Psyllid ID: psy222

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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-------180-------190-------200-------210-------220-----
Protein Sequence
MSDEQKSAKNSPSSHHSEVRDSKSSSQTVEPRDAKSSSGQTVKYWYPYCITYDPIQAGSIDGTDTIPHDRAILRALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWGGNRNSGQLRFGGRNKPWVKPVQLMNERELGEWRKQGGAGS
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHcccccccccccccccEEEEcccccccHHHHHHHHHHccccEEEEEEEcccccccccEEEEEEccHHHHHHHHHHHccccccccEEEEEcccccccccccccccccccccccccccccccccccccccccccccHHHccHHcccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccEEEccccccccccccccccccccccccccccHHccccccEccccccccccccccHHHHHHHHccccccccccccEEEEEEEccccccHHHHHHHHHHcccEEEEEEEEEccccccccEEEEEEccHHHHHHHHHHHcccEEcccEEEEEcccccccccccccccccccccccccccccccccccccccccccccHHHHHHHcccccccc
Coil and Loop (DISEMBL)
msdeqksaknspsshhsevrdsksssqtveprdaksssgqtvkywypycitydpiqagsidgtdtiphDRAILRALRstykphtsstdptrtLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFvtghskrygfleYDCEKACLAAIRALNRqnfqgseiivdfecgrvlpgwkprrlgggwggnrnsgqlrfggrnkpwvkpvqLMNERELGEWRKQGGAGS
Flexible Loop (DISEMBL)
msdeqksaknspsshhsevrdsksssqtveprdaksssgqtvkYWYPYCITYDPIQAGSIDGTDTIPHDRAILRALrstykphtsstdptrtlfIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECGRVLPGwkprrlgggwggnrnsgqlrfggrnkpwvkpvqlmnerelgewrkqggags
Low Complexity Region (SEG)
MSDEQKSAKNSPSSHHSEVRDSKSSSQTVEPRDAKSSSGQTVKYWYPYCITYDPIQAGSIDGTDTIPHDRAILRALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECGRVlpgwkprrlgggwggNRNSGQLRFGGRNKPWVKPVQLMNERELGEWRKQGGAGS
Disordered region (IsUnstruct)
****************************************TVKYWYPYCITYDPIQAGSIDGTDTIPHDRAILRALRST************TLFIGRLN*****ADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWGGNRNSGQLRFGGRNKPWVKPV*******************
Disordered Region (DISOPRED)
***********************************************YCITY***********************************DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECGRVL*****************************************************
Disordered Region (DISEMBL)
***************************************QTVKYWYPYCITYDPIQAGSIDGTDTIPHDRAILRALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWGGNRNSGQLRFGGRNKPWVKPVQLMNERELGE*********
Disordered Region (DISPRO)
****************************************TVKYWYPYCITYDPIQAGSIDGTDTIPHDRAILRALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECGRVLPGWKP************************************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSDEQKSAKNSPSSHHSEVRDSKSSSQTVEPRDAKSSSGQTVKYWYPYCITYDPIQAGSIDGTDTIPHDRAILRALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWGGNRNSGQLRFGGRNKPWVKPVQLMNERELGEWRKQGGAGS
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	225	2.2.26 [Sep-21-2011]
Q05AT9	272	U11/U12 small nuclear rib	N/A	N/A	0.728	0.602	0.515	7e-39
Q4KMD3	208	U11/U12 small nuclear rib	yes	N/A	0.746	0.807	0.491	2e-38
Q5U1W5	244	U11/U12 small nuclear rib	yes	N/A	0.728	0.672	0.515	5e-37
Q1LZH0	245	U11/U12 small nuclear rib	yes	N/A	0.728	0.669	0.509	5e-37
Q9D384	244	U11/U12 small nuclear rib	yes	N/A	0.728	0.672	0.509	1e-36
Q16560	246	U11/U12 small nuclear rib	yes	N/A	0.728	0.666	0.503	3e-36
Q42404	427	U1 small nuclear ribonucl	no	N/A	0.524	0.276	0.381	2e-18
O13829	261	U1 small nuclear ribonucl	yes	N/A	0.408	0.352	0.391	3e-14
Q55FQ0	459	U1 small nuclear ribonucl	yes	N/A	0.551	0.270	0.307	7e-13
P17133	448	U1 small nuclear ribonucl	yes	N/A	0.422	0.212	0.336	3e-11

>sp|Q05AT9|U1SBP_XENLA U11/U12 small nuclear ribonucleoprotein 35 kDa protein OS=Xenopus laevis GN=snrnp35 PE=2 SV=1

 Score =  160 bits (405), Expect = 7e-39,   Method: Compositional matrix adjust.
 Identities = 85/165 (51%), Positives = 110/165 (66%), Gaps = 1/165 (0%)

Query: 45  WYPYCITYDPIQAGSIDGTDTIPHDRAILRALRSTYKPHTSST-DPTRTLFIGRLNKNSR 103
           W P    YDP++AGSIDGTD  PHDRA+LRA+ S Y P+   T DP  TLF+ RL+  + 
Sbjct: 4   WTPIAKKYDPLKAGSIDGTDEEPHDRAVLRAMLSRYVPNKGVTGDPHLTLFVSRLSPQTT 63

Query: 104 EADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEII 163
           E  L++ F+ YG +  +R+VRDF+TG SK Y F+EY  E A + A R  N+      E+ 
Sbjct: 64  EEKLKEVFSRYGDIKRIRLVRDFITGFSKGYAFIEYKQENAIMKAHRDANKLVIDQREVF 123

Query: 164 VDFECGRVLPGWKPRRLGGGWGGNRNSGQLRFGGRNKPWVKPVQL 208
           VDFE  R L GW PRR GGG+GG + SGQLRFGGR++P+ KP+ L
Sbjct: 124 VDFELERNLKGWIPRRFGGGFGGKKESGQLRFGGRDRPFRKPINL 168

Xenopus laevis (taxid: 8355)

>sp|Q4KMD3|U1SBP_DANRE U11/U12 small nuclear ribonucleoprotein 35 kDa protein OS=Danio rerio GN=snrnp35 PE=2 SV=1

 Score =  159 bits (402), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 83/169 (49%), Positives = 109/169 (64%), Gaps = 1/169 (0%)

Query: 45  WYPYCITYDPIQAGSIDGTDTIPHDRAILRALRSTYKPHTSST-DPTRTLFIGRLNKNSR 103
           W P    YDP++AGSIDGTD  PHD  + RA+ + YKP+     DP  TLF+ RLN  + 
Sbjct: 3   WSPVAKVYDPLKAGSIDGTDVEPHDAGVWRAMLARYKPNRGVCGDPDLTLFVARLNPQTT 62

Query: 104 EADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEII 163
           E  L   F+++G +  +R+VRD VTG SKRY F+EY  E++   A R  N+      E++
Sbjct: 63  EEKLRDVFSKFGDIRRLRLVRDVVTGFSKRYAFIEYKEERSLKRAWRDANKLILDQYELL 122

Query: 164 VDFECGRVLPGWKPRRLGGGWGGNRNSGQLRFGGRNKPWVKPVQLMNER 212
           VD E  R LPGW+PRRLGGG GG + SGQLRFGGR++P+ KP+ L   R
Sbjct: 123 VDVEQERTLPGWRPRRLGGGQGGQKESGQLRFGGRDRPFRKPINLSTRR 171

Danio rerio (taxid: 7955)

>sp|Q5U1W5|U1SBP_RAT U11/U12 small nuclear ribonucleoprotein 35 kDa protein OS=Rattus norvegicus GN=Snrnp35 PE=2 SV=1

 Score =  154 bits (389), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 85/165 (51%), Positives = 109/165 (66%), Gaps = 1/165 (0%)

Query: 45  WYPYCITYDPIQAGSIDGTDTIPHDRAILRALRSTYKPHTSST-DPTRTLFIGRLNKNSR 103
           W P    YDP++AGSIDGTD  PHDRA+ RA+ + Y P+   T DP  TLF+ RLN  ++
Sbjct: 4   WMPIAKEYDPLKAGSIDGTDEDPHDRAVWRAMLARYVPNKGVTGDPLLTLFVARLNSQTK 63

Query: 104 EADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEII 163
           E  L++ F+ YG +  +R+VRD VTG SK Y F+EY  E+A L A R  +       EI 
Sbjct: 64  EEKLKEVFSRYGDIRRLRLVRDLVTGFSKGYAFIEYKEERALLKAYRDADGLVIDQHEIF 123

Query: 164 VDFECGRVLPGWKPRRLGGGWGGNRNSGQLRFGGRNKPWVKPVQL 208
           VD+E  R L GW PRRLGGG GG + SGQLRFGGR++P+ KP+ L
Sbjct: 124 VDYELERTLRGWIPRRLGGGLGGKKESGQLRFGGRDRPFRKPINL 168

Rattus norvegicus (taxid: 10116)

>sp|Q1LZH0|U1SBP_BOVIN U11/U12 small nuclear ribonucleoprotein 35 kDa protein OS=Bos taurus GN=SNRNP35 PE=2 SV=1

 Score =  154 bits (389), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 84/165 (50%), Positives = 109/165 (66%), Gaps = 1/165 (0%)

Query: 45  WYPYCITYDPIQAGSIDGTDTIPHDRAILRALRSTYKPHTSST-DPTRTLFIGRLNKNSR 103
           W P    YDP++AGSIDGTD  PHDRA+ RA+ + Y P+   T DP  TLF+ RLN  ++
Sbjct: 4   WMPIAKEYDPLKAGSIDGTDEDPHDRAVWRAMLARYTPNKGVTGDPLLTLFVARLNLQTK 63

Query: 104 EADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEII 163
           E  L++ F+ YG +  +R+VRD VTG SK Y F+EY  E++ L A R  +       EI 
Sbjct: 64  EEKLKEVFSRYGDIRRLRLVRDLVTGFSKGYAFIEYKDERSLLKAYRDADGLVIDQHEIF 123

Query: 164 VDFECGRVLPGWKPRRLGGGWGGNRNSGQLRFGGRNKPWVKPVQL 208
           VD+E  R L GW PRRLGGG GG + SGQLRFGGR++P+ KP+ L
Sbjct: 124 VDYELERTLKGWIPRRLGGGLGGKKESGQLRFGGRDRPFRKPINL 168

Bos taurus (taxid: 9913)

>sp|Q9D384|U1SBP_MOUSE U11/U12 small nuclear ribonucleoprotein 35 kDa protein OS=Mus musculus GN=Snrnp35 PE=2 SV=1

 Score =  153 bits (386), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 84/165 (50%), Positives = 109/165 (66%), Gaps = 1/165 (0%)

Query: 45  WYPYCITYDPIQAGSIDGTDTIPHDRAILRALRSTYKPHTSST-DPTRTLFIGRLNKNSR 103
           W P    YDP++AGSIDGTD  PHDRA+ RA+ + Y P+   T DP  TLF+ RLN  ++
Sbjct: 4   WMPIAKEYDPLKAGSIDGTDEDPHDRAVWRAMLARYVPNKGVTGDPLLTLFVARLNLQTK 63

Query: 104 EADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEII 163
           E  L++ F+ YG +  +R+VRD VTG SK Y F+EY  E+A + A R  +       EI 
Sbjct: 64  EEKLKEVFSRYGDIRRLRLVRDLVTGFSKGYAFIEYKEERALMKAYRDADGLVIDQHEIF 123

Query: 164 VDFECGRVLPGWKPRRLGGGWGGNRNSGQLRFGGRNKPWVKPVQL 208
           VD+E  R L GW PRRLGGG GG + SGQLRFGGR++P+ KP+ L
Sbjct: 124 VDYELERTLRGWIPRRLGGGLGGKKESGQLRFGGRDRPFRKPINL 168

Mus musculus (taxid: 10090)

>sp|Q16560|U1SBP_HUMAN U11/U12 small nuclear ribonucleoprotein 35 kDa protein OS=Homo sapiens GN=SNRNP35 PE=1 SV=1

 Score =  151 bits (382), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 83/165 (50%), Positives = 108/165 (65%), Gaps = 1/165 (0%)

Query: 45  WYPYCITYDPIQAGSIDGTDTIPHDRAILRALRSTYKPHTSST-DPTRTLFIGRLNKNSR 103
           W P    YDP++AGSIDGTD  PHDRA+ RA+ + Y P+     DP  TLF+ RLN  ++
Sbjct: 4   WMPIAKEYDPLKAGSIDGTDEDPHDRAVWRAMLARYVPNKGVIGDPLLTLFVARLNLQTK 63

Query: 104 EADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEII 163
           E  L++ F+ YG +  +R+VRD VTG SK Y F+EY  E+A + A R  +       EI 
Sbjct: 64  EDKLKEVFSRYGDIRRLRLVRDLVTGFSKGYAFIEYKEERAVIKAYRDADGLVIDQHEIF 123

Query: 164 VDFECGRVLPGWKPRRLGGGWGGNRNSGQLRFGGRNKPWVKPVQL 208
           VD+E  R L GW PRRLGGG GG + SGQLRFGGR++P+ KP+ L
Sbjct: 124 VDYELERTLKGWIPRRLGGGLGGKKESGQLRFGGRDRPFRKPINL 168

Homo sapiens (taxid: 9606)

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

 Score = 92.8 bits (229), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 45/118 (38%), Positives = 66/118 (55%)

Query: 84  TSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEK 143
            ++ DP +TLF+ RLN  S E+ +++ F  YG +  V +V D +T   K Y F+EY   +
Sbjct: 131 NATGDPYKTLFVSRLNYESSESKIKREFESYGPIKRVHLVTDQLTNKPKGYAFIEYMHTR 190

Query: 144 ACLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWGGNRNSGQLRFGGRNKP 201
              AA +  + Q   G  ++VD E GR +P W+PRRLGGG G +R  G     G  +P
Sbjct: 191 DMKAAYKQADGQKIDGRRVLVDVERGRTVPNWRPRRLGGGLGTSRVGGGEEIVGEQQP 248

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

Arabidopsis thaliana (taxid: 3702)

>sp|O13829|RU17_SCHPO U1 small nuclear ribonucleoprotein 70 kDa homolog OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=usp101 PE=1 SV=1

 Score = 78.6 bits (192), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 36/92 (39%), Positives = 57/92 (61%)

Query: 88  DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLA 147
           DP +T+F+ RL+ +++E+D+E+ F  YG +  +RVVR+ VTG S  Y F+ ++ E+    
Sbjct: 97  DPYKTMFLSRLSYDTKESDIEREFTRYGPIERIRVVRNKVTGKSMGYAFVVFERERDLKV 156

Query: 148 AIRALNRQNFQGSEIIVDFECGRVLPGWKPRR 179
           A +A       G  I+VD E GR + GW PR+
Sbjct: 157 AYKASAGLMLNGRRIVVDVERGRTVKGWLPRK 188

Involved in nuclear mRNA splicing (By similarity). Essential for growth.

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

>sp|Q55FQ0|RU17_DICDI U1 small nuclear ribonucleoprotein 70 kDa OS=Dictyostelium discoideum GN=snrnp70 PE=3 SV=1

 Score = 74.3 bits (181), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 39/127 (30%), Positives = 68/127 (53%), Gaps = 3/127 (2%)

Query: 68  HDRAILRALRS--TYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRD 125
           +D  I ++L++   Y    ++ DP +T+F+ R++  + +  LE  F ++G + S+ +V+D
Sbjct: 74  NDERISKSLKAWDPYSNSETTGDPYKTIFVSRISYKTTQQKLEFEFGQFGPIKSLFLVKD 133

Query: 126 FVTGHSKR-YGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGGW 184
                    Y F+E++ E+   AA +  +        I+VD E GRV+  WKPR+ GGG 
Sbjct: 134 SNNPEKHTGYAFIEFERERDMKAAYKQADGMKIDDRRIVVDIERGRVIKNWKPRKFGGGL 193

Query: 185 GGNRNSG 191
           G  R  G
Sbjct: 194 GNTRAGG 200

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

Dictyostelium discoideum (taxid: 44689)

>sp|P17133|RU17_DROME U1 small nuclear ribonucleoprotein 70 kDa OS=Drosophila melanogaster GN=snRNP-U1-70K PE=1 SV=2

 Score = 68.6 bits (166), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 32/95 (33%), Positives = 53/95 (55%)

Query: 84  TSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEK 143
            ++ DP RTLFI R+N ++ E+ L + F  YG +  + ++ D  +G  K Y F+EY+ E+
Sbjct: 95  NATEDPFRTLFIARINYDTSESKLRREFEFYGPIKKIVLIHDQESGKPKGYAFIEYEHER 154

Query: 144 ACLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPR 178
              AA +  + +      ++VD E  R + GW PR
Sbjct: 155 DMHAAYKHADGKKIDSKRVLVDVERARTVKGWLPR 189

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

Drosophila melanogaster (taxid: 7227)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	225
193631809	300	PREDICTED: u11/U12 small nuclear ribonuc	0.742	0.556	0.529	3e-46
321460332	240	hypothetical protein DAPPUDRAFT_308886 [	0.737	0.691	0.532	9e-46
449279308	254	U11/U12 small nuclear ribonucleoprotein	0.737	0.653	0.544	8e-45
395529739	283	PREDICTED: U11/U12 small nuclear ribonuc	0.728	0.579	0.545	1e-44
50756329	263	PREDICTED: U11/U12 small nuclear ribonuc	0.737	0.631	0.532	3e-44
326929594	265	PREDICTED: u11/U12 small nuclear ribonuc	0.737	0.626	0.526	5e-44
350536563	265	putative U11/U12 snRNP 35K [Taeniopygia	0.737	0.626	0.532	8e-44
126324312	261	PREDICTED: u11/U12 small nuclear ribonuc	0.728	0.628	0.533	8e-44
224161968	265	PREDICTED: U11/U12 small nuclear ribonuc	0.728	0.618	0.539	1e-43
322798651	178	hypothetical protein SINV_12300 [Solenop	0.72	0.910	0.521	1e-43

>gi|193631809|ref|XP_001951817.1| PREDICTED: u11/U12 small nuclear ribonucleoprotein 35 kDa protein-like [Acyrthosiphon pisum]

 Score =  190 bits (483), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 89/168 (52%), Positives = 116/168 (69%), Gaps = 1/168 (0%)

Query: 42  VKYWYPYCITYDPIQAGSIDGTDTIPHDRAILRALRSTYK-PHTSSTDPTRTLFIGRLNK 100
           VK WYP  I YD I+AGSIDGTD  PHD  I RAL S YK  + +  +P  T+F+GRL+ 
Sbjct: 15  VKCWYPKAIVYDAIKAGSIDGTDIEPHDAGITRALNSNYKISYKAKGNPLNTIFVGRLSL 74

Query: 101 NSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGS 160
           ++ E DLE  F  YGK+I++R+V+D +TG SKRY F+EY+  K  L       +   + S
Sbjct: 75  DTTEKDLENEFCRYGKMIALRLVKDLITGLSKRYAFIEYETFKMALNTYVLCKKLVLKNS 134

Query: 161 EIIVDFECGRVLPGWKPRRLGGGWGGNRNSGQLRFGGRNKPWVKPVQL 208
           ++ VDFECGR+LPGWKPRRLGGG+GG + SGQLRFGGR + +  P+ L
Sbjct: 135 QVFVDFECGRLLPGWKPRRLGGGFGGEKQSGQLRFGGRVRCFRPPLNL 182

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|321460332|gb|EFX71375.1| hypothetical protein DAPPUDRAFT_308886 [Daphnia pulex]

 Score =  189 bits (479), Expect = 9e-46,   Method: Compositional matrix adjust.
 Identities = 89/167 (53%), Positives = 115/167 (68%), Gaps = 1/167 (0%)

Query: 43  KYWYPYCITYDPIQAGSIDGTDTIPHDRAILRALRSTYKP-HTSSTDPTRTLFIGRLNKN 101
           K W PY   Y+PI+ GS DG D  PHD AI+RA  + Y P H  + +P  TLFIGRL+KN
Sbjct: 6   KRWSPYAEHYNPIEVGSKDGKDIEPHDNAIVRACNALYHPNHLLTNNPQTTLFIGRLDKN 65

Query: 102 SREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSE 161
             E DLE  F +YGK+ +V VVRD VTG+SKRYGF+E+  +  C  A   L++   +G +
Sbjct: 66  VTEKDLEDVFIKYGKLKNVTVVRDVVTGYSKRYGFVEFKNKHDCHEARSELHQTVLKGKK 125

Query: 162 IIVDFECGRVLPGWKPRRLGGGWGGNRNSGQLRFGGRNKPWVKPVQL 208
           I+V+FEC   LPGW PRRLGGG+GG + SGQLRFG  ++PW +PVQ+
Sbjct: 126 ILVEFECQHTLPGWIPRRLGGGFGGKKESGQLRFGCLDRPWKRPVQV 172

Source: Daphnia pulex

Species: Daphnia pulex

Genus: Daphnia

Family: Daphniidae

Order: Diplostraca

Class: Branchiopoda

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|449279308|gb|EMC86943.1| U11/U12 small nuclear ribonucleoprotein 35 kDa protein [Columba livia]

 Score =  186 bits (471), Expect = 8e-45,   Method: Compositional matrix adjust.
 Identities = 91/167 (54%), Positives = 112/167 (67%), Gaps = 1/167 (0%)

Query: 45  WYPYCITYDPIQAGSIDGTDTIPHDRAILRALRSTYKPHTSST-DPTRTLFIGRLNKNSR 103
           W P    YDP++AGSIDGTD  PHDRAI RA+ + Y P+   T DP  TLF+ RLN  + 
Sbjct: 4   WAPIAKEYDPLKAGSIDGTDEEPHDRAIWRAMLARYVPNKGVTGDPHLTLFVARLNLQTT 63

Query: 104 EADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEII 163
           E  L++AF+ YG +  +R+VRD VTG SK Y F+EY  E+A L A R  NR      EI 
Sbjct: 64  EEKLKEAFSRYGDIRKIRLVRDLVTGFSKGYAFIEYKEERALLKAHRDANRLVIDQHEIF 123

Query: 164 VDFECGRVLPGWKPRRLGGGWGGNRNSGQLRFGGRNKPWVKPVQLMN 210
           VDFE  R L GW PRRLGGG+GG + SGQLRFGGR++P+ KP+ L N
Sbjct: 124 VDFELERTLKGWIPRRLGGGFGGKKESGQLRFGGRDRPFRKPINLPN 170

Source: Columba livia

Species: Columba livia

Genus: Columba

Family: Columbidae

Order: Columbiformes

Class: Aves

Phylum: Chordata

Superkingdom: Eukaryota

>gi|395529739|ref|XP_003766966.1| PREDICTED: U11/U12 small nuclear ribonucleoprotein 35 kDa protein-like [Sarcophilus harrisii]

 Score =  185 bits (469), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 90/165 (54%), Positives = 112/165 (67%), Gaps = 1/165 (0%)

Query: 45  WYPYCITYDPIQAGSIDGTDTIPHDRAILRALRSTYKPHTS-STDPTRTLFIGRLNKNSR 103
           W P    YDP++AGSIDGTD  PHDRAI RA+R+ Y P+   S DP  TLF+GRLN  + 
Sbjct: 4   WMPIAKEYDPLKAGSIDGTDEEPHDRAIWRAIRARYVPNKGVSGDPYLTLFVGRLNLQTT 63

Query: 104 EADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEII 163
           E  L+  F+ YG +  +R+VRD VTG SKRY F+EY  E++ L A R  N       EI 
Sbjct: 64  EEKLKDVFSRYGDIRKLRLVRDVVTGFSKRYAFIEYREEQSLLKAYRDANGLVIDQHEIF 123

Query: 164 VDFECGRVLPGWKPRRLGGGWGGNRNSGQLRFGGRNKPWVKPVQL 208
           VD+E  RVL GW PRRLGGG+GG + SGQLRFGGR++P+ KP+ L
Sbjct: 124 VDYELERVLKGWIPRRLGGGFGGKKESGQLRFGGRDRPFRKPINL 168

Source: Sarcophilus harrisii

Species: Sarcophilus harrisii

Genus: Sarcophilus

Family: Dasyuridae

Order: Dasyuromorphia

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|50756329|ref|XP_415114.1| PREDICTED: U11/U12 small nuclear ribonucleoprotein 35 kDa protein [Gallus gallus]

 Score =  184 bits (466), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 89/167 (53%), Positives = 111/167 (66%), Gaps = 1/167 (0%)

Query: 45  WYPYCITYDPIQAGSIDGTDTIPHDRAILRALRSTYKPHTSST-DPTRTLFIGRLNKNSR 103
           W P    YDP++AGSIDGTD  PHDRAI RA+ + Y P+   T DP  TLF+ RLN  + 
Sbjct: 4   WAPIAKEYDPLKAGSIDGTDEEPHDRAIWRAMLARYVPNKGVTGDPHLTLFVARLNLQTT 63

Query: 104 EADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEII 163
           E  L++ F+ YG +  +R+VRD VTG SK Y F+EY  E+A L A R  NR      E+ 
Sbjct: 64  EEKLKEVFSRYGDIRKIRLVRDLVTGFSKGYAFIEYKEERALLKAHRDANRLVIDQHEVF 123

Query: 164 VDFECGRVLPGWKPRRLGGGWGGNRNSGQLRFGGRNKPWVKPVQLMN 210
           VDFE  R L GW PRRLGGG+GG + SGQLRFGGR++P+ KP+ L N
Sbjct: 124 VDFELERTLKGWIPRRLGGGFGGKKESGQLRFGGRDRPFRKPINLPN 170

Source: Gallus gallus

Species: Gallus gallus

Genus: Gallus

Family: Phasianidae

Order: Galliformes

Class: Aves

Phylum: Chordata

Superkingdom: Eukaryota

>gi|326929594|ref|XP_003210944.1| PREDICTED: u11/U12 small nuclear ribonucleoprotein 35 kDa protein-like [Meleagris gallopavo]

 Score =  183 bits (464), Expect = 5e-44,   Method: Compositional matrix adjust.
 Identities = 88/167 (52%), Positives = 111/167 (66%), Gaps = 1/167 (0%)

Query: 45  WYPYCITYDPIQAGSIDGTDTIPHDRAILRALRSTYKPHTSST-DPTRTLFIGRLNKNSR 103
           W P    YDP++AGSIDGTD  PHDRA+ RA+ + Y P+   T DP  TLF+ RLN  + 
Sbjct: 4   WAPIAKEYDPLKAGSIDGTDEEPHDRAVWRAMLARYVPNKGVTGDPHLTLFVARLNLQTT 63

Query: 104 EADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEII 163
           E  L++ F+ YG +  +R+VRD VTG SK Y F+EY  E+A L A R  NR      E+ 
Sbjct: 64  EEKLKEVFSRYGDIRKIRLVRDLVTGFSKGYAFIEYKEERALLKAHRDANRLVVDQHEVF 123

Query: 164 VDFECGRVLPGWKPRRLGGGWGGNRNSGQLRFGGRNKPWVKPVQLMN 210
           VDFE  R L GW PRRLGGG+GG + SGQLRFGGR++P+ KP+ L N
Sbjct: 124 VDFELERTLKGWIPRRLGGGFGGKKESGQLRFGGRDRPFRKPINLPN 170

Source: Meleagris gallopavo

Species: Meleagris gallopavo

Genus: Meleagris

Family: Phasianidae

Order: Galliformes

Class: Aves

Phylum: Chordata

Superkingdom: Eukaryota

>gi|350536563|ref|NP_001232485.1| putative U11/U12 snRNP 35K [Taeniopygia guttata] gi|197128442|gb|ACH44940.1| putative U11/U12 snRNP 35K [Taeniopygia guttata] gi|197128443|gb|ACH44941.1| putative U11/U12 snRNP 35K [Taeniopygia guttata] gi|197128444|gb|ACH44942.1| putative U11/U12 snRNP 35K [Taeniopygia guttata] gi|197128445|gb|ACH44943.1| putative U11/U12 snRNP 35K [Taeniopygia guttata]

 Score =  182 bits (462), Expect = 8e-44,   Method: Compositional matrix adjust.
 Identities = 89/167 (53%), Positives = 110/167 (65%), Gaps = 1/167 (0%)

Query: 45  WYPYCITYDPIQAGSIDGTDTIPHDRAILRALRSTYKPHTSST-DPTRTLFIGRLNKNSR 103
           W P    YDP++AGSIDGTD  PHDRAI RA+ + Y P+     DP  TLF+ RLN  + 
Sbjct: 4   WAPIAKEYDPLKAGSIDGTDEEPHDRAIWRAMLARYVPNKGVMGDPHLTLFVARLNLQTT 63

Query: 104 EADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEII 163
           E  L++ F+ YG +  +R+VRD VTG SK Y F+EY  E+A L A R  NR      EI 
Sbjct: 64  EEKLKEVFSRYGDIRKIRLVRDLVTGFSKGYAFIEYKEERALLKAHRDANRLVIDQHEIF 123

Query: 164 VDFECGRVLPGWKPRRLGGGWGGNRNSGQLRFGGRNKPWVKPVQLMN 210
           VDFE  R L GW PRRLGGG+GG + SGQLRFGGR++P+ KP+ L N
Sbjct: 124 VDFELERTLKGWIPRRLGGGFGGKKESGQLRFGGRDRPFRKPINLPN 170

Source: Taeniopygia guttata

Species: Taeniopygia guttata

Genus: Taeniopygia

Family: Estrildidae

Order: Passeriformes

Class: Aves

Phylum: Chordata

Superkingdom: Eukaryota

>gi|126324312|ref|XP_001375255.1| PREDICTED: u11/U12 small nuclear ribonucleoprotein 35 kDa protein-like [Monodelphis domestica]

 Score =  182 bits (462), Expect = 8e-44,   Method: Compositional matrix adjust.
 Identities = 88/165 (53%), Positives = 111/165 (67%), Gaps = 1/165 (0%)

Query: 45  WYPYCITYDPIQAGSIDGTDTIPHDRAILRALRSTYKPHTS-STDPTRTLFIGRLNKNSR 103
           W P    YDP++AGSIDGTD  PHDRAI RA+ + Y P+   S DP  TLF+GRLN  + 
Sbjct: 4   WMPIAKEYDPLKAGSIDGTDEEPHDRAIWRAMLARYVPNKGVSGDPHLTLFVGRLNLQTT 63

Query: 104 EADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEII 163
           E  L+  F+ YG +  +R+VRD VTG SKRY F+EY  E++ L A R  N       EI 
Sbjct: 64  EEKLKDVFSRYGDIRKLRLVRDVVTGFSKRYAFIEYKEERSLLKAYRDANGLVIDQHEIF 123

Query: 164 VDFECGRVLPGWKPRRLGGGWGGNRNSGQLRFGGRNKPWVKPVQL 208
           VD+E  R+L GW PRRLGGG+GG + SGQLRFGGR++P+ KP+ L
Sbjct: 124 VDYELERILKGWIPRRLGGGFGGKKESGQLRFGGRDRPFRKPINL 168

Source: Monodelphis domestica

Species: Monodelphis domestica

Genus: Monodelphis

Family: Didelphidae

Order: Didelphimorphia

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|224161968|ref|XP_002188436.1| PREDICTED: U11/U12 small nuclear ribonucleoprotein 35 kDa protein-like [Taeniopygia guttata]

 Score =  182 bits (461), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 89/165 (53%), Positives = 110/165 (66%), Gaps = 1/165 (0%)

Query: 47  PYCITYDPIQAGSIDGTDTIPHDRAILRALRSTYKPHTSST-DPTRTLFIGRLNKNSREA 105
           P    YDP++AGSIDGTD  PHDRAI RA+ + Y P+   T DP  TLF+ RLN  + E 
Sbjct: 6   PIAKEYDPLKAGSIDGTDEEPHDRAIWRAMMARYVPNKGVTGDPHLTLFVARLNLQTTEE 65

Query: 106 DLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD 165
            L++ F+ YG +  +R+VRD VTG SK Y F+EY  E+A L A R  NR      EI VD
Sbjct: 66  KLKEVFSRYGDIRKIRLVRDLVTGFSKGYAFIEYKEERALLKAHRDANRLVIDQHEIFVD 125

Query: 166 FECGRVLPGWKPRRLGGGWGGNRNSGQLRFGGRNKPWVKPVQLMN 210
           FE  R L GW PRRLGGG+GG + SGQLRFGGR++P+ KP+ L N
Sbjct: 126 FELERTLKGWIPRRLGGGFGGKKESGQLRFGGRDRPFRKPINLPN 170

Source: Taeniopygia guttata

Species: Taeniopygia guttata

Genus: Taeniopygia

Family: Estrildidae

Order: Passeriformes

Class: Aves

Phylum: Chordata

Superkingdom: Eukaryota

>gi|322798651|gb|EFZ20255.1| hypothetical protein SINV_12300 [Solenopsis invicta]

 Score =  182 bits (461), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 85/163 (52%), Positives = 113/163 (69%), Gaps = 1/163 (0%)

Query: 45  WYPYCITYDPIQAGSIDGTDTIPHDRAILRALRSTYKP-HTSSTDPTRTLFIGRLNKNSR 103
           W PY   YDP++AGSIDGTDT PHD+AI RAL   Y+P H   + P RTLF+ RL     
Sbjct: 7   WSPYAKEYDPLKAGSIDGTDTQPHDKAISRALLMHYEPPHNLESKPERTLFVARLGPKVT 66

Query: 104 EADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEII 163
           + DL++ F++YG+VIS +V+ D VTG S+ YGF+E   E     A+R       +G +I 
Sbjct: 67  KYDLKELFSKYGEVISAKVIVDVVTGLSQGYGFVEMKSEDEARRALRRTIDATLKGYKIF 126

Query: 164 VDFECGRVLPGWKPRRLGGGWGGNRNSGQLRFGGRNKPWVKPV 206
           VD+ECGR L GWKPRRLGGG+GG + SGQLRFGG+++P+ +P+
Sbjct: 127 VDYECGRTLKGWKPRRLGGGFGGKKESGQLRFGGKDRPFKRPI 169

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	225
UNIPROTKB|F1NJ85	245	SNRNP35 "Uncharacterized prote	0.737	0.677	0.461	9.5e-34
RGD|1310724	244	Snrnp35 "small nuclear ribonuc	0.728	0.672	0.442	2.3e-32
UNIPROTKB|Q5U1W5	244	Snrnp35 "U11/U12 small nuclear	0.728	0.672	0.442	2.3e-32
UNIPROTKB|Q1LZH0	245	SNRNP35 "U11/U12 small nuclear	0.728	0.669	0.436	4.7e-32
MGI|MGI:1923417	244	Snrnp35 "small nuclear ribonuc	0.728	0.672	0.436	6e-32
UNIPROTKB|I3LN96	246	SNRNP35 "Uncharacterized prote	0.728	0.666	0.436	1.3e-31
UNIPROTKB|F1P6U2	246	SNRNP35 "Uncharacterized prote	0.728	0.666	0.430	1.6e-31
UNIPROTKB|Q16560	246	SNRNP35 "U11/U12 small nuclear	0.728	0.666	0.430	3.3e-31
ZFIN|ZDB-GENE-050706-77	208	snrnp35 "small nuclear ribonuc	0.746	0.807	0.414	1.8e-30
TAIR|locus:2058141	333	AT2G43370 [Arabidopsis thalian	0.795	0.537	0.381	1.7e-27

UNIPROTKB|F1NJ85 SNRNP35 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 367 (134.2 bits), Expect = 9.5e-34, P = 9.5e-34
 Identities = 77/167 (46%), Positives = 98/167 (58%)

Query:    45 WYPYCITYDPIQAGSIDGTDTIPHDRAILRALRSTYKPHTSST-DPTRTLFIGRLNKNSR 103
             W P    YDP++AGSIDGTD  PHDRAI RA+ + Y P+   T DP  TLF+ RLN  + 
Sbjct:     9 WAPIAKEYDPLKAGSIDGTDEEPHDRAIWRAMLARYVPNKGVTGDPHLTLFVARLNLQTT 68

Query:   104 EADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEII 163
             E  L++ F+ YG +  +R+VRD VTG SK Y F+EY  E+A L A R  NR      E+ 
Sbjct:    69 EEKLKEVFSRYGDIRKIRLVRDLVTGFSKGYAFIEYKEERALLKAHRDANRLVIDQHEVF 128

Query:   164 VDFECGRVXXXXXXXXXXXXXXXNRNSGQLRFGGRNKPWVKPVQLMN 210
             VDFE  R                 + SGQLRFGGR++P+ KP+ L N
Sbjct:   129 VDFELERTLKGWIPRRLGGGFGGKKESGQLRFGGRDRPFRKPINLPN 175

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005689 "U12-type spliceosomal complex" evidence=IEA

RGD|1310724 Snrnp35 "small nuclear ribonucleoprotein 35 (U11/U12)" [Rattus norvegicus (taxid:10116)]

 Score = 354 (129.7 bits), Expect = 2.3e-32, P = 2.3e-32
 Identities = 73/165 (44%), Positives = 97/165 (58%)

Query:    45 WYPYCITYDPIQAGSIDGTDTIPHDRAILRALRSTYKPHTSST-DPTRTLFIGRLNKNSR 103
             W P    YDP++AGSIDGTD  PHDRA+ RA+ + Y P+   T DP  TLF+ RLN  ++
Sbjct:     4 WMPIAKEYDPLKAGSIDGTDEDPHDRAVWRAMLARYVPNKGVTGDPLLTLFVARLNSQTK 63

Query:   104 EADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEII 163
             E  L++ F+ YG +  +R+VRD VTG SK Y F+EY  E+A L A R  +       EI 
Sbjct:    64 EEKLKEVFSRYGDIRRLRLVRDLVTGFSKGYAFIEYKEERALLKAYRDADGLVIDQHEIF 123

Query:   164 VDFECGRVXXXXXXXXXXXXXXXNRNSGQLRFGGRNKPWVKPVQL 208
             VD+E  R                 + SGQLRFGGR++P+ KP+ L
Sbjct:   124 VDYELERTLRGWIPRRLGGGLGGKKESGQLRFGGRDRPFRKPINL 168

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISO

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0005689 "U12-type spliceosomal complex" evidence=IEA;ISO

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

UNIPROTKB|Q5U1W5 Snrnp35 "U11/U12 small nuclear ribonucleoprotein 35 kDa protein" [Rattus norvegicus (taxid:10116)]

 Score = 354 (129.7 bits), Expect = 2.3e-32, P = 2.3e-32
 Identities = 73/165 (44%), Positives = 97/165 (58%)

Query:    45 WYPYCITYDPIQAGSIDGTDTIPHDRAILRALRSTYKPHTSST-DPTRTLFIGRLNKNSR 103
             W P    YDP++AGSIDGTD  PHDRA+ RA+ + Y P+   T DP  TLF+ RLN  ++
Sbjct:     4 WMPIAKEYDPLKAGSIDGTDEDPHDRAVWRAMLARYVPNKGVTGDPLLTLFVARLNSQTK 63

Query:   104 EADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEII 163
             E  L++ F+ YG +  +R+VRD VTG SK Y F+EY  E+A L A R  +       EI 
Sbjct:    64 EEKLKEVFSRYGDIRRLRLVRDLVTGFSKGYAFIEYKEERALLKAYRDADGLVIDQHEIF 123

Query:   164 VDFECGRVXXXXXXXXXXXXXXXNRNSGQLRFGGRNKPWVKPVQL 208
             VD+E  R                 + SGQLRFGGR++P+ KP+ L
Sbjct:   124 VDYELERTLRGWIPRRLGGGLGGKKESGQLRFGGRDRPFRKPINL 168

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|Q1LZH0 SNRNP35 "U11/U12 small nuclear ribonucleoprotein 35 kDa protein" [Bos taurus (taxid:9913)]

 Score = 351 (128.6 bits), Expect = 4.7e-32, P = 4.7e-32
 Identities = 72/165 (43%), Positives = 97/165 (58%)

Query:    45 WYPYCITYDPIQAGSIDGTDTIPHDRAILRALRSTYKPHTSST-DPTRTLFIGRLNKNSR 103
             W P    YDP++AGSIDGTD  PHDRA+ RA+ + Y P+   T DP  TLF+ RLN  ++
Sbjct:     4 WMPIAKEYDPLKAGSIDGTDEDPHDRAVWRAMLARYTPNKGVTGDPLLTLFVARLNLQTK 63

Query:   104 EADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEII 163
             E  L++ F+ YG +  +R+VRD VTG SK Y F+EY  E++ L A R  +       EI 
Sbjct:    64 EEKLKEVFSRYGDIRRLRLVRDLVTGFSKGYAFIEYKDERSLLKAYRDADGLVIDQHEIF 123

Query:   164 VDFECGRVXXXXXXXXXXXXXXXNRNSGQLRFGGRNKPWVKPVQL 208
             VD+E  R                 + SGQLRFGGR++P+ KP+ L
Sbjct:   124 VDYELERTLKGWIPRRLGGGLGGKKESGQLRFGGRDRPFRKPINL 168

GO:0005689 "U12-type spliceosomal complex" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

MGI|MGI:1923417 Snrnp35 "small nuclear ribonucleoprotein 35 (U11/U12)" [Mus musculus (taxid:10090)]

 Score = 350 (128.3 bits), Expect = 6.0e-32, P = 6.0e-32
 Identities = 72/165 (43%), Positives = 97/165 (58%)

Query:    45 WYPYCITYDPIQAGSIDGTDTIPHDRAILRALRSTYKPHTSST-DPTRTLFIGRLNKNSR 103
             W P    YDP++AGSIDGTD  PHDRA+ RA+ + Y P+   T DP  TLF+ RLN  ++
Sbjct:     4 WMPIAKEYDPLKAGSIDGTDEDPHDRAVWRAMLARYVPNKGVTGDPLLTLFVARLNLQTK 63

Query:   104 EADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEII 163
             E  L++ F+ YG +  +R+VRD VTG SK Y F+EY  E+A + A R  +       EI 
Sbjct:    64 EEKLKEVFSRYGDIRRLRLVRDLVTGFSKGYAFIEYKEERALMKAYRDADGLVIDQHEIF 123

Query:   164 VDFECGRVXXXXXXXXXXXXXXXNRNSGQLRFGGRNKPWVKPVQL 208
             VD+E  R                 + SGQLRFGGR++P+ KP+ L
Sbjct:   124 VDYELERTLRGWIPRRLGGGLGGKKESGQLRFGGRDRPFRKPINL 168

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003674 "molecular_function" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISS

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0005689 "U12-type spliceosomal complex" evidence=ISO

GO:0006397 "mRNA processing" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0008380 "RNA splicing" evidence=IEA

UNIPROTKB|I3LN96 SNRNP35 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 347 (127.2 bits), Expect = 1.3e-31, P = 1.3e-31
 Identities = 72/165 (43%), Positives = 97/165 (58%)

Query:    45 WYPYCITYDPIQAGSIDGTDTIPHDRAILRALRSTYKPHTSST-DPTRTLFIGRLNKNSR 103
             W P    YDP++AGSIDGTD  PHDRAI RA+ + Y P+   T DP  TLF+ RLN  ++
Sbjct:     4 WVPIAKEYDPLKAGSIDGTDEDPHDRAIWRAMLARYTPNKGVTGDPLLTLFVARLNLQTK 63

Query:   104 EADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEII 163
             E  L++ F+ YG +  +R+VRD VTG SK Y F+EY  E++ L A R  +       EI 
Sbjct:    64 EEKLKEVFSRYGDIRRLRLVRDLVTGFSKGYAFIEYKEERSLLKAYRDADGLVIDQHEIF 123

Query:   164 VDFECGRVXXXXXXXXXXXXXXXNRNSGQLRFGGRNKPWVKPVQL 208
             VD+E  R                 + SGQLRFGGR++P+ +P+ L
Sbjct:   124 VDYELERTLKGWIPRRLGGGLGGKKESGQLRFGGRDRPFRQPINL 168

GO:0005689 "U12-type spliceosomal complex" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|F1P6U2 SNRNP35 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 346 (126.9 bits), Expect = 1.6e-31, P = 1.6e-31
 Identities = 71/165 (43%), Positives = 97/165 (58%)

Query:    45 WYPYCITYDPIQAGSIDGTDTIPHDRAILRALRSTYKPHTSST-DPTRTLFIGRLNKNSR 103
             W P    YDP++AGSIDGTD  PHDRA+ RA+ + Y P+   T DP  TLF+ RLN  ++
Sbjct:     4 WMPIAKEYDPLKAGSIDGTDEDPHDRAVWRAMLARYTPNKGVTGDPLLTLFVARLNLQTK 63

Query:   104 EADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEII 163
             E  L++ F+ YG +  +R+VRD VTG SK Y F+EY  E++ + A R  +       EI 
Sbjct:    64 EEKLKEVFSRYGDIRRLRLVRDLVTGLSKGYAFIEYKEERSLIKAYRDADGLVIDQHEIF 123

Query:   164 VDFECGRVXXXXXXXXXXXXXXXNRNSGQLRFGGRNKPWVKPVQL 208
             VD+E  R                 + SGQLRFGGR++P+ KP+ L
Sbjct:   124 VDYELERTLKGWIPRRLGGGLGGKKESGQLRFGGRDRPFRKPINL 168

GO:0005689 "U12-type spliceosomal complex" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|Q16560 SNRNP35 "U11/U12 small nuclear ribonucleoprotein 35 kDa protein" [Homo sapiens (taxid:9606)]

 Score = 343 (125.8 bits), Expect = 3.3e-31, P = 3.3e-31
 Identities = 71/165 (43%), Positives = 96/165 (58%)

Query:    45 WYPYCITYDPIQAGSIDGTDTIPHDRAILRALRSTYKPHTSST-DPTRTLFIGRLNKNSR 103
             W P    YDP++AGSIDGTD  PHDRA+ RA+ + Y P+     DP  TLF+ RLN  ++
Sbjct:     4 WMPIAKEYDPLKAGSIDGTDEDPHDRAVWRAMLARYVPNKGVIGDPLLTLFVARLNLQTK 63

Query:   104 EADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEII 163
             E  L++ F+ YG +  +R+VRD VTG SK Y F+EY  E+A + A R  +       EI 
Sbjct:    64 EDKLKEVFSRYGDIRRLRLVRDLVTGFSKGYAFIEYKEERAVIKAYRDADGLVIDQHEIF 123

Query:   164 VDFECGRVXXXXXXXXXXXXXXXNRNSGQLRFGGRNKPWVKPVQL 208
             VD+E  R                 + SGQLRFGGR++P+ KP+ L
Sbjct:   124 VDYELERTLKGWIPRRLGGGLGGKKESGQLRFGGRDRPFRKPINL 168

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005689 "U12-type spliceosomal complex" evidence=IDA

GO:0008380 "RNA splicing" evidence=IC

ZFIN|ZDB-GENE-050706-77 snrnp35 "small nuclear ribonucleoprotein 35 (U11/U12)" [Danio rerio (taxid:7955)]

 Score = 336 (123.3 bits), Expect = 1.8e-30, P = 1.8e-30
 Identities = 70/169 (41%), Positives = 95/169 (56%)

Query:    45 WYPYCITYDPIQAGSIDGTDTIPHDRAILRALRSTYKPHTSST-DPTRTLFIGRLNKNSR 103
             W P    YDP++AGSIDGTD  PHD  + RA+ + YKP+     DP  TLF+ RLN  + 
Sbjct:     3 WSPVAKVYDPLKAGSIDGTDVEPHDAGVWRAMLARYKPNRGVCGDPDLTLFVARLNPQTT 62

Query:   104 EADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEII 163
             E  L   F+++G +  +R+VRD VTG SKRY F+EY  E++   A R  N+      E++
Sbjct:    63 EEKLRDVFSKFGDIRRLRLVRDVVTGFSKRYAFIEYKEERSLKRAWRDANKLILDQYELL 122

Query:   164 VDFECGRVXXXXXXXXXXXXXXXNRNSGQLRFGGRNKPWVKPVQLMNER 212
             VD E  R                 + SGQLRFGGR++P+ KP+ L   R
Sbjct:   123 VDVEQERTLPGWRPRRLGGGQGGQKESGQLRFGGRDRPFRKPINLSTRR 171

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0005634 "nucleus" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

TAIR|locus:2058141 AT2G43370 [Arabidopsis thaliana (taxid:3702)]

 Score = 308 (113.5 bits), Expect = 1.7e-27, P = 1.7e-27
 Identities = 71/186 (38%), Positives = 100/186 (53%)

Query:    36 SSSGQTVKYWYPYCITYDPIQAGSIDGTDTIPHDRAILRAL----RSTYKPHTSST---D 88
             S  G  V     Y  +Y PIQAGSIDGTD  PHD  + RAL       Y P   S    D
Sbjct:     2 SGGGNNVVNKVFYATSYHPIQAGSIDGTDVAPHDNGVRRALLCYNAGLYDPSGDSKAVGD 61

Query:    89 PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAA 148
             P  TLF+GRL+ ++ E  L +  ++YG++ ++R+VR  VTG S+ YGF+EY+ EK  L A
Sbjct:    62 PYCTLFVGRLSHHTTEDTLREVMSKYGRIKNLRLVRHIVTGASRGYGFVEYETEKEMLRA 121

Query:   149 IRALNRQNFQGSEIIVDFECGRVXXXXXXXXXXXXXXXNRNSGQLRFGGRNKPWVKPVQL 208
                 +     G EIIVD+   ++                + SGQLRFGGR++P+  P++ 
Sbjct:   122 YEDAHHSLIDGREIIVDYNRQQLMPGWIPRRLGGGLGGRKESGQLRFGGRDRPFRAPLRP 181

Query:   209 MNEREL 214
             +   +L
Sbjct:   182 IPHEDL 187

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM;IDA

GO:0008150 "biological_process" evidence=ND

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

GO:0008284 "positive regulation of cell proliferation" evidence=RCA

GO:0048573 "photoperiodism, flowering" 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

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q1LZH0	U1SBP_BOVIN	No assigned EC number	0.5090	0.7288	0.6693	yes	N/A
Q9D384	U1SBP_MOUSE	No assigned EC number	0.5090	0.7288	0.6721	yes	N/A
Q4KMD3	U1SBP_DANRE	No assigned EC number	0.4911	0.7466	0.8076	yes	N/A
Q16560	U1SBP_HUMAN	No assigned EC number	0.5030	0.7288	0.6666	yes	N/A
Q5U1W5	U1SBP_RAT	No assigned EC number	0.5151	0.7288	0.6721	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	225
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	3e-39
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	4e-23
smart00360	73	smart00360, RRM, RNA recognition motif	1e-21
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	6e-18
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	2e-17
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	2e-16
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	4e-16
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	3e-15
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	6e-15
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	7e-14
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	1e-13
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	2e-12
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	2e-12
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	2e-12
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	2e-12
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	8e-12
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	1e-11
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	1e-11
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	3e-11
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	9e-11
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	1e-10
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	1e-10
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	1e-10
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	1e-10
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	2e-10
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	3e-10
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	3e-10
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	7e-10
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	1e-09
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	1e-09
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	2e-09
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	3e-09
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	3e-09
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	3e-09
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	5e-09
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	5e-09
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	6e-09
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	6e-09
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	1e-08
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	1e-08
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	1e-08
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	1e-08
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	1e-08
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	1e-08
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	2e-08
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	2e-08
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	2e-08
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	2e-08
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	3e-08
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	3e-08
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	3e-08
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	4e-08
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	4e-08
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	4e-08
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	6e-08
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	7e-08
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	9e-08
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	1e-07
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	1e-07
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	2e-07
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	2e-07
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	2e-07
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	2e-07
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	2e-07
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	3e-07
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	3e-07
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	3e-07
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	3e-07
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	4e-07
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	4e-07
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	4e-07
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	6e-07
cd12636	81	cd12636, RRM2_Bruno_like, RNA recognition motif 2	6e-07
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	7e-07
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	8e-07
cd12244	79	cd12244, RRM2_MSSP, RNA recognition motif 2 in the	8e-07
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	8e-07
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	9e-07
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	9e-07
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	9e-07
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	1e-06
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-06
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-06
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	1e-06
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	2e-06
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	2e-06
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	2e-06
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	2e-06
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	2e-06
cd12678	74	cd12678, RRM_SLTM, RNA recognition motif in Scaffo	3e-06
cd12594	74	cd12594, RRM1_SRSF4, RNA recognition motif 1 in ve	4e-06
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	4e-06
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	4e-06
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	5e-06
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	5e-06
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	5e-06
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	6e-06
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	6e-06
cd12358	73	cd12358, RRM1_VICKZ, RNA recognition motif 1 in th	6e-06
cd12631	84	cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif	7e-06
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	7e-06
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	7e-06
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	8e-06
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	9e-06
cd12596	70	cd12596, RRM1_SRSF6, RNA recognition motif 1 in ve	9e-06
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	9e-06
cd12635	81	cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2	1e-05
cd12679	76	cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in	1e-05
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	1e-05
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	1e-05
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	1e-05
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	2e-05
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	2e-05
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	2e-05
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	2e-05
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	2e-05
cd12773	84	cd12773, RRM2_HuR, RNA recognition motif 2 in vert	2e-05
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	2e-05
cd12466	70	cd12466, RRM2_AtRSp31_like, RNA recognition motif	2e-05
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	2e-05
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	2e-05
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	2e-05
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	2e-05
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	3e-05
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	3e-05
cd12573	79	cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA	3e-05
cd12471	75	cd12471, RRM1_MSSP2, RNA recognition motif 1 in ve	3e-05
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	3e-05
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	3e-05
cd12610	84	cd12610, RRM1_SECp43, RNA recognition motif 1 in t	4e-05
cd12360	78	cd12360, RRM_cwf2, RNA recognition motif in yeast	4e-05
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	4e-05
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	4e-05
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	4e-05
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	5e-05
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	5e-05
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	5e-05
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	6e-05
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	6e-05
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	6e-05
cd12494	72	cd12494, RRM3_hnRNPR, RNA recognition motif 3 in v	6e-05
cd12470	86	cd12470, RRM1_MSSP1, RNA recognition motif 1 in ve	6e-05
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	6e-05
cd12615	74	cd12615, RRM1_TIA1, RNA recognition motif 1 in nuc	7e-05
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	7e-05
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	9e-05
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	1e-04
cd12551	77	cd12551, RRM_II_PABPN1L, RNA recognition motif in	1e-04
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	1e-04
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	1e-04
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	1e-04
cd12484	78	cd12484, RRM1_RBM46, RNA recognition motif 1 found	1e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-04
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	2e-04
cd12401	76	cd12401, RRM_eIF4H, RNA recognition motif in eukar	2e-04
cd12556	85	cd12556, RRM2_RBM15B, RNA recognition motif 2 in p	2e-04
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	2e-04
cd12364	81	cd12364, RRM_RDM1, RNA recognition motif of RAD52	2e-04
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	2e-04
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	2e-04
cd12495	72	cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in v	2e-04
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	3e-04
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	3e-04
cd12595	70	cd12595, RRM1_SRSF5, RNA recognition motif 1 in ve	3e-04
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	3e-04
cd12474	86	cd12474, RRM2_MSSP2, RNA recognition motif 2 found	3e-04
cd12555	87	cd12555, RRM2_RBM15, RNA recognition motif 2 in ve	3e-04
cd12634	81	cd12634, RRM2_CELF1_2, RNA recognition motif 2 in	3e-04
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	3e-04
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	4e-04
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	4e-04
cd12472	80	cd12472, RRM1_RBMS3, RNA recognition motif 1 found	4e-04
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	4e-04
cd12416	98	cd12416, RRM4_RBM28_like, RNA recognition motif 4	4e-04
cd12537	85	cd12537, RRM1_RBM23, RNA recognition motif 1 in ve	4e-04
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	4e-04
cd12473	85	cd12473, RRM2_MSSP1, RNA recognition motif 2 found	5e-04
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	5e-04
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	5e-04
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	6e-04
cd12234	72	cd12234, RRM1_AtRSp31_like, RNA recognition motif	6e-04
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	6e-04
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	6e-04
cd12605	69	cd12605, RRM_RALYL, RNA recognition motif in verte	6e-04
cd12607	67	cd12607, RRM2_RBM4, RNA recognition motif 2 in ver	6e-04
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	8e-04
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	0.001
cd12536	85	cd12536, RRM1_RBM39, RNA recognition motif 1 in ve	0.001
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	0.001
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	0.001
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	0.001
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	0.001
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	0.001
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	0.001
cd12529	71	cd12529, RRM2_MEI2_like, RNA recognition motif 2 i	0.001
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	0.002
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	0.002
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	0.002
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	0.002
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	0.002
cd12645	81	cd12645, RRM_SRSF3, RNA recognition motif in verte	0.002
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	0.002
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	0.002
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	0.003
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	0.003
cd12475	88	cd12475, RRM2_RBMS3, RNA recognition motif 2 found	0.003
cd12331	79	cd12331, RRM_NRD1_SEB1_like, RNA recognition motif	0.003
cd12582	80	cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in	0.004
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	0.004
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	0.004
cd12622	74	cd12622, RRM3_PUB1, RNA recognition motif 3 in yea	0.004

>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 =  130 bits (328), Expect = 3e-39
 Identities = 47/93 (50%), Positives = 60/93 (64%)

Query: 88  DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLA 147
           DP  TLF+GRL+  + E  L + F+ YG +  +R+VRD VTG SK Y F+EY+ E+  L 
Sbjct: 1   DPYLTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALR 60

Query: 148 AIRALNRQNFQGSEIIVDFECGRVLPGWKPRRL 180
           A R  ++    GSEI VDFE  R LPGW PRRL
Sbjct: 61  AYRDAHKLVIDGSEIFVDFERERTLPGWIPRRL 93

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

 Score = 88.8 bits (221), Expect = 4e-23
 Identities = 36/90 (40%), Positives = 56/90 (62%)

Query: 91  RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
           +TLF+ RLN ++ E+ L + F EYG +  +R+VRD  TG  + Y F+E++ E+   AA +
Sbjct: 2   KTLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYK 61

Query: 151 ALNRQNFQGSEIIVDFECGRVLPGWKPRRL 180
             + +   G  ++VD E GR + GW PRRL
Sbjct: 62  YADGKKIDGRRVLVDVERGRTVKGWLPRRL 91

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|214636 smart00360, RRM, RNA recognition motif

 Score = 84.2 bits (209), Expect = 1e-21
 Identities = 30/73 (41%), Positives = 47/73 (64%)

Query: 92  TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
           TLF+G L  ++ E +L + F+++GKV SVR+VRD  TG SK + F+E++ E+    A+ A
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 152 LNRQNFQGSEIIV 164
           LN +   G  + 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 = 75.0 bits (185), Expect = 6e-18
 Identities = 28/73 (38%), Positives = 42/73 (57%)

Query: 92  TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
            L++G L  N  E DL+  F ++G+V S RV+ D  TG S+ +GF+E +  +   AAI  
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 152 LNRQNFQGSEIIV 164
           LN  +F G  + V
Sbjct: 61  LNGTDFGGRTLTV 73

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 = 73.1 bits (180), Expect = 2e-17
 Identities = 26/73 (35%), Positives = 45/73 (61%), Gaps = 1/73 (1%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           LF+G L  ++ E DL + F+++G++ SVR+VRD   G SK + F+E++  +    A+ AL
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRD-KDGKSKGFAFVEFESPEDAEKALEAL 59

Query: 153 NRQNFQGSEIIVD 165
           N +   G ++ 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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 70.7 bits (174), Expect = 2e-16
 Identities = 27/70 (38%), Positives = 45/70 (64%), Gaps = 1/70 (1%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           LF+G L  ++ E DL+  F+++G + S+R+VRD  TG SK + F+E++ E+    A+ AL
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDE-TGRSKGFAFVEFEDEEDAEKALEAL 59

Query: 153 NRQNFQGSEI 162
           N +   G E+
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|240681 cd12235, RRM_PPIL4, RNA recognition motif in peptidyl-prolyl cis-trans isomerase-like 4 (PPIase) and similar proteins

 Score = 70.4 bits (173), Expect = 4e-16
 Identities = 27/78 (34%), Positives = 43/78 (55%)

Query: 89  PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAA 148
           P   LF+ +LN  + + DLE  F+ +GK+ S  V+RD  TG S +Y F+E++ ++ C  A
Sbjct: 2   PENVLFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEA 61

Query: 149 IRALNRQNFQGSEIIVDF 166
              ++        I VDF
Sbjct: 62  YFKMDNVLIDDRRIHVDF 79

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

 Score = 73.1 bits (178), Expect = 3e-15
 Identities = 31/97 (31%), Positives = 49/97 (50%)

Query: 77  RSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGF 136
             + K    S +   TLF+G L  +  E DL + F ++G V  VR+VRD  TG S+ + F
Sbjct: 102 SESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAF 161

Query: 137 LEYDCEKACLAAIRALNRQNFQGSEIIVDFECGRVLP 173
           +E++ E++   AI  LN +  +G  + V        P
Sbjct: 162 VEFESEESAEKAIEELNGKELEGRPLRVQKAQPASQP 198

Length = 306

>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 = 66.5 bits (163), Expect = 6e-15
 Identities = 25/72 (34%), Positives = 33/72 (45%), Gaps = 8/72 (11%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           LF+G L   +   +L   F +YG V    VV        K YGF+  + E+    AI+AL
Sbjct: 2   LFVGNLPDATTSEELRALFEKYGTVTECDVV--------KNYGFVHMEEEEDAEDAIKAL 53

Query: 153 NRQNFQGSEIIV 164
           N   F G  I V
Sbjct: 54  NGYEFMGKRINV 65

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

>gnl|CDD|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 = 64.2 bits (157), Expect = 7e-14
 Identities = 25/74 (33%), Positives = 45/74 (60%)

Query: 92  TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
            LF+  L+  + E +LE  F+++G+V  V +++D  TG S+ +GF+ ++  +   AAIR 
Sbjct: 3   KLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRD 62

Query: 152 LNRQNFQGSEIIVD 165
           LN +  +G  I V+
Sbjct: 63  LNGKELEGRVIKVE 76

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|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 = 63.8 bits (156), Expect = 1e-13
 Identities = 29/73 (39%), Positives = 42/73 (57%)

Query: 94  FIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALN 153
           F+G +  ++ E  L + F+E G V+S R+V D  TG  K YGF E++  +   +AIR LN
Sbjct: 2   FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLN 61

Query: 154 RQNFQGSEIIVDF 166
              F G  + VDF
Sbjct: 62  GYEFNGRALRVDF 74

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

 Score = 60.8 bits (148), Expect = 2e-12
 Identities = 27/75 (36%), Positives = 42/75 (56%), Gaps = 1/75 (1%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVI-SVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
           LFIG L+    E  L   F+ +G ++ + +++RD  TG+SK + F+ YD  +A  AAI A
Sbjct: 4   LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEA 63

Query: 152 LNRQNFQGSEIIVDF 166
           +N Q      I V +
Sbjct: 64  MNGQYLCNRPITVSY 78

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

 Score = 60.5 bits (147), Expect = 2e-12
 Identities = 24/75 (32%), Positives = 44/75 (58%)

Query: 92  TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
           TLF+G L+ +  +  L+  F ++G V+  RV+ D  TG S+ +G+++++  +    AI A
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 152 LNRQNFQGSEIIVDF 166
           ++ +   G  I VDF
Sbjct: 61  MDGKELDGRPINVDF 75

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|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 = 60.3 bits (147), Expect = 2e-12
 Identities = 28/61 (45%), Positives = 37/61 (60%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           LFI  L     + DL Q FA +G VIS +V  D  TG SK +GF+ YD  ++  AAI+A+
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 153 N 153
           N
Sbjct: 61  N 61

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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 59.9 bits (146), Expect = 2e-12
 Identities = 21/70 (30%), Positives = 36/70 (51%), Gaps = 2/70 (2%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           L++  L  +  E DL + F+ YGKV  VR+VR+      + + F+E+   +   AA++ L
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRN--KDRPRGFAFVEFASPEDAEAALKKL 58

Query: 153 NRQNFQGSEI 162
           N     G  +
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 = 58.7 bits (143), Expect = 8e-12
 Identities = 23/61 (37%), Positives = 35/61 (57%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           LF+G+L K + E D+   F EYG +  V ++RD  TG SK   F+++   +    AI AL
Sbjct: 2   LFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEAL 61

Query: 153 N 153
           +
Sbjct: 62  H 62

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

 Score = 58.3 bits (142), Expect = 1e-11
 Identities = 23/65 (35%), Positives = 36/65 (55%), Gaps = 3/65 (4%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           L++G L+ +  EA L + F+  G V+S+RV RD +T  S  Y ++ +        A RAL
Sbjct: 2   LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPA---DAERAL 58

Query: 153 NRQNF 157
           +  NF
Sbjct: 59  DTLNF 63

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

 Score = 58.0 bits (141), Expect = 1e-11
 Identities = 24/70 (34%), Positives = 38/70 (54%)

Query: 91  RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
             ++I  L  N+ + DLE+    +GK+IS + + D  T   K YGF+++D  +A L AI 
Sbjct: 1   TNVYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIE 60

Query: 151 ALNRQNFQGS 160
            LN +  Q  
Sbjct: 61  GLNGRGVQAQ 70

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

 Score = 58.9 bits (142), Expect = 3e-11
 Identities = 35/105 (33%), Positives = 53/105 (50%), Gaps = 6/105 (5%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           LFIG L+  + +A L  AFA +G V+  +V+ D  TG S+ +GF+ ++ E A  AAI  +
Sbjct: 37  LFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEM 96

Query: 153 NRQNFQGSEIIVDFECGR------VLPGWKPRRLGGGWGGNRNSG 191
           + +   G  I V+    R         G      GGG+GG  + G
Sbjct: 97  DGKELNGRHIRVNPANDRPSAPRAYGGGGGYSGGGGGYGGGGDGG 141

Length = 144

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

 Score = 56.1 bits (136), Expect = 9e-11
 Identities = 26/82 (31%), Positives = 50/82 (60%), Gaps = 5/82 (6%)

Query: 91  RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
           RT+FI  L  ++ E +L++ F+++G+V   R+V+D +TGHSK   F+++  +++    + 
Sbjct: 1   RTVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLE 60

Query: 151 ALNRQNFQGSEIIVDFECGRVL 172
           A +  N + S + +D   GR L
Sbjct: 61  AAD--NAEDSGLSLD---GRRL 77

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|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 = 55.6 bits (134), Expect = 1e-10
 Identities = 27/73 (36%), Positives = 45/73 (61%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           LFIG L+ ++ E  LEQ F++YG++  V VV+D  T  S+ +GF+ ++       A+ A+
Sbjct: 3   LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAM 62

Query: 153 NRQNFQGSEIIVD 165
           N ++  G +I VD
Sbjct: 63  NGKSVDGRQIRVD 75

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

 Score = 55.5 bits (134), Expect = 1e-10
 Identities = 27/74 (36%), Positives = 39/74 (52%), Gaps = 8/74 (10%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEY----DCEKACLAA 148
           +F+G L+       L  AFA +G++   RVV+D  TG SK YGF+ +    D E     A
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAEN----A 57

Query: 149 IRALNRQNFQGSEI 162
           I+++N Q   G  I
Sbjct: 58  IQSMNGQWLGGRAI 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|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 = 55.2 bits (133), Expect = 1e-10
 Identities = 28/74 (37%), Positives = 42/74 (56%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           +F+G +   + E  L+  F+E G V+S R+V D  TG  K YGF EY  ++  L+A+R L
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 153 NRQNFQGSEIIVDF 166
           N     G ++ VD 
Sbjct: 61  NGYELNGRQLRVDN 74

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

 Score = 55.4 bits (134), Expect = 1e-10
 Identities = 20/73 (27%), Positives = 41/73 (56%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           L++  L+  ++ ADL+Q F++YGKV+  ++V +  +  ++ +GF+     +     I+ L
Sbjct: 2   LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQHL 61

Query: 153 NRQNFQGSEIIVD 165
           +R    G  I V+
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|240835 cd12389, RRM2_RAVER, RNA recognition motif 2 in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins

 Score = 55.0 bits (133), Expect = 2e-10
 Identities = 23/76 (30%), Positives = 35/76 (46%), Gaps = 2/76 (2%)

Query: 92  TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKAC-LAAIR 150
            L +G L     +    +  + +G V    +V    TG SK YGF+EY   KA  L A  
Sbjct: 1   LLCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEY-ASKASALKAKN 59

Query: 151 ALNRQNFQGSEIIVDF 166
            L+ +   G ++ VD+
Sbjct: 60  QLDGKQIGGRKLQVDW 75

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

 Score = 54.5 bits (132), Expect = 3e-10
 Identities = 19/74 (25%), Positives = 40/74 (54%), Gaps = 1/74 (1%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLA-AIRA 151
           LF+G L+ +  E+DLE+ F+ +G V  V +++    G  + + +++    +A L      
Sbjct: 2   LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKST 61

Query: 152 LNRQNFQGSEIIVD 165
           LN   ++GS + ++
Sbjct: 62  LNGTKWKGSVLKIE 75

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

 Score = 54.6 bits (132), Expect = 3e-10
 Identities = 26/72 (36%), Positives = 43/72 (59%)

Query: 92  TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
           TL++G L     EA +  AFAE G+V SV+++R+  TG S  YGF+E+   +A   A+++
Sbjct: 1   TLWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQS 60

Query: 152 LNRQNFQGSEII 163
           LN +    ++  
Sbjct: 61  LNGKPIPNTQQR 72

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

 Score = 53.6 bits (129), Expect = 7e-10
 Identities = 21/62 (33%), Positives = 38/62 (61%)

Query: 92  TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
            ++IG L     E +L++ F+++G V +VRV R   TG+SK YGF+++   +    A ++
Sbjct: 1   VIYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKS 60

Query: 152 LN 153
           +N
Sbjct: 61  MN 62

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|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family

 Score = 53.4 bits (129), Expect = 1e-09
 Identities = 25/73 (34%), Positives = 42/73 (57%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           ++IG L     E D+   F++YG+++ + +VRD  TG SK + FL Y+ +++ + A+  L
Sbjct: 12  IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNL 71

Query: 153 NRQNFQGSEIIVD 165
           N     G  I VD
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|241081 cd12637, RRM2_FCA, RNA recognition motif 2 in plant flowering time control protein FCA and similar proteins

 Score = 52.9 bits (127), Expect = 1e-09
 Identities = 23/61 (37%), Positives = 40/61 (65%), Gaps = 1/61 (1%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           LF+G LNK + E ++E+ F+ YG+V  + ++RD +   S+   F++Y  ++   AAI+AL
Sbjct: 2   LFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMK-QSRGCAFVKYSSKEMAQAAIKAL 60

Query: 153 N 153
           N
Sbjct: 61  N 61

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

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

 Score = 52.6 bits (127), Expect = 2e-09
 Identities = 18/72 (25%), Positives = 36/72 (50%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           L +G+L +N  +  L++ F+ YG V  V +  D      + Y ++E++  +    AI+ +
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 153 NRQNFQGSEIIV 164
           +     G E+ V
Sbjct: 61  DGGQIDGQEVTV 72

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

 Score = 52.2 bits (126), Expect = 3e-09
 Identities = 24/74 (32%), Positives = 43/74 (58%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           +F+  +++ ++E D+   FAE+G++ ++ +  D  TG  K Y  +EY+ +K   AAI  L
Sbjct: 9   IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68

Query: 153 NRQNFQGSEIIVDF 166
           N +   G  I VD+
Sbjct: 69  NGKELLGQTISVDW 82

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

 Score = 51.9 bits (125), Expect = 3e-09
 Identities = 15/76 (19%), Positives = 42/76 (55%), Gaps = 2/76 (2%)

Query: 91  RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
            ++F+G+L+ +  + +L + F+ +GK++ V ++      H+  + F++++ E+A   A+ 
Sbjct: 4   YSIFVGQLSPDVTKEELNERFSRHGKILEVNLI--KRANHTNAFAFIKFEREQAAARAVE 61

Query: 151 ALNRQNFQGSEIIVDF 166
           + N    +   + V +
Sbjct: 62  SENHSMLKNKTMHVQY 77

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

 Score = 51.9 bits (125), Expect = 3e-09
 Identities = 27/76 (35%), Positives = 42/76 (55%), Gaps = 2/76 (2%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           L++  L K   + +LE  F+ YG++I+ R++ D VTG S+  GF+ +D       AI+AL
Sbjct: 3   LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL 62

Query: 153 NRQNFQGS--EIIVDF 166
           N     G+   I V F
Sbjct: 63  NGTIPPGATEPITVKF 78

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

 Score = 50.8 bits (122), Expect = 5e-09
 Identities = 25/73 (34%), Positives = 45/73 (61%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           LF+G L+ ++ E  + +AF EYG++ SVR+  D  +G  K +G++E+  ++A  AA+ AL
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 153 NRQNFQGSEIIVD 165
              +  G  + +D
Sbjct: 61  GGTDLLGRPVRLD 73

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

 Score = 51.3 bits (123), Expect = 5e-09
 Identities = 23/74 (31%), Positives = 37/74 (50%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           L +  L +N  + ++   F+  G++ S +++RD VTG S  YGF+ Y   +    AI  L
Sbjct: 4   LIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTL 63

Query: 153 NRQNFQGSEIIVDF 166
           N    Q   I V +
Sbjct: 64  NGLRLQNKTIKVSY 77

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

 Score = 51.0 bits (122), Expect = 6e-09
 Identities = 27/66 (40%), Positives = 38/66 (57%), Gaps = 2/66 (3%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           LFI  L +   +A+L Q F  +G VIS +V  D  T  SK +GF+ +D   +  AAI+A+
Sbjct: 7   LFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAM 66

Query: 153 NRQNFQ 158
           N   FQ
Sbjct: 67  N--GFQ 70

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

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

 Score = 50.7 bits (122), Expect = 6e-09
 Identities = 21/57 (36%), Positives = 33/57 (57%), Gaps = 3/57 (5%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEY---DCEKACL 146
           L++G L+ N  E DL   F  +G++  V++ RD  TG SK YGF+++   +  K  L
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKAL 57

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|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 = 50.0 bits (120), Expect = 1e-08
 Identities = 18/67 (26%), Positives = 32/67 (47%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           LF+  L   + E +L + F  +G++  V +  D  T  SK + F+ +   +  + A   L
Sbjct: 2   LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61

Query: 153 NRQNFQG 159
           +   FQG
Sbjct: 62  DGSIFQG 68

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

 Score = 50.2 bits (121), Expect = 1e-08
 Identities = 23/84 (27%), Positives = 42/84 (50%), Gaps = 7/84 (8%)

Query: 89  PTRTLFIGRLNKNSREADLEQAFAEYGK--VISVRVVRDFVTGHSKRYGFLEY----DCE 142
           PT TL +  L+  + E D+ QA +      +  VR++RD +TG S+ + F+E+    D  
Sbjct: 1   PTNTLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDAT 60

Query: 143 KACLAAIRALNRQNFQGSEIIVDF 166
           +  + A+  L+     G  + V +
Sbjct: 61  QW-MDALNNLDPFVIDGRVVRVSY 83

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

 Score = 50.0 bits (120), Expect = 1e-08
 Identities = 22/76 (28%), Positives = 36/76 (47%)

Query: 91  RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
             L +  L ++  + +L   F   G + S ++VRD +TG S  YGF++Y  E     AI 
Sbjct: 1   TNLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAIN 60

Query: 151 ALNRQNFQGSEIIVDF 166
            LN    +   + V +
Sbjct: 61  TLNGFEIRNKRLKVSY 76

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

 Score = 50.0 bits (120), Expect = 1e-08
 Identities = 27/74 (36%), Positives = 44/74 (59%), Gaps = 2/74 (2%)

Query: 92  TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
           TLF+G L+ ++ + DLE+ F E G+V+ VR+ +D   G SK +G +E+  E+    A+  
Sbjct: 1   TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDD-DGRSKGFGHVEFATEEGAQKALE- 58

Query: 152 LNRQNFQGSEIIVD 165
            + +   G EI VD
Sbjct: 59  KSGEELLGREIRVD 72

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

 Score = 50.0 bits (120), Expect = 1e-08
 Identities = 27/78 (34%), Positives = 41/78 (52%), Gaps = 6/78 (7%)

Query: 92  TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFL---EYDCEKACLAA 148
            +F+  L  ++ E+ L Q F+ +G V +V+V+RD  T   K YGF+    Y  E+A   A
Sbjct: 3   CIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNY--EEAYS-A 59

Query: 149 IRALNRQNFQGSEIIVDF 166
           I +LN     G  + V F
Sbjct: 60  IASLNGYRLGGRVLQVSF 77

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

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

 Score = 50.0 bits (119), Expect = 1e-08
 Identities = 27/76 (35%), Positives = 44/76 (57%), Gaps = 2/76 (2%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           L++  L K   + ++EQ F++YG++I+ R++ D VTG S+  GF+ +D       AI+ L
Sbjct: 4   LYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIKGL 63

Query: 153 NRQNFQGSE--IIVDF 166
           N Q   G+   I V F
Sbjct: 64  NGQKPLGAAEPITVKF 79

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

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

 Score = 50.1 bits (119), Expect = 2e-08
 Identities = 25/68 (36%), Positives = 41/68 (60%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           L++  L K   + +LEQ F++YG++I+ R++ D VTG S+  GF+ +D       AI+ L
Sbjct: 5   LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 64

Query: 153 NRQNFQGS 160
           N Q   G+
Sbjct: 65  NGQKPSGA 72

This subgroup corresponds to the RRM2 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells and also regulates the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

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

 Score = 49.9 bits (119), Expect = 2e-08
 Identities = 25/68 (36%), Positives = 43/68 (63%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           L++  L K   + +LEQ F++YG++I+ R++RD +TG S+  GF+ +D       AI+ L
Sbjct: 3   LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKGL 62

Query: 153 NRQNFQGS 160
           N Q  +G+
Sbjct: 63  NGQKPEGA 70

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

 Score = 49.5 bits (119), Expect = 2e-08
 Identities = 25/73 (34%), Positives = 42/73 (57%), Gaps = 1/73 (1%)

Query: 92  TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
           T+F+ +L+   RE DL + F++ GKV  VR++RD  +  SK   ++E+  E++   A+  
Sbjct: 1   TVFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLAL-G 59

Query: 152 LNRQNFQGSEIIV 164
           L  Q   G  I+V
Sbjct: 60  LTGQRLLGQPIMV 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|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 53.0 bits (127), Expect = 2e-08
 Identities = 26/76 (34%), Positives = 40/76 (52%), Gaps = 2/76 (2%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           L++  L K   + +LE  F+ +G++I+ R++ D VTG SK  GF+ +D       AI+ L
Sbjct: 92  LYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTL 151

Query: 153 NRQNFQGS--EIIVDF 166
           N     G    I V F
Sbjct: 152 NGTTPSGCTEPITVKF 167

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

 Score = 49.1 bits (117), Expect = 3e-08
 Identities = 21/68 (30%), Positives = 34/68 (50%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           L++  L +   E +L + F  YG ++   ++RD  TG  +   F+ YD  +   AAI +L
Sbjct: 3   LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSL 62

Query: 153 NRQNFQGS 160
           N     GS
Sbjct: 63  NGTIPPGS 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|240809 cd12363, RRM_TRA2, RNA recognition motif in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar proteins

 Score = 49.2 bits (118), Expect = 3e-08
 Identities = 23/69 (33%), Positives = 36/69 (52%)

Query: 98  LNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNF 157
           L+  + E DL + F+ YG +  V+VV D  TG S+ +GF+ ++  +    A   LN    
Sbjct: 7   LSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGMEI 66

Query: 158 QGSEIIVDF 166
            G  I VD+
Sbjct: 67  DGRRIRVDY 75

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

 Score = 48.9 bits (117), Expect = 3e-08
 Identities = 25/85 (29%), Positives = 45/85 (52%), Gaps = 7/85 (8%)

Query: 90  TRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAI 149
           T  LF+  L  + +E DLE+ F+++G++  V V  D  +G SK + ++ +   +  + A 
Sbjct: 2   TGRLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAY 61

Query: 150 RALNRQNFQGSEIIVDFECGRVLPG 174
           + L+ + FQG  I        +LPG
Sbjct: 62  KELDGKVFQGRLI-------HILPG 79

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

 Score = 48.8 bits (116), Expect = 4e-08
 Identities = 26/61 (42%), Positives = 35/61 (57%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           LFI  L +   + DL Q F  +G VIS +V  D  T  SK +GF+ YD   +  AAI+A+
Sbjct: 7   LFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAAIQAM 66

Query: 153 N 153
           N
Sbjct: 67  N 67

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

 Score = 49.0 bits (116), Expect = 4e-08
 Identities = 25/68 (36%), Positives = 41/68 (60%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           L++  L K   + +LEQ F++YG++I+ R++ D VTG S+  GF+ +D       AI+ L
Sbjct: 8   LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 67

Query: 153 NRQNFQGS 160
           N Q   G+
Sbjct: 68  NGQKPPGA 75

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

 Score = 48.4 bits (116), Expect = 4e-08
 Identities = 18/62 (29%), Positives = 35/62 (56%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           +++  ++ +  E D++  F  +GK+ S  +  D  TG  K YGF+EY+  ++   AI ++
Sbjct: 3   IYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIASM 62

Query: 153 NR 154
           N 
Sbjct: 63  NL 64

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

 Score = 48.0 bits (115), Expect = 6e-08
 Identities = 20/58 (34%), Positives = 32/58 (55%), Gaps = 1/58 (1%)

Query: 92  TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEY-DCEKACLAA 148
            ++IG L     E +L + F+++G V  +R+ R   TG SK Y F+E+   E A + A
Sbjct: 1   VVYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVA 58

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

 Score = 48.2 bits (115), Expect = 7e-08
 Identities = 20/72 (27%), Positives = 37/72 (51%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           +++G ++    E  + QAF+ +G + S+ +  D VT   K + F+EY+  +A   A+  +
Sbjct: 3   VYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQM 62

Query: 153 NRQNFQGSEIIV 164
           N     G  I V
Sbjct: 63  NGVMLGGRNIKV 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|240812 cd12366, RRM1_RBM45, RNA recognition motif 1 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 47.7 bits (114), Expect = 9e-08
 Identities = 21/66 (31%), Positives = 34/66 (51%), Gaps = 3/66 (4%)

Query: 89  PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYD-CEKACLA 147
           P   LFI    K+  E DL +AFA +G++  + VV+D  T  SK   ++++     A   
Sbjct: 2   PNSRLFI-VCGKSVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAAR- 59

Query: 148 AIRALN 153
           A+  +N
Sbjct: 60  AMEEMN 65

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

 Score = 47.2 bits (113), Expect = 1e-07
 Identities = 22/80 (27%), Positives = 38/80 (47%), Gaps = 16/80 (20%)

Query: 91  RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVR--------DFVTGHSKRYGFLEYDCE 142
            TLF+  LN  + E  L++ F + G V SV + +          +   S  YGF+E+  +
Sbjct: 1   TTLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLL---SMGYGFVEFKSK 57

