
                      .........+||++||..++++++.++...||.+....++.+..+|-++||||.+|.+......|+..|||..+.+..|.
T Consensus       283 t~~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lv  362 (500)
T KOG0120|consen  283 TDVPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLV  362 (500)
T ss_pred             cCcccccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeE
Confidence            34556678999999999999999999999999999999999998999999999999999999999999999999999999


Q ss_pred             EEEecCcH
Q 030819          151 VEIAKSRA  158 (171)
Q Consensus       151 v~~~~~~~  158 (171)
                      |..+....
T Consensus       363 vq~A~~g~  370 (500)
T KOG0120|consen  363 VQRAIVGA  370 (500)
T ss_pred             eehhhccc
Confidence            98876443

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

Probab=98.58  E-value=3e-08  Score=80.90  Aligned_cols=88  Identities=20%  Similarity=0.396  Sum_probs=79.9

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 030819           72 STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFV  151 (171)
Q Consensus        72 ~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v  151 (171)
                      ....+.+++|+..|+..++..+|.++|..+|.|.+++++.|+.++.++|.+||+|.+.+++..|+. |.|..+.|.+|.|
T Consensus       174 ~eERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aia-LsGqrllg~pv~v  252 (549)
T KOG0147|consen  174 PEERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIA-LSGQRLLGVPVIV  252 (549)
T ss_pred             chHHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhh-hcCCcccCceeEe
Confidence            345567899999999999999999999999999999999999999999999999999999999996 9999999999999


Q ss_pred             EEecCcHHH
Q 030819          152 EIAKSRAEL  160 (171)
Q Consensus       152 ~~~~~~~~~  160 (171)
                      ......+..
T Consensus       253 q~sEaeknr  261 (549)
T KOG0147|consen  253 QLSEAEKNR  261 (549)
T ss_pred             cccHHHHHH
Confidence            887655544

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.47  E-value=7.9e-08  Score=74.54  Aligned_cols=84  Identities=24%  Similarity=0.513  Sum_probs=75.2

Q ss_pred             CCCCeEE-EcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 030819           75 QPKTRLF-VSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEI  153 (171)
Q Consensus        75 ~~~~~l~-V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~  153 (171)
                      ....++| |++++.++++++|+..|..+|.|..+++..++.++.++|||++.|.+...+..++.. +...+.+..+.+..
T Consensus       182 ~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~  260 (285)
T KOG4210|consen  182 GPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEE  260 (285)
T ss_pred             CccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCccccccc
Confidence            3445566 999999999999999999999999999999999999999999999999999999886 78889999999998


Q ss_pred             ecCcHH
Q 030819          154 AKSRAE  159 (171)
Q Consensus       154 ~~~~~~  159 (171)
                      ..++..
T Consensus       261 ~~~~~~  266 (285)
T KOG4210|consen  261 DEPRPK  266 (285)
T ss_pred             CCCCcc
Confidence            876643

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

Probab=98.45  E-value=1.2e-06  Score=69.64  Aligned_cols=76  Identities=24%  Similarity=0.383  Sum_probs=68.7

Q ss_pred             CCeEEEcCCCCC-CCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 030819           77 KTRLFVSGLSFR-TSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAK  155 (171)
Q Consensus        77 ~~~l~V~nl~~~-~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~  155 (171)
                      +..|.|.||... +|.+-|..+|..||+|.++.+..++.     .-|+|.|.+...|+-|+++|+|..+.|++|+|.+++
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkk-----d~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SK  371 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKK-----DNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSK  371 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCC-----cceeeeecchhHHHHHHHHhhcceecCceEEEeecc
Confidence            577888888775 99999999999999999999987762     579999999999999999999999999999999987


Q ss_pred             Cc
Q 030819          156 SR  157 (171)
Q Consensus       156 ~~  157 (171)
                      -.
T Consensus       372 H~  373 (492)
T KOG1190|consen  372 HT  373 (492)
T ss_pred             Cc
Confidence            54

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

Probab=98.39  E-value=1.6e-06  Score=70.24  Aligned_cols=80  Identities=20%  Similarity=0.373  Sum_probs=65.3

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      .......|-+.+|||++|+++|.++|+.++ |..+.+.  +.+|+..|-|||+|.+.++++.|++ .+...+..+-|.|-
T Consensus         6 e~~~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~--r~~Gr~sGeA~Ve~~seedv~~Alk-kdR~~mg~RYIEVf   81 (510)
T KOG4211|consen    6 EGSTAFEVRLRGLPWSATEKEILDFFSNCG-IENLEIP--RRNGRPSGEAYVEFTSEEDVEKALK-KDRESMGHRYIEVF   81 (510)
T ss_pred             CCCcceEEEecCCCccccHHHHHHHHhcCc-eeEEEEe--ccCCCcCcceEEEeechHHHHHHHH-hhHHHhCCceEEEE
Confidence            344566788999999999999999999985 7775544  4479999999999999999999999 56667777778886


Q ss_pred             EecC
Q 030819          153 IAKS  156 (171)
Q Consensus       153 ~~~~  156 (171)
                      -+..
T Consensus        82 ~~~~   85 (510)
T KOG4211|consen   82 TAGG   85 (510)
T ss_pred             ccCC
Confidence            6543

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

Probab=98.38  E-value=5.9e-07  Score=73.06  Aligned_cols=67  Identities=21%  Similarity=0.386  Sum_probs=61.7

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHh-cCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHH
Q 030819           72 STCQPKTRLFVSGLSFRTSEDSLRNAFQ-GFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG  138 (171)
Q Consensus        72 ~~~~~~~~l~V~nl~~~~~~~~l~~~f~-~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~  138 (171)
                      ..-++.+|||||+||.-++.++|-.+|. -||.|..+-|-.|++-+.++|-|=|+|.+-.+-.+||.+
T Consensus       365 q~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  365 QPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             cccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            3456789999999999999999999998 799999999999987899999999999999999999885

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

Probab=98.35  E-value=4.2e-06  Score=61.64  Aligned_cols=79  Identities=19%  Similarity=0.439  Sum_probs=70.2

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC-CeEEE
Q 030819           72 STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLD-GRVIF  150 (171)
Q Consensus        72 ~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~-g~~i~  150 (171)
                      ...++...+|+.|||.+++.+.|..+|.+|....+++++...     .+.|||+|.+...+..|...++|..|. .+.++
T Consensus       141 ~~~ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~~-----~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~  215 (221)
T KOG4206|consen  141 QMAPPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPPR-----SGIAFVEFLSDRQASAAQQALQGFKITKKNTMQ  215 (221)
T ss_pred             cCCCCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccCC-----CceeEEecchhhhhHHHhhhhccceeccCceEE
Confidence            346778899999999999999999999999999999998754     279999999999999999999999985 88899


Q ss_pred             EEEec
Q 030819          151 VEIAK  155 (171)
Q Consensus       151 v~~~~  155 (171)
                      |.+++
T Consensus       216 i~~a~  220 (221)
T KOG4206|consen  216 ITFAK  220 (221)
T ss_pred             ecccC
Confidence            88775

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

Probab=98.35  E-value=6.3e-07  Score=69.97  Aligned_cols=86  Identities=26%  Similarity=0.352  Sum_probs=77.3

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeE--------EEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLV--------EVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFL  144 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~--------~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i  144 (171)
                      ......+|||-+|+..+++++|.++|.++|.|.        .+.+-++++|+..||-|.|.|.+...|++|+.-+++..+
T Consensus        62 ~~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf  141 (351)
T KOG1995|consen   62 DKSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDF  141 (351)
T ss_pred             cccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccc
Confidence            345667999999999999999999999999875        356778889999999999999999999999999999999


Q ss_pred             CCeEEEEEEecCcH
Q 030819          145 DGRVIFVEIAKSRA  158 (171)
Q Consensus       145 ~g~~i~v~~~~~~~  158 (171)
                      ++..|+|..+..+.
T Consensus       142 ~gn~ikvs~a~~r~  155 (351)
T KOG1995|consen  142 CGNTIKVSLAERRT  155 (351)
T ss_pred             cCCCchhhhhhhcc
Confidence            99999998876554

>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=98.34  E-value=4.1e-06  Score=52.53  Aligned_cols=70  Identities=29%  Similarity=0.408  Sum_probs=47.9

Q ss_pred             CeEEEcCCCCCCCHH----HHHHHHhcCCC-eEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           78 TRLFVSGLSFRTSED----SLRNAFQGFGQ-LVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        78 ~~l~V~nl~~~~~~~----~l~~~f~~~G~-i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ..|||.|||-+....    -|++++..+|. |..+       +|   +.|++.|.+.+.|.+|...|+|-.+.|++|.|.
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v-------~~---~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~   72 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV-------SG---GTAILRFPNQEFAERAQKRMEGEDVFGNKISVS   72 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE---------T---T-EEEEESSHHHHHHHHHHHTT--SSSS--EEE
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE-------eC---CEEEEEeCCHHHHHHHHHhhcccccccceEEEE
Confidence            468999999988865    45667778874 5444       22   689999999999999999999999999999999


Q ss_pred             EecCc
Q 030819          153 IAKSR  157 (171)
Q Consensus       153 ~~~~~  157 (171)
                      +....
T Consensus        73 ~~~~~   77 (90)
T PF11608_consen   73 FSPKN   77 (90)
T ss_dssp             SS--S
T ss_pred             EcCCc
Confidence            98533

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

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

Probab=98.32  E-value=1.2e-06  Score=70.83  Aligned_cols=79  Identities=25%  Similarity=0.413  Sum_probs=63.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEE-EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 030819           75 QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVE-VNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEI  153 (171)
Q Consensus        75 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~-~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~  153 (171)
                      .....|-+.+||+.++++||.++|+..--+.. +.+..++ .+++.|-|||.|++.+.|+.||. -|...|..+-|.|-.
T Consensus       101 ~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~-rgR~tGEAfVqF~sqe~ae~Al~-rhre~iGhRYIEvF~  178 (510)
T KOG4211|consen  101 ANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQ-RGRPTGEAFVQFESQESAEIALG-RHRENIGHRYIEVFR  178 (510)
T ss_pred             CCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccC-CCCcccceEEEecCHHHHHHHHH-HHHHhhccceEEeeh
Confidence            45678999999999999999999997644444 4456666 78899999999999999999998 465677777777765


Q ss_pred             ec
Q 030819          154 AK  155 (171)
Q Consensus       154 ~~  155 (171)
                      +.
T Consensus       179 Ss  180 (510)
T KOG4211|consen  179 SS  180 (510)
T ss_pred             hH
Confidence            54

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

Probab=98.30  E-value=9.5e-07  Score=65.03  Aligned_cols=64  Identities=19%  Similarity=0.397  Sum_probs=54.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC
Q 030819           78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLD  145 (171)
Q Consensus        78 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~  145 (171)
                      .+|||.||.++++|++|+.+|+.|.....+++-. + .|.  ..+|++|++.+.|..||..|+|..|.
T Consensus       211 stlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~-~-~g~--~vaf~~~~~~~~at~am~~lqg~~~s  274 (284)
T KOG1457|consen  211 STLFIANLGPNCTEDELKQLLSRYPGFHILKIRA-R-GGM--PVAFADFEEIEQATDAMNHLQGNLLS  274 (284)
T ss_pred             hhHhhhccCCCCCHHHHHHHHHhCCCceEEEEec-C-CCc--ceEeecHHHHHHHHHHHHHhhcceec
Confidence            5899999999999999999999998766666532 2 444  38999999999999999999998773

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

Probab=98.24  E-value=1.2e-05  Score=63.47  Aligned_cols=81  Identities=23%  Similarity=0.283  Sum_probs=72.0

Q ss_pred             CCCCCCCeEEEcCCCCC-CCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q 030819           72 STCQPKTRLFVSGLSFR-TSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIF  150 (171)
Q Consensus        72 ~~~~~~~~l~V~nl~~~-~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~  150 (171)
                      ....++..+.|.+|... ++.+.|..+|..||.|..+++++.+.     |-|.|++.+..+.++|+..||+..+-|.+|.
T Consensus       282 ~g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk~-----gtamVemgd~~aver~v~hLnn~~lfG~kl~  356 (494)
T KOG1456|consen  282 GGGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTKP-----GTAMVEMGDAYAVERAVTHLNNIPLFGGKLN  356 (494)
T ss_pred             CCCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeeccc-----ceeEEEcCcHHHHHHHHHHhccCccccceEE
Confidence            45567889999999986 67789999999999999999987762     7899999999999999999999999999999


Q ss_pred             EEEecCc
Q 030819          151 VEIAKSR  157 (171)
Q Consensus       151 v~~~~~~  157 (171)
                      |+.++..
T Consensus       357 v~~SkQ~  363 (494)
T KOG1456|consen  357 VCVSKQN  363 (494)
T ss_pred             Eeecccc
Confidence            9988743

>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation

Probab=98.23  E-value=3.5e-06  Score=55.89  Aligned_cols=70  Identities=26%  Similarity=0.472  Sum_probs=44.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCc-----eeCCeEEEEE
Q 030819           78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGK-----FLDGRVIFVE  152 (171)
Q Consensus        78 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~-----~i~g~~i~v~  152 (171)
                      ..|.+.+++..++.++|++.|..||.|..|.+....      ..|+|.|.+.+.|+.|+..+...     .+.+..+.+.
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~------~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~   75 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGD------TEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLE   75 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-------SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCC------CEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEE
Confidence            568899999999999999999999999999886544      48999999999999999977644     4566555554


Q ss_pred             E
Q 030819          153 I  153 (171)
Q Consensus       153 ~  153 (171)
                      .
T Consensus        76 v   76 (105)
T PF08777_consen   76 V   76 (105)
T ss_dssp             -
T ss_pred             E
Confidence            4

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

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

Probab=98.09  E-value=5.1e-06  Score=64.92  Aligned_cols=78  Identities=21%  Similarity=0.360  Sum_probs=66.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCC--CeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 030819           74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFG--QLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFV  151 (171)
Q Consensus        74 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G--~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v  151 (171)
                      ......+|||||-|.+|++||.+.+..-|  ++.++++..++.+|+++|||++...+..+.++.|+.|.-..|.|..=.|
T Consensus        77 ~Grk~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V  156 (498)
T KOG4849|consen   77 EGRKYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTV  156 (498)
T ss_pred             cCceEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCee
Confidence            34456799999999999999999988766  5677777788889999999999999999999999999999998864333

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

Probab=98.05  E-value=6.8e-07  Score=76.43  Aligned_cols=141  Identities=17%  Similarity=0.195  Sum_probs=105.3

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCCCCCCCCCC-----CCCC
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPSPHSLSTC-----QPKT   78 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~   78 (171)
                      +++.||.++++.|....+.+.+...+..         .......+.-..+-+|.+++.+-.+..+...-..     -...
T Consensus       667 ~~~~fvsnl~~~~~~~dl~~~~~~~~~~---------e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~gK~  737 (881)
T KOG0128|consen  667 LIKIFVSNLSPKMSEEDLSERFSPSGTI---------EVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFGKI  737 (881)
T ss_pred             HHHHHHhhcchhhcCchhhhhcCccchh---------hhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhhhh
Confidence            3567778888888877777776554443         1111123344567778888888877765543222     2356


Q ss_pred             eEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 030819           79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIA  154 (171)
Q Consensus        79 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~  154 (171)
                      .++|.|.|+..|.+.|+.++.++|.+.+++++..+ .|+++|.++|.|.+..++.++........+.-+.+.|..+
T Consensus       738 ~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r-~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vs  812 (881)
T KOG0128|consen  738 SVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVR-AGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVS  812 (881)
T ss_pred             hhheeCCCCCCchHHHHhhccccCCccccchhhhh-ccccccceeccCCCcchhhhhcccchhhhhhhcCcccccc
Confidence            89999999999999999999999999999988888 8999999999999999999988877766665555555553

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

Probab=98.02  E-value=4.4e-06  Score=61.81  Aligned_cols=73  Identities=37%  Similarity=0.613  Sum_probs=63.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 030819           74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEI  153 (171)
Q Consensus        74 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~  153 (171)
                      ....+.+.|.+++..+.+.+|.+.|..+|.+.....        ..+++||+|...+++.+|+..|+|..+.++.|.+..
T Consensus        96 ~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~--------~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~~~  167 (216)
T KOG0106|consen   96 SRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA--------RRNFAFVEFSEQEDAKRALEKLDGKKLNGRRISVEK  167 (216)
T ss_pred             ccccceeeeccchhhhhHHHHhhhhcccCCCchhhh--------hccccceeehhhhhhhhcchhccchhhcCceeeecc
Confidence            455678999999999999999999999999854433        237999999999999999999999999999999954


Q ss_pred             e
Q 030819          154 A  154 (171)
Q Consensus       154 ~  154 (171)
                      .
T Consensus       168 ~  168 (216)
T KOG0106|consen  168 N  168 (216)
T ss_pred             c
Confidence            3

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=98.00  E-value=2.1e-05  Score=61.30  Aligned_cols=81  Identities=22%  Similarity=0.515  Sum_probs=63.0

Q ss_pred             CCeEEEcCCCCCCCHHH----H--HHHHhcCCCeEEEEEeecCCC-CCcceE--EEEEeCCHHHHHHHHHHhCCceeCCe
Q 030819           77 KTRLFVSGLSFRTSEDS----L--RNAFQGFGQLVEVNLVMDKIA-NRPRGF--AFLRYATEEESRRAIEGMHGKFLDGR  147 (171)
Q Consensus        77 ~~~l~V~nl~~~~~~~~----l--~~~f~~~G~i~~~~~~~~~~~-g~~~g~--~fv~f~~~~~a~~al~~l~g~~i~g~  147 (171)
                      ..-+||-+|++.+..++    |  .++|.+||.|..+.+-+.-.+ ....+.  .||+|...++|.+||...+|..++|+
T Consensus       114 KNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr  193 (480)
T COG5175         114 KNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGR  193 (480)
T ss_pred             cceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCc
Confidence            45789999999877655    3  478999999999877543311 111232  39999999999999999999999999


Q ss_pred             EEEEEEecCc
Q 030819          148 VIFVEIAKSR  157 (171)
Q Consensus       148 ~i~v~~~~~~  157 (171)
                      .|+..+...+
T Consensus       194 ~lkatYGTTK  203 (480)
T COG5175         194 VLKATYGTTK  203 (480)
T ss_pred             eEeeecCchH
Confidence            9999987644

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

Probab=97.96  E-value=4.2e-05  Score=63.11  Aligned_cols=144  Identities=17%  Similarity=0.275  Sum_probs=92.2

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCCCCCCC------------
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPSPHSL------------   71 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------------   71 (171)
                      -+++||++++...++....+.+..+++.         ..+.-..+..++-++++++..++.+.....+            
T Consensus       289 ~~ki~v~~lp~~l~~~q~~Ell~~fg~l---------k~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~  359 (500)
T KOG0120|consen  289 PNKIFVGGLPLYLTEDQVKELLDSFGPL---------KAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDK  359 (500)
T ss_pred             cchhhhccCcCccCHHHHHHHHHhcccc---------hhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCc
Confidence            3568999999999999888888887777         4444444444455556666555554432211            


Q ss_pred             ----------------------------------CCCCCCCeEEEcCCC--CC-CCH-------HHHHHHHhcCCCeEEE
Q 030819           72 ----------------------------------STCQPKTRLFVSGLS--FR-TSE-------DSLRNAFQGFGQLVEV  107 (171)
Q Consensus        72 ----------------------------------~~~~~~~~l~V~nl~--~~-~~~-------~~l~~~f~~~G~i~~~  107 (171)
                                                        ....+...|.+.|+=  .+ ..+       ++++.-+.+||.|..|
T Consensus       360 ~lvvq~A~~g~~~~~~~~~~~~~~~~~i~~~~~q~~g~~t~Vl~L~n~Vt~deLkdd~EyeeIlEdvr~ec~k~g~v~~v  439 (500)
T KOG0120|consen  360 KLVVQRAIVGASNANVNFNISQSQVPGIPLLMTQMAGIPTEVLCLTNVVTPDELKDDEEYEEILEDVRTECAKFGAVRSV  439 (500)
T ss_pred             eeEeehhhccchhccccCCccccccccchhhhcccCCCcchhhhhhhcCCHHHhcchHHHHHHHHHHHHHhcccCceeEE
Confidence                                              011111122222110  00 111       2444455789999999


Q ss_pred             EEeec-C--CCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 030819          108 NLVMD-K--IANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKS  156 (171)
Q Consensus       108 ~~~~~-~--~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~~  156 (171)
                      .+.++ .  ...-..|--||+|.+.+++++|+++|+|.++.++.|...|-..
T Consensus       440 ~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYyde  491 (500)
T KOG0120|consen  440 EIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYDE  491 (500)
T ss_pred             ecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecCH
Confidence            88876 2  1223457789999999999999999999999999988887543

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

Probab=97.87  E-value=8.3e-05  Score=59.35  Aligned_cols=84  Identities=25%  Similarity=0.337  Sum_probs=67.9

Q ss_pred             CCCCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC-eE
Q 030819           70 SLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDG-RV  148 (171)
Q Consensus        70 ~~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g-~~  148 (171)
                      .....++..++.+.|+|.+++|++|+.+|..-|...+....    -++.+-++++.+.+.|+|..|+-.+|...+.. ..
T Consensus       407 ~~ni~PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkf----f~kd~kmal~q~~sveeA~~ali~~hnh~lgen~h  482 (492)
T KOG1190|consen  407 YQNIFPPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKF----FQKDRKMALPQLESVEEAIQALIDLHNHYLGENHH  482 (492)
T ss_pred             ccccCCchhheeeccCCcccchhHHHHhhhcCCceEEeeee----cCCCcceeecccCChhHhhhhccccccccCCCCce
Confidence            33456788899999999999999999999988865443222    23445699999999999999999999999854 58


Q ss_pred             EEEEEecCc
Q 030819          149 IFVEIAKSR  157 (171)
Q Consensus       149 i~v~~~~~~  157 (171)
                      ++|.++++.
T Consensus       483 lRvSFSks~  491 (492)
T KOG1190|consen  483 LRVSFSKST  491 (492)
T ss_pred             EEEEeeccc
Confidence            999998763

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

Probab=97.86  E-value=9.9e-06  Score=60.77  Aligned_cols=73  Identities=12%  Similarity=0.218  Sum_probs=62.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCC--------CCcce----EEEEEeCCHHHHHHHHHHhCCce
Q 030819           76 PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIA--------NRPRG----FAFLRYATEEESRRAIEGMHGKF  143 (171)
Q Consensus        76 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~--------g~~~g----~~fv~f~~~~~a~~al~~l~g~~  143 (171)
                      ....||+++||+.....-|+++|..||.|-.|.+.....+        |.+.+    -|+|+|.+...|.++...||+..
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~  152 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTP  152 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCc
Confidence            4578999999999999999999999999999988766554        33322    47899999999999999999999


Q ss_pred             eCCeE
Q 030819          144 LDGRV  148 (171)
Q Consensus       144 i~g~~  148 (171)
                      |+|++
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            98864

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

Probab=97.79  E-value=7.8e-05  Score=43.13  Aligned_cols=52  Identities=23%  Similarity=0.556  Sum_probs=41.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHH
Q 030819           78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI  136 (171)
Q Consensus        78 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al  136 (171)
                      +.|-|.|.+++..+. +...|..||+|.+..+....      -+.++.|.+..+|++||
T Consensus         2 ~wI~V~Gf~~~~~~~-vl~~F~~fGeI~~~~~~~~~------~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAEE-VLEHFASFGEIVDIYVPEST------NWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHHH-HHHHHHhcCCEEEEEcCCCC------cEEEEEECCHHHHHhhC
Confidence            467788999876644 56688899999998875222      48999999999999985

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

Probab=97.76  E-value=0.00023  Score=59.02  Aligned_cols=78  Identities=23%  Similarity=0.491  Sum_probs=63.1

Q ss_pred             CCCCeEEEcCCCCCCCH------HHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC-Ce
Q 030819           75 QPKTRLFVSGLSFRTSE------DSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLD-GR  147 (171)
Q Consensus        75 ~~~~~l~V~nl~~~~~~------~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~-g~  147 (171)
                      .-...|+|.|+|.--..      .-|..+|+++|+|....+..+.+ |.++||.|++|.+..+|+.|+..|||..++ .+
T Consensus        56 g~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~-ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknH  134 (698)
T KOG2314|consen   56 GFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEE-GGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNH  134 (698)
T ss_pred             CcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCcc-CCeeeEEEEEecChhhHHHHHHhcccceecccc
Confidence            44568999999874332      35678899999999999888884 559999999999999999999999999984 45


Q ss_pred             EEEEEE
Q 030819          148 VIFVEI  153 (171)
Q Consensus       148 ~i~v~~  153 (171)
                      ...|..
T Consensus       135 tf~v~~  140 (698)
T KOG2314|consen  135 TFFVRL  140 (698)
T ss_pred             eEEeeh
Confidence            555543

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

Probab=97.74  E-value=0.00017  Score=61.20  Aligned_cols=75  Identities=19%  Similarity=0.320  Sum_probs=65.5

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 030819           79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEI  153 (171)
Q Consensus        79 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~  153 (171)
                      .|-|.|+|++++-+||.++|..|-.+-...+++-.+.|...|-|.|.|++.++|.+|...|++..|..+.|.+.+
T Consensus       869 V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~nd~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~V~l~i  943 (944)
T KOG4307|consen  869 VLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             EEEecCCCccccHHHHHHHhcccccCCCceeEeecCCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            777999999999999999999997665444444455899999999999999999999999999999999988764

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

Probab=97.62  E-value=0.00017  Score=62.63  Aligned_cols=148  Identities=16%  Similarity=0.218  Sum_probs=97.1

Q ss_pred             eeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccc----cCCCCCCCCCCCCCC-----CCCCC-CCCCC
Q 030819            6 FLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLR----QGRGRGACFPLACLP-----PSPHS-LSTCQ   75 (171)
Q Consensus         6 ~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~-----~~~~~-~~~~~   75 (171)
                      .||+|++.-.+++..+...|...+.+..--+-+++......+..-    +...-..++......     ....- .....
T Consensus       374 TLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~glG~~kst  453 (975)
T KOG0112|consen  374 TLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHIKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGLGQPKST  453 (975)
T ss_pred             hhhhcCcccchhhhhhhhhhhhhccccccccccCCCCcccchhhhhhhccccCcccchhhcCCccccCcccccccccccc
Confidence            478899999999999998888876664433322222211111110    000000000000000     00000 01345


Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC--eEEEEEE
Q 030819           76 PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDG--RVIFVEI  153 (171)
Q Consensus        76 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g--~~i~v~~  153 (171)
                      ..+.+|+++|..++....|...|..||.|..+.+-..    .  .|++|.|.+...++.|+..+-|..+.|  +.+.|.+
T Consensus       454 ~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~hg----q--~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvdl  527 (975)
T KOG0112|consen  454 PTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRHG----Q--PYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVDL  527 (975)
T ss_pred             cceeeccCCCCCCChHHHHHHHhhccCcceeeecccC----C--cceeeecccCccchhhHHHHhcCcCCCCCccccccc
Confidence            6789999999999999999999999999999776432    2  599999999999999999999999976  5788888


Q ss_pred             ecCcHH
Q 030819          154 AKSRAE  159 (171)
Q Consensus       154 ~~~~~~  159 (171)
                      +..-..
T Consensus       528 a~~~~~  533 (975)
T KOG0112|consen  528 ASPPGA  533 (975)
T ss_pred             ccCCCC
Confidence            875543

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

Probab=97.62  E-value=0.00043  Score=45.39  Aligned_cols=77  Identities=18%  Similarity=0.317  Sum_probs=51.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEe-ec-------CCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCe
Q 030819           76 PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLV-MD-------KIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGR  147 (171)
Q Consensus        76 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~-~~-------~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~  147 (171)
                      ....|.|.++|+. .-..+.+.|++||.|.+..-. .+       + ......+-.|.|.++.+|.+||. .||..+.|.
T Consensus         5 ~~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~-~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~   81 (100)
T PF05172_consen    5 SETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYP-IPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGS   81 (100)
T ss_dssp             GCCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG-----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTC
T ss_pred             CCeEEEEEccCHH-HHHHHHHHHHhcceEEEeeccccccccccccc-CCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCc
Confidence            3557889999987 556788999999999776400 00       0 01112488999999999999999 799999885


Q ss_pred             -EEEEEEec
Q 030819          148 -VIFVEIAK  155 (171)
Q Consensus       148 -~i~v~~~~  155 (171)
                       .+-|.+.+
T Consensus        82 ~mvGV~~~~   90 (100)
T PF05172_consen   82 LMVGVKPCD   90 (100)
T ss_dssp             EEEEEEE-H
T ss_pred             EEEEEEEcH
Confidence             45566653

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.

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

Probab=97.59  E-value=0.00074  Score=47.01  Aligned_cols=77  Identities=21%  Similarity=0.342  Sum_probs=52.3

Q ss_pred             CCCCCCeEEEcCCCC------CCCH---HHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCce
Q 030819           73 TCQPKTRLFVSGLSF------RTSE---DSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKF  143 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~------~~~~---~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~  143 (171)
                      -.++..||.|.-+.+      ...+   .+|.+.|..||.+.=+++..+        .-+|+|.+.++|.+|+. ++|..
T Consensus        23 ~GPpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaals-~dg~~   93 (146)
T PF08952_consen   23 QGPPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAALS-LDGIQ   93 (146)
T ss_dssp             ---TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHHH-GCCSE
T ss_pred             cCCCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHHc-cCCcE
Confidence            345566777775551      1222   367788899999887777643        57999999999999999 99999


Q ss_pred             eCCeEEEEEEecCcH
Q 030819          144 LDGRVIFVEIAKSRA  158 (171)
Q Consensus       144 i~g~~i~v~~~~~~~  158 (171)
                      ++|+.|+|....+..
T Consensus        94 v~g~~l~i~LKtpdW  108 (146)
T PF08952_consen   94 VNGRTLKIRLKTPDW  108 (146)
T ss_dssp             ETTEEEEEEE-----
T ss_pred             ECCEEEEEEeCCccH
Confidence            999999998876543

; PDB: 1UFW_A 2DNR_A.

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

Probab=97.43  E-value=0.00029  Score=55.97  Aligned_cols=80  Identities=24%  Similarity=0.408  Sum_probs=66.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCC-eEE--EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 030819           75 QPKTRLFVSGLSFRTSEDSLRNAFQGFGQ-LVE--VNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFV  151 (171)
Q Consensus        75 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~-i~~--~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v  151 (171)
                      .....|-+.+||++.+.++|.++|..|.. |..  +.++.+. .|+..|-|||+|.+.+.|.+|+...+.+...++-|.|
T Consensus       278 ~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~-qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEv  356 (508)
T KOG1365|consen  278 RSKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNG-QGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEV  356 (508)
T ss_pred             CCCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcC-CCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEE
Confidence            34668899999999999999999998864 444  6777766 8999999999999999999999988877666777777


Q ss_pred             EEec
Q 030819          152 EIAK  155 (171)
Q Consensus       152 ~~~~  155 (171)
                      -...
T Consensus       357 fp~S  360 (508)
T KOG1365|consen  357 FPCS  360 (508)
T ss_pred             eecc
Confidence            5543

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

Probab=97.38  E-value=0.00052  Score=56.33  Aligned_cols=65  Identities=22%  Similarity=0.473  Sum_probs=48.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCC---CCCcce---EEEEEeCCHHHHHHHHHHhC
Q 030819           75 QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKI---ANRPRG---FAFLRYATEEESRRAIEGMH  140 (171)
Q Consensus        75 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~---~g~~~g---~~fv~f~~~~~a~~al~~l~  140 (171)
                      .-+++||||+||++++|+.|...|..||.+. +.+.....   ---++|   |+|+.|+++.++..-+.+..
T Consensus       257 ~~S~KVFvGGlp~dise~~i~~~F~~FGs~~-VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~  327 (520)
T KOG0129|consen  257 RYSRKVFVGGLPWDITEAQINASFGQFGSVK-VDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACS  327 (520)
T ss_pred             ccccceeecCCCccccHHHHHhhcccccceE-eecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHh
Confidence            3457999999999999999999999999743 34442111   122466   99999999988888776554

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

Probab=97.35  E-value=0.0014  Score=51.52  Aligned_cols=79  Identities=20%  Similarity=0.442  Sum_probs=60.3

Q ss_pred             CCCCeEEEcCCCC----CCC-------HHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCce
Q 030819           75 QPKTRLFVSGLSF----RTS-------EDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKF  143 (171)
Q Consensus        75 ~~~~~l~V~nl~~----~~~-------~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~  143 (171)
                      ...++|.+.|+=.    ..+       .++|++-..+||.|..+.+.-.    .+.|.+-|.|.+.++|..|+..|+|..
T Consensus       263 r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d~----hPdGvvtV~f~n~eeA~~ciq~m~GR~  338 (382)
T KOG1548|consen  263 RADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYDR----HPDGVVTVSFRNNEEADQCIQTMDGRW  338 (382)
T ss_pred             cCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEecc----CCCceeEEEeCChHHHHHHHHHhcCee
Confidence            3456787777521    233       2455666789999999877522    245899999999999999999999999


Q ss_pred             eCCeEEEEEEecCc
Q 030819          144 LDGRVIFVEIAKSR  157 (171)
Q Consensus       144 i~g~~i~v~~~~~~  157 (171)
                      +.|+.|.......+
T Consensus       339 fdgRql~A~i~DG~  352 (382)
T KOG1548|consen  339 FDGRQLTASIWDGK  352 (382)
T ss_pred             ecceEEEEEEeCCc
Confidence            99999998875543

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

Probab=97.30  E-value=0.00051  Score=55.23  Aligned_cols=74  Identities=19%  Similarity=0.298  Sum_probs=59.4

Q ss_pred             CCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeec---CCC--CCc--------ceEEEEEeCCHHHHHH
Q 030819           68 PHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMD---KIA--NRP--------RGFAFLRYATEEESRR  134 (171)
Q Consensus        68 ~~~~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~---~~~--g~~--------~g~~fv~f~~~~~a~~  134 (171)
                      +......-++++|.+.|||.+-.-+.|..+|..+|.|+.|++...   +.+  +..        +-+|+|+|...+.|.+
T Consensus       222 p~~~~eel~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~K  301 (484)
T KOG1855|consen  222 PEFDEEELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARK  301 (484)
T ss_pred             CCccccccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHH
Confidence            334445568999999999999888999999999999999998765   222  212        4589999999999999


Q ss_pred             HHHHhCC
Q 030819          135 AIEGMHG  141 (171)
Q Consensus       135 al~~l~g  141 (171)
                      |-+.++.
T Consensus       302 A~e~~~~  308 (484)
T KOG1855|consen  302 ARELLNP  308 (484)
T ss_pred             HHHhhch
Confidence            9997743

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

Probab=97.24  E-value=0.00054  Score=55.11  Aligned_cols=80  Identities=21%  Similarity=0.346  Sum_probs=61.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCc-eeCCeEEEEEEecC
Q 030819           78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGK-FLDGRVIFVEIAKS  156 (171)
Q Consensus        78 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~-~i~g~~i~v~~~~~  156 (171)
                      ..+|++||.+..+..+|+.+|...---..-.++..      -||+||.+.+..-|.+|++.++|. .+.|.++.+..+.+
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~k------~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~   75 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLVK------SGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVP   75 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceeee------cceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhh
Confidence            36899999999999999999975311011112222      279999999999999999999998 48999999999888


Q ss_pred             cHHHHHh
Q 030819          157 RAELRQA  163 (171)
Q Consensus       157 ~~~~~~~  163 (171)
                      +..+.+.
T Consensus        76 kkqrsrk   82 (584)
T KOG2193|consen   76 KKQRSRK   82 (584)
T ss_pred             HHHHhhh
Confidence            7755443

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

Probab=97.19  E-value=0.0035  Score=39.40  Aligned_cols=56  Identities=14%  Similarity=0.306  Sum_probs=42.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC
Q 030819           76 PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMH  140 (171)
Q Consensus        76 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~  140 (171)
                      ..+..+|+ +|..+...||.++|..||.| .+.++.|-       -|||...+.+.+..++..+.
T Consensus         8 RdHVFhlt-FPkeWK~~DI~qlFspfG~I-~VsWi~dT-------SAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen    8 RDHVFHLT-FPKEWKTSDIYQLFSPFGQI-YVSWINDT-------SAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             GCCEEEEE---TT--HHHHHHHCCCCCCE-EEEEECTT-------EEEEEECCCHHHHHHHHHHT
T ss_pred             cceEEEEe-CchHhhhhhHHHHhccCCcE-EEEEEcCC-------cEEEEeecHHHHHHHHHHhc
Confidence            34566666 99999999999999999986 45566553       79999999999999998775

; 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.

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

Probab=97.04  E-value=0.0012  Score=55.20  Aligned_cols=78  Identities=17%  Similarity=0.309  Sum_probs=63.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhc-CCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee---CCeE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQG-FGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFL---DGRV  148 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~-~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i---~g~~  148 (171)
                      ....+..|||.||-.-.|.-+|+.++.. .|.|.+. |+ |+    .+..|||.|.+.++|.+...+|||..+   +++.
T Consensus       440 R~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~-Wm-Dk----IKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~  513 (718)
T KOG2416|consen  440 RKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEF-WM-DK----IKSHCYVSYSSVEEAAATREALHNVQWPPSNPKH  513 (718)
T ss_pred             CCCccceEeeecccccchHHHHHHHHhhccCchHHH-HH-HH----hhcceeEecccHHHHHHHHHHHhccccCCCCCce
Confidence            5567889999999999999999999995 5556665 32 32    346899999999999999999999986   6678


Q ss_pred             EEEEEecC
Q 030819          149 IFVEIAKS  156 (171)
Q Consensus       149 i~v~~~~~  156 (171)
                      |.+.|...
T Consensus       514 L~adf~~~  521 (718)
T KOG2416|consen  514 LIADFVRA  521 (718)
T ss_pred             eEeeecch
Confidence            88888754

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

Probab=97.01  E-value=0.0055  Score=36.46  Aligned_cols=55  Identities=16%  Similarity=0.339  Sum_probs=45.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcC---CCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHh
Q 030819           77 KTRLFVSGLSFRTSEDSLRNAFQGF---GQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM  139 (171)
Q Consensus        77 ~~~l~V~nl~~~~~~~~l~~~f~~~---G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l  139 (171)
                      ...|+|.|++ +++.++|+.+|..|   .....+.++-|.       -|-|.|.+.+.|.+||.+|
T Consensus         5 peavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdDt-------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    5 PEAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDDT-------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecCC-------cEEEEECCHHHHHHHHHcC
Confidence            3579999997 57888999999988   235688888775       5889999999999999764

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

Probab=96.94  E-value=0.0072  Score=48.13  Aligned_cols=94  Identities=13%  Similarity=0.174  Sum_probs=71.8

Q ss_pred             CCCCCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCC-eEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC
Q 030819           62 ACLPPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQ-LVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMH  140 (171)
Q Consensus        62 ~~~~~~~~~~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~-i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~  140 (171)
                      +.+|..+.......++..|...|-|..+||+.|..+|..-+. -.++++..-+ +.++ .-|.++|++.++|..||..+|
T Consensus       391 Fssp~qAsKNrIq~Ps~vLHffNaP~~vtEe~l~~i~nek~v~~~svkvFp~k-serS-ssGllEfe~~s~Aveal~~~N  468 (494)
T KOG1456|consen  391 FSSPEQASKNRIQPPSNVLHFFNAPLGVTEEQLIGICNEKDVPPTSVKVFPLK-SERS-SSGLLEFENKSDAVEALMKLN  468 (494)
T ss_pred             cCChhHhhcccccCCcceeEEecCCCccCHHHHHHHhhhcCCCcceEEeeccc-cccc-ccceeeeehHHHHHHHHHHhc
Confidence            344445555556778899999999999999999999986553 3555665554 4444 478999999999999999999


Q ss_pred             CceeCCe------EEEEEEecCc
Q 030819          141 GKFLDGR------VIFVEIAKSR  157 (171)
Q Consensus       141 g~~i~g~------~i~v~~~~~~  157 (171)
                      ...+.+.      .++++++.++
T Consensus       469 H~pi~~p~gs~PfilKlcfsts~  491 (494)
T KOG1456|consen  469 HYPIEGPNGSFPFILKLCFSTSK  491 (494)
T ss_pred             cccccCCCCCCCeeeeeeecccc
Confidence            9888653      5778877654

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

Probab=96.87  E-value=0.0031  Score=50.38  Aligned_cols=76  Identities=13%  Similarity=0.228  Sum_probs=60.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCC---CcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 030819           77 KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIAN---RPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEI  153 (171)
Q Consensus        77 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g---~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~  153 (171)
                      ...|-|.||++.++.++++.+|...|.|.++.|....+.-   ...-.|||.|.+...+..|-. |.+..+-+..|.|-.
T Consensus         7 ~~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQh-Ltntvfvdraliv~p   85 (479)
T KOG4676|consen    7 LGVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQH-LTNTVFVDRALIVRP   85 (479)
T ss_pred             CceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhh-hccceeeeeeEEEEe
Confidence            3489999999999999999999999999999887644322   234589999999999888865 777777666665554

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=96.84  E-value=0.0054  Score=47.32  Aligned_cols=65  Identities=17%  Similarity=0.347  Sum_probs=52.8

Q ss_pred             HHHHHHHHhcCCCeEEEEEeecCCCCCcce-EEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 030819           91 EDSLRNAFQGFGQLVEVNLVMDKIANRPRG-FAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAK  155 (171)
Q Consensus        91 ~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g-~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~  155 (171)
                      ++++++-.++||.|..|.+..++....... --||+|...++|.+|+--|||..+.|+.+..++..
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn  365 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYN  365 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheecc
Confidence            456777788999999988776653333322 45999999999999999999999999999988865

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

Probab=96.80  E-value=0.00071  Score=51.01  Aligned_cols=62  Identities=19%  Similarity=0.516  Sum_probs=50.0

Q ss_pred             HHHHHHh-cCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 030819           93 SLRNAFQ-GFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAK  155 (171)
Q Consensus        93 ~l~~~f~-~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~  155 (171)
                      ++..-|. +||+|+++.+..+. .-.-+|-.+|.|...++|++|++.||+.-+.|++|...+..
T Consensus        84 d~f~E~~~kygEiee~~Vc~Nl-~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~p  146 (260)
T KOG2202|consen   84 DVFTELEDKYGEIEELNVCDNL-GDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSP  146 (260)
T ss_pred             HHHHHHHHHhhhhhhhhhhccc-chhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecC
Confidence            3333334 89999998665443 44467889999999999999999999999999999998764

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

Probab=96.77  E-value=0.0024  Score=54.43  Aligned_cols=84  Identities=18%  Similarity=0.130  Sum_probs=67.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEE-EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVE-VNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFV  151 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~-~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v  151 (171)
                      ..+.+..|||..||..+++.++..+|...-.|++ |.+-.-+ +++.++.|||.|..++++..|+.--+-..+..+.|+|
T Consensus       430 P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~P-~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv  508 (944)
T KOG4307|consen  430 PGGAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRLP-TDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRV  508 (944)
T ss_pred             CCCccceEEeccCCccccccchhhhhhhhhhhhheeEeccCC-cccccchhhheeccccccchhhhcccccccCceEEEe
Confidence            4456789999999999999999999987666666 6666666 8889999999999988888887755555667778999


Q ss_pred             EEecCc
Q 030819          152 EIAKSR  157 (171)
Q Consensus       152 ~~~~~~  157 (171)
                      .-...+
T Consensus       509 ~si~~~  514 (944)
T KOG4307|consen  509 DSIADY  514 (944)
T ss_pred             echhhH
Confidence            765433

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=96.70  E-value=0.0023  Score=48.30  Aligned_cols=62  Identities=24%  Similarity=0.414  Sum_probs=56.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC
Q 030819           78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMH  140 (171)
Q Consensus        78 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~  140 (171)
                      ..|||.||+.-++.+.|.+-|..||+|..-.++.|. .++..+-++|.|...-.+..|+..+.
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~-r~k~t~eg~v~~~~k~~a~~a~rr~~   93 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDD-RGKPTREGIVEFAKKPNARKAARRCR   93 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeecc-cccccccchhhhhcchhHHHHHHHhc
Confidence            689999999999999999999999999887777776 78888999999999999999988764

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

Probab=96.67  E-value=0.008  Score=48.02  Aligned_cols=60  Identities=27%  Similarity=0.360  Sum_probs=49.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhc----CCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHH
Q 030819           78 TRLFVSGLSFRTSEDSLRNAFQG----FGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG  138 (171)
Q Consensus        78 ~~l~V~nl~~~~~~~~l~~~f~~----~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~  138 (171)
                      -.|-+.+||+++++.++.++|..    -|..+.+.++..+ .|+..|-|||.|..+++|+.||..
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            35667899999999999999962    2345666666665 799999999999999999999984

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

Probab=96.48  E-value=0.00015  Score=62.57  Aligned_cols=69  Identities=29%  Similarity=0.424  Sum_probs=59.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC
Q 030819           77 KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLD  145 (171)
Q Consensus        77 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~  145 (171)
                      ..++||.||+..+.+.+|...|..+|.+..+++......++.+|+|++.|...+.+.+|+....+..+.
T Consensus       667 ~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~g  735 (881)
T KOG0128|consen  667 LIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFG  735 (881)
T ss_pred             HHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhh
Confidence            357999999999999999999999999888877766668999999999999999999999865544433

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

Probab=96.25  E-value=0.00092  Score=58.21  Aligned_cols=82  Identities=17%  Similarity=0.308  Sum_probs=67.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ....+.+||+|||+..+++.+|+..|..+|.|.+|.+...+ -+.---|+|+.|.+...+..|+..+.+..|....+++.
T Consensus       368 D~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~-~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~g  446 (975)
T KOG0112|consen  368 DFRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPH-IKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIG  446 (975)
T ss_pred             chhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCC-CCcccchhhhhhhccccCcccchhhcCCccccCccccc
Confidence            44457899999999999999999999999999999987654 23333599999999999999999999988855555655


Q ss_pred             Eec
Q 030819          153 IAK  155 (171)
Q Consensus       153 ~~~  155 (171)
                      +..
T Consensus       447 lG~  449 (975)
T KOG0112|consen  447 LGQ  449 (975)
T ss_pred             ccc
Confidence            553

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=96.11  E-value=0.041  Score=38.21  Aligned_cols=76  Identities=16%  Similarity=0.230  Sum_probs=57.0

Q ss_pred             CCCCCCCeEEEcCCCCCCCH-H---HHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCe
Q 030819           72 STCQPKTRLFVSGLSFRTSE-D---SLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGR  147 (171)
Q Consensus        72 ~~~~~~~~l~V~nl~~~~~~-~---~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~  147 (171)
                      ..+++-.+|.|.=|..++.. +   .+..-++.||+|.++.+.     |+  .-|.|.|.+..+|=.|+.+++. ...|.
T Consensus        81 ~kepPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~c-----Gr--qsavVvF~d~~SAC~Av~Af~s-~~pgt  152 (166)
T PF15023_consen   81 TKEPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLC-----GR--QSAVVVFKDITSACKAVSAFQS-RAPGT  152 (166)
T ss_pred             CCCCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeec-----CC--ceEEEEehhhHHHHHHHHhhcC-CCCCc
Confidence            34566778989877666542 3   444556789999998763     32  4799999999999999998875 66788


Q ss_pred             EEEEEEec
Q 030819          148 VIFVEIAK  155 (171)
Q Consensus       148 ~i~v~~~~  155 (171)
                      .+++.|-.
T Consensus       153 m~qCsWqq  160 (166)
T PF15023_consen  153 MFQCSWQQ  160 (166)
T ss_pred             eEEeeccc
Confidence            88888854

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=95.99  E-value=0.0028  Score=49.60  Aligned_cols=81  Identities=21%  Similarity=0.432  Sum_probs=62.3

Q ss_pred             CCeEEEcCCCCCCCHH-HHH--HHHhcCCCeEEEEEeecCC----CCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEE
Q 030819           77 KTRLFVSGLSFRTSED-SLR--NAFQGFGQLVEVNLVMDKI----ANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVI  149 (171)
Q Consensus        77 ~~~l~V~nl~~~~~~~-~l~--~~f~~~G~i~~~~~~~~~~----~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i  149 (171)
                      ...+||-+|+.....+ .|+  +.|.+||.|..+.+-.+..    .+-+. -++|+|...++|..||...+|..++|+.+
T Consensus        77 knlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~-s~yITy~~~eda~rci~~v~g~~~dg~~l  155 (327)
T KOG2068|consen   77 KNLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTC-SVYITYEEEEDADRCIDDVDGFVDDGRAL  155 (327)
T ss_pred             hhhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCC-cccccccchHhhhhHHHHhhhHHhhhhhh
Confidence            4678899999876544 343  6788999999998877651    12222 37999999999999999999999999888


Q ss_pred             EEEEecCcH
Q 030819          150 FVEIAKSRA  158 (171)
Q Consensus       150 ~v~~~~~~~  158 (171)
                      +..++..+-
T Consensus       156 ka~~gttky  164 (327)
T KOG2068|consen  156 KASLGTTKY  164 (327)
T ss_pred             HHhhCCCcc
Confidence            877776553

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells

Probab=95.78  E-value=0.045  Score=39.92  Aligned_cols=62  Identities=16%  Similarity=0.250  Sum_probs=45.5

Q ss_pred             CHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC--CceeCCeEEEEEEecCc
Q 030819           90 SEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMH--GKFLDGRVIFVEIAKSR  157 (171)
Q Consensus        90 ~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~--g~~i~g~~i~v~~~~~~  157 (171)
                      ....|+.+|..|+.+........-      +-..|.|.+.+.|.+|...|+  +..+.|..+++.++...
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~sF------rRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~   71 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKSF------RRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPT   71 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETTT------TEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----S
T ss_pred             hHHHHHHHHHhcCCceEEEEcCCC------CEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEcccc
Confidence            457899999999988777665443      467999999999999999999  99999999999998543

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.

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

Probab=95.71  E-value=0.3  Score=32.58  Aligned_cols=68  Identities=16%  Similarity=0.227  Sum_probs=49.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCC-CeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC
Q 030819           77 KTRLFVSGLSFRTSEDSLRNAFQGFG-QLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDG  146 (171)
Q Consensus        77 ~~~l~V~nl~~~~~~~~l~~~f~~~G-~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g  146 (171)
                      ...+.+...|..++.++|..+.+.+- .|..++++++.  .-++=.+++.|.+.++|..-...+||..++.
T Consensus        13 ~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~--~pnrymVLikF~~~~~Ad~Fy~~fNGk~Fns   81 (110)
T PF07576_consen   13 STLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDG--TPNRYMVLIKFRDQESADEFYEEFNGKPFNS   81 (110)
T ss_pred             ceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCC--CCceEEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            34455555555566667765555544 47788888875  2355688999999999999999999998755

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

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

Probab=95.56  E-value=0.008  Score=43.36  Aligned_cols=54  Identities=7%  Similarity=0.157  Sum_probs=46.9

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCC
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPP   66 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   66 (171)
                      ++++|||+++|++++..++.-|+..+.+         .+..-+....+++++|++|......-
T Consensus        35 sA~Iyiggl~~~LtEgDil~VFSqyGe~---------vdinLiRDk~TGKSKGFaFLcYEDQR   88 (219)
T KOG0126|consen   35 SAYIYIGGLPYELTEGDILCVFSQYGEI---------VDINLIRDKKTGKSKGFAFLCYEDQR   88 (219)
T ss_pred             ceEEEECCCcccccCCcEEEEeeccCce---------EEEEEEecCCCCcccceEEEEecCcc
Confidence            5789999999999999999999998888         77777888899999999987665443

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

Probab=95.37  E-value=0.031  Score=40.48  Aligned_cols=82  Identities=13%  Similarity=0.154  Sum_probs=50.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhc-CCCe---EEEEEeecCCC-C-CcceEEEEEeCCHHHHHHHHHHhCCceeC---
Q 030819           75 QPKTRLFVSGLSFRTSEDSLRNAFQG-FGQL---VEVNLVMDKIA-N-RPRGFAFLRYATEEESRRAIEGMHGKFLD---  145 (171)
Q Consensus        75 ~~~~~l~V~nl~~~~~~~~l~~~f~~-~G~i---~~~~~~~~~~~-g-~~~g~~fv~f~~~~~a~~al~~l~g~~i~---  145 (171)
                      ....+|.|++||+.+|++++.+.+.. ++.-   ..+.-.....+ . ..-.-|||.|.+.+++..-...++|..+.   
T Consensus         5 ~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~k   84 (176)
T PF03467_consen    5 KEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSK   84 (176)
T ss_dssp             ----EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TT
T ss_pred             ccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCC
Confidence            34669999999999999998887776 6654   33321111111 1 12357899999999999999999998762   


Q ss_pred             C--eEEEEEEecC
Q 030819          146 G--RVIFVEIAKS  156 (171)
Q Consensus       146 g--~~i~v~~~~~  156 (171)
                      |  ....|++|.-
T Consensus        85 g~~~~~~VE~Apy   97 (176)
T PF03467_consen   85 GNEYPAVVEFAPY   97 (176)
T ss_dssp             S-EEEEEEEE-SS
T ss_pred             CCCcceeEEEcch
Confidence            2  2556666653

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.

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

Probab=95.29  E-value=0.0022  Score=47.91  Aligned_cols=59  Identities=10%  Similarity=0.051  Sum_probs=51.5

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCCCCCCC
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPSPHSL   71 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   71 (171)
                      +-++|||++.|+-..+.++..|+.++.+         .+.-.+.+..++|+||++|+.+....++..+
T Consensus        12 ~TKifVggL~w~T~~~~l~~yFeqfGeI---------~eavvitd~~t~rskGyGfVTf~d~~aa~rA   70 (247)
T KOG0149|consen   12 FTKIFVGGLAWETHKETLRRYFEQFGEI---------VEAVVITDKNTGRSKGYGFVTFRDAEAATRA   70 (247)
T ss_pred             EEEEEEcCcccccchHHHHHHHHHhCce---------EEEEEEeccCCccccceeeEEeecHHHHHHH
Confidence            5689999999999999999999999888         7777778888999999999999887765544

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=95.26  E-value=0.012  Score=48.06  Aligned_cols=74  Identities=20%  Similarity=0.297  Sum_probs=58.4

Q ss_pred             CCCeEEEcCCCCCCC-HHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 030819           76 PKTRLFVSGLSFRTS-EDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIA  154 (171)
Q Consensus        76 ~~~~l~V~nl~~~~~-~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~  154 (171)
                      +.+.+-+...++..+ -++|...|.+||.|..|.+-...      -.|.|+|.+..+|-.|-. .++..|+++.|+|.|-
T Consensus       371 dhs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~~------~~a~vTF~t~aeag~a~~-s~~avlnnr~iKl~wh  443 (526)
T KOG2135|consen  371 DHSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYSS------LHAVVTFKTRAEAGEAYA-SHGAVLNNRFIKLFWH  443 (526)
T ss_pred             ccchhhhhccCCCCchHhhhhhhhhhcCccccccccCch------hhheeeeeccccccchhc-cccceecCceeEEEEe
Confidence            344555666666644 58899999999999998874432      478999999999866655 7899999999999998


Q ss_pred             cC
Q 030819          155 KS  156 (171)
Q Consensus       155 ~~  156 (171)
                      .+
T Consensus       444 np  445 (526)
T KOG2135|consen  444 NP  445 (526)
T ss_pred             cC
Confidence            76

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

Probab=95.05  E-value=0.0023  Score=47.42  Aligned_cols=126  Identities=19%  Similarity=0.215  Sum_probs=91.3

Q ss_pred             eeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCCCCCCC---------CCCCC
Q 030819            6 FLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPSPHSL---------STCQP   76 (171)
Q Consensus         6 ~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------~~~~~   76 (171)
                      .|||+|.+...++.++.+-|-..+|+-+-       .+.+.   +....+ ++++.+....+...+         ...+.
T Consensus        11 tl~v~n~~~~v~eelL~ElfiqaGPV~kv-------~ip~~---~d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~   79 (267)
T KOG4454|consen   11 TLLVQNMYSGVSEELLSELFIQAGPVYKV-------GIPSG---QDQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEE   79 (267)
T ss_pred             HHHHHhhhhhhhHHHHHHHhhccCceEEE-------eCCCC---ccCCCc-eeeeecccccchhhhhhhcccchhccchh
Confidence            48999999999999999999888888321       11111   111222 556665554443322         23344


Q ss_pred             CCeEEEcC----CCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCce
Q 030819           77 KTRLFVSG----LSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKF  143 (171)
Q Consensus        77 ~~~l~V~n----l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~  143 (171)
                      ..+++.|+    |...++++.+.+.|..-|.+..+++..+. .|.++-++|+.+.-..+.-.++....+..
T Consensus        80 q~~~r~G~shapld~r~~~ei~~~v~s~a~p~~~~R~~~~~-d~rnrn~~~~~~qr~~~~P~~~~~y~~l~  149 (267)
T KOG4454|consen   80 QRTLRCGNSHAPLDERVTEEILYEVFSQAGPIEGVRIPTDN-DGRNRNFGFVTYQRLCAVPFALDLYQGLE  149 (267)
T ss_pred             hcccccCCCcchhhhhcchhhheeeecccCCCCCccccccc-cCCccCccchhhhhhhcCcHHhhhhcccC
Confidence            56888898    88899999999999999999999999888 48888999999987777777777666554

>KOG4410 consensus 5-formyltetrahydrofolate cyclo-ligase [Coenzyme transport and metabolism]

Probab=95.03  E-value=0.47  Score=36.81  Aligned_cols=59  Identities=14%  Similarity=0.241  Sum_probs=42.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCCe-EEEEEeecCCCCCcceEEEEEeCCH-------HHHHHHHHHh
Q 030819           75 QPKTRLFVSGLSFRTSEDSLRNAFQGFGQL-VEVNLVMDKIANRPRGFAFLRYATE-------EESRRAIEGM  139 (171)
Q Consensus        75 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i-~~~~~~~~~~~g~~~g~~fv~f~~~-------~~a~~al~~l  139 (171)
                      +-..-||++||+.++.-.||+.-+.+-|.+ .++.+.-      +.|-||..|.+.       .++.+++..+
T Consensus       328 ~~~~di~~~nl~rd~rv~dlk~~lr~~~~~pm~iswkg------~~~k~flh~~~~~~~~~~~~~~~~~~~s~  394 (396)
T KOG4410|consen  328 GAKTDIKLTNLSRDIRVKDLKSELRKRECTPMSISWKG------HFGKCFLHFGNRKGVPSTQDDMDKVLKSL  394 (396)
T ss_pred             ccccceeeccCccccchHHHHHHHHhcCCCceeEeeec------CCcceeEecCCccCCCCCchHHHHHhccC
Confidence            344569999999999999999999987753 4444432      347899999764       4555555444

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

Probab=94.67  E-value=0.087  Score=44.02  Aligned_cols=59  Identities=19%  Similarity=0.267  Sum_probs=46.4

Q ss_pred             CCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee---CC-eEEEEEEecCcHH
Q 030819          101 FGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFL---DG-RVIFVEIAKSRAE  159 (171)
Q Consensus       101 ~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i---~g-~~i~v~~~~~~~~  159 (171)
                      .|.-..+-+..|-.+....|||||.|.+.+++..+.++.||+..   ++ +...+.||+-++.
T Consensus       413 ~gtYDFlYLPiDF~nkcNvGYAFINm~sp~ai~~F~kAFnGk~W~~FnS~Kia~itYArIQGk  475 (549)
T KOG4660|consen  413 KGTYDFLYLPIDFKNKCNVGYAFINMTSPEAIIRFYKAFNGKKWEKFNSEKIASITYARIQGK  475 (549)
T ss_pred             cCccceEEeccccccccccceeEEeecCHHHHHHHHHHHcCCchhhhcceeeeeeehhhhhch
Confidence            45556677777877888899999999999999999999999864   43 4566777764443

>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=94.63  E-value=0.32  Score=29.85  Aligned_cols=67  Identities=22%  Similarity=0.399  Sum_probs=38.9

Q ss_pred             eEEEc-CCCCCCCHHHHHHHHhcCCC-----eEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           79 RLFVS-GLSFRTSEDSLRNAFQGFGQ-----LVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        79 ~l~V~-nl~~~~~~~~l~~~f~~~G~-----i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ++||. +--..++..+|..++..-+.     |-.+.+..        -|+||+-.. +.+..++..|++..+.|++++|+
T Consensus         2 rl~in~Gr~dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~--------~~S~vev~~-~~a~~v~~~l~~~~~~gk~v~ve   72 (74)
T PF03880_consen    2 RLFINVGRKDGLTPRDIVGAICNEAGIPGRDIGRIDIFD--------NFSFVEVPE-EVAEKVLEALNGKKIKGKKVRVE   72 (74)
T ss_dssp             EEEES-SGGGT--HHHHHHHHHTCTTB-GGGEEEEEE-S--------S-EEEEE-T-T-HHHHHHHHTT--SSS----EE
T ss_pred             EEEEEcccccCCCHHHHHHHHHhccCCCHHhEEEEEEee--------eEEEEEECH-HHHHHHHHHhcCCCCCCeeEEEE
Confidence            34443 33345788899999987654     44566643        388998864 68889999999999999999998


Q ss_pred             Ee
Q 030819          153 IA  154 (171)
Q Consensus       153 ~~  154 (171)
                      .|
T Consensus        73 ~A   74 (74)
T PF03880_consen   73 RA   74 (74)
T ss_dssp             E-
T ss_pred             EC
Confidence            65

; PDB: 2G0C_A 3MOJ_B.

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

Probab=94.63  E-value=0.041  Score=46.83  Aligned_cols=73  Identities=15%  Similarity=0.245  Sum_probs=60.7

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 030819           72 STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFV  151 (171)
Q Consensus        72 ~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v  151 (171)
                      ..-++..++||+|+...+..+-++.+...+|.|..+...         -|||..|..+....+|+..++-..++|..+.+
T Consensus        35 ~~~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~---------~fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~  105 (668)
T KOG2253|consen   35 QPLPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRD---------KFGFCEFLKHIGDLRASRLLTELNIDDQKLIE  105 (668)
T ss_pred             cCCCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhh---------hhcccchhhHHHHHHHHHHhcccCCCcchhhc
Confidence            355667899999999999999999999999987775432         28999999999999999999888888876655


Q ss_pred             EE
Q 030819          152 EI  153 (171)
Q Consensus       152 ~~  153 (171)
                      ..
T Consensus       106 ~~  107 (668)
T KOG2253|consen  106 NV  107 (668)
T ss_pred             cc
Confidence            43

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

Probab=94.52  E-value=0.013  Score=43.88  Aligned_cols=60  Identities=22%  Similarity=0.422  Sum_probs=42.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHH
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEES  132 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a  132 (171)
                      .......+++.+++..++..++...|..+|.+....+.............++.+.....+
T Consensus       221 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  280 (306)
T COG0724         221 LLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSKDGKIPKSRSFVGNEASKDA  280 (306)
T ss_pred             cccccceeeccccccccchhHHHHhccccccceeeeccCCCCCcccccccccchhHHHhh
Confidence            445667899999999999999999999999997776665553333434444333333333

>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes

Probab=94.50  E-value=0.33  Score=29.27  Aligned_cols=55  Identities=7%  Similarity=0.228  Sum_probs=43.1

Q ss_pred             CCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 030819           88 RTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFV  151 (171)
Q Consensus        88 ~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v  151 (171)
                      .++-.+++..+.+|+- .+  +..|+ +|     =||.|.+..+|+++....+|..+.+..|.+
T Consensus        11 ~~~v~d~K~~Lr~y~~-~~--I~~d~-tG-----fYIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYRW-DR--IRDDR-TG-----FYIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCCc-ce--EEecC-CE-----EEEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            4677899999999963 33  33444 33     389999999999999999999988877765

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=94.47  E-value=0.18  Score=39.24  Aligned_cols=64  Identities=22%  Similarity=0.384  Sum_probs=49.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeE
Q 030819           77 KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRV  148 (171)
Q Consensus        77 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~  148 (171)
                      ..=|-|.++++.- -..|..+|.+||.|.+.....   +|   -+-+|.|.++.+|++||. .+|..|+|..
T Consensus       197 D~WVTVfGFppg~-~s~vL~~F~~cG~Vvkhv~~~---ng---NwMhirYssr~~A~KALs-kng~ii~g~v  260 (350)
T KOG4285|consen  197 DTWVTVFGFPPGQ-VSIVLNLFSRCGEVVKHVTPS---NG---NWMHIRYSSRTHAQKALS-KNGTIIDGDV  260 (350)
T ss_pred             cceEEEeccCccc-hhHHHHHHHhhCeeeeeecCC---CC---ceEEEEecchhHHHHhhh-hcCeeeccce
Confidence            3456677888854 456778999999988765431   33   488999999999999998 6999998853

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=94.01  E-value=0.038  Score=48.40  Aligned_cols=75  Identities=17%  Similarity=0.258  Sum_probs=63.6

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee--CCeEEEEEEecC
Q 030819           79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFL--DGRVIFVEIAKS  156 (171)
Q Consensus        79 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i--~g~~i~v~~~~~  156 (171)
                      +.++.|.+-..+-..|..++..||.+.+....++-      -.+.|+|...+.|..|+++|+|.++  .|-+.+|.+++.
T Consensus       300 ~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~------N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~  373 (1007)
T KOG4574|consen  300 KQSLENNAVNLTSSSLATLCSDYGSVASAWTLRDL------NMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKT  373 (1007)
T ss_pred             hhhhhcccccchHHHHHHHHHhhcchhhheecccc------cchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEeccc
Confidence            45566777788888999999999999998877765      4899999999999999999999975  788899999885


Q ss_pred             cHH
Q 030819          157 RAE  159 (171)
Q Consensus       157 ~~~  159 (171)
                      -.-
T Consensus       374 ~~~  376 (1007)
T KOG4574|consen  374 LPM  376 (1007)
T ss_pred             ccc
Confidence            543

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=93.04  E-value=0.058  Score=42.13  Aligned_cols=79  Identities=20%  Similarity=0.133  Sum_probs=63.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 030819           75 QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEI  153 (171)
Q Consensus        75 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~  153 (171)
                      ....++|++++...+.+.+...++..+|......+........++|++.+.|...+.+..|+.......+.+..+....
T Consensus        86 ~~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl  164 (285)
T KOG4210|consen   86 GSSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDL  164 (285)
T ss_pred             cccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCcc
Confidence            4578999999999999998999999999887777777666888999999999999999999994333345555444443

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

Probab=92.56  E-value=0.024  Score=39.71  Aligned_cols=55  Identities=15%  Similarity=0.080  Sum_probs=42.0

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCCC
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPS   67 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   67 (171)
                      ..+|||+++.+++++..+...|...+++         .+.....+..+.++++++++.+..+..
T Consensus        34 ~~~lfVgnL~~~~te~~L~~~F~~~G~I---------~~v~i~~d~~tg~~kGfaFV~F~~~e~   88 (144)
T PLN03134         34 STKLFIGGLSWGTDDASLRDAFAHFGDV---------VDAKVIVDRETGRSRGFGFVNFNDEGA   88 (144)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCe---------EEEEEEecCCCCCcceEEEEEECCHHH
Confidence            4679999999999999999999998776         445555555566777777766665543

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=90.58  E-value=0.5  Score=39.89  Aligned_cols=71  Identities=10%  Similarity=0.323  Sum_probs=54.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhc--CCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCc--eeCCeEEEE
Q 030819           76 PKTRLFVSGLSFRTSEDSLRNAFQG--FGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGK--FLDGRVIFV  151 (171)
Q Consensus        76 ~~~~l~V~nl~~~~~~~~l~~~f~~--~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~--~i~g~~i~v  151 (171)
                      ..+.|.+.-||..+-.++++.+|+.  +-.+.+|.+-.+.       -=||+|++..+|+.|...|...  +|.|++|..
T Consensus       174 kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~-------nWyITfesd~DAQqAykylreevk~fqgKpImA  246 (684)
T KOG2591|consen  174 KRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND-------NWYITFESDTDAQQAYKYLREEVKTFQGKPIMA  246 (684)
T ss_pred             ceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC-------ceEEEeecchhHHHHHHHHHHHHHhhcCcchhh
Confidence            3467888999999999999999974  6778888876654       2489999999999998877543  466766554


Q ss_pred             EE
Q 030819          152 EI  153 (171)
Q Consensus       152 ~~  153 (171)
                      ++
T Consensus       247 RI  248 (684)
T KOG2591|consen  247 RI  248 (684)
T ss_pred             hh
Confidence            43

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=90.01  E-value=1.8  Score=35.78  Aligned_cols=69  Identities=16%  Similarity=0.302  Sum_probs=57.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCC-CeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC
Q 030819           76 PKTRLFVSGLSFRTSEDSLRNAFQGFG-QLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDG  146 (171)
Q Consensus        76 ~~~~l~V~nl~~~~~~~~l~~~f~~~G-~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g  146 (171)
                      ++..|+|-.+|-.++--||..+...+- .|.++++++|...  ++=..+|.|.+.++|....+.+||..++.
T Consensus        73 ~~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~p--nrymvLIkFr~q~da~~Fy~efNGk~Fn~  142 (493)
T KOG0804|consen   73 SSTMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGMP--NRYMVLIKFRDQADADTFYEEFNGKQFNS  142 (493)
T ss_pred             CCcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCCC--ceEEEEEEeccchhHHHHHHHcCCCcCCC
Confidence            388999999999999999999888654 5889999986522  23467999999999999999999998754

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

Probab=89.51  E-value=0.12  Score=42.55  Aligned_cols=70  Identities=13%  Similarity=0.127  Sum_probs=57.4

Q ss_pred             eeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCCCCCCC-----CCCCCCCe
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPSPHSL-----STCQPKTR   79 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~   79 (171)
                      +.+|||++.|+.+++.+...|...+++         .++.-.++..+++.+|++|+++..+..+..+     .....+++
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v---------~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~   89 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPV---------LSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRK   89 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCcc---------ceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCce
Confidence            779999999999999999999999999         8888889999999999999999887654432     23444566


Q ss_pred             EEEc
Q 030819           80 LFVS   83 (171)
Q Consensus        80 l~V~   83 (171)
                      |.|.
T Consensus        90 l~v~   93 (435)
T KOG0108|consen   90 LRVN   93 (435)
T ss_pred             EEee
Confidence            6653

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

Probab=89.39  E-value=0.11  Score=41.81  Aligned_cols=75  Identities=11%  Similarity=0.048  Sum_probs=56.8

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 030819           72 STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFV  151 (171)
Q Consensus        72 ~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v  151 (171)
                      ....-..+++|.+|+..+-..++.++|..+|.+....+.    .+...-+|-+.|....+...|+. .+|..+.-....+
T Consensus       146 kleeirRt~~v~sl~~~~~l~e~~e~f~r~Gev~ya~~a----sk~~s~~c~~sf~~qts~~halr-~~gre~k~qhsr~  220 (479)
T KOG4676|consen  146 KLEEIRRTREVQSLISAAILPESGESFERKGEVSYAHTA----SKSRSSSCSHSFRKQTSSKHALR-SHGRERKRQHSRR  220 (479)
T ss_pred             hhHHHHhhhhhhcchhhhcchhhhhhhhhcchhhhhhhh----ccCCCcchhhhHhhhhhHHHHHH-hcchhhhhhhhhh
Confidence            334445789999999999999999999999998887664    33344577899998888888888 6777654333333

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

Probab=85.68  E-value=0.18  Score=37.59  Aligned_cols=62  Identities=11%  Similarity=0.044  Sum_probs=50.3

Q ss_pred             eecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 030819            7 LPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPSPHSLSTCQPK   77 (171)
Q Consensus         7 ~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   77 (171)
                      ||||.+.-+.++.++...|-.++.+         .+.....+....+.|+++++++.....+..+..+...
T Consensus        13 lYVGGladeVtekvLhaAFIPFGDI---------~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMne   74 (298)
T KOG0111|consen   13 LYVGGLADEVTEKVLHAAFIPFGDI---------KDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNE   74 (298)
T ss_pred             EEeccchHHHHHHHHHhccccccch---------hhcccccchhcccccceeEEEeeccchhHHHhhcCch
Confidence            9999999999999999999888877         5555666777789999999999888776665444443

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

Probab=85.17  E-value=0.2  Score=38.99  Aligned_cols=54  Identities=13%  Similarity=0.156  Sum_probs=47.7

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCC
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPP   66 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   66 (171)
                      .+.|||+-+.|+.++..|...|+..+++         ..+....++-++++++++|+++..+-
T Consensus       101 y~TLFv~RLnydT~EskLrreF~~YG~I---------krirlV~d~vTgkskGYAFIeye~er  154 (335)
T KOG0113|consen  101 YKTLFVARLNYDTSESKLRREFEKYGPI---------KRIRLVRDKVTGKSKGYAFIEYEHER  154 (335)
T ss_pred             cceeeeeeccccccHHHHHHHHHhcCcc---------eeEEEeeecccCCccceEEEEeccHH
Confidence            4679999999999999999999999999         77778888889999999998776554

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

Probab=83.89  E-value=0.25  Score=35.58  Aligned_cols=55  Identities=13%  Similarity=-0.037  Sum_probs=40.2

Q ss_pred             eeeeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCCCCCCC
Q 030819            3 VLGFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPSPHSL   71 (171)
Q Consensus         3 ~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   71 (171)
                      +.+++||||+..+.+...|-..|...++.         .+.-..     ....+++|++|..+-.+..+
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~l---------rsvWvA-----rnPPGfAFVEFed~RDA~DA   63 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPL---------RSVWVA-----RNPPGFAFVEFEDPRDAEDA   63 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcc---------eeEEEe-----ecCCCceEEeccCcccHHHH
Confidence            46899999999999999999999998866         221111     24567778777777665544

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

Probab=82.90  E-value=0.29  Score=38.63  Aligned_cols=54  Identities=17%  Similarity=0.180  Sum_probs=47.2

Q ss_pred             eeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCCCCCC
Q 030819            6 FLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPSPHS   70 (171)
Q Consensus         6 ~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   70 (171)
                      .|+|.||.+.+.+-.+...|.+.+++         .+.+.+++.  +.+||++|+....+.+...
T Consensus        98 RLhVSNIPFrFRdpDL~aMF~kfG~V---------ldVEIIfNE--RGSKGFGFVTmen~~dadR  151 (376)
T KOG0125|consen   98 RLHVSNIPFRFRDPDLRAMFEKFGKV---------LDVEIIFNE--RGSKGFGFVTMENPADADR  151 (376)
T ss_pred             eeEeecCCccccCccHHHHHHhhCce---------eeEEEEecc--CCCCccceEEecChhhHHH
Confidence            58999999999999999999999999         889998885  6888999998887766544

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	171
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		2e-12
2lea_A	135	Solution Structure Of Human Srsf2 (Sc35) Rrm Length		6e-11
3cw1_K	216	Crystal Structure Of Human Spliceosomal U1 Snrnp Le		8e-11
2kn4_A	158	The Structure Of The Rrm Domain Of Sc35 Length = 15		8e-11
3pgw_S	437	Crystal Structure Of Human U1 Snrnp Length = 437		2e-10
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		2e-09
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		2e-09
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		2e-09
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		2e-09
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		2e-09
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		2e-09
2dnm_A	103	Solution Structure Of Rna Binding Domain In Srp46 S		3e-09
2rrb_A	96	Refinement Of Rna Binding Domain In Human Tra2 Beta		3e-09
2rra_A	99	Solution Structure Of Rna Binding Domain In Human T		4e-09
1whw_A	99	Solution Structure Of The N-Terminal Rna Binding Do		5e-09
2fc8_A	102	Solution Structure Of The Rrm_1 Domain Of Ncl Prote		6e-09
2kxn_B	129	Nmr Structure Of Human Tra2beta1 Rrm In Complex Wit		6e-09
2cqc_A	95	Solution Structure Of The Rna Recognition Motif In		1e-08
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		1e-08
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		1e-08
1sxl_A	97	Resonance Assignments And Solution Structure Of The		2e-08
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		2e-08
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		2e-08
1x4b_A	116	Solution Structure Of Rrm Domain In Heterogeneous N		2e-08
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		2e-08
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		3e-08
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		5e-08
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		6e-08
2cqd_A	116	Solution Structure Of The Rna Recognition Motif In		1e-07
4f25_A	115	Crystal Structure Of The Second Rrm Domain Of Human		1e-07
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		1e-07
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		1e-07
2k8g_A	95	Solution Structure Of Rrm2 Domain Of Pabp1 Length =		1e-07
1hd0_A	75	Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D		2e-07
3hi9_A	84	The X-Ray Crystal Structure Of The First Rna Recogn		2e-07
1wtb_A	79	Complex Structure Of The C-Terminal Rna-Binding Dom		2e-07
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		2e-07
2err_A	109	Nmr Structure Of The Rna Binding Domain Of Human Fo		3e-07
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		3e-07
2do4_A	100	Solution Structure Of The Rna Binding Domain Of Squ		3e-07
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		3e-07
1iqt_A	75	Solution Structure Of The C-Terminal Rna-Binding Do		4e-07
4fxv_A	99	Crystal Structure Of An Elav-Like Protein 1 (Elavl1		4e-07
3mdf_A	85	Crystal Structure Of The Rrm Domain Of Cyclophilin		5e-07
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		5e-07
3md1_A	83	Crystal Structure Of The Second Rrm Domain Of Yeast		6e-07
2cqb_A	102	Solution Structure Of The Rna Recognition Motif In		7e-07
2dh8_A	105	Solution Structure Of The N-Terminal Rna Binding Do		7e-07
2dgs_A	99	Solution Structure Of The Second Rna Binding Domain		8e-07
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		8e-07
2xb2_D	90	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		1e-06
2hyi_B	91	Structure Of The Human Exon Junction Complex With A		1e-06
2cq0_A	103	Solution Structure Of Rna Binding Domain In Eukaryo		1e-06
2j0s_D	89	The Crystal Structure Of The Exon Junction Complex		1e-06
1p27_B	106	Crystal Structure Of The Human Y14MAGOH COMPLEX Len		1e-06
2kyx_A	83	Solution Structure Of The Rrm Domain Of Cyp33 Lengt		1e-06
2j0q_D	109	The Crystal Structure Of The Exon Junction Complex		1e-06
2cq3_A	103	Solution Structure Of Rna Binding Domain In Rna Bin		2e-06
2ku7_A	140	Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric		2e-06
2yh0_A	198	Solution Structure Of The Closed Conformation Of Hu		2e-06
3ex7_B	126	The Crystal Structure Of Ejc In Its Transition Stat		2e-06
2e5h_A	94	Solution Structure Of Rna Binding Domain In Zinc Fi		2e-06
2mss_A	75	Musashi1 Rbd2, Nmr Length = 75		3e-06
3lpy_A	79	Crystal Structure Of The Rrm Domain Of Cyp33 Length		5e-06
2d9p_A	103	Solution Structure Of Rna Binding Domain 4 In Polya		5e-06
3s7r_A	87	Crystal Structure Of A Heterogeneous Nuclear Ribonu		5e-06
3vaf_A	174	Structure Of U2af65 Variant With Bru3 Dna Length =		6e-06
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		7e-06
2g4b_A	172	Structure Of U2af65 Variant With Polyuridine Tract		7e-06
2dnk_A	105	Solution Structure Of Rna Binding Domain In Bruno-L		1e-05
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		2e-05
2u2f_A	85	Solution Structure Of The Second Rna-Binding Domain		2e-05
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		3e-05
2rs2_A	109	1h, 13c, And 15n Chemical Shift Assignments For Mus		3e-05
1x4h_A	111	Solution Structure Of Rrm Domain In Rna-Binding Pro		4e-05
1h2t_Z	156	Structure Of The Human Nuclear Cap-Binding-Complex		4e-05
2cqg_A	103	Solution Structure Of The Rna Binding Domain Of Tar		4e-05
1uaw_A	77	Solution Structure Of The N-Terminal Rna-Binding Do		4e-05
1x5t_A	96	Solution Structure Of The Second Rrm Domain In Spli		5e-05
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		7e-05
1d9a_A	85	Solution Structure Of The Second Rna-Binding Domain		8e-05
1oo0_B	110	Crystal Structure Of The Drosophila Mago Nashi-Y14		9e-05
1x4g_A	109	Solution Structure Of Rrm Domain In Nucleolysin Tia		2e-04
1hl6_A	165	A Novel Mode Of Rbd-Protein Recognition In The Y14-		2e-04
2cpf_A	98	Solution Structure Of The Penultimate Rna Recogniti		2e-04
1h6k_Z	98	Nuclear Cap Binding Complex Length = 98		3e-04
2osq_A	74	Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein Length		8e-04
1x4e_A	85	Solution Structure Of Rrm Domain In Rna Binding Mot		9e-04

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 68.6 bits (166), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 34/88 (38%), Positives = 53/88 (60%)
Query: 74  CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESR 133
              + +LFV GLSF T+E SL   F  +GQ+ EV +V D+   R RGF F+ +   ++++
Sbjct: 9   ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAK 68
Query: 134 RAIEGMHGKFLDGRVIFVEIAKSRAELR 161
            A+  M+GK +DGR I V+ A   ++ R
Sbjct: 69  DAMMAMNGKSVDGRQIRVDQAGKSSDNR 96

>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm Length = 135

Iteration: 1
 Score = 63.5 bits (153), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 29/78 (37%), Positives = 50/78 (64%)
Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           T L V  L++RTS D+LR  F+ +G++ +V +  D+     RGFAF+R+  + ++  A++
Sbjct: 48  TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 107
Query: 138 GMHGKFLDGRVIFVEIAK 155
            M G  LDGR + V++A+
Sbjct: 108 AMDGAVLDGRELRVQMAR 125

>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp Length = 216

Iteration: 1
 Score = 63.2 bits (152), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 26/79 (32%), Positives = 48/79 (60%)
Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           LFV+ +++ T+E  LR  F+ +G +  +++V  K + +PRG+AF+ Y  E +   A +  
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 140 HGKFLDGRVIFVEIAKSRA 158
            GK +DGR + V++ + R 
Sbjct: 165 DGKKIDGRRVLVDVERGRT 183

>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35 Length = 158

Iteration: 1
 Score = 62.8 bits (151), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 29/82 (35%), Positives = 51/82 (62%)
Query: 74  CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESR 133
            +  T L V  L++RTS D+LR  F+ +G++ +V +  D+     RGFAF+R+  + ++ 
Sbjct: 67  VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAE 126
Query: 134 RAIEGMHGKFLDGRVIFVEIAK 155
            A++ M G  LDGR + V++A+
Sbjct: 127 DAMDAMDGAVLDGRELRVQMAR 148

>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp Length = 437

Iteration: 1
 Score = 62.0 bits (149), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 29/93 (31%), Positives = 52/93 (55%), Gaps = 2/93 (2%)
Query: 67  SPHSLSTCQPKT--RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFL 124
            PH+    Q      LFV+ +++ T+E  LR  F+ +G +  +++V  K + +PRG+AF+
Sbjct: 90  DPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFI 149
Query: 125 RYATEEESRRAIEGMHGKFLDGRVIFVEIAKSR 157
            Y  E +   A +   GK +DGR + V++ + R
Sbjct: 150 EYEHERDMHSAYKHADGKKIDGRRVLVDVERGR 182

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 58.5 bits (140), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 33/81 (40%), Positives = 50/81 (61%), Gaps = 1/81 (1%)
Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           +LF+ GLSF T+++SLR+ F+ +G L +  ++ D    R RGF F+ YAT EE   A+  
Sbjct: 15  KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 74
Query: 139 MHGKFLDGRVIFVEIAKSRAE 159
              K +DGRV+  + A SR +
Sbjct: 75  RPHK-VDGRVVEPKRAVSRED 94

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 58.5 bits (140), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 33/81 (40%), Positives = 50/81 (61%), Gaps = 1/81 (1%)
Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           +LF+ GLSF T+++SLR+ F+ +G L +  ++ D    R RGF F+ YAT EE   A+  
Sbjct: 13  KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 72
Query: 139 MHGKFLDGRVIFVEIAKSRAE 159
              K +DGRV+  + A SR +
Sbjct: 73  RPHK-VDGRVVEPKRAVSRED 92

>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi) G); A Human Telomeric Repeat Containing 6-Methyl-8-(2- Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi) Length = 195

Iteration: 1
 Score = 58.5 bits (140), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 33/81 (40%), Positives = 50/81 (61%), Gaps = 1/81 (1%)
Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           +LF+ GLSF T+++SLR+ F+ +G L +  ++ D    R RGF F+ YAT EE   A+  
Sbjct: 14  KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 73
Query: 139 MHGKFLDGRVIFVEIAKSRAE 159
              K +DGRV+  + A SR +
Sbjct: 74  RPHK-VDGRVVEPKRAVSRED 93

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 58.5 bits (140), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 33/81 (40%), Positives = 50/81 (61%), Gaps = 1/81 (1%)
Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           +LF+ GLSF T+++SLR+ F+ +G L +  ++ D    R RGF F+ YAT EE   A+  
Sbjct: 15  KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 74
Query: 139 MHGKFLDGRVIFVEIAKSRAE 159
              K +DGRV+  + A SR +
Sbjct: 75  RPHK-VDGRVVEPKRAVSRED 94

>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1 (up1) Using Segmental Isotope Labeling Length = 197

Iteration: 1
 Score = 58.2 bits (139), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 33/81 (40%), Positives = 50/81 (61%), Gaps = 1/81 (1%)
Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           +LF+ GLSF T+++SLR+ F+ +G L +  ++ D    R RGF F+ YAT EE   A+  
Sbjct: 16  KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 75
Query: 139 MHGKFLDGRVIFVEIAKSRAE 159
              K +DGRV+  + A SR +
Sbjct: 76  RPHK-VDGRVVEPKRAVSRED 95

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 58.2 bits (139), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 33/81 (40%), Positives = 50/81 (61%), Gaps = 1/81 (1%)
Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           +LF+ GLSF T+++SLR+ F+ +G L +  ++ D    R RGF F+ YAT EE   A+  
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67
Query: 139 MHGKFLDGRVIFVEIAKSRAE 159
              K +DGRV+  + A SR +
Sbjct: 68  RPHK-VDGRVVEPKRAVSRED 87

>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing Factor Length = 103

Iteration: 1
 Score = 57.8 bits (138), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 29/76 (38%), Positives = 47/76 (61%)
Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           L V  L++RTS DSLR  F+ +G++ +V +  +     PRGFAF+R+    +++ A   M
Sbjct: 16  LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAM 75
Query: 140 HGKFLDGRVIFVEIAK 155
            G  LDGR + V++A+
Sbjct: 76  DGAELDGRELRVQVAR 91

>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta Protein Length = 96

Iteration: 1
 Score = 57.4 bits (137), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 30/83 (36%), Positives = 49/83 (59%)
Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
            P   L V GLS  T+E  LR  F  +G + +V++V D+ + R RGFAF+ +   ++++ 
Sbjct: 10  DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 69
Query: 135 AIEGMHGKFLDGRVIFVEIAKSR 157
           A E  +G  LDGR I V+ + ++
Sbjct: 70  AKERANGMELDGRRIRVDFSITK 92

>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2 Beta Protein In Complex With Rna (Gaagaa) Length = 99

Iteration: 1
 Score = 57.4 bits (137), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 30/83 (36%), Positives = 49/83 (59%)
Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
            P   L V GLS  T+E  LR  F  +G + +V++V D+ + R RGFAF+ +   ++++ 
Sbjct: 13  DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 72
Query: 135 AIEGMHGKFLDGRVIFVEIAKSR 157
           A E  +G  LDGR I V+ + ++
Sbjct: 73  AKERANGMELDGRRIRVDFSITK 95

>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain From Hypothetical Protein Bab23448 Length = 99

Iteration: 1
 Score = 57.0 bits (136), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 27/85 (31%), Positives = 48/85 (56%)
Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           RLFV  LS+ +SE+ L   F  +G L E++  +D +  +P+GFAF+ +   E + +A   
Sbjct: 10  RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 139 MHGKFLDGRVIFVEIAKSRAELRQA 163
           + G+   GR++ V  +  + E  Q+
Sbjct: 70  VDGQVFQGRMLHVLPSTIKKEASQS 94

>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein Length = 102

Iteration: 1
 Score = 56.6 bits (135), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 28/82 (34%), Positives = 46/82 (56%), Gaps = 3/82 (3%)
Query: 74  CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESR 133
            QP   LFV GLS  T+E++L+ +F G    V   +V D+     +GF F+ + +EE+++
Sbjct: 12  SQPSKTLFVKGLSEDTTEETLKESFDG---SVRARIVTDRETGSSKGFGFVDFNSEEDAK 68
Query: 134 RAIEGMHGKFLDGRVIFVEIAK 155
            A E M    +DG  + ++ AK
Sbjct: 69  AAKEAMEDGEIDGNKVTLDWAK 90

>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With Aagaac Rna Length = 129