Query: 143 KACLAAIRALNRQNFQGSEI 162
           +A   A++ L     QG+ +
Sbjct: 58  EAAQKALKRL-----QGTVL 72

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

 Score = 47.2 bits (113), Expect = 1e-07
 Identities = 20/72 (27%), Positives = 42/72 (58%), Gaps = 1/72 (1%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           +++  L ++  +  L++ F +YGK+ S +V++D   G SK +GF+ ++  +A   A+  L
Sbjct: 4   VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKD-DEGKSKGFGFVNFENHEAAQKAVEEL 62

Query: 153 NRQNFQGSEIIV 164
           N +   G ++ V
Sbjct: 63  NGKEVNGKKLYV 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|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 50.7 bits (121), Expect = 2e-07
 Identities = 32/157 (20%), Positives = 60/157 (38%), Gaps = 11/157 (7%)

Query: 15  HHSEVRDSKSSSQTVEPRDAKSSSGQTVKYWYPYCITYDPIQAGSIDGTDTIPHDRAILR 74
             ++ R S    +    R       +  +    Y               +     R    
Sbjct: 10  LRNDTRRSDKGRERSRRRSRSRDRSRRRRDRDYY---RGRRGRSRSRSPNRYYRPRGDRS 66

Query: 75  ALRSTYKPHTSSTDP-------TRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFV 127
             R   +   ++ +P        RT+F+ +L   +RE DL + F++ GKV  V+ ++D  
Sbjct: 67  YRRDDRRSGRNTKEPLTEAERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRN 126

Query: 128 TGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV 164
           +  SK   ++E+   ++ + A+ AL  Q   G  IIV
Sbjct: 127 SRRSKGVAYVEFYDVESVIKAL-ALTGQMLLGRPIIV 162

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|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 = 46.5 bits (111), Expect = 2e-07
 Identities = 21/69 (30%), Positives = 36/69 (52%), Gaps = 6/69 (8%)

Query: 92  TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
           T+++G L     E +L++ F+ +G +  VRV +D      K Y F+ +D  +A   AI A
Sbjct: 2   TVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD------KGYAFVRFDTHEAAATAIVA 55

Query: 152 LNRQNFQGS 160
           +N  +  G 
Sbjct: 56  VNGTSINGQ 64

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

 Score = 46.5 bits (111), Expect = 2e-07
 Identities = 19/77 (24%), Positives = 38/77 (49%), Gaps = 8/77 (10%)

Query: 91  RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
           + L++  L  ++ E  L + F+EYG+V  V+ ++D        Y F+ ++     + A+ 
Sbjct: 2   KVLYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD--------YAFVHFEERDDAVKAME 53

Query: 151 ALNRQNFQGSEIIVDFE 167
            +N +  +GS I V   
Sbjct: 54  EMNGKELEGSPIEVSLA 70

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

 Score = 46.6 bits (111), Expect = 2e-07
 Identities = 20/78 (25%), Positives = 41/78 (52%)

Query: 92  TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
           +L++  +   +R  DL + F +YG ++ V +  DF T   + + +++++  +    A+  
Sbjct: 2   SLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYY 61

Query: 152 LNRQNFQGSEIIVDFECG 169
           L+R  F G EI + F  G
Sbjct: 62  LDRTRFLGREIEIQFAQG 79

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

 Score = 46.6 bits (111), Expect = 2e-07
 Identities = 20/73 (27%), Positives = 37/73 (50%), Gaps = 1/73 (1%)

Query: 92  TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
            LF+  L  +  + +LE+ F ++G V SVR+V    +G  K   ++EY+ E +   A+  
Sbjct: 4   KLFVSGLPFSVTKEELEKLFKKHGVVKSVRLV-TNRSGKPKGLAYVEYENESSASQAVLK 62

Query: 152 LNRQNFQGSEIIV 164
           ++    +   I V
Sbjct: 63  MDGTEIKEKTISV 75

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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 46.0 bits (110), Expect = 3e-07
 Identities = 14/56 (25%), Positives = 29/56 (51%), Gaps = 5/56 (8%)

Query: 111 FAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF 166
           F+ +G V  +++++         + F+E+  E+A   A++ LN   F G  + VD+
Sbjct: 5   FSPFGNVEKIKLLKK-----KPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDY 55

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

 Score = 46.5 bits (111), Expect = 3e-07
 Identities = 18/66 (27%), Positives = 34/66 (51%), Gaps = 1/66 (1%)

Query: 101 NSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGS 160
              EADL++ F+ +G V  V + R    G  K + F+++  +     AI+ +N +  +G 
Sbjct: 10  KCTEADLKKLFSPFGFVWEVTIPRKP-DGKKKGFAFVQFTSKADAEKAIKGVNGKKIKGR 68

Query: 161 EIIVDF 166
            + VD+
Sbjct: 69  PVAVDW 74

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

 Score = 46.1 bits (110), Expect = 3e-07
 Identities = 21/59 (35%), Positives = 33/59 (55%), Gaps = 4/59 (6%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYD----CEKACLA 147
           LF+G L ++  E DL + F++YG V SV +V D  TG  + + F+ +D     +K  L 
Sbjct: 2   LFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQ 60

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

 Score = 46.3 bits (110), Expect = 3e-07
 Identities = 18/61 (29%), Positives = 30/61 (49%)

Query: 91  RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
             LF+G LN  + ++ L + F  YGK+    V+ D  T  S+ +GF+ +        A+ 
Sbjct: 3   CKLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAME 62

Query: 151 A 151
           A
Sbjct: 63  A 63

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|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 = 46.1 bits (110), Expect = 4e-07
 Identities = 23/74 (31%), Positives = 36/74 (48%), Gaps = 2/74 (2%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVI--SVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
           L++G L   + + DLE A AE G V   S++       G SK + ++E+  E A  A   
Sbjct: 1   LYVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKE 60

Query: 151 ALNRQNFQGSEIIV 164
            L  + F G + +V
Sbjct: 61  KLEGREFNGKKCVV 74

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

 Score = 46.2 bits (109), Expect = 4e-07
 Identities = 25/61 (40%), Positives = 35/61 (57%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           LFI  L +   + DL Q F  +G V+S +V  D  T  SK +GF+ YD   +  AAI+A+
Sbjct: 10  LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQAM 69

Query: 153 N 153
           N
Sbjct: 70  N 70

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

>gnl|CDD|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 = 46.2 bits (110), Expect = 4e-07
 Identities = 23/63 (36%), Positives = 36/63 (57%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           LF+G++ +N  E DL   F ++GK+  + V++D  TG  K   FL Y   ++ L A  AL
Sbjct: 8   LFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALKAQSAL 67

Query: 153 NRQ 155
           + Q
Sbjct: 68  HEQ 70

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

 Score = 45.4 bits (107), Expect = 6e-07
 Identities = 24/76 (31%), Positives = 45/76 (59%), Gaps = 3/76 (3%)

Query: 91  RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
           +TLF+  L++++ E  L+++F      I+ R+V D  TG SK +GF+++  E+   AA  
Sbjct: 1   KTLFVKGLSEDTTEETLKESF---DGSIAARIVTDRDTGSSKGFGFVDFSSEEDAKAAKE 57

Query: 151 ALNRQNFQGSEIIVDF 166
           A+      G+++ +DF
Sbjct: 58  AMEDGEIDGNKVTLDF 73

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|241080 cd12636, RRM2_Bruno_like, RNA recognition motif 2 in Drosophila melanogaster Bruno protein and similar proteins

 Score = 45.6 bits (108), Expect = 6e-07
 Identities = 21/66 (31%), Positives = 34/66 (51%), Gaps = 1/66 (1%)

Query: 91  RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
           R LF+G L+K   E D+   FA +G +    V+RD   G S+   F+ +   +  L AI+
Sbjct: 2   RKLFVGMLSKKCNENDVRIMFAPFGSIEECTVLRD-QNGQSRGCAFVTFASRQCALNAIK 60

Query: 151 ALNRQN 156
           A++   
Sbjct: 61  AMHHSQ 66

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

 Score = 45.3 bits (107), Expect = 7e-07
 Identities = 21/63 (33%), Positives = 35/63 (55%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           LF+G + +   E ++   F E+G V+ V +++D  TGH +   F++Y        AIRAL
Sbjct: 2   LFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRAL 61

Query: 153 NRQ 155
           + Q
Sbjct: 62  HNQ 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|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 48.4 bits (115), Expect = 8e-07
 Identities = 22/79 (27%), Positives = 37/79 (46%)

Query: 88  DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLA 147
           +    L +  L +   + ++   F   G++ S ++VRD VTG S  YGF+ Y   +    
Sbjct: 1   ESKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEK 60

Query: 148 AIRALNRQNFQGSEIIVDF 166
           A+ +LN    Q   I V +
Sbjct: 61  AVNSLNGLRLQNKTIKVSY 79

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

 Score = 45.0 bits (107), Expect = 8e-07
 Identities = 23/68 (33%), Positives = 33/68 (48%), Gaps = 1/68 (1%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           L+I  L  +  E DLE     YG+VIS R++RD   G S+  GF   +  + C   I   
Sbjct: 3   LYISNLPLHMDEQDLETMLKPYGQVISTRILRD-SKGQSRGVGFARMESREKCEDIISKF 61

Query: 153 NRQNFQGS 160
           N +  +G 
Sbjct: 62  NGKYLKGE 69

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

 Score = 44.8 bits (107), Expect = 8e-07
 Identities = 24/73 (32%), Positives = 40/73 (54%), Gaps = 1/73 (1%)

Query: 92  TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
           ++F+G L  +  E +L + F + G V +VR+VRD  TG  K +G++ +   K  +A    
Sbjct: 1   SVFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFK-TKDSVALALK 59

Query: 152 LNRQNFQGSEIIV 164
           LN    +G +I V
Sbjct: 60  LNGIKLKGRKIRV 72

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

 Score = 48.4 bits (115), Expect = 9e-07
 Identities = 22/75 (29%), Positives = 36/75 (48%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           +F+  L+ ++ E  L Q F  +G V +V+++RD  T   K YGF+          AI +L
Sbjct: 272 IFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSL 331

Query: 153 NRQNFQGSEIIVDFE 167
           N        + V F+
Sbjct: 332 NGYTLGNRVLQVSFK 346

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

 Score = 45.1 bits (106), Expect = 9e-07
 Identities = 24/70 (34%), Positives = 39/70 (55%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           +F+G L+      D++ AFA +G++   RVV+D  TG SK YGF+ +  +     AI+ +
Sbjct: 4   VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 63

Query: 153 NRQNFQGSEI 162
             Q   G +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|241213 cd12769, RRM1_HuR, RNA recognition motif 1 in vertebrate Hu-antigen R (HuR)

 Score = 45.1 bits (106), Expect = 9e-07
 Identities = 26/74 (35%), Positives = 37/74 (50%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           L +  L +N  + +L   F+  G+V S +++RD V GHS  YGF+ Y   K    AI  L
Sbjct: 4   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINTL 63

Query: 153 NRQNFQGSEIIVDF 166
           N    Q   I V +
Sbjct: 64  NGLRLQSKTIKVSY 77

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

 Score = 45.1 bits (107), Expect = 1e-06
 Identities = 17/52 (32%), Positives = 29/52 (55%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
           LF+G L  +  E +L++ F E+G V+ VR+      G    +GF+ +D  +A
Sbjct: 6   LFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEA 57

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

 Score = 48.3 bits (115), Expect = 1e-06
 Identities = 24/71 (33%), Positives = 37/71 (52%)

Query: 92  TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
           +L++G L+ +  EA L   F  +G V+SVRV RD VT  S  YG++ +        A+  
Sbjct: 2   SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALET 61

Query: 152 LNRQNFQGSEI 162
           +N +   G  I
Sbjct: 62  MNFKRLGGKPI 72

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

 Score = 47.9 bits (114), Expect = 1e-06
 Identities = 19/94 (20%), Positives = 40/94 (42%), Gaps = 1/94 (1%)

Query: 71  AILRALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGH 130
           A LR      +           L++  L+    +  L + F+E G++ S +V+ D   G 
Sbjct: 266 AELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLD-EKGV 324

Query: 131 SKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV 164
           S+ +GF+ +   +    A+  ++ +   G  + V
Sbjct: 325 SRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYV 358

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

 Score = 44.7 bits (105), Expect = 1e-06
 Identities = 25/70 (35%), Positives = 38/70 (54%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           +F+G L+      D++ AFA +GK+   RVV+D  TG SK YGF+ +  +     AI  +
Sbjct: 4   VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63

Query: 153 NRQNFQGSEI 162
             Q   G +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|241021 cd12577, RRM1_Hrp1p, RNA recognition motif 1 in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins

 Score = 44.1 bits (104), Expect = 2e-06
 Identities = 18/48 (37%), Positives = 29/48 (60%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYD 140
           +FIG LN  + +  L + F ++G+V    V+RD  TG S+ +GFL + 
Sbjct: 1   MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFK 48

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

 Score = 44.3 bits (105), Expect = 2e-06
 Identities = 21/59 (35%), Positives = 31/59 (52%)

Query: 92  TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
            LF+G L  ++   DL   F   G   SVR++ D  TG SK   F+E+D  +A   A++
Sbjct: 2   ILFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALK 60

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

 Score = 43.7 bits (103), Expect = 2e-06
 Identities = 23/73 (31%), Positives = 35/73 (47%), Gaps = 8/73 (10%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           LF+G L   + E ++   F +YGKV+   ++        K YGF+  D + A   AIR L
Sbjct: 3   LFVGNLPPEATEQEIRSLFEQYGKVLECDII--------KNYGFVHMDDKTAADEAIRNL 54

Query: 153 NRQNFQGSEIIVD 165
           +     G  I V+
Sbjct: 55  HHYKLHGVAINVE 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|240859 cd12413, RRM1_RBM28_like, RNA recognition motif 1 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 44.1 bits (105), Expect = 2e-06
 Identities = 20/75 (26%), Positives = 39/75 (52%)

Query: 92  TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
           TLF+  L  ++ +  LE+ F+E G +    VV+D  +   + +G++ +  E+    A+  
Sbjct: 1   TLFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEE 60

Query: 152 LNRQNFQGSEIIVDF 166
             +  F G +I V+F
Sbjct: 61  KKKTKFGGRKIHVEF 75

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|240796 cd12350, RRM3_SHARP, RNA recognition motif 3 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 43.9 bits (104), Expect = 2e-06
 Identities = 21/73 (28%), Positives = 41/73 (56%), Gaps = 3/73 (4%)

Query: 90  TRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAI 149
           TRTLFIG L K +  +DL +AF  +G++I + + +    G +  Y F++Y    + + A+
Sbjct: 2   TRTLFIGNLEKTTTYSDLREAFERFGEIIDIDIKK---QGGNPAYAFIQYADIASVVKAM 58

Query: 150 RALNRQNFQGSEI 162
           R ++ +    + +
Sbjct: 59  RKMDGEYLGNNRV 71

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|241122 cd12678, RRM_SLTM, RNA recognition motif in Scaffold attachment factor (SAF)-like transcription modulator (SLTM) and similar proteins

 Score = 43.5 bits (102), Expect = 3e-06
 Identities = 23/73 (31%), Positives = 39/73 (53%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           L++  L+ N++ ADL+  F +YGKV+S +VV +  +  +K YG +           I  L
Sbjct: 2   LWVSGLSSNTKAADLKNLFGKYGKVLSAKVVTNARSPGAKCYGIVTMSSSAEVARCISHL 61

Query: 153 NRQNFQGSEIIVD 165
           +R    G +I V+
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|241038 cd12594, RRM1_SRSF4, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 4 (SRSF4)

 Score = 43.4 bits (102), Expect = 4e-06
 Identities = 30/87 (34%), Positives = 46/87 (52%), Gaps = 15/87 (17%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           ++IGRL+  +RE D+E+ F  YGK++ V    D   G    YGF+E+D  +    A+  L
Sbjct: 2   VYIGRLSYQARERDVERFFKGYGKILEV----DLKNG----YGFVEFDDLRDADDAVYEL 53

Query: 153 NRQNFQGSEIIVDFECGRVLPGWKPRR 179
           N ++  G  +IV+   G       PRR
Sbjct: 54  NGKDLCGERVIVEHARG-------PRR 73

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

 Score = 42.9 bits (101), Expect = 4e-06
 Identities = 20/73 (27%), Positives = 37/73 (50%), Gaps = 8/73 (10%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           +F+G +++++ + +L   F  YG V+S  V+R F         F+    E A   AI  L
Sbjct: 3   IFVGNVDEDTSQEELRALFEAYGAVLSCAVMRQF--------AFVHLRGEAAADRAIEEL 54

Query: 153 NRQNFQGSEIIVD 165
           N +   G +++V+
Sbjct: 55  NGRELHGRKLVVE 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|240829 cd12383, RRM_RBM42, RNA recognition motif in RNA-binding protein 42 (RBM42) and similar proteins

 Score = 43.4 bits (103), Expect = 4e-06
 Identities = 21/61 (34%), Positives = 33/61 (54%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           +F+G L     +  L +AF++Y      +VVRD  TG SK YGF+ +      L A++ +
Sbjct: 9   IFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAMKEM 68

Query: 153 N 153
           N
Sbjct: 69  N 69

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

 Score = 46.0 bits (109), Expect = 5e-06
 Identities = 25/83 (30%), Positives = 40/83 (48%), Gaps = 1/83 (1%)

Query: 83  HTSSTDPT-RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDC 141
           H     P    L++G L+ N  E +L Q F  +G +  V++ RD  TG SK +GF+++  
Sbjct: 178 HQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHD 237

Query: 142 EKACLAAIRALNRQNFQGSEIIV 164
            +    A+  +N     G  I V
Sbjct: 238 AEEAKEALEVMNGFELAGRPIKV 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|240791 cd12345, RRM2_SECp43_like, RNA recognition motif 2 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 43.0 bits (102), Expect = 5e-06
 Identities = 24/66 (36%), Positives = 34/66 (51%), Gaps = 4/66 (6%)

Query: 92  TLFIGRLNKNSREADLEQAF-AEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
           ++F+G L  +  +  L++ F A Y  V   +VV D VTG SK YGF+ +  E       R
Sbjct: 3   SIFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDE---DERDR 59

Query: 151 ALNRQN 156
           AL   N
Sbjct: 60  ALTEMN 65

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

 Score = 42.8 bits (101), Expect = 5e-06
 Identities = 18/73 (24%), Positives = 34/73 (46%), Gaps = 4/73 (5%)

Query: 92  TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
           T++ G    +   +D+++ F   G V  V ++   V  H+    F+ ++  +A   AI  
Sbjct: 1   TVYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRTVQPHA----FITFENLEAAQLAIET 56

Query: 152 LNRQNFQGSEIIV 164
           LN  +  G+ I V
Sbjct: 57  LNGASVDGNCIKV 69

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

 Score = 42.9 bits (102), Expect = 6e-06
 Identities = 21/61 (34%), Positives = 35/61 (57%), Gaps = 1/61 (1%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           +FI  L+K+     L   F+ +G ++S +V  D   G SK YGF+ ++ E+A + AI  +
Sbjct: 5   IFIKNLDKSIDNKALYDTFSAFGNILSCKVATD-ENGGSKGYGFVHFETEEAAVRAIEKV 63

Query: 153 N 153
           N
Sbjct: 64  N 64

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

 Score = 42.5 bits (100), Expect = 6e-06
 Identities = 22/73 (30%), Positives = 37/73 (50%), Gaps = 8/73 (10%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           +F+G ++      +L   F E+G+V+    V+D        Y F+  + E+  LAAI AL
Sbjct: 3   IFVGNVSATCTSDELRGLFEEFGRVVECDKVKD--------YAFVHMEREEEALAAIEAL 54

Query: 153 NRQNFQGSEIIVD 165
           N +  +G  I V+
Sbjct: 55  NGKEVKGRRINVE 67

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

 Score = 42.4 bits (100), Expect = 6e-06
 Identities = 25/74 (33%), Positives = 36/74 (48%), Gaps = 8/74 (10%)

Query: 93  LFIGRLNKNSREADLEQAFAEYG-KVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
           L+IG L+ +  E+DL Q F E+   V SV V +    G    Y F++   +     AI  
Sbjct: 1   LYIGNLSSDVNESDLRQLFEEHKIPVSSVLVKK---GG----YAFVDCPDQSWADKAIEK 53

Query: 152 LNRQNFQGSEIIVD 165
           LN +  QG  I V+
Sbjct: 54  LNGKILQGKVIEVE 67

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|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 = 42.9 bits (101), Expect = 7e-06
 Identities = 20/62 (32%), Positives = 33/62 (53%), Gaps = 2/62 (3%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYG--FLEYDCEKACLAAIR 150
           +F+G++ ++  E DL + F +YG V  + V+RD      +  G  F+ +   KA L A  
Sbjct: 4   MFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 63

Query: 151 AL 152
           AL
Sbjct: 64  AL 65

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

 Score = 42.8 bits (100), Expect = 7e-06
 Identities = 26/79 (32%), Positives = 38/79 (48%)

Query: 88  DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLA 147
           D    L +  L +N  + +L+  F   G++ S ++VRD +TG S  YGF+ Y   K    
Sbjct: 2   DSKTNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEK 61

Query: 148 AIRALNRQNFQGSEIIVDF 166
           AI  LN    Q   I V +
Sbjct: 62  AINTLNGLRLQTKTIKVSY 80

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

 Score = 42.2 bits (100), Expect = 7e-06
 Identities = 18/59 (30%), Positives = 36/59 (61%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
           LFIG L+ ++ E  L + F++YG+V+   +++D +TG S+ +GF+ +    +    + A
Sbjct: 1   LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAA 59

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

 Score = 42.2 bits (100), Expect = 8e-06
 Identities = 23/63 (36%), Positives = 39/63 (61%), Gaps = 11/63 (17%)

Query: 93  LFIGRLNKN--SREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
           +F+G LN +  S+E DLE+ F++YGK++ + +       H K YGF+++D E+   AA+ 
Sbjct: 3   VFVGNLNTDKVSKE-DLEEIFSKYGKILGISL-------H-KGYGFVQFDNEEDARAAVA 53

Query: 151 ALN 153
             N
Sbjct: 54  GEN 56

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

 Score = 42.3 bits (100), Expect = 9e-06
 Identities = 20/71 (28%), Positives = 40/71 (56%), Gaps = 2/71 (2%)

Query: 92  TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
            +F+G +  ++ E +L   F+ +G V  V+++ D   G SK YGF+ ++ ++     I A
Sbjct: 4   RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITD-RAGVSKGYGFVTFETQED-AEKILA 61

Query: 152 LNRQNFQGSEI 162
           +   NF+G ++
Sbjct: 62  MGNLNFRGKKL 72

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|241040 cd12596, RRM1_SRSF6, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 6 (SRSF6)

 Score = 42.2 bits (99), Expect = 9e-06
 Identities = 23/73 (31%), Positives = 42/73 (57%), Gaps = 8/73 (10%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           ++IGRL+ + RE D+++ F  YGK++ +    D   G    YGF+E++  +    A+  L
Sbjct: 2   VYIGRLSYHVREKDIQRFFGGYGKLLEI----DLKNG----YGFVEFEDSRDADDAVYEL 53

Query: 153 NRQNFQGSEIIVD 165
           N ++  G  +IV+
Sbjct: 54  NGKDLCGERVIVE 66

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

 Score = 42.4 bits (99), Expect = 9e-06
 Identities = 22/61 (36%), Positives = 34/61 (55%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           +FI  L +++ E  L Q F  +G V +V+V+RDF T   K +GF+     +    AI +L
Sbjct: 4   IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASL 63

Query: 153 N 153
           N
Sbjct: 64  N 64

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|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 = 42.0 bits (99), Expect = 1e-05
 Identities = 25/79 (31%), Positives = 40/79 (50%), Gaps = 4/79 (5%)

Query: 91  RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
           R LF+G L+K   E D+ + F  +G +    ++R    G+SK   F+++       AAI 
Sbjct: 2   RKLFVGMLSKQQTEDDVRRLFEPFGTIEECTILRG-PDGNSKGCAFVKFSSHAEAQAAIN 60

Query: 151 ALN-RQNFQG--SEIIVDF 166
           AL+  Q   G  S ++V F
Sbjct: 61  ALHGSQTMPGASSSLVVKF 79

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|241123 cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), and similar proteins

 Score = 42.0 bits (98), Expect = 1e-05
 Identities = 22/75 (29%), Positives = 39/75 (52%)

Query: 91  RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
           R L++  L+  +R  DL+  F++YGKV+  +VV +  +  ++ YGF+     +     I 
Sbjct: 2   RNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSEEATKCIN 61

Query: 151 ALNRQNFQGSEIIVD 165
            L+R    G  I V+
Sbjct: 62  HLHRTELHGRMISVE 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|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 = 41.7 bits (98), Expect = 1e-05
 Identities = 19/76 (25%), Positives = 37/76 (48%), Gaps = 9/76 (11%)

Query: 92  TLFIGRLN-KNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
           TLF+   +   +RE D+E+ F  +G ++   + + F         F+E++  +    A+ 
Sbjct: 1   TLFVVGFDPGTTREEDIEKLFEPFGPLVRCDIRKTF--------AFVEFEDSEDATKALE 52

Query: 151 ALNRQNFQGSEIIVDF 166
           AL+     GS + V+F
Sbjct: 53  ALHGSRIDGSVLTVEF 68

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

 Score = 42.1 bits (99), Expect = 1e-05
 Identities = 20/75 (26%), Positives = 34/75 (45%)

Query: 92  TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
           TLF+  L  +  + DL   F++   +    VV D  TG S+ YGF+ +   +    A+  
Sbjct: 1   TLFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAK 60

Query: 152 LNRQNFQGSEIIVDF 166
           L  +   G  + +D 
Sbjct: 61  LKNKKLHGRILRLDI 75

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

 Score = 41.4 bits (98), Expect = 1e-05
 Identities = 20/80 (25%), Positives = 37/80 (46%), Gaps = 10/80 (12%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           L++G L +   E  L  AF  +G +  +++  D+ T   + + F+E++  +   AAI   
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAI--- 57

Query: 153 NRQNFQGSEIIVDFECGRVL 172
              N   SE+      GR +
Sbjct: 58  --DNMNESEL-----FGRTI 70

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

 Score = 41.6 bits (98), Expect = 2e-05
 Identities = 17/55 (30%), Positives = 31/55 (56%)

Query: 90  TRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
           T+ +F+G L  N  E DL + F+++G V  V V+ D      + +GF+ ++ E +
Sbjct: 2   TKKIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDS 56

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

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

 Score = 41.6 bits (98), Expect = 2e-05
 Identities = 17/59 (28%), Positives = 33/59 (55%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
           LFIG L+  + +  L+  F+++G++    V++D  T  S+ +GF+ +       AA+ A
Sbjct: 2   LFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNA 60

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

 Score = 41.5 bits (98), Expect = 2e-05
 Identities = 17/71 (23%), Positives = 37/71 (52%), Gaps = 1/71 (1%)

Query: 94  FIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALN 153
           F+G ++  +   +L++ F   G +  + ++ D  TG  K + ++E+  + +   A+  LN
Sbjct: 3   FVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENAL-LLN 61

Query: 154 RQNFQGSEIIV 164
              F+G +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|240837 cd12391, RRM1_SART3, RNA recognition motif 1 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 41.5 bits (98), Expect = 2e-05
 Identities = 21/74 (28%), Positives = 46/74 (62%), Gaps = 2/74 (2%)

Query: 92  TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
           T+F+  L+ +  E +L + F++ G++  VR+V+++  G SK Y ++E++ E++   A+  
Sbjct: 1   TVFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYK-GKSKGYAYVEFENEESVQEAL-K 58

Query: 152 LNRQNFQGSEIIVD 165
           L+R+  +G  + V 
Sbjct: 59  LDRELIKGRPMFVS 72

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

 Score = 41.4 bits (98), Expect = 2e-05
 Identities = 17/63 (26%), Positives = 33/63 (52%)

Query: 92  TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
           T+ +  L++++ E DL + F  +G +  V + +D  TG S+ + F+ +   +    AI  
Sbjct: 1   TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEK 60

Query: 152 LNR 154
           LN 
Sbjct: 61  LNG 63

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

 Score = 41.5 bits (97), Expect = 2e-05
 Identities = 24/76 (31%), Positives = 38/76 (50%), Gaps = 2/76 (2%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           L+I  L +   + D+E  F+ +G++I+ RV+ D  TG S+   F+ +D       AI + 
Sbjct: 3   LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITSF 62

Query: 153 NRQNFQGS--EIIVDF 166
           N     GS   I V F
Sbjct: 63  NGHKPPGSSEPITVKF 78

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

 Score = 41.3 bits (96), Expect = 2e-05
 Identities = 24/74 (32%), Positives = 35/74 (47%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           L +  L +N  + +    F   G++ S ++VRD +TG S  YGF+ Y   K    AI  L
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64

Query: 153 NRQNFQGSEIIVDF 166
           N    Q   I V +
Sbjct: 65  NGLRLQTKTIKVSY 78

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

 Score = 41.0 bits (96), Expect = 2e-05
 Identities = 22/76 (28%), Positives = 40/76 (52%), Gaps = 9/76 (11%)

Query: 92  TLFIGRLNK-NSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
           TLF+   +  N+R  DLE+ F  YGK+++VR+ R+F         F++Y+ ++    A+ 
Sbjct: 1   TLFVINFDPINTRTRDLERHFEPYGKLVNVRIRRNF--------AFVQYETQEDATKALE 52

Query: 151 ALNRQNFQGSEIIVDF 166
           + N        I V++
Sbjct: 53  STNMSKVLDRVISVEY 68

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

 Score = 44.7 bits (105), Expect = 2e-05
 Identities = 21/72 (29%), Positives = 38/72 (52%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           +++G ++   RE  + +AF  +G + S+ +  D  TG  K + F+EY+  +A   A+  +
Sbjct: 110 VYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQM 169

Query: 153 NRQNFQGSEIIV 164
           N Q   G  I V
Sbjct: 170 NGQMLGGRNIKV 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|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 = 41.1 bits (97), Expect = 2e-05
 Identities = 15/61 (24%), Positives = 35/61 (57%), Gaps = 1/61 (1%)

Query: 106 DLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD 165
           +L + F+ +G+V SVR+ + F  G  + + F+E+  ++    A+ AL   +  G  ++++
Sbjct: 16  ELRELFSPFGQVKSVRLPKKF-DGSHRGFAFVEFVTKQEAQNAMEALKSTHLYGRHLVLE 74

Query: 166 F 166
           +
Sbjct: 75  Y 75

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

 Score = 41.3 bits (96), Expect = 2e-05
 Identities = 24/79 (30%), Positives = 36/79 (45%)

Query: 88  DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLA 147
           D    L +  L +N  + + +  F   G++ S ++VRD +TG S  YGF+ Y        
Sbjct: 1   DSKTNLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADK 60

Query: 148 AIRALNRQNFQGSEIIVDF 166
           AI  LN    Q   I V +
Sbjct: 61  AINTLNGLKLQTKTIKVSY 79

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

 Score = 40.8 bits (96), Expect = 2e-05
 Identities = 17/52 (32%), Positives = 35/52 (67%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
           +F+G L  +  E + ++ F+++GKV+  ++++D  TG S+ +GF+ +D E A
Sbjct: 2   IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESA 53

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

 Score = 40.8 bits (96), Expect = 3e-05
 Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 8/74 (10%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           ++IGRL   +RE D+E+ F  YG++  + +   F        GF+E++  +    A+  L
Sbjct: 2   VYIGRLPYRARERDVERFFKGYGRIREINLKNGF--------GFVEFEDPRDADDAVYEL 53

Query: 153 NRQNFQGSEIIVDF 166
           N +   G  +IV+ 
Sbjct: 54  NGKELCGERVIVEH 67

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

 Score = 41.2 bits (96), Expect = 3e-05
 Identities = 21/61 (34%), Positives = 33/61 (54%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           +F+  L+  + E+ L Q F  +G V +V+V+RDF T   K +GF+          AI +L
Sbjct: 4   IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63

Query: 153 N 153
           N
Sbjct: 64  N 64

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

 Score = 40.8 bits (95), Expect = 3e-05
 Identities = 19/70 (27%), Positives = 37/70 (52%), Gaps = 4/70 (5%)

Query: 90  TRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYD----CEKAC 145
           T+ +F+G L+ N+   D++Q F ++GKV    ++ D  T   + +GF+ ++     EK C
Sbjct: 3   TKKIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEKVC 62

Query: 146 LAAIRALNRQ 155
                 +N +
Sbjct: 63  EIHFHEINNK 72

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|240915 cd12471, RRM1_MSSP2, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 40.9 bits (95), Expect = 3e-05
 Identities = 21/67 (31%), Positives = 34/67 (50%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           L+I  L+  + + DL +    YGK++S + + D  T   K YGF+++D   A   A+ AL
Sbjct: 4   LYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 63

Query: 153 NRQNFQG 159
                Q 
Sbjct: 64  KASGVQA 70

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|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE

 Score = 40.9 bits (96), Expect = 3e-05
 Identities = 23/70 (32%), Positives = 41/70 (58%), Gaps = 2/70 (2%)

Query: 89  PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAA 148
           P R +F+G ++  + E DL + F++YG V  V++V D   G SK YGF+ ++ ++     
Sbjct: 2   PNR-IFVGGIDFKTNENDLRKFFSQYGTVKEVKIVND-RAGVSKGYGFVTFETQEDAQKI 59

Query: 149 IRALNRQNFQ 158
           ++  NR  F+
Sbjct: 60  LQEANRLCFR 69

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

 Score = 40.8 bits (96), Expect = 3e-05
 Identities = 23/75 (30%), Positives = 35/75 (46%)

Query: 92  TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
            L I  L +   + +    F   G V + ++VRD  TG+S  +GF++Y   +    AIR 
Sbjct: 2   NLIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRT 61

Query: 152 LNRQNFQGSEIIVDF 166
           LN    Q   I V +
Sbjct: 62  LNGLQLQNKRIKVAY 76

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|241054 cd12610, RRM1_SECp43, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43)

 Score = 40.8 bits (96), Expect = 4e-05
 Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 1/76 (1%)

Query: 92  TLFIGRLNKNSREADLEQAFAEYG-KVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
           +L++G L     E  +++AFA  G  V+SV+++R+ +TG    Y F+E+  E      + 
Sbjct: 1   SLWMGDLEPYMDENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERCLH 60

Query: 151 ALNRQNFQGSEIIVDF 166
            LN +   GS     F
Sbjct: 61  KLNGKPIPGSNPPKRF 76

This subgroup corresponds to the RRM1 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 = 84

>gnl|CDD|240806 cd12360, RRM_cwf2, RNA recognition motif in yeast pre-mRNA-splicing factor Cwc2 and similar proteins

 Score = 40.7 bits (96), Expect = 4e-05
 Identities = 20/78 (25%), Positives = 35/78 (44%), Gaps = 10/78 (12%)

Query: 90  TRTLFIGRLNKNSREADLEQA----FAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKAC 145
            RTL++G +   S    +E+     F E+G +  +RV+       SK   F+ Y    + 
Sbjct: 1   NRTLYVGGIKAGSALKQIEEILRRHFGEWGDIEDIRVL------PSKGIAFVRYKYRASA 54

Query: 146 LAAIRALNRQNFQGSEII 163
             A  A+  Q+  G E++
Sbjct: 55  EFAKEAMADQSLDGGEVL 72

This subfamily corresponds to the RRM of yeast protein Cwc2, also termed Complexed with CEF1 protein 2, or PRP19-associated complex protein 40 (Ntc40), or synthetic lethal with CLF1 protein 3, one of the components of the Prp19-associated complex [nineteen complex (NTC)] that can bind to RNA. NTC is composed of the scaffold protein Prp19 and a number of associated splicing factors, and plays a crucial role in intron removal during premature mRNA splicing in eukaryotes. Cwc2 functions as an RNA-binding protein that can bind both small nuclear RNAs (snRNAs) and pre-mRNA in vitro. It interacts directly with the U6 snRNA to link the NTC to the spliceosome during pre-mRNA splicing. In the N-terminal half, Cwc2 contains a CCCH-type zinc finger (ZnF domain), a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and an intervening loop, also termed RNA-binding loop or RB loop, between ZnF and RRM, all of which are necessary and sufficient for RNA binding. The ZnF is also responsible for mediating protein-protein interaction. The C-terminal flexible region of Cwc2 interacts with the WD40 domain of Prp19. Length = 78

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

 Score = 40.6 bits (95), Expect = 4e-05
 Identities = 19/70 (27%), Positives = 34/70 (48%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           +F+G L+    +A L  AF+ +      RV+ D  +G S+ YGF+ +  ++    AI  +
Sbjct: 2   IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEM 61

Query: 153 NRQNFQGSEI 162
           N +      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|240780 cd12334, RRM1_SF3B4, RNA recognition motif 1 in splicing factor 3B subunit 4 (SF3B4) and similar proteins

 Score = 40.3 bits (95), Expect = 4e-05
 Identities = 19/61 (31%), Positives = 36/61 (59%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           +++G L++   E  L + F + G V++V + +D VT   + YGF+E+  E+    AI+ +
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 153 N 153
           N
Sbjct: 61  N 61

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

 Score = 40.4 bits (94), Expect = 4e-05
 Identities = 19/70 (27%), Positives = 37/70 (52%), Gaps = 4/70 (5%)

Query: 91  RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYD----CEKACL 146
           + LF+G + +++ E  L   F EYGK+ ++ ++ D  +G  + +GF+ +D     +K  L
Sbjct: 1   KKLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIVL 60

Query: 147 AAIRALNRQN 156
                +N  N
Sbjct: 61  QKYHTINGHN 70

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

 Score = 40.5 bits (94), Expect = 5e-05
 Identities = 22/61 (36%), Positives = 34/61 (55%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           +F+  L+ +S E+ L Q F  +G V +V+V+RDF T   K +GF+          AI +L
Sbjct: 6   IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 153 N 153
           N
Sbjct: 66  N 66

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

 Score = 40.0 bits (94), Expect = 5e-05
 Identities = 24/75 (32%), Positives = 38/75 (50%), Gaps = 5/75 (6%)

Query: 92  TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
            LF+G L       +L++ F+++GKV S  V  D  TG SK YGF+ +           A
Sbjct: 1   KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLE---NA 57

Query: 152 LNRQN--FQGSEIIV 164
           L +Q    +G+++ V
Sbjct: 58  LQKQKHILEGNKLQV 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|240892 cd12446, RRM_RBM25, RNA recognition motif in eukaryotic RNA-binding protein 25 and similar proteins

 Score = 40.3 bits (95), Expect = 5e-05
 Identities = 25/75 (33%), Positives = 42/75 (56%), Gaps = 2/75 (2%)

Query: 91  RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEY-DCEKACLAAI 149
            T+F+G + +   +  + +   + GKV+S + V+D  TG  K +GF E+ D E A L A+
Sbjct: 1   TTVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGA-LRAL 59

Query: 150 RALNRQNFQGSEIIV 164
           R LN     G +++V
Sbjct: 60  RLLNGLELGGKKLLV 74

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

 Score = 42.9 bits (101), Expect = 6e-05
 Identities = 21/72 (29%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           +F+  L+K+     L   F+++G ++S +V  D   G S+ YGF+ ++ E++  AAI+ +
Sbjct: 91  IFVKNLDKSVDNKALFDTFSKFGNILSCKVATD-ENGKSRGYGFVHFEKEESAKAAIQKV 149

Query: 153 NRQNFQGSEIIV 164
           N       E+ V
Sbjct: 150 NGMLLNDKEVYV 161

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

 Score = 40.1 bits (94), Expect = 6e-05
 Identities = 18/50 (36%), Positives = 26/50 (52%), Gaps = 1/50 (2%)

Query: 90  TRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEY 139
           TRTLF+G L     E +L +AF  YG V  V + R      +  Y F+++
Sbjct: 2   TRTLFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGNA-YAFVKF 50

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

 Score = 40.1 bits (94), Expect = 6e-05
 Identities = 16/47 (34%), Positives = 30/47 (63%), Gaps = 3/47 (6%)

Query: 104 EADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFL---EYDCEKACLA 147
           E DL+  F+ +G+++ V+V +D  TG SK +GF+   +Y+ +   L+
Sbjct: 13  EQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVLS 59

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

 Score = 40.0 bits (93), Expect = 6e-05
 Identities = 20/72 (27%), Positives = 38/72 (52%), Gaps = 8/72 (11%)

Query: 91  RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
           + LF+  L     E  LE++F+E+GK+  V+ ++D        Y F+ ++   A + A+ 
Sbjct: 2   KVLFVRNLATTVTEEILEKSFSEFGKLERVKKLKD--------YAFVHFEERDAAVRAMD 53

Query: 151 ALNRQNFQGSEI 162
            +N +  +G EI
Sbjct: 54  EMNGKEIEGEEI 65

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

 Score = 40.2 bits (93), Expect = 6e-05
 Identities = 22/67 (32%), Positives = 34/67 (50%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           L+I  L  N+ + DL +    YGK++S + + D  T   K YGF+++D   A   A+ AL
Sbjct: 10  LYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAAQKAVSAL 69

Query: 153 NRQNFQG 159
                Q 
Sbjct: 70  KASGVQA 76

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

 Score = 40.0 bits (93), Expect = 6e-05
 Identities = 21/78 (26%), Positives = 40/78 (51%)

Query: 92  TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
           +LF+  +   +R  DL + F  YG ++ V V  DF T   + + +++++  +    A+  
Sbjct: 2   SLFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYN 61

Query: 152 LNRQNFQGSEIIVDFECG 169
           LNR+   G +I + F  G
Sbjct: 62  LNRKWVCGRQIEIQFAQG 79

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

 Score = 39.6 bits (92), Expect = 7e-05
 Identities = 21/75 (28%), Positives = 43/75 (57%), Gaps = 2/75 (2%)

Query: 92  TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
           TL++G L+++  EA + Q F++ G   S +++ D  T  +  Y F+E+   +   A++ A
Sbjct: 1   TLYVGNLSRDVTEALILQLFSQIGPCKSCKMIMD--TAGNDPYCFVEFFEHRHAAASLAA 58

Query: 152 LNRQNFQGSEIIVDF 166
           +N +   G E+ V++
Sbjct: 59  MNGRKIMGKEVKVNW 73

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

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

 Score = 40.1 bits (93), Expect = 7e-05
 Identities = 21/61 (34%), Positives = 33/61 (54%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           +F+  L  ++ E+ L Q F  +G V +V+V+RDF T   K +GF+          AI +L
Sbjct: 6   IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 153 N 153
           N
Sbjct: 66  N 66

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

 Score = 39.2 bits (92), Expect = 9e-05
 Identities = 17/63 (26%), Positives = 32/63 (50%)

Query: 103 READLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEI 162
              DL + F +YG+V  V + RD  T  S+ + F+ +  ++    A+ A++ +   G E+
Sbjct: 11  TPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDGKELDGREL 70

Query: 163 IVD 165
            V 
Sbjct: 71  RVQ 73

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|240722 cd12276, RRM2_MEI2_EAR1_like, RNA recognition motif 2 in Mei2-like proteins and terminal EAR1-like proteins

 Score = 39.1 bits (92), Expect = 1e-04
 Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 5/74 (6%)

Query: 92  TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
           TL +  L+    + +L   F+++G+V  +R          K   F+E+   +A  AA+ A
Sbjct: 3   TLLVFNLDSPISDQELRSLFSQFGEVKDIRETPL--RPSQK---FVEFYDIRAAEAALDA 57

Query: 152 LNRQNFQGSEIIVD 165
           LN + F G  + V 
Sbjct: 58  LNGRPFLGGRLKVK 71

This subfamily corresponds to the RRM2 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding proteins family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins. . Length = 71

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

 Score = 39.1 bits (91), Expect = 1e-04
 Identities = 21/73 (28%), Positives = 41/73 (56%), Gaps = 1/73 (1%)

Query: 92  TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
           ++++G ++  S   +LE  F+  G +  V ++ D  +GH K Y ++E+    +  AA+ A
Sbjct: 1   SVYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFATRDSVEAAV-A 59

Query: 152 LNRQNFQGSEIIV 164
           L+  +F+G  I V
Sbjct: 60  LDESSFRGRVIKV 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|240813 cd12367, RRM2_RBM45, RNA recognition motif 2 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 38.9 bits (91), Expect = 1e-04
 Identities = 18/50 (36%), Positives = 30/50 (60%), Gaps = 2/50 (4%)

Query: 100 KNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAI 149
           K+  E DL + F E+G +  V +V+D  TG SK +G++++   K   AA+
Sbjct: 10  KSYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKF--HKPSQAAV 57

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

 Score = 39.2 bits (92), Expect = 1e-04
 Identities = 20/68 (29%), Positives = 36/68 (52%)

Query: 92  TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
           T+++  L  +    DL + F++YGKV+ V +V+D  T  SK   F+ +   +     ++A
Sbjct: 3   TVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKA 62

Query: 152 LNRQNFQG 159
           LN +   G
Sbjct: 63  LNNKELFG 70

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

 Score = 38.8 bits (91), Expect = 1e-04
 Identities = 20/74 (27%), Positives = 40/74 (54%), Gaps = 5/74 (6%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           +++G L   + + +LE  F +YG + SV V R+   G    + F+E++  +    A+RAL
Sbjct: 2   VYVGNLGPRATKRELEDEFEKYGPLRSVWVARN-PPG----FAFVEFEDPRDAEDAVRAL 56

Query: 153 NRQNFQGSEIIVDF 166
           + +   G+ + V+ 
Sbjct: 57  DGRRICGNRVRVEL 70

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

 Score = 39.1 bits (91), Expect = 1e-04
 Identities = 18/63 (28%), Positives = 35/63 (55%), Gaps = 1/63 (1%)

Query: 91  RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
             +F+G++ ++  E +L   F   GK+   R++ +F +G ++ Y F+ Y  ++    AIR
Sbjct: 2   CEVFVGKIPRDMYEDELVPLFERAGKIYEFRLMMEF-SGENRGYAFVMYTTKEEAQLAIR 60

Query: 151 ALN 153
            LN
Sbjct: 61  ILN 63

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

 Score = 41.3 bits (97), Expect = 2e-04
 Identities = 17/93 (18%), Positives = 44/93 (47%), Gaps = 8/93 (8%)

Query: 65  TIPHDRAILRALRSTYKPHT---SSTDPTRT-LFIGRLNKNSREADLEQAFAEYGKVISV 120
            + +D+ +       +       ++     T L++  L+ +  E  L + FA++G++ S 
Sbjct: 152 MLLNDKEVYVGR---FIKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSA 208

Query: 121 RVVRDFVTGHSKRYGFLEYDCEKACLAAIRALN 153
            V++D  +G S+ + F+ ++  +    A+  +N
Sbjct: 209 AVMKD-GSGRSRGFAFVNFEKHEDAAKAVEEMN 240

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|241057 cd12613, RRM2_NGR1_NAM8_like, RNA recognition motif 2 in yeast negative growth regulatory protein NGR1, yeast protein NAM8 and similar proteins

 Score = 38.7 bits (90), Expect = 2e-04
 Identities = 19/69 (27%), Positives = 33/69 (47%), Gaps = 1/69 (1%)

Query: 92  TLFIGRLNKNSREADLEQAFAE-YGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
           ++F+G L+    E+DL   F   +    S +++ D VTG S+ YGF+ +  E     A+ 
Sbjct: 3   SIFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRALI 62

Query: 151 ALNRQNFQG 159
            +      G
Sbjct: 63  EMQGVYCGG 71

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

 Score = 38.5 bits (90), Expect = 2e-04
 Identities = 22/74 (29%), Positives = 38/74 (51%), Gaps = 2/74 (2%)

Query: 92  TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
           T F+G L  N+ + DL+  F +   V SVR+VRD  T   K + ++E++  ++   A+  
Sbjct: 3   TAFVGNLPFNTVQGDLDAIFKDL-SVKSVRLVRDKETDKFKGFCYVEFEDVESLKEAL-E 60

Query: 152 LNRQNFQGSEIIVD 165
            +   F    + VD
Sbjct: 61  YDGALFDDRSLRVD 74

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|241000 cd12556, RRM2_RBM15B, RNA recognition motif 2 in putative RNA binding motif protein 15B (RBM15B) from vertebrate

 Score = 38.8 bits (90), Expect = 2e-04
 Identities = 20/50 (40%), Positives = 29/50 (58%), Gaps = 1/50 (2%)

Query: 90  TRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEY 139
           TR LFIG L+ N  E +L +AF +YG +  V V++    G    Y FL++
Sbjct: 8   TRNLFIGNLDHNVSEVELRRAFDKYGIIEEV-VIKRPARGQGGAYAFLKF 56

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|241116 cd12672, RRM_DAZL, RNA recognition motif in vertebrate deleted in azoospermia-like (DAZL) proteins

 Score = 38.6 bits (90), Expect = 2e-04
 Identities = 18/48 (37%), Positives = 30/48 (62%), Gaps = 1/48 (2%)

Query: 92  TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEY 139
           T+F+G ++    E ++   FA+YG V  V+++ D  TG SK YGF+ +
Sbjct: 7   TVFVGGIDIRMDETEIRSFFAKYGSVKEVKIITD-RTGVSKGYGFVSF 53

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|240810 cd12364, RRM_RDM1, RNA recognition motif of RAD52 motif-containing protein 1 (RDM1) and similar proteins

 Score = 38.5 bits (90), Expect = 2e-04
 Identities = 21/81 (25%), Positives = 41/81 (50%), Gaps = 5/81 (6%)

Query: 91  RTLFIGRLNKNSREADLE----QAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACL 146
           +TL++  ++    E ++      AF+++G + SV+V  +        Y F+++   +A  
Sbjct: 1   KTLYVWGISPKLTEEEIYESLCSAFSQFGLLYSVKVFPNAAVATPGFYAFVKFYSARAAS 60

Query: 147 AAIRALNRQN-FQGSEIIVDF 166
            A +A N +  FQGS + V F
Sbjct: 61  RAQKACNGKWLFQGSPLKVRF 81

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|241037 cd12593, RRM_RBM11, RNA recognition motif in vertebrate RNA-binding protein 11 (RBM11)

 Score = 38.4 bits (89), Expect = 2e-04
 Identities = 24/74 (32%), Positives = 35/74 (47%), Gaps = 1/74 (1%)

Query: 91  RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
           RTLF+G L    RE  L + F + G +  V + +D   G  K +GF+ +   ++   AI 
Sbjct: 2   RTLFVGNLECRVREEILYELFLQAGPLTKVTICKD-KEGKPKSFGFVCFKHSESVPYAIA 60

Query: 151 ALNRQNFQGSEIIV 164
            LN     G  I V
Sbjct: 61  LLNGIRLYGRPIKV 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|240756 cd12310, RRM3_Spen, RNA recognition motif 3 in the Spen (split end) protein family

 Score = 38.0 bits (89), Expect = 2e-04
 Identities = 22/77 (28%), Positives = 34/77 (44%), Gaps = 10/77 (12%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYD-CEKACLAAIRA 151
           L++G L   +  A+LE+ F  +G       +R       + Y ++EY+  E A  AA  A
Sbjct: 1   LWVGGLGPWTSLAELEREFDRFGA------IRRIDYDPGRNYAYIEYESIEAAQ-AAKEA 53

Query: 152 LNRQNF--QGSEIIVDF 166
           L        G  + VDF
Sbjct: 54  LRGFPLGGPGRRLRVDF 70

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

 Score = 38.1 bits (88), Expect = 2e-04
 Identities = 20/76 (26%), Positives = 37/76 (48%), Gaps = 8/76 (10%)

Query: 91  RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
           + LF+  L     E  LE+AF ++GK+  V+ ++D        Y F+ +D     + A+ 
Sbjct: 2   KVLFVRNLANTVTEEILEKAFGQFGKLERVKKLKD--------YAFIHFDERDGAVKAME 53

Query: 151 ALNRQNFQGSEIIVDF 166
            +N +  +G  I + F
Sbjct: 54  EMNGKELEGENIEIVF 69

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

 Score = 38.2 bits (89), Expect = 3e-04
 Identities = 17/57 (29%), Positives = 34/57 (59%), Gaps = 4/57 (7%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCE----KAC 145
           +F+G L+ N+ E D+++ F+++GKV    ++ D  T   + +GF+ ++ E    K C
Sbjct: 2   IFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVC 58

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|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 37.9 bits (89), Expect = 3e-04
 Identities = 17/68 (25%), Positives = 40/68 (58%), Gaps = 3/68 (4%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           +F+G++ ++  E +L   F + G +  +R++ DF +G ++ Y F+ Y  ++A   A++ L
Sbjct: 4   VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDF-SGLNRGYAFVTYTNKEAAQRAVKQL 62

Query: 153 NRQNFQGS 160
           +  N++  
Sbjct: 63  H--NYEIR 68

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

 Score = 38.0 bits (88), Expect = 3e-04
 Identities = 19/48 (39%), Positives = 29/48 (60%), Gaps = 8/48 (16%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYD 140
           +FIGRLN  +RE D+E+ F  YG++  + + R F        GF+E+D
Sbjct: 2   VFIGRLNPAAREKDVERFFKGYGRIRDIDLKRGF--------GFVEFD 41

This subgroup corresponds to the RRM1 of SRSF5, also termed delayed-early protein HRS, or pre-mRNA-splicing factor SRp40, or splicing factor, arginine/serine-rich 5 (SFRS5). SFSF5 is an essential splicing regulatory serine/arginine (SR) protein that regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and it is necessary for enhancer activation. SRSF5 also functions as a factor required for insulin-regulated splice site selection for protein kinase C (PKC) betaII mRNA. It is involved in the regulation of PKCbetaII exon inclusion by insulin via its increased phosphorylation by a phosphatidylinositol 3-kinase (PI 3-kinase) signaling pathway. Moreover, SRSF5 can regulate alternative splicing in exon 9 of glucocorticoid receptor pre-mRNA in a dose-dependent manner. SRSF5 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. The specific RNA binding by SRSF5 requires the phosphorylation of its SR domain. . Length = 70

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

 Score = 38.1 bits (89), Expect = 3e-04
 Identities = 22/75 (29%), Positives = 37/75 (49%), Gaps = 1/75 (1%)

Query: 91  RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
           RTLF+G L+    E  L + F + G +  V++ +D   G  K + F+ +  E +   AI+
Sbjct: 2   RTLFVGNLDARVTEEILYELFLQAGPLEGVKIPKD-PNGKPKSFAFVTFKHEVSVPYAIQ 60

Query: 151 ALNRQNFQGSEIIVD 165
            LN     G E+ + 
Sbjct: 61  LLNGIRLFGRELRIK 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|240918 cd12474, RRM2_MSSP2, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 38.1 bits (88), Expect = 3e-04
 Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 1/61 (1%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           L+I  L  +  E +LE     +G+VIS R++RD  +G S+  GF   +  + C A I   
Sbjct: 3   LYISNLPLSMDEQELESMLKPFGQVISTRILRD-ASGTSRGVGFARMESTEKCEAIITHF 61

Query: 153 N 153
           N
Sbjct: 62  N 62

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

>gnl|CDD|240999 cd12555, RRM2_RBM15, RNA recognition motif 2 in vertebrate RNA binding motif protein 15 (RBM15)

 Score = 38.0 bits (88), Expect = 3e-04
 Identities = 19/50 (38%), Positives = 29/50 (58%), Gaps = 1/50 (2%)

Query: 91  RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYD 140
           RTLF+G L+    E DL +AF  +G +  V + R    G +  YGFL+++
Sbjct: 8   RTLFLGNLDITVTETDLRRAFDRFGVITEVDIKRP-GRGQTSTYGFLKFE 56

This subgroup corresponds to the RRM2 of RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, 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 possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contain 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. This family also includes a RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is N-terminally fused to megakaryoblastic leukemia 1 protein (MKL1) at the C-terminus in a translocation involving chromosome 1 and 22, resulting in acute megakaryoblastic leukemia. The fusion protein could interact with the mRNA export machinery. Although it maintains the specific transactivator function of MKL1, the fusion protein cannot activate RTE-mediated mRNA expression and has lost the post-transcriptional activator function of RBM15. However, it has transdominant suppressor function contributing to its oncogenic properties. . Length = 87

>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 = 38.1 bits (88), Expect = 3e-04
 Identities = 24/79 (30%), Positives = 42/79 (53%), Gaps = 4/79 (5%)

Query: 91  RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
           R LFIG ++K   E D+   F+ +G++   R++R    G S+   F+ +        AI+
Sbjct: 2   RKLFIGMVSKKCNENDIRVMFSPFGQIEECRILRG-PDGLSRGCAFVTFTTRAMAQTAIK 60

Query: 151 ALNR-QNFQG--SEIIVDF 166
           A+++ Q  +G  S I+V F
Sbjct: 61  AMHQAQTMEGCSSPIVVKF 79

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

 Score = 38.0 bits (89), Expect = 3e-04
 Identities = 20/81 (24%), Positives = 40/81 (49%), Gaps = 11/81 (13%)

Query: 92  TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFV-------TGHSKRYGFLEYDCEKA 144
            L+IG L+    E  L + F++YGK+       DF+        G  + Y F+ ++ ++ 
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKF----DFLFHKSGPLKGQPRGYCFVTFETKEE 56

Query: 145 CLAAIRALNRQNFQGSEIIVD 165
              A+++LN +   G +++V 
Sbjct: 57  AEKALKSLNGKTALGKKLVVR 77

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

 Score = 37.8 bits (87), Expect = 4e-04
 Identities = 21/61 (34%), Positives = 34/61 (55%)

Query: 91  RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
           R LFIG L+  + +  L + F ++G +    V+RD  T  S+ +GF+ Y C +   AA+ 
Sbjct: 3   RKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAMS 62

Query: 151 A 151
           A
Sbjct: 63  A 63

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

 Score = 37.6 bits (88), Expect = 4e-04
 Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 1/74 (1%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           + +  L K   E  L + F   G+V  V+V+R    G S+R+GF+ +  E+    A++  
Sbjct: 3   IIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTR-DGKSRRFGFVGFKSEEDAQQAVKYF 61

Query: 153 NRQNFQGSEIIVDF 166
           N+     S+I V+ 
Sbjct: 62  NKTFIDTSKISVEL 75

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

 Score = 37.9 bits (87), Expect = 4e-04
 Identities = 20/67 (29%), Positives = 33/67 (49%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           L+I  L   + + DL +    YGK++S + + D  T   K YGF+++D   A   A+ +L
Sbjct: 7   LYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQKAVASL 66

Query: 153 NRQNFQG 159
                Q 
Sbjct: 67  KANGVQA 73

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

 Score = 38.0 bits (88), Expect = 4e-04
 Identities = 20/78 (25%), Positives = 41/78 (52%)

Query: 92  TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
           +LF+  +  ++R  DL + F  YG ++ V V  DF T   + + +++++  +    A+  
Sbjct: 2   SLFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHN 61

Query: 152 LNRQNFQGSEIIVDFECG 169
           L+R+   G +I + F  G
Sbjct: 62  LDRKWICGRQIEIQFAQG 79

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

 Score = 38.0 bits (89), Expect = 4e-04
 Identities = 21/62 (33%), Positives = 33/62 (53%), Gaps = 6/62 (9%)

Query: 98  LNKNSREADLEQAFAEYGKVISVRVVRD------FVTGHSKRYGFLEYDCEKACLAAIRA 151
           L +   +A  E+A  +  K+  V+++RD         G SK YGF+E+   +  L A+RA
Sbjct: 17  LKELFLKAVSERAGKKKPKIKQVKIMRDLKRVDPNGKGKSKGYGFVEFTNHEHALKALRA 76

Query: 152 LN 153
           LN
Sbjct: 77  LN 78

This subfamily corresponds to the RRM4 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 98

>gnl|CDD|240981 cd12537, RRM1_RBM23, RNA recognition motif 1 in vertebrate probable RNA-binding protein 23 (RBM23)

 Score = 37.7 bits (87), Expect = 4e-04
 Identities = 26/74 (35%), Positives = 36/74 (48%), Gaps = 1/74 (1%)

Query: 91  RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
           RT+F  +L    R  DLE  F+  GKV  VR++ D  +  SK   ++E+ CE   +    
Sbjct: 2   RTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEF-CEIQSVPLAI 60

Query: 151 ALNRQNFQGSEIIV 164
            L  Q   G  IIV
Sbjct: 61  GLTGQRLLGVPIIV 74

This subgroup corresponds to the RRM1 of RBM23, also termed RNA-binding region-containing protein 4, or splicing factor SF2, which may function as a pre-mRNA splicing factor. It shows high sequence homology to RNA-binding protein 39 (RBM39 or 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). In contrast to RBM39, RBM23 contains only two RRMs. . Length = 85

>gnl|CDD|241036 cd12592, RRM_RBM7, RNA recognition motif in vertebrate RNA-binding protein 7 (RBM7)

 Score = 37.6 bits (87), Expect = 4e-04
 Identities = 21/72 (29%), Positives = 36/72 (50%), Gaps = 1/72 (1%)

Query: 91  RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
           RTLF+G L+    E  + + F + G VI V++ +D   G  K++ F+ +  E +   A+ 
Sbjct: 2   RTLFVGNLDPKVTEELIFELFLQAGPVIKVKIPKD-KDGKPKQFAFVNFKHEVSVPYAMN 60

Query: 151 ALNRQNFQGSEI 162
            LN     G  +
Sbjct: 61  LLNGIKLYGRPL 72

This subfamily corresponds to the RRM of RBM7, a 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. RBM7 interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20. It 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. RBM7 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. . Length = 75

>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 = 5e-04
 Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 1/61 (1%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           L+I  L  +  E +LE     +G+VIS R++RD  +G S+  GF   +  + C A I   
Sbjct: 3   LYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVISHF 61

Query: 153 N 153
           N
Sbjct: 62  N 62

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

 Score = 37.4 bits (87), Expect = 5e-04
 Identities = 22/67 (32%), Positives = 33/67 (49%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           LFI  L     E DLE+ F++YG +  V +  D +T   K + F+ Y   +  + A   L
Sbjct: 5   LFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAEL 64

Query: 153 NRQNFQG 159
           +   FQG
Sbjct: 65  DGTVFQG 71

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

 Score = 37.3 bits (87), Expect = 5e-04
 Identities = 19/62 (30%), Positives = 34/62 (54%)

Query: 92  TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
           T+++  L KN+    L+  F++YG V+ V + R   TG  K + F+E++  +    A + 
Sbjct: 1   TVYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKH 60

Query: 152 LN 153
           LN
Sbjct: 61  LN 62

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

 Score = 37.2 bits (87), Expect = 6e-04
 Identities = 16/63 (25%), Positives = 29/63 (46%), Gaps = 1/63 (1%)

Query: 104 EADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEII 163
           E DLE+ F   G+V  V++  D  +G S+    + ++  +    AI+  N     G  + 
Sbjct: 14  EEDLEELFGRVGEVKKVKINYD-RSGRSEGTADVVFEKREDAERAIKQFNGVLLDGQPMQ 72

Query: 164 VDF 166
           V+ 
Sbjct: 73  VEL 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|240680 cd12234, RRM1_AtRSp31_like, RNA recognition motif in Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins from plants

 Score = 37.1 bits (86), Expect = 6e-04
 Identities = 19/67 (28%), Positives = 35/67 (52%), Gaps = 8/67 (11%)

Query: 91  RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
           R +F G    ++R++++E+ F +YG+V  V    D  +G    + F+  + E+    AIR
Sbjct: 1   RPVFCGNFEYDARQSEIERLFGKYGRVDRV----DMKSG----FAFVYMEDERDAEDAIR 52

Query: 151 ALNRQNF 157
            L+   F
Sbjct: 53  GLDNFEF 59

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

>gnl|CDD|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 = 36.9 bits (86), Expect = 6e-04
 Identities = 14/34 (41%), Positives = 23/34 (67%)

Query: 90  TRTLFIGRLNKNSREADLEQAFAEYGKVISVRVV 123
           + TL+IG L+K   E DL+  F EYG++ S+ ++
Sbjct: 2   STTLWIGHLSKKVTEEDLKNLFEEYGEIQSIDMI 35

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

 Score = 37.0 bits (86), Expect = 6e-04
 Identities = 11/52 (21%), Positives = 28/52 (53%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
           +F+G L+  + E  + + F ++G ++ + +  D  T   + + F+ +D E+ 
Sbjct: 2   IFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEP 53

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|241049 cd12605, RRM_RALYL, RNA recognition motif in vertebrate RNA-binding Raly-like protein (RALYL)

 Score = 36.9 bits (85), Expect = 6e-04
 Identities = 23/74 (31%), Positives = 38/74 (51%), Gaps = 9/74 (12%)

Query: 93  LFIGRLNKN-SREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
           +FIG LN    ++AD+E  FA+YGK++   V         K Y F++Y  E+   AA+  
Sbjct: 4   VFIGNLNTAIVKKADIEAIFAKYGKIVGCSV--------HKGYAFVQYISERHARAAVAG 55

Query: 152 LNRQNFQGSEIIVD 165
            N +   G  + ++
Sbjct: 56  ENARIIAGQPLDIN 69

This subgroup corresponds to the RRM of RALYL, also termed heterogeneous nuclear ribonucleoprotein C-like 3, or hnRNP core protein C-like 3, a putative RNA-binding protein that shows high sequence homology with Raly, an RNA-binding protein playing a critical role in embryonic development. The biological role of RALYL remains unclear. Like Raly, RALYL contains 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. . Length = 69

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

 Score = 36.9 bits (85), Expect = 6e-04
 Identities = 21/72 (29%), Positives = 34/72 (47%), Gaps = 8/72 (11%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           L +G ++ +    +L   F EYG VI   +V+D        Y F+  +  +  + AIR L
Sbjct: 3   LHVGNISSSCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEAIRGL 54

Query: 153 NRQNFQGSEIIV 164
           +   FQG  + V
Sbjct: 55  DNTEFQGKRMHV 66

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

 Score = 39.5 bits (92), Expect = 8e-04
 Identities = 32/136 (23%), Positives = 56/136 (41%), Gaps = 5/136 (3%)

Query: 33  DAKSSSGQTVKYWYPYCITYDPIQAGSIDGTDTIPHDRAILRALRSTYKPHTSSTDPTRT 92
           D+   S   +K   P+   Y P+   + + +   P D A            T+  D    
Sbjct: 243 DSIIYSNVFLKIRRPH--DYIPVPQITPEVSQKNPDDNAKNVEKLVNS---TTVLDSKDR 297

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           ++IG L     E  +++    +G + +  +++D  TG SK Y F EY        AI AL
Sbjct: 298 IYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAAL 357

Query: 153 NRQNFQGSEIIVDFEC 168
           N ++   +++ V   C
Sbjct: 358 NGKDTGDNKLHVQRAC 373

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

 Score = 36.6 bits (85), Expect = 0.001
 Identities = 17/63 (26%), Positives = 31/63 (49%), Gaps = 2/63 (3%)

Query: 103 READLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEI 162
           R+ DL Q F ++G ++ V ++  F    SK +GF+ +        A   L+    +G +I
Sbjct: 13  RDPDLRQMFGQFGPILDVEII--FNERGSKGFGFVTFANSADADRAREKLHGTVVEGRKI 70

Query: 163 IVD 165
            V+
Sbjct: 71  EVN 73

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|240980 cd12536, RRM1_RBM39, RNA recognition motif 1 in vertebrate RNA-binding protein 39 (RBM39)

 Score = 36.6 bits (84), Expect = 0.001
 Identities = 26/75 (34%), Positives = 37/75 (49%), Gaps = 1/75 (1%)

Query: 90  TRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAI 149
            RT+F  +L    R  DLE+ F+  GKV  VR++ D  +  SK   ++E+    +   AI
Sbjct: 1   ARTVFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFVDVSSVPLAI 60

Query: 150 RALNRQNFQGSEIIV 164
             L  Q   G  IIV
Sbjct: 61  -GLTGQRVLGVPIIV 74

This subgroup corresponds to the RRM1 of RBM39, also termed hepatocellular carcinoma protein 1, or RNA-binding region-containing protein 2, or splicing factor 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. 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|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 = 36.5 bits (85), Expect = 0.001
 Identities = 22/75 (29%), Positives = 39/75 (52%), Gaps = 2/75 (2%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVIS-VRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
           L +  L  +  EA+L++ F+++G  I+ V+++R    G S+R  F+ Y  E+    A   
Sbjct: 3   LIVKNLPASLTEAELKEHFSKHGGEITDVKLLRT-EDGKSRRIAFIGYKTEEEAQKAKDY 61

Query: 152 LNRQNFQGSEIIVDF 166
            N      S+I V+F
Sbjct: 62  FNNTYINTSKISVEF 76

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

 Score = 36.6 bits (84), Expect = 0.001
 Identities = 20/61 (32%), Positives = 33/61 (54%)

Query: 91  RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
           R LFIG L+  + E  L   + ++GK+    V+RD  +  S+ +GF+ + C     AA+ 
Sbjct: 3   RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAMA 62

Query: 151 A 151
           A
Sbjct: 63  A 63

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

 Score = 36.4 bits (84), Expect = 0.001
 Identities = 16/48 (33%), Positives = 27/48 (56%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYD 140
           LF+G L  +  E DL + F+++G V    V+ D  TG  + +GF+ + 
Sbjct: 2   LFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQ 49

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|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 = 36.4 bits (85), Expect = 0.001
 Identities = 21/61 (34%), Positives = 30/61 (49%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           +FIG L     E  +++    +GK+ +  +V+D  TG SK Y F EY        AI  L
Sbjct: 3   IFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAGL 62

Query: 153 N 153
           N
Sbjct: 63  N 63

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

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

 Score = 36.4 bits (84), Expect = 0.001
 Identities = 15/45 (33%), Positives = 32/45 (71%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFL 137
           +F+G L+ ++ + DL++ F+++G+V+   +  D VTG S+ +GF+
Sbjct: 1   MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFV 45

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

 Score = 36.1 bits (83), Expect = 0.001
 Identities = 18/67 (26%), Positives = 35/67 (52%), Gaps = 4/67 (5%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYD----CEKACLAA 148
           +F+G L+ N+   D++Q F ++GKV    ++ D  T   + +GF+ ++     EK C   
Sbjct: 2   IFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61

Query: 149 IRALNRQ 155
              +N +
Sbjct: 62  FHEINNK 68

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|240973 cd12529, RRM2_MEI2_like, RNA recognition motif 2 in plant Mei2-like proteins

 Score = 35.9 bits (83), Expect = 0.001
 Identities = 21/71 (29%), Positives = 36/71 (50%), Gaps = 5/71 (7%)

Query: 92  TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
           TL +  L+ +    DL Q F  YG++  +R      T + + + F+E+   ++  AA++A
Sbjct: 3   TLVVFNLDPSVSNDDLHQIFGAYGEIKEIRE-----TPNKRHHKFIEFYDVRSAEAALKA 57

Query: 152 LNRQNFQGSEI 162
           LNR    G  I
Sbjct: 58  LNRSEIAGKRI 68

This subgroup corresponds to the RRM2 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 is highly conserved between plants and fungi. To date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear. . Length = 71

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

 Score = 38.1 bits (88), Expect = 0.002
 Identities = 14/61 (22%), Positives = 34/61 (55%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           +++  ++ +  E D++  F  +G+++  ++ R       K YGF+EY+  ++   AI ++
Sbjct: 207 IYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASM 266

Query: 153 N 153
           N
Sbjct: 267 N 267

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

 Score = 36.0 bits (83), Expect = 0.002
 Identities = 22/74 (29%), Positives = 38/74 (51%), Gaps = 1/74 (1%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           L++G L+    E  L+Q F   G V +V+++ D        YGF+EY        A++ L
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPD-KNNKGVNYGFVEYHQSHDAEIALQTL 59

Query: 153 NRQNFQGSEIIVDF 166
           N +  + +EI V++
Sbjct: 60  NGRQIENNEIRVNW 73

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

 Score = 35.9 bits (83), Expect = 0.002
 Identities = 17/61 (27%), Positives = 33/61 (54%), Gaps = 1/61 (1%)

Query: 106 DLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD 165
           D+   F+ YG++ SVRV + F    ++ + F+E+   K  L A+ AL   +  G  +++ 
Sbjct: 16  DVRTLFSSYGQLKSVRVPKKF-DQSARGFAFVEFSTAKEALNAMNALKDTHLLGRRLVLQ 74

Query: 166 F 166
           +
Sbjct: 75  Y 75

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

 Score = 35.7 bits (83), Expect = 0.002
 Identities = 21/72 (29%), Positives = 41/72 (56%), Gaps = 3/72 (4%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           L++G L++   E  L + F++ G + S +++R+   G+   Y F+EY   ++  AA++ +
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIRE--HGNDP-YAFVEYYDHRSAAAALQTM 57

Query: 153 NRQNFQGSEIIV 164
           N +   G EI V
Sbjct: 58  NGRLILGQEIKV 69

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

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

 Score = 35.7 bits (83), Expect = 0.002
 Identities = 19/65 (29%), Positives = 32/65 (49%), Gaps = 7/65 (10%)

Query: 91  RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEY-DCEKACLAAI 149
            TL++G L +   E DL   F ++G++ S+ VV        ++  F+ +   E A  AA 
Sbjct: 2   TTLYVGGLGERVTEKDLRDHFYQFGEIRSITVV------PRQQCAFVTFTTREAAEKAAE 55

Query: 150 RALNR 154
           R  N+
Sbjct: 56  RLFNK 60

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|241089 cd12645, RRM_SRSF3, RNA recognition motif in vertebrate serine/arginine-rich splicing factor 3 (SRSF3)

 Score = 35.8 bits (82), Expect = 0.002
 Identities = 21/77 (27%), Positives = 39/77 (50%), Gaps = 5/77 (6%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           +++G L  N  + +LE+AF  YG + SV V R+        + F+E++  +    A+R L
Sbjct: 7   VYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVREL 61

Query: 153 NRQNFQGSEIIVDFECG 169
           + +   G  + V+   G
Sbjct: 62  DGRTLCGCRVRVELSNG 78

This subgroup corresponds to the RRM of SRSF3, also termed pre-mRNA-splicing factor SRp20, a splicing regulatory serine/arginine (SR) protein that 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. SRSF3 can shuttle between the nucleus and cytoplasm. It contains 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 = 81

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

 Score = 35.7 bits (83), Expect = 0.002
 Identities = 17/59 (28%), Positives = 33/59 (55%), Gaps = 4/59 (6%)

Query: 91  RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEY----DCEKAC 145
             +F+G L  ++ +  L + F+++G++    V+ D  TG S+ YGF+ +      E+AC
Sbjct: 1   TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERAC 59

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

 Score = 35.3 bits (82), Expect = 0.002
 Identities = 17/64 (26%), Positives = 33/64 (51%), Gaps = 4/64 (6%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           L++  L+ +  +  L + F+ +G + S +V+ D   G SK +GF+   C  +   A +A+
Sbjct: 4   LYVKNLDDSIDDERLREEFSPFGTITSAKVMTD-EKGRSKGFGFV---CFSSPEEATKAV 59

Query: 153 NRQN 156
              N
Sbjct: 60  TEMN 63

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

 Score = 35.1 bits (81), Expect = 0.003
 Identities = 18/74 (24%), Positives = 38/74 (51%), Gaps = 3/74 (4%)

Query: 92  TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
           T+++G L  + RE ++E  F +YG ++ + +    +      Y F+E++  +    AIR 
Sbjct: 1   TVYVGNLPGDIREREVEDLFYKYGPIVDIDLK---LPPRPPGYAFIEFEDARDAEDAIRG 57

Query: 152 LNRQNFQGSEIIVD 165
            +  +F G  + V+
Sbjct: 58  RDGYDFDGQRLRVE 71

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

 Score = 35.3 bits (81), Expect = 0.003
 Identities = 15/45 (33%), Positives = 31/45 (68%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFL 137
           +FIG L+ ++ + DL+  F+++G+V+   +  D +TG S+ +GF+
Sbjct: 1   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFV 45

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

 Score = 35.5 bits (81), Expect = 0.003
 Identities = 22/65 (33%), Positives = 32/65 (49%), Gaps = 2/65 (3%)

Query: 89  PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAA 148
           PT  L+I  L  +  E +LE     +G VIS R++RD   G S+  GF   +  + C   
Sbjct: 1   PT-NLYISNLPVSMDEQELENMLKPFGHVISTRILRD-ANGVSRGVGFARMESTEKCEVV 58

Query: 149 IRALN 153
           I+  N
Sbjct: 59  IQHFN 63

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|240777 cd12331, RRM_NRD1_SEB1_like, RNA recognition motif in Saccharomyces cerevisiae protein Nrd1, Schizosaccharomyces pombe Rpb7-binding protein seb1 and similar proteins

 Score = 35.2 bits (81), Expect = 0.003
 Identities = 18/68 (26%), Positives = 30/68 (44%), Gaps = 6/68 (8%)

Query: 90  TRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAI 149
           +RTLF G +  N  E DL   F  +G+V S       +  + KR+ F++    +    A 
Sbjct: 3   SRTLFPGGVTFNMIEYDLRSGFGRFGEVQSC------ILNNDKRHAFVKMYNRRDAENAR 56

Query: 150 RALNRQNF 157
            A+ +   
Sbjct: 57  EAMEQYKS 64

This subfamily corresponds to the RRM of Nrd1 and Seb1. Nrd1 is a novel heterogeneous nuclear ribonucleoprotein (hnRNP)-like RNA-binding protein encoded by gene NRD1 (for nuclear pre-mRNA down-regulation) from yeast S. cerevisiae. It is implicated in 3' end formation of small nucleolar and small nuclear RNAs transcribed by polymerase II, and plays a critical role in pre-mRNA metabolism. Nrd1 contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a short arginine-, serine-, and glutamate-rich segment similar to the regions rich in RE and RS dipeptides (RE/RS domains) in many metazoan splicing factors, and a proline- and glutamine-rich C-terminal domain (P+Q domain) similar to domains found in several yeast hnRNPs. Disruption of NRD1 gene is lethal to yeast cells. Its N-terminal domain is sufficient for viability, which may facilitate interactions with RNA polymerase II where Nrd1 may function as an auxiliary factor. By contrast, the RRM, RE/RS domains, and P+Q domain are dispensable. Seb1 is an RNA-binding protein encoded by gene seb1 (for seven binding) from fission yeast S. pombe. It is essential for cell viability and bound directly to Rpb7 subunit of RNA polymerase II. Seb1 is involved in processing of polymerase II transcripts. It also contains one RRM motif and a region rich in arginine-serine dipeptides (RS domain). Length = 79

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

 Score = 35.0 bits (80), Expect = 0.004
 Identities = 13/50 (26%), Positives = 30/50 (60%)

Query: 91  RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYD 140
           + +F+G + +++ E  L   F +YGK+ ++ V+ D  +G  + + F+ +D
Sbjct: 1   KKIFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFD 50

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

 Score = 37.3 bits (86), Expect = 0.004
 Identities = 21/90 (23%), Positives = 41/90 (45%), Gaps = 4/90 (4%)

Query: 77  RSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGF 136
                 + S T+    L +  L ++  + +L   F   G + + R++RD+ TG+S  Y F
Sbjct: 98  SDDNDTNNSGTN----LIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAF 153

Query: 137 LEYDCEKACLAAIRALNRQNFQGSEIIVDF 166
           +++  E     AI+ LN    +   + V +
Sbjct: 154 VDFGSEADSQRAIKNLNGITVRNKRLKVSY 183

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

 Score = 34.6 bits (80), Expect = 0.004
 Identities = 19/74 (25%), Positives = 36/74 (48%), Gaps = 6/74 (8%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           LF+G L  +  E + ++ F++YG+V  V + ++      K +GF+  D       A   L
Sbjct: 4   LFVGNLPNDITEEEFKELFSKYGEVSEVFLNKE------KGFGFIRLDTRTNAEKAKAEL 57

Query: 153 NRQNFQGSEIIVDF 166
           +    +G ++ V F
Sbjct: 58  DGIMRKGRQLRVRF 71

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

 Score = 34.8 bits (80), Expect = 0.004
 Identities = 21/97 (21%), Positives = 36/97 (37%), Gaps = 24/97 (24%)

Query: 92  TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
           T+++G +   + +ADL   F  +G ++  R   D      + + F++ D  +    AI  
Sbjct: 2   TVYVGNIPPYTTQADLIPLFQNFGYILEFRHQPD------RGFAFVKLDTHEQAAMAIVQ 55

Query: 152 LNRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWGGNR 188
           L      G                  R L  GWG +R
Sbjct: 56  LQGFPVHG------------------RPLRCGWGKDR 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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	225
KOG0113|consensus	335		99.91
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.89
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.86
KOG0121|consensus	153		99.75
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.74
KOG0105|consensus	241		99.73
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.72
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.71
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.71
KOG0122|consensus	270		99.71
KOG0107|consensus	195		99.7
KOG4207|consensus	256		99.7
KOG0149|consensus	247		99.66
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.65
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.65
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.63
KOG0125|consensus	376		99.62
PLN03120	260	nucleic acid binding protein; Provisional	99.62
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.61
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.6
KOG0130|consensus	170		99.59
PLN03213	759	repressor of silencing 3; Provisional	99.58
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.57
KOG0148|consensus	321		99.57
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.56
PLN03121	243	nucleic acid binding protein; Provisional	99.55
KOG0148|consensus	321		99.55
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.55
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.54
KOG0126|consensus	219		99.54
smart00362	72	RRM_2 RNA recognition motif.	99.54
KOG0117|consensus	506		99.53
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.53
KOG0415|consensus	479		99.52
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.51
KOG0131|consensus	203		99.5
smart00360	71	RRM RNA recognition motif.	99.5
KOG0145|consensus	360		99.5
KOG0116|consensus	419		99.49
KOG0117|consensus	506		99.49
KOG0111|consensus	298		99.48
KOG0144|consensus	510		99.48
KOG0108|consensus	435		99.47
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.47
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.46
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.45
KOG0114|consensus	124		99.44
KOG4212|consensus	608		99.43
KOG0144|consensus	510		99.42
KOG0127|consensus	678		99.42
KOG0127|consensus	678		99.38
KOG0145|consensus	360		99.36
KOG0146|consensus	371		99.36
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.34
smart00361	70	RRM_1 RNA recognition motif.	99.34
KOG0124|consensus	544		99.33
KOG0109|consensus	346		99.32
KOG4208|consensus	214		99.3
KOG0147|consensus	549		99.27
KOG0131|consensus	203		99.25
KOG4205|consensus	311		99.24
KOG0109|consensus	346		99.19
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.18
KOG0132|consensus	894		99.16
KOG0123|consensus	369		99.16
KOG4206|consensus	221		99.16
KOG4205|consensus	311		99.13
KOG0110|consensus	725		99.07
KOG0146|consensus	371		99.07
KOG4212|consensus	608		99.06
KOG0533|consensus	243		99.05
KOG0153|consensus	377		99.04
KOG4661|consensus	940		99.04
KOG0124|consensus	544		99.0
KOG4209|consensus	231		98.98
KOG0123|consensus	369		98.98
KOG0110|consensus	725		98.97
KOG0106|consensus	216		98.9
KOG1548|consensus	382		98.9
KOG1995|consensus	351		98.82
KOG4454|consensus	267		98.8
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.75
KOG1457|consensus	284		98.74
KOG0226|consensus	290		98.71
KOG0151|consensus	877		98.68
KOG4211|consensus	510		98.64
KOG4660|consensus	549		98.55
KOG4210|consensus	285		98.39
KOG0120|consensus	500		98.37
KOG4849|consensus	498		98.34
KOG0147|consensus	549		98.32
KOG1190|consensus	492		98.27
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.14
KOG1457|consensus	284		98.13
KOG4206|consensus	221		98.07
KOG4211|consensus	510		98.04
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.01
KOG3152|consensus	278		98.01
KOG0106|consensus	216		98.0
KOG0105|consensus	241		97.81
KOG1456|consensus	494		97.79
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.74
KOG1190|consensus	492		97.64
KOG0129|consensus	520		97.63
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.61
KOG4307|consensus	944		97.6
KOG1548|consensus	382		97.53
KOG0120|consensus	500		97.5
KOG2416|consensus	718		97.44
KOG1456|consensus	494		97.41
KOG0129|consensus	520		97.4
KOG2314|consensus	698		97.39
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.26
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	97.23
KOG1855|consensus	484		97.11
KOG1365|consensus	508		97.08
KOG1365|consensus	508		96.92
KOG4676|consensus	479		96.9
KOG0112|consensus	975		96.9
KOG2202|consensus	260		96.88
KOG1996|consensus	378		96.88
KOG0128|consensus	881		96.84
KOG2193|consensus	584		96.75
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	96.72
KOG4307|consensus	944		96.72
KOG0128|consensus	881		96.56
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	96.51
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	96.36
KOG0112|consensus	975		95.99
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	95.93
KOG0115|consensus	275		95.87
KOG2253|consensus	668		95.86
KOG2068|consensus	327		95.86
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	95.3
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	95.27
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	94.93
KOG2591|consensus	684		94.48
KOG4210|consensus	285		94.22
KOG4660|consensus	549		94.15
KOG2135|consensus	526		93.86
KOG4285|consensus	350		93.62
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	93.58
KOG4574|consensus	1007		91.98
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	91.93
KOG2193|consensus	584		89.79
KOG0804|consensus	493		89.54
KOG2318|consensus	650		87.48
KOG4676|consensus	479		87.29
KOG4410|consensus	396		82.75

>KOG0113|consensus

Probab=99.91  E-value=6.6e-24  Score=172.34  Aligned_cols=166  Identities=40%  Similarity=0.708  Sum_probs=138.8

Q ss_pred             CCCccccccccCccccCCCCCcccCcccHHHHHHHhccCCCCC-CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEE
Q psy222           42 VKYWYPYCITYDPIQAGSIDGTDTIPHDRAILRALRSTYKPHT-SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISV  120 (225)
Q Consensus        42 ~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v  120 (225)
                      +..+.+++...++++...++..+..++. ...+.+..+..... ...++-+||||+.|+++++|..|+..|+.||.|..|
T Consensus        53 ~p~~~p~~t~~e~~er~~~~k~e~~~~~-~~~~l~~wdP~~dp~a~gDPy~TLFv~RLnydT~EskLrreF~~YG~Ikri  131 (335)
T KOG0113|consen   53 APPKFPVETPEEPLERGRREKTEKIPHK-LERRLKLWDPNNDPNAIGDPYKTLFVARLNYDTSESKLRREFEKYGPIKRI  131 (335)
T ss_pred             CCCcCcccchhhHHHhhhhhhhhhhHHH-HHHHHHhcCCCCCCcccCCccceeeeeeccccccHHHHHHHHHhcCcceeE
Confidence            3456777777777777777766666664 33333333222222 566889999999999999999999999999999999


Q ss_pred             EEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEeeCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCC
Q psy222          121 RVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWGGNR-NSGQLRFGGRN  199 (225)
Q Consensus       121 ~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~~~~~~~~~~~r~~gg~gg~~-~~g~~~~gg~~  199 (225)
                      .|++++.||+++|||||+|.++.++.+|.+..+|..|+|+.|.|++-..+..++|.|++.+||.||.+ ..+...++++.
T Consensus       132 rlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDvERgRTvkgW~PRRLGGGLGg~r~~~~~~~~~~R~  211 (335)
T KOG0113|consen  132 RLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDVERGRTVKGWLPRRLGGGLGGRRYESRQLRFGGRE  211 (335)
T ss_pred             EEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEecccccccccccccccCCcCCcccccccccccccc
Confidence            99999999999999999999999999999999999999999999999999999999999999999987 45666788888


Q ss_pred             CCCCCCccC
Q psy222          200 KPWVKPVQL  208 (225)
Q Consensus       200 ~~~~~p~~~  208 (225)
                      +++..|...
T Consensus       212 R~~~s~~~g  220 (335)
T KOG0113|consen  212 RPFRSPLNG  220 (335)
T ss_pred             ccccCCCCC
Confidence            887777654

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

Probab=99.89  E-value=6.7e-22  Score=150.20  Aligned_cols=87  Identities=32%  Similarity=0.521  Sum_probs=81.6

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q psy222           86 STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD  165 (225)
Q Consensus        86 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~  165 (225)
                      .....++|||+|||+.++|++|+++|.+||.|..|.|+.++.+++++|||||+|.+.++|++||+.||+..|+++.|+|+
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            34566799999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeeCCCC
Q psy222          166 FECGRVL  172 (225)
Q Consensus       166 ~a~~~~~  172 (225)
                      ++.++..
T Consensus       110 ~a~~~~~  116 (144)
T PLN03134        110 PANDRPS  116 (144)
T ss_pred             eCCcCCC
Confidence            9987654

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.86  E-value=4.6e-21  Score=164.85  Aligned_cols=84  Identities=21%  Similarity=0.425  Sum_probs=77.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCC--cEEEEEE
Q psy222           89 PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQG--SEIIVDF  166 (225)
Q Consensus        89 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g--~~l~V~~  166 (225)
                      ...+|||+|||+.++|++|+++|++||.|+.|.|++++.+++.++||||+|.+.++|++||+.||+..|.+  ++|+|.+
T Consensus       192 ~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~  271 (346)
T TIGR01659       192 KDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRL  271 (346)
T ss_pred             ccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEE
Confidence            45689999999999999999999999999999999999899999999999999999999999999999876  6899999


Q ss_pred             eeCCCC
Q psy222          167 ECGRVL  172 (225)
Q Consensus       167 a~~~~~  172 (225)
                      +.....
T Consensus       272 a~~~~~  277 (346)
T TIGR01659       272 AEEHGK  277 (346)
T ss_pred             CCcccc
Confidence            887543

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

>KOG0121|consensus

Probab=99.75  E-value=3.8e-18  Score=123.02  Aligned_cols=82  Identities=17%  Similarity=0.331  Sum_probs=78.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF  166 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~  166 (225)
                      ...+++|||+||++.++|++|.++|+.+|.|..|.+-.|+.+..++|||||+|.+.++|+.|++.+++..|++++|+|+|
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            34678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ee
Q psy222          167 EC  168 (225)
Q Consensus       167 a~  168 (225)
                      ..
T Consensus       113 D~  114 (153)
T KOG0121|consen  113 DA  114 (153)
T ss_pred             cc
Confidence            65

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.74  E-value=1.5e-17  Score=143.88  Aligned_cols=84  Identities=26%  Similarity=0.441  Sum_probs=79.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEe
Q psy222           88 DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFE  167 (225)
Q Consensus        88 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a  167 (225)
                      ..+.+|||+|||+.+++++|+++|++||.|..|+|+++..++.++|||||+|.+.++|.+||..|||..|+|+.|+|.|+
T Consensus       267 ~~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~  346 (352)
T TIGR01661       267 GAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFK  346 (352)
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEc
Confidence            34557999999999999999999999999999999999989999999999999999999999999999999999999999


Q ss_pred             eCCC
Q psy222          168 CGRV  171 (225)
Q Consensus       168 ~~~~  171 (225)
                      ..+.
T Consensus       347 ~~~~  350 (352)
T TIGR01661       347 TNKA  350 (352)
T ss_pred             cCCC
Confidence            8764

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

>KOG0105|consensus

Probab=99.73  E-value=2.5e-17  Score=125.95  Aligned_cols=79  Identities=22%  Similarity=0.517  Sum_probs=71.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEe
Q psy222           88 DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFE  167 (225)
Q Consensus        88 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a  167 (225)
                      ...++|||+|||.++.+.+|+++|-+||.|..|.|...   .....||||+|++..+|+.||..-+|..++|+.|+|+++
T Consensus         4 r~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r---~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfp   80 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNR---PGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFP   80 (241)
T ss_pred             cccceEEecCCCcchhhccHHHHHhhhcceEEEEeccC---CCCCCeeEEEecCccchhhhhhcccccccCcceEEEEec
Confidence            45689999999999999999999999999999988643   224679999999999999999999999999999999998


Q ss_pred             eC
Q psy222          168 CG  169 (225)
Q Consensus       168 ~~  169 (225)
                      +.
T Consensus        81 rg   82 (241)
T KOG0105|consen   81 RG   82 (241)
T ss_pred             cC
Confidence            75

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.72  E-value=3.5e-17  Score=140.90  Aligned_cols=85  Identities=22%  Similarity=0.432  Sum_probs=79.8

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      ......++|||+|||+++++++|+++|+.||.|+.|+|+.+..+++++|||||+|.++++|++||+.|++..|.+++|+|
T Consensus       102 ~~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V  181 (346)
T TIGR01659       102 DTNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKV  181 (346)
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeee
Confidence            34456789999999999999999999999999999999999989999999999999999999999999999999999999


Q ss_pred             EEeeC
Q psy222          165 DFECG  169 (225)
Q Consensus       165 ~~a~~  169 (225)
                      .++++
T Consensus       182 ~~a~p  186 (346)
T TIGR01659       182 SYARP  186 (346)
T ss_pred             ecccc
Confidence            98864

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

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.71  E-value=4.8e-17  Score=140.76  Aligned_cols=83  Identities=27%  Similarity=0.442  Sum_probs=78.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEee
Q psy222           89 PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFEC  168 (225)
Q Consensus        89 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~  168 (225)
                      +..+|||+|||+.+++++|+++|+.||.|..|+|++++.+++++|||||+|.+.++|++||+.||+..|.|+.|.|.+++
T Consensus         2 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a~   81 (352)
T TIGR01661         2 SKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYAR   81 (352)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeec
Confidence            45799999999999999999999999999999999999899999999999999999999999999999999999999987


Q ss_pred             CCC
Q psy222          169 GRV  171 (225)
Q Consensus       169 ~~~  171 (225)
                      +..
T Consensus        82 ~~~   84 (352)
T TIGR01661        82 PSS   84 (352)
T ss_pred             ccc
Confidence            644

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

>PF00076 RRM_1: RNA recognition motif

Probab=99.71  E-value=1e-16  Score=106.29  Aligned_cols=70  Identities=33%  Similarity=0.691  Sum_probs=67.0

Q ss_pred             EEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEE
Q psy222           93 LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEII  163 (225)
Q Consensus        93 l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~  163 (225)
                      |||+|||+.+++++|+++|++||.|..+.+..+ .++..++||||+|.+.++|++|++.|++..|.|+.|+
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            799999999999999999999999999999987 5888999999999999999999999999999999885

(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 ....

>KOG0122|consensus

Probab=99.71  E-value=7.6e-17  Score=128.16  Aligned_cols=85  Identities=27%  Similarity=0.443  Sum_probs=81.4

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q psy222           86 STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD  165 (225)
Q Consensus        86 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~  165 (225)
                      ...+.++|-|.||+.+++|++|+++|..||.|..|.|.+|+.||.++|||||.|.+.++|.+||..|||+-++.-.|+|+
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            34577899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeeCC
Q psy222          166 FECGR  170 (225)
Q Consensus       166 ~a~~~  170 (225)
                      |++|+
T Consensus       265 wskP~  269 (270)
T KOG0122|consen  265 WSKPS  269 (270)
T ss_pred             ecCCC
Confidence            99885

>KOG0107|consensus

Probab=99.70  E-value=3.5e-16  Score=118.68  Aligned_cols=80  Identities=29%  Similarity=0.573  Sum_probs=73.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEe
Q psy222           88 DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFE  167 (225)
Q Consensus        88 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a  167 (225)
                      .-.++|||+||+..+++.+|+.+|..||.|..|.|...     +.|||||+|++..+|+.|+..|+|..|.|..|+|+++
T Consensus         8 ~~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn-----PPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S   82 (195)
T KOG0107|consen    8 NGNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARN-----PPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELS   82 (195)
T ss_pred             CCCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeec-----CCCceEEeccCcccHHHHHhhcCCccccCceEEEEee
Confidence            34679999999999999999999999999999998865     4899999999999999999999999999999999999


Q ss_pred             eCCCC
Q psy222          168 CGRVL  172 (225)
Q Consensus       168 ~~~~~  172 (225)
                      +.+..
T Consensus        83 ~G~~r   87 (195)
T KOG0107|consen   83 TGRPR   87 (195)
T ss_pred             cCCcc
Confidence            87654

>KOG4207|consensus

Probab=99.70  E-value=1.4e-16  Score=123.91  Aligned_cols=84  Identities=23%  Similarity=0.391  Sum_probs=79.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF  166 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~  166 (225)
                      .....+|-|-||.+.++.++|+.+|++||.|-+|.|++|+.|...+|||||.|....+|+.|+++|+|..|+|+.|.|++
T Consensus        10 v~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~   89 (256)
T KOG4207|consen   10 VEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQM   89 (256)
T ss_pred             cccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehh
Confidence            34456899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeCC
Q psy222          167 ECGR  170 (225)
Q Consensus       167 a~~~  170 (225)
                      |+-.
T Consensus        90 aryg   93 (256)
T KOG4207|consen   90 ARYG   93 (256)
T ss_pred             hhcC
Confidence            9853

>KOG0149|consensus

Probab=99.66  E-value=1.8e-16  Score=125.50  Aligned_cols=79  Identities=23%  Similarity=0.435  Sum_probs=73.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEeeC
Q psy222           90 TRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECG  169 (225)
Q Consensus        90 ~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~~  169 (225)
                      -.+||||+|+|++..+.|+++|++||+|+++.|+.|+.++++|||+||+|.+.+.|++|++. ..-.|+||+..+.+|.-
T Consensus        12 ~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNcnlA~l   90 (247)
T KOG0149|consen   12 FTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKANCNLASL   90 (247)
T ss_pred             EEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC-CCCcccccccccchhhh
Confidence            36899999999999999999999999999999999999999999999999999999999985 45679999999998763

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

Probab=99.65  E-value=5.3e-16  Score=140.84  Aligned_cols=89  Identities=19%  Similarity=0.354  Sum_probs=82.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEee
Q psy222           89 PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFEC  168 (225)
Q Consensus        89 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~  168 (225)
                      ..++|||+||++++++++|+++|+.||.|..|+|++++.+++.+|||||+|.+.++|.+||+.||+..|+|+.|+|.++.
T Consensus       203 ~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi  282 (612)
T TIGR01645       203 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCV  282 (612)
T ss_pred             ccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecC
Confidence            45799999999999999999999999999999999998889999999999999999999999999999999999999998


Q ss_pred             CCCCCCCCC
Q psy222          169 GRVLPGWKP  177 (225)
Q Consensus       169 ~~~~~~~~~  177 (225)
                      ..+...+.+
T Consensus       283 ~pP~~~~~p  291 (612)
T TIGR01645       283 TPPDALLQP  291 (612)
T ss_pred             CCccccCCC
Confidence            765555543

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.

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

Probab=99.65  E-value=2.8e-15  Score=135.89  Aligned_cols=78  Identities=26%  Similarity=0.480  Sum_probs=71.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcC--CceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q psy222           88 DPTRTLFIGRLNKNSREADLEQAFAEY--GKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD  165 (225)
Q Consensus        88 ~~~~~l~V~nLp~~~te~~L~~~F~~~--G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~  165 (225)
                      ...++|||+||++.+++++|+++|++|  |.|+.|.++        ++||||+|.+.++|++||+.||+..|+|+.|+|.
T Consensus       231 ~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~--------rgfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~  302 (578)
T TIGR01648       231 AKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI--------RDYAFVHFEDREDAVKAMDELNGKELEGSEIEVT  302 (578)
T ss_pred             ccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee--------cCeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            345789999999999999999999999  999999876        4599999999999999999999999999999999


Q ss_pred             EeeCCCCC
Q psy222          166 FECGRVLP  173 (225)
Q Consensus       166 ~a~~~~~~  173 (225)
                      ++++....
T Consensus       303 ~Akp~~~~  310 (578)
T TIGR01648       303 LAKPVDKK  310 (578)
T ss_pred             EccCCCcc
Confidence            99986544

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.

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.63  E-value=3.2e-15  Score=99.47  Aligned_cols=70  Identities=27%  Similarity=0.575  Sum_probs=64.6

Q ss_pred             EEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEE
Q psy222           93 LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEII  163 (225)
Q Consensus        93 l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~  163 (225)
                      |||+|||+.+++++|+++|..||.|..+.+..++. +..+++|||+|.+.++|.+|+..+++..|+|+.|+
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            79999999999999999999999999999999876 88999999999999999999999998999999874

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 ....

>KOG0125|consensus

Probab=99.62  E-value=1.1e-15  Score=126.08  Aligned_cols=86  Identities=27%  Similarity=0.423  Sum_probs=78.6

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      ..+...++|||.|||+...|.||+.+|.+||.|++|.|+.+  ..-+|||+||+|++.++|++|-++|||..|.||+|.|
T Consensus        91 ~s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfN--ERGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEV  168 (376)
T KOG0125|consen   91 SSKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFN--ERGSKGFGFVTMENPADADRARAELHGTVVEGRKIEV  168 (376)
T ss_pred             CCCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEec--cCCCCccceEEecChhhHHHHHHHhhcceeeceEEEE
Confidence            44556689999999999999999999999999999999987  3457999999999999999999999999999999999


Q ss_pred             EEeeCCCC
Q psy222          165 DFECGRVL  172 (225)
Q Consensus       165 ~~a~~~~~  172 (225)
                      ..|..|..
T Consensus       169 n~ATarV~  176 (376)
T KOG0125|consen  169 NNATARVH  176 (376)
T ss_pred             eccchhhc
Confidence            99987654

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.62  E-value=3.7e-15  Score=121.47  Aligned_cols=77  Identities=12%  Similarity=0.204  Sum_probs=71.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEeeC
Q psy222           90 TRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECG  169 (225)
Q Consensus        90 ~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~~  169 (225)
                      .++|||+|||+.+++++|+++|+.||.|.+|.|+.++.   .++||||+|.++++|+.||. |+|..|.|+.|.|.++..
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~   79 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAED   79 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccC
Confidence            47999999999999999999999999999999998853   46899999999999999996 999999999999999875


Q ss_pred             C
Q psy222          170 R  170 (225)
Q Consensus       170 ~  170 (225)
                      .
T Consensus        80 ~   80 (260)
T PLN03120         80 Y   80 (260)
T ss_pred             C
Confidence            3

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

Probab=99.61  E-value=1.3e-15  Score=136.36  Aligned_cols=81  Identities=28%  Similarity=0.506  Sum_probs=77.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEee
Q psy222           89 PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFEC  168 (225)
Q Consensus        89 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~  168 (225)
                      ..++|||+|||..+++++|+++|++||.|..|.|+.+..+++.+|||||+|.+.++|.+||..|+|..|.|+.|+|.++.
T Consensus       185 ~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~  264 (457)
T TIGR01622       185 NFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQ  264 (457)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEcc
Confidence            36899999999999999999999999999999999998888999999999999999999999999999999999999976


Q ss_pred             C
Q psy222          169 G  169 (225)
Q Consensus       169 ~  169 (225)
                      .
T Consensus       265 ~  265 (457)
T TIGR01622       265 D  265 (457)
T ss_pred             C
Confidence            3

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.

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

Probab=99.60  E-value=3e-15  Score=135.95  Aligned_cols=81  Identities=26%  Similarity=0.459  Sum_probs=77.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEe
Q psy222           88 DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFE  167 (225)
Q Consensus        88 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a  167 (225)
                      ...++|||+||++.+++++|+++|.+||.|.+|.|+.++.+++++|||||+|.+.++|++||+.|||..|.|+.|+|...
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            45689999999999999999999999999999999999999999999999999999999999999999999999999865


Q ss_pred             e
Q psy222          168 C  168 (225)
Q Consensus       168 ~  168 (225)
                      .
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.

>KOG0130|consensus

Probab=99.59  E-value=8.7e-15  Score=106.66  Aligned_cols=92  Identities=27%  Similarity=0.463  Sum_probs=85.5

Q ss_pred             CCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCC
Q psy222           80 YKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQG  159 (225)
Q Consensus        80 ~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g  159 (225)
                      ..|.++..-.+..|||.++...++|++|...|..||.|..|+|..|+.||-.+|||+|+|.+.+.|++|+..||+..|.+
T Consensus        62 ~~pgPqrSVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~  141 (170)
T KOG0130|consen   62 MRPGPQRSVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLG  141 (170)
T ss_pred             cCCCCccceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhC
Confidence            34555667778899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cEEEEEEeeCCC
Q psy222          160 SEIIVDFECGRV  171 (225)
Q Consensus       160 ~~l~V~~a~~~~  171 (225)
                      +.|.|.|+.-+.
T Consensus       142 q~v~VDw~Fv~g  153 (170)
T KOG0130|consen  142 QNVSVDWCFVKG  153 (170)
T ss_pred             CceeEEEEEecC
Confidence            999999998654

>PLN03213 repressor of silencing 3; Provisional

Probab=99.58  E-value=5.9e-15  Score=127.69  Aligned_cols=78  Identities=18%  Similarity=0.350  Sum_probs=72.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCH--HHHHHHHHHhCCCccCCcEEEEE
Q psy222           88 DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCE--KACLAAIRALNRQNFQGSEIIVD  165 (225)
Q Consensus        88 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~--~~a~~Al~~l~g~~l~g~~l~V~  165 (225)
                      ....+||||||++.+++++|+.+|..||.|..|.|++.  +|  +|||||+|...  .++.+||..|||..|+|+.|+|.
T Consensus         8 ~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRE--TG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVN   83 (759)
T PLN03213          8 GGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRT--KG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLE   83 (759)
T ss_pred             CcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecc--cC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEe
Confidence            34579999999999999999999999999999999944  66  99999999987  78999999999999999999999


Q ss_pred             EeeC
Q psy222          166 FECG  169 (225)
Q Consensus       166 ~a~~  169 (225)
                      .|++
T Consensus        84 KAKP   87 (759)
T PLN03213         84 KAKE   87 (759)
T ss_pred             eccH
Confidence            9986

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

Probab=99.57  E-value=1.7e-14  Score=130.71  Aligned_cols=82  Identities=27%  Similarity=0.467  Sum_probs=77.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEe
Q psy222           88 DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFE  167 (225)
Q Consensus        88 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a  167 (225)
                      ...++|||+|||+.+++++|+++|..||.|..+.|+.+..++.++|||||+|.+.+.|..||..|++..|.|+.|.|.++
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            34579999999999999999999999999999999999889999999999999999999999999999999999999998


Q ss_pred             eC
Q psy222          168 CG  169 (225)
Q Consensus       168 ~~  169 (225)
                      ..
T Consensus       373 ~~  374 (509)
T TIGR01642       373 CV  374 (509)
T ss_pred             cc
Confidence            65

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

>KOG0148|consensus

Probab=99.57  E-value=1.4e-14  Score=116.84  Aligned_cols=81  Identities=21%  Similarity=0.445  Sum_probs=76.2

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      ...++.++||||||+..++|++|++.|+.||.|.+|+|..+      +||+||.|.+.+.|..||..||+.+|.|+.+++
T Consensus       159 Qssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~------qGYaFVrF~tkEaAahAIv~mNntei~G~~VkC  232 (321)
T KOG0148|consen  159 QSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD------QGYAFVRFETKEAAAHAIVQMNNTEIGGQLVRC  232 (321)
T ss_pred             cCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc------cceEEEEecchhhHHHHHHHhcCceeCceEEEE
Confidence            66778899999999999999999999999999999999987      799999999999999999999999999999999


Q ss_pred             EEeeCCC
Q psy222          165 DFECGRV  171 (225)
Q Consensus       165 ~~a~~~~  171 (225)
                      .|-+...
T Consensus       233 sWGKe~~  239 (321)
T KOG0148|consen  233 SWGKEGD  239 (321)
T ss_pred             eccccCC
Confidence            9987643

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

Probab=99.56  E-value=1.7e-14  Score=132.38  Aligned_cols=78  Identities=31%  Similarity=0.537  Sum_probs=75.2

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEeeC
Q psy222           92 TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECG  169 (225)
Q Consensus        92 ~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~~  169 (225)
                      +|||+|||.+++|++|+++|++||.|..|+|+++..+++++|||||+|.+.++|++||..|++..|.|+.|+|.|+..
T Consensus         2 sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~   79 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQR   79 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeecccc
Confidence            799999999999999999999999999999999998999999999999999999999999999999999999999753

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

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.55  E-value=3e-14  Score=114.51  Aligned_cols=77  Identities=14%  Similarity=0.148  Sum_probs=70.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEee
Q psy222           89 PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFEC  168 (225)
Q Consensus        89 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~  168 (225)
                      .+.+|||+||++.+|+++|++||+.||.|.+|.|+++.   ..++||||+|.+++.++.||. |+|..|.++.|.|....
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~---et~gfAfVtF~d~~aaetAll-LnGa~l~d~~I~It~~~   79 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG---EYACTAYVTFKDAYALETAVL-LSGATIVDQRVCITRWG   79 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC---CcceEEEEEECCHHHHHHHHh-cCCCeeCCceEEEEeCc
Confidence            46799999999999999999999999999999999884   345799999999999999996 99999999999988765


Q ss_pred             C
Q psy222          169 G  169 (225)
Q Consensus       169 ~  169 (225)
                      .
T Consensus        80 ~   80 (243)
T PLN03121         80 Q   80 (243)
T ss_pred             c
Confidence            3

>KOG0148|consensus

Probab=99.55  E-value=1.2e-14  Score=117.29  Aligned_cols=82  Identities=29%  Similarity=0.521  Sum_probs=79.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEeeC
Q psy222           90 TRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECG  169 (225)
Q Consensus        90 ~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~~  169 (225)
                      ...|||+.|...++-++|++.|.+||+|.+++|++|..|+++|||+||.|.+.++|++||..|||.-|+.|.|+..||..
T Consensus        62 hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATR  141 (321)
T KOG0148|consen   62 HFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATR  141 (321)
T ss_pred             ceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeecccccc
Confidence            56899999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             CC
Q psy222          170 RV  171 (225)
Q Consensus       170 ~~  171 (225)
                      ++
T Consensus       142 Kp  143 (321)
T KOG0148|consen  142 KP  143 (321)
T ss_pred             Cc
Confidence            65

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

Probab=99.55  E-value=3.9e-14  Score=126.76  Aligned_cols=84  Identities=29%  Similarity=0.408  Sum_probs=77.9

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      ....+.++|||+|||+.+++++|+++|++||.|..|.|+.++.+++.+|||||+|.+.++|++||. |++..|.|+.|.|
T Consensus        84 ~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v  162 (457)
T TIGR01622        84 EAERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIV  162 (457)
T ss_pred             ccccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEE
Confidence            344567899999999999999999999999999999999999899999999999999999999998 8999999999999


Q ss_pred             EEeeC
Q psy222          165 DFECG  169 (225)
Q Consensus       165 ~~a~~  169 (225)
                      .++..
T Consensus       163 ~~~~~  167 (457)
T TIGR01622       163 QSSQA  167 (457)
T ss_pred             eecch
Confidence            88653

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

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

Probab=99.54  E-value=4.4e-14  Score=129.62  Aligned_cols=83  Identities=19%  Similarity=0.416  Sum_probs=78.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF  166 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~  166 (225)
                      .....+|||+||++.+++++|+++|++||.|.+|+|+.+ .++.++|||||+|.+.++|.+||..||+..|.|++|.|.+
T Consensus       282 ~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d-~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~  360 (562)
T TIGR01628       282 KAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLD-EKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVAL  360 (562)
T ss_pred             ccCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEEC-CCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEe
Confidence            456678999999999999999999999999999999999 5899999999999999999999999999999999999999


Q ss_pred             eeCC
Q psy222          167 ECGR  170 (225)
Q Consensus       167 a~~~  170 (225)
                      +..+
T Consensus       361 a~~k  364 (562)
T TIGR01628       361 AQRK  364 (562)
T ss_pred             ccCc
Confidence            9864

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

>KOG0126|consensus

Probab=99.54  E-value=8.4e-16  Score=117.30  Aligned_cols=85  Identities=28%  Similarity=0.502  Sum_probs=78.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF  166 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~  166 (225)
                      -.++.-|||||||+..||.+|..+|++||+|+.|.|++|+.||+++||||+.|++-.+---|+.-|||..|.|+.|+|..
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            44667899999999999999999999999999999999999999999999999998888888999999999999999998


Q ss_pred             eeCCC
Q psy222          167 ECGRV  171 (225)
Q Consensus       167 a~~~~  171 (225)
                      .....
T Consensus       112 v~~Yk  116 (219)
T KOG0126|consen  112 VSNYK  116 (219)
T ss_pred             ccccc
Confidence            65433

>smart00362 RRM_2 RNA recognition motif

Probab=99.54  E-value=6.2e-14  Score=92.22  Aligned_cols=72  Identities=36%  Similarity=0.677  Sum_probs=67.0

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q psy222           92 TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD  165 (225)
Q Consensus        92 ~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~  165 (225)
                      +|||.|||..+++++|+++|.+||.|..+.+..+.  +..+++|||+|.+.+.|+.|+..|++..|.++.|.|+
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            58999999999999999999999999999998775  6778999999999999999999999999999998873

>KOG0117|consensus

Probab=99.53  E-value=4.5e-14  Score=120.83  Aligned_cols=77  Identities=26%  Similarity=0.458  Sum_probs=71.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEee
Q psy222           89 PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFEC  168 (225)
Q Consensus        89 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~  168 (225)
                      .-+.|||.||+.++||+.|+++|.+||.|+.|+.++|        ||||.|.+.++|.+|++.||++.|+|..|.|.+|+
T Consensus       258 ~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD--------YaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAK  329 (506)
T KOG0117|consen  258 KVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD--------YAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAK  329 (506)
T ss_pred             heeeeeeeccchhhhHHHHHHHHHhccceEEeecccc--------eeEEeecchHHHHHHHHHhcCceecCceEEEEecC
Confidence            3478999999999999999999999999999998855        99999999999999999999999999999999999


Q ss_pred             CCCCC
Q psy222          169 GRVLP  173 (225)
Q Consensus       169 ~~~~~  173 (225)
                      +....
T Consensus       330 P~~k~  334 (506)
T KOG0117|consen  330 PVDKK  334 (506)
T ss_pred             Chhhh
Confidence            85543

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

Probab=99.53  E-value=3.7e-14  Score=128.61  Aligned_cols=79  Identities=20%  Similarity=0.439  Sum_probs=71.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccC-CcEEEEEE
Q psy222           88 DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQ-GSEIIVDF  166 (225)
Q Consensus        88 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~-g~~l~V~~  166 (225)
                      ...++|||+|||++++|++|+++|++||.|..|+|++| .+++++|||||+|.+.++|++||+.||+..|. ++.|.|.+
T Consensus        56 ~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~  134 (578)
T TIGR01648        56 GRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCI  134 (578)
T ss_pred             CCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC-CCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCccccccc
Confidence            34689999999999999999999999999999999999 69999999999999999999999999998885 66666654


Q ss_pred             e
Q psy222          167 E  167 (225)
Q Consensus       167 a  167 (225)
                      +
T Consensus       135 S  135 (578)
T TIGR01648       135 S  135 (578)
T ss_pred             c
Confidence            4

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.

>KOG0415|consensus

Probab=99.52  E-value=2.4e-14  Score=119.44  Aligned_cols=109  Identities=27%  Similarity=0.505  Sum_probs=94.0

Q ss_pred             cccHHHHHHHhccCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHH
Q psy222           67 PHDRAILRALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACL  146 (225)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~  146 (225)
                      ++..++..++..+ .|.....+|.+.|||-.|.+.++.++|.-+|+.||.|..|.|+++..||.+..||||+|.+.++|+
T Consensus       217 a~~~A~iLEmvGD-lpdAd~~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE  295 (479)
T KOG0415|consen  217 AKAQAVILEMVGD-LPDADVKPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCE  295 (479)
T ss_pred             HHhhHhHHHHhcC-CcccccCCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHH
Confidence            3344455555555 345567888899999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhCCCccCCcEEEEEEeeCCCCCCCC
Q psy222          147 AAIRALNRQNFQGSEIIVDFECGRVLPGWK  176 (225)
Q Consensus       147 ~Al~~l~g~~l~g~~l~V~~a~~~~~~~~~  176 (225)
                      +|...|++..|+++.|+|.|++.-....|+
T Consensus       296 ~AyFKMdNvLIDDrRIHVDFSQSVsk~k~r  325 (479)
T KOG0415|consen  296 QAYFKMDNVLIDDRRIHVDFSQSVSKVKYR  325 (479)
T ss_pred             HHHhhhcceeeccceEEeehhhhhhhhhcc
Confidence            999999999999999999999865444444

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

Probab=99.51  E-value=1e-13  Score=114.02  Aligned_cols=79  Identities=35%  Similarity=0.610  Sum_probs=76.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEee
Q psy222           90 TRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFEC  168 (225)
Q Consensus        90 ~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~  168 (225)
                      .++|||+|||+.+++++|+++|..||.|..|.+..++.++..+|||||+|.+.++|..|+..|++..|.|+.|.|.++.
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            5899999999999999999999999999999999998899999999999999999999999999999999999999965

>KOG0131|consensus

Probab=99.50  E-value=3.5e-14  Score=108.52  Aligned_cols=82  Identities=29%  Similarity=0.468  Sum_probs=78.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF  166 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~  166 (225)
                      .....+|||+||+..++++.|.++|-+.|.|+.+++++++.+...+|||||+|.++++|+-|++.||...|.|++|+|..
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            44567999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ee
Q psy222          167 EC  168 (225)
Q Consensus       167 a~  168 (225)
                      +.
T Consensus        86 as   87 (203)
T KOG0131|consen   86 AS   87 (203)
T ss_pred             cc
Confidence            87

>smart00360 RRM RNA recognition motif

Probab=99.50  E-value=1.6e-13  Score=89.88  Aligned_cols=71  Identities=37%  Similarity=0.659  Sum_probs=66.6

Q ss_pred             EcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q psy222           95 IGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD  165 (225)
Q Consensus        95 V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~  165 (225)
                      |+|||..+++++|+.+|.+||.|..+.+..++.++.+++||||+|.+.++|..|+..|++..+.++.|+|.
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            57999999999999999999999999999887778899999999999999999999999999999998873

>KOG0145|consensus

Probab=99.50  E-value=8.9e-14  Score=111.80  Aligned_cols=85  Identities=29%  Similarity=0.466  Sum_probs=79.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF  166 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~  166 (225)
                      .+....|.|.-||..+|+++|+.+|...|+|++|++++|+.+|.+.||+||.|.++++|++|+..|||..|..+.|+|.+
T Consensus        38 ~~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSy  117 (360)
T KOG0145|consen   38 DESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSY  117 (360)
T ss_pred             CcccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEe
Confidence            34456789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeCCC
Q psy222          167 ECGRV  171 (225)
Q Consensus       167 a~~~~  171 (225)
                      |++-.
T Consensus       118 ARPSs  122 (360)
T KOG0145|consen  118 ARPSS  122 (360)
T ss_pred             ccCCh
Confidence            99743

>KOG0116|consensus

Probab=99.49  E-value=3.3e-13  Score=117.68  Aligned_cols=87  Identities=20%  Similarity=0.305  Sum_probs=72.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEe
Q psy222           88 DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFE  167 (225)
Q Consensus        88 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a  167 (225)
                      ....+|||.|||.++++.+|+++|..||.|+...|..-...++...|+||+|.+.+.++.||++ +-..|++++|.|+..
T Consensus       286 ~~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek  364 (419)
T KOG0116|consen  286 ADGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEK  364 (419)
T ss_pred             ecccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEec
Confidence            3445699999999999999999999999999887765432344448999999999999999996 677899999999998


Q ss_pred             eCCCCCCC
Q psy222          168 CGRVLPGW  175 (225)
Q Consensus       168 ~~~~~~~~  175 (225)
                      ++......
T Consensus       365 ~~~~~g~~  372 (419)
T KOG0116|consen  365 RPGFRGNG  372 (419)
T ss_pred             cccccccc
Confidence            87554433

>KOG0117|consensus

Probab=99.49  E-value=1.4e-13  Score=117.84  Aligned_cols=83  Identities=22%  Similarity=0.426  Sum_probs=77.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCcc-CCcEEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNF-QGSEIIVD  165 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l-~g~~l~V~  165 (225)
                      ..-++.||||.||.++.|++|.-+|.+.|.|-+++|++|+.+|.++|||||.|.+.++|+.||+.||+++| .|+.|.|+
T Consensus        80 p~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc  159 (506)
T KOG0117|consen   80 PPRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVC  159 (506)
T ss_pred             CCCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEE
Confidence            45679999999999999999999999999999999999999999999999999999999999999999988 57888888


Q ss_pred             EeeC
Q psy222          166 FECG  169 (225)
Q Consensus       166 ~a~~  169 (225)
                      .+..
T Consensus       160 ~Sva  163 (506)
T KOG0117|consen  160 VSVA  163 (506)
T ss_pred             Eeee
Confidence            7653

>KOG0111|consensus

Probab=99.48  E-value=3e-14  Score=111.95  Aligned_cols=85  Identities=25%  Similarity=0.506  Sum_probs=80.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEe
Q psy222           88 DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFE  167 (225)
Q Consensus        88 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a  167 (225)
                      ...++||||+|..+++|.-|...|-.||.|..|.++.|..+++.+||+||+|...++|.+||.-||+.+|.|+.|+|.+|
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~A   87 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLA   87 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeec
Confidence            34579999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eCCCC
Q psy222          168 CGRVL  172 (225)
Q Consensus       168 ~~~~~  172 (225)
                      +|...
T Consensus        88 kP~ki   92 (298)
T KOG0111|consen   88 KPEKI   92 (298)
T ss_pred             CCccc
Confidence            98443

>KOG0144|consensus

Probab=99.48  E-value=1.2e-13  Score=117.73  Aligned_cols=84  Identities=31%  Similarity=0.574  Sum_probs=76.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCc-cCC--cEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQN-FQG--SEII  163 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~-l~g--~~l~  163 (225)
                      ....-++||+-||..++|.+|+++|++||.|.+|.|++|+.|+..+|||||.|.+.++|.+|+.+||+.. |.|  .+|.
T Consensus        31 d~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvq  110 (510)
T KOG0144|consen   31 DGSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQ  110 (510)
T ss_pred             CchhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCccee
Confidence            3555689999999999999999999999999999999999999999999999999999999999998864 555  6789


Q ss_pred             EEEeeCC
Q psy222          164 VDFECGR  170 (225)
Q Consensus       164 V~~a~~~  170 (225)
                      |++|...
T Consensus       111 vk~Ad~E  117 (510)
T KOG0144|consen  111 VKYADGE  117 (510)
T ss_pred             ecccchh
Confidence            9998753

>KOG0108|consensus

Probab=99.47  E-value=1.3e-13  Score=120.80  Aligned_cols=82  Identities=33%  Similarity=0.558  Sum_probs=79.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEeeCC
Q psy222           91 RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECGR  170 (225)
Q Consensus        91 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~~~  170 (225)
                      +.|||||||+++++++|..+|+..|.|..++++.|+.+|+.+||+|++|.+.++|+.|++.||+.++.|++|+|.|+..+
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            89999999999999999999999999999999999999999999999999999999999999999999999999999865


Q ss_pred             CC
Q psy222          171 VL  172 (225)
Q Consensus       171 ~~  172 (225)
                      ..
T Consensus        99 ~~  100 (435)
T KOG0108|consen   99 KN  100 (435)
T ss_pred             ch
Confidence            43

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

Probab=99.47  E-value=3.3e-13  Score=121.59  Aligned_cols=79  Identities=20%  Similarity=0.252  Sum_probs=73.2

Q ss_pred             CCCCCeEEEcCCCC-CCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q psy222           87 TDPTRTLFIGRLNK-NSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD  165 (225)
Q Consensus        87 ~~~~~~l~V~nLp~-~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~  165 (225)
                      ..++++|||+||++ .+++++|+++|+.||.|..|+|+.++     +|||||+|.+.++|+.||..||+..|.|+.|+|.
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            34678999999998 69999999999999999999999874     6899999999999999999999999999999999


Q ss_pred             EeeCC
Q psy222          166 FECGR  170 (225)
Q Consensus       166 ~a~~~  170 (225)
                      +++..
T Consensus       347 ~s~~~  351 (481)
T TIGR01649       347 PSKQQ  351 (481)
T ss_pred             Ecccc
Confidence            98764

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).

>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=99.46  E-value=1e-12  Score=86.84  Aligned_cols=74  Identities=42%  Similarity=0.697  Sum_probs=68.3

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEE
Q psy222           92 TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF  166 (225)
Q Consensus        92 ~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~  166 (225)
                      +|||+|||+.+++++|+++|..||.|..+.+..+..+ ..+++|||+|.+.++|..|+..+++..+.++.|.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~-~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDT-KSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCC-CcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            4899999999999999999999999999999987644 6789999999999999999999999999999998864

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).

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

Probab=99.45  E-value=4.3e-13  Score=120.89  Aligned_cols=75  Identities=21%  Similarity=0.378  Sum_probs=68.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHh--CCCccCCcEEEEEE
Q psy222           89 PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL--NRQNFQGSEIIVDF  166 (225)
Q Consensus        89 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l--~g~~l~g~~l~V~~  166 (225)
                      ++++|||+|||+.+++++|+++|++||.|..|.|+.+      ++||||+|.+.++|++||..|  ++..|.|+.|.|.+
T Consensus         1 ps~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~~------k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~   74 (481)
T TIGR01649         1 PSPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPG------KRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNY   74 (481)
T ss_pred             CccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEECC------CCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEe
Confidence            4679999999999999999999999999999999854      579999999999999999864  77889999999999


Q ss_pred             eeC
Q psy222          167 ECG  169 (225)
Q Consensus       167 a~~  169 (225)
                      +..
T Consensus        75 s~~   77 (481)
T TIGR01649        75 STS   77 (481)
T ss_pred             cCC
Confidence            864

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).

>KOG0114|consensus

Probab=99.44  E-value=1.2e-12  Score=91.32  Aligned_cols=82  Identities=17%  Similarity=0.257  Sum_probs=73.7

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      .+....+.|||.|||+.+|.+++.++|.+||.|..|+|-..+   ..+|-|||.|++..+|.+|+..|+|..++++.|.|
T Consensus        13 lppevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k---~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~v   89 (124)
T KOG0114|consen   13 LPPEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTK---ETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVV   89 (124)
T ss_pred             CChhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCcc---CcCceEEEEehHhhhHHHHHHHhcccccCCceEEE
Confidence            445567889999999999999999999999999999997654   45889999999999999999999999999999999


Q ss_pred             EEeeC
Q psy222          165 DFECG  169 (225)
Q Consensus       165 ~~a~~  169 (225)
                      -+-.+
T Consensus        90 lyyq~   94 (124)
T KOG0114|consen   90 LYYQP   94 (124)
T ss_pred             EecCH
Confidence            88654

>KOG4212|consensus

Probab=99.43  E-value=1.5e-12  Score=111.43  Aligned_cols=79  Identities=23%  Similarity=0.382  Sum_probs=74.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHh-cCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEee
Q psy222           90 TRTLFIGRLNKNSREADLEQAFA-EYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFEC  168 (225)
Q Consensus        90 ~~~l~V~nLp~~~te~~L~~~F~-~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~  168 (225)
                      .+.+||.|||+++.|.+|+++|. +.|+|+.|.|+.|. +++.+|||.|+|++++.+++|++.||.+.+.|+.|+|+...
T Consensus        44 ~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~-~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd~  122 (608)
T KOG4212|consen   44 DRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDE-SGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKEDH  122 (608)
T ss_pred             cceEEEecCcchhhhHhHHHHHHHhcCceEeeeeeccc-CCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEeccC
Confidence            35699999999999999999995 78999999999996 89999999999999999999999999999999999999876


Q ss_pred             C
Q psy222          169 G  169 (225)
Q Consensus       169 ~  169 (225)
                      .
T Consensus       123 d  123 (608)
T KOG4212|consen  123 D  123 (608)
T ss_pred             c
Confidence            5

>KOG0144|consensus

Probab=99.42  E-value=2.1e-13  Score=116.35  Aligned_cols=84  Identities=27%  Similarity=0.547  Sum_probs=76.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCc-cCC--cEEEEE
Q psy222           89 PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQN-FQG--SEIIVD  165 (225)
Q Consensus        89 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~-l~g--~~l~V~  165 (225)
                      ..++|||+-|+..++|.+|+++|++||.|++|.|+++. .+.++|||||.|.+.+-|..||+.||+.. +.|  .+|.|+
T Consensus       123 ~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~-~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVk  201 (510)
T KOG0144|consen  123 EERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDP-DGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVK  201 (510)
T ss_pred             cchhhhhhhccccccHHHHHHHHHhhCccchhhheecc-cccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEE
Confidence            36789999999999999999999999999999999996 78999999999999999999999999974 555  589999


Q ss_pred             EeeCCCCC
Q psy222          166 FECGRVLP  173 (225)
Q Consensus       166 ~a~~~~~~  173 (225)
                      ||.+...+
T Consensus       202 FADtqkdk  209 (510)
T KOG0144|consen  202 FADTQKDK  209 (510)
T ss_pred             ecccCCCc
Confidence            99875543

>KOG0127|consensus

Probab=99.42  E-value=6.9e-13  Score=116.14  Aligned_cols=85  Identities=22%  Similarity=0.441  Sum_probs=77.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF  166 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~  166 (225)
                      ..+..+|+|.||||.|.+.+|+.+|+.||.|..|.|++.. .++.+|||||.|....+|..||+.||+..|+|++|-|+|
T Consensus       114 ~~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~-dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDW  192 (678)
T KOG0127|consen  114 DLPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKK-DGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDW  192 (678)
T ss_pred             cCccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCC-CCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEee
Confidence            4447799999999999999999999999999999999776 556669999999999999999999999999999999999


Q ss_pred             eeCCCC
Q psy222          167 ECGRVL  172 (225)
Q Consensus       167 a~~~~~  172 (225)
                      |-++..
T Consensus       193 AV~Kd~  198 (678)
T KOG0127|consen  193 AVDKDT  198 (678)
T ss_pred             eccccc
Confidence            987553

>KOG0127|consensus

Probab=99.38  E-value=1.7e-12  Score=113.67  Aligned_cols=86  Identities=26%  Similarity=0.423  Sum_probs=77.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHh-----CC-CccCC
Q psy222           86 STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL-----NR-QNFQG  159 (225)
Q Consensus        86 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l-----~g-~~l~g  159 (225)
                      ......+|||.|||+++++++|..+|++||.|..+.|+.++.|++++|.|||.|.+..+|+.||...     .+ ..|+|
T Consensus       288 n~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~G  367 (678)
T KOG0127|consen  288 NITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLLDG  367 (678)
T ss_pred             cccccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcCccCCCceEEEec
Confidence            3455689999999999999999999999999999999999999999999999999999999999865     23 57899


Q ss_pred             cEEEEEEeeCCC
Q psy222          160 SEIIVDFECGRV  171 (225)
Q Consensus       160 ~~l~V~~a~~~~  171 (225)
                      +.|.|..|-.|.
T Consensus       368 R~Lkv~~Av~Rk  379 (678)
T KOG0127|consen  368 RLLKVTLAVTRK  379 (678)
T ss_pred             cEEeeeeccchH
Confidence            999999997653

>KOG0145|consensus

Probab=99.36  E-value=4.2e-12  Score=102.22  Aligned_cols=82  Identities=28%  Similarity=0.458  Sum_probs=77.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEee
Q psy222           89 PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFEC  168 (225)
Q Consensus        89 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~  168 (225)
                      ....|||=||.++++|.-|.++|.+||.|..|+|++|..|.++|||+||...+-++|..||..|||+.+.++.|.|.|..
T Consensus       277 ~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsFKt  356 (360)
T KOG0145|consen  277 GGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKT  356 (360)
T ss_pred             CeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccceEEEEEEec
Confidence            35789999999999999999999999999999999999889999999999999999999999999999999999999976


Q ss_pred             CC
Q psy222          169 GR  170 (225)
Q Consensus       169 ~~  170 (225)
                      .+
T Consensus       357 nk  358 (360)
T KOG0145|consen  357 NK  358 (360)
T ss_pred             CC
Confidence            54

>KOG0146|consensus

Probab=99.36  E-value=1.1e-12  Score=106.03  Aligned_cols=89  Identities=27%  Similarity=0.382  Sum_probs=84.4

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      ...+++|+|||=.||.++.+.+|..+|-.||.|.+.++..|+.|..+|.|+||.|.+..+++.||..|||..|+=++|+|
T Consensus       280 reGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKV  359 (371)
T KOG0146|consen  280 REGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKV  359 (371)
T ss_pred             hcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhh
Confidence            55778999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeeCCCCC
Q psy222          165 DFECGRVLP  173 (225)
Q Consensus       165 ~~a~~~~~~  173 (225)
                      .+.+++...
T Consensus       360 QLKRPkdan  368 (371)
T KOG0146|consen  360 QLKRPKDAN  368 (371)
T ss_pred             hhcCccccC
Confidence            999887643

>PF13893 RRM_5: RNA recognition motif

Probab=99.34  E-value=7.5e-12  Score=79.57  Aligned_cols=56  Identities=23%  Similarity=0.567  Sum_probs=50.9

Q ss_pred             HHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEe
Q psy222          107 LEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFE  167 (225)
Q Consensus       107 L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a  167 (225)
                      |.++|++||.|..+.+..+.     +++|||+|.+.++|.+|+..||+..|.|++|+|.+|
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            67899999999999997653     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 ....

>smart00361 RRM_1 RNA recognition motif

Probab=99.34  E-value=5.9e-12  Score=83.91  Aligned_cols=61  Identities=23%  Similarity=0.448  Sum_probs=55.1

Q ss_pred             HHHHHHHHh----cCCceeEEE-EeecCCC--CccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222          104 EADLEQAFA----EYGKVISVR-VVRDFVT--GHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus       104 e~~L~~~F~----~~G~v~~v~-i~~~~~~--g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      +++|+++|.    +||.|..|. |+.++.+  +..+||+||+|.+.++|.+|+..|||..|.|+.|++
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            578888888    999999995 7777656  889999999999999999999999999999999876

>KOG0124|consensus

Probab=99.33  E-value=9.6e-13  Score=110.38  Aligned_cols=78  Identities=27%  Similarity=0.488  Sum_probs=74.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEe
Q psy222           90 TRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFE  167 (225)
Q Consensus        90 ~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a  167 (225)
                      -|+||||.|.+++.|+.|+..|..||.|.+|.+-+|..|+++||||||+|+-++.|+-|++.||+..++|+.|+|...
T Consensus       113 McRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrP  190 (544)
T KOG0124|consen  113 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRP  190 (544)
T ss_pred             hHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCC
Confidence            479999999999999999999999999999999999999999999999999999999999999999999999998743

>KOG0109|consensus

Probab=99.32  E-value=2.6e-12  Score=104.82  Aligned_cols=73  Identities=34%  Similarity=0.599  Sum_probs=69.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEeeCC
Q psy222           91 RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECGR  170 (225)
Q Consensus        91 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~~~  170 (225)
                      .+|||+|||..+++.+|+.+|++||.|++|.|+        |.|+||..++...++.||.-||+..|+|..|+|+-++.+
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIv--------KNYgFVHiEdktaaedairNLhgYtLhg~nInVeaSksK   74 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIV--------KNYGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSK   74 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeee--------cccceEEeecccccHHHHhhcccceecceEEEEEecccc
Confidence            479999999999999999999999999999998        559999999999999999999999999999999999876


Q ss_pred             C
Q psy222          171 V  171 (225)
Q Consensus       171 ~  171 (225)
                      .
T Consensus        75 s   75 (346)
T KOG0109|consen   75 S   75 (346)
T ss_pred             C
Confidence            3

>KOG4208|consensus

Probab=99.30  E-value=1.1e-11  Score=96.64  Aligned_cols=84  Identities=19%  Similarity=0.334  Sum_probs=76.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcC-CceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEY-GKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD  165 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~-G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~  165 (225)
                      .....-+||..||.-+.+.+|..+|.+| |.|..+++-+++.||.++|||||+|.+++.|+.|.+.||++.|.++.|.|.
T Consensus        46 ~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~  125 (214)
T KOG4208|consen   46 QEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECH  125 (214)
T ss_pred             cCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeE
Confidence            3445578999999999999999999988 778888888999999999999999999999999999999999999999999


Q ss_pred             EeeCC
Q psy222          166 FECGR  170 (225)
Q Consensus       166 ~a~~~  170 (225)
                      +..+.
T Consensus       126 vmppe  130 (214)
T KOG4208|consen  126 VMPPE  130 (214)
T ss_pred             EeCch
Confidence            97764

>KOG0147|consensus

Probab=99.27  E-value=1e-11  Score=108.98  Aligned_cols=86  Identities=33%  Similarity=0.507  Sum_probs=78.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF  166 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~  166 (225)
                      ..+...|||+||..++++++|+.+|+.||.|..|.++.+..||..+||+||+|.+.++|.+|++.|||.+|-|+.|+|..
T Consensus       275 ~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~  354 (549)
T KOG0147|consen  275 TGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSV  354 (549)
T ss_pred             ccchhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEE
Confidence            34444599999999999999999999999999999999988999999999999999999999999999999999999988


Q ss_pred             eeCCCC
Q psy222          167 ECGRVL  172 (225)
Q Consensus       167 a~~~~~  172 (225)
                      -..+..
T Consensus       355 v~~r~~  360 (549)
T KOG0147|consen  355 VTERVD  360 (549)
T ss_pred             eeeecc
Confidence            776443

>KOG0131|consensus

Probab=99.25  E-value=1.8e-11  Score=93.83  Aligned_cols=85  Identities=32%  Similarity=0.499  Sum_probs=78.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEE-EEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISV-RVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD  165 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v-~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~  165 (225)
                      ...+.+|||+||.++++|..|.+.|+.||.+... +|+++..|+..++|+||.|.+.+.+.+|+..||++.+..++|.|.
T Consensus        93 l~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~  172 (203)
T KOG0131|consen   93 LDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPITVS  172 (203)
T ss_pred             ccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCceEEE
Confidence            4455799999999999999999999999987654 889998899999999999999999999999999999999999999


Q ss_pred             EeeCCC
Q psy222          166 FECGRV  171 (225)
Q Consensus       166 ~a~~~~  171 (225)
                      ++..+.
T Consensus       173 ya~k~~  178 (203)
T KOG0131|consen  173 YAFKKD  178 (203)
T ss_pred             EEEecC
Confidence            998654

>KOG4205|consensus

Probab=99.24  E-value=2e-11  Score=102.90  Aligned_cols=113  Identities=23%  Similarity=0.435  Sum_probs=93.3

Q ss_pred             ccCCCCCcccCcccHHHHHHHhccCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEE
Q psy222           56 QAGSIDGTDTIPHDRAILRALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYG  135 (225)
Q Consensus        56 ~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~a  135 (225)
                      ..+.||++.+++. ++..+....    .........+|||++||.++++++++++|.+||.|..+.++.|..+.+.++|+
T Consensus        68 ~~h~~dgr~ve~k-~av~r~~~~----~~~~~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFg  142 (311)
T KOG4205|consen   68 RTHKLDGRSVEPK-RAVSREDQT----KVGRHLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFG  142 (311)
T ss_pred             cccccCCccccce-eccCccccc----ccccccceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccce
Confidence            4577999999987 332222111    11223367799999999999999999999999999999999999999999999


Q ss_pred             EEEeCCHHHHHHHHHHhCCCccCCcEEEEEEeeCCCCCC
Q psy222          136 FLEYDCEKACLAAIRALNRQNFQGSEIIVDFECGRVLPG  174 (225)
Q Consensus       136 fV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~~~~~~~  174 (225)
                      ||.|.+++.+.+++. ..-+.|.++.+.|+.|.++....
T Consensus       143 fv~~~~e~sVdkv~~-~~f~~~~gk~vevkrA~pk~~~~  180 (311)
T KOG4205|consen  143 FVTFDSEDSVDKVTL-QKFHDFNGKKVEVKRAIPKEVMQ  180 (311)
T ss_pred             eeEeccccccceecc-cceeeecCceeeEeeccchhhcc
Confidence            999999999999988 57889999999999999876543

>KOG0109|consensus

Probab=99.19  E-value=3e-11  Score=98.74  Aligned_cols=78  Identities=28%  Similarity=0.608  Sum_probs=72.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF  166 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~  166 (225)
                      .....+|+|+||.+.++..+|+..|.+||.|.+|.|+        ++|+||.|...++|..|++.|++.+|+|++|+|++
T Consensus        75 sk~stkl~vgNis~tctn~ElRa~fe~ygpviecdiv--------kdy~fvh~d~~eda~~air~l~~~~~~gk~m~vq~  146 (346)
T KOG0109|consen   75 SKASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIV--------KDYAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQL  146 (346)
T ss_pred             CCCccccccCCCCccccCHHHhhhhcccCCceeeeee--------cceeEEEEeeccchHHHHhcccccccccceeeeee
Confidence            4567899999999999999999999999999999998        55999999999999999999999999999999999


Q ss_pred             eeCCCC
Q psy222          167 ECGRVL  172 (225)
Q Consensus       167 a~~~~~  172 (225)
                      +..|..
T Consensus       147 stsrlr  152 (346)
T KOG0109|consen  147 STSRLR  152 (346)
T ss_pred             eccccc
Confidence            987654

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

Probab=99.18  E-value=7.4e-11  Score=107.02  Aligned_cols=76  Identities=20%  Similarity=0.330  Sum_probs=62.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcC------------CceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhC
Q psy222           86 STDPTRTLFIGRLNKNSREADLEQAFAEY------------GKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALN  153 (225)
Q Consensus        86 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~------------G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~  153 (225)
                      .....++|||+|||+.+++++|+++|..|            +.|..+.+      .+.++||||+|.+.++|..||. |+
T Consensus       171 ~~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~------~~~kg~afVeF~~~e~A~~Al~-l~  243 (509)
T TIGR01642       171 ATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNI------NKEKNFAFLEFRTVEEATFAMA-LD  243 (509)
T ss_pred             CCccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEE------CCCCCEEEEEeCCHHHHhhhhc-CC
Confidence            34456899999999999999999999975            22333333      3357999999999999999996 99


Q ss_pred             CCccCCcEEEEEEee
Q psy222          154 RQNFQGSEIIVDFEC  168 (225)
Q Consensus       154 g~~l~g~~l~V~~a~  168 (225)
                      +..|.|+.|+|....
T Consensus       244 g~~~~g~~l~v~r~~  258 (509)
T TIGR01642       244 SIIYSNVFLKIRRPH  258 (509)
T ss_pred             CeEeeCceeEecCcc
Confidence            999999999987543

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

>KOG0132|consensus

Probab=99.16  E-value=2.3e-10  Score=104.09  Aligned_cols=82  Identities=22%  Similarity=0.399  Sum_probs=75.1

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      ...--++|||||.|+..++|.+|..+|+.||.|.+|.++..      ++||||...+..+|++||.+|+...+.++.|+|
T Consensus       416 ~isV~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~------R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki  489 (894)
T KOG0132|consen  416 HISVCSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP------RGCAFIKMVRRQDAEKALQKLSNVKVADKTIKI  489 (894)
T ss_pred             ceeEeeeeeeeccccchhhHHHHHHHHHhcccceeEeeccC------CceeEEEEeehhHHHHHHHHHhcccccceeeEE
Confidence            44556789999999999999999999999999999998865      789999999999999999999999999999999


Q ss_pred             EEeeCCCC
Q psy222          165 DFECGRVL  172 (225)
Q Consensus       165 ~~a~~~~~  172 (225)
                      .|+.....
T Consensus       490 ~Wa~g~G~  497 (894)
T KOG0132|consen  490 AWAVGKGP  497 (894)
T ss_pred             eeeccCCc
Confidence            99987544

>KOG0123|consensus

Probab=99.16  E-value=1.2e-10  Score=101.20  Aligned_cols=77  Identities=30%  Similarity=0.526  Sum_probs=72.2

Q ss_pred             EEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEeeCCCC
Q psy222           93 LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECGRVL  172 (225)
Q Consensus        93 l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~~~~~  172 (225)
                      |||.||+..++..+|.++|+.||.|++|++.++. .| .+|| ||+|.+++.|.+||..|||..+.+++|.|.....+..
T Consensus        79 ~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~-~g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~e  155 (369)
T KOG0123|consen   79 VFIKNLDESIDNKSLYDTFSEFGNILSCKVATDE-NG-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERKEE  155 (369)
T ss_pred             eeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcC-CC-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccchhh
Confidence            9999999999999999999999999999999996 55 8999 9999999999999999999999999999988876443

>KOG4206|consensus

Probab=99.16  E-value=1.5e-10  Score=91.63  Aligned_cols=80  Identities=25%  Similarity=0.531  Sum_probs=72.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHH----HHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEE
Q psy222           88 DPTRTLFIGRLNKNSREADLEQ----AFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEII  163 (225)
Q Consensus        88 ~~~~~l~V~nLp~~~te~~L~~----~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~  163 (225)
                      .+..||||.||+..+..++|+.    +|++||.|..|....   +.+.+|-|||.|.+.+.|-.|+..|+|..|-|+.++
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            3455999999999999998887    999999999988763   677899999999999999999999999999999999


Q ss_pred             EEEeeCC
Q psy222          164 VDFECGR  170 (225)
Q Consensus       164 V~~a~~~  170 (225)
                      |.+|+..
T Consensus        84 iqyA~s~   90 (221)
T KOG4206|consen   84 IQYAKSD   90 (221)
T ss_pred             eecccCc
Confidence            9999864

>KOG4205|consensus

Probab=99.13  E-value=5.8e-11  Score=100.18  Aligned_cols=83  Identities=25%  Similarity=0.453  Sum_probs=76.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEee
Q psy222           89 PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFEC  168 (225)
Q Consensus        89 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~  168 (225)
                      ..++|||++|+|+++++.|+++|.+||+|.+|.+++++.+++.++|+||+|++.+.+..+|. ...+.|+++.|.++-|.
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 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLN-ARTHKLDGRSVEPKRAV   83 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeec-ccccccCCccccceecc
Confidence            67899999999999999999999999999999999999999999999999999999888887 35678999999999888


Q ss_pred             CCCC
Q psy222          169 GRVL  172 (225)
Q Consensus       169 ~~~~  172 (225)
                      ++..
T Consensus        84 ~r~~   87 (311)
T KOG4205|consen   84 SRED   87 (311)
T ss_pred             Cccc
Confidence            7653

>KOG0110|consensus

Probab=99.07  E-value=5.8e-11  Score=107.03  Aligned_cols=83  Identities=14%  Similarity=0.423  Sum_probs=76.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF  166 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~  166 (225)
                      ......|+|.|||+.++-.+|+.+|..||.|..|+|+.....+..+|||||+|-+..+|.+|+..|..+.|.|+.|+++|
T Consensus       610 kk~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEw  689 (725)
T KOG0110|consen  610 KKKGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEW  689 (725)
T ss_pred             ccccceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhcccceechhhheeh
Confidence            33467999999999999999999999999999999997755677899999999999999999999999999999999999


Q ss_pred             eeC
Q psy222          167 ECG  169 (225)
Q Consensus       167 a~~  169 (225)
                      |..
T Consensus       690 A~~  692 (725)
T KOG0110|consen  690 AKS  692 (725)
T ss_pred             hcc
Confidence            975

>KOG0146|consensus

Probab=99.07  E-value=2.1e-10  Score=92.84  Aligned_cols=83  Identities=31%  Similarity=0.532  Sum_probs=74.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCc-cCC--cEEEEE
Q psy222           89 PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQN-FQG--SEIIVD  165 (225)
Q Consensus        89 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~-l~g--~~l~V~  165 (225)
                      +.++||||-|...-.|++++.+|..||.|.+|.+++.. .|.+||||||.|.+..+|+.||..|||.. +-|  ..|+|+
T Consensus        18 ~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~-dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK   96 (371)
T KOG0146|consen   18 DDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGP-DGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVK   96 (371)
T ss_pred             cchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCC-CCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEE
Confidence            56799999999999999999999999999999999886 78899999999999999999999999975 444  579999


Q ss_pred             EeeCCCC
Q psy222          166 FECGRVL  172 (225)
Q Consensus       166 ~a~~~~~  172 (225)
                      ++....+
T Consensus        97 ~ADTdkE  103 (371)
T KOG0146|consen   97 FADTDKE  103 (371)
T ss_pred             eccchHH
Confidence            9976443

>KOG4212|consensus

Probab=99.06  E-value=3.7e-10  Score=96.95  Aligned_cols=77  Identities=19%  Similarity=0.266  Sum_probs=69.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q psy222           86 STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD  165 (225)
Q Consensus        86 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~  165 (225)
                      .....|+|||.|||.++||..|++-|..||.|..+.|+   ..++.+|  .|.|.++++|++|+..|++..|+|+.|.|.
T Consensus       532 aarKa~qIiirNlP~dfTWqmlrDKfre~G~v~yadim---e~GkskG--VVrF~s~edAEra~a~Mngs~l~Gr~I~V~  606 (608)
T KOG4212|consen  532 AARKACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIM---ENGKSKG--VVRFFSPEDAERACALMNGSRLDGRNIKVT  606 (608)
T ss_pred             ccccccEEEEecCCccccHHHHHHHHHhccceehhhhh---ccCCccc--eEEecCHHHHHHHHHHhccCcccCceeeee
Confidence            34567899999999999999999999999999999985   3577776  899999999999999999999999999998


Q ss_pred             Ee
Q psy222          166 FE  167 (225)
Q Consensus       166 ~a  167 (225)
                      +.
T Consensus       607 y~  608 (608)
T KOG4212|consen  607 YF  608 (608)
T ss_pred             eC
Confidence            73

>KOG0533|consensus

Probab=99.05  E-value=4.8e-09  Score=85.44  Aligned_cols=82  Identities=20%  Similarity=0.295  Sum_probs=75.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEee
Q psy222           89 PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFEC  168 (225)
Q Consensus        89 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~  168 (225)
                      ...+|+|.|||+.+++++|+++|..|+.+..+.|..++ .|.+.|.|-|.|...++|++|++.|++..|+|+.|++.+..
T Consensus        82 ~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~-~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~  160 (243)
T KOG0533|consen   82 RSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDR-AGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIIS  160 (243)
T ss_pred             CcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCC-CCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEec
Confidence            34789999999999999999999999999999999886 89999999999999999999999999999999999999876


Q ss_pred             CCC
Q psy222          169 GRV  171 (225)
Q Consensus       169 ~~~  171 (225)
                      ...
T Consensus       161 ~~~  163 (243)
T KOG0533|consen  161 SPS  163 (243)
T ss_pred             Ccc
Confidence            533

>KOG0153|consensus

Probab=99.04  E-value=1.4e-09  Score=90.88  Aligned_cols=78  Identities=24%  Similarity=0.454  Sum_probs=68.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHh-CCCccCCcEEEE
Q psy222           86 STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL-NRQNFQGSEIIV  164 (225)
Q Consensus        86 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l-~g~~l~g~~l~V  164 (225)
                      ....-.+|||++|...++|.+|+.+|.+||.|..|.+...      +++|||+|.+.+.|+.|.+.+ +...|+|++|.|
T Consensus       224 eD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~------~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i  297 (377)
T KOG0153|consen  224 EDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR------KGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKI  297 (377)
T ss_pred             cccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc------cccceeeehhhHHHHHHHHhhcceeeecceEEEE
Confidence            3445579999999999999999999999999999998865      569999999999999998754 545689999999


Q ss_pred             EEeeC
Q psy222          165 DFECG  169 (225)
Q Consensus       165 ~~a~~  169 (225)
                      .|..+
T Consensus       298 ~Wg~~  302 (377)
T KOG0153|consen  298 KWGRP  302 (377)
T ss_pred             EeCCC
Confidence            99887

>KOG4661|consensus

Probab=99.04  E-value=2.5e-09  Score=94.60  Aligned_cols=83  Identities=27%  Similarity=0.494  Sum_probs=77.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF  166 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~  166 (225)
                      ..-.++|||.+|...+...+|+.+|++||.|+-.+|+++..+.-.++|+||++.+.++|.+||..||.+.|.|+.|.|+-
T Consensus       402 s~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEk  481 (940)
T KOG4661|consen  402 STLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEK  481 (940)
T ss_pred             cccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeee
Confidence            44567999999999999999999999999999999999977777889999999999999999999999999999999999


Q ss_pred             eeC
Q psy222          167 ECG  169 (225)
Q Consensus       167 a~~  169 (225)
                      ++.
T Consensus       482 aKN  484 (940)
T KOG4661|consen  482 AKN  484 (940)
T ss_pred             ccc
Confidence            875

>KOG0124|consensus

Probab=99.00  E-value=8.6e-10  Score=92.85  Aligned_cols=81  Identities=20%  Similarity=0.399  Sum_probs=75.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEee
Q psy222           89 PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFEC  168 (225)
Q Consensus        89 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~  168 (225)
                      .-++|||..+.++.+|++|+..|+.||.|+.|.+.+....+.++||+|++|.+......||..||-..|+|+.|+|--+-
T Consensus       209 ~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~v  288 (544)
T KOG0124|consen  209 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCV  288 (544)
T ss_pred             hhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEeccccc
Confidence            45799999999999999999999999999999999998888899999999999999999999999999999999998765


Q ss_pred             C
Q psy222          169 G  169 (225)
Q Consensus       169 ~  169 (225)
                      .
T Consensus       289 T  289 (544)
T KOG0124|consen  289 T  289 (544)
T ss_pred             C
Confidence            4

>KOG4209|consensus

Probab=98.98  E-value=3.4e-09  Score=86.34  Aligned_cols=85  Identities=19%  Similarity=0.346  Sum_probs=79.2

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      ....+...+||+|+.+.++.+++..+|+.||.|..+.|+.++..+++++|+||+|.+.+.++.+|. |++..|.++.+.|
T Consensus        96 ~~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~v  174 (231)
T KOG4209|consen   96 QKEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEV  174 (231)
T ss_pred             hhccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCccccccccee
Confidence            445567899999999999999999999999999999999999899999999999999999999999 9999999999999


Q ss_pred             EEeeCC
Q psy222          165 DFECGR  170 (225)
Q Consensus       165 ~~a~~~  170 (225)
                      .+.+.+
T Consensus       175 t~~r~~  180 (231)
T KOG4209|consen  175 TLKRTN  180 (231)
T ss_pred             eeeeee
Confidence            998765

>KOG0123|consensus

Probab=98.98  E-value=1.9e-09  Score=93.77  Aligned_cols=74  Identities=27%  Similarity=0.443  Sum_probs=69.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEeeCC
Q psy222           91 RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECGR  170 (225)
Q Consensus        91 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~~~  170 (225)
                      ..||||   +.+|+..|.++|+.+|.|++++|.+|. |  +.|||||.|.++++|++||..||...|.|++|+|-|+...
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            368999   899999999999999999999999997 6  9999999999999999999999999999999999998753

>KOG0110|consensus

Probab=98.97  E-value=1.8e-09  Score=97.56  Aligned_cols=76  Identities=26%  Similarity=0.468  Sum_probs=69.2

Q ss_pred             EEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCC---ccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEee
Q psy222           93 LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTG---HSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFEC  168 (225)
Q Consensus        93 l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g---~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~  168 (225)
                      |||.||++.++.++|..+|..+|.|..|.|...+...   .+.||+||+|.+.++|+.|++.|+|+.|+|+.|.|+++.
T Consensus       518 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  518 LFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISE  596 (725)
T ss_pred             hhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEecc
Confidence            9999999999999999999999999999887654221   234999999999999999999999999999999999998

>KOG0106|consensus

Probab=98.90  E-value=1.8e-09  Score=86.20  Aligned_cols=71  Identities=28%  Similarity=0.600  Sum_probs=66.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEeeC
Q psy222           91 RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECG  169 (225)
Q Consensus        91 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~~  169 (225)
                      ..|||++||+.+.+.+|+.||..||.|..|.+.        .+|+||+|.+..+|..|+..||+.+|.+-.+.|++++.
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 PRVYIGRLPYRARERDVERFFKGYGKIPDADMK--------NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARG   72 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceee--------cccceeccCchhhhhcccchhcCceecceeeeeecccc
Confidence            369999999999999999999999999999876        57999999999999999999999999998888998875

>KOG1548|consensus

Probab=98.90  E-value=5.7e-09  Score=87.32  Aligned_cols=79  Identities=16%  Similarity=0.294  Sum_probs=73.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCCcee--------EEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcE
Q psy222           90 TRTLFIGRLNKNSREADLEQAFAEYGKVI--------SVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSE  161 (225)
Q Consensus        90 ~~~l~V~nLp~~~te~~L~~~F~~~G~v~--------~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~  161 (225)
                      ...|||.|||.++|-+++.++|++||.|.        .|+|.++. .|+.+|-|++.|.-.++++-||..|++..|.|+.
T Consensus       134 Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~-~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~~  212 (382)
T KOG1548|consen  134 NTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDN-QGKLKGDALCCYIKRESVELAIKILDEDELRGKK  212 (382)
T ss_pred             CceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecC-CCCccCceEEEeecccHHHHHHHHhCcccccCcE
Confidence            45699999999999999999999999875        48888886 5999999999999999999999999999999999


Q ss_pred             EEEEEeeC
Q psy222          162 IIVDFECG  169 (225)
Q Consensus       162 l~V~~a~~  169 (225)
                      |+|+.|+=
T Consensus       213 ~rVerAkf  220 (382)
T KOG1548|consen  213 LRVERAKF  220 (382)
T ss_pred             EEEehhhh
Confidence            99999873

>KOG1995|consensus

Probab=98.82  E-value=2.2e-08  Score=84.33  Aligned_cols=89  Identities=22%  Similarity=0.250  Sum_probs=80.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCcee--------EEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccC
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVI--------SVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQ  158 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~--------~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~  158 (225)
                      ....-+|||.+||..+++++|.++|.+|+.|.        .|.|.+++.|++.|+-|.|.|.+...|+.||..+++..|.
T Consensus        63 ~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~  142 (351)
T KOG1995|consen   63 KSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFC  142 (351)
T ss_pred             ccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhcccccc
Confidence            45567999999999999999999999999875        4778889999999999999999999999999999999999


Q ss_pred             CcEEEEEEeeCCCCCCC
Q psy222          159 GSEIIVDFECGRVLPGW  175 (225)
Q Consensus       159 g~~l~V~~a~~~~~~~~  175 (225)
                      +.+|+|.+|..+..-++
T Consensus       143 gn~ikvs~a~~r~~ve~  159 (351)
T KOG1995|consen  143 GNTIKVSLAERRTGVES  159 (351)
T ss_pred             CCCchhhhhhhccCccc
Confidence            99999999987764443

>KOG4454|consensus

Probab=98.80  E-value=2.4e-09  Score=84.47  Aligned_cols=80  Identities=20%  Similarity=0.315  Sum_probs=72.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEe
Q psy222           88 DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFE  167 (225)
Q Consensus        88 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a  167 (225)
                      +..++|||+|+...++|+.|.++|-+.|.|..|.|..++ .++.+ ||||.|.++..+.-|++.|||..+.+..+.|.+.
T Consensus         7 e~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~-d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r   84 (267)
T KOG4454|consen    7 EMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQ-DQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLR   84 (267)
T ss_pred             chhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCc-cCCCc-eeeeecccccchhhhhhhcccchhccchhhcccc
Confidence            345799999999999999999999999999999998876 56667 9999999999999999999999999998888876


Q ss_pred             eC
Q psy222          168 CG  169 (225)
Q Consensus       168 ~~  169 (225)
                      ..
T Consensus        85 ~G   86 (267)
T KOG4454|consen   85 CG   86 (267)
T ss_pred             cC
Confidence            54

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

Probab=98.75  E-value=1e-07  Score=67.09  Aligned_cols=79  Identities=18%  Similarity=0.240  Sum_probs=68.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhc--CCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccC----CcEEEE
Q psy222           91 RTLFIGRLNKNSREADLEQAFAE--YGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQ----GSEIIV  164 (225)
Q Consensus        91 ~~l~V~nLp~~~te~~L~~~F~~--~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~----g~~l~V  164 (225)
                      +||.|.|||...+.+.|.+++..  .|..-.+.++.|..+..+.|||||.|.+.+.|.+-.+.++|..+.    .+.+.|
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            58999999999999999988864  356777889999889999999999999999999999999999875    466788


Q ss_pred             EEeeC
Q psy222          165 DFECG  169 (225)
Q Consensus       165 ~~a~~  169 (225)
                      .+|+-
T Consensus        82 ~yAri   86 (97)
T PF04059_consen   82 SYARI   86 (97)
T ss_pred             ehhHh
Confidence            88763

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

>KOG1457|consensus

Probab=98.74  E-value=9.6e-08  Score=75.76  Aligned_cols=85  Identities=20%  Similarity=0.303  Sum_probs=69.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeec-CCCCccceEEEEEeCCHHHHHHHHHHhCCCccC---CcEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRD-FVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQ---GSEI  162 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~-~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~---g~~l  162 (225)
                      ...-+||||.+||.++...+|..+|..|--.+.+.|... +.....+-+|||.|.+...|++|+.+|||..|+   +..|
T Consensus        31 ~~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stL  110 (284)
T KOG1457|consen   31 PGAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTL  110 (284)
T ss_pred             ccccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCcee
Confidence            345689999999999999999999999876666666543 222234579999999999999999999999986   5789


Q ss_pred             EEEEeeCCC
Q psy222          163 IVDFECGRV  171 (225)
Q Consensus       163 ~V~~a~~~~  171 (225)
                      +|++|+...
T Consensus       111 hiElAKSNt  119 (284)
T KOG1457|consen  111 HIELAKSNT  119 (284)
T ss_pred             EeeehhcCc
Confidence            999998643

>KOG0226|consensus

Probab=98.71  E-value=1.7e-08  Score=81.36  Aligned_cols=85  Identities=24%  Similarity=0.364  Sum_probs=77.3

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      .......+||++.|..+++++.|-..|.+|-.....++++++.|++.+||+||.|.+..++..|+..|+|..++.+.|++
T Consensus       185 ew~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpikl  264 (290)
T KOG0226|consen  185 EWDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKL  264 (290)
T ss_pred             cCccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHh
Confidence            44556689999999999999999999999998889999999999999999999999999999999999999999999887


Q ss_pred             EEeeC
Q psy222          165 DFECG  169 (225)
Q Consensus       165 ~~a~~  169 (225)
                      .-...
T Consensus       265 RkS~w  269 (290)
T KOG0226|consen  265 RKSEW  269 (290)
T ss_pred             hhhhH
Confidence            65543

>KOG0151|consensus

Probab=98.68  E-value=3.9e-08  Score=89.06  Aligned_cols=85  Identities=19%  Similarity=0.308  Sum_probs=75.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCC---CCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFV---TGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEII  163 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~---~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~  163 (225)
                      .+.+++|||+||++.++++.|...|..||.|..|+|++.+.   ....+.|+||.|-+..+|++|++.|+|..+....++
T Consensus       171 DP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K  250 (877)
T KOG0151|consen  171 DPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMK  250 (877)
T ss_pred             CCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeee
Confidence            44568999999999999999999999999999999998752   234567899999999999999999999999999999


Q ss_pred             EEEeeCCC
Q psy222          164 VDFECGRV  171 (225)
Q Consensus       164 V~~a~~~~  171 (225)
                      +-|.+.-.
T Consensus       251 ~gWgk~V~  258 (877)
T KOG0151|consen  251 LGWGKAVP  258 (877)
T ss_pred             eccccccc
Confidence            99997543

>KOG4211|consensus

Probab=98.64  E-value=1.4e-07  Score=82.45  Aligned_cols=78  Identities=17%  Similarity=0.274  Sum_probs=66.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEe
Q psy222           88 DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFE  167 (225)
Q Consensus        88 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a  167 (225)
                      ....-|-+.+|||++|+++|.+||+-|+ |..+.+.+.  +|+..|-|||+|.+++++++||+ .+...+..+-|.|--+
T Consensus         8 ~~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r~--~Gr~sGeA~Ve~~seedv~~Alk-kdR~~mg~RYIEVf~~   83 (510)
T KOG4211|consen    8 STAFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPRR--NGRPSGEAYVEFTSEEDVEKALK-KDRESMGHRYIEVFTA   83 (510)
T ss_pred             CcceEEEecCCCccccHHHHHHHHhcCc-eeEEEEecc--CCCcCcceEEEeechHHHHHHHH-hhHHHhCCceEEEEcc
Confidence            3456778899999999999999999987 777666554  79999999999999999999999 4777888888988877


Q ss_pred             eC
Q psy222          168 CG  169 (225)
Q Consensus       168 ~~  169 (225)
                      ..
T Consensus        84 ~~   85 (510)
T KOG4211|consen   84 GG   85 (510)
T ss_pred             CC
Confidence            54

>KOG4660|consensus

Probab=98.55  E-value=5.5e-08  Score=86.04  Aligned_cols=72  Identities=24%  Similarity=0.368  Sum_probs=64.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEII  163 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~  163 (225)
                      .-+..+|+|-|||..+++++|..+|+.||+|..|+.-     -..++.+||+|.+..+|++|+++|++..|.++.|+
T Consensus        72 ~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t-----~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   72 DMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRET-----PNKRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             cCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcc-----cccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            3456899999999999999999999999999997653     33588999999999999999999999999998887

>KOG4210|consensus

Probab=98.39  E-value=3.6e-07  Score=76.83  Aligned_cols=86  Identities=23%  Similarity=0.448  Sum_probs=76.7

Q ss_pred             CCCCCCeEE-EcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           86 STDPTRTLF-IGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        86 ~~~~~~~l~-V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      ......++| |++|+..+++++|+.+|..+|.|..+++..+..++..++|+||+|.....+..++.. ....+.++++.|
T Consensus       180 ~~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~  258 (285)
T KOG4210|consen  180 SSGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRL  258 (285)
T ss_pred             ccCccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCccccc
Confidence            344556777 999999999999999999999999999999999999999999999999999999886 788899999999