Iteration: 1
 Score = 56.6 bits (135), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 30/83 (36%), Positives = 49/83 (59%)
Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
            P   L V GLS  T+E  LR  F  +G + +V++V D+ + R RGFAF+ +   ++++ 
Sbjct: 44  DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 103
Query: 135 AIEGMHGKFLDGRVIFVEIAKSR 157
           A E  +G  LDGR I V+ + ++
Sbjct: 104 AKERANGMELDGRRIRVDFSITK 126

>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In ArginineSERINE-Rich Splicing Factor 10 Length = 95

Iteration: 1
 Score = 55.8 bits (133), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 30/77 (38%), Positives = 45/77 (58%)
Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
            P   L V GLS  T+E  LR  F  +G + +V++V D+ + R RGFAF+ +   ++++ 
Sbjct: 13  DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 72
Query: 135 AIEGMHGKFLDGRVIFV 151
           A E  +G  LDGR I V
Sbjct: 73  AKERANGMELDGRRIRV 89

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 55.8 bits (133), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 25/69 (36%), Positives = 41/69 (59%)
Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           T L+V+ L    ++D L   F  +G +V+ N++ DK+  RPRG AF+RY   EE++ AI 
Sbjct: 90  TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 149
Query: 138 GMHGKFLDG 146
            ++    +G
Sbjct: 150 ALNNVIPEG 158

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 55.5 bits (132), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 25/69 (36%), Positives = 41/69 (59%)
Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           T L+V+ L    ++D L   F  +G +V+ N++ DK+  RPRG AF+RY   EE++ AI 
Sbjct: 101 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 160
Query: 138 GMHGKFLDG 146
            ++    +G
Sbjct: 161 ALNNVIPEG 169

>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second Rna-Binding Domain Of Sex-Lethal Determined By Multidimensional Heteronuclear Magnetic Resonance Spectroscopy Length = 97

Iteration: 1
 Score = 55.5 bits (132), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 25/69 (36%), Positives = 41/69 (59%)
Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           T L+V+ L    ++D L   F  +G +V+ N++ DK+  RPRG AF+RY   EE++ AI 
Sbjct: 14  TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 73
Query: 138 GMHGKFLDG 146
            ++    +G
Sbjct: 74  ALNNVIPEG 82

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 55.5 bits (132), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 27/81 (33%), Positives = 47/81 (58%)
Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           RL+V  L F  +ED LR  F+ FG++  + L+MD    R +G+ F+ ++  E +++A+E 
Sbjct: 28  RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 139 MHGKFLDGRVIFVEIAKSRAE 159
           ++G  L GR + V     R +
Sbjct: 88  LNGFELAGRPMKVGHVTERTD 108

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 54.7 bits (130), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 29/77 (37%), Positives = 47/77 (61%), Gaps = 1/77 (1%)
Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           +LF+ GL+  T+E  L+  F   G + EV L+ D+ + + RGFAF+ +    +++ A + 
Sbjct: 9   KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTS-KSRGFAFITFENPADAKNAAKD 67
Query: 139 MHGKFLDGRVIFVEIAK 155
           M+GK L G+ I VE AK
Sbjct: 68  MNGKSLHGKAIKVEQAK 84

>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear Ribonucleaoproteins A2B1 Length = 116

Iteration: 1
 Score = 54.7 bits (130), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 29/81 (35%), Positives = 50/81 (61%), Gaps = 1/81 (1%)
Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           +LF+ GLSF T+E+SLRN ++ +G+L +  ++ D  + R RGF F+ +++  E   A+  
Sbjct: 29  KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM-A 87
Query: 139 MHGKFLDGRVIFVEIAKSRAE 159
                +DGRV+  + A +R E
Sbjct: 88  ARPHSIDGRVVEPKRAVAREE 108

>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To Ssdna From A Portion Of Fuse Length = 216

Iteration: 1
 Score = 54.7 bits (130), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 24/74 (32%), Positives = 43/74 (58%)
Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           +R++V  + +   ED++R AF  FG +  +++  D +  + +GFAF+ Y   E ++ A+E
Sbjct: 29  SRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALE 88
Query: 138 GMHGKFLDGRVIFV 151
            M+   L GR I V
Sbjct: 89  QMNSVMLGGRNIKV 102

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 54.7 bits (130), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 24/73 (32%), Positives = 42/73 (57%)
Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           R++V  + +   ED++R AF  FG +  +++  D +  + +GFAF+ Y   E ++ A+E 
Sbjct: 15  RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 74
Query: 139 MHGKFLDGRVIFV 151
           M+   L GR I V
Sbjct: 75  MNSVMLGGRNIKV 87

>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In Complex With Rrm1-2 Of Pabp And Poly(A) Length = 213

Iteration: 1
 Score = 53.5 bits (127), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 27/80 (33%), Positives = 44/80 (55%), Gaps = 2/80 (2%)
Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           +F+  L       +L + F  FG ++   +V D+  N  +G+ F+ + T+E + RAIE M
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKM 163
Query: 140 HGKFLDGRVIFVEIAKSRAE 159
           +G  L+ R +FV   KSR E
Sbjct: 164 NGMLLNDRKVFVGRFKSRKE 183

>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In Complex With Polyadenylate Rna Length = 190

Iteration: 1
 Score = 53.5 bits (127), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 27/80 (33%), Positives = 44/80 (55%), Gaps = 2/80 (2%)
Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           +F+  L       +L + F  FG ++   +V D+  N  +G+ F+ + T+E + RAIE M
Sbjct: 101 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKM 158
Query: 140 HGKFLDGRVIFVEIAKSRAE 159
           +G  L+ R +FV   KSR E
Sbjct: 159 NGMLLNDRKVFVGRFKSRKE 178

>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna- Binding Region Containing Protein 1 Length = 116

Iteration: 1
 Score = 52.4 bits (124), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 26/77 (33%), Positives = 44/77 (57%), Gaps = 1/77 (1%)
Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           T++FV GL + T++ SLR  F+GFG + E  ++ D+   + RG+ F+  A    + RA +
Sbjct: 18  TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACK 77
Query: 138 GMHGKFLDGRVIFVEIA 154
             +   +DGR   V +A
Sbjct: 78  DPN-PIIDGRKANVNLA 93

>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1 At Ph 6.0 Length = 115

Iteration: 1
 Score = 52.4 bits (124), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 27/80 (33%), Positives = 44/80 (55%), Gaps = 2/80 (2%)
Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           +F+  L       +L + F  FG ++   +V D+  N  +G+ F+ + T+E + RAIE M
Sbjct: 8   IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKM 65
Query: 140 HGKFLDGRVIFVEIAKSRAE 159
           +G  L+ R +FV   KSR E
Sbjct: 66  NGMLLNDRKVFVGRFKSRKE 85

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 52.4 bits (124), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 26/84 (30%), Positives = 46/84 (54%)
Query: 77  KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
           +T L V+ L    ++D LR+ F   G++    L+ DK+A    G+ F+ Y T +++ RAI
Sbjct: 2   RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 61
Query: 137 EGMHGKFLDGRVIFVEIAKSRAEL 160
             ++G  L  + I V  A+  +E+
Sbjct: 62  NTLNGLRLQSKTIKVSYARPSSEV 85

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 52.4 bits (124), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 26/84 (30%), Positives = 46/84 (54%)
Query: 77  KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
           +T L V+ L    ++D LR+ F   G++    L+ DK+A    G+ F+ Y T +++ RAI
Sbjct: 2   RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 61
Query: 137 EGMHGKFLDGRVIFVEIAKSRAEL 160
             ++G  L  + I V  A+  +E+
Sbjct: 62  NTLNGLRLQSKTIKVSYARPSSEV 85

>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1 Length = 95

Iteration: 1
 Score = 52.4 bits (124), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 27/80 (33%), Positives = 44/80 (55%), Gaps = 2/80 (2%)
Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           +F+  L       +L + F  FG ++   +V D+  N  +G+ F+ + T+E + RAIE M
Sbjct: 14  IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKM 71
Query: 140 HGKFLDGRVIFVEIAKSRAE 159
           +G  L+ R +FV   KSR E
Sbjct: 72  NGMLLNDRKVFVGRFKSRKE 91

>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0 Rbd1), Nmr Length = 75

Iteration: 1
 Score = 52.0 bits (123), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 24/70 (34%), Positives = 42/70 (60%), Gaps = 1/70 (1%)
Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           +F+ GLS+ T++  L++ F  FG++V+  L +D I  R RGF F+ +   E   + ++  
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 140 HGKFLDGRVI 149
             K L+G+VI
Sbjct: 62  EHK-LNGKVI 70

>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition Motif (Rrm1) Of The Au-Rich Element (Are) Binding Protein Hur At 2.0 Angstrom Resolution Length = 84

Iteration: 1
 Score = 51.6 bits (122), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 25/79 (31%), Positives = 43/79 (54%)
Query: 77  KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
           +T L V+ L    ++D LR+ F   G++    L+ DK+A    G+ F+ Y T +++ RAI
Sbjct: 4   RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 63
Query: 137 EGMHGKFLDGRVIFVEIAK 155
             ++G  L  + I V  A+
Sbjct: 64  NTLNGLRLQSKTIKVSYAR 82

>pdb|1WTB|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of Hnrnp D (Auf1) With Telomere Dna Length = 79

Iteration: 1
 Score = 51.6 bits (122), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 23/59 (38%), Positives = 36/59 (61%)
Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           ++FV GLS  T E+ +R  F GFG++  + L MD   N+ RGF F+ +  EE  ++ +E
Sbjct: 3   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 61

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 51.6 bits (122), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 23/71 (32%), Positives = 40/71 (56%), Gaps = 2/71 (2%)
Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           ++F+ GL++ T+ED+LR  F  +G + ++ ++ D    R RGF FL +         ++ 
Sbjct: 5   KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 139 MHGKFLDGRVI 149
            H   LDG+VI
Sbjct: 65  QH--ILDGKVI 73

>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In Complex With Ugcaugu Length = 109

Iteration: 1
 Score = 51.2 bits (121), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 31/99 (31%), Positives = 54/99 (54%), Gaps = 5/99 (5%)
Query: 62  ACLPPSPH--SLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPR 119
             +P   H  + +  QPK RL VS + FR  +  LR  F  FG++++V ++ ++  +  +
Sbjct: 13  GLVPRGSHMNTENKSQPK-RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS--K 69
Query: 120 GFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKSRA 158
           GF F+ +    ++ RA E +HG  ++GR I V  A +R 
Sbjct: 70  GFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARV 108

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 51.2 bits (121), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 25/68 (36%), Positives = 41/68 (60%)
Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           L+V  L F  +ED LR  F+ FG++  + L+ D    R +G+ F+ ++  E +RRA+E +
Sbjct: 8   LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 140 HGKFLDGR 147
           +G  L GR
Sbjct: 68  NGFELAGR 75

>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 = 51.2 bits (121), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 26/85 (30%), Positives = 48/85 (56%), Gaps = 1/85 (1%)
Query: 72  STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEE 131
           ST   K +LF+SGL F  +++ L    +  G + ++ LV ++ A +P+G A++ Y  E +
Sbjct: 12  STSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQ 70
Query: 132 SRRAIEGMHGKFLDGRVIFVEIAKS 156
           + +A+  M G  +   +I V I+ S
Sbjct: 71  ASQAVMKMDGMTIKENIIKVAISNS 95

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score = 50.8 bits (120), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 21/76 (27%), Positives = 44/76 (57%)
Query: 72  STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEE 131
           S+      LFV  L+    +++LRNAF+ F   +  +++ D      RG+ F+ + ++++
Sbjct: 82  SSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDD 141
Query: 132 SRRAIEGMHGKFLDGR 147
           ++ A++ M G+ L+GR
Sbjct: 142 AQNAMDSMQGQDLNGR 157

>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1) Length = 75

Iteration: 1
 Score = 50.8 bits (120), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 23/58 (39%), Positives = 35/58 (60%)
Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           +FV GLS  T E+ +R  F GFG++  + L MD   N+ RGF F+ +  EE  ++ +E
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 59

>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From Homo Sapiens At 1.90 A Resolution Length = 99

Iteration: 1
 Score = 50.4 bits (119), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 25/78 (32%), Positives = 42/78 (53%)
Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           T L V+ L    ++D LR+ F   G++    L+ DK+A    G+ F+ Y T +++ RAI 
Sbjct: 20  TNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 79
Query: 138 GMHGKFLDGRVIFVEIAK 155
            ++G  L  + I V  A+
Sbjct: 80  TLNGLRLQSKTIKVSYAR 97

>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33 Length = 85

Iteration: 1
 Score = 50.4 bits (119), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 28/84 (33%), Positives = 44/84 (52%)
Query: 72  STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEE 131
           S    K  L+V GL+    +  L  AF  FG + ++ + +D    + RGFAF+ +   E+
Sbjct: 2   SMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAED 61
Query: 132 SRRAIEGMHGKFLDGRVIFVEIAK 155
           +  AI+ M+   L GR I V +AK
Sbjct: 62  AAAAIDNMNESELFGRTIRVNLAK 85

>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U Binding Splicing Factor 60kda (Puf60) From Homo Sapiens At 2.50 A Resolution Length = 200

Iteration: 1
 Score = 50.4 bits (119), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 23/73 (31%), Positives = 40/73 (54%)
Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           R++V  + +   ED++R AF  FG +  ++   D +  + +GFAF+ Y   E ++ A+E 
Sbjct: 14  RVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQ 73
Query: 139 MHGKFLDGRVIFV 151
            +   L GR I V
Sbjct: 74  XNSVXLGGRNIKV 86

>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast Poly(U)-Binding Protein (Pub1) Length = 83

Iteration: 1
 Score = 50.1 bits (118), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 21/75 (28%), Positives = 45/75 (60%)
Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           LFV  L+    +++LRNAF+ F   +  +++ D      RG+ F+ + ++++++ A++ M
Sbjct: 4   LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 140 HGKFLDGRVIFVEIA 154
            G+ L+GR + +  A
Sbjct: 64  QGQDLNGRPLRINWA 78

>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In Peptidyl- Prolyl Cis-Trans Isomerase E Length = 102

Iteration: 1
 Score = 50.1 bits (118), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 29/89 (32%), Positives = 45/89 (50%)
Query: 67  SPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRY 126
           S  S      K  L+V GL+    +  L  AF  FG + ++ + +D    + RGFAF+ +
Sbjct: 2   SSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 61
Query: 127 ATEEESRRAIEGMHGKFLDGRVIFVEIAK 155
              E++  AI+ M+   L GR I V +AK
Sbjct: 62  ELAEDAAAAIDNMNESELFGRTIRVNLAK 90

>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Daz-Associated Protein 1 Length = 105

Iteration: 1
 Score = 49.7 bits (117), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 18/48 (37%), Positives = 35/48 (72%)
Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRY 126
           +LFV GL + T++++LR+ F  +G++V+  ++ DK  N+ RGF F+++
Sbjct: 18  KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKF 65

>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In Daz- Associated Protein 1 Length = 99

Iteration: 1
 Score = 49.7 bits (117), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 29/90 (32%), Positives = 47/90 (52%), Gaps = 5/90 (5%)
Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           ++FV G+     E  LR  F+ FG + EV ++ D    RPRGF F+ +  E+   +A+  
Sbjct: 12  KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN- 70
Query: 139 MHGKFLDGRVIFVEIAKSRAELRQAFKNNP 168
           MH   + G+ + V+    RAE R +  + P
Sbjct: 71  MHFHDIMGKKVEVK----RAEPRDSKSSGP 96

>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage Stimulation Factor 64 Kda Subunit Length = 104

Iteration: 1
 Score = 49.7 bits (117), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 24/85 (28%), Positives = 47/85 (55%), Gaps = 3/85 (3%)
Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           +FV  + +  +E+ L++ F   G +V   LV D+   +P+G+ F  Y  +E +  A+  +
Sbjct: 11  VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 140 HGKFLDGRVIFVEIA---KSRAELR 161
           +G+   GR + V+ A   K++ EL+
Sbjct: 71  NGREFSGRALRVDNAASEKNKEELK 95

>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd Machinery Length = 90

Iteration: 1
 Score = 49.3 bits (116), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 21/73 (28%), Positives = 46/73 (63%)
Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           LFV+G+    +E+ + + F  +G++  ++L +D+     +G+  + Y T +E++ A+EG+
Sbjct: 10  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 140 HGKFLDGRVIFVE 152
           +G+ L G+ I V+
Sbjct: 70  NGQDLMGQPISVD 82

>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A Trapped Dead-Box Helicase Bound To Rna Length = 91

Iteration: 1
 Score = 49.3 bits (116), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 21/73 (28%), Positives = 46/73 (63%)
Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           LFV+G+    +E+ + + F  +G++  ++L +D+     +G+  + Y T +E++ A+EG+
Sbjct: 12  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 140 HGKFLDGRVIFVE 152
           +G+ L G+ I V+
Sbjct: 72  NGQDLMGQPISVD 84

>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic Translation Initiation Factor 3 Subunit 4 Length = 103

Iteration: 1
 Score = 49.3 bits (116), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 27/74 (36%), Positives = 41/74 (55%)
Query: 82  VSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHG 141
           V+ LS  T E  L+  F+ FG +  + L  DK   + +GFAF+ +   E++ RAI G+ G
Sbjct: 20  VTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSG 79
Query: 142 KFLDGRVIFVEIAK 155
              D  ++ VE AK
Sbjct: 80  FGYDHLILNVEWAK 93

>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2 A Resolution Length = 89

Iteration: 1
 Score = 49.3 bits (116), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 21/73 (28%), Positives = 46/73 (63%)
Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           LFV+G+    +E+ + + F  +G++  ++L +D+     +G+  + Y T +E++ A+EG+
Sbjct: 10  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 140 HGKFLDGRVIFVE 152
           +G+ L G+ I V+
Sbjct: 70  NGQDLMGQPISVD 82

>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX Length = 106

Iteration: 1
 Score = 48.9 bits (115), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 21/73 (28%), Positives = 46/73 (63%)
Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           LFV+G+    +E+ + + F  +G++  ++L +D+     +G+  + Y T +E++ A+EG+
Sbjct: 26  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 140 HGKFLDGRVIFVE 152
           +G+ L G+ I V+
Sbjct: 86  NGQDLMGQPISVD 98

>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33 Length = 83

Iteration: 1
 Score = 48.9 bits (115), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 27/79 (34%), Positives = 43/79 (54%)
Query: 77  KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
           K  L+V GL+    +  L  AF  FG + ++ + +D    + RGFAF+ +   E++  AI
Sbjct: 5   KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 64
Query: 137 EGMHGKFLDGRVIFVEIAK 155
           + M+   L GR I V +AK
Sbjct: 65  DNMNESELFGRTIRVNLAK 83

>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 109

Iteration: 1
 Score = 48.9 bits (115), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 21/73 (28%), Positives = 46/73 (63%)
Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           LFV+G+    +E+ + + F  +G++  ++L +D+     +G+  + Y T +E++ A+EG+
Sbjct: 10  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 140 HGKFLDGRVIFVE 152
           +G+ L G+ I V+
Sbjct: 70  NGQDLMGQPISVD 82

>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding Motif Protein 9 Length = 103

Iteration: 1
 Score = 48.5 bits (114), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 26/80 (32%), Positives = 46/80 (57%), Gaps = 2/80 (2%)
Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           RL VS + FR  +  LR  F  FG++++V ++ ++  +  +GF F+ +    ++ RA E 
Sbjct: 17  RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS--KGFGFVTFENSADADRAREK 74
Query: 139 MHGKFLDGRVIFVEIAKSRA 158
           +HG  ++GR I V  A +R 
Sbjct: 75  LHGTVVEGRKIEVNNATARV 94

>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein Length = 140

Iteration: 1
 Score = 48.5 bits (114), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 26/78 (33%), Positives = 42/78 (53%)
Query: 77  KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
           K  L+V GL+    +  L  AF  FG + ++ + +D    + RGFAF+ +   E++  AI
Sbjct: 63  KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 122
Query: 137 EGMHGKFLDGRVIFVEIA 154
           + M+   L GR I V +A
Sbjct: 123 DNMNESELFGRTIRVNLA 140

>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human U2af65 Tandem Rrm1 And Rrm2 Domains Length = 198

Iteration: 1
 Score = 48.5 bits (114), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 28/94 (29%), Positives = 46/94 (48%), Gaps = 2/94 (2%)
Query: 68  PHSLSTCQPKT--RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLR 125
           P  +ST  P +  +LF+ GL    ++D ++     FG L   NLV D      +G+AF  
Sbjct: 103 PGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCE 162
Query: 126 YATEEESRRAIEGMHGKFLDGRVIFVEIAKSRAE 159
           Y     + +AI G++G  L  + + V+ A   A+
Sbjct: 163 YVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAK 196

>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State Length = 126

Iteration: 1
 Score = 48.5 bits (114), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 21/73 (28%), Positives = 46/73 (63%)
Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           LFV+G+    +E+ + + F  +G++  ++L +D+     +G+  + Y T +E++ A+EG+
Sbjct: 25  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 140 HGKFLDGRVIFVE 152
           +G+ L G+ I V+
Sbjct: 85  NGQDLMGQPISVD 97

>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger Cchc-Type And Rna Binding Motif 1 Length = 94

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 23/78 (29%), Positives = 44/78 (56%)
Query: 77  KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
           K+ ++VS L F  + + L   F  +G++V+V ++ DK   + +G AF+ +  ++ ++   
Sbjct: 16  KSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCT 75
Query: 137 EGMHGKFLDGRVIFVEIA 154
             ++ K L GRVI   IA
Sbjct: 76  RAINNKQLFGRVIKASIA 93

>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr Length = 75

Iteration: 1
 Score = 48.1 bits (113), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 25/84 (29%), Positives = 44/84 (52%), Gaps = 10/84 (11%)
Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           +FV GLS  T+ + +++ F+ FG++ +  L+ DK  NR RGF F+ + +E+   +  E  
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-- 59
Query: 140 HGKFLDGRVIFVEIAKSRAELRQA 163
                   + F EI     E ++A
Sbjct: 60  --------IHFHEINNKMVECKKA 75

>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33 Length = 79

Iteration: 1
 Score = 47.0 bits (110), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 26/78 (33%), Positives = 42/78 (53%)
Query: 77  KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
           K  L+V GL+    +  L  AF  FG + ++ + +D    + RGFAF+ +   E++  AI
Sbjct: 2   KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 61
Query: 137 EGMHGKFLDGRVIFVEIA 154
           + M+   L GR I V +A
Sbjct: 62  DNMNESELFGRTIRVNLA 79

>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In Polyadenylation Binding Protein 3 Length = 103

Iteration: 1
 Score = 47.0 bits (110), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 25/84 (29%), Positives = 49/84 (58%), Gaps = 3/84 (3%)
Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           L+V  L     ++ LR AF  FG +    ++M+    R +GF F+ +++ EE+ +A+  M
Sbjct: 18  LYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEM 75
Query: 140 HGKFLDGRVIFVEIAKSRAELRQA 163
           +G+ +  + ++V +A+ R E RQ+
Sbjct: 76  NGRIVATKPLYVALAQ-RKEERQS 98

>pdb|3S7R|A Chain A, Crystal Structure Of A Heterogeneous Nuclear Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15 A Resolution Length = 87

Iteration: 1
 Score = 47.0 bits (110), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 24/71 (33%), Positives = 39/71 (54%), Gaps = 1/71 (1%)
Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           + FV GLS+ TS+  L++ F  FG++V+  +  D    R RGF F+ +       + ++ 
Sbjct: 13  KXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQ 72
Query: 139 MHGKFLDGRVI 149
              + LDGRVI
Sbjct: 73  KEHR-LDGRVI 82

>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna Length = 174

Iteration: 1
 Score = 46.6 bits (109), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 25/87 (28%), Positives = 40/87 (45%)
Query: 68  PHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYA 127
           PH         +LF+ GL    ++D ++     FG L   NLV D      +G+AF  Y 
Sbjct: 87  PHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYV 146
Query: 128 TEEESRRAIEGMHGKFLDGRVIFVEIA 154
               + +AI G++G  L  + + V+ A
Sbjct: 147 DINVTDQAIAGLNGMQLGDKKLLVQRA 173

>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In Cytotoxic Granule-Associated Rna Binding Protein 1 Length = 115

Iteration: 1
 Score = 46.6 bits (109), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 23/93 (24%), Positives = 50/93 (53%), Gaps = 1/93 (1%)
Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           +FV  LS   + + ++ AF  FG++ +  +V D    + +G+ F+ +  + ++  AI+ M
Sbjct: 18  VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 140 HGKFLDGRVIFVEIAKSRAEL-RQAFKNNPRQN 171
            G++L GR I    A  +    +  +++N +Q+
Sbjct: 78  GGQWLGGRQIRTNWATRKPPAPKSTYESNTKQS 110

>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract Length = 172

Iteration: 1
 Score = 46.6 bits (109), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 25/87 (28%), Positives = 40/87 (45%)
Query: 68  PHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYA 127
           PH         +LF+ GL    ++D ++     FG L   NLV D      +G+AF  Y 
Sbjct: 85  PHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYV 144
Query: 128 TEEESRRAIEGMHGKFLDGRVIFVEIA 154
               + +AI G++G  L  + + V+ A
Sbjct: 145 DINVTDQAIAGLNGMQLGDKKLLVQRA 171

>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4 Rna Binding Protein Length = 105

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 22/63 (34%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           +LFV  L+ + SED +R  F+ FG + E  ++     N  +G AF++Y++  E++ AI  
Sbjct: 17  KLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNS-KGCAFVKYSSHAEAQAAINA 75
Query: 139 MHG 141
           +HG
Sbjct: 76  LHG 78

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 45.4 bits (106), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 21/76 (27%), Positives = 41/76 (53%)
Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
            +FV  LS   + + +++AF  FG++ +  +V D    + +G+ F+ +  + ++  AI  
Sbjct: 17  HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 76
Query: 139 MHGKFLDGRVIFVEIA 154
           M G++L GR I    A
Sbjct: 77  MGGQWLGGRQIRTNWA 92

>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of Hu2af65 Length = 85

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 24/81 (29%), Positives = 40/81 (49%)
Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           +LF+ GL    ++D ++     FG L   NLV D      +G+AF  Y     + +AI G
Sbjct: 3   KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62
Query: 139 MHGKFLDGRVIFVEIAKSRAE 159
           ++G  L  + + V+ A   A+
Sbjct: 63  LNGMQLGDKKLLVQRASVGAK 83

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 44.3 bits (103), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 18/63 (28%), Positives = 37/63 (58%)
Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           L+VSGL    ++  L   F  +G+++   +++D++    RG  F+R+    E+  AI+G+
Sbjct: 91  LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150
Query: 140 HGK 142
           +G+
Sbjct: 151 NGQ 153

>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1 Rbd1:r(Guagu) Complex Length = 109

Iteration: 1
 Score = 44.3 bits (103), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 17/51 (33%), Positives = 33/51 (64%)
Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATE 129
           ++F+ GLS++T+++ LR  F  FG++ E  ++ D +  R RGF F+ +  +
Sbjct: 27  KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQ 77

>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28 Length = 111

Iteration: 1
 Score = 44.3 bits (103), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 27/86 (31%), Positives = 47/86 (54%), Gaps = 6/86 (6%)
Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR----- 134
           +F+  LSF + E++L    Q FG L  V +V+       +G AF ++ T+E +++     
Sbjct: 18  VFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAA 77
Query: 135 AIEGMHGKF-LDGRVIFVEIAKSRAE 159
           ++E   G   LDGR + V++A +R E
Sbjct: 78  SLEAEGGGLKLDGRQLKVDLAVTRDE 103

>pdb|1H2T|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc) In Complex With A Cap Analogue M7gpppg Length = 156

Iteration: 1
 Score = 43.9 bits (102), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 24/83 (28%), Positives = 43/83 (51%)
Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           L+V  LSF T+E+ +   F   G + ++ + +DK+     GF F+ Y +  ++  A+  +
Sbjct: 42  LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 101
Query: 140 HGKFLDGRVIFVEIAKSRAELRQ 162
           +G  LD R+I  +      E RQ
Sbjct: 102 NGTRLDDRIIRTDWDAGFKEGRQ 124

>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna- Binding Protein-43 Length = 103

Iteration: 1
 Score = 43.9 bits (102), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 23/83 (27%), Positives = 41/83 (49%), Gaps = 2/83 (2%)
Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
           Q  + L V GL ++T+E  L+  F  FG+++ V +  D      +GF F+R+   E   +
Sbjct: 13  QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVK 72
Query: 135 AIEGMHGKFLDGRVIFVEIAKSR 157
            +   H   +DGR    ++  S+
Sbjct: 73  VMSQRH--MIDGRWCDCKLPNSK 93

>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of Mouse Musashi1 Length = 77

Iteration: 1
 Score = 43.9 bits (102), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 17/51 (33%), Positives = 33/51 (64%)
Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATE 129
           ++F+ GLS++T+++ LR  F  FG++ E  ++ D +  R RGF F+ +  +
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQ 52

>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing Factor 3b Length = 96

Iteration: 1
 Score = 43.9 bits (102), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 24/78 (30%), Positives = 41/78 (52%), Gaps = 1/78 (1%)
Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVM-DKIANRPRGFAFLRYATEEESRRAI 136
           + +F+  L     E  L + F  FG +++   +M D      +G+AF+ +A+ + S  AI
Sbjct: 6   SGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAI 65
Query: 137 EGMHGKFLDGRVIFVEIA 154
           E M+G++L  R I V  A
Sbjct: 66  EAMNGQYLCNRPITVSYA 83

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 43.5 bits (101), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 18/63 (28%), Positives = 36/63 (57%)
Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           L+VSGL    S+  +   F  +G+++   +++D+     RG  F+R+    E+  AI+G+
Sbjct: 93  LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 152
Query: 140 HGK 142
           +G+
Sbjct: 153 NGQ 155

>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2) Of Hu Antigen C (Huc) Length = 85

Iteration: 1
 Score = 43.1 bits (100), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 18/63 (28%), Positives = 36/63 (57%)
Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           L+VSGL    S+  +   F  +G+++   +++D+     RG  F+R+    E+  AI+G+
Sbjct: 4   LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 140 HGK 142
           +G+
Sbjct: 64  NGQ 66

>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex Length = 110

Iteration: 1
 Score = 42.7 bits (99), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 19/73 (26%), Positives = 41/73 (56%)
Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           LFV+ +     ED ++  F  +G++  ++L +D+     +G+A + Y T +++  A E +
Sbjct: 29  LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 140 HGKFLDGRVIFVE 152
           +G  + G+ I V+
Sbjct: 89  NGAEIMGQTIQVD 101

>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar Length = 109

Iteration: 1
 Score = 42.0 bits (97), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 19/81 (23%), Positives = 44/81 (54%), Gaps = 6/81 (7%)
Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           ++  G++   ++  +R  F  FGQ++E+ +  +K      G++F+R++T E +  AI  +
Sbjct: 28  VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK------GYSFVRFSTHESAAHAIVSV 81
Query: 140 HGKFLDGRVIFVEIAKSRAEL 160
           +G  ++G V+     K   ++
Sbjct: 82  NGTTIEGHVVKCYWGKESPDM 102

>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago Complex Length = 165

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 19/73 (26%), Positives = 41/73 (56%)
Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           LFV+ +     ED ++  F  +G++  ++L +D+     +G+A + Y T +++  A E +
Sbjct: 75  LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 140 HGKFLDGRVIFVE 152
           +G  + G+ I V+
Sbjct: 135 NGAEIMGQTIQVD 147

>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition Motif Of Hypothetical Rna-Binding Protein Rbm19 Length = 98

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/81 (27%), Positives = 44/81 (54%), Gaps = 7/81 (8%)
Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRP-----RGFAFLRYATEEESRR 134
           LF+  L+F T+E++L+  F   G +   +  + K  N+       GF F+ Y   E++++
Sbjct: 8   LFIKNLNFSTTEETLKGVFSKVGAIK--SCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65
Query: 135 AIEGMHGKFLDGRVIFVEIAK 155
           A++ + G  +DG  + V I++
Sbjct: 66  ALKQLQGHTVDGHKLEVRISE 86

>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex Length = 98

Iteration: 1
 Score = 40.8 bits (94), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 21/70 (30%), Positives = 39/70 (55%), Gaps = 1/70 (1%)
Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           L+V  LSF T+E+ +   F   G + ++ + +DK+     GF F+ Y +  ++  A+  +
Sbjct: 21  LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKT-ACGFCFVEYYSRADAENAMRYI 79
Query: 140 HGKFLDGRVI 149
           +G  LD R+I
Sbjct: 80  NGTRLDDRII 89

>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein Length = 74

Iteration: 1
 Score = 39.7 bits (91), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 26/65 (40%), Positives = 32/65 (49%), Gaps = 8/65 (12%)
Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           TRLFV        E  L   F  FG + EV     KI N   GFAF+ +   E + +AIE
Sbjct: 5   TRLFVRPFPLDVQESELNEIFGPFGPMKEV-----KILN---GFAFVEFEEAESAAKAIE 56
Query: 138 GMHGK 142
            +HGK
Sbjct: 57  EVHGK 61

>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif, Single-Stranded Interacting Protein 2 Length = 85

Iteration: 1
 Score = 39.7 bits (91), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 14/61 (22%), Positives = 34/61 (55%)
Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           L++ GL   T++  L    Q +G++V    ++DK  N+ +G+ F+ + +   +++A+  +
Sbjct: 8   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67
Query: 140 H 140
Sbjct: 68  K 68

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	171
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	3e-32
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	1e-31
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	3e-31
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	1e-30
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	4e-30
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	5e-30
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	6e-30
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	7e-30
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	8e-30
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	2e-29
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	4e-29
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	5e-29
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	6e-29
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	1e-28
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	1e-28
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	2e-28
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	3e-28
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	3e-28
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	5e-28
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	7e-28
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	9e-28
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	1e-27
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	1e-27
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	1e-27
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	2e-27
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	3e-27
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-27
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	5e-27
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	7e-27
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	8e-27
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	9e-27
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	1e-26
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	2e-26
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	4e-26
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	5e-26
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	6e-26
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	1e-25
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	1e-25
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	1e-25
1x4e_A	85	RNA binding motif, single-stranded interacting pro	1e-25
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	2e-25
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	3e-25
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	5e-25
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	5e-25
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	5e-25
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	9e-25
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	1e-24
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	2e-24
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	3e-24
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	4e-24
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	4e-24
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	4e-24
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	5e-24
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	6e-24
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	8e-24
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	1e-23
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	1e-23
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	1e-23
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	3e-17
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	1e-23
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	2e-23
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	2e-23
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	2e-23
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	5e-22
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	2e-23
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	3e-23
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	3e-23
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	3e-23
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	4e-23
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	5e-23
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	7e-18
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	5e-23
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	4e-19
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-14
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	9e-23
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	2e-21
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	1e-22
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	1e-22
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	1e-22
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	1e-22
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	2e-22
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	3e-22
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	3e-22
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	4e-22
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	6e-16
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	4e-22
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-21
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	6e-22
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	6e-22
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	7e-22
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	9e-15
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	8e-22
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	9e-22
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-18
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	1e-21
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	1e-21
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-21
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	2e-21
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	3e-21
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	3e-21
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	3e-21
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	4e-21
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	4e-21
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	8e-21
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	2e-20
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	9e-21
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	1e-20
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	1e-20
1x5o_A	114	RNA binding motif, single-stranded interacting pro	1e-20
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	1e-20
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	2e-20
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	2e-20
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-20
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	4e-20
1x5p_A	97	Negative elongation factor E; structure genomics,	7e-20
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	9e-20
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-19
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-14
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	2e-19
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	5e-19
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	7e-19
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	1e-18
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	8e-19
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	1e-18
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	1e-18
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	1e-18
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	1e-18
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	2e-18
2dis_A	109	Unnamed protein product; structural genomics, RRM	3e-18
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	8e-18
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	8e-18
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	8e-18
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	1e-17
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	1e-17
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	9e-17
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	2e-17
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	2e-17
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	2e-17
2div_A	99	TRNA selenocysteine associated protein; structural	3e-17
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	6e-17
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	9e-17
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	1e-16
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	1e-16
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	2e-16
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	2e-16
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	5e-16
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	6e-16
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	7e-16
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	3e-15
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	4e-15
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	5e-15
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	6e-15
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	7e-15
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	8e-15
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	8e-15
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	9e-15
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	4e-10
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	1e-14
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	1e-14
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	2e-14
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	2e-13
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	2e-13
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	6e-13
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	3e-13
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	4e-13
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	4e-13
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	4e-13
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	8e-13
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	1e-12
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	5e-11
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	1e-12
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	2e-12
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-12
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-11
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	2e-12
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	3e-12
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	1e-11
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	2e-11
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	3e-11
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	5e-11
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	1e-10
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	1e-10
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	1e-10
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	2e-10
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	2e-10
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	3e-08
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	4e-08
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	8e-08
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	3e-07
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	3e-06
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	3e-06
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	3e-05
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	7e-05
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	1e-04
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	5e-04
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	6e-04

>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 =  109 bits (276), Expect = 3e-32
 Identities = 31/82 (37%), Positives = 46/82 (56%)

Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
            P   L V GLS  T+E  LR  F  +G + +V++V D+ + R RGFAF+ +   ++++ 
Sbjct: 13  DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 72

Query: 135 AIEGMHGKFLDGRVIFVEIAKS 156
           A E  +G  LDGR I V    S
Sbjct: 73  AKERANGMELDGRRIRVSGPSS 94

>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 =  108 bits (272), Expect = 1e-31
 Identities = 35/93 (37%), Positives = 54/93 (58%)

Query: 67  SPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRY 126
           S  S      + +LFV GLSF T+E SL   F  +GQ+ EV +V D+   R RGF F+ +
Sbjct: 2   SSGSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTF 61

Query: 127 ATEEESRRAIEGMHGKFLDGRVIFVEIAKSRAE 159
              ++++ A+  M+GK +DGR I V+ A   ++
Sbjct: 62  ENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSD 94

>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 =  108 bits (272), Expect = 3e-31
 Identities = 30/93 (32%), Positives = 51/93 (54%)

Query: 65  PPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFL 124
                + +   P   L V GLS  T+E  LR  F  +G + +V++V D+ + R RGFAF+
Sbjct: 34  SRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFV 93

Query: 125 RYATEEESRRAIEGMHGKFLDGRVIFVEIAKSR 157
            +   ++++ A E  +G  LDGR I V+ + ++
Sbjct: 94  YFENVDDAKEAKERANGMELDGRRIRVDFSITK 126

>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 =  106 bits (266), Expect = 1e-30
 Identities = 29/84 (34%), Positives = 47/84 (55%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
               L V  L++RTS DSLR  F+ +G++ +V +  +     PRGFAF+R+    +++ A
Sbjct: 12  GMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDA 71

Query: 136 IEGMHGKFLDGRVIFVEIAKSRAE 159
              M G  LDGR + V++A+    
Sbjct: 72  EAAMDGAELDGRELRVQVARYGRR 95

>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 =  104 bits (262), Expect = 4e-30
 Identities = 27/84 (32%), Positives = 42/84 (50%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
               + V+ LS  T E  L+  F+ FG +  + L  DK   + +GFAF+ +   E++ RA
Sbjct: 14  DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARA 73

Query: 136 IEGMHGKFLDGRVIFVEIAKSRAE 159
           I G+ G   D  ++ VE AK    
Sbjct: 74  IAGVSGFGYDHLILNVEWAKPSTN 97

>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 =  105 bits (263), Expect = 5e-30
 Identities = 30/96 (31%), Positives = 51/96 (53%), Gaps = 1/96 (1%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
              +LF+ GL+  T+E  L+  F   G + EV L+ D+  ++ RGFAF+ +    +++ A
Sbjct: 6   HPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNA 64

Query: 136 IEGMHGKFLDGRVIFVEIAKSRAELRQAFKNNPRQN 171
            + M+GK L G+ I VE AK  +      +  P  +
Sbjct: 65  AKDMNGKSLHGKAIKVEQAKKPSFQSGGRRRPPASS 100

>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 =  104 bits (261), Expect = 6e-30
 Identities = 27/88 (30%), Positives = 48/88 (54%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
              RLFV  LS+ +SE+ L   F  +G L E++  +D +  +P+GFAF+ +   E + +A
Sbjct: 7   GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKA 66

Query: 136 IEGMHGKFLDGRVIFVEIAKSRAELRQA 163
              + G+   GR++ V  +  + E  Q+
Sbjct: 67  YAEVDGQVFQGRMLHVLPSTIKKEASQS 94

>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 =  103 bits (260), Expect = 7e-30
 Identities = 23/79 (29%), Positives = 44/79 (55%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
            K+ ++VS L F  + + L   F  +G++V+V ++ DK   + +G AF+ +  ++ ++  
Sbjct: 15  SKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNC 74

Query: 136 IEGMHGKFLDGRVIFVEIA 154
              ++ K L GRVI   IA
Sbjct: 75  TRAINNKQLFGRVIKASIA 93

>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 =  104 bits (261), Expect = 8e-30
 Identities = 27/84 (32%), Positives = 43/84 (51%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
            K  L+V GL+    +  L  AF  FG + ++ + +D    + RGFAF+ +   E++  A
Sbjct: 11  TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 70

Query: 136 IEGMHGKFLDGRVIFVEIAKSRAE 159
           I+ M+   L GR I V +AK    
Sbjct: 71  IDNMNESELFGRTIRVNLAKPMRI 94

>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 =  103 bits (258), Expect = 2e-29
 Identities = 28/88 (31%), Positives = 48/88 (54%), Gaps = 3/88 (3%)

Query: 72  STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEE 131
           +  QP   LFV GLS  T+E++L+ +F      V   +V D+     +GF F+ + +EE+
Sbjct: 10  ARSQPSKTLFVKGLSEDTTEETLKESF---DGSVRARIVTDRETGSSKGFGFVDFNSEED 66

Query: 132 SRRAIEGMHGKFLDGRVIFVEIAKSRAE 159
           ++ A E M    +DG  + ++ AK + E
Sbjct: 67  AKAAKEAMEDGEIDGNKVTLDWAKPKGE 94

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score =  102 bits (256), Expect = 4e-29
 Identities = 26/93 (27%), Positives = 48/93 (51%), Gaps = 1/93 (1%)

Query: 65  PPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFL 124
                  ST   K +LF+SGL F  +++ L    +  G + ++ LV ++ A +P+G A++
Sbjct: 5   SSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYV 63

Query: 125 RYATEEESRRAIEGMHGKFLDGRVIFVEIAKSR 157
            Y  E ++ +A+  M G  +   +I V I+ S 
Sbjct: 64  EYENESQASQAVMKMDGMTIKENIIKVAISNSG 96

>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 =  101 bits (254), Expect = 5e-29
 Identities = 14/85 (16%), Positives = 45/85 (52%), Gaps = 1/85 (1%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIA-NRPRGFAFLRYATEEESRR 134
             T++ +  L+   ++D +   F  +G++  +++ ++++  +  +G+A++ +   +E+ +
Sbjct: 3   KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEK 62

Query: 135 AIEGMHGKFLDGRVIFVEIAKSRAE 159
           A++ M G  +DG+ I      +   
Sbjct: 63  ALKHMDGGQIDGQEITATAVLAPWP 87

>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 =  101 bits (255), Expect = 6e-29
 Identities = 26/85 (30%), Positives = 45/85 (52%), Gaps = 2/85 (2%)

Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
               RL VS + FR  +  LR  F  FG++++V ++ ++     +GF F+ +    ++ R
Sbjct: 13  STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADR 70

Query: 135 AIEGMHGKFLDGRVIFVEIAKSRAE 159
           A E +HG  ++GR I V  A +R  
Sbjct: 71  AREKLHGTVVEGRKIEVNNATARVM 95

>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 =  102 bits (257), Expect = 1e-28
 Identities = 29/82 (35%), Positives = 50/82 (60%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
             T L V  L++RTS D+LR  F+ +G++ +V +  D+     RGFAF+R+  + ++  A
Sbjct: 69  GMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDA 128

Query: 136 IEGMHGKFLDGRVIFVEIAKSR 157
           ++ M G  LDGR + V++A+  
Sbjct: 129 MDAMDGAVLDGRELRVQMARYG 150

>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 =  100 bits (252), Expect = 1e-28
 Identities = 27/80 (33%), Positives = 43/80 (53%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
            K  L+V GL+    +  L  AF  FG + ++ + +D    + RGFAF+ +   E++  A
Sbjct: 6   TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 65

Query: 136 IEGMHGKFLDGRVIFVEIAK 155
           I+ M+   L GR I V +AK
Sbjct: 66  IDNMNESELFGRTIRVNLAK 85

>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 =  100 bits (251), Expect = 2e-28
 Identities = 27/84 (32%), Positives = 46/84 (54%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
             + L+V  L F  +ED LR  F+ FG++  + L+ D    R +G+ F+ ++  E +RRA
Sbjct: 4   GSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRA 63

Query: 136 IEGMHGKFLDGRVIFVEIAKSRAE 159
           +E ++G  L GR + V     R +
Sbjct: 64  LEQLNGFELAGRPMRVGHVTERLD 87

>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 =  101 bits (254), Expect = 3e-28
 Identities = 26/133 (19%), Positives = 55/133 (41%), Gaps = 1/133 (0%)

Query: 38  IKRRDFDSLFSLRQGRGRGACFPLACLPPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNA 97
            K R F S  + R+                            LFV+ +     ED ++  
Sbjct: 33  RKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEK 92

Query: 98  FQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKSR 157
           F  +G++  ++L +D+     +G+A + Y T +++  A E ++G  + G+ I V+    +
Sbjct: 93  FCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVK 152

Query: 158 AELRQAFKNNPRQ 170
              ++  K+  R+
Sbjct: 153 GP-KRVKKSEKRR 164

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score =  100 bits (252), Expect = 3e-28
 Identities = 29/82 (35%), Positives = 50/82 (60%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
             T L V  L++RTS D+LR  F+ +G++ +V +  D+     RGFAF+R+  + ++  A
Sbjct: 46  GMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDA 105

Query: 136 IEGMHGKFLDGRVIFVEIAKSR 157
           ++ M G  LDGR + V++A+  
Sbjct: 106 MDAMDGAVLDGRELRVQMARYG 127

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A Length = 115

 Score = 99.7 bits (249), Expect = 5e-28
 Identities = 23/97 (23%), Positives = 50/97 (51%), Gaps = 1/97 (1%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
               +FV  LS   + + ++ AF  FG++ +  +V D    + +G+ F+ +  + ++  A
Sbjct: 14  NHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENA 73

Query: 136 IEGMHGKFLDGRVIFVEIAKSRAEL-RQAFKNNPRQN 171
           I+ M G++L GR I    A  +    +  +++N +Q+
Sbjct: 74  IQQMGGQWLGGRQIRTNWATRKPPAPKSTYESNTKQS 110

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 98.9 bits (247), Expect = 7e-28
 Identities = 20/88 (22%), Positives = 42/88 (47%), Gaps = 6/88 (6%)

Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQGFGQL--VEVNLVMDKIANRPRGFAFLRYATEEES 132
                + +  ++  T  DS+  A   +  L    + L+ DK   + RGFAF++ ++  ++
Sbjct: 7   HHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDA 66

Query: 133 RRAIEGMHGKF----LDGRVIFVEIAKS 156
            + ++ +        +DG+ I V+ AKS
Sbjct: 67  SQLLQILQSLHPPLKIDGKTIGVDFAKS 94

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score =  100 bits (250), Expect = 9e-28
 Identities = 28/90 (31%), Positives = 45/90 (50%)

Query: 65  PPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFL 124
             S  S  +   K  L+V GL+    +  L  AF  FG + ++ + +D    + RGFAF+
Sbjct: 51  GGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFV 110

Query: 125 RYATEEESRRAIEGMHGKFLDGRVIFVEIA 154
            +   E++  AI+ M+   L GR I V +A
Sbjct: 111 EFELAEDAAAAIDNMNESELFGRTIRVNLA 140

>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 = 99.0 bits (247), Expect = 1e-27
 Identities = 26/91 (28%), Positives = 45/91 (49%), Gaps = 6/91 (6%)

Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
                +F+  LSF + E++L    Q FG L  V +V+       +G AF ++ T+E +++
Sbjct: 13  TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQK 72

Query: 135 AIEGMH------GKFLDGRVIFVEIAKSRAE 159
            +          G  LDGR + V++A +R E
Sbjct: 73  CLAAASLEAEGGGLKLDGRQLKVDLAVTRDE 103

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 98.9 bits (247), Expect = 1e-27
 Identities = 26/80 (32%), Positives = 45/80 (56%), Gaps = 2/80 (2%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
            RL VS + FR  +  LR  F  FG++++V ++ ++     +GF F+ +    ++ RA E
Sbjct: 30  KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRARE 87

Query: 138 GMHGKFLDGRVIFVEIAKSR 157
            +HG  ++GR I V  A +R
Sbjct: 88  KLHGTVVEGRKIEVNNATAR 107

>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 = 98.9 bits (247), Expect = 1e-27
 Identities = 27/84 (32%), Positives = 47/84 (55%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
              RL+V  L F  +ED LR  F+ FG++  + L+MD    R +G+ F+ ++  E +++A
Sbjct: 25  GPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKA 84

Query: 136 IEGMHGKFLDGRVIFVEIAKSRAE 159
           +E ++G  L GR + V     R +
Sbjct: 85  LEQLNGFELAGRPMKVGHVTERTD 108

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 97.7 bits (244), Expect = 2e-27
 Identities = 22/85 (25%), Positives = 47/85 (55%)

Query: 74  CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESR 133
                 LFV+G+    +E+ + + F  +G++  ++L +D+     +G+  + Y T +E++
Sbjct: 20  SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 79

Query: 134 RAIEGMHGKFLDGRVIFVEIAKSRA 158
            A+EG++G+ L G+ I V+    R 
Sbjct: 80  AAMEGLNGQDLMGQPISVDWCFVRG 104

>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 = 98.2 bits (245), Expect = 3e-27
 Identities = 23/98 (23%), Positives = 52/98 (53%)

Query: 74  CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESR 133
                 LFV+G+    +E+ + + F  +G++  ++L +D+     +G+  + Y T +E++
Sbjct: 19  SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 78

Query: 134 RAIEGMHGKFLDGRVIFVEIAKSRAELRQAFKNNPRQN 171
            A+EG++G+ L G+ I V+    R   +   +   R++
Sbjct: 79  AAMEGLNGQDLMGQPISVDWCFVRGPPKGKRRGGRRRS 116

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} Length = 83

 Score = 96.8 bits (242), Expect = 3e-27
 Identities = 21/80 (26%), Positives = 45/80 (56%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
             LFV  L+    +++LRNAF+ F   +  +++ D      RG+ F+ + ++++++ A++
Sbjct: 2   FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61

Query: 138 GMHGKFLDGRVIFVEIAKSR 157
            M G+ L+GR + +  A   
Sbjct: 62  SMQGQDLNGRPLRINWAAKL 81

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 97.1 bits (242), Expect = 5e-27
 Identities = 12/91 (13%), Positives = 41/91 (45%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
           P   +  + L+    E  L++  + +G++ EV +++     +  G A + + +   ++  
Sbjct: 5   PLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKET 64

Query: 136 IEGMHGKFLDGRVIFVEIAKSRAELRQAFKN 166
           ++ +H   + G +I  ++     +  + ++ 
Sbjct: 65  VKNLHLTSVMGNIIHAQLDIKGQQRMKYYEL 95

>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 = 97.4 bits (243), Expect = 7e-27
 Identities = 29/146 (19%), Positives = 57/146 (39%), Gaps = 22/146 (15%)

Query: 22  IHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPSPHSLSTCQPKTRLF 81
           + ++T        P   +   FDS     +G   G                      +L 
Sbjct: 1   MASMTGGQQMGRDPDKWQHDLFDSGCGGGEGVETG---------------------AKLL 39

Query: 82  VSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHG 141
           VS L F  S+  ++  F  FG L +  +  D+ + R  G A + +    ++ +A++   G
Sbjct: 40  VSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKG 98

Query: 142 KFLDGRVIFVEIAKSRAELRQAFKNN 167
             LDGR + +++  S+ +L     ++
Sbjct: 99  VPLDGRPMDIQLVASQIDLEHHHHHH 124

>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 = 96.2 bits (240), Expect = 8e-27
 Identities = 14/96 (14%), Positives = 43/96 (44%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
           P   +++  + +  +E+ + +     G ++ + ++ D    R +G+AF+ +   E S  A
Sbjct: 1   PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60

Query: 136 IEGMHGKFLDGRVIFVEIAKSRAELRQAFKNNPRQN 171
           +  ++G  L  R +    + +      + +++   +
Sbjct: 61  VRNLNGYQLGSRFLKCGYSSNSDISGVSLEHHHHHH 96

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 98.1 bits (244), Expect = 9e-27
 Identities = 20/98 (20%), Positives = 44/98 (44%), Gaps = 4/98 (4%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFG--QLVEVNLVMDKIANRPRGFAFLRYATEEESR 133
            +  ++V   S+ T++  L    +  G   +VE+    ++   + +G+A +  A+E    
Sbjct: 54  RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVH 113

Query: 134 RAIEGMHGKFLDGRVIFVEIAKSRAELRQAFKNNPRQN 171
           + +E + GK L+G  + V  A  +      F+   R+ 
Sbjct: 114 KLLELLPGKVLNGEKVDVRPATRQN--LSQFEAQARKR 149

>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 = 97.1 bits (242), Expect = 1e-26
 Identities = 21/95 (22%), Positives = 44/95 (46%)

Query: 65  PPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFL 124
            P             L V+ +     E  LR  F+ +G +  V +V D+   + RG+ F+
Sbjct: 30  IPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFV 89

Query: 125 RYATEEESRRAIEGMHGKFLDGRVIFVEIAKSRAE 159
           ++ +   +++AI G++G  +  + + V +A S  +
Sbjct: 90  KFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQ 124

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C Length = 90

 Score = 95.0 bits (237), Expect = 2e-26
 Identities = 15/88 (17%), Positives = 40/88 (45%), Gaps = 2/88 (2%)

Query: 77  KTRLFVSGLSFRTSEDSLRNAFQGFG--QLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
           +  L++  L++ T+++ L  A    G   ++E+    ++   + +GFA +   +E  S++
Sbjct: 1   RIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKK 60

Query: 135 AIEGMHGKFLDGRVIFVEIAKSRAELRQ 162
            ++ +  + L G+   V  +        
Sbjct: 61  LMDLLPKRELHGQNPVVTPSNKLEHHHH 88

>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 = 94.7 bits (236), Expect = 4e-26
 Identities = 22/92 (23%), Positives = 41/92 (44%), Gaps = 3/92 (3%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
            +LF+  +     E  L+  F+ FG++ E+ ++ D+     +G AFL Y   E + +A  
Sbjct: 14  IKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQS 73

Query: 138 GMHGKFL---DGRVIFVEIAKSRAELRQAFKN 166
            +H +       R I V+ A S +       +
Sbjct: 74  ALHEQKTLPGMNRPIQVKPADSESRGGSGPSS 105

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 95.1 bits (237), Expect = 5e-26
 Identities = 29/101 (28%), Positives = 48/101 (47%), Gaps = 1/101 (0%)

Query: 65  PPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFL 124
               H        T++FV GL + T++ SLR  F+GFG + E  ++ D+   + RG+ F+
Sbjct: 5   SSGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFV 64

Query: 125 RYATEEESRRAIEGMHGKFLDGRVIFVEIAKSRAELRQAFK 165
             A    + RA +  +   +DGR   V +A   A+ R    
Sbjct: 65  TMADRAAAERACKDPNPI-IDGRKANVNLAYLGAKPRSLQT 104

>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 = 96.0 bits (239), Expect = 6e-26
 Identities = 24/88 (27%), Positives = 44/88 (50%)

Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
           +    L+V  LSF T+E+ +   F   G + ++ + +DK+     GF F+ Y +  ++  
Sbjct: 37  KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAEN 96

Query: 135 AIEGMHGKFLDGRVIFVEIAKSRAELRQ 162
           A+  ++G  LD R+I  +      E RQ
Sbjct: 97  AMRYINGTRLDDRIIRTDWDAGFKEGRQ 124

>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 = 93.5 bits (233), Expect = 1e-25
 Identities = 21/89 (23%), Positives = 43/89 (48%), Gaps = 3/89 (3%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDK---IANRPRGFAFLRYATEEESRR 134
           + LF+  L+F T+E++L+  F   G +    +   K         GF F+ Y   E++++
Sbjct: 6   SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65

Query: 135 AIEGMHGKFLDGRVIFVEIAKSRAELRQA 163
           A++ + G  +DG  + V I++   +    
Sbjct: 66  ALKQLQGHTVDGHKLEVRISERATKPASG 94

>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 = 93.9 bits (234), Expect = 1e-25
 Identities = 20/97 (20%), Positives = 43/97 (44%)

Query: 65  PPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFL 124
                          LFV+ +     ED ++  F  +G++  ++L +D+     +G+A +
Sbjct: 14  DELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALV 73

Query: 125 RYATEEESRRAIEGMHGKFLDGRVIFVEIAKSRAELR 161
            Y T +++  A E ++G  + G+ I V+    +   R
Sbjct: 74  EYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKR 110

>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 = 93.5 bits (233), Expect = 1e-25
 Identities = 22/85 (25%), Positives = 43/85 (50%)

Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
           +    +FV  + +  +E+ L++ F   G +V   LV D+   +P+G+ F  Y  +E +  
Sbjct: 6   RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALS 65

Query: 135 AIEGMHGKFLDGRVIFVEIAKSRAE 159
           A+  ++G+   GR + V+ A S   
Sbjct: 66  AMRNLNGREFSGRALRVDNAASEKN 90

>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 = 93.0 bits (232), Expect = 1e-25
 Identities = 15/79 (18%), Positives = 39/79 (49%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           + L++ GL   T++  L    Q +G++V    ++DK  N+ +G+ F+ + +   +++A+ 
Sbjct: 6   SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 65

Query: 138 GMHGKFLDGRVIFVEIAKS 156
            +    +  ++       S
Sbjct: 66  ALKASGVQAQMAKQSGPSS 84

>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 = 93.1 bits (232), Expect = 2e-25
 Identities = 23/94 (24%), Positives = 47/94 (50%)

Query: 66  PSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLR 125
           P   S +  +P   L++  LS R +E  L + F  F +     +    +  R RG AF+ 
Sbjct: 14  PMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFIT 73

Query: 126 YATEEESRRAIEGMHGKFLDGRVIFVEIAKSRAE 159
           +  +E + +A+  ++G  L G+++ +E  K++ +
Sbjct: 74  FPNKEIAWQALHLVNGYKLYGKILVIEFGKNKKQ 107

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 92.3 bits (230), Expect = 3e-25
 Identities = 22/86 (25%), Positives = 40/86 (46%), Gaps = 2/86 (2%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           + L V GL ++T+E  L+  F  FG+++ V +  D      +GF F+R+   E   + + 
Sbjct: 16  SDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS 75

Query: 138 GMHGKFLDGRVIFVEIAKSRAELRQA 163
             H   +DGR    ++  S+      
Sbjct: 76  QRH--MIDGRWCDCKLPNSKQSQDSG 99

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 91.5 bits (228), Expect = 5e-25
 Identities = 21/82 (25%), Positives = 41/82 (50%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
               +FV  LS   +  ++  AF  FG++ +  +V D    + +G+ F+ +  + ++  A
Sbjct: 5   SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENA 64

Query: 136 IEGMHGKFLDGRVIFVEIAKSR 157
           I+ M G++L GR I    A  +
Sbjct: 65  IQQMGGQWLGGRQIRTNWATRK 86

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 91.6 bits (228), Expect = 5e-25
 Identities = 23/88 (26%), Positives = 40/88 (45%), Gaps = 6/88 (6%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
            ++RLFV  L    +E+ +R  F+ +G+  EV +      ++ +GF F+R  T   +  A
Sbjct: 14  QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFI------HKDKGFGFIRLETRTLAEIA 67

Query: 136 IEGMHGKFLDGRVIFVEIAKSRAELRQA 163
              +    L G+ + V  A   A L   
Sbjct: 68  KVELDNMPLRGKQLRVRFACHSASLTSG 95

>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 = 92.0 bits (229), Expect = 5e-25
 Identities = 24/96 (25%), Positives = 45/96 (46%), Gaps = 2/96 (2%)

Query: 66  PSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIA-NRPRGFAFL 124
            S   +   Q  +++ V  + F+ ++  +R  F  FG+L  V L          RGF F+
Sbjct: 4   GSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFV 63

Query: 125 RYATEEESRRAIEGM-HGKFLDGRVIFVEIAKSRAE 159
            + T++++++A   + H   L GR + +E A S   
Sbjct: 64  DFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVT 99

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A Length = 115

 Score = 91.5 bits (228), Expect = 9e-25
 Identities = 27/94 (28%), Positives = 46/94 (48%), Gaps = 2/94 (2%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
             +F+  L       +L + F  FG ++   +V D+  N  +G+ F+ + T+E + RAIE
Sbjct: 6   GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIE 63

Query: 138 GMHGKFLDGRVIFVEIAKSRAELRQAFKNNPRQN 171
            M+G  L+ R +FV   KSR E         ++ 
Sbjct: 64  KMNGMLLNDRKVFVGRFKSRKEREAELGARAKEF 97

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 90.3 bits (225), Expect = 1e-24
 Identities = 24/85 (28%), Positives = 42/85 (49%), Gaps = 1/85 (1%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVM-DKIANRPRGFAFLRYATEEESRR 134
             + +F+  L     E  L + F  FG +++   +M D      +G+AF+ +A+ + S  
Sbjct: 4   GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDA 63

Query: 135 AIEGMHGKFLDGRVIFVEIAKSRAE 159
           AIE M+G++L  R I V  A  +  
Sbjct: 64  AIEAMNGQYLCNRPITVSYAFKKDS 88

>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 = 90.0 bits (224), Expect = 2e-24
 Identities = 18/95 (18%), Positives = 40/95 (42%), Gaps = 5/95 (5%)

Query: 67  SPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRY 126
            P +    +    L    LSF  +ED L+  F+   ++      +     + +G A++ +
Sbjct: 6   DPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIR-----LVSQDGKSKGIAYIEF 60

Query: 127 ATEEESRRAIEGMHGKFLDGRVIFVEIAKSRAELR 161
            +E ++ + +E   G  +DGR + +     +   R
Sbjct: 61  KSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGGTR 95

>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 = 90.0 bits (224), Expect = 3e-24
 Identities = 19/88 (21%), Positives = 44/88 (50%), Gaps = 4/88 (4%)

Query: 72  STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEE 131
           +       L +S LS+  +E++L+  F+    +     V      + +G+AF+ +A+ E+
Sbjct: 10  TWSGESKTLVLSNLSYSATEETLQEVFEKATFIK----VPQNQNGKSKGYAFIEFASFED 65

Query: 132 SRRAIEGMHGKFLDGRVIFVEIAKSRAE 159
           ++ A+   + + ++GR I +E+   R  
Sbjct: 66  AKEALNSCNKREIEGRAIRLELQGPRGS 93

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score = 89.6 bits (223), Expect = 4e-24
 Identities = 24/86 (27%), Positives = 43/86 (50%), Gaps = 1/86 (1%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
            +LFV GL + T++++LR+ F  +G++V+  ++ DK  N+ RGF F+++         + 
Sbjct: 17  GKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLA 76

Query: 138 GMHGKFLDGRVIFVEIAKSRAELRQA 163
                 LDGR I  +    R      
Sbjct: 77  -SRPHTLDGRNIDPKPCTPRGMQPSG 101

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 90.1 bits (224), Expect = 4e-24
 Identities = 22/105 (20%), Positives = 45/105 (42%), Gaps = 1/105 (0%)

Query: 67  SPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRY 126
           S  +L   +  + +FV+ L ++     L+  F   G +V  +++ DK   + RG   + +
Sbjct: 5   SSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTF 63

Query: 127 ATEEESRRAIEGMHGKFLDGRVIFVEIAKSRAELRQAFKNNPRQN 171
               E+ +AI   +G+ L  R + V++ +        F     Q 
Sbjct: 64  EQSIEAVQAISMFNGQLLFDRPMHVKMDERALPKGDFFPPERPQQ 108

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 91.8 bits (228), Expect = 4e-24
 Identities = 22/102 (21%), Positives = 46/102 (45%), Gaps = 1/102 (0%)

Query: 66  PSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLR 125
                    +   +L VS L F  S+  ++  F  FG L +  +  D+ + R  G A + 
Sbjct: 77  SGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVH 135

Query: 126 YATEEESRRAIEGMHGKFLDGRVIFVEIAKSRAELRQAFKNN 167
           +    ++ +A++   G  LDGR + +++  S+ +L     ++
Sbjct: 136 FERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLEHHHHHH 177

>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 = 89.3 bits (222), Expect = 5e-24
 Identities = 21/82 (25%), Positives = 43/82 (52%), Gaps = 1/82 (1%)

Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
           +   +L VS L F  S+  ++  F  FG L +  +  D+ + R  G A + +  + ++ +
Sbjct: 27  ETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALK 85

Query: 135 AIEGMHGKFLDGRVIFVEIAKS 156
           A++  +G  LDGR + +++  S
Sbjct: 86  AMKQYNGVPLDGRPMNIQLVTS 107

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 89.8 bits (223), Expect = 6e-24
 Identities = 22/97 (22%), Positives = 40/97 (41%), Gaps = 8/97 (8%)

Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVE--------VNLVMDKIANRPRGFAFLRY 126
                +FV GL    + +S+ + F+  G +          +NL  D+   + +G A + +
Sbjct: 5   SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSF 64

Query: 127 ATEEESRRAIEGMHGKFLDGRVIFVEIAKSRAELRQA 163
                ++ AI+   GK   G  I V  A  RA+  + 
Sbjct: 65  DDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADFNRG 101

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 89.3 bits (222), Expect = 8e-24
 Identities = 29/86 (33%), Positives = 50/86 (58%), Gaps = 1/86 (1%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
            +LF+ GLSF T+E+SLRN ++ +G+L +  ++ D  + R RGF F+ +++  E   A+ 
Sbjct: 28  RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA 87

Query: 138 GMHGKFLDGRVIFVEIAKSRAELRQA 163
                 +DGRV+  + A +R E    
Sbjct: 88  -ARPHSIDGRVVEPKRAVAREESGSG 112

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score = 88.9 bits (221), Expect = 1e-23
 Identities = 23/95 (24%), Positives = 44/95 (46%), Gaps = 1/95 (1%)

Query: 65  PPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFL 124
              P          ++F+ GLS++T+++ LR  F  FG++ E  ++ D +  R RGF F+
Sbjct: 13  GLVPRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFV 72

Query: 125 RYATEEESRRAIEGMHGKFLDGRVIFVEIAKSRAE 159
            +  +    + +       LD + I  ++A  R  
Sbjct: 73  TFMDQAGVDKVLA-QSRHELDSKTIDPKVAFPRRA 106

>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 = 88.5 bits (220), Expect = 1e-23
 Identities = 19/87 (21%), Positives = 44/87 (50%), Gaps = 6/87 (6%)

Query: 77  KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
              ++  G++   ++  +R  F  FGQ++E+ +  +K      G++F+R++T E +  AI
Sbjct: 25  NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK------GYSFVRFSTHESAAHAI 78

Query: 137 EGMHGKFLDGRVIFVEIAKSRAELRQA 163
             ++G  ++G V+     K   ++   
Sbjct: 79  VSVNGTTIEGHVVKCYWGKESPDMTSG 105

>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 = 90.9 bits (226), Expect = 1e-23
 Identities = 26/95 (27%), Positives = 42/95 (44%)

Query: 65  PPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFL 124
            P   S        +LF+ GL    ++D ++     FG L   NLV D      +G+AF 
Sbjct: 102 VPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFC 161

Query: 125 RYATEEESRRAIEGMHGKFLDGRVIFVEIAKSRAE 159
            Y     + +AI G++G  L  + + V+ A   A+
Sbjct: 162 EYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAK 196

>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 = 74.3 bits (183), Expect = 3e-17
 Identities = 19/98 (19%), Positives = 41/98 (41%), Gaps = 6/98 (6%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNL-----VMDKIANRPRGFAFLRYATEEESR 133
           RL+V  + F  +E+++ + F    +L  +       V+    N+ + FAFL + + +E+ 
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 134 RAIEGMHGKFLDGRVIFVEIAKSRAELRQAFKNNPRQN 171
           +A+    G    G+ + +        L    +N     
Sbjct: 66  QAMA-FDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYV 102

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori} Length = 90

 Score = 87.6 bits (218), Expect = 1e-23
 Identities = 21/89 (23%), Positives = 39/89 (43%), Gaps = 1/89 (1%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
            ++V  L +  + + ++  F  FG++  V L+ D+   +P+GF F+    E     AI  
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESV-SEAIAK 61

Query: 139 MHGKFLDGRVIFVEIAKSRAELRQAFKNN 167
           +      GR I V  A  +  L     ++
Sbjct: 62  LDNTDFMGRTIRVTEANPKKSLEHHHHHH 90

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score = 88.1 bits (219), Expect = 2e-23
 Identities = 18/93 (19%), Positives = 41/93 (44%), Gaps = 4/93 (4%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
             +FV G+  R  E  +R+ F  +G + EV ++ D+     +G+ F+ +  + + ++ +E
Sbjct: 10  NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE 68

Query: 138 GMHGKFLDGRVIFVEIAKSRAELRQAFKNNPRQ 170
                   G+ + +  A  +      +   PR 
Sbjct: 69  SQIN--FHGKKLKLGPAIRKQN-LSTYHVQPRP 98

>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 = 88.1 bits (219), Expect = 2e-23
 Identities = 22/84 (26%), Positives = 42/84 (50%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
               ++V GL  + SE  L   F   G +V  ++  D++  + +G+ F+ + +EE++  A
Sbjct: 14  QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA 73

Query: 136 IEGMHGKFLDGRVIFVEIAKSRAE 159
           I+ M    L G+ I V  A +  +
Sbjct: 74  IKIMDMIKLYGKPIRVNKASAHNK 97

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 90.8 bits (226), Expect = 2e-23
 Identities = 20/93 (21%), Positives = 43/93 (46%)

Query: 65  PPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFL 124
           P         +   R++V+ +    S+D +++ F+ FG++    L  D    + +G+ F+
Sbjct: 113 PIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFI 172

Query: 125 RYATEEESRRAIEGMHGKFLDGRVIFVEIAKSR 157
            Y   + S+ A+  M+   L G+ + V  A + 
Sbjct: 173 EYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTP 205

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 87.4 bits (217), Expect = 5e-22
 Identities = 25/106 (23%), Positives = 49/106 (46%), Gaps = 1/106 (0%)

Query: 66  PSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLR 125
            +          +R++V  + +   ED++R AF  FG +  +++  D +  + +GFAF+ 
Sbjct: 17  SAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVE 76

Query: 126 YATEEESRRAIEGMHGKFLDGRVIFVEIAKSRAELRQAFKNNPRQN 171
           Y   E ++ A+E M+   L GR I V    +  +  Q   +   + 
Sbjct: 77  YEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQ-AQPIIDQLAEE 121

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 87.6 bits (218), Expect = 2e-23
 Identities = 26/85 (30%), Positives = 43/85 (50%), Gaps = 1/85 (1%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           ++FV G+     E  LR  F+ FG + EV ++ D    RPRGF F+ +  E+   +A+  
Sbjct: 12  KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN- 70

Query: 139 MHGKFLDGRVIFVEIAKSRAELRQA 163
           MH   + G+ + V+ A+ R      
Sbjct: 71  MHFHDIMGKKVEVKRAEPRDSKSSG 95

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 87.2 bits (217), Expect = 3e-23
 Identities = 20/82 (24%), Positives = 40/82 (48%), Gaps = 2/82 (2%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
              ++FV  L F  +   L++ F   G ++  ++ M+    + +G   +++ + E + RA
Sbjct: 7   GACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMEN--GKSKGCGVVKFESPEVAERA 64

Query: 136 IEGMHGKFLDGRVIFVEIAKSR 157
              M+G  L GR I V I ++ 
Sbjct: 65  CRMMNGMKLSGREIDVRIDRNA 86

>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 = 87.3 bits (217), Expect = 3e-23
 Identities = 20/87 (22%), Positives = 34/87 (39%), Gaps = 2/87 (2%)

Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
                LF+  L+   S   L+ A            V+D      R F ++ + + E+  +
Sbjct: 15  TTPFNLFIGNLNPNKSVAELKVAISELFA-KNDLAVVDVRTGTNRKFGYVDFESAEDLEK 73

Query: 135 AIEGMHGKFLDGRVIFVEIAKSRAELR 161
           A+E + G  + G  I +E  K R   R
Sbjct: 74  ALE-LTGLKVFGNEIKLEKPKGRDGTR 99

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 87.3 bits (217), Expect = 3e-23
 Identities = 22/89 (24%), Positives = 48/89 (53%), Gaps = 2/89 (2%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
             L+V  L     ++ LR AF  FG +    ++M+    R +GF F+ +++ EE+ +A+ 
Sbjct: 16  VNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEG--GRSKGFGFVCFSSPEEATKAVT 73

Query: 138 GMHGKFLDGRVIFVEIAKSRAELRQAFKN 166
            M+G+ +  + ++V +A+ + E +    +
Sbjct: 74  EMNGRIVATKPLYVALAQRKEERQSGPSS 102

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C Length = 229

 Score = 90.5 bits (224), Expect = 4e-23
 Identities = 15/97 (15%), Positives = 43/97 (44%), Gaps = 2/97 (2%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFG--QLVEVNLVMDKIANRPRGFAFLRYATEEESR 133
            +  L++  L++ T+++ L  A    G   ++E+    ++   + +GFA +   +E  S+
Sbjct: 67  KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSK 126

Query: 134 RAIEGMHGKFLDGRVIFVEIAKSRAELRQAFKNNPRQ 170
           + ++ +  + L G+   V     +   +   ++    
Sbjct: 127 KLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTT 163

>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 = 88.8 bits (221), Expect = 5e-23
 Identities = 23/80 (28%), Positives = 38/80 (47%)

Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
               +LF+ GL    ++D ++     FG L   NLV D      +G+AF  Y     + +
Sbjct: 92  PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQ 151

Query: 135 AIEGMHGKFLDGRVIFVEIA 154
           AI G++G  L  + + V+ A
Sbjct: 152 AIAGLNGMQLGDKKLLVQRA 171

>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 = 75.3 bits (186), Expect = 7e-18
 Identities = 20/92 (21%), Positives = 41/92 (44%), Gaps = 6/92 (6%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNL-----VMDKIANRPRGFAFLRYATEEESR 133
           RL+V  + F  +E+++ + F    +L  +       V+    N+ + FAFL + + +E+ 
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 134 RAIEGMHGKFLDGRVIFVEIAKSRAELRQAFK 165
           +A+    G    G+ + +        L  A K
Sbjct: 66  QAMA-FDGIIFQGQSLKIRRPHDYQPLPGAHK 96

>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 = 91.2 bits (227), Expect = 5e-23
 Identities = 18/93 (19%), Positives = 34/93 (36%)

Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
                L V+ L    ++       + FG L    LV  +   + +G+ F  Y  ++ + R
Sbjct: 93  PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAAR 152

Query: 135 AIEGMHGKFLDGRVIFVEIAKSRAELRQAFKNN 167
           A   + GK L  R ++V    +         + 
Sbjct: 153 AKSDLLGKPLGPRTLYVHWTDAGQLTPALLHSR 185

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 80.8 bits (200), Expect = 4e-19
 Identities = 20/86 (23%), Positives = 29/86 (33%), Gaps = 2/86 (2%)

Query: 78  TRLFVSGLSFRTSE-DSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
             L V  L    ++ D+L  A           L   +   + +GFA L Y T E +  A 
Sbjct: 185 RCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEMAEEAQ 243

Query: 137 EGMHGKFLDGRVIFVEIAKSRAELRQ 162
           +   G  L G  + V         R 
Sbjct: 244 QQADGLSLGGSHLRVSFCAPGPPGRS 269

>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 = 68.1 bits (167), Expect = 2e-14
 Identities = 13/103 (12%), Positives = 35/103 (33%), Gaps = 21/103 (20%)

Query: 77  KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
           + ++ + GL    +   + +    +        +     ++ +G AF+     E++  AI
Sbjct: 22  RRKILIRGLPGDVTNQEVHDLLSDYE-------LKYCFVDKYKGTAFVTLLNGEQAEAAI 74

Query: 137 EGMHGKFLDGRVIFVEIAKSRA--------------ELRQAFK 165
              H   L  R + V++  + A              +  +  +
Sbjct: 75  NAFHQSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVR 117

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 88.0 bits (219), Expect = 9e-23
 Identities = 27/87 (31%), Positives = 46/87 (52%), Gaps = 2/87 (2%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           ++F+ GL++ T+ED+LR  F  +G + ++ ++ D    R RGF FL +         ++ 
Sbjct: 5   KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64

Query: 139 MHGKFLDGRVIFVEIAKSRAELRQAFK 165
            H   LDG+VI  + A  R E  +  K
Sbjct: 65  QH--ILDGKVIDPKRAIPRDEQDKTGK 89

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 84.1 bits (209), Expect = 2e-21
 Identities = 18/83 (21%), Positives = 35/83 (42%), Gaps = 1/83 (1%)

Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
               ++FV G+            F  +G +++  L++DK   + RGF F+ Y + +   R
Sbjct: 85  DKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDR 144

Query: 135 AIEGMHGKFLDGRVIFVEIAKSR 157
             +         R I ++ A+ R
Sbjct: 145 VCQ-NKFIDFKDRKIEIKRAEPR 166

>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 = 85.8 bits (213), Expect = 1e-22
 Identities = 24/81 (29%), Positives = 35/81 (43%), Gaps = 1/81 (1%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
               +FV  L  R  E+ L   F   G L +V +  D+   +P+ F F+ +   E    A
Sbjct: 15  ADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYA 73

Query: 136 IEGMHGKFLDGRVIFVEIAKS 156
           I  ++G  L GR I V    S
Sbjct: 74  IALLNGIRLYGRPINVSGPSS 94

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 84.9 bits (211), Expect = 1e-22
 Identities = 21/76 (27%), Positives = 42/76 (55%), Gaps = 1/76 (1%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           ++F+ GLS++T+++ LR  F  FG++ E  ++ D +  R RGF F+ +  +    + +  
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA- 60

Query: 139 MHGKFLDGRVIFVEIA 154
                LD + I  ++A
Sbjct: 61  QSRHELDSKTIDPKVA 76

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A Length = 115

 Score = 86.2 bits (214), Expect = 1e-22
 Identities = 20/92 (21%), Positives = 43/92 (46%), Gaps = 1/92 (1%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
               LF+  L     +  L   F  FG +V   + +DK  N  + F F+ Y     ++ A
Sbjct: 24  EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAA 83

Query: 136 IEGMHGKFLDGRVIFVEIAKSRAELRQAFKNN 167
           I+ M+G  +  + + V++ +S+ +  ++  ++
Sbjct: 84  IQSMNGFQIGMKRLKVQLKRSKND-SKSGPSS 114

>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 = 85.8 bits (213), Expect = 1e-22
 Identities = 27/100 (27%), Positives = 45/100 (45%), Gaps = 8/100 (8%)

Query: 72  STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEE 131
           S       LFV  L+   +E+ L  AF  FG+L  V           + +AF+ +   + 
Sbjct: 6   SGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKK--------LKDYAFIHFDERDG 57

Query: 132 SRRAIEGMHGKFLDGRVIFVEIAKSRAELRQAFKNNPRQN 171
           + +A+E M+GK L+G  I +  AK   + R+  K   +  
Sbjct: 58  AVKAMEEMNGKDLEGENIEIVFAKPPDQKRKERKAQRQAA 97

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A Length = 87

 Score = 84.5 bits (210), Expect = 2e-22
 Identities = 26/77 (33%), Positives = 43/77 (55%), Gaps = 1/77 (1%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
            ++FV GLS+ TS+  L++ F  FG++V+  + MD    R RGF F+ +       + ++
Sbjct: 12  GKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD 71

Query: 138 GMHGKFLDGRVIFVEIA 154
               + LDGRVI  + A
Sbjct: 72  QKEHR-LDGRVIDPKKA 87

>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 = 84.6 bits (210), Expect = 3e-22
 Identities = 22/90 (24%), Positives = 44/90 (48%), Gaps = 8/90 (8%)

Query: 70  SLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATE 129
           S S+ +  T+L V  +S   +   LR  F+ +G ++E ++V        + +AF+     
Sbjct: 3   SGSSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERA 54

Query: 130 EESRRAIEGMHGKFLDGRVIFVEIAKSRAE 159
           E++  AI G+      G+ + V+++ SR  
Sbjct: 55  EDAVEAIRGLDNTEFQGKRMHVQLSTSRLR 84

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score = 84.1 bits (209), Expect = 3e-22
 Identities = 18/82 (21%), Positives = 39/82 (47%), Gaps = 1/82 (1%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
               ++V  + +  + + L   F G G +  V ++ DK +  P+GFA++ ++ +E  R +
Sbjct: 5   DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTS 64

Query: 136 IEGMHGKFLDGRVIFVEIAKSR 157
           +  +      GR I V   ++ 
Sbjct: 65  LA-LDESLFRGRQIKVIPKRTN 85

>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 = 87.3 bits (217), Expect = 4e-22
 Identities = 27/93 (29%), Positives = 45/93 (48%), Gaps = 2/93 (2%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
             +F+  L       +L + F  FG ++   +V D   N  +G+ F+ + T+E + RAIE
Sbjct: 104 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIE 161

Query: 138 GMHGKFLDGRVIFVEIAKSRAELRQAFKNNPRQ 170
            M+G  L+ R +FV   KSR E         ++
Sbjct: 162 KMNGMLLNDRKVFVGRFKSRKEREAELGARAKE 194

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 71.2 bits (175), Expect = 6e-16
 Identities = 17/76 (22%), Positives = 36/76 (47%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
           P   L+V  L    +E  L   F   G ++ + +  D I  R  G+A++ +    ++ RA
Sbjct: 14  PMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERA 73

Query: 136 IEGMHGKFLDGRVIFV 151
           ++ M+   + G+ + +
Sbjct: 74  LDTMNFDVIKGKPVRI 89

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 87.0 bits (216), Expect = 4e-22
 Identities = 32/90 (35%), Positives = 52/90 (57%), Gaps = 1/90 (1%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           +LF+ GLSF T+++SLR+ F+ +G L +  ++ D    R RGF F+ YAT EE   A+  
Sbjct: 15  KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN- 73

Query: 139 MHGKFLDGRVIFVEIAKSRAELRQAFKNNP 168
                +DGRV+  + A SR + ++   +  
Sbjct: 74  ARPHKVDGRVVEPKRAVSREDSQRPGAHLT 103

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 85.8 bits (213), Expect = 1e-21
 Identities = 22/103 (21%), Positives = 45/103 (43%), Gaps = 1/103 (0%)

Query: 61  LACLPPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRG 120
            A                ++FV G+   T E  LR+ F+ +G++  + ++ D+ + + RG
Sbjct: 88  RAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRG 147

Query: 121 FAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKSRAELRQA 163
           FAF+ +   +   + +       ++G    V  A S+ E+  A
Sbjct: 148 FAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKALSKQEMASA 189

>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 = 83.4 bits (207), Expect = 6e-22
 Identities = 20/82 (24%), Positives = 44/82 (53%), Gaps = 8/82 (9%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
            ++FV  +S   +   LR+ F+  G+++E ++V        + +AF+    E +++ AI 
Sbjct: 10  WKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEADAKAAIA 61

Query: 138 GMHGKFLDGRVIFVEIAKSRAE 159
            ++GK + G+ I VE++    +
Sbjct: 62  QLNGKEVKGKRINVELSTKGQK 83

>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 = 85.3 bits (211), Expect = 6e-22
 Identities = 22/119 (18%), Positives = 43/119 (36%), Gaps = 5/119 (4%)

Query: 39  KRRDFDSLFSLRQGRGRGACFPLACLPPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAF 98
                D  ++             +          +C    +++V  L    ++  L  AF
Sbjct: 35  NDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNKTELERAF 94

Query: 99  QGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKSR 157
             +G L  V      +A  P GFAF+ +    ++  A+  + G+ L G  + VE++   
Sbjct: 95  GYYGPLRSV-----WVARNPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGE 148

>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 = 85.7 bits (213), Expect = 7e-22
 Identities = 21/79 (26%), Positives = 45/79 (56%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
               LFV  L+    +++LRNAF+ F   +  +++ D      RG+ F+ + ++++++ A
Sbjct: 86  DTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNA 145

Query: 136 IEGMHGKFLDGRVIFVEIA 154
           ++ M G+ L+GR + +  A
Sbjct: 146 MDSMQGQDLNGRPLRINWA 164

>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 = 67.2 bits (165), Expect = 9e-15
 Identities = 19/82 (23%), Positives = 42/82 (51%), Gaps = 1/82 (1%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           L+V  L    +ED L+  FQ  G +  + +++DK  N+   +AF+ Y    ++  A++ +
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTL 61

Query: 140 HGKFLDGRVIFVEIAKSRAELR 161
           +GK ++  ++ +  A    +  
Sbjct: 62  NGKQIENNIVKINWAFQSQQSS 83

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 84.4 bits (209), Expect = 8e-22
 Identities = 17/83 (20%), Positives = 36/83 (43%), Gaps = 1/83 (1%)

Query: 77  KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
           K  ++V  + + ++   L   F   G +  + ++ DK +  P+G+A++ +A       A+
Sbjct: 36  KRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV 95

Query: 137 EGMHGKFLDGRVIFVEIAKSRAE 159
             M      GR I V   ++   
Sbjct: 96  A-MDETVFRGRTIKVLPKRTNMP 117

>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 = 85.7 bits (213), Expect = 9e-22
 Identities = 17/94 (18%), Positives = 37/94 (39%), Gaps = 5/94 (5%)

Query: 65  PPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFL 124
            P        +    L    LSF  +ED L+  F+         + +     + +G A++
Sbjct: 87  KPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDAL-----EIRLVSQDGKSKGIAYI 141

Query: 125 RYATEEESRRAIEGMHGKFLDGRVIFVEIAKSRA 158
            + +E ++ + +E   G  +DGR + +     + 
Sbjct: 142 EFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKG 175

>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 = 77.6 bits (192), Expect = 1e-18
 Identities = 19/92 (20%), Positives = 36/92 (39%), Gaps = 2/92 (2%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
               LF+  L+   S   L+ A        ++  V+D      R F ++ + + E+  +A
Sbjct: 12  TPFNLFIGNLNPNKSVAELKVAISELFAKNDLA-VVDVRTGTNRKFGYVDFESAEDLEKA 70

Query: 136 IEGMHGKFLDGRVIFVEIAKSRAELRQAFKNN 167
           +E + G  + G  I +E  K R   +      
Sbjct: 71  LE-LTGLKVFGNEIKLEKPKGRDSKKVRAART 101

>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 = 83.1 bits (206), Expect = 1e-21
 Identities = 21/96 (21%), Positives = 38/96 (39%), Gaps = 8/96 (8%)

Query: 67  SPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVE--------VNLVMDKIANRP 118
             H   +      +FV GL    + +S+ + F+  G +          +NL  D+   + 
Sbjct: 3   HHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKL 62

Query: 119 RGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIA 154
           +G A + +     ++ AI+   GK   G  I V  A
Sbjct: 63  KGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFA 98

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 83.1 bits (206), Expect = 1e-21
 Identities = 26/87 (29%), Positives = 38/87 (43%), Gaps = 8/87 (9%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
             TRLFV        E  L   F  FG + EV +          GFAF+ +   E + +A
Sbjct: 30  SNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKI--------LNGFAFVEFEEAESAAKA 81

Query: 136 IEGMHGKFLDGRVIFVEIAKSRAELRQ 162
           IE +HGK    + + V  +K  A+  +
Sbjct: 82  IEEVHGKSFANQPLEVVYSKLPAKRYR 108

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 82.7 bits (205), Expect = 2e-21
 Identities = 18/80 (22%), Positives = 32/80 (40%), Gaps = 6/80 (7%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           T  ++  +    +E  L   FQ FG +++     +K      G  F++Y T E++   I 
Sbjct: 28  TTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEK------GCCFIKYDTHEQAAVCIV 81

Query: 138 GMHGKFLDGRVIFVEIAKSR 157
            +      GR +     K R
Sbjct: 82  ALANFPFQGRNLRTGWGKER 101

>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 = 82.3 bits (204), Expect = 3e-21
 Identities = 25/98 (25%), Positives = 45/98 (45%), Gaps = 4/98 (4%)

Query: 65  PPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFL 124
             S  S S      +LFV  L+ + SE+ +   FQ FG + E  ++        +G AF+
Sbjct: 3   SGSSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFV 61

Query: 125 RYATEEESRRAIEGMHGKFL---DGRVIFVEIAKSRAE 159
           ++++  E++ AI  +HG          + V+ A +  E
Sbjct: 62  KFSSHTEAQAAIHALHGSQTMPGASSSLVVKFADTDKE 99

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 81.4 bits (202), Expect = 3e-21
 Identities = 22/76 (28%), Positives = 46/76 (60%), Gaps = 1/76 (1%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           ++FV GLS  T+ + +++ F+ FG++ +  L+ DK  NR RGF F+ + +E+   +  E 
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE- 59

Query: 139 MHGKFLDGRVIFVEIA 154
           +H   ++ +++  + A
Sbjct: 60  IHFHEINNKMVECKKA 75

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 82.4 bits (204), Expect = 3e-21
 Identities = 18/85 (21%), Positives = 40/85 (47%), Gaps = 1/85 (1%)

Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
           +    +F   L+ R     L + F   G++ +V ++ D+ + R +G A++ +   +    
Sbjct: 23  RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPL 82

Query: 135 AIEGMHGKFLDGRVIFVEIAKSRAE 159
           AI  + G+ L G  I V+ +++   
Sbjct: 83  AIG-LTGQRLLGVPIIVQASQAEKN 106

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 82.4 bits (204), Expect = 4e-21
 Identities = 17/80 (21%), Positives = 39/80 (48%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
               LF+  L    ++  L + F  FG ++   + +DK  +  + F F+ +   + ++ A
Sbjct: 39  EGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVA 98

Query: 136 IEGMHGKFLDGRVIFVEIAK 155
           I+ M+G  +  + + V++ K
Sbjct: 99  IKAMNGFQVGTKRLKVQLKK 118

>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 = 81.6 bits (202), Expect = 4e-21
 Identities = 22/91 (24%), Positives = 39/91 (42%), Gaps = 6/91 (6%)

Query: 72  STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEE 131
            T      L+V  L   TSE+ +   F          +       + R +AF+ ++  E+
Sbjct: 10  DTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK------KIRDYAFVHFSNRED 63

Query: 132 SRRAIEGMHGKFLDGRVIFVEIAKSRAELRQ 162
           +  A++ ++GK LDG  I V +AK   +   
Sbjct: 64  AVEAMKALNGKVLDGSPIEVTLAKPVDKDSS 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 = 83.0 bits (206), Expect = 8e-21
 Identities = 27/82 (32%), Positives = 46/82 (56%), Gaps = 2/82 (2%)

Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
              T L+V+ L    ++D L   F  +G +V+ N++ DK+  RPRG AF+RY   EE++ 
Sbjct: 87  IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQE 146

Query: 135 AIEGMHGKFLDG--RVIFVEIA 154
           AI  ++    +G  + + V +A
Sbjct: 147 AISALNNVIPEGGSQPLSVRLA 168

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 81.9 bits (203), Expect = 2e-20
 Identities = 20/89 (22%), Positives = 41/89 (46%)

Query: 77  KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
            T L V+ L    ++  L   F+  G +    ++ D       G+AF+ + +E +S+RAI
Sbjct: 3   NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 62

Query: 137 EGMHGKFLDGRVIFVEIAKSRAELRQAFK 165
           + ++G  +  + + V  A+   E  +   
Sbjct: 63  KVLNGITVRNKRLKVSYARPGGESIKDTN 91

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 113

 Score = 81.3 bits (201), Expect = 9e-21
 Identities = 20/90 (22%), Positives = 42/90 (46%), Gaps = 8/90 (8%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVE--------VNLVMDKIANRPRGFAFLRYATE 129
           + ++V GL+   + D L + F+  G +          +++ +DK   +P+G A + Y   
Sbjct: 16  SAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDP 75

Query: 130 EESRRAIEGMHGKFLDGRVIFVEIAKSRAE 159
             ++ A+E   GK   G  + V +A+ +  
Sbjct: 76  PTAKAAVEWFDGKDFQGSKLKVSLARKKPP 105

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 80.8 bits (200), Expect = 1e-20
 Identities = 23/91 (25%), Positives = 40/91 (43%), Gaps = 5/91 (5%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           +++V  L     +  L  AF  +G L  V      IA  P GFAF+ +    ++  A+ G
Sbjct: 2   KVYVGNLGTGAGKGELERAFSYYGPLRTV-----WIARNPPGFAFVEFEDPRDAEDAVRG 56

Query: 139 MHGKFLDGRVIFVEIAKSRAELRQAFKNNPR 169
           + GK + G  + VE++       +  +   R
Sbjct: 57  LDGKVICGSRVRVELSTGMPRRSRFDRPPAR 87

>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 = 80.3 bits (199), Expect = 1e-20
 Identities = 18/82 (21%), Positives = 42/82 (51%), Gaps = 8/82 (9%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
            +LF+  L    +E  +R+ F+ +G+++E +++        + + F+    +  +  AI 
Sbjct: 9   VKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIR 60

Query: 138 GMHGKFLDGRVIFVEIAKSRAE 159
            +H   L G  I VE +K++++
Sbjct: 61  NLHHYKLHGVNINVEASKNKSK 82

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 80.8 bits (200), Expect = 1e-20
 Identities = 20/78 (25%), Positives = 33/78 (42%), Gaps = 1/78 (1%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           T L++S L     E  L N  + FGQ++   ++ D  +   RG  F R  + E+    I 
Sbjct: 26  TNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIG 84

Query: 138 GMHGKFLDGRVIFVEIAK 155
             +GKF+          +
Sbjct: 85  HFNGKFIKTPPGVSAPTE 102

>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 = 80.0 bits (198), Expect = 1e-20
 Identities = 22/85 (25%), Positives = 38/85 (44%), Gaps = 7/85 (8%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
              +L++  LS   + D LR  F          L +        G+AF+ Y  +  + RA
Sbjct: 7   GMNKLYIGNLSPAVTADDLRQLFGDRK------LPLAGQVLLKSGYAFVDYPDQNWAIRA 60

Query: 136 IEGMHGKF-LDGRVIFVEIAKSRAE 159
           IE + GK  L G+++ V+ + S+  
Sbjct: 61  IETLSGKVELHGKIMEVDYSVSKKL 85

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score = 79.5 bits (197), Expect = 2e-20
 Identities = 24/76 (31%), Positives = 41/76 (53%), Gaps = 1/76 (1%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           ++FV GLS  T E+ +R  F GFG++  + L MD   N+ RGF F+ +  EE  ++ +E 
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME- 59

Query: 139 MHGKFLDGRVIFVEIA 154
                +      +++A
Sbjct: 60  KKYHNVGLSKCEIKVA 75

>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 = 80.4 bits (199), Expect = 2e-20
 Identities = 17/80 (21%), Positives = 34/80 (42%), Gaps = 3/80 (3%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
            R++V  L        + + F  +G + +++L   +       FAF+ +    ++  A+ 
Sbjct: 23  CRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR---GGPPFAFVEFEDPRDAEDAVY 79

Query: 138 GMHGKFLDGRVIFVEIAKSR 157
           G  G   DG  + VE  +S 
Sbjct: 80  GRDGYDYDGYRLRVEFPRSG 99

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 81.9 bits (203), Expect = 2e-20
 Identities = 23/83 (27%), Positives = 42/83 (50%)

Query: 77  KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
           KT L V+ L    +++  R+ F   G++    LV DKI  +  G+ F+ Y   +++ +AI
Sbjct: 2   KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61

Query: 137 EGMHGKFLDGRVIFVEIAKSRAE 159
             ++G  L  + I V  A+  + 
Sbjct: 62  NTLNGLRLQTKTIKVSYARPSSA 84

>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 = 81.1 bits (201), Expect = 4e-20
 Identities = 22/79 (27%), Positives = 42/79 (53%), Gaps = 2/79 (2%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
             L+VSGL    ++  L   F  +G+++   +++D++    RG  F+R+    E+  AI+
Sbjct: 89  ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 148

Query: 138 GMHGKFLDG--RVIFVEIA 154
           G++G+   G    I V+ A
Sbjct: 149 GLNGQKPSGATEPITVKFA 167

>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 = 78.5 bits (194), Expect = 7e-20
 Identities = 19/89 (21%), Positives = 40/89 (44%), Gaps = 8/89 (8%)

Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
           +    L+V G     +   LR AF  FG ++++++   +        AF+ Y   E + +
Sbjct: 13  RKGNTLYVYGEDM--TPTLLRGAFSPFGNIIDLSMDPPR------NCAFVTYEKMESADQ 64

Query: 135 AIEGMHGKFLDGRVIFVEIAKSRAELRQA 163
           A+  ++G  ++   + V IA+ +  L   
Sbjct: 65  AVAELNGTQVESVQLKVNIARKQPMLDSG 93

>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 = 82.7 bits (205), Expect = 9e-20
 Identities = 20/84 (23%), Positives = 41/84 (48%), Gaps = 3/84 (3%)

Query: 76  PKTRLFVSGLSFR-TSEDSLRNAFQGFGQLVEVNLVMDKIAN-RPRGFAFLRYATEEESR 133
               + +  LS     E+ LR +F+GFG + ++N+   +  +      AF+ +  ++ + 
Sbjct: 209 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAE 268

Query: 134 RAIEGMHGKFLDGRVIFVEIAKSR 157
           RA++ M+   L  R I V +A  +
Sbjct: 269 RALQ-MNRSLLGNREISVSLADKK 291

>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 = 82.0 bits (203), Expect = 2e-19
 Identities = 12/88 (13%), Positives = 41/88 (46%)

Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
             +  L+++      ++ ++R+  Q    +     +     N  R FA++   ++E++R 
Sbjct: 115 LTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARY 174

Query: 135 AIEGMHGKFLDGRVIFVEIAKSRAELRQ 162
            +E ++G  ++G  +  +++    + ++
Sbjct: 175 CVEKLNGLKIEGYTLVTKVSNPLEKSKR 202

>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 = 68.5 bits (168), Expect = 1e-14
 Identities = 14/99 (14%), Positives = 32/99 (32%), Gaps = 16/99 (16%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           + V  L    +++ +   F+  G ++ V++       +   FA + +A  + +  AI   
Sbjct: 44  VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSL--KKNFRFARIEFARYDGALAAITKT 101

Query: 140 HGKFLDGRVIFVEIAKSR-------------AELRQAFK 165
           H   +    I V                     +R   +
Sbjct: 102 HKV-VGQNEIIVSHLTECTLWMTNFPPSYTQRNIRDLLQ 139

>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 = 77.3 bits (191), Expect = 2e-19
 Identities = 15/94 (15%), Positives = 37/94 (39%)

Query: 65  PPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFL 124
             S  + S     T + V  + F  S D + + F G+  +     +       P G A +
Sbjct: 3   SGSSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMV 62

Query: 125 RYATEEESRRAIEGMHGKFLDGRVIFVEIAKSRA 158
            + + +E+  A+  ++ + +  R + + +    +
Sbjct: 63  AFESRDEATAAVIDLNDRPIGSRKVKLVLGSGPS 96

>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 = 76.2 bits (188), Expect = 5e-19
 Identities = 17/92 (18%), Positives = 36/92 (39%)

Query: 65  PPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFL 124
             S  S S     T + V  + F  S D + + F G+  +     +       P G A +
Sbjct: 3   SGSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMV 62

Query: 125 RYATEEESRRAIEGMHGKFLDGRVIFVEIAKS 156
            + + +E+  A+  ++ + +  R + +    S
Sbjct: 63  AFESRDEATAAVIDLNDRPIGSRKVKLSGPSS 94

>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 = 78.0 bits (193), Expect = 7e-19
 Identities = 21/80 (26%), Positives = 38/80 (47%), Gaps = 4/80 (5%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
            +LF+  +S + +E+ +R  F  FGQ+ E  ++        RG AF+ + T   ++ AI+
Sbjct: 96  RKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIK 154

Query: 138 GMHGKFL---DGRVIFVEIA 154
            MH           + V+ A
Sbjct: 155 AMHQAQTMEGCSSPMVVKFA 174

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 77.7 bits (192), Expect = 1e-18
 Identities = 23/92 (25%), Positives = 46/92 (50%), Gaps = 3/92 (3%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRP--RGFAFLRYATEEESRRA 135
            ++FV  +    SE  LR  F+ +G + E+N++ D+  N P  +G  F+ + T + +  A
Sbjct: 4   IKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63

Query: 136 IEGMHG-KFLDGRVIFVEIAKSRAELRQAFKN 166
              +H  K L G    +++  + +E   A ++
Sbjct: 64  QNALHNMKVLPGMHHPIQMKPADSEKNNAVED 95

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 75.8 bits (187), Expect = 8e-19
 Identities = 21/85 (24%), Positives = 40/85 (47%), Gaps = 2/85 (2%)

Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
           +P    +V  L F T +  +   F+    +  V LV DK  ++ +GF ++ +   +  + 
Sbjct: 13  EPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKE 71

Query: 135 AIEGMHGKFLDGRVIFVEIAKSRAE 159
           A+    G  L  R + V+IA+ R +
Sbjct: 72  ALT-YDGALLGDRSLRVDIAEGRKQ 95

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 75.3 bits (186), Expect = 1e-18
 Identities = 20/83 (24%), Positives = 41/83 (49%), Gaps = 9/83 (10%)

Query: 76  PKTRLFVSGLSFRT-SEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
           PK+RLF+  L  +  S++ L   F  +G ++++N+           F F+++   +  R 
Sbjct: 9   PKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRD 60

Query: 135 AIEGMHGKFLDGRVIFVEIAKSR 157
           AIE    +   G+ + +E++ S 
Sbjct: 61  AIECESQEMNFGKKLILEVSSSN 83

>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 = 75.9 bits (187), Expect = 1e-18
 Identities = 21/107 (19%), Positives = 45/107 (42%), Gaps = 2/107 (1%)

Query: 65  PPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFL 124
             S         K    ++ + F  ++  +    +G         V+     +  G A +
Sbjct: 3   SGSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALV 62

Query: 125 RYATEEESRRAIEGMHGKFLDGRVIFVEIAKSRAELRQAFKNNPRQN 171
           ++  E+++R++   +H K L+GR  FV +  +  ++R+  KN P Q 
Sbjct: 63  QFKNEDDARKSER-LHRKKLNGREAFVHVV-TLEDMREIEKNPPAQG 107

>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 = 75.0 bits (185), Expect = 1e-18
 Identities = 27/85 (31%), Positives = 42/85 (49%), Gaps = 8/85 (9%)

Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
            P TRL+V GL   TS  +L   F  FG +  ++ V      +   FA+++Y + + ++ 
Sbjct: 15  NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHV------KGDSFAYIQYESLDAAQA 68

Query: 135 AIEGMHGKFLDG--RVIFVEIAKSR 157
           A   M G  L G  R + V+ AKS 
Sbjct: 69  ACAKMRGFPLGGPDRRLRVDFAKSG 93

>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 = 75.5 bits (186), Expect = 1e-18
 Identities = 18/89 (20%), Positives = 42/89 (47%), Gaps = 9/89 (10%)

Query: 76  PKTRLFVSGLSF-RTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
             +R+F+  L+     +  +   F  +G++   ++         +G+AF++Y+ E  +R 
Sbjct: 26  INSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARA 77

Query: 135 AIEGMHGKFLDGRVIFVEIAKSRAELRQA 163
           A+ G +G+ L G+ + + +A      R  
Sbjct: 78  AVLGENGRVLAGQTLDINMAGEPKPDRSG 106

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 74.8 bits (184), Expect = 2e-18
 Identities = 11/85 (12%), Positives = 32/85 (37%), Gaps = 3/85 (3%)

Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
           Q   +L +  +      + L +    +G +     V             + Y++++++R+
Sbjct: 13  QRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTD---SETAVVNVTYSSKDQARQ 69

Query: 135 AIEGMHGKFLDGRVIFVEIAKSRAE 159
           A++ ++G  L+   + V        
Sbjct: 70  ALDKLNGFQLENFTLKVAYIPDEMA 94

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 74.4 bits (183), Expect = 3e-18
 Identities = 18/92 (19%), Positives = 35/92 (38%), Gaps = 4/92 (4%)

Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLV-EVNLVMD-KIANRPRGFAFLRYATEEES 132
               RLF+ G+      + +        + V +V +        + RGFAF+ Y +   +
Sbjct: 6   SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAA 65

Query: 133 RRAIEGMHGKF--LDGRVIFVEIAKSRAELRQ 162
             A   +      L G  I V+ A+   ++ +
Sbjct: 66  AMARRKLMPGRIQLWGHQIAVDWAEPEIDVDE 97

>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 = 73.5 bits (181), Expect = 8e-18
 Identities = 17/86 (19%), Positives = 38/86 (44%), Gaps = 3/86 (3%)

Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKI-ANRPRGFAFLRYATEEESR 133
            P    F+  L +  +E+S++  F+G   +  V L  +     R +GF +  +   +   
Sbjct: 13  SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLL 71

Query: 134 RAIEGMHGKFLDGRVIFVEIAKSRAE 159
            A+  ++ + L  + I V++A    +
Sbjct: 72  SALS-LNEESLGNKRIRVDVADQAQD 96

>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 = 73.6 bits (181), Expect = 8e-18
 Identities = 12/89 (13%), Positives = 39/89 (43%), Gaps = 3/89 (3%)

Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
           +    L++  L ++ + + + + F  +G + ++ +         RG A++ Y    +++ 
Sbjct: 6   EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTP---ETRGTAYVVYEDIFDAKN 62

Query: 135 AIEGMHGKFLDGRVIFVEIAKSRAELRQA 163
           A++ + G  +  R + V    +    ++ 
Sbjct: 63  AVDHLSGFNVSNRYLVVLYYNANRAFQKM 91

>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 = 73.0 bits (180), Expect = 8e-18
 Identities = 18/86 (20%), Positives = 38/86 (44%), Gaps = 3/86 (3%)

Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKI-ANRPRGFAFLRYATEEESR 133
            P    F+  L +  +E+S++  F+G   +  V L  +     R +GF +  +   +   
Sbjct: 17  SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLL 75

Query: 134 RAIEGMHGKFLDGRVIFVEIAKSRAE 159
            A+  ++ + L  R I V++A    +
Sbjct: 76  SALS-LNEESLGNRRIRVDVADQAQD 100

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 72.8 bits (179), Expect = 1e-17
 Identities = 14/70 (20%), Positives = 33/70 (47%)

Query: 81  FVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMH 140
            +        + +L + F   G++V +   +D+   + +GF F+   +  ++++ I+  H
Sbjct: 16  VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75

Query: 141 GKFLDGRVIF 150
           GK LD +   
Sbjct: 76  GKRLDLKHRL 85

>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 = 76.7 bits (189), Expect = 1e-17
 Identities = 22/101 (21%), Positives = 39/101 (38%), Gaps = 5/101 (4%)

Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
                L V  LS   S + L  AF  FG + +  +V+D    R  G  F+ +A +  +R+
Sbjct: 94  THGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDD-RGRATGKGFVEFAAKPPARK 152

Query: 135 AIEGMHGKFL----DGRVIFVEIAKSRAELRQAFKNNPRQN 171
           A+E             R + VE  +   +     +   ++ 
Sbjct: 153 ALERCGDGAFLLTTTPRPVIVEPMEQFDDEDGLPEKLMQKT 193

>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 = 74.3 bits (183), Expect = 9e-17
 Identities = 23/85 (27%), Positives = 37/85 (43%), Gaps = 6/85 (7%)

Query: 77  KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
           + RLFV  L    +E+  +  F+ +G+  EV +  D      RGF F+R  +   +  A 
Sbjct: 22  RCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAK 75

Query: 137 EGMHGKFLDGRVIFVEIAKSRAELR 161
             + G  L  R + +  A   A L 
Sbjct: 76  AELDGTILKSRPLRIRFATHGAALT 100

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 72.7 bits (179), Expect = 2e-17
 Identities = 20/95 (21%), Positives = 41/95 (43%), Gaps = 3/95 (3%)

Query: 65  PPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFL 124
             S       QP+T L+V  LS   +E  +   F   G      ++ +  +N P  + F+
Sbjct: 4   GSSGMMEDDGQPRT-LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFV 60

Query: 125 RYATEEESRRAIEGMHGKFLDGRVIFVEIAKSRAE 159
            +    ++  A+  M+G+ + G+ + V  A + + 
Sbjct: 61  EFYEHRDAAAALAAMNGRKILGKEVKVNWATTPSS 95

>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 = 72.3 bits (178), Expect = 2e-17
 Identities = 21/94 (22%), Positives = 42/94 (44%), Gaps = 9/94 (9%)

Query: 66  PSPHSLSTCQPKTRLFVSGLSFRT-SEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFL 124
            S         K+RLF+  L  +  S++ L   F  +G ++++N+           F F+
Sbjct: 11  SSGLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFI 62

Query: 125 RYATEEESRRAIEGMHGKFLDGRVIFVEIAKSRA 158
           ++   +  R AIE    +   G+ + +E++ S A
Sbjct: 63  QFDNPQSVRDAIEXESQEMNFGKKLILEVSSSNA 96

>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 = 73.3 bits (180), Expect = 2e-17
 Identities = 20/109 (18%), Positives = 42/109 (38%), Gaps = 5/109 (4%)

Query: 66  PSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNL-----VMDKIANRPRG 120
               S    +P  R++V  L+    E  L+  F  +             +      R +G
Sbjct: 34  SVFRSYEPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKG 93

Query: 121 FAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKSRAELRQAFKNNPR 169
            AF+    E+ + +A++  +G  L G+ + V+ A+S    +   +   +
Sbjct: 94  QAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFARSARPKQDPKEGKRK 142

>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 = 72.0 bits (177), Expect = 3e-17
 Identities = 16/79 (20%), Positives = 34/79 (43%), Gaps = 1/79 (1%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVE-VNLVMDKIANRPRGFAFLRYATEEESRR 134
               L++  L     E+ +  AF   G+ V  V ++ +++   P G+ F+ +A    + +
Sbjct: 8   MAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEK 67

Query: 135 AIEGMHGKFLDGRVIFVEI 153
            +  ++GK L G       
Sbjct: 68  CLHKINGKPLPGATPAKRF 86

>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 = 71.4 bits (175), Expect = 6e-17
 Identities = 21/87 (24%), Positives = 42/87 (48%), Gaps = 6/87 (6%)

Query: 77  KTRLFVSGLSFRTSEDSL---RNAFQGFGQLVEVNLVMDKI---ANRPRGFAFLRYATEE 130
           K  +FV GLS R ++  +      F  FG++ +V +        +  P   A++ Y   E
Sbjct: 15  KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSE 74

Query: 131 ESRRAIEGMHGKFLDGRVIFVEIAKSR 157
           ++ RAI+ ++   +DGR +   +  ++
Sbjct: 75  DALRAIQCVNNVVVDGRTLKASLGTTK 101

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 88

 Score = 70.3 bits (173), Expect = 9e-17
 Identities = 16/82 (19%), Positives = 36/82 (43%), Gaps = 7/82 (8%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           + +FV   +   +ED LR  F  +G +++V +         R FAF+ +A ++ ++    
Sbjct: 6   SGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF-----RAFAFVTFADDQIAQSLCG 60

Query: 138 GMHGKFLDGRVIFVEIAKSRAE 159
                 + G  + +  A+ +  
Sbjct: 61  EDL--IIKGISVHISNAEPKHN 80

>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 = 70.5 bits (173), Expect = 1e-16
 Identities = 24/98 (24%), Positives = 47/98 (47%), Gaps = 3/98 (3%)

Query: 66  PSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLR 125
            S +S  T      + + GL F  S++ +   F G   +     +      R  G AF++
Sbjct: 5   SSGNSPDTANDGF-VRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQ 63

Query: 126 YATEEESRRAIEGMHGKFLDGRVIFVEIAKSRAELRQA 163
           +A++E + +A++  H + +  R I +  + SRAE+R +
Sbjct: 64  FASQEIAEKALK-KHKERIGHRYIEIFKS-SRAEVRTS 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 = 69.9 bits (172), Expect = 1e-16
 Identities = 17/89 (19%), Positives = 44/89 (49%), Gaps = 7/89 (7%)

Query: 75  QPKTRLFVSGLSFRTSEDSLRNA----FQGFGQLVEVNLVMDKIANRPRGFAFLRYATEE 130
           +P   ++++ L+ +  +D L+ +    F  FGQ++++ +       + RG AF+ +    
Sbjct: 6   RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL---KMRGQAFVIFKEVS 62

Query: 131 ESRRAIEGMHGKFLDGRVIFVEIAKSRAE 159
            +  A+  M G     + + ++ AK+ ++
Sbjct: 63  SATNALRSMQGFPFYDKPMRIQYAKTDSD 91

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89

 Score = 69.2 bits (170), Expect = 2e-16
 Identities = 14/82 (17%), Positives = 37/82 (45%), Gaps = 7/82 (8%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           +++FV   +   + + L+  F  +G++V+V +         R FAF+ +A ++ ++    
Sbjct: 12  SKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPF-----RAFAFVTFADDKVAQSLCG 66

Query: 138 GMHGKFLDGRVIFVEIAKSRAE 159
                 + G  + +  A+ +  
Sbjct: 67  EDL--IIKGISVHISNAEPKHN 86

>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 = 69.0 bits (169), Expect = 2e-16
 Identities = 13/85 (15%), Positives = 34/85 (40%), Gaps = 7/85 (8%)

Query: 77  KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
            + + V  L   ++   + +  + +        +     +R +  AF+     E+++ AI
Sbjct: 5   SSGILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQNAI 57

Query: 137 EGMHGKFLDGRVIFVEIAKSRAELR 161
           +  H     G+ + V++  + A L 
Sbjct: 58  QMFHQYSFRGKDLIVQLQPTDALLC 82

>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 = 69.0 bits (169), Expect = 5e-16
 Identities = 17/87 (19%), Positives = 41/87 (47%), Gaps = 4/87 (4%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           + V G+ F   E+ +R+ F G  ++  V+L+ D    R  G   +++ + +++  A++  
Sbjct: 19  VSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDH-VGRNNGNGLVKFLSPQDTFEALK-R 75

Query: 140 HGKFLDGRVIFVEIAKSRAELRQAFKN 166
           +   +  R + V  A +  +   A  +
Sbjct: 76  NRMLMIQRYVEVSPA-TERQWVAAGGH 101

>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 = 69.1 bits (169), Expect = 6e-16
 Identities = 12/96 (12%), Positives = 37/96 (38%), Gaps = 2/96 (2%)

Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
           +    +++ GL F      + + F+    + +   +      +  G  F+ +  E + + 
Sbjct: 23  EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKA 82

Query: 135 AIEGMHGKFLDGRVIFVEIAKSRAELRQAFKNNPRQ 170
           A+   H +++  R I V    ++  + +      ++
Sbjct: 83  ALC-RHKQYMGNRFIQVHPI-TKKGMLEKIDMIRKR 116

>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 = 68.8 bits (168), Expect = 7e-16
 Identities = 18/97 (18%), Positives = 42/97 (43%), Gaps = 2/97 (2%)

Query: 65  PPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFL 124
                + +       + + GL F  +++ +   F G   +     +      +  G AF+
Sbjct: 30  MGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFV 89

Query: 125 RYATEEESRRAIEGMHGKFLDGRVIFVEIAKSRAELR 161
           ++A++E + +A+   H + +  R I V  + S+ E+R
Sbjct: 90  QFASQELAEKALG-KHKERIGHRYIEVFKS-SQEEVR 124

>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 = 67.6 bits (165), Expect = 3e-15
 Identities = 19/96 (19%), Positives = 39/96 (40%), Gaps = 3/96 (3%)

Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
                + + GL ++ +E+ + N F      V V++ +     R  G A + +AT EE+  
Sbjct: 44  TTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGP-DGRVTGEADVEFATHEEAVA 101

Query: 135 AIEGMHGKFLDGRVIFVEIAKSRAELRQAFKNNPRQ 170
           A+       +  R I + +  +      A+ +   Q
Sbjct: 102 AMS-KDRANMQHRYIELFLNSTTGASNGAYSSQVMQ 136

>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 = 66.8 bits (163), Expect = 4e-15
 Identities = 17/95 (17%), Positives = 30/95 (31%), Gaps = 6/95 (6%)

Query: 77  KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
           KT +    L   T    ++  F  FG L  V L            A + +    E+R+A 
Sbjct: 10  KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLL------PEGGITAIVEFLEPLEARKAF 63

Query: 137 EGMHGKFLDGRVIFVEIAKSRAELRQAFKNNPRQN 171
             +         +++E A          K + +  
Sbjct: 64  RHLAYSKFHHVPLYLEWAPIGVFGAAPQKKDSQHE 98

>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 = 65.8 bits (161), Expect = 5e-15
 Identities = 23/79 (29%), Positives = 40/79 (50%), Gaps = 7/79 (8%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           T L+V GL    +E  LRN F  FG++  + +V  +        AF+++AT + +  A E
Sbjct: 13  TTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQ------QCAFIQFATRQAAEVAAE 66

Query: 138 GMHGKF-LDGRVIFVEIAK 155
               K  ++GR + V+  +
Sbjct: 67  KSFNKLIVNGRRLNVKWGR 85

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 70.6 bits (172), Expect = 6e-15
 Identities = 27/94 (28%), Positives = 50/94 (53%)

Query: 66  PSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLR 125
           P     +       LFV+ +++ T+E  LR  F+ +G +  +++V  K + +PRG+AF+ 
Sbjct: 91  PHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIE 150

Query: 126 YATEEESRRAIEGMHGKFLDGRVIFVEIAKSRAE 159
           Y  E +   A +   GK +DGR + V++ + R  
Sbjct: 151 YEHERDMHSAYKHADGKKIDGRRVLVDVERGRTV 184

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 66.0 bits (161), Expect = 7e-15
 Identities = 19/99 (19%), Positives = 36/99 (36%), Gaps = 3/99 (3%)

Query: 65  PPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFL 124
           P   H       + R+ +  L    S   L++  +        + V  +      G   L
Sbjct: 16  PRGSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR---DFDGTGAL 72

Query: 125 RYATEEESRRAIEGMHGKFLDGRVIFVEIAKSRAELRQA 163
            + +EE    A+E ++     G VI VE   +   +R++
Sbjct: 73  EFPSEEILVEALERLNNIEFRGSVITVERDDNPPPIRRS 111

>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 = 65.5 bits (160), Expect = 8e-15
 Identities = 17/84 (20%), Positives = 37/84 (44%), Gaps = 4/84 (4%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           + + GL +R +E+ + N F      + V++ +     R  G A + +AT E++  A+   
Sbjct: 18  VHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-K 74

Query: 140 HGKFLDGRVIFVEIAKSRAELRQA 163
               +  R + + +  S A    +
Sbjct: 75  DKANMQHRYVELFLN-STAGTSGS 97

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 65.4 bits (160), Expect = 8e-15
 Identities = 20/95 (21%), Positives = 43/95 (45%), Gaps = 3/95 (3%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAF-QGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
           P+  LFV  L+    +  L   F + +       +V+D+     +G+ F+++  E E +R
Sbjct: 8   PEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKR 66

Query: 135 AIEGMHGK-FLDGRVIFVEIAKSRAELRQAFKNNP 168
           A+    G   L  + + + +A  +A   +  ++ P
Sbjct: 67  ALTECQGAVGLGSKPVRLSVAIPKASRVKPVESGP 101

>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 = 69.1 bits (168), Expect = 9e-15
 Identities = 17/92 (18%), Positives = 45/92 (48%), Gaps = 7/92 (7%)

Query: 75  QPKTRLFVSGLSFRTSEDSLRNA----FQGFGQLVEVNLVMDKIANRPRGFAFLRYATEE 130
           +P   ++++ L+ +  +D L+ +    F  FGQ++++ +       + RG AF+ +    
Sbjct: 7   RPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSL---KMRGQAFVIFKEVS 63

Query: 131 ESRRAIEGMHGKFLDGRVIFVEIAKSRAELRQ 162
            +  A+  M G     + + ++ AK+ +++  
Sbjct: 64  SATNALRSMQGFPFYDKPMRIQYAKTDSDIIA 95

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 56.0 bits (134), Expect = 4e-10
 Identities = 24/107 (22%), Positives = 37/107 (34%), Gaps = 6/107 (5%)

Query: 50  RQGRGRGACFPLACLPPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNL 109
                      +    P    LS   P   LF++ L   T+E  L   F  F    EV L
Sbjct: 180 IPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRL 239

Query: 110 VMDKIANRPRGFAFLRYATEEESRRAIEGMHG-KFLDGRVIFVEIAK 155
           V  +        AF+ +  E ++  A + + G K      + +  AK
Sbjct: 240 VPGR-----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK 281

>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 = 65.0 bits (159), Expect = 1e-14
 Identities = 17/77 (22%), Positives = 37/77 (48%), Gaps = 3/77 (3%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           + + G  F  +E ++          V + +V +       G+ F+ ++ EEE ++A++  
Sbjct: 13  VKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNA-HGNKTGYIFVDFSNEEEVKQALK-C 69

Query: 140 HGKFLDGRVIFVEIAKS 156
           + +++ GR I V   KS
Sbjct: 70  NREYMGGRYIEVFREKS 86

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 65.7 bits (160), Expect = 1e-14
 Identities = 11/89 (12%), Positives = 40/89 (44%), Gaps = 7/89 (7%)

Query: 75  QPKTRLFVSGLSFRTSEDSLRNA----FQGFGQLVEVNLVMDKIANRPRGFAFLRYATEE 130
           +P   + ++ ++    ++ L+          G ++++ +    +++   G A++ +AT+E
Sbjct: 27  EPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVV---DLSDDNSGKAYIVFATQE 83

Query: 131 ESRRAIEGMHGKFLDGRVIFVEIAKSRAE 159
            ++  +E   G    G  + +  +++   
Sbjct: 84  SAQAFVEAFQGYPFQGNPLVITFSETPQS 112

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 64.5 bits (157), Expect = 2e-14
 Identities = 17/93 (18%), Positives = 32/93 (34%), Gaps = 5/93 (5%)

Query: 65  PPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFL 124
            P             ++V  L        L+ A +  G +      +      PR  AFL
Sbjct: 7   GPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVP-----LRLTWQGPRRRAFL 61

Query: 125 RYATEEESRRAIEGMHGKFLDGRVIFVEIAKSR 157
            Y     +++A+  + G  L    + V +A+ +
Sbjct: 62  HYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQ 94

>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 = 62.2 bits (151), Expect = 2e-13
 Identities = 15/94 (15%), Positives = 39/94 (41%), Gaps = 4/94 (4%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLV--MDKIANRPRGFAFLRYATEEESRRAIE 137
           +   GL +  + + + N F         N +  +     + RG A +   +E++ ++A+E
Sbjct: 14  IRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE 73

Query: 138 GMHGKFLDGRVIFVEIAKSRAELRQAFKNNPRQN 171
             H  ++  R + V    +  ++    K+   ++
Sbjct: 74  -KHRMYMGQRYVEVYEI-NNEDVDALMKSLQVKS 105

>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 = 64.1 bits (156), Expect = 2e-13
 Identities = 21/94 (22%), Positives = 40/94 (42%), Gaps = 5/94 (5%)

Query: 65  PPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFL 124
           P S +  +   P   L +S +    SE+ L+  F   G +V+      K   + R  A +
Sbjct: 108 PGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVK----GFKFFQKDRKMALI 163

Query: 125 RYATEEESRRAIEGMHG-KFLDGRVIFVEIAKSR 157
           +  + EE+ +A+  +H     +   + V  +KS 
Sbjct: 164 QMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST 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 = 63.0 bits (153), Expect = 6e-13
 Identities = 20/80 (25%), Positives = 38/80 (47%), Gaps = 6/80 (7%)

Query: 80  LFVSGLS-FRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           L VS L+  R +  SL   F  +G +  V     KI    +  A ++ A   +++ A+  
Sbjct: 6   LLVSNLNPERVTPQSLFILFGVYGDVQRV-----KILFNKKENALVQMADGNQAQLAMSH 60

Query: 139 MHGKFLDGRVIFVEIAKSRA 158
           ++G  L G+ I + ++K + 
Sbjct: 61  LNGHKLHGKPIRITLSKHQN 80

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 61.8 bits (150), Expect = 3e-13
 Identities = 21/96 (21%), Positives = 39/96 (40%), Gaps = 7/96 (7%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVE----VNLVMDKIANRPRGFAFLRYATEEESRRA 135
           + + GL F  + + +   F     +      +  V      RP G AF+ +A EE ++ A
Sbjct: 26  VRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP-DGRPTGDAFVLFACEEYAQNA 84

Query: 136 IEGMHGKFLDGRVIFVEIAKSRAELRQAFKNNPRQN 171
           +   H   L  R I +  + + AE++Q        +
Sbjct: 85  LR-KHKDLLGKRYIELFRS-TAAEVQQVLNRFSSAS 118

>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 = 61.0 bits (148), Expect = 4e-13
 Identities = 16/106 (15%), Positives = 35/106 (33%), Gaps = 9/106 (8%)

Query: 65  PPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFL 124
             S  S         + V GL     E  L  A + FG +  V +         +  A +
Sbjct: 3   SGSSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMM------MPFKRQALV 56

Query: 125 RYATEEESRRAIEGM--HGKFLDGRVIFVEIAKSRAELRQAFKNNP 168
            +   + ++  +        ++ G+  F   + S+  + +   + P
Sbjct: 57  EFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSK-RITRPGNSGP 101

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 108

 Score = 61.4 bits (149), Expect = 4e-13
 Identities = 18/110 (16%), Positives = 35/110 (31%), Gaps = 21/110 (19%)

Query: 50  RQGRGRGACFPLACLPPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNL 109
             G   G        PPS  S      + R+ VSGL    S   L++  +  G +   ++
Sbjct: 2   SSGSSGG--------PPSRRS------ENRVVVSGLPPSGSWQDLKDHMREAGDVCYADV 47

Query: 110 VMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKSRAE 159
             D       G   + +  +E+   A+  +               + + +
Sbjct: 48  YRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVD 90

>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 = 61.5 bits (149), Expect = 4e-13
 Identities = 17/95 (17%), Positives = 41/95 (43%), Gaps = 6/95 (6%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGF---GQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
           + + GL +  S + ++N          +  V+ +  +   R  G AF+   +E++ + A+
Sbjct: 20  VKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTR-EGRQSGEAFVELESEDDVKLAL 78

Query: 137 EGMHGKFLDGRVIFVEIAKSRAELRQAFKNNPRQN 171
           +    + +  R I V  +  R E+    K++   +
Sbjct: 79  K-KDRESMGHRYIEVFKS-HRTEMDWVLKHSGPNS 111

>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 = 60.7 bits (147), Expect = 8e-13
 Identities = 18/105 (17%), Positives = 40/105 (38%), Gaps = 9/105 (8%)

Query: 65  PPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFL 124
                S S   P   + +  L    +E  + +    FG++  + ++      + +  AF+
Sbjct: 19  SHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLML------KGKNQAFI 72

Query: 125 RYATEEESRRAIE--GMHGKFLDGRVIFVEIAKSRAELRQAFKNN 167
              TEE +   +         L G+ I+++ +  + EL+     N
Sbjct: 73  EMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHK-ELKTDSSPN 116

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 62.4 bits (151), Expect = 1e-12
 Identities = 6/85 (7%), Positives = 22/85 (25%)

Query: 65  PPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFL 124
           P          P   L         +E++        G     ++ +    +       L
Sbjct: 111 PEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLL 170

Query: 125 RYATEEESRRAIEGMHGKFLDGRVI 149
            + ++ ++   +  ++   +     
Sbjct: 171 EWDSKSDALETLGFLNHYQMKNPNG 195

>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 = 57.8 bits (139), Expect = 5e-11
 Identities = 21/97 (21%), Positives = 38/97 (39%), Gaps = 6/97 (6%)

Query: 76  PKTRLFVSGLS-FRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
               L V GL   + + D + N F  +G + +V  +  K      G A +  A      R
Sbjct: 3   DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDR 57

Query: 135 AIEGMHGKFLDGRVIFVEIAKSRAELRQAFKNNPRQN 171
           AI  ++  F+ G+ + V ++K  A +          +
Sbjct: 58  AITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGS 94

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 59.7 bits (145), Expect = 1e-12
 Identities = 9/84 (10%), Positives = 32/84 (38%), Gaps = 2/84 (2%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           +++ G     + D ++   +  GQ++ + +         +G  F+ + + E +++ +E  
Sbjct: 14  VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETP 72

Query: 140 HGKFLDGRVIFVEIAKSRAELRQA 163
             K+     + +         +  
Sbjct: 73  GQKY-KETDLLILFKDDYFAKKNE 95

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 59.7 bits (145), Expect = 2e-12
 Identities = 14/79 (17%), Positives = 31/79 (39%), Gaps = 8/79 (10%)

Query: 78  TRLFVSGLSFRTSE------DSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEE 131
           + + V  +     +      + +   F  FG++        +   + +G+ FL YA+   
Sbjct: 16  SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITND--FYPEEDGKTKGYIFLEYASPAH 73

Query: 132 SRRAIEGMHGKFLDGRVIF 150
           +  A++   G  LD +  F
Sbjct: 74  AVDAVKNADGYKLDKQHTF 92

>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 = 61.9 bits (150), Expect = 2e-12
 Identities = 22/94 (23%), Positives = 40/94 (42%), Gaps = 5/94 (5%)

Query: 65  PPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFL 124
           P S +  +   P   L +S +    SE+ L+  F   G +V+      K     R  A +
Sbjct: 139 PGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK----DRKMALI 194

Query: 125 RYATEEESRRAIEGMHGKFL-DGRVIFVEIAKSR 157
           +  + EE+ +A+  +H   L +   + V  +KS 
Sbjct: 195 QMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST 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 = 59.6 bits (144), Expect = 1e-11
 Identities = 20/84 (23%), Positives = 39/84 (46%), Gaps = 6/84 (7%)

Query: 76  PKTRLFVSGLS-FRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
             + L VS L+  R +  SL   F  +G +  V     KI    +  A ++ A   +++ 
Sbjct: 33  GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRV-----KILFNKKENALVQMADGNQAQL 87

Query: 135 AIEGMHGKFLDGRVIFVEIAKSRA 158
           A+  ++G  L G+ I + ++K + 
Sbjct: 88  AMSHLNGHKLHGKPIRITLSKHQN 111

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 59.0 bits (143), Expect = 2e-12
 Identities = 15/85 (17%), Positives = 29/85 (34%), Gaps = 8/85 (9%)

Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
                + + GL     E  L  A Q FG +  V ++        +  A + +     +  
Sbjct: 19  PASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVM------PKKRQALVEFEDVLGACN 72

Query: 135 AIEGMHGK--FLDGRVIFVEIAKSR 157
           A+        ++ G   FV  + S+
Sbjct: 73  AVNYAADNQIYIAGHPAFVNYSTSQ 97

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 58.7 bits (142), Expect = 3e-12
 Identities = 17/103 (16%), Positives = 39/103 (37%), Gaps = 9/103 (8%)

Query: 67  SPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRY 126
             H   +  P   + +  L    +E  + +    FG++  + +       + +  AF+  
Sbjct: 6   HHHHHGSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLM------LKGKNQAFIEM 59

Query: 127 ATEEESRRAIE--GMHGKFLDGRVIFVEIAKSRAELRQAFKNN 167
            TEE +   +         L G+ I+++ +  + EL+     N
Sbjct: 60  NTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHK-ELKTDSSPN 101

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A Length = 136

 Score = 58.5 bits (141), Expect = 1e-11
 Identities = 17/96 (17%), Positives = 39/96 (40%), Gaps = 6/96 (6%)

Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQGF---GQLVEVNLVMDKIANRPRGFAFLRYATEEE 131
                + + GL +  S + ++N             V+ +  +   R  G AF+   +E++
Sbjct: 42  GEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTR-EGRQSGEAFVELGSEDD 100

Query: 132 SRRAIEGMHGKFLDGRVIFVEIAKSRAELRQAFKNN 167
            + A++    + +  R I V  +  R E+    K++
Sbjct: 101 VKMALK-KDRESMGHRYIEVFKS-HRTEMDWVLKHS 134

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115

 Score = 57.1 bits (138), Expect = 2e-11
 Identities = 12/81 (14%), Positives = 28/81 (34%), Gaps = 7/81 (8%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           R+ VSGL    S   L++  +  G +   ++  D       G   + +  +E+   A+  
Sbjct: 18  RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRK 70

Query: 139 MHGKFLDGRVIFVEIAKSRAE 159
           +               + + +
Sbjct: 71  LDNTKFRSHEGETAYIRVKVD 91

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 56.2 bits (136), Expect = 3e-11
 Identities = 20/91 (21%), Positives = 30/91 (32%), Gaps = 7/91 (7%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
            +FVSG         L   F  FG +  V  VMDK       FA +           +  
Sbjct: 10  SVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDK---DKGVFAIVEMGDVGAREAVLS- 63

Query: 139 MHGKFLDGRVIFVEIAKSRAELRQAFKNNPR 169
                L G  + V   + + E +     +P+
Sbjct: 64  QSQHSLGGHRLRVRPREQK-EFQSPASKSPK 93

>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 = 56.1 bits (135), Expect = 5e-11
 Identities = 19/75 (25%), Positives = 33/75 (44%), Gaps = 8/75 (10%)

Query: 72  STCQPKTRLFVS--GLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATE 129
           +       L V+  GL    S + L    +  G +  + +  +K       ++F RY T 
Sbjct: 20  TVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK------PYSFARYRTT 73

Query: 130 EESRRAIEGMHGKFL 144
           EES+RA   ++GK +
Sbjct: 74  EESKRAYVTLNGKEV 88

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 55.0 bits (132), Expect = 1e-10
 Identities = 18/87 (20%), Positives = 38/87 (43%), Gaps = 5/87 (5%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANR--PRGFAFLRYATEEESRRAI 136
           ++FV GL     ED +  +F+ FG LV       +  +   P+G+AFL +  E   +  I
Sbjct: 10  KVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALI 69

Query: 137 EGMHGKFLDGRVIFVEIAKSRAELRQA 163
           +    +      +++ ++    + +  
Sbjct: 70  DACLEEDGK---LYLCVSSPTIKDKPV 93

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 53.9 bits (130), Expect = 1e-10
 Identities = 14/79 (17%), Positives = 31/79 (39%), Gaps = 8/79 (10%)

Query: 78  TRLFVSGL------SFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEE 131
           + + V  +           ++ +   F  FG++        +   + +G+ FL YA+   
Sbjct: 2   SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITND--FYPEEDGKTKGYIFLEYASPAH 59

Query: 132 SRRAIEGMHGKFLDGRVIF 150
           +  A++   G  LD +  F
Sbjct: 60  AVDAVKNADGYKLDKQHTF 78

>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 = 54.4 bits (131), Expect = 1e-10
 Identities = 16/93 (17%), Positives = 33/93 (35%), Gaps = 8/93 (8%)

Query: 67  SPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRY 126
           S        P   L +  L    +E  +      FG++  + +       + +  AFL  
Sbjct: 5   SSGDKMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILM------LKGKNQAFLEL 58

Query: 127 ATEEESRRAIE--GMHGKFLDGRVIFVEIAKSR 157
           ATEE +   +         L  + I+++ +  +
Sbjct: 59  ATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHK 91

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3 Length = 104

 Score = 54.5 bits (131), Expect = 2e-10
 Identities = 13/62 (20%), Positives = 35/62 (56%), Gaps = 1/62 (1%)

Query: 91  EDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIF 150
           E+      + +G++ E+N V D + +   G  ++++  EE++ +A+  ++ ++ +G+ I 
Sbjct: 41  EEVFTEMEEKYGEVEEMN-VCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIH 99

Query: 151 VE 152
            E
Sbjct: 100 AE 101

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 54.0 bits (130), Expect = 2e-10
 Identities = 17/76 (22%), Positives = 37/76 (48%), Gaps = 6/76 (7%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNL-----VMDKIANRPRGFAFLRYATEEESR 133
           RL+V  + F  +E+++ + F    +L  +       V+    N+ + FAFL + + +E+ 
Sbjct: 8   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 67

Query: 134 RAIEGMHGKFLDGRVI 149
           +A+    G    G+ +
Sbjct: 68  QAMA-FDGIIFQGQSL 82

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 50.2 bits (119), Expect = 3e-08
 Identities = 14/91 (15%), Positives = 26/91 (28%), Gaps = 15/91 (16%)

Query: 78  TRLFVSGLSF---------RTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYAT 128
             L+V G+              E  +R  F   G +  +  V  K         F+++  
Sbjct: 135 KTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESK------NCGFVKFKY 188

Query: 129 EEESRRAIEGMHGKFLDGRVIFVEIAKSRAE 159
           +  +  A E M  + L          +    
Sbjct: 189 QANAEFAKEAMSNQTLLLPSDKEWDDRREGT 219

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 49.4 bits (117), Expect = 4e-08
 Identities = 12/105 (11%), Positives = 35/105 (33%), Gaps = 2/105 (1%)

Query: 58  CFPLACLPPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANR 117
             P   LP              +++ G     + D ++   +  GQ++ + +        
Sbjct: 90  RSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKA 148

Query: 118 PRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKSRAELRQ 162
            +G  F+ + + E +++ +E    K+     + +         + 
Sbjct: 149 FKGSIFVVFDSIESAKKFVETPGQKY-KETDLLILFKDDYFAKKN 192

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster} Length = 89

 Score = 47.0 bits (111), Expect = 8e-08
 Identities = 18/76 (23%), Positives = 29/76 (38%), Gaps = 6/76 (7%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           L +  L+ +    +LR      G LV  +          +G A  +Y T EE+ +A   +
Sbjct: 10  LLLKNLTAQIDGPTLRTLCMQHGPLVSFHP------YLNQGIALCKYTTREEANKAQMAL 63

Query: 140 HGKFLDGRVIFVEIAK 155
           +   L    IF E   
Sbjct: 64  NNCVLANTTIFAESPS 79

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 112

 Score = 45.9 bits (109), Expect = 3e-07
 Identities = 16/62 (25%), Positives = 28/62 (45%), Gaps = 4/62 (6%)

Query: 91  EDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIF 150
            + LR     FGQ+ ++ L        P G A + +   EE+   I+ + G++  GR I 
Sbjct: 40  REDLRVECSKFGQIRKLLL----FDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQIT 95

Query: 151 VE 152
            +
Sbjct: 96  AQ 97

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A Length = 105

 Score = 42.9 bits (101), Expect = 3e-06
 Identities = 10/64 (15%), Positives = 31/64 (48%), Gaps = 2/64 (3%)

Query: 91  EDSLRNAFQGFGQLVEVNL--VMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRV 148
            + +R+    +G +  + +   +D +     G  F+ + +  + ++A++G+ G+    RV
Sbjct: 29  VEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRV 88

Query: 149 IFVE 152
           +  +
Sbjct: 89  VVTK 92

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A Length = 114

 Score = 43.1 bits (102), Expect = 3e-06
 Identities = 11/62 (17%), Positives = 29/62 (46%), Gaps = 4/62 (6%)

Query: 91  EDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIF 150
           +D +       G ++ + +  DK  N  +G  +++  +   +  A+  +HG++  G++I 
Sbjct: 31  KDDVIEECNKHGGVIHIYV--DK--NSAQGNVYVKCPSIAAAIAAVNALHGRWFAGKMIT 86

Query: 151 VE 152
             
Sbjct: 87  AA 88

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 40.3 bits (94), Expect = 3e-05
 Identities = 17/88 (19%), Positives = 29/88 (32%), Gaps = 16/88 (18%)

Query: 80  LFVSGLSFRTSEDSLRNAFQ-----GFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
           + V GL     ++ L   F+     G G ++           R      L +    ++ R
Sbjct: 11  VEVRGLPPAVPDELLTLYFENRRRSGGGPVLSW--------QRLGCGGVLTFREPADAER 62

Query: 135 AIE-GMHGKFLDGRVIFVEIAKSRAELR 161
            +    H   L G  + +  A  RA  R
Sbjct: 63  VLAQADHE--LHGAQLSLRPAPPRAPAR 88

>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* Length = 345

 Score = 40.9 bits (95), Expect = 7e-05
 Identities = 18/72 (25%), Positives = 30/72 (41%), Gaps = 8/72 (11%)

Query: 73  TCQPKTRLFVS--GLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEE 130
                  L V+  GL    S + L    +  G +  +      +    + ++F RY T E
Sbjct: 14  VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDAL------LMPPNKPYSFARYRTTE 67

Query: 131 ESRRAIEGMHGK 142
           ES+RA   ++GK
Sbjct: 68  ESKRAYVTLNGK 79

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} PDB: 3us5_A 2dny_A Length = 118

 Score = 39.0 bits (91), Expect = 1e-04
 Identities = 13/67 (19%), Positives = 29/67 (43%), Gaps = 4/67 (5%)

Query: 91  EDSLRNAFQGFGQLVEVNLVMDKIANRPR----GFAFLRYATEEESRRAIEGMHGKFLDG 146
           E  +      FG +  V +  +K             F+ ++   E+ +AI+ ++G++  G
Sbjct: 39  EGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG 98

Query: 147 RVIFVEI 153
           R +  E+
Sbjct: 99  RKVVAEV 105

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 37.3 bits (86), Expect = 5e-04
 Identities = 20/91 (21%), Positives = 34/91 (37%), Gaps = 4/91 (4%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           R+ V  L +  + D L   F  FG  V   +   K     +  A L+YA    ++ A   
Sbjct: 30  RIIVENLFYPVTLDVLHQIFSKFGT-VLKIITFTK---NNQFQALLQYADPVSAQHAKLS 85

Query: 139 MHGKFLDGRVIFVEIAKSRAELRQAFKNNPR 169
           + G+ +      + I  S+        NN +
Sbjct: 86  LDGQNIYNACCTLRIDFSKLTSLNVKYNNDK 116

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 96

 Score = 36.6 bits (84), Expect = 6e-04
 Identities = 19/92 (20%), Positives = 35/92 (38%), Gaps = 5/92 (5%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
             T L+V  L       S+ N  +   +L +      K+ +     A LR+  ++ + RA
Sbjct: 8   CHTLLYVYNLPANKDGKSVSNRLR---RLSDN--CGGKVLSITGCSAILRFINQDSAERA 62

Query: 136 IEGMHGKFLDGRVIFVEIAKSRAELRQAFKNN 167
            + M  + + G  I V       EL +    +
Sbjct: 63  QKRMENEDVFGNRIIVSFTPKNRELCETSGPS 94

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	171
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.92
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.91
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.91
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.89
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.89
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.89
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.88
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.88
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.88
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.88
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.88
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.88
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.88
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.88
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.88
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.88
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.88
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.88
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.88
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.87
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.87
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.87
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.87
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.87
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.87
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.87
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.87
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.87
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.87
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.87
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.87
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.87
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.87
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.87
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.87
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.87
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.87
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.87
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.87
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.86
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.86
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.86
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.86
2div_A	99	TRNA selenocysteine associated protein; structural	99.86
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.86
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.86
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.86
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.86
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.86
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.86
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.86
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.86
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.86
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.86
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.86
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.86
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.86
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.85
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.85
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.85
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.85
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.85
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.85
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.85
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.85
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.85
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.85
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.85
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.85
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.85
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.85
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.85
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.85
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.85
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.85
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.85
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.85
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.84
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.84
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.84
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.84
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.84
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.84
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.84
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.84
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.84
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.84
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.84
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.84
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.84
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.84
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.84
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.84
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.84
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.84
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.83
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.83
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.83
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.83
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.83
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.83
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.83
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.83
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.83
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.83
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.82
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.82
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.82
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.82
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.82
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.82
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.82
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.82
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.82
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.82
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.82
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.82
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.82
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.82
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.82
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.82
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.82
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.82
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.81
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.81
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.81
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.81
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.81
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.81
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.81
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.81
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.81
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.81
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.81
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.81
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.81
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.8
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.8
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.8
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.8
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.68
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.8
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.8
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.8
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.79
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.79
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.79
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.79
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.79
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.79
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.79
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.79
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.79
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.78
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.78
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.78
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.78
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.78
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.78
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.78
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.77
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.77
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.77
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.77
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.77
1x5p_A	97	Negative elongation factor E; structure genomics,	99.76
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.76
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.76
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.76
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.76
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.76
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.75
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.75
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.75
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.75
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.75
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.75
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.74
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.74
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.74
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.74
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.73
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.73
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.72
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.72
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.72
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.72
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.72
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.71
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.7
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.7
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.68
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.65
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.65
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.64
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.64
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.62
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.61
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.58
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.57
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.56
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.52
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.51
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.45
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.34
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.32
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	99.15
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	99.11
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.88
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	98.04
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.94
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.78
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.64
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.6
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.58
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	97.28
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	96.86
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	96.58
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	96.36
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	96.31
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	96.17
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	95.15
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	94.75
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	94.11
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	93.97
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	93.95
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	93.89
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	93.89
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	92.5
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	93.3
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	93.19
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	92.95
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	92.9
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	92.9
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	92.67
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	92.55
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	92.52
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	92.49
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	92.47
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	92.47
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	92.43
1x4e_A	85	RNA binding motif, single-stranded interacting pro	92.33
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	92.02
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	91.96
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	91.86
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	91.85
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	91.57
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	91.56
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	91.54
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	91.36
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	91.23
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	91.22
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	91.19
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	91.03
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	90.98
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	90.92
2div_A	99	TRNA selenocysteine associated protein; structural	90.74
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	90.72
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	90.66
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	90.65
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	90.55
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	90.45
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	90.44
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	90.39
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	90.35
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	90.25
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	90.24
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	90.23
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	90.18
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	90.13
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	90.07
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	90.03
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	89.99
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	89.85
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	89.82
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	89.82
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	89.78
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	89.75
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	89.74
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	89.63
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	89.49
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	89.41
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	89.36
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	89.35
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	89.27
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	89.11
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	89.05
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	88.59
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	88.47
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	88.3
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	88.26
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	88.1
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	88.1
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	87.81
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	87.7
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	87.7
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	87.59
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	87.3
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	87.17
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	87.05
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	87.04
2dis_A	109	Unnamed protein product; structural genomics, RRM	86.83
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	86.49
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	86.28
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	86.15
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	86.05
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	86.04
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	85.93
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	85.92
1x5o_A	114	RNA binding motif, single-stranded interacting pro	85.88
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	85.77
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	85.41
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	85.41
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	85.3
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	84.95
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	84.93
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	84.84
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	84.6
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	84.36
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	84.26
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	84.13
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	83.95
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	83.94
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	83.68
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	83.65
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	83.22
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	82.55
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	82.52
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	81.69
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	81.65
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	81.53
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	81.41
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	81.39
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	81.38
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	80.15

>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=99.92  E-value=2e-24  Score=141.65  Aligned_cols=82  Identities=30%  Similarity=0.523  Sum_probs=79.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 030819           75 QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIA  154 (171)
Q Consensus        75 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~  154 (171)
                      -.+++|||+|||+++++++|+++|++||.|.++.++.++.+|.++|||||+|.+.++|++|++.|||..+.|+.|+|.|+
T Consensus        17 ~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~A   96 (99)
T 4fxv_A           17 FQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYA   96 (99)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cC
Q 030819          155 KS  156 (171)
Q Consensus       155 ~~  156 (171)
                      +|
T Consensus        97 kP   98 (99)
T 4fxv_A           97 RP   98 (99)
T ss_dssp             CB
T ss_pred             eC
Confidence            86

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.91  E-value=1.4e-23  Score=140.09  Aligned_cols=90  Identities=13%  Similarity=0.272  Sum_probs=84.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 030819           74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEI  153 (171)
Q Consensus        74 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~  153 (171)
                      .++.++|||+|||+++++++|+++|++||.|.++.++.|+.+|+++|||||+|.+.++|++|++.|||..++|+.|+|.+
T Consensus         3 ~~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~   82 (110)
T 3s8s_A            3 QIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQL   82 (110)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            35678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCcHHHHHh
Q 030819          154 AKSRAELRQA  163 (171)
Q Consensus       154 ~~~~~~~~~~  163 (171)
                      +.....+++.
T Consensus        83 a~~~~~~~~~   92 (110)
T 3s8s_A           83 DIKGQQRMKY   92 (110)
T ss_dssp             CSTTHHHHHH
T ss_pred             CCCCcHHHHH
Confidence            9877665543

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.91  E-value=1.9e-25  Score=165.30  Aligned_cols=150  Identities=23%  Similarity=0.380  Sum_probs=117.6

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCCCCCC-------------
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPSPHS-------------   70 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------------   70 (171)
                      .+.|||+|++++++++.+...|...+++         .+.....+..++++++++++.+.....+..             
T Consensus        15 ~~tlfVgnLp~~~te~~L~~~F~~~G~I---------~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~   85 (213)
T 4f02_A           15 MASLYVGDLHPDVTEAMLYEKFSPAGPI---------LSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGK   85 (213)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCE---------EEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhhCCE---------EEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCc
Confidence            3579999999999999999999998876         333333333344555566655543321110             


Q ss_pred             -----------CCCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHh
Q 030819           71 -----------LSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM  139 (171)
Q Consensus        71 -----------~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l  139 (171)
                                 ........+|||+|||+.+++++|+++|++||.|..+.++.+.  +.++|||||+|.+.++|.+|++.|
T Consensus        86 ~i~~~~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~--~~~~g~~fV~f~~~~~a~~Ai~~l  163 (213)
T 4f02_A           86 PVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKM  163 (213)
T ss_dssp             ECEEEECCCCTHHHHHCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESSHHHHHHHHHHH
T ss_pred             ccccccccccccccccccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccC--CCCceEEEEEeCCHHHHHHHHHHh
Confidence                       0112245789999999999999999999999999999999885  457999999999999999999999


Q ss_pred             CCceeCCeEEEEEEecCcHHHHHhh
Q 030819          140 HGKFLDGRVIFVEIAKSRAELRQAF  164 (171)
Q Consensus       140 ~g~~i~g~~i~v~~~~~~~~~~~~~  164 (171)
                      ||..|+|+.|+|.+++++.++....
T Consensus       164 ng~~~~g~~i~V~~a~~~~~~~~~~  188 (213)
T 4f02_A          164 NGMLLNDRKVFVGRFKSRKEREAEL  188 (213)
T ss_dssp             TTCEETTEECEEEECCCHHHHHHHH
T ss_pred             CCCEECCEEEEEEEcCCCcccchhh
Confidence            9999999999999999887665443

>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=99.89  E-value=1e-24  Score=154.67  Aligned_cols=144  Identities=19%  Similarity=0.310  Sum_probs=118.3

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCCCCCCC------------
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPSPHSL------------   71 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------------   71 (171)
                      .+.|||+++++++++..+...|...+++         .+........++++++++++.+..+..+..+            
T Consensus         3 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i---------~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~g~~i   73 (167)
T 2cjk_A            3 SCKMFIGGLNWDTTEDNLREYFGKYGTV---------TDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQHILDGKVI   73 (167)
T ss_dssp             GGEEEECSCCTTCCHHHHHHHHTTTCCE---------EEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHSCCEETTEEC
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhCCCE---------EEEEEEECCCCCCccceEEEEEccHHHHHHHHhcccccCCeEc
Confidence            3679999999999999999999988766         3333333434566777777766554422110            


Q ss_pred             --------CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCce
Q 030819           72 --------STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKF  143 (171)
Q Consensus        72 --------~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~  143 (171)
                              ....+..+|||+|||+++++++|+++|++||.|..+.+..++.+|.++|||||+|.+.++|.+|++ ++|..
T Consensus        74 ~v~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~  152 (167)
T 2cjk_A           74 DPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFID  152 (167)
T ss_dssp             CCEECCCHHHHHHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEEC
T ss_pred             ccccccchhhccCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEE
Confidence                    112245699999999999999999999999999999999998899999999999999999999998 89999


Q ss_pred             eCCeEEEEEEecCc
Q 030819          144 LDGRVIFVEIAKSR  157 (171)
Q Consensus       144 i~g~~i~v~~~~~~  157 (171)
                      +.|+.|+|.++.++
T Consensus       153 ~~g~~i~V~~a~pk  166 (167)
T 2cjk_A          153 FKDRKIEIKRAEPR  166 (167)
T ss_dssp             SSSSCEEEEECCCC
T ss_pred             eCCeEEEEeecCCC
Confidence            99999999999876

>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=99.89  E-value=7.2e-24  Score=153.97  Aligned_cols=149  Identities=19%  Similarity=0.288  Sum_probs=108.0

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCC-----------------
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPP-----------------   66 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----------------   66 (171)
                      .+.|||+++++++++..+...|...+++..         .........+++++++++.+..+.                 
T Consensus        13 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~---------v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~g~~   83 (196)
T 1l3k_A           13 LRKLFIGGLSFETTDESLRSHFEQWGTLTD---------CVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRV   83 (196)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHGGGSCEEE---------EEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEE---------EEEEEcCCCCCccceEEEEeCCHHHHHHHHhcCCCEECCEE
Confidence            357999999999999999999999877622         111122122233333333332211                 


Q ss_pred             ----------CCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHH
Q 030819           67 ----------SPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI  136 (171)
Q Consensus        67 ----------~~~~~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al  136 (171)
                                ............+|||+|||+++++++|+++|+.||.|..+.+..++.+|.++|||||+|.+.++|.+|+
T Consensus        84 l~v~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~  163 (196)
T 1l3k_A           84 VEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV  163 (196)
T ss_dssp             CEEEECCC-----------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHH
T ss_pred             eeeecccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHH
Confidence                      0011122345689999999999999999999999999999999999989999999999999999999999


Q ss_pred             HHhCCceeCCeEEEEEEecCcHHHHH
Q 030819          137 EGMHGKFLDGRVIFVEIAKSRAELRQ  162 (171)
Q Consensus       137 ~~l~g~~i~g~~i~v~~~~~~~~~~~  162 (171)
                      .. +|..++|+.|.|.++.++.....
T Consensus       164 ~~-~~~~~~G~~i~v~~a~~k~~~~~  188 (196)
T 1l3k_A          164 IQ-KYHTVNGHNCEVRKALSKQEMAS  188 (196)
T ss_dssp             HC-SCCEETTEECEEEECC-------
T ss_pred             Hh-CCcEECCEEEEEEecCChhHhcc
Confidence            85 89999999999999998876654

>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=99.89  E-value=2.6e-22  Score=128.07  Aligned_cols=83  Identities=25%  Similarity=0.499  Sum_probs=77.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 030819           75 QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIA  154 (171)
Q Consensus        75 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~  154 (171)
                      .+.++|||+|||+++++++|+++|++||.|.++.++.++.+|.++|||||+|.+.++|++|++.|||..+.|+.|+|.++
T Consensus         4 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   83 (87)
T 3bs9_A            4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA   83 (87)
T ss_dssp             --CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEec
Confidence            45789999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             cCc
Q 030819          155 KSR  157 (171)
Q Consensus       155 ~~~  157 (171)
                      +++
T Consensus        84 ~~k   86 (87)
T 3bs9_A           84 TRK   86 (87)
T ss_dssp             C--
T ss_pred             CCC
Confidence            875

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.88  E-value=3.9e-22  Score=130.41  Aligned_cols=85  Identities=24%  Similarity=0.380  Sum_probs=80.3

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEE--------EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCc
Q 030819           71 LSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVE--------VNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGK  142 (171)
Q Consensus        71 ~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~--------~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~  142 (171)
                      .....+.++|||+|||+++++++|+++|++||.|..        +.+..++.+|+++|||||+|.+.++|++|++.|||.
T Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~   86 (99)
T 2la6_A            7 HHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGK   86 (99)
T ss_dssp             CCSCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTC
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCC
Confidence            445667899999999999999999999999999999        999999889999999999999999999999999999


Q ss_pred             eeCCeEEEEEEec
Q 030819          143 FLDGRVIFVEIAK  155 (171)
Q Consensus       143 ~i~g~~i~v~~~~  155 (171)
                      .+.|+.|+|.+++
T Consensus        87 ~~~g~~l~V~~A~   99 (99)
T 2la6_A           87 EFSGNPIKVSFAT   99 (99)
T ss_dssp             BSSSSBCEEEECC
T ss_pred             EeCCcEEEEEecC
Confidence            9999999999974

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.88  E-value=2.1e-23  Score=147.39  Aligned_cols=141  Identities=20%  Similarity=0.373  Sum_probs=109.5

Q ss_pred             eeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCC-------------------
Q 030819            6 FLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPP-------------------   66 (171)
Q Consensus         6 ~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------------------   66 (171)
                      .|||+|+++++++..+.+.|...+++..-..         ... +.++.++.+++.+....                   
T Consensus         2 ~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i---------~~~-~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i   71 (166)
T 3md3_A            2 VLYVGNLDKAITEDILKQYFQVGGPIANIKI---------MID-KNNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIV   71 (166)
T ss_dssp             EEEEEEEETTCCHHHHHHHHGGGSCEEEEEE---------ECC-CC-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             EEEECCCCCcCCHHHHHHHHHhcCCeEEEEE---------EEC-CCCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCee
Confidence            5899999999999999999998877632111         000 01112222222221111                   


Q ss_pred             -----CCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCC
Q 030819           67 -----SPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHG  141 (171)
Q Consensus        67 -----~~~~~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g  141 (171)
                           .........+..+|||+|||+.+++++|+++|++||.|..+.+..++.+|.++|||||+|.+.++|.+|+..|||
T Consensus        72 ~v~~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g  151 (166)
T 3md3_A           72 KINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQG  151 (166)
T ss_dssp             EEEECCCCCCCCCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTT
T ss_pred             EEEEcCCCCCCCCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCC
Confidence                 111223455678999999999999999999999999999999999988999999999999999999999999999


Q ss_pred             ceeCCeEEEEEEecC
Q 030819          142 KFLDGRVIFVEIAKS  156 (171)
Q Consensus       142 ~~i~g~~i~v~~~~~  156 (171)
                      ..+.|+.|+|.|++.
T Consensus       152 ~~~~g~~i~v~~a~~  166 (166)
T 3md3_A          152 QDLNGRPLRINWAAK  166 (166)
T ss_dssp             CEETTEECEEEESCC
T ss_pred             CccCCcEEEEEecCC
Confidence            999999999999863

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} SCOP: d.58.7.0

Probab=99.88  E-value=5.3e-22  Score=125.53  Aligned_cols=82  Identities=26%  Similarity=0.558  Sum_probs=78.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 030819           77 KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKS  156 (171)
Q Consensus        77 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~~  156 (171)
                      +.+|||+|||+++++++|+++|++||.|.++.++.++.+|.++|||||+|.+.++|++|+..|||..+.|+.|+|.++++
T Consensus         1 t~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~   80 (83)
T 3md1_A            1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK   80 (83)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCc
Confidence            35899999999999999999999999999999999988999999999999999999999999999999999999999987


Q ss_pred             cH
Q 030819          157 RA  158 (171)
Q Consensus       157 ~~  158 (171)
                      +.
T Consensus        81 ~~   82 (83)
T 3md1_A           81 LE   82 (83)
T ss_dssp             CC
T ss_pred             CC
Confidence            63

>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=99.88  E-value=7.1e-22  Score=132.59  Aligned_cols=89  Identities=22%  Similarity=0.402  Sum_probs=83.0

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q 030819           71 LSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIF  150 (171)
Q Consensus        71 ~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~  150 (171)
                      ....++.++|||+|||+++++++|+++|.+||.|..+.++.++.++.++|||||+|.+.++|++|++.|||..+.|+.|+
T Consensus        19 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   98 (115)
T 2cpz_A           19 QKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLK   98 (115)
T ss_dssp             CCCCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CcCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            34456678999999999999999999999999999999999998999999999999999999999999999999999999


Q ss_pred             EEEecCcHH
Q 030819          151 VEIAKSRAE  159 (171)
Q Consensus       151 v~~~~~~~~  159 (171)
                      |.+++++..
T Consensus        99 V~~a~~~~~  107 (115)
T 2cpz_A           99 VQLKRSKND  107 (115)
T ss_dssp             EECCCCSCC
T ss_pred             EEEcCCCCc
Confidence            999987653

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.88  E-value=8e-22  Score=127.78  Aligned_cols=86  Identities=36%  Similarity=0.556  Sum_probs=81.0

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q 030819           71 LSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIF  150 (171)
Q Consensus        71 ~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~  150 (171)
                      ....++.++|||+|||+++++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|++|+..|||..+.|+.|+
T Consensus         9 ~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   88 (95)
T 2cqc_A            9 RANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR   88 (95)
T ss_dssp             CCSCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            34556788999999999999999999999999999999999998999999999999999999999999999999999999


Q ss_pred             EEEecC
Q 030819          151 VEIAKS  156 (171)
Q Consensus       151 v~~~~~  156 (171)
                      |.++++
T Consensus        89 v~~a~~   94 (95)
T 2cqc_A           89 VSGPSS   94 (95)
T ss_dssp             EECCSC
T ss_pred             EEecCC
Confidence            999875

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.88  E-value=8.9e-22  Score=127.38  Aligned_cols=85  Identities=27%  Similarity=0.493  Sum_probs=80.1

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q 030819           71 LSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIF  150 (171)
Q Consensus        71 ~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~  150 (171)
                      ....++.++|||+|||+++++++|+++|.+||.|..+.+..++.++.++|||||+|.+.++|++|++.|||..+.|+.|+
T Consensus        10 ~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   89 (94)
T 2e5h_A           10 GGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIK   89 (94)
T ss_dssp             CSCCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEE
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEE
Confidence            34456788999999999999999999999999999999999998899999999999999999999999999999999999


Q ss_pred             EEEec
Q 030819          151 VEIAK  155 (171)
Q Consensus       151 v~~~~  155 (171)
                      |.+++
T Consensus        90 v~~ak   94 (94)
T 2e5h_A           90 ASIAI   94 (94)
T ss_dssp             EEECC
T ss_pred             EEecC
Confidence            99985

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.88  E-value=1.5e-22  Score=131.71  Aligned_cols=83  Identities=23%  Similarity=0.415  Sum_probs=76.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCC--eEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCc----eeCCe
Q 030819           74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQ--LVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGK----FLDGR  147 (171)
Q Consensus        74 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~--i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~----~i~g~  147 (171)
                      ...-.+|||+|||+++|+++|+++|++||.  +.++++++|+.+|+++|||||+|.+.++|++|++.|||.    .++|+
T Consensus         6 ~~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr   85 (95)
T 2lkz_A            6 HHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGK   85 (95)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTE
T ss_pred             CCccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCE
Confidence            344579999999999999999999999995  678999999999999999999999999999999999997    58999


Q ss_pred             EEEEEEecC
Q 030819          148 VIFVEIAKS  156 (171)
Q Consensus       148 ~i~v~~~~~  156 (171)
                      +|.|+|+++
T Consensus        86 ~i~V~~Aks   94 (95)
T 2lkz_A           86 TIGVDFAKS   94 (95)
T ss_dssp             EEEEEECCC
T ss_pred             EEEEEEccC
Confidence            999999975

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.88  E-value=4.1e-23  Score=133.31  Aligned_cols=82  Identities=23%  Similarity=0.411  Sum_probs=76.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCC-CeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC-CceeCCeEEEEEEe
Q 030819           77 KTRLFVSGLSFRTSEDSLRNAFQGFG-QLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMH-GKFLDGRVIFVEIA  154 (171)
Q Consensus        77 ~~~l~V~nl~~~~~~~~l~~~f~~~G-~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~-g~~i~g~~i~v~~~  154 (171)
                      +.+|||+|||+++++++|+++|++|| .|.+++++.++.+|.++|||||+|.+.++|++|++.++ +..+.|++|+|.++
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a   80 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYS   80 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEc
Confidence            46899999999999999999999999 79999999999999999999999999999999999874 55799999999999


Q ss_pred             cCcH
Q 030819          155 KSRA  158 (171)
Q Consensus       155 ~~~~  158 (171)
                      .++.
T Consensus        81 ~~~~   84 (91)
T 2lxi_A           81 DPKP   84 (91)
T ss_dssp             CSCC
T ss_pred             CCCC
Confidence            8765

>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=99.88  E-value=5e-22  Score=126.21  Aligned_cols=82  Identities=33%  Similarity=0.573  Sum_probs=78.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 030819           74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEI  153 (171)
Q Consensus        74 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~  153 (171)
                      ..+.++|||+|||+++++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|.+|++.|||..+.|+.|+|.+
T Consensus         4 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   83 (85)
T 3mdf_A            4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   83 (85)
T ss_dssp             CCCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            45688999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ec
Q 030819          154 AK  155 (171)
Q Consensus       154 ~~  155 (171)
                      ++
T Consensus        84 ak   85 (85)
T 3mdf_A           84 AK   85 (85)
T ss_dssp             CC
T ss_pred             cC
Confidence            85

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.88  E-value=1.6e-23  Score=154.28  Aligned_cols=146  Identities=18%  Similarity=0.384  Sum_probs=114.2

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCCCCCC-------------
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPSPHS-------------   70 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------------   70 (171)
                      ++.|||+++.+++++..+...|...+++         .+.........++.++++++.+.....+..             
T Consensus        28 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i---------~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~   98 (216)
T 2qfj_A           28 MSRVYVGSIYYELGEDTIRQAFAPFGPI---------KSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGR   98 (216)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHGGGSCE---------EEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-C
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhCCCE---------EEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCe
Confidence            4679999999999999999999988766         222222222233444444444432221000             


Q ss_pred             ---------C-----------CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHH
Q 030819           71 ---------L-----------STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEE  130 (171)
Q Consensus        71 ---------~-----------~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~  130 (171)
                               .           .......+|||+|||.++++++|+++|++||.|..+.+..++.+|.++|||||+|.+.+
T Consensus        99 ~l~v~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~  178 (216)
T 2qfj_A           99 NIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQ  178 (216)
T ss_dssp             CCEEECCSCCGGGHHHHHHHHHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHH
T ss_pred             eEEEecCCCccccchhhhhhhcccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHH
Confidence                     0           01244579999999999999999999999999999999999889999999999999999


Q ss_pred             HHHHHHHHhCCceeCCeEEEEEEecCcH
Q 030819          131 ESRRAIEGMHGKFLDGRVIFVEIAKSRA  158 (171)
Q Consensus       131 ~a~~al~~l~g~~i~g~~i~v~~~~~~~  158 (171)
                      +|.+|+..|||..+.|+.|+|.++.++.
T Consensus       179 ~A~~A~~~l~g~~~~g~~i~V~~a~~~~  206 (216)
T 2qfj_A          179 SSQDAVSSMNLFDLGGQYLRVGKAVTPP  206 (216)
T ss_dssp             HHHHHHHHHTTCBCSSSBCEEEECSSCS
T ss_pred             HHHHHHHHccCCEeCCcEEEEEEecCCC
Confidence            9999999999999999999999998764

>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=99.88  E-value=3.6e-22  Score=134.21  Aligned_cols=84  Identities=32%  Similarity=0.613  Sum_probs=75.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 030819           76 PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAK  155 (171)
Q Consensus        76 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~  155 (171)
                      ...+|||+|||+++++++|+++|++||.|.+++++.++  +.++|||||+|.+.++|++|++.|+|..++|+.|+|.+++
T Consensus         4 ~~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~--~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~   81 (115)
T 4f25_A            4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK   81 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESS
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            35689999999999999999999999999999999986  4589999999999999999999999999999999999998


Q ss_pred             CcHHHH
Q 030819          156 SRAELR  161 (171)
Q Consensus       156 ~~~~~~  161 (171)
                      ++..+.
T Consensus        82 ~~~~~~   87 (115)
T 4f25_A           82 SRKERE   87 (115)
T ss_dssp             CCCC--
T ss_pred             Cccccc
Confidence            765443

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.88  E-value=4.5e-22  Score=133.49  Aligned_cols=89  Identities=24%  Similarity=0.480  Sum_probs=83.0

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 030819           72 STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFV  151 (171)
Q Consensus        72 ~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v  151 (171)
                      ....+.++|||+|||+.+++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|++|++.|+|..+.|+.|+|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   89 (115)
T 2dgo_A           10 KDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRT   89 (115)
T ss_dssp             CCSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEE
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            34567889999999999999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             EEecCcHHH
Q 030819          152 EIAKSRAEL  160 (171)
Q Consensus       152 ~~~~~~~~~  160 (171)
                      .+++++...
T Consensus        90 ~~a~~~~~~   98 (115)
T 2dgo_A           90 NWATRKPPA   98 (115)
T ss_dssp             EESSCCCCC
T ss_pred             EEccCCCCC
Confidence            999876543

>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=99.88  E-value=7.5e-22  Score=130.30  Aligned_cols=89  Identities=26%  Similarity=0.413  Sum_probs=83.0

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q 030819           71 LSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIF  150 (171)
Q Consensus        71 ~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~  150 (171)
                      .....+.++|||+|||+++++++|+++|++||.|..+.+..++.++.++|||||+|.+.++|++|+..|+|..+.|+.|+
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   88 (105)
T 1x5u_A            9 ISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIR   88 (105)
T ss_dssp             CCCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCE
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEE
Confidence            34556789999999999999999999999999999999999998999999999999999999999999999999999999


Q ss_pred             EEEecCcHH
Q 030819          151 VEIAKSRAE  159 (171)
Q Consensus       151 v~~~~~~~~  159 (171)
                      |.+++++..
T Consensus        89 v~~a~~~~~   97 (105)
T 1x5u_A           89 VNKASAHNK   97 (105)
T ss_dssp             EEETTTTSC
T ss_pred             EEECCCCCc
Confidence            999987653

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.87  E-value=8.2e-22  Score=127.80  Aligned_cols=85  Identities=32%  Similarity=0.579  Sum_probs=80.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 030819           75 QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIA  154 (171)
Q Consensus        75 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~  154 (171)
                      .+.++|||+|||+++++++|+++|++||.|..+.+..++.+++++|||||+|.+.++|++|++.|||..+.|+.|+|.++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   82 (95)
T 2dnz_A            3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHV   82 (95)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEES
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEc
Confidence            46789999999999999999999999999999999999989999999999999999999999999999999999999999


Q ss_pred             cCcHH
Q 030819          155 KSRAE  159 (171)
Q Consensus       155 ~~~~~  159 (171)
                      +++..
T Consensus        83 ~~~~~   87 (95)
T 2dnz_A           83 TERLD   87 (95)
T ss_dssp             SCCCC
T ss_pred             ccccC
Confidence            87653

>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=99.87  E-value=9e-22  Score=128.00  Aligned_cols=86  Identities=16%  Similarity=0.431  Sum_probs=81.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 030819           76 PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAK  155 (171)
Q Consensus        76 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~  155 (171)
                      ++++|||+|||.++++++|+++|++||.|.++.+..++.+|.++|||||+|.+.++|.+|++.|+|..+.|+.|+|.+++
T Consensus         1 P~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   80 (96)
T 2x1f_A            1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSS   80 (96)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcC
Confidence            46799999999999999999999999999999999999899999999999999999999999999999999999999998


Q ss_pred             CcHHHH
Q 030819          156 SRAELR  161 (171)
Q Consensus       156 ~~~~~~  161 (171)
                      ++....
T Consensus        81 ~~~~~~   86 (96)
T 2x1f_A           81 NSDISG   86 (96)
T ss_dssp             CSSGGG
T ss_pred             CCCCCC
Confidence            776543

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.87  E-value=1.1e-21  Score=129.19  Aligned_cols=86  Identities=31%  Similarity=0.505  Sum_probs=81.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ...+.++|||+|||+++++++|+++|.+||.|..+.++.++.++.++|||||+|.+.++|++|+..|||..+.|+.|+|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   90 (103)
T 2cq0_A           11 RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVE   90 (103)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            45668999999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             EecCcH
Q 030819          153 IAKSRA  158 (171)
Q Consensus       153 ~~~~~~  158 (171)
                      +++++.
T Consensus        91 ~a~~~~   96 (103)
T 2cq0_A           91 WAKPST   96 (103)
T ss_dssp             ESSCCC
T ss_pred             ECCCCC
Confidence            998765

>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=99.87  E-value=5.2e-22  Score=132.03  Aligned_cols=88  Identities=31%  Similarity=0.579  Sum_probs=82.5

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q 030819           71 LSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIF  150 (171)
Q Consensus        71 ~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~  150 (171)
                      ....++.++|||+|||+.+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|++.|+|..+.|+.|+
T Consensus        20 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~   99 (108)
T 2jrs_A           20 QKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMK   99 (108)
T ss_dssp             CCSCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCE
T ss_pred             ccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            34556778999999999999999999999999999999999988999999999999999999999999999999999999


Q ss_pred             EEEecCcH
Q 030819          151 VEIAKSRA  158 (171)
Q Consensus       151 v~~~~~~~  158 (171)
                      |.+++++.
T Consensus       100 V~~a~~k~  107 (108)
T 2jrs_A          100 VGHVTERT  107 (108)
T ss_dssp             EECSCSSC
T ss_pred             EEEcccCC
Confidence            99998764

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.87  E-value=1.1e-21  Score=128.15  Aligned_cols=88  Identities=30%  Similarity=0.594  Sum_probs=82.6

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ...+.++|||+|||+++++++|+++|.+||.|..+.++.++.++.++|||||+|.+.++|++|+..|||..+.|+.|+|.
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   83 (99)
T 1whw_A            4 GSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVL   83 (99)
T ss_dssp             CCCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            34567899999999999999999999999999999999999899999999999999999999999999999999999999


Q ss_pred             EecCcHHH
Q 030819          153 IAKSRAEL  160 (171)
Q Consensus       153 ~~~~~~~~  160 (171)
                      +++++...
T Consensus        84 ~a~~~~~~   91 (99)
T 1whw_A           84 PSTIKKEA   91 (99)
T ss_dssp             ECCCCSTT
T ss_pred             EcCCCccc
Confidence            99987643

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.87  E-value=2.9e-21  Score=126.43  Aligned_cols=85  Identities=29%  Similarity=0.596  Sum_probs=80.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ...+.++|||+|||+++++++|+++|.+||.|..+.+..++ +|+++|||||+|.+.++|++|++.|||..+.|+.|+|.
T Consensus        13 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   91 (100)
T 2do4_A           13 TSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVA   91 (100)
T ss_dssp             SCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            44567899999999999999999999999999999999998 99999999999999999999999999999999999999


Q ss_pred             EecCcH
Q 030819          153 IAKSRA  158 (171)
Q Consensus       153 ~~~~~~  158 (171)
                      +++++.
T Consensus        92 ~a~~~~   97 (100)
T 2do4_A           92 ISNSGP   97 (100)
T ss_dssp             ECCCCS
T ss_pred             ECCCCC
Confidence            998764

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.87  E-value=1.4e-21  Score=127.71  Aligned_cols=86  Identities=30%  Similarity=0.572  Sum_probs=81.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ...+.++|||+|||+++++++|+++|.+||.|..+.++.++.++.++|||||+|.+.++|++|++ |++..+.|+.|+|.
T Consensus         6 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V~   84 (99)
T 2dgs_A            6 SGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVK   84 (99)
T ss_dssp             CCSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEEE
Confidence            45667899999999999999999999999999999999999899999999999999999999999 99999999999999


Q ss_pred             EecCcHH
Q 030819          153 IAKSRAE  159 (171)
Q Consensus       153 ~~~~~~~  159 (171)
                      +++++..
T Consensus        85 ~a~~~~~   91 (99)
T 2dgs_A           85 RAEPRDS   91 (99)
T ss_dssp             ECCCCCC
T ss_pred             ECCCCcc
Confidence            9987653

>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=99.87  E-value=1.5e-22  Score=143.50  Aligned_cols=142  Identities=24%  Similarity=0.353  Sum_probs=110.1

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCCC----------------
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPS----------------   67 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----------------   67 (171)
                      .+.|||++++.++++..+...|...+++..         .........++.++++++.+..+..                
T Consensus         3 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~---------v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~   73 (168)
T 1b7f_A            3 NTNLIVNYLPQDMTDRELYALFRAIGPINT---------CRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNK   73 (168)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEE---------EECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCeeE---------EEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCc
Confidence            367999999999999999999998877622         1111121222333333333322111                


Q ss_pred             ------CCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCC
Q 030819           68 ------PHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHG  141 (171)
Q Consensus        68 ------~~~~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g  141 (171)
                            +.......+..+|||+|||..+++++|+++|++||.|..+.+..++.+|.++|||||+|.+.++|.+|+..|||
T Consensus        74 ~l~v~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g  153 (168)
T 1b7f_A           74 RLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNN  153 (168)
T ss_dssp             ECEEEECCCCSSTTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTT
T ss_pred             EEEEEecCCCcccCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcC
Confidence                  11112345678999999999999999999999999999999999988999999999999999999999999999


Q ss_pred             ceeCC--eEEEEEEe
Q 030819          142 KFLDG--RVIFVEIA  154 (171)
Q Consensus       142 ~~i~g--~~i~v~~~  154 (171)
                      ..+.|  ++|+|.+|
T Consensus       154 ~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A          154 VIPEGGSQPLSVRLA  168 (168)
T ss_dssp             CCCTTCSSCCEEEEC
T ss_pred             CEecCCCeEEEEEeC
Confidence            99988  99999886

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.87  E-value=6.6e-22  Score=130.78  Aligned_cols=86  Identities=26%  Similarity=0.498  Sum_probs=80.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ...++++|||+|||+++++++|+++|+.||.|..+.+..++.+|.++|||||+|.+.++|++|+..|||..+.|+.|+|.
T Consensus        19 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   98 (106)
T 1p27_B           19 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD   98 (106)
T ss_dssp             CBTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEE
Confidence            34567899999999999999999999999999999999999899999999999999999999999999999999999999