Q ss_pred             EEeeCCCC
Q psy222          165 DFECGRVL  172 (225)
Q Consensus       165 ~~a~~~~~  172 (225)
                      ....++..
T Consensus       259 ~~~~~~~~  266 (285)
T KOG4210|consen  259 EEDEPRPK  266 (285)
T ss_pred             ccCCCCcc
Confidence            99887643

>KOG0120|consensus

Probab=98.37  E-value=3e-07  Score=81.83  Aligned_cols=85  Identities=25%  Similarity=0.396  Sum_probs=78.8

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      ......+.|||++||..+++.++.+++..||.+....++.+..++.++||||.+|.+......|+..|||..+.+..|+|
T Consensus       284 ~~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvv  363 (500)
T KOG0120|consen  284 DVPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVV  363 (500)
T ss_pred             CcccccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEe
Confidence            33445679999999999999999999999999999999999888999999999999999999999999999999999999


Q ss_pred             EEeeC
Q psy222          165 DFECG  169 (225)
Q Consensus       165 ~~a~~  169 (225)
                      ..|..
T Consensus       364 q~A~~  368 (500)
T KOG0120|consen  364 QRAIV  368 (500)
T ss_pred             ehhhc
Confidence            99875

>KOG4849|consensus

Probab=98.34  E-value=2.1e-06  Score=72.27  Aligned_cols=79  Identities=20%  Similarity=0.328  Sum_probs=67.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCC--ceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYG--KVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G--~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      ......+|||||-|++|+++|.+.+..-|  .+.++++..++.+|.+||||+|...+...+.+.++.|..+.|.|+.-.|
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            33445789999999999999998887666  4677888888889999999999999999999999999999999875444


Q ss_pred             E
Q psy222          165 D  165 (225)
Q Consensus       165 ~  165 (225)
                      -
T Consensus       157 ~  157 (498)
T KOG4849|consen  157 L  157 (498)
T ss_pred             e
Confidence            3

>KOG0147|consensus

Probab=98.32  E-value=2.2e-07  Score=82.19  Aligned_cols=84  Identities=30%  Similarity=0.415  Sum_probs=77.0

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      .+..+.++||+-.|...+++.+|.+||+.+|.|..|.|+.|+.++..+|.|||+|.+.+.+..||. |.|+.+.|.+|.|
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            344556899999999999999999999999999999999999999999999999999999999997 8999999999999


Q ss_pred             EEeeC
Q psy222          165 DFECG  169 (225)
Q Consensus       165 ~~a~~  169 (225)
                      .....
T Consensus       253 q~sEa  257 (549)
T KOG0147|consen  253 QLSEA  257 (549)
T ss_pred             cccHH
Confidence            88653

>KOG1190|consensus

Probab=98.27  E-value=3.9e-06  Score=72.05  Aligned_cols=77  Identities=18%  Similarity=0.273  Sum_probs=69.5

Q ss_pred             CCeEEEcCCCC-CCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEee
Q psy222           90 TRTLFIGRLNK-NSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFEC  168 (225)
Q Consensus        90 ~~~l~V~nLp~-~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~  168 (225)
                      ...|-|.||.. .+|.+.|..+|..||.|.+|+|+.++     +--|+|.|.+...|+-|++.|+|+.|.|++|+|.+++
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nk-----kd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SK  371 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNK-----KDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSK  371 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecC-----CcceeeeecchhHHHHHHHHhhcceecCceEEEeecc
Confidence            57888899855 58999999999999999999999886     4569999999999999999999999999999999998


Q ss_pred             CCC
Q psy222          169 GRV  171 (225)
Q Consensus       169 ~~~  171 (225)
                      -..
T Consensus       372 H~~  374 (492)
T KOG1190|consen  372 HTN  374 (492)
T ss_pred             Ccc
Confidence            644

>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=98.14  E-value=1.1e-05  Score=54.53  Aligned_cols=67  Identities=22%  Similarity=0.357  Sum_probs=46.9

Q ss_pred             eEEEcCCCCCCCHHHHH----HHHhcCC-ceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEE
Q psy222           92 TLFIGRLNKNSREADLE----QAFAEYG-KVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF  166 (225)
Q Consensus        92 ~l~V~nLp~~~te~~L~----~~F~~~G-~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~  166 (225)
                      .|||.|||.+.+...|+    .++..|| .|..|.          .+.|+|.|.+.+.|.+|++.|+|-.+-|++|.|.+
T Consensus         4 ~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v~----------~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~   73 (90)
T PF11608_consen    4 LLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSVS----------GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSF   73 (90)
T ss_dssp             EEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEES
T ss_pred             EEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEe----------CCEEEEEeCCHHHHHHHHHhhcccccccceEEEEE
Confidence            68999999999887654    5566776 454442          35799999999999999999999999999999999


Q ss_pred             ee
Q psy222          167 EC  168 (225)
Q Consensus       167 a~  168 (225)
                      ..
T Consensus        74 ~~   75 (90)
T PF11608_consen   74 SP   75 (90)
T ss_dssp             S-
T ss_pred             cC
Confidence            74

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

>KOG1457|consensus

Probab=98.13  E-value=2.5e-06  Score=67.86  Aligned_cols=69  Identities=22%  Similarity=0.346  Sum_probs=56.3

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCcc
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNF  157 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l  157 (225)
                      .....+.+|||.||..+++|++|+.+|+.|--...++|...  .|  -.+|||+|++.+.|..|+..|+|..|
T Consensus       205 ~~~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~--~g--~~vaf~~~~~~~~at~am~~lqg~~~  273 (284)
T KOG1457|consen  205 SGARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRAR--GG--MPVAFADFEEIEQATDAMNHLQGNLL  273 (284)
T ss_pred             ccchhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecC--CC--cceEeecHHHHHHHHHHHHHhhccee
Confidence            34456679999999999999999999999987766666532  23  34899999999999999998888765

>KOG4206|consensus

Probab=98.07  E-value=1.8e-05  Score=63.04  Aligned_cols=79  Identities=18%  Similarity=0.325  Sum_probs=69.0

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccC-CcEEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQ-GSEII  163 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~-g~~l~  163 (225)
                      ...++...+|+.|||..++.+.|..+|.+|.....|+++...     ++.|||+|.+...+..|...|++..|- ...+.
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            336677899999999999999999999999999999988664     789999999999999999999998876 77888


Q ss_pred             EEEee
Q psy222          164 VDFEC  168 (225)
Q Consensus       164 V~~a~  168 (225)
                      |.++.
T Consensus       216 i~~a~  220 (221)
T KOG4206|consen  216 ITFAK  220 (221)
T ss_pred             ecccC
Confidence            87764

>KOG4211|consensus

Probab=98.04  E-value=1.5e-05  Score=69.95  Aligned_cols=79  Identities=18%  Similarity=0.197  Sum_probs=64.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCceeE-EEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEE
Q psy222           88 DPTRTLFIGRLNKNSREADLEQAFAEYGKVIS-VRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF  166 (225)
Q Consensus        88 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~-v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~  166 (225)
                      .....|-+.+||+.|++++|.+||+..-.|.. |.++.+. .+++.|-|||.|++.+.|++||.. |...|..+-|.|-.
T Consensus       101 ~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~-rgR~tGEAfVqF~sqe~ae~Al~r-hre~iGhRYIEvF~  178 (510)
T KOG4211|consen  101 ANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQ-RGRPTGEAFVQFESQESAEIALGR-HRENIGHRYIEVFR  178 (510)
T ss_pred             CCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccC-CCCcccceEEEecCHHHHHHHHHH-HHHhhccceEEeeh
Confidence            35568899999999999999999997655544 4455554 677999999999999999999985 77778888888876


Q ss_pred             ee
Q psy222          167 EC  168 (225)
Q Consensus       167 a~  168 (225)
                      +.
T Consensus       179 Ss  180 (510)
T KOG4211|consen  179 SS  180 (510)
T ss_pred             hH
Confidence            64

>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=98.01  E-value=1.6e-05  Score=56.95  Aligned_cols=71  Identities=21%  Similarity=0.443  Sum_probs=44.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCC-----ccCCcEEEEE
Q psy222           91 RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQ-----NFQGSEIIVD  165 (225)
Q Consensus        91 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~-----~l~g~~l~V~  165 (225)
                      +.|+|.+++..++.++|+++|+.||.|..|.+...      ..-|||.|.+.+.|+.|+..+.-.     .|.+..+.+.
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G------~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~   75 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRG------DTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLE   75 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-------SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCC------CCEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEE
Confidence            56889999999999999999999999999988643      236999999999999999876544     4566666655


Q ss_pred             Ee
Q psy222          166 FE  167 (225)
Q Consensus       166 ~a  167 (225)
                      +-
T Consensus        76 vL   77 (105)
T PF08777_consen   76 VL   77 (105)
T ss_dssp             --
T ss_pred             EC
Confidence            43

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

>KOG3152|consensus

Probab=98.01  E-value=1.4e-05  Score=64.81  Aligned_cols=73  Identities=16%  Similarity=0.305  Sum_probs=61.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCC--------Cccce----EEEEEeCCHHHHHHHHHHhCCCc
Q psy222           89 PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVT--------GHSKR----YGFLEYDCEKACLAAIRALNRQN  156 (225)
Q Consensus        89 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~--------g~~kg----~afV~F~~~~~a~~Al~~l~g~~  156 (225)
                      ..-.||+++||+.+...-|+++|+.||.|-.|.|.....+        +..+.    -+.|+|.+...|..+...||+..
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            5678999999999999999999999999999988776544        22222    25799999999999999999999


Q ss_pred             cCCcE
Q psy222          157 FQGSE  161 (225)
Q Consensus       157 l~g~~  161 (225)
                      |+|+.
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99864

>KOG0106|consensus

Probab=98.00  E-value=4e-06  Score=67.17  Aligned_cols=71  Identities=21%  Similarity=0.388  Sum_probs=62.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD  165 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~  165 (225)
                      ....+.|+|.+++..+.+.+|.++|.++|.+....+        ..+++||+|...+++.+||..|++..|.++.|.+.
T Consensus        96 ~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~--------~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~~  166 (216)
T KOG0106|consen   96 SRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA--------RRNFAFVEFSEQEDAKRALEKLDGKKLNGRRISVE  166 (216)
T ss_pred             ccccceeeeccchhhhhHHHHhhhhcccCCCchhhh--------hccccceeehhhhhhhhcchhccchhhcCceeeec
Confidence            445578899999999999999999999999854443        25689999999999999999999999999999993

>KOG0105|consensus

Probab=97.81  E-value=0.00028  Score=54.85  Aligned_cols=66  Identities=26%  Similarity=0.345  Sum_probs=58.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCC
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQG  159 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g  159 (225)
                      ......|.|.+||...+|.+|++++.+.|.|+...+.+|       |++.|+|...++++-||..|....+..
T Consensus       112 rrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD-------g~GvV~~~r~eDMkYAvr~ld~~~~~s  177 (241)
T KOG0105|consen  112 RRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD-------GVGVVEYLRKEDMKYAVRKLDDQKFRS  177 (241)
T ss_pred             cccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc-------cceeeeeeehhhHHHHHHhhccccccC
Confidence            334568999999999999999999999999999999876       478999999999999999998877643

>KOG1456|consensus

Probab=97.79  E-value=0.00089  Score=57.31  Aligned_cols=81  Identities=17%  Similarity=0.259  Sum_probs=64.8

Q ss_pred             CCCCCCCeEEEc--CCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccC--Cc
Q psy222           85 SSTDPTRTLFIG--RLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQ--GS  160 (225)
Q Consensus        85 ~~~~~~~~l~V~--nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~--g~  160 (225)
                      ....+.+.|.+.  |--+.+|-+-|..+...+|.|..|.|.+.  ++.   -|.|+|++.+.|++|.+.|||..|.  -+
T Consensus       115 es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkk--ngV---QAmVEFdsv~~AqrAk~alNGADIYsGCC  189 (494)
T KOG1456|consen  115 ESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKK--NGV---QAMVEFDSVEVAQRAKAALNGADIYSGCC  189 (494)
T ss_pred             CCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEec--cce---eeEEeechhHHHHHHHhhcccccccccce
Confidence            344455555544  54566899999999999999999998865  333   4899999999999999999999874  47


Q ss_pred             EEEEEEeeCC
Q psy222          161 EIIVDFECGR  170 (225)
Q Consensus       161 ~l~V~~a~~~  170 (225)
                      +|+|++|++.
T Consensus       190 TLKIeyAkP~  199 (494)
T KOG1456|consen  190 TLKIEYAKPT  199 (494)
T ss_pred             eEEEEecCcc
Confidence            8999999874

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.74  E-value=8.2e-05  Score=62.68  Aligned_cols=81  Identities=11%  Similarity=0.276  Sum_probs=62.5

Q ss_pred             CCCeEEEcCCCCCCCHHH----H--HHHHhcCCceeEEEEeecCCCCc-cce--EEEEEeCCHHHHHHHHHHhCCCccCC
Q psy222           89 PTRTLFIGRLNKNSREAD----L--EQAFAEYGKVISVRVVRDFVTGH-SKR--YGFLEYDCEKACLAAIRALNRQNFQG  159 (225)
Q Consensus        89 ~~~~l~V~nLp~~~te~~----L--~~~F~~~G~v~~v~i~~~~~~g~-~kg--~afV~F~~~~~a~~Al~~l~g~~l~g  159 (225)
                      ...-+||-+|++.+..++    |  .++|.+||.|..|.|.+....-. ..+  -.||+|.+.++|.+||...+|..++|
T Consensus       113 QKNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DG  192 (480)
T COG5175         113 QKNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDG  192 (480)
T ss_pred             ecceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccC
Confidence            345789999988876655    3  48999999999987765431111 112  24999999999999999999999999


Q ss_pred             cEEEEEEeeC
Q psy222          160 SEIIVDFECG  169 (225)
Q Consensus       160 ~~l~V~~a~~  169 (225)
                      +.|+..+-..
T Consensus       193 r~lkatYGTT  202 (480)
T COG5175         193 RVLKATYGTT  202 (480)
T ss_pred             ceEeeecCch
Confidence            9999888653

>KOG1190|consensus

Probab=97.64  E-value=0.00016  Score=62.44  Aligned_cols=79  Identities=16%  Similarity=0.284  Sum_probs=65.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCc-EEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGS-EIIVD  165 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~-~l~V~  165 (225)
                      .+++.+|.+.|||.+++|++|+.+|..-|.........    ++.+-+|++.+.+.++|-.|+..++.+.+... .|+|.
T Consensus       411 ~PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkff----~kd~kmal~q~~sveeA~~ali~~hnh~lgen~hlRvS  486 (492)
T KOG1190|consen  411 FPPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFF----QKDRKMALPQLESVEEAIQALIDLHNHYLGENHHLRVS  486 (492)
T ss_pred             CCchhheeeccCCcccchhHHHHhhhcCCceEEeeeec----CCCcceeecccCChhHhhhhccccccccCCCCceEEEE
Confidence            46778999999999999999999999888765543332    33456999999999999999999999998765 89999


Q ss_pred             EeeC
Q psy222          166 FECG  169 (225)
Q Consensus       166 ~a~~  169 (225)
                      |++.
T Consensus       487 FSks  490 (492)
T KOG1190|consen  487 FSKS  490 (492)
T ss_pred             eecc
Confidence            9864

>KOG0129|consensus

Probab=97.63  E-value=0.00017  Score=63.82  Aligned_cols=67  Identities=27%  Similarity=0.401  Sum_probs=61.4

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHh-cCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHH
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFA-EYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA  151 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~-~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~  151 (225)
                      ..-++.+|||||+||.-++.++|..+|. -||.|+.+-|-+|.+-+-++|-+-|+|.+-..-.+||.+
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            4566789999999999999999999998 899999999999977888999999999999999999874

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

Probab=97.61  E-value=0.00017  Score=45.00  Aligned_cols=52  Identities=19%  Similarity=0.402  Sum_probs=41.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHH
Q psy222           91 RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAI  149 (225)
Q Consensus        91 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al  149 (225)
                      +.|-|.+.+.+..+. +..+|..||.|+.+.+..      ...+.||.|.+..+|++||
T Consensus         2 ~wI~V~Gf~~~~~~~-vl~~F~~fGeI~~~~~~~------~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAEE-VLEHFASFGEIVDIYVPE------STNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHHH-HHHHHHhcCCEEEEEcCC------CCcEEEEEECCHHHHHhhC
Confidence            467788888876644 556888999999988762      2458999999999999985

>KOG4307|consensus

Probab=97.60  E-value=0.00026  Score=64.76  Aligned_cols=79  Identities=13%  Similarity=0.164  Sum_probs=66.5

Q ss_pred             CCCC-eEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEE
Q psy222           88 DPTR-TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF  166 (225)
Q Consensus        88 ~~~~-~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~  166 (225)
                      .+++ .|-|.|+|+.++-++|-+||.-|-.+-.-.+++-.+.|+..|-|.|.|++.++|.+|...|+++.|..++|.|.+
T Consensus       864 ~pGp~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  864 SPGPRVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             CCCCeEEEecCCCccccHHHHHHHhcccccCCCceeEeecCCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            3444 778899999999999999999997654433333345899999999999999999999999999999999998875

>KOG1548|consensus

Probab=97.53  E-value=0.00036  Score=59.03  Aligned_cols=81  Identities=17%  Similarity=0.310  Sum_probs=63.9

Q ss_pred             CCCCCCCeEEEcCCCC----CCC-------HHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhC
Q psy222           85 SSTDPTRTLFIGRLNK----NSR-------EADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALN  153 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~----~~t-------e~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~  153 (225)
                      ......++|.|.||=.    ..+       .++|.+-..+||.|..|.|.    ..++.|.+.|.|.+.++|..||+.|+
T Consensus       260 sk~r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~----d~hPdGvvtV~f~n~eeA~~ciq~m~  335 (382)
T KOG1548|consen  260 SKARADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVY----DRHPDGVVTVSFRNNEEADQCIQTMD  335 (382)
T ss_pred             ccccCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEe----ccCCCceeEEEeCChHHHHHHHHHhc
Confidence            3344567899988832    223       23555667899999999886    33468999999999999999999999


Q ss_pred             CCccCCcEEEEEEeeC
Q psy222          154 RQNFQGSEIIVDFECG  169 (225)
Q Consensus       154 g~~l~g~~l~V~~a~~  169 (225)
                      |..|+|+.|...+-..
T Consensus       336 GR~fdgRql~A~i~DG  351 (382)
T KOG1548|consen  336 GRWFDGRQLTASIWDG  351 (382)
T ss_pred             CeeecceEEEEEEeCC
Confidence            9999999999887654

>KOG0120|consensus

Probab=97.50  E-value=0.00032  Score=62.84  Aligned_cols=63  Identities=19%  Similarity=0.335  Sum_probs=51.7

Q ss_pred             HHHHHHhcCCceeEEEEeecCCC---CccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEee
Q psy222          106 DLEQAFAEYGKVISVRVVRDFVT---GHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFEC  168 (225)
Q Consensus       106 ~L~~~F~~~G~v~~v~i~~~~~~---g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~  168 (225)
                      +++.-+++||.|..|.|.++...   .-..|-.||+|.+.+++++|.+.|+|.+|.++.|+..|-.
T Consensus       425 dvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYyd  490 (500)
T KOG0120|consen  425 DVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYD  490 (500)
T ss_pred             HHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecC
Confidence            34566678999999999887212   2345678999999999999999999999999999988754

>KOG2416|consensus

Probab=97.44  E-value=0.00045  Score=62.23  Aligned_cols=83  Identities=22%  Similarity=0.301  Sum_probs=68.4

Q ss_pred             CCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHh-cCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCcc--
Q psy222           81 KPHTSSTDPTRTLFIGRLNKNSREADLEQAFA-EYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNF--  157 (225)
Q Consensus        81 ~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~-~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l--  157 (225)
                      .+.+.....++.|||.||-.-+|.-+|+.++. .+|.|+..  +.|+    .|..|||.|.+.++|...+.+|||..+  
T Consensus       435 vpSPsR~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~--WmDk----IKShCyV~yss~eEA~atr~AlhnV~WP~  508 (718)
T KOG2416|consen  435 VPSPSRKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEF--WMDK----IKSHCYVSYSSVEEAAATREALHNVQWPP  508 (718)
T ss_pred             CCCCCCCCccceEeeecccccchHHHHHHHHhhccCchHHH--HHHH----hhcceeEecccHHHHHHHHHHHhccccCC
Confidence            34446778889999999999999999999998 56667666  3333    477899999999999999999999876  


Q ss_pred             -CCcEEEEEEeeC
Q psy222          158 -QGSEIIVDFECG  169 (225)
Q Consensus       158 -~g~~l~V~~a~~  169 (225)
                       +.+.|.|.|...
T Consensus       509 sNPK~L~adf~~~  521 (718)
T KOG2416|consen  509 SNPKHLIADFVRA  521 (718)
T ss_pred             CCCceeEeeecch
Confidence             457788988864

>KOG1456|consensus

Probab=97.41  E-value=0.0014  Score=56.17  Aligned_cols=81  Identities=19%  Similarity=0.199  Sum_probs=71.7

Q ss_pred             CCCCCCCeEEEcCCCCC-CCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEE
Q psy222           85 SSTDPTRTLFIGRLNKN-SREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEII  163 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~-~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~  163 (225)
                      ....+++.+.|-+|... +.-+.|..+|=.||.|+.|++++.+     .|-|.|+..+..++++|+..||+..+-|.+|.
T Consensus       282 ~g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk-----~gtamVemgd~~aver~v~hLnn~~lfG~kl~  356 (494)
T KOG1456|consen  282 GGGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK-----PGTAMVEMGDAYAVERAVTHLNNIPLFGGKLN  356 (494)
T ss_pred             CCCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc-----cceeEEEcCcHHHHHHHHHHhccCccccceEE
Confidence            45567789999999876 6678899999999999999999876     56799999999999999999999999999999


Q ss_pred             EEEeeCC
Q psy222          164 VDFECGR  170 (225)
Q Consensus       164 V~~a~~~  170 (225)
                      |.+++..
T Consensus       357 v~~SkQ~  363 (494)
T KOG1456|consen  357 VCVSKQN  363 (494)
T ss_pred             Eeecccc
Confidence            9998753

>KOG0129|consensus

Probab=97.40  E-value=0.00065  Score=60.27  Aligned_cols=66  Identities=24%  Similarity=0.406  Sum_probs=50.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCC---CCccce---EEEEEeCCHHHHHHHHHHhC
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFV---TGHSKR---YGFLEYDCEKACLAAIRALN  153 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~---~g~~kg---~afV~F~~~~~a~~Al~~l~  153 (225)
                      ..-.++||||+||++++|+.|...|..||.+ .|.+.....   --.++|   |+|+.|+++..+..-|.++.
T Consensus       256 ~~~S~KVFvGGlp~dise~~i~~~F~~FGs~-~VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~  327 (520)
T KOG0129|consen  256 PRYSRKVFVGGLPWDITEAQINASFGQFGSV-KVDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACS  327 (520)
T ss_pred             cccccceeecCCCccccHHHHHhhcccccce-EeecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHh
Confidence            3456899999999999999999999999975 555553211   122466   99999999998888776543

>KOG2314|consensus

Probab=97.39  E-value=0.0015  Score=58.65  Aligned_cols=79  Identities=19%  Similarity=0.277  Sum_probs=63.2

Q ss_pred             CCCeEEEcCCCCCCCH------HHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccC-CcE
Q psy222           89 PTRTLFIGRLNKNSRE------ADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQ-GSE  161 (225)
Q Consensus        89 ~~~~l~V~nLp~~~te------~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~-g~~  161 (225)
                      -...|+|.|+|.--..      ..|..+|+++|.|+.+.++-+.. |..+||.|++|.+...|+.|++.|||+.|+ .++
T Consensus        57 ~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~-ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHt  135 (698)
T KOG2314|consen   57 FDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEE-GGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHT  135 (698)
T ss_pred             cceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCcc-CCeeeEEEEEecChhhHHHHHHhcccceecccce
Confidence            3457889999975332      24568999999999999988864 448999999999999999999999999875 466


Q ss_pred             EEEEEee
Q psy222          162 IIVDFEC  168 (225)
Q Consensus       162 l~V~~a~  168 (225)
                      +.|..-+
T Consensus       136 f~v~~f~  142 (698)
T KOG2314|consen  136 FFVRLFK  142 (698)
T ss_pred             EEeehhh
Confidence            7776543

>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=97.26  E-value=0.0014  Score=46.44  Aligned_cols=77  Identities=16%  Similarity=0.166  Sum_probs=50.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCCceeEEE-EeecC------CCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcE-
Q psy222           90 TRTLFIGRLNKNSREADLEQAFAEYGKVISVR-VVRDF------VTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSE-  161 (225)
Q Consensus        90 ~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~-i~~~~------~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~-  161 (225)
                      ..-|.|-+.|.. .-..|.++|++||.|++.. +..+.      ........-.|.|.++.+|++||. .||..|.|.. 
T Consensus         6 ~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~~m   83 (100)
T PF05172_consen    6 ETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGSLM   83 (100)
T ss_dssp             CCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTCEE
T ss_pred             CeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCcEE
Confidence            346778899988 4567888999999998764 11100      001124578999999999999999 5999999865 


Q ss_pred             EEEEEee
Q psy222          162 IIVDFEC  168 (225)
Q Consensus       162 l~V~~a~  168 (225)
                      +-|.+.+
T Consensus        84 vGV~~~~   90 (100)
T PF05172_consen   84 VGVKPCD   90 (100)
T ss_dssp             EEEEE-H
T ss_pred             EEEEEcH
Confidence            4466663

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=97.23  E-value=0.0022  Score=48.32  Aligned_cols=74  Identities=24%  Similarity=0.415  Sum_probs=52.6

Q ss_pred             CCCCCeEEEcCCC------CCCCH---HHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCcc
Q psy222           87 TDPTRTLFIGRLN------KNSRE---ADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNF  157 (225)
Q Consensus        87 ~~~~~~l~V~nLp------~~~te---~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l  157 (225)
                      .++-.||.|.=+.      ..+.+   .+|.+.|..||.+.-++++.+        .-+|+|.+-..|.+|+. |+|..+
T Consensus        24 GPpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaals-~dg~~v   94 (146)
T PF08952_consen   24 GPPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAALS-LDGIQV   94 (146)
T ss_dssp             --TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHHH-GCCSEE
T ss_pred             CCCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHHc-cCCcEE
Confidence            3455577776554      12332   256678889999998888744        36899999999999999 899999


Q ss_pred             CCcEEEEEEeeC
Q psy222          158 QGSEIIVDFECG  169 (225)
Q Consensus       158 ~g~~l~V~~a~~  169 (225)
                      .|+.|+|++..+
T Consensus        95 ~g~~l~i~LKtp  106 (146)
T PF08952_consen   95 NGRTLKIRLKTP  106 (146)
T ss_dssp             TTEEEEEEE---
T ss_pred             CCEEEEEEeCCc
Confidence            999999999765

; PDB: 1UFW_A 2DNR_A.

>KOG1855|consensus

Probab=97.11  E-value=0.00062  Score=59.13  Aligned_cols=68  Identities=25%  Similarity=0.377  Sum_probs=56.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeec---CCC--Cc--------cceEEEEEeCCHHHHHHHHHHhC
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRD---FVT--GH--------SKRYGFLEYDCEKACLAAIRALN  153 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~---~~~--g~--------~kg~afV~F~~~~~a~~Al~~l~  153 (225)
                      ..+.++|.+-|||.+-.-+.|.++|..||.|..|+|+..   ...  +.        .+-+|||+|...+.|.+|.+.|+
T Consensus       228 el~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~  307 (484)
T KOG1855|consen  228 ELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLN  307 (484)
T ss_pred             ccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhc
Confidence            357899999999999888999999999999999999865   211  11        25589999999999999999875


Q ss_pred             C
Q psy222          154 R  154 (225)
Q Consensus       154 g  154 (225)
                      .
T Consensus       308 ~  308 (484)
T KOG1855|consen  308 P  308 (484)
T ss_pred             h
Confidence            4

>KOG1365|consensus

Probab=97.08  E-value=0.00094  Score=57.33  Aligned_cols=79  Identities=13%  Similarity=0.123  Sum_probs=65.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCc-eeE--EEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q psy222           89 PTRTLFIGRLNKNSREADLEQAFAEYGK-VIS--VRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD  165 (225)
Q Consensus        89 ~~~~l~V~nLp~~~te~~L~~~F~~~G~-v~~--v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~  165 (225)
                      ....|-+.+||+..+.++|..||..|-. |..  |+++.+. .|++.|-|||+|.+.+.|..|....+.+....+.|.|-
T Consensus       279 ~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~-qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvf  357 (508)
T KOG1365|consen  279 SKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNG-QGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVF  357 (508)
T ss_pred             CCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcC-CCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEe
Confidence            3567889999999999999999988864 333  6666664 78999999999999999999999888877778888887


Q ss_pred             Eee
Q psy222          166 FEC  168 (225)
Q Consensus       166 ~a~  168 (225)
                      -+.
T Consensus       358 p~S  360 (508)
T KOG1365|consen  358 PCS  360 (508)
T ss_pred             ecc
Confidence            654

>KOG1365|consensus

Probab=96.92  E-value=0.00084  Score=57.62  Aligned_cols=73  Identities=22%  Similarity=0.249  Sum_probs=54.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcC----CceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q psy222           91 RTLFIGRLNKNSREADLEQAFAEY----GKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD  165 (225)
Q Consensus        91 ~~l~V~nLp~~~te~~L~~~F~~~----G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~  165 (225)
                      -.|-+.+||+++++.++.+||..-    +..+.|.+++.. .|+..|-|||.|..+++|+.||.. |...|+-+-|.+-
T Consensus       162 vivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rp-dgrpTGdAFvlfa~ee~aq~aL~k-hrq~iGqRYIElF  238 (508)
T KOG1365|consen  162 VIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRP-DGRPTGDAFVLFACEEDAQFALRK-HRQNIGQRYIELF  238 (508)
T ss_pred             eEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECC-CCCcccceEEEecCHHHHHHHHHH-HHHHHhHHHHHHH
Confidence            355667999999999999999632    234456555543 788999999999999999999985 5555655554443

>KOG4676|consensus

Probab=96.90  E-value=0.0013  Score=56.68  Aligned_cols=77  Identities=13%  Similarity=0.221  Sum_probs=61.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCC---CCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEe
Q psy222           91 RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFV---TGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFE  167 (225)
Q Consensus        91 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~---~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a  167 (225)
                      ..|.|.||.+.++.++++.||...|.|..+.|+....   -....-.|||.|.+...+..|.. |.++.|-++.|.|...
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQh-Ltntvfvdraliv~p~   86 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQH-LTNTVFVDRALIVRPY   86 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhh-hccceeeeeeEEEEec
Confidence            3799999999999999999999999999998876321   12334589999999999999987 6777777776666554


Q ss_pred             e
Q psy222          168 C  168 (225)
Q Consensus       168 ~  168 (225)
                      -
T Consensus        87 ~   87 (479)
T KOG4676|consen   87 G   87 (479)
T ss_pred             C
Confidence            3

>KOG0112|consensus

Probab=96.90  E-value=0.0012  Score=62.24  Aligned_cols=78  Identities=22%  Similarity=0.396  Sum_probs=68.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCC--cEEE
Q psy222           86 STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQG--SEII  163 (225)
Q Consensus        86 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g--~~l~  163 (225)
                      ...+...+||++|..++....|...|..||.|..|.+-..      .-||||.|.+...++.|++.|.+..|++  +.|.
T Consensus       451 kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~hg------q~yayi~yes~~~aq~a~~~~rgap~G~P~~r~r  524 (975)
T KOG0112|consen  451 KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRHG------QPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLR  524 (975)
T ss_pred             ccccceeeccCCCCCCChHHHHHHHhhccCcceeeecccC------CcceeeecccCccchhhHHHHhcCcCCCCCcccc
Confidence            4556789999999999999999999999999988876432      4599999999999999999999999987  6799


Q ss_pred             EEEeeC
Q psy222          164 VDFECG  169 (225)
Q Consensus       164 V~~a~~  169 (225)
                      |.|+.+
T Consensus       525 vdla~~  530 (975)
T KOG0112|consen  525 VDLASP  530 (975)
T ss_pred             cccccC
Confidence            999975

>KOG2202|consensus

Probab=96.88  E-value=0.00057  Score=55.66  Aligned_cols=62  Identities=19%  Similarity=0.384  Sum_probs=50.2

Q ss_pred             HHHHHHh-cCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEee
Q psy222          106 DLEQAFA-EYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFEC  168 (225)
Q Consensus       106 ~L~~~F~-~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~  168 (225)
                      +|...|. +||+|+.+.|..+. .-...|=+||.|..+++|++|+..||+.-|.|++|..++..
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            4444454 89999988765543 33457789999999999999999999999999999988864

>KOG1996|consensus

Probab=96.88  E-value=0.0036  Score=52.04  Aligned_cols=65  Identities=22%  Similarity=0.297  Sum_probs=51.8

Q ss_pred             HHHHHHHHhcCCceeEEEEeecCCCCccce-EEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEee
Q psy222          104 EADLEQAFAEYGKVISVRVVRDFVTGHSKR-YGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFEC  168 (225)
Q Consensus       104 e~~L~~~F~~~G~v~~v~i~~~~~~g~~kg-~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~  168 (225)
                      ++++++.+.+||.|..|.|......-.... -.||+|...+.|.+|+-.|||..|+|+.+...|-.
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            356778899999999998877642222221 36999999999999999999999999998877754

>KOG0128|consensus

Probab=96.84  E-value=0.00094  Score=62.50  Aligned_cols=79  Identities=15%  Similarity=0.168  Sum_probs=71.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEeeC
Q psy222           90 TRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECG  169 (225)
Q Consensus        90 ~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~~  169 (225)
                      ...|||.|+|+..|.++|+.++..+|.+.++.+++.+ .|+++|.|||.|.++.++.+++..++...+.-+.+.|....+
T Consensus       736 K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r-~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsnp  814 (881)
T KOG0128|consen  736 KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVR-AGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNP  814 (881)
T ss_pred             hhhhheeCCCCCCchHHHHhhccccCCccccchhhhh-ccccccceeccCCCcchhhhhcccchhhhhhhcCccccccCC
Confidence            4579999999999999999999999999999988876 899999999999999999999988887778777788888665

>KOG2193|consensus

Probab=96.75  E-value=0.0016  Score=56.57  Aligned_cols=74  Identities=23%  Similarity=0.342  Sum_probs=57.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCC-ccCCcEEEEEEeeC
Q psy222           91 RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQ-NFQGSEIIVDFECG  169 (225)
Q Consensus        91 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~-~l~g~~l~V~~a~~  169 (225)
                      ..+|++||.+.++..+|+.+|...-.-..-.++.      -.||+||++.+...|.+|++.++++ .+.|.++.|...-+
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 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLV------KSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVP   75 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceee------ecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhh
Confidence            3689999999999999999996431111111221      2579999999999999999999997 58999999998765


Q ss_pred             C
Q psy222          170 R  170 (225)
Q Consensus       170 ~  170 (225)
                      +
T Consensus        76 k   76 (584)
T KOG2193|consen   76 K   76 (584)
T ss_pred             H
Confidence            3

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

Probab=96.72  E-value=0.011  Score=37.95  Aligned_cols=54  Identities=19%  Similarity=0.281  Sum_probs=44.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcC---CceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHh
Q psy222           91 RTLFIGRLNKNSREADLEQAFAEY---GKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL  152 (225)
Q Consensus        91 ~~l~V~nLp~~~te~~L~~~F~~~---G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l  152 (225)
                      ..|+|.++.. ++.++|+.+|..|   .....|.++-|.       -|-|.|.+.+.|.+||..|
T Consensus         6 eavhirGvd~-lsT~dI~~y~~~y~~~~~~~~IEWIdDt-------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    6 EAVHIRGVDE-LSTDDIKAYFSEYFDEEGPFRIEWIDDT-------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             ceEEEEcCCC-CCHHHHHHHHHHhcccCCCceEEEecCC-------cEEEEECCHHHHHHHHHcC
Confidence            4799999964 6778899999988   235689999774       4789999999999999764

>KOG4307|consensus

Probab=96.72  E-value=0.0014  Score=60.29  Aligned_cols=82  Identities=16%  Similarity=0.031  Sum_probs=66.1

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeE-EEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVIS-VRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEII  163 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~-v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~  163 (225)
                      .....+..|||..||..+++.++-.+|...-.|++ |.|.+-. +++.++.|||.|.+++++..|+..-+.+.++.+.|+
T Consensus       429 ~P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~P-~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~ir  507 (944)
T KOG4307|consen  429 FPGGAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRLP-TDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIR  507 (944)
T ss_pred             CCCCccceEEeccCCccccccchhhhhhhhhhhhheeEeccCC-cccccchhhheeccccccchhhhcccccccCceEEE
Confidence            55667789999999999999999999987666776 5555544 778889999999998888888875566667778888


Q ss_pred             EEEe
Q psy222          164 VDFE  167 (225)
Q Consensus       164 V~~a  167 (225)
                      |.-.
T Consensus       508 v~si  511 (944)
T KOG4307|consen  508 VDSI  511 (944)
T ss_pred             eech
Confidence            8754

>KOG0128|consensus

Probab=96.56  E-value=0.00014  Score=67.78  Aligned_cols=70  Identities=19%  Similarity=0.238  Sum_probs=58.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCcc
Q psy222           88 DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNF  157 (225)
Q Consensus        88 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l  157 (225)
                      ....++||.||+..+.+++|...|..++.+..+++.....+++.+|+|||+|...+.+.+||.......+
T Consensus       665 R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~  734 (881)
T KOG0128|consen  665 RDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFF  734 (881)
T ss_pred             HHHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhh
Confidence            3456899999999999999999999999888877664455788999999999999999999985444333

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

Probab=96.51  E-value=0.012  Score=40.05  Aligned_cols=55  Identities=16%  Similarity=0.370  Sum_probs=42.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCC
Q psy222           91 RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNR  154 (225)
Q Consensus        91 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g  154 (225)
                      +..||. +|..+...+|.++|+.||.| .|.++.+.       -|||...+.+.|..++..+.-
T Consensus        10 HVFhlt-FPkeWK~~DI~qlFspfG~I-~VsWi~dT-------SAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen   10 HVFHLT-FPKEWKTSDIYQLFSPFGQI-YVSWINDT-------SAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             CEEEEE---TT--HHHHHHHCCCCCCE-EEEEECTT-------EEEEEECCCHHHHHHHHHHTT
T ss_pred             eEEEEe-CchHhhhhhHHHHhccCCcE-EEEEEcCC-------cEEEEeecHHHHHHHHHHhcc
Confidence            345555 99999999999999999977 77777664       699999999999999887753

; 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.

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=96.36  E-value=0.083  Score=49.60  Aligned_cols=69  Identities=9%  Similarity=0.098  Sum_probs=49.7

Q ss_pred             eEEEc-CCCCCCCHHHHHHHHhcCCcee-----EEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q psy222           92 TLFIG-RLNKNSREADLEQAFAEYGKVI-----SVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD  165 (225)
Q Consensus        92 ~l~V~-nLp~~~te~~L~~~F~~~G~v~-----~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~  165 (225)
                      ++||. +--..++..+|-.++..-+.|.     .|.|.        ..|.||+.. ...+...+..|++..+.|+.|.|+
T Consensus       488 ~~~~~~g~~~~~~~~~~~~~i~~~~~~~~~~ig~i~i~--------~~~s~v~~~-~~~~~~~~~~~~~~~~~~~~~~~~  558 (629)
T PRK11634        488 LYRIEVGRDDGVEVRHIVGAIANEGDISSRYIGNIKLF--------ASHSTIELP-KGMPGEVLQHFTRTRILNKPMNMQ  558 (629)
T ss_pred             EEEEecccccCCCHHHHHHHHHhhcCCChhhCCcEEEe--------CCceEEEcC-hhhHHHHHHHhccccccCCceEEE
Confidence            45553 3345678888877776554443     45554        348999987 566788889999999999999999


Q ss_pred             EeeC
Q psy222          166 FECG  169 (225)
Q Consensus       166 ~a~~  169 (225)
                      .+..
T Consensus       559 ~~~~  562 (629)
T PRK11634        559 LLGD  562 (629)
T ss_pred             ECCC
Confidence            8753

>KOG0112|consensus

Probab=95.99  E-value=0.0021  Score=60.61  Aligned_cols=83  Identities=22%  Similarity=0.266  Sum_probs=68.7

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      .....+.+||++||+..+++.+|+..|..+|.|..|.|.+.+ -+....|+||.|.+...+..|+..+.+..|....+++
T Consensus       367 DD~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~-~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~  445 (975)
T KOG0112|consen  367 DDFRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPH-IKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRI  445 (975)
T ss_pred             cchhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCC-CCcccchhhhhhhccccCcccchhhcCCccccCcccc
Confidence            344567899999999999999999999999999999987664 2334558999999999999999989888887666666


Q ss_pred             EEee
Q psy222          165 DFEC  168 (225)
Q Consensus       165 ~~a~  168 (225)
                      .+..
T Consensus       446 glG~  449 (975)
T KOG0112|consen  446 GLGQ  449 (975)
T ss_pred             cccc
Confidence            6654

>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=95.93  E-value=0.014  Score=45.84  Aligned_cols=81  Identities=11%  Similarity=0.099  Sum_probs=50.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhc-CCce---eEEEEeecCCC--CccceEEEEEeCCHHHHHHHHHHhCCCccCC---
Q psy222           89 PTRTLFIGRLNKNSREADLEQAFAE-YGKV---ISVRVVRDFVT--GHSKRYGFLEYDCEKACLAAIRALNRQNFQG---  159 (225)
Q Consensus        89 ~~~~l~V~nLp~~~te~~L~~~F~~-~G~v---~~v~i~~~~~~--g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g---  159 (225)
                      ...+|.|++||+.+||+++.+.+.. ++..   ..+.-......  .....-|||.|.+.+++..-+..++|+.|.+   
T Consensus         6 ~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~kg   85 (176)
T PF03467_consen    6 EGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSKG   85 (176)
T ss_dssp             ---EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TTS
T ss_pred             cCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCCC
Confidence            4468999999999999998886665 5544   33331122111  1123458999999999999999999988754   


Q ss_pred             --cEEEEEEeeC
Q psy222          160 --SEIIVDFECG  169 (225)
Q Consensus       160 --~~l~V~~a~~  169 (225)
                        ....|++|--
T Consensus        86 ~~~~~~VE~Apy   97 (176)
T PF03467_consen   86 NEYPAVVEFAPY   97 (176)
T ss_dssp             -EEEEEEEE-SS
T ss_pred             CCcceeEEEcch
Confidence              3466777654

Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.

>KOG0115|consensus

Probab=95.87  E-value=0.012  Score=48.14  Aligned_cols=65  Identities=23%  Similarity=0.320  Sum_probs=55.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCc
Q psy222           91 RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQN  156 (225)
Q Consensus        91 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~  156 (225)
                      ..|||.||+..+.-+.|...|+.||.|....++-|. .++..+-++|.|...-.+.+|+..+.-.-
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~-r~k~t~eg~v~~~~k~~a~~a~rr~~~~g   96 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDD-RGKPTREGIVEFAKKPNARKAARRCREGG   96 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeecc-cccccccchhhhhcchhHHHHHHHhccCc
Confidence            689999999999999999999999999887666663 57777889999999999999998774433

>KOG2253|consensus

Probab=95.86  E-value=0.0069  Score=55.45  Aligned_cols=76  Identities=22%  Similarity=0.299  Sum_probs=65.8

Q ss_pred             CCCCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEE
Q psy222           83 HTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEI  162 (225)
Q Consensus        83 ~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l  162 (225)
                      .....++..+|||+||...+..+-++.++..||.|..+..+.         |+|.+|........|+..|+...+++..+
T Consensus        33 ~~~~~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~---------fgf~~f~~~~~~~ra~r~~t~~~~~~~kl  103 (668)
T KOG2253|consen   33 VFQPLPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK---------FGFCEFLKHIGDLRASRLLTELNIDDQKL  103 (668)
T ss_pred             cccCCCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh---------hcccchhhHHHHHHHHHHhcccCCCcchh
Confidence            336677888999999999999999999999999988776542         99999999999999999999999999887


Q ss_pred             EEEEe
Q psy222          163 IVDFE  167 (225)
Q Consensus       163 ~V~~a  167 (225)
                      .+...
T Consensus       104 ~~~~d  108 (668)
T KOG2253|consen  104 IENVD  108 (668)
T ss_pred             hccch
Confidence            76653

>KOG2068|consensus

Probab=95.86  E-value=0.0034  Score=53.09  Aligned_cols=79  Identities=16%  Similarity=0.259  Sum_probs=60.8

Q ss_pred             CCeEEEcCCCCCCCHH-HHH--HHHhcCCceeEEEEeecCC----CCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEE
Q psy222           90 TRTLFIGRLNKNSREA-DLE--QAFAEYGKVISVRVVRDFV----TGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEI  162 (225)
Q Consensus        90 ~~~l~V~nLp~~~te~-~L~--~~F~~~G~v~~v~i~~~~~----~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l  162 (225)
                      .+-+||-+|+.....+ .|+  ++|.+||.|..|.+..+..    .+... -+||+|...++|..||...+|..++++.|
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            3567888998876554 443  7899999999998877651    12222 37999999999999999999999999887


Q ss_pred             EEEEeeC
Q psy222          163 IVDFECG  169 (225)
Q Consensus       163 ~V~~a~~  169 (225)
                      +..+...
T Consensus       156 ka~~gtt  162 (327)
T KOG2068|consen  156 KASLGTT  162 (327)
T ss_pred             HHhhCCC
Confidence            7777654

>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=95.30  E-value=0.25  Score=35.60  Aligned_cols=68  Identities=10%  Similarity=0.093  Sum_probs=50.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCC-ceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCC
Q psy222           90 TRTLFIGRLNKNSREADLEQAFAEYG-KVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQG  159 (225)
Q Consensus        90 ~~~l~V~nLp~~~te~~L~~~F~~~G-~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g  159 (225)
                      ...+.+...|+.++-++|..+.+.+- .|..++|+++.  ..++-.+++.|.+.+.|..-...+||+.|.-
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            33445555666666677766666554 47788999874  3356689999999999999999999998754

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

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=95.27  E-value=0.13  Score=38.70  Aligned_cols=74  Identities=16%  Similarity=0.294  Sum_probs=53.9

Q ss_pred             CCCCCeEEEcCCCCCCCH-H---HHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEE
Q psy222           87 TDPTRTLFIGRLNKNSRE-A---DLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEI  162 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te-~---~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l  162 (225)
                      .++-.+|.|.=|..++.. +   .+...++.||.|.+|.+.       .+.-|.|.|.+..+|.+|+.+++. ...|..+
T Consensus        83 epPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~c-------GrqsavVvF~d~~SAC~Av~Af~s-~~pgtm~  154 (166)
T PF15023_consen   83 EPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLC-------GRQSAVVVFKDITSACKAVSAFQS-RAPGTMF  154 (166)
T ss_pred             CCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeec-------CCceEEEEehhhHHHHHHHHhhcC-CCCCceE
Confidence            456678888766555432 3   445667899999998765       245799999999999999998765 4556666


Q ss_pred             EEEEee
Q psy222          163 IVDFEC  168 (225)
Q Consensus       163 ~V~~a~  168 (225)
                      ...|-.
T Consensus       155 qCsWqq  160 (166)
T PF15023_consen  155 QCSWQQ  160 (166)
T ss_pred             Eeeccc
Confidence            666643

>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=94.93  E-value=0.15  Score=33.83  Aligned_cols=67  Identities=18%  Similarity=0.310  Sum_probs=38.7

Q ss_pred             eEEEc-CCCCCCCHHHHHHHHhcCCc-----eeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q psy222           92 TLFIG-RLNKNSREADLEQAFAEYGK-----VISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD  165 (225)
Q Consensus        92 ~l~V~-nLp~~~te~~L~~~F~~~G~-----v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~  165 (225)
                      ++||. +--..++..+|..++...+.     |-.|.|.        ..|+||+... +.+..++..|++..+.|++++|+
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 RLFINVGRKDGLTPRDIVGAICNEAGIPGRDIGRIDIF--------DNFSFVEVPE-EVAEKVLEALNGKKIKGKKVRVE   72 (74)
T ss_dssp             EEEES-SGGGT--HHHHHHHHHTCTTB-GGGEEEEEE---------SS-EEEEE-T-T-HHHHHHHHTT--SSS----EE
T ss_pred             EEEEEcccccCCCHHHHHHHHHhccCCCHHhEEEEEEe--------eeEEEEEECH-HHHHHHHHHhcCCCCCCeeEEEE
Confidence            45553 33445788888888876544     4466765        3389999874 57889999999999999999998


Q ss_pred             Ee
Q psy222          166 FE  167 (225)
Q Consensus       166 ~a  167 (225)
                      .|
T Consensus        73 ~A   74 (74)
T PF03880_consen   73 RA   74 (74)
T ss_dssp             E-
T ss_pred             EC
Confidence            75

; PDB: 2G0C_A 3MOJ_B.

>KOG2591|consensus

Probab=94.48  E-value=0.072  Score=48.16  Aligned_cols=71  Identities=15%  Similarity=0.295  Sum_probs=54.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHh--cCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCC--CccCCcEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFA--EYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNR--QNFQGSEI  162 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~--~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g--~~l~g~~l  162 (225)
                      ....|.|.|.-||..+..++++.+|.  .|-.+.+|.+..+.       -=||+|.+..+|+.|.++|..  +.|.|+.|
T Consensus       172 ~~kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~-------nWyITfesd~DAQqAykylreevk~fqgKpI  244 (684)
T KOG2591|consen  172 NHKRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND-------NWYITFESDTDAQQAYKYLREEVKTFQGKPI  244 (684)
T ss_pred             CcceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC-------ceEEEeecchhHHHHHHHHHHHHHhhcCcch
Confidence            44567888999999999999999996  46777888776542       258999999999999887644  24555554


Q ss_pred             EE
Q psy222          163 IV  164 (225)
Q Consensus       163 ~V  164 (225)
                      ..
T Consensus       245 mA  246 (684)
T KOG2591|consen  245 MA  246 (684)
T ss_pred             hh
Confidence            43

>KOG4210|consensus

Probab=94.22  E-value=0.037  Score=46.75  Aligned_cols=84  Identities=19%  Similarity=0.188  Sum_probs=67.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEe
Q psy222           88 DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFE  167 (225)
Q Consensus        88 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a  167 (225)
                      ....++|++++.+.+.+.++..++..+|.+..+.+.........+++++|.|...+.+..||.....+.+.++.+...+.
T Consensus        86 ~~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~  165 (285)
T KOG4210|consen   86 GSSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLN  165 (285)
T ss_pred             cccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCccc
Confidence            35678999999999999989999999998877776665567788999999999999999999954445666766666665


Q ss_pred             eCCC
Q psy222          168 CGRV  171 (225)
Q Consensus       168 ~~~~  171 (225)
                      ..+.
T Consensus       166 ~~~~  169 (285)
T KOG4210|consen  166 TRRG  169 (285)
T ss_pred             cccc
Confidence            5433

>KOG4660|consensus

Probab=94.15  E-value=0.083  Score=47.66  Aligned_cols=81  Identities=17%  Similarity=0.218  Sum_probs=59.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHH-hcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccC---C-cEE
Q psy222           88 DPTRTLFIGRLNKNSREADLEQAF-AEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQ---G-SEI  162 (225)
Q Consensus        88 ~~~~~l~V~nLp~~~te~~L~~~F-~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~---g-~~l  162 (225)
                      ...+++.|.|+|...|-..|.+.. ...|.-..+.++.|-.+..+.|||||.|.+.+.+..+.+++||+.+.   . +.+
T Consensus       386 ~~rtt~~iknipNK~T~~ml~~~d~~~~gtYDFlYLPiDF~nkcNvGYAFINm~sp~ai~~F~kAFnGk~W~~FnS~Kia  465 (549)
T KOG4660|consen  386 CPRTTLMIKNIPNKYTSKMLLAADEKNKGTYDFLYLPIDFKNKCNVGYAFINMTSPEAIIRFYKAFNGKKWEKFNSEKIA  465 (549)
T ss_pred             CchhhhHhhccCchhhHHhhhhhhccccCccceEEeccccccccccceeEEeecCHHHHHHHHHHHcCCchhhhcceeee
Confidence            344566777777665555444333 24566667888888778888999999999999999999999998753   2 446


Q ss_pred             EEEEee
Q psy222          163 IVDFEC  168 (225)
Q Consensus       163 ~V~~a~  168 (225)
                      .+.||+
T Consensus       466 ~itYAr  471 (549)
T KOG4660|consen  466 SITYAR  471 (549)
T ss_pred             eeehhh
Confidence            666765

>KOG2135|consensus

Probab=93.86  E-value=0.037  Score=49.03  Aligned_cols=73  Identities=14%  Similarity=0.139  Sum_probs=58.4

Q ss_pred             CCeEEEcCCCCCC-CHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEee
Q psy222           90 TRTLFIGRLNKNS-READLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFEC  168 (225)
Q Consensus        90 ~~~l~V~nLp~~~-te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~  168 (225)
                      .+.|-+.-+|+.. +-++|..+|.+||.|..|.+-..      -.-|.|+|.+..+|-.|.. .++..|+++.|+|.|-.
T Consensus       372 hs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~------~~~a~vTF~t~aeag~a~~-s~~avlnnr~iKl~whn  444 (526)
T KOG2135|consen  372 HSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYS------SLHAVVTFKTRAEAGEAYA-SHGAVLNNRFIKLFWHN  444 (526)
T ss_pred             cchhhhhccCCCCchHhhhhhhhhhcCccccccccCc------hhhheeeeeccccccchhc-cccceecCceeEEEEec
Confidence            3455555556554 45889999999999999988644      2358999999999977776 68999999999999987


Q ss_pred             C
Q psy222          169 G  169 (225)
Q Consensus       169 ~  169 (225)
                      +
T Consensus       445 p  445 (526)
T KOG2135|consen  445 P  445 (526)
T ss_pred             C
Confidence            6

>KOG4285|consensus

Probab=93.62  E-value=0.27  Score=41.37  Aligned_cols=71  Identities=11%  Similarity=0.114  Sum_probs=51.4

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEE-EEEEeeCC
Q psy222           92 TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEI-IVDFECGR  170 (225)
Q Consensus        92 ~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l-~V~~a~~~  170 (225)
                      =|-|-++|+.-. .-|..+|++||.|++....      ..-.+-+|.|.+.-+|++||.+ ||..|++..+ -|+-+..+
T Consensus       199 WVTVfGFppg~~-s~vL~~F~~cG~Vvkhv~~------~ngNwMhirYssr~~A~KALsk-ng~ii~g~vmiGVkpCtDk  270 (350)
T KOG4285|consen  199 WVTVFGFPPGQV-SIVLNLFSRCGEVVKHVTP------SNGNWMHIRYSSRTHAQKALSK-NGTIIDGDVMIGVKPCTDK  270 (350)
T ss_pred             eEEEeccCccch-hHHHHHHHhhCeeeeeecC------CCCceEEEEecchhHHHHhhhh-cCeeeccceEEeeeecCCH
Confidence            344557777643 4567889999998775433      2245889999999999999994 9999988654 36654443

>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=93.58  E-value=0.2  Score=39.52  Aligned_cols=60  Identities=22%  Similarity=0.356  Sum_probs=44.4

Q ss_pred             HHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhC--CCccCCcEEEEEEeeC
Q psy222          104 EADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALN--RQNFQGSEIIVDFECG  169 (225)
Q Consensus       104 e~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~--g~~l~g~~l~V~~a~~  169 (225)
                      ...|+++|..|+.+..+.++..-      +=..|.|.+.+.|..|...|+  +..+.|..|+|-++..
T Consensus         9 ~~~l~~l~~~~~~~~~~~~L~sF------rRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~   70 (184)
T PF04847_consen    9 LAELEELFSTYDPPVQFSPLKSF------RRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQP   70 (184)
T ss_dssp             HHHHHHHHHTT-SS-EEEEETTT------TEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----
T ss_pred             HHHHHHHHHhcCCceEEEEcCCC------CEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEccc
Confidence            47899999999998888776442      236799999999999999999  8999999999999854

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.

>KOG4574|consensus

Probab=91.98  E-value=0.14  Score=48.63  Aligned_cols=74  Identities=19%  Similarity=0.282  Sum_probs=61.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCcc--CCcEEEEEEee
Q psy222           91 RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNF--QGSEIIVDFEC  168 (225)
Q Consensus        91 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l--~g~~l~V~~a~  168 (225)
                      .+.++.|.+-..+-..|..+|..||.|.++..+++      -..|.|+|...+.|-.|+.+|+|+++  -|-+.+|.+|+
T Consensus       299 p~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~------~N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak  372 (1007)
T KOG4574|consen  299 PKQSLENNAVNLTSSSLATLCSDYGSVASAWTLRD------LNMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAK  372 (1007)
T ss_pred             chhhhhcccccchHHHHHHHHHhhcchhhheeccc------ccchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEecc
Confidence            35556666667788889999999999999988776      34799999999999999999999874  57789999988


Q ss_pred             CC
Q psy222          169 GR  170 (225)
Q Consensus       169 ~~  170 (225)
                      .-
T Consensus       373 ~~  374 (1007)
T KOG4574|consen  373 TL  374 (1007)
T ss_pred             cc
Confidence            63

>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes

Probab=91.93  E-value=0.86  Score=29.65  Aligned_cols=55  Identities=15%  Similarity=0.186  Sum_probs=42.3

Q ss_pred             CCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222          101 NSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus       101 ~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      .++-++|+..|..|. ...|.  .++     .| =||.|.+..+|++|....++..+-...|.+
T Consensus        11 ~~~v~d~K~~Lr~y~-~~~I~--~d~-----tG-fYIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYR-WDRIR--DDR-----TG-FYIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCC-cceEE--ecC-----CE-EEEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            356789999999997 33443  332     23 479999999999999999999887777654

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>KOG2193|consensus

Probab=89.79  E-value=0.034  Score=48.60  Aligned_cols=76  Identities=21%  Similarity=0.262  Sum_probs=62.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEe-ecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEe
Q psy222           89 PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVV-RDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFE  167 (225)
Q Consensus        89 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~-~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a  167 (225)
                      ..+.+-|.|||+...|+.|..++.+||.+..|..+ ++..+    ...-|+|...+.+..||..|++..|....++|.|-
T Consensus        79 rsrk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~et----avvnvty~~~~~~~~ai~kl~g~Q~en~~~k~~Yi  154 (584)
T KOG2193|consen   79 RSRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDSET----AVVNVTYSAQQQHRQAIHKLNGPQLENQHLKVGYI  154 (584)
T ss_pred             HhhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccchHH----HHHHHHHHHHHHHHHHHHhhcchHhhhhhhhcccC
Confidence            34568899999999999999999999999988654 33322    23347888999999999999999999999999886


Q ss_pred             e
Q psy222          168 C  168 (225)
Q Consensus       168 ~  168 (225)
                      .
T Consensus       155 P  155 (584)
T KOG2193|consen  155 P  155 (584)
T ss_pred             c
Confidence            4

>KOG0804|consensus

Probab=89.54  E-value=1.4  Score=39.17  Aligned_cols=68  Identities=16%  Similarity=0.244  Sum_probs=57.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcC-CceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCC
Q psy222           90 TRTLFIGRLNKNSREADLEQAFAEY-GKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQG  159 (225)
Q Consensus        90 ~~~l~V~nLp~~~te~~L~~~F~~~-G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g  159 (225)
                      ...|+|=.+|..++-.+|..|+..| -.|..++|++|..  -++-..+|.|.+.++|....+.+||+.|..
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~--pnrymvLIkFr~q~da~~Fy~efNGk~Fn~  142 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGM--PNRYMVLIKFRDQADADTFYEEFNGKQFNS  142 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCC--CceEEEEEEeccchhHHHHHHHcCCCcCCC
Confidence            7789999999999999999998765 4588999999642  234468999999999999999999998764

>KOG2318|consensus

Probab=87.48  E-value=3.8  Score=37.66  Aligned_cols=83  Identities=20%  Similarity=0.319  Sum_probs=62.7

Q ss_pred             CCCCCCCeEEEcCCCCC-CCHHHHHHHHhcC----CceeEEEEeecC----------CCCc-------------------
Q psy222           85 SSTDPTRTLFIGRLNKN-SREADLEQAFAEY----GKVISVRVVRDF----------VTGH-------------------  130 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~-~te~~L~~~F~~~----G~v~~v~i~~~~----------~~g~-------------------  130 (225)
                      .....+++|-|-||.|. +...+|..+|..|    |.|.+|.|....          ..|.                   
T Consensus       169 ~~~~~T~RLAVvNMDWd~v~AkDL~v~~nSFlP~gGsilSV~IYpSeFGkeRM~eEeV~GP~~el~~~~e~~~~s~sD~e  248 (650)
T KOG2318|consen  169 VLGEETKRLAVVNMDWDRVKAKDLFVLFNSFLPKGGSILSVKIYPSEFGKERMKEEEVHGPPKELFKPVEEYKESESDDE  248 (650)
T ss_pred             ccccccceeeEeccccccccHHHHHHHHHhhcCCCCceeEEEechhhhhHHHhhhhcccCChhhhccccccCcccccchh
Confidence            34567889999999997 7788999999876    578888875422          1111                   


Q ss_pred             ------------------cceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEe
Q psy222          131 ------------------SKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFE  167 (225)
Q Consensus       131 ------------------~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a  167 (225)
                                        ..-||.|+|.+...|.+....++|..|...-..+.+.
T Consensus       249 e~~~~~~~kLR~Yq~~rLkYYyAVvecDsi~tA~~vYe~CDG~EfEsS~~~~DLR  303 (650)
T KOG2318|consen  249 EEEDVDREKLRQYQLNRLKYYYAVVECDSIETAKAVYEECDGIEFESSANKLDLR  303 (650)
T ss_pred             hhhhHHHHHHHHHHhhhheeEEEEEEecCchHHHHHHHhcCcceeccccceeeee
Confidence                              1237999999999999999999999987655555443

>KOG4676|consensus

Probab=87.29  E-value=0.076  Score=46.04  Aligned_cols=72  Identities=11%  Similarity=0.049  Sum_probs=56.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEe
Q psy222           91 RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFE  167 (225)
Q Consensus        91 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a  167 (225)
                      ++|+|++|+..+...++-+.|..+|.|...++.    .+....+|-|.|........|+. ++|..+.-+...+.+.
T Consensus       152 Rt~~v~sl~~~~~l~e~~e~f~r~Gev~ya~~a----sk~~s~~c~~sf~~qts~~halr-~~gre~k~qhsr~ai~  223 (479)
T KOG4676|consen  152 RTREVQSLISAAILPESGESFERKGEVSYAHTA----SKSRSSSCSHSFRKQTSSKHALR-SHGRERKRQHSRRAII  223 (479)
T ss_pred             hhhhhhcchhhhcchhhhhhhhhcchhhhhhhh----ccCCCcchhhhHhhhhhHHHHHH-hcchhhhhhhhhhhhc
Confidence            689999999999999999999999998877764    34456678899998888888888 5777765444444333

>KOG4410|consensus

Probab=82.75  E-value=5  Score=33.72  Aligned_cols=58  Identities=16%  Similarity=0.240  Sum_probs=40.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCce-eEEEEeecCCCCccceEEEEEeCCH-------HHHHHHHHHh
Q psy222           89 PTRTLFIGRLNKNSREADLEQAFAEYGKV-ISVRVVRDFVTGHSKRYGFLEYDCE-------KACLAAIRAL  152 (225)
Q Consensus        89 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v-~~v~i~~~~~~g~~kg~afV~F~~~-------~~a~~Al~~l  152 (225)
                      ...-|||+||+.++.-.+|+..+.+-+.+ .++.+.     | +.+-||+.|.+.       .++.+++..+
T Consensus       329 ~~~di~~~nl~rd~rv~dlk~~lr~~~~~pm~iswk-----g-~~~k~flh~~~~~~~~~~~~~~~~~~~s~  394 (396)
T KOG4410|consen  329 AKTDIKLTNLSRDIRVKDLKSELRKRECTPMSISWK-----G-HFGKCFLHFGNRKGVPSTQDDMDKVLKSL  394 (396)
T ss_pred             cccceeeccCccccchHHHHHHHHhcCCCceeEeee-----c-CCcceeEecCCccCCCCCchHHHHHhccC
Confidence            34569999999999999999999877653 344432     1 356799999764       3455555444

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	225
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		1e-09
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		2e-08
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		2e-04
3pgw_S	437	Crystal Structure Of Human U1 Snrnp Length = 437		3e-08
1p27_B	106	Crystal Structure Of The Human Y14MAGOH COMPLEX Len		5e-08
3cw1_K	216	Crystal Structure Of Human Spliceosomal U1 Snrnp Le		6e-08
2hyi_B	91	Structure Of The Human Exon Junction Complex With A		9e-08
3ex7_B	126	The Crystal Structure Of Ejc In Its Transition Stat		9e-08
2xb2_D	90	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		9e-08
2j0s_D	89	The Crystal Structure Of The Exon Junction Complex		1e-07
1oo0_B	110	Crystal Structure Of The Drosophila Mago Nashi-Y14		2e-07
2j0q_D	109	The Crystal Structure Of The Exon Junction Complex		2e-07
1hl6_A	165	A Novel Mode Of Rbd-Protein Recognition In The Y14-		2e-07
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		3e-07
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		3e-07
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		5e-07
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		5e-07
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		6e-07
1d9a_A	85	Solution Structure Of The Second Rna-Binding Domain		2e-06
3hi9_A	84	The X-Ray Crystal Structure Of The First Rna Recogn		2e-06
2fc8_A	102	Solution Structure Of The Rrm_1 Domain Of Ncl Prote		2e-06
2dgp_A	106	Solution Structure Of The N-Terminal Rna Binding Do		3e-06
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		6e-06
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		7e-06
4fxv_A	99	Crystal Structure Of An Elav-Like Protein 1 (Elavl1		7e-06
2cpz_A	115	Solution Structure Of Rna Binding Domain 3 In Cug T		1e-05
2dgq_A	108	Solution Structure Of The N-Terminal Rna Binding Do		2e-05
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		3e-05
2khc_A	118	Bruno Rrm3+ Length = 118		3e-05
1x4e_A	85	Solution Structure Of Rrm Domain In Rna Binding Mot		3e-05
1x5u_A	105	Solution Structure Of Rrm Domain In Splicing Factor		4e-05
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		6e-05
1x5t_A	96	Solution Structure Of The Second Rrm Domain In Spli		7e-05
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		7e-05
2yh0_A	198	Solution Structure Of The Closed Conformation Of Hu		9e-05
2cqg_A	103	Solution Structure Of The Rna Binding Domain Of Tar		9e-05
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		1e-04
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		1e-04
1d8z_A	89	Solution Structure Of The First Rna-Binding Domain		2e-04
2dh8_A	105	Solution Structure Of The N-Terminal Rna Binding Do		2e-04
2jwn_A	124	Solution Nmr Structure Of The Protease-Resistent Do		2e-04
1x5o_A	114	Solution Structure Of Rrm Domain In Rna Binding Mot		2e-04
2dnk_A	105	Solution Structure Of Rna Binding Domain In Bruno-L		2e-04
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		2e-04
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		3e-04
1u6f_A	139	Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit		4e-04
2dnq_A	90	Solution Structure Of Rna Binding Domain 1 In Rna-B		4e-04
2dgu_A	103	Solution Structure Of The Rna Binding Domain In Het		4e-04
2ki2_A	90	Solution Structure Of Ss-Dna Binding Protein 12rnp2		6e-04
2cq4_A	114	Solution Structure Of Rna Binding Domain In Rna Bin		7e-04
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		9e-04
2km8_B	84	Interdomain Rrm Packing Contributes To Rna Recognit		9e-04

>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 = 60.1 bits (144), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 30/75 (40%), Positives = 45/75 (60%)
Query: 91  RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
           R++F+G +   + E  L+  F+E G V+S R+V D  TG  K YGF EY  ++  L+A+R
Sbjct: 9   RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 68
Query: 151 ALNRQNFQGSEIIVD 165
            LN + F G  + VD
Sbjct: 69  NLNGREFSGRALRVD 83

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 56.2 bits (134), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 36/123 (29%), Positives = 65/123 (52%), Gaps = 4/123 (3%)
Query: 38  SGQTVKYWYPYCITYDPIQAGSIDGTDTIPHDRAILRALRSTYKPHTSSTDPTRTLFIGR 97
           +GQ++ Y +   I  DP  A      +T+   R   + ++ +Y   +S++     L++  
Sbjct: 40  TGQSLGYGFVNYI--DPKDAEK--AINTLNGLRLQTKTIKVSYARPSSASIRDANLYVSG 95
Query: 98  LNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNF 157
           L K   + +LEQ F++YG++I+ R++ D VTG S+  GF+ +D       AI+ LN Q  
Sbjct: 96  LPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKP 155
Query: 158 QGS 160
            G+
Sbjct: 156 SGA 158

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/74 (32%), Positives = 35/74 (47%)
Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           L +  L +N  + +    F   G++ S ++VRD +TG S  YGF+ Y   K    AI  L
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 153 NRQNFQGSEIIVDF 166
           N    Q   I V +
Sbjct: 65  NGLRLQTKTIKVSY 78

>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp Length = 437

Iteration: 1
 Score = 55.1 bits (131), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 27/96 (28%), Positives = 49/96 (51%), Gaps = 3/96 (3%)
Query: 79  TYKPHTSST---DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYG 135
            + PH       D  +TLF+ R+N ++ E+ L + F  YG +  + +V    +G  + Y 
Sbjct: 88  MWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYA 147
Query: 136 FLEYDCEKACLAAIRALNRQNFQGSEIIVDFECGRV 171
           F+EY+ E+   +A +  + +   G  ++VD E GR 
Sbjct: 148 FIEYEHERDMHSAYKHADGKKIDGRRVLVDVERGRT 183

>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX Length = 106

Iteration: 1
 Score = 54.3 bits (129), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 26/74 (35%), Positives = 43/74 (58%)
Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           LF+  +++ + E D+   FAEYG++ ++ +  D  TG+ K Y  +EY+  K   AA+  L
Sbjct: 26  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 153 NRQNFQGSEIIVDF 166
           N Q+  G  I VD+
Sbjct: 86  NGQDLMGQPISVDW 99

>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp Length = 216

Iteration: 1
 Score = 54.3 bits (129), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 27/95 (28%), Positives = 49/95 (51%), Gaps = 3/95 (3%)
Query: 80  YKPHTSST---DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGF 136
           + PH       D  +TLF+ R+N ++ E+ L + F  YG +  + +V    +G  + Y F
Sbjct: 89  WDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAF 148
Query: 137 LEYDCEKACLAAIRALNRQNFQGSEIIVDFECGRV 171
           +EY+ E+   +A +  + +   G  ++VD E GR 
Sbjct: 149 IEYEHERDMHSAYKHADGKKIDGRRVLVDVERGRT 183

>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 = 53.5 bits (127), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 26/74 (35%), Positives = 43/74 (58%)
Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           LF+  +++ + E D+   FAEYG++ ++ +  D  TG+ K Y  +EY+  K   AA+  L
Sbjct: 12  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 153 NRQNFQGSEIIVDF 166
           N Q+  G  I VD+
Sbjct: 72  NGQDLMGQPISVDW 85

>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State Length = 126

Iteration: 1
 Score = 53.5 bits (127), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 26/74 (35%), Positives = 43/74 (58%)
Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           LF+  +++ + E D+   FAEYG++ ++ +  D  TG+ K Y  +EY+  K   AA+  L
Sbjct: 25  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 153 NRQNFQGSEIIVDF 166
           N Q+  G  I VD+
Sbjct: 85  NGQDLMGQPISVDW 98

>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 = 53.5 bits (127), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 26/74 (35%), Positives = 43/74 (58%)
Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           LF+  +++ + E D+   FAEYG++ ++ +  D  TG+ K Y  +EY+  K   AA+  L
Sbjct: 10  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 153 NRQNFQGSEIIVDF 166
           N Q+  G  I VD+
Sbjct: 70  NGQDLMGQPISVDW 83

>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2 A Resolution Length = 89

Iteration: 1
 Score = 53.1 bits (126), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 26/74 (35%), Positives = 43/74 (58%)
Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           LF+  +++ + E D+   FAEYG++ ++ +  D  TG+ K Y  +EY+  K   AA+  L
Sbjct: 10  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 153 NRQNFQGSEIIVDF 166
           N Q+  G  I VD+
Sbjct: 70  NGQDLMGQPISVDW 83

>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex Length = 110

Iteration: 1
 Score = 52.8 bits (125), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 25/75 (33%), Positives = 44/75 (58%)
Query: 92  TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
            LF+  +++ ++E ++++ F +YG++ ++ +  D  TG SK Y  +EY+  K  LAA  A
Sbjct: 28  ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 87
Query: 152 LNRQNFQGSEIIVDF 166
           LN     G  I VD+
Sbjct: 88  LNGAEIMGQTIQVDW 102

>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 109

Iteration: 1
 Score = 52.8 bits (125), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 26/74 (35%), Positives = 43/74 (58%)
Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           LF+  +++ + E D+   FAEYG++ ++ +  D  TG+ K Y  +EY+  K   AA+  L
Sbjct: 10  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 153 NRQNFQGSEIIVDF 166
           N Q+  G  I VD+
Sbjct: 70  NGQDLMGQPISVDW 83

>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago Complex Length = 165

Iteration: 1
 Score = 52.8 bits (125), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 25/74 (33%), Positives = 44/74 (59%)
Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           LF+  +++ ++E ++++ F +YG++ ++ +  D  TG SK Y  +EY+  K  LAA  AL
Sbjct: 75  LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 153 NRQNFQGSEIIVDF 166
           N     G  I VD+
Sbjct: 135 NGAEIMGQTIQVDW 148

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 52.0 bits (123), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 36/132 (27%), Positives = 68/132 (51%), Gaps = 8/132 (6%)
Query: 38  SGQTVKYWYPYCITY-DPIQAGSIDGTDTIPHDRAILRALRSTYKPHTSSTDPTRTLFIG 96
           +GQ++ Y +   + Y DP  A      +T+   +   + ++ +Y   +S++     L++ 
Sbjct: 42  TGQSLGYGF---VNYSDPNDADK--AINTLNGLKLQTKTIKVSYARPSSASIRDANLYVS 96
Query: 97  RLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQN 156
            L K   + ++EQ F++YG++I+ R++ D  TG S+  GF+ +D       AI+ LN Q 
Sbjct: 97  GLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQK 156
Query: 157 FQGSE--IIVDF 166
             G+   I V F
Sbjct: 157 PLGAAEPITVKF 168

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 51.6 bits (122), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 26/73 (35%), Positives = 45/73 (61%)
Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           LF+G L+ ++ E  LEQ F++YG++  V VV+D  T  S+ +GF+ ++       A+ A+
Sbjct: 15  LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 153 NRQNFQGSEIIVD 165
           N ++  G +I VD
Sbjct: 75  NGKSVDGRQIRVD 87

>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 = 51.2 bits (121), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 24/70 (34%), Positives = 39/70 (55%)
Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           +F+G L+      D++ AFA +G++   RVV+D  TG SK YGF+ +  +     AI+ +
Sbjct: 18  VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 153 NRQNFQGSEI 162
             Q   G +I
Sbjct: 78  GGQWLGGRQI 87

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 51.2 bits (121), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 25/70 (35%), Positives = 38/70 (54%)
Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           +F+G L+      D++ AFA +GK+   RVV+D  TG SK YGF+ +  +     AI  +
Sbjct: 18  VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 153 NRQNFQGSEI 162
             Q   G +I
Sbjct: 78  GGQWLGGRQI 87

>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 = 6e-07,   Method: Compositional matrix adjust.
 Identities = 25/80 (31%), Positives = 42/80 (52%)
Query: 80  YKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEY 139
           ++   SS+D T  LF+G LN N  +  L  AF ++   +S  V+ D  TG S+ YGF+ +
Sbjct: 77  FQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSF 136
Query: 140 DCEKACLAAIRALNRQNFQG 159
             +     A+ ++  Q+  G
Sbjct: 137 TSQDDAQNAMDSMQGQDLNG 156

>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2) Of Hu Antigen C (Huc) Length = 85

Iteration: 1
 Score = 49.3 bits (116), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 26/76 (34%), Positives = 43/76 (56%), Gaps = 2/76 (2%)
Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           L++  L K   + ++EQ F++YG++I+ R++ D  TG S+  GF+ +D       AI+ L
Sbjct: 4   LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 153 NRQNFQGSE--IIVDF 166
           N Q   G+   I V F
Sbjct: 64  NGQKPLGAAEPITVKF 79

>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 = 49.3 bits (116), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 29/79 (36%), Positives = 40/79 (50%), Gaps = 1/79 (1%)
Query: 89  PTRT-LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLA 147
           P RT L +  L +N  + +L   F+  G+V S +++RD V GHS  YGF+ Y   K    
Sbjct: 2   PGRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAER 61
Query: 148 AIRALNRQNFQGSEIIVDF 166
           AI  LN    Q   I V +
Sbjct: 62  AINTLNGLRLQSKTIKVSY 80

>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein Length = 102

Iteration: 1
 Score = 49.3 bits (116), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 23/78 (29%), Positives = 47/78 (60%), Gaps = 3/78 (3%)
Query: 89  PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAA 148
           P++TLF+  L++++ E  L+++F      +  R+V D  TG SK +GF++++ E+   AA
Sbjct: 14  PSKTLFVKGLSEDTTEETLKESFD---GSVRARIVTDRETGSSKGFGFVDFNSEEDAKAA 70
Query: 149 IRALNRQNFQGSEIIVDF 166
             A+      G+++ +D+
Sbjct: 71  KEAMEDGEIDGNKVTLDW 88

>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Bruno-Like 4 Rna-Binding Protein Length = 106

Iteration: 1
 Score = 48.5 bits (114), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 27/64 (42%), Positives = 39/64 (60%), Gaps = 2/64 (3%)
Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEK-ACLAAIRA 151
           LFIG++ +N  E DL+  F E+GK+  + V++D  TG  K   FL Y CE+ + L A  A
Sbjct: 16  LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTY-CERESALKAQSA 74
Query: 152 LNRQ 155
           L+ Q
Sbjct: 75  LHEQ 78

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 41.2 bits (95), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 26/97 (26%), Positives = 45/97 (46%), Gaps = 2/97 (2%)
Query: 74  RALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKR 133
           + ++ +Y   +S       L+I  L +   + D+E  F+ +G++I+ RV+ D  TG S+ 
Sbjct: 72  KTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRG 131
Query: 134 YGFLEYDCEKACLAAIRALNRQNFQGSE--IIVDFEC 168
             F+ +D       AI + N     GS   I V F  
Sbjct: 132 VAFIRFDKRSEAEEAITSFNGHKPPGSSEPITVKFAA 168

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 41.2 bits (95), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 26/97 (26%), Positives = 45/97 (46%), Gaps = 2/97 (2%)
Query: 74  RALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKR 133
           + ++ +Y   +S       L+I  L +   + D+E  F+ +G++I+ RV+ D  TG S+ 
Sbjct: 72  KTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRG 131
Query: 134 YGFLEYDCEKACLAAIRALNRQNFQGSE--IIVDFEC 168
             F+ +D       AI + N     GS   I V F  
Sbjct: 132 VAFIRFDKRSEAEEAITSFNGHKPPGSSEPITVXFAA 168

>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 = 47.4 bits (111), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 26/74 (35%), Positives = 37/74 (50%)
Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           L +  L +N  + +L   F+  G+V S +++RD V GHS  YGF+ Y   K    AI  L
Sbjct: 22  LIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 81
Query: 153 NRQNFQGSEIIVDF 166
           N    Q   I V +
Sbjct: 82  NGLRLQSKTIKVSY 95

>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet Repeat Rna-Binding Protein 1 Length = 115

Iteration: 1
 Score = 46.6 bits (109), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 24/62 (38%), Positives = 35/62 (56%)
Query: 92  TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
            LFI  L +   + DL Q F  +G V+S +V  D  T  SK +GF+ YD   +  AAI++
Sbjct: 27  NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS 86
Query: 152 LN 153
           +N
Sbjct: 87  MN 88

>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Bruno-Like 6 Rna-Binding Protein Length = 108

Iteration: 1
 Score = 45.8 bits (107), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 22/64 (34%), Positives = 36/64 (56%)
Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           LF+G++ +   E DL+  F E+G++  + V++D +TG  K   FL Y    + L A  AL
Sbjct: 18  LFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQSAL 77
Query: 153 NRQN 156
           + Q 
Sbjct: 78  HEQK 81

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 43.1 bits (100), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 18/58 (31%), Positives = 34/58 (58%)
Query: 88  DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKAC 145
           D T  +F+G +  + R  + E+ F+++G +I  +++ D  TG S+ +GF+ YD   A 
Sbjct: 85  DKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAV 142

>pdb|2KHC|A Chain A, Bruno Rrm3+ Length = 118

Iteration: 1
 Score = 45.1 bits (105), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 23/61 (37%), Positives = 33/61 (54%)
Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           LFI  L +   + DL   F  +G VIS +V  D  T  SK +GF+ +D   +   AI+A+
Sbjct: 43  LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 153 N 153
           N
Sbjct: 103 N 103

>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif, Single-Stranded Interacting Protein 2 Length = 85

Iteration: 1
 Score = 45.1 bits (105), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 21/66 (31%), Positives = 33/66 (50%)
Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           L+I  L   + + DL +    YGK++S + + D  T   K YGF+++D   A   A+ AL
Sbjct: 8   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67
Query: 153 NRQNFQ 158
                Q
Sbjct: 68  KASGVQ 73

>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b Length = 105

Iteration: 1
 Score = 44.7 bits (104), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 22/74 (29%), Positives = 41/74 (55%)
Query: 92  TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
           T+++G L++   E  L + F + G V++  + +D VTG  + YGF+E+  E+    AI+ 
Sbjct: 17  TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKI 76
Query: 152 LNRQNFQGSEIIVD 165
           ++     G  I V+
Sbjct: 77  MDMIKLYGKPIRVN 90

>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 = 44.3 bits (103), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 18/67 (26%), Positives = 39/67 (58%)
Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           +++  ++++  + D++  F  +GK+ S  + RD  TG  K YGF+EY+  ++   A+ ++
Sbjct: 128 IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 187
Query: 153 NRQNFQG 159
           N  +  G
Sbjct: 188 NLFDLGG 194

>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 = 7e-05,   Method: Compositional matrix adjust.
 Identities = 25/75 (33%), Positives = 39/75 (52%), Gaps = 1/75 (1%)
Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISV-RVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
           +FIG L+    E  L   F+ +G ++   +++RD  TG+SK Y F+ +    A  AAI A
Sbjct: 8   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 152 LNRQNFQGSEIIVDF 166
           +N Q      I V +
Sbjct: 68  MNGQYLCNRPITVSY 82