Q ss_pred             EecCcH
Q 030819          153 IAKSRA  158 (171)
Q Consensus       153 ~~~~~~  158 (171)
                      +++++.
T Consensus        99 ~a~~~~  104 (106)
T 1p27_B           99 WCFVRG  104 (106)
T ss_dssp             ESEESS
T ss_pred             eecCCC
Confidence            997653

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.87  E-value=1.5e-22  Score=132.85  Aligned_cols=87  Identities=21%  Similarity=0.432  Sum_probs=81.5

Q ss_pred             CCCCeEEEcCCCC------CCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC-e
Q 030819           75 QPKTRLFVSGLSF------RTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDG-R  147 (171)
Q Consensus        75 ~~~~~l~V~nl~~------~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g-~  147 (171)
                      ..+++|||+|||+      ++++++|+++|++||.|.++.++.++.+|+++|||||+|.+.++|++|++.|||..+.| +
T Consensus         4 ~~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r   83 (100)
T 3ns6_A            4 GSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKH   83 (100)
T ss_dssp             CGGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSC
T ss_pred             CcCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCe
Confidence            3467999999999      99999999999999999999999999899999999999999999999999999999999 9


Q ss_pred             EEEEEEecCcHHHH
Q 030819          148 VIFVEIAKSRAELR  161 (171)
Q Consensus       148 ~i~v~~~~~~~~~~  161 (171)
                      .|+|.++.++....
T Consensus        84 ~l~V~~a~~~~~~~   97 (100)
T 3ns6_A           84 RLFLYTMKDVERYN   97 (100)
T ss_dssp             BCEEEESHHHHHHH
T ss_pred             EEEEEECchhhhhh
Confidence            99999998766543

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.87  E-value=9.2e-22  Score=129.23  Aligned_cols=87  Identities=31%  Similarity=0.520  Sum_probs=81.9

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ...+.++|||+|||+++++++|+++|.+||.|..+.++.++.++.++|||||+|.+.++|++|++.|||..+.|+.|+|.
T Consensus         8 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   87 (102)
T 2cqb_A            8 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN   87 (102)
T ss_dssp             SCCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            44578899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             EecCcHH
Q 030819          153 IAKSRAE  159 (171)
Q Consensus       153 ~~~~~~~  159 (171)
                      +++++..
T Consensus        88 ~a~~~~~   94 (102)
T 2cqb_A           88 LAKPMRI   94 (102)
T ss_dssp             ECCCCCC
T ss_pred             eCCCCCC
Confidence            9987653

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.87  E-value=8.3e-22  Score=129.71  Aligned_cols=86  Identities=34%  Similarity=0.575  Sum_probs=81.4

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ...+.++|||+|||+++++++|+++|.+||.|..+.+..++.++.++|||||+|.+.++|++|+..|||..+.|+.|+|.
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   88 (103)
T 2dnm_A            9 DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQ   88 (103)
T ss_dssp             CCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            45567899999999999999999999999999999999999899999999999999999999999999999999999999


Q ss_pred             EecCcH
Q 030819          153 IAKSRA  158 (171)
Q Consensus       153 ~~~~~~  158 (171)
                      ++++..
T Consensus        89 ~a~~~~   94 (103)
T 2dnm_A           89 VARYGR   94 (103)
T ss_dssp             ECSSCC
T ss_pred             ECCcCC
Confidence            998654

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.87  E-value=2e-21  Score=128.65  Aligned_cols=89  Identities=26%  Similarity=0.537  Sum_probs=82.6

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeec-CCCCCcceEEEEEeCCHHHHHHHHHHh-CCceeCCeE
Q 030819           71 LSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMD-KIANRPRGFAFLRYATEEESRRAIEGM-HGKFLDGRV  148 (171)
Q Consensus        71 ~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~-~~~g~~~g~~fv~f~~~~~a~~al~~l-~g~~i~g~~  148 (171)
                      .....+.++|||+|||+++++++|+++|.+||.|..+.++.+ +.++.++|||||+|.+.++|++|+..| |+..+.|+.
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~   88 (107)
T 2cph_A            9 VPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRR   88 (107)
T ss_dssp             SCCSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCB
T ss_pred             cccCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCE
Confidence            345567899999999999999999999999999999999998 789999999999999999999999999 999999999


Q ss_pred             EEEEEecCcHH
Q 030819          149 IFVEIAKSRAE  159 (171)
Q Consensus       149 i~v~~~~~~~~  159 (171)
                      |+|.+++++..
T Consensus        89 l~v~~a~~~~~   99 (107)
T 2cph_A           89 LVLEWADSEVT   99 (107)
T ss_dssp             CEEEECCCCCC
T ss_pred             EEEEeCCCCCC
Confidence            99999987653

>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=99.87  E-value=2.1e-22  Score=143.39  Aligned_cols=147  Identities=20%  Similarity=0.328  Sum_probs=109.3

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCCC----------------
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPS----------------   67 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----------------   67 (171)
                      .+.|||+|++++++++.+...|...+.......    ............++++++++.+..+..                
T Consensus         4 ~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~----~~~~~v~~~~~~~~~g~afV~f~~~~~A~~A~~~~~~~~~g~~   79 (172)
T 2g4b_A            4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQ----APGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQS   79 (172)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCS----SSSCSEEEEEEETTTTEEEEEESSHHHHHHHGGGTTCEETTEE
T ss_pred             ccEEEEcCCCcccCHHHHHHHHHHHhhhccccc----CCCCceeeeEecCCCCEEEEEeCCHHHHHHHHHhCCcEecCce
Confidence            367999999999999999999988722111000    000011111222334444443322211                


Q ss_pred             -----CCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCc
Q 030819           68 -----PHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGK  142 (171)
Q Consensus        68 -----~~~~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~  142 (171)
                           +..........+|||+|||+.+++++|+++|++||.|..+.+..++.+|.++|||||+|.+.++|.+|+..|||.
T Consensus        80 i~v~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~  159 (172)
T 2g4b_A           80 LKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGM  159 (172)
T ss_dssp             CEEECCSSCCCCTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTC
T ss_pred             eeecCCcccCCCCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCC
Confidence                 111223345789999999999999999999999999999999999889999999999999999999999999999


Q ss_pred             eeCCeEEEEEEe
Q 030819          143 FLDGRVIFVEIA  154 (171)
Q Consensus       143 ~i~g~~i~v~~~  154 (171)
                      .+.|+.|.|.+|
T Consensus       160 ~~~g~~l~V~~A  171 (172)
T 2g4b_A          160 QLGDKKLLVQRA  171 (172)
T ss_dssp             EETTEECEEEEC
T ss_pred             EECCeEEEEEeC
Confidence            999999999987

>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=99.87  E-value=6.5e-22  Score=131.71  Aligned_cols=86  Identities=22%  Similarity=0.424  Sum_probs=81.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ...+.++|||+|||+++++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..|||..+.|+.|+|.
T Consensus        22 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  101 (110)
T 1oo0_B           22 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD  101 (110)
T ss_dssp             CBTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            34567899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             EecCcH
Q 030819          153 IAKSRA  158 (171)
Q Consensus       153 ~~~~~~  158 (171)
                      +++++.
T Consensus       102 ~a~~~~  107 (110)
T 1oo0_B          102 WCFVKG  107 (110)
T ss_dssp             ESEESS
T ss_pred             EcccCC
Confidence            998654

>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=99.87  E-value=3.1e-21  Score=128.48  Aligned_cols=87  Identities=30%  Similarity=0.542  Sum_probs=81.9

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC------CceeCC
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMH------GKFLDG  146 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~------g~~i~g  146 (171)
                      ...+.++|||+|||+++++++|+++|.+||.|..+.++.++.++.++|||||+|.+.++|.+|+..||      +..+.|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g   90 (111)
T 1x4h_A           11 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDG   90 (111)
T ss_dssp             CCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSS
T ss_pred             cCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcC
Confidence            45568899999999999999999999999999999999999899999999999999999999999999      999999


Q ss_pred             eEEEEEEecCcHH
Q 030819          147 RVIFVEIAKSRAE  159 (171)
Q Consensus       147 ~~i~v~~~~~~~~  159 (171)
                      +.|+|.++.++..
T Consensus        91 ~~l~v~~a~~~~~  103 (111)
T 1x4h_A           91 RQLKVDLAVTRDE  103 (111)
T ss_dssp             CEEEEECCCCCCC
T ss_pred             EEEEEEECCCCcc
Confidence            9999999987653

>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=99.87  E-value=2.1e-22  Score=129.60  Aligned_cols=83  Identities=18%  Similarity=0.424  Sum_probs=72.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCC--CeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 030819           78 TRLFVSGLSFRTSEDSLRNAFQGFG--QLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAK  155 (171)
Q Consensus        78 ~~l~V~nl~~~~~~~~l~~~f~~~G--~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~  155 (171)
                      .+|||+|||+++++++|+++|++||  .|.++.++.++.+|+++|||||+|.+.++|++|++.|||..+.|+.|+|.++.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            4799999999999999999999999  99999999999999999999999999999999999999999999999999998


Q ss_pred             CcHHH
Q 030819          156 SRAEL  160 (171)
Q Consensus       156 ~~~~~  160 (171)
                      +....
T Consensus        82 ~~~~~   86 (90)
T 3p5t_L           82 KLEHH   86 (90)
T ss_dssp             -----
T ss_pred             CCccc
Confidence            76543

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.87  E-value=1.2e-22  Score=147.70  Aligned_cols=85  Identities=28%  Similarity=0.504  Sum_probs=80.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 030819           74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEI  153 (171)
Q Consensus        74 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~  153 (171)
                      ..+.++|||+|||+.+++++|+++|++||.|..+.+..++.+|.++|||||+|.+.++|.+|+..|||..+.|+.|+|.+
T Consensus       111 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  190 (198)
T 2yh0_A          111 PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR  190 (198)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            35679999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ecCcH
Q 030819          154 AKSRA  158 (171)
Q Consensus       154 ~~~~~  158 (171)
                      ++++.
T Consensus       191 a~~~~  195 (198)
T 2yh0_A          191 ASVGA  195 (198)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            98764

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.87  E-value=2.6e-21  Score=130.34  Aligned_cols=84  Identities=20%  Similarity=0.397  Sum_probs=78.9

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 030819           72 STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFV  151 (171)
Q Consensus        72 ~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v  151 (171)
                      ....+.++|||+|||+++++++|+++|++||.|.++.++.++.+|+++|||||+|.+.++|++|++.|||..+.|+.|+|
T Consensus        35 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V  114 (118)
T 2khc_A           35 IEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKV  114 (118)
T ss_dssp             CCCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            34566789999999999999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             EEec
Q 030819          152 EIAK  155 (171)
Q Consensus       152 ~~~~  155 (171)
                      ++++
T Consensus       115 ~~ak  118 (118)
T 2khc_A          115 QLKK  118 (118)
T ss_dssp             EEC-
T ss_pred             EecC
Confidence            9975

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.87  E-value=1.2e-21  Score=127.25  Aligned_cols=85  Identities=27%  Similarity=0.504  Sum_probs=80.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEE-EEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 030819           75 QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEV-NLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEI  153 (171)
Q Consensus        75 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~-~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~  153 (171)
                      .+.++|||+|||+++++++|+++|++||.|..+ .++.++.++.++|||||+|.+.++|++|+..|||..+.|+.|+|.+
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   82 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSY   82 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            467899999999999999999999999999999 9999988999999999999999999999999999999999999999


Q ss_pred             ecCcHH
Q 030819          154 AKSRAE  159 (171)
Q Consensus       154 ~~~~~~  159 (171)
                      +.++..
T Consensus        83 a~~~~~   88 (96)
T 1x5t_A           83 AFKKDS   88 (96)
T ss_dssp             SCCCCC
T ss_pred             ecccCC
Confidence            987653

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.86  E-value=1.8e-21  Score=137.47  Aligned_cols=85  Identities=21%  Similarity=0.416  Sum_probs=79.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCC--CeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           75 QPKTRLFVSGLSFRTSEDSLRNAFQGFG--QLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        75 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G--~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ...++|||+|||+++++++|+++|..||  .|.++.++.|+.+|+++|||||+|.+.++|++||+.|||..+.|+.|+|.
T Consensus        53 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~  132 (156)
T 3n9u_C           53 NRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVR  132 (156)
T ss_dssp             ---CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEE
Confidence            3568999999999999999999999999  99999999999999999999999999999999999999999999999999


Q ss_pred             EecCcHH
Q 030819          153 IAKSRAE  159 (171)
Q Consensus       153 ~~~~~~~  159 (171)
                      ++.++..
T Consensus       133 ~a~~~~~  139 (156)
T 3n9u_C          133 PATRQNL  139 (156)
T ss_dssp             ECCHHHH
T ss_pred             EcCCCcc
Confidence            9986643

>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=99.86  E-value=5e-21  Score=126.32  Aligned_cols=86  Identities=26%  Similarity=0.434  Sum_probs=80.6

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC---eEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDG---RVI  149 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g---~~i  149 (171)
                      ..++.++|||+|||+++++++|+++|.+||.|..+.+..++ +|.++|||||+|.+.++|++|++.|||..+.|   +.|
T Consensus        11 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l   89 (105)
T 2dnh_A           11 RGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSL   89 (105)
T ss_dssp             SCCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccE
Confidence            44568999999999999999999999999999999999998 89999999999999999999999999999988   999


Q ss_pred             EEEEecCcHH
Q 030819          150 FVEIAKSRAE  159 (171)
Q Consensus       150 ~v~~~~~~~~  159 (171)
                      +|.+++++..
T Consensus        90 ~V~~a~~~~~   99 (105)
T 2dnh_A           90 VVKFADTDKE   99 (105)
T ss_dssp             EEEESCSSCC
T ss_pred             EEEECccCcc
Confidence            9999987654

>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=99.86  E-value=4.3e-21  Score=127.03  Aligned_cols=84  Identities=25%  Similarity=0.470  Sum_probs=79.3

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 030819           72 STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFV  151 (171)
Q Consensus        72 ~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v  151 (171)
                      ....+.++|||+|||+.+++++|+++|.+||.|..+.++.++ +|+++|||||+|.+.++|++|++.|||..+.|+.|+|
T Consensus        24 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V  102 (107)
T 3ulh_A           24 AGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNI  102 (107)
T ss_dssp             CCCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEE
Confidence            345668899999999999999999999999999999999999 9999999999999999999999999999999999999


Q ss_pred             EEecC
Q 030819          152 EIAKS  156 (171)
Q Consensus       152 ~~~~~  156 (171)
                      .++.+
T Consensus       103 ~~a~s  107 (107)
T 3ulh_A          103 QLVTS  107 (107)
T ss_dssp             EEECC
T ss_pred             EEeCC
Confidence            99863

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.86  E-value=1.5e-21  Score=128.24  Aligned_cols=87  Identities=38%  Similarity=0.672  Sum_probs=81.9

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ...+.++|||+|||+++++++|+++|.+||.|..+.++.++.++.++|||||+|.+.++|.+|++.|||..+.|+.|+|.
T Consensus         8 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   87 (102)
T 1x5s_A            8 MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVD   87 (102)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            45567899999999999999999999999999999999999899999999999999999999999999999999999999


Q ss_pred             EecCcHH
Q 030819          153 IAKSRAE  159 (171)
Q Consensus       153 ~~~~~~~  159 (171)
                      +++++..
T Consensus        88 ~a~~~~~   94 (102)
T 1x5s_A           88 QAGKSSD   94 (102)
T ss_dssp             EEECCCC
T ss_pred             ECCCCCC
Confidence            9987653

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.86  E-value=1.8e-21  Score=127.19  Aligned_cols=86  Identities=20%  Similarity=0.415  Sum_probs=80.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeE-EEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeE---
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLV-EVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRV---  148 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~-~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~---  148 (171)
                      ...+.++|||+|||+++++++|+++|.+||.|. .+.++.++.++.++|||||+|.+.++|++|++.|||..+.|+.   
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~   84 (99)
T 2div_A            5 SSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAK   84 (99)
T ss_dssp             CCSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCE
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcce
Confidence            445688999999999999999999999999999 9999999989999999999999999999999999999999999   


Q ss_pred             -EEEEEecCcH
Q 030819          149 -IFVEIAKSRA  158 (171)
Q Consensus       149 -i~v~~~~~~~  158 (171)
                       |+|.|+++..
T Consensus        85 ~l~v~~a~~~~   95 (99)
T 2div_A           85 RFKLNYATYSG   95 (99)
T ss_dssp             ECCEEETTCCS
T ss_pred             eEEEeecCCCC
Confidence             9999997653

>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=99.86  E-value=1.3e-21  Score=131.02  Aligned_cols=86  Identities=22%  Similarity=0.417  Sum_probs=80.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 030819           74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEI  153 (171)
Q Consensus        74 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~  153 (171)
                      ....++|||+|||+++++++|+++|..||.|..+.++.++.+|.++|||||+|.+.++|++|+ .|||..+.|+.|+|.+
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~  100 (114)
T 2cq4_A           22 ERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQA  100 (114)
T ss_dssp             HHHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEE
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEe
Confidence            345689999999999999999999999999999999999988999999999999999999999 8999999999999999


Q ss_pred             ecCcHHH
Q 030819          154 AKSRAEL  160 (171)
Q Consensus       154 ~~~~~~~  160 (171)
                      ++++...
T Consensus       101 a~~~~~~  107 (114)
T 2cq4_A          101 SQAEKNR  107 (114)
T ss_dssp             HHHHHHH
T ss_pred             cCCCccC
Confidence            9876644

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.86  E-value=3.3e-21  Score=133.41  Aligned_cols=89  Identities=22%  Similarity=0.414  Sum_probs=83.3

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q 030819           71 LSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIF  150 (171)
Q Consensus        71 ~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~  150 (171)
                      .....+.++|||+|||+++++++|+++|+.||.|.++.++.++.+|+++|||||+|.+.++|.+|++.|||..+.|+.|+
T Consensus        36 ~~~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  115 (139)
T 1u6f_A           36 NPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLK  115 (139)
T ss_dssp             SCCTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEE
Confidence            44566789999999999999999999999999999999999998999999999999999999999999999999999999


Q ss_pred             EEEecCcHH
Q 030819          151 VEIAKSRAE  159 (171)
Q Consensus       151 v~~~~~~~~  159 (171)
                      |.+++++..
T Consensus       116 v~~a~~~~~  124 (139)
T 1u6f_A          116 VALAASGHQ  124 (139)
T ss_dssp             EEESSCCCC
T ss_pred             EEECCCCCC
Confidence            999987653

>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=99.86  E-value=1.4e-21  Score=129.17  Aligned_cols=88  Identities=25%  Similarity=0.425  Sum_probs=82.0

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee---CCeE
Q 030819           72 STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFL---DGRV  148 (171)
Q Consensus        72 ~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i---~g~~  148 (171)
                      ....+.++|||+|||+++++++|+++|++||.|..+.++.++.+|+++|||||+|.+.++|.+|+..|||..+   .|+.
T Consensus         8 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~   87 (106)
T 2dgp_A            8 MKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRP   87 (106)
T ss_dssp             CCCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCce
Confidence            3456788999999999999999999999999999999999998999999999999999999999999999987   8999


Q ss_pred             EEEEEecCcHH
Q 030819          149 IFVEIAKSRAE  159 (171)
Q Consensus       149 i~v~~~~~~~~  159 (171)
                      |+|.++.++..
T Consensus        88 l~v~~a~~~~~   98 (106)
T 2dgp_A           88 IQVKPADSESR   98 (106)
T ss_dssp             CEEEECCCCSC
T ss_pred             EEEEECCcccc
Confidence            99999987653

>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=99.86  E-value=5.6e-21  Score=121.92  Aligned_cols=81  Identities=32%  Similarity=0.590  Sum_probs=76.2

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ...+.++|||+|||+++++++|+++|++||.|..+.++.++.+|+++|||||+|.+.++|++|++ +++..++|+.|.|.
T Consensus         7 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v~   85 (87)
T 3s7r_A            7 NEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDPK   85 (87)
T ss_dssp             CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEEE
Confidence            45678899999999999999999999999999999999999899999999999999999999997 58889999999998


Q ss_pred             Ee
Q 030819          153 IA  154 (171)
Q Consensus       153 ~~  154 (171)
                      +|
T Consensus        86 ~A   87 (87)
T 3s7r_A           86 KA   87 (87)
T ss_dssp             EC
T ss_pred             eC
Confidence            75

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.86  E-value=4.5e-21  Score=126.17  Aligned_cols=87  Identities=26%  Similarity=0.570  Sum_probs=80.9

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q 030819           71 LSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIF  150 (171)
Q Consensus        71 ~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~  150 (171)
                      .....+.++|||+|||+++++++|+++|.+||.|..+.+..+  ++.++|||||+|.+.++|.+|+..|||..+.|+.|+
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   86 (103)
T 2d9p_A            9 RITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLY   86 (103)
T ss_dssp             CCCCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCE
T ss_pred             ccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEE
Confidence            345567899999999999999999999999999999999987  899999999999999999999999999999999999


Q ss_pred             EEEecCcHH
Q 030819          151 VEIAKSRAE  159 (171)
Q Consensus       151 v~~~~~~~~  159 (171)
                      |.+++++..
T Consensus        87 V~~a~~~~~   95 (103)
T 2d9p_A           87 VALAQRKEE   95 (103)
T ss_dssp             EEECSSCCC
T ss_pred             EEEeccccc
Confidence            999987654

>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=99.86  E-value=2.6e-22  Score=141.89  Aligned_cols=141  Identities=22%  Similarity=0.326  Sum_probs=108.3

Q ss_pred             eeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCCC-----------------
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPS-----------------   67 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----------------   67 (171)
                      +.|||+|+++++++..+...|...+++..         .........++.++.+++.+..+..                 
T Consensus         3 ~~l~v~nlp~~~~~~~l~~~f~~~G~i~~---------v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~   73 (167)
T 1fxl_A            3 TNLIVNYLPQNMTQEEFRSLFGSIGEIES---------CKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKT   73 (167)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEE---------EEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             ceEEEcCCCCCCCHHHHHHHHHhcCCeEE---------EEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCce
Confidence            57999999999999999999988876622         1111111122333333333322211                 


Q ss_pred             -----CCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCc
Q 030819           68 -----PHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGK  142 (171)
Q Consensus        68 -----~~~~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~  142 (171)
                           ..+........+|||+|||+.+++++|+++|++||.|..+.+..++.+|.++|||||+|.+.++|.+|+..|||.
T Consensus        74 l~v~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~  153 (167)
T 1fxl_A           74 IKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQ  153 (167)
T ss_dssp             CEEEECCCCCGGGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTC
T ss_pred             EEEEecCCCcccCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCC
Confidence                 011123345689999999999999999999999999999999999889999999999999999999999999999


Q ss_pred             eeCCeE--EEEEEe
Q 030819          143 FLDGRV--IFVEIA  154 (171)
Q Consensus       143 ~i~g~~--i~v~~~  154 (171)
                      .+.|+.  |+|.||
T Consensus       154 ~~~g~~~~i~v~~A  167 (167)
T 1fxl_A          154 KPSGATEPITVKFA  167 (167)
T ss_dssp             CCTTCSSCCEEEEC
T ss_pred             ccCCCccceEEEeC
Confidence            999964  888875

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.86  E-value=3.4e-21  Score=128.78  Aligned_cols=88  Identities=23%  Similarity=0.415  Sum_probs=82.1

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeE--------EEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCce
Q 030819           72 STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLV--------EVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKF  143 (171)
Q Consensus        72 ~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~--------~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~  143 (171)
                      ....+.++|||+|||+++++++|+++|.+||.|.        .+.+..++.+++++|||||+|.+.++|++|++.|||..
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~   89 (113)
T 2cpe_A           10 DEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKD   89 (113)
T ss_dssp             CCCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCE
T ss_pred             ccCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCc
Confidence            3456789999999999999999999999999999        69999998899999999999999999999999999999


Q ss_pred             eCCeEEEEEEecCcHH
Q 030819          144 LDGRVIFVEIAKSRAE  159 (171)
Q Consensus       144 i~g~~i~v~~~~~~~~  159 (171)
                      +.|+.|+|.+++++..
T Consensus        90 ~~g~~l~V~~a~~~~~  105 (113)
T 2cpe_A           90 FQGSKLKVSLARKKPP  105 (113)
T ss_dssp             ETTEECEEECSSCCCC
T ss_pred             cCCCEEEEEECCCCCC
Confidence            9999999999987654

>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=99.86  E-value=8.5e-22  Score=129.77  Aligned_cols=90  Identities=24%  Similarity=0.536  Sum_probs=83.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 030819           75 QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIA  154 (171)
Q Consensus        75 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~  154 (171)
                      .+.++|||+|||+.+++++|+++|++||.|..+.+..++.+|.++|||||+|.+.++|.+|++.|||..+.|+.|+|.++
T Consensus         6 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   85 (104)
T 1p1t_A            6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNA   85 (104)
T ss_dssp             HHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEET
T ss_pred             CCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeC
Confidence            35689999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             cCcHHHHHhh
Q 030819          155 KSRAELRQAF  164 (171)
Q Consensus       155 ~~~~~~~~~~  164 (171)
                      .++.......
T Consensus        86 ~~~~~~~~~~   95 (104)
T 1p1t_A           86 ASEKNKEELK   95 (104)
T ss_dssp             TCTTHHHHHH
T ss_pred             CCccchhhhc
Confidence            9877665433

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.86  E-value=2.4e-21  Score=126.29  Aligned_cols=84  Identities=25%  Similarity=0.516  Sum_probs=78.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCC---CCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 030819           75 QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKI---ANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFV  151 (171)
Q Consensus        75 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~---~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v  151 (171)
                      .+.++|||+|||+++++++|+++|++||.|..+.+..++.   ++.++|||||+|.+.++|++|+..|||..+.|+.|+|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   82 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEV   82 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEE
Confidence            5678999999999999999999999999999999998876   5689999999999999999999999999999999999


Q ss_pred             EEecCcH
Q 030819          152 EIAKSRA  158 (171)
Q Consensus       152 ~~~~~~~  158 (171)
                      .+++++.
T Consensus        83 ~~a~~~~   89 (98)
T 2cpf_A           83 RISERAT   89 (98)
T ss_dssp             ECSSCSS
T ss_pred             EEccCCC
Confidence            9998764

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.86  E-value=7.3e-21  Score=125.21  Aligned_cols=85  Identities=25%  Similarity=0.508  Sum_probs=79.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ...+.++|||+|||+++++++|+++|.+|| |..+.++.++.+++++|||||+|.+.++|++|+ .|||..+.|+.|+|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~   88 (103)
T 2dng_A           11 PTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVD   88 (103)
T ss_dssp             CSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEE
Confidence            445678999999999999999999999997 999999999989999999999999999999999 899999999999999


Q ss_pred             EecCcHH
Q 030819          153 IAKSRAE  159 (171)
Q Consensus       153 ~~~~~~~  159 (171)
                      +++++..
T Consensus        89 ~a~~~~~   95 (103)
T 2dng_A           89 IAEGRKQ   95 (103)
T ss_dssp             ECCCCCC
T ss_pred             EecCCCC
Confidence            9987653

>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=99.86  E-value=8.4e-23  Score=145.59  Aligned_cols=142  Identities=20%  Similarity=0.264  Sum_probs=106.0

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccC--CCCCCCCCCCCCCC---------------
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQG--RGRGACFPLACLPP---------------   66 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~---------------   66 (171)
                      .+.|||+|+++++++..+...|...+++..-..         ......+  ++++++++.+..+.               
T Consensus         3 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i---------~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~   73 (175)
T 3nmr_A            3 AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINV---------LRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVL   73 (175)
T ss_dssp             CEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEE---------EEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCC
T ss_pred             ceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEE---------EecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEc
Confidence            468999999999999999999998877632111         1111010  22222222221110               


Q ss_pred             -----------CCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHH
Q 030819           67 -----------SPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA  135 (171)
Q Consensus        67 -----------~~~~~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~a  135 (171)
                                 ............+|||+|||+.+++++|+++|++||.|..+.+..++ +|.++|||||+|.+.++|.+|
T Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~-~g~~~g~afV~f~~~~~A~~A  152 (175)
T 3nmr_A           74 PGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTA  152 (175)
T ss_dssp             TTCSSCCEEEECGGGCCSCGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHH
T ss_pred             cCCccceEEccccccccccCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECC-CCCEEEEEEEEECCHHHHHHH
Confidence                       00111233467899999999999999999999999999999999987 799999999999999999999


Q ss_pred             HHHhCCceeC---CeEEEEEEec
Q 030819          136 IEGMHGKFLD---GRVIFVEIAK  155 (171)
Q Consensus       136 l~~l~g~~i~---g~~i~v~~~~  155 (171)
                      +..|||..+.   +++|.|.|+.
T Consensus       153 ~~~l~g~~~~~g~~~~l~V~~ad  175 (175)
T 3nmr_A          153 IKAMHQAQTMEGCSSPMVVKFAD  175 (175)
T ss_dssp             HHHHTTSCCCTTCSSCCEEEECC
T ss_pred             HHHhcCCcccCCCCCCeEEEecC
Confidence            9999999875   4899999873

>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=99.86  E-value=4.1e-21  Score=124.46  Aligned_cols=83  Identities=29%  Similarity=0.421  Sum_probs=78.3

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ...+.++|||+|||+.+++++|+++|++||.|..+.+..++ ++.++|||||+|.+.++|++|++.|||..+.|+.|+|.
T Consensus        12 ~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   90 (95)
T 2ywk_A           12 QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVS   90 (95)
T ss_dssp             CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEE
Confidence            44567899999999999999999999999999999999998 59999999999999999999999999999999999999


Q ss_pred             EecC
Q 030819          153 IAKS  156 (171)
Q Consensus       153 ~~~~  156 (171)
                      +++.
T Consensus        91 ~a~~   94 (95)
T 2ywk_A           91 GPSS   94 (95)
T ss_dssp             CCCC
T ss_pred             EcCC
Confidence            9874

>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=99.86  E-value=2.2e-21  Score=132.94  Aligned_cols=87  Identities=34%  Similarity=0.589  Sum_probs=81.8

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 030819           72 STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFV  151 (171)
Q Consensus        72 ~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v  151 (171)
                      ...++.++|||+|||+++++++|+++|++||.|..+.++.++.+|+++|||||+|.+.++|++|+..|+|..+.|+.|+|
T Consensus        41 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V  120 (129)
T 2kxn_B           41 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV  120 (129)
T ss_dssp             SCCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            34566789999999999999999999999999999999999989999999999999999999999999999999999999


Q ss_pred             EEecCcH
Q 030819          152 EIAKSRA  158 (171)
Q Consensus       152 ~~~~~~~  158 (171)
                      .+++++.
T Consensus       121 ~~a~~~~  127 (129)
T 2kxn_B          121 DFSITKR  127 (129)
T ss_dssp             SCCSSSS
T ss_pred             EEecCCC
Confidence            9998754

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=1.8e-21  Score=128.38  Aligned_cols=87  Identities=10%  Similarity=0.242  Sum_probs=79.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 030819           74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEI  153 (171)
Q Consensus        74 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~  153 (171)
                      ..+.++|||+|||+++++++|+++|++||.|.++.++.++. |.++|||||+|.+.++|.+|+. ++|..+.|+.|.|.+
T Consensus         8 ~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~   85 (103)
T 1s79_A            8 DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILF   85 (103)
T ss_dssp             CSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEE
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEE
Confidence            34568999999999999999999999999999999999986 9999999999999999999999 899999999999999


Q ss_pred             ecCcHHHHH
Q 030819          154 AKSRAELRQ  162 (171)
Q Consensus       154 ~~~~~~~~~  162 (171)
                      +......+.
T Consensus        86 ~~~~~~~k~   94 (103)
T 1s79_A           86 KDDYFAKKN   94 (103)
T ss_dssp             HHHHHHHHH
T ss_pred             chHHHHHHH
Confidence            887655543

>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=99.85  E-value=3.7e-21  Score=125.41  Aligned_cols=85  Identities=15%  Similarity=0.237  Sum_probs=79.2

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ..+..++|||+|||+++++++|+++|.+||.|..+.++.++.+|+++|||||+|.+.++|++|++.|||..+.|+.|+|.
T Consensus        11 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~   90 (98)
T 2cqp_A           11 GKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLV   90 (98)
T ss_dssp             CCCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            44557899999999999999999999999999988888888899999999999999999999999999999999999999


Q ss_pred             EecCc
Q 030819          153 IAKSR  157 (171)
Q Consensus       153 ~~~~~  157 (171)
                      ++..+
T Consensus        91 ~a~~~   95 (98)
T 2cqp_A           91 LGSGP   95 (98)
T ss_dssp             ESSCS
T ss_pred             EcCCC
Confidence            98754

>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=99.85  E-value=8.4e-21  Score=125.13  Aligned_cols=85  Identities=20%  Similarity=0.433  Sum_probs=79.3

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCC-CCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIA-NRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFV  151 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~-g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v  151 (171)
                      ...+.++|||+|||+++++++|+++|..|| |..+.++.++.+ |+++|||||+|.+.++|++|| .|++..+.|+.|+|
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V   88 (104)
T 1wi8_A           11 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRV   88 (104)
T ss_dssp             CSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEE
T ss_pred             CCCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEE
Confidence            345678999999999999999999999999 999999999987 999999999999999999999 89999999999999


Q ss_pred             EEecCcHH
Q 030819          152 EIAKSRAE  159 (171)
Q Consensus       152 ~~~~~~~~  159 (171)
                      .+++++..
T Consensus        89 ~~a~~~~~   96 (104)
T 1wi8_A           89 DVADQAQD   96 (104)
T ss_dssp             EECCCCCC
T ss_pred             EEccCCCC
Confidence            99987654

>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=5.1e-21  Score=122.18  Aligned_cols=84  Identities=17%  Similarity=0.451  Sum_probs=78.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCC-cceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 030819           75 QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANR-PRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEI  153 (171)
Q Consensus        75 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~-~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~  153 (171)
                      ...++|||+|||+++++++|+++|++||.|..+.+..++.++. ++|||||+|.+.++|++|+..|||..+.|+.|+|.+
T Consensus         2 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   81 (88)
T 4a8x_A            2 MKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATA   81 (88)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEE
Confidence            3467999999999999999999999999999999999887766 899999999999999999999999999999999999


Q ss_pred             ecCcH
Q 030819          154 AKSRA  158 (171)
Q Consensus       154 ~~~~~  158 (171)
                      +.+..
T Consensus        82 a~~~~   86 (88)
T 4a8x_A           82 VLAPW   86 (88)
T ss_dssp             ECCCC
T ss_pred             CCCCC
Confidence            97653

>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=99.85  E-value=7.6e-22  Score=129.39  Aligned_cols=88  Identities=22%  Similarity=0.408  Sum_probs=75.6

Q ss_pred             CCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecC-CCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCe
Q 030819           69 HSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDK-IANRPRGFAFLRYATEEESRRAIEGMHGKFLDGR  147 (171)
Q Consensus        69 ~~~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~-~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~  147 (171)
                      .........++|||+|||+++++++|+++|++|| |.++.++.++ .+|+++|||||+|.+.++|.+|+ .|+|..+.|+
T Consensus        11 ~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~   88 (100)
T 2j76_E           11 RSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNR   88 (100)
T ss_dssp             ---------CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTB
T ss_pred             CCcCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCe
Confidence            3344567789999999999999999999999999 9999999988 58999999999999999999999 7999999999


Q ss_pred             EEEEEEecCcH
Q 030819          148 VIFVEIAKSRA  158 (171)
Q Consensus       148 ~i~v~~~~~~~  158 (171)
                      .|+|.+++++.
T Consensus        89 ~l~V~~a~~~~   99 (100)
T 2j76_E           89 RIRVDVADQAQ   99 (100)
T ss_dssp             CCCCEECCCSC
T ss_pred             EEEEEeccCCC
Confidence            99999998753

>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=1.1e-20  Score=126.98  Aligned_cols=86  Identities=30%  Similarity=0.551  Sum_probs=80.2

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q 030819           71 LSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIF  150 (171)
Q Consensus        71 ~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~  150 (171)
                      .....+.++|||+|||+++++++|+++|.+||.|..+.++.++.+++++|||||+|.+.++|++|++.+++ .+.|+.|+
T Consensus        11 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~   89 (116)
T 2cqd_A           11 SQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKAN   89 (116)
T ss_dssp             CCCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECE
T ss_pred             CcCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEE
Confidence            33456789999999999999999999999999999999999998999999999999999999999999998 89999999


Q ss_pred             EEEecCc
Q 030819          151 VEIAKSR  157 (171)
Q Consensus       151 v~~~~~~  157 (171)
                      |.++...
T Consensus        90 V~~a~~~   96 (116)
T 2cqd_A           90 VNLAYLG   96 (116)
T ss_dssp             EEESTTT
T ss_pred             EEEcccC
Confidence            9999754

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A

Probab=99.85  E-value=6.4e-21  Score=122.06  Aligned_cols=80  Identities=23%  Similarity=0.576  Sum_probs=76.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 030819           77 KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKS  156 (171)
Q Consensus        77 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~~  156 (171)
                      .++|||+|||+++++++|+++|++||.|..+.+..++.++.++|||||+|.+.++|++|+ .|||..+.|+.|+|.++++
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~~   84 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKRT   84 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEccC
Confidence            579999999999999999999999999999999999889999999999999999999999 8999999999999999876


Q ss_pred             c
Q 030819          157 R  157 (171)
Q Consensus       157 ~  157 (171)
                      .
T Consensus        85 ~   85 (89)
T 3ucg_A           85 N   85 (89)
T ss_dssp             T
T ss_pred             C
Confidence            4

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.85  E-value=5.7e-21  Score=127.15  Aligned_cols=87  Identities=25%  Similarity=0.491  Sum_probs=76.2

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q 030819           71 LSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIF  150 (171)
Q Consensus        71 ~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~  150 (171)
                      .....+.++|||+|||+++++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|.+|+..+ +..+.|+.|+
T Consensus        19 ~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~   97 (109)
T 2rs2_A           19 SHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTID   97 (109)
T ss_dssp             -------CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEE
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEE
Confidence            445667899999999999999999999999999999999999989999999999999999999999975 5899999999


Q ss_pred             EEEecCcH
Q 030819          151 VEIAKSRA  158 (171)
Q Consensus       151 v~~~~~~~  158 (171)
                      |.++.++.
T Consensus        98 V~~a~~~~  105 (109)
T 2rs2_A           98 PKVAFPRR  105 (109)
T ss_dssp             EEECCCCC
T ss_pred             EEEccCCC
Confidence            99998764

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens}

Probab=99.85  E-value=5.5e-21  Score=128.62  Aligned_cols=84  Identities=35%  Similarity=0.615  Sum_probs=79.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 030819           74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEI  153 (171)
Q Consensus        74 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~  153 (171)
                      ..+.++|||+|||+++++++|+++|++||.|..+.+..++ +|.++|||||+|.+.++|++|++.|+|..+.|+.|+|.+
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~   82 (116)
T 2fy1_A            4 ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQ   82 (116)
T ss_dssp             TCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            4557899999999999999999999999999999999998 999999999999999999999999999999999999999


Q ss_pred             ecCcH
Q 030819          154 AKSRA  158 (171)
Q Consensus       154 ~~~~~  158 (171)
                      ++++.
T Consensus        83 a~~~~   87 (116)
T 2fy1_A           83 AKKPS   87 (116)
T ss_dssp             CCCSS
T ss_pred             CCCCC
Confidence            98654

>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=99.85  E-value=3.7e-21  Score=130.97  Aligned_cols=85  Identities=26%  Similarity=0.502  Sum_probs=80.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ...+.++|||+|||+++++++|+++|.+||.|..+.++.++.++.++|||||+|.+.++|++|++.|||..+.|+.|.|.
T Consensus        18 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   97 (126)
T 3ex7_B           18 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD   97 (126)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            44567899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             EecCc
Q 030819          153 IAKSR  157 (171)
Q Consensus       153 ~~~~~  157 (171)
                      ++.++
T Consensus        98 ~a~~~  102 (126)
T 3ex7_B           98 WCFVR  102 (126)
T ss_dssp             ESEES
T ss_pred             EecCC
Confidence            98644

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=2.8e-20  Score=122.37  Aligned_cols=86  Identities=30%  Similarity=0.606  Sum_probs=78.8

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q 030819           71 LSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIF  150 (171)
Q Consensus        71 ~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~  150 (171)
                      .....+.++|||+|||+++++++|+++|.+||.|..+.++.++.  .++|||||+|.+.++|++|+..|||..+.|+.|+
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   86 (103)
T 2cq3_A            9 SESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIE   86 (103)
T ss_dssp             SCCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            34556679999999999999999999999999999999998863  3889999999999999999999999999999999


Q ss_pred             EEEecCcH
Q 030819          151 VEIAKSRA  158 (171)
Q Consensus       151 v~~~~~~~  158 (171)
                      |.+++++.
T Consensus        87 v~~a~~~~   94 (103)
T 2cq3_A           87 VNNATARV   94 (103)
T ss_dssp             EEECCSSC
T ss_pred             EEEcccCC
Confidence            99998765

>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=99.85  E-value=6.5e-21  Score=135.72  Aligned_cols=90  Identities=22%  Similarity=0.408  Sum_probs=80.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ...+.++|||+|||+.+++++|+.+|.+||.|..+.++.++.+|.++|||||+|.+.++|.+||..|||..|.|+.|.|.
T Consensus        68 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  147 (165)
T 1rk8_A           68 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD  147 (165)
T ss_dssp             CCC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             EecCcHHHHH
Q 030819          153 IAKSRAELRQ  162 (171)
Q Consensus       153 ~~~~~~~~~~  162 (171)
                      |+.++...+.
T Consensus       148 ~a~~~~~~~~  157 (165)
T 1rk8_A          148 WCFVKGPKRV  157 (165)
T ss_dssp             ESEECC----
T ss_pred             EecCCCCCCC
Confidence            9987665443

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.85  E-value=2.6e-20  Score=124.60  Aligned_cols=84  Identities=21%  Similarity=0.412  Sum_probs=78.9

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ...+.++|||+|||+++++++|+++|.+||.|.++.+..++ +++++|||||+|.+.++|++|+..|||..+.|+.|+|.
T Consensus        11 ~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   89 (114)
T 2do0_A           11 AGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVK   89 (114)
T ss_dssp             CCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEE
Confidence            44567899999999999999999999999999999999998 69999999999999999999999999999999999999


Q ss_pred             EecCc
Q 030819          153 IAKSR  157 (171)
Q Consensus       153 ~~~~~  157 (171)
                      +++..
T Consensus        90 ~a~~~   94 (114)
T 2do0_A           90 MDERA   94 (114)
T ss_dssp             ECSCC
T ss_pred             EcccC
Confidence            98743

>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=99.85  E-value=8e-21  Score=127.38  Aligned_cols=88  Identities=18%  Similarity=0.308  Sum_probs=81.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCe-EEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQL-VEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFV  151 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i-~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v  151 (171)
                      ...+..+|||+|||+++++++|+++|..||.| ..+.++.++ +|+++|||||+|.+.++|++||.. |+..+.|+.|.|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v   88 (114)
T 2cpy_A           11 VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFV   88 (114)
T ss_dssp             CCSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEE
T ss_pred             CCCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEE
Confidence            45567899999999999999999999999999 889999999 999999999999999999999996 999999999999


Q ss_pred             EEecCcHHHHH
Q 030819          152 EIAKSRAELRQ  162 (171)
Q Consensus       152 ~~~~~~~~~~~  162 (171)
                      .++.++.....
T Consensus        89 ~~a~~~~~~~~   99 (114)
T 2cpy_A           89 HVVTLEDMREI   99 (114)
T ss_dssp             EEECHHHHHHH
T ss_pred             EECCHHHHHHH
Confidence            99987765544

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.85  E-value=3.7e-20  Score=125.75  Aligned_cols=85  Identities=25%  Similarity=0.453  Sum_probs=80.2

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ....+++|||+|||+.+++++|+++|++||.|..+.+..++ +|.++|||||+|.+.++|.+|+..|+|..+.|+.|+|.
T Consensus        31 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  109 (124)
T 2kt5_A           31 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQ  109 (124)
T ss_dssp             CCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            45667899999999999999999999999999999999998 99999999999999999999999999999999999999


Q ss_pred             EecCcH
Q 030819          153 IAKSRA  158 (171)
Q Consensus       153 ~~~~~~  158 (171)
                      ++.+..
T Consensus       110 ~a~~~~  115 (124)
T 2kt5_A          110 LVASQI  115 (124)
T ss_dssp             EECCTT
T ss_pred             EeCCCC
Confidence            997643

>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=99.85  E-value=2.1e-20  Score=122.97  Aligned_cols=86  Identities=16%  Similarity=0.306  Sum_probs=78.6

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 030819           72 STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFV  151 (171)
Q Consensus        72 ~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v  151 (171)
                      ....+.++|||+|||+++++++|+++|.+||.|..+.++.++.  .++|||||+|.+.++|++|+..|+|..+.|+.|+|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   87 (103)
T 2cqi_A           10 EDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHT--SNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKV   87 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCC--SSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCC--CCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEE
Confidence            3456789999999999999999999999999999999998863  36899999999999999999999999999999999


Q ss_pred             EEecCcHH
Q 030819          152 EIAKSRAE  159 (171)
Q Consensus       152 ~~~~~~~~  159 (171)
                      .+++++..
T Consensus        88 ~~a~~~~~   95 (103)
T 2cqi_A           88 NWATTPSS   95 (103)
T ss_dssp             EECCCTTC
T ss_pred             EECCCCcc
Confidence            99987653

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.85  E-value=5.9e-21  Score=126.01  Aligned_cols=88  Identities=28%  Similarity=0.522  Sum_probs=82.1

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 030819           72 STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFV  151 (171)
Q Consensus        72 ~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v  151 (171)
                      ....+.++|||+|||+++++++|+++|.+||.|..+.++.++.++.++|||||+|.+.++|++|+.. ++..+.|+.|.|
T Consensus        11 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V   89 (105)
T 2dh8_A           11 SGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDP   89 (105)
T ss_dssp             CCSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEE
Confidence            3456789999999999999999999999999999999999988999999999999999999999998 999999999999


Q ss_pred             EEecCcHHH
Q 030819          152 EIAKSRAEL  160 (171)
Q Consensus       152 ~~~~~~~~~  160 (171)
                      .++.++...
T Consensus        90 ~~a~~~~~~   98 (105)
T 2dh8_A           90 KPCTPRGMQ   98 (105)
T ss_dssp             CCSCCSSCC
T ss_pred             EEccCCCCC
Confidence            999877643

>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=99.85  E-value=1.1e-20  Score=122.86  Aligned_cols=82  Identities=20%  Similarity=0.280  Sum_probs=76.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHH----HHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEE
Q 030819           74 CQPKTRLFVSGLSFRTSEDSLR----NAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVI  149 (171)
Q Consensus        74 ~~~~~~l~V~nl~~~~~~~~l~----~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i  149 (171)
                      ..+.++|||+|||+++++++|+    ++|++||.|.++.++.++.+   +|||||+|.+.++|++|++.|||..+.|+.|
T Consensus         6 ~~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l   82 (96)
T 2dgx_A            6 SGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSKKI   82 (96)
T ss_dssp             CSSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCeEE
Confidence            4457899999999999999999    99999999999999998754   7999999999999999999999999999999


Q ss_pred             EEEEecCcH
Q 030819          150 FVEIAKSRA  158 (171)
Q Consensus       150 ~v~~~~~~~  158 (171)
                      +|.+++++.
T Consensus        83 ~V~~a~~~~   91 (96)
T 2dgx_A           83 LVSLATGAS   91 (96)
T ss_dssp             EEEECCCSS
T ss_pred             EEEEcCCCC
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=99.85  E-value=4.5e-22  Score=152.58  Aligned_cols=151  Identities=19%  Similarity=0.166  Sum_probs=114.0

Q ss_pred             eeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCC------------------
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPP------------------   66 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------------------   66 (171)
                      +.|||+++++++++..+...|...+++...         ........++.++++++.+....                  
T Consensus        96 ~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~---------~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~  166 (284)
T 3smz_A           96 ALLCVANLPPSLTQQQFEELVRPFGSLERC---------FLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRT  166 (284)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHGGGSCEEEE---------EEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHhcCCeeEE---------EEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcE
Confidence            469999999999999999999887765221         11111111222222222221111                  


Q ss_pred             -------CCCCCCCCCCCCeEEEcCCCCCC-CHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHH
Q 030819           67 -------SPHSLSTCQPKTRLFVSGLSFRT-SEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG  138 (171)
Q Consensus        67 -------~~~~~~~~~~~~~l~V~nl~~~~-~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~  138 (171)
                             .........+..+|||+|||+.+ ++++|+++|+.||.|..+.+..+. +|.++|+|||+|.+.++|.+|+..
T Consensus       167 i~v~~a~~~~~~~~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~A~~~  245 (284)
T 3smz_A          167 LYVHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEMAEEAQQQ  245 (284)
T ss_dssp             CEEEECCGGGCCTTTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECS-SCCEEEEEEEECSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCCcccCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECC-CCCcccEEEEEeCCHHHHHHHHHH
Confidence                   11112234567899999999995 999999999999999999999988 899999999999999999999999


Q ss_pred             hCCceeCCeEEEEEEecCcHHHHHhhh
Q 030819          139 MHGKFLDGRVIFVEIAKSRAELRQAFK  165 (171)
Q Consensus       139 l~g~~i~g~~i~v~~~~~~~~~~~~~~  165 (171)
                      |||..+.|+.|+|.++.++...++..+
T Consensus       246 l~g~~~~g~~l~v~~a~~~~~~~~~~~  272 (284)
T 3smz_A          246 ADGLSLGGSHLRVSFCAPGPPGRSMLA  272 (284)
T ss_dssp             HTTCEETTEECEEEECCSSSCHHHHHH
T ss_pred             hCCCccCCeEEEEEEecCCCcccchhh
Confidence            999999999999999998876655444

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.85  E-value=5.9e-21  Score=125.76  Aligned_cols=87  Identities=22%  Similarity=0.424  Sum_probs=81.2

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhc-CCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCce-eCCeEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQG-FGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKF-LDGRVIF  150 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~-~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~-i~g~~i~  150 (171)
                      ...+.++|||+|||+++++++|+++|.+ ||.|..+.++.++ +|.++|||||+|.+.++|.+|+..|+|.. +.|+.|+
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~   83 (104)
T 2dhg_A            5 SSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVR   83 (104)
T ss_dssp             CSSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEE
Confidence            3456789999999999999999999999 9999999999999 99999999999999999999999999999 9999999


Q ss_pred             EEEecCcHHH
Q 030819          151 VEIAKSRAEL  160 (171)
Q Consensus       151 v~~~~~~~~~  160 (171)
                      |.++.++...
T Consensus        84 v~~a~~~~~~   93 (104)
T 2dhg_A           84 LSVAIPKASR   93 (104)
T ss_dssp             CCBCCCCCSC
T ss_pred             EEEccCCCcC
Confidence            9999876543

>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=9.9e-22  Score=124.93  Aligned_cols=83  Identities=18%  Similarity=0.411  Sum_probs=77.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 030819           74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEI  153 (171)
Q Consensus        74 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~  153 (171)
                      ..+.++|||+|||+++++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|++.|||..+.|+.|++.+
T Consensus         2 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~   81 (85)
T 1x4e_A            2 SSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSG   81 (85)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecC
Confidence            35678999999999999999999999999999999999988999999999999999999999999999999999998877


Q ss_pred             ecC
Q 030819          154 AKS  156 (171)
Q Consensus       154 ~~~  156 (171)
                      +++
T Consensus        82 ~~s   84 (85)
T 1x4e_A           82 PSS   84 (85)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            653

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=9.1e-21  Score=126.16  Aligned_cols=85  Identities=31%  Similarity=0.621  Sum_probs=78.5

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q 030819           71 LSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIF  150 (171)
Q Consensus        71 ~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~  150 (171)
                      .....+.++|||+|||.++++++|+++|++||.|..+.+..++  +.++|||||+|.+.++|++|++.|+|..+.|+.|+
T Consensus        23 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~  100 (109)
T 2err_A           23 TENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIE  100 (109)
T ss_dssp             CSCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECE
T ss_pred             ccCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            4456678999999999999999999999999999999999885  34889999999999999999999999999999999


Q ss_pred             EEEecCc
Q 030819          151 VEIAKSR  157 (171)
Q Consensus       151 v~~~~~~  157 (171)
                      |.+++++
T Consensus       101 V~~a~~~  107 (109)
T 2err_A          101 VNNATAR  107 (109)
T ss_dssp             EEECCCS
T ss_pred             EEECCCC
Confidence            9999875

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X

Probab=99.84  E-value=2.4e-20  Score=131.49  Aligned_cols=86  Identities=24%  Similarity=0.451  Sum_probs=81.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ...+.++|||+|||+++++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|++||+.||+..|.|+.|+|.
T Consensus        35 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  114 (156)
T 1h2v_Z           35 LLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTD  114 (156)
T ss_dssp             TTTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            34567899999999999999999999999999999999999899999999999999999999999999999999999999


Q ss_pred             EecCcH
Q 030819          153 IAKSRA  158 (171)
Q Consensus       153 ~~~~~~  158 (171)
                      |+++..
T Consensus       115 ~a~~~~  120 (156)
T 1h2v_Z          115 WDAGFK  120 (156)
T ss_dssp             EESCCC
T ss_pred             ECCCCC
Confidence            997643

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.84  E-value=1.6e-20  Score=121.01  Aligned_cols=84  Identities=24%  Similarity=0.445  Sum_probs=78.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ...+.++|||+|||+++++++|+++|.+||.|..+.+..+  +|.++|||||+|.+.++|++|+..|+|..+.|+.|+|.
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~--~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~   81 (92)
T 2dgv_A            4 GSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVR   81 (92)
T ss_dssp             SSSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            3456789999999999999999999999999999999874  89999999999999999999999999999999999999


Q ss_pred             EecCcH
Q 030819          153 IAKSRA  158 (171)
Q Consensus       153 ~~~~~~  158 (171)
                      ++++..
T Consensus        82 ~a~~~~   87 (92)
T 2dgv_A           82 IDRNAS   87 (92)
T ss_dssp             ECSCCS
T ss_pred             EcCCCC
Confidence            998754

>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=99.84  E-value=4.3e-20  Score=121.44  Aligned_cols=86  Identities=26%  Similarity=0.518  Sum_probs=79.3

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 030819           72 STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFV  151 (171)
Q Consensus        72 ~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v  151 (171)
                      ....+.++|||+|||+++++++|+++|.+||.|..+.++.++.+|+++|||||+|.+.++|++|+.  ++..++|+.|.|
T Consensus        10 ~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~v   87 (103)
T 2cqg_A           10 RAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDC   87 (103)
T ss_dssp             CCCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEE
T ss_pred             CccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEEE
Confidence            345667899999999999999999999999999999999999899999999999999999999998  477999999999


Q ss_pred             EEecCcHH
Q 030819          152 EIAKSRAE  159 (171)
Q Consensus       152 ~~~~~~~~  159 (171)
                      .++.++..
T Consensus        88 ~~a~~~~~   95 (103)
T 2cqg_A           88 KLPNSKQS   95 (103)
T ss_dssp             ECCCTTCC
T ss_pred             EecCCCCc
Confidence            99987654

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.84  E-value=2.8e-21  Score=132.65  Aligned_cols=85  Identities=26%  Similarity=0.418  Sum_probs=79.6

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEE--EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCc----eeCC
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVE--VNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGK----FLDG  146 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~--~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~----~i~g  146 (171)
                      ...+.++|||+|||+++++++|+++|.+||.|..  |+++.|+.+|+++|||||+|.+. +|.+|+..|||.    .+.|
T Consensus        19 ~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~g   97 (131)
T 2m2b_A           19 SENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDG   97 (131)
T ss_dssp             CSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGG
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCC
Confidence            4456789999999999999999999999999976  99999999999999999999999 999999999999    9999


Q ss_pred             eEEEEEEecCcH
Q 030819          147 RVIFVEIAKSRA  158 (171)
Q Consensus       147 ~~i~v~~~~~~~  158 (171)
                      +.|+|.+++++.
T Consensus        98 r~l~V~~a~~~~  109 (131)
T 2m2b_A           98 KTINVEFAKGSK  109 (131)
T ss_dssp             CCCCCEECCCSC
T ss_pred             EEEEEEECCCCC
Confidence            999999998753

>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=99.84  E-value=5e-21  Score=124.07  Aligned_cols=83  Identities=17%  Similarity=0.237  Sum_probs=76.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 030819           74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEI  153 (171)
Q Consensus        74 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~  153 (171)
                      .++.++|||+|||+++++++|+++|.+||.|..+.++.++.+++++|||||+|.+.++|++|++.|||..+.|+.|+|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~   91 (95)
T 2ek1_A           12 KPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSG   91 (95)
T ss_dssp             ---CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEe
Confidence            34568999999999999999999999999999888888888999999999999999999999999999999999999998


Q ss_pred             ecC
Q 030819          154 AKS  156 (171)
Q Consensus       154 ~~~  156 (171)
                      +.+
T Consensus        92 a~s   94 (95)
T 2ek1_A           92 PSS   94 (95)
T ss_dssp             CC-
T ss_pred             ccC
Confidence            764

>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=4.6e-20  Score=118.66  Aligned_cols=83  Identities=20%  Similarity=0.383  Sum_probs=77.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ......+|||+|||+++++++|+++|..| .|..+.++.+ .+|+++|||||+|.+.++|++|+. |||..+.|+.|.|.
T Consensus         6 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~   82 (91)
T 2dgw_A            6 SGTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVF   82 (91)
T ss_dssp             CCCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEE
T ss_pred             CCCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEE
Confidence            44567899999999999999999999999 9999999999 599999999999999999999999 99999999999999


Q ss_pred             EecCcH
Q 030819          153 IAKSRA  158 (171)
Q Consensus       153 ~~~~~~  158 (171)
                      ++.++.
T Consensus        83 ~a~~~~   88 (91)
T 2dgw_A           83 REKSGP   88 (91)
T ss_dssp             EESSCC
T ss_pred             ECCcCC
Confidence            998764

>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=99.84  E-value=6.5e-20  Score=121.82  Aligned_cols=84  Identities=20%  Similarity=0.378  Sum_probs=76.4

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 030819           72 STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFV  151 (171)
Q Consensus        72 ~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v  151 (171)
                      ....+.++|||+|||+++++++|+++|.+||.|..+.+..   ++.++|||||+|.+.++|++|++.||+..+.|+.|+|
T Consensus        17 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   93 (109)
T 1x4a_A           17 PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN---RRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRV   93 (109)
T ss_dssp             CCCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECC---SSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEE---CCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEE
Confidence            3455678999999999999999999999999999999855   4557899999999999999999999999999999999


Q ss_pred             EEecCcH
Q 030819          152 EIAKSRA  158 (171)
Q Consensus       152 ~~~~~~~  158 (171)
                      .+++++.
T Consensus        94 ~~a~~~~  100 (109)
T 1x4a_A           94 EFPRSGR  100 (109)
T ss_dssp             ECCCCCC
T ss_pred             EEcccCC
Confidence            9998764

>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=6.4e-20  Score=122.74  Aligned_cols=84  Identities=25%  Similarity=0.493  Sum_probs=78.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee--------
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFL--------  144 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i--------  144 (171)
                      ...+.++|||+|||+++++++|+++|..||.|..+.++.++ ++.++|||||+|.+.++|++|+..|||..+        
T Consensus        21 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~   99 (114)
T 1x5o_A           21 QEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSA   99 (114)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccC
Confidence            44567899999999999999999999999999999999998 999999999999999999999999999999        


Q ss_pred             CCeEEEEEEecCc
Q 030819          145 DGRVIFVEIAKSR  157 (171)
Q Consensus       145 ~g~~i~v~~~~~~  157 (171)
                      .+++|.|.|+.++
T Consensus       100 ~~~~l~v~~a~p~  112 (114)
T 1x5o_A          100 PTEPLLCKFSGPS  112 (114)
T ss_dssp             CSSCBEEEECCCS
T ss_pred             CCCceeEEccCCC
Confidence            5788999999865

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.84  E-value=1.1e-20  Score=129.08  Aligned_cols=89  Identities=12%  Similarity=0.324  Sum_probs=78.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHH----HHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLR----NAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRV  148 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~----~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~  148 (171)
                      ...+..+|||+|||+.+++++|+    ++|++||.|.+|.+..   +++++|||||+|.+.++|..|+..|||..+.|+.
T Consensus        25 ~~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~---~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~  101 (127)
T 2a3j_A           25 HTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNP  101 (127)
T ss_dssp             CCSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC---CCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc---CCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCE
Confidence            34567899999999999999876    6999999999987743   7889999999999999999999999999999999


Q ss_pred             EEEEEecCcHHHHHhh
Q 030819          149 IFVEIAKSRAELRQAF  164 (171)
Q Consensus       149 i~v~~~~~~~~~~~~~  164 (171)
                      |+|.|++.+.......
T Consensus       102 l~V~~a~~~~~~~~~~  117 (127)
T 2a3j_A          102 LVITFSETPQSQVAED  117 (127)
T ss_dssp             CEEEECCCCCHHHHCC
T ss_pred             EEEEEccCcchhcccc
Confidence            9999999887665433

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.84  E-value=2.9e-20  Score=128.47  Aligned_cols=83  Identities=31%  Similarity=0.561  Sum_probs=78.0

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 030819           72 STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFV  151 (171)
Q Consensus        72 ~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v  151 (171)
                      ....+.++|||+|||+.+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|++|++.|||..+.|+.|+|
T Consensus        58 ~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  137 (140)
T 2ku7_A           58 GSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRV  137 (140)
T ss_dssp             SSCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEE
T ss_pred             CCCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            34567899999999999999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             EEe
Q 030819          152 EIA  154 (171)
Q Consensus       152 ~~~  154 (171)
                      .+|
T Consensus       138 ~~A  140 (140)
T 2ku7_A          138 NLA  140 (140)
T ss_dssp             EC-
T ss_pred             EeC
Confidence            875

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=99.84  E-value=2.2e-20  Score=131.81  Aligned_cols=86  Identities=34%  Similarity=0.632  Sum_probs=81.2

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ......+|||+|||+++++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|++|+..|||..+.|+.|+|.
T Consensus        66 ~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  145 (158)
T 2kn4_A           66 DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQ  145 (158)
T ss_dssp             CCCBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            34567899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             EecCcH
Q 030819          153 IAKSRA  158 (171)
Q Consensus       153 ~~~~~~  158 (171)
                      +++++.
T Consensus       146 ~a~~~~  151 (158)
T 2kn4_A          146 MARYGR  151 (158)
T ss_dssp             EECCSS
T ss_pred             ECCCCC
Confidence            998754

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=1.4e-20  Score=126.45  Aligned_cols=85  Identities=34%  Similarity=0.608  Sum_probs=79.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 030819           74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEI  153 (171)
Q Consensus        74 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~  153 (171)
                      ..+.++|||+|||+++++++|+++|..||.|..+.++.++.++.++|||||+|.+.++|++||.. ++..+.|+.|+|.+
T Consensus        24 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~  102 (116)
T 1x4b_A           24 KEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKR  102 (116)
T ss_dssp             HHHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEEC
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEE
Confidence            34568999999999999999999999999999999999998999999999999999999999997 99999999999999


Q ss_pred             ecCcHH
Q 030819          154 AKSRAE  159 (171)
Q Consensus       154 ~~~~~~  159 (171)
                      +.++..
T Consensus       103 a~~~~~  108 (116)
T 1x4b_A          103 AVAREE  108 (116)
T ss_dssp             CSSCCC
T ss_pred             CCCCcc
Confidence            987754

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.84  E-value=3.5e-20  Score=125.00  Aligned_cols=86  Identities=16%  Similarity=0.202  Sum_probs=79.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCC---eEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQ---LVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVI  149 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~---i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i  149 (171)
                      .....++|||+|||+++++++|+++|..||.   |..+.++.++. |+++|||||+|.+.++|++||+ +|+..+.|+.|
T Consensus        13 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i   90 (118)
T 2db1_A           13 EGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALK-KDRESMGHRYI   90 (118)
T ss_dssp             CBCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEE
Confidence            3456789999999999999999999999999   89999999985 9999999999999999999999 99999999999


Q ss_pred             EEEEecCcHHH
Q 030819          150 FVEIAKSRAEL  160 (171)
Q Consensus       150 ~v~~~~~~~~~  160 (171)
                      +|.++..+...
T Consensus        91 ~V~~a~~~~~~  101 (118)
T 2db1_A           91 EVFKSHRTEMD  101 (118)
T ss_dssp             EEEEECHHHHH
T ss_pred             EEEECCHHHHH
Confidence            99999766533

>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=1e-20  Score=124.61  Aligned_cols=81  Identities=16%  Similarity=0.322  Sum_probs=73.6

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCC--ceeCCeEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHG--KFLDGRVIF  150 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g--~~i~g~~i~  150 (171)
                      .+.+.++|||+|||+++++++|+++|++||.|.++.++.+      +|||||+|.+.++|.+|++.|++  ..+.|++|.
T Consensus        12 ~~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~   85 (105)
T 1sjq_A           12 SGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIY   85 (105)
T ss_dssp             CCCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            4567889999999999999999999999999999999875      49999999999999999998864  689999999


Q ss_pred             EEEecCcHH
Q 030819          151 VEIAKSRAE  159 (171)
Q Consensus       151 v~~~~~~~~  159 (171)
                      |.+++++..
T Consensus        86 V~~A~~~~~   94 (105)
T 1sjq_A           86 IQFSNHKEL   94 (105)
T ss_dssp             BCCCSSSSC
T ss_pred             EEEcCCCCC
Confidence            999987653

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.84  E-value=4.8e-21  Score=118.95  Aligned_cols=75  Identities=29%  Similarity=0.604  Sum_probs=72.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 030819           79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIA  154 (171)
Q Consensus        79 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~  154 (171)
                      +|||+|||+++++++|+++|++||.|..+.+..++.+|.++|||||+|.+.++|++|++ ++|..++|+.|.|.+|
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECCEEEEEEeC
Confidence            58999999999999999999999999999999999899999999999999999999998 9999999999999875

>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=99.84  E-value=1.1e-20  Score=128.39  Aligned_cols=86  Identities=14%  Similarity=0.297  Sum_probs=78.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ......+|||+|||+++++++|+++|..||.|..+.++.+..+|+++|||||+|.+.++|++||. |||..+.|+.|.|.
T Consensus        21 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~   99 (124)
T 1wel_A           21 PHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVH   99 (124)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEE
Confidence            34567899999999999999999999999999886666666699999999999999999999999 99999999999999


Q ss_pred             EecCcHH
Q 030819          153 IAKSRAE  159 (171)
Q Consensus       153 ~~~~~~~  159 (171)
                      ++..+..
T Consensus       100 ~a~~~~~  106 (124)
T 1wel_A          100 PITKKGM  106 (124)
T ss_dssp             EECHHHH
T ss_pred             ECCHHHH
Confidence            9987653

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.83  E-value=3e-20  Score=121.33  Aligned_cols=80  Identities=19%  Similarity=0.248  Sum_probs=72.6

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCce--eCCeEE
Q 030819           72 STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKF--LDGRVI  149 (171)
Q Consensus        72 ~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~--i~g~~i  149 (171)
                      ...+++++|||+|||+++++++|+++|++||.|.++.+++.      ||+|||+|.+.++|.+|++.|++..  +.|++|
T Consensus        16 ~~~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~------kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i   89 (100)
T 3r27_A           16 HKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVLGACNAVNYAADNQIYIAGHPA   89 (100)
T ss_dssp             -CCCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCEEETTEEE
T ss_pred             ccCCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhcCCCceeCCcEE
Confidence            35567899999999999999999999999999999998754      4899999999999999999999875  789999


Q ss_pred             EEEEecCc
Q 030819          150 FVEIAKSR  157 (171)
Q Consensus       150 ~v~~~~~~  157 (171)
                      .|.+++++
T Consensus        90 ~V~~S~~k   97 (100)
T 3r27_A           90 FVNYSTSQ   97 (100)
T ss_dssp             EEEECSCS
T ss_pred             EEEecccc
Confidence            99999875

>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=99.83  E-value=4.4e-22  Score=142.25  Aligned_cols=139  Identities=17%  Similarity=0.223  Sum_probs=104.5

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCCC----------------
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPS----------------   67 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----------------   67 (171)
                      .+.|||+|+++++++..+...|...+....          ..+.....++.++++++.+..+..                
T Consensus        13 ~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~----------~~~~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~   82 (175)
T 1fje_B           13 PFNLFIGNLNPNKSVAELKVAISELFAKND----------LAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNE   82 (175)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHHHHHT----------CCCCEEEEETTTTEEEEEESSHHHHHHHHHGGGEEETTEE
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHHhCCcce----------EEEEECCCCccccEEEEEECCHHHHHHHHhcCCCEeCCeE
Confidence            367999999999999988877766544311          011112233444444443332211                


Q ss_pred             -------CCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC
Q 030819           68 -------PHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMH  140 (171)
Q Consensus        68 -------~~~~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~  140 (171)
                             +.......+..+|||+|||+.+++++|+++|+.||.|..+     ..++.++|||||+|.+.++|.+|+..||
T Consensus        83 l~v~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~A~~A~~~l~  157 (175)
T 1fje_B           83 IKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQ  157 (175)
T ss_dssp             EEEECCCCSSCSTTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-----CSSSSCCSEEEEECSSHHHHHHHHHHHT
T ss_pred             EEEecCCCccccccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-----cCCCCCceEEEEEECCHHHHHHHHHHhC
Confidence                   1112234467899999999999999999999999988766     4488999999999999999999999999


Q ss_pred             CceeCCeEEEEEEecCc
Q 030819          141 GKFLDGRVIFVEIAKSR  157 (171)
Q Consensus       141 g~~i~g~~i~v~~~~~~  157 (171)
                      |..+.|+.|+|.|++++
T Consensus       158 g~~~~g~~i~v~~a~~k  174 (175)
T 1fje_B          158 GAEIDGRSVSLYYTGEK  174 (175)
T ss_dssp             EEEETTEEEEEEECSSC
T ss_pred             CCEECCeEEEEEecCCC
Confidence            99999999999999876

>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=99.83  E-value=1.8e-20  Score=140.09  Aligned_cols=85  Identities=18%  Similarity=0.411  Sum_probs=79.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCC--CeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 030819           76 PKTRLFVSGLSFRTSEDSLRNAFQGFG--QLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEI  153 (171)
Q Consensus        76 ~~~~l~V~nl~~~~~~~~l~~~f~~~G--~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~  153 (171)
                      ..++|||+||++++++++|+++|.+||  .|.+|.|+.++.+|+++|||||+|.+.++|++||+.|||..|.|+.|+|.+
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~  146 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTP  146 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEE
Confidence            567999999999999999999999999  999999999999999999999999999999999999999999999999999


Q ss_pred             ecCcHHH
Q 030819          154 AKSRAEL  160 (171)
Q Consensus       154 ~~~~~~~  160 (171)
                      +++....
T Consensus       147 a~~~~~~  153 (229)
T 3q2s_C          147 VNKQFLS  153 (229)
T ss_dssp             CCHHHHH
T ss_pred             CCCCccc
Confidence            9876544

>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=99.83  E-value=1.7e-20  Score=124.60  Aligned_cols=87  Identities=20%  Similarity=0.315  Sum_probs=79.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCC-eEEEEEe-ecCCCCCcceEEEEEeCCHHHHHHHHHHhC--CceeCCeEE
Q 030819           74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQ-LVEVNLV-MDKIANRPRGFAFLRYATEEESRRAIEGMH--GKFLDGRVI  149 (171)
Q Consensus        74 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~-i~~~~~~-~~~~~g~~~g~~fv~f~~~~~a~~al~~l~--g~~i~g~~i  149 (171)
                      ..+.++|||+|||+++++++|+++|.+||. |..+.++ .++.+|.++|||||+|.+.++|.+|+..|+  +..+.|+.|
T Consensus         5 s~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l   84 (109)
T 2dis_A            5 SSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQI   84 (109)
T ss_dssp             CCCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCC
T ss_pred             ccCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeE
Confidence            345789999999999999999999999998 9999998 788889999999999999999999999996  589999999


Q ss_pred             EEEEecCcHHH
Q 030819          150 FVEIAKSRAEL  160 (171)
Q Consensus       150 ~v~~~~~~~~~  160 (171)
                      +|.+++++...
T Consensus        85 ~V~~a~~~~~~   95 (109)
T 2dis_A           85 AVDWAEPEIDV   95 (109)
T ss_dssp             EEEESCSSCST
T ss_pred             EEEEcCCCCCc
Confidence            99999877643

>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=99.83  E-value=9.6e-20  Score=119.60  Aligned_cols=82  Identities=18%  Similarity=0.264  Sum_probs=73.4

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC--CceeCCeE
Q 030819           71 LSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMH--GKFLDGRV  148 (171)
Q Consensus        71 ~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~--g~~i~g~~  148 (171)
                      ....+++++|||+|||+++++++|+++|++||.|.++.++.+      +|||||+|.+.++|.+|++.|+  +..+.|++
T Consensus         9 ~~~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~   82 (101)
T 2cq1_A            9 KMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQP   82 (101)
T ss_dssp             CCCSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEE
T ss_pred             CccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCcE
Confidence            345567889999999999999999999999999999988765      5999999999999999999874  67899999


Q ss_pred             EEEEEecCcH
Q 030819          149 IFVEIAKSRA  158 (171)
Q Consensus       149 i~v~~~~~~~  158 (171)
                      |.|.+++++.
T Consensus        83 l~V~~a~~~~   92 (101)
T 2cq1_A           83 IYIQYSNHKE   92 (101)
T ss_dssp             CEEEECSCSS
T ss_pred             EEEEEcCccc
Confidence            9999998664

>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=99.83  E-value=2.7e-20  Score=124.22  Aligned_cols=85  Identities=25%  Similarity=0.413  Sum_probs=77.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHH---HHHhcCCCeEEEEEeecCCCC---CcceEEEEEeCCHHHHHHHHHHhCCceeCCe
Q 030819           74 CQPKTRLFVSGLSFRTSEDSLR---NAFQGFGQLVEVNLVMDKIAN---RPRGFAFLRYATEEESRRAIEGMHGKFLDGR  147 (171)
Q Consensus        74 ~~~~~~l~V~nl~~~~~~~~l~---~~f~~~G~i~~~~~~~~~~~g---~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~  147 (171)
                      .....+|||+|||+++++++|+   ++|.+||.|.++.+..++.++   .++|||||+|.+.++|++|++.|||..+.|+
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr   91 (111)
T 2cpi_A           12 VVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGR   91 (111)
T ss_dssp             CCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             ccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCE
Confidence            3457899999999999999999   999999999999999887644   5669999999999999999999999999999


Q ss_pred             EEEEEEecCcH
Q 030819          148 VIFVEIAKSRA  158 (171)
Q Consensus       148 ~i~v~~~~~~~  158 (171)
                      .|+|.++.++.
T Consensus        92 ~l~V~~a~~k~  102 (111)
T 2cpi_A           92 TLKASLGTTKY  102 (111)
T ss_dssp             EEEEESCCCCS
T ss_pred             EEEEEeccccc
Confidence            99999998765

>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=3.7e-20  Score=125.68  Aligned_cols=82  Identities=21%  Similarity=0.509  Sum_probs=77.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 030819           76 PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAK  155 (171)
Q Consensus        76 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~  155 (171)
                      +.++|||+|||+++++++|+++|.+||.|..+.+..++.+|.++|||||+|.+.++|++|+ .|+|..+.|+.|+|.+++
T Consensus        35 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~  113 (124)
T 2jwn_A           35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKR  113 (124)
T ss_dssp             HHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECC
Confidence            4689999999999999999999999999999999999889999999999999999999999 799999999999999998


Q ss_pred             CcH
Q 030819          156 SRA  158 (171)
Q Consensus       156 ~~~  158 (171)
                      +..
T Consensus       114 ~~~  116 (124)
T 2jwn_A          114 TNM  116 (124)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            643

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.83  E-value=9e-21  Score=118.16  Aligned_cols=76  Identities=28%  Similarity=0.587  Sum_probs=73.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 030819           78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIA  154 (171)
Q Consensus        78 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~  154 (171)
                      ++|||+|||+++++++|+++|++||.|..+.+..++.+|+++|||||+|.+.++|++|++.++ ..++|+.|+|.++
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a   76 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            479999999999999999999999999999999999899999999999999999999999999 9999999999986

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.83  E-value=4.3e-20  Score=122.74  Aligned_cols=83  Identities=31%  Similarity=0.497  Sum_probs=73.2

Q ss_pred             CCCCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEE
Q 030819           70 SLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVI  149 (171)
Q Consensus        70 ~~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i  149 (171)
                      ......+.++|||+|||+++++++|+++|++||.|..+.+.        +|||||+|.+.++|++|+..|||..+.|+.|
T Consensus        24 ~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l   95 (108)
T 2jvo_A           24 RQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPL   95 (108)
T ss_dssp             ----CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTEEC
T ss_pred             ccCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCeEE
Confidence            34456778999999999999999999999999999999987        4899999999999999999999999999999


Q ss_pred             EEEEecCcHHH
Q 030819          150 FVEIAKSRAEL  160 (171)
Q Consensus       150 ~v~~~~~~~~~  160 (171)
                      .|.+++++..+
T Consensus        96 ~V~~a~~~~~r  106 (108)
T 2jvo_A           96 EVVYSKLPAKR  106 (108)
T ss_dssp             EEESCSCCC--
T ss_pred             EEEEecCCCCC
Confidence            99999876544

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.83  E-value=2.7e-20  Score=123.05  Aligned_cols=83  Identities=17%  Similarity=0.292  Sum_probs=75.7

Q ss_pred             CCCCCCeEEEcCCCCCC------CHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC
Q 030819           73 TCQPKTRLFVSGLSFRT------SEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDG  146 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~------~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g  146 (171)
                      .....++|||+|||+.+      ++++|+++|++||.|..+.+.  +.+|+++|||||+|.+.++|.+|+..|||..+.|
T Consensus        11 ~~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~--~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g   88 (105)
T 2nlw_A           11 ADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDK   88 (105)
T ss_dssp             CCSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC--CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECST
T ss_pred             CCCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee--CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCC
Confidence            34457899999999999      789999999999999999887  3589999999999999999999999999999999


Q ss_pred             e-EEEEEEecCc
Q 030819          147 R-VIFVEIAKSR  157 (171)
Q Consensus       147 ~-~i~v~~~~~~  157 (171)
                      + .|+|.++...
T Consensus        89 ~~~l~V~~a~~~  100 (105)
T 2nlw_A           89 QHTFRVNLFTDF  100 (105)
T ss_dssp             TCEEEEECSCCC
T ss_pred             CceEEEEEcchH
Confidence            8 9999998754

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.82  E-value=1.1e-19  Score=119.12  Aligned_cols=82  Identities=22%  Similarity=0.473  Sum_probs=74.9

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ...+.++|||+|||+++++++|+++|.+||.|   .++.+ .+++++|||||+|.+.++|++|+..|||..+.|+.|+|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   86 (101)
T 2fc9_A           11 WSGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLE   86 (101)
T ss_dssp             CSCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEE
Confidence            45678999999999999999999999999977   55666 489999999999999999999999999999999999999


Q ss_pred             EecCcH
Q 030819          153 IAKSRA  158 (171)
Q Consensus       153 ~~~~~~  158 (171)
                      +++++.
T Consensus        87 ~a~~~~   92 (101)
T 2fc9_A           87 LQGPRG   92 (101)
T ss_dssp             ECSSCC
T ss_pred             EcCCCC
Confidence            998764

>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=99.82  E-value=9.2e-20  Score=118.82  Aligned_cols=82  Identities=24%  Similarity=0.488  Sum_probs=72.2

Q ss_pred             CCCCCCCCCCeEEEcCCCC-CCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCe
Q 030819           69 HSLSTCQPKTRLFVSGLSF-RTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGR  147 (171)
Q Consensus        69 ~~~~~~~~~~~l~V~nl~~-~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~  147 (171)
                      ......++.++|||+|||+ ++++++|+++|++||.|..+.+.        +|||||+|.+.++|.+|+..|||..+.|+
T Consensus        14 ~~~~~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~   85 (97)
T 2xnq_A           14 LVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGK   85 (97)
T ss_dssp             -----CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTE
T ss_pred             cccCCCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCE
Confidence            3345667789999999998 99999999999999999999883        58999999999999999999999999999


Q ss_pred             EEEEEEecCcH
Q 030819          148 VIFVEIAKSRA  158 (171)
Q Consensus       148 ~i~v~~~~~~~  158 (171)
                      .|+|.+++++.
T Consensus        86 ~l~V~~a~~~~   96 (97)
T 2xnq_A           86 KLILEVSSSNA   96 (97)
T ss_dssp             ECEEEECCCCC
T ss_pred             EEEEEecCCCC
Confidence            99999998753

>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=99.82  E-value=8.7e-20  Score=120.42  Aligned_cols=81  Identities=16%  Similarity=0.272  Sum_probs=72.6

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCc--eeCCeEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGK--FLDGRVIF  150 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~--~i~g~~i~  150 (171)
                      ..++.++|||+|||+++++++|+++|++||.|..+.++.+      +|||||+|.+.++|.+|++.|++.  .+.|++|.
T Consensus        11 ~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~   84 (104)
T 1wex_A           11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAF   84 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            4466789999999999999999999999999999998764      489999999999999999988765  48999999


Q ss_pred             EEEecCcHH
Q 030819          151 VEIAKSRAE  159 (171)
Q Consensus       151 v~~~~~~~~  159 (171)
                      |.+++.+..
T Consensus        85 V~~a~~~~~   93 (104)
T 1wex_A           85 FNYSTSKRI   93 (104)
T ss_dssp             EEECSSSSC
T ss_pred             EEEccCccc
Confidence            999987653

>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=99.82  E-value=8.3e-20  Score=120.47  Aligned_cols=84  Identities=21%  Similarity=0.357  Sum_probs=76.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEE-EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVE-VNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFV  151 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~-~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v  151 (171)
                      ......+|||+|||+++++++|+++|..||.|.. +.++.+ .+|+++|||||+|.+.++|++||.. ++..+.|+.|.|
T Consensus        11 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v   88 (104)
T 1wg5_A           11 DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEI   88 (104)
T ss_dssp             SCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEE
Confidence            4456789999999999999999999999999987 888888 5999999999999999999999997 999999999999


Q ss_pred             EEecCcH
Q 030819          152 EIAKSRA  158 (171)
Q Consensus       152 ~~~~~~~  158 (171)
                      .++..+.
T Consensus        89 ~~~~~~~   95 (104)
T 1wg5_A           89 FKSSRAE   95 (104)
T ss_dssp             EEECTTT
T ss_pred             EECCHHH
Confidence            9987543

>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=9.3e-21  Score=130.78  Aligned_cols=86  Identities=34%  Similarity=0.632  Sum_probs=81.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ...+.++|||+|||+++++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|+..|+|..+.|+.|+|.
T Consensus        43 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~  122 (135)
T 2lea_A           43 DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQ  122 (135)
T ss_dssp             SGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            44567899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             EecCcH
Q 030819          153 IAKSRA  158 (171)
Q Consensus       153 ~~~~~~  158 (171)
                      ++++..
T Consensus       123 ~a~~~~  128 (135)
T 2lea_A          123 MARYGR  128 (135)
T ss_dssp             ECCCCC
T ss_pred             ECCCCC
Confidence            998754

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.82  E-value=1.2e-19  Score=115.02  Aligned_cols=74  Identities=24%  Similarity=0.386  Sum_probs=69.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 030819           76 PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAK  155 (171)
Q Consensus        76 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~  155 (171)
                      .+..|||+||++.+++++|+++|.+||+|.++.+..      ++|||||+|.+.++|++|++.||+..+.|+.|+|.++.
T Consensus         6 ~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~   79 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             CCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             ccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            467899999999999999999999999999999865      46999999999999999999999999999999999993

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.82  E-value=1.4e-19  Score=118.72  Aligned_cols=85  Identities=33%  Similarity=0.603  Sum_probs=77.4

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 030819           72 STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFV  151 (171)
Q Consensus        72 ~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v  151 (171)
                      ....+.++|||+|||+++++++|+++|..|+   .+.++.++.++.++|||||+|.+.++|++|+..|||..+.|+.|+|
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   86 (102)
T 2fc8_A           10 ARSQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTL   86 (102)
T ss_dssp             SSSCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            3456789999999999999999999999874   6777888889999999999999999999999999999999999999


Q ss_pred             EEecCcHH
Q 030819          152 EIAKSRAE  159 (171)
Q Consensus       152 ~~~~~~~~  159 (171)
                      .+++++..
T Consensus        87 ~~a~~~~~   94 (102)
T 2fc8_A           87 DWAKPKGE   94 (102)
T ss_dssp             EECCCCCS
T ss_pred             EEecCCCC
Confidence            99987654

>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=99.82  E-value=3.7e-20  Score=127.82  Aligned_cols=86  Identities=16%  Similarity=0.196  Sum_probs=79.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCC---eEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQ---LVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVI  149 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~---i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i  149 (171)
                      .....++|||+|||+++++++|+++|+.||.   |..+.++.++. |+++|||||+|.+.++|++|++ +|+..+.|+.|
T Consensus        40 ~~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i  117 (136)
T 2hgl_A           40 EGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRESMGHRYI  117 (136)
T ss_dssp             SCCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEE
Confidence            4456789999999999999999999999999   89999999995 9999999999999999999999 99999999999


Q ss_pred             EEEEecCcHHH
Q 030819          150 FVEIAKSRAEL  160 (171)
Q Consensus       150 ~v~~~~~~~~~  160 (171)
                      .|.++.++...
T Consensus       118 ~V~~a~~~e~~  128 (136)
T 2hgl_A          118 EVFKSHRTEMD  128 (136)
T ss_dssp             EEEECCHHHHH
T ss_pred             EEEECChHHHH
Confidence            99998766533

>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=99.82  E-value=1.8e-20  Score=124.31  Aligned_cols=87  Identities=15%  Similarity=0.246  Sum_probs=79.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCC---eEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQ---LVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVI  149 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~---i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i  149 (171)
                      ......+|||+|||+++++++|+++|..||.   |..+.++.++. |+++|||||+|.+.++|++||. +++..+.|+.|
T Consensus         7 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i   84 (107)
T 2lmi_A            7 EVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALE-KHRMYMGQRYV   84 (107)
T ss_dssp             CCSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCC
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEE
Confidence            4566889999999999999999999999988   89999999985 9999999999999999999999 99999999999


Q ss_pred             EEEEecCcHHHH
Q 030819          150 FVEIAKSRAELR  161 (171)
Q Consensus       150 ~v~~~~~~~~~~  161 (171)
                      +|.++.++...+
T Consensus        85 ~V~~a~~~~~~~   96 (107)
T 2lmi_A           85 EVYEINNEDVDA   96 (107)
T ss_dssp             CCEECCHHHHHH
T ss_pred             EEEECCHHHHHH
Confidence            999998766443

>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=99.82  E-value=3.6e-21  Score=123.58  Aligned_cols=82  Identities=26%  Similarity=0.553  Sum_probs=74.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEecCc
Q 030819           78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKSR  157 (171)
Q Consensus        78 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~~~  157 (171)
                      ++|||+|||+++++++|+++|++||.|.++.+..++.+|.++|||||+|.+.+ |.+|+..|||..+.|+.|+|.++.+.
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~~   80 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANPK   80 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC---
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCCC
Confidence            58999999999999999999999999999999999989999999999999999 99999999999999999999999876


Q ss_pred             HHH
Q 030819          158 AEL  160 (171)
Q Consensus       158 ~~~  160 (171)
                      ...
T Consensus        81 ~~~   83 (90)
T 2ki2_A           81 KSL   83 (90)
T ss_dssp             ---
T ss_pred             CCC
Confidence            543

>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=99.82  E-value=3.3e-20  Score=121.90  Aligned_cols=79  Identities=14%  Similarity=0.231  Sum_probs=72.1

Q ss_pred             CCCCCeEEEcCCCC-CCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCc--eeCCeEEE
Q 030819           74 CQPKTRLFVSGLSF-RTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGK--FLDGRVIF  150 (171)
Q Consensus        74 ~~~~~~l~V~nl~~-~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~--~i~g~~i~  150 (171)
                      ..++++|||+|||+ ++++++|+++|++||.|.++.++.++      |||||+|.+.++|.+|++.|++.  .+.|++|.
T Consensus        12 ~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~k------g~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~   85 (102)
T 1x4d_A           12 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI------NEAFIEMATTEDAQAAVDYYTTTPALVFGKPVR   85 (102)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS------SCEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcCC------CEEEEEECCHHHHHHHHHHHcCCCceECCcEEE
Confidence            34688999999999 99999999999999999999998764      89999999999999999999865  59999999


Q ss_pred             EEEecCcH
Q 030819          151 VEIAKSRA  158 (171)
Q Consensus       151 v~~~~~~~  158 (171)
                      |.+++...
T Consensus        86 V~~a~~~~   93 (102)
T 1x4d_A           86 VHLSQKYK   93 (102)
T ss_dssp             EEEECCCT
T ss_pred             EEECCCCC
Confidence            99998654

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ...

Probab=99.82  E-value=2.2e-20  Score=121.41  Aligned_cols=86  Identities=20%  Similarity=0.430  Sum_probs=77.4

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHH----HHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLR----NAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRV  148 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~----~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~  148 (171)
                      ..+++++|||+|||+++++++|+    ++|++||.|..+.+..   +|.++|||||+|.+.++|.+|+..|||..+.|+.
T Consensus         4 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   80 (97)
T 1nu4_A            4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKP   80 (97)
T ss_dssp             --CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcE
Confidence            34568899999999999999999    9999999999998863   6778899999999999999999999999999999


Q ss_pred             EEEEEecCcHHHH
Q 030819          149 IFVEIAKSRAELR  161 (171)
Q Consensus       149 i~v~~~~~~~~~~  161 (171)
                      |+|.+++++....
T Consensus        81 l~v~~a~~~~~~~   93 (97)
T 1nu4_A           81 MRIQYAKTDSDII   93 (97)
T ss_dssp             CEEEECSSCCTHH
T ss_pred             EEEEEccCCCccc
Confidence            9999999876554

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.82  E-value=1.6e-19  Score=114.61  Aligned_cols=77  Identities=29%  Similarity=0.468  Sum_probs=71.6

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHh-CCceeCCeEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM-HGKFLDGRVIFV  151 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l-~g~~i~g~~i~v  151 (171)
                      ...+.++|||+|||+++++++|+++|.+||.|..+.+..+      +|||||+|.+.++|.+|+..| +|..+.|+.|+|
T Consensus         8 ~~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~------kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v   81 (85)
T 2ytc_A            8 EDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNV   81 (85)
T ss_dssp             SCSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTTTCEETTEECCE
T ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC------CCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEE
Confidence            4566789999999999999999999999999999999864      489999999999999999998 999999999999


Q ss_pred             EEec
Q 030819          152 EIAK  155 (171)
Q Consensus       152 ~~~~  155 (171)
                      .|++
T Consensus        82 ~~ak   85 (85)
T 2ytc_A           82 KWGR   85 (85)
T ss_dssp             EECC
T ss_pred             EecC
Confidence            9985

>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=99.82  E-value=1e-20  Score=145.04  Aligned_cols=139  Identities=15%  Similarity=0.195  Sum_probs=113.2

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCCCCCCC------------
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPSPHSL------------   71 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------------   71 (171)
                      .+.|||+|+++++++..+...|...+ +..               ....+.++++++.+..+..+..+            
T Consensus        22 ~~~l~V~nLp~~~te~~l~~~F~~~G-i~~---------------~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~   85 (284)
T 3smz_A           22 RRKILIRGLPGDVTNQEVHDLLSDYE-LKY---------------CFVDKYKGTAFVTLLNGEQAEAAINAFHQSRLRER   85 (284)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHTTTSC-EEE---------------EEEETTTTEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHcC-CEE---------------EEEecCCCEEEEEeCCHHHHHHHHHHcCCCeeCCe
Confidence            36799999999999999999998866 311               11134455555555443322110            


Q ss_pred             ----CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCe
Q 030819           72 ----STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGR  147 (171)
Q Consensus        72 ----~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~  147 (171)
                          ...+...+|||+|||+++++++|+++|..||.|..+.++.++.+|.++|||||+|.+.++|.+|+..|+|..+.|+
T Consensus        86 ~i~v~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~  165 (284)
T 3smz_A           86 ELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPR  165 (284)
T ss_dssp             ECEEEECCCSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             EEEEEecCCCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCc
Confidence                1234568999999999999999999999999999999999988999999999999999999999999999999999


Q ss_pred             EEEEEEecCcH
Q 030819          148 VIFVEIAKSRA  158 (171)
Q Consensus       148 ~i~v~~~~~~~  158 (171)
                      .|.|.++.+..
T Consensus       166 ~i~v~~a~~~~  176 (284)
T 3smz_A          166 TLYVHWTDAGQ  176 (284)
T ss_dssp             ECEEEECCGGG
T ss_pred             EEEEEECCCCC
Confidence            99999997654

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.82  E-value=1.6e-19  Score=133.36  Aligned_cols=89  Identities=21%  Similarity=0.438  Sum_probs=80.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      +..+.++|||+|||+++++++|+++|++||.|.+|.++.++.+++++|||||+|.+.++|.+|+..+++..+.|+.|++.
T Consensus        11 p~~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~   90 (213)
T 4f02_A           11 PSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIM   90 (213)
T ss_dssp             ----CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcccccc
Confidence            34567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EecCcHHHH
Q 030819          153 IAKSRAELR  161 (171)
Q Consensus       153 ~~~~~~~~~  161 (171)
                      ++.......
T Consensus        91 ~~~~~~~~~   99 (213)
T 4f02_A           91 WSQRDPSLR   99 (213)
T ss_dssp             ECCCCTHHH
T ss_pred             ccccccccc
Confidence            988665443

>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=99.82  E-value=8e-20  Score=121.31  Aligned_cols=80  Identities=19%  Similarity=0.302  Sum_probs=73.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC-----eE
Q 030819           74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDG-----RV  148 (171)
Q Consensus        74 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g-----~~  148 (171)
                      ....++|||+|||+++++++|+++|.+||.|..+.++.+       |||||+|.+.++|++||+.|||..+.|     +.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~   84 (108)
T 1x4c_A           12 RRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAY   84 (108)
T ss_dssp             CSCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceE
Confidence            355789999999999999999999999999999999875       799999999999999999999999999     99


Q ss_pred             EEEEEecCcHHH
Q 030819          149 IFVEIAKSRAEL  160 (171)
Q Consensus       149 i~v~~~~~~~~~  160 (171)
                      |+|.++.++...
T Consensus        85 i~V~~a~~~~~~   96 (108)
T 1x4c_A           85 IRVKVDGPRSPS   96 (108)
T ss_dssp             EEEEESSCCSCC
T ss_pred             EEEEeCCCCCCC
Confidence            999999886543

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.82  E-value=4.1e-21  Score=125.93  Aligned_cols=84  Identities=23%  Similarity=0.305  Sum_probs=76.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ...+..+|||+|||+++++++|+++|.+||.|.. .++.++.+|.++|||||+|.+.++|++|++ |||..+.|+.|+|.
T Consensus        13 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~   90 (101)
T 1fj7_A           13 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLE   90 (101)
T ss_dssp             TCSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEE
Confidence            4456789999999999999999999999999887 666777789999999999999999999999 99999999999999


Q ss_pred             EecCcH
Q 030819          153 IAKSRA  158 (171)
Q Consensus       153 ~~~~~~  158 (171)
                      +++++.
T Consensus        91 ~a~~~~   96 (101)
T 1fj7_A           91 KPKGRD   96 (101)
T ss_dssp             CCSCCC
T ss_pred             EcCCCC
Confidence            998764

>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=5.3e-20  Score=122.76  Aligned_cols=84  Identities=18%  Similarity=0.151  Sum_probs=72.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCC-CeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFG-QLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFV  151 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G-~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v  151 (171)
                      .+....+|||+|||+++++++|+++|++|| .|..+.+..    ..++|||||+|.+.++|++|++.|||..+.|+.|+|
T Consensus        24 ~p~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~----~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V   99 (111)
T 2jvr_A           24 LPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNT----RDFDGTGALEFPSEEILVEALERLNNIEFRGSVITV   99 (111)
T ss_dssp             -CCCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSS----CSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEc----CCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEE
Confidence            344578999999999999999999999999 899988753    247899999999999999999999999999999999


Q ss_pred             EEecCcHHH
Q 030819          152 EIAKSRAEL  160 (171)
Q Consensus       152 ~~~~~~~~~  160 (171)
                      .+++.....
T Consensus       100 ~~a~~~p~~  108 (111)
T 2jvr_A          100 ERDDNPPPI  108 (111)
T ss_dssp             EESCC----
T ss_pred             EECCCCCCC
Confidence            999866543

>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=99.81  E-value=1.3e-19  Score=122.14  Aligned_cols=81  Identities=16%  Similarity=0.318  Sum_probs=73.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCC--ceeCCeEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHG--KFLDGRVIF  150 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g--~~i~g~~i~  150 (171)
                      ..+++++|||+|||+++++++|+++|++||.|.++.++.+      +|||||+|.+.++|.+|++.|++  ..+.|++|.
T Consensus        27 ~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~  100 (119)
T 2ad9_A           27 AGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIY  100 (119)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeEEE
Confidence            4456789999999999999999999999999999999876      49999999999999999998874  579999999


Q ss_pred             EEEecCcHH
Q 030819          151 VEIAKSRAE  159 (171)
Q Consensus       151 v~~~~~~~~  159 (171)
                      |.+++++..
T Consensus       101 V~~a~~k~~  109 (119)
T 2ad9_A          101 IQFSNHKEL  109 (119)
T ss_dssp             EEECSSSSC
T ss_pred             EEEccCCCC
Confidence            999987653

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.81  E-value=1.4e-19  Score=120.37  Aligned_cols=83  Identities=20%  Similarity=0.369  Sum_probs=75.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 030819           75 QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIA  154 (171)
Q Consensus        75 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~  154 (171)
                      ....+|||+|||+++++++|+++|+.| .|..+.++.++ .|+++|||||+|.+.++|++|| .+|+..+.|+.|.|..+
T Consensus        14 ~~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a   90 (109)
T 2dnn_A           14 PDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDH-VGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPA   90 (109)
T ss_dssp             HHHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCT-TCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECC-CCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEEC
Confidence            445799999999999999999999999 89999999998 5999999999999999999999 59999999999999988


Q ss_pred             cCcHHH
Q 030819          155 KSRAEL  160 (171)
Q Consensus       155 ~~~~~~  160 (171)
                      ..+.-.
T Consensus        91 ~~~~~~   96 (109)
T 2dnn_A           91 TERQWV   96 (109)
T ss_dssp             CHHHHH
T ss_pred             Cccchh
Confidence            765433

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=3.3e-20  Score=124.25  Aligned_cols=87  Identities=24%  Similarity=0.433  Sum_probs=74.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ...+.++|||+|||+++++++|+++|.+||.|..+.+..+..+++++|||||+|.+.++|++|+..|||..+.|+.|+|.
T Consensus        21 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~  100 (115)
T 2cpx_A           21 PGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIE  100 (115)
T ss_dssp             CCSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            34567899999999999999999999999998433222222278899999999999999999999999999999999999


Q ss_pred             EecCcHH
Q 030819          153 IAKSRAE  159 (171)
Q Consensus       153 ~~~~~~~  159 (171)
                      +++++..
T Consensus       101 ~a~~~~~  107 (115)
T 2cpx_A          101 FGKNKKQ  107 (115)
T ss_dssp             ECCCCSC
T ss_pred             EccCCCC
Confidence            9987653

>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=99.81  E-value=1.1e-19  Score=119.58  Aligned_cols=83  Identities=18%  Similarity=0.306  Sum_probs=75.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ......+|||+|||+++++++|+++|..||. ..+.++.++ +|+++|||||+|.+.++|++||+ +|+..+.|+.|+|.
T Consensus        11 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~-~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~   87 (102)
T 1wez_A           11 QSTTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELF   87 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCc-eEEEEEECC-CCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEE
Confidence            4456789999999999999999999999995 599999998 99999999999999999999995 79999999999999


Q ss_pred             EecCcH
Q 030819          153 IAKSRA  158 (171)
Q Consensus       153 ~~~~~~  158 (171)
                      ++....
T Consensus        88 ~~~~~~   93 (102)
T 1wez_A           88 LNSTAG   93 (102)
T ss_dssp             EECCCC
T ss_pred             ECCCCC
Confidence            887543

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} SCOP: d.58.7.1 PDB: 2f9d_A 2f9j_A 2fho_B

Probab=99.81  E-value=1.7e-19  Score=120.81  Aligned_cols=82  Identities=15%  Similarity=0.353  Sum_probs=75.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 030819           74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEI  153 (171)
Q Consensus        74 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~  153 (171)
                      ++++++|||+|||+++++++|+++|+.||.|..+.++.+   +.++|||||+|.+.++|.+|+..|||..+.|+.|+|.+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   81 (115)
T 3lqv_A            5 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLY   81 (115)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            456789999999999999999999999999999999865   45589999999999999999999999999999999999


Q ss_pred             ecCcH
Q 030819          154 AKSRA  158 (171)
Q Consensus       154 ~~~~~  158 (171)
                      +.++.
T Consensus        82 a~~~~   86 (115)
T 3lqv_A           82 YNANR   86 (115)
T ss_dssp             CCHHH
T ss_pred             ecCCh
Confidence            98644

>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=99.81  E-value=3.5e-19  Score=115.88  Aligned_cols=80  Identities=33%  Similarity=0.517  Sum_probs=73.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC--CeEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLD--GRVIF  150 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~--g~~i~  150 (171)
                      ..++.++|||+|||+++++++|+++|++||.|..+.+..+      +|||||+|.+.++|++|++.|||..+.  |+.|+
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~   86 (97)
T 1why_A           13 KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLR   86 (97)
T ss_dssp             CCCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEE
Confidence            3456789999999999999999999999999999998754      589999999999999999999999999  99999


Q ss_pred             EEEecCcH
Q 030819          151 VEIAKSRA  158 (171)
Q Consensus       151 v~~~~~~~  158 (171)
                      |.+++++.
T Consensus        87 V~~a~~~~   94 (97)
T 1why_A           87 VDFAKSGP   94 (97)
T ss_dssp             EEECCCCC
T ss_pred             EEECCCCC
Confidence            99998764

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.81  E-value=3.1e-19  Score=128.44  Aligned_cols=85  Identities=25%  Similarity=0.453  Sum_probs=80.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ...++++|||+|||+.+++++|+++|.+||.|..|.+..++ ++.++|||||+|.+.++|.+|++.|+|..+.|+.|+|.
T Consensus        84 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~  162 (177)
T 2f3j_A           84 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQ  162 (177)
T ss_dssp             SCTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            44567899999999999999999999999999999999998 99999999999999999999999999999999999999


Q ss_pred             EecCcH
Q 030819          153 IAKSRA  158 (171)
Q Consensus       153 ~~~~~~  158 (171)
                      ++....
T Consensus       163 ~a~~~~  168 (177)
T 2f3j_A          163 LVASQI  168 (177)
T ss_dssp             EESSGG
T ss_pred             EecCCC
Confidence            997654

>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=99.81  E-value=2e-19  Score=117.46  Aligned_cols=80  Identities=30%  Similarity=0.453  Sum_probs=74.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ...+.++|||+|||+++++++|+++|.+||.|..+.+..+      +|||||+|.+.++|++|++.|+|..+.|+.|+|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~   84 (99)
T 2cpj_A           11 TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVR   84 (99)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEE
Confidence            4456789999999999999999999999999999998755      4899999999999999999999999999999999


Q ss_pred             EecCcH
Q 030819          153 IAKSRA  158 (171)
Q Consensus       153 ~~~~~~  158 (171)
                      +++++.
T Consensus        85 ~a~~~~   90 (99)
T 2cpj_A           85 FACHSA   90 (99)
T ss_dssp             ESSCCS
T ss_pred             EcCCCC
Confidence            998764

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.81  E-value=2.1e-19  Score=115.37  Aligned_cols=79  Identities=23%  Similarity=0.501  Sum_probs=73.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ...+.++|||+|||+++++++|+++|.+||.|..+.+.        +|||||+|.+.++|++|+..|||..+.|+.|+|.
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   75 (90)
T 2dnq_A            4 GSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVE   75 (90)
T ss_dssp             CSSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEE
Confidence            34567899999999999999999999999999999986        4899999999999999999999999999999999


Q ss_pred             EecCcHH
Q 030819          153 IAKSRAE  159 (171)
Q Consensus       153 ~~~~~~~  159 (171)
                      +++++..
T Consensus        76 ~a~~~~~   82 (90)
T 2dnq_A           76 ASKNKSK   82 (90)
T ss_dssp             CSSCCCC
T ss_pred             ECCCCCC
Confidence            9987653

>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=99.81  E-value=1.4e-19  Score=120.67  Aligned_cols=81  Identities=15%  Similarity=0.270  Sum_probs=72.0

Q ss_pred             CCCCCCeEEEcCCCCC-CCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCC--ceeCCeEE
Q 030819           73 TCQPKTRLFVSGLSFR-TSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHG--KFLDGRVI  149 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~-~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g--~~i~g~~i  149 (171)
                      ...++++|||+|||++ +++++|+++|++||.|.++.+++.      +|||||+|.+.++|..|++.|++  ..+.|+.|
T Consensus        21 ~~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l   94 (112)
T 1x4f_A           21 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCV   94 (112)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCC
T ss_pred             cCCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEecC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEE
Confidence            4556889999999998 999999999999999999999753      59999999999999999998865  45899999


Q ss_pred             EEEEecCcHH
Q 030819          150 FVEIAKSRAE  159 (171)
Q Consensus       150 ~v~~~~~~~~  159 (171)
                      .|.+++.+..
T Consensus        95 ~V~~a~~~~~  104 (112)
T 1x4f_A           95 KVDLSEKYKK  104 (112)
T ss_dssp             EEEEECSCSS
T ss_pred             EEEECccccc
Confidence            9999986643

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.81  E-value=3.4e-20  Score=116.84  Aligned_cols=73  Identities=19%  Similarity=0.365  Sum_probs=67.7

Q ss_pred             CCeEEEcCCCCCC------CHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCe-EE
Q 030819           77 KTRLFVSGLSFRT------SEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGR-VI  149 (171)
Q Consensus        77 ~~~l~V~nl~~~~------~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~-~i  149 (171)
                      +++|||+|||+.+      ++++|+++|++||.|.++.+.  +.+|+++|||||+|.+.++|.+|+..|||..+.|+ .|
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~--~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l   78 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF   78 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC--CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec--CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeE
Confidence            3689999999999      779999999999999999887  45899999999999999999999999999999998 88


Q ss_pred             EE
Q 030819          150 FV  151 (171)
Q Consensus       150 ~v  151 (171)
                      +|
T Consensus        79 ~V   80 (81)
T 2krb_A           79 RV   80 (81)
T ss_dssp             CC
T ss_pred             Ee
Confidence            76

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.81  E-value=2.8e-19  Score=116.37  Aligned_cols=81  Identities=21%  Similarity=0.381  Sum_probs=72.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      .....++|||+|||+++++++|+++|.+||.|. +.++.    +.++|||||+|.+.++|++|+..|||..+.|+.|+|.
T Consensus        15 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~----~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   89 (97)
T 2e5j_A           15 GAPLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTW----QGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVA   89 (97)
T ss_dssp             SSCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEE----ETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEc----CCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            445578999999999999999999999999996 66654    3577999999999999999999999999999999999


Q ss_pred             EecCcH
Q 030819          153 IAKSRA  158 (171)
Q Consensus       153 ~~~~~~  158 (171)
                      +++++.
T Consensus        90 ~a~~~~   95 (97)
T 2e5j_A           90 LARQQR   95 (97)
T ss_dssp             ECCCCC
T ss_pred             EcCCCC
Confidence            998764

>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=99.81  E-value=2.5e-20  Score=141.71  Aligned_cols=137  Identities=23%  Similarity=0.235  Sum_probs=109.6

Q ss_pred             eeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCCCCCCC-------------
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPSPHSL-------------   71 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------------   71 (171)
                      +.|||+|+++++++..+...|...+++..               ....+.++++++.+..+..+..+             
T Consensus        23 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~---------------v~i~~~kg~afV~f~~~~~A~~A~~~l~g~~i~g~~   87 (261)
T 3sde_A           23 CRLFVGNLPTDITEEDFKRLFERYGEPSE---------------VFINRDRGFGFIRLESRTLAEIAKAELDGTILKSRP   87 (261)
T ss_dssp             GEEEEESCCTTCCHHHHHHHTGGGCCCSE---------------EEEETTTTEEEEECSSHHHHHHHHHHHTTCEETTEE
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCCEEE---------------EEEeCCCcEEEEEECCHHHHHHHHHHcCCcEECCce
Confidence            57999999999999999999999887722               11123456666666544322111             


Q ss_pred             ---CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCC-ceeC--
Q 030819           72 ---STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHG-KFLD--  145 (171)
Q Consensus        72 ---~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g-~~i~--  145 (171)
                         ....++.+|||+|||+.+++++|+++|..||.|..+.++.+. +|.++|||||+|.+.++|.+|+..|++ ..+.  
T Consensus        88 l~v~~a~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~  166 (261)
T 3sde_A           88 LRIRFATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDD-RGRATGKGFVEFAAKPPARKALERCGDGAFLLTT  166 (261)
T ss_dssp             CEEEECCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET-TSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSS
T ss_pred             eEeeecccCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCC-CCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecC
Confidence               122356799999999999999999999999999999999995 999999999999999999999999954 4444  


Q ss_pred             -CeEEEEEEecCc
Q 030819          146 -GRVIFVEIAKSR  157 (171)
Q Consensus       146 -g~~i~v~~~~~~  157 (171)
                       +++|.|.++.+.
T Consensus       167 ~~r~i~v~~~~~~  179 (261)
T 3sde_A          167 TPRPVIVEPMEQF  179 (261)
T ss_dssp             SCCBCEEEECCCE
T ss_pred             CCceEEEeecccc
Confidence             899999998755

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.80  E-value=1.8e-19  Score=118.07  Aligned_cols=78  Identities=22%  Similarity=0.363  Sum_probs=72.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 030819           74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEI  153 (171)
Q Consensus        74 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~  153 (171)
                      ....++|||+|||.++++++|+++|.+||.|.++.+..      ++|||||+|.+.++|.+|+..|||..++|+.|+|.|
T Consensus        24 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   97 (101)
T 2la4_A           24 PPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYP------EKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGW   97 (101)
T ss_dssp             CSSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCB
T ss_pred             CCCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEe
Confidence            34578999999999999999999999999999999873      459999999999999999999999999999999999


Q ss_pred             ecCc
Q 030819          154 AKSR  157 (171)
Q Consensus       154 ~~~~  157 (171)
                      ++++
T Consensus        98 a~~~  101 (101)
T 2la4_A           98 GKER  101 (101)
T ss_dssp             CCCC
T ss_pred             ccCC
Confidence            9864

>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=99.80  E-value=1.9e-20  Score=144.09  Aligned_cols=142  Identities=19%  Similarity=0.221  Sum_probs=104.6

Q ss_pred             eeeecCceeecccchhhcccCCcCC-CCCCCCccccccccccccccccCCCCCCCCCCCCC-------------------
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHS-PAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACL-------------------   64 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------------------   64 (171)
                      +.|||++++++++...+...|...+ ++.......         .. .+..++++++.+..                   
T Consensus       118 ~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~---------~~-~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~  187 (292)
T 2ghp_A          118 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPS---------LR-FNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGY  187 (292)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-----------------CCEEEEECSSHHHHHHHHHHHTTCEETTE
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEe---------CC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCc
Confidence            5799999999999999999999887 553211100         00 01122222222211                   


Q ss_pred             --------CCCCCC--CCCCCCCCeEEEcCCCCC-CCHHHHHHHHhcCCCeEEEEEeecCC-CCCcceEEEEEeCCHHHH
Q 030819           65 --------PPSPHS--LSTCQPKTRLFVSGLSFR-TSEDSLRNAFQGFGQLVEVNLVMDKI-ANRPRGFAFLRYATEEES  132 (171)
Q Consensus        65 --------~~~~~~--~~~~~~~~~l~V~nl~~~-~~~~~l~~~f~~~G~i~~~~~~~~~~-~g~~~g~~fv~f~~~~~a  132 (171)
                              +.....  .....+..+|||+|||+. +++++|+++|..||.|..+.+..+.. +|.++|||||+|.+.++|
T Consensus       188 ~l~v~~a~~~~~~~~~~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A  267 (292)
T 2ghp_A          188 TLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSA  267 (292)
T ss_dssp             ECEEEECCCC---------CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHH
T ss_pred             EEEEEECCCCcccccccccCCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHH
Confidence                    111100  124456789999999999 99999999999999999999999885 499999999999999999


Q ss_pred             HHHHHHhCCceeCCeEEEEEEecCc
Q 030819          133 RRAIEGMHGKFLDGRVIFVEIAKSR  157 (171)
Q Consensus       133 ~~al~~l~g~~i~g~~i~v~~~~~~  157 (171)
                      .+|+ .|||..+.|+.|.|.|++++
T Consensus       268 ~~A~-~l~g~~~~g~~i~V~~a~~k  291 (292)
T 2ghp_A          268 ERAL-QMNRSLLGNREISVSLADKK  291 (292)
T ss_dssp             HHHG-GGTTEEETTEEEEEEECCCC
T ss_pred             HHHH-HhcCCEECCcEEEEEEecCC
Confidence            9999 99999999999999999876

>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=99.80  E-value=2.9e-20  Score=115.30  Aligned_cols=75  Identities=32%  Similarity=0.583  Sum_probs=71.5

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 030819           79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIA  154 (171)
Q Consensus        79 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~  154 (171)
                      +|||+|||+++++++|+++|++||.|..+.+..++.+|.++|||||+|.+.++|++|++ +++..+.|+.|.|.++
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~-~~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHT-TSSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHH-hCCCeECCEEEEEEEC
Confidence            58999999999999999999999999999999999899999999999999999999999 5899999999999875

>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=1.1e-19  Score=117.93  Aligned_cols=82  Identities=21%  Similarity=0.446  Sum_probs=74.0

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 030819           72 STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFV  151 (171)
Q Consensus        72 ~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v  151 (171)
                      ....+.++|||+|||+++++++|+++|..||.|..+     ..++.++|||||+|.+.++|.+|+..|+|..+.|+.|+|
T Consensus        11 ~~~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   85 (96)
T 1fjc_A           11 KKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSL   85 (96)
T ss_dssp             STTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            345567899999999999999999999999988766     237899999999999999999999999999999999999


Q ss_pred             EEecCcH
Q 030819          152 EIAKSRA  158 (171)
Q Consensus       152 ~~~~~~~  158 (171)
                      .++.++.
T Consensus        86 ~~a~~~~   92 (96)
T 1fjc_A           86 YYTGEKG   92 (96)
T ss_dssp             EECSSSC
T ss_pred             EEcCCCC
Confidence            9998764

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.68  E-value=3.5e-21  Score=129.44  Aligned_cols=88  Identities=25%  Similarity=0.413  Sum_probs=81.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEE--------EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC
Q 030819           74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVE--------VNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLD  145 (171)
Q Consensus        74 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~--------~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~  145 (171)
                      ..+.++|||+|||+++++++|+++|.+||.|..        +.++.++.++.++|||||+|.+.++|++|+..|||..+.
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~   83 (116)
T 2lcw_A            4 NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFS   83 (116)
Confidence            356789999999999999999999999999998        899999889999999999999999999999999999999


Q ss_pred             CeEEEEEEecCcHHHH
Q 030819          146 GRVIFVEIAKSRAELR  161 (171)
Q Consensus       146 g~~i~v~~~~~~~~~~  161 (171)
                      |+.|+|.+++++....
T Consensus        84 g~~l~V~~a~~~~~~~   99 (116)
T 2lcw_A           84 GNPIKVSFATRRADFN   99 (116)
Confidence            9999999998876553

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=1.6e-18  Score=113.17  Aligned_cols=79  Identities=30%  Similarity=0.544  Sum_probs=72.2

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcC--CCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEE
Q 030819           72 STCQPKTRLFVSGLSFRTSEDSLRNAFQGF--GQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVI  149 (171)
Q Consensus        72 ~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~--G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i  149 (171)
                      ....+.++|||+|||+.+++++|+++|.+|  |.|..+.+.        +|||||+|.+.++|.+|+..|||..+.|+.|
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   81 (99)
T 2cpd_A           10 DTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKVLDGSPI   81 (99)
T ss_dssp             SCSSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSEEETTEEE
T ss_pred             cccCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEE
Confidence            345567899999999999999999999999  899988764        4799999999999999999999999999999


Q ss_pred             EEEEecCcH
Q 030819          150 FVEIAKSRA  158 (171)
Q Consensus       150 ~v~~~~~~~  158 (171)
                      +|.+++++.
T Consensus        82 ~v~~a~~~~   90 (99)
T 2cpd_A           82 EVTLAKPVD   90 (99)
T ss_dssp             EEECCCCCC
T ss_pred             EEEECCCCC
Confidence            999998765

>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=99.80  E-value=4.3e-19  Score=117.88  Aligned_cols=82  Identities=22%  Similarity=0.558  Sum_probs=75.3

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      .....++|||+|||+.+++++|+++|.+||.|..+.+..+      +|||||+|.+.++|.+|+..|+|..+.|+.|+|.
T Consensus        21 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~------~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   94 (109)
T 1x4g_A           21 SSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCY   94 (109)
T ss_dssp             SCSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            3456789999999999999999999999999999999876      4899999999999999999999999999999999


Q ss_pred             EecCcHHH
Q 030819          153 IAKSRAEL  160 (171)
Q Consensus       153 ~~~~~~~~  160 (171)
                      |++++...
T Consensus        95 ~a~~~~~~  102 (109)
T 1x4g_A           95 WGKESPDM  102 (109)
T ss_dssp             CCCCCCSS
T ss_pred             ecCCCCCC
Confidence            99887643

>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=99.80  E-value=9.3e-19  Score=123.47  Aligned_cols=83  Identities=28%  Similarity=0.505  Sum_probs=79.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 030819           76 PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAK  155 (171)
Q Consensus        76 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~  155 (171)
                      +.++|||+|||+++++++|+++|+.||.|.++.++.++.+|.++|||||+|.+.++|.+|++.|+|..+.|+.|+|.++.
T Consensus         1 s~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~   80 (167)
T 1fxl_A            1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYAR   80 (167)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CcceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecC
Confidence            36799999999999999999999999999999999999899999999999999999999999999999999999999998


Q ss_pred             CcH
Q 030819          156 SRA  158 (171)
Q Consensus       156 ~~~  158 (171)
                      +..
T Consensus        81 ~~~   83 (167)
T 1fxl_A           81 PSS   83 (167)
T ss_dssp             CCC
T ss_pred             CCc
Confidence            654

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.79  E-value=3.1e-19  Score=120.47  Aligned_cols=81  Identities=19%  Similarity=0.279  Sum_probs=73.4

Q ss_pred             CeEEEcCC----CCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCC----HHH----HHHHHH--HhCCce
Q 030819           78 TRLFVSGL----SFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYAT----EEE----SRRAIE--GMHGKF  143 (171)
Q Consensus        78 ~~l~V~nl----~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~----~~~----a~~al~--~l~g~~  143 (171)
                      ..|||+||    |+.+++.+|+.+|+.||+|.++.++.|+.||.++|||||+|.+    +++    |.+|+.  .++|..
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~   82 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCF   82 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCe
Confidence            68999999    9999999999999999999999999999999999999999996    323    888888  789999


Q ss_pred             eCCeEEEEEEecCcH
Q 030819          144 LDGRVIFVEIAKSRA  158 (171)
Q Consensus       144 i~g~~i~v~~~~~~~  158 (171)
                      |+|+.|+|.+.+...
T Consensus        83 I~Gr~irV~ln~~g~   97 (136)
T 2j8a_A           83 IMGFKFEVILNKHSI   97 (136)
T ss_dssp             ETTEEEEEEECCTTH
T ss_pred             ecCcEEEEEECcccH
Confidence            999999999987543

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.79  E-value=8e-20  Score=119.94  Aligned_cols=84  Identities=20%  Similarity=0.461  Sum_probs=76.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 030819           74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEI  153 (171)
Q Consensus        74 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~  153 (171)
                      ....++|||+|||+++++++|+++|+.||.|..+.++.++ +|+++|||||+|.+.++|++|+.  ++..++|+.|.|.+
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~   82 (102)
T 2xs2_A            6 KIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGP   82 (102)
T ss_dssp             EEEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEE
Confidence            3456899999999999999999999999999999999998 99999999999999999999998  99999999999999


Q ss_pred             ecCcHHH
Q 030819          154 AKSRAEL  160 (171)
Q Consensus       154 ~~~~~~~  160 (171)
                      +.++...
T Consensus        83 a~~~~~~   89 (102)
T 2xs2_A           83 AIRKQNL   89 (102)
T ss_dssp             EEECC--
T ss_pred             CCcCcch
Confidence            8766544

>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=99.79  E-value=2.9e-19  Score=117.56  Aligned_cols=80  Identities=30%  Similarity=0.490  Sum_probs=72.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ...+.++|||+|||+++++++|+++|.+||.|..+.+.        +|||||+|.+.++|++|++.|||..+.|+.|+|.
T Consensus         7 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   78 (103)
T 2dgu_A            7 GMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIV   78 (103)
T ss_dssp             CCCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEE
Confidence            34567899999999999999999999999999999886        3699999999999999999999999999999999


Q ss_pred             EecCcHHH
Q 030819          153 IAKSRAEL  160 (171)
Q Consensus       153 ~~~~~~~~  160 (171)
                      +++++...
T Consensus        79 ~a~~~~~~   86 (103)
T 2dgu_A           79 FAKPPDQK   86 (103)
T ss_dssp             ECCCCCCC
T ss_pred             EcCCCccc
Confidence            99876543

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=1.4e-18  Score=111.90  Aligned_cols=78  Identities=26%  Similarity=0.533  Sum_probs=72.4

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ...+.++|||+|||+++++++|+++|++||.|..+.+..        +||||+|.+.++|.+|+..|||..+.|+.|+|.
T Consensus         6 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   77 (92)
T 2dgt_A            6 SGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQ   77 (92)
T ss_dssp             CCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECS--------SEEEEEESCHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEE
Confidence            456678999999999999999999999999999999863        599999999999999999999999999999999


Q ss_pred             EecCcH
Q 030819          153 IAKSRA  158 (171)
Q Consensus       153 ~~~~~~  158 (171)
                      +++++.
T Consensus        78 ~a~~~~   83 (92)
T 2dgt_A           78 LSTSRL   83 (92)
T ss_dssp             ESSCCC
T ss_pred             EccCCC
Confidence            998764

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens}

Probab=99.79  E-value=5e-20  Score=128.07  Aligned_cols=86  Identities=22%  Similarity=0.406  Sum_probs=74.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEE------EEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCe
Q 030819           74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEV------NLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGR  147 (171)
Q Consensus        74 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~------~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~  147 (171)
                      ..+.++|||+|||+++++++|+.+|..||.|..+      .+.. ..+|.++|||||+|.+.++|.+|+..|||..+.|+
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~-~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~  120 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRL-MKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGK  120 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEE-EEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEe-ccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCc
Confidence            4567899999999999999999999999998764      1111 23789999999999999999999999999999999


Q ss_pred             EEEEEEecCcHHH
Q 030819          148 VIFVEIAKSRAEL  160 (171)
Q Consensus       148 ~i~v~~~~~~~~~  160 (171)
                      .|.|.++++...+
T Consensus       121 ~l~V~~a~~~~~~  133 (143)
T 3egn_A          121 PMVVQFARSARPK  133 (143)
T ss_dssp             ECEEEECCCSCC-
T ss_pred             EEEEEECCCCCCc
Confidence            9999999765433

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=3.8e-19  Score=120.68  Aligned_cols=85  Identities=21%  Similarity=0.298  Sum_probs=76.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCCe----EEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q 030819           75 QPKTRLFVSGLSFRTSEDSLRNAFQGFGQL----VEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIF  150 (171)
Q Consensus        75 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i----~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~  150 (171)
                      .+..+|||+|||+++++++|+++|++||.|    ..+.++.++ +|+++|||||+|.+.++|++||.. |+..+.|+.|.
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~-~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~   98 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP-DGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIE   98 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECT-TSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECC-CCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEE
Confidence            457899999999999999999999999975    689999886 899999999999999999999995 99999999999


Q ss_pred             EEEecCcHHHH
Q 030819          151 VEIAKSRAELR  161 (171)
Q Consensus       151 v~~~~~~~~~~  161 (171)
                      |..+..+...+
T Consensus        99 V~~a~~~e~~~  109 (123)
T 2dha_A           99 LFRSTAAEVQQ  109 (123)
T ss_dssp             CEEECHHHHHH
T ss_pred             EEECCHHHHHH
Confidence            99987665443

>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=99.79  E-value=8.1e-19  Score=124.11  Aligned_cols=83  Identities=23%  Similarity=0.388  Sum_probs=79.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 030819           76 PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAK  155 (171)
Q Consensus        76 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~  155 (171)
                      ++++|||+|||+++++++|+++|+.||.|.++.++.++.+|.++|||||+|.+.++|.+|++.|+|..+.|+.|.|.++.
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~   81 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYAR   81 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecC
Confidence            46899999999999999999999999999999999998899999999999999999999999999999999999999988


Q ss_pred             CcH
Q 030819          156 SRA  158 (171)
Q Consensus       156 ~~~  158 (171)
                      +..
T Consensus        82 ~~~   84 (168)
T 1b7f_A           82 PGG   84 (168)
T ss_dssp             CCS
T ss_pred             CCc
Confidence            654

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A

Probab=99.79  E-value=5.1e-19  Score=123.90  Aligned_cols=82  Identities=24%  Similarity=0.501  Sum_probs=75.5

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 030819           72 STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFV  151 (171)
Q Consensus        72 ~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v  151 (171)
                      ....+.++|||+|||+++++++|+++|++||.|.++.++.+     ++|||||+|.+.++|.+|+..|||..+.|+.|+|
T Consensus        68 ~~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  142 (150)
T 2i2y_A           68 DSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRV  142 (150)
T ss_dssp             SSSTTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEE
Confidence            34566789999999999999999999999999999999876     4699999999999999999999999999999999


Q ss_pred             EEecCcH
Q 030819          152 EIAKSRA  158 (171)
Q Consensus       152 ~~~~~~~  158 (171)
                      .+++++.
T Consensus       143 ~~a~~~~  149 (150)
T 2i2y_A          143 ELSNGEK  149 (150)
T ss_dssp             EECCCCC
T ss_pred             EEcCCCC
Confidence            9998763

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.79  E-value=3.1e-19  Score=116.01  Aligned_cols=80  Identities=26%  Similarity=0.547  Sum_probs=71.1

Q ss_pred             CCCCCCeEEEcCCCC-CCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 030819           73 TCQPKTRLFVSGLSF-RTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFV  151 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~-~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v  151 (171)
                      ..++.++|||+|||+ .+++++|+++|.+||.|..+.+.        +|||||+|.+.++|.+|+..|+|..+.|+.|+|
T Consensus         6 ~~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   77 (96)
T 2kvi_A            6 NIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLIL   77 (96)
T ss_dssp             ---CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCE
T ss_pred             cCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEE
Confidence            456788999999998 99999999999999999999884        589999999999999999999999999999999


Q ss_pred             EEecCcHHH
Q 030819          152 EIAKSRAEL  160 (171)
Q Consensus       152 ~~~~~~~~~  160 (171)
                      .+++++...
T Consensus        78 ~~a~~~~~~   86 (96)
T 2kvi_A           78 EVSSSNARP   86 (96)
T ss_dssp             EEEECCCC-
T ss_pred             EEcCcCCCC
Confidence            999766543

>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=1.1e-18  Score=141.59  Aligned_cols=86  Identities=30%  Similarity=0.645  Sum_probs=80.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ...+.++|||+|||+.+++++|..+|.+||.|..|.|+.++.+|+++|||||+|.+.++|.+||..|||..|.|+.|.|.
T Consensus        98 ~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~  177 (437)
T 3pgw_S           98 QGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD  177 (437)
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             EecCcH
Q 030819          153 IAKSRA  158 (171)
Q Consensus       153 ~~~~~~  158 (171)
                      ++.++.
T Consensus       178 ~a~~~~  183 (437)
T 3pgw_S          178 VERGRT  183 (437)
T ss_pred             EeCCCC
Confidence            998653

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.78  E-value=7.2e-20  Score=119.94  Aligned_cols=76  Identities=26%  Similarity=0.545  Sum_probs=71.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEecCc
Q 030819           78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKSR  157 (171)
Q Consensus        78 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~~~  157 (171)
                      ++|||+|||+++++++|+++|++||.|..+.+..+     ++|||||+|.+.++|++|++.|+|..+.|+.|+|.+++++
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   75 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGM   75 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS-----SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC-----CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCC
Confidence            48999999999999999999999999999999876     5699999999999999999999999999999999999876


Q ss_pred             H
Q 030819          158 A  158 (171)
Q Consensus       158 ~  158 (171)
                      .
T Consensus        76 ~   76 (101)
T 2hvz_A           76 P   76 (101)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.78  E-value=1.6e-18  Score=115.21  Aligned_cols=78  Identities=22%  Similarity=0.529  Sum_probs=71.3

Q ss_pred             CCCCCCeEEEcCCCCC-CCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 030819           73 TCQPKTRLFVSGLSFR-TSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFV  151 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~-~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v  151 (171)
                      .....++|||+|||++ +++++|+++|.+||.|..+.+        ++|||||+|.+.++|++|++.|+|..+.|+.|+|
T Consensus        23 ~~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   94 (110)
T 1wf1_A           23 PKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDI   94 (110)
T ss_dssp             CTTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCE
T ss_pred             CCCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEE
Confidence            3445689999999999 999999999999999999988        3589999999999999999999999999999999


Q ss_pred             EEecCcH
Q 030819          152 EIAKSRA  158 (171)
Q Consensus       152 ~~~~~~~  158 (171)
                      .++++..
T Consensus        95 ~~a~~~~  101 (110)
T 1wf1_A           95 NMAGEPK  101 (110)
T ss_dssp             EESCCCC
T ss_pred             EECCCCC
Confidence            9998543

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.78  E-value=1.6e-18  Score=111.17  Aligned_cols=78  Identities=26%  Similarity=0.488  Sum_probs=72.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ...+.++|||+|||+++++++|+++|++||.|..+.+..        +||||+|.+.++|++|+..|||..+.|+.|+|.
T Consensus         5 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   76 (90)
T 2dnp_A            5 SSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK--------DYAFVHMEKEADAKAAIAQLNGKEVKGKRINVE   76 (90)
T ss_dssp             SSCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECS--------SCEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            445678999999999999999999999999999999863        599999999999999999999999999999999


Q ss_pred             EecCcH
Q 030819          153 IAKSRA  158 (171)
Q Consensus       153 ~~~~~~  158 (171)
                      +++++.
T Consensus        77 ~a~~~~   82 (90)
T 2dnp_A           77 LSTKGQ   82 (90)
T ss_dssp             ESCCCC
T ss_pred             ECCCCC
Confidence            998764

>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=4.2e-19  Score=118.44  Aligned_cols=75  Identities=21%  Similarity=0.238  Sum_probs=69.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 030819           76 PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAK  155 (171)
Q Consensus        76 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~  155 (171)
                      ..++|||+|||+++++++|+++|.+||.|..+.+..      ++|||||+|.+.++|++|+..|||..+.|+.|.|.|++
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   82 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAP   82 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            467999999999999999999999999999998864      45899999999999999999999999999999999987


Q ss_pred             C
Q 030819          156 S  156 (171)
Q Consensus       156 ~  156 (171)
                      .
T Consensus        83 ~   83 (111)
T 1whx_A           83 I   83 (111)
T ss_dssp             T
T ss_pred             C
Confidence            4

>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=99.78  E-value=6.5e-19  Score=113.65  Aligned_cols=80  Identities=28%  Similarity=0.421  Sum_probs=70.6

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCC-eEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCC-ceeCCeEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQ-LVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHG-KFLDGRVIF  150 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~-i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g-~~i~g~~i~  150 (171)
                      ...+.++|||+|||+++++++|+++|.+||. |..+.+.       ++|||||+|.+.++|++|++.||| ..+.|+.|+
T Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~   76 (93)
T 2cqh_A            4 GSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIME   76 (93)
T ss_dssp             CCCCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEE
Confidence            3456789999999999999999999999999 6655552       358999999999999999999999 999999999


Q ss_pred             EEEecCcHH
Q 030819          151 VEIAKSRAE  159 (171)
Q Consensus       151 v~~~~~~~~  159 (171)
                      |.+++++..
T Consensus        77 v~~a~~~~~   85 (93)
T 2cqh_A           77 VDYSVSKKL   85 (93)
T ss_dssp             EEECCCCCC
T ss_pred             EEEccCccc
Confidence            999987653

>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=99.78  E-value=3.7e-19  Score=136.17  Aligned_cols=78  Identities=26%  Similarity=0.383  Sum_probs=71.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC-CeEEEEE
Q 030819           74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLD-GRVIFVE  152 (171)
Q Consensus        74 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~-g~~i~v~  152 (171)
                      ..+.++|||+|||..+++++|+++|++||.|.++.+..++     +|||||+|.+.++|.+|+..|||..+. |+.|+|.
T Consensus       204 ~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~  278 (282)
T 3pgw_A          204 NPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKIS  278 (282)
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC-----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEE
Confidence            3467899999999999999999999999999999998654     489999999999999999999999998 9999999


Q ss_pred             EecC
Q 030819          153 IAKS  156 (171)
Q Consensus       153 ~~~~  156 (171)
                      |++.
T Consensus       279 ~akk  282 (282)
T 3pgw_A          279 FAKK  282 (282)
T ss_pred             EecC
Confidence            9863

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.77  E-value=1.3e-18  Score=112.88  Aligned_cols=81  Identities=14%  Similarity=0.231  Sum_probs=73.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEE-EeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVN-LVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFV  151 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~-~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v  151 (171)
                      .....++|||+|||+++++++|+++|.+||.|..++ ++.++.++    .|||+|.+.++|.+|+..|||..+.|+.|+|
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~----~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V   86 (96)
T 2e44_A           11 KRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETA----VVNVTYSSKDQARQALDKLNGFQLENFTLKV   86 (96)
T ss_dssp             CCCSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSE----EEEEEESSHHHHHHHHHHHTTCBCSSCBCEE
T ss_pred             CCCCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCC----EEEEEECCHHHHHHHHHHhCCCEECCcEEEE
Confidence            334578999999999999999999999999999994 77776443    4999999999999999999999999999999


Q ss_pred             EEecCc
Q 030819          152 EIAKSR  157 (171)
Q Consensus       152 ~~~~~~  157 (171)
                      .++.++
T Consensus        87 ~~a~~~   92 (96)
T 2e44_A           87 AYIPDE   92 (96)
T ss_dssp             EECCCC
T ss_pred             EEcCcc
Confidence            999876

>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=99.77  E-value=6.2e-19  Score=120.02  Aligned_cols=82  Identities=22%  Similarity=0.368  Sum_probs=73.9

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeE--EEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLV--EVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIF  150 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~--~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~  150 (171)
                      ......+|||+|||+++++++|+++|+.| .|.  .+.++.++. |+++|||||+|.+.++|++|++ +++..+.|+.|.
T Consensus        38 ~~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~-~~~~~l~gR~I~  114 (126)
T 2hgm_A           38 DSANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALG-KHKERIGHRYIE  114 (126)
T ss_dssp             CSSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHT-TTTCCBTTBCCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHH-HCCCEECCEEEE
Confidence            34567899999999999999999999999 677  899999985 9999999999999999999998 578999999999


Q ss_pred             EEEecCc
Q 030819          151 VEIAKSR  157 (171)
Q Consensus       151 v~~~~~~  157 (171)
                      |..+..+
T Consensus       115 V~~a~~~  121 (126)
T 2hgm_A          115 VFKSSQE  121 (126)
T ss_dssp             CEEECHH
T ss_pred             EEECCHH
Confidence            9988643

>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=99.77  E-value=2.6e-18  Score=124.44  Aligned_cols=87  Identities=37%  Similarity=0.604  Sum_probs=78.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ...+.++|||+|||+++++++|+++|+.||.|.++.++.++.+|.++|||||+|.+.++|.+|+.. ++..+.|+.|.|.
T Consensus         9 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v~   87 (196)
T 1l3k_A            9 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPK   87 (196)
T ss_dssp             CCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeeee
Confidence            455678999999999999999999999999999999999998999999999999999999999985 9999999999999


Q ss_pred             EecCcHHH
Q 030819          153 IAKSRAEL  160 (171)
Q Consensus       153 ~~~~~~~~  160 (171)
                      ++.+....
T Consensus        88 ~~~~~~~~   95 (196)
T 1l3k_A           88 RAVSREDS   95 (196)
T ss_dssp             ECCC----
T ss_pred             cccCcccc
Confidence            99876543

>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=99.77  E-value=8e-20  Score=140.56  Aligned_cols=146  Identities=15%  Similarity=0.195  Sum_probs=106.0

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCCCCCCC------------
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPSPHSL------------   71 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------------   71 (171)
                      .+.|||+++++++++..+...|...+++..         .......  ...++++++.+..+..+..+            
T Consensus        41 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~---------v~i~~~~--~~~~g~afV~f~~~~~A~~A~~~~~~~~~g~~  109 (292)
T 2ghp_A           41 LTTVLVKNLPKSYNQNKVYKYFKHCGPIIH---------VDVADSL--KKNFRFARIEFARYDGALAAITKTHKVVGQNE  109 (292)
T ss_dssp             -CEEEEEEECTTCCHHHHHHHHGGGSCEEE---------EEEEECT--TSSSEEEEEEESSHHHHHHHHTTTTCEETTEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEE---------EEEEECC--CCCcEEEEEEECCHHHHHHHHHhCCcEeCCcE
Confidence            467999999999999999999998876621         1111111  11245555555433321110            


Q ss_pred             --CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCC-CeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeE
Q 030819           72 --STCQPKTRLFVSGLSFRTSEDSLRNAFQGFG-QLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRV  148 (171)
Q Consensus        72 --~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G-~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~  148 (171)
                        ......++|||+|||+.+++++|+++|..|| .|..+.++.++ .|.++|||||+|.+.++|.+|+..|+|..+.|+.
T Consensus       110 i~v~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~-~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~  188 (292)
T 2ghp_A          110 IIVSHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLR-FNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYT  188 (292)
T ss_dssp             CEEEECCSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC--------CCEEEEECSSHHHHHHHHHHHTTCEETTEE
T ss_pred             EEEEECCCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcE
Confidence              1123578999999999999999999999999 99999999888 4889999999999999999999999999999999


Q ss_pred             EEEEEecCcHHHH
Q 030819          149 IFVEIAKSRAELR  161 (171)
Q Consensus       149 i~v~~~~~~~~~~  161 (171)
                      |.|.++.+.....
T Consensus       189 l~v~~a~~~~~~~  201 (292)
T 2ghp_A          189 LVTKVSNPLEKSK  201 (292)
T ss_dssp             CEEEECCCC----
T ss_pred             EEEEECCCCcccc
Confidence            9999998776543

>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=99.77  E-value=3.6e-18  Score=109.52  Aligned_cols=79  Identities=19%  Similarity=0.388  Sum_probs=63.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCce--eCCeEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKF--LDGRVIF  150 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~--i~g~~i~  150 (171)
                      ...+..+|||+|||+++++++|+++|++||.|.++.++.+     ++|||||+|.+.++|++    ++|..  +.|+.|.
T Consensus         7 ~~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~   77 (89)
T 3d2w_A            7 HHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQS----LCGEDLIIKGISVH   77 (89)
T ss_dssp             ----CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHH----HTTCEEEETTEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHH----HcCCCcccCCEEEE
Confidence            4566789999999999999999999999999999999764     67999999999999883    56665  4699999


Q ss_pred             EEEecCcHHH
Q 030819          151 VEIAKSRAEL  160 (171)
Q Consensus       151 v~~~~~~~~~  160 (171)
                      |.++.++...
T Consensus        78 v~~a~~k~~~   87 (89)
T 3d2w_A           78 ISNAEPKHNK   87 (89)
T ss_dssp             EEECC-----
T ss_pred             EEEcCCCCcC
Confidence            9999887643

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=1.2e-17  Score=108.62  Aligned_cols=79  Identities=25%  Similarity=0.480  Sum_probs=71.3

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ...+.++|||+||  ++++++|+++|.+||.|..+.+.      .++|||||+|.+.++|.+|+..|+|..+.|+.|+|.
T Consensus        11 ~~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~   82 (97)
T 1x5p_A           11 APRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVN   82 (97)
T ss_dssp             CCCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            4456789999996  89999999999999999999884      456899999999999999999999999999999999


Q ss_pred             EecCcHH
Q 030819          153 IAKSRAE  159 (171)
Q Consensus       153 ~~~~~~~  159 (171)
                      +++++..
T Consensus        83 ~a~~~~~   89 (97)
T 1x5p_A           83 IARKQPM   89 (97)
T ss_dssp             CCSSCCC
T ss_pred             ECCCCCC
Confidence            9987653

>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=99.76  E-value=3.1e-18  Score=109.47  Aligned_cols=76  Identities=16%  Similarity=0.298  Sum_probs=70.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 030819           75 QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIA  154 (171)
Q Consensus        75 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~  154 (171)
                      ...++|||+|||+++++++|+++|.+| .|.++.+.      +++|||||+|.+.++|++|++.|||..+.|+.|+|.++
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a   75 (88)
T 1wg1_A            3 SGSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQ   75 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe------CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEc
Confidence            356899999999999999999999999 99999884      56799999999999999999999999999999999998


Q ss_pred             cCc
Q 030819          155 KSR  157 (171)
Q Consensus       155 ~~~  157 (171)
                      ...
T Consensus        76 ~~~   78 (88)
T 1wg1_A           76 PTD   78 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            653

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.76  E-value=1.5e-17  Score=112.74  Aligned_cols=75  Identities=13%  Similarity=0.234  Sum_probs=67.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceE-EEEEeCCHHHHHHHHHHhCCceeCC--eEEEEEEe
Q 030819           78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGF-AFLRYATEEESRRAIEGMHGKFLDG--RVIFVEIA  154 (171)
Q Consensus        78 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~-~fv~f~~~~~a~~al~~l~g~~i~g--~~i~v~~~  154 (171)
                      ..|||+||++.+++++|+++|++||.|.++.+.. +     .|| |||+|.+.++|..|++.|||..|.|  +.|+|.++
T Consensus        26 l~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~-~-----~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~A   99 (124)
T 2e5i_A           26 LLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFK-R-----NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYA   99 (124)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEE-S-----SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECC
T ss_pred             EEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEe-C-----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEe
Confidence            3468999999999999999999999999999864 2     176 9999999999999999999999987  68999999


Q ss_pred             cCcH
Q 030819          155 KSRA  158 (171)
Q Consensus       155 ~~~~  158 (171)
                      +++.
T Consensus       100 k~~~  103 (124)
T 2e5i_A          100 RPTR  103 (124)
T ss_dssp             SCSC
T ss_pred             cCCc
Confidence            8764

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.76  E-value=3.8e-18  Score=110.32  Aligned_cols=78  Identities=23%  Similarity=0.322  Sum_probs=70.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 030819           75 QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIA  154 (171)
Q Consensus        75 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~  154 (171)
                      ...++|||+|||+++++++|+++|.+||.|.++  +.++.+|.   ||||+|.+.++|++|+. |+|..++|+.|.|.++
T Consensus         6 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a   79 (94)
T 2e5g_A            6 SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPR   79 (94)
T ss_dssp             TTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECCCBCS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEEC
Confidence            346799999999999999999999999999987  55665665   99999999999999999 9999999999999988


Q ss_pred             cCcH
Q 030819          155 KSRA  158 (171)
Q Consensus       155 ~~~~  158 (171)
                      .++.
T Consensus        80 ~~~~   83 (94)
T 2e5g_A           80 EQKE   83 (94)
T ss_dssp             CCSC
T ss_pred             CcCC
Confidence            7654

>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=99.76  E-value=3.2e-19  Score=123.47  Aligned_cols=84  Identities=20%  Similarity=0.290  Sum_probs=75.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ......+|||+|||+++++++|+++|++|| |..+.++.++. |+++|||||+|.+.++|++|| .+|+..+.|+.|+|.
T Consensus        42 ~~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~-g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~  118 (139)
T 2hgn_A           42 QSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELF  118 (139)
T ss_dssp             ---CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSS-SCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCC-CCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEE
Confidence            345578999999999999999999999999 77999999984 999999999999999999999 689999999999999


Q ss_pred             EecCcHH
Q 030819          153 IAKSRAE  159 (171)
Q Consensus       153 ~~~~~~~  159 (171)
                      .+.....
T Consensus       119 ~a~~~~~  125 (139)
T 2hgn_A          119 LNSTTGA  125 (139)
T ss_dssp             ECCCSCC
T ss_pred             ECCCCCC
Confidence            9876543

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=2.7e-18  Score=114.59  Aligned_cols=78  Identities=23%  Similarity=0.376  Sum_probs=69.6

Q ss_pred             CCCCCeEEE--cCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee-----CC
Q 030819           74 CQPKTRLFV--SGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFL-----DG  146 (171)
Q Consensus        74 ~~~~~~l~V--~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i-----~g  146 (171)
                      ..+..+|||  +||++++++++|+++|++||.|..+.+..+      +|||||+|.+.++|++|++.|||..+     .|
T Consensus        22 ~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~------rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g   95 (114)
T 2cq2_A           22 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQK   95 (114)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEEECTTSCE
T ss_pred             CCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHhCCCEEccccCCC
Confidence            345789999  789999999999999999999999887643      58999999999999999999999988     68


Q ss_pred             eEEEEEEecCc
Q 030819          147 RVIFVEIAKSR  157 (171)
Q Consensus       147 ~~i~v~~~~~~  157 (171)
                      .+|.|.+++..
T Consensus        96 ~~l~v~~a~~~  106 (114)
T 2cq2_A           96 ITLYLNFVEKV  106 (114)
T ss_dssp             EECEEEEESCC
T ss_pred             cEEEEEecccC
Confidence            89999998743

>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=99.75  E-value=5.7e-18  Score=119.62  Aligned_cols=79  Identities=20%  Similarity=0.345  Sum_probs=71.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC--eEEEEEE
Q 030819           76 PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDG--RVIFVEI  153 (171)
Q Consensus        76 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g--~~i~v~~  153 (171)
                      ...+|||+||++.+++++|+++|++||.|.++.+..+.    ++|||||+|.+.++|++|++.|||..|.|  +.|+|+|
T Consensus        45 ~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~----~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~  120 (164)
T 1sjr_A           45 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF  120 (164)
T ss_dssp             CEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESS----SCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEE
T ss_pred             ceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCC----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEE
Confidence            34679999999999999999999999999999986432    46899999999999999999999999965  9999999


Q ss_pred             ecCcH
Q 030819          154 AKSRA  158 (171)
Q Consensus       154 ~~~~~  158 (171)
                      ++++.
T Consensus       121 Ak~~~  125 (164)
T 1sjr_A          121 SKLTS  125 (164)
T ss_dssp             CSSSS
T ss_pred             ecCCc
Confidence            98763

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.75  E-value=1.3e-17  Score=113.67  Aligned_cols=78  Identities=22%  Similarity=0.403  Sum_probs=70.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceE-EEEEeCCHHHHHHHHHHhCCceeCC--eEEEE
Q 030819           75 QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGF-AFLRYATEEESRRAIEGMHGKFLDG--RVIFV  151 (171)
Q Consensus        75 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~-~fv~f~~~~~a~~al~~l~g~~i~g--~~i~v  151 (171)
                      ..--.|||+||++.+++++|+++|++||.|.++.+..+.     +|| |||+|.+.++|++|++.|||..+.|  +.|+|
T Consensus        26 s~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~-----~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI  100 (130)
T 3zzy_A           26 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN-----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRI  100 (130)
T ss_dssp             CSEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEET-----TEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEE
T ss_pred             CceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCC-----CCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEE
Confidence            334578899999999999999999999999999887542     477 9999999999999999999999988  89999


Q ss_pred             EEecCc
Q 030819          152 EIAKSR  157 (171)
Q Consensus       152 ~~~~~~  157 (171)
                      +|+++.
T Consensus       101 ~~ak~~  106 (130)
T 3zzy_A          101 DFSKLT  106 (130)
T ss_dssp             EECSCS
T ss_pred             EecCCC
Confidence            999875

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.75  E-value=5.9e-18  Score=119.22  Aligned_cols=79  Identities=24%  Similarity=0.471  Sum_probs=74.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEecCc
Q 030819           78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKSR  157 (171)
Q Consensus        78 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~~~  157 (171)
                      ++|||+|||+++++++|+++|++||.|.++.+..++ +++++|||||+|.+.++|.+|+..|+|..+.|+.|.|.++.+.
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~   79 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQS   79 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCC-C-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECC-CCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCC
Confidence            589999999999999999999999999999999998 6889999999999999999999999999999999999998654

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.75  E-value=4.1e-18  Score=108.99  Aligned_cols=75  Identities=23%  Similarity=0.327  Sum_probs=66.7

Q ss_pred             CCCCe-EEEcCCCCCCCHHH----HHHHHhcC-CCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeE
Q 030819           75 QPKTR-LFVSGLSFRTSEDS----LRNAFQGF-GQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRV  148 (171)
Q Consensus        75 ~~~~~-l~V~nl~~~~~~~~----l~~~f~~~-G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~  148 (171)
                      ++..+ |||+|||..+++++    |+++|.+| |.|.++       ++   |+|||.|.+.++|.+|++.|+|..+.|++
T Consensus         6 ~p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~   75 (96)
T 2diu_A            6 SGCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRMENEDVFGNR   75 (96)
T ss_dssp             CCSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSC
T ss_pred             CCcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcCCccCCce
Confidence            34555 99999999999987    55899999 599987       44   99999999999999999999999999999


Q ss_pred             EEEEEecCcHH
Q 030819          149 IFVEIAKSRAE  159 (171)
Q Consensus       149 i~v~~~~~~~~  159 (171)
                      |+|.+++.+.+
T Consensus        76 i~v~~A~~~sd   86 (96)
T 2diu_A           76 IIVSFTPKNRE   86 (96)
T ss_dssp             CEEESSCCSCC
T ss_pred             EEEEecCCCcc
Confidence            99999987653

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.75  E-value=1e-18  Score=127.23  Aligned_cols=79  Identities=23%  Similarity=0.347  Sum_probs=72.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCC-CeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC-CeEEEE
Q 030819           74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFG-QLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLD-GRVIFV  151 (171)
Q Consensus        74 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G-~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~-g~~i~v  151 (171)
                      .++..+|||+|||..+++++|+++|..|| .|..+.+..+.     +|+|||+|.+.++|.+|+..|||..+. |+.|+|
T Consensus       117 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v  191 (198)
T 1qm9_A          117 FPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD-----RKMALIQMGSVEEAVQALIDLHNHDLGENHHLRV  191 (198)
T ss_dssp             CCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESSTT-----SSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCE
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEE
Confidence            45689999999999999999999999999 99999986542     589999999999999999999999999 999999


Q ss_pred             EEecCc
Q 030819          152 EIAKSR  157 (171)
Q Consensus       152 ~~~~~~  157 (171)
                      .|++++
T Consensus       192 ~~a~~~  197 (198)
T 1qm9_A          192 SFSKST  197 (198)
T ss_dssp             EEECCC
T ss_pred             Eeeccc
Confidence            999864

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.75  E-value=4.6e-18  Score=113.82  Aligned_cols=78  Identities=27%  Similarity=0.471  Sum_probs=66.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCC---CCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q 030819           74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIA---NRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIF  150 (171)
Q Consensus        74 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~---g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~  150 (171)
                      ....++|||+|||+++++++|+++|++||.|. +.++.++.+   |+++|||||+|.+.++|++|++.|+  .++|+.+.
T Consensus         5 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~   81 (114)
T 2dnl_A            5 SSGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYL   81 (114)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEE
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEE
Confidence            34578999999999999999999999999999 888888766   7999999999999999999999883  35555555


Q ss_pred             EEEe
Q 030819          151 VEIA  154 (171)
Q Consensus       151 v~~~  154 (171)
                      +..+
T Consensus        82 ~~~~   85 (114)
T 2dnl_A           82 CVSS   85 (114)
T ss_dssp             EECC
T ss_pred             eccC
Confidence            5433

>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=1.3e-17  Score=122.54  Aligned_cols=77  Identities=26%  Similarity=0.367  Sum_probs=71.7

Q ss_pred             CCCCeEEEcCCC-CCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 030819           75 QPKTRLFVSGLS-FRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEI  153 (171)
Q Consensus        75 ~~~~~l~V~nl~-~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~  153 (171)
                      .++++|||+||| +.+++++|+++|++||.|.+++++.++     +|||||+|.+.++|++|++.|||..+.|+.|+|.+
T Consensus         2 ~~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~~-----~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   76 (205)
T 3tyt_A            2 ADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCV   76 (205)
T ss_dssp             CCCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTS-----TTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEE
Confidence            457899999999 899999999999999999999997653     69999999999999999999999999999999999


Q ss_pred             ecC
Q 030819          154 AKS  156 (171)
Q Consensus       154 ~~~  156 (171)
                      ++.
T Consensus        77 s~~   79 (205)
T 3tyt_A           77 SKQ   79 (205)
T ss_dssp             CSC
T ss_pred             ccC
Confidence            864

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.74  E-value=9.8e-18  Score=123.17  Aligned_cols=83  Identities=29%  Similarity=0.560  Sum_probs=75.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 030819           76 PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAK  155 (171)
Q Consensus        76 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~  155 (171)
                      +.++|||+|||+++++++|+++|+.||.|.++.++.++.+|.++|||||+|.+.++|.+|++.|+|..+.|+.|.|.++.
T Consensus        27 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~  106 (216)
T 2qfj_A           27 IMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPS  106 (216)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCS
T ss_pred             cCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCC
Confidence            45799999999999999999999999999999999998899999999999999999999999999999999999999987


Q ss_pred             CcH
Q 030819          156 SRA  158 (171)
Q Consensus       156 ~~~  158 (171)
                      ...
T Consensus       107 ~~~  109 (216)
T 2qfj_A          107 NIG  109 (216)
T ss_dssp             CCG
T ss_pred             Ccc
Confidence            654

>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=99.74  E-value=4.3e-18  Score=114.19  Aligned_cols=77  Identities=19%  Similarity=0.336  Sum_probs=67.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeE-----E
Q 030819           75 QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRV-----I  149 (171)
Q Consensus        75 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~-----i  149 (171)
                      ...++|||+|||+++++++|+++|.+||.|.++.++.+       |||||+|.+.++|++||+.|||..++|+.     |
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i   86 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYI   86 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEE
Confidence            35689999999999999999999999999999999765       89999999999999999999999999988     8


Q ss_pred             EEEEecCcH
Q 030819          150 FVEIAKSRA  158 (171)
Q Consensus       150 ~v~~~~~~~  158 (171)
                      +|..+.++.
T Consensus        87 ~v~~~~~~~   95 (115)
T 3beg_B           87 RVKVDGPRS   95 (115)
T ss_dssp             EEEECC---
T ss_pred             EeccCCCCC
Confidence            888776644

>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=99.73  E-value=1.2e-18  Score=128.21  Aligned_cols=78  Identities=9%  Similarity=0.189  Sum_probs=68.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCCe--EEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCe----E
Q 030819           75 QPKTRLFVSGLSFRTSEDSLRNAFQGFGQL--VEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGR----V  148 (171)
Q Consensus        75 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i--~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~----~  148 (171)
                      +++.+|||+|||+++++++|+++|++||.|  ..+++..++  +.++|+|||+|.+.++|.+||..|||..+.|.    +
T Consensus       121 ~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~--~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p  198 (205)
T 3tyt_A          121 HPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK--SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYP  198 (205)
T ss_dssp             CCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCC--SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSC
T ss_pred             CCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCC--CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcc
Confidence            567899999999999999999999999999  888888765  55679999999999999999999999999876    4


Q ss_pred             EEEEEe
Q 030819          149 IFVEIA  154 (171)
Q Consensus       149 i~v~~~  154 (171)
                      +.|.++
T Consensus       199 ~~vk~~  204 (205)
T 3tyt_A          199 YTLKLC  204 (205)
T ss_dssp             EECEEE
T ss_pred             eEEEec
Confidence            665554

>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=99.73  E-value=1.7e-17  Score=117.30  Aligned_cols=83  Identities=30%  Similarity=0.600  Sum_probs=76.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 030819           76 PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAK  155 (171)
Q Consensus        76 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~  155 (171)
                      ++++|||+|||+++++++|+++|+.||.|.++.++.++.+|.++|||||+|.+.++|.+|+..  +..+.|+.|.|.++.
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g~~i~v~~~~   79 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT--QHILDGKVIDPKRAI   79 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS--CCEETTEECCCEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc--ccccCCeEccccccc
Confidence            467999999999999999999999999999999999988999999999999999999999984  678999999999988


Q ss_pred             CcHHH
Q 030819          156 SRAEL  160 (171)
Q Consensus       156 ~~~~~  160 (171)
                      ++...
T Consensus        80 ~~~~~   84 (167)
T 2cjk_A           80 PRDEQ   84 (167)
T ss_dssp             CHHHH
T ss_pred             chhhc
Confidence            76543

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=99.72  E-value=2.9e-17  Score=116.68  Aligned_cols=82  Identities=24%  Similarity=0.408  Sum_probs=74.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCC--CcceEEEEEeCCHHHHHHHHHHhCCceeC---CeEEE
Q 030819           76 PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIAN--RPRGFAFLRYATEEESRRAIEGMHGKFLD---GRVIF  150 (171)
Q Consensus        76 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g--~~~g~~fv~f~~~~~a~~al~~l~g~~i~---g~~i~  150 (171)
                      +.++|||+|||+++++++|+++|++||.|.++.++.++.++  +++|||||+|.+.++|++|++.|+|..+.   ++.+.
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~   81 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQ   81 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCE
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceE
Confidence            46799999999999999999999999999999999999776  89999999999999999999999998875   57788


Q ss_pred             EEEecCc
Q 030819          151 VEIAKSR  157 (171)
Q Consensus       151 v~~~~~~  157 (171)
                      +.++.+.
T Consensus        82 ~~~~~~~   88 (175)
T 3nmr_A           82 MKPADSE   88 (175)
T ss_dssp             EEECGGG
T ss_pred             Ecccccc
Confidence            8877644

>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=99.72  E-value=4.7e-17  Score=118.55  Aligned_cols=83  Identities=11%  Similarity=0.257  Sum_probs=74.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 030819           76 PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAK  155 (171)
Q Consensus        76 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~  155 (171)
                      ..++|||+|||+++++++|+++|++||.|..+++..+. +|.++|||||+|.+.++|.+|+..+ +..+.|+.|.|.+++
T Consensus       108 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~-~~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~Gr~l~V~~~~  185 (193)
T 2voo_A          108 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKD  185 (193)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESSHHHHHHHHHCT-TCEETTEECEEEETT
T ss_pred             ccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHhC-CCeECCEEEEEEEhH
Confidence            35899999999999999999999999999999999987 6999999999999999999999865 469999999999987


Q ss_pred             CcHHH
Q 030819          156 SRAEL  160 (171)
Q Consensus       156 ~~~~~  160 (171)
                      .-.+.
T Consensus       186 ~y~~~  190 (193)
T 2voo_A          186 DYFAK  190 (193)
T ss_dssp             TC---
T ss_pred             HHHHH
Confidence            65443

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.72  E-value=4.5e-17  Score=107.53  Aligned_cols=84  Identities=14%  Similarity=0.232  Sum_probs=74.3

Q ss_pred             CCCCeEEEcCCCC-----CCCHHHHHHHHhcCCCeEEEEEeecCCC-CCcceEEEEEeCCHHHHHHHHHHhCCceeCCeE
Q 030819           75 QPKTRLFVSGLSF-----RTSEDSLRNAFQGFGQLVEVNLVMDKIA-NRPRGFAFLRYATEEESRRAIEGMHGKFLDGRV  148 (171)
Q Consensus        75 ~~~~~l~V~nl~~-----~~~~~~l~~~f~~~G~i~~~~~~~~~~~-g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~  148 (171)
                      .++++|+|.|+..     +.++++|++.|++||.|.++.++.++.+ +.++|||||+|.+.++|.+|+..|||..+.|+.
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~   85 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRV   85 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcE
Confidence            4678999999963     2368999999999999999999988654 688999999999999999999999999999999


Q ss_pred             EEEEEecCcH
Q 030819          149 IFVEIAKSRA  158 (171)
Q Consensus       149 i~v~~~~~~~  158 (171)
                      |.|.++....
T Consensus        86 i~v~~a~~~~   95 (105)
T 2pe8_A           86 VKACFYNLDK   95 (105)
T ss_dssp             CEEEECCHHH
T ss_pred             EEEEEcCHHH
Confidence            9999997643

>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=99.72  E-value=2.1e-18  Score=128.60  Aligned_cols=79  Identities=23%  Similarity=0.342  Sum_probs=72.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCC-CeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC-CeEEEE
Q 030819           74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFG-QLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLD-GRVIFV  151 (171)
Q Consensus        74 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G-~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~-g~~i~v  151 (171)
                      .++..+|||+|||+.+++++|+++|.+|| .|..+.++.+     .+|||||+|.+.++|.+|+..|+|..+. |+.|+|
T Consensus       148 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v  222 (229)
T 2adc_A          148 FPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRV  222 (229)
T ss_dssp             CCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS-----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEE
T ss_pred             CCCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC-----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEE
Confidence            35578999999999999999999999999 9999998653     2589999999999999999999999999 999999


Q ss_pred             EEecCc
Q 030819          152 EIAKSR  157 (171)
Q Consensus       152 ~~~~~~  157 (171)
                      .|++++
T Consensus       223 ~~a~~~  228 (229)
T 2adc_A          223 SFSKST  228 (229)
T ss_dssp             EECSSC
T ss_pred             EEecCC
Confidence            999864

>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=99.72  E-value=2.9e-17  Score=104.39  Aligned_cols=72  Identities=24%  Similarity=0.556  Sum_probs=66.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcC----C-------CeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCce
Q 030819           75 QPKTRLFVSGLSFRTSEDSLRNAFQGF----G-------QLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKF  143 (171)
Q Consensus        75 ~~~~~l~V~nl~~~~~~~~l~~~f~~~----G-------~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~  143 (171)
                      .+.++|||+|||+++++++|+++|.+|    |       .|.++.+..+      +|||||+|.+.++|.+|+ .|||..
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~-~l~g~~   76 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAM-AFDGII   76 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHG-GGTTCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHH-hcCCCE
Confidence            457899999999999999999999999    8       8999988755      499999999999999999 899999


Q ss_pred             eCCeEEEEEE
Q 030819          144 LDGRVIFVEI  153 (171)
Q Consensus       144 i~g~~i~v~~  153 (171)
                      +.|+.|+|+.
T Consensus        77 ~~g~~l~V~r   86 (87)
T 2hzc_A           77 FQGQSLKIRR   86 (87)
T ss_dssp             ETTEECEEEC
T ss_pred             ECCeEEEEeC
Confidence            9999999874

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A

Probab=99.71  E-value=9.3e-17  Score=122.80  Aligned_cols=83  Identities=20%  Similarity=0.434  Sum_probs=76.3

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHH----HHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLR----NAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRV  148 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~----~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~  148 (171)
                      ...+.++|||+|||+++++++|+    ++|..||.|.+|.+..   +|+++|||||+|.+.++|.+|++.|||..+.|+.
T Consensus         5 ~~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   81 (282)
T 3pgw_A            5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKP   81 (282)
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcE
Confidence            45668999999999999999976    8999999999998875   7889999999999999999999999999999999


Q ss_pred             EEEEEecCcH
Q 030819          149 IFVEIAKSRA  158 (171)
Q Consensus       149 i~v~~~~~~~  158 (171)
                      |+|.+++...
T Consensus        82 l~v~~a~~~~   91 (282)
T 3pgw_A           82 MRIQYAKTDS   91 (282)
T ss_pred             EEEEEeccCc
Confidence            9999997655

>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=99.70  E-value=1.6e-17  Score=106.03  Aligned_cols=78  Identities=21%  Similarity=0.382  Sum_probs=66.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 030819           75 QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIA  154 (171)
Q Consensus        75 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~  154 (171)
                      .+.++|||+|||+++++++|+++|++||.|.++.++.+     ++|||||+|.+.++|++|+..  ...+.|..|.|.++
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~~--~~~~~g~~l~v~~a   75 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCGE--DLIIKGISVHISNA   75 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTTC--EEEETTEEEEEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHHhcC--CceeCCEEEEEEec
Confidence            45789999999999999999999999999999998754     579999999999999764321  23459999999999


Q ss_pred             cCcHH
Q 030819          155 KSRAE  159 (171)
Q Consensus       155 ~~~~~  159 (171)
                      .++..
T Consensus        76 ~~~~~   80 (88)
T 1wf0_A           76 EPKHN   80 (88)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87653

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.70  E-value=4.1e-17  Score=122.14  Aligned_cols=82  Identities=20%  Similarity=0.360  Sum_probs=71.3

Q ss_pred             CCCCCCeEEEcCCCCCC---------CHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCce
Q 030819           73 TCQPKTRLFVSGLSFRT---------SEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKF  143 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~---------~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~  143 (171)
                      .....++|||+||+..+         ++++|+.+|++||.|.++.++.+      +|||||+|.+.++|+.|++.|+|..
T Consensus       130 ~~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~------kG~AFV~F~~~~~Ae~A~~am~g~~  203 (240)
T 3u1l_A          130 FRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES------KNCGFVKFKYQANAEFAKEAMSNQT  203 (240)
T ss_dssp             -CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHHHTTCC
T ss_pred             cccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECC------CCEEEEEeCCHHHHHHHHHHhCCCE
Confidence            35568899999999998         79999999999999999999864      5999999999999999999999999


Q ss_pred             e------------CCeEEEEEEecCcHHH
Q 030819          144 L------------DGRVIFVEIAKSRAEL  160 (171)
Q Consensus       144 i------------~g~~i~v~~~~~~~~~  160 (171)
                      +            .|+.|.|.|++.....
T Consensus       204 l~~~~~~e~~~~~~gr~L~V~wA~~~pnp  232 (240)
T 3u1l_A          204 LLLPSDKEWDDRREGTGLLVKWANEDPDP  232 (240)
T ss_dssp             CCCTTSTTGGGGGGSCCCEEEECC-----
T ss_pred             EeccccccccccCCCCEEEEEEccCCCCH
Confidence            9            8999999999876543

>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=9.9e-17  Score=119.52  Aligned_cols=80  Identities=24%  Similarity=0.394  Sum_probs=74.2

Q ss_pred             CCCCCCeEEEcCCCC-CCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 030819           73 TCQPKTRLFVSGLSF-RTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFV  151 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~-~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v  151 (171)
                      ..+++++|||+|||+ ++++++|+++|++||.|.++.++.++     +|||||+|.+.++|++|++.|+|..+.|+.|.|
T Consensus        30 ~~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v  104 (229)
T 2adc_A           30 AGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRI  104 (229)
T ss_dssp             GCCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEE
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            446789999999999 99999999999999999999998775     689999999999999999999999999999999


Q ss_pred             EEecCc
Q 030819          152 EIAKSR  157 (171)
Q Consensus       152 ~~~~~~  157 (171)
                      .+++..
T Consensus       105 ~~a~~~  110 (229)
T 2adc_A          105 TLSKHQ  110 (229)
T ss_dssp             ECCSCC
T ss_pred             EEecCc
Confidence            998754

>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=99.65  E-value=7.4e-16  Score=116.93  Aligned_cols=78  Identities=28%  Similarity=0.508  Sum_probs=71.9

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ...+.++|||+|||+++++++|+++|+.||.|..+.+..+      +|||||+|.+.++|.+|+..|+|..+.|+.|.|.
T Consensus        18 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~   91 (261)
T 3sde_A           18 TYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIR   91 (261)
T ss_dssp             SSCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CcEEEEEECCHHHHHHHHHHcCCcEECCceeEee
Confidence            4456789999999999999999999999999999998654      4999999999999999999999999999999999


Q ss_pred             EecC
Q 030819          153 IAKS  156 (171)
Q Consensus       153 ~~~~  156 (171)
                      ++.+
T Consensus        92 ~a~~   95 (261)
T 3sde_A           92 FATH   95 (261)
T ss_dssp             ECCC
T ss_pred             eccc
Confidence            9865

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.65  E-value=4.3e-17  Score=116.16  Aligned_cols=85  Identities=24%  Similarity=0.310  Sum_probs=73.8

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 030819           72 STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFV  151 (171)
Q Consensus        72 ~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v  151 (171)
                      ....+.++|||+|||+++++++|+++|..||.+.. .++.+..+|.++|||||+|.+.++|.+|++ |+|..+.|+.|.|
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~-~~~~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~v   85 (175)
T 1fje_B            8 SESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKL   85 (175)
T ss_dssp             SSCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEE
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEEECCCCccccEEEEEECCHHHHHHHHh-cCCCEeCCeEEEE
Confidence            34567889999999999999999999999998766 334444588899999999999999999995 9999999999999


Q ss_pred             EEecCcH
Q 030819          152 EIAKSRA  158 (171)
Q Consensus       152 ~~~~~~~  158 (171)
                      .++.++.
T Consensus        86 ~~~~~~~   92 (175)
T 1fje_B           86 EKPKGRD   92 (175)
T ss_dssp             ECCCCSS
T ss_pred             ecCCCcc
Confidence            9988653

>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=3.1e-16  Score=113.99  Aligned_cols=77  Identities=25%  Similarity=0.416  Sum_probs=71.9

Q ss_pred             CCCeEEEcCCCC-CCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 030819           76 PKTRLFVSGLSF-RTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIA  154 (171)
Q Consensus        76 ~~~~l~V~nl~~-~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~  154 (171)
                      .+++|||+|||+ ++++++|+++|+.||.|.++.+..++     +|||||+|.+.++|.+|+..|+|..+.|+.|.|.++
T Consensus         2 ~~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a   76 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLS   76 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEEC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEe
Confidence            468999999999 99999999999999999999998765     689999999999999999999999999999999998


Q ss_pred             cCc
Q 030819          155 KSR  157 (171)
Q Consensus       155 ~~~  157 (171)
                      +..
T Consensus        77 ~~~   79 (198)
T 1qm9_A           77 KHQ   79 (198)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            754

>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=99.64  E-value=2.7e-15  Score=99.93  Aligned_cols=82  Identities=21%  Similarity=0.415  Sum_probs=70.5

Q ss_pred             CCCCCCeEEEcCCCCCCC-----------HHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCC
Q 030819           73 TCQPKTRLFVSGLSFRTS-----------EDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHG  141 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~-----------~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g  141 (171)
                      .+.++++|+|.||.....           +++|+++|.+||.|.++.+ .++   .++|||||+|.+.++|.+|+..|||
T Consensus        11 ~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~lng   86 (112)
T 2dit_A           11 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTLDG   86 (112)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHSTT
T ss_pred             CCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHcCC
Confidence            445688999999954432           5899999999999999965 554   3789999999999999999999999


Q ss_pred             ceeCCeEEEEEEecCcH
Q 030819          142 KFLDGRVIFVEIAKSRA  158 (171)
Q Consensus       142 ~~i~g~~i~v~~~~~~~  158 (171)
                      ..+.|+.|+|.++.++.
T Consensus        87 ~~~~gr~l~v~~a~~~~  103 (112)
T 2dit_A           87 RWFGGRQITAQAWDGTT  103 (112)
T ss_dssp             CEETTEECEEEECCSCC
T ss_pred             CEECCcEEEEEEeCCCC
Confidence            99999999999998754

>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=99.62  E-value=3e-16  Score=103.41  Aligned_cols=72  Identities=18%  Similarity=0.498  Sum_probs=65.0

Q ss_pred             EcCCCCCCCHHHHHHHH------------hcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEE
Q 030819           82 VSGLSFRTSEDSLRNAF------------QGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVI  149 (171)
Q Consensus        82 V~nl~~~~~~~~l~~~f------------~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i  149 (171)
                      +.||++.+++++|++.|            ++||.|.++.+..+. +++++|||||+|.+.++|.+|+..|||..++|+.|
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~-~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i   98 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPI   98 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCC-CCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEE
Confidence            56778888888777766            999999999999887 58899999999999999999999999999999999


Q ss_pred             EEEEe
Q 030819          150 FVEIA  154 (171)
Q Consensus       150 ~v~~~  154 (171)
                      +|.++
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            99986

>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=99.61  E-value=4.2e-15  Score=98.02  Aligned_cols=84  Identities=13%  Similarity=0.297  Sum_probs=72.0

Q ss_pred             CCCCeEEEcCC--CCCCC--------HHHHHHHHhcCCCeEEEEEeecCCC--CCcceEEEEEeCCHHHHHHHHHHhCCc
Q 030819           75 QPKTRLFVSGL--SFRTS--------EDSLRNAFQGFGQLVEVNLVMDKIA--NRPRGFAFLRYATEEESRRAIEGMHGK  142 (171)
Q Consensus        75 ~~~~~l~V~nl--~~~~~--------~~~l~~~f~~~G~i~~~~~~~~~~~--g~~~g~~fv~f~~~~~a~~al~~l~g~  142 (171)
                      .+++.|.+.|+  +.++.        +++|++.|++||.|.++.++.++.+  +.++|++||+|.+.++|.+|+..|||.
T Consensus         3 ~ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~   82 (105)
T 3v4m_A            3 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   82 (105)
T ss_dssp             SCCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCC
Confidence            45778899987  33333        3689999999999999999988754  367899999999999999999999999


Q ss_pred             eeCCeEEEEEEecCcH
Q 030819          143 FLDGRVIFVEIAKSRA  158 (171)
Q Consensus       143 ~i~g~~i~v~~~~~~~  158 (171)
                      .++|+.|+|.+.....
T Consensus        83 ~f~GR~i~v~~~~~~~   98 (105)
T 3v4m_A           83 KFANRVVVTKYCDPDS   98 (105)
T ss_dssp             EETTEECEEEEECHHH
T ss_pred             EeCCCEEEEEEeCHHH
Confidence            9999999999987544

>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=99.58  E-value=6.6e-15  Score=104.30  Aligned_cols=75  Identities=21%  Similarity=0.512  Sum_probs=67.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcC----C-------CeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee
Q 030819           76 PKTRLFVSGLSFRTSEDSLRNAFQGF----G-------QLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFL  144 (171)
Q Consensus        76 ~~~~l~V~nl~~~~~~~~l~~~f~~~----G-------~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i  144 (171)
                      +.++|||+|||+++++++|+++|++|    |       .|.++.+..      ++|||||+|.+.++|.+|+ .++|..+
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~------~~g~afV~f~~~~~A~~A~-~~~~~~~   75 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQ------DKNFAFLEFRSVDETTQAM-AFDGIIF   75 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEET------TTTEEEEEESSHHHHHHHG-GGTTCEE
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecC------CCCEEEEEeCCHHHHHHHH-HhCCcEe
Confidence            46899999999999999999999999    6       677776644      3599999999999999999 7999999


Q ss_pred             CCeEEEEEEecCc
Q 030819          145 DGRVIFVEIAKSR  157 (171)
Q Consensus       145 ~g~~i~v~~~~~~  157 (171)
                      .|+.|.|.++...
T Consensus        76 ~g~~i~v~~~~~~   88 (172)
T 2g4b_A           76 QGQSLKIRRPHDY   88 (172)
T ss_dssp             TTEECEEECCSSC
T ss_pred             cCceeeecCCccc
Confidence            9999999987654

>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=99.57  E-value=1.9e-14  Score=96.73  Aligned_cols=82  Identities=17%  Similarity=0.321  Sum_probs=71.4

Q ss_pred             CCCeEEEcCCCC--C---CCHHHHHHHHhcCCCeEEEEEeecCC----CCCcceEEEEEeCCHHHHHHHHHHhCCceeCC
Q 030819           76 PKTRLFVSGLSF--R---TSEDSLRNAFQGFGQLVEVNLVMDKI----ANRPRGFAFLRYATEEESRRAIEGMHGKFLDG  146 (171)
Q Consensus        76 ~~~~l~V~nl~~--~---~~~~~l~~~f~~~G~i~~~~~~~~~~----~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g  146 (171)
                      ++++|++.|+-.  +   --+++|++.|++||.|.++.++.++.    ++.++|++||+|.+.++|.+|+..|||..++|
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~G   98 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG   98 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECC
Confidence            578999999842  1   23689999999999999999998864    45788999999999999999999999999999


Q ss_pred             eEEEEEEecCc
Q 030819          147 RVIFVEIAKSR  157 (171)
Q Consensus       147 ~~i~v~~~~~~  157 (171)
                      +.|+|.+....
T Consensus        99 R~i~v~~~~~~  109 (118)
T 3ue2_A           99 RKVVAEVYDQE  109 (118)
T ss_dssp             EECEEEEECHH
T ss_pred             cEEEEEEcChH
Confidence            99999998653