>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 = 43.9 bits (102), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 23/69 (33%), Positives = 39/69 (56%), Gaps = 3/69 (4%)
Query: 89  PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAA 148
           P  +L++G L+ +  EA L + F+  G ++S+RV RD +T  S  Y ++ +   +    A
Sbjct: 14  PMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNF---QQPADA 70
Query: 149 IRALNRQNF 157
            RAL+  NF
Sbjct: 71  ERALDTMNF 79

>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human U2af65 Tandem Rrm1 And Rrm2 Domains Length = 198

Iteration: 1
 Score = 43.5 bits (101), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 31/104 (29%), Positives = 44/104 (42%), Gaps = 6/104 (5%)
Query: 67  PHDRAILRALR---STYKPHTSST---DPTRTLFIGRLNKNSREADLEQAFAEYGKVISV 120
           PHD   L  +    S Y P   ST   D    LFIG L     +  +++    +G + + 
Sbjct: 85  PHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAF 144
Query: 121 RVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV 164
            +V+D  TG SK Y F EY        AI  LN       +++V
Sbjct: 145 NLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLV 188

>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna- Binding Protein-43 Length = 103

Iteration: 1
 Score = 43.5 bits (101), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 19/50 (38%), Positives = 32/50 (64%)
Query: 90  TRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEY 139
           T  L +  L   + E DL++ F+ +G+V+ V+V +D  TGHSK +GF+ +
Sbjct: 15  TSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRF 64

>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 = 43.1 bits (100), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/69 (33%), Positives = 39/69 (56%), Gaps = 3/69 (4%)
Query: 89  PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAA 148
           P  +L++G L+ +  EA L + F+  G ++S+RV RD +T  S  Y ++ +   +    A
Sbjct: 9   PMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNF---QQPADA 65
Query: 149 IRALNRQNF 157
            RAL+  NF
Sbjct: 66  ERALDTMNF 74

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 42.7 bits (99), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 18/67 (26%), Positives = 39/67 (58%)
Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           +++  ++++  + D++  F  +GK+ S  + RD  TG  K YGF+EY+  ++   A+ ++
Sbjct: 113 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 172
Query: 153 NRQNFQG 159
           N  +  G
Sbjct: 173 NLFDLGG 179

>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1) Of Hu Antigen C (Huc) Length = 89

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/79 (30%), Positives = 35/79 (44%)
Query: 88  DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLA 147
           D    L +  L +N  + + +  F   G + S ++VRD +TG S  YGF+ Y        
Sbjct: 2   DSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADK 61
Query: 148 AIRALNRQNFQGSEIIVDF 166
           AI  LN    Q   I V +
Sbjct: 62  AINTLNGLKLQTKTIKVSY 80

>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Daz-Associated Protein 1 Length = 105

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 18/70 (25%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           LF+G L+ ++ +  L   F++YG+V+   +++D  T  S+ +GF+++  +  C+  + A 
Sbjct: 19  LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFK-DPNCVGTVLAS 77
Query: 153 NRQNFQGSEI 162
                 G  I
Sbjct: 78  RPHTLDGRNI 87

>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of Xenopus Laevis Epabp2 Length = 124

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 21/74 (28%), Positives = 41/74 (55%), Gaps = 1/74 (1%)
Query: 91  RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
           R++++G ++  S   DLE  F+  G +  + ++ D  +GH K Y ++E+  E+  + A  
Sbjct: 37  RSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEF-AERNSVDAAV 95
Query: 151 ALNRQNFQGSEIIV 164
           A++   F+G  I V
Sbjct: 96  AMDETVFRGRTIKV 109

>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif, Single-Stranded Interacting Protein 1 Length = 114

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/66 (36%), Positives = 35/66 (53%), Gaps = 2/66 (3%)
Query: 88  DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLA 147
           DPT  L+I  L  +  E +LE     +G+VIS R++RD  +G S+  GF   +  + C A
Sbjct: 24  DPTN-LYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEA 81
Query: 148 AIRALN 153
            I   N
Sbjct: 82  VIGHFN 87

>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4 Rna Binding Protein Length = 105

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 27/79 (34%), Positives = 40/79 (50%), Gaps = 4/79 (5%)
Query: 91  RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
           R LF+G LNK   E D+ + F  +G +    ++R    G+SK   F++Y       AAI 
Sbjct: 16  RKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRG-PDGNSKGCAFVKYSSHAEAQAAIN 74
Query: 151 ALN-RQNFQG--SEIIVDF 166
           AL+  Q   G  S ++V F
Sbjct: 75  ALHGSQTMPGASSSLVVKF 93

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/68 (33%), Positives = 37/68 (54%), Gaps = 1/68 (1%)
Query: 86  STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKAC 145
           S  P R L++G L+ N  E  L   F  +G++ S++++ D  TG SK YGF+ +   +  
Sbjct: 23  SAGPMR-LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECA 81
Query: 146 LAAIRALN 153
             A+  LN
Sbjct: 82  KKALEQLN 89

>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U Binding Splicing Factor 60kda (Puf60) From Homo Sapiens At 2.50 A Resolution Length = 200

Iteration: 1
 Score = 41.6 bits (96), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 18/67 (26%), Positives = 38/67 (56%)
Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           +++  ++++  + D++  F  +GK+ S  + RD  TG  K YGF+EY+  ++   A+ + 
Sbjct: 112 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSX 171
Query: 153 NRQNFQG 159
           N  +  G
Sbjct: 172 NLFDLGG 178

>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From Trypanosoma Cruzi Length = 139

Iteration: 1
 Score = 41.6 bits (96), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 23/70 (32%), Positives = 33/70 (47%)
Query: 88  DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLA 147
           D  R L +  +     E  L Q F  YG + SV++V D  T  S+ YGF+++    +   
Sbjct: 40  DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQ 99
Query: 148 AIRALNRQNF 157
           AI  LN  N 
Sbjct: 100 AIAGLNGFNI 109

>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding Protein 30 Length = 90

Iteration: 1
 Score = 41.2 bits (95), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 24/82 (29%), Positives = 39/82 (47%), Gaps = 8/82 (9%)
Query: 84  TSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEK 143
           +S +     LFIG L + + E ++   F +YGKV+   ++        K YGF+  + + 
Sbjct: 2   SSGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKT 53
Query: 144 ACLAAIRALNRQNFQGSEIIVD 165
           A   AIR L+     G  I V+
Sbjct: 54  AAEDAIRNLHHYKLHGVNINVE 75

>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In Heterogeneous Nuclear Ribonucleoprotein Q Length = 103

Iteration: 1
 Score = 41.2 bits (95), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 21/83 (25%), Positives = 41/83 (49%), Gaps = 8/83 (9%)
Query: 84  TSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEK 143
           +S     + LF+  L     E  LE+AF+++GK+  V+ ++D        Y F+ +D   
Sbjct: 5   SSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERD 56
Query: 144 ACLAAIRALNRQNFQGSEIIVDF 166
             + A+  +N ++ +G  I + F
Sbjct: 57  GAVKAMEEMNGKDLEGENIEIVF 79

>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2 Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori Length = 90

Iteration: 1
 Score = 40.8 bits (94), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 21/72 (29%), Positives = 42/72 (58%), Gaps = 1/72 (1%)
Query: 91  RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
           R +++G L  ++    +++ F+++GKV +V+++ D  T   K +GF+E   E++   AI 
Sbjct: 2   RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQ-EESVSEAIA 60
Query: 151 ALNRQNFQGSEI 162
            L+  +F G  I
Sbjct: 61  KLDNTDFMGRTI 72

>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding Motif Protein 23 Length = 114

Iteration: 1
 Score = 40.4 bits (93), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 26/75 (34%), Positives = 36/75 (48%), Gaps = 1/75 (1%)
Query: 90  TRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAI 149
            RT+F  +L    R  DLE  F+  GKV  VR++ D  +  SK   ++E+ CE   +   
Sbjct: 25  ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEF-CEIQSVPLA 83
Query: 150 RALNRQNFQGSEIIV 164
             L  Q   G  IIV
Sbjct: 84  IGLTGQRLLGVPIIV 98

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 40.4 bits (93), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 21/67 (31%), Positives = 35/67 (52%)
Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           L++G L+ N  E  L   F  +GK+ ++ +++D  TG SK YGF+ +   +    A+  L
Sbjct: 8   LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 153 NRQNFQG 159
           N     G
Sbjct: 68  NGFELAG 74

>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition In The Rna15, Hrp1, Anchor Rna 3' Processing Ternary Complex Length = 84

Iteration: 1
 Score = 40.4 bits (93), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 19/65 (29%), Positives = 38/65 (58%)
Query: 89  PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAA 148
           P+R +++G +  +  E  +    +  G VI+++++ D  TG SK Y F+E+   ++  +A
Sbjct: 3   PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 62
Query: 149 IRALN 153
           +R LN
Sbjct: 63  VRNLN 67

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	225
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	3e-23
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	2e-22
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	2e-22
1x4e_A	85	RNA binding motif, single-stranded interacting pro	6e-22
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	8e-22
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	2e-21
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	2e-21
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	3e-21
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	4e-21
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	4e-21
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	5e-21
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	6e-21
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	8e-21
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	3e-20
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	3e-20
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	3e-20
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	4e-20
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	5e-20
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	7e-20
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	8e-20
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	9e-20
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	3e-19
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	9e-20
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	1e-19
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	2e-19
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	2e-19
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	2e-19
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	1e-16
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	2e-19
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	3e-19
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	3e-19
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	3e-19
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	3e-19
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	3e-19
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	3e-19
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	4e-19
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	3e-18
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	4e-19
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	4e-19
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	4e-19
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	7e-19
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	9e-19
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	1e-18
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-18
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-16
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	7e-11
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	1e-18
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	1e-18
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-18
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	3e-18
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	6e-18
1x5o_A	114	RNA binding motif, single-stranded interacting pro	6e-18
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	6e-18
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	3e-17
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	7e-18
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	7e-18
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	7e-18
2div_A	99	TRNA selenocysteine associated protein; structural	8e-18
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	8e-18
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	8e-18
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	9e-18
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-15
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	1e-17
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	1e-17
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	2e-17
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	2e-17
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	2e-17
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	3e-17
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	4e-17
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	3e-12
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	4e-17
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	5e-17
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	4e-15
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	5e-17
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	5e-17
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	5e-17
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	5e-17
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	6e-17
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	6e-17
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	8e-17
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	1e-13
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	9e-17
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	9e-17
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	6e-15
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	9e-17
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	1e-16
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	2e-16
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	2e-16
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	2e-16
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	3e-16
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	3e-16
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	4e-16
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	6e-16
2dis_A	109	Unnamed protein product; structural genomics, RRM	8e-16
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	2e-15
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	2e-15
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	3e-15
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	3e-15
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	6e-15
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	6e-15
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	8e-15
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	9e-15
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	2e-14
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-14
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	6e-14
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	6e-14
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-13
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-12
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	9e-14
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	9e-14
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	3e-12
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	1e-13
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	1e-13
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	1e-13
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-13
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-05
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-13
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	3e-13
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	3e-13
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	4e-13
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	5e-13
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	8e-13
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	9e-13
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	1e-12
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	1e-12
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	1e-12
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	1e-12
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	1e-12
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	1e-12
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	3e-12
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	3e-12
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	3e-12
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	3e-12
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	5e-12
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	8e-12
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	8e-12
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	8e-12
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	8e-12
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	1e-11
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	1e-10
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	1e-11
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	2e-11
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	4e-11
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	4e-11
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	7e-11
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	8e-11
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	8e-11
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	1e-10
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	2e-10
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	3e-10
1x5p_A	97	Negative elongation factor E; structure genomics,	3e-10
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	4e-10
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	4e-10
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	1e-09
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	5e-10
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	8e-10
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-09
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	7e-09
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	3e-09
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	7e-09
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	2e-08
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	2e-08
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	3e-08
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	3e-08
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	5e-08
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	5e-08
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	5e-08
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	6e-08
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	8e-08
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	9e-08
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	1e-07
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	2e-07
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	4e-07
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	1e-06
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	2e-06
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	3e-06
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	9e-06
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	1e-05
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	3e-05
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	4e-05
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	2e-04
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	3e-04
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	8e-04

>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 = 90.2 bits (224), Expect = 3e-23
 Identities = 28/106 (26%), Positives = 40/106 (37%), Gaps = 5/106 (4%)

Query: 85  SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
              D  R L +  +     E  L Q F  YG + SV++V D  T  S+ YGF+++    +
Sbjct: 37  PEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSS 96

Query: 145 CLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWGGNRNS 190
              AI  LN  N     + V             R    G  G+ N 
Sbjct: 97  AQQAIAGLNGFNILNKRLKVALAASG-----HQRPGIAGAVGDGNG 137

>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 = 86.5 bits (215), Expect = 2e-22
 Identities = 19/78 (24%), Positives = 40/78 (51%)

Query: 89  PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAA 148
           P+R +++G +  +  E  +    +  G VI+++++ D  TG SK Y F+E+   ++  +A
Sbjct: 1   PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60

Query: 149 IRALNRQNFQGSEIIVDF 166
           +R LN        +   +
Sbjct: 61  VRNLNGYQLGSRFLKCGY 78

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 87.1 bits (216), Expect = 2e-22
 Identities = 16/78 (20%), Positives = 31/78 (39%)

Query: 89  PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAA 148
           P + +   RLN N RE  L+    +YG+V  V ++    T        + +   +     
Sbjct: 5   PLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKET 64

Query: 149 IRALNRQNFQGSEIIVDF 166
           ++ L+  +  G+ I    
Sbjct: 65  VKNLHLTSVMGNIIHAQL 82

>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 = 84.9 bits (211), Expect = 6e-22
 Identities = 22/77 (28%), Positives = 36/77 (46%), Gaps = 1/77 (1%)

Query: 86  STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKAC 145
           S+  +  L+I  L   + + DL +    YGK++S + + D  T   K YGF+++D   A 
Sbjct: 2   SSGSSG-LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAA 60

Query: 146 LAAIRALNRQNFQGSEI 162
             A+ AL     Q    
Sbjct: 61  QKAVTALKASGVQAQMA 77

>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 = 85.0 bits (211), Expect = 8e-22
 Identities = 32/103 (31%), Positives = 49/103 (47%), Gaps = 5/103 (4%)

Query: 85  SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
           +     R++F+G +   + E  L+  F+E G V+S R+V D  TG  K YGF EY  ++ 
Sbjct: 3   AVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQET 62

Query: 145 CLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWGGN 187
            L+A+R LN + F G  + VD          K +      G  
Sbjct: 63  ALSAMRNLNGREFSGRALRVDNAASE-----KNKEELKSLGTG 100

>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 = 83.8 bits (208), Expect = 2e-21
 Identities = 25/95 (26%), Positives = 52/95 (54%), Gaps = 3/95 (3%)

Query: 85  SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
           + + P++TLF+  L++++ E  L+++F      +  R+V D  TG SK +GF++++ E+ 
Sbjct: 10  ARSQPSKTLFVKGLSEDTTEETLKESF---DGSVRARIVTDRETGSSKGFGFVDFNSEED 66

Query: 145 CLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRR 179
             AA  A+      G+++ +D+   +   G  P  
Sbjct: 67  AKAAKEAMEDGEIDGNKVTLDWAKPKGEGGSGPSS 101

>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 = 83.8 bits (208), Expect = 2e-21
 Identities = 20/82 (24%), Positives = 36/82 (43%)

Query: 85  SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
           ++ DP   L +  L+  + E DL + F++YG +  V +V D  +  S+ + F+ ++    
Sbjct: 10  ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDD 69

Query: 145 CLAAIRALNRQNFQGSEIIVDF 166
              A    N     G  I V  
Sbjct: 70  AKEAKERANGMELDGRRIRVSG 91

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 83.5 bits (207), Expect = 3e-21
 Identities = 14/88 (15%), Positives = 33/88 (37%), Gaps = 6/88 (6%)

Query: 85  SSTDPTRTLFIGRLNKNSREADLEQAFAEYGK--VISVRVVRDFVTGHSKRYGFLEYDCE 142
                  T+ +  +  ++    +  A + Y    V ++R+++D  T  ++ + F++    
Sbjct: 4   HHHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSA 63

Query: 143 KACLAAIRALN----RQNFQGSEIIVDF 166
                 ++ L          G  I VDF
Sbjct: 64  MDASQLLQILQSLHPPLKIDGKTIGVDF 91

>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 = 83.5 bits (207), Expect = 4e-21
 Identities = 29/114 (25%), Positives = 53/114 (46%), Gaps = 5/114 (4%)

Query: 66  IPHDRAILRALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRD 125
           I     +        +P    +     LF+  +++ ++E ++++ F +YG++ ++ +  D
Sbjct: 2   IHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLD 61

Query: 126 FVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRR 179
             TG SK Y  +EY+  K  LAA  ALN     G  I VD+   +      P+R
Sbjct: 62  RRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVK-----GPKR 110

>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 = 83.4 bits (207), Expect = 4e-21
 Identities = 19/91 (20%), Positives = 34/91 (37%)

Query: 88  DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLA 147
           D   TL +  L   +    L + F +YG+V  V + R+  T   + + F+ +   +    
Sbjct: 11  DGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQD 70

Query: 148 AIRALNRQNFQGSEIIVDFECGRVLPGWKPR 178
           A  A++     G E+ V            P 
Sbjct: 71  AEAAMDGAELDGRELRVQVARYGRRDLSGPS 101

>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 = 84.0 bits (208), Expect = 5e-21
 Identities = 24/113 (21%), Positives = 43/113 (38%)

Query: 54  PIQAGSIDGTDTIPHDRAILRALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAE 113
                   G+              S +  + ++ DP   L +  L+  + E DL + F++
Sbjct: 10  HSSGLVPRGSHMASMTGGQQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSK 69

Query: 114 YGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF 166
           YG +  V +V D  +  S+ + F+ ++       A    N     G  I VDF
Sbjct: 70  YGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDF 122

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 84.1 bits (208), Expect = 6e-21
 Identities = 20/97 (20%), Positives = 39/97 (40%)

Query: 70  RAILRALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTG 129
              +            S    R L++G L +   +  L  AF  +G +  +++  D+ T 
Sbjct: 43  ERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETE 102

Query: 130 HSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF 166
             + + F+E++  +   AAI  +N     G  I V+ 
Sbjct: 103 KHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL 139

>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 = 82.3 bits (204), Expect = 8e-21
 Identities = 20/79 (25%), Positives = 37/79 (46%)

Query: 88  DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLA 147
               T+++  L  +    DL + F++YGKV+ V +++D  T  SK   F+ +  + +   
Sbjct: 14  PSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQN 73

Query: 148 AIRALNRQNFQGSEIIVDF 166
             RA+N +   G  I    
Sbjct: 74  CTRAINNKQLFGRVIKASI 92

>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 = 81.1 bits (201), Expect = 3e-20
 Identities = 18/82 (21%), Positives = 41/82 (50%)

Query: 85  SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
              D   T+ +  L++++RE DL++ F  +G +  + + +D  TG SK + F+ +   + 
Sbjct: 10  RRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRRED 69

Query: 145 CLAAIRALNRQNFQGSEIIVDF 166
              AI  ++   +    + V++
Sbjct: 70  AARAIAGVSGFGYDHLILNVEW 91

>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 = 81.2 bits (201), Expect = 3e-20
 Identities = 20/95 (21%), Positives = 43/95 (45%), Gaps = 4/95 (4%)

Query: 85  SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
           + +  ++TL +  L+ ++ E  L++ F +   +     V     G SK Y F+E+   + 
Sbjct: 10  TWSGESKTLVLSNLSYSATEETLQEVFEKATFI----KVPQNQNGKSKGYAFIEFASFED 65

Query: 145 CLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRR 179
              A+ + N++  +G  I ++ +  R  P   P  
Sbjct: 66  AKEALNSCNKREIEGRAIRLELQGPRGSPNSGPSS 100

>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 = 82.6 bits (204), Expect = 3e-20
 Identities = 20/90 (22%), Positives = 39/90 (43%)

Query: 77  RSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGF 136
            S +  H    +   +L +  L   +    L + F +YG+V  V + RD  T  S+ + F
Sbjct: 57  GSHHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAF 116

Query: 137 LEYDCEKACLAAIRALNRQNFQGSEIIVDF 166
           + +  ++    A+ A++     G E+ V  
Sbjct: 117 VRFHDKRDAEDAMDAMDGAVLDGRELRVQM 146

>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 = 80.8 bits (200), Expect = 4e-20
 Identities = 22/82 (26%), Positives = 38/82 (46%)

Query: 85  SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
             +     L++G L+ N  E  L   F  +G++ S++++ D  TG SK YGF+ +   + 
Sbjct: 21  KGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSEC 80

Query: 145 CLAAIRALNRQNFQGSEIIVDF 166
              A+  LN     G  + V  
Sbjct: 81  AKKALEQLNGFELAGRPMKVGH 102

>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 = 80.3 bits (199), Expect = 5e-20
 Identities = 25/100 (25%), Positives = 43/100 (43%), Gaps = 6/100 (6%)

Query: 87  TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACL 146
           +  +  L++G L+ N  E  L   F  +GK+ ++ +++D  TG SK YGF+ +   +   
Sbjct: 2   SSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECAR 61

Query: 147 AAIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWGG 186
            A+  LN     G  + V      V    +     G   G
Sbjct: 62  RALEQLNGFELAGRPMRVGH----VTE--RLDGGSGPSSG 95

>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 = 80.0 bits (198), Expect = 7e-20
 Identities = 25/102 (24%), Positives = 43/102 (42%), Gaps = 5/102 (4%)

Query: 85  SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
           S +  +  LF+  L+  S E DLE+ F+ YG +  +    D +T   K + F+ +   + 
Sbjct: 3   SGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEH 62

Query: 145 CLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWGG 186
            + A   ++ Q FQG  + V     +     K     G   G
Sbjct: 63  AVKAYAEVDGQVFQGRMLHVLPSTIK-----KEASQSGPSSG 99

>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 = 79.5 bits (197), Expect = 8e-20
 Identities = 22/75 (29%), Positives = 41/75 (54%), Gaps = 1/75 (1%)

Query: 91  RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
           R +++G L  ++    +++ F+++GKV +V+++ D  T   K +GF+E   E     AI 
Sbjct: 2   RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESV-SEAIA 60

Query: 151 ALNRQNFQGSEIIVD 165
            L+  +F G  I V 
Sbjct: 61  KLDNTDFMGRTIRVT 75

>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 = 9e-20
 Identities = 19/84 (22%), Positives = 37/84 (44%), Gaps = 2/84 (2%)

Query: 85  SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
             +     L++  L +   +  L+  F +YG ++   ++RD +TG  +   F+ Y+  + 
Sbjct: 84  GESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREE 143

Query: 145 CLAAIRALNRQNFQGS--EIIVDF 166
              AI ALN    +G    + V  
Sbjct: 144 AQEAISALNNVIPEGGSQPLSVRL 167

>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 = 80.3 bits (199), Expect = 3e-19
 Identities = 19/76 (25%), Positives = 37/76 (48%)

Query: 91  RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
             L +  L ++  + +L   F   G + + R++RD+ TG+S  Y F+++  E     AI+
Sbjct: 4   TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63

Query: 151 ALNRQNFQGSEIIVDF 166
            LN    +   + V +
Sbjct: 64  VLNGITVRNKRLKVSY 79

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 80.0 bits (198), Expect = 9e-20
 Identities = 27/93 (29%), Positives = 47/93 (50%)

Query: 74  RALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKR 133
              +   +P    +     LF+  +++ + E D+   FAEYG++ ++ +  D  TG+ K 
Sbjct: 7   SVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKG 66

Query: 134 YGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF 166
           Y  +EY+  K   AA+  LN Q+  G  I VD+
Sbjct: 67  YTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 99

>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 = 79.1 bits (196), Expect = 1e-19
 Identities = 20/81 (24%), Positives = 38/81 (46%)

Query: 85  SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
           S     R L++G L +   +  L  AF  +G +  +++  D+ T   + + F+E++  + 
Sbjct: 2   SMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAED 61

Query: 145 CLAAIRALNRQNFQGSEIIVD 165
             AAI  +N     G  I V+
Sbjct: 62  AAAAIDNMNESELFGRTIRVN 82

>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 = 78.7 bits (195), Expect = 2e-19
 Identities = 20/82 (24%), Positives = 39/82 (47%), Gaps = 2/82 (2%)

Query: 86  STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRD-FVTGHSKRYGFLEYDCEKA 144
           S  PT+ + IGRL +N  +  + + F+ YGK+  + +  +      SK Y ++E++    
Sbjct: 1   SMKPTK-VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDE 59

Query: 145 CLAAIRALNRQNFQGSEIIVDF 166
              A++ ++     G EI    
Sbjct: 60  AEKALKHMDGGQIDGQEITATA 81

>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 = 80.6 bits (199), Expect = 2e-19
 Identities = 30/128 (23%), Positives = 57/128 (44%), Gaps = 5/128 (3%)

Query: 61  DGTDTIPHDRAILRALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISV 120
           +  + I     +        +P    +     LF+  +++ ++E ++++ F +YG++ ++
Sbjct: 43  NTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNI 102

Query: 121 RVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRRL 180
            +  D  TG SK Y  +EY+  K  LAA  ALN     G  I VD+   +      P+R+
Sbjct: 103 HLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVK-----GPKRV 157

Query: 181 GGGWGGNR 188
                  R
Sbjct: 158 KKSEKRRR 165

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 82.0 bits (203), Expect = 2e-19
 Identities = 22/90 (24%), Positives = 39/90 (43%)

Query: 77  RSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGF 136
           R +      +      +++G +     E  + QAFA +G + S+ +  D VT   K + F
Sbjct: 15  RGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAF 74

Query: 137 LEYDCEKACLAAIRALNRQNFQGSEIIVDF 166
           +EY+  +A   A+  +N     G  I V  
Sbjct: 75  VEYEVPEAAQLALEQMNSVMLGGRNIKVGR 104

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 74.7 bits (184), Expect = 1e-16
 Identities = 20/99 (20%), Positives = 42/99 (42%), Gaps = 1/99 (1%)

Query: 69  DRAILRALRSTYKPHT-SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFV 127
            R                       +++  ++++  + D++  F  +GK+ S  + RD  
Sbjct: 103 GRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPT 162

Query: 128 TGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF 166
           TG  K YGF+EY+  ++   A+ ++N  +  G  + V  
Sbjct: 163 TGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGK 201

>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 = 78.9 bits (195), Expect = 2e-19
 Identities = 28/88 (31%), Positives = 41/88 (46%), Gaps = 4/88 (4%)

Query: 83  HTSSTDPTRT-LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDC 141
            +   D     LFIG++ +N  E DL+  F E+GK+  + V++D  TG  K   FL Y  
Sbjct: 5   SSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCE 64

Query: 142 EKACLAAIRALNRQN---FQGSEIIVDF 166
            ++ L A  AL+ Q         I V  
Sbjct: 65  RESALKAQSALHEQKTLPGMNRPIQVKP 92

>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 = 79.3 bits (196), Expect = 3e-19
 Identities = 33/122 (27%), Positives = 55/122 (45%), Gaps = 2/122 (1%)

Query: 74  RALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKR 133
              +   +P    +     LF+  +++ + E D+   FAEYG++ ++ +  D  TG+ K 
Sbjct: 6   SVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKG 65

Query: 134 YGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWGGNRNSGQL 193
           Y  +EY+  K   AA+  LN Q+  G  I VD+    V    K +R GG         + 
Sbjct: 66  YTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW--CFVRGPPKGKRRGGRRRSRSPDRRR 123

Query: 194 RF 195
           R 
Sbjct: 124 RL 125

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 78.5 bits (194), Expect = 3e-19
 Identities = 19/83 (22%), Positives = 37/83 (44%), Gaps = 1/83 (1%)

Query: 84  TSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEK 143
            S++     LFI  L  +  + +LE+    +G V  +R+V +   G  K   ++EY+ E 
Sbjct: 11  YSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENES 69

Query: 144 ACLAAIRALNRQNFQGSEIIVDF 166
               A+  ++    + + I V  
Sbjct: 70  QASQAVMKMDGMTIKENIIKVAI 92

>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 = 78.0 bits (193), Expect = 3e-19
 Identities = 26/102 (25%), Positives = 40/102 (39%), Gaps = 14/102 (13%)

Query: 85  SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
           SS   +  L +G ++      +L   F EYG VI   +V+D+         F+  +  + 
Sbjct: 5   SSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKDY--------AFVHMERAED 56

Query: 145 CLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWGG 186
            + AIR L+   FQG  + V     R       R   G   G
Sbjct: 57  AVEAIRGLDNTEFQGKRMHVQLSTSR------LRTASGPSSG 92

>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 = 78.4 bits (194), Expect = 3e-19
 Identities = 26/83 (31%), Positives = 46/83 (55%)

Query: 84  TSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEK 143
           +        LF+G L+ ++ E  LEQ F++YG++  V VV+D  T  S+ +GF+ ++   
Sbjct: 6   SGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENID 65

Query: 144 ACLAAIRALNRQNFQGSEIIVDF 166
               A+ A+N ++  G +I VD 
Sbjct: 66  DAKDAMMAMNGKSVDGRQIRVDQ 88

>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 = 78.9 bits (195), Expect = 3e-19
 Identities = 19/105 (18%), Positives = 43/105 (40%), Gaps = 4/105 (3%)

Query: 62  GTDTIPHDRAILRALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVR 121
           G+     +      + S+Y P     +P + L++  L+    E DL   FA + +     
Sbjct: 1   GSSGSSGEEIRKIPMFSSYNPG----EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPP 56

Query: 122 VVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF 166
           +    +TG  +   F+ +  ++    A+  +N     G  ++++F
Sbjct: 57  IQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF 101

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 78.5 bits (194), Expect = 3e-19
 Identities = 26/105 (24%), Positives = 47/105 (44%), Gaps = 6/105 (5%)

Query: 82  PHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDC 141
              S  +   T+++G L++   E  L + F + G V++  + +D VTG  + YGF+E+  
Sbjct: 7   GPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLS 66

Query: 142 EKACLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWGG 186
           E+    AI+ ++     G  I V+            + L G   G
Sbjct: 67  EEDADYAIKIMDMIKLYGKPIRVNKASAH------NKNLSGPSSG 105

>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 = 79.9 bits (198), Expect = 4e-19
 Identities = 30/88 (34%), Positives = 49/88 (55%), Gaps = 3/88 (3%)

Query: 81  KPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYD 140
           +P ++S      L++  L K   + +LEQ F++YG++I+ R++ D VTG S+  GF+ +D
Sbjct: 80  RPSSASIRDAN-LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFD 138

Query: 141 CEKACLAAIRALNRQNFQGSE--IIVDF 166
                  AI+ LN Q   G+   I V F
Sbjct: 139 KRIEAEEAIKGLNGQKPSGATEPITVKF 166

>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 = 77.6 bits (192), Expect = 3e-18
 Identities = 24/75 (32%), Positives = 35/75 (46%)

Query: 92  TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
            L +  L +N  + +    F   G++ S ++VRD +TG S  YGF+ Y   K    AI  
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 152 LNRQNFQGSEIIVDF 166
           LN    Q   I V +
Sbjct: 64  LNGLRLQTKTIKVSY 78

>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 = 78.0 bits (193), Expect = 4e-19
 Identities = 19/83 (22%), Positives = 38/83 (45%)

Query: 84  TSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEK 143
           +      R L++G L +   +  L  AF  +G +  +++  D+ T   + + F+E++  +
Sbjct: 6   SGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 65

Query: 144 ACLAAIRALNRQNFQGSEIIVDF 166
              AAI  +N     G  I V+ 
Sbjct: 66  DAAAAIDNMNESELFGRTIRVNL 88

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 78.6 bits (194), Expect = 4e-19
 Identities = 31/111 (27%), Positives = 43/111 (38%)

Query: 56  QAGSIDGTDTIPHDRAILRALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYG 115
           Q GS     T P     L A  +              LFI  L +   + DL   F  +G
Sbjct: 6   QFGSASALSTSPLASVALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFG 65

Query: 116 KVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF 166
            VIS +V  D  T  SK +GF+ +D   +   AI+A+N        + V  
Sbjct: 66  NVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQL 116

>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 = 79.5 bits (196), Expect = 4e-19
 Identities = 23/121 (19%), Positives = 49/121 (40%), Gaps = 4/121 (3%)

Query: 74  RALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKR 133
           +  R   +        + TL++G L+  + E  + + F++ G +  + +  D +   +  
Sbjct: 23  QHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACG 82

Query: 134 YGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWGGNRNSGQL 193
           + F+EY        A+R +N        I  D++ G      + R+ G G  G +   + 
Sbjct: 83  FCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFK----EGRQYGRGRSGGQVRDEY 138

Query: 194 R 194
           R
Sbjct: 139 R 139

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 78.6 bits (194), Expect = 7e-19
 Identities = 19/90 (21%), Positives = 38/90 (42%)

Query: 77  RSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGF 136
             +Y       +   +L +  L   +    L + F +YG+V  V + RD  T  S+ + F
Sbjct: 34  SMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAF 93

Query: 137 LEYDCEKACLAAIRALNRQNFQGSEIIVDF 166
           + +  ++    A+ A++     G E+ V  
Sbjct: 94  VRFHDKRDAEDAMDAMDGAVLDGRELRVQM 123

>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 = 76.9 bits (190), Expect = 9e-19
 Identities = 24/102 (23%), Positives = 41/102 (40%), Gaps = 14/102 (13%)

Query: 84  TSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEK 143
           + S+  T  +F+G ++      +L   F   G+VI   VV+D+         F+  + E 
Sbjct: 3   SGSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKDY--------AFVHMEKEA 54

Query: 144 ACLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWG 185
              AAI  LN +  +G  I V+            ++ G   G
Sbjct: 55  DAKAAIAQLNGKEVKGKRINVELSTKG------QKKSGPSSG 90

>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 = 77.4 bits (191), Expect = 1e-18
 Identities = 27/92 (29%), Positives = 40/92 (43%), Gaps = 1/92 (1%)

Query: 74  RALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKR 133
             +R      +      RT+F  +L    R  DLE  F+  GKV  VR++ D  +  SK 
Sbjct: 9   SPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKG 68

Query: 134 YGFLEYDCEKACLAAIRALNRQNFQGSEIIVD 165
             ++E+   ++   AI  L  Q   G  IIV 
Sbjct: 69  IAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQ 99

>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 = 81.2 bits (201), Expect = 1e-18
 Identities = 17/75 (22%), Positives = 29/75 (38%)

Query: 92  TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
            L +  L  +  +   E+    +G +    +V    TG SK YGF EY  + +   A   
Sbjct: 97  LLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSD 156

Query: 152 LNRQNFQGSEIIVDF 166
           L  +      + V +
Sbjct: 157 LLGKPLGPRTLYVHW 171

>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 = 75.8 bits (187), Expect = 1e-16
 Identities = 19/95 (20%), Positives = 35/95 (36%), Gaps = 2/95 (2%)

Query: 73  LRALRSTYKPHTSSTDPTRTLFIGRLNKNSREAD-LEQAFAEYGKVISVRVVRDFVTGHS 131
           L    +     T +   +R L + RL     + D L +A +        ++      G  
Sbjct: 167 LYVHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACG-QDGQL 225

Query: 132 KRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF 166
           K +  LEY+  +    A +  +  +  GS + V F
Sbjct: 226 KGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSF 260

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 59.6 bits (145), Expect = 7e-11
 Identities = 14/91 (15%), Positives = 29/91 (31%), Gaps = 7/91 (7%)

Query: 76  LRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYG 135
           +R   +         R + I  L  +    ++    ++Y  +    V         K   
Sbjct: 8   IRKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTA 60

Query: 136 FLEYDCEKACLAAIRALNRQNFQGSEIIVDF 166
           F+     +   AAI A ++   +  E+ V  
Sbjct: 61  FVTLLNGEQAEAAINAFHQSRLRERELSVQL 91

>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 = 76.4 bits (189), Expect = 1e-18
 Identities = 19/77 (24%), Positives = 42/77 (54%), Gaps = 1/77 (1%)

Query: 89  PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAA 148
             R++++G ++  +   +LE  F   G V  V ++ D  +GH K + ++E+  +++   +
Sbjct: 5   DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTS 64

Query: 149 IRALNRQNFQGSEIIVD 165
           + AL+   F+G +I V 
Sbjct: 65  L-ALDESLFRGRQIKVI 80

>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 = 77.4 bits (191), Expect = 1e-18
 Identities = 26/109 (23%), Positives = 45/109 (41%), Gaps = 1/109 (0%)

Query: 86  STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKAC 145
             D    LFIG LN+ + E  L+  F ++G +  V +++D  T  S+ + F+ ++     
Sbjct: 3   EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITFENPADA 61

Query: 146 LAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWGGNRNSGQLR 194
             A + +N ++  G  I V+            RR          SG L 
Sbjct: 62  KNAAKDMNGKSLHGKAIKVEQAKKPSFQSGGRRRPPASSRNRSPSGSLE 110

>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 = 75.6 bits (187), Expect = 2e-18
 Identities = 21/74 (28%), Positives = 39/74 (52%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           LF+G LN N  +  L  AF ++   +S  V+ D  TG S+ YGF+ +  +     A+ ++
Sbjct: 4   LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63

Query: 153 NRQNFQGSEIIVDF 166
             Q+  G  + +++
Sbjct: 64  QGQDLNGRPLRINW 77

>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 = 76.2 bits (188), Expect = 3e-18
 Identities = 25/72 (34%), Positives = 37/72 (51%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           LFI  L +   + DL Q F  +G V+S +V  D  T  SK +GF+ YD   +  AAI+++
Sbjct: 28  LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87

Query: 153 NRQNFQGSEIIV 164
           N        + V
Sbjct: 88  NGFQIGMKRLKV 99

>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 = 75.5 bits (186), Expect = 6e-18
 Identities = 23/88 (26%), Positives = 40/88 (45%), Gaps = 6/88 (6%)

Query: 85  SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
           S     +T+FI  L+ +S E  L +   ++G +  VRVV    T HSK   F ++  ++A
Sbjct: 10  SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEA 69

Query: 145 CLAAIRALNRQN------FQGSEIIVDF 166
               + A + +         G ++ VD 
Sbjct: 70  AQKCLAAASLEAEGGGLKLDGRQLKVDL 97

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 75.4 bits (186), Expect = 6e-18
 Identities = 24/80 (30%), Positives = 38/80 (47%), Gaps = 2/80 (2%)

Query: 85  SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
              DPT  L+I  L  +  E +LE     +G+VIS R++RD  +G S+  GF   +  + 
Sbjct: 21  QEQDPTN-LYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEK 78

Query: 145 CLAAIRALNRQNFQGSEIIV 164
           C A I   N +  +    + 
Sbjct: 79  CEAVIGHFNGKFIKTPPGVS 98

>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 = 76.9 bits (190), Expect = 6e-18
 Identities = 21/76 (27%), Positives = 33/76 (43%), Gaps = 2/76 (2%)

Query: 91  RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTG--HSKRYGFLEYDCEKACLAA 148
             +F+G++ +   E DL + F +YG V  + V+RD       SK   F+ +   KA L A
Sbjct: 4   IKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63

Query: 149 IRALNRQNFQGSEIIV 164
             AL+           
Sbjct: 64  QNALHNMKVLPGMHHP 79

>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 = 75.0 bits (185), Expect = 3e-17
 Identities = 21/89 (23%), Positives = 41/89 (46%), Gaps = 4/89 (4%)

Query: 81  KPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYD 140
               ++    R LFIG ++K   E D+   F+ +G++   R++R    G S+   F+ + 
Sbjct: 86  DSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRG-PDGLSRGCAFVTFT 144

Query: 141 CEKACLAAIRALNRQNF---QGSEIIVDF 166
                  AI+A+++        S ++V F
Sbjct: 145 TRAMAQTAIKAMHQAQTMEGCSSPMVVKF 173

>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 = 74.5 bits (184), Expect = 7e-18
 Identities = 24/102 (23%), Positives = 43/102 (42%), Gaps = 14/102 (13%)

Query: 85  SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
           S +     LFIG L + + E ++   F +YGKV+   +++++        GF+  + + A
Sbjct: 3   SGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKNY--------GFVHIEDKTA 54

Query: 145 CLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWGG 186
              AIR L+     G  I V+    +       +   G   G
Sbjct: 55  AEDAIRNLHHYKLHGVNINVEASKNK------SKASSGPSSG 90

>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 = 74.5 bits (184), Expect = 7e-18
 Identities = 24/79 (30%), Positives = 39/79 (49%)

Query: 87  TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACL 146
                 +F+G L+     A +  AFA +G++   RVV+D  TG SK YGF+ +  +    
Sbjct: 3   LGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAE 62

Query: 147 AAIRALNRQNFQGSEIIVD 165
            AI+ +  Q   G +I  +
Sbjct: 63  NAIQQMGGQWLGGRQIRTN 81

>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 = 74.5 bits (184), Expect = 7e-18
 Identities = 15/76 (19%), Positives = 31/76 (40%), Gaps = 2/76 (2%)

Query: 93  LFIGRLNKNSREADLEQAFAEYG--KVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
           L+IG L   + + DL +A    G   ++ ++   +   G SK +  +    E +    + 
Sbjct: 4   LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63

Query: 151 ALNRQNFQGSEIIVDF 166
            L ++   G   +V  
Sbjct: 64  LLPKRELHGQNPVVTP 79

>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 = 74.7 bits (184), Expect = 8e-18
 Identities = 21/84 (25%), Positives = 40/84 (47%), Gaps = 1/84 (1%)

Query: 84  TSSTDPTRTLFIGRLNKNSREADLEQAFAEYG-KVISVRVVRDFVTGHSKRYGFLEYDCE 142
           + S+    +L++G L     E  + +AFA  G  V+SV+++R+ +TG    Y F+E+   
Sbjct: 3   SGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADL 62

Query: 143 KACLAAIRALNRQNFQGSEIIVDF 166
                 +  +N +   G+     F
Sbjct: 63  ATAEKCLHKINGKPLPGATPAKRF 86

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 74.5 bits (184), Expect = 8e-18
 Identities = 19/81 (23%), Positives = 34/81 (41%), Gaps = 2/81 (2%)

Query: 84  TSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEK 143
           +S +     +F+  L  +     L+  F E G V+   +  +   G SK  G ++++  +
Sbjct: 2   SSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPE 59

Query: 144 ACLAAIRALNRQNFQGSEIIV 164
               A R +N     G EI V
Sbjct: 60  VAERACRMMNGMKLSGREIDV 80

>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 = 74.6 bits (184), Expect = 8e-18
 Identities = 23/85 (27%), Positives = 37/85 (43%), Gaps = 1/85 (1%)

Query: 82  PHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDC 141
              +  +  RT+F+G L    RE  L + F + G +  V + +D   G  K +GF+ +  
Sbjct: 8   MFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKD-REGKPKSFGFVCFKH 66

Query: 142 EKACLAAIRALNRQNFQGSEIIVDF 166
            ++   AI  LN     G  I V  
Sbjct: 67  PESVSYAIALLNGIRLYGRPINVSG 91

>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 = 76.4 bits (189), Expect = 9e-18
 Identities = 25/87 (28%), Positives = 46/87 (52%)

Query: 80  YKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEY 139
           ++   SS+D T  LF+G LN N  +  L  AF ++   +S  V+ D  TG S+ YGF+ +
Sbjct: 77  FQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSF 136

Query: 140 DCEKACLAAIRALNRQNFQGSEIIVDF 166
             +     A+ ++  Q+  G  + +++
Sbjct: 137 TSQDDAQNAMDSMQGQDLNGRPLRINW 163

>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 = 69.9 bits (172), Expect = 3e-15
 Identities = 18/76 (23%), Positives = 39/76 (51%), Gaps = 1/76 (1%)

Query: 91  RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
           R L++G L+K   E  L+Q F   G + +++++ D     +  Y F+EY        A++
Sbjct: 1   RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMID-KNNKNVNYAFVEYHQSHDANIALQ 59

Query: 151 ALNRQNFQGSEIIVDF 166
            LN +  + + + +++
Sbjct: 60  TLNGKQIENNIVKINW 75

>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 = 75.1 bits (185), Expect = 1e-17
 Identities = 21/84 (25%), Positives = 41/84 (48%), Gaps = 1/84 (1%)

Query: 82  PHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDC 141
                    R++++G ++  S   DLE  F+  G +  + ++ D  +GH K Y ++E+  
Sbjct: 28  AEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAE 87

Query: 142 EKACLAAIRALNRQNFQGSEIIVD 165
             +  AA+ A++   F+G  I V 
Sbjct: 88  RNSVDAAV-AMDETVFRGRTIKVL 110

>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 = 74.2 bits (183), Expect = 1e-17
 Identities = 27/85 (31%), Positives = 40/85 (47%), Gaps = 4/85 (4%)

Query: 85  SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
           S     R LF+G LNK   E D+ + F  +G +    V+R    G SK   F+++     
Sbjct: 10  SRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTE 68

Query: 145 CLAAIRALN-RQNFQGSE--IIVDF 166
             AAI AL+  Q   G+   ++V F
Sbjct: 69  AQAAIHALHGSQTMPGASSSLVVKF 93

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 73.4 bits (181), Expect = 2e-17
 Identities = 25/104 (24%), Positives = 47/104 (45%), Gaps = 13/104 (12%)

Query: 85  SSTDPTRTLFIGRLN-KNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEK 143
            +  P   LFIG L  KN  + DL + F+ YG ++ + +   F        GF+++D  +
Sbjct: 5   HNIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAF--------GFIQFDNPQ 56

Query: 144 ACLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWGGN 187
           +   AI   +++   G ++I++          +P+   G  G N
Sbjct: 57  SVRDAIECESQEMNFGKKLILEVSSSNA----RPQFDHGDHGTN 96

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 97

 Score = 73.4 bits (181), Expect = 2e-17
 Identities = 19/80 (23%), Positives = 36/80 (45%), Gaps = 8/80 (10%)

Query: 89  PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAA 148
           PT  L++G L  N+  A L + F  +G + ++  V+         + +++Y+   A  AA
Sbjct: 16  PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAA 69

Query: 149 IRALNRQNFQGSE--IIVDF 166
              +      G +  + VDF
Sbjct: 70  CAKMRGFPLGGPDRRLRVDF 89

>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 = 73.9 bits (182), Expect = 2e-17
 Identities = 25/81 (30%), Positives = 42/81 (51%)

Query: 86  STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKAC 145
            T     +F+G L+      D++ AFA +G++   RVV+D  TG SK YGF+ +  +   
Sbjct: 11  DTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDA 70

Query: 146 LAAIRALNRQNFQGSEIIVDF 166
             AI+ +  Q   G +I  ++
Sbjct: 71  ENAIQQMGGQWLGGRQIRTNW 91

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 75.0 bits (184), Expect = 3e-17
 Identities = 13/88 (14%), Positives = 32/88 (36%), Gaps = 2/88 (2%)

Query: 81  KPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYG--KVISVRVVRDFVTGHSKRYGFLE 138
             ++   +    +++G  +  + +  L Q     G   V+ ++   +   G SK Y  + 
Sbjct: 46  YTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVV 105

Query: 139 YDCEKACLAAIRALNRQNFQGSEIIVDF 166
              E +    +  L  +   G ++ V  
Sbjct: 106 VASENSVHKLLELLPGKVLNGEKVDVRP 133

>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 = 74.9 bits (185), Expect = 4e-17
 Identities = 22/82 (26%), Positives = 41/82 (50%), Gaps = 2/82 (2%)

Query: 85  SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
           S +     LFIG LN N   A+L+ A +E      + VV    TG ++++G+++++  + 
Sbjct: 8   SESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAED 66

Query: 145 CLAAIRALNRQNFQGSEIIVDF 166
              A+  L      G+EI ++ 
Sbjct: 67  LEKAL-ELTGLKVFGNEIKLEK 87

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 61.9 bits (151), Expect = 3e-12
 Identities = 15/79 (18%), Positives = 29/79 (36%), Gaps = 5/79 (6%)

Query: 88  DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLA 147
              RTL    L+ N  E +L++ F +  ++  V        G SK   ++E+  E     
Sbjct: 97  RAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEK 151

Query: 148 AIRALNRQNFQGSEIIVDF 166
            +         G  + + +
Sbjct: 152 NLEEKQGAEIDGRSVSLYY 170

>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 = 73.1 bits (180), Expect = 4e-17
 Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 2/74 (2%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           +FI  L+K+     L   F+ +G ++S +VV D     SK YGF+ ++ ++A   AI  +
Sbjct: 8   IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKM 65

Query: 153 NRQNFQGSEIIVDF 166
           N       ++ V  
Sbjct: 66  NGMLLNDRKVFVGR 79

>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 = 75.4 bits (186), Expect = 5e-17
 Identities = 20/83 (24%), Positives = 43/83 (51%)

Query: 84  TSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEK 143
           ++ + P  +L++G L+ +  EA L + F+  G ++S+RV RD +T  S  Y ++ +    
Sbjct: 9   SAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPA 68

Query: 144 ACLAAIRALNRQNFQGSEIIVDF 166
               A+  +N    +G  + + +
Sbjct: 69  DAERALDTMNFDVIKGKPVRIMW 91

>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 = 70.4 bits (173), Expect = 4e-15
 Identities = 24/94 (25%), Positives = 43/94 (45%), Gaps = 3/94 (3%)

Query: 73  LRALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSK 132
           +R + S   P    +     +FI  L+K+     L   F+ +G ++S +VV D     SK
Sbjct: 87  VRIMWSQRDPSLRKSGVGN-IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSK 143

Query: 133 RYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF 166
            YGF+ ++ ++A   AI  +N       ++ V  
Sbjct: 144 GYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGR 177

>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 = 72.7 bits (179), Expect = 5e-17
 Identities = 19/83 (22%), Positives = 39/83 (46%), Gaps = 2/83 (2%)

Query: 84  TSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEK 143
           + S    + L +  +    R+ DL Q F ++GK++ V ++ +     SK +GF+ ++   
Sbjct: 9   SESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGFVTFENSA 66

Query: 144 ACLAAIRALNRQNFQGSEIIVDF 166
               A   L+    +G +I V+ 
Sbjct: 67  DADRAREKLHGTVVEGRKIEVNN 89

>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 = 72.8 bits (179), Expect = 5e-17
 Identities = 29/106 (27%), Positives = 46/106 (43%), Gaps = 17/106 (16%)

Query: 84  TSSTDP---TRTLFIGRLNKNS-READLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEY 139
           T+  DP      +FIG LN    +++D+E  F++YG+V    V         K Y F++Y
Sbjct: 18  TNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQY 69

Query: 140 DCEKACLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWG 185
             E+   AA+   N +   G  + ++          KP R G   G
Sbjct: 70  SNERHARAAVLGENGRVLAGQTLDINMAGEP-----KPDRSGPSSG 110

>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 = 72.7 bits (179), Expect = 5e-17
 Identities = 14/91 (15%), Positives = 43/91 (47%), Gaps = 2/91 (2%)

Query: 78  STYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDF-VTGHSKRYGF 136
           S           T  + +  +   + + ++ + F+ +G++ +VR+ +    TG  + +GF
Sbjct: 3   SGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGF 62

Query: 137 LEYDCEKACLAAIRAL-NRQNFQGSEIIVDF 166
           +++  ++    A  AL +  +  G  +++++
Sbjct: 63  VDFITKQDAKKAFNALCHSTHLYGRRLVLEW 93

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 72.3 bits (178), Expect = 5e-17
 Identities = 23/98 (23%), Positives = 45/98 (45%), Gaps = 11/98 (11%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           +++G L   + + +LE+AF+ YG + +V + R+        + F+E++  +    A+R L
Sbjct: 3   VYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGL 57

Query: 153 NRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWGGNRNS 190
           + +   GS + V+   G       PRR        R  
Sbjct: 58  DGKVICGSRVRVELSTGM------PRRSRFDRPPARRK 89

>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 = 77.6 bits (190), Expect = 6e-17
 Identities = 40/152 (26%), Positives = 68/152 (44%), Gaps = 3/152 (1%)

Query: 71  AILRALRSTYKPHT---SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFV 127
             +      + PH    +  D  +TLF+ R+N ++ E+ L + F  YG +  + +V    
Sbjct: 80  QEVETELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKR 139

Query: 128 TGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWGGN 187
           +G  + Y F+EY+ E+   +A +  + +   G  ++VD E GR + GW+PRRLGGG GG 
Sbjct: 140 SGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGT 199

Query: 188 RNSGQLRFGGRNKPWVKPVQLMNERELGEWRK 219
           R  G       +                   +
Sbjct: 200 RRGGADVNIRHSGRDDTSRYDERPGPSPLPHR 231

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 72.7 bits (179), Expect = 6e-17
 Identities = 24/105 (22%), Positives = 48/105 (45%), Gaps = 3/105 (2%)

Query: 68  HDRAILRALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFV 127
           H  +     R ++    + + P R L +  +    R+ DL Q F ++GK++ V ++ +  
Sbjct: 8   HHHSSGLVPRGSHMNTENKSQPKR-LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN-- 64

Query: 128 TGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECGRVL 172
              SK +GF+ ++       A   L+    +G +I V+    RV+
Sbjct: 65  ERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARVM 109

>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 = 74.2 bits (183), Expect = 8e-17
 Identities = 21/80 (26%), Positives = 33/80 (41%)

Query: 86  STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKAC 145
                  LFIG L     +  +++    +G + +  +V+D  TG SK Y F EY      
Sbjct: 90  PLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVT 149

Query: 146 LAAIRALNRQNFQGSEIIVD 165
             AI  LN       +++V 
Sbjct: 150 DQAIAGLNGMQLGDKKLLVQ 169

>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 = 65.3 bits (160), Expect = 1e-13
 Identities = 15/79 (18%), Positives = 28/79 (35%), Gaps = 6/79 (7%)

Query: 91  RTLFIGRLNKNSREADLEQAFAEYGKVISV-----RVVRDFVTGHSKRYGFLEYDCEKAC 145
           R L++G +     E  +   F    ++  +       V        K + FLE+      
Sbjct: 5   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64

Query: 146 LAAIRALNRQNFQGSEIIV 164
             A+ A +   FQG  + +
Sbjct: 65  TQAM-AFDGIIFQGQSLKI 82

>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 = 71.9 bits (177), Expect = 9e-17
 Identities = 21/89 (23%), Positives = 43/89 (48%), Gaps = 2/89 (2%)

Query: 78  STYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFL 137
           S            RTL++G L+++  E  + Q F++ G   S +++ +  +     Y F+
Sbjct: 3   SGSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFV 60

Query: 138 EYDCEKACLAAIRALNRQNFQGSEIIVDF 166
           E+   +   AA+ A+N +   G E+ V++
Sbjct: 61  EFYEHRDAAAALAAMNGRKILGKEVKVNW 89

>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 = 74.7 bits (184), Expect = 9e-17
 Identities = 23/100 (23%), Positives = 38/100 (38%)

Query: 67  PHDRAILRALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDF 126
               +   ++       T   D    LFIG L     +  +++    +G + +  +V+D 
Sbjct: 91  LPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDS 150

Query: 127 VTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF 166
            TG SK Y F EY        AI  LN       +++V  
Sbjct: 151 ATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR 190

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 69.7 bits (171), Expect = 6e-15
 Identities = 15/84 (17%), Positives = 28/84 (33%), Gaps = 6/84 (7%)

Query: 88  DPTRTLFIGRLNKNSREADLEQAFAEYGKVISV-----RVVRDFVTGHSKRYGFLEYDCE 142
              R L++G +     E  +   F    ++  +       V        K + FLE+   
Sbjct: 2   AMARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV 61

Query: 143 KACLAAIRALNRQNFQGSEIIVDF 166
                A+ A +   FQG  + +  
Sbjct: 62  DETTQAM-AFDGIIFQGQSLKIRR 84

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 71.9 bits (177), Expect = 9e-17
 Identities = 19/81 (23%), Positives = 35/81 (43%), Gaps = 3/81 (3%)

Query: 89  PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTG---HSKRYGFLEYDCEKAC 145
            +  LFI  LN ++ E  L+  F++ G + S  + +         S  +GF+EY   +  
Sbjct: 4   GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQA 63

Query: 146 LAAIRALNRQNFQGSEIIVDF 166
             A++ L      G ++ V  
Sbjct: 64  QKALKQLQGHTVDGHKLEVRI 84

>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 = 75.1 bits (184), Expect = 1e-16
 Identities = 18/119 (15%), Positives = 40/119 (33%), Gaps = 2/119 (1%)

Query: 85  SSTDPTRTLFIGRLNKNSREADLEQAFAEYG--KVISVRVVRDFVTGHSKRYGFLEYDCE 142
           + T     L+IG L   + + DL +A    G   ++ ++   +   G SK +  +    E
Sbjct: 63  TYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSE 122

Query: 143 KACLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWGGNRNSGQLRFGGRNKP 201
            +    +  L ++   G   +V     + L  ++ +       G  +            
Sbjct: 123 ASSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTTQSGQMSGEGKAGPPGGSS 181

>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 = 71.1 bits (175), Expect = 2e-16
 Identities = 15/83 (18%), Positives = 30/83 (36%), Gaps = 5/83 (6%)

Query: 84  TSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEK 143
           +      RTL    L+ N  E +L++ F +  ++  V        G SK   ++E+  E 
Sbjct: 10  SKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEA 64

Query: 144 ACLAAIRALNRQNFQGSEIIVDF 166
                +         G  + + +
Sbjct: 65  DAEKNLEEKQGAEIDGRSVSLYY 87

>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 = 72.6 bits (178), Expect = 2e-16
 Identities = 23/90 (25%), Positives = 41/90 (45%), Gaps = 5/90 (5%)

Query: 81  KPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYD 140
             H  S      +++G L  N  + +LE+AF  YG + SV V R+        + F+E++
Sbjct: 64  HMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFE 118

Query: 141 CEKACLAAIRALNRQNFQGSEIIVDFECGR 170
             +    A+R L+ +   G  + V+   G 
Sbjct: 119 DPRDAADAVRELDGRTLCGCRVRVELSNGE 148

>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 = 71.2 bits (175), Expect = 2e-16
 Identities = 15/79 (18%), Positives = 32/79 (40%), Gaps = 3/79 (3%)

Query: 88  DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLA 147
           +  R L+I  L       ++   F +YG +  +RV     T  ++   ++ Y+       
Sbjct: 6   EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN---TPETRGTAYVVYEDIFDAKN 62

Query: 148 AIRALNRQNFQGSEIIVDF 166
           A+  L+  N     ++V +
Sbjct: 63  AVDHLSGFNVSNRYLVVLY 81

>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 = 70.7 bits (174), Expect = 3e-16
 Identities = 25/81 (30%), Positives = 41/81 (50%), Gaps = 1/81 (1%)

Query: 87  TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISV-RVVRDFVTGHSKRYGFLEYDCEKAC 145
           +  +  +FIG L+    E  L   F+ +G ++   +++RD  TG+SK Y F+ +    A 
Sbjct: 2   SSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDAS 61

Query: 146 LAAIRALNRQNFQGSEIIVDF 166
            AAI A+N Q      I V +
Sbjct: 62  DAAIEAMNGQYLCNRPITVSY 82

>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 = 70.7 bits (174), Expect = 3e-16
 Identities = 16/86 (18%), Positives = 36/86 (41%), Gaps = 2/86 (2%)

Query: 81  KPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYD 140
                +      L++  L+    +  L +AF+ +G + S +V+ +   G SK +GF+ + 
Sbjct: 6   SGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFS 63

Query: 141 CEKACLAAIRALNRQNFQGSEIIVDF 166
             +    A+  +N +      + V  
Sbjct: 64  SPEEATKAVTEMNGRIVATKPLYVAL 89

>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 = 70.4 bits (173), Expect = 4e-16
 Identities = 20/83 (24%), Positives = 41/83 (49%), Gaps = 8/83 (9%)

Query: 84  TSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEK 143
           +S     + LF+  L     E  LE+AF+++GK+  V+ ++D+         F+ +D   
Sbjct: 5   SSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKDY--------AFIHFDERD 56

Query: 144 ACLAAIRALNRQNFQGSEIIVDF 166
             + A+  +N ++ +G  I + F
Sbjct: 57  GAVKAMEEMNGKDLEGENIEIVF 79

>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 = 70.0 bits (172), Expect = 6e-16
 Identities = 16/112 (14%), Positives = 40/112 (35%), Gaps = 8/112 (7%)

Query: 74  RALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKR 133
             +         + +    +++G L  + R  D+E  F +YG +  + +           
Sbjct: 6   SGMSGGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPP 62

Query: 134 YGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWG 185
           + F+E++  +    A+   +  ++ G  + V+F         +    G   G
Sbjct: 63  FAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSG-----RGTGSGPSSG 109

>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 = 69.8 bits (171), Expect = 8e-16
 Identities = 21/87 (24%), Positives = 39/87 (44%), Gaps = 4/87 (4%)

Query: 84  TSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVI-SVRVVRD-FVTGHSKRYGFLEYDC 141
           +S +     LFIG + K  +  ++ +  A+  + +  V V         ++ + F+EY+ 
Sbjct: 2   SSGSSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYES 61

Query: 142 EKACLAAIRALNRQNFQ--GSEIIVDF 166
            +A   A R L     Q  G +I VD+
Sbjct: 62  HRAAAMARRKLMPGRIQLWGHQIAVDW 88

>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 = 68.0 bits (167), Expect = 2e-15
 Identities = 18/83 (21%), Positives = 33/83 (39%), Gaps = 7/83 (8%)

Query: 85  SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
           S +     L+IG L+      DL Q F +    ++ +            Y F++Y  +  
Sbjct: 3   SGSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQ------VLLKSGYAFVDYPDQNW 56

Query: 145 CLAAIRALN-RQNFQGSEIIVDF 166
            + AI  L+ +    G  + VD+
Sbjct: 57  AIRAIETLSGKVELHGKIMEVDY 79

>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 = 68.5 bits (168), Expect = 2e-15
 Identities = 17/85 (20%), Positives = 34/85 (40%), Gaps = 6/85 (7%)

Query: 82  PHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDC 141
               +    + L++  L  ++ E  +E+ F         RV +       + Y F+ +  
Sbjct: 7   GDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK------IRDYAFVHFSN 60

Query: 142 EKACLAAIRALNRQNFQGSEIIVDF 166
            +  + A++ALN +   GS I V  
Sbjct: 61  REDAVEAMKALNGKVLDGSPIEVTL 85

>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 = 68.1 bits (167), Expect = 3e-15
 Identities = 19/81 (23%), Positives = 35/81 (43%), Gaps = 6/81 (7%)

Query: 86  STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKAC 145
           +      LF+G L  +  E ++ + F +YGK   V + +D      K +GF+  +     
Sbjct: 11  TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLA 64

Query: 146 LAAIRALNRQNFQGSEIIVDF 166
             A   L+    +G ++ V F
Sbjct: 65  EIAKVELDNMPLRGKQLRVRF 85

>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 = 67.7 bits (166), Expect = 3e-15
 Identities = 22/81 (27%), Positives = 41/81 (50%), Gaps = 2/81 (2%)

Query: 85  SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
           S +     LFIG LN N   A+L+ A +E      + VV    TG ++++G+++++  + 
Sbjct: 12  SESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVDFESAED 70

Query: 145 CLAAIRALNRQNFQGSEIIVD 165
              A+  L      G+EI ++
Sbjct: 71  LEKAL-ELTGLKVFGNEIKLE 90

>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 = 67.3 bits (165), Expect = 6e-15
 Identities = 21/94 (22%), Positives = 36/94 (38%), Gaps = 8/94 (8%)

Query: 81  KPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVIS--------VRVVRDFVTGHSK 132
             H  S     T+F+  L +N     +   F + G + +        + +  D  TG  K
Sbjct: 4   HHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLK 63

Query: 133 RYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF 166
               + +D   +  AAI   + + F G+ I V F
Sbjct: 64  GEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSF 97

>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 = 67.7 bits (166), Expect = 6e-15
 Identities = 30/110 (27%), Positives = 44/110 (40%), Gaps = 6/110 (5%)

Query: 75  ALRSTYKPHTSSTDPTRT-LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKR 133
               +   H S  D T T +F+G L  ++ +A L + F  +G +    V+ D  TG S+ 
Sbjct: 1   GSSGSSGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRG 60

Query: 134 YGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGG 183
           YGF+      A   A +  N     G +            G KPR L  G
Sbjct: 61  YGFVTMADRAAAERACKDPN-PIIDGRKA----NVNLAYLGAKPRSLQTG 105

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 66.9 bits (164), Expect = 8e-15
 Identities = 17/99 (17%), Positives = 40/99 (40%), Gaps = 8/99 (8%)

Query: 68  HDRAILRALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFV 127
           H  + L    S              LF+     + +E++L + F  +G +  V+++  F 
Sbjct: 9   HHSSGLVPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNGF- 67

Query: 128 TGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF 166
                   F+E++  ++   AI  ++ ++F    + V +
Sbjct: 68  -------AFVEFEEAESAAKAIEEVHGKSFANQPLEVVY 99

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 66.9 bits (164), Expect = 9e-15
 Identities = 27/108 (25%), Positives = 46/108 (42%), Gaps = 7/108 (6%)

Query: 78  STYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFL 137
           S        T+P  T ++G L  N+ + D++  F +   + SVR+VRD  T   K + ++
Sbjct: 3   SGSSGKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYV 61

Query: 138 EYDCEKACLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWG 185
           E+D   +   A+   +        + VD   GR     K  + G   G
Sbjct: 62  EFDEVDSLKEAL-TYDGALLGDRSLRVDIAEGR-----KQDKSGPSSG 103

>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 = 65.8 bits (161), Expect = 2e-14
 Identities = 17/91 (18%), Positives = 40/91 (43%), Gaps = 9/91 (9%)

Query: 77  RSTYKPHTSSTDPTRTLFIGRLNKNS-READLEQAFAEYGKVISVRVVRDFVTGHSKRYG 135
             +       +     LFIG L   +  + DL + F+ YG ++ + +           +G
Sbjct: 9   HHSSGLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFG 60

Query: 136 FLEYDCEKACLAAIRALNRQNFQGSEIIVDF 166
           F+++D  ++   AI   +++   G ++I++ 
Sbjct: 61  FIQFDNPQSVRDAIEXESQEMNFGKKLILEV 91

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 65.4 bits (160), Expect = 2e-14
 Identities = 21/90 (23%), Positives = 34/90 (37%), Gaps = 7/90 (7%)

Query: 78  STYKPHTSSTDPT-RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGF 136
                   S  P   T +IG +   + EADL   F  +G ++  +   +      K   F
Sbjct: 14  QAVDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE------KGCCF 67

Query: 137 LEYDCEKACLAAIRALNRQNFQGSEIIVDF 166
           ++YD  +     I AL    FQG  +   +
Sbjct: 68  IKYDTHEQAAVCIVALANFPFQGRNLRTGW 97

>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 = 63.8 bits (156), Expect = 6e-14
 Identities = 21/87 (24%), Positives = 43/87 (49%), Gaps = 8/87 (9%)

Query: 82  PHTSSTDPT-RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYD 140
             +S  D T  TL++G L     E DL   F ++G++ ++ VV+       ++  F+++ 
Sbjct: 3   SGSSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFA 56

Query: 141 C-EKACLAAIRALNRQNFQGSEIIVDF 166
             + A +AA ++ N+    G  + V +
Sbjct: 57  TRQAAEVAAEKSFNKLIVNGRRLNVKW 83

>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 = 68.1 bits (167), Expect = 6e-14
 Identities = 8/76 (10%), Positives = 27/76 (35%)

Query: 91  RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
            TL++     +  + ++     +   V     +       S+R+ +++   ++     + 
Sbjct: 118 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 177

Query: 151 ALNRQNFQGSEIIVDF 166
            LN    +G  ++   
Sbjct: 178 KLNGLKIEGYTLVTKV 193

>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 = 67.3 bits (165), Expect = 1e-13
 Identities = 20/96 (20%), Positives = 37/96 (38%), Gaps = 8/96 (8%)

Query: 74  RALRSTYKPHTSSTDPTR-----TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVT 128
               +      ++   TR     T+ +  L K+  +  + + F   G +I V V      
Sbjct: 20  SPAAAGLTSKKANEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS--L 77

Query: 129 GHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV 164
             + R+  +E+      LAAI   ++     +EIIV
Sbjct: 78  KKNFRFARIEFARYDGALAAITKTHKV-VGQNEIIV 112

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 64.2 bits (157), Expect = 1e-12
 Identities = 17/88 (19%), Positives = 34/88 (38%), Gaps = 3/88 (3%)

Query: 81  KPHTSSTDPTRTLFIGRLNKN-SREADLEQAFAEYGKVISVRVVRDF-VTGHSKRYGFLE 138
           K   S+T   R + I  L+     E  L ++F  +G +  + +         +    F+ 
Sbjct: 201 KRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMV 260

Query: 139 YDCEKACLAAIRALNRQNFQGSEIIVDF 166
           ++ + +   A+  +NR      EI V  
Sbjct: 261 FENKDSAERAL-QMNRSLLGNREISVSL 287

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 64.9 bits (158), Expect = 9e-14
 Identities = 13/90 (14%), Positives = 37/90 (41%), Gaps = 7/90 (7%)

Query: 81  KPHTSSTDPTRTLFIGRLNKNSREADLEQA----FAEYGKVISVRVVRDFVTGHSKRYGF 136
                 T+P++ + I  +N    +  L+       +  G ++ + V     +  +    +
Sbjct: 20  GSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAY 76

Query: 137 LEYDCEKACLAAIRALNRQNFQGSEIIVDF 166
           + +  +++  A + A     FQG+ +++ F
Sbjct: 77  IVFATQESAQAFVEAFQGYPFQGNPLVITF 106

>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 = 67.4 bits (165), Expect = 9e-14
 Identities = 18/73 (24%), Positives = 29/73 (39%), Gaps = 1/73 (1%)

Query: 88  DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLA 147
                L +  L+       LEQAF+++G V    VV D   G +   GF+E+  +     
Sbjct: 94  THGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARK 152

Query: 148 AIRALNRQNFQGS 160
           A+       F  +
Sbjct: 153 ALERCGDGAFLLT 165

>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 = 63.2 bits (154), Expect = 3e-12
 Identities = 19/86 (22%), Positives = 34/86 (39%), Gaps = 6/86 (6%)

Query: 81  KPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYD 140
           KP   +      LF+G L  +  E D ++ F  YG+   V + RD      + +GF+  +
Sbjct: 13  KPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLE 66

Query: 141 CEKACLAAIRALNRQNFQGSEIIVDF 166
                  A   L+    +   + + F
Sbjct: 67  SRTLAEIAKAELDGTILKSRPLRIRF 92

>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 = 63.8 bits (156), Expect = 1e-13
 Identities = 16/82 (19%), Positives = 35/82 (42%), Gaps = 1/82 (1%)

Query: 85  SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
           +  +    L +  L+    +AD+++ FAE+G +    V  D  +G S     + ++ +  
Sbjct: 24  AGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKAD 82

Query: 145 CLAAIRALNRQNFQGSEIIVDF 166
            L A++  N     G  + +  
Sbjct: 83  ALKAMKQYNGVPLDGRPMNIQL 104

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 64.3 bits (157), Expect = 1e-13
 Identities = 25/111 (22%), Positives = 40/111 (36%), Gaps = 11/111 (9%)

Query: 89  PTRTLFIGRLNKNSREADLEQAFAEYGKV--------ISVRVVRDFVTGHSKRYGFLEYD 140
              T+F+  L +N     +   F + G +          + +  D  TG  K    + +D
Sbjct: 6   DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFD 65

Query: 141 CEKACLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWGGNRNSG 191
              +  AAI   + + F G+ I V F   R       R  G G GG  +  
Sbjct: 66  DPPSAKAAIDWFDGKEFSGNPIKVSFATRR---ADFNRGGGNGRGGLEHHH 113

>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 = 63.9 bits (156), Expect = 1e-13
 Identities = 15/89 (16%), Positives = 40/89 (44%), Gaps = 7/89 (7%)

Query: 79  TYKPHTSSTDPTR-TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFL 137
            ++   + + P   T++ G +     +  + Q F+ +G+++ +RV  +      K Y F+
Sbjct: 13  RFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFV 66

Query: 138 EYDCEKACLAAIRALNRQNFQGSEIIVDF 166
            +   ++   AI ++N    +G  +   +
Sbjct: 67  RFSTHESAAHAIVSVNGTTIEGHVVKCYW 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 = 66.8 bits (162), Expect = 2e-13
 Identities = 15/85 (17%), Positives = 42/85 (49%), Gaps = 7/85 (8%)

Query: 86  STDPTRTLFIGRLNKNSREADLEQA----FAEYGKVISVRVVRDFVTGHSKRYGFLEYDC 141
            T P  T++I  LN+  ++ +L+++    F+++G+++ + V R   +   +   F+ +  
Sbjct: 5   ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKE 61

Query: 142 EKACLAAIRALNRQNFQGSEIIVDF 166
             +   A+R++    F    + + +
Sbjct: 62  VSSATNALRSMQGFPFYDKPMRIQY 86

>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 = 43.7 bits (102), Expect = 2e-05
 Identities = 21/110 (19%), Positives = 33/110 (30%), Gaps = 5/110 (4%)

Query: 54  PIQAGSIDGTDTIPHDRAILRALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAE 113
           P    +             L   +       S   P   LF+  L + + E  L   F +
Sbjct: 171 PPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQ 230

Query: 114 YGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEII 163
           +     VR+V            F+E+D E    AA  AL       +  +
Sbjct: 231 FPGFKEVRLVPG-----RHDIAFVEFDNEVQAGAARDALQGFKITQNNAM 275

>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 = 63.5 bits (155), Expect = 2e-13
 Identities = 21/107 (19%), Positives = 40/107 (37%), Gaps = 6/107 (5%)

Query: 84  TSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEK 143
             +     T+F+  L+       L++ F+  G V+   ++ D   G S+  G + ++   
Sbjct: 9   LQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSI 67

Query: 144 ACLAAIRALNRQNFQGSEIIVDF-----ECGRVLPGWKPRRLGGGWG 185
             + AI   N Q      + V         G   P  +P++ G   G
Sbjct: 68  EAVQAISMFNGQLLFDRPMHVKMDERALPKGDFFPPERPQQSGPSSG 114

>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 = 62.6 bits (153), Expect = 3e-13
 Identities = 21/75 (28%), Positives = 39/75 (52%), Gaps = 3/75 (4%)

Query: 90  TRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAI 149
             T+F+G ++    E ++   FA YG V  V+++ D  TG SK YGF+ +  +      +
Sbjct: 9   PNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIV 67

Query: 150 RALNRQNFQGSEIIV 164
              ++ NF G ++ +
Sbjct: 68  E--SQINFHGKKLKL 80

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 62.4 bits (152), Expect = 3e-13
 Identities = 15/79 (18%), Positives = 29/79 (36%), Gaps = 5/79 (6%)

Query: 94  FIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALN 153
            I        +  L   F++ GKV+++    D  TG +K + F+E          I++ +
Sbjct: 16  VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75

Query: 154 RQNFQGSEIIV-----DFE 167
            +       +      D E
Sbjct: 76  GKRLDLKHRLFLYTMKDVE 94

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 62.2 bits (151), Expect = 4e-13
 Identities = 18/94 (19%), Positives = 34/94 (36%), Gaps = 5/94 (5%)

Query: 77  RSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGF 136
                P          +++G L +++R +DL++A  E G  + +R+         +R  F
Sbjct: 6   SGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELG-SVPLRLTWQ----GPRRRAF 60

Query: 137 LEYDCEKACLAAIRALNRQNFQGSEIIVDFECGR 170
           L Y    A   A+  L         + V     +
Sbjct: 61  LHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQ 94

>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 = 62.4 bits (152), Expect = 5e-13
 Identities = 19/83 (22%), Positives = 34/83 (40%), Gaps = 8/83 (9%)

Query: 91  RTLFIGRLNKNSREADLEQAFAEYGKVIS--------VRVVRDFVTGHSKRYGFLEYDCE 142
             +++  LN +    DL   F + G V          + +  D  TG  K    + Y+  
Sbjct: 16  SAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDP 75

Query: 143 KACLAAIRALNRQNFQGSEIIVD 165
               AA+   + ++FQGS++ V 
Sbjct: 76  PTAKAAVEWFDGKDFQGSKLKVS 98

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 61.3 bits (149), Expect = 8e-13
 Identities = 18/84 (21%), Positives = 30/84 (35%), Gaps = 8/84 (9%)

Query: 85  SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
             T  +  + I  L     EADL +A  E+G +  V V+        KR   +E++    
Sbjct: 16  HKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP------KKRQALVEFEDVLG 69

Query: 145 CLAAIRALNRQNFQ--GSEIIVDF 166
              A+           G    V++
Sbjct: 70  ACNAVNYAADNQIYIAGHPAFVNY 93

>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 = 61.1 bits (149), Expect = 9e-13
 Identities = 15/85 (17%), Positives = 41/85 (48%), Gaps = 7/85 (8%)

Query: 86  STDPTRTLFIGRLNKNSREADLEQA----FAEYGKVISVRVVRDFVTGHSKRYGFLEYDC 141
            T P  T++I  LN+  ++ +L+++    F+ +G+++ + V R   +   +   F+ +  
Sbjct: 4   ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKE 60

Query: 142 EKACLAAIRALNRQNFQGSEIIVDF 166
             +   A+R++    F    + + +
Sbjct: 61  VSSATNALRSMQGFPFYDKPMRIQY 85

>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 = 62.0 bits (151), Expect = 1e-12
 Identities = 15/82 (18%), Positives = 32/82 (39%), Gaps = 1/82 (1%)

Query: 85  SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
              +    L +  L+    +AD+++ FAE+G +    V  D  +G S     + ++    
Sbjct: 30  EGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADVHFERRAD 88

Query: 145 CLAAIRALNRQNFQGSEIIVDF 166
            L A++        G  + +  
Sbjct: 89  ALKAMKQYKGVPLDGRPMDIQL 110

>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 = 61.1 bits (149), Expect = 1e-12
 Identities = 21/96 (21%), Positives = 43/96 (44%), Gaps = 4/96 (4%)

Query: 73  LRALRSTYKPHTS-STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVT-GH 130
           +R     +   +     P  T F+G L  +  E  +++ F     + +VR+ R+      
Sbjct: 1   MRGSHHHHHHRSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPER 59

Query: 131 SKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF 166
            K +G+ E++   + L+A+ +LN ++     I VD 
Sbjct: 60  LKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRVDV 94

>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 = 62.2 bits (151), Expect = 1e-12
 Identities = 22/87 (25%), Positives = 36/87 (41%), Gaps = 5/87 (5%)

Query: 85  SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVIS--VRVVRDFV---TGHSKRYGFLEY 139
              +P   +++  L K+ +E DL+  F  Y    S   R++ D      G  K   F+  
Sbjct: 40  EPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGL 99

Query: 140 DCEKACLAAIRALNRQNFQGSEIIVDF 166
             EKA   A++  N     G  ++V F
Sbjct: 100 PNEKAAAKALKEANGYVLFGKPMVVQF 126

>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 = 62.5 bits (153), Expect = 1e-12
 Identities = 18/62 (29%), Positives = 37/62 (59%)

Query: 90  TRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAI 149
           +  +FIG LN ++ E +L + F +YG V  +++++D  TG S+ +GFL ++   +    +
Sbjct: 3   SCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVV 62

Query: 150 RA 151
           + 
Sbjct: 63  KT 64

>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 = 62.5 bits (153), Expect = 1e-12
 Identities = 20/79 (25%), Positives = 40/79 (50%), Gaps = 1/79 (1%)

Query: 88  DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLA 147
           D T  +F+G +  + R  + E+ F+++G +I  +++ D  TG S+ +GF+ YD   A   
Sbjct: 85  DKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDR 144

Query: 148 AIRALNRQNFQGSEIIVDF 166
                   +F+  +I +  
Sbjct: 145 VC-QNKFIDFKDRKIEIKR 162

>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 = 60.7 bits (148), Expect = 1e-12
 Identities = 17/83 (20%), Positives = 43/83 (51%), Gaps = 3/83 (3%)

Query: 85  SSTDPTRT--LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCE 142
           S +  +++  +F+G +  N  E +L + F ++G V  V ++ D      + +GF+ ++ E
Sbjct: 3   SGSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDE 62

Query: 143 KACLAAIRALNRQNFQGSEIIVD 165
           ++   A+  ++  +  G ++ V 
Sbjct: 63  QSVDQAV-NMHFHDIMGKKVEVK 84

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 61.9 bits (151), Expect = 3e-12
 Identities = 20/64 (31%), Positives = 33/64 (51%)

Query: 88  DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLA 147
           +  R LFIG L+  + +  L   F ++G +    V+RD  T  S+ +GF+ Y   +   A
Sbjct: 11  EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 70

Query: 148 AIRA 151
           A+ A
Sbjct: 71  AMNA 74

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 61.9 bits (151), Expect = 3e-12
 Identities = 20/107 (18%), Positives = 42/107 (39%), Gaps = 6/107 (5%)

Query: 60  IDGTDTIPHDRAILRALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVIS 119
           +DG   +   RA+ R        H       + +F+G + +++ E  L   F +YGK+  
Sbjct: 79  VDGR-VVEPKRAVSREDSQRPGAH----LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEV 133

Query: 120 VRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF 166
           + ++ D  +G  + + F+ +D   +    +         G    V  
Sbjct: 134 IEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQKYHTVNGHNCEVRK 179

>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 = 3e-12
 Identities = 10/74 (13%), Positives = 37/74 (50%), Gaps = 2/74 (2%)

Query: 91  RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
           R+++I     ++   D+++   + G+V+++++ R       K   F+ +D  ++    + 
Sbjct: 12  RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFV- 69

Query: 151 ALNRQNFQGSEIIV 164
               Q ++ +++++
Sbjct: 70  ETPGQKYKETDLLI 83

>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 = 60.0 bits (146), Expect = 3e-12
 Identities = 22/106 (20%), Positives = 43/106 (40%), Gaps = 8/106 (7%)

Query: 81  KPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFV-TGHSKRYGFLEY 139
                   P  T F+G L  +  E  +++ F     + +VR+ R+       K +G+ E+
Sbjct: 6   SGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEF 64

Query: 140 DCEKACLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWG 185
           +   + L+A+ +LN ++     I VD          + +  G   G
Sbjct: 65  EDLDSLLSAL-SLNEESLGNKRIRVDVADQA-----QDKDSGPSSG 104

>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 = 58.7 bits (143), Expect = 5e-12
 Identities = 14/62 (22%), Positives = 32/62 (51%)

Query: 90  TRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAI 149
              +F+G L+ ++ + DL+  F ++G+V+   +  D  TG S+ +GF+ +    +    +
Sbjct: 11  AGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVL 70

Query: 150 RA 151
             
Sbjct: 71  DQ 72

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 119

 Score = 59.5 bits (144), Expect = 8e-12
 Identities = 20/101 (19%), Positives = 40/101 (39%), Gaps = 8/101 (7%)