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.56  E-value=1.1e-14  Score=105.40  Aligned_cols=75  Identities=23%  Similarity=0.538  Sum_probs=65.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcC----C-------CeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee
Q 030819           76 PKTRLFVSGLSFRTSEDSLRNAFQGF----G-------QLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFL  144 (171)
Q Consensus        76 ~~~~l~V~nl~~~~~~~~l~~~f~~~----G-------~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i  144 (171)
                      ..++|||+|||+++++++|+++|..|    |       .|.++.+      +.++|||||+|.+.++|++|+ .|||..+
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~------~~~~g~afV~F~~~~~A~~Al-~l~g~~~   75 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI------NQDKNFAFLEFRSVDETTQAM-AFDGIIF   75 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEE------ETTTTEEEEEESCSHHHHHHG-GGTTEEE
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEe------cCCCCEEEEEeCCHHHHHHHH-HhcCCEE
Confidence            46899999999999999999999999    5       5666655      345699999999999999999 7999999


Q ss_pred             CCeEEEEEEecCc
Q 030819          145 DGRVIFVEIAKSR  157 (171)
Q Consensus       145 ~g~~i~v~~~~~~  157 (171)
                      .|+.|+|.++...
T Consensus        76 ~g~~i~v~~~~~~   88 (198)
T 2yh0_A           76 QGQSLKIRRPHDY   88 (198)
T ss_dssp             TTEEEEEECCCCC
T ss_pred             cCceEEEeCCCCC
Confidence            9999999998754

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.52  E-value=1.5e-13  Score=89.62  Aligned_cols=65  Identities=18%  Similarity=0.233  Sum_probs=57.5

Q ss_pred             CCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEecCcH
Q 030819           87 FRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKSRA  158 (171)
Q Consensus        87 ~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~~~~  158 (171)
                      ..+++++|+++|++||.|.++.++     ++++|||||+|.+.++|+.|+..++  .+.|++|+|.|++++.
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~~--~~~g~~l~V~~a~~~~   91 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNEV--GLVDNPLKISWLEGQP   91 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHTCC--BCSSSBCEEECSSCCC
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHhcC--CCCCCeEEEEEccCCC
Confidence            468999999999999999999987     4678999999999999999999754  4679999999998664

>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*

Probab=99.51  E-value=6.2e-14  Score=110.02  Aligned_cols=78  Identities=23%  Similarity=0.382  Sum_probs=66.2

Q ss_pred             CCCCCCCeEEEcC--CCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee---CC
Q 030819           72 STCQPKTRLFVSG--LSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFL---DG  146 (171)
Q Consensus        72 ~~~~~~~~l~V~n--l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i---~g  146 (171)
                      ....++.+|||+|  |+..+++++|+++|++||.|.++.+..      .||||||+|.+.++|++|++.|||..+   .|
T Consensus        13 ~~~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g   86 (345)
T 3tht_A           13 TVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLG   86 (345)
T ss_dssp             CCSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTTCEEECTTS
T ss_pred             ecCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCccccccC
Confidence            3456788999998  688999999999999999999987643      359999999999999999999999987   34


Q ss_pred             e--EEEEEEec
Q 030819          147 R--VIFVEIAK  155 (171)
Q Consensus       147 ~--~i~v~~~~  155 (171)
                      +  .|.|.+..
T Consensus        87 ~~~~ly~~~~~   97 (345)
T 3tht_A           87 QKITLYLNFVE   97 (345)
T ss_dssp             CEEECEEEECS
T ss_pred             CceEEEEEEee
Confidence            4  56667663

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A

Probab=99.45  E-value=1.2e-12  Score=87.34  Aligned_cols=84  Identities=11%  Similarity=0.244  Sum_probs=68.0

Q ss_pred             CCCCeEEEcCCCCCCC----------HHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee
Q 030819           75 QPKTRLFVSGLSFRTS----------EDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFL  144 (171)
Q Consensus        75 ~~~~~l~V~nl~~~~~----------~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i  144 (171)
                      .+++.|.+.|+=....          +++|++.|++||.|.++.+..+.    .+|++||+|.+.++|.+|+..|||..+
T Consensus         5 ~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG~~f   80 (114)
T 3s6e_A            5 LATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGRWF   80 (114)
T ss_dssp             CCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTCEE
T ss_pred             CCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCCEE
Confidence            3466777777643221          35889999999999999886543    479999999999999999999999999


Q ss_pred             CCeEEEEEEecCcHHHHH
Q 030819          145 DGRVIFVEIAKSRAELRQ  162 (171)
Q Consensus       145 ~g~~i~v~~~~~~~~~~~  162 (171)
                      +|+.|.|.++....-...
T Consensus        81 ~GR~i~v~~~~~~~y~~~   98 (114)
T 3s6e_A           81 AGKMITAAYVPLPTYHNL   98 (114)
T ss_dssp             TTEECEEEEECHHHHHHH
T ss_pred             CCEEEEEEEEcHHHHHHh
Confidence            999999999976554443

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.34  E-value=8.1e-12  Score=79.11  Aligned_cols=75  Identities=21%  Similarity=0.337  Sum_probs=64.5

Q ss_pred             CCCCCeEEEcCCC----CCCCH----HHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeC
Q 030819           74 CQPKTRLFVSGLS----FRTSE----DSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLD  145 (171)
Q Consensus        74 ~~~~~~l~V~nl~----~~~~~----~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~  145 (171)
                      .++..||+|.-.+    .++..    .+|.+.|.+||.|..++++.++        +||+|.+.++|.+|+. |+|..+.
T Consensus         4 GPpd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~-mnG~~v~   74 (91)
T 2dnr_A            4 GSSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFLEGSSALNVLS-LNGKELL   74 (91)
T ss_dssp             CCSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEESSHHHHHHGGG-GTTCEET
T ss_pred             CCCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEECChHHHHHHHh-cCCeEeC
Confidence            4667789888776    23333    6899999999999999998764        8999999999999998 9999999


Q ss_pred             CeEEEEEEecCc
Q 030819          146 GRVIFVEIAKSR  157 (171)
Q Consensus       146 g~~i~v~~~~~~  157 (171)
                      |+.|+|.++.+.
T Consensus        75 Gr~LkV~lkt~d   86 (91)
T 2dnr_A           75 NRTITIALKSPS   86 (91)
T ss_dssp             TEEEEEEECCCS
T ss_pred             CeEEEEEeCCCC
Confidence            999999998764

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.32  E-value=8.8e-12  Score=83.62  Aligned_cols=81  Identities=14%  Similarity=0.105  Sum_probs=70.5

Q ss_pred             CCCCCCCCeEEEcCCCCC-CCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCC-HHHHHHHHHHhC--CceeCC
Q 030819           71 LSTCQPKTRLFVSGLSFR-TSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYAT-EEESRRAIEGMH--GKFLDG  146 (171)
Q Consensus        71 ~~~~~~~~~l~V~nl~~~-~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~-~~~a~~al~~l~--g~~i~g  146 (171)
                      +..-+++..|||+||+++ ++.++|+++|++||.|..|.+..+..      .|||.|.+ .++|..|+..++  +..|.|
T Consensus        12 ~~~~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~~~i~g   85 (121)
T 1owx_A           12 SLEEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGNLQLRN   85 (121)
T ss_dssp             CCSCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCBCTTS
T ss_pred             cccccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCCcEEeC
Confidence            345678999999999999 99999999999999999999988773      69999999 899999999995  667889


Q ss_pred             eEEEEEEecCc
Q 030819          147 RVIFVEIAKSR  157 (171)
Q Consensus       147 ~~i~v~~~~~~  157 (171)
                      ..++++.-...
T Consensus        86 ~~~~~evL~Ge   96 (121)
T 1owx_A           86 KEVTWEVLEGE   96 (121)
T ss_dssp             SSEEEEECCHH
T ss_pred             cEEEEEECCCH
Confidence            88888776543

>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=99.15  E-value=1e-10  Score=74.37  Aligned_cols=75  Identities=15%  Similarity=0.228  Sum_probs=64.0

Q ss_pred             CCCCCCeEEEcCCCCC-----CCH----HHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCce
Q 030819           73 TCQPKTRLFVSGLSFR-----TSE----DSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKF  143 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~-----~~~----~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~  143 (171)
                      ..++..||+|.-++..     +..    .+|.+.|..||.|..++++.++        +||+|.+.++|.+||. |+|..
T Consensus        11 ~GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~-ldG~~   81 (95)
T 1ufw_A           11 QGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLD-VDGMK   81 (95)
T ss_dssp             CCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHH-GGGSE
T ss_pred             cCCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHh-cCCee
Confidence            4567889999988743     222    5789999999999999998774        9999999999999999 99999


Q ss_pred             eCCeEEEEEEecC
Q 030819          144 LDGRVIFVEIAKS  156 (171)
Q Consensus       144 i~g~~i~v~~~~~  156 (171)
                      ++|+.|+|.+..+
T Consensus        82 v~Gr~L~V~~k~~   94 (95)
T 1ufw_A           82 VKGRAVKISGPSS   94 (95)
T ss_dssp             ETTEEEEEECCCC
T ss_pred             eCCeEEEEeccCC
Confidence            9999999987643

>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=99.11  E-value=3e-10  Score=83.85  Aligned_cols=69  Identities=19%  Similarity=0.367  Sum_probs=61.3

Q ss_pred             CCHHHHHHHHhcCCCeEEEEEeecC----CCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEecCc
Q 030819           89 TSEDSLRNAFQGFGQLVEVNLVMDK----IANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKSR  157 (171)
Q Consensus        89 ~~~~~l~~~f~~~G~i~~~~~~~~~----~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~~~  157 (171)
                      -.+++|.+.|.+||.|.++.+..+.    .++.++|++||+|.+.++|.+|+..|||..++|+.|.+.+....
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~~~  213 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQE  213 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECCHH
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcCHH
Confidence            3568999999999999999998554    35589999999999999999999999999999999999997643

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.88  E-value=2.2e-08  Score=65.08  Aligned_cols=75  Identities=17%  Similarity=0.158  Sum_probs=68.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcC-----CCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEE
Q 030819           75 QPKTRLFVSGLSFRTSEDSLRNAFQGF-----GQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVI  149 (171)
Q Consensus        75 ~~~~~l~V~nl~~~~~~~~l~~~f~~~-----G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i  149 (171)
                      ...++|-+-+||..+++..|+.+...+     |.|..+.+..|.      |-|+|+|.+...|-+|.-.|+|..+.|+.|
T Consensus        19 ~~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH------~GAivef~d~~~AgKasLaL~G~ef~gr~L   92 (117)
T 2l9w_A           19 ELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF------NGAIIIFRDSKFAAKMLMILNGSQFQGKVI   92 (117)
T ss_dssp             TTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTT------TEEEEECSCHHHHHHHHHHHSSEEETTEEE
T ss_pred             cCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCC------CceEEEEccchhhHHHHhhcCCeeecCeEE
Confidence            447789999999999999999999999     999999999887      689999999999999998999999999999


Q ss_pred             EEEEec
Q 030819          150 FVEIAK  155 (171)
Q Consensus       150 ~v~~~~  155 (171)
                      ++.-..
T Consensus        93 r~gTv~   98 (117)
T 2l9w_A           93 RSGTIN   98 (117)
T ss_dssp             EEECHH
T ss_pred             EecCHH
Confidence            987544

>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=98.04  E-value=1.9e-05  Score=50.88  Aligned_cols=75  Identities=9%  Similarity=0.074  Sum_probs=61.8

Q ss_pred             CCeEEEcCCCCCC-C----HHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 030819           77 KTRLFVSGLSFRT-S----EDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFV  151 (171)
Q Consensus        77 ~~~l~V~nl~~~~-~----~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v  151 (171)
                      ..+|+|.||+.++ .    .+.++.+|..|+++......+.-      .-..|.|.+.++|.+|-..||+..++|+.|+|
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSF------RRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~   78 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF------KRVRINFSNPLSAADARLRLHKTEFLGKEMKL   78 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTT------TEEEEECSSTTHHHHHHHTSTTSEETTEECEE
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcc------eEEEEEeCChHHHHHHHHHhccceecCceeEE
Confidence            5689999998865 2    25779999999988776555432      25689999999999999999999999999999


Q ss_pred             EEecCc
Q 030819          152 EIAKSR  157 (171)
Q Consensus       152 ~~~~~~  157 (171)
                      .++.+.
T Consensus        79 YFgq~~   84 (104)
T 1wey_A           79 YFAQTL   84 (104)
T ss_dssp             ECCCCS
T ss_pred             EecCCC
Confidence            998743

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=97.94  E-value=6.5e-05  Score=47.76  Aligned_cols=57  Identities=19%  Similarity=0.304  Sum_probs=47.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHh
Q 030819           74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM  139 (171)
Q Consensus        74 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l  139 (171)
                      ....+.+++ ++|+++...||.++|+.||. ..|+++.|-       -|||.|.+++.|..|+..+
T Consensus        13 p~r~HVf~l-~FP~ewKt~DI~~lFs~fgg-v~I~WidDT-------sAlvvf~~~~~a~~al~~i   69 (100)
T 1whv_A           13 PKRDHVLHV-TFPKEWKTSDLYQLFSAFGN-IQISWIDDT-------SAFVSLSQPEQVQIAVNTS   69 (100)
T ss_dssp             CCCCSEEEE-ECCTTCCHHHHHHHHTTTCS-CCCEEEETT-------EEEEECSCHHHHHHHHHHH
T ss_pred             CCCCeEEEE-eCChhhhhHHHHHHhhccCC-EEEEEEcCC-------eEEEEecCHHHHHHHHHhc
Confidence            344566777 99999999999999999994 566777664       8999999999999999866

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.78  E-value=0.00042  Score=44.50  Aligned_cols=73  Identities=15%  Similarity=0.156  Sum_probs=58.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhc-----CCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEE
Q 030819           75 QPKTRLFVSGLSFRTSEDSLRNAFQG-----FGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVI  149 (171)
Q Consensus        75 ~~~~~l~V~nl~~~~~~~~l~~~f~~-----~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i  149 (171)
                      ....+|.|.|||+.+.++.|.-+|++     -|+|..+....        +-|+|+|.+.+.|++.|.. ..+.+++..|
T Consensus         6 ~~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~k-~~H~L~~~~L   76 (104)
T 2dhx_A            6 SGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLAQ-ADHELHGAQL   76 (104)
T ss_dssp             CCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHTC-SCCBSSSSBC
T ss_pred             cCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhcC-CcceecCeEE
Confidence            44679999999999999999999986     25677776532        4789999999999999873 3567888888


Q ss_pred             EEEEecC
Q 030819          150 FVEIAKS  156 (171)
Q Consensus       150 ~v~~~~~  156 (171)
                      .|....+
T Consensus        77 sV~P~~~   83 (104)
T 2dhx_A           77 SLRPAPP   83 (104)
T ss_dssp             EEEECCC
T ss_pred             EEEcCCC
Confidence            8876543

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=97.64  E-value=0.00038  Score=46.02  Aligned_cols=75  Identities=16%  Similarity=0.290  Sum_probs=59.2

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC-eEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDG-RVIFV  151 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g-~~i~v  151 (171)
                      .....+-|.|.++|+.. -+.+...|++||.|.+....    ++  ..+-.|.|.++.+|++||. .||..+.| -.|-|
T Consensus        20 ~~~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~----~~--~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV   91 (119)
T 1wwh_A           20 DHLDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMS----NT--GNWMHIRYQSKLQARKALS-KDGRIFGESIMIGV   91 (119)
T ss_dssp             -CGGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEEC----SS--SSEEEEEESSHHHHHHHHT-TTTCEETTTEECEE
T ss_pred             CCCCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccC----CC--CCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEE
Confidence            34456789999999985 56788899999999987762    12  2488999999999999999 69999975 66777


Q ss_pred             EEec
Q 030819          152 EIAK  155 (171)
Q Consensus       152 ~~~~  155 (171)
                      ..-.
T Consensus        92 ~p~~   95 (119)
T 1wwh_A           92 KPCI   95 (119)
T ss_dssp             EECC
T ss_pred             EECC
Confidence            6644

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=97.60  E-value=0.00073  Score=42.63  Aligned_cols=78  Identities=13%  Similarity=0.190  Sum_probs=60.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCC--cceEEEEEeCCHHHHHHHHHHhCCceeC---Ce--EEE
Q 030819           78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANR--PRGFAFLRYATEEESRRAIEGMHGKFLD---GR--VIF  150 (171)
Q Consensus        78 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~--~~g~~fv~f~~~~~a~~al~~l~g~~i~---g~--~i~  150 (171)
                      .+|.|++||+.+|++++.+.+.....+.....+..+.+.+  .-+-|+|.|.+.+++..-.+.++|..+.   |.  +..
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D~kg~~~~a~   81 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPAI   81 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEECE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEcCCCCEeeeE
Confidence            4789999999999999999999988877776665553332  3357899999999999999999999872   22  345


Q ss_pred             EEEec
Q 030819          151 VEIAK  155 (171)
Q Consensus       151 v~~~~  155 (171)
                      |++|.
T Consensus        82 VE~AP   86 (91)
T 1uw4_A           82 VEFAP   86 (91)
T ss_dssp             EEECS
T ss_pred             EEEcC
Confidence            56554

>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=97.58  E-value=0.00011  Score=46.76  Aligned_cols=54  Identities=20%  Similarity=0.321  Sum_probs=46.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC
Q 030819           78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMH  140 (171)
Q Consensus        78 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~  140 (171)
                      +.++| ++|+++...||.++|+.|| -..|+++.|-       -|||.|.+++.|..|+..+.
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fg-gv~I~WidDT-------sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFG-NIQISWIDDT-------SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSE-EEEEEEEETT-------EEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccC-CEEEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            45566 9999999999999999999 5677777764       89999999999999999764

>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=97.28  E-value=1.4e-06  Score=57.53  Aligned_cols=28  Identities=11%  Similarity=0.110  Sum_probs=25.8

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCC
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      ...|||+|+.+++++..+.+.|...+++
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v   32 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNI   32 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCE
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCE
Confidence            4679999999999999999999998877

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=96.86  E-value=0.0013  Score=44.13  Aligned_cols=77  Identities=16%  Similarity=0.263  Sum_probs=55.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCCCeEE-EEEeec--------CCCC-----CcceEEEEEeCCHHHHHHHHHHhCCc
Q 030819           77 KTRLFVSGLSFRTSEDSLRNAFQGFGQLVE-VNLVMD--------KIAN-----RPRGFAFLRYATEEESRRAIEGMHGK  142 (171)
Q Consensus        77 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~-~~~~~~--------~~~g-----~~~g~~fv~f~~~~~a~~al~~l~g~  142 (171)
                      ...|.|.++|++.. ..+.+.|++||.|.+ ......        +.+.     ....+-.|.|.+..+|.+||. .||.
T Consensus         7 e~~VtVFGFp~~~~-~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG~   84 (132)
T 3p3d_A            7 ELAILVFGYPETMA-NQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENGA   84 (132)
T ss_dssp             -CEEEEECCCGGGH-HHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTTC
T ss_pred             ceEEEEEecCHHHH-HHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCCe
Confidence            45788999987654 557789999999876 211100        0000     123577999999999999999 7999


Q ss_pred             eeCCeEEEEEEec
Q 030819          143 FLDGRVIFVEIAK  155 (171)
Q Consensus       143 ~i~g~~i~v~~~~  155 (171)
                      .+.|..|-|.+-.
T Consensus        85 ii~G~mIGV~Py~   97 (132)
T 3p3d_A           85 VFNGVLLGVIPYT   97 (132)
T ss_dssp             EETTEECEEEECC
T ss_pred             EeCcEEEEEEECC
Confidence            9999988887764

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=96.58  E-value=0.0085  Score=38.04  Aligned_cols=80  Identities=9%  Similarity=0.092  Sum_probs=55.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCC--cceEEEEEeCCHHHHHHHHHHhCCceeCC-----eE
Q 030819           76 PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANR--PRGFAFLRYATEEESRRAIEGMHGKFLDG-----RV  148 (171)
Q Consensus        76 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~--~~g~~fv~f~~~~~a~~al~~l~g~~i~g-----~~  148 (171)
                      .+-+|.|+.||+.+||+++.+.+...-.+.....+..+.+.+  .-.-|+|.|.+.+++..-.+.++|..+.+     .+
T Consensus         8 ~~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~kg~~~~   87 (97)
T 2l08_A            8 HSHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKGLEYP   87 (97)
T ss_dssp             CCCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECTTCCEEE
T ss_pred             cceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeCCCCEee
Confidence            356899999999999999887777654443332222222211  12468999999999999999999998622     24


Q ss_pred             EEEEEec
Q 030819          149 IFVEIAK  155 (171)
Q Consensus       149 i~v~~~~  155 (171)
                      ..|++|.
T Consensus        88 a~VE~AP   94 (97)
T 2l08_A           88 AVVEFAP   94 (97)
T ss_dssp             EEEEECC
T ss_pred             eEEEecC
Confidence            5566654

>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=96.36  E-value=0.0046  Score=42.40  Aligned_cols=35  Identities=6%  Similarity=0.162  Sum_probs=28.4

Q ss_pred             EEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCc
Q 030819          106 EVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGK  142 (171)
Q Consensus       106 ~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~  142 (171)
                      .+.++.+.  .+++|||||+|.+.++|++|+..+++.
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            34566665  368999999999999999999887753

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=96.31  E-value=0.0024  Score=51.88  Aligned_cols=55  Identities=11%  Similarity=0.182  Sum_probs=41.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHH
Q 030819           77 KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE  137 (171)
Q Consensus        77 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~  137 (171)
                      .++|+|. .|..+++.+|.++|.+||.|.++.+..++  |   -|+.|+|.+.+++..++.
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~--g---~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF--G---LYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS--S---EEEEEECC---CCHHHHS
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC--C---eEEEEEeCCHHHHHHHHh
Confidence            4689997 68899999999999999999998876543  3   699999999999887765

>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=96.17  E-value=0.002  Score=44.04  Aligned_cols=42  Identities=10%  Similarity=0.075  Sum_probs=37.3

Q ss_pred             CCCcceEEEEEeCCHHHHHHHHHHh-CCceeCCeEEEEEEecCc
Q 030819          115 ANRPRGFAFLRYATEEESRRAIEGM-HGKFLDGRVIFVEIAKSR  157 (171)
Q Consensus       115 ~g~~~g~~fv~f~~~~~a~~al~~l-~g~~i~g~~i~v~~~~~~  157 (171)
                      ....+|+++++|.+.++|++|++.+ ||..++| .|.+.++..+
T Consensus         9 g~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~   51 (150)
T 2i2y_A            9 GKTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKT   51 (150)
T ss_dssp             CSSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTE
T ss_pred             cccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCc
Confidence            3467899999999999999999999 9999999 9999987653

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=95.15  E-value=0.0055  Score=36.52  Aligned_cols=54  Identities=11%  Similarity=0.006  Sum_probs=38.9

Q ss_pred             eeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPS   67 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   67 (171)
                      +.+||+|++++.++..+...|...+++         .+.....+...+++++.+++.+..+..
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v---------~~v~i~~~~~~~~~~g~afV~f~~~~~   54 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEV---------KECLVMRDPLTKRSRGFGFVTFMDQAG   54 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCC---------CCEEEECCCCSSSCSSEEEECCCCTTH
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCE---------EEEEEecCCCCCCcCceEEEEEcCHHH
Confidence            579999999999999999999998877         333333333445667777776665543

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=94.75  E-value=0.0078  Score=38.02  Aligned_cols=57  Identities=7%  Similarity=0.062  Sum_probs=40.9

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCCC
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPS   67 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   67 (171)
                      |-.|||+|++++.+++.+...|...+...-       .+.....+..+++++|++|+.+..+..
T Consensus         9 m~tlfV~nL~~~~tee~L~~~F~~~G~i~v-------~~v~i~~d~~tg~srG~aFV~f~~~~~   65 (95)
T 2lkz_A            9 MDTIILRNIAPHTVVDSIMTALSPYASLAV-------NNIRLIKDKQTQQNRGFAFVQLSSAMD   65 (95)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHSTTTCCCCG-------GGEECCCCSSSSSCSSEEEEECSSSHH
T ss_pred             cCEEEEeCCCCcCCHHHHHHHHHhhCCccE-------EEEEEEecCCCCCCceEeEEEECCHHH
Confidence            456999999999999999999999876421       233334445556777787776665543

>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=94.11  E-value=0.00085  Score=43.69  Aligned_cols=88  Identities=13%  Similarity=0.136  Sum_probs=58.6

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCCCCCCC-----CCCCCCC
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPSPHSL-----STCQPKT   78 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~   78 (171)
                      ...|||+|+++++++..+...|...+++         .+....   ..+..++++++.+.....+..+     ...-.++
T Consensus         8 ~~~l~V~nlp~~~t~~~l~~~F~~~G~v---------~~v~i~---~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~   75 (115)
T 3lqv_A            8 NRILYIRNLPYKITAEEMYDIFGKYGPI---------RQIRVG---NTPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNR   75 (115)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCE---------EEEEEE---CSTTTTTCEEEEESSHHHHHHHHHHHTTCBSSSC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCe---------EEEEEe---eCCCCCcEEEEEECCHHHHHHHHHHcCCCEECCe
Confidence            4579999999999999999999988776         222111   1234477788777665433221     1222344


Q ss_pred             eEEE---------cCCCCCCCHHHHHHHHhcCCC
Q 030819           79 RLFV---------SGLSFRTSEDSLRNAFQGFGQ  103 (171)
Q Consensus        79 ~l~V---------~nl~~~~~~~~l~~~f~~~G~  103 (171)
                      .|.|         .+++...++++|.++|++||-
T Consensus        76 ~l~v~~a~~~~~~~~~~~~~~~~~l~~~~~~~g~  109 (115)
T 3lqv_A           76 YLVVLYYNANRAFQKMDTKKKEEQLKLLKEKYGI  109 (115)
T ss_dssp             BCEEEECCHHHHTTTSCHHHHHHHHHHHHHHHCC
T ss_pred             EEEEEEecCChhhhhhhHhHhHHHHHHHHHHhCC
Confidence            5554         355666788999999999984

>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease, hydrolase, magnesium, metal nonsense-mediated mRNA decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus}

Probab=93.97  E-value=0.23  Score=40.82  Aligned_cols=55  Identities=20%  Similarity=0.349  Sum_probs=45.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC
Q 030819           77 KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMH  140 (171)
Q Consensus        77 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~  140 (171)
                      ...++|+ +|..+...+|.++|+.||. .+++++.+.       .|||.|.+.+.|..++..+.
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~-v~V~widdt-------~a~V~~~~~~~a~~~l~~~~  494 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGN-IQISWIDDT-------SAFVSLSQPEQVQIAVNTSK  494 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCC-CEEEECSSS-------EEEEECSCHHHHHHHHHHHT
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCC-EEEEEEcCC-------eEEEEECCHHHHHHHHHHHH
Confidence            4566676 8999999999999999995 466666553       79999999999999999875

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=93.95  E-value=0.013  Score=38.96  Aligned_cols=54  Identities=7%  Similarity=0.013  Sum_probs=39.8

Q ss_pred             eeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLP   65 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   65 (171)
                      ..|||+|+.++++++.+...|...+.+..       .+...+.+..++++++++|+.+...
T Consensus        24 ~~lfV~nL~~~~te~~L~~~F~~~G~v~~-------~~v~i~~d~~tg~~rG~aFV~f~~~   77 (131)
T 2m2b_A           24 DTIILRNLNPHSTMDSILGALAPYAVLSS-------SNVRVIKDKQTQLNRGFAFIQLSTI   77 (131)
T ss_dssp             CEEEECSCCTTCCSHHHHHHHGGGCCCCT-------TTEECCBCSSSSSBCSCEEEECCHH
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCcce-------eeEEEEEcCCCCCcceEEEEEECCH
Confidence            46999999999999999999999887722       1133444444667778887776654

>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=93.89  E-value=0.0067  Score=37.39  Aligned_cols=54  Identities=6%  Similarity=0.070  Sum_probs=37.4

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCC
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPP   66 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   66 (171)
                      ++.+||+++.+++++..+...|...+++         .+.....+..++++++++++.+....
T Consensus         1 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i---------~~v~i~~~~~~~~~~g~afV~f~~~~   54 (90)
T 2ki2_A            1 MRNIYVGNLVYSATSEQVKELFSQFGKV---------FNVKLIYDRETKKPKGFGFVEMQEES   54 (90)
T ss_dssp             CEEEEEEEECTTSSHHHHTTTHHHHTCC---------SEEEECCCSSSCCCCEEEEEEECTTH
T ss_pred             CcEEEECCCCCCCCHHHHHHHHHhcCCE---------EEEEEEEcCCCCCcceEEEEEECCHH
Confidence            4689999999999999999999998776         33333333334555566665554443

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=93.89  E-value=0.00092  Score=42.46  Aligned_cols=28  Identities=11%  Similarity=-0.083  Sum_probs=24.8

Q ss_pred             eeeecCceeecccchhhcccCCcCCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPAP   32 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~   32 (171)
                      +.|||+++.+++++..+...|...+++.
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~   28 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLR   28 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeE
Confidence            4799999999999999999999888763

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=92.50  E-value=0.014  Score=37.81  Aligned_cols=66  Identities=12%  Similarity=0.019  Sum_probs=44.7

Q ss_pred             eeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCCCCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPSPHSL   71 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   71 (171)
                      ..|||+|+.+++++..+...|...+++...... .........+..+++.++++++.+.....+..+
T Consensus         8 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~-~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A   73 (116)
T 2lcw_A            8 NTIFVQGLGENVTIESVADYFKQIGIIKTNKKT-GQPMINLYTDRETGKLKGEATVSFDDPPSAKAA   73 (116)
Confidence            569999999999999999999998877221000 000023333444567788999988877766544

>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=93.30  E-value=0.013  Score=34.63  Aligned_cols=52  Identities=10%  Similarity=0.057  Sum_probs=37.6

Q ss_pred             eeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCC
Q 030819            6 FLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPP   66 (171)
Q Consensus         6 ~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   66 (171)
                      .+||++++++.++..+...|...+++         .+.........++.++++++.+..+.
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i---------~~v~i~~~~~~~~~~g~afV~f~~~~   52 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEV---------ESIELPMDNKTNKRRGFCFITFKEEE   52 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCC---------SEECCCCSCCCSSSCCCEEEECSSSH
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCe---------EEEEEEecCCCCCcCCEEEEEECCHH
Confidence            48999999999999999999998777         33333333344566777777666554

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=93.19  E-value=0.012  Score=36.62  Aligned_cols=53  Identities=15%  Similarity=0.145  Sum_probs=37.9

Q ss_pred             eeeecCceeecccchhhcccCCcCC-CCCCCCccccccccccccccccCCCCCCCCCCCCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHS-PAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPP   66 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   66 (171)
                      -.|||+|++++.+++.+...|...+ ++         .+...+.+..++++++++++.+..+.
T Consensus         2 ~~i~v~nLp~~~te~~l~~~F~~~G~~v---------~~v~i~~d~~t~~~rg~aFV~F~~~~   55 (91)
T 2lxi_A            2 NIVMLRMLPQAATEDDIRGQLQSHGVQA---------REVRLMRNKSSGQSRGFAFVEFSHLQ   55 (91)
T ss_dssp             CEEEEETCCSSCCHHHHHHHHHHHTCCC---------SBCCSSSCSSSCCCSSEEEEECSSHH
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCEe---------EEEEEEecCCCCCcCceEEEEecCHH
Confidence            4689999999999999999999877 44         33333444445666777766655443

>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=92.95  E-value=0.014  Score=38.45  Aligned_cols=53  Identities=11%  Similarity=-0.001  Sum_probs=37.3

Q ss_pred             eeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPP   66 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   66 (171)
                      +.|||+++.++.++..+...|...+++         .+...+....+++.++++++.+....
T Consensus        26 ~~l~V~nLp~~~te~~l~~~F~~~G~v---------~~~~~~~~~~~g~~~G~afV~F~~~~   78 (124)
T 1wel_A           26 FCVYLKGLPFEAENKHVIDFFKKLDIV---------EDSIYIAYGPNGKATGEGFVEFRNEA   78 (124)
T ss_dssp             CEEEEECCCTTCCHHHHHHHSCSSCBC---------TTTCEEEECTTSSEEEEEEEEBSSSH
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCc---------cceEEEEECCCCCCCeEEEEEECCHH
Confidence            579999999999999999999998877         22223333334556666666555443

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=92.90  E-value=0.028  Score=36.32  Aligned_cols=54  Identities=17%  Similarity=0.058  Sum_probs=37.4

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCCCCCCcccccccccccccccc---CCCCCCCCCCCCCCCC
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQ---GRGRGACFPLACLPPS   67 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~   67 (171)
                      .+.|||+++.+++++..+...|...+++.          ........+   ++.++++++.+..+..
T Consensus         8 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~----------~~~~~~~~~~~~g~~~G~aFV~f~~~~~   64 (114)
T 2dnl_A            8 SRKVFVGGLPPDIDEDEITASFRRFGPLV----------VDWPHKAESKSYFPPKGYAFLLFQEESS   64 (114)
T ss_dssp             CCCEEEECCCTTCCHHHHHHHTTTTCCCC----------EECTTSSSSCCCSCTTSEEEECCSSHHH
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCEE----------EEEeecCCCCCCCCcccEEEEEECCHHH
Confidence            57899999999999999999999988772          111222222   4566677666655443

>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=92.90  E-value=0.0047  Score=39.23  Aligned_cols=51  Identities=16%  Similarity=-0.007  Sum_probs=34.9

Q ss_pred             eeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACL   64 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   64 (171)
                      ..|||+|++++++++.+...|...+++         .+.....+..++++++++++.+..
T Consensus        20 t~lfV~nLp~~~te~~L~~~F~~~G~I---------~~v~i~~d~~tg~~kG~afV~f~~   70 (99)
T 4fxv_A           20 TNLIVNYLPQNMTQDELRSLFSSIGEV---------ESAKLIRDKVAGHSLGYGFVNYVT   70 (99)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCE---------EEEEEEECSSSCCEEEEEEEEESS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCE---------EEeEeeecCCCCcccccEEEEECC
Confidence            359999999999999999999988776         333333333344555555544443

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=92.67  E-value=0.015  Score=37.45  Aligned_cols=27  Identities=7%  Similarity=-0.032  Sum_probs=24.6

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      +.|||+++.++++++.+...|...+++
T Consensus        26 ~~lfV~nLp~~~te~~L~~~F~~~G~i   52 (109)
T 2rs2_A           26 CKMFIGGLSWQTTQEGLREYFGQFGEV   52 (109)
T ss_dssp             CCEEEESCCTTCCHHHHHHHHTTTSCE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHccCCe
Confidence            579999999999999999999988776

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=92.55  E-value=0.0086  Score=40.29  Aligned_cols=53  Identities=8%  Similarity=-0.041  Sum_probs=45.8

Q ss_pred             eeeeeecCce----eecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCC
Q 030819            3 VLGFLPVPTT----YFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACL   64 (171)
Q Consensus         3 ~~~~~~v~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   64 (171)
                      |...|||+++    .++.++..+...|...+.+         .+.....+..+++++|++++.+..
T Consensus         1 mp~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV---------~~~~li~Dp~Tg~slGfgfVef~d   57 (136)
T 2j8a_A            1 MSCEIVVYPAQDSTTTNIQDISIKNYFKKYGEI---------SHFEAFNDPNSALPLHVYLIKYAS   57 (136)
T ss_dssp             -CCEEEEEESSSSCCCCCCHHHHHHHHHTTSCC---------SEEEEEECTTTCCEEEEEEEECC-
T ss_pred             CCcEEEEeCCCCCCCCCCCHHHHHHHHHhcCCe---------EEEEEEecCCCCceeeEEEEEECC
Confidence            3468999999    9999999999999999998         777788888888999999887775

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=92.52  E-value=0.0029  Score=40.13  Aligned_cols=58  Identities=9%  Similarity=0.058  Sum_probs=42.5

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCCCCCCC
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPSPHSL   71 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   71 (171)
                      .+.|||+++.++++++.+...|...+++         .+....... .++.++++++.+.....+..+
T Consensus         9 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i---------~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A   66 (102)
T 2xs2_A            9 PNTVFVGGIDVRMDETEIRSFFARYGSV---------KEVKIITDR-TGVSKGYGFVSFYNDVDVQKI   66 (102)
T ss_dssp             EEEEEEECCCTTCCHHHHHHHHGGGSCE---------EEEEEEECT-TSCEEEEEEEEESSCCCHHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCe---------EEEEEEECC-CCCccceEEEEECCHHHHHHH
Confidence            5789999999999999999999887766         333333333 566777888877766654433

>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=92.49  E-value=0.01  Score=36.64  Aligned_cols=51  Identities=8%  Similarity=0.004  Sum_probs=35.1

Q ss_pred             eeecCceeecccchhhcccCCcCC--CCCCCCccccccccccccccccCCCCCCCCCCCCCC
Q 030819            6 FLPVPTTYFNINQNLLIHNLTRHS--PAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLP   65 (171)
Q Consensus         6 ~~~v~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   65 (171)
                      .|||+|+.++.+++.+...|...+  .+         .+.....+..+++++|++++.+...
T Consensus         3 ~l~V~nL~~~~t~~~l~~~F~~~G~~~v---------~~v~i~~~~~~g~~kG~afV~f~~~   55 (90)
T 3p5t_L            3 ALYIGNLTWWTTDEDLTEAVHSLGVNDI---------LEIKFFENRANGQSKGFALVGVGSE   55 (90)
T ss_dssp             -CEEESCCTTCCHHHHHHHHHTTTCCCC---------CCEEEEECTTTCCEEEEEEECC-CH
T ss_pred             EEEEeCCCCCCCHHHHHHHHHHhCCCce---------EEEEEEecCCCCccCcEEEEEECCH
Confidence            589999999999999999999887  44         3333334444556666666665544

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=92.47  E-value=0.03  Score=35.20  Aligned_cols=27  Identities=11%  Similarity=0.039  Sum_probs=24.5

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      +.|||+++.+++++..+...|...+++
T Consensus        13 ~~l~V~nLp~~~t~~~l~~~f~~~G~i   39 (102)
T 2cqb_A           13 RVLYVGGLAEEVDDKVLHAAFIPFGDI   39 (102)
T ss_dssp             SCEEEESCCSSCCHHHHHHHHTTTSCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHhhccCCE
Confidence            569999999999999999999988776

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=92.47  E-value=0.018  Score=34.04  Aligned_cols=51  Identities=18%  Similarity=0.078  Sum_probs=34.6

Q ss_pred             eeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCC
Q 030819            6 FLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLP   65 (171)
Q Consensus         6 ~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   65 (171)
                      ++||+++++++++..+...|...+++         .+.........+++++++++.+..+
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i---------~~v~i~~~~~~~~~~g~afV~f~~~   51 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKV---------DDAMLMFDKTTNRHRGFGFVTFESE   51 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCC---------SEECCCBCSSSTTSCBEEEEECSCH
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCE---------EEEEEEecCCCCCcCcEEEEEECCH
Confidence            48999999999999999999998776         2322233333445555665555443

>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=92.43  E-value=0.03  Score=35.74  Aligned_cols=54  Identities=7%  Similarity=0.049  Sum_probs=34.6

Q ss_pred             eeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLP   65 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   65 (171)
                      +.|||+|+.++.++..+...|...++...      -.+........ ++.++++++.+...
T Consensus        12 ~~l~V~nLp~~~te~~l~~~F~~~g~~~~------v~~v~i~~~~~-g~~~G~afV~F~~~   65 (107)
T 2lmi_A           12 FLIRAQGLPWSCTMEDVLNFFSDCRIRNG------ENGIHFLLNRD-GKRRGDALIEMESE   65 (107)
T ss_dssp             CEEEEECCCSSCCSHHHHHHTTTSCBTTT------TTTEECCCCTT-STTCSEEEEEBSSH
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCcCC------cceEEEEECCC-CCEeeEEEEEECCH
Confidence            56999999999999999999988666210      02222223322 55666666555443

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=92.33  E-value=0.027  Score=34.16  Aligned_cols=28  Identities=7%  Similarity=-0.172  Sum_probs=24.9

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCC
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      .+.|||+++++++++..+...|...+++
T Consensus         5 ~~~l~v~nlp~~~t~~~l~~~f~~~G~i   32 (85)
T 1x4e_A            5 SSGLYIRGLQPGTTDQDLVKLCQPYGKI   32 (85)
T ss_dssp             CCEEEEESCCTTCCHHHHHTTSTTTSCE
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhcCCe
Confidence            3579999999999999999999987766

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=92.02  E-value=0.0093  Score=38.64  Aligned_cols=52  Identities=12%  Similarity=0.071  Sum_probs=39.6

Q ss_pred             eeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLP   65 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   65 (171)
                      ..|||+++.++++++.+.+.|...+++         .+.....+..++++++++++.+...
T Consensus         7 ~~lfV~nL~~~~te~~L~~~F~~~G~i---------~~v~i~~d~~tg~~rG~aFV~f~~~   58 (110)
T 3s8s_A            7 KEVTFARLNDNVRETFLKDMCRKYGEV---------EEVEILLHPRTRKHLGLARVLFTST   58 (110)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHTTTSCE---------EEEEEEECTTTCCEEEEEEEEESSH
T ss_pred             cEEEEECCCCCCCHHHHHHHHHhcCCe---------eEEEEEECCCCCceeeEEEEEECCH
Confidence            469999999999999999999998887         4555555555566777777655443

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=91.96  E-value=0.022  Score=35.99  Aligned_cols=54  Identities=13%  Similarity=-0.003  Sum_probs=36.8

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCC
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPP   66 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   66 (171)
                      .+.|||+++.+++++..+...|...+++         .+........+++.++++++.+..+.
T Consensus        13 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i---------~~v~i~~~~~~~~~~g~afV~f~~~~   66 (103)
T 2dnm_A           13 MITLKVDNLTYRTSPDSLRRVFEKYGRV---------GDVYIPREPHTKAPRGFAFVRFHDRR   66 (103)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHTTTSCE---------EEEECCBCSSSCSBCSCEEEEESSSS
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhcCCE---------EEEEEEeCCCCCCCCeEEEEEECCHH
Confidence            3679999999999999999999987766         33333333333455566665554443

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=91.86  E-value=0.013  Score=37.50  Aligned_cols=52  Identities=8%  Similarity=-0.067  Sum_probs=38.1

Q ss_pred             eeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPP   66 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   66 (171)
                      ..|||++++++.++..+...|...+++         .+........ ++++|++++.+..+.
T Consensus        12 ~~lfV~~Lp~~~te~~L~~~F~~~G~v---------~~v~i~~d~~-g~~rG~aFV~F~~~e   63 (103)
T 1s79_A           12 RSVYIKGFPTDATLDDIKEWLEDKGQV---------LNIQMRRTLH-KAFKGSIFVVFDSIE   63 (103)
T ss_dssp             GCEEEECCCTTCCHHHHHHHHHTSSCE---------EEEEEECCCT-TSCCCEEEEEESSHH
T ss_pred             CEEEEECCCCCCCHHHHHHHHhhcCCE---------EEEEEEECCC-CCCccEEEEEECCHH
Confidence            469999999999999999999998877         3333333333 667777777665543

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=91.85  E-value=0.028  Score=36.32  Aligned_cols=51  Identities=16%  Similarity=0.066  Sum_probs=35.3

Q ss_pred             eeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACL   64 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   64 (171)
                      +.|||+++.+++++..+...|...+++         ..........+++.++++++.+..
T Consensus        28 ~~l~V~nLp~~~te~~l~~~F~~~G~i---------~~v~i~~~~~~g~~~g~afV~f~~   78 (116)
T 1x4b_A           28 RKLFIGGLSFETTEESLRNYYEQWGKL---------TDCVVMRDPASKRSRGFGFVTFSS   78 (116)
T ss_dssp             TEEEEECCTTCCCHHHHHHHHTSSCCC---------SEEEEECCTTTSSCCSEEEEECSS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCE---------EEEEEEECCCCCCcCceEEEEeCC
Confidence            579999999999999999999988877         333333333344555555544443

>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=91.57  E-value=0.02  Score=36.42  Aligned_cols=53  Identities=15%  Similarity=0.198  Sum_probs=37.5

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCCCCCCccccccc-cccccccccCCCCCCCCCCCCCCC
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRD-FDSLFSLRQGRGRGACFPLACLPP   66 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~   66 (171)
                      .+.|||++++++.++..+...|...+.+         .+ ...... .+++.++++++.+..+.
T Consensus        15 ~~~l~V~nLp~~~te~~l~~~F~~~G~v---------~~~v~i~~~-~~g~~~G~afV~F~~~~   68 (104)
T 1wg5_A           15 DGFVRLRGLPFGCSKEEIVQFFSGLEIV---------PNGMTLPVD-FQGRSTGEAFVQFASQE   68 (104)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHTTTCCEE---------EEEEECCBC-SSSCBCSEEEEEESSHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCc---------ceeEEEEEC-CCCCcceEEEEEECCHH
Confidence            3679999999999999999999887665         22 222233 45667777777665544

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=91.56  E-value=0.023  Score=35.62  Aligned_cols=28  Identities=11%  Similarity=-0.028  Sum_probs=24.8

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCC
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      .+.|||+++.++++++.+...|...+++
T Consensus        10 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i   37 (99)
T 2dgs_A           10 SNKIFVGGIPHNCGETELREYFKKFGVV   37 (99)
T ss_dssp             CCEEEEESCCSSCCHHHHHHHHSSSSCE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCe
Confidence            3579999999999999999999987766

>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=91.54  E-value=0.023  Score=36.66  Aligned_cols=51  Identities=14%  Similarity=0.087  Sum_probs=35.1

Q ss_pred             eeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACL   64 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   64 (171)
                      +.|||+++.+++++..+...|...+.+         .+.....+..+++.++++++.+..
T Consensus        26 ~~l~V~nlp~~~t~~~l~~~F~~~G~i---------~~v~i~~~~~~g~~~g~afV~f~~   76 (114)
T 2cq4_A           26 RTVFCMQLAARIRPRDLEDFFSAVGKV---------RDVRIISDRNSRRSKGIAYVEFCE   76 (114)
T ss_dssp             TEEEEESCCTTCCHHHHHHHHTTTSCE---------EEEEECCSCCSSSCCCCEEEEESC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhCCCE---------eEEEEEecCCCCccCcEEEEEeCc
Confidence            579999999999999999999887766         333333333334555565554443

>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=91.36  E-value=0.03  Score=35.56  Aligned_cols=53  Identities=9%  Similarity=0.014  Sum_probs=37.1

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCCC
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPS   67 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   67 (171)
                      .+.|||+|++++.+++.+.+.|...++.          +....... +++.++++++.+..+..
T Consensus        15 ~~~l~V~nLp~~~te~~l~~~F~~~G~~----------~v~i~~d~-~g~~~G~afV~F~~~~~   67 (102)
T 1wez_A           15 GHCVHMRGLPYRATENDIYNFFSPLNPM----------RVHIEIGP-DGRVTGEADVEFATHED   67 (102)
T ss_dssp             SCEEEEESCCTTCCHHHHHHSSCSCCCS----------EEEEEESS-SSCEEEEEEEECSSSHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHcCce----------EEEEEECC-CCCEeeEEEEEECCHHH
Confidence            3579999999999999999999886632          22222332 46667777777665543

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=91.23  E-value=0.023  Score=36.80  Aligned_cols=51  Identities=6%  Similarity=-0.140  Sum_probs=34.5

Q ss_pred             eeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACL   64 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   64 (171)
                      +.|||+++.+++++..+...|...+++         .+.....+...++.++++++.+..
T Consensus        41 ~~l~V~nlp~~~t~~~l~~~F~~~G~i---------~~~~i~~~~~~g~~~g~afV~f~~   91 (118)
T 2khc_A           41 CNLFIYHLPQEFTDTDLASTFLPFGNV---------ISAKVFIDKQTSLSKCFGFVSFDN   91 (118)
T ss_dssp             EEEEEECSCTTCCHHHHHHHTTTSCEE---------EEEEECCCSSSSCCCCEEEEEEES
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCE---------EEEEEEeCCCCCCcCcEEEEEECC
Confidence            579999999999999999999887765         333333333344555555544443

>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=91.22  E-value=0.031  Score=37.21  Aligned_cols=56  Identities=11%  Similarity=0.132  Sum_probs=39.3

Q ss_pred             eeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPSPH   69 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   69 (171)
                      +.|||+|++++.+++.+...|... .+.       ..+........ ++.+|++++.+..+..+.
T Consensus        43 ~~lfVgnLp~~~te~dL~~~F~~~-~i~-------~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~   98 (126)
T 2hgm_A           43 GFVRLRGLPFGCTKEEIVQFFSGL-EIV-------PNGITLPVDPE-GKITGEAFVQFASQELAE   98 (126)
T ss_dssp             CEEEEECCCTTCCHHHHHHHTTTS-CEE-------EEEEECCCCSS-SSSCSEEEEEESSTTHHH
T ss_pred             CEEEEeCCCCCCCHHHHHHHHhcC-Cce-------eeEEEEEECCC-CCCceEEEEEECCHHHHH
Confidence            579999999999999999999885 220       00233333333 778888888887766443

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=91.19  E-value=0.032  Score=34.61  Aligned_cols=28  Identities=11%  Similarity=0.057  Sum_probs=25.3

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCC
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      .+.|||+++++++++..+...|...+++
T Consensus         5 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i   32 (96)
T 1x5t_A            5 SSGIFIGNLDPEIDEKLLYDTFSAFGVI   32 (96)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHHHTTSCB
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCe
Confidence            4679999999999999999999988776

>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=91.03  E-value=0.049  Score=34.21  Aligned_cols=26  Identities=0%  Similarity=-0.100  Sum_probs=22.9

Q ss_pred             eeeeecCceeecccchhhcccCCcCC
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHS   29 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~   29 (171)
                      .+.|||+|+.++++++.+...|...+
T Consensus        19 ~~~l~V~nLp~~~t~~~l~~~F~~~G   44 (100)
T 2j76_E           19 PYTAFLGNLPYDVTEESIKEFFRGLN   44 (100)
T ss_dssp             -CEEEESCCSSCCSSSHHHHHSCSSC
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhcC
Confidence            46799999999999999999998866

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=90.98  E-value=0.0086  Score=37.94  Aligned_cols=54  Identities=9%  Similarity=0.080  Sum_probs=40.5

Q ss_pred             eeeeecCceee------cccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCC
Q 030819            4 LGFLPVPTTYF------NINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPP   66 (171)
Q Consensus         4 ~~~~~v~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   66 (171)
                      .+.|||+|+++      +..+..+...|...+++         .+.....+..++++++++++.+..+.
T Consensus         6 ~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i---------~~v~i~~d~~tg~~kG~afV~f~~~~   65 (100)
T 3ns6_A            6 DQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKV---------VNMEFPIDEATGKTKGFLFVECGSMN   65 (100)
T ss_dssp             GGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCE---------EEEECCEETTTTEECSEEEEEESSHH
T ss_pred             CcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCE---------eEEEEEEcCCCCccceEEEEEECCHH
Confidence            46799999999      99999999999998877         44444455555677777776665543

>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=90.92  E-value=0.013  Score=35.77  Aligned_cols=50  Identities=22%  Similarity=0.217  Sum_probs=34.1

Q ss_pred             eeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLAC   63 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   63 (171)
                      +.|||+++++++++..+...|...+++         .+........+++.++++++.+.
T Consensus        12 ~~l~V~nlp~~~t~~~l~~~F~~~G~i---------~~v~i~~~~~~g~~~g~afV~f~   61 (87)
T 3s7r_A           12 GKMFVGGLSWDTSKKDLKDYFTKFGEV---------VDCTIKMDPNTGRSRGFGFILFK   61 (87)
T ss_dssp             TEEEEECCCTTCCHHHHHHHHTTTSCE---------EEEEEEECTTTCCEEEEEEEEES
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhCCCE---------EEEEEeecCCCCccccEEEEEEC
Confidence            579999999999999999999887766         33333333333445555554443

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=90.74  E-value=0.02  Score=35.89  Aligned_cols=29  Identities=7%  Similarity=0.037  Sum_probs=26.0

Q ss_pred             eeeeeecCceeecccchhhcccCCcCCCC
Q 030819            3 VLGFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         3 ~~~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      ..+.|||+++.+++++..+...|...+++
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i   36 (99)
T 2div_A            8 MAASLWMGDLEPYMDENFISRAFATMGET   36 (99)
T ss_dssp             SSSEEEECSCCTTCCHHHHHHHHHHTTCC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHhCCc
Confidence            35689999999999999999999998876

>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=90.72  E-value=0.036  Score=34.57  Aligned_cols=27  Identities=7%  Similarity=0.107  Sum_probs=24.8

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      +.|||++++++++++.+...|...+++
T Consensus        16 ~~l~v~nLp~~~t~~~l~~~F~~~G~v   42 (98)
T 2cqp_A           16 TIIKVQNMPFTVSIDEILDFFYGYQVI   42 (98)
T ss_dssp             EEEEEESCCTTCCHHHHHHHTTTSCCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHcCCc
Confidence            679999999999999999999988777

>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=90.66  E-value=0.024  Score=35.90  Aligned_cols=27  Identities=11%  Similarity=-0.080  Sum_probs=24.6

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      +.|||+++.+++++..+...|...+++
T Consensus        14 ~~l~V~nlp~~~t~~~l~~~F~~~G~i   40 (106)
T 2dgp_A           14 IKLFIGQIPRNLDEKDLKPLFEEFGKI   40 (106)
T ss_dssp             EEEEEESCCTTCCHHHHHHHHHHHSCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCe
Confidence            579999999999999999999988776

>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=90.65  E-value=0.034  Score=37.50  Aligned_cols=54  Identities=9%  Similarity=0.058  Sum_probs=35.3

Q ss_pred             eeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLP   65 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   65 (171)
                      +.|||+|+.++.++..+...|...+.+..      -.+........ +++++++++.+..+
T Consensus        45 ~~lfVgnLp~~~te~dL~~~F~~~G~v~~------v~~v~i~~d~~-g~srG~aFV~F~~~   98 (136)
T 2hgl_A           45 FVVKLRGLPWSCSVEDVQNFLSDCTIHDG------AAGVHFIYTRE-GRQSGEAFVELGSE   98 (136)
T ss_dssp             CEEEEESCCTTCCHHHHHHHTTTCCCSSS------STTEEEEECSS-SCEEEEEEEECSSH
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCcCc------eeEEEEEECCC-CCCCeEEEEEECCH
Confidence            56999999999999999999999776210      02222233322 55666666555443

>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=90.55  E-value=0.017  Score=42.42  Aligned_cols=56  Identities=9%  Similarity=-0.002  Sum_probs=43.8

Q ss_pred             eeeecCceeecccchhhcccCCcCC--CCCCCCccccccccccccccccCCCCCCCCCCCCCCCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHS--PAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPSPH   69 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   69 (171)
                      +.|||+|+.+++++..|...|...+  .+         .+...+.+..++++++++|+.+.....+.
T Consensus        69 ~~lfVgnL~~~~te~~L~~~F~~~G~~~v---------~~v~i~~d~~tg~skGfaFV~f~~~~~a~  126 (229)
T 3q2s_C           69 IALYIGNLTWWTTDEDLTEAVHSLGVNDI---------LEIKFFENRANGQSKGFALVGVGSEASSK  126 (229)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHHTTTCCCE---------EEEEEEECTTTCCEEEEEEEEESCTTHHH
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHHHCCcce---------EEEEEEecCCCCccceEEEEEECCHHHHH
Confidence            5699999999999999999999877  45         44445555567788889998887765433

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A

Probab=90.45  E-value=0.021  Score=34.86  Aligned_cols=52  Identities=10%  Similarity=0.024  Sum_probs=35.1

Q ss_pred             eeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLP   65 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   65 (171)
                      +.+||++++++.++..+...|...+++         .+.....+...++.++++++.+..+
T Consensus         7 ~~l~V~nlp~~~t~~~l~~~F~~~G~i---------~~v~i~~~~~~~~~~g~afV~f~~~   58 (89)
T 3ucg_A            7 RSIYVGNVDYGATAEELEAHFHGCGSV---------NRVTILCDKFSGHPKGFAYIEFSDK   58 (89)
T ss_dssp             TEEEEESCCTTCCHHHHHHHHGGGCCE---------EEEEEEESCSSSSCCEEEEEEESST
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhCCCE---------EEEEEEecCCCCCcceEEEEEECCH
Confidence            579999999999999999999987766         3333333333445555555544443

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=90.44  E-value=0.031  Score=35.26  Aligned_cols=28  Identities=7%  Similarity=-0.063  Sum_probs=25.0

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCC
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      .+.|||+++.++++++.+...|...+++
T Consensus        15 ~~~l~V~nlp~~~t~~~l~~~f~~~G~i   42 (103)
T 2cq0_A           15 NATIRVTNLSEDTRETDLQELFRPFGSI   42 (103)
T ss_dssp             SEEEEEESCCTTCCHHHHHTTSTTTCCE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCe
Confidence            3679999999999999999999987766

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=90.39  E-value=0.023  Score=35.61  Aligned_cols=28  Identities=7%  Similarity=-0.118  Sum_probs=25.3

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCC
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      .+.|||+|+.++++++.+...|...+.+
T Consensus        13 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i   40 (99)
T 2la6_A           13 NNTIFVQGLGENVTIESVADYFKQIGII   40 (99)
T ss_dssp             CSEEEEECCCSSCCHHHHHHHHTTTSCB
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCE
Confidence            4679999999999999999999988776

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=90.35  E-value=0.016  Score=36.73  Aligned_cols=53  Identities=19%  Similarity=0.093  Sum_probs=36.2

Q ss_pred             eeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPP   66 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   66 (171)
                      +.|||+++.+++++..+...|...+++         .+.........++.++++++.+..+.
T Consensus        17 ~~l~V~nlp~~~t~~~l~~~F~~~G~v---------~~v~i~~~~~~g~~~g~afV~f~~~~   69 (105)
T 2dh8_A           17 GKLFVGGLDWSTTQETLRSYFSQYGEV---------VDCVIMKDKTTNQSRGFGFVKFKDPN   69 (105)
T ss_dssp             SEECCBSCCTTCCHHHHHHHHHTTSCE---------EEEEEEECSSSCCEEEEEEEEESSTT
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCe---------EEEEEeeCCCCCCcceEEEEEECCHH
Confidence            579999999999999999999887766         33333333334455556655555443

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=90.25  E-value=0.06  Score=34.73  Aligned_cols=49  Identities=14%  Similarity=0.040  Sum_probs=33.0

Q ss_pred             eeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACL   64 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   64 (171)
                      +.|||+|++++.++..+.+.|... .+         .+....... .++.++++++.+..
T Consensus        17 ~~v~V~nLp~~~te~dl~~~F~~~-~v---------~~v~i~~d~-~g~~~G~afV~F~~   65 (109)
T 2dnn_A           17 LYVSVHGMPFSAMENDVRDFFHGL-RV---------DAVHLLKDH-VGRNNGNGLVKFLS   65 (109)
T ss_dssp             HEEEEECCCSSCCHHHHHHHTTTS-CC---------CEEEECCCT-TCCCCSEEEEECSS
T ss_pred             CEEEEeCCCCCCCHHHHHHHhccC-Ce---------eEEEEEECC-CCCCCeEEEEEECC
Confidence            479999999999999999999875 33         222223332 25566666655544

>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=90.24  E-value=0.036  Score=34.31  Aligned_cols=27  Identities=7%  Similarity=0.096  Sum_probs=24.7

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      +.|||++++++++++.+...|...+++
T Consensus        16 ~~l~V~nlp~~~t~~~l~~~F~~~G~i   42 (95)
T 2ek1_A           16 TVIKVQNMPFTVSIDEILDFFYGYQVI   42 (95)
T ss_dssp             EEEEEECCCTTCCHHHHHHHTTTSCBC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCc
Confidence            679999999999999999999987776

>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=90.23  E-value=0.015  Score=46.91  Aligned_cols=56  Identities=20%  Similarity=0.261  Sum_probs=43.3

Q ss_pred             eeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPSPH   69 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   69 (171)
                      +.|||+|+.+++++..|...|...+++         ..+..+....++..++++|+.|.....+.
T Consensus       103 ~~lfV~nL~~~~te~~L~~~F~~~G~I---------~~v~i~~d~~tg~~kG~aFV~F~~~e~A~  158 (437)
T 3pgw_S          103 KTLFVARVNYDTTESKLRREFEVYGPI---------KRIHMVYSKRSGKPRGYAFIEYEHERDMH  158 (437)
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHcCCe---------eEEEeeccCCCCCccceEEEeeccHHHHH
Confidence            579999999999999999999998887         44444445456777888888877665443

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=90.18  E-value=0.049  Score=34.93  Aligned_cols=28  Identities=7%  Similarity=-0.089  Sum_probs=25.1

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCC
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      .+.|||+|+.++++++.+...|...+++
T Consensus        15 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i   42 (113)
T 2cpe_A           15 NSAIYVQGLNDSVTLDDLADFFKQCGVV   42 (113)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHHTTTSCB
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCE
Confidence            3579999999999999999999988776

>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=90.13  E-value=0.084  Score=35.65  Aligned_cols=52  Identities=8%  Similarity=-0.012  Sum_probs=37.9

Q ss_pred             eeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPS   67 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   67 (171)
                      ..|||+|+.++.+++.+.+.|...+ +         .+.....+. .+++++++++.+..+..
T Consensus        47 ~~lfV~nLp~~~te~dL~~~F~~~G-i---------~~v~i~~d~-~g~srGfaFV~F~~~e~   98 (139)
T 2hgn_A           47 HCVHMRGLPYKATENDIYNFFSPLN-P---------VRVHIEIGP-DGRVTGEADVEFATHEE   98 (139)
T ss_dssp             CCEECCSCCTTCCHHHHHHHHCSCC-C---------SEEECCCSS-SSCSSCCCEEECSHHHH
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcC-C---------eEEEEEECC-CCCCceEEEEEeCCHHH
Confidence            5799999999999999999999876 3         122223333 36788888887765543

>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=90.07  E-value=0.028  Score=35.52  Aligned_cols=27  Identities=15%  Similarity=0.106  Sum_probs=24.3

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      +.|||+++.+++++..+...|...+++
T Consensus        16 ~~l~V~nlp~~~t~~~l~~~F~~~G~i   42 (105)
T 1x5u_A           16 ATVYVGGLDEKVSEPLLWELFLQAGPV   42 (105)
T ss_dssp             TEEEEECCCTTCCHHHHHHHHHTTSCE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCe
Confidence            579999999999999999999887766

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=90.03  E-value=0.098  Score=31.83  Aligned_cols=28  Identities=7%  Similarity=-0.082  Sum_probs=25.7

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCC
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      .+.|||+++++++++..+...|...+++
T Consensus         5 ~~~l~V~nLp~~~te~~l~~~F~~~G~i   32 (88)
T 1wf0_A            5 SSGVFVGRCTGDMTEDELREFFSQYGDV   32 (88)
T ss_dssp             CCEEEEESCCSSSCHHHHHHHSTTTSCC
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHHcCCe
Confidence            4679999999999999999999998877

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=89.99  E-value=0.036  Score=34.26  Aligned_cols=28  Identities=21%  Similarity=0.158  Sum_probs=24.9

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCC
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      .+.|||+++.+++++..+...|...+++
T Consensus         5 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v   32 (95)
T 2dnz_A            5 SSGLYVGSLHFNITEDMLRGIFEPFGKI   32 (95)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHTTTSCE
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhcCCE
Confidence            4679999999999999999999887766

>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=89.85  E-value=0.021  Score=34.38  Aligned_cols=27  Identities=15%  Similarity=0.046  Sum_probs=24.3

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      +.|||+|++++++++.+...|...+++
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i   28 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSY   28 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTE
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCe
Confidence            579999999999999999999887766

>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=89.82  E-value=0.034  Score=35.49  Aligned_cols=27  Identities=7%  Similarity=-0.027  Sum_probs=24.2

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      +.|||+++.+++++..+...|...+++
T Consensus        27 ~~l~V~nlp~~~t~~~l~~~F~~~G~i   53 (110)
T 1oo0_B           27 WILFVTSIHEEAQEDEIQEKFCDYGEI   53 (110)
T ss_dssp             EEEEEESCCTTCCHHHHHHHHGGGSCE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCE
Confidence            569999999999999999999887766

>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=89.82  E-value=0.028  Score=36.28  Aligned_cols=27  Identities=7%  Similarity=-0.047  Sum_probs=24.5

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      +.|||+++.+++++..+...|...+++
T Consensus        26 ~~l~V~nLp~~~t~~~l~~~F~~~G~i   52 (115)
T 2cpz_A           26 ANLFIYHLPQEFGDQDLLQMFMPFGNV   52 (115)
T ss_dssp             CCEEEESCCSSCCHHHHHHHHGGGSCC
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCe
Confidence            569999999999999999999988776

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=89.78  E-value=0.034  Score=34.73  Aligned_cols=27  Identities=19%  Similarity=0.164  Sum_probs=24.2

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      +.|||+++.+++++..+...|...+++
T Consensus         9 ~~l~V~nlp~~~t~~~l~~~F~~~G~i   35 (99)
T 1whw_A            9 GRLFVRNLSYTSSEEDLEKLFSAYGPL   35 (99)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHHTTSCE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCE
Confidence            579999999999999999999887765

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=89.75  E-value=0.048  Score=33.60  Aligned_cols=27  Identities=15%  Similarity=0.168  Sum_probs=24.1

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      +.|||+++++++++..+...|...+++
T Consensus        17 ~~l~V~nlp~~~t~~~l~~~f~~~G~v   43 (94)
T 2e5h_A           17 STVYVSNLPFSLTNNDLYRIFSKYGKV   43 (94)
T ss_dssp             TSEEEESCCTTSCHHHHHHHTTTTSCE
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCCe
Confidence            469999999999999999999887766

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=89.74  E-value=0.032  Score=36.02  Aligned_cols=27  Identities=7%  Similarity=-0.046  Sum_probs=24.3

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      +.|||+++.++++++.+...|...+++
T Consensus        18 ~~l~V~nlp~~~t~~~l~~~F~~~G~i   44 (116)
T 2cqd_A           18 TKIFVGGLPYHTTDASLRKYFEGFGDI   44 (116)
T ss_dssp             SEEEEECCCSSCCHHHHHHHHHTTSCE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhCCCe
Confidence            579999999999999999999887766

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=89.63  E-value=0.016  Score=39.93  Aligned_cols=49  Identities=10%  Similarity=0.066  Sum_probs=34.4

Q ss_pred             eeeecCceeecccchhhcccCCcCC--CCCCCCccccccccccccccccCCCCCCCCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHS--PAPATPFTIKRRDFDSLFSLRQGRGRGACFPLA   62 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   62 (171)
                      ..|||+|+.+++++..+...|...+  .+         .+.....+..+++.+|++|+.+
T Consensus        56 ~~lfVgnLp~~~te~~L~~~F~~~G~i~v---------~~v~i~~d~~tg~skGfaFV~f  106 (156)
T 3n9u_C           56 AAVYVGSFSWWTTDQQLIQVIRSIGVYDV---------VELKFAENRANGQSKGYAEVVV  106 (156)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCE---------EEEEEEECTTTCCEEEEEEEEE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHHCCccE---------EEEEEEecCCCCccceEEEEEE
Confidence            4799999999999999999999887  44         3333334444455556655443

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=89.49  E-value=0.029  Score=35.81  Aligned_cols=28  Identities=11%  Similarity=0.016  Sum_probs=24.6

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCC
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      ...|||+++.+++++..+...|...+++
T Consensus        15 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i   42 (111)
T 1x4h_A           15 GKTVFIRNLSFDSEEEALGEVLQQFGDL   42 (111)
T ss_dssp             CCCEEEESCCTTCCHHHHHHHHHTTSCE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhcCCe
Confidence            3569999999999999999999887765

>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=89.41  E-value=0.063  Score=33.86  Aligned_cols=25  Identities=0%  Similarity=-0.073  Sum_probs=22.8

Q ss_pred             eeeecCceeecccchhhcccCCcCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHS   29 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~   29 (171)
                      +.|||+++.++++++.+...|...+
T Consensus        16 ~~l~V~nlp~~~t~~~l~~~F~~~G   40 (104)
T 1wi8_A           16 YTAFLGNLPYDVTEESIKEFFRGLN   40 (104)
T ss_dssp             EEEEEESCCSSCCHHHHHHHTTTSC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHCC
Confidence            6799999999999999999998865

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B

Probab=89.36  E-value=0.032  Score=34.75  Aligned_cols=27  Identities=4%  Similarity=0.151  Sum_probs=24.3

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      ..|||+++.+++++..+...|...+++
T Consensus         3 ~~l~V~nLp~~~t~~~l~~~F~~~G~i   29 (96)
T 2x1f_A            3 RVVYLGSIPYDQTEEQILDLCSNVGPV   29 (96)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCE
T ss_pred             cEEEEECCCCCCCHHHHHHHHHhcCCE
Confidence            579999999999999999999887765

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=89.35  E-value=0.075  Score=35.50  Aligned_cols=53  Identities=13%  Similarity=0.010  Sum_probs=37.7

Q ss_pred             eeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPP   66 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   66 (171)
                      ..|||+++.+++++..+...|...+++         .+.........++.++++++.+....
T Consensus        48 ~~l~V~nLp~~~te~~L~~~F~~~G~i---------~~v~i~~~~~~g~~~G~afV~F~~~~  100 (135)
T 2lea_A           48 TSLKVDNLTYRTSPDTLRRVFEKYGRV---------GDVYIPRDRYTKESRGFAFVRFHDKR  100 (135)
T ss_dssp             CCEEEECCCSSCHHHHHHHHHGGGSCC---------SEEECCCCSSSSSCCSCCEEECSCHH
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCE---------EEEEEEecCCCCccceEEEEEECCHH
Confidence            469999999999999999999998876         33333333344566677776665443

>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=89.27  E-value=0.056  Score=35.09  Aligned_cols=27  Identities=22%  Similarity=0.287  Sum_probs=24.7

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      +.|||+++.+++++..+...|...+++
T Consensus         8 ~~l~V~nLp~~~t~~~l~~~F~~~G~i   34 (116)
T 2fy1_A            8 GKLFIGGLNRETNEKMLKAVFGKHGPI   34 (116)
T ss_dssp             CEEEEECCTTTCCHHHHHHHHHTSSCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCE
Confidence            579999999999999999999988776

>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=89.11  E-value=0.045  Score=35.81  Aligned_cols=27  Identities=7%  Similarity=-0.066  Sum_probs=24.3

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      +.|||+|+.+++++..+...|...+++
T Consensus        23 ~~l~V~nlp~~~t~~~l~~~F~~~G~i   49 (126)
T 3ex7_B           23 WILFVTGVHEEATEEDIHDKFAEYGEI   49 (126)
T ss_dssp             EEEEEESCCTTCCHHHHHHHHHTTSCE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCe
Confidence            579999999999999999999887766

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=89.05  E-value=0.042  Score=34.52  Aligned_cols=27  Identities=22%  Similarity=0.217  Sum_probs=24.4

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      ..|||+++.+++++..+...|...+++
T Consensus        13 ~~l~v~nLp~~~t~~~l~~~f~~~G~i   39 (102)
T 1x5s_A           13 GKLFVGGLSFDTNEQSLEQVFSKYGQI   39 (102)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHHHSCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCCe
Confidence            579999999999999999999887766

>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=88.59  E-value=0.023  Score=35.89  Aligned_cols=27  Identities=11%  Similarity=-0.001  Sum_probs=24.3

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      +.|||+++.+++++..+...|...+++
T Consensus        16 ~~l~v~nlp~~~t~~~l~~~F~~~G~i   42 (103)
T 2cqg_A           16 SDLIVLGLPWKTTEQDLKEYFSTFGEV   42 (103)
T ss_dssp             CCEEEESCCSSCCHHHHHHHHGGGSCE
T ss_pred             CEEEEEcCCCcCCHHHHHHHHHhcCCe
Confidence            569999999999999999999887766

>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=88.47  E-value=0.14  Score=33.29  Aligned_cols=28  Identities=0%  Similarity=-0.079  Sum_probs=25.4

Q ss_pred             eeeeecCceeec-ccchhhcccCCcCCCC
Q 030819            4 LGFLPVPTTYFN-INQNLLIHNLTRHSPA   31 (171)
Q Consensus         4 ~~~~~v~~~~~~-~~~~~~~~~~~~~~~~   31 (171)
                      ...|||+|+.++ +++..+...|...+.+
T Consensus        25 ~~~l~V~NLp~~~~te~~L~~lF~~fG~V   53 (112)
T 1x4f_A           25 GRVIHLSNLPHSGYSDSAVLKLAEPYGKI   53 (112)
T ss_dssp             CCEEEEESCCCSSCCSHHHHTTTTTTSCC
T ss_pred             CCEEEEeCCCCccCCHHHHHHHHHhcCCE
Confidence            457999999998 9999999999998887

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=88.30  E-value=0.029  Score=35.57  Aligned_cols=27  Identities=7%  Similarity=-0.066  Sum_probs=24.4

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      +.|||+++.+++++..+...|...+++
T Consensus        24 ~~l~V~nlp~~~t~~~l~~~f~~~G~i   50 (106)
T 1p27_B           24 WILFVTGVHEEATEEDIHDKFAEYGEI   50 (106)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHGGGSCE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHhccCCe
Confidence            569999999999999999999887766

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=88.26  E-value=0.048  Score=35.54  Aligned_cols=27  Identities=4%  Similarity=-0.096  Sum_probs=23.9

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      +.|||+++.++.++..+...|...+..
T Consensus        18 ~~l~V~nLp~~~te~~l~~~F~~~G~~   44 (118)
T 2db1_A           18 YVVKLRGLPWSCSIEDVQNFLSDCTIH   44 (118)
T ss_dssp             CEEEEESCCTTCCHHHHHHHTTTSCBT
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHHcCCc
Confidence            569999999999999999999887663

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=88.10  E-value=0.063  Score=35.47  Aligned_cols=27  Identities=11%  Similarity=0.190  Sum_probs=24.4

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      +.|||+|++|+.++..+.+.|...+++
T Consensus        24 ~~v~V~nLp~~~te~dl~~~F~~~g~v   50 (123)
T 2dha_A           24 VIVRMRGLPFTATAEEVVAFFGQHCPI   50 (123)
T ss_dssp             CEEEECSCCTTCCHHHHHHHHHTTSCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhhCCc
Confidence            579999999999999999999987765

>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=88.10  E-value=0.05  Score=33.55  Aligned_cols=28  Identities=7%  Similarity=-0.115  Sum_probs=25.3

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCC
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      ...|||+++++++++..+...|...+++
T Consensus        11 ~~~l~V~~Lp~~~te~~L~~~F~~~G~i   38 (89)
T 3d2w_A           11 GSKVFVGRCTEDMTAEELQQFFCQYGEV   38 (89)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHTTTSCE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHhccCCE
Confidence            3579999999999999999999998876

>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=87.81  E-value=0.18  Score=32.34  Aligned_cols=27  Identities=11%  Similarity=0.039  Sum_probs=24.0

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      ..|||+++.+++++..+...|...+.+
T Consensus        16 ~~l~V~nLp~~~t~~~l~~~F~~~g~v   42 (114)
T 2cpy_A           16 VCAHITNIPFSITKMDVLQFLEGIPVD   42 (114)
T ss_dssp             CEEEEESCCTTSCHHHHHHHTTTSCCC
T ss_pred             cEEEEeCcCCcCCHHHHHHHHHhCCCc
Confidence            579999999999999999999887655

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=87.70  E-value=0.046  Score=34.57  Aligned_cols=27  Identities=15%  Similarity=0.095  Sum_probs=24.2

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      +.|||+++.+++++..+...|...+++
T Consensus        16 ~~l~V~nlp~~~t~~~l~~~F~~~G~i   42 (107)
T 2cph_A           16 SKILVRNIPFQANQREIRELFSTFGEL   42 (107)
T ss_dssp             CCEEEESCCTTCCHHHHHHHHHTTSCE
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHccCCe
Confidence            579999999999999999999887765

>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=87.70  E-value=0.051  Score=36.07  Aligned_cols=51  Identities=18%  Similarity=0.167  Sum_probs=34.5

Q ss_pred             eeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACL   64 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   64 (171)
                      +.|||+++.+++++..+...|...+++         .+.........++.++++++.+..
T Consensus        47 ~~l~V~nLp~~~te~~L~~~F~~~G~I---------~~v~i~~d~~tg~~~G~afV~F~~   97 (129)
T 2kxn_B           47 CCLGVFGLSLYTTERDLREVFSKYGPI---------ADVSIVYDQQSRRSRGFAFVYFEN   97 (129)
T ss_dssp             SCBCEETCTTSCCHHHHHHHHTTTSCE---------EEEEEECCSSSSCCCCEEEEEESC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCe---------EEEEEEecCCCCccceEEEEEECC
Confidence            569999999999999999999887766         333333333334555555544443

>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=87.59  E-value=0.034  Score=33.59  Aligned_cols=27  Identities=11%  Similarity=0.039  Sum_probs=24.2

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      +.|||+++++++++..+...|...+++
T Consensus         8 ~~l~V~nl~~~~~~~~l~~~f~~~G~i   34 (85)
T 3mdf_A            8 RVLYVGGLAEEVDDKVLHAAFIPFGDI   34 (85)
T ss_dssp             SEEEEECCCTTCCHHHHHHHHGGGSCE
T ss_pred             CEEEEECCCCCCCHHHHHHHHhccCCE
Confidence            569999999999999999999887766

>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=87.30  E-value=0.034  Score=33.73  Aligned_cols=27  Identities=7%  Similarity=-0.089  Sum_probs=24.2

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      ..|||+++.+++++..+...|...+++
T Consensus         7 ~~l~v~nlp~~~t~~~l~~~F~~~G~i   33 (87)
T 3bs9_A            7 FHVFVGDLSPEITTAAIAAAFAPFGRI   33 (87)
T ss_dssp             EEEEEESCCTTCCHHHHHHHHGGGSCE
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCE
Confidence            579999999999999999999887765

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=87.17  E-value=0.089  Score=34.31  Aligned_cols=28  Identities=11%  Similarity=0.040  Sum_probs=24.6

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCC
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      .+.|||+++.++.++..+...|...+++
T Consensus        35 ~~~l~V~nlp~~~t~~~l~~~F~~~G~v   62 (124)
T 2kt5_A           35 GAKLLVSNLDFGVSDADIQELFAEFGTL   62 (124)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHHHTTSCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCe
Confidence            3579999999999999999999887766

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=87.05  E-value=0.057  Score=34.28  Aligned_cols=54  Identities=11%  Similarity=0.041  Sum_probs=37.3

Q ss_pred             eeeeeecCceeecc------cchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCCC
Q 030819            3 VLGFLPVPTTYFNI------NQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPS   67 (171)
Q Consensus         3 ~~~~~~v~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   67 (171)
                      +.+.|||+|++++.      ++..+...|...+++         .+....  ..++++++++++.+..+..
T Consensus        14 ~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v---------~~v~i~--~~~g~~~G~afV~f~~~~~   73 (105)
T 2nlw_A           14 IDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKI---------TNDFYP--EEDGKTKGYIFLEYASPAH   73 (105)
T ss_dssp             CCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCE---------EEEECC--CBTTBSCCEEEEEECSSSH
T ss_pred             CCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCE---------EEEEee--CCCCCeeeEEEEEECCHHH
Confidence            35679999999998      567888889887776         222222  2345677777777766554

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=87.04  E-value=0.036  Score=36.22  Aligned_cols=27  Identities=7%  Similarity=-0.012  Sum_probs=24.3

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      +.|||+++.++++++.+...|...+++
T Consensus        37 ~~l~V~nlp~~~t~~~l~~~F~~~G~i   63 (124)
T 2jwn_A           37 RSVYVGNVDYGSTAQDLEAHFSSCGSI   63 (124)
T ss_dssp             TEEEEEEECTTCCHHHHHHHHHTTSCE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCE
Confidence            469999999999999999999987766

>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=86.83  E-value=0.047  Score=34.72  Aligned_cols=26  Identities=4%  Similarity=-0.042  Sum_probs=23.4

Q ss_pred             eeeecCceeecccchhhcccCCcCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSP   30 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~   30 (171)
                      +.|||+++.++++++.+...|...++
T Consensus         9 ~~l~V~nLp~~~t~~~l~~~f~~~G~   34 (109)
T 2dis_A            9 CRLFIGGIPKMKKREEILEEIAKVTE   34 (109)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHST
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhcC
Confidence            57999999999999999999988765

>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=86.49  E-value=0.039  Score=35.37  Aligned_cols=28  Identities=21%  Similarity=0.129  Sum_probs=24.8

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCC
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      .+.|||+++.+++++..+...|...+++
T Consensus        26 ~~~l~V~nLp~~~te~~l~~~F~~~G~i   53 (108)
T 2jrs_A           26 PMRLYVGSLHFNITEDMLRGIFEPFGRI   53 (108)
T ss_dssp             CEEEEEECCCSSCCHHHHHHHHTTTSCE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCe
Confidence            3579999999999999999999887766

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=86.28  E-value=0.044  Score=35.24  Aligned_cols=27  Identities=7%  Similarity=-0.124  Sum_probs=24.4

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      +.|||+++.+++++..+...|...+.+
T Consensus        16 ~~l~V~nlp~~~t~~~l~~~F~~~G~i   42 (115)
T 2dgo_A           16 FHVFVGDLSPEITTEDIKAAFAPFGRI   42 (115)
T ss_dssp             EEEEEESCCTTCCHHHHHHHHGGGSCE
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCe
Confidence            579999999999999999999887766

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=86.15  E-value=0.12  Score=36.20  Aligned_cols=51  Identities=12%  Similarity=0.028  Sum_probs=35.1

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCC
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACL   64 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   64 (171)
                      .+.|||+|+.++++++.+...|...+++         ......... .++.++++++.+..
T Consensus        88 ~~~l~V~nLp~~~te~~L~~~F~~~G~I---------~~v~i~~d~-~g~~kG~afV~F~~  138 (177)
T 2f3j_A           88 GAKLLVSNLDFGVSDADIQELFAEFGTL---------KKAAVDYDR-SGRSLGTADVHFER  138 (177)
T ss_dssp             CEEEEEECCCSCCCHHHHHHHHHHTSCC---------SEEEECCCT-TSSCSCCEEEEESC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCe---------EEEEEEECC-CCCEeeEEEEEeCC
Confidence            3689999999999999999999988776         333333332 44555555544443

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=86.05  E-value=0.078  Score=32.49  Aligned_cols=24  Identities=13%  Similarity=0.171  Sum_probs=21.9

Q ss_pred             eeeecCceeecccchhhcccCCcC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRH   28 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~   28 (171)
                      +.|||++++++++++.+...|...
T Consensus        11 ~~l~v~nLp~~~t~~~l~~~F~~~   34 (91)
T 2dgw_A           11 HTVKLRGAPFNVTEKNVMEFLAPL   34 (91)
T ss_dssp             CEEEEECCCSSCCHHHHHHHHTTS
T ss_pred             cEEEEECCCCCCCHHHHHHHHhhC
Confidence            579999999999999999999876

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=86.04  E-value=0.19  Score=32.02  Aligned_cols=28  Identities=14%  Similarity=0.043  Sum_probs=25.3

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCC
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      .+.|||+++.++++++.+...|...+++
T Consensus        29 ~~~l~V~nLp~~~te~~l~~~F~~~G~i   56 (109)
T 2err_A           29 PKRLHVSNIPFRFRDPDLRQMFGQFGKI   56 (109)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHGGGTCCC
T ss_pred             CCEEEEECCCCcCCHHHHHHHHHhcCCE
Confidence            3579999999999999999999998877

>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=85.93  E-value=0.15  Score=32.52  Aligned_cols=28  Identities=4%  Similarity=-0.138  Sum_probs=25.3

Q ss_pred             eeeeecCceee-cccchhhcccCCcCCCC
Q 030819            4 LGFLPVPTTYF-NINQNLLIHNLTRHSPA   31 (171)
Q Consensus         4 ~~~~~v~~~~~-~~~~~~~~~~~~~~~~~   31 (171)
                      ...|||+|+++ ++++..+...|...+.+
T Consensus        15 ~~~l~V~nLp~~~~te~dL~~lF~~fG~V   43 (102)
T 1x4d_A           15 RRVVHIMDFQRGKNLRYQLLQLVEPFGVI   43 (102)
T ss_dssp             CCEEEEESCCCSSSHHHHHHTTTGGGSCE
T ss_pred             CCEEEEeCCCCCcCCHHHHHHHHHhcCCE
Confidence            45799999999 99999999999998877

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=85.92  E-value=0.089  Score=34.88  Aligned_cols=27  Identities=11%  Similarity=0.039  Sum_probs=23.8

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      ..|||+++.+++++..+...|...+++
T Consensus        64 ~~l~v~nlp~~~~~~~l~~~f~~~G~i   90 (140)
T 2ku7_A           64 RVLYVGGLAEEVDDKVLHAAFIPFGDI   90 (140)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHGGGSCE
T ss_pred             cEEEEEeCCCCCCHHHHHHHHHhcCCE
Confidence            469999999999999999999887766

>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=85.88  E-value=0.068  Score=34.29  Aligned_cols=27  Identities=11%  Similarity=0.091  Sum_probs=24.2

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      +.|||+++++++++..+...|...+.+
T Consensus        26 ~~l~V~nlp~~~t~~~l~~~F~~~G~i   52 (114)
T 1x5o_A           26 TNLYISNLPLSMDEQELENMLKPFGQV   52 (114)
T ss_dssp             TEEEEESCCTTCCHHHHHHTTTTTSCE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCE
Confidence            569999999999999999999887765

>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=85.77  E-value=0.047  Score=34.34  Aligned_cols=27  Identities=11%  Similarity=0.113  Sum_probs=24.5

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      ..|||+++.+++++..+...|...+++
T Consensus         9 ~~l~V~nlp~~~~~~~l~~~f~~~G~i   35 (104)
T 1p1t_A            9 RSVFVGNIPYEATEEQLKDIFSEVGPV   35 (104)
T ss_dssp             SCEEEESCCTTSCHHHHHHHHHTTSCC
T ss_pred             cEEEEeCCCCcCCHHHHHHHHHhcCCe
Confidence            569999999999999999999988776

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=85.41  E-value=0.066  Score=33.68  Aligned_cols=25  Identities=16%  Similarity=-0.164  Sum_probs=22.3

Q ss_pred             eeeeecCceeecccchhhcccCCcC
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRH   28 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~   28 (171)
                      .+.|||+++.+++++..+...|...
T Consensus        15 ~~~l~V~nLp~~~t~~~l~~~F~~~   39 (103)
T 2dng_A           15 PYTAYVGNLPFNTVQGDIDAIFKDL   39 (103)
T ss_dssp             CEEEEEESCCTTCCHHHHHHHTTTS
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhC
Confidence            3579999999999999999999875

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=85.41  E-value=0.06  Score=34.64  Aligned_cols=28  Identities=4%  Similarity=-0.015  Sum_probs=25.5

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCC
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      .+.|||+|++++++++.+...|...+.+
T Consensus        16 ~~~LfV~nLp~~vte~dL~~lF~~fG~V   43 (105)
T 1sjq_A           16 SRVIHIRKLPIDVTEGEVISLGLPFGKV   43 (105)
T ss_dssp             CCEEEECSCCTTSCHHHHHHHHHHHCCE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCE
Confidence            4679999999999999999999998877

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=85.30  E-value=0.025  Score=35.55  Aligned_cols=51  Identities=14%  Similarity=-0.052  Sum_probs=34.4

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCC
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACL   64 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   64 (171)
                      .+.|||+|+.+++++..+...|...+++         .. ..+.....++.++++++.+..
T Consensus        17 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v---------~~-~~~~~~~~g~~~g~afV~f~~   67 (101)
T 1fj7_A           17 PFNLFIGNLNPNKSVAELKVAISELFAK---------ND-LAVVDVRTGTNRKFGYVDFES   67 (101)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHHHH---------HT-CCCCEEEEETTTTEEEEEESS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCc---------ce-EEEecCCCCCcCcEEEEEECC
Confidence            3579999999999999999998886654         11 222333345566666655543

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=84.95  E-value=0.074  Score=33.42  Aligned_cols=28  Identities=14%  Similarity=0.018  Sum_probs=24.8

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCC
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      .+.|||+++.+++++..+...|...+++
T Consensus        15 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i   42 (103)
T 2d9p_A           15 VVNLYVKNLDDGIDDERLRKAFSPFGTI   42 (103)
T ss_dssp             CCCEEEECCCTTCCHHHHHHTTTTTSCE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCE
Confidence            3579999999999999999999987766

>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=84.93  E-value=0.057  Score=34.06  Aligned_cols=28  Identities=7%  Similarity=-0.159  Sum_probs=24.8

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCC
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      .+.|||+++.+++++..+...|...+++
T Consensus        15 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i   42 (105)
T 2dnh_A           15 DRKLFVGMLNKQQSEEDVLRLFQPFGVI   42 (105)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHTTTSCE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCe
Confidence            3579999999999999999999887765

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=84.84  E-value=0.038  Score=34.86  Aligned_cols=27  Identities=11%  Similarity=0.054  Sum_probs=24.4