Query: 68  HDRAILRALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFV 127
           H  + L    S      S+  P+R + I +L  +  E ++      +GKV ++ +++   
Sbjct: 9   HHSSGLVPRGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-- 66

Query: 128 TGHSKRYGFLEYDCEKACLAAIR--ALNRQNFQGSEIIVDF 166
               K   F+E + E+A    +          +G  I + F
Sbjct: 67  ----KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQF 103

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 59.1 bits (143), Expect = 8e-12
 Identities = 18/86 (20%), Positives = 36/86 (41%), Gaps = 8/86 (9%)

Query: 83  HTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCE 142
           H  S  P+R + I +L  +  E ++      +GKV ++ +++       K   F+E + E
Sbjct: 9   HHGSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTE 62

Query: 143 KACLAAIRAL--NRQNFQGSEIIVDF 166
           +A    +          +G  I + F
Sbjct: 63  EAANTMVNYYTSVTPVLRGQPIYIQF 88

>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 = 59.0 bits (143), Expect = 8e-12
 Identities = 12/83 (14%), Positives = 31/83 (37%), Gaps = 8/83 (9%)

Query: 86  STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKAC 145
               +  + +  L ++  EADL +A  ++G +  V ++        KR   +E++   + 
Sbjct: 11  KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSA 64

Query: 146 LAAIRALNRQNFQ--GSEIIVDF 166
              +           G +   ++
Sbjct: 65  KECVTFAADVPVYIAGQQAFFNY 87

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 58.6 bits (142), Expect = 8e-12
 Identities = 14/85 (16%), Positives = 25/85 (29%), Gaps = 3/85 (3%)

Query: 82  PHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDC 141
                    R L I  +  + +   L+    +YG V S   V             + Y  
Sbjct: 7   GSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET---AVVNVTYSS 63

Query: 142 EKACLAAIRALNRQNFQGSEIIVDF 166
           +     A+  LN    +   + V +
Sbjct: 64  KDQARQALDKLNGFQLENFTLKVAY 88

>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 = 60.9 bits (147), Expect = 1e-11
 Identities = 13/78 (16%), Positives = 21/78 (26%)

Query: 89  PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAA 148
           P+  L          E +  +   E G      V            G LE+D +   L  
Sbjct: 122 PSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALET 181

Query: 149 IRALNRQNFQGSEIIVDF 166
           +  LN    +       +
Sbjct: 182 LGFLNHYQMKNPNGPYPY 199

>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 = 1e-10
 Identities = 19/114 (16%), Positives = 35/114 (30%), Gaps = 6/114 (5%)

Query: 89  PTRTLFIGRLN-KNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLA 147
            +  L +  L+        +   F  YG V  V+ ++            +E     A   
Sbjct: 3   DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS-----KPGAAMVEMADGYAVDR 57

Query: 148 AIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWGGNRNSGQLRFGGRNKP 201
           AI  LN     G ++ V       +   +   L  G    ++  + R    + P
Sbjct: 58  AITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTP 111

>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 = 58.2 bits (141), Expect = 1e-11
 Identities = 12/77 (15%), Positives = 32/77 (41%), Gaps = 7/77 (9%)

Query: 90  TRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAI 149
           +  + +  L ++S   ++     +Y        ++      +KR  F+     +    AI
Sbjct: 5   SSGILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQNAI 57

Query: 150 RALNRQNFQGSEIIVDF 166
           +  ++ +F+G ++IV  
Sbjct: 58  QMFHQYSFRGKDLIVQL 74

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 56.3 bits (137), Expect = 4e-11
 Identities = 15/59 (25%), Positives = 31/59 (52%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
           +FIG L+  + +  L + F ++G+V    V+RD +T  S+ +GF+ +  +      +  
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 58.7 bits (142), Expect = 4e-11
 Identities = 17/100 (17%), Positives = 35/100 (35%), Gaps = 1/100 (1%)

Query: 67  PHDRAILRALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDF 126
           P        L  +        +    L +  L+    +AD+++ FAE+G +    V  D 
Sbjct: 65  PLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD- 123

Query: 127 VTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF 166
            +G S     + ++     L A++        G  + +  
Sbjct: 124 RSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL 163

>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 = 56.1 bits (136), Expect = 7e-11
 Identities = 19/66 (28%), Positives = 36/66 (54%)

Query: 88  DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLA 147
             T  L +  L   + E DL++ F+ +G+V+ V+V +D  TGHSK +GF+ +   +  + 
Sbjct: 13  QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVK 72

Query: 148 AIRALN 153
            +   +
Sbjct: 73  VMSQRH 78

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 55.2 bits (134), Expect = 8e-11
 Identities = 14/59 (23%), Positives = 29/59 (49%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
           +F+G L+ N+   D++  F ++GKV    ++ D  T   + +GF+ ++ E         
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60

>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 = 56.1 bits (136), Expect = 8e-11
 Identities = 17/71 (23%), Positives = 34/71 (47%), Gaps = 1/71 (1%)

Query: 82  PHTSSTDPT-RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYD 140
           P  S    +   +FIG L+  + +  L + F ++G+V    V+RD +T  S+ +GF+ + 
Sbjct: 16  PRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFM 75

Query: 141 CEKACLAAIRA 151
            +      +  
Sbjct: 76  DQAGVDKVLAQ 86

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score = 54.8 bits (133), Expect = 1e-10
 Identities = 14/73 (19%), Positives = 33/73 (45%), Gaps = 1/73 (1%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           +F+G L+ ++ E  + + F  +G+V S+ +  D  T   + + F+ +  E+     +   
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK- 60

Query: 153 NRQNFQGSEIIVD 165
              N   S+  + 
Sbjct: 61  KYHNVGLSKCEIK 73

>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 = 55.2 bits (133), Expect = 2e-10
 Identities = 16/82 (19%), Positives = 34/82 (41%), Gaps = 8/82 (9%)

Query: 87  TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACL 146
             P+R L I +L     E ++      +GKV ++ +++       K   FLE   E+A +
Sbjct: 12  GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAI 65

Query: 147 AAIR--ALNRQNFQGSEIIVDF 166
             +   +    + +   I + +
Sbjct: 66  TMVNYYSAVTPHLRNQPIYIQY 87

>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 = 54.9 bits (133), Expect = 3e-10
 Identities = 16/67 (23%), Positives = 35/67 (52%)

Query: 85  SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
           S  D    LF+G L+ ++ +  L   F++YG+V+   +++D  T  S+ +GF+++     
Sbjct: 11  SGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNC 70

Query: 145 CLAAIRA 151
               + +
Sbjct: 71  VGTVLAS 77

>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 = 54.2 bits (131), Expect = 3e-10
 Identities = 14/89 (15%), Positives = 34/89 (38%), Gaps = 8/89 (8%)

Query: 78  STYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFL 137
           S       +     TL++    ++     L  AF+ +G +I + +         +   F+
Sbjct: 3   SGSSGERRAPRKGNTLYVY--GEDMTPTLLRGAFSPFGNIIDLSMDPP------RNCAFV 54

Query: 138 EYDCEKACLAAIRALNRQNFQGSEIIVDF 166
            Y+  ++   A+  LN    +  ++ V+ 
Sbjct: 55  TYEKMESADQAVAELNGTQVESVQLKVNI 83

>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 = 54.6 bits (132), Expect = 4e-10
 Identities = 19/64 (29%), Positives = 33/64 (51%)

Query: 88  DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLA 147
           +  R LFIG L+  + E  L   + ++GK+    V+RD  +  S+ +GF+ +       A
Sbjct: 25  EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDA 84

Query: 148 AIRA 151
           A+ A
Sbjct: 85  AMAA 88

>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 = 56.4 bits (136), Expect = 4e-10
 Identities = 15/78 (19%), Positives = 25/78 (32%), Gaps = 6/78 (7%)

Query: 90  TRTLFIGRLN-KNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAA 148
              L +  LN +      L   F  YG V  V+++ +      K    ++         A
Sbjct: 3   NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KKENALVQMADGNQAQLA 57

Query: 149 IRALNRQNFQGSEIIVDF 166
           +  LN     G  I +  
Sbjct: 58  MSHLNGHKLHGKPIRITL 75

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 54.9 bits (132), Expect = 1e-09
 Identities = 15/94 (15%), Positives = 35/94 (37%), Gaps = 5/94 (5%)

Query: 74  RALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKR 133
           R  +   K   +   P+ TL +  +  +  E DL+  F+  G V+             ++
Sbjct: 104 RFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRK 159

Query: 134 YGFLEYDCEKACLAAIRALNRQNFQGSEII-VDF 166
              ++    +  + A+  L+  +   +  + V F
Sbjct: 160 MALIQMGSVEEAVQALIDLHNHDLGENHHLRVSF 193

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 53.8 bits (130), Expect = 5e-10
 Identities = 23/79 (29%), Positives = 36/79 (45%), Gaps = 2/79 (2%)

Query: 83  HTSSTDPTRTLFIGRLNKNSREADLEQAFAE-YGKVISVRVVRDFVTGHSKRYGFLEYDC 141
            + S+ P  +LF+G L  +  +  L + F + Y      +VV D  TG SK YGF+++  
Sbjct: 2   SSGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLD-QTGVSKGYGFVKFTD 60

Query: 142 EKACLAAIRALNRQNFQGS 160
           E     A+         GS
Sbjct: 61  ELEQKRALTECQGAVGLGS 79

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 53.1 bits (128), Expect = 8e-10
 Identities = 16/81 (19%), Positives = 34/81 (41%), Gaps = 6/81 (7%)

Query: 84  TSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEK 143
           +S +   R++F+    +    A L + F  +G V SV + +D        +  +E     
Sbjct: 2   SSGSSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKD-----KGVFAIVEMGDVG 56

Query: 144 ACLAAIRALNRQNFQGSEIIV 164
           A  A + + ++ +  G  + V
Sbjct: 57  AREAVL-SQSQHSLGGHRLRV 76

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 55.4 bits (133), Expect = 1e-09
 Identities = 15/86 (17%), Positives = 26/86 (30%), Gaps = 6/86 (6%)

Query: 82  PHTSSTDPTRTLFIGRLN-KNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYD 140
               +      L +  LN +      L   F  YG V  V+++ +      K    ++  
Sbjct: 26  IPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KKENALVQMA 80

Query: 141 CEKACLAAIRALNRQNFQGSEIIVDF 166
                  A+  LN     G  I +  
Sbjct: 81  DGNQAQLAMSHLNGHKLHGKPIRITL 106

>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 = 53.1 bits (127), Expect = 7e-09
 Identities = 13/79 (16%), Positives = 31/79 (39%), Gaps = 5/79 (6%)

Query: 89  PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAA 148
           P+ TL +  +  +  E DL+  F+  G V+             ++   ++    +  + A
Sbjct: 150 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQA 205

Query: 149 IRALNRQNFQGSEII-VDF 166
           +  L+  +   +  + V F
Sbjct: 206 LIDLHNHDLGENHHLRVSF 224

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 52.0 bits (125), Expect = 3e-09
 Identities = 13/69 (18%), Positives = 28/69 (40%), Gaps = 7/69 (10%)

Query: 104 EADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEII 163
           +  + + F+++GK+ +     +   G +K Y FLEY      + A++  +          
Sbjct: 35  KNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF 92

Query: 164 V-----DFE 167
                 DF+
Sbjct: 93  RVNLFTDFD 101

>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 = 51.0 bits (122), Expect = 7e-09
 Identities = 10/76 (13%), Positives = 26/76 (34%), Gaps = 6/76 (7%)

Query: 91  RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
             +    L   +  A++++ F+ +G +  V +              +E+        A R
Sbjct: 11  TVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFR 64

Query: 151 ALNRQNFQGSEIIVDF 166
            L    F    + +++
Sbjct: 65  HLAYSKFHHVPLYLEW 80

>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 = 49.4 bits (118), Expect = 2e-08
 Identities = 15/79 (18%), Positives = 28/79 (35%), Gaps = 6/79 (7%)

Query: 91  RTLFIGRLNKNSREADLEQAFAEYGKVISVRV-----VRDFVTGHSKRYGFLEYDCEKAC 145
           R L++G +     E  +   F    ++  +       V        K + FLE+      
Sbjct: 7   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 66

Query: 146 LAAIRALNRQNFQGSEIIV 164
             A+ A +   FQG  + +
Sbjct: 67  TQAM-AFDGIIFQGQSLKI 84

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 50.0 bits (119), Expect = 2e-08
 Identities = 16/70 (22%), Positives = 31/70 (44%), Gaps = 2/70 (2%)

Query: 84  TSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDF--VTGHSKRYGFLEYDC 141
           +S +  +R +F+G L  +  E ++  +F  +G ++     +         K Y FL +  
Sbjct: 2   SSGSSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQE 61

Query: 142 EKACLAAIRA 151
           E +  A I A
Sbjct: 62  ESSVQALIDA 71

>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 = 49.5 bits (118), Expect = 3e-08
 Identities = 16/81 (19%), Positives = 29/81 (35%), Gaps = 13/81 (16%)

Query: 85  SSTDPTRTLFI--GRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCE 142
           + +  T++L +  G L        L     + G V ++ +  +      K Y F  Y   
Sbjct: 20  TVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTT 73

Query: 143 KACLAAIRALNRQNFQGSEII 163
           +    A   LN     G E++
Sbjct: 74  EESKRAYVTLN-----GKEVV 89

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 51.3 bits (122), Expect = 3e-08
 Identities = 19/119 (15%), Positives = 38/119 (31%), Gaps = 15/119 (12%)

Query: 53  DPIQAGSIDGTDTIPHDRAILRALRSTYKPHTSSTDPTRTLFIGRLNKN---------SR 103
           + I   ++         R      R       S     +TL++G ++             
Sbjct: 97  EDIGKLALRTEVLDCFGREKFADYREDMGGIGSFRKKNKTLYVGGIDGALNSKHLKPAQI 156

Query: 104 EADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEI 162
           E+ +   F+  G +  +R V       SK  GF+++  +     A  A++ Q       
Sbjct: 157 ESRIRFVFSRLGDIDRIRYV------ESKNCGFVKFKYQANAEFAKEAMSNQTLLLPSD 209

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 108

 Score = 48.6 bits (116), Expect = 5e-08
 Identities = 21/99 (21%), Positives = 34/99 (34%), Gaps = 11/99 (11%)

Query: 92  TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
            + +  L  +    DL+    E G V    V RD         G +E+  ++    A+R 
Sbjct: 17  RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRK 69

Query: 152 LNRQNFQGSEIIVDF----ECGRVLPGWKPRRLGGGWGG 186
           L+   F+  E    +      G   P +   R  G   G
Sbjct: 70  LDNTKFRSHEGETAYIRVKVDGPRSPSYGRSRSSGPSSG 108

>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 = 49.0 bits (117), Expect = 5e-08
 Identities = 27/123 (21%), Positives = 46/123 (37%), Gaps = 12/123 (9%)

Query: 77  RSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGF 136
           R  Y P +  ++    + +  L  +    DL+    E G V    V RD         G 
Sbjct: 5   RGRYGPPSRRSE--NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGV 55

Query: 137 LEYDCEKACLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWGGNRNSGQLRFG 196
           +E+  ++    A+R L+   F+  E    +   RV     PR    G   +R+  + R  
Sbjct: 56  VEFVRKEDMTYAVRKLDNTKFRSHEGETAY--IRVKVD-GPRSPSYGRSRSRSRSRSRSR 112

Query: 197 GRN 199
            R+
Sbjct: 113 SRS 115

>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 = 48.0 bits (115), Expect = 5e-08
 Identities = 13/85 (15%), Positives = 34/85 (40%), Gaps = 7/85 (8%)

Query: 81  KPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYD 140
           +           +F+GR  ++    +L+Q F +YG+V+ V + +       + + F+ + 
Sbjct: 2   RGSHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFA 56

Query: 141 CEKACLAAIRALNRQNFQGSEIIVD 165
            +K   +          +G  + + 
Sbjct: 57  DDKVAQSLCG--EDLIIKGISVHIS 79

>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 = 48.1 bits (115), Expect = 6e-08
 Identities = 10/86 (11%), Positives = 27/86 (31%), Gaps = 2/86 (2%)

Query: 82  PHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVI-SVRVVRDFVTGHSKRYGFLEYD 140
             +S       + +  +       ++   F  Y  +  SV +  +   G       + ++
Sbjct: 7   GASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNE-KGMPTGEAMVAFE 65

Query: 141 CEKACLAAIRALNRQNFQGSEIIVDF 166
                 AA+  LN +     ++ +  
Sbjct: 66  SRDEATAAVIDLNDRPIGSRKVKLVL 91

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 47.7 bits (114), Expect = 8e-08
 Identities = 8/85 (9%), Positives = 25/85 (29%)

Query: 82  PHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDC 141
             +S       + +  +       ++   F  Y  +     ++    G       + ++ 
Sbjct: 7   GSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFES 66

Query: 142 EKACLAAIRALNRQNFQGSEIIVDF 166
                AA+  LN +     ++ +  
Sbjct: 67  RDEATAAVIDLNDRPIGSRKVKLSG 91

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 47.4 bits (113), Expect = 9e-08
 Identities = 11/60 (18%), Positives = 25/60 (41%), Gaps = 2/60 (3%)

Query: 104 EADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEII 163
           +  + + F+++GK+ +     +   G +K Y FLEY      + A++  +          
Sbjct: 21  KNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF 78

>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 = 47.9 bits (114), Expect = 1e-07
 Identities = 13/81 (16%), Positives = 32/81 (39%), Gaps = 6/81 (7%)

Query: 92  TLFIGRLNKNSREADL---EQAFAEYGKVISVRVVRDFVTGHSKR---YGFLEYDCEKAC 145
            +F+  L++   + ++    + F ++GK+  V +        S+      ++ Y   +  
Sbjct: 17  LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 76

Query: 146 LAAIRALNRQNFQGSEIIVDF 166
           L AI+ +N     G  +    
Sbjct: 77  LRAIQCVNNVVVDGRTLKASL 97

>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 = 46.8 bits (112), Expect = 2e-07
 Identities = 12/76 (15%), Positives = 33/76 (43%), Gaps = 7/76 (9%)

Query: 90  TRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAI 149
           +  +F+GR   +  E +L + F++YG V+ V + +       + + F+ +  ++   +  
Sbjct: 5   SSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLC 59

Query: 150 RALNRQNFQGSEIIVD 165
                   +G  + + 
Sbjct: 60  G--EDLIIKGISVHIS 73

>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 = 46.3 bits (110), Expect = 4e-07
 Identities = 15/89 (16%), Positives = 27/89 (30%), Gaps = 3/89 (3%)

Query: 77  RSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVI-SVRVVRDFVTGHSKRYG 135
            S                I  +  +  + D+ Q          +V V+ D   G      
Sbjct: 2   SSGSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQA 60

Query: 136 FLEYDCEKACLAAIRALNRQNFQGSEIIV 164
            +++  E     + R L+R+   G E  V
Sbjct: 61  LVQFKNEDDARKSER-LHRKKLNGREAFV 88

>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 = 46.7 bits (110), Expect = 1e-06
 Identities = 11/87 (12%), Positives = 39/87 (44%), Gaps = 2/87 (2%)

Query: 80  YKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEY 139
                 +    R+++I     ++   D+++   + G+V+++++ R       K   F+ +
Sbjct: 99  VTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVF 157

Query: 140 DCEKACLAAIRALNRQNFQGSEIIVDF 166
           D  ++    +     Q ++ +++++ F
Sbjct: 158 DSIESAKKFVETPG-QKYKETDLLILF 183

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 44.4 bits (105), Expect = 2e-06
 Identities = 17/72 (23%), Positives = 26/72 (36%), Gaps = 3/72 (4%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           + +  L +     DL+    E              T      G LE+  E+  + A+  L
Sbjct: 31  ITMKNLPEGCSWQDLKDLARENSLET---TFSSVNTRDFDGTGALEFPSEEILVEALERL 87

Query: 153 NRQNFQGSEIIV 164
           N   F+GS I V
Sbjct: 88  NNIEFRGSVITV 99

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 112

 Score = 44.2 bits (104), Expect = 3e-06
 Identities = 15/84 (17%), Positives = 33/84 (39%), Gaps = 9/84 (10%)

Query: 86  STDPTRTLFIGRL-NKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
             +  R + +  L +    ++ + +    YGK+ +  ++R       K   F+E +  + 
Sbjct: 21  KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR------MKSQAFIEMETRED 74

Query: 145 CLAAIR--ALNRQNFQGSEIIVDF 166
            +A +         FQG  + VD 
Sbjct: 75  AMAMVDHCLKKALWFQGRCVKVDL 98

>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 = 42.2 bits (99), Expect = 9e-06
 Identities = 13/63 (20%), Positives = 27/63 (42%), Gaps = 1/63 (1%)

Query: 104 EADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEII 163
           E    +   +YG+V  + V  + +  H     ++++  E+    A+  LN + F G  I 
Sbjct: 41  EEVFTEMEEKYGEVEEMNVCDN-LGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIH 99

Query: 164 VDF 166
            + 
Sbjct: 100 AEL 102

>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 = 41.9 bits (99), Expect = 1e-05
 Identities = 20/83 (24%), Positives = 38/83 (45%), Gaps = 3/83 (3%)

Query: 82  PHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDC 141
              SS     T+ +     N  E ++ +  A   K +++R+VR+   G+   Y F+++  
Sbjct: 2   SSGSSGTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNA-HGNKTGYIFVDFSN 59

Query: 142 EKACLAAIRALNRQNFQGSEIIV 164
           E+    A++  NR+   G  I V
Sbjct: 60  EEEVKQALK-CNREYMGGRYIEV 81

>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 = 41.4 bits (97), Expect = 3e-05
 Identities = 15/90 (16%), Positives = 30/90 (33%), Gaps = 3/90 (3%)

Query: 77  RSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVI-SVRVVRDFVTGHSKRYG 135
                   S  +    +++  L   +    +   F +   V  S+ +      G +   G
Sbjct: 12  GQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGP-NGKATGEG 70

Query: 136 FLEYDCEKACLAAIRALNRQNFQGSEIIVD 165
           F+E+  E    AA+   ++Q      I V 
Sbjct: 71  FVEFRNEADYKAAL-CRHKQYMGNRFIQVH 99

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 40.5 bits (95), Expect = 4e-05
 Identities = 16/89 (17%), Positives = 37/89 (41%), Gaps = 4/89 (4%)

Query: 77  RSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGF 136
            S+ KP   + D    + +  +  ++ E D+   F    +V +V +++D   G +   G 
Sbjct: 4   GSSGKPLPINPDD-LYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDH-VGRNNGNGL 60

Query: 137 LEYDCEKACLAAIRALNRQNFQGSEIIVD 165
           +++   +    A++  NR       + V 
Sbjct: 61  VKFLSPQDTFEALK-RNRMLMIQRYVEVS 88

>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 = 39.0 bits (91), Expect = 2e-04
 Identities = 14/63 (22%), Positives = 27/63 (42%), Gaps = 2/63 (3%)

Query: 106 DLEQAFAEYGKVISVRVVR--DFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEII 163
           D+    ++YG V S+ + R  D V        F+E+     C  A++ L  + F    ++
Sbjct: 31  DVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVV 90

Query: 164 VDF 166
             +
Sbjct: 91  TKY 93

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 102

 Score = 37.9 bits (88), Expect = 3e-04
 Identities = 9/69 (13%), Positives = 20/69 (28%), Gaps = 7/69 (10%)

Query: 86  STDPTRTLFIGRL-NKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
             +  R + I       +    L Q    +G + +  ++            F+E    + 
Sbjct: 11  RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILN------KINEAFIEMATTED 64

Query: 145 CLAAIRALN 153
             AA+    
Sbjct: 65  AQAAVDYYT 73

>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 = 36.6 bits (85), Expect = 8e-04
 Identities = 12/81 (14%), Positives = 29/81 (35%), Gaps = 3/81 (3%)

Query: 82  PHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDC 141
             +  +     + +  L   + E D+   F+     + V +      G       +E+  
Sbjct: 7   GSSFQSTTGHCVHMRGLPYRATENDIYNFFSPL-NPMRVHIEIGP-DGRVTGEADVEFAT 64

Query: 142 EKACLAAIRALNRQNFQGSEI 162
            +  +AA+ A ++ N Q   +
Sbjct: 65  HEDAVAAM-AKDKANMQHRYV 84

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	225
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.89
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.88
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.87
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.87
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.87
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.87
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.87
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.87
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.86
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.86
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.86
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.86
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.86
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.86
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.86
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.86
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.86
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.86
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.86
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.86
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.86
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.86
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.86
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.85
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.85
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.85
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.85
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.85
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.85
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.85
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.85
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.85
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.85
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.85
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.85
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.85
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.85
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.84
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.84
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.84
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.84
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.84
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.84
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.84
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.83
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.83
2div_A	99	TRNA selenocysteine associated protein; structural	99.83
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.83
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.83
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.83
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.83
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.83
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.83
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.83
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.83
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.83
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.83
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.82
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.82
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.82
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.82
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.82
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.82
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.82
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.82
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.82
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.82
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.82
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.82
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.82
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.82
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.82
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.81
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.81
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.81
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.81
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.81
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.81
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.81
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.81
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.81
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.81
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.81
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.81
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.81
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.81
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.81
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.8
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.8
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.8
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.8
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.8
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.8
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.8
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.8
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.8
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.8
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.8
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.8
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.8
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.8
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.8
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.79
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.79
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.79
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.67
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.79
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.79
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.79
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.79
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.79
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.79
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.79
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.78
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.78
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.78
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.78
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.78
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.78
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.78
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.78
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.78
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.78
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.78
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.77
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.77
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.77
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.77
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.77
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.77
1x5p_A	97	Negative elongation factor E; structure genomics,	99.76
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.76
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.76
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.76
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.76
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.76
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.76
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.76
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.76
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.76
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.76
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.75
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.75
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.74
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.74
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.74
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.74
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.74
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.74
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.74
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.73
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.73
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.73
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.73
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.73
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.73
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.72
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.72
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.72
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.72
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.71
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.71
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.71
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.7
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.7
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.7
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.7
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.7
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.7
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.69
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.69
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.69
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.69
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.68
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.67
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.67
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.66
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.65
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.65
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.65
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.65
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.64
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.62
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.62
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.62
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.62
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.61
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.6
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.59
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.58
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.58
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.58
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.58
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.57
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.55
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.54
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.53
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.53
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.53
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.53
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.51
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.49
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.46
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.37
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.25
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.24
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	99.06
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.99
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.53
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.78
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.71
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.69
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.53
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.44
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.14
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	96.99
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	96.47
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	96.29
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	95.94
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	95.52
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	92.24
2g0c_A	76	ATP-dependent RNA helicase DBPA; RNA recognition m	81.37

>4fxv_A ELAV-like protein 1; RNA recognition motif, putative RNA-binding domain, transcri structural genomics, joint center for structural genomics; 1.90A {Homo sapiens}

Probab=99.89  E-value=6.8e-23  Score=145.26  Aligned_cols=83  Identities=31%  Similarity=0.462  Sum_probs=79.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF  166 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~  166 (225)
                      ...+++|||+|||+++++++|+++|++||.|..|.|++++.++.++|||||+|.+.++|++||+.||+..|.|+.|+|++
T Consensus        16 ~~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~   95 (99)
T 4fxv_A           16 YFQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSY   95 (99)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            34567999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeC
Q psy222          167 ECG  169 (225)
Q Consensus       167 a~~  169 (225)
                      |+|
T Consensus        96 AkP   98 (99)
T 4fxv_A           96 ARP   98 (99)
T ss_dssp             CCB
T ss_pred             eeC
Confidence            975

>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=99.88  E-value=3.5e-22  Score=152.74  Aligned_cols=86  Identities=20%  Similarity=0.317  Sum_probs=81.3

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q psy222           86 STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD  165 (225)
Q Consensus        86 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~  165 (225)
                      ...+.++|||+|||+.+++++|+++|++||.|..|.|+.++.++..++||||+|.+.++|++||+.||+..|.++.|+|+
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             EeeCCC
Q psy222          166 FECGRV  171 (225)
Q Consensus       166 ~a~~~~  171 (225)
                      ++++..
T Consensus       115 ~a~~~~  120 (156)
T 1h2v_Z          115 WDAGFK  120 (156)
T ss_dssp             EESCCC
T ss_pred             ECCCCC
Confidence            998754

>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=99.87  E-value=1.4e-21  Score=172.38  Aligned_cols=102  Identities=35%  Similarity=0.759  Sum_probs=92.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q psy222           86 STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD  165 (225)
Q Consensus        86 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~  165 (225)
                      ...+.++|||+|||+.+++++|+.+|++||.|+.|.|+.++.+++++|||||+|.+.++|++||..||++.|.|+.|.|.
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            34566899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             EeeCCCCCCCCCCCCCCCCCCC
Q psy222          166 FECGRVLPGWKPRRLGGGWGGN  187 (225)
Q Consensus       166 ~a~~~~~~~~~~~r~~gg~gg~  187 (225)
                      ++.++...+|.+.+.+||+|++
T Consensus       178 ~a~~~~~~~~~~~~~ggG~gg~  199 (437)
T 3pgw_S          178 VERGRTVKGWRPRRLGGGLGGT  199 (437)
T ss_pred             EeCCCCCCCCCCCCcCCCCCCC
Confidence            9999888888877665555443

>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=1.6e-21  Score=136.66  Aligned_cols=84  Identities=27%  Similarity=0.466  Sum_probs=80.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEe
Q psy222           88 DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFE  167 (225)
Q Consensus        88 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a  167 (225)
                      .+.++|||+|||+.+++++|+++|++||.|..|.|+.++.+++++|||||+|.+.++|++||+.||+..|.|+.|+|.++
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            46789999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             eCCC
Q psy222          168 CGRV  171 (225)
Q Consensus       168 ~~~~  171 (225)
                      .++.
T Consensus        83 ~~~~   86 (95)
T 2dnz_A           83 TERL   86 (95)
T ss_dssp             SCCC
T ss_pred             cccc
Confidence            8765

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.87  E-value=1.2e-21  Score=141.48  Aligned_cols=82  Identities=20%  Similarity=0.287  Sum_probs=78.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEe
Q psy222           88 DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFE  167 (225)
Q Consensus        88 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a  167 (225)
                      .+.++|||+|||+.+++++|+++|++||.|..|.|++++.+++++|||||+|.+.++|++||+.||+..|+|+.|+|.++
T Consensus         4 ~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a   83 (110)
T 3s8s_A            4 IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLD   83 (110)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            46789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             eC
Q psy222          168 CG  169 (225)
Q Consensus       168 ~~  169 (225)
                      ..
T Consensus        84 ~~   85 (110)
T 3s8s_A           84 IK   85 (110)
T ss_dssp             ST
T ss_pred             CC
Confidence            64

>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=2.5e-21  Score=136.82  Aligned_cols=88  Identities=20%  Similarity=0.406  Sum_probs=81.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q psy222           86 STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD  165 (225)
Q Consensus        86 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~  165 (225)
                      ...+.++|||+|||+.+++++|+++|++||.|..|.|+.++.++..+|||||+|.+.++|++||+ |++..|.|+.|+|.
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            45677899999999999999999999999999999999998899999999999999999999999 99999999999999


Q ss_pred             EeeCCCCCC
Q psy222          166 FECGRVLPG  174 (225)
Q Consensus       166 ~a~~~~~~~  174 (225)
                      ++.++....
T Consensus        85 ~a~~~~~~~   93 (99)
T 2dgs_A           85 RAEPRDSKS   93 (99)
T ss_dssp             ECCCCCCCC
T ss_pred             ECCCCcccC
Confidence            998765443

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.87  E-value=2.4e-21  Score=145.22  Aligned_cols=88  Identities=27%  Similarity=0.430  Sum_probs=82.4

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      ....+.++|||+|||+.+++++|+++|+.||.|..|.|+.++.+++.+|||||+|.+.++|++||+.||+..|.|+.|+|
T Consensus        37 ~~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  116 (139)
T 1u6f_A           37 PEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKV  116 (139)
T ss_dssp             CCTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            34566789999999999999999999999999999999999989999999999999999999999999999999999999


Q ss_pred             EEeeCCCC
Q psy222          165 DFECGRVL  172 (225)
Q Consensus       165 ~~a~~~~~  172 (225)
                      .+++++..
T Consensus       117 ~~a~~~~~  124 (139)
T 1u6f_A          117 ALAASGHQ  124 (139)
T ss_dssp             EESSCCCC
T ss_pred             EECCCCCC
Confidence            99987643

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*

Probab=99.87  E-value=9.1e-22  Score=145.08  Aligned_cols=89  Identities=31%  Similarity=0.477  Sum_probs=83.0

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      ....+.++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||+.||+..|.|+.|+|
T Consensus        17 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   96 (126)
T 3ex7_B           17 QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISV   96 (126)
T ss_dssp             CCCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEE
Confidence            45566789999999999999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             EEeeCCCCC
Q psy222          165 DFECGRVLP  173 (225)
Q Consensus       165 ~~a~~~~~~  173 (225)
                      .++.++..+
T Consensus        97 ~~a~~~~~~  105 (126)
T 3ex7_B           97 DWCFVRGPP  105 (126)
T ss_dssp             EESEESSSC
T ss_pred             EEecCCCCC
Confidence            999876543

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.86  E-value=4.9e-21  Score=139.20  Aligned_cols=87  Identities=23%  Similarity=0.355  Sum_probs=80.6

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      ....+.++|||+|||+.+++++|+++|++||.|..|.|+.++.+++.+|||||+|.+.++|++||+.|++ .|.|+.|+|
T Consensus        12 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V   90 (116)
T 2cqd_A           12 QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANV   90 (116)
T ss_dssp             CCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEE
Confidence            4455778999999999999999999999999999999999988999999999999999999999999998 899999999


Q ss_pred             EEeeCCCC
Q psy222          165 DFECGRVL  172 (225)
Q Consensus       165 ~~a~~~~~  172 (225)
                      +++.....
T Consensus        91 ~~a~~~~~   98 (116)
T 2cqd_A           91 NLAYLGAK   98 (116)
T ss_dssp             EESTTTCC
T ss_pred             EEcccCCC
Confidence            99986543

>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=99.86  E-value=5.2e-22  Score=161.19  Aligned_cols=81  Identities=19%  Similarity=0.356  Sum_probs=76.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCC--ceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEE
Q psy222           89 PTRTLFIGRLNKNSREADLEQAFAEYG--KVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF  166 (225)
Q Consensus        89 ~~~~l~V~nLp~~~te~~L~~~F~~~G--~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~  166 (225)
                      ..++|||+||++++++++|+++|++||  .|+.|.|++++.+++++|||||+|.+.++|++||+.||++.|.|+.|+|.+
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             eeC
Q psy222          167 ECG  169 (225)
Q Consensus       167 a~~  169 (225)
                      +++
T Consensus       147 a~~  149 (229)
T 3q2s_C          147 VNK  149 (229)
T ss_dssp             CCH
T ss_pred             CCC
Confidence            864

>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=99.86  E-value=3.8e-21  Score=139.58  Aligned_cols=88  Identities=28%  Similarity=0.380  Sum_probs=82.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q psy222           86 STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD  165 (225)
Q Consensus        86 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~  165 (225)
                      ...+.++|||+|||+++++++|+++|++||.|..|.|+.++.++..+|||||+|.+.++|++||+.||+..|.|+.|+|.
T Consensus        21 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~  100 (115)
T 2cpz_A           21 EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQ  100 (115)
T ss_dssp             CCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34566899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             EeeCCCCC
Q psy222          166 FECGRVLP  173 (225)
Q Consensus       166 ~a~~~~~~  173 (225)
                      +++++...
T Consensus       101 ~a~~~~~~  108 (115)
T 2cpz_A          101 LKRSKNDS  108 (115)
T ss_dssp             CCCCSCCC
T ss_pred             EcCCCCcC
Confidence            99876543

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.86  E-value=4.1e-21  Score=135.62  Aligned_cols=86  Identities=24%  Similarity=0.346  Sum_probs=81.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF  166 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~  166 (225)
                      ..+.++|||+|||+.+++++|+++|++||.|..|.|+.++.++..+|||||+|.+.++|++||..||+..|.|+.|+|.+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   84 (99)
T 1whw_A            5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLP   84 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            45678999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             eeCCCC
Q psy222          167 ECGRVL  172 (225)
Q Consensus       167 a~~~~~  172 (225)
                      +.++..
T Consensus        85 a~~~~~   90 (99)
T 1whw_A           85 STIKKE   90 (99)
T ss_dssp             CCCCST
T ss_pred             cCCCcc
Confidence            988654

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.86  E-value=2.7e-21  Score=137.62  Aligned_cols=88  Identities=20%  Similarity=0.306  Sum_probs=82.1

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      ....+.++|||+|||+.+++++|+++|++||.|..|.|+.++.++..+|||||+|.+.++|++||+.||+..|.|+.|+|
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   87 (103)
T 2dnm_A            8 PDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRV   87 (103)
T ss_dssp             SCCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEE
T ss_pred             CCCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEE
Confidence            34556789999999999999999999999999999999999888999999999999999999999999999999999999


Q ss_pred             EEeeCCCC
Q psy222          165 DFECGRVL  172 (225)
Q Consensus       165 ~~a~~~~~  172 (225)
                      .+++....
T Consensus        88 ~~a~~~~~   95 (103)
T 2dnm_A           88 QVARYGRR   95 (103)
T ss_dssp             EECSSCCS
T ss_pred             EECCcCCC
Confidence            99987543

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.86  E-value=1.7e-21  Score=138.40  Aligned_cols=88  Identities=22%  Similarity=0.452  Sum_probs=82.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF  166 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~  166 (225)
                      ..+.++|||+|||+.+++++|+++|++||.|..|.|+.++.+++.+|||||+|.+.++|++||+.||+..|.|+.|+|.+
T Consensus         9 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   88 (102)
T 2cqb_A            9 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   88 (102)
T ss_dssp             CCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEe
Confidence            45678999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             eeCCCCCC
Q psy222          167 ECGRVLPG  174 (225)
Q Consensus       167 a~~~~~~~  174 (225)
                      +.++....
T Consensus        89 a~~~~~~~   96 (102)
T 2cqb_A           89 AKPMRIKE   96 (102)
T ss_dssp             CCCCCCCC
T ss_pred             CCCCCCCC
Confidence            98866443

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens}

Probab=99.86  E-value=5.7e-21  Score=139.14  Aligned_cols=84  Identities=25%  Similarity=0.453  Sum_probs=79.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF  166 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~  166 (225)
                      ..+.++|||+|||+.+++++|+++|++||.|..|.|+.+. ++..+|||||+|.+.++|++||+.||+..|.|+.|+|.+
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            4567899999999999999999999999999999999998 899999999999999999999999999999999999999


Q ss_pred             eeCCC
Q psy222          167 ECGRV  171 (225)
Q Consensus       167 a~~~~  171 (225)
                      ++++.
T Consensus        83 a~~~~   87 (116)
T 2fy1_A           83 AKKPS   87 (116)
T ss_dssp             CCCSS
T ss_pred             CCCCC
Confidence            98754

>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=3.9e-21  Score=136.48  Aligned_cols=87  Identities=30%  Similarity=0.477  Sum_probs=81.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q psy222           86 STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD  165 (225)
Q Consensus        86 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~  165 (225)
                      ...+.++|||+|||+.+++++|+++|++||.|..|.|+.++.++..+|||||+|.+.++|++||+.||+..|.|+.|+|.
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            34567899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             EeeCCCC
Q psy222          166 FECGRVL  172 (225)
Q Consensus       166 ~a~~~~~  172 (225)
                      ++.++..
T Consensus        88 ~a~~~~~   94 (102)
T 1x5s_A           88 QAGKSSD   94 (102)
T ss_dssp             EEECCCC
T ss_pred             ECCCCCC
Confidence            9997653

>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=99.86  E-value=4.6e-21  Score=136.81  Aligned_cols=87  Identities=26%  Similarity=0.433  Sum_probs=82.1

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      ....+.++|||+|||+.+++++|+++|++||.|..|.|+.++.++..+|||||+|.+.++|++||..||+..|.|+.|+|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   89 (105)
T 1x5u_A           10 SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRV   89 (105)
T ss_dssp             CCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            44567789999999999999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             EEeeCCC
Q psy222          165 DFECGRV  171 (225)
Q Consensus       165 ~~a~~~~  171 (225)
                      .++.++.
T Consensus        90 ~~a~~~~   96 (105)
T 1x5u_A           90 NKASAHN   96 (105)
T ss_dssp             EETTTTS
T ss_pred             EECCCCC
Confidence            9998754

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.86  E-value=2.5e-21  Score=135.90  Aligned_cols=85  Identities=29%  Similarity=0.472  Sum_probs=80.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEE-EEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEE
Q psy222           88 DPTRTLFIGRLNKNSREADLEQAFAEYGKVISV-RVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF  166 (225)
Q Consensus        88 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v-~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~  166 (225)
                      .+.++|||+|||+.+++++|+++|++||.|..| .|+.++.++..+|||||+|.+.++|++||..||+..|.|+.|+|.+
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             eeCCCC
Q psy222          167 ECGRVL  172 (225)
Q Consensus       167 a~~~~~  172 (225)
                      +.++..
T Consensus        83 a~~~~~   88 (96)
T 1x5t_A           83 AFKKDS   88 (96)
T ss_dssp             SCCCCC
T ss_pred             ecccCC
Confidence            987653

>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=99.86  E-value=3.7e-21  Score=132.53  Aligned_cols=83  Identities=29%  Similarity=0.518  Sum_probs=77.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEe
Q psy222           88 DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFE  167 (225)
Q Consensus        88 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a  167 (225)
                      .+.++|||+|||+.+++++|+++|++||.|..|.|+.++.++..+|||||+|.+.++|++|++.||+..|.|+.|+|.++
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            45679999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             eCC
Q psy222          168 CGR  170 (225)
Q Consensus       168 ~~~  170 (225)
                      +++
T Consensus        84 ~~k   86 (87)
T 3bs9_A           84 TRK   86 (87)
T ss_dssp             C--
T ss_pred             CCC
Confidence            875

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.86  E-value=4e-21  Score=136.74  Aligned_cols=88  Identities=20%  Similarity=0.401  Sum_probs=82.5

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      ....+.++|||+|||+.+++++|+++|++||.|..|.|+.++.++..+|||||+|.+.++|++||..||+..|.|+.|+|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   89 (103)
T 2cq0_A           10 RRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNV   89 (103)
T ss_dssp             CCCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEE
Confidence            34567789999999999999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             EEeeCCCC
Q psy222          165 DFECGRVL  172 (225)
Q Consensus       165 ~~a~~~~~  172 (225)
                      .++.++..
T Consensus        90 ~~a~~~~~   97 (103)
T 2cq0_A           90 EWAKPSTN   97 (103)
T ss_dssp             EESSCCCC
T ss_pred             EECCCCCC
Confidence            99987653

>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=99.86  E-value=6.8e-21  Score=137.19  Aligned_cols=89  Identities=27%  Similarity=0.380  Sum_probs=82.9

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhC------CCccC
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALN------RQNFQ  158 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~------g~~l~  158 (225)
                      ....+.++|||+|||+.+++++|+++|.+||.|..|.|++++.++..+|||||+|.+.++|++||..||      +..|.
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~   89 (111)
T 1x4h_A           10 SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLD   89 (111)
T ss_dssp             CCCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESS
T ss_pred             CcCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEc
Confidence            445677899999999999999999999999999999999999899999999999999999999999999      99999


Q ss_pred             CcEEEEEEeeCCCCC
Q psy222          159 GSEIIVDFECGRVLP  173 (225)
Q Consensus       159 g~~l~V~~a~~~~~~  173 (225)
                      |+.|+|.++.++...
T Consensus        90 g~~l~v~~a~~~~~~  104 (111)
T 1x4h_A           90 GRQLKVDLAVTRDEA  104 (111)
T ss_dssp             SCEEEEECCCCCCCC
T ss_pred             CEEEEEEECCCCccC
Confidence            999999999876543

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.86  E-value=4.9e-22  Score=138.66  Aligned_cols=83  Identities=17%  Similarity=0.338  Sum_probs=76.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCC-ceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhC-CCccCCcEEEEEEe
Q psy222           90 TRTLFIGRLNKNSREADLEQAFAEYG-KVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALN-RQNFQGSEIIVDFE  167 (225)
Q Consensus        90 ~~~l~V~nLp~~~te~~L~~~F~~~G-~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~-g~~l~g~~l~V~~a  167 (225)
                      +++|||+|||+++|+++|+++|++|| .|..|+|++++.++.++|||||+|.+.++|++||+.|+ +..|+|++|+|.++
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            36899999999999999999999999 79999999999999999999999999999999999774 56799999999999


Q ss_pred             eCCCC
Q psy222          168 CGRVL  172 (225)
Q Consensus       168 ~~~~~  172 (225)
                      .++..
T Consensus        81 ~~~~~   85 (91)
T 2lxi_A           81 DPKPK   85 (91)
T ss_dssp             CSCCC
T ss_pred             CCCCC
Confidence            87653

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.86  E-value=6.4e-21  Score=135.70  Aligned_cols=86  Identities=27%  Similarity=0.419  Sum_probs=79.8

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      ....+.++|||+|||+.+++++|+++|++|| |..|.|+.++.+++++|||||+|.+.++|++|| .||+..|.|+.|+|
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V   87 (103)
T 2dng_A           10 LPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRV   87 (103)
T ss_dssp             CCSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEE
T ss_pred             CCCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEE
Confidence            3455678999999999999999999999997 999999999989999999999999999999999 79999999999999


Q ss_pred             EEeeCCCC
Q psy222          165 DFECGRVL  172 (225)
Q Consensus       165 ~~a~~~~~  172 (225)
                      .++.++..
T Consensus        88 ~~a~~~~~   95 (103)
T 2dng_A           88 DIAEGRKQ   95 (103)
T ss_dssp             EECCCCCC
T ss_pred             EEecCCCC
Confidence            99987654

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.85  E-value=5e-21  Score=134.93  Aligned_cols=86  Identities=23%  Similarity=0.366  Sum_probs=79.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCC---CCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           88 DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFV---TGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        88 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~---~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      .+.++|||+|||+++++++|+++|++||.|..|.|+.++.   ++..+|||||+|.+.++|++||..||+..|.|+.|+|
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            4678999999999999999999999999999999998876   5689999999999999999999999999999999999


Q ss_pred             EEeeCCCCC
Q psy222          165 DFECGRVLP  173 (225)
Q Consensus       165 ~~a~~~~~~  173 (225)
                      .++.++...
T Consensus        83 ~~a~~~~~~   91 (98)
T 2cpf_A           83 RISERATKP   91 (98)
T ss_dssp             ECSSCSSCC
T ss_pred             EEccCCCCC
Confidence            999876543

>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=6e-21  Score=136.10  Aligned_cols=86  Identities=23%  Similarity=0.375  Sum_probs=79.9

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCC-CccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVT-GHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEII  163 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~-g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~  163 (225)
                      ....+.++|||+|||+.+++++|+++|+.|| |..|.|+.++.+ ++.+|||||+|.+.++|++|| .||+..|.|+.|+
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~   87 (104)
T 1wi8_A           10 LPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIR   87 (104)
T ss_dssp             CCSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECE
T ss_pred             CCCCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEE
Confidence            4456778999999999999999999999999 999999999887 999999999999999999999 8999999999999


Q ss_pred             EEEeeCCCC
Q psy222          164 VDFECGRVL  172 (225)
Q Consensus       164 V~~a~~~~~  172 (225)
                      |.++.++..
T Consensus        88 V~~a~~~~~   96 (104)
T 1wi8_A           88 VDVADQAQD   96 (104)
T ss_dssp             EEECCCCCC
T ss_pred             EEEccCCCC
Confidence            999987653

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.85  E-value=2.3e-20  Score=135.41  Aligned_cols=88  Identities=28%  Similarity=0.496  Sum_probs=82.3

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      ....+.++|||+|||+.+++++|+++|++||.|..|.|+.++.++..+|||||+|.+.++|++||+.||+..|.|+.|+|
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            34557789999999999999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             EEeeCCCC
Q psy222          165 DFECGRVL  172 (225)
Q Consensus       165 ~~a~~~~~  172 (225)
                      .++.++..
T Consensus        90 ~~a~~~~~   97 (115)
T 2dgo_A           90 NWATRKPP   97 (115)
T ss_dssp             EESSCCCC
T ss_pred             EEccCCCC
Confidence            99987653

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.85  E-value=1e-20  Score=134.58  Aligned_cols=87  Identities=18%  Similarity=0.373  Sum_probs=80.9

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      ....+.++|||+|||+.+++++|+++|++||.|..|.|+.+  ++..++||||+|.+.++|++||+.||+..|.|+.|+|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   87 (103)
T 2d9p_A           10 ITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYV   87 (103)
T ss_dssp             CCCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEE
Confidence            44557889999999999999999999999999999999988  8899999999999999999999999999999999999


Q ss_pred             EEeeCCCCC
Q psy222          165 DFECGRVLP  173 (225)
Q Consensus       165 ~~a~~~~~~  173 (225)
                      .++.++..+
T Consensus        88 ~~a~~~~~~   96 (103)
T 2d9p_A           88 ALAQRKEER   96 (103)
T ss_dssp             EECSSCCCC
T ss_pred             EEecccccC
Confidence            999886543

>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=99.85  E-value=7.7e-21  Score=129.78  Aligned_cols=82  Identities=27%  Similarity=0.527  Sum_probs=78.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEeeC
Q psy222           90 TRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECG  169 (225)
Q Consensus        90 ~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~~  169 (225)
                      +++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++|+..||+..|.|+.|+|.++++
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            36899999999999999999999999999999999988999999999999999999999999999999999999999987


Q ss_pred             CC
Q psy222          170 RV  171 (225)
Q Consensus       170 ~~  171 (225)
                      +.
T Consensus        81 ~~   82 (83)
T 3md1_A           81 LE   82 (83)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.85  E-value=1.1e-20  Score=135.28  Aligned_cols=88  Identities=16%  Similarity=0.435  Sum_probs=82.1

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeec-CCCCccceEEEEEeCCHHHHHHHHHHh-CCCccCCcEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRD-FVTGHSKRYGFLEYDCEKACLAAIRAL-NRQNFQGSEI  162 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~-~~~g~~kg~afV~F~~~~~a~~Al~~l-~g~~l~g~~l  162 (225)
                      ....+.++|||+|||+.+++++|+++|++||.|..|.|+.+ +.++..+|||||+|.+.++|++||..| |+..|.|+.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l   89 (107)
T 2cph_A           10 PKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRL   89 (107)
T ss_dssp             CCSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBC
T ss_pred             ccCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEE
Confidence            34567789999999999999999999999999999999998 788999999999999999999999999 9999999999


Q ss_pred             EEEEeeCCCC
Q psy222          163 IVDFECGRVL  172 (225)
Q Consensus       163 ~V~~a~~~~~  172 (225)
                      +|.++.++..
T Consensus        90 ~v~~a~~~~~   99 (107)
T 2cph_A           90 VLEWADSEVT   99 (107)
T ss_dssp             EEEECCCCCC
T ss_pred             EEEeCCCCCC
Confidence            9999987653

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=6.8e-21  Score=136.14  Aligned_cols=87  Identities=31%  Similarity=0.468  Sum_probs=82.0

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      ....+.++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||..||+..|.|+.|+|
T Consensus        18 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   97 (106)
T 1p27_B           18 QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISV   97 (106)
T ss_dssp             CCBTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEE
Confidence            44556789999999999999999999999999999999999989999999999999999999999999999999999999


Q ss_pred             EEeeCCC
Q psy222          165 DFECGRV  171 (225)
Q Consensus       165 ~~a~~~~  171 (225)
                      .++.++.
T Consensus        98 ~~a~~~~  104 (106)
T 1p27_B           98 DWCFVRG  104 (106)
T ss_dssp             EESEESS
T ss_pred             EeecCCC
Confidence            9998764

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.85  E-value=1.3e-20  Score=133.33  Aligned_cols=86  Identities=22%  Similarity=0.331  Sum_probs=80.6

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      ....+.++|||+|||+.+++++|+++|++||.|..|.|+.++ +++.+|||||+|.+.++|++||+.||+..|.|+.|+|
T Consensus        12 ~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   90 (100)
T 2do4_A           12 STSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKV   90 (100)
T ss_dssp             SSCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            345567899999999999999999999999999999999998 8999999999999999999999999999999999999


Q ss_pred             EEeeCCC
Q psy222          165 DFECGRV  171 (225)
Q Consensus       165 ~~a~~~~  171 (225)
                      .++.++.
T Consensus        91 ~~a~~~~   97 (100)
T 2do4_A           91 AISNSGP   97 (100)
T ss_dssp             EECCCCS
T ss_pred             EECCCCC
Confidence            9998764

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A

Probab=99.85  E-value=9.4e-21  Score=135.42  Aligned_cols=87  Identities=31%  Similarity=0.434  Sum_probs=81.3

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCcc---CCcE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNF---QGSE  161 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l---~g~~  161 (225)
                      ....+.++|||+|||+.+++++|+++|++||.|..|.|+.++.+++.+|||||+|.+.++|++||+.||+..+   .++.
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            4456778999999999999999999999999999999999988999999999999999999999999999987   8999


Q ss_pred             EEEEEeeCCC
Q psy222          162 IIVDFECGRV  171 (225)
Q Consensus       162 l~V~~a~~~~  171 (225)
                      |+|.++.++.
T Consensus        88 l~v~~a~~~~   97 (106)
T 2dgp_A           88 IQVKPADSES   97 (106)
T ss_dssp             CEEEECCCCS
T ss_pred             EEEEECCccc
Confidence            9999998754

>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=3e-20  Score=132.15  Aligned_cols=91  Identities=24%  Similarity=0.428  Sum_probs=82.0

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      ....+.++|||+|||+.+++++|+++|++||.|..|.|+.+..  ..++||||+|.+.++|++||..||+..|.|+.|+|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   87 (103)
T 2cq3_A           10 ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEV   87 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            4456778999999999999999999999999999999998853  37999999999999999999999999999999999


Q ss_pred             EEeeCCCCCCCCC
Q psy222          165 DFECGRVLPGWKP  177 (225)
Q Consensus       165 ~~a~~~~~~~~~~  177 (225)
                      .++.++....+.+
T Consensus        88 ~~a~~~~~~~~~~  100 (103)
T 2cq3_A           88 NNATARVMTNSGP  100 (103)
T ss_dssp             EECCSSCCCCCSS
T ss_pred             EEcccCCCCCCCC
Confidence            9999877655443

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=9.7e-21  Score=136.95  Aligned_cols=88  Identities=22%  Similarity=0.329  Sum_probs=81.9

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCcee--------EEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCc
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVI--------SVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQN  156 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~--------~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~  156 (225)
                      ....+.++|||+|||+.+++++|+++|++||.|.        .|.|+.++.+++.+|||||+|.+.++|++||+.||+..
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            3456778999999999999999999999999998        69999998899999999999999999999999999999


Q ss_pred             cCCcEEEEEEeeCCCC
Q psy222          157 FQGSEIIVDFECGRVL  172 (225)
Q Consensus       157 l~g~~l~V~~a~~~~~  172 (225)
                      |.|+.|+|.+++++..
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            9999999999987553

>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=99.85  E-value=9.1e-21  Score=129.99  Aligned_cols=82  Identities=23%  Similarity=0.501  Sum_probs=78.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF  166 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~  166 (225)
                      ..+.++|||+|||+.+++++|+++|++||.|..|.|+.++.++..+|||||+|.+.++|++|++.||+..|.|+.|+|++
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            45678999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ee
Q psy222          167 EC  168 (225)
Q Consensus       167 a~  168 (225)
                      ++
T Consensus        84 ak   85 (85)
T 3mdf_A           84 AK   85 (85)
T ss_dssp             CC
T ss_pred             cC
Confidence            74

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A

Probab=99.85  E-value=3e-20  Score=132.55  Aligned_cols=87  Identities=29%  Similarity=0.428  Sum_probs=80.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCC---cEE
Q psy222           86 STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQG---SEI  162 (225)
Q Consensus        86 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g---~~l  162 (225)
                      ...+.++|||+|||+.+++++|+++|++||.|..|.|+.++ ++..+|||||+|.+.++|++||+.||+..|.+   +.|
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            34567899999999999999999999999999999999997 89999999999999999999999999999998   999


Q ss_pred             EEEEeeCCCCC
Q psy222          163 IVDFECGRVLP  173 (225)
Q Consensus       163 ~V~~a~~~~~~  173 (225)
                      +|.++.++..+
T Consensus        90 ~V~~a~~~~~~  100 (105)
T 2dnh_A           90 VVKFADTDKES  100 (105)
T ss_dssp             EEEESCSSCCC
T ss_pred             EEEECccCccc
Confidence            99999876543

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.85  E-value=1.6e-21  Score=137.04  Aligned_cols=83  Identities=17%  Similarity=0.337  Sum_probs=76.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCc--eeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCC----ccCCc
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGK--VISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQ----NFQGS  160 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~--v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~----~l~g~  160 (225)
                      ...-.+|||+|||+.+|+++|+++|++||.  |..|+|++|+.+++++|||||+|.+.++|++||+.||+.    .|+|+
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            345579999999999999999999999995  679999999999999999999999999999999999997    48999


Q ss_pred             EEEEEEeeC
Q psy222          161 EIIVDFECG  169 (225)
Q Consensus       161 ~l~V~~a~~  169 (225)
                      +|.|++|+.
T Consensus        86 ~i~V~~Aks   94 (95)
T 2lkz_A           86 TIGVDFAKS   94 (95)
T ss_dssp             EEEEEECCC
T ss_pred             EEEEEEccC
Confidence            999999874

>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=99.84  E-value=1.8e-21  Score=135.28  Aligned_cols=82  Identities=18%  Similarity=0.339  Sum_probs=72.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCC--ceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEee
Q psy222           91 RTLFIGRLNKNSREADLEQAFAEYG--KVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFEC  168 (225)
Q Consensus        91 ~~l~V~nLp~~~te~~L~~~F~~~G--~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~  168 (225)
                      .+|||+|||+++++++|+++|++||  .|..|.|+.++.+++++|||||+|.+.++|++||+.||+..|+|+.|+|.++.
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             CCCC
Q psy222          169 GRVL  172 (225)
Q Consensus       169 ~~~~  172 (225)
                      +...
T Consensus        82 ~~~~   85 (90)
T 3p5t_L           82 KLEH   85 (90)
T ss_dssp             ----
T ss_pred             CCcc
Confidence            7553

>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=99.84  E-value=1.3e-20  Score=132.40  Aligned_cols=83  Identities=23%  Similarity=0.434  Sum_probs=79.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEee
Q psy222           89 PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFEC  168 (225)
Q Consensus        89 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~  168 (225)
                      +.++|||+|||+.+++++|+++|++||.|..|.|+.++.++..+|||||+|.+.++|++|++.||+..|+|+.|+|.++.
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            46799999999999999999999999999999999998899999999999999999999999999999999999999998


Q ss_pred             CCC
Q psy222          169 GRV  171 (225)
Q Consensus       169 ~~~  171 (225)
                      ++.
T Consensus        81 ~~~   83 (96)
T 2x1f_A           81 NSD   83 (96)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            754

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.84  E-value=2.1e-20  Score=132.08  Aligned_cols=84  Identities=24%  Similarity=0.357  Sum_probs=79.9

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeE--------EEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCc
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVIS--------VRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQN  156 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~--------v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~  156 (225)
                      ....+.++|||+|||+.+++++|+++|++||.|..        |.|+.++.+++.+|||||+|.+.++|++||+.||+..
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~   87 (99)
T 2la6_A            8 HSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKE   87 (99)
T ss_dssp             CSCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCB
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCE
Confidence            55677899999999999999999999999999999        9999998899999999999999999999999999999


Q ss_pred             cCCcEEEEEEee
Q psy222          157 FQGSEIIVDFEC  168 (225)
Q Consensus       157 l~g~~l~V~~a~  168 (225)
                      |.|+.|+|++|+
T Consensus        88 ~~g~~l~V~~A~   99 (99)
T 2la6_A           88 FSGNPIKVSFAT   99 (99)
T ss_dssp             SSSSBCEEEECC
T ss_pred             eCCcEEEEEecC
Confidence            999999999974

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=1.8e-20  Score=131.17  Aligned_cols=85  Identities=24%  Similarity=0.354  Sum_probs=80.1

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      ....+.++|||+|||+.+++++|+++|++||.|..|.|+.++.++..+|||||+|.+.++|++||..||+..|.|+.|+|
T Consensus        10 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   89 (95)
T 2cqc_A           10 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   89 (95)
T ss_dssp             CSCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            44566789999999999999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             EEeeC
Q psy222          165 DFECG  169 (225)
Q Consensus       165 ~~a~~  169 (225)
                      .+++.
T Consensus        90 ~~a~~   94 (95)
T 2cqc_A           90 SGPSS   94 (95)
T ss_dssp             ECCSC
T ss_pred             EecCC
Confidence            99864

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.84  E-value=2.1e-20  Score=133.14  Aligned_cols=85  Identities=24%  Similarity=0.357  Sum_probs=80.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhc-CCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCc-cCCcEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAE-YGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQN-FQGSEIIV  164 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~-~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~-l~g~~l~V  164 (225)
                      ..+.++|||+|||+.+++++|+++|++ ||.|..|.|+.++ ++..+|||||+|.+.++|++||+.|++.. |.|+.|+|
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v   84 (104)
T 2dhg_A            6 SGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRL   84 (104)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEE
Confidence            456789999999999999999999999 9999999999998 99999999999999999999999999999 99999999


Q ss_pred             EEeeCCCC
Q psy222          165 DFECGRVL  172 (225)
Q Consensus       165 ~~a~~~~~  172 (225)
                      .++.++..
T Consensus        85 ~~a~~~~~   92 (104)
T 2dhg_A           85 SVAIPKAS   92 (104)
T ss_dssp             CBCCCCCS
T ss_pred             EEccCCCc
Confidence            99987543

>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=99.84  E-value=1.4e-20  Score=135.44  Aligned_cols=87  Identities=29%  Similarity=0.496  Sum_probs=82.0

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      ....+.++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||..||+..|.|+.|+|
T Consensus        21 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V  100 (110)
T 1oo0_B           21 QRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQV  100 (110)
T ss_dssp             CCBTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEE
Confidence            44567789999999999999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             EEeeCCC
Q psy222          165 DFECGRV  171 (225)
Q Consensus       165 ~~a~~~~  171 (225)
                      .++.++.
T Consensus       101 ~~a~~~~  107 (110)
T 1oo0_B          101 DWCFVKG  107 (110)
T ss_dssp             EESEESS
T ss_pred             EEcccCC
Confidence            9998754

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.84  E-value=1.8e-20  Score=131.01  Aligned_cols=84  Identities=24%  Similarity=0.377  Sum_probs=79.1

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      ....+.++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||+.||+..|.|+.|+|
T Consensus        11 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   90 (94)
T 2e5h_A           11 GLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKA   90 (94)
T ss_dssp             SCCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEE
Confidence            34556789999999999999999999999999999999999888999999999999999999999999999999999999


Q ss_pred             EEee
Q psy222          165 DFEC  168 (225)
Q Consensus       165 ~~a~  168 (225)
                      ++|+
T Consensus        91 ~~ak   94 (94)
T 2e5h_A           91 SIAI   94 (94)
T ss_dssp             EECC
T ss_pred             EecC
Confidence            9974

>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=99.83  E-value=2.4e-20  Score=135.51  Aligned_cols=80  Identities=28%  Similarity=0.466  Sum_probs=74.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEeeC
Q psy222           90 TRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECG  169 (225)
Q Consensus        90 ~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~~  169 (225)
                      ..+|||+|||+.+++++|+++|++||.|..|+|++++  +.++|||||+|.+.++|++||+.|++..|+|+.|+|.++.+
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~--~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~   82 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   82 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSC
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            4689999999999999999999999999999999985  45799999999999999999999999999999999999986


Q ss_pred             CC
Q psy222          170 RV  171 (225)
Q Consensus       170 ~~  171 (225)
                      +.
T Consensus        83 ~~   84 (115)
T 4f25_A           83 RK   84 (115)
T ss_dssp             CC
T ss_pred             cc
Confidence            54

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.83  E-value=1.3e-19  Score=131.14  Aligned_cols=85  Identities=19%  Similarity=0.290  Sum_probs=79.4

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      ....+.++|||+|||+.+++++|+++|.+||.|..|.|+.++ +++.++||||+|.+.++|++||+.||+..|.|+.|+|
T Consensus        10 ~~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   88 (114)
T 2do0_A           10 QAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHV   88 (114)
T ss_dssp             CCCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEE
Confidence            345567899999999999999999999999999999999997 6999999999999999999999999999999999999


Q ss_pred             EEeeCC
Q psy222          165 DFECGR  170 (225)
Q Consensus       165 ~~a~~~  170 (225)
                      +++...
T Consensus        89 ~~a~~~   94 (114)
T 2do0_A           89 KMDERA   94 (114)
T ss_dssp             EECSCC
T ss_pred             EEcccC
Confidence            998753

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.83  E-value=2.1e-20  Score=131.91  Aligned_cols=84  Identities=21%  Similarity=0.425  Sum_probs=79.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCcee-EEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcE----
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVI-SVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSE----  161 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~-~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~----  161 (225)
                      ..+.++|||+|||+.+++++|+++|++||.|. .|.|++++.++.++|||||+|.+.++|++||+.||+..|.|+.    
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~   85 (99)
T 2div_A            6 SGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKR   85 (99)
T ss_dssp             CSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEE
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCccee
Confidence            45678999999999999999999999999999 9999999989999999999999999999999999999999999    


Q ss_pred             EEEEEeeCC
Q psy222          162 IIVDFECGR  170 (225)
Q Consensus       162 l~V~~a~~~  170 (225)
                      |+|.++++.
T Consensus        86 l~v~~a~~~   94 (99)
T 2div_A           86 FKLNYATYS   94 (99)
T ss_dssp             CCEEETTCC
T ss_pred             EEEeecCCC
Confidence            999998763

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.83  E-value=1.8e-20  Score=133.74  Aligned_cols=87  Identities=22%  Similarity=0.429  Sum_probs=81.2

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      ....+.++|||+|||+.+++++|+++|++||.|..|.|+.++.++..+|||||+|.+.++|++||.. ++..|.|+.|+|
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            3456778999999999999999999999999999999999988999999999999999999999998 999999999999


Q ss_pred             EEeeCCCC
Q psy222          165 DFECGRVL  172 (225)
Q Consensus       165 ~~a~~~~~  172 (225)
                      .++.++..
T Consensus        90 ~~a~~~~~   97 (105)
T 2dh8_A           90 KPCTPRGM   97 (105)
T ss_dssp             CCSCCSSC
T ss_pred             EEccCCCC
Confidence            99987653

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.83  E-value=4.2e-21  Score=136.18  Aligned_cols=82  Identities=15%  Similarity=0.206  Sum_probs=78.3

Q ss_pred             CCCeEEEcCCCC------CCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCC-cE
Q psy222           89 PTRTLFIGRLNK------NSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQG-SE  161 (225)
Q Consensus        89 ~~~~l~V~nLp~------~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g-~~  161 (225)
                      ..++|||+|||+      .+++++|+++|++||.|..|.|++++.|++++|||||+|.+.++|++||+.||+..|.| +.
T Consensus         5 ~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~   84 (100)
T 3ns6_A            5 SDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHR   84 (100)
T ss_dssp             GGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCB
T ss_pred             cCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCeE
Confidence            457999999999      99999999999999999999999999899999999999999999999999999999999 99


Q ss_pred             EEEEEeeCC
Q psy222          162 IIVDFECGR  170 (225)
Q Consensus       162 l~V~~a~~~  170 (225)
                      |+|.++.++
T Consensus        85 l~V~~a~~~   93 (100)
T 3ns6_A           85 LFLYTMKDV   93 (100)
T ss_dssp             CEEEESHHH
T ss_pred             EEEEECchh
Confidence            999999764

>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=99.83  E-value=3.2e-20  Score=133.47  Aligned_cols=87  Identities=26%  Similarity=0.450  Sum_probs=81.5

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      ....+.++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||+.|++..|.|+.|+|
T Consensus        21 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V  100 (108)
T 2jrs_A           21 KGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKV  100 (108)
T ss_dssp             CSCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            33556789999999999999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             EEeeCCC
Q psy222          165 DFECGRV  171 (225)
Q Consensus       165 ~~a~~~~  171 (225)
                      .+++++.
T Consensus       101 ~~a~~k~  107 (108)
T 2jrs_A          101 GHVTERT  107 (108)
T ss_dssp             ECSCSSC
T ss_pred             EEcccCC
Confidence            9998753

>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=99.83  E-value=6.5e-20  Score=130.41  Aligned_cols=86  Identities=23%  Similarity=0.440  Sum_probs=78.2

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      ....+.++|||+|||+.+++++|+++|++||.|..|.|+.++.  ..+|||||+|.+.++|++||..||+..|.|+.|+|
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            3456778999999999999999999999999999999998853  36899999999999999999999999999999999


Q ss_pred             EEeeCCCC
Q psy222          165 DFECGRVL  172 (225)
Q Consensus       165 ~~a~~~~~  172 (225)
                      .+++++..
T Consensus        88 ~~a~~~~~   95 (103)
T 2cqi_A           88 NWATTPSS   95 (103)
T ss_dssp             EECCCTTC
T ss_pred             EECCCCcc
Confidence            99987553

>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=99.83  E-value=3.7e-20  Score=127.66  Aligned_cols=82  Identities=22%  Similarity=0.437  Sum_probs=77.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCc-cceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEe
Q psy222           89 PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGH-SKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFE  167 (225)
Q Consensus        89 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~-~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a  167 (225)
                      ..++|||+|||+++++++|+++|++||.|..|.|+.+..++. .+|||||+|.+.++|++|++.||+..|+|+.|+|.++
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   82 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAV   82 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEEC
Confidence            467999999999999999999999999999999999876665 8999999999999999999999999999999999999


Q ss_pred             eCC
Q psy222          168 CGR  170 (225)
Q Consensus       168 ~~~  170 (225)
                      .+.
T Consensus        83 ~~~   85 (88)
T 4a8x_A           83 LAP   85 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            764

>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=99.83  E-value=9e-20  Score=129.77  Aligned_cols=79  Identities=25%  Similarity=0.487  Sum_probs=72.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF  166 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~  166 (225)
                      ..+.++|||+|||+.+++++|+++|++||.|..|.|+        ++||||+|.+.++|++||+.||+..|.|+.|+|.+
T Consensus         8 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   79 (103)
T 2dgu_A            8 MAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVF   79 (103)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEE
Confidence            4467899999999999999999999999999999987        55999999999999999999999999999999999


Q ss_pred             eeCCCCC
Q psy222          167 ECGRVLP  173 (225)
Q Consensus       167 a~~~~~~  173 (225)
                      +.++...
T Consensus        80 a~~~~~~   86 (103)
T 2dgu_A           80 AKPPDQK   86 (103)
T ss_dssp             CCCCCCC
T ss_pred             cCCCccc
Confidence            9876543

>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=99.83  E-value=1.1e-19  Score=129.27  Aligned_cols=86  Identities=24%  Similarity=0.416  Sum_probs=79.3

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q psy222           86 STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD  165 (225)
Q Consensus        86 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~  165 (225)
                      ...+.++|||+|||+.+++++|+++|.+||.|..|.|+.++.++.++|||||+|.+.++|++||.  +++.|+|+.|.|.
T Consensus        11 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~v~   88 (103)
T 2cqg_A           11 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCK   88 (103)
T ss_dssp             CCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEE
T ss_pred             ccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEEEE
Confidence            35567899999999999999999999999999999999998899999999999999999999998  4779999999999


Q ss_pred             EeeCCCCC
Q psy222          166 FECGRVLP  173 (225)
Q Consensus       166 ~a~~~~~~  173 (225)
                      ++.++...
T Consensus        89 ~a~~~~~~   96 (103)
T 2cqg_A           89 LPNSKQSQ   96 (103)
T ss_dssp             CCCTTCCC
T ss_pred             ecCCCCcC
Confidence            99886543

>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=99.83  E-value=1.1e-19  Score=130.58  Aligned_cols=83  Identities=17%  Similarity=0.409  Sum_probs=75.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q psy222           86 STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD  165 (225)
Q Consensus        86 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~  165 (225)
                      ...+.++|||+|||+.+++++|+++|++||.|..|.|+.+   +..++||||+|.+.++|++||+.||+..|.|+.|+|+
T Consensus        18 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   94 (109)
T 1x4a_A           18 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVE   94 (109)
T ss_dssp             CCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            3456789999999999999999999999999999999654   4578999999999999999999999999999999999


Q ss_pred             EeeCCC
Q psy222          166 FECGRV  171 (225)
Q Consensus       166 ~a~~~~  171 (225)
                      +++++.
T Consensus        95 ~a~~~~  100 (109)
T 1x4a_A           95 FPRSGR  100 (109)
T ss_dssp             CCCCCC
T ss_pred             EcccCC
Confidence            998754

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A

Probab=99.83  E-value=7.8e-20  Score=130.82  Aligned_cols=82  Identities=20%  Similarity=0.356  Sum_probs=78.2

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q psy222           86 STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD  165 (225)
Q Consensus        86 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~  165 (225)
                      ...+.++|||+|||+.+++++|+++|.+||.|..|.|+.++ +++.+|||||+|.+.++|++||+.||+..|.|+.|+|+
T Consensus        25 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~  103 (107)
T 3ulh_A           25 GVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQ  103 (107)
T ss_dssp             CCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            45677899999999999999999999999999999999998 99999999999999999999999999999999999999


Q ss_pred             Eee
Q psy222          166 FEC  168 (225)
Q Consensus       166 ~a~  168 (225)
                      ++.
T Consensus       104 ~a~  106 (107)
T 3ulh_A          104 LVT  106 (107)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            985

>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=99.83  E-value=3.3e-20  Score=137.56  Aligned_cols=87  Identities=25%  Similarity=0.403  Sum_probs=81.8

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      ....+.++|||+|||+.+++++|+++|++||.|..|.|+.++.+++.+|||||+|.+.++|++||+.||+..|.|+.|+|
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            44567789999999999999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             EEeeCCC
Q psy222          165 DFECGRV  171 (225)
Q Consensus       165 ~~a~~~~  171 (225)
                      +++.++.
T Consensus       121 ~~a~~~~  127 (129)
T 2kxn_B          121 DFSITKR  127 (129)
T ss_dssp             SCCSSSS
T ss_pred             EEecCCC
Confidence            9998754

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.82  E-value=3.3e-20  Score=133.93  Aligned_cols=86  Identities=14%  Similarity=0.252  Sum_probs=78.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHH---HHHhcCCceeEEEEeecCCCC---ccceEEEEEeCCHHHHHHHHHHhCCCccCCc
Q psy222           87 TDPTRTLFIGRLNKNSREADLE---QAFAEYGKVISVRVVRDFVTG---HSKRYGFLEYDCEKACLAAIRALNRQNFQGS  160 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~---~~F~~~G~v~~v~i~~~~~~g---~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~  160 (225)
                      ....++|||+|||+.+++++|+   ++|++||.|..|.|+.++.++   .++|||||+|.+.++|++||+.||+..|+|+
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            4456799999999999999999   999999999999999887644   5569999999999999999999999999999


Q ss_pred             EEEEEEeeCCCC
Q psy222          161 EIIVDFECGRVL  172 (225)
Q Consensus       161 ~l~V~~a~~~~~  172 (225)
                      .|+|.++.++..
T Consensus        92 ~l~V~~a~~k~~  103 (111)
T 2cpi_A           92 TLKASLGTTKYC  103 (111)
T ss_dssp             EEEEESCCCCSC
T ss_pred             EEEEEecccccc
Confidence            999999998653

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.82  E-value=4.4e-20  Score=141.28  Aligned_cols=82  Identities=16%  Similarity=0.279  Sum_probs=77.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCC--ceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEE
Q psy222           89 PTRTLFIGRLNKNSREADLEQAFAEYG--KVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF  166 (225)
Q Consensus        89 ~~~~l~V~nLp~~~te~~L~~~F~~~G--~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~  166 (225)
                      ..++|||+|||+++++++|+++|++||  .|..|.|+.++.+++++|||||+|.+.++|++||..||+..|+|+.|+|.+
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~  133 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRP  133 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEE
Confidence            567999999999999999999999999  999999999999999999999999999999999999999999999999999


Q ss_pred             eeCC
Q psy222          167 ECGR  170 (225)
Q Consensus       167 a~~~  170 (225)
                      +.++
T Consensus       134 a~~~  137 (156)
T 3n9u_C          134 ATRQ  137 (156)
T ss_dssp             CCHH
T ss_pred             cCCC
Confidence            9764

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.82  E-value=9.2e-20  Score=126.86  Aligned_cols=83  Identities=22%  Similarity=0.343  Sum_probs=77.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF  166 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~  166 (225)
                      ..+.++|||+|||+.+++++|+++|++||.|..|.|+.+  ++..+|||||+|.+.++|++||+.||+..|.|+.|+|.+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~--~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~   82 (92)
T 2dgv_A            5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRI   82 (92)
T ss_dssp             SSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            456789999999999999999999999999999999974  788999999999999999999999999999999999999


Q ss_pred             eeCCC
Q psy222          167 ECGRV  171 (225)
Q Consensus       167 a~~~~  171 (225)
                      +++..
T Consensus        83 a~~~~   87 (92)
T 2dgv_A           83 DRNAS   87 (92)
T ss_dssp             CSCCS
T ss_pred             cCCCC
Confidence            98754

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.82  E-value=4.7e-20  Score=133.96  Aligned_cols=83  Identities=25%  Similarity=0.414  Sum_probs=78.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEee
Q psy222           89 PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFEC  168 (225)
Q Consensus        89 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~  168 (225)
                      +.++|||+|||+.+++++|+++|.+||.|..|.|+.++.++..+|||||+|.+.++|++||.. ++..|.|+.|+|.++.
T Consensus        26 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a~  104 (116)
T 1x4b_A           26 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAV  104 (116)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECCS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEECC
Confidence            346999999999999999999999999999999999988999999999999999999999997 9999999999999998


Q ss_pred             CCCC
Q psy222          169 GRVL  172 (225)
Q Consensus       169 ~~~~  172 (225)
                      ++..
T Consensus       105 ~~~~  108 (116)
T 1x4b_A          105 AREE  108 (116)
T ss_dssp             SCCC
T ss_pred             CCcc
Confidence            7653

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.82  E-value=3.2e-20  Score=135.25  Aligned_cols=83  Identities=29%  Similarity=0.424  Sum_probs=78.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q psy222           86 STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD  165 (225)
Q Consensus        86 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~  165 (225)
                      ...+.++|||+|||+++++++|+++|++||.|..|.|++++.+++.+|||||+|.+.++|++||+.||+..|+|+.|+|+
T Consensus        36 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~  115 (118)
T 2khc_A           36 EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQ  115 (118)
T ss_dssp             CCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             Eee
Q psy222          166 FEC  168 (225)
Q Consensus       166 ~a~  168 (225)
                      +++
T Consensus       116 ~ak  118 (118)
T 2khc_A          116 LKK  118 (118)
T ss_dssp             EC-
T ss_pred             ecC
Confidence            974

>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=1.2e-19  Score=130.39  Aligned_cols=78  Identities=23%  Similarity=0.320  Sum_probs=73.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCC-----cE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQG-----SE  161 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g-----~~  161 (225)
                      ....++|||+|||+++++++|+++|.+||.|..|.|+.+       |||||+|.+.++|++||+.||++.|.|     +.
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            456789999999999999999999999999999999865       799999999999999999999999999     99


Q ss_pred             EEEEEeeCCC
Q psy222          162 IIVDFECGRV  171 (225)
Q Consensus       162 l~V~~a~~~~  171 (225)
                      |+|+++.++.
T Consensus        85 i~V~~a~~~~   94 (108)
T 1x4c_A           85 IRVKVDGPRS   94 (108)
T ss_dssp             EEEEESSCCS
T ss_pred             EEEEeCCCCC
Confidence            9999998854

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A

Probab=99.82  E-value=8.5e-20  Score=125.79  Aligned_cols=81  Identities=20%  Similarity=0.417  Sum_probs=75.9

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q psy222           86 STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD  165 (225)
Q Consensus        86 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~  165 (225)
                      ...+.++|||+|||+.+++++|+++|++||.|..|.|+.++.+++++|||||+|.+.++|++||+ +++..|+|+.|.|+
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            35577899999999999999999999999999999999998899999999999999999999997 58889999999998


Q ss_pred             Ee
Q psy222          166 FE  167 (225)
Q Consensus       166 ~a  167 (225)
                      +|
T Consensus        86 ~A   87 (87)
T 3s7r_A           86 KA   87 (87)
T ss_dssp             EC
T ss_pred             eC
Confidence            75

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.82  E-value=1.4e-19  Score=125.78  Aligned_cols=84  Identities=24%  Similarity=0.304  Sum_probs=78.3

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q psy222           86 STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD  165 (225)
Q Consensus        86 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~  165 (225)
                      .....++|||+|||+.+++++|+++|+.| .|..|.|+++ .+++++|||||+|.+.++|++||. ||+..|.|+.|.|.
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            34567899999999999999999999999 8999999999 689999999999999999999999 99999999999999


Q ss_pred             EeeCCCC
Q psy222          166 FECGRVL  172 (225)
Q Consensus       166 ~a~~~~~  172 (225)
                      ++.++..
T Consensus        83 ~a~~~~~   89 (91)
T 2dgw_A           83 REKSGPS   89 (91)
T ss_dssp             EESSCCC
T ss_pred             ECCcCCC
Confidence            9987643

>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=99.82  E-value=7.8e-20  Score=128.55  Aligned_cols=82  Identities=18%  Similarity=0.296  Sum_probs=76.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHH----HHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLE----QAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEI  162 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~----~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l  162 (225)
                      ..+.++|||+|||+.+++++|+    ++|++||.|..|.|+.++.+   ++||||+|.+.++|++||+.||+..|+|+.|
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            3456799999999999999999    99999999999999988755   8899999999999999999999999999999


Q ss_pred             EEEEeeCCC
Q psy222          163 IVDFECGRV  171 (225)
Q Consensus       163 ~V~~a~~~~  171 (225)
                      +|.+++++.
T Consensus        83 ~V~~a~~~~   91 (96)
T 2dgx_A           83 LVSLATGAS   91 (96)
T ss_dssp             EEEECCCSS
T ss_pred             EEEEcCCCC
Confidence            999998754

>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=99.82  E-value=6.6e-20  Score=128.33  Aligned_cols=83  Identities=28%  Similarity=0.435  Sum_probs=77.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q psy222           86 STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD  165 (225)
Q Consensus        86 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~  165 (225)
                      ...+.++|||+|||+.+++++|+++|++||.|..|.|+.++ ++..+|||||+|.+.++|++||+.||+..|.|+.|+|.
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            34566899999999999999999999999999999999997 48899999999999999999999999999999999999


Q ss_pred             EeeC
Q psy222          166 FECG  169 (225)
Q Consensus       166 ~a~~  169 (225)
                      +++.
T Consensus        91 ~a~~   94 (95)
T 2ywk_A           91 GPSS   94 (95)
T ss_dssp             CCCC
T ss_pred             EcCC
Confidence            9863

>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=128.39  Aligned_cols=84  Identities=27%  Similarity=0.540  Sum_probs=76.8

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      ....+.++|||+|||+.+++++|+++|+.|+   .|.++.++.+++.+|||||+|.+.++|++||+.||+..|.|+.|+|
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            4456778999999999999999999999773   7788888889999999999999999999999999999999999999


Q ss_pred             EEeeCCC
Q psy222          165 DFECGRV  171 (225)
Q Consensus       165 ~~a~~~~  171 (225)
                      .+++++.
T Consensus        87 ~~a~~~~   93 (102)
T 2fc8_A           87 DWAKPKG   93 (102)
T ss_dssp             EECCCCC
T ss_pred             EEecCCC
Confidence            9998754

>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=99.82  E-value=8.6e-20  Score=126.15  Aligned_cols=80  Identities=24%  Similarity=0.490  Sum_probs=76.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEeeC
Q psy222           90 TRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECG  169 (225)
Q Consensus        90 ~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~~  169 (225)
                      .++|||+|||+.+++++|+++|++||.|..|.|+.++.+++++|||||+|.+.++|++|+ .||+..|.|+.|+|.++++
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            469999999999999999999999999999999999889999999999999999999999 8999999999999999876


Q ss_pred             C
Q psy222          170 R  170 (225)
Q Consensus       170 ~  170 (225)
                      .
T Consensus        85 ~   85 (89)
T 3ucg_A           85 N   85 (89)
T ss_dssp             T
T ss_pred             C
Confidence            3

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.82  E-value=3.2e-20  Score=130.75  Aligned_cols=85  Identities=9%  Similarity=0.139  Sum_probs=79.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q psy222           86 STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD  165 (225)
Q Consensus        86 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~  165 (225)
                      .....++|||+|||+.+++++|+++|.+||.|..+.++.++.+++++|||||+|.+.++|++||+.||+..|.|+.|+|+
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            34556899999999999999999999999999988888888899999999999999999999999999999999999999


Q ss_pred             EeeCC
Q psy222          166 FECGR  170 (225)
Q Consensus       166 ~a~~~  170 (225)
                      ++..+
T Consensus        91 ~a~~~   95 (98)
T 2cqp_A           91 LGSGP   95 (98)
T ss_dssp             ESSCS
T ss_pred             EcCCC
Confidence            98754

>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=99.82  E-value=6.4e-20  Score=130.57  Aligned_cols=83  Identities=13%  Similarity=0.163  Sum_probs=75.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q psy222           86 STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD  165 (225)
Q Consensus        86 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~  165 (225)
                      .....++|||+|||+.+++++|+++|++|| +..|.|++++ +++++|||||+|.+.++|++||+ +|+..|+++.|+|.
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 QSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELF   87 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcC-ceEEEEEECC-CCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEE
Confidence            345668999999999999999999999999 5599999997 89999999999999999999996 79999999999999


Q ss_pred             EeeCCC
Q psy222          166 FECGRV  171 (225)
Q Consensus       166 ~a~~~~  171 (225)
                      ++.+..
T Consensus        88 ~~~~~~   93 (102)
T 1wez_A           88 LNSTAG   93 (102)
T ss_dssp             EECCCC
T ss_pred             ECCCCC
Confidence            987643

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A

Probab=99.82  E-value=1e-19  Score=140.34  Aligned_cols=88  Identities=28%  Similarity=0.482  Sum_probs=81.4

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      ....+.++|||+|||+.+++++|+.+|++||.|..|.|+.++.++.++|||||+|.+.++|++||..||+..|.|+.|.|
T Consensus        67 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V  146 (165)
T 1rk8_A           67 QRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQV  146 (165)
T ss_dssp             CCCC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            44566789999999999999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             EEeeCCCC
Q psy222          165 DFECGRVL  172 (225)
Q Consensus       165 ~~a~~~~~  172 (225)
                      .++.++..
T Consensus       147 ~~a~~~~~  154 (165)
T 1rk8_A          147 DWCFVKGP  154 (165)
T ss_dssp             EESEECC-
T ss_pred             EEecCCCC
Confidence            99987553

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=6.5e-20  Score=130.69  Aligned_cols=83  Identities=22%  Similarity=0.362  Sum_probs=74.9

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCC--CccCCcEEE
Q psy222           86 STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNR--QNFQGSEII  163 (225)
Q Consensus        86 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g--~~l~g~~l~  163 (225)
                      ...+.++|||+|||+.+++++|+++|++||.|..|.|+++      +|||||+|.+.++|++|++.|++  ..|.|++|+
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            4567789999999999999999999999999999999865      79999999999999999998864  789999999


Q ss_pred             EEEeeCCCCCC
Q psy222          164 VDFECGRVLPG  174 (225)
Q Consensus       164 V~~a~~~~~~~  174 (225)
                      |.+++++....
T Consensus        86 V~~A~~~~~~~   96 (105)
T 1sjq_A           86 IQFSNHKELKT   96 (105)
T ss_dssp             BCCCSSSSCCC
T ss_pred             EEEcCCCCCCc
Confidence            99998866543

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.81  E-value=1.2e-19  Score=133.37  Aligned_cols=80  Identities=26%  Similarity=0.505  Sum_probs=76.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEeeC
Q psy222           90 TRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECG  169 (225)
Q Consensus        90 ~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~~  169 (225)
                      .++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++|| .||+..|+|+.|+|.++++
T Consensus        36 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~  114 (124)
T 2jwn_A           36 KRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKRT  114 (124)
T ss_dssp             HTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESSC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCC
Confidence            469999999999999999999999999999999999889999999999999999999999 7999999999999999886


Q ss_pred             C
Q psy222          170 R  170 (225)
Q Consensus       170 ~  170 (225)
                      .
T Consensus       115 ~  115 (124)
T 2jwn_A          115 N  115 (124)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.81  E-value=3.2e-20  Score=129.92  Aligned_cols=82  Identities=9%  Similarity=0.109  Sum_probs=75.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEe
Q psy222           88 DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFE  167 (225)
Q Consensus        88 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a  167 (225)
                      .+.++|||+|||+.+++++|+++|.+||.|..+.++.++.+++.+|||||+|.+.++|++||+.||+..|.|+.|+|.++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a   92 (95)
T 2ek1_A           13 PGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGP   92 (95)
T ss_dssp             --CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEec
Confidence            35689999999999999999999999999999999998889999999999999999999999999999999999999987


Q ss_pred             eC
Q psy222          168 CG  169 (225)
Q Consensus       168 ~~  169 (225)
                      ..
T Consensus        93 ~s   94 (95)
T 2ek1_A           93 SS   94 (95)
T ss_dssp             C-
T ss_pred             cC
Confidence            53

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.81  E-value=2.9e-20  Score=138.16  Aligned_cols=84  Identities=24%  Similarity=0.385  Sum_probs=78.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeE--EEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCC----ccCCc
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVIS--VRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQ----NFQGS  160 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~--v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~----~l~g~  160 (225)
                      ..+.++|||+|||+++++++|+++|++||.|..  |+|++++.+++++|||||+|.+. +|++||..||+.    .|+|+
T Consensus        20 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr   98 (131)
T 2m2b_A           20 ENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGK   98 (131)
T ss_dssp             SCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCE
Confidence            456789999999999999999999999999976  99999999999999999999999 999999999999    99999


Q ss_pred             EEEEEEeeCCC
Q psy222          161 EIIVDFECGRV  171 (225)
Q Consensus       161 ~l~V~~a~~~~  171 (225)
                      .|+|++++++.
T Consensus        99 ~l~V~~a~~~~  109 (131)
T 2m2b_A           99 TINVEFAKGSK  109 (131)
T ss_dssp             CCCCEECCCSC
T ss_pred             EEEEEECCCCC
Confidence            99999998754

>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=2.3e-19  Score=124.49  Aligned_cols=78  Identities=29%  Similarity=0.552  Sum_probs=72.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF  166 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~  166 (225)
                      ..+.++|||+|||+++++++|+++|++||.|..|.|+        ++||||+|.+.++|++||+.||+..|.|+.|+|.+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   76 (90)
T 2dnq_A            5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEA   76 (90)
T ss_dssp             SSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEC
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEE
Confidence            4567899999999999999999999999999999987        67999999999999999999999999999999999


Q ss_pred             eeCCCC
Q psy222          167 ECGRVL  172 (225)
Q Consensus       167 a~~~~~  172 (225)
                      ++++..
T Consensus        77 a~~~~~   82 (90)
T 2dnq_A           77 SKNKSK   82 (90)
T ss_dssp             SSCCCC
T ss_pred             CCCCCC
Confidence            987653

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.81  E-value=1.4e-19  Score=128.22  Aligned_cols=82  Identities=22%  Similarity=0.423  Sum_probs=74.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q psy222           86 STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD  165 (225)
Q Consensus        86 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~  165 (225)
                      ...+.++|||+|||+.+++++|+++|++||.|   .|+.+ .+++.+|||||+|.+.++|++||..||+..|.|+.|+|.
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            45577899999999999999999999999976   56666 588899999999999999999999999999999999999


Q ss_pred             EeeCCC
Q psy222          166 FECGRV  171 (225)
Q Consensus       166 ~a~~~~  171 (225)
                      +++++.
T Consensus        87 ~a~~~~   92 (101)
T 2fc9_A           87 LQGPRG   92 (101)
T ss_dssp             ECSSCC
T ss_pred             EcCCCC
Confidence            998764

>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=99.81  E-value=7.7e-20  Score=130.11  Aligned_cols=83  Identities=36%  Similarity=0.627  Sum_probs=78.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEee
Q psy222           89 PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFEC  168 (225)
Q Consensus        89 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~  168 (225)
                      +.++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||+.||+..|.|+.|+|.++.
T Consensus         7 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   86 (104)
T 1p1t_A            7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAA   86 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETT
T ss_pred             CccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeCC
Confidence            45799999999999999999999999999999999998899999999999999999999999999999999999999998


Q ss_pred             CCC
Q psy222          169 GRV  171 (225)
Q Consensus       169 ~~~  171 (225)
                      ++.
T Consensus        87 ~~~   89 (104)
T 1p1t_A           87 SEK   89 (104)
T ss_dssp             CTT
T ss_pred             Ccc
Confidence            754

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.81  E-value=1.2e-19  Score=130.66  Aligned_cols=87  Identities=21%  Similarity=0.339  Sum_probs=76.7

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      ....+.++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||..+ +..|.|+.|.|
T Consensus        20 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V   98 (109)
T 2rs2_A           20 HMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDP   98 (109)
T ss_dssp             ------CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEE
Confidence            44556789999999999999999999999999999999999889999999999999999999999976 58999999999


Q ss_pred             EEeeCCCC
Q psy222          165 DFECGRVL  172 (225)
Q Consensus       165 ~~a~~~~~  172 (225)
                      .++.++..
T Consensus        99 ~~a~~~~~  106 (109)
T 2rs2_A           99 KVAFPRRA  106 (109)
T ss_dssp             EECCCCCC
T ss_pred             EEccCCCC
Confidence            99987653

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=7.1e-20  Score=130.56  Aligned_cols=81  Identities=14%  Similarity=0.304  Sum_probs=75.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF  166 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~  166 (225)
                      ..+.++|||+|||+++++++|+++|++||.|..|.|++++. +.++|||||+|.+.++|++||. +++..|+|+.|.|.+
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            34567999999999999999999999999999999999986 9999999999999999999999 899999999999998


Q ss_pred             eeC
Q psy222          167 ECG  169 (225)
Q Consensus       167 a~~  169 (225)
                      +..
T Consensus        86 ~~~   88 (103)
T 1s79_A           86 KDD   88 (103)
T ss_dssp             HHH
T ss_pred             chH
Confidence            764

>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=99.81  E-value=2.1e-20  Score=135.44  Aligned_cols=82  Identities=32%  Similarity=0.399  Sum_probs=77.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEee
Q psy222           89 PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFEC  168 (225)
Q Consensus        89 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~  168 (225)
                      ..++|||+|||+.+++++|+++|++||.|..|.|+.++.++..+|||||+|.+.++|++|| .||+..|.|+.|+|.++.
T Consensus        24 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~  102 (114)
T 2cq4_A           24 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQ  102 (114)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEecC
Confidence            3469999999999999999999999999999999999988999999999999999999999 899999999999999998


Q ss_pred             CCC
Q psy222          169 GRV  171 (225)
Q Consensus       169 ~~~  171 (225)
                      ++.
T Consensus       103 ~~~  105 (114)
T 2cq4_A          103 AEK  105 (114)
T ss_dssp             HHH
T ss_pred             CCc
Confidence            643

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=99.81  E-value=2.2e-19  Score=137.21  Aligned_cols=86  Identities=21%  Similarity=0.353  Sum_probs=81.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q psy222           86 STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD  165 (225)
Q Consensus        86 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~  165 (225)
                      .....++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||..||+..|.|+.|+|.
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             EeeCCC
Q psy222          166 FECGRV  171 (225)
Q Consensus       166 ~a~~~~  171 (225)
                      ++.++.
T Consensus       146 ~a~~~~  151 (158)
T 2kn4_A          146 MARYGR  151 (158)
T ss_dssp             EECCSS
T ss_pred             ECCCCC
Confidence            998754

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=2.3e-19  Score=128.74  Aligned_cols=87  Identities=24%  Similarity=0.365  Sum_probs=79.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCc-eeEEEEe-ecCCCCccceEEEEEeCCHHHHHHHHHHhC--CCccCCcEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGK-VISVRVV-RDFVTGHSKRYGFLEYDCEKACLAAIRALN--RQNFQGSEI  162 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~-v~~v~i~-~~~~~g~~kg~afV~F~~~~~a~~Al~~l~--g~~l~g~~l  162 (225)
                      ..+.++|||+|||+.+++++|+++|.+||. |..|.|+ .++.++..+|||||+|.+.++|++||..|+  +..|.|+.|
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            346789999999999999999999999998 9999998 788888999999999999999999999996  589999999


Q ss_pred             EEEEeeCCCCC
Q psy222          163 IVDFECGRVLP  173 (225)
Q Consensus       163 ~V~~a~~~~~~  173 (225)
                      +|.++.++...
T Consensus        85 ~V~~a~~~~~~   95 (109)
T 2dis_A           85 AVDWAEPEIDV   95 (109)
T ss_dssp             EEEESCSSCST
T ss_pred             EEEEcCCCCCc
Confidence            99999986543

>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=99.81  E-value=2.7e-19  Score=127.67  Aligned_cols=85  Identities=13%  Similarity=0.155  Sum_probs=77.6

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeE-EEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           86 STDPTRTLFIGRLNKNSREADLEQAFAEYGKVIS-VRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        86 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~-v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      .....++|||+|||+.+++++|+++|.+||.|.. |.|+.+ .+++++|||||+|.+.++|++||.. ++..|+++.|.|
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            3456789999999999999999999999999987 888888 6899999999999999999999997 999999999999


Q ss_pred             EEeeCCCC
Q psy222          165 DFECGRVL  172 (225)
Q Consensus       165 ~~a~~~~~  172 (225)
                      .++..+..
T Consensus        89 ~~~~~~~~   96 (104)
T 1wg5_A           89 FKSSRAEV   96 (104)
T ss_dssp             EEECTTTS
T ss_pred             EECCHHHH
Confidence            99876543

>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=99.81  E-value=4.2e-19  Score=126.04  Aligned_cols=84  Identities=20%  Similarity=0.365  Sum_probs=74.9

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhC--CCccCCcEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALN--RQNFQGSEI  162 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~--g~~l~g~~l  162 (225)
                      ....+.++|||+|||+.+++++|+++|++||.|..|.|+.+      +|||||+|.+.++|++|++.|+  +..|.|++|
T Consensus        10 ~~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l   83 (101)
T 2cq1_A           10 MDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPI   83 (101)
T ss_dssp             CCSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEEC
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCcEE
Confidence            34567789999999999999999999999999999988864      7999999999999999999774  678999999


Q ss_pred             EEEEeeCCCCCC
Q psy222          163 IVDFECGRVLPG  174 (225)
Q Consensus       163 ~V~~a~~~~~~~  174 (225)
                      +|.+++.+....
T Consensus        84 ~V~~a~~~~~~~   95 (101)
T 2cq1_A           84 YIQYSNHKELKT   95 (101)
T ss_dssp             EEEECSCSSCCC
T ss_pred             EEEEcCcccCcC
Confidence            999999876554

>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=99.81  E-value=1.3e-19  Score=128.88  Aligned_cols=81  Identities=14%  Similarity=0.181  Sum_probs=72.9

Q ss_pred             CCCCCCCeEEEcCCCC-CCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCC--ccCCcE
Q psy222           85 SSTDPTRTLFIGRLNK-NSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQ--NFQGSE  161 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~-~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~--~l~g~~  161 (225)
                      ....+.++|||+|||+ .+++++|+++|++||.|..|.|+++      ++||||+|.+.++|++||+.|++.  .|.|++
T Consensus        10 ~~~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~   83 (102)
T 1x4d_A           10 GRVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKP   83 (102)
T ss_dssp             CCCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEE
T ss_pred             CCCCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHHcCCCceECCcE
Confidence            3455788999999999 9999999999999999999999865      589999999999999999999865  599999


Q ss_pred             EEEEEeeCCC
Q psy222          162 IIVDFECGRV  171 (225)
Q Consensus       162 l~V~~a~~~~  171 (225)
                      |+|.+++.+.
T Consensus        84 l~V~~a~~~~   93 (102)
T 1x4d_A           84 VRVHLSQKYK   93 (102)
T ss_dssp             CEEEEECCCT
T ss_pred             EEEEECCCCC
Confidence            9999998643

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens}

Probab=99.80  E-value=4.5e-20  Score=130.73  Aligned_cols=85  Identities=24%  Similarity=0.388  Sum_probs=75.5

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecC-CCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDF-VTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEII  163 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~-~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~  163 (225)
                      ......++|||+|||+++++++|+++|++|| |..|.|+.++ .+++++|||||+|.+.++|++|| .|++..|.|+.|+
T Consensus        14 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~   91 (100)
T 2j76_E           14 LPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIR   91 (100)
T ss_dssp             ------CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCC
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEE
Confidence            4456778999999999999999999999999 9999999997 58999999999999999999999 7999999999999


Q ss_pred             EEEeeCCC
Q psy222          164 VDFECGRV  171 (225)
Q Consensus       164 V~~a~~~~  171 (225)
                      |.+++++.
T Consensus        92 V~~a~~~~   99 (100)
T 2j76_E           92 VDVADQAQ   99 (100)
T ss_dssp             CEECCCSC
T ss_pred             EEeccCCC
Confidence            99998754

>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=99.80  E-value=5.1e-20  Score=133.45  Aligned_cols=87  Identities=17%  Similarity=0.365  Sum_probs=74.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF  166 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~  166 (225)
                      ..+.++|||+|||+.+++++|+++|.+||.|..|.+..+..+++.+|||||+|.+.++|++||..||+..|.|+.|+|.+
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~  101 (115)
T 2cpx_A           22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF  101 (115)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            45678999999999999999999999999984332222222788899999999999999999999999999999999999


Q ss_pred             eeCCCCC
Q psy222          167 ECGRVLP  173 (225)
Q Consensus       167 a~~~~~~  173 (225)
                      +.++...
T Consensus       102 a~~~~~~  108 (115)
T 2cpx_A          102 GKNKKQR  108 (115)
T ss_dssp             CCCCSCC
T ss_pred             ccCCCCC
Confidence            9876543

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=2.6e-20  Score=127.87  Aligned_cols=80  Identities=26%  Similarity=0.425  Sum_probs=75.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEe
Q psy222           88 DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFE  167 (225)
Q Consensus        88 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a  167 (225)
                      .+.++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||+.||+..|.|+.|+|.++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~   82 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGP   82 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCC
Confidence            46789999999999999999999999999999999999889999999999999999999999999999999998877654

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.80  E-value=5.7e-19  Score=122.98  Aligned_cols=79  Identities=29%  Similarity=0.578  Sum_probs=72.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q psy222           86 STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD  165 (225)
Q Consensus        86 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~  165 (225)
                      ...+.++|||+|||+.+++++|+++|++||.|..|.|+        ++||||+|.+.++|++||..||+..|.|+.|+|.
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 SGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQ   77 (92)
T ss_dssp             CCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEEC--------SSEEEEEESCHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEE--------CCEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEE
Confidence            35577899999999999999999999999999999997        3499999999999999999999999999999999


Q ss_pred             EeeCCCC
Q psy222          166 FECGRVL  172 (225)
Q Consensus       166 ~a~~~~~  172 (225)
                      +++++..
T Consensus        78 ~a~~~~~   84 (92)
T 2dgt_A           78 LSTSRLR   84 (92)
T ss_dssp             ESSCCCS
T ss_pred             EccCCCC
Confidence            9987543

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.80  E-value=5.8e-19  Score=129.72  Aligned_cols=86  Identities=17%  Similarity=0.327  Sum_probs=80.6

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q psy222           86 STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD  165 (225)
Q Consensus        86 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~  165 (225)
                      ...+.++|||+|||+.+++++|+++|++||.|..|.|+.++ +++.+|||||+|.+.++|++||..||+..|.|+.|+|.
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            45567899999999999999999999999999999999998 89999999999999999999999999999999999999


Q ss_pred             EeeCCCC
Q psy222          166 FECGRVL  172 (225)
Q Consensus       166 ~a~~~~~  172 (225)
                      ++.+...
T Consensus       110 ~a~~~~~  116 (124)
T 2kt5_A          110 LVASQID  116 (124)
T ss_dssp             EECCTTC
T ss_pred             EeCCCCC
Confidence            9987543

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.80  E-value=6.9e-20  Score=122.72  Aligned_cols=75  Identities=19%  Similarity=0.396  Sum_probs=72.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEe
Q psy222           92 TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFE  167 (225)
Q Consensus        92 ~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a  167 (225)
                      +|||+|||+++++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|++|++ |++..|+|+.|.|++|
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            59999999999999999999999999999999998899999999999999999999998 8999999999999875

>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=99.80  E-value=3.9e-19  Score=125.04  Aligned_cols=80  Identities=23%  Similarity=0.454  Sum_probs=73.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccC--CcEEE
Q psy222           86 STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQ--GSEII  163 (225)
Q Consensus        86 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~--g~~l~  163 (225)
                      ...+.++|||+|||+.+++++|+++|++||.|..|.++++      ++||||+|.+.++|++|++.||+..|.  ++.|+
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      789999999999999999999999999  99999


Q ss_pred             EEEeeCCC
Q psy222          164 VDFECGRV  171 (225)
Q Consensus       164 V~~a~~~~  171 (225)
                      |.+++++.
T Consensus        87 V~~a~~~~   94 (97)
T 1why_A           87 VDFAKSGP   94 (97)
T ss_dssp             EEECCCCC
T ss_pred             EEECCCCC
Confidence            99998754

>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=99.80  E-value=4.4e-19  Score=126.65  Aligned_cols=81  Identities=15%  Similarity=0.287  Sum_probs=72.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCC--ccCCcEEE
Q psy222           86 STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQ--NFQGSEII  163 (225)
Q Consensus        86 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~--~l~g~~l~  163 (225)
                      ...+.++|||+|||+.+++++|+++|++||.|..|.|+++      +|||||+|.+.++|++|++.|++.  .|.|++|+
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            3457789999999999999999999999999999998854      789999999999999999988764  59999999


Q ss_pred             EEEeeCCCC
Q psy222          164 VDFECGRVL  172 (225)
Q Consensus       164 V~~a~~~~~  172 (225)
                      |.+++.+..
T Consensus        85 V~~a~~~~~   93 (104)
T 1wex_A           85 FNYSTSKRI   93 (104)
T ss_dssp             EEECSSSSC
T ss_pred             EEEccCccc
Confidence            999987654

>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=99.80  E-value=5e-19  Score=128.06  Aligned_cols=83  Identities=27%  Similarity=0.485  Sum_probs=77.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCcc--------C
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNF--------Q  158 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l--------~  158 (225)
                      ..+.++|||+|||+.+++++|+++|++||.|..|.|+.++ ++..+|||||+|.+.++|++||..||+..|        .
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~  100 (114)
T 1x5o_A           22 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAP  100 (114)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCC
Confidence            4466899999999999999999999999999999999998 999999999999999999999999999999        5


Q ss_pred             CcEEEEEEeeCC
Q psy222          159 GSEIIVDFECGR  170 (225)
Q Consensus       159 g~~l~V~~a~~~  170 (225)
                      +++|.|.|+.++
T Consensus       101 ~~~l~v~~a~p~  112 (114)
T 1x5o_A          101 TEPLLCKFSGPS  112 (114)
T ss_dssp             SSCBEEEECCCS
T ss_pred             CCceeEEccCCC
Confidence            788999999864

>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=8.9e-19  Score=123.63  Aligned_cols=80  Identities=23%  Similarity=0.407  Sum_probs=72.9

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcC--CceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEY--GKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEI  162 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~--G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l  162 (225)
                      ....+.++|||+|||+.+++++|+++|++|  |.|..|.++        ++||||+|.+.++|++||..||+..|.|+.|
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            445567899999999999999999999999  999998875        6799999999999999999999999999999


Q ss_pred             EEEEeeCCCC
Q psy222          163 IVDFECGRVL  172 (225)
Q Consensus       163 ~V~~a~~~~~  172 (225)
                      +|.+++++..
T Consensus        82 ~v~~a~~~~~   91 (99)
T 2cpd_A           82 EVTLAKPVDK   91 (99)
T ss_dssp             EEECCCCCCC
T ss_pred             EEEECCCCCC
Confidence            9999987653

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.80  E-value=3.1e-19  Score=125.99  Aligned_cols=81  Identities=22%  Similarity=0.326  Sum_probs=73.2

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCc--cCCcEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQN--FQGSEI  162 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~--l~g~~l  162 (225)
                      ....+.++|||+|||+.+++++|+++|++||.|..|.+++.      +|||||+|.+.++|.+|+..|++..  |.|++|
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            44567899999999999999999999999999999999853      7899999999999999999999876  789999


Q ss_pred             EEEEeeCCC
Q psy222          163 IVDFECGRV  171 (225)
Q Consensus       163 ~V~~a~~~~  171 (225)
                      .|.+++.+.
T Consensus        90 ~V~~S~~k~   98 (100)
T 3r27_A           90 FVNYSTSQK   98 (100)
T ss_dssp             EEEECSCSC
T ss_pred             EEEeccccc
Confidence            999998753

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.80  E-value=9.8e-20  Score=136.06  Aligned_cols=88  Identities=20%  Similarity=0.338  Sum_probs=81.8

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      ....+.++|||+|||+.+++++|+++|++||.|..|.|+.++.+++.+|||||+|.+.++|++||..||+..|.|+.|+|
T Consensus        42 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V  121 (135)
T 2lea_A           42 PDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRV  121 (135)
T ss_dssp             SSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            44556789999999999999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             EEeeCCCC
Q psy222          165 DFECGRVL  172 (225)
Q Consensus       165 ~~a~~~~~  172 (225)
                      .++++...
T Consensus       122 ~~a~~~~~  129 (135)
T 2lea_A          122 QMARYGRP  129 (135)
T ss_dssp             EECCCCCC
T ss_pred             EECCCCCC
Confidence            99987543

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=3.1e-19  Score=128.44  Aligned_cols=85  Identities=24%  Similarity=0.430  Sum_probs=78.3

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      ....+.++|||+|||+.+++++|+++|++||.|..|.|+.++  +..+|||||+|.+.++|++|++.||+..|.|+.|+|
T Consensus        24 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V  101 (109)
T 2err_A           24 ENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEV  101 (109)
T ss_dssp             SCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEE
T ss_pred             cCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            445677899999999999999999999999999999999885  458999999999999999999999999999999999


Q ss_pred             EEeeCCC
Q psy222          165 DFECGRV  171 (225)
Q Consensus       165 ~~a~~~~  171 (225)
                      .++.++.
T Consensus       102 ~~a~~~~  108 (109)
T 2err_A          102 NNATARV  108 (109)
T ss_dssp             EECCCSC
T ss_pred             EECCCCc
Confidence            9998753

>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=99.80  E-value=4.9e-19  Score=124.96  Aligned_cols=81  Identities=25%  Similarity=0.495  Sum_probs=74.7

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      ....+.++|||+|||+.+++++|+++|++||.|..|.|+.+      ++||||+|.+.++|++||+.||+..|.|+.|+|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v   83 (99)
T 2cpj_A           10 KTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRV   83 (99)
T ss_dssp             CCCCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEE
T ss_pred             CcCCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEE
Confidence            44567789999999999999999999999999999999854      789999999999999999999999999999999


Q ss_pred             EEeeCCC
Q psy222          165 DFECGRV  171 (225)
Q Consensus       165 ~~a~~~~  171 (225)
                      .+++++.
T Consensus        84 ~~a~~~~   90 (99)
T 2cpj_A           84 RFACHSA   90 (99)
T ss_dssp             EESSCCS
T ss_pred             EEcCCCC
Confidence            9998754

>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=99.80  E-value=3.1e-20  Score=134.70  Aligned_cols=83  Identities=16%  Similarity=0.152  Sum_probs=77.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCce-eEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKV-ISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD  165 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v-~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~  165 (225)
                      ..+.++|||+|||+.+++++|+++|+.||.| ..|.|++++ +++.+|||||+|.+.++|++||+. |+..|.|+.|.|.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~   89 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVH   89 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEE
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEE
Confidence            4567899999999999999999999999999 889999998 999999999999999999999996 9999999999999


Q ss_pred             EeeCCC
Q psy222          166 FECGRV  171 (225)
Q Consensus       166 ~a~~~~  171 (225)
                      ++.++.
T Consensus        90 ~a~~~~   95 (114)
T 2cpy_A           90 VVTLED   95 (114)
T ss_dssp             EECHHH
T ss_pred             ECCHHH
Confidence            998643

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=6.1e-19  Score=126.70  Aligned_cols=80  Identities=18%  Similarity=0.388  Sum_probs=74.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF  166 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~  166 (225)
                      ....++|||+|||+.+++++|+++|++||.|..|.|+.+      ++||||+|.+.++|++||..|++..|.|+.|+|.+
T Consensus        22 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~------~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   95 (109)
T 1x4g_A           22 SPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYW   95 (109)
T ss_dssp             CSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEe
Confidence            346789999999999999999999999999999999876      78999999999999999999999999999999999


Q ss_pred             eeCCCC
Q psy222          167 ECGRVL  172 (225)
Q Consensus       167 a~~~~~  172 (225)
                      ++++..
T Consensus        96 a~~~~~  101 (109)
T 1x4g_A           96 GKESPD  101 (109)
T ss_dssp             CCCCCS
T ss_pred             cCCCCC
Confidence            987654

>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=99.79  E-value=4e-19  Score=129.55  Aligned_cols=84  Identities=21%  Similarity=0.362  Sum_probs=75.3

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCC--CccCCcEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNR--QNFQGSEI  162 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g--~~l~g~~l  162 (225)
                      ....+.++|||+|||+.+++++|+++|++||.|..|.|+.+      +|||||+|.+.++|++|++.|++  ..|.|++|
T Consensus        26 ~~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l   99 (119)
T 2ad9_A           26 SAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPI   99 (119)
T ss_dssp             SCSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCC
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeEE
Confidence            34557789999999999999999999999999999999875      79999999999999999998874  68999999


Q ss_pred             EEEEeeCCCCCC
Q psy222          163 IVDFECGRVLPG  174 (225)
Q Consensus       163 ~V~~a~~~~~~~  174 (225)
                      +|.+++++....
T Consensus       100 ~V~~a~~k~~~~  111 (119)
T 2ad9_A          100 YIQFSNHKELKT  111 (119)
T ss_dssp             EEEECSSSSCCC
T ss_pred             EEEEccCCCCCc
Confidence            999998866543

>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=125.39  Aligned_cols=78  Identities=24%  Similarity=0.519  Sum_probs=71.7

Q ss_pred             CCCCCeEEEcCCCC-CCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q psy222           87 TDPTRTLFIGRLNK-NSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD  165 (225)
Q Consensus        87 ~~~~~~l~V~nLp~-~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~  165 (225)
                      ..+.++|||+|||+ .+++++|+++|++||.|..|.|.        +|||||+|.+.++|++||..||+..|.|+.|+|.
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   78 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILE   78 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            45788999999999 99999999999999999999984        7899999999999999999999999999999999


Q ss_pred             EeeCCCC
Q psy222          166 FECGRVL  172 (225)
Q Consensus       166 ~a~~~~~  172 (225)
                      +++++..
T Consensus        79 ~a~~~~~   85 (96)
T 2kvi_A           79 VSSSNAR   85 (96)
T ss_dssp             EEECCCC
T ss_pred             EcCcCCC
Confidence            9987553

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.67  E-value=5.3e-21  Score=139.06  Aligned_cols=85  Identities=24%  Similarity=0.363  Sum_probs=79.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeE--------EEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccC
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVIS--------VRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQ  158 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~--------v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~  158 (225)
                      ..+.++|||+|||+.+++++|+++|++||.|..        |.|+.++.++..+|||||+|.+.++|++||..||+..|.
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            446789999999999999999999999999998        899999888999999999999999999999999999999


Q ss_pred             CcEEEEEEeeCCC
Q psy222          159 GSEIIVDFECGRV  171 (225)
Q Consensus       159 g~~l~V~~a~~~~  171 (225)
                      |+.|+|.++.++.
T Consensus        84 g~~l~V~~a~~~~   96 (116)
T 2lcw_A           84 GNPIKVSFATRRA   96 (116)
Confidence            9999999998754

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.79  E-value=1e-19  Score=122.40  Aligned_cols=76  Identities=21%  Similarity=0.385  Sum_probs=73.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEe
Q psy222           91 RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFE  167 (225)
Q Consensus        91 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a  167 (225)
                      ++|||+|||+++++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|++|+..++ ..|+|+.|.|++|
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            479999999999999999999999999999999998889999999999999999999999998 9999999999986

>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=99.79  E-value=4.6e-20  Score=127.94  Aligned_cols=81  Identities=27%  Similarity=0.491  Sum_probs=74.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEeeCC
Q psy222           91 RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECGR  170 (225)
Q Consensus        91 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~~~  170 (225)
                      ++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.+ |++|+..||+..|.|+.|+|++|.+.
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            58999999999999999999999999999999999889999999999999999 99999999999999999999999875


Q ss_pred             CC
Q psy222          171 VL  172 (225)
Q Consensus       171 ~~  172 (225)
                      ..
T Consensus        81 ~~   82 (90)
T 2ki2_A           81 KS   82 (90)
T ss_dssp             --
T ss_pred             CC
Confidence            53

>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=99.79  E-value=5.5e-19  Score=123.23  Aligned_cols=80  Identities=23%  Similarity=0.418  Sum_probs=71.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCc-eeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCC-CccCCcEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGK-VISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNR-QNFQGSEIIV  164 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~-v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g-~~l~g~~l~V  164 (225)
                      ..+.++|||+|||+++++++|+++|++||. |..+.+.       .+|||||+|.+.++|++||+.||+ ..|.|+.|+|
T Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v   77 (93)
T 2cqh_A            5 SSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEV   77 (93)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEE
Confidence            456789999999999999999999999999 6655553       478999999999999999999999 9999999999


Q ss_pred             EEeeCCCCC
Q psy222          165 DFECGRVLP  173 (225)
Q Consensus       165 ~~a~~~~~~  173 (225)
                      .+++++..+
T Consensus        78 ~~a~~~~~~   86 (93)
T 2cqh_A           78 DYSVSKKLR   86 (93)
T ss_dssp             EECCCCCCC
T ss_pred             EEccCcccc
Confidence            999876543

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.79  E-value=4.3e-19  Score=132.72  Aligned_cols=83  Identities=24%  Similarity=0.516  Sum_probs=77.6

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      ....+.++|||+|||+.+++++|+++|++||.|..|.|+.++.+++.+|||||+|.+.++|++||+.||+..|.|+.|+|
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            33456789999999999999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             EEe
Q psy222          165 DFE  167 (225)
Q Consensus       165 ~~a  167 (225)
                      ++|
T Consensus       138 ~~A  140 (140)
T 2ku7_A          138 NLA  140 (140)
T ss_dssp             EC-
T ss_pred             EeC
Confidence            985

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.79  E-value=4.1e-19  Score=126.89  Aligned_cols=84  Identities=14%  Similarity=0.249  Sum_probs=76.4

Q ss_pred             CCCCCCCeEEEcCCCCCC------CHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccC
Q psy222           85 SSTDPTRTLFIGRLNKNS------READLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQ  158 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~------te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~  158 (225)
                      ......++|||+|||+.+      ++++|+++|++||.|..|.|+  +.+++++|||||+|.+.++|++||..|||..|.
T Consensus        10 ~~~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~--~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~   87 (105)
T 2nlw_A           10 EADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLD   87 (105)
T ss_dssp             SCCSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC--CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECS
T ss_pred             CCCCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee--CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccC
Confidence            344557899999999999      789999999999999999988  358999999999999999999999999999999


Q ss_pred             Cc-EEEEEEeeCC
Q psy222          159 GS-EIIVDFECGR  170 (225)
Q Consensus       159 g~-~l~V~~a~~~  170 (225)
                      |+ .|+|.++...
T Consensus        88 g~~~l~V~~a~~~  100 (105)
T 2nlw_A           88 KQHTFRVNLFTDF  100 (105)
T ss_dssp             TTCEEEEECSCCC
T ss_pred             CCceEEEEEcchH
Confidence            98 9999998754

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.79  E-value=7.7e-19  Score=123.57  Aligned_cols=82  Identities=22%  Similarity=0.382  Sum_probs=73.5

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      ......++|||+|||+.+++++|+++|++||.|. +.++++    ..+|||||+|.+.++|++||+.||+..|.|+.|+|
T Consensus        14 ~~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~----~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   88 (97)
T 2e5j_A           14 EGAPLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ----GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRV   88 (97)
T ss_dssp             SSSCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE----TTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEE
T ss_pred             CCCCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC----CCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEE
Confidence            3455678999999999999999999999999996 677654    47899999999999999999999999999999999


Q ss_pred             EEeeCCC
Q psy222          165 DFECGRV  171 (225)
Q Consensus       165 ~~a~~~~  171 (225)
                      .+++++.
T Consensus        89 ~~a~~~~   95 (97)
T 2e5j_A           89 ALARQQR   95 (97)
T ss_dssp             EECCCCC
T ss_pred             EEcCCCC
Confidence            9998754

>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=99.79  E-value=5.8e-20  Score=137.80  Aligned_cols=82  Identities=16%  Similarity=0.178  Sum_probs=74.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF  166 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~  166 (225)
                      ....++|||+|||+++++++|+++|++|| |+.|.|+.++. ++++|||||+|.+.++|++|| .+|+..|+++.|+|.+
T Consensus        43 ~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~-g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~  119 (139)
T 2hgn_A           43 STTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFL  119 (139)
T ss_dssp             --CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSS-SCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCC-CCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEE
Confidence            44668999999999999999999999999 77999999974 999999999999999999999 6899999999999999


Q ss_pred             eeCCC
Q psy222          167 ECGRV  171 (225)
Q Consensus       167 a~~~~  171 (225)
                      +.++.
T Consensus       120 a~~~~  124 (139)
T 2hgn_A          120 NSTTG  124 (139)
T ss_dssp             CCCSC
T ss_pred             CCCCC
Confidence            88654

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.78  E-value=4e-19  Score=129.68  Aligned_cols=82  Identities=15%  Similarity=0.127  Sum_probs=76.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCc---eeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGK---VISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEII  163 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~---v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~  163 (225)
                      ....++|||+|||+++++++|+++|+.||.   |..|.|+.++. ++++|||||+|.+.++|++||+ ||++.|+|+.|+
T Consensus        14 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~   91 (118)
T 2db1_A           14 GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALK-KDRESMGHRYIE   91 (118)
T ss_dssp             BCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEE
Confidence            446789999999999999999999999999   89999999975 9999999999999999999999 999999999999


Q ss_pred             EEEeeCC
Q psy222          164 VDFECGR  170 (225)
Q Consensus       164 V~~a~~~  170 (225)
                      |.++..+
T Consensus        92 V~~a~~~   98 (118)
T 2db1_A           92 VFKSHRT   98 (118)
T ss_dssp             EEEECHH
T ss_pred             EEECCHH
Confidence            9998753

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.78  E-value=4.3e-19  Score=121.51  Aligned_cols=74  Identities=15%  Similarity=0.174  Sum_probs=70.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEee
Q psy222           89 PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFEC  168 (225)
Q Consensus        89 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~  168 (225)
                      .+..|||+||++.++|++|+++|.+||.|.+++++.      ++|||||+|.++++|++|++.||+..|.|++|+|++|.
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            456899999999999999999999999999999975      48999999999999999999999999999999999985

>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=99.78  E-value=1.6e-19  Score=132.86  Aligned_cols=83  Identities=16%  Similarity=0.142  Sum_probs=76.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF  166 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~  166 (225)
                      ..+.++|||+|||+.+++++|+++|..||.|..+.++.+..+++++|||||+|.+.++|++||. ||+..|+|+.|.|.+
T Consensus        22 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~  100 (124)
T 1wel_A           22 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHP  100 (124)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEE
Confidence            4466899999999999999999999999999887667666799999999999999999999999 999999999999999


Q ss_pred             eeCC
Q psy222          167 ECGR  170 (225)
Q Consensus       167 a~~~  170 (225)
                      +..+
T Consensus       101 a~~~  104 (124)
T 1wel_A          101 ITKK  104 (124)
T ss_dssp             ECHH
T ss_pred             CCHH
Confidence            9753

>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=99.78  E-value=5e-19  Score=128.55  Aligned_cols=76  Identities=25%  Similarity=0.355  Sum_probs=66.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcE-----E
Q psy222           88 DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSE-----I  162 (225)
Q Consensus        88 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~-----l  162 (225)
                      ...++|||+|||+++++++|+++|++||.|..|.|+.+       |||||+|.+.++|++||+.||+..|+|+.     |
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            35689999999999999999999999999999999855       89999999999999999999999999988     7


Q ss_pred             EEEEeeCC
Q psy222          163 IVDFECGR  170 (225)
Q Consensus       163 ~V~~a~~~  170 (225)
                      +|..+.++
T Consensus        87 ~v~~~~~~   94 (115)
T 3beg_B           87 RVKVDGPR   94 (115)
T ss_dssp             EEEECC--
T ss_pred             EeccCCCC
Confidence            77776653

>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=1.2e-18  Score=125.31  Aligned_cols=77  Identities=27%  Similarity=0.507  Sum_probs=71.0

Q ss_pred             CCCCCeEEEcCCCCC-CCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q psy222           87 TDPTRTLFIGRLNKN-SREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD  165 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~-~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~  165 (225)
                      ....++|||+|||+. +++++|+++|++||.|..|.|        .++||||+|.+.++|++||+.||+..|.|+.|+|.
T Consensus        24 ~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   95 (110)
T 1wf1_A           24 KSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDIN   95 (110)
T ss_dssp             TTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEE
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            345589999999999 999999999999999999998        37899999999999999999999999999999999


Q ss_pred             EeeCCC
Q psy222          166 FECGRV  171 (225)
Q Consensus       166 ~a~~~~  171 (225)
                      ++++..
T Consensus        96 ~a~~~~  101 (110)
T 1wf1_A           96 MAGEPK  101 (110)
T ss_dssp             ESCCCC
T ss_pred             ECCCCC
Confidence            998543

>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=99.78  E-value=5.6e-19  Score=127.43  Aligned_cols=82  Identities=18%  Similarity=0.251  Sum_probs=72.7

Q ss_pred             CCCCCeEEEcCCCCC-CCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCC--CccCCcEEE
Q psy222           87 TDPTRTLFIGRLNKN-SREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNR--QNFQGSEII  163 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~-~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g--~~l~g~~l~  163 (225)
                      ..+.++|||+|||++ +++++|+++|++||.|..|.|++.      +|||||+|.+.++|++|++.|++  ..|.|+.|+
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~   95 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVK   95 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCE
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEecC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            456789999999998 999999999999999999999743      79999999999999999998864  569999999


Q ss_pred             EEEeeCCCCCC
Q psy222          164 VDFECGRVLPG  174 (225)
Q Consensus       164 V~~a~~~~~~~  174 (225)
                      |.+++.+....
T Consensus        96 V~~a~~~~~~~  106 (112)
T 1x4f_A           96 VDLSEKYKKLV  106 (112)
T ss_dssp             EEEECSCSSSS
T ss_pred             EEECccccccc
Confidence            99998765443

>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=1.8e-18  Score=119.97  Aligned_cols=78  Identities=29%  Similarity=0.486  Sum_probs=72.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q psy222           86 STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD  165 (225)
Q Consensus        86 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~  165 (225)
                      ...+.++|||+|||+.+++++|+++|++||.|..|.|+        ++||||+|.+.++|++||+.||+..|.|+.|+|.
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 SSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVE   76 (90)
T ss_dssp             SSCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            34567899999999999999999999999999999997        3499999999999999999999999999999999


Q ss_pred             EeeCCC
Q psy222          166 FECGRV  171 (225)
Q Consensus       166 ~a~~~~  171 (225)
                      +++++.
T Consensus        77 ~a~~~~   82 (90)
T 2dnp_A           77 LSTKGQ   82 (90)
T ss_dssp             ESCCCC
T ss_pred             ECCCCC
Confidence            998753

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.78  E-value=1.2e-18  Score=128.74  Aligned_cols=84  Identities=15%  Similarity=0.356  Sum_probs=75.0

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHH----HHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCc
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLE----QAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGS  160 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~----~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~  160 (225)
                      ....+.++|||+|||+.+++++|+    ++|++||.|..|.+..   +++.+|||||+|.+.++|+.||..|||..|.|+
T Consensus        24 ~~~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~---~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr  100 (127)
T 2a3j_A           24 PHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAFVEAFQGYPFQGN  100 (127)
T ss_dssp             CCCSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC---CCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTS
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc---CCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCC
Confidence            345567899999999999999876    6999999999988753   677899999999999999999999999999999


Q ss_pred             EEEEEEeeCCC
Q psy222          161 EIIVDFECGRV  171 (225)
Q Consensus       161 ~l~V~~a~~~~  171 (225)
                      .|+|.+++.+.
T Consensus       101 ~l~V~~a~~~~  111 (127)
T 2a3j_A          101 PLVITFSETPQ  111 (127)
T ss_dssp             CCEEEECCCCC
T ss_pred             EEEEEEccCcc
Confidence            99999998643

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.78  E-value=7.9e-20  Score=129.50  Aligned_cols=84  Identities=27%  Similarity=0.418  Sum_probs=76.3

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q psy222           86 STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD  165 (225)
Q Consensus        86 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~  165 (225)
                      ...+.++|||+|||+.+++++|+++|++||.|.. .++.+..++.++|||||+|.+.++|++||+ ||+..|.|+.|+|.
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            3446789999999999999999999999999888 666776788899999999999999999999 99999999999999


Q ss_pred             EeeCCC
Q psy222          166 FECGRV  171 (225)
Q Consensus       166 ~a~~~~  171 (225)
                      +++++.
T Consensus        91 ~a~~~~   96 (101)
T 1fj7_A           91 KPKGRD   96 (101)
T ss_dssp             CCSCCC
T ss_pred             EcCCCC
Confidence            998754

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A

Probab=99.78  E-value=4.3e-19  Score=132.63  Aligned_cols=83  Identities=13%  Similarity=0.103  Sum_probs=77.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCc---eeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEE
Q psy222           86 STDPTRTLFIGRLNKNSREADLEQAFAEYGK---VISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEI  162 (225)
Q Consensus        86 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~---v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l  162 (225)
                      .....++|||+|||+++|+++|+++|++||.   |..|.|++++. ++++|||||+|.+.++|++||+ ||+..|+|+.|
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            3456789999999999999999999999999   88999999986 9999999999999999999999 99999999999


Q ss_pred             EEEEeeCC
Q psy222          163 IVDFECGR  170 (225)
Q Consensus       163 ~V~~a~~~  170 (225)
                      +|.++.++
T Consensus       118 ~V~~a~~~  125 (136)
T 2hgl_A          118 EVFKSHRT  125 (136)
T ss_dssp             EEEECCHH
T ss_pred             EEEECChH
Confidence            99998653

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.78  E-value=5.6e-19  Score=127.46  Aligned_cols=80  Identities=21%  Similarity=0.230  Sum_probs=72.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCC-ceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYG-KVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD  165 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G-~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~  165 (225)
                      ....++|||+|||+++++++|+++|++|| .|..|.|+..    ..+|||||+|.+.++|++||+.||+..|.|+.|+|+
T Consensus        25 p~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~----~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~  100 (111)
T 2jvr_A           25 PAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR----DFDGTGALEFPSEEILVEALERLNNIEFRGSVITVE  100 (111)
T ss_dssp             CCCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSC----SSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcC----CCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            34567999999999999999999999999 8999988633    378999999999999999999999999999999999


Q ss_pred             EeeCC
Q psy222          166 FECGR  170 (225)
Q Consensus       166 ~a~~~  170 (225)
                      ++...
T Consensus       101 ~a~~~  105 (111)
T 2jvr_A          101 RDDNP  105 (111)
T ss_dssp             ESCC-
T ss_pred             ECCCC
Confidence            98754

>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=99.77  E-value=2.1e-18  Score=118.17  Aligned_cols=77  Identities=22%  Similarity=0.451  Sum_probs=71.4

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHh-CCCccCCcEEEE
Q psy222           86 STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL-NRQNFQGSEIIV  164 (225)
Q Consensus        86 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l-~g~~l~g~~l~V  164 (225)
                      ...+.++|||+|||+.+++++|+++|++||.|..|.++++      +|||||+|.+.++|++|+..| ++..|.|+.|+|
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            3456789999999999999999999999999999999864      789999999999999999988 999999999999


Q ss_pred             EEee
Q psy222          165 DFEC  168 (225)
Q Consensus       165 ~~a~  168 (225)
                      ++++
T Consensus        82 ~~ak   85 (85)
T 2ytc_A           82 KWGR   85 (85)
T ss_dssp             EECC
T ss_pred             EecC
Confidence            9974

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.77  E-value=1.3e-18  Score=123.23  Aligned_cols=76  Identities=25%  Similarity=0.542  Sum_probs=71.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEeeCC
Q psy222           91 RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECGR  170 (225)
Q Consensus        91 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~~~  170 (225)
                      ++|||+|||+.+++++|+++|++||.|..|.|+.+     .+|||||+|.+.++|++|++.|++..|.|+.|+|.+++++
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     5899999999999999999999999999999999999875


Q ss_pred             C
Q psy222          171 V  171 (225)
Q Consensus       171 ~  171 (225)
                      .
T Consensus        76 ~   76 (101)
T 2hvz_A           76 P   76 (101)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.77  E-value=2.8e-18  Score=124.32  Aligned_cols=81  Identities=17%  Similarity=0.294  Sum_probs=74.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF  166 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~  166 (225)
                      ..+.++|||+|||+.+++++|+++|++||.|..|.|+.+   +..+|||||+|.+.++|++|+..||+..|.|+.|.|.+
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   44589999999999999999999999999999999999


Q ss_pred             eeCC
Q psy222          167 ECGR  170 (225)
Q Consensus       167 a~~~  170 (225)
                      +.++
T Consensus        82 a~~~   85 (115)
T 3lqv_A           82 YNAN   85 (115)
T ss_dssp             CCHH
T ss_pred             ecCC
Confidence            9863

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.77  E-value=1.2e-18  Score=123.33  Aligned_cols=77  Identities=26%  Similarity=0.426  Sum_probs=71.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEe
Q psy222           88 DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFE  167 (225)
Q Consensus        88 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a  167 (225)
                      ...++|||+|||+++++++|+++|++||.|..|.|+.      .+|||||+|.+.++|++|+..||+..|+|+.|+|.++
T Consensus        25 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   98 (101)
T 2la4_A           25 PRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYP------EKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWG   98 (101)
T ss_dssp             SSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBC
T ss_pred             CCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEec
Confidence            4568999999999999999999999999999999983      4799999999999999999999999999999999998


Q ss_pred             eCC
Q psy222          168 CGR  170 (225)
Q Consensus       168 ~~~  170 (225)
                      +++
T Consensus        99 ~~~  101 (101)
T 2la4_A           99 KER  101 (101)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            763

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.77  E-value=3.5e-18  Score=119.49  Aligned_cols=79  Identities=22%  Similarity=0.309  Sum_probs=70.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEe
Q psy222           88 DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFE  167 (225)
Q Consensus        88 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a  167 (225)
                      ...++|||+|||+++++++|+++|++||.|..|  +.++.+++   ||||+|.+.++|++||. ||+..|+|+.|+|.++
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            356799999999999999999999999999987  55555665   99999999999999999 9999999999999988


Q ss_pred             eCCCC
Q psy222          168 CGRVL  172 (225)
Q Consensus       168 ~~~~~  172 (225)
                      .++..
T Consensus        80 ~~~~~   84 (94)
T 2e5g_A           80 EQKEF   84 (94)
T ss_dssp             CCSCC
T ss_pred             CcCCC
Confidence            76543

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.77  E-value=6.4e-19  Score=119.89  Aligned_cols=72  Identities=17%  Similarity=0.311  Sum_probs=67.4

Q ss_pred             CeEEEcCCCCCC------CHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCc-EEE
Q psy222           91 RTLFIGRLNKNS------READLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGS-EII  163 (225)
Q Consensus        91 ~~l~V~nLp~~~------te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~-~l~  163 (225)
                      ++|||+|||+.+      ++++|+++|++||.|..|.|+  +.+++++|||||+|.+.++|++||..||+..|.|+ +|+
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~--~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~   79 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFR   79 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC--CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCC
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec--CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEE
Confidence            689999999999      779999999999999999988  35889999999999999999999999999999999 887


Q ss_pred             E
Q psy222          164 V  164 (225)
Q Consensus       164 V  164 (225)
                      |
T Consensus        80 V   80 (81)
T 2krb_A           80 V   80 (81)
T ss_dssp             C
T ss_pred             e
Confidence            6

>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=7.1e-18  Score=118.58  Aligned_cols=81  Identities=16%  Similarity=0.296  Sum_probs=72.6

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      ....+.++|||+||  .+++++|+++|++||.|..|.|.      ..+|||||+|.+.++|++||..||+..|.|+.|+|
T Consensus        10 ~~~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v   81 (97)
T 1x5p_A           10 RAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKV   81 (97)
T ss_dssp             CCCCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            34557789999996  89999999999999999999985      35789999999999999999999999999999999


Q ss_pred             EEeeCCCCC
Q psy222          165 DFECGRVLP  173 (225)
Q Consensus       165 ~~a~~~~~~  173 (225)
                      .++.++...
T Consensus        82 ~~a~~~~~~   90 (97)
T 1x5p_A           82 NIARKQPML   90 (97)
T ss_dssp             ECCSSCCCC
T ss_pred             EECCCCCCC
Confidence            999876543

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.76  E-value=2.4e-18  Score=123.63  Aligned_cols=79  Identities=16%  Similarity=0.392  Sum_probs=72.6

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      ....+.++|||+|||+.+++++|+++|++||.|..|.|+        +|||||+|.+.++|++|+..||+..|.|+.|.|
T Consensus        26 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V   97 (108)
T 2jvo_A           26 EGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEV   97 (108)
T ss_dssp             --CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEE
Confidence            335567899999999999999999999999999999987        689999999999999999999999999999999


Q ss_pred             EEeeCCC
Q psy222          165 DFECGRV  171 (225)
Q Consensus       165 ~~a~~~~  171 (225)
                      .+++++.
T Consensus        98 ~~a~~~~  104 (108)
T 2jvo_A           98 VYSKLPA  104 (108)
T ss_dssp             ESCSCCC
T ss_pred             EEecCCC
Confidence            9998754

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A

Probab=99.76  E-value=3.5e-19  Score=119.18  Aligned_cols=75  Identities=19%  Similarity=0.364  Sum_probs=71.6

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEe
Q psy222           92 TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFE  167 (225)
Q Consensus        92 ~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a  167 (225)
                      +|||+|||+.+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|++||+ +++..|.|+.|.|++|
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            59999999999999999999999999999999998889999999999999999999999 5899999999999875

>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=99.76  E-value=4.7e-18  Score=119.70  Aligned_cols=78  Identities=23%  Similarity=0.495  Sum_probs=71.6

Q ss_pred             CCCCCCCeEEEcCCCC-CCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEE
Q psy222           85 SSTDPTRTLFIGRLNK-NSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEII  163 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~-~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~  163 (225)
                      ....+.++|||+|||+ .+++++|+++|++||.|..|.|.        +|||||+|.+.++|++||..||+..|.|+.|+
T Consensus        17 ~~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~   88 (97)
T 2xnq_A           17 RGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLI   88 (97)
T ss_dssp             --CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTEECE
T ss_pred             CCCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            4466789999999998 99999999999999999999983        78999999999999999999999999999999


Q ss_pred             EEEeeCC
Q psy222          164 VDFECGR  170 (225)
Q Consensus       164 V~~a~~~  170 (225)
                      |++++.+
T Consensus        89 V~~a~~~   95 (97)
T 2xnq_A           89 LEVSSSN   95 (97)
T ss_dssp             EEECCCC
T ss_pred             EEecCCC
Confidence            9998764

>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=99.76  E-value=1.2e-18  Score=122.38  Aligned_cols=82  Identities=18%  Similarity=0.421  Sum_probs=75.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHH----HHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLE----QAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEI  162 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~----~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l  162 (225)
                      ..+.++|||+|||+.+++++|+    ++|++||.|..|.++.   ++..+|||||+|.+.++|++|+..||+..|.|+.|
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   81 (97)
T 1nu4_A            5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPM   81 (97)
T ss_dssp             -CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEE
Confidence            4577899999999999999999    9999999999999873   56788999999999999999999999999999999


Q ss_pred             EEEEeeCCC
Q psy222          163 IVDFECGRV  171 (225)
Q Consensus       163 ~V~~a~~~~  171 (225)
                      +|.+++++.
T Consensus        82 ~v~~a~~~~   90 (97)
T 1nu4_A           82 RIQYAKTDS   90 (97)
T ss_dssp             EEEECSSCC
T ss_pred             EEEEccCCC
Confidence            999998754

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.76  E-value=1.2e-18  Score=122.14  Aligned_cols=80  Identities=19%  Similarity=0.297  Sum_probs=72.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF  166 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~  166 (225)
                      ..+.++|||+|||+.+++++|+++|++||.|..+     ..++..+|||||+|.+.++|++||..|++..|.|+.|+|.+
T Consensus        13 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   87 (96)
T 1fjc_A           13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY   87 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            4467899999999999999999999999988766     23788999999999999999999999999999999999999


Q ss_pred             eeCCC
Q psy222          167 ECGRV  171 (225)
Q Consensus       167 a~~~~  171 (225)
                      +.++.
T Consensus        88 a~~~~   92 (96)
T 1fjc_A           88 TGEKG   92 (96)
T ss_dssp             CSSSC
T ss_pred             cCCCC
Confidence            98754

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.76  E-value=2.9e-18  Score=133.79  Aligned_cols=85  Identities=18%  Similarity=0.346  Sum_probs=79.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q psy222           86 STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD  165 (225)
Q Consensus        86 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~  165 (225)
                      ...+.++|||+|||+.+++++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|++||+.||+..|.|+.|+|.
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 89999999999999999999999999999999999999


Q ss_pred             EeeCCC
Q psy222          166 FECGRV  171 (225)
Q Consensus       166 ~a~~~~  171 (225)
                      ++....
T Consensus       163 ~a~~~~  168 (177)
T 2f3j_A          163 LVASQI  168 (177)
T ss_dssp             EESSGG
T ss_pred             EecCCC
Confidence            997643

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens}

Probab=99.76  E-value=5.4e-19  Score=126.69  Aligned_cols=83  Identities=12%  Similarity=0.069  Sum_probs=77.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCc---eeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEE
Q psy222           86 STDPTRTLFIGRLNKNSREADLEQAFAEYGK---VISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEI  162 (225)
Q Consensus        86 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~---v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l  162 (225)
                      .....++|||+|||+++++++|+++|+.||.   |..|.|+.++. ++++|||||+|.+.++|++||. ||+..|+|+.|
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            4557789999999999999999999999998   89999999986 9999999999999999999999 99999999999


Q ss_pred             EEEEeeCC
Q psy222          163 IVDFECGR  170 (225)
Q Consensus       163 ~V~~a~~~  170 (225)
                      +|.++.++
T Consensus        85 ~V~~a~~~   92 (107)
T 2lmi_A           85 EVYEINNE   92 (107)
T ss_dssp             CCEECCHH
T ss_pred             EEEECCHH
Confidence            99998753

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.76  E-value=4.2e-18  Score=136.36  Aligned_cols=83  Identities=24%  Similarity=0.464  Sum_probs=77.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF  166 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~  166 (225)
                      ..+.++|||+|||+++++++|+++|++||.|.+|+|++++.+++++|||||+|.+.++|++||+.|++..+.|+.|+|.+
T Consensus        12 ~~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~   91 (213)
T 4f02_A           12 SYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMW   91 (213)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCccccccc
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeC
Q psy222          167 ECG  169 (225)
Q Consensus       167 a~~  169 (225)
                      +..
T Consensus        92 ~~~   94 (213)
T 4f02_A           92 SQR   94 (213)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            865

>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=99.76  E-value=3e-19  Score=140.33  Aligned_cols=86  Identities=16%  Similarity=0.360  Sum_probs=76.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF  166 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~  166 (225)
                      ..+.++|||+|||+.+++++|+++|+.||.|..|.|+.+..++.++|||||+|.+.++|.+||.. ++..|+|+.|.|.+
T Consensus       101 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~  179 (196)
T 1l3k_A          101 HLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRK  179 (196)
T ss_dssp             --CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEE
T ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEe
Confidence            34568999999999999999999999999999999999988999999999999999999999995 89999999999999


Q ss_pred             eeCCCCC
Q psy222          167 ECGRVLP  173 (225)
Q Consensus       167 a~~~~~~  173 (225)
                      +.++...
T Consensus       180 a~~k~~~  186 (196)
T 1l3k_A          180 ALSKQEM  186 (196)
T ss_dssp             CC-----
T ss_pred             cCChhHh
Confidence            9886643

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.76  E-value=2.5e-18  Score=123.68  Aligned_cols=77  Identities=16%  Similarity=0.221  Sum_probs=72.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEeeC
Q psy222           90 TRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECG  169 (225)
Q Consensus        90 ~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~~  169 (225)
                      .++|||+|||+.+++++|+++|+.| .|..|.|+.++ .++++|||||+|.+.++|++|| .||+..|+|+.|.|..+.+
T Consensus        16 ~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a~~   92 (109)
T 2dnn_A           16 DLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDH-VGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPATE   92 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCT-TCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECCH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECC-CCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCc
Confidence            4699999999999999999999999 89999999997 4999999999999999999999 5899999999999998865

>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=99.75  E-value=2e-18  Score=132.80  Aligned_cols=118  Identities=22%  Similarity=0.299  Sum_probs=91.9

Q ss_pred             CccccccccCccccCCCCCcccCcccHHHHHHHhccCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEe
Q psy222           44 YWYPYCITYDPIQAGSIDGTDTIPHDRAILRALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVV  123 (225)
Q Consensus        44 ~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~  123 (225)
                      .|+.|....++..+..+++..+....      +...+..........++|||+|||+.+++++|+++|++||.|..|.++
T Consensus        54 afV~f~~~~~A~~A~~~~~~~~~g~~------i~v~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~  127 (172)
T 2g4b_A           54 AFLEFRSVDETTQAMAFDGIIFQGQS------LKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLV  127 (172)
T ss_dssp             EEEEESSHHHHHHHGGGTTCEETTEE------CEEECCSSCCCCTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEE
T ss_pred             EEEEeCCHHHHHHHHHhCCcEecCce------eeecCCcccCCCCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEE
Confidence            46666655444444444444443321      111111122334457899999999999999999999999999999999


Q ss_pred             ecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEe
Q psy222          124 RDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFE  167 (225)
Q Consensus       124 ~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a  167 (225)
                      .++.++.++|||||+|.+.++|++|+..||+..|+|+.|.|++|
T Consensus       128 ~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A          128 KDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             ECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             ecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeC
Confidence            99889999999999999999999999999999999999999987

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.75  E-value=5.7e-18  Score=122.21  Aligned_cols=77  Identities=14%  Similarity=0.229  Sum_probs=71.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEee
Q psy222           89 PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFEC  168 (225)
Q Consensus        89 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~  168 (225)
                      ..++|||+|||+.+++++|+++|++||.|..|.|+.      .++||||+|.+.++|++||+.||+..|.|+.|.|.|+.
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            457999999999999999999999999999998874      47899999999999999999999999999999999998


Q ss_pred             CCC
Q psy222          169 GRV  171 (225)
Q Consensus       169 ~~~  171 (225)
                      ...
T Consensus        83 ~~~   85 (111)
T 1whx_A           83 IGV   85 (111)
T ss_dssp             TTT
T ss_pred             CCc
Confidence            644

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.74  E-value=2.2e-18  Score=126.54  Aligned_cols=80  Identities=13%  Similarity=0.145  Sum_probs=73.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCce----eEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEE
Q psy222           88 DPTRTLFIGRLNKNSREADLEQAFAEYGKV----ISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEII  163 (225)
Q Consensus        88 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v----~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~  163 (225)
                      .+.++|||+|||+++++++|+++|++||.|    ..|.|+.+. +++++|||||+|.+.++|++||+. |++.|.++.|.
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            456899999999999999999999999875    689999985 899999999999999999999995 99999999999


Q ss_pred             EEEeeC
Q psy222          164 VDFECG  169 (225)
Q Consensus       164 V~~a~~  169 (225)
                      |..+.+
T Consensus        99 V~~a~~  104 (123)
T 2dha_A           99 LFRSTA  104 (123)
T ss_dssp             CEEECH
T ss_pred             EEECCH
Confidence            998865

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A

Probab=99.74  E-value=5.3e-18  Score=128.57  Aligned_cols=81  Identities=27%  Similarity=0.547  Sum_probs=75.4

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      ....+.++|||+|||+.+++++|+++|++||.|..|.|+.+     ++|||||+|.+.++|++||..||+..|.|+.|+|
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            44566789999999999999999999999999999999876     4899999999999999999999999999999999


Q ss_pred             EEeeCC
Q psy222          165 DFECGR  170 (225)
Q Consensus       165 ~~a~~~  170 (225)
                      .++.++
T Consensus       143 ~~a~~~  148 (150)
T 2i2y_A          143 ELSNGE  148 (150)
T ss_dssp             EECCCC
T ss_pred             EEcCCC
Confidence            999875

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.74  E-value=6.6e-18  Score=118.35  Aligned_cols=81  Identities=20%  Similarity=0.216  Sum_probs=73.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEE-EEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISV-RVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD  165 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v-~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~  165 (225)
                      ....++|||+|||+.+++++|+++|++||.|..| .|+.++.++    .|||+|.+.++|++||..||+..|.|+.|+|.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~----~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~   87 (96)
T 2e44_A           12 RQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETA----VVNVTYSSKDQARQALDKLNGFQLENFTLKVA   87 (96)
T ss_dssp             CCSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSE----EEEEEESSHHHHHHHHHHHTTCBCSSCBCEEE
T ss_pred             CCCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCC----EEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            3456899999999999999999999999999999 588776443    39999999999999999999999999999999


Q ss_pred             EeeCCC
Q psy222          166 FECGRV  171 (225)
Q Consensus       166 ~a~~~~  171 (225)
                      ++.++.
T Consensus        88 ~a~~~~   93 (96)
T 2e44_A           88 YIPDEM   93 (96)
T ss_dssp             ECCCCC
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=99.74  E-value=6.6e-19  Score=132.56  Aligned_cols=84  Identities=25%  Similarity=0.399  Sum_probs=74.6

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEE--------EEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCc
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISV--------RVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQN  156 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v--------~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~  156 (225)
                      ....+.++|||+|||+.+++++|+++|++||.|..|        .+.   .+++.+|||||+|.+.++|++||..||+..
T Consensus        40 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~---~~g~~~g~afV~f~~~~~A~~Ai~~lng~~  116 (143)
T 3egn_A           40 EPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLM---KEGRMKGQAFIGLPNEKAAAKALKEANGYV  116 (143)
T ss_dssp             CCCSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEE---EETTTEEEEEEECSSHHHHHHHHHHHTTBE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEec---cCCCcccEEEEEeCCHHHHHHHHHHhCCCE
Confidence            346678999999999999999999999999998764        222   368899999999999999999999999999


Q ss_pred             cCCcEEEEEEeeCCC
Q psy222          157 FQGSEIIVDFECGRV  171 (225)
Q Consensus       157 l~g~~l~V~~a~~~~  171 (225)
                      |.|+.|+|.++++..
T Consensus       117 ~~g~~l~V~~a~~~~  131 (143)
T 3egn_A          117 LFGKPMVVQFARSAR  131 (143)
T ss_dssp             ETTEECEEEECCCSC
T ss_pred             eCCcEEEEEECCCCC
Confidence            999999999998643

>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=1.7e-17  Score=132.20  Aligned_cols=86  Identities=23%  Similarity=0.498  Sum_probs=81.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEe
Q psy222           88 DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFE  167 (225)
Q Consensus        88 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a  167 (225)
                      ...++|||+|||+.+++++|+++|++||.|..|.|+.++.+++++|||||+|.+.++|.+||..||+..|+|+.|+|.++
T Consensus       123 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a  202 (216)
T 2qfj_A          123 RAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA  202 (216)
T ss_dssp             TTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEEC
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEe
Confidence            45689999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             eCCCCC
Q psy222          168 CGRVLP  173 (225)
Q Consensus       168 ~~~~~~  173 (225)
                      .++..+
T Consensus       203 ~~~~~~  208 (216)
T 2qfj_A          203 VTPPMP  208 (216)
T ss_dssp             SSCSST
T ss_pred             cCCCCC
Confidence            886543

>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=99.74  E-value=2.2e-17  Score=126.06  Aligned_cols=82  Identities=29%  Similarity=0.450  Sum_probs=78.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEeeC
Q psy222           90 TRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECG  169 (225)
Q Consensus        90 ~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~~  169 (225)
                      .++|||+|||+.+++++|+++|+.||.|..|.++.++.++.++|||||+|.+.++|++|++.|++..|.|+.|.|.++.+
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~   81 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecCC
Confidence            57999999999999999999999999999999999988999999999999999999999999999999999999999876


Q ss_pred             CC
Q psy222          170 RV  171 (225)
Q Consensus       170 ~~  171 (225)
                      ..
T Consensus        82 ~~   83 (167)
T 1fxl_A           82 SS   83 (167)
T ss_dssp             CC
T ss_pred             Cc
Confidence            43

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.74  E-value=2.6e-17  Score=125.48  Aligned_cols=84  Identities=30%  Similarity=0.574  Sum_probs=79.7

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      ....+.++|||+|||+.+++++|+++|++||.|..+.++.+..++.++|||||+|.+.++|.+|+..||+..|+|+.|+|
T Consensus        82 ~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  161 (166)
T 3md3_A           82 SSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRI  161 (166)
T ss_dssp             CCCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Confidence            44566789999999999999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             EEee
Q psy222          165 DFEC  168 (225)
Q Consensus       165 ~~a~  168 (225)
                      .+|+
T Consensus       162 ~~a~  165 (166)
T 3md3_A          162 NWAA  165 (166)
T ss_dssp             EESC
T ss_pred             EecC
Confidence            9986

>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=99.73  E-value=1e-17  Score=121.01  Aligned_cols=81  Identities=20%  Similarity=0.281  Sum_probs=72.0

Q ss_pred             CCCCCCCeEEE--cCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCcc-----
Q psy222           85 SSTDPTRTLFI--GRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNF-----  157 (225)
Q Consensus        85 ~~~~~~~~l~V--~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l-----  157 (225)
                      ....++++|||  +||++.+++++|+++|++||.|..|.|+.+      +|||||+|.+.++|++|++.|||..|     
T Consensus        20 ~~~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~------rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg   93 (114)
T 2cq2_A           20 TVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEVVDDLG   93 (114)
T ss_dssp             CCSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEEECTTS
T ss_pred             CCCCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHhCCCEEccccC
Confidence            34557789999  779999999999999999999999988642      78999999999999999999999988     


Q ss_pred             CCcEEEEEEeeCCC
Q psy222          158 QGSEIIVDFECGRV  171 (225)
Q Consensus       158 ~g~~l~V~~a~~~~  171 (225)
                      .+++|.|.++...+
T Consensus        94 ~g~~l~v~~a~~~p  107 (114)
T 2cq2_A           94 QKITLYLNFVEKVQ  107 (114)
T ss_dssp             CEEECEEEEESCCC
T ss_pred             CCcEEEEEecccCc
Confidence            68899999998644

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.73  E-value=4.9e-18  Score=120.38  Aligned_cols=81  Identities=26%  Similarity=0.489  Sum_probs=76.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEe
Q psy222           88 DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFE  167 (225)
Q Consensus        88 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a  167 (225)
                      .+.++|||+|||+.+++++|+++|++||.|..|.|+.++ ++..+|||||+|.+.++|++||.  ++..|+|+.|.|.++
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~a   83 (102)
T 2xs2_A            7 IMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPA   83 (102)
T ss_dssp             EEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEEC
Confidence            355799999999999999999999999999999999998 99999999999999999999999  899999999999999


Q ss_pred             eCCC
Q psy222          168 CGRV  171 (225)
Q Consensus       168 ~~~~  171 (225)
                      ..+.
T Consensus        84 ~~~~   87 (102)
T 2xs2_A           84 IRKQ   87 (102)
T ss_dssp             EECC
T ss_pred             CcCc
Confidence            8654

>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=99.73  E-value=1.6e-17  Score=127.22  Aligned_cols=83  Identities=23%  Similarity=0.415  Sum_probs=78.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEee
Q psy222           89 PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFEC  168 (225)
Q Consensus        89 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~  168 (225)
                      +.++|||+|||+.+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|++|++.|++..|.|+.|.|.++.
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             CCC
Q psy222          169 GRV  171 (225)
Q Consensus       169 ~~~  171 (225)
                      +..
T Consensus        82 ~~~   84 (168)
T 1b7f_A           82 PGG   84 (168)
T ss_dssp             CCS
T ss_pred             CCc
Confidence            643

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A

Probab=99.73  E-value=5.1e-18  Score=125.03  Aligned_cols=81  Identities=11%  Similarity=0.148  Sum_probs=73.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCcee--EEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVI--SVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~--~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      ....++|||+|||+.+++++|+++|+.| .|.  .|.|+.++. |+++|||||+|.+.++|++||+. ++..|+|+.|.|
T Consensus        39 ~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~~-~~~~l~gR~I~V  115 (126)
T 2hgm_A           39 SANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALGK-HKERIGHRYIEV  115 (126)
T ss_dssp             SSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHTT-TTCCBTTBCCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHHH-CCCEECCEEEEE
Confidence            4456899999999999999999999999 577  899999985 99999999999999999999994 779999999999


Q ss_pred             EEeeCC
Q psy222          165 DFECGR  170 (225)
Q Consensus       165 ~~a~~~  170 (225)
                      ..+..+
T Consensus       116 ~~a~~~  121 (126)
T 2hgm_A          116 FKSSQE  121 (126)
T ss_dssp             EEECHH
T ss_pred             EECCHH
Confidence            988653

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.73  E-value=6.7e-18  Score=123.21  Aligned_cols=78  Identities=13%  Similarity=0.195  Sum_probs=71.4

Q ss_pred             CeEEEcCC----CCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCC----HHH----HHHHHH--HhCCCc
Q psy222           91 RTLFIGRL----NKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDC----EKA----CLAAIR--ALNRQN  156 (225)
Q Consensus        91 ~~l~V~nL----p~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~----~~~----a~~Al~--~l~g~~  156 (225)
                      ..|||+||    |+.+++.+|+.+|++||.|.+|.++.|+.||.++|||||+|.+    +++    |.+|+.  .|++..
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            58999999    9999999999999999999999999999999999999999996    333    888888  789999


Q ss_pred             cCCcEEEEEEee
Q psy222          157 FQGSEIIVDFEC  168 (225)
Q Consensus       157 l~g~~l~V~~a~  168 (225)
                      |+|+.|+|.+-+
T Consensus        83 I~Gr~irV~ln~   94 (136)
T 2j8a_A           83 IMGFKFEVILNK   94 (136)
T ss_dssp             ETTEEEEEEECC
T ss_pred             ecCcEEEEEECc
Confidence            999999999865

>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=99.73  E-value=1.4e-17  Score=115.07  Aligned_cols=76  Identities=17%  Similarity=0.330  Sum_probs=70.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEe
Q psy222           88 DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFE  167 (225)
Q Consensus        88 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a  167 (225)
                      ...++|||+|||+.+++++|+++|++| .|..|.|.      +.+|||||+|.+.++|++|++.||+..|.|+.|+|+++
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            356799999999999999999999999 99999884      46899999999999999999999999999999999998


Q ss_pred             eCC
Q psy222          168 CGR  170 (225)
Q Consensus       168 ~~~  170 (225)
                      ...
T Consensus        76 ~~~   78 (88)
T 1wg1_A           76 PTD   78 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            754

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.72  E-value=3.6e-17  Score=120.73  Aligned_cols=78  Identities=19%  Similarity=0.279  Sum_probs=70.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceE-EEEEeCCHHHHHHHHHHhCCCccCC--cEEEEEE
Q psy222           90 TRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRY-GFLEYDCEKACLAAIRALNRQNFQG--SEIIVDF  166 (225)
Q Consensus        90 ~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~-afV~F~~~~~a~~Al~~l~g~~l~g--~~l~V~~  166 (225)
                      --.|||+||++.+++++|+++|++||.|.+|.|+...     +|| |||+|.+.++|++|++.|||..|.+  +.|+|+|
T Consensus        28 VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~-----~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~  102 (130)
T 3zzy_A           28 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN-----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF  102 (130)
T ss_dssp             EEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEET-----TEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEE
T ss_pred             eEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCC-----CCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEe
Confidence            3478899999999999999999999999999888642     678 9999999999999999999999988  8999999


Q ss_pred             eeCCCC
Q psy222          167 ECGRVL  172 (225)
Q Consensus       167 a~~~~~  172 (225)
                      +++...
T Consensus       103 ak~~~l  108 (130)
T 3zzy_A          103 SKLTSL  108 (130)
T ss_dssp             CSCSSC
T ss_pred             cCCCce
Confidence            987543

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.72  E-value=4.2e-17  Score=128.19  Aligned_cols=84  Identities=26%  Similarity=0.404  Sum_probs=80.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEe
Q psy222           88 DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFE  167 (225)
Q Consensus        88 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a  167 (225)
                      .+.++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++|++.||+..|+|+.|.|.++
T Consensus       112 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  191 (198)
T 2yh0_A          112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  191 (198)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            56789999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             eCCC
Q psy222          168 CGRV  171 (225)
Q Consensus       168 ~~~~  171 (225)
                      .++.
T Consensus       192 ~~~~  195 (198)
T 2yh0_A          192 SVGA  195 (198)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8754

>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=99.72  E-value=3.6e-17  Score=125.14  Aligned_cols=78  Identities=18%  Similarity=0.220  Sum_probs=71.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCC--cEEEEEEe
Q psy222           90 TRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQG--SEIIVDFE  167 (225)
Q Consensus        90 ~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g--~~l~V~~a  167 (225)
                      ..+|||+||++.+++++|+++|++||.|.+|.|....    .++||||+|.+.++|++|++.|||..|.+  +.|+|+++
T Consensus        46 vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~----~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~A  121 (164)
T 1sjr_A           46 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS  121 (164)
T ss_dssp             EEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESS----SCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEEC
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCC----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEe
Confidence            4578999999999999999999999999999987542    57899999999999999999999999965  99999999


Q ss_pred             eCCC
Q psy222          168 CGRV  171 (225)
Q Consensus       168 ~~~~  171 (225)
                      +++.
T Consensus       122 k~~~  125 (164)
T 1sjr_A          122 KLTS  125 (164)
T ss_dssp             SSSS
T ss_pred             cCCc
Confidence            9764

>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=99.72  E-value=1.4e-17  Score=127.56  Aligned_cols=83  Identities=23%  Similarity=0.462  Sum_probs=77.7

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCC--cEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQG--SEI  162 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g--~~l  162 (225)
                      ....+.++|||+|||..+++++|+++|++||.|..+.++.+..++.++|||||+|.+.++|.+|+..||+..|.|  ++|
T Consensus        84 ~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l  163 (168)
T 1b7f_A           84 GESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPL  163 (168)
T ss_dssp             SSTTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCC
T ss_pred             cccCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEE
Confidence            344567899999999999999999999999999999999998899999999999999999999999999999988  999


Q ss_pred             EEEEe
Q psy222          163 IVDFE  167 (225)
Q Consensus       163 ~V~~a  167 (225)
                      +|.+|
T Consensus       164 ~V~~A  168 (168)
T 1b7f_A          164 SVRLA  168 (168)
T ss_dssp             EEEEC
T ss_pred             EEEeC
Confidence            99986

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=4.1e-17  Score=112.80  Aligned_cols=75  Identities=24%  Similarity=0.357  Sum_probs=66.9

Q ss_pred             CCCCCe-EEEcCCCCCCCHHH----HHHHHhcC-CceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCc
Q psy222           87 TDPTRT-LFIGRLNKNSREAD----LEQAFAEY-GKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGS  160 (225)
Q Consensus        87 ~~~~~~-l~V~nLp~~~te~~----L~~~F~~~-G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~  160 (225)
                      .++..+ |||+|||+.+++++    |+++|++| |.|.+|       ++   |+|||.|.+.++|++|++.|+|..|.|+
T Consensus         5 ~~p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr   74 (96)
T 2diu_A            5 SSGCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRMENEDVFGN   74 (96)
T ss_dssp             CCCSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSS
T ss_pred             CCCcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcCCccCCc
Confidence            345667 99999999999988    55899999 599988       33   9999999999999999999999999999


Q ss_pred             EEEEEEeeCCC
Q psy222          161 EIIVDFECGRV  171 (225)
Q Consensus       161 ~l~V~~a~~~~  171 (225)
                      +|+|.+|+.+.
T Consensus        75 ~i~v~~A~~~s   85 (96)
T 2diu_A           75 RIIVSFTPKNR   85 (96)
T ss_dssp             CCEEESSCCSC
T ss_pred             eEEEEecCCCc
Confidence            99999998754