Q ss_pred             eeeecCceeecccchhhcccCCc-CCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTR-HSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~-~~~~   31 (171)
                      +.|||+++.++++++.+...|.. .+.+
T Consensus        10 ~~l~V~nLp~~~t~~~l~~~F~~~~G~v   37 (104)
T 2dhg_A           10 YSLFVGDLTPDVDDGMLYEFFVKVYPSC   37 (104)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHHCTTE
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHHhCCCe
Confidence            57999999999999999999988 7766

>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=84.60  E-value=0.076  Score=34.06  Aligned_cols=27  Identities=11%  Similarity=0.087  Sum_probs=24.0

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      +.|||+|+.++++++.+...|...+.+
T Consensus        26 ~~l~V~nLp~~~t~~~l~~~f~~~G~v   52 (115)
T 2cpx_A           26 KVLYLKNLSPRVTERDLVSLFARFQEK   52 (115)
T ss_dssp             SEEEEECCCTTCCHHHHHHHTHHHHHS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCc
Confidence            579999999999999999999887665

>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=84.36  E-value=0.061  Score=36.66  Aligned_cols=28  Identities=11%  Similarity=0.057  Sum_probs=25.1

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCC
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      .+.|||+++.+++++..+...|...+++
T Consensus        39 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i   66 (156)
T 1h2v_Z           39 SCTLYVGNLSFYTTEEQIYELFSKSGDI   66 (156)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCe
Confidence            4679999999999999999999987766

>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=84.26  E-value=0.066  Score=36.94  Aligned_cols=27  Identities=7%  Similarity=-0.027  Sum_probs=24.4

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      +.|||+|+.+++++..+...|...+++
T Consensus        73 ~~l~V~nLp~~~t~~~L~~~F~~~G~i   99 (165)
T 1rk8_A           73 WILFVTSIHEEAQEDEIQEKFCDYGEI   99 (165)
T ss_dssp             EEEEEESCCTTCCHHHHHHHHGGGSCE
T ss_pred             CEEEEeCCCCCCCHHHHHHHhhcCCCE
Confidence            469999999999999999999988776

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=84.13  E-value=0.045  Score=34.17  Aligned_cols=78  Identities=15%  Similarity=0.169  Sum_probs=53.6

Q ss_pred             eeeeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCCCCCCC-----CCCCCC
Q 030819            3 VLGFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPSPHSL-----STCQPK   77 (171)
Q Consensus         3 ~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~   77 (171)
                      +++-|||+|+.+.+++..+...|...+++         .++..      ..++|++++++..+..+..+     ...-.+
T Consensus         6 ~~~wL~VgNL~~~~te~~L~~lF~q~G~V---------~~~~l------~~~kGfaFVey~~~~eA~~Ai~~Ln~~~l~g   70 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDGPTLRTLCMQHGPL---------VSFHP------YLNQGIALCKYTTREEANKAQMALNNCVLAN   70 (89)
T ss_dssp             CCCEEEEECCCTTCCCHHHHHHHHHHSCE---------EEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTEEETT
T ss_pred             ccceEEEeCCCccCCHHHHHHHHHhhCCE---------EEEEE------cCCCcEEEEEECCHHHHHHHHHHhcCCEECC
Confidence            46779999999999999999999999998         33222      23688888888777544432     122234


Q ss_pred             CeEEEcCCCCCCCHHHHHHHHh
Q 030819           78 TRLFVSGLSFRTSEDSLRNAFQ   99 (171)
Q Consensus        78 ~~l~V~nl~~~~~~~~l~~~f~   99 (171)
                      ++|.|.    ..+++++..+|.
T Consensus        71 r~I~V~----~A~e~~~~~~~~   88 (89)
T 2wbr_A           71 TTIFAE----SPSENEVQSIMQ   88 (89)
T ss_dssp             EEEEEE----CCCHHHHHHHHC
T ss_pred             cEEEEE----ECCHHHHHHHhh
Confidence            556552    236777777664

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=83.95  E-value=0.048  Score=33.67  Aligned_cols=27  Identities=15%  Similarity=0.057  Sum_probs=24.0

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      +.|||+++.+++++..+...|...+++
T Consensus        16 ~~l~v~nlp~~~t~~~l~~~f~~~G~v   42 (95)
T 2cqc_A           16 CCLGVFGLSLYTTERDLREVFSKYGPI   42 (95)
T ss_dssp             GCEEEESCCSSCCHHHHHHHHHTTSCE
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCCe
Confidence            569999999999999999999887766

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=83.94  E-value=0.06  Score=33.67  Aligned_cols=27  Identities=15%  Similarity=0.050  Sum_probs=24.1

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      +.|||+++.+++++..+...|...+++
T Consensus        18 ~~l~v~nlp~~~t~~~l~~~F~~~G~i   44 (100)
T 2do4_A           18 HKLFISGLPFSCTKEELEEICKAHGTV   44 (100)
T ss_dssp             SCEEEESCCTTCCHHHHHHHHTTTSCE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhCCCe
Confidence            569999999999999999999887765

>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=83.68  E-value=0.22  Score=30.90  Aligned_cols=27  Identities=15%  Similarity=0.010  Sum_probs=24.6

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      +.|||+++.+++++..+...|...+++
T Consensus        16 ~~l~V~nlp~~~t~~~l~~~F~~~G~i   42 (99)
T 2cpj_A           16 SRLFVGNLPPDITEEEMRKLFEKYGKA   42 (99)
T ss_dssp             TEEEEESCCTTCCHHHHHHHTSTTCCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHhhcCCe
Confidence            479999999999999999999998776

>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=83.65  E-value=0.17  Score=32.35  Aligned_cols=28  Identities=4%  Similarity=-0.008  Sum_probs=24.5

Q ss_pred             eeeeecCceeecccchhhc---ccCCcCCCC
Q 030819            4 LGFLPVPTTYFNINQNLLI---HNLTRHSPA   31 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~---~~~~~~~~~   31 (171)
                      ...|||+++++++++..+.   ..|...+++
T Consensus        15 ~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i   45 (111)
T 2cpi_A           15 KNLVFVVGLSQRLADPEVLKRPEYFGKFGKI   45 (111)
T ss_dssp             SSCEEEEEECTTTCCHHHHHSTTTTTTTSCE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhhccCCE
Confidence            3569999999999999998   889887776

>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=83.22  E-value=0.065  Score=33.07  Aligned_cols=27  Identities=11%  Similarity=0.111  Sum_probs=24.3

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      ..|||+++++++++..+...|...+++
T Consensus        17 ~~l~v~nlp~~~~~~~l~~~F~~~G~i   43 (95)
T 2ywk_A           17 RTVFVGNLEARVREEILYELFLQAGPL   43 (95)
T ss_dssp             GEEEEECCCTTCCHHHHHHHHGGGSCE
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCCE
Confidence            579999999999999999999887766

>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=82.55  E-value=0.062  Score=32.55  Aligned_cols=27  Identities=4%  Similarity=0.044  Sum_probs=24.4

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      +.|||+|+.+++++..+...|...+++
T Consensus         5 ~~l~V~nlp~~~t~~~l~~~F~~~G~i   31 (88)
T 4a8x_A            5 TKVHIGRLTRNVTKDHIMEIFSTYGKI   31 (88)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHTTSCE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhCCCE
Confidence            579999999999999999999887766

>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=82.52  E-value=0.072  Score=33.68  Aligned_cols=28  Identities=14%  Similarity=0.113  Sum_probs=24.6

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCC
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      .+.|||+|+.+++++..+...|...+++
T Consensus        29 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i   56 (107)
T 3ulh_A           29 GGKLLVSNLDFGVSDADIQELFAEFGTL   56 (107)
T ss_dssp             SEEEEEESCCTTCCHHHHHHHHHTTSCE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCe
Confidence            3679999999999999999999887765

>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=81.69  E-value=0.22  Score=31.50  Aligned_cols=27  Identities=7%  Similarity=-0.074  Sum_probs=24.7

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      ..|||+|+.+++++..+...|...+.+
T Consensus        16 ~~l~V~nLp~~~te~~L~~~F~~fG~v   42 (101)
T 2cq1_A           16 RVLHIRKLPGEVTETEVIALGLPFGKV   42 (101)
T ss_dssp             SEEEEESCCTTCCHHHHHHTTTTTSCE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCE
Confidence            579999999999999999999988776

>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=81.65  E-value=0.16  Score=33.30  Aligned_cols=27  Identities=4%  Similarity=0.010  Sum_probs=25.0

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      ..|||+|+.++++++.+...|...+.+
T Consensus        32 ~~LfVgNLp~~vte~dL~~lF~~fG~V   58 (119)
T 2ad9_A           32 RVIHIRKLPIDVTEGEVISLGLPFGKV   58 (119)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHTTTSCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCE
Confidence            569999999999999999999998887

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=81.53  E-value=0.043  Score=36.60  Aligned_cols=27  Identities=19%  Similarity=0.092  Sum_probs=24.1

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      ..|||+++.++++++.+...|...+++
T Consensus        43 ~~l~V~nLp~~~~~~~l~~~F~~~G~i   69 (139)
T 1u6f_A           43 RNLMVNYIPTTVDEVQLRQLFERYGPI   69 (139)
T ss_dssp             SEEEEESCSTTCCHHHHHHHHHHHSCE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCe
Confidence            579999999999999999999887766

>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=81.41  E-value=0.026  Score=36.91  Aligned_cols=49  Identities=12%  Similarity=-0.009  Sum_probs=35.0

Q ss_pred             eeeec--CceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCCCC
Q 030819            5 GFLPV--PTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPSP   68 (171)
Q Consensus         5 ~~~~v--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   68 (171)
                      ..|||  |++.++.+++.+...|...+.+         .+...      ...++++|+.+..+..+
T Consensus        26 ~~L~V~Ng~L~~~~te~~L~~~F~~fG~v---------~~v~i------~~~rgfaFV~f~~~~~A   76 (114)
T 2cq2_A           26 QSLVVANGGLGNGVSRNQLLPVLEKCGLV---------DALLM------PPNKPYSFARYRTTEES   76 (114)
T ss_dssp             SEEEEETCTGGGTCCHHHHHHHHHHHSCE---------EEEEC------CTTCSCEEEEESSHHHH
T ss_pred             CEEEEECCCCCCCCCHHHHHHHHHhcCCe---------EEEEE------eCCCCEEEEEECCHHHH
Confidence            35999  8899999999999999998866         11111      12367888777765543

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=81.39  E-value=0.2  Score=31.22  Aligned_cols=28  Identities=7%  Similarity=-0.136  Sum_probs=25.0

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCC
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      .+.|||+++.+++++..+...|...+.+
T Consensus        27 ~~~l~V~nlp~~~~~~~l~~~f~~~G~i   54 (101)
T 2la4_A           27 VTTAYIGNIPHFATEADLIPLFQNFGFI   54 (101)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHTTSCC
T ss_pred             CCEEEEcCCCcccCHHHHHHHHHhCCCE
Confidence            3679999999999999999999888776

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=81.38  E-value=0.047  Score=33.97  Aligned_cols=27  Identities=11%  Similarity=0.091  Sum_probs=24.3

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      +.|||+++.++++++.+...|...+++
T Consensus         6 ~~l~V~nLp~~~t~~~l~~~F~~~G~i   32 (98)
T 2cpf_A            6 SGLFIKNLNFSTTEETLKGVFSKVGAI   32 (98)
T ss_dssp             CCEEEESCCTTCCHHHHHHHHHTTSCE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCe
Confidence            579999999999999999999887766

>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=80.15  E-value=0.22  Score=31.14  Aligned_cols=28  Identities=14%  Similarity=0.043  Sum_probs=24.7

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCC
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      .+.|||+++.+++++..+...|...+++
T Consensus        15 ~~~l~V~nlp~~~t~~~l~~~f~~~G~v   42 (103)
T 2cq3_A           15 PKRLHVSNIPFRFRDPDLRQMFGQFGKI   42 (103)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHGGGTSCE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCe
Confidence            3579999999999999999999887765

---

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	171
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	6e-22
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	8e-22
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	3e-20
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	2e-19
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	7e-19
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-18
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	2e-18
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	3e-18
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	3e-18
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	3e-18
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-18
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	5e-18
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	5e-18
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	6e-18
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	6e-18
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	7e-18
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	7e-18
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	1e-17
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	1e-17
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	2e-17
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	2e-17
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	3e-17
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	5e-17
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	5e-17
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	5e-17
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	8e-17
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	8e-17
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	1e-16
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	1e-16
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	1e-16
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	1e-16
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	1e-16
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	2e-16
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	2e-16
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	2e-16
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	3e-16
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	1e-15
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	1e-15
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	2e-10
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	1e-15
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-15
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	2e-15
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	4e-15
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	7e-15
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	8e-15
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	8e-15
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	8e-15
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	2e-14
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	3e-14
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	5e-14
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	5e-14
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	8e-14
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	1e-13
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	2e-13
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	2e-13
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	2e-13
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	7e-13
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	9e-13
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	2e-12
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	4e-12
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	9e-12
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	1e-11
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	1e-11
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 2e-11
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	2e-11
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	2e-11
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-11
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	7e-11
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	1e-10
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-10
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	2e-10
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	7e-10
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	9e-10
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	1e-09
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-09
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	3e-09
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	6e-09
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	2e-08
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	5e-08
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	9e-08
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	1e-07
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	2e-07
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	5e-07
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	2e-06
d1x4fa1	99	d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus)	0.003

>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 = 82.7 bits (204), Expect = 6e-22
 Identities = 24/88 (27%), Positives = 44/88 (50%)

Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
           +    L+V  LSF T+E+ +   F   G + ++ + +DK+     GF F+ Y +  ++  
Sbjct: 5   KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAEN 64

Query: 135 AIEGMHGKFLDGRVIFVEIAKSRAELRQ 162
           A+  ++G  LD R+I  +      E RQ
Sbjct: 65  AMRYINGTRLDDRIIRTDWDAGFKEGRQ 92

>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 = 82.3 bits (203), Expect = 8e-22
 Identities = 23/89 (25%), Positives = 45/89 (50%), Gaps = 2/89 (2%)

Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMD-KIANRPRGFAFLRYATEEESR 133
           Q  +++ V  + F+ ++  +R  F  FG+L  V L          RGF F+ + T+++++
Sbjct: 6   QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAK 65

Query: 134 RAIEGM-HGKFLDGRVIFVEIAKSRAELR 161
           +A   + H   L GR + +E A S   ++
Sbjct: 66  KAFNALCHSTHLYGRRLVLEWADSEVTVQ 94

>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 = 78.1 bits (192), Expect = 3e-20
 Identities = 23/85 (27%), Positives = 41/85 (48%), Gaps = 2/85 (2%)

Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
           Q  + L V GL ++T+E  L+  F  FG+++ V +  D      +GF F+R+   E   +
Sbjct: 6   QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVK 65

Query: 135 AIEGMHGKFLDGRVIFVEIAKSRAE 159
            +   H   +DGR    ++  S+  
Sbjct: 66  VMSQRHM--IDGRWCDCKLPNSKQS 88

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 75.3 bits (185), Expect = 2e-19
 Identities = 16/76 (21%), Positives = 37/76 (48%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           L+V  L    +E  L   F   G ++ + +  D I  R  G+A++ +    ++ RA++ M
Sbjct: 3   LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 62

Query: 140 HGKFLDGRVIFVEIAK 155
           +   + G+ + +  ++
Sbjct: 63  NFDVIKGKPVRIMWSQ 78

>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 = 74.2 bits (182), Expect = 7e-19
 Identities = 21/78 (26%), Positives = 40/78 (51%), Gaps = 1/78 (1%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           +L VS L F  S+  ++  F  FG L +   V    + R  G A + +  + ++ +A++ 
Sbjct: 2   KLLVSNLDFGVSDADIQELFAEFGTLKKAA-VHYDRSGRSLGTADVHFERKADALKAMKQ 60

Query: 139 MHGKFLDGRVIFVEIAKS 156
            +G  LDGR + +++  S
Sbjct: 61  YNGVPLDGRPMNIQLVTS 78

>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 = 73.9 bits (181), Expect = 1e-18
 Identities = 24/81 (29%), Positives = 40/81 (49%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           +LF+ GL    ++D ++     FG L   NLV D      +G+AF  Y     + +AI G
Sbjct: 3   KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62

Query: 139 MHGKFLDGRVIFVEIAKSRAE 159
           ++G  L  + + V+ A   A+
Sbjct: 63  LNGMQLGDKKLLVQRASVGAK 83

>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 = 73.5 bits (180), Expect = 2e-18
 Identities = 19/79 (24%), Positives = 39/79 (49%)

Query: 77  KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
            T L V+ L    ++  L   F+  G +    ++ D       G+AF+ + +E +S+RAI
Sbjct: 2   NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 61

Query: 137 EGMHGKFLDGRVIFVEIAK 155
           + ++G  +  + + V  A+
Sbjct: 62  KVLNGITVRNKRLKVSYAR 80

>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 = 72.7 bits (178), Expect = 3e-18
 Identities = 27/79 (34%), Positives = 46/79 (58%), Gaps = 2/79 (2%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           T L+V+ L    ++D L   F  +G +V+ N++ DK+  RPRG AF+RY   EE++ AI 
Sbjct: 7   TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 66

Query: 138 GMHGKFLDG--RVIFVEIA 154
            ++    +G  + + V +A
Sbjct: 67  ALNNVIPEGGSQPLSVRLA 85

>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 = 73.2 bits (179), Expect = 3e-18
 Identities = 27/86 (31%), Positives = 48/86 (55%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
            RLFV  LS+ +SE+ L   F  +G L E++  +D +  +P+GFAF+ +   E + +A  
Sbjct: 9   GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

Query: 138 GMHGKFLDGRVIFVEIAKSRAELRQA 163
            + G+   GR++ V  +  + E  Q+
Sbjct: 69  EVDGQVFQGRMLHVLPSTIKKEASQS 94

>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 = 72.8 bits (178), Expect = 3e-18
 Identities = 27/83 (32%), Positives = 43/83 (51%)

Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
             K  L+V GL+    +  L  AF  FG + ++ + +D    + RGFAF+ +   E++  
Sbjct: 3   TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 62

Query: 135 AIEGMHGKFLDGRVIFVEIAKSR 157
           AI+ M+   L GR I V +AK  
Sbjct: 63  AIDNMNESELFGRTIRVNLAKPM 85

>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 = 72.6 bits (178), Expect = 4e-18
 Identities = 20/88 (22%), Positives = 41/88 (46%), Gaps = 9/88 (10%)

Query: 75  QPKTRLFVSGLS-FRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESR 133
              +R+F+  L+     +  +   F  +G++V  ++          GFAF++Y  E  +R
Sbjct: 13  SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHK--------GFAFVQYVNERNAR 64

Query: 134 RAIEGMHGKFLDGRVIFVEIAKSRAELR 161
            A+ G  G+ + G+V+ + +A      R
Sbjct: 65  AAVAGEDGRMIAGQVLDINLAAEPKVNR 92

>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 = 72.8 bits (178), Expect = 5e-18
 Identities = 20/86 (23%), Positives = 40/86 (46%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
               LF+  L     +  L   F  FG +V   + +DK  N  + F F+ Y     ++ A
Sbjct: 17  EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAA 76

Query: 136 IEGMHGKFLDGRVIFVEIAKSRAELR 161
           I+ M+G  +  + + V++ +S+ + +
Sbjct: 77  IQSMNGFQIGMKRLKVQLKRSKNDSK 102

>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 = 72.1 bits (176), Expect = 5e-18
 Identities = 23/79 (29%), Positives = 41/79 (51%)

Query: 77  KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
           KT L V+ L    +++  R+ F   G++    LV DKI  +  G+ F+ Y   +++ +AI
Sbjct: 2   KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61

Query: 137 EGMHGKFLDGRVIFVEIAK 155
             ++G  L  + I V  A+
Sbjct: 62  NTLNGLRLQTKTIKVSYAR 80

>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 = 72.4 bits (177), Expect = 6e-18
 Identities = 22/84 (26%), Positives = 42/84 (50%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
               ++V GL  + SE  L   F   G +V  ++  D++  + +G+ F+ + +EE++  A
Sbjct: 8   QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA 67

Query: 136 IEGMHGKFLDGRVIFVEIAKSRAE 159
           I+ M    L G+ I V  A +  +
Sbjct: 68  IKIMDMIKLYGKPIRVNKASAHNK 91

>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 = 72.8 bits (178), Expect = 6e-18
 Identities = 29/85 (34%), Positives = 51/85 (60%), Gaps = 1/85 (1%)

Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
           +   +LF+ GLSF T+E+SLRN ++ +G+L +  ++ D  + R RGF F+ +++  E   
Sbjct: 18  EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDA 77

Query: 135 AIEGMHGKFLDGRVIFVEIAKSRAE 159
           A+       +DGRV+  + A +R E
Sbjct: 78  AMA-ARPHSIDGRVVEPKRAVAREE 101

>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 = 72.7 bits (178), Expect = 7e-18
 Identities = 15/108 (13%), Positives = 41/108 (37%), Gaps = 11/108 (10%)

Query: 64  LPPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAF 123
           LPP        +    L++  L ++ + + + + F  +G + ++           RG A+
Sbjct: 2   LPP--------EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQI---RVGNTPETRGTAY 50

Query: 124 LRYATEEESRRAIEGMHGKFLDGRVIFVEIAKSRAELRQAFKNNPRQN 171
           + Y    +++ A + + G  +  R + V    +    ++       + 
Sbjct: 51  VVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNANRAFQKMDTKKKEEQ 98

>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 = 72.0 bits (176), Expect = 7e-18
 Identities = 14/86 (16%), Positives = 42/86 (48%), Gaps = 1/86 (1%)

Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQG-FGQLVEVNLVMDKIANRPRGFAFLRYATEEESR 133
           +P   ++++ L+ +  +D L+ +    F +  ++  ++   + + RG AF+ +     + 
Sbjct: 1   RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSAT 60

Query: 134 RAIEGMHGKFLDGRVIFVEIAKSRAE 159
            A+  M G     + + ++ AK+ ++
Sbjct: 61  NALRSMQGFPFYDKPMRIQYAKTDSD 86

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 71.2 bits (174), Expect = 1e-17
 Identities = 21/76 (27%), Positives = 42/76 (55%), Gaps = 1/76 (1%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           ++F+ GLS++T+++ LR  F  FG++ E  ++ D +  R RGF F+ +  +    + +  
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA- 60

Query: 139 MHGKFLDGRVIFVEIA 154
                LD + I  ++A
Sbjct: 61  QSRHELDSKTIDPKVA 76

>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 = 71.6 bits (175), Expect = 1e-17
 Identities = 13/79 (16%), Positives = 33/79 (41%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
             T + V  + F  S D + + F G+  +     +       P G A + + + +E+  A
Sbjct: 8   GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAA 67

Query: 136 IEGMHGKFLDGRVIFVEIA 154
           +  ++ + +  R + + + 
Sbjct: 68  VIDLNDRPIGSRKVKLVLG 86

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 70.8 bits (173), Expect = 2e-17
 Identities = 21/81 (25%), Positives = 41/81 (50%), Gaps = 3/81 (3%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDK---IANRPRGFAFLRYATEEESRRAI 136
           LF+  L+F T+E++L+  F   G +    +   K         GF F+ Y   E++++A+
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 137 EGMHGKFLDGRVIFVEIAKSR 157
           + + G  +DG  + V I++  
Sbjct: 61  KQLQGHTVDGHKLEVRISERA 81

>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 = 70.9 bits (173), Expect = 2e-17
 Identities = 26/83 (31%), Positives = 45/83 (54%), Gaps = 2/83 (2%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
              RL VS + FR  +  LR  F  FG++++V ++ ++     +GF F+ +    ++ RA
Sbjct: 10  TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRA 67

Query: 136 IEGMHGKFLDGRVIFVEIAKSRA 158
            E +HG  ++GR I V  A +R 
Sbjct: 68  REKLHGTVVEGRKIEVNNATARV 90

>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 = 70.5 bits (172), Expect = 3e-17
 Identities = 30/77 (38%), Positives = 45/77 (58%)

Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
            P   L V GLS  T+E  LR  F  +G + +V++V D+ + R RGFAF+ +   ++++ 
Sbjct: 7   DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 66

Query: 135 AIEGMHGKFLDGRVIFV 151
           A E  +G  LDGR I V
Sbjct: 67  AKERANGMELDGRRIRV 83

>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 = 69.6 bits (170), Expect = 5e-17
 Identities = 24/84 (28%), Positives = 38/84 (45%), Gaps = 6/84 (7%)

Query: 77  KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
           ++RLFV  L    +E+ +R  F+ +G+  EV +  DK       F F+R  T   +  A 
Sbjct: 8   RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG------FGFIRLETRTLAEIAK 61

Query: 137 EGMHGKFLDGRVIFVEIAKSRAEL 160
             +    L G+ + V  A   A L
Sbjct: 62  VELDNMPLRGKQLRVRFACHSASL 85

>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 = 69.7 bits (170), Expect = 5e-17
 Identities = 19/80 (23%), Positives = 42/80 (52%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
             LFV+ +     ED ++  F  +G++  ++L +D+     +G+A + Y T +++  A E
Sbjct: 8   WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 67

Query: 138 GMHGKFLDGRVIFVEIAKSR 157
            ++G  + G+ I V+    +
Sbjct: 68  ALNGAEIMGQTIQVDWCFVK 87

>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 = 70.0 bits (171), Expect = 5e-17
 Identities = 18/85 (21%), Positives = 43/85 (50%), Gaps = 6/85 (7%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
               ++  G++   ++  +R  F  FGQ++E+ +         +G++F+R++T E +  A
Sbjct: 17  KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVF------PEKGYSFVRFSTHESAAHA 70

Query: 136 IEGMHGKFLDGRVIFVEIAKSRAEL 160
           I  ++G  ++G V+     K   ++
Sbjct: 71  IVSVNGTTIEGHVVKCYWGKESPDM 95

>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 = 69.3 bits (169), Expect = 8e-17
 Identities = 27/82 (32%), Positives = 44/82 (53%), Gaps = 2/82 (2%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
             +F+  L       +L + F  FG ++   +V D+  N  +G+ F+ + T+E + RAIE
Sbjct: 9   GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIE 66

Query: 138 GMHGKFLDGRVIFVEIAKSRAE 159
            M+G  L+ R +FV   KSR E
Sbjct: 67  KMNGMLLNDRKVFVGRFKSRKE 88

>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 = 69.3 bits (169), Expect = 8e-17
 Identities = 17/89 (19%), Positives = 33/89 (37%), Gaps = 4/89 (4%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVE--VNLVMDKIANRPRGFAFLRYATEEESRRA 135
            RLF+ G+      + +        + V   +         + RGFAF+ Y +   +  A
Sbjct: 2   CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 61

Query: 136 IEGMHGK--FLDGRVIFVEIAKSRAELRQ 162
              +      L G  I V+ A+   ++ +
Sbjct: 62  RRKLMPGRIQLWGHQIAVDWAEPEIDVDE 90

>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 = 68.9 bits (168), Expect = 1e-16
 Identities = 27/82 (32%), Positives = 42/82 (51%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
               + V+ LS  T E  L+  F+ FG +  + L  DK   + +GFAF+ +   E++ RA
Sbjct: 7   DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARA 66

Query: 136 IEGMHGKFLDGRVIFVEIAKSR 157
           I G+ G   D  ++ VE AK  
Sbjct: 67  IAGVSGFGYDHLILNVEWAKPS 88

>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 = 68.5 bits (167), Expect = 1e-16
 Identities = 24/76 (31%), Positives = 42/76 (55%), Gaps = 1/76 (1%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           ++FV GLS  T E+ +R  F GFG++  + L MD   N+ RGF F+ +  EE  ++ +E 
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 139 MHGKFLDGRVIFVEIA 154
            +   +      +++A
Sbjct: 61  KY-HNVGLSKCEIKVA 75

>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 = 68.9 bits (168), Expect = 1e-16
 Identities = 17/82 (20%), Positives = 33/82 (40%), Gaps = 3/82 (3%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
              R++V  L        + + F  +G + +++L           FAF+ +    ++  A
Sbjct: 13  NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDA 69

Query: 136 IEGMHGKFLDGRVIFVEIAKSR 157
           + G  G   DG  + VE  +S 
Sbjct: 70  VYGRDGYDYDGYRLRVEFPRSG 91

>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 = 68.6 bits (167), Expect = 1e-16
 Identities = 23/81 (28%), Positives = 40/81 (49%), Gaps = 1/81 (1%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIAN-RPRGFAFLRYATEEESRRAIEG 138
           +F+  L     E  L + F  FG +++   +M        +G+AF+ +A+ + S  AIE 
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 139 MHGKFLDGRVIFVEIAKSRAE 159
           M+G++L  R I V  A  +  
Sbjct: 61  MNGQYLCNRPITVSYAFKKDS 81

>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 = 68.9 bits (168), Expect = 1e-16
 Identities = 17/85 (20%), Positives = 37/85 (43%), Gaps = 3/85 (3%)

Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
           QP+T L+V  LS   +E  +   F   G      ++ +        + F+ +    ++  
Sbjct: 7   QPRT-LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEH--TSNDPYCFVEFYEHRDAAA 63

Query: 135 AIEGMHGKFLDGRVIFVEIAKSRAE 159
           A+  M+G+ + G+ + V  A + + 
Sbjct: 64  ALAAMNGRKILGKEVKVNWATTPSS 88

>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 = 68.7 bits (167), Expect = 2e-16
 Identities = 23/94 (24%), Positives = 47/94 (50%)

Query: 66  PSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLR 125
           P   S +  +P   L++  LS R +E  L + F  F +     +    +  R RG AF+ 
Sbjct: 7   PMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFIT 66

Query: 126 YATEEESRRAIEGMHGKFLDGRVIFVEIAKSRAE 159
           +  +E + +A+  ++G  L G+++ +E  K++ +
Sbjct: 67  FPNKEIAWQALHLVNGYKLYGKILVIEFGKNKKQ 100

>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 = 68.2 bits (166), Expect = 2e-16
 Identities = 22/79 (27%), Positives = 42/79 (53%), Gaps = 2/79 (2%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
             L+VSGL    ++  L   F  +G+++   +++D++    RG  F+R+    E+  AI+
Sbjct: 7   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 66

Query: 138 GMHGKFLDGRV--IFVEIA 154
           G++G+   G    I V+ A
Sbjct: 67  GLNGQKPSGATEPITVKFA 85

>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 = 68.2 bits (166), Expect = 2e-16
 Identities = 34/83 (40%), Positives = 52/83 (62%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           +LFV GLSF T+E SL   F  +GQ+ EV +V D+   R RGF F+ +   ++++ A+  
Sbjct: 7   KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 66

Query: 139 MHGKFLDGRVIFVEIAKSRAELR 161
           M+GK +DGR I V+ A   ++ R
Sbjct: 67  MNGKSVDGRQIRVDQAGKSSDNR 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 = 67.8 bits (165), Expect = 3e-16
 Identities = 31/78 (39%), Positives = 47/78 (60%), Gaps = 1/78 (1%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           +LF+ GLSF T+++SLR+ F+ +G L +  ++ D    R RGF F+ YAT EE   A+  
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN- 66

Query: 139 MHGKFLDGRVIFVEIAKS 156
                +DGRV+  + A S
Sbjct: 67  ARPHKVDGRVVEPKRAVS 84

>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 = 66.7 bits (162), Expect = 1e-15
 Identities = 20/91 (21%), Positives = 39/91 (42%), Gaps = 8/91 (8%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLV--------MDKIANRPRGFAFLRYA 127
             + ++V GL+   + D L + F+  G +              +DK   +P+G A + Y 
Sbjct: 7   DNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYE 66

Query: 128 TEEESRRAIEGMHGKFLDGRVIFVEIAKSRA 158
               ++ A+E   GK   G  + V +A+ + 
Sbjct: 67  DPPTAKAAVEWFDGKDFQGSKLKVSLARKKP 97

>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 = 68.9 bits (167), Expect = 1e-15
 Identities = 21/90 (23%), Positives = 44/90 (48%), Gaps = 1/90 (1%)

Query: 74  CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESR 133
                ++FV G+   T E  LR+ F+ +G++  + ++ D+ + + RGFAF+ +   +   
Sbjct: 94  HLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVD 153

Query: 134 RAIEGMHGKFLDGRVIFVEIAKSRAELRQA 163
           + +       ++G    V  A S+ E+  A
Sbjct: 154 KIVI-QKYHTVNGHNCEVRKALSKQEMASA 182

>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 = 54.6 bits (130), Expect = 2e-10
 Identities = 26/65 (40%), Positives = 39/65 (60%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           +LF+ GLSF T+++SLR+ F+ +G L +  ++ D    R RGF F+ YAT EE   A+  
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67

Query: 139 MHGKF 143
              K 
Sbjct: 68  RPHKV 72

>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 = 66.6 bits (162), Expect = 1e-15
 Identities = 18/94 (19%), Positives = 40/94 (42%), Gaps = 5/94 (5%)

Query: 68  PHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYA 127
           P +    +    L    LSF  +ED L+  F+       + + +     + +G A++ + 
Sbjct: 7   PCTSKKVRAARTLLAKNLSFNITEDELKEVFEDA-----LEIRLVSQDGKSKGIAYIEFK 61

Query: 128 TEEESRRAIEGMHGKFLDGRVIFVEIAKSRAELR 161
           +E ++ + +E   G  +DGR + +     +   R
Sbjct: 62  SEADAEKNLEEKQGAEIDGRSVSLYYTGEKGGTR 95

>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 = 65.4 bits (159), Expect = 2e-15
 Identities = 24/76 (31%), Positives = 44/76 (57%), Gaps = 1/76 (1%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           ++F+ GLS+ T++  L++ F  FG++V+  L +D I  R RGF F+ +   E   + ++ 
Sbjct: 1   KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD- 59

Query: 139 MHGKFLDGRVIFVEIA 154
                L+G+VI  + A
Sbjct: 60  QKEHKLNGKVIDPKRA 75

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.9 bits (160), Expect = 2e-15
 Identities = 28/84 (33%), Positives = 47/84 (55%), Gaps = 1/84 (1%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           T++FV GL + T++ SLR  F+GFG + E  ++ D+   + RG+ F+  A    + RA +
Sbjct: 11  TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACK 70

Query: 138 GMHGKFLDGRVIFVEIAKSRAELR 161
             +   +DGR   V +A   A+ R
Sbjct: 71  DPNPI-IDGRKANVNLAYLGAKPR 93

>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 = 65.1 bits (158), Expect = 4e-15
 Identities = 18/83 (21%), Positives = 40/83 (48%), Gaps = 1/83 (1%)

Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
           +    +F   L+ R     L + F   G++ +V ++ D+ + R +G A++ +   +    
Sbjct: 16  RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPL 75

Query: 135 AIEGMHGKFLDGRVIFVEIAKSR 157
           AI  + G+ L G  I V+ +++ 
Sbjct: 76  AIG-LTGQRLLGVPIIVQASQAE 97

>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 = 64.9 bits (157), Expect = 7e-15
 Identities = 20/96 (20%), Positives = 44/96 (45%), Gaps = 2/96 (2%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
            K    ++ + F  ++  +    +G         V+     +  G A +++  E+++R++
Sbjct: 7   AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKS 66

Query: 136 IEGMHGKFLDGRVIFVEIAKSRAELRQAFKNNPRQN 171
              +H K L+GR  FV +  +  ++R+  KN P Q 
Sbjct: 67  ER-LHRKKLNGREAFVHVV-TLEDMREIEKNPPAQG 100

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 64.4 bits (156), Expect = 8e-15
 Identities = 26/91 (28%), Positives = 45/91 (49%), Gaps = 6/91 (6%)

Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
                +F+  LSF + E++L    Q FG L  V +V+       +G AF ++ T+E +++
Sbjct: 6   TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQK 65

Query: 135 AIEGMH------GKFLDGRVIFVEIAKSRAE 159
            +          G  LDGR + V++A +R E
Sbjct: 66  CLAAASLEAEGGGLKLDGRQLKVDLAVTRDE 96

>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 = 64.0 bits (155), Expect = 8e-15
 Identities = 12/78 (15%), Positives = 37/78 (47%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
             L+++      ++ ++R+  Q    +     +     N  R FA++   ++E++R  +E
Sbjct: 2   CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 61

Query: 138 GMHGKFLDGRVIFVEIAK 155
            ++G  ++G  +  +++ 
Sbjct: 62  KLNGLKIEGYTLVTKVSN 79

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 64.4 bits (156), Expect = 8e-15
 Identities = 25/97 (25%), Positives = 48/97 (49%), Gaps = 3/97 (3%)

Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
           +    +FV  + +  +E+ L++ F   G +V   LV D+   +P+G+ F  Y  +E +  
Sbjct: 6   RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALS 65

Query: 135 AIEGMHGKFLDGRVIFVEIAKS---RAELRQAFKNNP 168
           A+  ++G+   GR + V+ A S   + EL+      P
Sbjct: 66  AMRNLNGREFSGRALRVDNAASEKNKEELKSLGTGAP 102

>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 = 63.2 bits (153), Expect = 2e-14
 Identities = 21/82 (25%), Positives = 37/82 (45%), Gaps = 7/82 (8%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           +L++  LS   + D LR  F            +        G+AF+ Y  +  + RAIE 
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKL------PLAGQVLLKSGYAFVDYPDQNWAIRAIET 56

Query: 139 MHGKF-LDGRVIFVEIAKSRAE 159
           + GK  L G+++ V+ + S+  
Sbjct: 57  LSGKVELHGKIMEVDYSVSKKL 78

>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 = 62.1 bits (150), Expect = 3e-14
 Identities = 22/76 (28%), Positives = 46/76 (60%), Gaps = 1/76 (1%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           ++FV GLS  T+ + +++ F+ FG++ +  L+ DK  NR RGF F+ + +E+   +  E 
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE- 59

Query: 139 MHGKFLDGRVIFVEIA 154
           +H   ++ +++  + A
Sbjct: 60  IHFHEINNKMVECKKA 75

>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 = 62.0 bits (150), Expect = 5e-14
 Identities = 21/79 (26%), Positives = 38/79 (48%), Gaps = 6/79 (7%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
            L+V  L   TSE+ +   F        +     +   + R +AF+ ++  E++  A++ 
Sbjct: 10  ILYVRNLMLSTSEEMIEKEFN------NIKPGAVERVKKIRDYAFVHFSNREDAVEAMKA 63

Query: 139 MHGKFLDGRVIFVEIAKSR 157
           ++GK LDG  I V +AK  
Sbjct: 64  LNGKVLDGSPIEVTLAKPV 82

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 108

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.3 bits (151), Expect = 5e-14
 Identities = 19/94 (20%), Positives = 36/94 (38%), Gaps = 4/94 (4%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
           P  R+ V  L +  + D L   F  FG ++++           +  A L+YA    ++ A
Sbjct: 6   PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHA 61

Query: 136 IEGMHGKFLDGRVIFVEIAKSRAELRQAFKNNPR 169
              + G+ +      + I  S+        NN +
Sbjct: 62  KLSLDGQNIYNACCTLRIDFSKLTSLNVKYNNDK 95

>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 = 61.2 bits (148), Expect = 8e-14
 Identities = 17/82 (20%), Positives = 36/82 (43%), Gaps = 7/82 (8%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           + +FV   +   +ED LR  F  +G +++V      I    R FAF+ +A ++ ++    
Sbjct: 6   SGVFVGRCTGDMTEDELREFFSQYGDVMDV-----FIPKPFRAFAFVTFADDQIAQSLC- 59

Query: 138 GMHGKFLDGRVIFVEIAKSRAE 159
                 + G  + +  A+ +  
Sbjct: 60  -GEDLIIKGISVHISNAEPKHN 80

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.5 bits (146), Expect = 1e-13
 Identities = 18/76 (23%), Positives = 39/76 (51%), Gaps = 1/76 (1%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           ++FV G+   T E  LR+ F+ +G++  + ++ D+ + + RGFAF+ +   +   + +  
Sbjct: 4   KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI- 62

Query: 139 MHGKFLDGRVIFVEIA 154
                ++G    V  A
Sbjct: 63  QKYHTVNGHNCEVRKA 78

>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 = 60.9 bits (147), Expect = 2e-13
 Identities = 15/85 (17%), Positives = 34/85 (40%), Gaps = 1/85 (1%)

Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
            P    F+  L +  +E+S++  F+G                R +GF +  +   +    
Sbjct: 13  SPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLS 72

Query: 135 AIEGMHGKFLDGRVIFVEIAKSRAE 159
           A+  ++ + L  + I V++A    +
Sbjct: 73  ALS-LNEESLGNKRIRVDVADQAQD 96

>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 = 60.5 bits (146), Expect = 2e-13
 Identities = 13/86 (15%), Positives = 33/86 (38%), Gaps = 7/86 (8%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           + + V  L   ++   + +  + +              +R +  AF+     E+++ AI+
Sbjct: 6   SGILVKNLPQDSNCQEVHDLLKDYDL-------KYCYVDRNKRTAFVTLLNGEQAQNAIQ 58

Query: 138 GMHGKFLDGRVIFVEIAKSRAELRQA 163
             H     G+ + V++  + A L   
Sbjct: 59  MFHQYSFRGKDLIVQLQPTDALLCSG 84

>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 = 61.5 bits (148), Expect = 2e-13
 Identities = 21/94 (22%), Positives = 44/94 (46%)

Query: 66  PSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLR 125
           P             L V+ +     E  LR  F+ +G +  V +V D+   + RG+ F++
Sbjct: 31  PPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVK 90

Query: 126 YATEEESRRAIEGMHGKFLDGRVIFVEIAKSRAE 159
           + +   +++AI G++G  +  + + V +A S  +
Sbjct: 91  FQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQ 124

>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 = 59.3 bits (143), Expect = 7e-13
 Identities = 27/85 (31%), Positives = 41/85 (48%), Gaps = 8/85 (9%)

Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
            P TRL+V GL   TS  +L   F  FG +  ++ V          FA+++Y + + ++ 
Sbjct: 15  NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDS------FAYIQYESLDAAQA 68

Query: 135 AIEGMHGKFLDG--RVIFVEIAKSR 157
           A   M G  L G  R + V+ AKS 
Sbjct: 69  ACAKMRGFPLGGPDRRLRVDFAKSG 93

>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 = 58.5 bits (141), Expect = 9e-13
 Identities = 19/83 (22%), Positives = 39/83 (46%), Gaps = 8/83 (9%)

Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
           +    L+V G     +   LR AF  FG ++++++         R  AF+ Y   E + +
Sbjct: 3   RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQ 54

Query: 135 AIEGMHGKFLDGRVIFVEIAKSR 157
           A+  ++G  ++   + V IA+ +
Sbjct: 55  AVAELNGTQVESVQLKVNIARKQ 77

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 57.9 bits (139), Expect = 2e-12
 Identities = 20/79 (25%), Positives = 38/79 (48%), Gaps = 6/79 (7%)

Query: 77  KTRLFVSGLSFRTSEDSLRNAFQG---FGQLVEVNLVMDKIANR---PRGFAFLRYATEE 130
           K  +FV GLS R ++  +    +    FG++ +V +           P   A++ Y   E
Sbjct: 8   KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSE 67

Query: 131 ESRRAIEGMHGKFLDGRVI 149
           ++ RAI+ ++   +DGR +
Sbjct: 68  DALRAIQCVNNVVVDGRTL 86

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.1 bits (137), Expect = 4e-12
 Identities = 17/82 (20%), Positives = 38/82 (46%), Gaps = 6/82 (7%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNL-----VMDKIANRPRGFAFLRYATEEESR 133
           RL+V  + F  +E+++ + F    +L  +       V+    N+ + FAFL + + +E+ 
Sbjct: 3   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 134 RAIEGMHGKFLDGRVIFVEIAK 155
           +A+    G    G+ + +    
Sbjct: 63  QAMA-FDGIIFQGQSLKIRRPH 83

>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 = 56.3 bits (135), Expect = 9e-12
 Identities = 15/95 (15%), Positives = 27/95 (28%), Gaps = 13/95 (13%)

Query: 65  PPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFL 124
           PP+  S        R+ VSGL    S   L+         +     +     +  G   +
Sbjct: 9   PPTRRS------DFRVLVSGLPPSGSWQDLK-------DHMREAGDVCYADVQKDGMGMV 55

Query: 125 RYATEEESRRAIEGMHGKFLDGRVIFVEIAKSRAE 159
            Y  +E+   A+  +               +   E
Sbjct: 56  EYLRKEDMEYALRKLDDTKFRSHEGETSYIRVYPE 90

>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 = 55.2 bits (132), Expect = 1e-11
 Identities = 14/70 (20%), Positives = 37/70 (52%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           L++ GL   T++  L    Q +G++V    ++DK  N+ +G+ F+ + +   +++A+  +
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 140 HGKFLDGRVI 149
               +  ++ 
Sbjct: 61  KASGVQAQMA 70

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.9 bits (134), Expect = 1e-11
 Identities = 17/81 (20%), Positives = 27/81 (33%), Gaps = 1/81 (1%)

Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
           Q  T L++S L     E  L          V    ++   +   RG  F R  + E+   
Sbjct: 16  QDPTNLYISNLPLSMDEQELE-NMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEA 74

Query: 135 AIEGMHGKFLDGRVIFVEIAK 155
            I   +GKF+          +
Sbjct: 75  VIGHFNGKFIKTPPGVSAPTE 95

>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 = 55.8 bits (134), Expect = 2e-11
 Identities = 13/75 (17%), Positives = 38/75 (50%), Gaps = 1/75 (1%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           + + +        E+      + +G++ E+N V D + +   G  ++++  EE++ +A+ 
Sbjct: 28  SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMN-VCDNLGDHLVGNVYVKFRREEDAEKAVI 86

Query: 138 GMHGKFLDGRVIFVE 152
            ++ ++ +G+ I  E
Sbjct: 87  DLNNRWFNGQPIHAE 101

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 55.1 bits (132), Expect = 2e-11
 Identities = 21/82 (25%), Positives = 41/82 (50%), Gaps = 3/82 (3%)

Query: 78  TRLFVSGLSFR-TSEDSLRNAFQGFGQLVEVNLVMD-KIANRPRGFAFLRYATEEESRRA 135
             + +  LS     E+ LR +F+GFG + ++N+    K  +     AF+ +  ++ + RA
Sbjct: 5   REIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERA 64

Query: 136 IEGMHGKFLDGRVIFVEIAKSR 157
           ++ M+   L  R I V +A  +
Sbjct: 65  LQ-MNRSLLGNREISVSLADKK 85

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.3 bits (133), Expect = 2e-11
 Identities = 16/75 (21%), Positives = 30/75 (40%), Gaps = 4/75 (5%)

Query: 87  FRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDG 146
                + LR     FGQ+ ++ L        P G A + +   EE+   I+ + G++  G
Sbjct: 29  LNEIREDLRVECSKFGQIRKLLLFDRH----PDGVASVSFRDPEEADYCIQTLDGRWFGG 84

Query: 147 RVIFVEIAKSRAELR 161
           R I  +      + +
Sbjct: 85  RQITAQAWDGTTDYQ 99

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {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: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.1 bits (132), Expect = 3e-11
 Identities = 14/88 (15%), Positives = 31/88 (35%), Gaps = 3/88 (3%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
               + + GL +R +E+ + N F     +            R  G A + +AT E++  A
Sbjct: 14  TGHCVHMRGLPYRATENDIYNFFSPLNPMRVHI--EIGPDGRVTGEADVEFATHEDAVAA 71

Query: 136 IEGMHGKFLDGRVIFVEIAKSRAELRQA 163
           +       +  R + + +  +       
Sbjct: 72  MA-KDKANMQHRYVELFLNSTAGTSGSG 98

>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 = 54.2 bits (129), Expect = 7e-11
 Identities = 19/102 (18%), Positives = 34/102 (33%), Gaps = 6/102 (5%)

Query: 70  SLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATE 129
           S S+ + KT +    L   T    ++  F  FG L  V L            A + +   
Sbjct: 3   SGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEP 56

Query: 130 EESRRAIEGMHGKFLDGRVIFVEIAKSRAELRQAFKNNPRQN 171
            E+R+A   +         +++E A          K + +  
Sbjct: 57  LEARKAFRHLAYSKFHHVPLYLEWAPIGVFGAAPQKKDSQHE 98

>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 = 53.6 bits (128), Expect = 1e-10
 Identities = 19/81 (23%), Positives = 38/81 (46%), Gaps = 6/81 (7%)

Query: 78  TRLFVSGLSFR-TSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
           + L VS L+    +  SL   F  +G +  V     KI    +  A ++ A   +++ A+
Sbjct: 3   SVLLVSNLNPERVTPQSLFILFGVYGDVQRV-----KILFNKKENALVQMADGNQAQLAM 57

Query: 137 EGMHGKFLDGRVIFVEIAKSR 157
             ++G  L G+ I + ++K +
Sbjct: 58  SHLNGHKLHGKPIRITLSKHQ 78

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.3 bits (127), Expect = 1e-10
 Identities = 21/89 (23%), Positives = 43/89 (48%), Gaps = 2/89 (2%)

Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
                + + GL F  S++ +   F G   +     +      R  G AF+++A++E + +
Sbjct: 13  ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEK 72

Query: 135 AIEGMHGKFLDGRVIFVEIAKSRAELRQA 163
           A++  H + +  R I +  + SRAE+R +
Sbjct: 73  ALK-KHKERIGHRYIEIFKS-SRAEVRTS 99

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 53.0 bits (126), Expect = 2e-10
 Identities = 21/91 (23%), Positives = 37/91 (40%), Gaps = 4/91 (4%)

Query: 69  HSLSTCQPKT--RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRY 126
           H +   +  T   LF+  L+   S   L+ A            V+D      R F ++ +
Sbjct: 3   HMVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFA-KNDLAVVDVRTGTNRKFGYVDF 61

Query: 127 ATEEESRRAIEGMHGKFLDGRVIFVEIAKSR 157
            + E+  +A+E + G  + G  I +E  K R
Sbjct: 62  ESAEDLEKALE-LTGLKVFGNEIKLEKPKGR 91

>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 = 51.6 bits (123), Expect = 7e-10
 Identities = 22/94 (23%), Positives = 39/94 (41%), Gaps = 9/94 (9%)

Query: 72  STCQPKTRLFVS--GLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATE 129
           +       L V+  GL    S + L    +  G +  + +  +K       ++F RY T 
Sbjct: 13  TVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKP------YSFARYRTT 66

Query: 130 EESRRAIEGMHGKFL-DGRVIFVEIAKSRAELRQ 162
           EES+RA   ++GK + D     + +  +  E  Q
Sbjct: 67  EESKRAYVTLNGKEVVDDLGQKITLYLNFVEKVQ 100

>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 = 50.9 bits (121), Expect = 9e-10
 Identities = 19/83 (22%), Positives = 36/83 (43%), Gaps = 5/83 (6%)

Query: 76  PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRA 135
           P   L +S +    SE+ L+  F   G +V+      K   + R  A ++  + EE+ +A
Sbjct: 9   PSATLHLSNIPPSVSEEDLKVLFSSNGGVVK----GFKFFQKDRKMALIQMGSVEEAVQA 64

Query: 136 IEGMHGK-FLDGRVIFVEIAKSR 157
           +  +H     +   + V  +KS 
Sbjct: 65  LIDLHNHDLGENHHLRVSFSKST 87

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 50.3 bits (120), Expect = 1e-09
 Identities = 11/72 (15%), Positives = 30/72 (41%), Gaps = 8/72 (11%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           T + V G    ++   L   F  +G +++         +    +  +RY ++ ++R+A+ 
Sbjct: 5   TWVTVFGFPQASASYILL-QFAQYGNILKHV------MSNTGNWMHIRYQSKLQARKALS 57

Query: 138 GMHGKFLDGRVI 149
              G+     ++
Sbjct: 58  -KDGRIFGESIM 68

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.4 bits (120), Expect = 2e-09
 Identities = 10/72 (13%), Positives = 32/72 (44%), Gaps = 2/72 (2%)

Query: 85  LSFRTSEDSLRNAFQGFGQLVEVNLV--MDKIANRPRGFAFLRYATEEESRRAIEGMHGK 142
             +    + +R+    +G +  + +   +D +     G  F+ + +  + ++A++G+ G+
Sbjct: 22  EEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR 81

Query: 143 FLDGRVIFVEIA 154
               RV+  +  
Sbjct: 82  KFANRVVVTKYC 93

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 49.1 bits (116), Expect = 3e-09
 Identities = 14/75 (18%), Positives = 30/75 (40%), Gaps = 3/75 (4%)

Query: 78  TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE 137
           T + V  L    +++ +   F+  G ++ V++       +   FA + +A  + +  AI 
Sbjct: 1   TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSL--KKNFRFARIEFARYDGALAAIT 58

Query: 138 GMHGKFLDGRVIFVE 152
               K +    I V 
Sbjct: 59  -KTHKVVGQNEIIVS 72

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 112

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.1 bits (116), Expect = 6e-09
 Identities = 13/88 (14%), Positives = 34/88 (38%), Gaps = 1/88 (1%)

Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
           +    +++ GL F      + + F+    + +   +      +  G  F+ +  E + + 
Sbjct: 16  EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKA 75

Query: 135 AIEGMHGKFLDGRVIFVEIAKSRAELRQ 162
           A+   H +++  R I V     +  L +
Sbjct: 76  ALC-RHKQYMGNRFIQVHPITKKGMLEK 102

>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 = 47.4 bits (112), Expect = 2e-08
 Identities = 9/79 (11%), Positives = 32/79 (40%), Gaps = 2/79 (2%)

Query: 77  KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAI 136
              +++ G     + D ++   +  GQ++ +  +   +    +G  F+ + + E +++ +
Sbjct: 6   NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQ-MRRTLHKAFKGSIFVVFDSIESAKKFV 64

Query: 137 EGMHGKFLDGRVIFVEIAK 155
           E   G+      + +    
Sbjct: 65  E-TPGQKYKETDLLILFKD 82

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 113

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 = 46.7 bits (110), Expect = 5e-08
 Identities = 12/93 (12%), Positives = 29/93 (31%), Gaps = 7/93 (7%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATE-EESRRAIEG 138
            F   L  +T  + L   F   G++  ++ V             + +  + +E+    + 
Sbjct: 14  KFSGDLDDQTCREDLHILFSNHGEIKWIDFVR------GAKEGIILFKEKAKEALGKAKD 67

Query: 139 MHGKFLDGRVIFVEIAKSRAELRQAFKNNPRQN 171
            +   L  R   V       E+ +       ++
Sbjct: 68  ANNGNLQLRNKEVTWEVLEGEVEKEALKKIIED 100

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.3 bits (106), Expect = 9e-08
 Identities = 10/81 (12%), Positives = 23/81 (28%), Gaps = 7/81 (8%)

Query: 79  RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           R+ VSGL    S   L+         +     +        G   + +  +E+   A+  
Sbjct: 2   RVVVSGLPPSGSWQDLK-------DHMREAGDVCYADVYRDGTGVVEFVRKEDMTYAVRK 54

Query: 139 MHGKFLDGRVIFVEIAKSRAE 159
           +               + + +
Sbjct: 55  LDNTKFRSHEGETAYIRVKVD 75

>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 = 45.5 bits (107), Expect = 1e-07
 Identities = 11/85 (12%), Positives = 32/85 (37%), Gaps = 9/85 (10%)

Query: 80  LFVSGL-SFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEG 138
           + +      +     L    + FG +    ++           AF+  AT E+++ A++ 
Sbjct: 11  VHIMDFQRGKNLRYQLLQLVEPFGVISNHLILN------KINEAFIEMATTEDAQAAVDY 64

Query: 139 --MHGKFLDGRVIFVEIAKSRAELR 161
                  + G+ + V +++    ++
Sbjct: 65  YTTTPALVFGKPVRVHLSQKYKRIK 89

>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 = 44.5 bits (104), Expect = 2e-07
 Identities = 18/89 (20%), Positives = 35/89 (39%), Gaps = 9/89 (10%)

Query: 75  QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRR 134
            P   L +  L    +E  +      FG+      V + +  + +  AFL  ATEE +  
Sbjct: 6   APSRVLHIRKLPGEVTETEVIALGLPFGK------VTNILMLKGKNQAFLELATEEAAIT 59

Query: 135 AIEGMHGK--FLDGRVIFVEIAKSRAELR 161
            +         L  + I+++ +  + EL+
Sbjct: 60  MVNYYSAVTPHLRNQPIYIQYSNHK-ELK 87

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-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: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.4 bits (101), Expect = 5e-07
 Identities = 14/81 (17%), Positives = 30/81 (37%), Gaps = 7/81 (8%)

Query: 80  LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM 139
           + + GL    +   + +    +              ++ +G AF+     E++  AI   
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDYEL-------KYCFVDKYKGTAFVTLLNGEQAEAAINTF 53

Query: 140 HGKFLDGRVIFVEIAKSRAEL 160
           H   L  R + V++  + A L
Sbjct: 54  HQSRLRERELSVQLQPTDALL 74

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 42.1 bits (98), Expect = 2e-06
 Identities = 7/87 (8%), Positives = 23/87 (26%), Gaps = 11/87 (12%)

Query: 76  PKTRLFVSGL-----SFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEE 130
             + L          S   +     + F+ + +                    + ++   
Sbjct: 4   GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK------SFKRVRINFSNPL 57

Query: 131 ESRRAIEGMHGKFLDGRVIFVEIAKSR 157
            +  A   +H     G+ + +  A++ 
Sbjct: 58  SAADARLRLHKTEFLGKEMKLYFAQTL 84

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {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: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 33.8 bits (76), Expect = 0.003
 Identities = 10/87 (11%), Positives = 33/87 (37%), Gaps = 5/87 (5%)

Query: 75  QPKTRLFVSGL-SFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESR 133
           +    + +S L     S+ ++    + +G++    L+      + + F  +    +  + 
Sbjct: 16  ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR----MKSQAFIEMETREDAMAM 71

Query: 134 RAIEGMHGKFLDGRVIFVEIAKSRAEL 160
                    +  GR + V++++   +L
Sbjct: 72  VDHCLKKALWFQGRCVKVDLSEKYKKL 98

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	171
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.91
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.91
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.91
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.91
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.91
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.91
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.91
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.91
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.9
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.9
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.9
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.9
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.9
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.89
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.89
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.89
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.89
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.89
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.89
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.89
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.89
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.89
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.89
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.88
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.88
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.88
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.88
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.88
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.88
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.88
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.87
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.87
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.87
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.87
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.87
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.87
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.86
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.86
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.86
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.86
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.86
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.85
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.85
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.85
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.85
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.85
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.84
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.84
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.84
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.84
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.83
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.83
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.83
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.83
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.82
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.82
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.82
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.82
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.82
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.82
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.81
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.81
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.81
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.81
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.81
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.8
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.8
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.8
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.8
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.8
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.8
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.79
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.79
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.79
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.78
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.77
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.77
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.74
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.7
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.69
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	99.68
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.65
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.63
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.63
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.56
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.53
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.45
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	98.01
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.75
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.59
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	97.35
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	96.47
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	96.19
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	96.09
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	95.89
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	95.5
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	95.47
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	95.35
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	95.19
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	95.15
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	95.11
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	94.88
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	94.85
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	94.82
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	94.58
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	94.48
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	94.2
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	94.2
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	94.17
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	94.1
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	94.01
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	93.98
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	93.9
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	93.81
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	93.72
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	93.47
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	93.23
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	93.1
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	92.54
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	92.3
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	92.22
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	92.18
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	92.09
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	91.98
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	91.97
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	91.94
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	91.22
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	91.01
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	90.71
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	90.09
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	90.08
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	89.82
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	89.59
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	89.57
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	88.32
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	88.24
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	87.95
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	86.81
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	84.88
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	84.8
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	84.28
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	83.55
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	82.37
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	81.01
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	80.7
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	80.2

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.91  E-value=1.4e-24  Score=136.06  Aligned_cols=80  Identities=24%  Similarity=0.403  Sum_probs=77.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 030819           77 KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKS  156 (171)
Q Consensus        77 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~~  156 (171)
                      +++|||+|||+++++++|+++|++||.|.++.++.++.+|+++|||||+|.+.++|++|++.|||..+.|+.|+|.|++|
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~p   81 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   81 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            57899999999999999999999999999999999998999999999999999999999999999999999999999986

>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=99.91  E-value=2.3e-24  Score=136.90  Aligned_cols=83  Identities=23%  Similarity=0.438  Sum_probs=79.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 030819           75 QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIA  154 (171)
Q Consensus        75 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~  154 (171)
                      .++.+|||+|||+++++++|+++|++||.|.+++++.++.+|+++|||||+|.+.++|++|+..|||..+.|+.|+|+|+
T Consensus         5 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~a   84 (88)
T d1rk8a_           5 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC   84 (88)
T ss_dssp             C-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            45789999999999999999999999999999999999989999999999999999999999999999999999999999


Q ss_pred             cCc
Q 030819          155 KSR  157 (171)
Q Consensus       155 ~~~  157 (171)
                      .++
T Consensus        85 ~~k   87 (88)
T d1rk8a_          85 FVK   87 (88)
T ss_dssp             EEC
T ss_pred             cCC
Confidence            875

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.91  E-value=1.7e-24  Score=138.85  Aligned_cols=85  Identities=26%  Similarity=0.481  Sum_probs=80.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 030819           75 QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIA  154 (171)
Q Consensus        75 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~  154 (171)
                      ..+++|||+|||+++++++|+++|++||.|.++.++.++.+|.++|||||+|.+.++|..|++.|||..++|+.|+|.|+
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a   84 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD   84 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCcHH
Q 030819          155 KSRAE  159 (171)
Q Consensus       155 ~~~~~  159 (171)
                      .+..+
T Consensus        85 ~~~~~   89 (93)
T d1h2vz_          85 AGFKE   89 (93)
T ss_dssp             SCCCT
T ss_pred             CCCCC
Confidence            76543

>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=99.91  E-value=2.7e-24  Score=137.09  Aligned_cols=85  Identities=32%  Similarity=0.511  Sum_probs=80.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 030819           74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEI  153 (171)
Q Consensus        74 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~  153 (171)
                      ..+..+|||+|||.++++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|++.|||..+.|+.|+|.|
T Consensus         5 ~~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~   84 (90)
T d2cq0a1           5 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEW   84 (90)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            34567999999999999999999999999999999999998999999999999999999999999999999999999999


Q ss_pred             ecCcH
Q 030819          154 AKSRA  158 (171)
Q Consensus       154 ~~~~~  158 (171)
                      ++++.
T Consensus        85 akp~~   89 (90)
T d2cq0a1          85 AKPST   89 (90)
T ss_dssp             SSCCC
T ss_pred             eeCCC
Confidence            98864

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.91  E-value=6.4e-24  Score=133.02  Aligned_cols=80  Identities=29%  Similarity=0.518  Sum_probs=77.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 030819           77 KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKS  156 (171)
Q Consensus        77 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~~  156 (171)
                      .++|||+|||+++++++|+++|++||.|.+++++.+..+|.++|||||+|.+.++|+.|+..|||..+.|+.|+|.|++|
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            46799999999999999999999999999999999998999999999999999999999999999999999999999986

>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=99.91  E-value=1.9e-24  Score=140.88  Aligned_cols=87  Identities=23%  Similarity=0.417  Sum_probs=81.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ..+++++|||+|||+++++++|+++|..||.|.++.++.++.+|.++|||||+|.+.++|+.||+.|||..+.|+.|+|+
T Consensus        14 ~~p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~   93 (102)
T d2cpza1          14 EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQ   93 (102)
T ss_dssp             CCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            33567889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EecCcHH
Q 030819          153 IAKSRAE  159 (171)
Q Consensus       153 ~~~~~~~  159 (171)
                      |++++.+
T Consensus        94 ~a~~k~~  100 (102)
T d2cpza1          94 LKRSKND  100 (102)
T ss_dssp             CCCCSCC
T ss_pred             EeCCCCC
Confidence            9988754

>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=99.91  E-value=3.2e-24  Score=137.52  Aligned_cols=85  Identities=26%  Similarity=0.409  Sum_probs=80.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 030819           74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEI  153 (171)
Q Consensus        74 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~  153 (171)
                      ....++|||+|||+++++++|+++|++||.|.++.++.++.+|.++|||||+|.+.++|++|++.|||..+.|+.|+|.+
T Consensus         6 ~~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   85 (93)
T d1x5ua1           6 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNK   85 (93)
T ss_dssp             CCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34467999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCcH
Q 030819          154 AKSRA  158 (171)
Q Consensus       154 ~~~~~  158 (171)
                      |+++.
T Consensus        86 A~~~~   90 (93)
T d1x5ua1          86 ASAHN   90 (93)
T ss_dssp             TTTTS
T ss_pred             cCCCC
Confidence            98764

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.91  E-value=3.2e-24  Score=136.46  Aligned_cols=83  Identities=33%  Similarity=0.556  Sum_probs=79.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 030819           76 PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAK  155 (171)
Q Consensus        76 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~  155 (171)
                      ..++|||+|||+++++++|+++|++||+|.++.++.++.+|.++|||||+|.+.++|++|+..|||..++|+.|+|.+++
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~   83 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK   83 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            46799999999999999999999999999999999999899999999999999999999999999999999999999998


Q ss_pred             CcH
Q 030819          156 SRA  158 (171)
Q Consensus       156 ~~~  158 (171)
                      ++.
T Consensus        84 p~~   86 (89)
T d2cqba1          84 PMR   86 (89)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            753

>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=99.90  E-value=6.3e-24  Score=132.49  Aligned_cols=78  Identities=21%  Similarity=0.439  Sum_probs=75.7

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 030819           79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKS  156 (171)
Q Consensus        79 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~~  156 (171)
                      +|||+|||+++++++|+++|.+||+|.+++++.++.+|+++|||||+|.+.++|..|++.|+|..+.|++|+|.|++.
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~~   79 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQR   79 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECCC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            699999999999999999999999999999999999999999999999999999999999999999999999999853

>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=135.41  Aligned_cols=86  Identities=30%  Similarity=0.617  Sum_probs=80.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 030819           74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEI  153 (171)
Q Consensus        74 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~  153 (171)
                      ....++|||+|||+++++++|+++|.+||.|.++.++.++.+|+++|||||+|.+.++|++||+.|||..+.|+.|+|.+
T Consensus         5 ~~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~   84 (99)
T d1whwa_           5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLP   84 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCcHH
Q 030819          154 AKSRAE  159 (171)
Q Consensus       154 ~~~~~~  159 (171)
                      ++++..
T Consensus        85 a~~~~~   90 (99)
T d1whwa_          85 STIKKE   90 (99)
T ss_dssp             CCCCST
T ss_pred             CCCCCc
Confidence            988753

>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=99.90  E-value=2.9e-23  Score=130.29  Aligned_cols=78  Identities=38%  Similarity=0.623  Sum_probs=74.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 030819           74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFV  151 (171)
Q Consensus        74 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v  151 (171)
                      +++.++|||+|||+++++++|+++|++||.|.++.++.++.+|+++|||||+|.+.++|..|+..|||..+.|++|+|
T Consensus         6 p~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           6 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            345789999999999999999999999999999999999989999999999999999999999999999999999987

>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=99.90  E-value=8.3e-24  Score=133.41  Aligned_cols=81  Identities=30%  Similarity=0.537  Sum_probs=77.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEecCc
Q 030819           78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKSR  157 (171)
Q Consensus        78 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~~~  157 (171)
                      ++|||+|||+++++++|+++|++||+|.++.++.|+.+|.++|||||+|.+.++|..|++.|||..+.|++|.|.++.+.
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~   81 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG   81 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            57999999999999999999999999999999999999999999999999999999999999999999999999999865


Q ss_pred             H
Q 030819          158 A  158 (171)
Q Consensus       158 ~  158 (171)
                      .
T Consensus        82 ~   82 (85)
T d2u2fa_          82 A   82 (85)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.90  E-value=7.5e-24  Score=137.70  Aligned_cols=82  Identities=22%  Similarity=0.419  Sum_probs=77.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 030819           76 PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAK  155 (171)
Q Consensus        76 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~  155 (171)
                      +.++|||+|||+++++++|+++|+.||.|.+++++.++.+|+++|||||+|.+.++|.+|+. |||..+.|+.|+|.++.
T Consensus        17 ~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a~   95 (101)
T d2cq4a1          17 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQ   95 (101)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECC
Confidence            35799999999999999999999999999999999999899999999999999999999996 99999999999999987


Q ss_pred             CcH
Q 030819          156 SRA  158 (171)
Q Consensus       156 ~~~  158 (171)
                      ++.
T Consensus        96 ~~~   98 (101)
T d2cq4a1          96 AEK   98 (101)
T ss_dssp             HHH
T ss_pred             CCC
Confidence            654

>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=6.3e-23  Score=140.71  Aligned_cols=85  Identities=24%  Similarity=0.438  Sum_probs=80.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 030819           74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEI  153 (171)
Q Consensus        74 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~  153 (171)
                      ....++|||+|||+++++++|+++|++||.|.++.++.++.+|+++|||||+|.+.++|..|++.|||..|.|+.|+|.+
T Consensus        39 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~  118 (139)
T d1u6fa1          39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVAL  118 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            34557899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCcH
Q 030819          154 AKSRA  158 (171)
Q Consensus       154 ~~~~~  158 (171)
                      ++++.
T Consensus       119 a~~~~  123 (139)
T d1u6fa1         119 AASGH  123 (139)
T ss_dssp             SSCCC
T ss_pred             cCCCC
Confidence            97654

>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=3.6e-23  Score=130.44  Aligned_cols=80  Identities=34%  Similarity=0.641  Sum_probs=75.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC--eEEEEE
Q 030819           75 QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDG--RVIFVE  152 (171)
Q Consensus        75 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g--~~i~v~  152 (171)
                      ...++|||+|||+++++++|+++|++||.|.+++++.++.+|+++|||||+|.+.++|.+|++.|||..+.|  ++|+|.
T Consensus         4 ~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~   83 (85)
T d1b7fa2           4 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR   83 (85)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEE
Confidence            356789999999999999999999999999999999999999999999999999999999999999999976  789999


Q ss_pred             Ee
Q 030819          153 IA  154 (171)
Q Consensus       153 ~~  154 (171)
                      ||
T Consensus        84 ~A   85 (85)
T d1b7fa2          84 LA   85 (85)
T ss_dssp             EC
T ss_pred             EC
Confidence            86

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.89  E-value=3.2e-23  Score=133.04  Aligned_cols=85  Identities=27%  Similarity=0.563  Sum_probs=78.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCC-CCCcceEEEEEeCCHHHHHHHHHHh-CCceeCCeEEEE
Q 030819           74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKI-ANRPRGFAFLRYATEEESRRAIEGM-HGKFLDGRVIFV  151 (171)
Q Consensus        74 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~-~g~~~g~~fv~f~~~~~a~~al~~l-~g~~i~g~~i~v  151 (171)
                      .....+|||+|||+++++++|+++|++||.|..+.++.+.. +|.++|||||+|.+.++|.+|+..| ||..+.|++|+|
T Consensus         5 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V   84 (94)
T d2cpha1           5 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVL   84 (94)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEE
Confidence            34567899999999999999999999999999999988753 7999999999999999999999998 899999999999


Q ss_pred             EEecCcH
Q 030819          152 EIAKSRA  158 (171)
Q Consensus       152 ~~~~~~~  158 (171)
                      .|+.++.
T Consensus        85 ~~A~~~~   91 (94)
T d2cpha1          85 EWADSEV   91 (94)
T ss_dssp             EECCCCC
T ss_pred             EEcCCCC
Confidence            9998753

>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=3.8e-23  Score=130.34  Aligned_cols=79  Identities=28%  Similarity=0.591  Sum_probs=74.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC--eEEEEEE
Q 030819           76 PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDG--RVIFVEI  153 (171)
Q Consensus        76 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g--~~i~v~~  153 (171)
                      .+++|||+|||+++++++|+++|++||.|.+++++.++.+|.++|||||+|.+.++|.+|++.|||..+.|  ++|+|.|
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~   84 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKF   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEe
Confidence            35789999999999999999999999999999999999899999999999999999999999999999987  5699988


Q ss_pred             e
Q 030819          154 A  154 (171)
Q Consensus       154 ~  154 (171)
                      |
T Consensus        85 A   85 (85)
T d1fxla2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.89  E-value=5.4e-23  Score=129.32  Aligned_cols=80  Identities=39%  Similarity=0.635  Sum_probs=75.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 030819           76 PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAK  155 (171)
Q Consensus        76 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~  155 (171)
                      ..++|||+|||+++++++|+++|++||.|..+.++.|+.+|+++|||||+|.+.++|++|++ +++..++|+.|+|..|.
T Consensus         5 ~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEeee
Confidence            45799999999999999999999999999999999999999999999999999999999998 69999999999999875


Q ss_pred             C
Q 030819          156 S  156 (171)
Q Consensus       156 ~  156 (171)
                      +
T Consensus        84 s   84 (84)
T d1l3ka1          84 S   84 (84)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.89  E-value=3.2e-24  Score=153.17  Aligned_cols=147  Identities=18%  Similarity=0.292  Sum_probs=111.5

Q ss_pred             eeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCC---------------------
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLAC---------------------   63 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------------------   63 (171)
                      -.|||+|+++++++..+.+.|...+.+..         .........+..++.+++.+.                     
T Consensus         7 r~lfV~nLp~~~te~~L~~~F~~~G~v~~---------~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~   77 (183)
T d1u1qa_           7 RKLFIGGLSFETTDESLRSHFEQWGTLTD---------CVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVV   77 (183)
T ss_dssp             HEEEEESCCTTCCHHHHHHHHGGGSCEEE---------EEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHcCCEEE---------EEeeecccCCCccCceecccCCHHHHHHHHHhcCCcccccch
Confidence            36999999999999999999999887622         111111111111122221111                     


Q ss_pred             -----C-CCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHH
Q 030819           64 -----L-PPSPHSLSTCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE  137 (171)
Q Consensus        64 -----~-~~~~~~~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~  137 (171)
                           . .............++|||+|||+.+++++|+++|+.||.|..+.+..+..+|.++|||||+|.+.++|.+|++
T Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~  157 (183)
T d1u1qa_          78 EPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI  157 (183)
T ss_dssp             EEEECCCTTGGGSTTTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT
T ss_pred             hhhhhhhcccccccccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH
Confidence                 0 0111112344567899999999999999999999999999999999999899999999999999999999997


Q ss_pred             HhCCceeCCeEEEEEEecCcHHHH
Q 030819          138 GMHGKFLDGRVIFVEIAKSRAELR  161 (171)
Q Consensus       138 ~l~g~~i~g~~i~v~~~~~~~~~~  161 (171)
                       +++..++|+.|+|.++.++.++.
T Consensus       158 -~~~~~~~G~~i~V~~A~~k~e~~  180 (183)
T d1u1qa_         158 -QKYHTVNGHNCEVRKALSKQEMA  180 (183)
T ss_dssp             -SSCEEETTEEEEEEECCCHHHHH
T ss_pred             -hCCCeECCEEEEEEecCCccccc
Confidence             79999999999999999887654

>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=99.89  E-value=3e-23  Score=135.61  Aligned_cols=86  Identities=26%  Similarity=0.571  Sum_probs=80.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 030819           77 KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKS  156 (171)
Q Consensus        77 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~~  156 (171)
                      .++|||+|||+++++++|+++|++||.|.++.++.++.+|+++|||||+|.+.++|..|++.|||..+.|+.|+|.++.+
T Consensus         8 ~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~~   87 (104)
T d1p1ta_           8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAAS   87 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTC
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             cHHHHH
Q 030819          157 RAELRQ  162 (171)
Q Consensus       157 ~~~~~~  162 (171)
                      ......
T Consensus        88 ~~~~~~   93 (104)
T d1p1ta_          88 EKNKEE   93 (104)
T ss_dssp             TTHHHH
T ss_pred             CCCccc
Confidence            655443

>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=99.89  E-value=8.5e-23  Score=129.97  Aligned_cols=82  Identities=27%  Similarity=0.532  Sum_probs=76.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 030819           75 QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIA  154 (171)
Q Consensus        75 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~  154 (171)
                      ....+|||+|||+++++++|+++|++||.|..+.++.|+.+|.++|||||+|.+.++|++||+.  ...++|+.|.|.++
T Consensus         6 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~--~~~l~Gr~i~v~~a   83 (90)
T d2cqga1           6 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWCDCKLP   83 (90)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTEEEEEECC
T ss_pred             cCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhc--CCccCCEEeEEEeC
Confidence            4567899999999999999999999999999999999998999999999999999999999984  45899999999999


Q ss_pred             cCcH
Q 030819          155 KSRA  158 (171)
Q Consensus       155 ~~~~  158 (171)
                      .++.
T Consensus        84 ~~k~   87 (90)
T d2cqga1          84 NSKQ   87 (90)
T ss_dssp             CTTC
T ss_pred             CCCC
Confidence            8754

>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=99.89  E-value=7.5e-23  Score=126.93  Aligned_cols=77  Identities=27%  Similarity=0.514  Sum_probs=74.3

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 030819           79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKS  156 (171)
Q Consensus        79 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~~  156 (171)
                      +|||+|||+++++++|+++|++||.|.++.+..++ +|+++|||||+|.+.++|.+|++.|||..++|++|+|+++.+
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~S   78 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVTS   78 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEECC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEee-ccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            69999999999999999999999999999999987 899999999999999999999999999999999999999864

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.89  E-value=4.8e-23  Score=128.69  Aligned_cols=79  Identities=15%  Similarity=0.332  Sum_probs=69.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 030819           78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKS  156 (171)
Q Consensus        78 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~~  156 (171)
                      ++|||+|||+++++++|+++|++||.|..+.++.+..+|+++|||||+|.+.++|.+|++.|||..+.|++|+|.+++|
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            6999999999999999999999999999888888888999999999999999999999999999999999999999986

>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=99.88  E-value=4.6e-23  Score=131.26  Aligned_cols=83  Identities=40%  Similarity=0.693  Sum_probs=78.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 030819           76 PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAK  155 (171)
Q Consensus        76 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~  155 (171)
                      +..+|||+|||+++++++|+++|++||.|..+.++.++.+|.++|||||+|.++++|+.|+..|+|..++|+.|+|.++.
T Consensus         4 ~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a~   83 (90)
T d1x5sa1           4 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAG   83 (90)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEE
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            46789999999999999999999999999999999988899999999999999999999999999999999999999997


Q ss_pred             CcH
Q 030819          156 SRA  158 (171)
Q Consensus       156 ~~~  158 (171)
                      ++.
T Consensus        84 ~~~   86 (90)
T d1x5sa1          84 KSS   86 (90)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            664

>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=99.88  E-value=8.7e-23  Score=129.99  Aligned_cols=83  Identities=18%  Similarity=0.339  Sum_probs=76.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 030819           74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEI  153 (171)
Q Consensus        74 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~  153 (171)
                      ..+.++|||+|||.++++++|+++|+.||.|..+.+..++.++  +|||||+|.+.++|.+|+..|+|..+.|+.|+|.|
T Consensus         5 ~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~--~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~   82 (90)
T d2cqia1           5 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNW   82 (90)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSS--CCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCcc--ceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            4556799999999999999999999999999999999887544  78999999999999999999999999999999999


Q ss_pred             ecCcH
Q 030819          154 AKSRA  158 (171)
Q Consensus       154 ~~~~~  158 (171)
                      +++..
T Consensus        83 a~~~~   87 (90)
T d2cqia1          83 ATTPS   87 (90)
T ss_dssp             CCCTT
T ss_pred             cCCCC
Confidence            98654

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.88  E-value=1.9e-22  Score=131.51  Aligned_cols=83  Identities=33%  Similarity=0.600  Sum_probs=76.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 030819           75 QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIA  154 (171)
Q Consensus        75 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~  154 (171)
                      ...++|||+|||+.+++++|+++|++||.|.++.++.++.+|+++|||||+|.+.++|++|++.+++ .++|+.|+|.++
T Consensus         8 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a   86 (103)
T d2cqda1           8 TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLA   86 (103)
T ss_dssp             CSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEES
T ss_pred             CCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEEc
Confidence            3456899999999999999999999999999999999998999999999999999999999998875 799999999998


Q ss_pred             cCcH
Q 030819          155 KSRA  158 (171)
Q Consensus       155 ~~~~  158 (171)
                      ..+.
T Consensus        87 ~~~~   90 (103)
T d2cqda1          87 YLGA   90 (103)
T ss_dssp             TTTC
T ss_pred             CCCC
Confidence            7543

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.88  E-value=7.1e-23  Score=128.49  Aligned_cols=79  Identities=29%  Similarity=0.545  Sum_probs=74.5

Q ss_pred             EEEcCCCCCCCHHHHHHHHhcCCCeEEE-EEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEecCcH
Q 030819           80 LFVSGLSFRTSEDSLRNAFQGFGQLVEV-NLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKSRA  158 (171)
Q Consensus        80 l~V~nl~~~~~~~~l~~~f~~~G~i~~~-~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~~~~  158 (171)
                      |||+|||+++++++|+++|.+||.|.++ .++.++.+|+++|||||+|.+.++|++|++.|+|..++|++|+|.++.++.
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k~   80 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKD   80 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCCC
Confidence            7999999999999999999999998664 788898899999999999999999999999999999999999999998764

>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=99.88  E-value=5.6e-22  Score=126.93  Aligned_cols=84  Identities=31%  Similarity=0.638  Sum_probs=77.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ......+|||+|||+++++++|+++|++||.|.++.++.++  +.++|||||+|.+.++|.+|+..|||..+.|+.|+|.
T Consensus         7 ~~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~--~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~   84 (93)
T d2cq3a1           7 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN   84 (93)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT--TTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccc--cCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            44556789999999999999999999999999999999886  3468999999999999999999999999999999999


Q ss_pred             EecCcH
Q 030819          153 IAKSRA  158 (171)
Q Consensus       153 ~~~~~~  158 (171)
                      +++++.
T Consensus        85 ~A~~r~   90 (93)
T d2cq3a1          85 NATARV   90 (93)
T ss_dssp             ECCSSC
T ss_pred             ecCcCC
Confidence            998764

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.88  E-value=6.4e-23  Score=133.69  Aligned_cols=82  Identities=34%  Similarity=0.615  Sum_probs=77.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 030819           76 PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAK  155 (171)
Q Consensus        76 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~  155 (171)
                      ..++|||+|||+++++++|+++|.+||.|..+.+..|+.++.++|||||+|.+.++|.+|++ ++|..|+|+.|.|.++.
T Consensus        19 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~   97 (103)
T d1x4ba1          19 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAV   97 (103)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCS
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECc
Confidence            34799999999999999999999999999999999999899999999999999999999997 79999999999999998


Q ss_pred             CcH
Q 030819          156 SRA  158 (171)
Q Consensus       156 ~~~  158 (171)
                      ++.
T Consensus        98 ~ke  100 (103)
T d1x4ba1          98 ARE  100 (103)
T ss_dssp             SCC
T ss_pred             ccC
Confidence            764

>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=99.88  E-value=2.9e-23  Score=128.43  Aligned_cols=76  Identities=28%  Similarity=0.586  Sum_probs=73.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 030819           78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIA  154 (171)
Q Consensus        78 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~  154 (171)
                      ++|||+|||+++++++|+++|++||.|.++.++.|+.+|+++|||||+|.+.++|++|++ +++..++|+.|.|..|
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            579999999999999999999999999999999999999999999999999999999998 7999999999999876

>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=2.1e-22  Score=126.84  Aligned_cols=78  Identities=27%  Similarity=0.566  Sum_probs=72.8

Q ss_pred             EEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCC---CcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 030819           80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIAN---RPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKS  156 (171)
Q Consensus        80 l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g---~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~~  156 (171)
                      |||+|||+++++++|+++|++||.|.++.++.++.++   .++|||||+|.+.++|.+|++.|||..++|+.|+|.+++.
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~~   80 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISER   80 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSC
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            7999999999999999999999999999999887665   4689999999999999999999999999999999999864


Q ss_pred             c
Q 030819          157 R  157 (171)
Q Consensus       157 ~  157 (171)
                      .
T Consensus        81 ~   81 (85)
T d2cpfa1          81 A   81 (85)
T ss_dssp             S
T ss_pred             C
Confidence            3

>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=99.87  E-value=5.9e-22  Score=123.06  Aligned_cols=77  Identities=23%  Similarity=0.477  Sum_probs=73.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 030819           77 KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIA  154 (171)
Q Consensus        77 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~  154 (171)
                      .++|||+|||+++|+++|+++|++||.|..+.+..++.++.++|||||+|.+.+++.+|++ ++|..|+|+.|+|..|
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEEC
Confidence            4689999999999999999999999999999999999999999999999999999999996 8999999999999876

>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=99.87  E-value=4.7e-22  Score=128.35  Aligned_cols=85  Identities=29%  Similarity=0.541  Sum_probs=78.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC------CceeCCe
Q 030819           74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMH------GKFLDGR  147 (171)
Q Consensus        74 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~------g~~i~g~  147 (171)
                      ..++++|||+|||+++++++|+++|.+||.|..+.+..++.++.++|||||+|.+.++|.+|++.|+      |..+.|+
T Consensus         5 ~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr   84 (98)
T d1x4ha1           5 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGR   84 (98)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSC
T ss_pred             CCCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCE
Confidence            3457899999999999999999999999999999999999899999999999999999999999886      5678999


Q ss_pred             EEEEEEecCcH
Q 030819          148 VIFVEIAKSRA  158 (171)
Q Consensus       148 ~i~v~~~~~~~  158 (171)
                      .|+|+++.++.
T Consensus        85 ~l~v~~a~~k~   95 (98)
T d1x4ha1          85 QLKVDLAVTRD   95 (98)
T ss_dssp             EEEEECCCCCC
T ss_pred             EEEEEECCCCC
Confidence            99999998764

>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=99.87  E-value=1.3e-22  Score=124.83  Aligned_cols=75  Identities=32%  Similarity=0.661  Sum_probs=71.2

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 030819           79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIA  154 (171)
Q Consensus        79 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~  154 (171)
                      +|||+|||+++++++|+++|++||.|..+.+..++.+++++|||||+|.+.++|++||+ +++..++|+.|.|..|
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeEC
Confidence            58999999999999999999999999999999999999999999999999999999998 7999999999998643

>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=2.3e-22  Score=127.72  Aligned_cols=81  Identities=33%  Similarity=0.642  Sum_probs=75.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 030819           77 KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKS  156 (171)
Q Consensus        77 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~~  156 (171)
                      ..+|||+|||+++++++|+++|++||.|..+.++.++  +.++|||||+|.+.++|++|++.|||..++|+.|.|.++++
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~   85 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   85 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBT--TBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeec--CCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            4579999999999999999999999999999999886  34789999999999999999999999999999999999987


Q ss_pred             cHH
Q 030819          157 RAE  159 (171)
Q Consensus       157 ~~~  159 (171)
                      +.+
T Consensus        86 ~~~   88 (89)
T d1cvja2          86 RKE   88 (89)
T ss_dssp             TTT
T ss_pred             CCC
Confidence            653

>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=99.87  E-value=9.2e-23  Score=125.47  Aligned_cols=75  Identities=32%  Similarity=0.583  Sum_probs=70.9

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 030819           79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIA  154 (171)
Q Consensus        79 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~  154 (171)
                      +|||+|||+++++++|+++|++||.|.++.++.++.+++++|||||+|.+.++|++||+ .++..++|+.|.|..|
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~-~~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTT-CSSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHh-hCCCEECCEEeEEEEC
Confidence            58999999999999999999999999999999999999999999999999999999998 5778899999998764

>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=8.7e-22  Score=127.79  Aligned_cols=86  Identities=23%  Similarity=0.424  Sum_probs=78.2

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeE--------EEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLV--------EVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFL  144 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~--------~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i  144 (171)
                      ......+|||+|||+++++++|+++|+.||.|.        .+.+..++.+|+++|||||+|.+.++|.+|++.|||..+
T Consensus         4 ~~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~   83 (101)
T d2cpea1           4 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   83 (101)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEE
Confidence            345678999999999999999999999999874        466778888899999999999999999999999999999


Q ss_pred             CCeEEEEEEecCcH
Q 030819          145 DGRVIFVEIAKSRA  158 (171)
Q Consensus       145 ~g~~i~v~~~~~~~  158 (171)
                      +|+.|+|.+++++.
T Consensus        84 ~gr~i~V~~a~~~~   97 (101)
T d2cpea1          84 QGSKLKVSLARKKP   97 (101)
T ss_dssp             TTEECEEECSSCCC
T ss_pred             CCEEEEEEEcCCCC
Confidence            99999999998754

>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=1.3e-21  Score=129.64  Aligned_cols=80  Identities=15%  Similarity=0.347  Sum_probs=73.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 030819           75 QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIA  154 (171)
Q Consensus        75 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~  154 (171)
                      +.+++|||+|||.++++++|+++|++||.|.+|++..   ++.++|||||+|.+.++|..|++.|||..+.|+.|+|.++
T Consensus         5 ~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~---~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a   81 (114)
T d2f9da1           5 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN---TPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYY   81 (114)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEC---STTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccc---cCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            4578999999999999999999999999999998865   4567899999999999999999999999999999999998


Q ss_pred             cCc
Q 030819          155 KSR  157 (171)
Q Consensus       155 ~~~  157 (171)
                      ...
T Consensus        82 ~~~   84 (114)
T d2f9da1          82 NAN   84 (114)
T ss_dssp             CHH
T ss_pred             CCC
Confidence            643

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.86  E-value=4.8e-22  Score=125.47  Aligned_cols=81  Identities=26%  Similarity=0.472  Sum_probs=71.3

Q ss_pred             CCCeEEEcCCCCCCC-HHHHHHHHhcCCCeEEEEEeec-CCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 030819           76 PKTRLFVSGLSFRTS-EDSLRNAFQGFGQLVEVNLVMD-KIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEI  153 (171)
Q Consensus        76 ~~~~l~V~nl~~~~~-~~~l~~~f~~~G~i~~~~~~~~-~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~  153 (171)
                      .+++|||+|||++++ +++|+++|++||.|.++.+..+ ..+++++|||||+|.+.++|.+|++ |||..+.|+.|+|.+
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~~   81 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSL   81 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEEE
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEEE
Confidence            468999999999875 6679999999999999998764 5689999999999999999999996 999999999999999


Q ss_pred             ecCc
Q 030819          154 AKSR  157 (171)
Q Consensus       154 ~~~~  157 (171)
                      ++++
T Consensus        82 a~~k   85 (86)
T d2ghpa3          82 ADKK   85 (86)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9875

>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=1.1e-22  Score=132.29  Aligned_cols=85  Identities=25%  Similarity=0.436  Sum_probs=79.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 030819           74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEI  153 (171)
Q Consensus        74 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~  153 (171)
                      ..++++|||+|||.++++++|+++|.+||.|..+.+..+..+|+++|||||+|.+.++|.+|++.|||..+.|+.|+|+|
T Consensus        15 ~~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   94 (102)
T d2cpxa1          15 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF   94 (102)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            34578999999999999999999999999999998888877899999999999999999999999999999999999999


Q ss_pred             ecCcH
Q 030819          154 AKSRA  158 (171)
Q Consensus       154 ~~~~~  158 (171)
                      ++++.
T Consensus        95 ak~k~   99 (102)
T d2cpxa1          95 GKNKK   99 (102)
T ss_dssp             CCCCS
T ss_pred             CCCcc
Confidence            98764

>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=99.86  E-value=9.3e-23  Score=130.07  Aligned_cols=83  Identities=22%  Similarity=0.318  Sum_probs=75.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      .+....+|||+|||+++++++|+++|++||.|..+.++.+. +|+++|||||+|.+.++|++||+ |||..++|+.|+|+
T Consensus         9 ~~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~-~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~   86 (91)
T d1fjeb1           9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLE   86 (91)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEE-EETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEE
T ss_pred             CCCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecC-CCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEE
Confidence            34456799999999999999999999999999988887654 89999999999999999999997 99999999999999


Q ss_pred             EecCc
Q 030819          153 IAKSR  157 (171)
Q Consensus       153 ~~~~~  157 (171)
                      +++++
T Consensus        87 ~ak~k   91 (91)
T d1fjeb1          87 KPKGR   91 (91)
T ss_dssp             CCCCS
T ss_pred             ecCCC
Confidence            99875

>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=99.85  E-value=7.6e-22  Score=121.33  Aligned_cols=75  Identities=29%  Similarity=0.604  Sum_probs=72.2

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 030819           79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIA  154 (171)
Q Consensus        79 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~  154 (171)
                      +|||+|||+++++++|+++|++||.|..+.+..++.++.++|||||+|.+.++|++|++ +||..++|++|+|++|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECCeEEEEEEC
Confidence            58999999999999999999999999999999999899999999999999999999997 9999999999999875

>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=99.85  E-value=2.4e-21  Score=124.61  Aligned_cols=78  Identities=24%  Similarity=0.558  Sum_probs=72.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 030819           75 QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIA  154 (171)
Q Consensus        75 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~  154 (171)
                      +..++|||+|||.++++++|+++|++||.|.++.+..++      |||||+|.+.++|..|+..|||..++|+.|+|.|+
T Consensus        16 ~~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~k------g~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~a   89 (96)
T d1x4ga1          16 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK------GYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWG   89 (96)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETTT------TEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEecc------eEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            346799999999999999999999999999999998764      89999999999999999999999999999999999


Q ss_pred             cCcH
Q 030819          155 KSRA  158 (171)
Q Consensus       155 ~~~~  158 (171)
                      +++.
T Consensus        90 k~~p   93 (96)
T d1x4ga1          90 KESP   93 (96)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8754

>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=99.85  E-value=1.8e-21  Score=126.39  Aligned_cols=82  Identities=26%  Similarity=0.451  Sum_probs=75.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 030819           74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEI  153 (171)
Q Consensus        74 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~  153 (171)
                      ..+.++|||+|||+++++++|+++|++||.|..+.+..+. ++.++|||||+|.+.++|.+|++.|||..|.|+++.|.+
T Consensus        15 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~-~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~   93 (101)
T d1x5oa1          15 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAP   93 (101)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCC
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeeccc-ccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCC
Confidence            3456799999999999999999999999999999998886 899999999999999999999999999999999988877


Q ss_pred             ecC
Q 030819          154 AKS  156 (171)
Q Consensus       154 ~~~  156 (171)
                      ++|
T Consensus        94 ~~P   96 (101)
T d1x5oa1          94 TEP   96 (101)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            765

>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=99.85  E-value=5.3e-21  Score=120.31  Aligned_cols=77  Identities=12%  Similarity=0.312  Sum_probs=72.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 030819           77 KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAK  155 (171)
Q Consensus        77 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~  155 (171)
                      .++|||+|||.++++++|+++|+.||.|..+.+..++ +|.++|||||+|.+.++|++||+ ++|..+.|+.|.|.|+.
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~-~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeec-cCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            5799999999999999999999999999999998876 89999999999999999999997 79999999999999864

>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=99.85  E-value=5.2e-21  Score=122.81  Aligned_cols=82  Identities=21%  Similarity=0.388  Sum_probs=74.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ...+.++|||+|||+++++++|+++|..||.|..+.+..   ++.++|||||+|.+.++|+.||+.|||..+.|++|+|+
T Consensus        10 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~---~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~   86 (95)
T d1x4aa1          10 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN---RRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVE   86 (95)
T ss_dssp             CCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECC---SSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEecc---cccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            345567999999999999999999999999999988754   34568999999999999999999999999999999999


Q ss_pred             EecCc
Q 030819          153 IAKSR  157 (171)
Q Consensus       153 ~~~~~  157 (171)
                      |+++.
T Consensus        87 ~a~~~   91 (95)
T d1x4aa1          87 FPRSG   91 (95)
T ss_dssp             CCCCC
T ss_pred             eccCC
Confidence            99864

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.84  E-value=7.8e-21  Score=119.01  Aligned_cols=79  Identities=29%  Similarity=0.404  Sum_probs=71.4

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee-CCeEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFL-DGRVIFV  151 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i-~g~~i~v  151 (171)
                      ..+++++|||+|||.++++++|..+|+.||.|.++++..++     +|||||+|.+.++|.+|+..|||..+ .|+.|+|
T Consensus         4 ~~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v   78 (83)
T d2b0ga1           4 EQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFTTELQSNAAKEALQGFKITPTHAMKI   78 (83)
T ss_dssp             CCSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTT-----CSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeeccc-----ceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEE
Confidence            45567899999999999999999999999999999997543     58999999999999999999999988 5689999


Q ss_pred             EEecC
Q 030819          152 EIAKS  156 (171)
Q Consensus       152 ~~~~~  156 (171)
                      .|++.
T Consensus        79 ~~akk   83 (83)
T d2b0ga1          79 TFAKK   83 (83)
T ss_dssp             EECCC
T ss_pred             EEecC
Confidence            99873

>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=99.84  E-value=3.5e-21  Score=123.85  Aligned_cols=83  Identities=20%  Similarity=0.442  Sum_probs=74.5

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 030819           72 STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFV  151 (171)
Q Consensus        72 ~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v  151 (171)
                      ....+.++|||+|||+++++++|+++|.+||.|..+..     ++.++|||||+|.+.++|++|++.|||..++|+.|+|
T Consensus        11 ~~~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~-----~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V   85 (96)
T d1fjca_          11 KKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ-----DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSL   85 (96)
T ss_dssp             STTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE-----TTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEE
T ss_pred             CcCCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee-----cCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEE
Confidence            34456789999999999999999999999998766543     7889999999999999999999999999999999999


Q ss_pred             EEecCcHH
Q 030819          152 EIAKSRAE  159 (171)
Q Consensus       152 ~~~~~~~~  159 (171)
                      .|+.++..
T Consensus        86 ~~a~~k~~   93 (96)
T d1fjca_          86 YYTGEKGG   93 (96)
T ss_dssp             EECSSSCC
T ss_pred             EEeCCCCC
Confidence            99987753

>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=99.84  E-value=8.6e-21  Score=120.08  Aligned_cols=79  Identities=24%  Similarity=0.363  Sum_probs=71.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee-CCeEEEEEE
Q 030819           75 QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFL-DGRVIFVEI  153 (171)
Q Consensus        75 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i-~g~~i~v~~  153 (171)
                      +++++|||+|||+++++++|+++|++||.|..+.+..    ++.+|||||+|.+.++|.+|+..|||..+ +|+.|+|+|
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~----~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~   83 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFF----QKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSF   83 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEEC----SSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEee----ecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEe
Confidence            5678999999999999999999999999998877654    34568999999999999999999999998 589999999


Q ss_pred             ecCc
Q 030819          154 AKSR  157 (171)
Q Consensus       154 ~~~~  157 (171)
                      ++++
T Consensus        84 sk~~   87 (88)
T d2adca2          84 SKST   87 (88)
T ss_dssp             CSSC
T ss_pred             CCCC
Confidence            9864

>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=99.84  E-value=1.5e-20  Score=122.47  Aligned_cols=82  Identities=21%  Similarity=0.446  Sum_probs=72.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecC-CCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 030819           75 QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDK-IANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEI  153 (171)
Q Consensus        75 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~-~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~  153 (171)
                      .+.++|||+|||+++++++|+++|+.|| +.++.++.++ .+++++|||||+|.+.++|++|+. ||+..++|+.|+|.+
T Consensus        13 ~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~-~~~~~~~gr~l~V~~   90 (104)
T d1wi8a_          13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLGNKRIRVDV   90 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHG-GGTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHH-cCCCEECCEEEEEEE
Confidence            4568999999999999999999999999 7777777655 468899999999999999987775 999999999999999


Q ss_pred             ecCcH
Q 030819          154 AKSRA  158 (171)
Q Consensus       154 ~~~~~  158 (171)
                      +.++.
T Consensus        91 a~~~~   95 (104)
T d1wi8a_          91 ADQAQ   95 (104)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            98754

>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=99.83  E-value=4.4e-21  Score=122.20  Aligned_cols=83  Identities=20%  Similarity=0.447  Sum_probs=74.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHH----HHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 030819           76 PKTRLFVSGLSFRTSEDSLRN----AFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFV  151 (171)
Q Consensus        76 ~~~~l~V~nl~~~~~~~~l~~----~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v  151 (171)
                      |+++|||+|||+++++++|++    +|++||.|.++.+..   +++++|||||+|.+.++|..|+..+||..+.|+.|+|
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~---~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v   78 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI   78 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee---eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            578999999999999998864    589999999987743   5678899999999999999999999999999999999


Q ss_pred             EEecCcHHHH
Q 030819          152 EIAKSRAELR  161 (171)
Q Consensus       152 ~~~~~~~~~~  161 (171)
                      .|++++.+..
T Consensus        79 ~~ak~~~~~~   88 (91)
T d1nu4a_          79 QYAKTDSDII   88 (91)
T ss_dssp             EECSSCCTHH
T ss_pred             EEeCCCchhh
Confidence            9999876554

>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=99.83  E-value=8.2e-21  Score=119.66  Aligned_cols=81  Identities=16%  Similarity=0.254  Sum_probs=71.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 030819           74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEI  153 (171)
Q Consensus        74 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~  153 (171)
                      .+...+|||+|||+++++++|+++|..||.+....++.+..+|.++|+|||+|.+.++|.+|++.||+..+.|++|+|.+
T Consensus         6 ~p~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l   85 (86)
T d2cqpa1           6 KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVL   85 (86)
T ss_dssp             CCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34466899999999999999999999999987643344445899999999999999999999999999999999999987


Q ss_pred             e
Q 030819          154 A  154 (171)
Q Consensus       154 ~  154 (171)
                      +
T Consensus        86 ~   86 (86)
T d2cqpa1          86 G   86 (86)
T ss_dssp             S
T ss_pred             C
Confidence            5

>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=99.83  E-value=1e-20  Score=117.40  Aligned_cols=76  Identities=24%  Similarity=0.456  Sum_probs=69.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 030819           74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEI  153 (171)
Q Consensus        74 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~  153 (171)
                      +..+++|||+|++  +|+++|+++|++||.|.++.+..++      |||||+|.+.++|..|+..|||..++|+.|+|.|
T Consensus         2 p~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~~------~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~   73 (79)
T d2bz2a1           2 PRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPR------NCAFVTYEKMESADQAVAELNGTQVESVQLKVNI   73 (79)
T ss_dssp             CCCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETTT------TEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEECCC--CCHHHHHHHHhccCccceeeeccCC------CEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3457899999986  8999999999999999999987554      8999999999999999999999999999999999


Q ss_pred             ecCc
Q 030819          154 AKSR  157 (171)
Q Consensus       154 ~~~~  157 (171)
                      ++++
T Consensus        74 a~~~   77 (79)
T d2bz2a1          74 ARKQ   77 (79)
T ss_dssp             CCSS
T ss_pred             ecCC
Confidence            9865

>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=99.83  E-value=2.8e-21  Score=117.90  Aligned_cols=71  Identities=20%  Similarity=0.498  Sum_probs=68.2

Q ss_pred             EEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q 030819           80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIF  150 (171)
Q Consensus        80 l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~  150 (171)
                      |||+|||+++++++|+++|++||.|..+.+..++.++.++|||||+|.+.++|++|+..|||..+.|+.|+
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEECc
Confidence            79999999999999999999999999999999998999999999999999999999999999999998764

>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=99.82  E-value=2.1e-20  Score=117.75  Aligned_cols=75  Identities=31%  Similarity=0.468  Sum_probs=70.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 030819           77 KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKS  156 (171)
Q Consensus        77 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~~  156 (171)
                      .++|||+|||+++++++|+++|++||.|.++.+..++      |||||+|.+.++|++|+..|||..+.|+.|+|+|+..
T Consensus         8 ~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~k------~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~   81 (86)
T d2cpja1           8 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK------GFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACH   81 (86)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETTT------TEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeeccc------ceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            4689999999999999999999999999999998664      8999999999999999999999999999999999976


Q ss_pred             c
Q 030819          157 R  157 (171)
Q Consensus       157 ~  157 (171)
                      .
T Consensus        82 ~   82 (86)
T d2cpja1          82 S   82 (86)
T ss_dssp             C
T ss_pred             c
Confidence            5

>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=1.4e-20  Score=119.41  Aligned_cols=77  Identities=26%  Similarity=0.413  Sum_probs=69.9

Q ss_pred             CCCeEEEcCCCCCCCHHHH---HHHHhcCCCeEEEEEeecCCCCCc---ceEEEEEeCCHHHHHHHHHHhCCceeCCeEE
Q 030819           76 PKTRLFVSGLSFRTSEDSL---RNAFQGFGQLVEVNLVMDKIANRP---RGFAFLRYATEEESRRAIEGMHGKFLDGRVI  149 (171)
Q Consensus        76 ~~~~l~V~nl~~~~~~~~l---~~~f~~~G~i~~~~~~~~~~~g~~---~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i  149 (171)
                      ...+|||+|||+++++++|   .++|++||.|..+.++.++.++.+   +|||||+|.+.++|.+|++.|||..+.|+.|
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~l   86 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTL   86 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEE
Confidence            3568999999999999999   678999999999999988766554   4999999999999999999999999999999


Q ss_pred             EEE
Q 030819          150 FVE  152 (171)
Q Consensus       150 ~v~  152 (171)
                      +|.
T Consensus        87 kvS   89 (89)
T d2cpia1          87 KAS   89 (89)
T ss_dssp             EEE
T ss_pred             EEC
Confidence            985

>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=99.82  E-value=7e-20  Score=115.33  Aligned_cols=77  Identities=27%  Similarity=0.440  Sum_probs=70.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 030819           76 PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAK  155 (171)
Q Consensus        76 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~  155 (171)
                      ..++|||+|||+++++++|+++|++||.|..+.+..      ++|||||+|.+.++|.+|+..|||..+.|+.|+|.|++
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~------~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~ak   80 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK------IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAK   80 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE------CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcc------ccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEecc
Confidence            357899999999999999999999999988877644      45899999999999999999999999999999999998


Q ss_pred             CcH
Q 030819          156 SRA  158 (171)
Q Consensus       156 ~~~  158 (171)
                      |+.
T Consensus        81 P~~   83 (86)
T d2cpda1          81 PVD   83 (86)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            764

>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=99.82  E-value=4.8e-21  Score=119.20  Aligned_cols=75  Identities=28%  Similarity=0.495  Sum_probs=68.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCc-eeCCeEEEEEEecC
Q 030819           78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGK-FLDGRVIFVEIAKS  156 (171)
Q Consensus        78 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~-~i~g~~i~v~~~~~  156 (171)
                      .+|||+|||+++++++|+++|++||.|..+.+...      +|||||+|.+.++|.+|++.|||. .+.|++|+|+|+.+
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~------rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~   75 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK------SGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVS   75 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEE------TTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEecc------cceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCC
Confidence            37999999999999999999999999877766554      489999999999999999999996 69999999999998


Q ss_pred             cH
Q 030819          157 RA  158 (171)
Q Consensus       157 ~~  158 (171)
                      +.
T Consensus        76 k~   77 (80)
T d2cqha1          76 KK   77 (80)
T ss_dssp             CC
T ss_pred             cC
Confidence            65

>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=99.82  E-value=1.6e-20  Score=120.75  Aligned_cols=84  Identities=20%  Similarity=0.339  Sum_probs=74.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCCC-eEEEEEeecC-CCCCcceEEEEEeCCHHHHHHHHHHhCCc--eeCCeEEEEE
Q 030819           77 KTRLFVSGLSFRTSEDSLRNAFQGFGQ-LVEVNLVMDK-IANRPRGFAFLRYATEEESRRAIEGMHGK--FLDGRVIFVE  152 (171)
Q Consensus        77 ~~~l~V~nl~~~~~~~~l~~~f~~~G~-i~~~~~~~~~-~~g~~~g~~fv~f~~~~~a~~al~~l~g~--~i~g~~i~v~  152 (171)
                      +++|||+|||.++++++|+++|++||+ |..+.++.+. .+|+++|||||+|.+.++|..|++.|++.  .+.|+.|+|.
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~   80 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVD   80 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEE
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEE
Confidence            368999999999999999999999996 8999998875 46889999999999999999999999755  4579999999


Q ss_pred             EecCcHHH
Q 030819          153 IAKSRAEL  160 (171)
Q Consensus       153 ~~~~~~~~  160 (171)
                      |++++.+.
T Consensus        81 ~A~p~~~~   88 (96)
T d2disa1          81 WAEPEIDV   88 (96)
T ss_dssp             ESCSSCST
T ss_pred             EcCCCCCC
Confidence            99876543

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=5.2e-20  Score=118.66  Aligned_cols=76  Identities=25%  Similarity=0.611  Sum_probs=68.6

Q ss_pred             CCCCCeEEEcCCC-CCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           74 CQPKTRLFVSGLS-FRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        74 ~~~~~~l~V~nl~-~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      .....+|||+||| ..+++++|+++|++||.|.++.+        ++|||||+|.+.++|++|+..|||..+.|+.|+|+
T Consensus        12 ~~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i--------~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~   83 (98)
T d1wf2a_          12 RSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDIN   83 (98)
T ss_dssp             SSCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE--------ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEE
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE--------eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            3445689999997 56889999999999999999988        35999999999999999999999999999999999


Q ss_pred             EecCc
Q 030819          153 IAKSR  157 (171)
Q Consensus       153 ~~~~~  157 (171)
                      ++++.
T Consensus        84 ~a~~~   88 (98)
T d1wf2a_          84 LAAEP   88 (98)
T ss_dssp             ETTSC
T ss_pred             ECCCC
Confidence            99764

>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=99.81  E-value=4.5e-20  Score=120.03  Aligned_cols=86  Identities=17%  Similarity=0.283  Sum_probs=74.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEE
Q 030819           74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEI  153 (171)
Q Consensus        74 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~  153 (171)
                      +....+|||+|||+++++++|+++|..||.+..+.++....+|+++|+|||+|.+.++|++||+ +||..|+|+.|.|.+
T Consensus         5 ~~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~   83 (103)
T d2cpya1           5 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHV   83 (103)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEE
T ss_pred             CCCceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEE
Confidence            3446789999999999999999999999998775555555599999999999999999999997 999999999999999


Q ss_pred             ecCcHHH
Q 030819          154 AKSRAEL  160 (171)
Q Consensus       154 ~~~~~~~  160 (171)
                      +......
T Consensus        84 ~~~~~~~   90 (103)
T d2cpya1          84 VTLEDMR   90 (103)
T ss_dssp             ECHHHHH
T ss_pred             CCHHHhh
Confidence            8655433

>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=4.2e-20  Score=121.64  Aligned_cols=77  Identities=21%  Similarity=0.234  Sum_probs=70.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 030819           75 QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIA  154 (171)
Q Consensus        75 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~  154 (171)
                      ...++|||+|||+.+++++|+++|..||.|..+.+..      .+|||||+|.+.++|.+|++.|||..+.|++|.|+|+
T Consensus         8 r~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~------~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a   81 (111)
T d1whxa_           8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWA   81 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeec------cCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEEC
Confidence            3457999999999999999999999999999998743      3589999999999999999999999999999999998


Q ss_pred             cCc
Q 030819          155 KSR  157 (171)
Q Consensus       155 ~~~  157 (171)
                      ...
T Consensus        82 ~~~   84 (111)
T d1whxa_          82 PIG   84 (111)
T ss_dssp             ETT
T ss_pred             CCC
Confidence            643

>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=99.81  E-value=4.3e-20  Score=121.26  Aligned_cols=76  Identities=25%  Similarity=0.428  Sum_probs=70.1

Q ss_pred             CCeEEEcCCCC-CCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 030819           77 KTRLFVSGLSF-RTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAK  155 (171)
Q Consensus        77 ~~~l~V~nl~~-~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~  155 (171)
                      +++|||+||++ .+++++|+++|+.||.|..+.++.++     +|||||+|.+.++|.+|++.|||..+.|+.|+|.+++
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~-----kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~   76 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   76 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCS
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc-----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            57999999965 59999999999999999999998764     5899999999999999999999999999999999987


Q ss_pred             Cc
Q 030819          156 SR  157 (171)
Q Consensus       156 ~~  157 (171)
                      ..
T Consensus        77 ~~   78 (109)
T d2adca1          77 HQ   78 (109)
T ss_dssp             CC
T ss_pred             CC
Confidence            44

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=2e-19  Score=117.16  Aligned_cols=85  Identities=19%  Similarity=0.272  Sum_probs=76.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ......+|||+|||+++++++|+++|..+|.+....++.+..+++++|||||+|.+.++|++|++ +|+..|.|+.|.|.
T Consensus        11 ~~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~   89 (104)
T d1wg5a_          11 DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIF   89 (104)
T ss_dssp             SCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEE
Confidence            34456689999999999999999999999999887777777799999999999999999999997 89999999999999


Q ss_pred             EecCcH
Q 030819          153 IAKSRA  158 (171)
Q Consensus       153 ~~~~~~  158 (171)
                      ++.+..
T Consensus        90 ~~~~~~   95 (104)
T d1wg5a_          90 KSSRAE   95 (104)
T ss_dssp             EECTTT
T ss_pred             ECCHHH
Confidence            987654

>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=99.81  E-value=1.1e-19  Score=116.89  Aligned_cols=79  Identities=34%  Similarity=0.553  Sum_probs=71.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCC--eEEEE
Q 030819           74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDG--RVIFV  151 (171)
Q Consensus        74 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g--~~i~v  151 (171)
                      .++.++|||+|||+++++++|+++|++||.|..+++..++      +||||+|.+.++|..|++.||+..+.|  ++|+|
T Consensus        14 ~~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~------~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v   87 (97)
T d1whya_          14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGD------SFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRV   87 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSSS------CCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEE
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeeccc------cEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEE
Confidence            3567899999999999999999999999999999987654      899999999999999999999999976  58999


Q ss_pred             EEecCcH
Q 030819          152 EIAKSRA  158 (171)
Q Consensus       152 ~~~~~~~  158 (171)
                      +|+++.+
T Consensus        88 ~~ak~~~   94 (97)
T d1whya_          88 DFAKSGP   94 (97)
T ss_dssp             EECCCCC
T ss_pred             EeCCCCC
Confidence            9998653

>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=99.80  E-value=9.4e-20  Score=118.32  Aligned_cols=84  Identities=18%  Similarity=0.283  Sum_probs=75.0

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q 030819           72 STCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFV  151 (171)
Q Consensus        72 ~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v  151 (171)
                      .....+.+|||+|||+++|+++|+++|..|| +..+.++.+. ++.++|||||+|.+.++|++|++ +|+..|.|+.|+|
T Consensus        10 ~~~~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~~-~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V   86 (102)
T d1weza_          10 FQSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVEL   86 (102)
T ss_dssp             CCCSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEE
T ss_pred             CcCCCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEec-CCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEE
Confidence            3456678999999999999999999999998 4577777776 78999999999999999999987 8999999999999


Q ss_pred             EEecCcH
Q 030819          152 EIAKSRA  158 (171)
Q Consensus       152 ~~~~~~~  158 (171)
                      .++....
T Consensus        87 ~~s~~~~   93 (102)
T d1weza_          87 FLNSTAG   93 (102)
T ss_dssp             EEECCCC
T ss_pred             EEcCCCC
Confidence            9988654

>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=99.80  E-value=1.9e-19  Score=110.49  Aligned_cols=74  Identities=19%  Similarity=0.241  Sum_probs=67.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 030819           78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIA  154 (171)
Q Consensus        78 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~  154 (171)
                      ++|||+|||+++++++|+++|..||.|..+++..++. + .+|||||+|.+.++|.+|+. +++..|+|++|.|...
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~-~-~~~~afV~F~~~~~a~~Al~-~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK-K-NFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTT-S-SSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecc-c-cceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            4899999999999999999999999999999998873 3 35799999999999999996 8999999999999764

>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=4e-19  Score=112.26  Aligned_cols=79  Identities=20%  Similarity=0.283  Sum_probs=71.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHh--CCceeCCeEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM--HGKFLDGRVIF  150 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l--~g~~i~g~~i~  150 (171)
                      ..+++++|||+|||+++++++|+++|++||.|.++.+..++      |+|||+|.+.++|++|+..+  ++..+.|++|+
T Consensus         4 ~~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~~------~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~   77 (88)
T d2cq1a1           4 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGK------NQAFLELATEEAAITMVNYYSAVTPHLRNQPIY   77 (88)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETTT------TEEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcccccccccccccc------eEEEEEeCCHHHHHHHHHHHccCCCccCCCEEE
Confidence            45678999999999999999999999999999999987654      79999999999999999865  56789999999


Q ss_pred             EEEecCc
Q 030819          151 VEIAKSR  157 (171)
Q Consensus       151 v~~~~~~  157 (171)
                      |.|++.+
T Consensus        78 v~~sk~~   84 (88)
T d2cq1a1          78 IQYSNHK   84 (88)
T ss_dssp             EEECSCS
T ss_pred             EEECCCC
Confidence            9999765

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=9.2e-21  Score=119.71  Aligned_cols=73  Identities=16%  Similarity=0.253  Sum_probs=67.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEecCcH
Q 030819           79 RLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKSRA  158 (171)
Q Consensus        79 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~~~~  158 (171)
                      +|||+|||+++++++|+++|++||.|.++.+..+       |||||+|.+.++|++||..|||..+.|+.|+|.+++.+.
T Consensus         2 rvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~~   74 (87)
T d3begb1           2 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKV   74 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEE
T ss_pred             eEEEECCCCcCCHHHHHHHHhhhccccccccccc-------ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecCc
Confidence            6999999999999999999999999999988653       799999999999999999999999999999988776443

>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=99.80  E-value=4.6e-20  Score=116.69  Aligned_cols=77  Identities=21%  Similarity=0.396  Sum_probs=69.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 030819           75 QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIA  154 (171)
Q Consensus        75 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~  154 (171)
                      ...++|||+|||+++++++|+++|++||.|.++.+.     ..++|||||+|.+.++|++|+.  ++..++|+.|+|.++
T Consensus         3 ~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~-----~~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a   75 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIP-----KPFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNA   75 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECC-----SSCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEe-----eccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeC
Confidence            457899999999999999999999999999998764     3457999999999999999985  788899999999999


Q ss_pred             cCcH
Q 030819          155 KSRA  158 (171)
Q Consensus       155 ~~~~  158 (171)
                      +++.
T Consensus        76 ~~k~   79 (88)
T d1wf0a_          76 EPKH   79 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8764

>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=99.80  E-value=1.6e-19  Score=114.11  Aligned_cols=76  Identities=17%  Similarity=0.326  Sum_probs=66.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEec
Q 030819           76 PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAK  155 (171)
Q Consensus        76 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~  155 (171)
                      ...+|||+|||+++++++|+++|++|| +..+.+      +.++|||||+|.+.++|++|++.|||..+.|++|+|++++
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~------~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~   76 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV------DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE------EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcC-ceeeee------eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            357899999999999999999999999 333333      3456999999999999999999999999999999999997


Q ss_pred             CcH
Q 030819          156 SRA  158 (171)
Q Consensus       156 ~~~  158 (171)
                      .+.
T Consensus        77 ~~~   79 (88)
T d1wg1a_          77 TDA   79 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            653

>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=99.79  E-value=2.9e-19  Score=115.13  Aligned_cols=77  Identities=16%  Similarity=0.238  Sum_probs=70.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 030819           75 QPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIA  154 (171)
Q Consensus        75 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~  154 (171)
                      ....+|||+|||+++++++|+++|.+||.|..+.+..       +|||||+|.+.++|++||+.|||..+.|+.|+|.+.
T Consensus        13 ~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~   85 (98)
T d1wg4a_          13 RSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYI   85 (98)
T ss_dssp             SCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEE
Confidence            4567899999999999999999999999999998853       389999999999999999999999999999999998


Q ss_pred             cCcH
Q 030819          155 KSRA  158 (171)
Q Consensus       155 ~~~~  158 (171)
                      +.+.
T Consensus        86 ~~~~   89 (98)
T d1wg4a_          86 RVYP   89 (98)
T ss_dssp             EEEC
T ss_pred             ecCC
Confidence            7553

>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=99.79  E-value=1.9e-19  Score=118.04  Aligned_cols=81  Identities=20%  Similarity=0.328  Sum_probs=72.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee--CCeEEEE
Q 030819           74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFL--DGRVIFV  151 (171)
Q Consensus        74 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i--~g~~i~v  151 (171)
                      +.+...|||+|||+.+|+++|+++|++||.|..+.+..++    .+|+|||+|.+.++|+.|+..|||..+  .|..|+|
T Consensus         4 ~s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v   79 (108)
T d2adba1           4 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRI   79 (108)
T ss_dssp             CCCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEE
T ss_pred             CCCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEE
Confidence            3456789999999999999999999999999999998764    479999999999999999999999998  5788999


Q ss_pred             EEecCcH
Q 030819          152 EIAKSRA  158 (171)
Q Consensus       152 ~~~~~~~  158 (171)
                      .+++++.
T Consensus        80 ~~s~~~~   86 (108)
T d2adba1          80 DFSKLTS   86 (108)
T ss_dssp             EECSSCS
T ss_pred             EecCCcc
Confidence            9987653

>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=99.79  E-value=1.2e-19  Score=119.65  Aligned_cols=86  Identities=14%  Similarity=0.297  Sum_probs=76.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ......+|||+|||+++++++|+++|+.||.+..+.++.+..+|.++|+|||+|.+.++|++|+. +||..|+|+.|.|.
T Consensus        14 ~~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~   92 (112)
T d1wela1          14 PHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVH   92 (112)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEE
T ss_pred             CCCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEE
Confidence            34457799999999999999999999999998776566666699999999999999999999997 99999999999999


Q ss_pred             EecCcHH
Q 030819          153 IAKSRAE  159 (171)
Q Consensus       153 ~~~~~~~  159 (171)
                      .+..+..
T Consensus        93 ~~~~~~~   99 (112)
T d1wela1          93 PITKKGM   99 (112)
T ss_dssp             EECHHHH
T ss_pred             EcChHHH
Confidence            9876653

>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=6.9e-19  Score=107.89  Aligned_cols=71  Identities=18%  Similarity=0.345  Sum_probs=64.0

Q ss_pred             EEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEecCc
Q 030819           80 LFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKSR  157 (171)
Q Consensus        80 l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~~~  157 (171)
                      |||+|||+++++++|+++|++|| +..+.+      ++++|||||+|.+.++|++|+..|||..+.|++|+|++++..
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~------~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d   71 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee------cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            79999999999999999999999 555444      345699999999999999999999999999999999999754

>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=99.77  E-value=6.1e-19  Score=113.79  Aligned_cols=81  Identities=16%  Similarity=0.271  Sum_probs=71.4

Q ss_pred             CCCCCCCeEEEcCCCCC-CCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHH--HhCCceeCCeE
Q 030819           72 STCQPKTRLFVSGLSFR-TSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIE--GMHGKFLDGRV  148 (171)
Q Consensus        72 ~~~~~~~~l~V~nl~~~-~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~--~l~g~~i~g~~  148 (171)
                      ....++++|||+|||.+ +++++|.++|+.||.|.++.+..++      |+|||+|.+.++|.+|++  .+++..+.|+.
T Consensus        13 ~~~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~k------~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~   86 (99)
T d1x4fa1          13 QKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMK------SQAFIEMETREDAMAMVDHCLKKALWFQGRC   86 (99)
T ss_dssp             CSSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETTT------TEEEEECSSHHHHHHHHHHHHHSCCCSSSSC
T ss_pred             cCCCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeecC------CcEEEEecchHHHHHHHHHHhcCCceECCEE
Confidence            34556789999999985 8999999999999999999997654      899999999999999998  46788899999


Q ss_pred             EEEEEecCcH
Q 030819          149 IFVEIAKSRA  158 (171)
Q Consensus       149 i~v~~~~~~~  158 (171)
                      |+|.+++.+.
T Consensus        87 l~V~~s~~~~   96 (99)
T d1x4fa1          87 VKVDLSEKYK   96 (99)
T ss_dssp             CEEEEECSCS
T ss_pred             EEEEEcCCcc
Confidence            9999997653

>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=99.77  E-value=3.5e-18  Score=111.14  Aligned_cols=80  Identities=18%  Similarity=0.282  Sum_probs=71.2

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC--CceeCCeEEE
Q 030819           73 TCQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMH--GKFLDGRVIF  150 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~--g~~i~g~~i~  150 (171)
                      ..+++.+|||+|||+++++++|..+|.+||.|..+.+.+++      |+|||+|.+.++|++|+..|+  +..+.|++|+
T Consensus        11 ~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~k------~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~   84 (104)
T d1wexa_          11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFK------RQALVEFENIDSAKECVTFAADVPVYIAGQQAF   84 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETTT------TEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEecc------eeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEE
Confidence            45678899999999999999999999999999999987654      899999999999999999874  5567899999


Q ss_pred             EEEecCcH
Q 030819          151 VEIAKSRA  158 (171)
Q Consensus       151 v~~~~~~~  158 (171)
                      |.|++.+.
T Consensus        85 v~~s~~~~   92 (104)
T d1wexa_          85 FNYSTSKR   92 (104)
T ss_dssp             EEECSSSS
T ss_pred             EEEcCCCc
Confidence            99997654

>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=99.74  E-value=4.2e-18  Score=107.69  Aligned_cols=80  Identities=14%  Similarity=0.208  Sum_probs=71.1

Q ss_pred             CCCCCCeEEEcCCCCC-CCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHh--CCceeCCeEE
Q 030819           73 TCQPKTRLFVSGLSFR-TSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGM--HGKFLDGRVI  149 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~-~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l--~g~~i~g~~i  149 (171)
                      ...++++|||+|||.. +|+++|.++|+.||.|..+.+..++      ++|||+|.+.++|..|+..|  ++..+.|++|
T Consensus         4 ~~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~k------~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l   77 (89)
T d1x4da1           4 RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI------NEAFIEMATTEDAQAAVDYYTTTPALVFGKPV   77 (89)
T ss_dssp             CCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS------SCEEEEESSHHHHHHHHHHHHHSCCEETTEEC
T ss_pred             CCCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeeccc------eEEEEEEcchhhHHHHHHHHhhCCCccCCceE
Confidence            3466789999999986 7899999999999999999998765      69999999999999999966  6778999999


Q ss_pred             EEEEecCcH
Q 030819          150 FVEIAKSRA  158 (171)
Q Consensus       150 ~v~~~~~~~  158 (171)
                      +|.|+++..
T Consensus        78 ~V~~s~~~~   86 (89)
T d1x4da1          78 RVHLSQKYK   86 (89)
T ss_dssp             EEEEECCCT
T ss_pred             EEEECCCcc
Confidence            999997543

>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=9.2e-18  Score=109.04  Aligned_cols=79  Identities=10%  Similarity=0.063  Sum_probs=69.7

Q ss_pred             CCCCeEEEcCCCCCC-CH----HHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEE
Q 030819           75 QPKTRLFVSGLSFRT-SE----DSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVI  149 (171)
Q Consensus        75 ~~~~~l~V~nl~~~~-~~----~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i  149 (171)
                      ....+|||+||+.++ ++    ++|+.+|..||.|.++.+.+.      +|||||+|.+.++|.+|+..|||..+.|+.|
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l   76 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS------FKRVRINFSNPLSAADARLRLHKTEFLGKEM   76 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT------TTEEEEECSSTTHHHHHHHTSTTSEETTEEC
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecC------CCEEEEEECCHHHHHHHHHHhcccccCCCEe
Confidence            456799999999986 43    569999999999999988754      4899999999999999999999999999999


Q ss_pred             EEEEecCcHH
Q 030819          150 FVEIAKSRAE  159 (171)
Q Consensus       150 ~v~~~~~~~~  159 (171)
                      +|.|++++..
T Consensus        77 ~v~~a~~~~~   86 (104)
T d1weya_          77 KLYFAQTLHI   86 (104)
T ss_dssp             EEECCCCSSC
T ss_pred             EEeecccCCC
Confidence            9999986643

>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=99.69  E-value=1.3e-19  Score=115.03  Aligned_cols=77  Identities=21%  Similarity=0.453  Sum_probs=67.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEe-----ecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEE
Q 030819           78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLV-----MDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVE  152 (171)
Q Consensus        78 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~-----~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~  152 (171)
                      ++|||+|||+++++++|+++|+.||.+..+.+.     .+..+++++|||||+|.+.++|++|++ |||..+.|+.|+|.
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~Gr~l~V~   80 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIR   80 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSSSSCCCCB
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEECCEEEEEC
Confidence            689999999999999999999999987665443     345578899999999999999999986 99999999999997


Q ss_pred             Eec
Q 030819          153 IAK  155 (171)
Q Consensus       153 ~~~  155 (171)
                      .++
T Consensus        81 r~k   83 (90)
T d1u2fa_          81 RPH   83 (90)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            543

>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=99.68  E-value=3e-18  Score=111.36  Aligned_cols=76  Identities=14%  Similarity=0.346  Sum_probs=71.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 030819           78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIA  154 (171)
Q Consensus        78 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~  154 (171)
                      ..++|.+++.++++++|+++|++||+|.++.|..+. +|+++|+|||+|.+.++|.+|+..|||..++|++|+|+++
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~-~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCC-CCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            357888888899999999999999999999998775 8999999999999999999999999999999999999985

>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=99.65  E-value=2.9e-16  Score=103.31  Aligned_cols=76  Identities=14%  Similarity=0.115  Sum_probs=65.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCH-HHHHHHHHHhCCceeCCeEEEEEEec
Q 030819           77 KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATE-EESRRAIEGMHGKFLDGRVIFVEIAK  155 (171)
Q Consensus        77 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~-~~a~~al~~l~g~~i~g~~i~v~~~~  155 (171)
                      ...+||+|||+.+|+++|+++|.+||+|.+|.++.++      |||||.|.+. ++|..|+..+++..+.++.+.|.++.
T Consensus        11 ~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~k------g~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~   84 (113)
T d1owxa_          11 CLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGA------KEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEV   84 (113)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTC------SEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEE
T ss_pred             CeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecCC------ceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEee
Confidence            3456999999999999999999999999999998654      8999999985 78999999999999988777777766


Q ss_pred             CcH
Q 030819          156 SRA  158 (171)
Q Consensus       156 ~~~  158 (171)
                      .+.
T Consensus        85 ~~~   87 (113)
T d1owxa_          85 LEG   87 (113)
T ss_dssp             CCH
T ss_pred             ccc
Confidence            543

>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=99.63  E-value=4.3e-16  Score=100.47  Aligned_cols=65  Identities=29%  Similarity=0.414  Sum_probs=58.7

Q ss_pred             CCCCCeEEEc--CCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCcee
Q 030819           74 CQPKTRLFVS--GLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFL  144 (171)
Q Consensus        74 ~~~~~~l~V~--nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i  144 (171)
                      ..+..++||.  |||.++|+++|+++|++||.|..+.+..++      |||||+|.+.++|.+|+..|||..+
T Consensus        15 ~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~k------~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK------PYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTTC------SCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccCc------cEEEEEECCHHHHHHHHHHhCCCCC
Confidence            4556788885  599999999999999999999999887654      7999999999999999999999987

>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=99.63  E-value=8e-16  Score=108.92  Aligned_cols=81  Identities=40%  Similarity=0.648  Sum_probs=74.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 030819           77 KTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKS  156 (171)
Q Consensus        77 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~~  156 (171)
                      .++|||+|||+++++++|+++|++||.|..+.++.+..++.++|||||+|.+.++|.+|+. +++..++++.+.+....+
T Consensus         6 ~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~-~~~~~~~~~~~~~~~~~~   84 (183)
T d1u1qa_           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAVS   84 (183)
T ss_dssp             HHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHH-hcCCcccccchhhhhhhh
Confidence            4799999999999999999999999999999999999999999999999999999999998 577888888888887665


Q ss_pred             cH
Q 030819          157 RA  158 (171)
Q Consensus       157 ~~  158 (171)
                      ..
T Consensus        85 ~~   86 (183)
T d1u1qa_          85 RE   86 (183)
T ss_dssp             TT
T ss_pred             cc
Confidence            44

>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=99.56  E-value=6.6e-15  Score=90.98  Aligned_cols=75  Identities=17%  Similarity=0.321  Sum_probs=63.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCe-EEEEEEe
Q 030819           76 PKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGR-VIFVEIA  154 (171)
Q Consensus        76 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~-~i~v~~~  154 (171)
                      +.+.|+|+|+|++++++.| +.|++||.|.++.+..+      +|||||+|.+.++|++||. +||..++|+ .|.|...
T Consensus         3 ~~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~~------~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~   74 (81)
T d1wwha1           3 DDTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSNT------GNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPC   74 (81)
T ss_dssp             GGGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECSS------SSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEEC
T ss_pred             cccEEEEECCChHHHHHHH-HHHHhhhhhheEEecCC------CCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeC
Confidence            3567999999999887655 57999999999987443      4899999999999999996 999999997 4678877


Q ss_pred             cCcH
Q 030819          155 KSRA  158 (171)
Q Consensus       155 ~~~~  158 (171)
                      ..+.
T Consensus        75 ~~k~   78 (81)
T d1wwha1          75 IDKN   78 (81)
T ss_dssp             CCHH
T ss_pred             CChh
Confidence            6654

>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=99.53  E-value=2.9e-14  Score=91.39  Aligned_cols=82  Identities=20%  Similarity=0.380  Sum_probs=69.0

Q ss_pred             CCCCCCeEEEcCC--CCCCC---------HHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCC
Q 030819           73 TCQPKTRLFVSGL--SFRTS---------EDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHG  141 (171)
Q Consensus        73 ~~~~~~~l~V~nl--~~~~~---------~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g  141 (171)
                      ....+++|+|.|+  |.++.         +++|++.|++||.|..+.+..+    ..+|++||.|.+.++|.+|+..|||
T Consensus         4 ~~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~lng   79 (99)
T d2dita1           4 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLDG   79 (99)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHHSTT
T ss_pred             CCCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC----CCccEEEEEECCHHHHHHHHHHhCC
Confidence            3456789999998  54321         3689999999999999987654    4569999999999999999999999


Q ss_pred             ceeCCeEEEEEEecCcH
Q 030819          142 KFLDGRVIFVEIAKSRA  158 (171)
Q Consensus       142 ~~i~g~~i~v~~~~~~~  158 (171)
                      ..++|+.|+|.+..++.
T Consensus        80 ~~~~gr~i~v~~~~g~~   96 (99)
T d2dita1          80 RWFGGRQITAQAWDGTT   96 (99)
T ss_dssp             CEETTEECEEEECCSCC
T ss_pred             cEECCEEEEEEEeCCcC
Confidence            99999999999987654

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.45  E-value=7e-14  Score=90.36  Aligned_cols=84  Identities=13%  Similarity=0.297  Sum_probs=70.5

Q ss_pred             CCCCeEEEcCC--CCCCC--------HHHHHHHHhcCCCeEEEEEeecCCC--CCcceEEEEEeCCHHHHHHHHHHhCCc
Q 030819           75 QPKTRLFVSGL--SFRTS--------EDSLRNAFQGFGQLVEVNLVMDKIA--NRPRGFAFLRYATEEESRRAIEGMHGK  142 (171)
Q Consensus        75 ~~~~~l~V~nl--~~~~~--------~~~l~~~f~~~G~i~~~~~~~~~~~--g~~~g~~fv~f~~~~~a~~al~~l~g~  142 (171)
                      +|++.|.|.|+  +.++.        .++|++.|++||.|.++.+.++..+  ....|++||+|.+.++|.+|+..|||.
T Consensus         2 ~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr   81 (104)
T d1o0pa_           2 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   81 (104)
T ss_dssp             CCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSC
T ss_pred             CCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCC
Confidence            46788999999  44433        3578999999999999999876644  334689999999999999999999999


Q ss_pred             eeCCeEEEEEEecCcH
Q 030819          143 FLDGRVIFVEIAKSRA  158 (171)
Q Consensus       143 ~i~g~~i~v~~~~~~~  158 (171)
                      .++|+.|.|.+.....
T Consensus        82 ~f~gR~v~v~f~~~~~   97 (104)
T d1o0pa_          82 KFANRVVVTKYCDPDS   97 (104)
T ss_dssp             CSSSSCCEEEEECHHH
T ss_pred             EECCeEEEEEEcCHHH
Confidence            9999999999987543

>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=98.01  E-value=9e-06  Score=49.29  Aligned_cols=73  Identities=15%  Similarity=0.232  Sum_probs=58.3

Q ss_pred             CCCCCCeEEEcCCCCCCCH---------HHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCce
Q 030819           73 TCQPKTRLFVSGLSFRTSE---------DSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKF  143 (171)
Q Consensus        73 ~~~~~~~l~V~nl~~~~~~---------~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~  143 (171)
                      ..++..+|.|.=..+...+         .+|.+.|..||+|.=++++.+        --+|+|.+-++|.+|+. ++|.+
T Consensus        11 qGPpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al~-l~g~~   81 (95)
T d1ufwa_          11 QGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVLD-VDGMK   81 (95)
T ss_dssp             CCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHHH-GGGSE
T ss_pred             cCCCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHhc-cCCeE
Confidence            4566678888554433222         477888999999999998765        57999999999999999 89999


Q ss_pred             eCCeEEEEEEe
Q 030819          144 LDGRVIFVEIA  154 (171)
Q Consensus       144 i~g~~i~v~~~  154 (171)
                      +.|+.|+|...
T Consensus        82 v~G~~l~It~~   92 (95)
T d1ufwa_          82 VKGRAVKISGP   92 (95)
T ss_dssp             ETTEEEEEECC
T ss_pred             EcceEEEEecC
Confidence            99999998754

>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=97.75  E-value=0.00015  Score=41.66  Aligned_cols=62  Identities=19%  Similarity=0.289  Sum_probs=52.0

Q ss_pred             HHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEEEecC
Q 030819           92 DSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMHGKFLDGRVIFVEIAKS  156 (171)
Q Consensus        92 ~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~g~~i~g~~i~v~~~~~  156 (171)
                      +.|...|.++|.|..+.+.... .|.  -.|-|...+.++|.-|+..||..+|++++|.|.++..
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~-dg~--~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~~   72 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHT-DYQ--LKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATG   72 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCC-STT--CCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             HHHHHHHHhheeEEEEEEEecc-CCc--EEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEecC
Confidence            3456778899999999886544 233  4799999999999999999999999999999998753

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.59  E-value=0.00037  Score=42.38  Aligned_cols=78  Identities=12%  Similarity=0.149  Sum_probs=62.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCC--cceEEEEEeCCHHHHHHHHHHhCCceeCC-----eEEE
Q 030819           78 TRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANR--PRGFAFLRYATEEESRRAIEGMHGKFLDG-----RVIF  150 (171)
Q Consensus        78 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~--~~g~~fv~f~~~~~a~~al~~l~g~~i~g-----~~i~  150 (171)
                      ++|.|++||+.+|++++.+.+...|.+........+.+.+  .-.-|+|.|.+.+++....+..+|..+.+     .+-.
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D~~g~~~~a~   81 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPAI   81 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEECE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEcCCCCEeeeE
Confidence            5789999999999999999999999988877766554433  23578999999999999999999998722     1445


Q ss_pred             EEEec
Q 030819          151 VEIAK  155 (171)
Q Consensus       151 v~~~~  155 (171)
                      |++|.
T Consensus        82 VE~AP   86 (91)
T d1uw4a_          82 VEFAP   86 (91)
T ss_dssp             EEECS
T ss_pred             EEEcC
Confidence            66654

>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=97.35  E-value=2.1e-05  Score=46.71  Aligned_cols=54  Identities=11%  Similarity=0.006  Sum_probs=43.7

Q ss_pred             eeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPS   67 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   67 (171)
                      |+|||+|+++++++..+.+.|...+++         .+.....+..++++++++++.+..+..
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i---------~~v~i~~d~~tg~~kG~aFV~f~~~~~   54 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEV---------KECLVMRDPLTKRSRGFGFVTFMDQAG   54 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCC---------CCEEEECCCCSSSCSSEEEECCCCTTH
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCc---------ceeeeecccCCCCccceEEEEECCHHH
Confidence            899999999999999999999998887         444445555667788888887776554

>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=96.47  E-value=9.6e-05  Score=43.49  Aligned_cols=54  Identities=9%  Similarity=0.047  Sum_probs=43.6

Q ss_pred             eeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCCCC
Q 030819            6 FLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPSP   68 (171)
Q Consensus         6 ~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   68 (171)
                      +|||+|++++++++.+...|...+++         .+.....+..+++++|++++.+..+..+
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I---------~~v~i~~d~~t~~~rG~~FV~f~~~~~a   54 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEV---------ESIELPMDNKTNKRRGFCFITFKEEEPV   54 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCE---------EEEECCCCTTTCCTTCCEEEEESSSHHH
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCc---------ccccccccccccccccEEEEEECCHHHH
Confidence            58999999999999999999998877         5555555666678888998888766543

>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=96.19  E-value=0.00025  Score=42.54  Aligned_cols=54  Identities=17%  Similarity=0.087  Sum_probs=43.1

Q ss_pred             eeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPS   67 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   67 (171)
                      ++|||+|++++++++.+...|...+++         .+.....+..++++++++++.+..+..
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v---------~~v~i~~d~~tg~~rg~aFV~f~~~~~   55 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPL---------KAFNLVKDSATGLSKGYAFCEYVDINV   55 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCE---------EEEEEECCCSSSCCCCEEEEEESSSHH
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCcc---------ceEEeeccccccccceeEEEEECCHHH
Confidence            579999999999999999999998887         555555555667778888877765554

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.09  E-value=0.027  Score=34.18  Aligned_cols=59  Identities=15%  Similarity=0.265  Sum_probs=47.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC
Q 030819           74 CQPKTRLFVSGLSFRTSEDSLRNAFQGFGQLVEVNLVMDKIANRPRGFAFLRYATEEESRRAIEGMH  140 (171)
Q Consensus        74 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~~fv~f~~~~~a~~al~~l~  140 (171)
                      .+...-||.-.+|..+...+|.++|..||.|. +.++.+-       -|||...+.+.+..++..+.
T Consensus        12 ~p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~-VswIddT-------Sa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          12 QPKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQ-ISWIDDT-------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCCCSEEEEECCTTCCHHHHHHHHTTTCSCC-CEEEETT-------EEEEECSCHHHHHHHHHHHH
T ss_pred             CCCcceeEEEeCCcccchhHHHHHhcCCCceE-EEEecCc-------eEEEEecCHHHHHHHHHHhc
Confidence            44456788999999999999999999999864 3444442       69999999999999887554

>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=95.89  E-value=0.00019  Score=42.03  Aligned_cols=52  Identities=15%  Similarity=0.126  Sum_probs=39.0

Q ss_pred             eeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCC
Q 030819            6 FLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPP   66 (171)
Q Consensus         6 ~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   66 (171)
                      +|||+|+++++++..+...|...+++         .+.....+..++++++++++.+..+.
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i---------~~~~i~~d~~t~~~kg~afV~f~~~~   52 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEV---------VDCTLKLDPITGRSRGFGFVLFKESE   52 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCE---------EEEECCCBTTTTBCCSEEEEEESSHH
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccc---------cccccccCCCCCCcCceEEEEECCHH
Confidence            58999999999999999999998877         44444444455667777776665543

>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=95.50  E-value=0.0015  Score=39.27  Aligned_cols=49  Identities=14%  Similarity=0.113  Sum_probs=34.0

Q ss_pred             eeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCC
Q 030819            6 FLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLAC   63 (171)
Q Consensus         6 ~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   63 (171)
                      .|||+|++++.+++.+.+.|...+++         .+.....+..+++.+|++++.+.
T Consensus         7 tlfV~nLp~~~te~~l~~~F~~~G~i---------~~v~i~~d~~~~~~kg~afV~f~   55 (89)
T d2cqba1           7 VLYVGGLAEEVDDKVLHAAFIPFGDI---------TDIQIPLDYETEKHRGFAFVEFE   55 (89)
T ss_dssp             CEEEESCCSSCCHHHHHHHHTTTSCC---------CCEECCCCSSSCCCSSEEEECCS
T ss_pred             EEEEeCCCCcCCHHHHHHHHhhCCeE---------EecccccccccccccceeEEEEC
Confidence            49999999999999999999998877         33333333334455555544433

>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=95.47  E-value=0.00069  Score=39.96  Aligned_cols=27  Identities=11%  Similarity=-0.156  Sum_probs=25.5

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      |.|||+|++++++++.+.+.|...+++
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v   28 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVV   28 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcE
Confidence            789999999999999999999998877

>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=95.35  E-value=0.00026  Score=43.05  Aligned_cols=53  Identities=13%  Similarity=0.014  Sum_probs=40.2

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCC
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLP   65 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   65 (171)
                      ...|||+|++++.++..+...|...+++         .+...+.+..+++++|++++.+..+
T Consensus         8 ~~~lfV~nLp~~~te~~l~~~F~~~G~i---------~~v~i~~d~~tg~srG~aFV~f~~~   60 (90)
T d2cqga1           8 TSDLIVLGLPWKTTEQDLKEYFSTFGEV---------LMVQVKKDLKTGHSKGFGFVRFTEY   60 (90)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHHGGGSCE---------EEEEEEECSSSCSEEEEEEEEESSH
T ss_pred             CCeEEEECCCCCCCHHHHHHHHHhhccc---------ceeeeccCCCCcccCCEEEEEECCH
Confidence            3579999999999999999999998877         4555555555667777777555443

>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=95.19  E-value=0.0016  Score=40.41  Aligned_cols=53  Identities=15%  Similarity=0.051  Sum_probs=38.7

Q ss_pred             eeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPP   66 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   66 (171)
                      ..|||+|+++++++..+...|...+.+         .+.....+..+...++++|+.+....
T Consensus        21 ~~lfVgnLp~~~te~~L~~~F~~~G~i---------~~~~i~~d~~~~~~kg~aFV~f~~~~   73 (103)
T d1x4ba1          21 RKLFIGGLSFETTEESLRNYYEQWGKL---------TDCVVMRDPASKRSRGFGFVTFSSMA   73 (103)
T ss_dssp             TEEEEECCTTCCCHHHHHHHHTSSCCC---------SEEEEECCTTTSSCCSEEEEECSSHH
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHhhCcc---------cceeecccccCCCccCeEEEEECCHH
Confidence            469999999999999999999998887         44444444444566666666555443

>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=95.15  E-value=0.00091  Score=41.08  Aligned_cols=28  Identities=18%  Similarity=0.133  Sum_probs=25.4

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCC
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      .+.|||+|++++++++.+...|...+++
T Consensus         8 ~~~lfV~nL~~~~t~~~l~~~F~~~g~v   35 (99)
T d1whwa_           8 SGRLFVRNLSYTSSEEDLEKLFSAYGPL   35 (99)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHHTTSCE
T ss_pred             CCEEEEECCCCcCCHHHHHHHHHhcCCc
Confidence            5789999999999999999999887766

>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=95.11  E-value=0.00049  Score=41.95  Aligned_cols=29  Identities=10%  Similarity=0.036  Sum_probs=26.5

Q ss_pred             eeeeeecCceeecccchhhcccCCcCCCC
Q 030819            3 VLGFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         3 ~~~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      -.|.|||+|+++++++..+...|...+++
T Consensus         6 ~s~tlfV~nlp~~~te~~l~~~F~~~G~i   34 (93)
T d1h2vz_           6 KSCTLYVGNLSFYTTEEQIYELFSKSGDI   34 (93)
T ss_dssp             TCCEEEEESCCTTCCHHHHHHHHGGGSCE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCc
Confidence            36889999999999999999999998877

>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=94.88  E-value=0.0019  Score=37.20  Aligned_cols=26  Identities=12%  Similarity=0.001  Sum_probs=24.1

Q ss_pred             eeecCceeecccchhhcccCCcCCCC
Q 030819            6 FLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         6 ~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      +|||+|++++.+++.+.+.|...++.
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i   26 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKV   26 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCc
Confidence            58999999999999999999998776

>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=94.85  E-value=0.0016  Score=40.21  Aligned_cols=54  Identities=15%  Similarity=0.078  Sum_probs=43.0

Q ss_pred             eeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPS   67 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   67 (171)
                      ..|||+++.++.+++.+...|...+.+         .+........+++++|++++.+..+..
T Consensus        19 ~tifV~nL~~~~te~~l~~~F~~~G~V---------~~v~i~~d~~tg~~kG~afV~F~~~e~   72 (101)
T d2cq4a1          19 RTVFCMQLAARIRPRDLEDFFSAVGKV---------RDVRIISDRNSRRSKGIAYVEFCEIQS   72 (101)
T ss_dssp             TEEEEESCCTTCCHHHHHHHHTTTSCE---------EEEEECCSCCSSSCCCCEEEEESCGGG
T ss_pred             CEEEEECCCCCCCHHHHHHHHcCCCeE---------EEEEeeecCCCccccceEEEEECCHHH
Confidence            359999999999999999999998877         455555666667888888877766544

>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=94.82  E-value=0.00048  Score=41.17  Aligned_cols=50  Identities=16%  Similarity=0.108  Sum_probs=37.3

Q ss_pred             eeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCC
Q 030819            6 FLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACL   64 (171)
Q Consensus         6 ~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   64 (171)
                      .|||+|+++++++..+...|...+++         .+........+++++|++++.+..
T Consensus         8 ~lfV~nlp~~~te~~l~~~F~~~G~i---------~~v~i~~d~~tg~~kG~afV~f~~   57 (84)
T d1l3ka1           8 KLFIGGLSFETTDESLRSHFEQWGTL---------TDCVVMRDPNTKRSRGFGFVTYAT   57 (84)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCE---------EEEEEEECTTTCCEEEEEEEEESS
T ss_pred             EEEEECCCCCCCHHHHHHHHHhhccc---------cceeecccccCCCcccEEEEEEcC
Confidence            69999999999999999999998877         444444454456666666655543

>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=94.58  E-value=0.0012  Score=39.74  Aligned_cols=27  Identities=22%  Similarity=0.217  Sum_probs=24.9

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      ++|||+|++++.++..+...|...+++
T Consensus         6 ~kifV~nLp~~~t~~~l~~~F~~~G~i   32 (90)
T d1x5sa1           6 GKLFVGGLSFDTNEQSLEQVFSKYGQI   32 (90)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHHHSCC
T ss_pred             CEEEEECCCCcCCHHHHHHhhhccccc
Confidence            579999999999999999999988776

>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=94.48  E-value=0.0016  Score=40.23  Aligned_cols=53  Identities=11%  Similarity=0.061  Sum_probs=39.5

Q ss_pred             eeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPP   66 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   66 (171)
                      ..|||+|+++++++..+.+.|...+++         .+.....+..++++++++++.+....
T Consensus        11 ~~lfV~nLp~~~te~~l~~~F~~~G~i---------~~v~i~~d~~tg~~kg~afV~f~~~~   63 (103)
T d2cqda1          11 TKIFVGGLPYHTTDASLRKYFEGFGDI---------EEAVVITDRQTGKSRGYGFVTMADRA   63 (103)
T ss_dssp             SEEEEECCCSSCCHHHHHHHHHTTSCE---------EEEEESCCSSSCCCCSEEEEEESSHH
T ss_pred             cEEEEeCCCCcCcHHHHHHHHhhcccc---------cceeccccccccccCCeEEEEECCHH
Confidence            469999999999999999999998876         44444455555667777776655444

>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=94.20  E-value=0.0039  Score=35.62  Aligned_cols=49  Identities=8%  Similarity=-0.046  Sum_probs=34.8

Q ss_pred             eecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCC
Q 030819            7 LPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACL   64 (171)
Q Consensus         7 ~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   64 (171)
                      |||+|+++++++..+.+.|...+++         ...........+..++.+++.+..
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v---------~~~~~~~~~~~~~~~g~afV~f~~   49 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKI---------VSTKAILDKTTNKCKGYGFVDFDS   49 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCE---------EEEEEECCSSSCSCCSEEEEEESC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccc---------cccccccccccccccceeEEEECC
Confidence            7999999999999999999998877         333333344445555665555443

>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=94.20  E-value=0.0013  Score=40.60  Aligned_cols=50  Identities=6%  Similarity=-0.082  Sum_probs=36.2

Q ss_pred             eeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLAC   63 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   63 (171)
                      +.|||+|++++++++.+...|...+++         .+.........++.++++++.+.
T Consensus        19 ~~l~V~nLp~~~te~~l~~~F~~~G~i---------~~~~~~~~~~~g~~kG~afV~f~   68 (102)
T d2cpza1          19 ANLFIYHLPQEFGDQDLLQMFMPFGNV---------VSAKVFIDKQTNLSKCFGFVSYD   68 (102)
T ss_dssp             CCEEEESCCSSCCHHHHHHHHGGGSCC---------SEEEEEECSSSCSEEEEEEEECS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhhccc---------cccceeeecccCCCccceEEEeC
Confidence            469999999999999999999998877         44444455444555555554443

>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=94.17  E-value=0.0013  Score=38.48  Aligned_cols=27  Identities=15%  Similarity=0.171  Sum_probs=25.1

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      |+|||+|++++.+++.+.+.|...+++
T Consensus         1 grl~V~nLp~~~~~~~l~~~F~~~G~v   27 (78)
T d1no8a_           1 GKLLVSNLDFGVSDADIQELFAEFGTL   27 (78)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHHHHSCE
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCC
Confidence            689999999999999999999998777

>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=94.10  E-value=0.0021  Score=38.95  Aligned_cols=52  Identities=13%  Similarity=0.020  Sum_probs=37.6

Q ss_pred             eeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLP   65 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   65 (171)
                      +.|||+|+++++++..+...|...+++         .+.....+..+++.++++++.+...
T Consensus        10 ~tlfV~nLp~~~t~~~l~~~F~~~G~v---------~~v~~~~d~~tg~~kg~afV~f~~~   61 (93)
T d1x5ua1          10 ATVYVGGLDEKVSEPLLWELFLQAGPV---------VNTHMPKDRVTGQHQGYGFVEFLSE   61 (93)
T ss_dssp             TEEEEECCCTTCCHHHHHHHHHTTSCE---------EEEECCBCSSSCSBCSCEEEEESSH
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCc---------cccceeecccccccccceEEEECCH
Confidence            469999999999999999999998876         3433344444556666666555443

>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=94.01  E-value=0.0029  Score=37.89  Aligned_cols=61  Identities=8%  Similarity=0.040  Sum_probs=42.8

Q ss_pred             eeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCCCCCC
Q 030819            6 FLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPPSPHS   70 (171)
Q Consensus         6 ~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   70 (171)
                      .|||+|++++.+++.+.+.|...+........    ...........+.++++++.+..+..+..
T Consensus         3 rlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~----~~~~~~~~~~~~~kg~afV~f~~~e~a~~   63 (90)
T d1u2fa_           3 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQA----PGNPVLAVQINQDKNFAFLEFRSVDETTQ   63 (90)
T ss_dssp             EEEECSCCTTCCTTHHHHHHHHHHTTTTSCCS----SSCSEEECCEETTTTEEEEEESSCTTTTT
T ss_pred             EEEEcCCCCccchHHHHHHHHhhCcEEEEEEe----ccceeeecccCCCceEEEEEeCCHHHHHH
Confidence            58999999999999999999887766332211    11122334456778889988887776654

>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=93.98  E-value=0.00098  Score=39.04  Aligned_cols=27  Identities=7%  Similarity=-0.084  Sum_probs=24.8

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      -+|||+|++++++++.+...|...+++
T Consensus         3 r~lfV~nLp~~~te~~l~~~F~~~G~i   29 (79)
T d1l3ka2           3 KKIFVGGIKEDTEEHHLRDYFEQYGKI   29 (79)
T ss_dssp             SEEEEECCTTTCCHHHHHHHHTTTSCE
T ss_pred             CEEEECCCCCcCCHHHHHHHHHHhccc
Confidence            369999999999999999999998877

>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=93.90  E-value=0.00099  Score=39.23  Aligned_cols=51  Identities=14%  Similarity=0.124  Sum_probs=36.4

Q ss_pred             eeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCC
Q 030819            6 FLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLP   65 (171)
Q Consensus         6 ~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   65 (171)
                      -|||+|++++++++.+.+.|...+++         .+.....+..++++++++++.+..+
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i---------~~v~i~~d~~tg~~~g~aFV~f~~~   52 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPI---------LSIRVCRDMITRRSLGYAYVNFQQP   52 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCE---------EEEEEEECTTTCCEEEEEEEEESSH
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCE---------eEEEEEecccccCCCCceEEEECCH
Confidence            58999999999999999999998876         4444444444455566666555443

>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=93.81  E-value=0.0022  Score=38.97  Aligned_cols=52  Identities=10%  Similarity=0.109  Sum_probs=36.0

Q ss_pred             eeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLP   65 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   65 (171)
                      +.|||+|++++.+++.+...|...+++         .+.........+.+++++++.+...
T Consensus         9 ~tlfV~nLp~~~te~~l~~~f~~~G~v---------~~~~~~~~~~~~~~~g~afV~F~~~   60 (98)
T d1x4ha1           9 KTVFIRNLSFDSEEEALGEVLQQFGDL---------KYVRVVLHPDTEHSKGCAFAQFMTQ   60 (98)
T ss_dssp             CCEEEESCCTTCCHHHHHHHHHTTSCE---------EEEECCBCSSSCCBCSEEEEEESSH
T ss_pred             CEEEEcCCCCcCCHHHHHHHHhccccc---------eeeeeccccccccccceEEEEEcCH
Confidence            569999999999999999999998765         3333333434445556666555433

>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=93.72  E-value=0.0015  Score=38.89  Aligned_cols=51  Identities=18%  Similarity=0.010  Sum_probs=36.2

Q ss_pred             eeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACL   64 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   64 (171)
                      +.|||+|++.+.++..+.+.|...+++         .+.....+...++.++++++.+..
T Consensus         7 ~~lfV~nLp~~~te~~L~~~F~~~G~v---------~~v~i~~d~~~g~~kg~afV~f~~   57 (85)
T d1fxla2           7 ANLYVSGLPKTMTQKELEQLFSQYGRI---------ITSRILVDQVTGVSRGVGFIRFDK   57 (85)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHGGGSCE---------EEEEEEECTTTCCEEEEEEEEESS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCc---------cccccccccccccCCCeeEEEEcC
Confidence            469999999999999999999998877         444444443344555555554443

>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=93.47  E-value=0.0024  Score=38.87  Aligned_cols=55  Identities=11%  Similarity=-0.020  Sum_probs=37.7

Q ss_pred             eeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccc-cccCCCCCCCCCCCCCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFS-LRQGRGRGACFPLACLPPS   67 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~   67 (171)
                      |+|||++++.++++..+.+.|...++.-        .+.....+ ...+++++++++.+..+..
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~g~~i--------~~v~~~~~~~~~~~~rg~aFV~F~~~~~   57 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKVTEGV--------LDVIVYASAADKMKNRGFAFVEYESHRA   57 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHSTTE--------EEEECCSSSCTTTTTCCEEEEEESSHHH
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHhCCcc--------eEEEEeeeccccccCCCeEEEEEcCHHH
Confidence            7999999999999999999999977520        11111111 1245677777777766543

>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=93.23  E-value=0.0044  Score=37.11  Aligned_cols=28  Identities=7%  Similarity=-0.063  Sum_probs=25.5

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCC
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      .+.|||+|++.++++..+.+.|...+++
T Consensus         8 ~~~i~V~nLp~~~t~~~l~~~f~~~G~v   35 (90)
T d2cq0a1           8 NATIRVTNLSEDTRETDLQELFRPFGSI   35 (90)
T ss_dssp             SEEEEEESCCTTCCHHHHHTTSTTTCCE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhccc
Confidence            3679999999999999999999998876

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=93.10  E-value=0.0017  Score=38.24  Aligned_cols=27  Identities=15%  Similarity=0.004  Sum_probs=24.6

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      +.|||+|++.+++++.+.+.|...+++
T Consensus         3 t~l~V~nLp~~~t~~~l~~~F~~~G~v   29 (82)
T d1b7fa1           3 TNLIVNYLPQDMTDRELYALFRAIGPI   29 (82)
T ss_dssp             SEEEEECCCTTCCHHHHHHHHHTTSCE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCc
Confidence            359999999999999999999998876

>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=92.54  E-value=0.0032  Score=36.95  Aligned_cols=28  Identities=7%  Similarity=-0.043  Sum_probs=25.2

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCC
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      |..|||+|++++++++.+.+.|...+.+
T Consensus         1 mn~l~V~nLp~~~te~~L~~~F~~~G~i   28 (80)
T d2cqha1           1 MNKLYIGNLSPAVTADDLRQLFGDRKLP   28 (80)
T ss_dssp             CCCEEEECCCTTCCHHHHHHHHHHTTCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCcE
Confidence            4679999999999999999999987766

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.30  E-value=0.02  Score=34.91  Aligned_cols=51  Identities=12%  Similarity=0.064  Sum_probs=35.0

Q ss_pred             eecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCC
Q 030819            7 LPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLPP   66 (171)
Q Consensus         7 ~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   66 (171)
                      |||+|++++.+++.+.+.|...+.+..         ...+.....++.+|++++.+..+.
T Consensus        11 v~v~nLp~~~t~~~l~~~F~~~g~i~~---------~~~~~~~~~g~~~G~afV~F~s~~   61 (103)
T d2cpya1          11 AHITNIPFSITKMDVLQFLEGIPVDEN---------AVHVLVDNNGQGLGQALVQFKNED   61 (103)
T ss_dssp             EEEESCCTTSCHHHHHHHTTTSCCCST---------TEEECCCTTSSCSSCEEEECSSHH
T ss_pred             EEEeCCCCCCCHHHHhhhhcccceEEE---------EEEEEeCCCCCcCccEEEEECCHH
Confidence            999999999999999999988776622         222223334566666665554443

>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=92.22  E-value=0.0027  Score=37.44  Aligned_cols=51  Identities=18%  Similarity=0.167  Sum_probs=35.7

Q ss_pred             eeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACL   64 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   64 (171)
                      +.|||+|+.++.+++.+...|...+++         .+.....+...++.++++++.+..
T Consensus        10 ~~l~V~nL~~~~te~~l~~~F~~~G~i---------~~v~i~~~~~~~~~~g~afV~f~~   60 (83)
T d2cqca1          10 CCLGVFGLSLYTTERDLREVFSKYGPI---------ADVSIVYDQQSRRSRGFAFVYFEN   60 (83)
T ss_dssp             GCEEEESCCSSCCHHHHHHHHHTTSCE---------EEEEEEECSSSSSEEEEEEEEESS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCC---------ccccccccccccccccceEEEECC
Confidence            469999999999999999999998876         333333443344555555554443

>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=92.18  E-value=0.0036  Score=37.05  Aligned_cols=51  Identities=20%  Similarity=0.066  Sum_probs=36.2

Q ss_pred             eeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCC
Q 030819            6 FLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLP   65 (171)
Q Consensus         6 ~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   65 (171)
                      .|||+|+++++++..+...|...+++         .+.....+...+++++++++.+..+
T Consensus         8 ~lfV~nlp~~~te~~l~~~F~~~G~i---------~~~~~~~d~~~g~~~g~afV~f~~~   58 (85)
T d1b7fa2           8 NLYVTNLPRTITDDQLDTIFGKYGSI---------VQKNILRDKLTGRPRGVAFVRYNKR   58 (85)
T ss_dssp             EEEEESCCTTCCHHHHHHHHTSSSCE---------EEEEEEECTTTCCEEEEEEEEESSH
T ss_pred             EEEEeCCCCCCCHHHHHHHHHhhCCE---------eeeeeecccccccCceeEEEEECCH
Confidence            49999999999999999999998876         3333333334455566666555544

>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=92.09  E-value=0.0024  Score=37.50  Aligned_cols=26  Identities=15%  Similarity=-0.081  Sum_probs=24.1

Q ss_pred             eeecCceeecccchhhcccCCcCCCC
Q 030819            6 FLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         6 ~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      .|||+|+++++++..+.+.|...+++
T Consensus         4 ~l~V~nLp~~~te~~l~~~f~~~G~v   29 (82)
T d1fxla1           4 NLIVNYLPQNMTQEEFRSLFGSIGEI   29 (82)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHTTSCE
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCc
Confidence            49999999999999999999998876

>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=91.98  E-value=0.0043  Score=38.17  Aligned_cols=51  Identities=14%  Similarity=0.157  Sum_probs=36.1

Q ss_pred             eeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCCCC
Q 030819            6 FLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLACLP   65 (171)
Q Consensus         6 ~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   65 (171)
                      .|||+|+++++++..+.+.|...+.+         .+.....+..++++++++++.+...
T Consensus        10 tl~V~nLp~~~te~~l~~~f~~~G~i---------~~v~i~~~~~tg~~~g~afV~f~~~   60 (104)
T d1p1ta_          10 SVFVGNIPYEATEEQLKDIFSEVGPV---------VSFRLVYDRETGKPKGYGFCEYQDQ   60 (104)
T ss_dssp             CEEEESCCTTSCHHHHHHHHHTTSCC---------SEEEEEEETTTTEEEEEEEEECSCH
T ss_pred             EEEEECCCCcCCHHHHHHhhhccccc---------cccccccccceeccCCceEEEECCH
Confidence            59999999999999999999988776         4444444444445556666555433

>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=91.97  E-value=0.0076  Score=35.33  Aligned_cols=25  Identities=12%  Similarity=0.155  Sum_probs=23.1

Q ss_pred             eecCceeecccchhhcccCCcCCCC
Q 030819            7 LPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         7 ~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      |||+|+++++++..+.+.|...+++
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i   25 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVI   25 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCB
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCce
Confidence            7999999999999999999988776

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.94  E-value=0.0061  Score=37.50  Aligned_cols=27  Identities=11%  Similarity=0.236  Sum_probs=24.0

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      ++|||.|++|+.+++.+.+.|...+++
T Consensus        16 ~~v~v~nLP~~~te~dI~~~F~~~g~v   42 (104)
T d1wg5a_          16 GFVRLRGLPFGCSKEEIVQFFSGLEIV   42 (104)
T ss_dssp             CEEEEESCCTTCCHHHHHHHTTTCCEE
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCc
Confidence            469999999999999999999886655

>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=91.22  E-value=0.019  Score=33.91  Aligned_cols=27  Identities=15%  Similarity=0.010  Sum_probs=25.1

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      +.|||+|++.+++++.+.+.|...+++
T Consensus         9 ~~l~V~nLp~~~~~~~l~~~F~~~G~i   35 (86)
T d2cpja1           9 SRLFVGNLPPDITEEEMRKLFEKYGKA   35 (86)
T ss_dssp             TEEEEESCCTTCCHHHHHHHTSTTCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCc
Confidence            579999999999999999999998877

>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=91.01  E-value=0.016  Score=35.44  Aligned_cols=25  Identities=0%  Similarity=-0.073  Sum_probs=22.6

Q ss_pred             eeeecCceeecccchhhcccCCcCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHS   29 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~   29 (171)
                      +.|||+|+.+++++..+.+.|...+
T Consensus        16 ~~v~V~nLp~~~te~~l~~~f~~~g   40 (104)
T d1wi8a_          16 YTAFLGNLPYDVTEESIKEFFRGLN   40 (104)
T ss_dssp             EEEEEESCCSSCCHHHHHHHTTTSC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhc
Confidence            5799999999999999999998754

>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=90.71  E-value=0.0065  Score=36.19  Aligned_cols=27  Identities=7%  Similarity=-0.027  Sum_probs=24.4

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      ..|||+|++.+.++..+...|...+++
T Consensus         8 ~~l~V~nL~~~~t~~~l~~~F~~~G~i   34 (88)
T d1rk8a_           8 WILFVTSIHEEAQEDEIQEKFCDYGEI   34 (88)
T ss_dssp             EEEEEESCCTTCCHHHHHHHHGGGSCE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHcCCc
Confidence            359999999999999999999998776

>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=90.09  E-value=0.02  Score=35.60  Aligned_cols=26  Identities=8%  Similarity=0.069  Sum_probs=23.2

Q ss_pred             eeecCceeecccchhhcccCCcCCCC
Q 030819            6 FLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         6 ~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      .|||+|++|+++...+.+.|...+++
T Consensus        20 ~i~v~nLp~~~t~~di~~~F~~~g~~   45 (112)
T d1wela1          20 CVYLKGLPFEAENKHVIDFFKKLDIV   45 (112)
T ss_dssp             EEEEECCCTTCCHHHHHHHSCSSCBC
T ss_pred             EEEEecCCCcCcHHHHhhHHhhcccc
Confidence            59999999999999999999876665

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

Probab=90.08  E-value=0.004  Score=40.43  Aligned_cols=50  Identities=16%  Similarity=0.090  Sum_probs=34.8

Q ss_pred             eeeecCceeecccchhhcccCCcCCCCCCCCccccccccccccccccCCCCCCCCCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPAPATPFTIKRRDFDSLFSLRQGRGRGACFPLAC   63 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   63 (171)
                      ..|||+|+.+++++..+...|...+++         .+.....+..+++.++++++.+.
T Consensus        43 ~~l~V~nLp~~~te~~l~~~F~~~G~i---------~~v~i~~d~~t~~~rg~afV~f~   92 (139)
T d1u6fa1          43 RNLMVNYIPTTVDEVQLRQLFERYGPI---------ESVKIVCDRETRQSRGYGFVKFQ   92 (139)
T ss_dssp             SEEEEESCSTTCCHHHHHHHHHHHSCE---------EEEEEEEETTTTEEEEEEEEEES
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhhccc---------cccccccccccccccceeeEEEC
Confidence            359999999999999999999998876         34434444434455555554433

>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=89.82  E-value=0.054  Score=31.87  Aligned_cols=29  Identities=7%  Similarity=-0.117  Sum_probs=26.3

Q ss_pred             eeeeeecCceeecccchhhcccCCcCCCC
Q 030819            3 VLGFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         3 ~~~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      ....|||++++++++++.+.+.|...+++
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v   32 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDV   32 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCc
Confidence            35679999999999999999999998877

>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=89.59  E-value=0.023  Score=33.30  Aligned_cols=27  Identities=7%  Similarity=0.107  Sum_probs=24.4

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      ..|||.|++++.+++.+.+.|...+++
T Consensus        10 ~~l~v~nLp~~~~~~di~~~F~~~~~~   36 (86)
T d2cqpa1          10 TIIKVQNMPFTVSIDEILDFFYGYQVI   36 (86)
T ss_dssp             EEEEEESCCTTCCHHHHHHHTTTSCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhhcccc
Confidence            359999999999999999999998776

>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=89.57  E-value=0.014  Score=35.17  Aligned_cols=27  Identities=15%  Similarity=0.095  Sum_probs=24.5

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      ..|||+|+++++++..+...|...+++
T Consensus         9 ~~l~V~nLp~~~~e~~l~~~F~~~G~i   35 (94)
T d2cpha1           9 SKILVRNIPFQANQREIRELFSTFGEL   35 (94)
T ss_dssp             CCEEEESCCTTCCHHHHHHHHHTTSCE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCc
Confidence            469999999999999999999987766

>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=88.32  E-value=0.0055  Score=36.14  Aligned_cols=25  Identities=12%  Similarity=0.162  Sum_probs=23.4

Q ss_pred             eecCceeecccchhhcccCCcCCCC
Q 030819            7 LPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         7 ~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      |||+|++++.+++.+.+.|...+++
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v   25 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAI   25 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCE
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCc
Confidence            7999999999999999999998876

>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=88.24  E-value=0.017  Score=35.05  Aligned_cols=27  Identities=11%  Similarity=0.087  Sum_probs=24.2

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      +.|||+|++.++++..+...|...+++
T Consensus        19 ~tl~V~nLp~~~t~~~l~~~f~~~G~v   45 (102)
T d2cpxa1          19 KVLYLKNLSPRVTERDLVSLFARFQEK   45 (102)
T ss_dssp             SEEEEECCCTTCCHHHHHHHTHHHHHS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHhhccce
Confidence            579999999999999999999887766

>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=87.95  E-value=0.021  Score=34.76  Aligned_cols=27  Identities=11%  Similarity=0.091  Sum_probs=24.6

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      +.|||+|+++++++..+...|...+++
T Consensus        19 ~~lfV~nLp~~~te~~L~~~F~~~G~i   45 (101)
T d1x5oa1          19 TNLYISNLPLSMDEQELENMLKPFGQV   45 (101)
T ss_dssp             TEEEEESCCTTCCHHHHHHTTTTTSCE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHhhcccc
Confidence            469999999999999999999998766

>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=86.81  E-value=0.014  Score=34.36  Aligned_cols=26  Identities=4%  Similarity=-0.121  Sum_probs=24.1

Q ss_pred             eeecCceeecccchhhcccCCcCCCC
Q 030819            6 FLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         6 ~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      .|||+|++++.++..+...|...+++
T Consensus         8 tvfV~nlp~~~te~~l~~~F~~~G~v   33 (85)
T d1zh5a2           8 SVYIKGFPTDATLDDIKEWLEDKGQV   33 (85)
T ss_dssp             EEEEECCCTTCCHHHHHHHHTTSCCE
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhccc
Confidence            59999999999999999999998876

>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=84.88  E-value=0.046  Score=32.24  Aligned_cols=27  Identities=11%  Similarity=0.140  Sum_probs=24.4

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      +.|||+|+++++++..+.+.|...+.+
T Consensus         9 ~~l~V~nLp~~~t~~~l~~~F~~~G~v   35 (89)
T d1cvja2           9 GNIFIKNLDKSIDNKALYDTFSAFGNI   35 (89)
T ss_dssp             TEEEEESCCSSCCHHHHHHHHHTTSCE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCc
Confidence            469999999999999999999887766

>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=84.80  E-value=0.059  Score=32.95  Aligned_cols=27  Identities=4%  Similarity=-0.049  Sum_probs=24.7

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      ..|||+|++++.+++.|.+.|...+++
T Consensus        11 ~~l~V~nLp~~~t~~~L~~~F~~fG~I   37 (111)
T d1whxa_          11 TVILAKNLPAGTLAAEIQETFSRFGSL   37 (111)
T ss_dssp             EEEEEESCCTTCCHHHHHHHHHTTSCE
T ss_pred             CEEEEECCCCCCCHHHHHhhhhccCCc
Confidence            469999999999999999999998776

>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=84.28  E-value=0.11  Score=31.14  Aligned_cols=27  Identities=7%  Similarity=-0.055  Sum_probs=24.6

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      ..|||+|++++.++..+.+.|...+++
T Consensus         9 ~~i~V~nLp~~~te~~l~~~F~~~G~i   35 (101)
T d2cpea1           9 SAIYVQGLNDSVTLDDLADFFKQCGVV   35 (101)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHTTTSCB
T ss_pred             CEEEEECCCCcCCHHHHHHHHHHCceE
Confidence            469999999999999999999988776

>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=83.55  E-value=0.049  Score=32.43  Aligned_cols=27  Identities=15%  Similarity=0.073  Sum_probs=24.8

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      ..|||+|+++++++..+.+.|...+++
T Consensus        12 ~~l~v~nLp~~~t~~~L~~~F~~~G~v   38 (93)
T d2cq3a1          12 KRLHVSNIPFRFRDPDLRQMFGQFGKI   38 (93)
T ss_dssp             CEEEEESCCTTCCHHHHHHHGGGTSCE
T ss_pred             CEEEEECCCCCCCHHHHHHHHhhccee
Confidence            469999999999999999999998876

>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=82.37  E-value=0.055  Score=31.59  Aligned_cols=27  Identities=11%  Similarity=0.265  Sum_probs=24.1

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      ..|||+|++++++++.+.+.|...++.
T Consensus         9 k~l~V~nLp~~~te~~l~~~F~~~g~i   35 (86)
T d2cpda1           9 KILYVRNLMLSTSEEMIEKEFNNIKPG   35 (86)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHHTTSTT
T ss_pred             CEEEEcCCCCCCCHHHHHHhhccccee
Confidence            469999999999999999999887765

>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=81.01  E-value=0.071  Score=32.80  Aligned_cols=28  Identities=11%  Similarity=0.154  Sum_probs=25.2

Q ss_pred             eeeeecCceeecccchhhcccCCcCCCC
Q 030819            4 LGFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         4 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      ...|||+|+.++++...+...|...+++
T Consensus         7 ~r~l~V~nLp~~~te~~l~~~F~~~G~v   34 (114)
T d2f9da1           7 NRILYIRNLPYKITAEEMYDIFGKYGPI   34 (114)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHhhcCCe
Confidence            3469999999999999999999998876

>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=80.70  E-value=0.093  Score=30.88  Aligned_cols=25  Identities=4%  Similarity=-0.085  Sum_probs=21.4

Q ss_pred             eecCceeecccchhh---cccCCcCCCC
Q 030819            7 LPVPTTYFNINQNLL---IHNLTRHSPA   31 (171)
Q Consensus         7 ~~v~~~~~~~~~~~~---~~~~~~~~~~   31 (171)
                      +||+|++++.+++.+   .+.|...+++
T Consensus        11 vyV~nLp~~~t~~~l~~~~e~F~~~G~I   38 (89)
T d2cpia1          11 VFVVGLSQRLADPEVLKRPEYFGKFGKI   38 (89)
T ss_dssp             EEEEEECTTTCCHHHHHSTTTTTTTSCE
T ss_pred             EEEECCCCccCHHHHHHHHHHhcccCCc
Confidence            899999999999988   5668777766

>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=80.20  E-value=0.17  Score=31.15  Aligned_cols=27  Identities=7%  Similarity=-0.210  Sum_probs=24.8

Q ss_pred             eeeecCceeecccchhhcccCCcCCCC
Q 030819            5 GFLPVPTTYFNINQNLLIHNLTRHSPA   31 (171)
Q Consensus         5 ~~~~v~~~~~~~~~~~~~~~~~~~~~~   31 (171)
                      ...|||++..+.++..+...|...+++
T Consensus        12 ~~~fvgnL~~~~tee~Lk~~F~~fG~V   38 (113)
T d1owxa_          12 LLKFSGDLDDQTCREDLHILFSNHGEI   38 (113)
T ss_dssp             EEEEEESCCSSCCHHHHHHHTCSSCCE
T ss_pred             eEEEECCCCCCCCHHHHHHHHHhcCCh
Confidence            446999999999999999999998888