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.71  E-value=4e-17  Score=130.66  Aligned_cols=81  Identities=27%  Similarity=0.448  Sum_probs=75.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEee
Q psy222           89 PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFEC  168 (225)
Q Consensus        89 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~  168 (225)
                      ...+|||+|||+.+++++|+++|++||.|..|+|+++.  +..+|||||+|.+.++|++||+.||+..|+|+.|+|.++.
T Consensus       102 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~--~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~  179 (213)
T 4f02_A          102 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK  179 (213)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             ccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccC--CCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            45689999999999999999999999999999999884  5579999999999999999999999999999999999998


Q ss_pred             CCC
Q psy222          169 GRV  171 (225)
Q Consensus       169 ~~~  171 (225)
                      ++.
T Consensus       180 ~~~  182 (213)
T 4f02_A          180 SRK  182 (213)
T ss_dssp             CHH
T ss_pred             CCc
Confidence            643

>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=99.71  E-value=2e-17  Score=126.63  Aligned_cols=81  Identities=25%  Similarity=0.481  Sum_probs=77.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEee
Q psy222           89 PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFEC  168 (225)
Q Consensus        89 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~  168 (225)
                      +.++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|.+|++ +++..|.|+.|.|.++.
T Consensus        86 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a~  164 (167)
T 2cjk_A           86 KTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAE  164 (167)
T ss_dssp             HCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEECC
T ss_pred             CCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeecC
Confidence            35689999999999999999999999999999999998899999999999999999999998 89999999999999998


Q ss_pred             CC
Q psy222          169 GR  170 (225)
Q Consensus       169 ~~  170 (225)
                      ++
T Consensus       165 pk  166 (167)
T 2cjk_A          165 PR  166 (167)
T ss_dssp             CC
T ss_pred             CC
Confidence            75

>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=99.70  E-value=6e-17  Score=127.11  Aligned_cols=85  Identities=26%  Similarity=0.432  Sum_probs=78.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q psy222           86 STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD  165 (225)
Q Consensus        86 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~  165 (225)
                      ...+.++|||+|||+++++++|+++|+.||.|..|.|+.++.++.++|||||+|.+.++|++||.. ++..|.|+.|.|.
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            345678999999999999999999999999999999999988999999999999999999999985 8999999999999


Q ss_pred             EeeCCC
Q psy222          166 FECGRV  171 (225)
Q Consensus       166 ~a~~~~  171 (225)
                      ++..+.
T Consensus        88 ~~~~~~   93 (196)
T 1l3k_A           88 RAVSRE   93 (196)
T ss_dssp             ECCC--
T ss_pred             cccCcc
Confidence            987643

>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=114.57  Aligned_cols=78  Identities=15%  Similarity=0.334  Sum_probs=66.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEe
Q psy222           88 DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFE  167 (225)
Q Consensus        88 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a  167 (225)
                      .+.++|||+|||+.+++++|+++|++||.|..|.|+.+     ++|||||+|.+.++|++|+..  ...+.++.|.|.++
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            45689999999999999999999999999999999865     589999999999999865331  33468999999998


Q ss_pred             eCCCC
Q psy222          168 CGRVL  172 (225)
Q Consensus       168 ~~~~~  172 (225)
                      .++..
T Consensus        76 ~~~~~   80 (88)
T 1wf0_A           76 EPKHN   80 (88)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87653

>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=99.70  E-value=5.4e-17  Score=112.46  Aligned_cols=77  Identities=18%  Similarity=0.421  Sum_probs=63.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCc--cCCcEEE
Q psy222           86 STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQN--FQGSEII  163 (225)
Q Consensus        86 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~--l~g~~l~  163 (225)
                      ...+..+|||+|||+++++++|+++|++||.|..|.|+++     ++|||||+|.+.++|++    |++..  +.++.|.
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            3557789999999999999999999999999999999875     68999999999999883    45655  5699999


Q ss_pred             EEEeeCCC
Q psy222          164 VDFECGRV  171 (225)
Q Consensus       164 V~~a~~~~  171 (225)
                      |.++.++.
T Consensus        78 v~~a~~k~   85 (89)
T 3d2w_A           78 ISNAEPKH   85 (89)
T ss_dssp             EEECC---
T ss_pred             EEEcCCCC
Confidence            99998754

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.70  E-value=1e-16  Score=117.59  Aligned_cols=75  Identities=16%  Similarity=0.141  Sum_probs=67.7

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceE-EEEEeCCHHHHHHHHHHhCCCccCC--cEEEEEEee
Q psy222           92 TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRY-GFLEYDCEKACLAAIRALNRQNFQG--SEIIVDFEC  168 (225)
Q Consensus        92 ~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~-afV~F~~~~~a~~Al~~l~g~~l~g--~~l~V~~a~  168 (225)
                      .|||+||++.+++++|+++|++||.|..|.|+. +     .|| |||+|.+.++|+.|++.|||..|.|  +.|+|.+|+
T Consensus        27 ~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~-~-----~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~Ak  100 (124)
T 2e5i_A           27 LLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFK-R-----NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYAR  100 (124)
T ss_dssp             EEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEE-S-----SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCS
T ss_pred             EEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEe-C-----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEec
Confidence            468999999999999999999999999999875 2     276 9999999999999999999999987  699999998


Q ss_pred             CCCC
Q psy222          169 GRVL  172 (225)
Q Consensus       169 ~~~~  172 (225)
                      ++..
T Consensus       101 ~~~l  104 (124)
T 2e5i_A          101 PTRL  104 (124)
T ss_dssp             CSCC
T ss_pred             CCcc
Confidence            7653

>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=99.70  E-value=2.2e-17  Score=126.03  Aligned_cols=81  Identities=35%  Similarity=0.585  Sum_probs=75.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcE--EEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSE--IIV  164 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~--l~V  164 (225)
                      ....++|||+|||+.+++++|+++|++||.|..+.++.+..++.++|||||+|.+.++|.+|++.||+..|.|+.  |.|
T Consensus        85 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v  164 (167)
T 1fxl_A           85 SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITV  164 (167)
T ss_dssp             GGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEE
T ss_pred             cCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEE
Confidence            445689999999999999999999999999999999999889999999999999999999999999999999965  888


Q ss_pred             EEe
Q psy222          165 DFE  167 (225)
Q Consensus       165 ~~a  167 (225)
                      .||
T Consensus       165 ~~A  167 (167)
T 1fxl_A          165 KFA  167 (167)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            775

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.70  E-value=1e-16  Score=116.07  Aligned_cols=79  Identities=22%  Similarity=0.311  Sum_probs=67.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCC---CccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVT---GHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEII  163 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~---g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~  163 (225)
                      ....++|||+|||+.+++++|+++|++||.|. +.++.+..+   |+++|||||+|.+.++|++||+.|+  .++|+.|.
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            34568999999999999999999999999999 888888766   7999999999999999999999883  36666666


Q ss_pred             EEEee
Q psy222          164 VDFEC  168 (225)
Q Consensus       164 V~~a~  168 (225)
                      +..+.
T Consensus        82 ~~~~~   86 (114)
T 2dnl_A           82 CVSSP   86 (114)
T ss_dssp             EECCS
T ss_pred             eccCC
Confidence            65443

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A

Probab=99.69  E-value=8e-17  Score=128.42  Aligned_cols=79  Identities=19%  Similarity=0.177  Sum_probs=73.1

Q ss_pred             CCCCeEEEcCCC-CCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEE
Q psy222           88 DPTRTLFIGRLN-KNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF  166 (225)
Q Consensus        88 ~~~~~l~V~nLp-~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~  166 (225)
                      .+.++|||+||| +.+++++|+++|++||.|.+|+|+.++     +|||||+|.+.++|++||+.|||..|.|+.|+|.+
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            357899999999 899999999999999999999998763     79999999999999999999999999999999999


Q ss_pred             eeCCC
Q psy222          167 ECGRV  171 (225)
Q Consensus       167 a~~~~  171 (225)
                      ++...
T Consensus        77 s~~~~   81 (205)
T 3tyt_A           77 SKQPA   81 (205)
T ss_dssp             CSCSC
T ss_pred             ccCCc
Confidence            97543

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.69  E-value=1.3e-16  Score=121.66  Aligned_cols=80  Identities=23%  Similarity=0.436  Sum_probs=74.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEeeCC
Q psy222           91 RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECGR  170 (225)
Q Consensus        91 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~~~  170 (225)
                      ++|||+|||+.+++++|+++|++||.|..|.|+.++ +++.+|||||+|.+.++|++|++.|++..|.|+.|.|.++.+.
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            589999999999999999999999999999999987 5778999999999999999999999999999999999998764


Q ss_pred             C
Q psy222          171 V  171 (225)
Q Consensus       171 ~  171 (225)
                      .
T Consensus        80 ~   80 (166)
T 3md3_A           80 Q   80 (166)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.69  E-value=6e-17  Score=111.20  Aligned_cols=72  Identities=25%  Similarity=0.476  Sum_probs=66.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcC----C-------ceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCc
Q psy222           88 DPTRTLFIGRLNKNSREADLEQAFAEY----G-------KVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQN  156 (225)
Q Consensus        88 ~~~~~l~V~nLp~~~te~~L~~~F~~~----G-------~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~  156 (225)
                      .+.++|||+|||+.+++++|+++|++|    |       .|..+.+..+      +|||||+|.+.++|++|+ .||+..
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~-~l~g~~   76 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAM-AFDGII   76 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHG-GGTTCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHH-hcCCCE
Confidence            456899999999999999999999999    8       8999998754      799999999999999999 899999


Q ss_pred             cCCcEEEEEE
Q psy222          157 FQGSEIIVDF  166 (225)
Q Consensus       157 l~g~~l~V~~  166 (225)
                      |.|+.|+|+.
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            9999999873

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.68  E-value=1.1e-16  Score=127.48  Aligned_cols=82  Identities=26%  Similarity=0.403  Sum_probs=74.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEee
Q psy222           89 PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFEC  168 (225)
Q Consensus        89 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~  168 (225)
                      +.++|||+|||+++++++|+++|+.||.|..|.|++++.++..+|||||+|.+.++|++||+.|++..|.|+.|.|.++.
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            35699999999999999999999999999999999998899999999999999999999999999999999999998876


Q ss_pred             CC
Q psy222          169 GR  170 (225)
Q Consensus       169 ~~  170 (225)
                      ..
T Consensus       107 ~~  108 (216)
T 2qfj_A          107 NI  108 (216)
T ss_dssp             CC
T ss_pred             Cc
Confidence            43

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.67  E-value=5.5e-16  Score=110.67  Aligned_cols=83  Identities=19%  Similarity=0.253  Sum_probs=73.5

Q ss_pred             CCCCCeEEEcCCCC-----CCCHHHHHHHHhcCCceeEEEEeecCCC-CccceEEEEEeCCHHHHHHHHHHhCCCccCCc
Q psy222           87 TDPTRTLFIGRLNK-----NSREADLEQAFAEYGKVISVRVVRDFVT-GHSKRYGFLEYDCEKACLAAIRALNRQNFQGS  160 (225)
Q Consensus        87 ~~~~~~l~V~nLp~-----~~te~~L~~~F~~~G~v~~v~i~~~~~~-g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~  160 (225)
                      ..++++|+|.||..     +-++++|+++|++||.|.+|.|+.++.+ ++++||+||+|.+.++|.+|+..|||..|+|+
T Consensus         5 ~~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr   84 (105)
T 2pe8_A            5 KCPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGR   84 (105)
T ss_dssp             GSCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCc
Confidence            34678999999963     2378999999999999999999988644 67899999999999999999999999999999


Q ss_pred             EEEEEEeeC
Q psy222          161 EIIVDFECG  169 (225)
Q Consensus       161 ~l~V~~a~~  169 (225)
                      .|+|.++.+
T Consensus        85 ~i~v~~a~~   93 (105)
T 2pe8_A           85 VVKACFYNL   93 (105)
T ss_dssp             ECEEEECCH
T ss_pred             EEEEEEcCH
Confidence            999999875

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=99.67  E-value=3.4e-16  Score=120.36  Aligned_cols=81  Identities=26%  Similarity=0.501  Sum_probs=74.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccC---CcEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQ---GSEII  163 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~---g~~l~  163 (225)
                      ..+.++|||+|||+.+++++|+++|++||.|..|.++.+. ++.++|||||+|.+.++|.+|++.||+..+.   +++|+
T Consensus        92 ~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~  170 (175)
T 3nmr_A           92 AVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMV  170 (175)
T ss_dssp             CGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCE
T ss_pred             cCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECC-CCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeE
Confidence            3467899999999999999999999999999999999986 6899999999999999999999999998776   39999


Q ss_pred             EEEee
Q psy222          164 VDFEC  168 (225)
Q Consensus       164 V~~a~  168 (225)
                      |.||.
T Consensus       171 V~~ad  175 (175)
T 3nmr_A          171 VKFAD  175 (175)
T ss_dssp             EEECC
T ss_pred             EEecC
Confidence            99973

>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=99.66  E-value=5e-16  Score=119.46  Aligned_cols=83  Identities=27%  Similarity=0.391  Sum_probs=74.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCC--ccceEEEEEeCCHHHHHHHHHHhCCCccC---CcEEE
Q psy222           89 PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTG--HSKRYGFLEYDCEKACLAAIRALNRQNFQ---GSEII  163 (225)
Q Consensus        89 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g--~~kg~afV~F~~~~~a~~Al~~l~g~~l~---g~~l~  163 (225)
                      +.++|||+|||+.+++++|+++|++||.|..|.|++++.++  +++|||||+|.+.++|++|++.|++..+.   ++.+.
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            46799999999999999999999999999999999998776  89999999999999999999999998775   57788


Q ss_pred             EEEeeCCC
Q psy222          164 VDFECGRV  171 (225)
Q Consensus       164 V~~a~~~~  171 (225)
                      |.++....
T Consensus        82 ~~~~~~~~   89 (175)
T 3nmr_A           82 MKPADSEK   89 (175)
T ss_dssp             EEECGGGC
T ss_pred             Eccccccc
Confidence            88876543

>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=99.65  E-value=7.8e-16  Score=127.79  Aligned_cols=83  Identities=18%  Similarity=0.422  Sum_probs=76.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHH----HHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcE
Q psy222           86 STDPTRTLFIGRLNKNSREADLE----QAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSE  161 (225)
Q Consensus        86 ~~~~~~~l~V~nLp~~~te~~L~----~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~  161 (225)
                      ...+.++|||+|||+.+++++|+    ++|++||.|..|.|++   +++.+|||||+|.+.++|++||+.||+..|.|+.
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            35678899999999999999976    8999999999999885   6778999999999999999999999999999999


Q ss_pred             EEEEEeeCCC
Q psy222          162 IIVDFECGRV  171 (225)
Q Consensus       162 l~V~~a~~~~  171 (225)
                      |+|.++....
T Consensus        82 l~v~~a~~~~   91 (282)
T 3pgw_A           82 MRIQYAKTDS   91 (282)
T ss_pred             EEEEEeccCc
Confidence            9999997644

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A

Probab=99.65  E-value=6.5e-16  Score=122.04  Aligned_cols=78  Identities=14%  Similarity=0.340  Sum_probs=72.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEeeC
Q psy222           90 TRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECG  169 (225)
Q Consensus        90 ~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~~  169 (225)
                      .++|||+|||+.+++++|+++|++||.|..|.|+++. ++..+|||||+|.+.++|++||..+ +..|+|+.|.|.++..
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~-~~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~Gr~l~V~~~~~  186 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKDD  186 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESSHHHHHHHHHCT-TCEETTEECEEEETTT
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHhC-CCeECCEEEEEEEhHH
Confidence            4799999999999999999999999999999999986 6889999999999999999999865 5699999999998765

>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=3.9e-16  Score=120.47  Aligned_cols=80  Identities=19%  Similarity=0.312  Sum_probs=73.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q psy222           86 STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD  165 (225)
Q Consensus        86 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~  165 (225)
                      ...+.++|||+|||+.+++++|+++|++||.|..+     ..++..+|||||+|.+.++|.+||..||+..|.|+.|+|.
T Consensus        95 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  169 (175)
T 1fje_B           95 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLY  169 (175)
T ss_dssp             TTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-----CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEE
T ss_pred             ccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-----cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            34466899999999999999999999999988766     3578899999999999999999999999999999999999


Q ss_pred             EeeCC
Q psy222          166 FECGR  170 (225)
Q Consensus       166 ~a~~~  170 (225)
                      ++.++
T Consensus       170 ~a~~k  174 (175)
T 1fje_B          170 YTGEK  174 (175)
T ss_dssp             ECSSC
T ss_pred             ecCCC
Confidence            99875

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.65  E-value=3.5e-16  Score=127.04  Aligned_cols=80  Identities=20%  Similarity=0.417  Sum_probs=71.4

Q ss_pred             CCCCCeEEEcCCCCCC---------CHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCcc
Q psy222           87 TDPTRTLFIGRLNKNS---------READLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNF  157 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~---------te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l  157 (225)
                      ....++|||+||+..+         ++++|+.+|++||.|..|.|+..      +|||||+|.+.++|+.|++.|++..|
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~------kG~AFV~F~~~~~Ae~A~~am~g~~l  204 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES------KNCGFVKFKYQANAEFAKEAMSNQTL  204 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHHHTTCCC
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECC------CCEEEEEeCCHHHHHHHHHHhCCCEE
Confidence            4567899999999998         79999999999999999999854      79999999999999999999999999


Q ss_pred             ------------CCcEEEEEEeeCCCC
Q psy222          158 ------------QGSEIIVDFECGRVL  172 (225)
Q Consensus       158 ------------~g~~l~V~~a~~~~~  172 (225)
                                  .|+.|.|.||+..+.
T Consensus       205 ~~~~~~e~~~~~~gr~L~V~wA~~~pn  231 (240)
T 3u1l_A          205 LLPSDKEWDDRREGTGLLVKWANEDPD  231 (240)
T ss_dssp             CCTTSTTGGGGGGSCCCEEEECC----
T ss_pred             eccccccccccCCCCEEEEEEccCCCC
Confidence                        899999999987543

>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=99.64  E-value=2.8e-16  Score=120.15  Aligned_cols=79  Identities=25%  Similarity=0.508  Sum_probs=73.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEee
Q psy222           89 PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFEC  168 (225)
Q Consensus        89 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~  168 (225)
                      +.++|||+|||+++++++|+++|++||.|..|.|++++.++.++|||||+|.+.++|++||..  +..|.|+.|.|.++.
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            467999999999999999999999999999999999988999999999999999999999994  678999999998876


Q ss_pred             C
Q psy222          169 G  169 (225)
Q Consensus       169 ~  169 (225)
                      +
T Consensus        80 ~   80 (167)
T 2cjk_A           80 P   80 (167)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.62  E-value=8.7e-16  Score=124.15  Aligned_cols=81  Identities=19%  Similarity=0.273  Sum_probs=75.4

Q ss_pred             CCCCCCCeEEEcCCCC-CCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEE
Q psy222           85 SSTDPTRTLFIGRLNK-NSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEII  163 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~-~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~  163 (225)
                      ....+.++|||+|||+ .+++++|+++|++||.|..|.|+.++     +|||||+|.+.++|++||+.|++..|.|+.|.
T Consensus        29 ~~~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~  103 (229)
T 2adc_A           29 LAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIR  103 (229)
T ss_dssp             GGCCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCE
T ss_pred             CCCCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEE
Confidence            4456789999999999 99999999999999999999999875     78999999999999999999999999999999


Q ss_pred             EEEeeCC
Q psy222          164 VDFECGR  170 (225)
Q Consensus       164 V~~a~~~  170 (225)
                      |.++...
T Consensus       104 v~~a~~~  110 (229)
T 2adc_A          104 ITLSKHQ  110 (229)
T ss_dssp             EECCSCC
T ss_pred             EEEecCc
Confidence            9999865

>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=99.62  E-value=9.2e-16  Score=127.96  Aligned_cols=83  Identities=18%  Similarity=0.306  Sum_probs=76.5

Q ss_pred             CCCCCeEEEcCCCCC-CCHHHHHHHHhcCCceeEEEEeecCC-CCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           87 TDPTRTLFIGRLNKN-SREADLEQAFAEYGKVISVRVVRDFV-TGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~-~te~~L~~~F~~~G~v~~v~i~~~~~-~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      ..+.++|||+|||+. +++++|+++|+.||.|..|.|+.+.. |+.++|||||+|.+.++|.+|| .||+..|.|+.|.|
T Consensus       207 ~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~~i~V  285 (292)
T 2ghp_A          207 TLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISV  285 (292)
T ss_dssp             CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEEEE
T ss_pred             CCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-HhcCCEECCcEEEE
Confidence            456789999999999 99999999999999999999998875 5899999999999999999999 99999999999999


Q ss_pred             EEeeCC
Q psy222          165 DFECGR  170 (225)
Q Consensus       165 ~~a~~~  170 (225)
                      .++.++
T Consensus       286 ~~a~~k  291 (292)
T 2ghp_A          286 SLADKK  291 (292)
T ss_dssp             EECCCC
T ss_pred             EEecCC
Confidence            999875

>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=99.62  E-value=5.1e-15  Score=106.72  Aligned_cols=82  Identities=16%  Similarity=0.226  Sum_probs=70.5

Q ss_pred             CCCCCCeEEEcCCCCCCC-----------HHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCC
Q psy222           86 STDPTRTLFIGRLNKNSR-----------EADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNR  154 (225)
Q Consensus        86 ~~~~~~~l~V~nLp~~~t-----------e~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g  154 (225)
                      ...+.++|+|.||.....           +++|+++|++||.|..|.| .++   ..+|||||+|.+.++|++|+..||+
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            345788999999944432           5799999999999999966 443   3799999999999999999999999


Q ss_pred             CccCCcEEEEEEeeCCC
Q psy222          155 QNFQGSEIIVDFECGRV  171 (225)
Q Consensus       155 ~~l~g~~l~V~~a~~~~  171 (225)
                      ..|+|+.|+|.++.++.
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

>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=99.62  E-value=2.5e-15  Score=124.76  Aligned_cols=78  Identities=24%  Similarity=0.356  Sum_probs=72.6

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccC-CcEEEE
Q psy222           86 STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQ-GSEIIV  164 (225)
Q Consensus        86 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~-g~~l~V  164 (225)
                      ...+.++|||+|||..+++++|+++|++||.|..|.|+.++     +|||||+|.+.++|++||..||+..|. |+.|+|
T Consensus       203 ~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v  277 (282)
T 3pgw_A          203 ENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKI  277 (282)
T ss_pred             CCCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC-----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEE
Confidence            44567899999999999999999999999999999999664     689999999999999999999999999 999999


Q ss_pred             EEee
Q psy222          165 DFEC  168 (225)
Q Consensus       165 ~~a~  168 (225)
                      .|++
T Consensus       278 ~~ak  281 (282)
T 3pgw_A          278 SFAK  281 (282)
T ss_pred             EEec
Confidence            9986

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=99.61  E-value=4.7e-15  Score=123.15  Aligned_cols=84  Identities=20%  Similarity=0.257  Sum_probs=79.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEe
Q psy222           88 DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFE  167 (225)
Q Consensus        88 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a  167 (225)
                      ...++|||+|||+.+++++|+++|+.||.|..|.++.+..++.++|||||+|.+.++|.+|+..|++..|.|+.|.|.++
T Consensus        93 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a  172 (284)
T 3smz_A           93 PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWT  172 (284)
T ss_dssp             CCSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEC
Confidence            35679999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             eCCC
Q psy222          168 CGRV  171 (225)
Q Consensus       168 ~~~~  171 (225)
                      .+..
T Consensus       173 ~~~~  176 (284)
T 3smz_A          173 DAGQ  176 (284)
T ss_dssp             CGGG
T ss_pred             CCCC
Confidence            8654

>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=99.60  E-value=4e-15  Score=123.60  Aligned_cols=85  Identities=19%  Similarity=0.210  Sum_probs=79.2

Q ss_pred             CCCCCCeEEEcCCCCCC-CHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           86 STDPTRTLFIGRLNKNS-READLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        86 ~~~~~~~l~V~nLp~~~-te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      ...+.++|||+|||+.+ ++++|+++|+.||.|..|.|+.+. ++.++|||||+|.+.++|.+|+..||+..|.|+.|+|
T Consensus       180 ~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v  258 (284)
T 3smz_A          180 ALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRV  258 (284)
T ss_dssp             TTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECS-SCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             ccCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECC-CCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEE
Confidence            34567899999999995 999999999999999999999986 8999999999999999999999999999999999999


Q ss_pred             EEeeCCC
Q psy222          165 DFECGRV  171 (225)
Q Consensus       165 ~~a~~~~  171 (225)
                      .++.++.
T Consensus       259 ~~a~~~~  265 (284)
T 3smz_A          259 SFCAPGP  265 (284)
T ss_dssp             EECCSSS
T ss_pred             EEecCCC
Confidence            9998754

>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=99.59  E-value=2.5e-15  Score=119.70  Aligned_cols=78  Identities=19%  Similarity=0.274  Sum_probs=70.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCce--eEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCc----E
Q psy222           88 DPTRTLFIGRLNKNSREADLEQAFAEYGKV--ISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGS----E  161 (225)
Q Consensus        88 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v--~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~----~  161 (225)
                      .+.++|||+|||+.+++++|+++|++||.|  ..|+++.++  +..+|||||+|.+.++|.+||..||+..|.+.    +
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            467899999999999999999999999999  899998774  55579999999999999999999999999886    6


Q ss_pred             EEEEEe
Q psy222          162 IIVDFE  167 (225)
Q Consensus       162 l~V~~a  167 (225)
                      +.|+++
T Consensus       199 ~~vk~~  204 (205)
T 3tyt_A          199 YTLKLC  204 (205)
T ss_dssp             EECEEE
T ss_pred             eEEEec
Confidence            777775

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.58  E-value=2.2e-15  Score=118.61  Aligned_cols=77  Identities=19%  Similarity=0.295  Sum_probs=72.3

Q ss_pred             CCeEEEcCCCC-CCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEee
Q psy222           90 TRTLFIGRLNK-NSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFEC  168 (225)
Q Consensus        90 ~~~l~V~nLp~-~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~  168 (225)
                      .++|||+|||+ .+++++|+++|++||.|..|.|+.++     +|||||+|.+.++|++|+..||+..|.|+.|.|.++.
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~   77 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   77 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECC
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEec
Confidence            57999999999 99999999999999999999998774     7899999999999999999999999999999999998


Q ss_pred             CCC
Q psy222          169 GRV  171 (225)
Q Consensus       169 ~~~  171 (225)
                      ...
T Consensus        78 ~~~   80 (198)
T 1qm9_A           78 HQN   80 (198)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            643

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.58  E-value=4.5e-15  Score=116.85  Aligned_cols=79  Identities=16%  Similarity=0.325  Sum_probs=72.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCC-ceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccC-CcEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYG-KVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQ-GSEIIV  164 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G-~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~-g~~l~V  164 (225)
                      ..+.++|||+|||+.+++++|+++|+.|| .|..|.|+.+.     +|||||+|.+.++|.+|+..||+..|. |+.|+|
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            35678999999999999999999999999 99999997642     789999999999999999999999999 999999


Q ss_pred             EEeeCC
Q psy222          165 DFECGR  170 (225)
Q Consensus       165 ~~a~~~  170 (225)
                      .|++++
T Consensus       192 ~~a~~~  197 (198)
T 1qm9_A          192 SFSKST  197 (198)
T ss_dssp             EEECCC
T ss_pred             Eeeccc
Confidence            999864

>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=99.58  E-value=8.3e-15  Score=118.35  Aligned_cols=79  Identities=16%  Similarity=0.346  Sum_probs=72.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCC-ceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccC-CcEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYG-KVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQ-GSEIIV  164 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G-~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~-g~~l~V  164 (225)
                      ..+.++|||+|||+.+++++|+++|++|| .|..|.|+.+     .+|||||+|.+.++|.+||..||+..|. |+.|+|
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            34578999999999999999999999999 9999999753     3789999999999999999999999999 999999


Q ss_pred             EEeeCC
Q psy222          165 DFECGR  170 (225)
Q Consensus       165 ~~a~~~  170 (225)
                      .|++++
T Consensus       223 ~~a~~~  228 (229)
T 2adc_A          223 SFSKST  228 (229)
T ss_dssp             EECSSC
T ss_pred             EEecCC
Confidence            999864

>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=99.58  E-value=6.2e-15  Score=121.44  Aligned_cols=79  Identities=22%  Similarity=0.420  Sum_probs=72.5

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      ....+.++|||+|||+++++++|+++|+.||.|..|.|.++      +|||||+|.+.++|.+||..|++..|.|+.|.|
T Consensus        17 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v   90 (261)
T 3sde_A           17 KTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAELDGTILKSRPLRI   90 (261)
T ss_dssp             CSSCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CcEEEEEECCHHHHHHHHHHcCCcEECCceeEe
Confidence            34456689999999999999999999999999999999754      789999999999999999999999999999999


Q ss_pred             EEeeC
Q psy222          165 DFECG  169 (225)
Q Consensus       165 ~~a~~  169 (225)
                      .++.+
T Consensus        91 ~~a~~   95 (261)
T 3sde_A           91 RFATH   95 (261)
T ss_dssp             EECCC
T ss_pred             eeccc
Confidence            99865

>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=99.57  E-value=7e-16  Score=119.04  Aligned_cols=84  Identities=27%  Similarity=0.418  Sum_probs=73.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q psy222           86 STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD  165 (225)
Q Consensus        86 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~  165 (225)
                      ...+.++|||+|||+.+++++|+++|..||.+.. .++.+..++..+|||||+|.+.++|++||+ ||+..|.|+.|.|.
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~-~~~~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~v~   86 (175)
T 1fje_B            9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLE   86 (175)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEEECCCCccccEEEEEECCHHHHHHHHh-cCCCEeCCeEEEEe
Confidence            4557789999999999999999999999998766 333444578889999999999999999995 99999999999999


Q ss_pred             EeeCCC
Q psy222          166 FECGRV  171 (225)
Q Consensus       166 ~a~~~~  171 (225)
                      ++.++.
T Consensus        87 ~~~~~~   92 (175)
T 1fje_B           87 KPKGRD   92 (175)
T ss_dssp             CCCCSS
T ss_pred             cCCCcc
Confidence            988643

>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=99.55  E-value=1.9e-14  Score=102.61  Aligned_cols=82  Identities=18%  Similarity=0.288  Sum_probs=71.3

Q ss_pred             CCCCeEEEcCC--CCCCC--------HHHHHHHHhcCCceeEEEEeecCCC--CccceEEEEEeCCHHHHHHHHHHhCCC
Q psy222           88 DPTRTLFIGRL--NKNSR--------EADLEQAFAEYGKVISVRVVRDFVT--GHSKRYGFLEYDCEKACLAAIRALNRQ  155 (225)
Q Consensus        88 ~~~~~l~V~nL--p~~~t--------e~~L~~~F~~~G~v~~v~i~~~~~~--g~~kg~afV~F~~~~~a~~Al~~l~g~  155 (225)
                      .+++.|.|.|+  |..+.        +++|+++|++||.|.+|.|++++.+  +..+||+||+|.+.++|.+|+..|||.
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            46788999998  44443        3689999999999999999988754  367999999999999999999999999


Q ss_pred             ccCCcEEEEEEeeC
Q psy222          156 NFQGSEIIVDFECG  169 (225)
Q Consensus       156 ~l~g~~l~V~~a~~  169 (225)
                      .|+|+.|+|.++..
T Consensus        83 ~f~GR~i~v~~~~~   96 (105)
T 3v4m_A           83 KFANRVVVTKYCDP   96 (105)
T ss_dssp             EETTEECEEEEECH
T ss_pred             EeCCCEEEEEEeCH
Confidence            99999999999864

>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=99.54  E-value=3.3e-14  Score=117.09  Aligned_cols=84  Identities=23%  Similarity=0.253  Sum_probs=75.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCC-CccC---CcEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNR-QNFQ---GSEI  162 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g-~~l~---g~~l  162 (225)
                      ..+..+|||+|||+.+++++|+++|+.||.|..|.|+.+ .++.++|||||+|.+.++|.+||..||+ ..+.   +++|
T Consensus        93 a~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i  171 (261)
T 3sde_A           93 ATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPV  171 (261)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEE-TTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBC
T ss_pred             cccCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeC-CCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceE
Confidence            345689999999999999999999999999999999999 4899999999999999999999999955 4444   8999


Q ss_pred             EEEEeeCCC
Q psy222          163 IVDFECGRV  171 (225)
Q Consensus       163 ~V~~a~~~~  171 (225)
                      .|.++....
T Consensus       172 ~v~~~~~~~  180 (261)
T 3sde_A          172 IVEPMEQFD  180 (261)
T ss_dssp             EEEECCCEE
T ss_pred             EEeeccccC
Confidence            999998643

>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=99.53  E-value=4.1e-15  Score=105.95  Aligned_cols=72  Identities=18%  Similarity=0.380  Sum_probs=63.9

Q ss_pred             EcCCCCCCCHHHHHHHH------------hcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEE
Q psy222           95 IGRLNKNSREADLEQAF------------AEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEI  162 (225)
Q Consensus        95 V~nLp~~~te~~L~~~F------------~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l  162 (225)
                      +.+|++.+++++|+++|            ++||.|..|.|+++. +++++|||||+|.+.++|++|+..|||..|+|+.|
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            56677777777777666            999999999999886 57889999999999999999999999999999999


Q ss_pred             EEEEe
Q psy222          163 IVDFE  167 (225)
Q Consensus       163 ~V~~a  167 (225)
                      +|.++
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            99986

>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=99.53  E-value=2e-14  Score=119.82  Aligned_cols=83  Identities=11%  Similarity=0.227  Sum_probs=71.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCC-ceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEE
Q psy222           88 DPTRTLFIGRLNKNSREADLEQAFAEYG-KVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF  166 (225)
Q Consensus        88 ~~~~~l~V~nLp~~~te~~L~~~F~~~G-~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~  166 (225)
                      ...++|||+|||+.+++++|+++|..|| .|..|.|+.+. .+..+|||||+|.+.++|.+|+..|++..|.|+.|.|.+
T Consensus       115 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~-~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  193 (292)
T 2ghp_A          115 LTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLR-FNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKV  193 (292)
T ss_dssp             CCSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC--------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            3678999999999999999999999999 99999999886 478899999999999999999999999999999999999


Q ss_pred             eeCCC
Q psy222          167 ECGRV  171 (225)
Q Consensus       167 a~~~~  171 (225)
                      +.+..
T Consensus       194 a~~~~  198 (292)
T 2ghp_A          194 SNPLE  198 (292)
T ss_dssp             CCCC-
T ss_pred             CCCCc
Confidence            88654

>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=99.53  E-value=4.3e-14  Score=102.83  Aligned_cols=81  Identities=17%  Similarity=0.278  Sum_probs=71.3

Q ss_pred             CCCeEEEcCCC--CCC---CHHHHHHHHhcCCceeEEEEeecCC----CCccceEEEEEeCCHHHHHHHHHHhCCCccCC
Q psy222           89 PTRTLFIGRLN--KNS---READLEQAFAEYGKVISVRVVRDFV----TGHSKRYGFLEYDCEKACLAAIRALNRQNFQG  159 (225)
Q Consensus        89 ~~~~l~V~nLp--~~~---te~~L~~~F~~~G~v~~v~i~~~~~----~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g  159 (225)
                      ++++|+|.|+-  .++   .+++|++.|++||.|.+|.|++++.    ++..+||+||+|.+.++|.+|+..|||..|+|
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            67899999983  222   3689999999999999999998864    45678999999999999999999999999999


Q ss_pred             cEEEEEEeeC
Q psy222          160 SEIIVDFECG  169 (225)
Q Consensus       160 ~~l~V~~a~~  169 (225)
                      +.|+|.++..
T Consensus        99 R~i~v~~~~~  108 (118)
T 3ue2_A           99 RKVVAEVYDQ  108 (118)
T ss_dssp             EECEEEEECH
T ss_pred             cEEEEEEcCh
Confidence            9999999864

>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=99.53  E-value=2.4e-14  Score=109.88  Aligned_cols=75  Identities=23%  Similarity=0.423  Sum_probs=66.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcC----C-------ceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCcc
Q psy222           89 PTRTLFIGRLNKNSREADLEQAFAEY----G-------KVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNF  157 (225)
Q Consensus        89 ~~~~l~V~nLp~~~te~~L~~~F~~~----G-------~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l  157 (225)
                      +.++|||+|||+.+++++|+++|++|    |       .|..+.+..      .+|||||+|.+.++|++|+ .||+..|
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            46799999999999999999999999    6       667776653      3799999999999999999 7999999


Q ss_pred             CCcEEEEEEeeCC
Q psy222          158 QGSEIIVDFECGR  170 (225)
Q Consensus       158 ~g~~l~V~~a~~~  170 (225)
                      .|+.|.|.++...
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

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.51  E-value=4e-14  Score=111.04  Aligned_cols=76  Identities=22%  Similarity=0.397  Sum_probs=66.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcC----C-------ceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCcc
Q psy222           89 PTRTLFIGRLNKNSREADLEQAFAEY----G-------KVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNF  157 (225)
Q Consensus        89 ~~~~l~V~nLp~~~te~~L~~~F~~~----G-------~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l  157 (225)
                      ..++|||+|||+.+++++|+++|+.|    |       .|..+.+.      ..+|||||+|.+.++|++|| .||+..|
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 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN------QDKNFAFLEFRSVDETTQAM-AFDGIIF   75 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEEE------TTTTEEEEEESCSHHHHHHG-GGTTEEE
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEec------CCCCEEEEEeCCHHHHHHHH-HhcCCEE
Confidence            46899999999999999999999999    4       55555553      35899999999999999999 7999999


Q ss_pred             CCcEEEEEEeeCCC
Q psy222          158 QGSEIIVDFECGRV  171 (225)
Q Consensus       158 ~g~~l~V~~a~~~~  171 (225)
                      .|+.|.|.++....
T Consensus        76 ~g~~i~v~~~~~~~   89 (198)
T 2yh0_A           76 QGQSLKIRRPHDYQ   89 (198)
T ss_dssp             TTEEEEEECCCCCC
T ss_pred             cCceEEEeCCCCCC
Confidence            99999999987643

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.49  E-value=3.3e-13  Score=95.25  Aligned_cols=65  Identities=14%  Similarity=0.220  Sum_probs=57.5

Q ss_pred             CCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEeeCCC
Q psy222          100 KNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECGRV  171 (225)
Q Consensus       100 ~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~~~~  171 (225)
                      ..+++++|+++|++||.|..|.|+     ++.+|||||+|.+.++|+.||+.++  .+.++.|+|.|++++.
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            468999999999999999999998     3569999999999999999999744  4679999999998754

>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=99.46  E-value=1.5e-13  Score=117.05  Aligned_cols=78  Identities=19%  Similarity=0.309  Sum_probs=67.2

Q ss_pred             CCCCCCCeEEEcC--CCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccC---C
Q psy222           85 SSTDPTRTLFIGR--LNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQ---G  159 (225)
Q Consensus        85 ~~~~~~~~l~V~n--Lp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~---g  159 (225)
                      ....++.+|||+|  |++.++|++|+++|++||.|..|.+..      .||||||+|.+.++|++|++.|||..+.   |
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            4467889999999  588999999999999999999987753      3799999999999999999999999873   4


Q ss_pred             c--EEEEEEee
Q psy222          160 S--EIIVDFEC  168 (225)
Q Consensus       160 ~--~l~V~~a~  168 (225)
                      +  .|.|.++.
T Consensus        87 ~~~~ly~~~~~   97 (345)
T 3tht_A           87 QKITLYLNFVE   97 (345)
T ss_dssp             CEEECEEEECS
T ss_pred             CceEEEEEEee
Confidence            4  57777774

>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=99.37  E-value=3.6e-12  Score=92.04  Aligned_cols=78  Identities=18%  Similarity=0.218  Sum_probs=66.0

Q ss_pred             CCCCeEEEcCCCCCC----------CHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCcc
Q psy222           88 DPTRTLFIGRLNKNS----------READLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNF  157 (225)
Q Consensus        88 ~~~~~l~V~nLp~~~----------te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l  157 (225)
                      .+++.|.|.|+=..-          .+++|+++|++||.|.+|.|.++.    .+||+||+|.+.++|.+|++.|||..|
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            467788888873321          135789999999999999997653    489999999999999999999999999


Q ss_pred             CCcEEEEEEeeC
Q psy222          158 QGSEIIVDFECG  169 (225)
Q Consensus       158 ~g~~l~V~~a~~  169 (225)
                      +|+.|+|.++..
T Consensus        81 ~GR~i~v~~~~~   92 (114)
T 3s6e_A           81 AGKMITAAYVPL   92 (114)
T ss_dssp             TTEECEEEEECH
T ss_pred             CCEEEEEEEEcH
Confidence            999999999863

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.25  E-value=2.2e-11  Score=83.33  Aligned_cols=74  Identities=22%  Similarity=0.348  Sum_probs=63.5

Q ss_pred             CCCCCeEEEcCCC----CCCCH----HHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccC
Q psy222           87 TDPTRTLFIGRLN----KNSRE----ADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQ  158 (225)
Q Consensus        87 ~~~~~~l~V~nLp----~~~te----~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~  158 (225)
                      .++..||+|.-++    .++..    .+|.+.|.+||.|..++++.++        +||+|.+.++|.+||. |||..+.
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            3566789998776    23434    5788999999999999999774        8999999999999999 9999999


Q ss_pred             CcEEEEEEeeC
Q psy222          159 GSEIIVDFECG  169 (225)
Q Consensus       159 g~~l~V~~a~~  169 (225)
                      |+.|+|+++++
T Consensus        75 Gr~LkV~lkt~   85 (91)
T 2dnr_A           75 NRTITIALKSP   85 (91)
T ss_dssp             TEEEEEEECCC
T ss_pred             CeEEEEEeCCC
Confidence            99999999875

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.24  E-value=2.8e-11  Score=87.82  Aligned_cols=79  Identities=16%  Similarity=0.184  Sum_probs=69.7

Q ss_pred             CCCCCCCeEEEcCCCCC-CCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCC-HHHHHHHHHHhC--CCccCCc
Q psy222           85 SSTDPTRTLFIGRLNKN-SREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDC-EKACLAAIRALN--RQNFQGS  160 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~-~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~-~~~a~~Al~~l~--g~~l~g~  160 (225)
                      ..-.+++.|||+||++. +++++|+++|++||.|..|.++.+..      .|||.|.+ ..+|..|+..|+  +..|.+.
T Consensus        13 ~~~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~~~i~g~   86 (121)
T 1owx_A           13 LEEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGNLQLRNK   86 (121)
T ss_dssp             CSCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCBCTTSS
T ss_pred             ccccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCCcEEeCc
Confidence            45678899999999999 99999999999999999999987742      59999999 899999999995  6789999


Q ss_pred             EEEEEEeeC
Q psy222          161 EIIVDFECG  169 (225)
Q Consensus       161 ~l~V~~a~~  169 (225)
                      .+++++...
T Consensus        87 ~~~~evL~G   95 (121)
T 1owx_A           87 EVTWEVLEG   95 (121)
T ss_dssp             SEEEEECCH
T ss_pred             EEEEEECCC
Confidence            888887653

>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=99.06  E-value=1.4e-10  Score=79.70  Aligned_cols=73  Identities=12%  Similarity=0.259  Sum_probs=62.6

Q ss_pred             CCCCCeEEEcCCCCC-----CCH----HHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCcc
Q psy222           87 TDPTRTLFIGRLNKN-----SRE----ADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNF  157 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~-----~te----~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l  157 (225)
                      .++.-||+|.-++..     +..    .+|.+.|.+||.|..++|+.++        +||+|.+.++|.+||+ |+|..+
T Consensus        12 GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~-ldG~~v   82 (95)
T 1ufw_A           12 GPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLD-VDGMKV   82 (95)
T ss_dssp             CCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHH-GGGSEE
T ss_pred             CCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHh-cCCeee
Confidence            456679999888742     322    4688999999999999999874        9999999999999999 999999


Q ss_pred             CCcEEEEEEee
Q psy222          158 QGSEIIVDFEC  168 (225)
Q Consensus       158 ~g~~l~V~~a~  168 (225)
                      +|+.|+|.+..
T Consensus        83 ~Gr~L~V~~k~   93 (95)
T 1ufw_A           83 KGRAVKISGPS   93 (95)
T ss_dssp             TTEEEEEECCC
T ss_pred             CCeEEEEeccC
Confidence            99999999854

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=98.99  E-value=1.4e-09  Score=87.10  Aligned_cols=68  Identities=19%  Similarity=0.282  Sum_probs=60.7

Q ss_pred             CCHHHHHHHHhcCCceeEEEEeecC----CCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEeeC
Q psy222          102 SREADLEQAFAEYGKVISVRVVRDF----VTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECG  169 (225)
Q Consensus       102 ~te~~L~~~F~~~G~v~~v~i~~~~----~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~~  169 (225)
                      -.+++|++.|++||.|..+.|+++.    .+++.+|++||+|.+.++|.+|+..|||..|.|+.|.|.+...
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~~  212 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQ  212 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECCH
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcCH
Confidence            3467899999999999999998654    3458999999999999999999999999999999999999753

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.53  E-value=5.3e-07  Score=63.24  Aligned_cols=74  Identities=18%  Similarity=0.181  Sum_probs=66.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcC-----CceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEY-----GKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSE  161 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~-----G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~  161 (225)
                      ....++|-|=|||..+++..|+.++..+     |.+..|.+..|.      +-|+|+|.+...|-+|.-.|+|..|.|++
T Consensus        18 ~~~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH------~GAivef~d~~~AgKasLaL~G~ef~gr~   91 (117)
T 2l9w_A           18 KELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF------NGAIIIFRDSKFAAKMLMILNGSQFQGKV   91 (117)
T ss_dssp             TTTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTT------TEEEEECSCHHHHHHHHHHHSSEEETTEE
T ss_pred             ccCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCC------CceEEEEccchhhHHHHhhcCCeeecCeE
Confidence            3446788888999999999999999999     999999999873      46999999999999999889999999999


Q ss_pred             EEEEE
Q psy222          162 IIVDF  166 (225)
Q Consensus       162 l~V~~  166 (225)
                      |++--
T Consensus        92 Lr~gT   96 (117)
T 2l9w_A           92 IRSGT   96 (117)
T ss_dssp             EEEEC
T ss_pred             EEecC
Confidence            99863

>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=0.00037  Score=48.33  Aligned_cols=73  Identities=14%  Similarity=0.125  Sum_probs=60.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhc-----CCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEE
Q psy222           89 PTRTLFIGRLNKNSREADLEQAFAE-----YGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEII  163 (225)
Q Consensus        89 ~~~~l~V~nLp~~~te~~L~~~F~~-----~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~  163 (225)
                      ...+|.|.|||..+.++.|.-+|+.     -|.|..+....        +-|+|+|.+...|++.|+. ..+.|.+..|.
T Consensus         7 ~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~k-~~H~L~~~~Ls   77 (104)
T 2dhx_A            7 GGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLAQ-ADHELHGAQLS   77 (104)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHTC-SCCBSSSSBCE
T ss_pred             CccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhcC-CcceecCeEEE
Confidence            4578999999999999999999986     25688887653        4589999999999999983 47889999999


Q ss_pred             EEEeeCC
Q psy222          164 VDFECGR  170 (225)
Q Consensus       164 V~~a~~~  170 (225)
                      |.-..++
T Consensus        78 V~P~~~~   84 (104)
T 2dhx_A           78 LRPAPPR   84 (104)
T ss_dssp             EEECCCC
T ss_pred             EEcCCCC
Confidence            9765544

>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=97.71  E-value=0.00023  Score=48.58  Aligned_cols=78  Identities=10%  Similarity=0.122  Sum_probs=60.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCc--cceEEEEEeCCHHHHHHHHHHhCCCccCCc-----EEE
Q psy222           91 RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGH--SKRYGFLEYDCEKACLAAIRALNRQNFQGS-----EII  163 (225)
Q Consensus        91 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~--~kg~afV~F~~~~~a~~Al~~l~g~~l~g~-----~l~  163 (225)
                      .+|.|++||+.+||+++.+.+.....+.....+..+.+..  .-.-|||.|.+.+++....+.++|+.|.+.     +..
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            4789999999999999999999888766666554443322  234689999999999999999999987553     345


Q ss_pred             EEEee
Q psy222          164 VDFEC  168 (225)
Q Consensus       164 V~~a~  168 (225)
                      |++|-
T Consensus        82 VE~AP   86 (91)
T 1uw4_A           82 VEFAP   86 (91)
T ss_dssp             EEECS
T ss_pred             EEEcC
Confidence            66653

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=97.69  E-value=0.0001  Score=51.37  Aligned_cols=76  Identities=21%  Similarity=0.276  Sum_probs=63.0

Q ss_pred             CCCeEEEcCCCCCC-CH----HHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEE
Q psy222           89 PTRTLFIGRLNKNS-RE----ADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEII  163 (225)
Q Consensus        89 ~~~~l~V~nLp~~~-te----~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~  163 (225)
                      -.++|+|.||+.++ ..    +.++++|..|+.+....++..-     + =..|.|.+.++|.+|-..||+..|.|..|+
T Consensus         4 ~pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSF-----R-Rirv~F~~~~~A~~AR~~Lh~~~f~g~~~r   77 (104)
T 1wey_A            4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF-----K-RVRINFSNPLSAADARLRLHKTEFLGKEMK   77 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTT-----T-EEEEECSSTTHHHHHHHTSTTSEETTEECE
T ss_pred             CCceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcc-----e-EEEEEeCChHHHHHHHHHhccceecCceeE
Confidence            35689999998865 22    5678999999998887777542     2 257999999999999999999999999999


Q ss_pred             EEEeeCC
Q psy222          164 VDFECGR  170 (225)
Q Consensus       164 V~~a~~~  170 (225)
                      |-++++.
T Consensus        78 ~YFgq~~   84 (104)
T 1wey_A           78 LYFAQTL   84 (104)
T ss_dssp             EECCCCS
T ss_pred             EEecCCC
Confidence            9998853

>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=97.53  E-value=0.00031  Score=48.19  Aligned_cols=55  Identities=20%  Similarity=0.346  Sum_probs=47.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhC
Q psy222           90 TRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALN  153 (225)
Q Consensus        90 ~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~  153 (225)
                      .+.++| .+|.++...+|.++|+.|| -..|+++.|.       -|||.|.+++.|..|+..+.
T Consensus        16 ~HVf~l-~FP~ewKt~DI~~lFs~fg-gv~I~WidDT-------sAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           16 DHVLHV-TFPKEWKTSDLYQLFSAFG-NIQISWIDDT-------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CSEEEE-ECCTTCCHHHHHHHHTTTC-SCCCEEEETT-------EEEEECSCHHHHHHHHHHHH
T ss_pred             CeEEEE-eCChhhhhHHHHHHhhccC-CEEEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            345666 9999999999999999999 4478888774       69999999999999998763

>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=97.44  E-value=0.00019  Score=49.43  Aligned_cols=53  Identities=21%  Similarity=0.352  Sum_probs=46.2

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhC
Q psy222           92 TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALN  153 (225)
Q Consensus        92 ~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~  153 (225)
                      .++| ++|.++...+|..+|+.|| -..|+++.|.       -|||.|.+++.|..|+..+.
T Consensus         8 V~~l-~FP~ewKt~Di~~lFs~fg-gv~I~WidDT-------sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            8 VLHV-TFPKEWKTSDLYQLFSAFG-NIQISWIDDT-------SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEE-ECCTTCCHHHHHHHTTTSE-EEEEEEEETT-------EEEEEEEEECHHHHHHHHHT
T ss_pred             EEEE-eCChhhhhHHHHHHHhccC-CEEEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            4566 9999999999999999999 5588888774       69999999999999999764

>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=97.14  E-value=0.0019  Score=46.15  Aligned_cols=71  Identities=14%  Similarity=0.158  Sum_probs=56.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCC-cEEEEEEe
Q psy222           89 PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQG-SEIIVDFE  167 (225)
Q Consensus        89 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g-~~l~V~~a  167 (225)
                      ..+-|.|-++|... -..|..+|++||.|++....    +  ...+-.|.|.+..+|++||. .||..|.+ -.|-|...
T Consensus        23 ~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~----~--~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~p~   94 (119)
T 1wwh_A           23 DDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMS----N--TGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPC   94 (119)
T ss_dssp             GGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEEC----S--SSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEEC
T ss_pred             CCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccC----C--CCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEEC
Confidence            45678888999885 56678889999999987762    1  24588999999999999999 59999986 55666654

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=96.99  E-value=0.0011  Score=45.49  Aligned_cols=79  Identities=13%  Similarity=0.113  Sum_probs=54.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCc--cceEEEEEeCCHHHHHHHHHHhCCCccCCc-----EE
Q psy222           90 TRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGH--SKRYGFLEYDCEKACLAAIRALNRQNFQGS-----EI  162 (225)
Q Consensus        90 ~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~--~kg~afV~F~~~~~a~~Al~~l~g~~l~g~-----~l  162 (225)
                      .-+|.|+.||+.+||+++.+.+...-.+.....+..+.+.+  .-.-|||.|.+.+++..-.+.++|+.|.+.     +.
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~kg~~~~a   88 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKGLEYPA   88 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECTTCCEEEE
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeCCCCEeee
Confidence            45799999999999999887776654432222221111111  123589999999999999999999987553     45


Q ss_pred             EEEEee
Q psy222          163 IVDFEC  168 (225)
Q Consensus       163 ~V~~a~  168 (225)
                      .|++|-
T Consensus        89 ~VE~AP   94 (97)
T 2l08_A           89 VVEFAP   94 (97)
T ss_dssp             EEEECC
T ss_pred             EEEecC
Confidence            566653

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=96.47  E-value=0.0015  Score=57.41  Aligned_cols=54  Identities=15%  Similarity=0.240  Sum_probs=41.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHH
Q psy222           91 RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR  150 (225)
Q Consensus        91 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~  150 (225)
                      ++|||. +|..+++.+|.++|++||.|..+.+..++     .-||.|+|.+.+++..++.
T Consensus        54 rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~-----g~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           54 RTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF-----GLYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             TEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS-----SEEEEEECC---CCHHHHS
T ss_pred             ceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC-----CeEEEEEeCCHHHHHHHHh
Confidence            589997 89999999999999999999998887653     4699999999999887765

>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=96.29  E-value=0.0049  Score=45.79  Aligned_cols=36  Identities=8%  Similarity=-0.053  Sum_probs=29.6

Q ss_pred             EEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCc
Q psy222          119 SVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQN  156 (225)
Q Consensus       119 ~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~  156 (225)
                      .++|+++.  .+.+|||||+|.+.++|++|+..+++..
T Consensus         2 ~~kl~ln~--~~~~G~~fV~f~~~~~A~~al~~~~~~~   37 (158)
T 2kn4_A            2 QYKLILNG--KTLKGETTTEAVDAATAEKVFKQYANDN   37 (158)
T ss_dssp             EEEEEEEC--SSCEEEEEEECSSHHHHHHHHHHHHHHH
T ss_pred             cEEEEecC--ccccchhHHHHHHHHhHHHHHHhhcccC
Confidence            46677774  3689999999999999999998887643

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=95.94  E-value=0.008  Score=43.51  Aligned_cols=77  Identities=18%  Similarity=0.254  Sum_probs=54.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCceeE-EEEeec------------CCCC-ccceEEEEEeCCHHHHHHHHHHhCCCc
Q psy222           91 RTLFIGRLNKNSREADLEQAFAEYGKVIS-VRVVRD------------FVTG-HSKRYGFLEYDCEKACLAAIRALNRQN  156 (225)
Q Consensus        91 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~-v~i~~~------------~~~g-~~kg~afV~F~~~~~a~~Al~~l~g~~  156 (225)
                      .-|.|-+.|...+ ..+.++|++||.|++ +.+...            +... ....+-.|.|.+..+|.+||. .||..
T Consensus         8 ~~VtVFGFp~~~~-~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG~i   85 (132)
T 3p3d_A            8 LAILVFGYPETMA-NQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENGAV   85 (132)
T ss_dssp             CEEEEECCCGGGH-HHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTTCE
T ss_pred             eEEEEEecCHHHH-HHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCCeE
Confidence            4567778887765 556778999999876 221110            0000 134577999999999999999 59999


Q ss_pred             cCCcEEEEEEeeC
Q psy222          157 FQGSEIIVDFECG  169 (225)
Q Consensus       157 l~g~~l~V~~a~~  169 (225)
                      |.|..|-|....+
T Consensus        86 i~G~mIGV~Py~~   98 (132)
T 3p3d_A           86 FNGVLLGVIPYTK   98 (132)
T ss_dssp             ETTEECEEEECCH
T ss_pred             eCcEEEEEEECCH
Confidence            9999887877653

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A

Probab=95.52  E-value=0.0077  Score=44.39  Aligned_cols=40  Identities=15%  Similarity=-0.008  Sum_probs=36.6

Q ss_pred             CccceEEEEEeCCHHHHHHHHHHh-CCCccCCcEEEEEEeeC
Q psy222          129 GHSKRYGFLEYDCEKACLAAIRAL-NRQNFQGSEIIVDFECG  169 (225)
Q Consensus       129 g~~kg~afV~F~~~~~a~~Al~~l-~g~~l~g~~l~V~~a~~  169 (225)
                      ...+|+++|+|.+.++|++|++.| |+..|+| .|.|.++..
T Consensus        10 ~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~   50 (150)
T 2i2y_A           10 KTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATK   50 (150)
T ss_dssp             SSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTT
T ss_pred             ccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccC
Confidence            457899999999999999999999 9999999 999998765

>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=92.24  E-value=0.41  Score=42.56  Aligned_cols=55  Identities=20%  Similarity=0.347  Sum_probs=45.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCC
Q psy222           91 RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNR  154 (225)
Q Consensus        91 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g  154 (225)
                      +.++|+ +|..+...+|.++|+.||. ..|.++.+.       .|||.|.+.+.|..++..++.
T Consensus       441 ~vl~v~-f~~~~~~~~i~~~fs~fg~-v~V~widdt-------~a~V~~~~~~~a~~~l~~~~~  495 (507)
T 3d45_A          441 HVLHVT-FPKEWKTSDLYQLFSAFGN-IQISWIDDT-------SAFVSLSQPEQVQIAVNTSKY  495 (507)
T ss_dssp             GEEEEE-CCTTCCHHHHHHHGGGGCC-CEEEECSSS-------EEEEECSCHHHHHHHHHHHTT
T ss_pred             cEEEEe-CCCCCCHHHHHHHHHhcCC-EEEEEEcCC-------eEEEEECCHHHHHHHHHHHHh
Confidence            466665 8999999999999999994 477776553       699999999999999998853

>2g0c_A ATP-dependent RNA helicase DBPA; RNA recognition motif, hydrolase; 1.70A {Bacillus subtilis} PDB: 3moj_B

Probab=81.37  E-value=3.2  Score=26.33  Aligned_cols=68  Identities=12%  Similarity=0.221  Sum_probs=41.0

Q ss_pred             eEEEc-CCCCCCCHHHHHHHHhcCCc-----eeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q psy222           92 TLFIG-RLNKNSREADLEQAFAEYGK-----VISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD  165 (225)
Q Consensus        92 ~l~V~-nLp~~~te~~L~~~F~~~G~-----v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~  165 (225)
                      +|||. +--..+...+|..++..-+.     |-.|.|.        ..|.||+... ..+..++..|++..+.|+.+.|+
T Consensus         2 ~~~i~~Grk~~~~p~~ivg~i~~~~gi~~~~IG~I~i~--------d~~s~v~v~~-~~~~~~~~~l~~~~i~g~~~~v~   72 (76)
T 2g0c_A            2 KLYFNGGKKKKIRAVDFVGTIAKIDGVSADDIGIITIM--------DNASYVEILN-GKGPHVLKVMKNTTVKGKQLKVN   72 (76)
T ss_dssp             EEEESCCCC----CHHHHHHHHTSTTCCGGGEEEEEEC--------SSCEEEEECT-TCHHHHHHHHTTCCC---CCCEE
T ss_pred             EEEEeCCCccCCCHHHHHHHHHHccCCChhhccEEEEe--------CCcEEEEECH-HHHHHHHHHhccccCcCceEEEE
Confidence            45663 22334566677766654433     4456664        2389999874 55778888899999999999988


Q ss_pred             Eee
Q psy222          166 FEC  168 (225)
Q Consensus       166 ~a~  168 (225)
                      .++
T Consensus        73 ~~~   75 (76)
T 2g0c_A           73 KAN   75 (76)
T ss_dssp             ECC
T ss_pred             ECC
Confidence            764

---

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	225
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	7e-16
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	9e-15
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	1e-14
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	2e-14
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	6e-14
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	1e-13
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	1e-13
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	2e-13
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:) 5e-13
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	1e-12
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	1e-12
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	2e-12
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	2e-12
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	5e-12
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	6e-12
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	7e-12
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	9e-12
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	9e-12
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-11
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	1e-11
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	1e-11
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-11
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	2e-11
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	2e-11
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	2e-11
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	3e-11
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	3e-11
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	5e-11
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	1e-10
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	2e-10
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	2e-10
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	2e-10
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	2e-10
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	3e-10
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	3e-10
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	3e-10
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	3e-10
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	6e-10
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	6e-10
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	1e-09
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	1e-08
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	1e-09
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	1e-09
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	2e-09
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	2e-09
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	3e-09
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	4e-09
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	5e-09
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	7e-09
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	7e-09
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	1e-08
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	3e-08
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	3e-08
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	4e-08
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	5e-08
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	1e-07
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	2e-07
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	4e-07
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	6e-07
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	7e-07
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	8e-07
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	1e-06
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	3e-06
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	3e-06
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	3e-06
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	6e-06
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	7e-06
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	7e-06
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	1e-05
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	2e-05
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	2e-05
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	3e-05
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	8e-05
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-04
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	5e-04
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	0.001
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	0.001
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	0.004

>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 = 67.6 bits (165), Expect = 7e-16
 Identities = 19/75 (25%), Positives = 39/75 (52%)

Query: 92  TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
           +L++G L+ +  EA L + F+  G ++S+RV RD +T  S  Y ++ +        A+  
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 152 LNRQNFQGSEIIVDF 166
           +N    +G  + + +
Sbjct: 62  MNFDVIKGKPVRIMW 76

>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 = 65.3 bits (159), Expect = 9e-15
 Identities = 13/81 (16%), Positives = 42/81 (51%), Gaps = 2/81 (2%)

Query: 88  DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDF-VTGHSKRYGFLEYDCEKACL 146
             T  + +  +   + + ++ + F+ +G++ +VR+ +    TG  + +GF+++  ++   
Sbjct: 6   QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAK 65

Query: 147 AAIRAL-NRQNFQGSEIIVDF 166
            A  AL +  +  G  +++++
Sbjct: 66  KAFNALCHSTHLYGRRLVLEW 86

>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 = 64.6 bits (157), Expect = 1e-14
 Identities = 19/78 (24%), Positives = 36/78 (46%), Gaps = 2/78 (2%)

Query: 91  RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
             L++  L +   +  L+  F +YG ++   ++RD +TG  +   F+ Y+  +    AI 
Sbjct: 7   TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 66

Query: 151 ALNRQNFQGSE--IIVDF 166
           ALN    +G    + V  
Sbjct: 67  ALNNVIPEGGSQPLSVRL 84

>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 = 64.7 bits (157), Expect = 2e-14
 Identities = 23/82 (28%), Positives = 43/82 (52%)

Query: 85  SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
           S  +   T+++G L++   E  L + F + G V++  + +D VTG  + YGF+E+  E+ 
Sbjct: 4   SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEED 63

Query: 145 CLAAIRALNRQNFQGSEIIVDF 166
              AI+ ++     G  I V+ 
Sbjct: 64  ADYAIKIMDMIKLYGKPIRVNK 85

>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 = 62.8 bits (152), Expect = 6e-14
 Identities = 20/80 (25%), Positives = 36/80 (45%)

Query: 85  SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
           ++ DP   L +  L+  + E DL + F++YG +  V +V D  +  S+ + F+ ++    
Sbjct: 4   ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDD 63

Query: 145 CLAAIRALNRQNFQGSEIIV 164
              A    N     G  I V
Sbjct: 64  AKEAKERANGMELDGRRIRV 83

>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 = 62.3 bits (151), Expect = 1e-13
 Identities = 17/83 (20%), Positives = 37/83 (44%)

Query: 88  DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLA 147
             + TL++G L+  + E  + + F++ G +  + +  D +   +  + F+EY        
Sbjct: 5   KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAEN 64

Query: 148 AIRALNRQNFQGSEIIVDFECGR 170
           A+R +N        I  D++ G 
Sbjct: 65  AMRYINGTRLDDRIIRTDWDAGF 87

>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 = 61.9 bits (150), Expect = 1e-13
 Identities = 19/75 (25%), Positives = 37/75 (49%)

Query: 92  TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
            L +  L ++  + +L   F   G + + R++RD+ TG+S  Y F+++  E     AI+ 
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 152 LNRQNFQGSEIIVDF 166
           LN    +   + V +
Sbjct: 64  LNGITVRNKRLKVSY 78

>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 = 61.6 bits (149), Expect = 2e-13
 Identities = 19/78 (24%), Positives = 37/78 (47%)

Query: 89  PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAA 148
             R L++G L +   +  L  AF  +G +  +++  D+ T   + + F+E++  +   AA
Sbjct: 4   TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 63

Query: 149 IRALNRQNFQGSEIIVDF 166
           I  +N     G  I V+ 
Sbjct: 64  IDNMNESELFGRTIRVNL 81

>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 = 61.2 bits (148), Expect = 5e-13
 Identities = 13/74 (17%), Positives = 28/74 (37%), Gaps = 1/74 (1%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           + +        E    +   +YG+V  + V  +    H     ++++  E+    A+  L
Sbjct: 30  VEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDL 88

Query: 153 NRQNFQGSEIIVDF 166
           N + F G  I  + 
Sbjct: 89  NNRWFNGQPIHAEL 102

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.3 bits (143), Expect = 1e-12
 Identities = 29/84 (34%), Positives = 47/84 (55%), Gaps = 2/84 (2%)

Query: 85  SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
           S++     L++  L K   + +LEQ F++YG++I+ R++ D VTG S+  GF+ +D    
Sbjct: 1   SASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIE 60

Query: 145 CLAAIRALNRQNFQGSE--IIVDF 166
              AI+ LN Q   G+   I V F
Sbjct: 61  AEEAIKGLNGQKPSGATEPITVKF 84

>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 = 59.2 bits (143), Expect = 1e-12
 Identities = 16/74 (21%), Positives = 33/74 (44%), Gaps = 1/74 (1%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           L +  L+    +AD+++ FAE+G +    V  D  +G S     + ++ +   L A++  
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQY 61

Query: 153 NRQNFQGSEIIVDF 166
           N     G  + +  
Sbjct: 62  NGVPLDGRPMNIQL 75

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]} Length = 114

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.0 bits (145), Expect = 2e-12
 Identities = 14/79 (17%), Positives = 30/79 (37%), Gaps = 3/79 (3%)

Query: 88  DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLA 147
           +  R L+I  L       ++   F +YG +  +R      T  ++   ++ Y+       
Sbjct: 5   EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIR---VGNTPETRGTAYVVYEDIFDAKN 61

Query: 148 AIRALNRQNFQGSEIIVDF 166
           A   L+  N     ++V +
Sbjct: 62  ACDHLSGFNVCNRYLVVLY 80

>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 = 59.3 bits (143), Expect = 2e-12
 Identities = 18/79 (22%), Positives = 41/79 (51%)

Query: 88  DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLA 147
           D   T+ +  L++++RE DL++ F  +G +  + + +D  TG SK + F+ +   +    
Sbjct: 6   DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAAR 65

Query: 148 AIRALNRQNFQGSEIIVDF 166
           AI  ++   +    + V++
Sbjct: 66  AIAGVSGFGYDHLILNVEW 84

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.3 bits (140), Expect = 5e-12
 Identities = 15/82 (18%), Positives = 36/82 (43%)

Query: 85  SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
           +  +P + L++  L+    E DL   FA + +     +    +TG  +   F+ +  ++ 
Sbjct: 13  NPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEI 72

Query: 145 CLAAIRALNRQNFQGSEIIVDF 166
              A+  +N     G  ++++F
Sbjct: 73  AWQALHLVNGYKLYGKILVIEF 94

>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 = 58.2 bits (140), Expect = 6e-12
 Identities = 30/105 (28%), Positives = 45/105 (42%), Gaps = 6/105 (5%)

Query: 83  HTSSTDPT-RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDC 141
           H S  D T   +F+G L  ++ +A L + F  +G +    V+ D  TG S+ YGF+    
Sbjct: 2   HGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMAD 61

Query: 142 EKACLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWGG 186
             A   A +  N     G +  V+        G KPR L  G+  
Sbjct: 62  RAAAERACKDPN-PIIDGRKANVNLAY----LGAKPRSLQTGFAI 101

>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 = 57.4 bits (138), Expect = 7e-12
 Identities = 20/82 (24%), Positives = 42/82 (51%), Gaps = 2/82 (2%)

Query: 85  SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
                 RTL++G L+++  E  + Q F++ G   S +++ +     +  Y F+E+   + 
Sbjct: 3   EDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITE--HTSNDPYCFVEFYEHRD 60

Query: 145 CLAAIRALNRQNFQGSEIIVDF 166
             AA+ A+N +   G E+ V++
Sbjct: 61  AAAALAAMNGRKILGKEVKVNW 82

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.0 bits (137), Expect = 9e-12
 Identities = 24/76 (31%), Positives = 35/76 (46%)

Query: 91  RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
             L +  L +N  + +    F   G++ S ++VRD +TG S  YGF+ Y   K    AI 
Sbjct: 3   TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62

Query: 151 ALNRQNFQGSEIIVDF 166
            LN    Q   I V +
Sbjct: 63  TLNGLRLQTKTIKVSY 78

>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 = 57.3 bits (138), Expect = 9e-12
 Identities = 27/90 (30%), Positives = 39/90 (43%), Gaps = 1/90 (1%)

Query: 77  RSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGF 136
           R      +      RT+F  +L    R  DLE  F+  GKV  VR++ D  +  SK   +
Sbjct: 5   REPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAY 64

Query: 137 LEYDCEKACLAAIRALNRQNFQGSEIIVDF 166
           +E+   ++   AI  L  Q   G  IIV  
Sbjct: 65  VEFCEIQSVPLAI-GLTGQRLLGVPIIVQA 93

>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 = 56.9 bits (137), Expect = 1e-11
 Identities = 21/76 (27%), Positives = 33/76 (43%)

Query: 91  RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
             LFIG L     +  +++    +G + +  +V+D  TG SK Y F EY        AI 
Sbjct: 2   HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 61

Query: 151 ALNRQNFQGSEIIVDF 166
            LN       +++V  
Sbjct: 62  GLNGMQLGDKKLLVQR 77

>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 = 57.0 bits (137), Expect = 1e-11
 Identities = 19/77 (24%), Positives = 33/77 (42%), Gaps = 3/77 (3%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVV---RDFVTGHSKRYGFLEYDCEKACLAAI 149
           LFI  LN ++ E  L+  F++ G + S  +           S  +GF+EY   +    A+
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 150 RALNRQNFQGSEIIVDF 166
           + L      G ++ V  
Sbjct: 61  KQLQGHTVDGHKLEVRI 77

>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 = 56.6 bits (136), Expect = 1e-11
 Identities = 21/78 (26%), Positives = 35/78 (44%), Gaps = 1/78 (1%)

Query: 88  DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLA 147
           +  R LFIG L+  + +  L   F ++G +    V+RD  T  S+ +GF+ Y   +   A
Sbjct: 4   EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 63

Query: 148 AIRALNRQNFQGSEIIVD 165
           A+ A       G  +   
Sbjct: 64  AMNA-RPHKVDGRVVEPK 80

>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 = 56.8 bits (137), Expect = 2e-11
 Identities = 26/106 (24%), Positives = 46/106 (43%), Gaps = 17/106 (16%)

Query: 84  TSSTDP---TRTLFIGRLNKNS-READLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEY 139
           +  TDP      +FIG LN    +++D+E  F++YGK++   V + F         F++Y
Sbjct: 6   SGKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGF--------AFVQY 57

Query: 140 DCEKACLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWG 185
             E+   AA+   + +   G  + ++          K  R G   G
Sbjct: 58  VNERNARAAVAGEDGRMIAGQVLDINLAAEP-----KVNRSGPSSG 98

>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 = 56.5 bits (136), Expect = 2e-11
 Identities = 20/81 (24%), Positives = 38/81 (46%), Gaps = 2/81 (2%)

Query: 86  STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKAC 145
           +   T  L +  L   + E DL++ F+ +G+V+ V+V +D  TGHSK +GF+ +   +  
Sbjct: 4   AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQ 63

Query: 146 LAAIRALNRQNFQGSEIIVDF 166
           +  +   +     G       
Sbjct: 64  VKVMSQRH--MIDGRWCDCKL 82

>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 = 56.1 bits (135), Expect = 2e-11
 Identities = 14/81 (17%), Positives = 36/81 (44%), Gaps = 6/81 (7%)

Query: 86  STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKAC 145
           S+    T++ G +     +  + Q F+ +G+++ +RV  +        Y F+ +   ++ 
Sbjct: 14  SSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK------GYSFVRFSTHESA 67

Query: 146 LAAIRALNRQNFQGSEIIVDF 166
             AI ++N    +G  +   +
Sbjct: 68  AHAIVSVNGTTIEGHVVKCYW 88

>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 = 56.2 bits (135), Expect = 2e-11
 Identities = 10/79 (12%), Positives = 33/79 (41%), Gaps = 1/79 (1%)

Query: 89  PTRTLFIGRLNKNSREADLEQAFAEY-GKVISVRVVRDFVTGHSKRYGFLEYDCEKACLA 147
           P  T++I  LN+  ++ +L+++      +   +  +    +   +   F+ +    +   
Sbjct: 2   PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 61

Query: 148 AIRALNRQNFQGSEIIVDF 166
           A+R++    F    + + +
Sbjct: 62  ALRSMQGFPFYDKPMRIQY 80

>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 = 55.8 bits (134), Expect = 3e-11
 Identities = 19/84 (22%), Positives = 40/84 (47%), Gaps = 2/84 (2%)

Query: 83  HTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCE 142
           ++ S    + L +  +    R+ DL Q F ++GK++ V ++ +     SK +GF+ ++  
Sbjct: 4   NSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGFVTFENS 61

Query: 143 KACLAAIRALNRQNFQGSEIIVDF 166
                A   L+    +G +I V+ 
Sbjct: 62  ADADRAREKLHGTVVEGRKIEVNN 85

>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 = 55.4 bits (133), Expect = 3e-11
 Identities = 18/74 (24%), Positives = 35/74 (47%), Gaps = 1/74 (1%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           +FIG L+  + +  L + F ++G+V    V+RD +T  S+ +GF+ +  +      + A 
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-AQ 61

Query: 153 NRQNFQGSEIIVDF 166
           +R       I    
Sbjct: 62  SRHELDSKTIDPKV 75

>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 = 55.4 bits (133), Expect = 5e-11
 Identities = 17/87 (19%), Positives = 31/87 (35%), Gaps = 6/87 (6%)

Query: 81  KPHTSS-TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEY 139
            P TS      RTL    L+ N  E +L++ F +      + +      G SK   ++E+
Sbjct: 6   DPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDA-----LEIRLVSQDGKSKGIAYIEF 60

Query: 140 DCEKACLAAIRALNRQNFQGSEIIVDF 166
             E      +         G  + + +
Sbjct: 61  KSEADAEKNLEEKQGAEIDGRSVSLYY 87

>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 = 53.9 bits (129), Expect = 1e-10
 Identities = 8/83 (9%), Positives = 25/83 (30%)

Query: 84  TSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEK 143
           +S       + +  +       ++   F  Y  +     ++    G       + ++   
Sbjct: 3   SSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRD 62

Query: 144 ACLAAIRALNRQNFQGSEIIVDF 166
              AA+  LN +     ++ +  
Sbjct: 63  EATAAVIDLNDRPIGSRKVKLVL 85

>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 = 53.9 bits (129), Expect = 2e-10
 Identities = 17/79 (21%), Positives = 32/79 (40%), Gaps = 6/79 (7%)

Query: 88  DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLA 147
              + L++  L  ++ E  +E+ F         RV         + Y F+ +   +  + 
Sbjct: 6   SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV------KKIRDYAFVHFSNREDAVE 59

Query: 148 AIRALNRQNFQGSEIIVDF 166
           A++ALN +   GS I V  
Sbjct: 60  AMKALNGKVLDGSPIEVTL 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 = 54.3 bits (130), Expect = 2e-10
 Identities = 17/80 (21%), Positives = 32/80 (40%), Gaps = 1/80 (1%)

Query: 87  TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACL 146
             P  T F+G L  +  E  +++ F                    K +G+ E++   + L
Sbjct: 12  KSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLL 71

Query: 147 AAIRALNRQNFQGSEIIVDF 166
           +A+ +LN ++     I VD 
Sbjct: 72  SAL-SLNEESLGNKRIRVDV 90

>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 = 53.5 bits (128), Expect = 2e-10
 Identities = 19/77 (24%), Positives = 35/77 (45%), Gaps = 2/77 (2%)

Query: 90  TRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAI 149
              +FI  L+K+     L   F+ +G ++S +VV D        YGF+ ++ ++A   AI
Sbjct: 8   VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSK--GYGFVHFETQEAAERAI 65

Query: 150 RALNRQNFQGSEIIVDF 166
             +N       ++ V  
Sbjct: 66  EKMNGMLLNDRKVFVGR 82

>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 = 53.2 bits (127), Expect = 2e-10
 Identities = 25/76 (32%), Positives = 44/76 (57%)

Query: 91  RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
             LF+  +++ ++E ++++ F +YG++ ++ +  D  TG SK Y  +EY+  K  LAA  
Sbjct: 8   WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 67

Query: 151 ALNRQNFQGSEIIVDF 166
           ALN     G  I VD+
Sbjct: 68  ALNGAEIMGQTIQVDW 83

>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 = 53.5 bits (128), Expect = 3e-10
 Identities = 20/79 (25%), Positives = 36/79 (45%), Gaps = 1/79 (1%)

Query: 88  DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLA 147
           +  R LFIG L+  + E  L   + ++GK+    V+RD  +  S+ +GF+ +       A
Sbjct: 18  EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDA 77

Query: 148 AIRALNRQNFQGSEIIVDF 166
           A+ A    +  G  +    
Sbjct: 78  AM-AARPHSIDGRVVEPKR 95

>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 = 53.2 bits (127), Expect = 3e-10
 Identities = 14/79 (17%), Positives = 27/79 (34%), Gaps = 6/79 (7%)

Query: 91  RTLFIGRLNKNSREADLEQAFAEYGKVISVRV-----VRDFVTGHSKRYGFLEYDCEKAC 145
           R L++G +     E  +   F    ++  +       V        K + FLE+      
Sbjct: 2   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 61

Query: 146 LAAIRALNRQNFQGSEIIV 164
             A+   +   FQG  + +
Sbjct: 62  TQAMA-FDGIIFQGQSLKI 79

>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 = 53.2 bits (127), Expect = 3e-10
 Identities = 19/86 (22%), Positives = 33/86 (38%), Gaps = 8/86 (9%)

Query: 89  PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVV--------RDFVTGHSKRYGFLEYD 140
               +++  LN +    DL   F + G V   +           D  TG  K    + Y+
Sbjct: 7   DNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYE 66

Query: 141 CEKACLAAIRALNRQNFQGSEIIVDF 166
                 AA+   + ++FQGS++ V  
Sbjct: 67  DPPTAKAAVEWFDGKDFQGSKLKVSL 92

>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 = 52.8 bits (126), Expect = 3e-10
 Identities = 25/75 (33%), Positives = 39/75 (52%), Gaps = 1/75 (1%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISV-RVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
           +FIG L+    E  L   F+ +G ++   +++RD  TG+SK Y F+ +    A  AAI A
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 152 LNRQNFQGSEIIVDF 166
           +N Q      I V +
Sbjct: 61  MNGQYLCNRPITVSY 75

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.9 bits (124), Expect = 6e-10
 Identities = 14/72 (19%), Positives = 33/72 (45%), Gaps = 1/72 (1%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           +F+G L+ ++ E  + + F  +G+V S+ +  D  T   + + F+ +  E+     +   
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK- 60

Query: 153 NRQNFQGSEIIV 164
              N   S+  +
Sbjct: 61  KYHNVGLSKCEI 72

>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 = 51.9 bits (124), Expect = 6e-10
 Identities = 17/72 (23%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           +FIG L+ ++ + DL+  F+++G+V+   +  D +TG S+ +GF+ +   ++    +   
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVM-DQ 60

Query: 153 NRQNFQGSEIIV 164
                 G  I  
Sbjct: 61  KEHKLNGKVIDP 72

>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 = 53.9 bits (128), Expect = 1e-09
 Identities = 20/71 (28%), Positives = 34/71 (47%)

Query: 88  DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLA 147
           +  R LFIG L+  + +  L   F ++G +    V+RD  T  S+ +GF+ Y   +   A
Sbjct: 4   EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 63

Query: 148 AIRALNRQNFQ 158
           A+ A   +   
Sbjct: 64  AMNARPHKVDG 74

>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 = 50.8 bits (120), Expect = 1e-08
 Identities = 18/123 (14%), Positives = 42/123 (34%), Gaps = 1/123 (0%)

Query: 44  YWYPYCITYDPIQAGSIDGTDTIPHDRAILRALRSTYKPHTSSTDPTRTLFIGRLNKNSR 103
            +  Y    +   A +              RA+         +    + +F+G + +++ 
Sbjct: 51  GFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTE 110

Query: 104 EADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEII 163
           E  L   F +YGK+  + ++ D  +G  + + F+ +D   +    +         G    
Sbjct: 111 EHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQKYHTVNGHNCE 169

Query: 164 VDF 166
           V  
Sbjct: 170 VRK 172

>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 = 51.6 bits (123), Expect = 1e-09
 Identities = 25/78 (32%), Positives = 37/78 (47%)

Query: 89  PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAA 148
               LFI  L +   + DL Q F  +G V+S +V  D  T  SK +GF+ YD   +  AA
Sbjct: 17  EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAA 76

Query: 149 IRALNRQNFQGSEIIVDF 166
           I+++N        + V  
Sbjct: 77  IQSMNGFQIGMKRLKVQL 94

>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 = 50.9 bits (121), Expect = 1e-09
 Identities = 8/76 (10%), Positives = 27/76 (35%)

Query: 91  RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
            TL++     +  + ++     +   V     +       S+R+ +++   ++     + 
Sbjct: 2   CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 61

Query: 151 ALNRQNFQGSEIIVDF 166
            LN    +G  ++   
Sbjct: 62  KLNGLKIEGYTLVTKV 77

>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 = 51.3 bits (122), Expect = 2e-09
 Identities = 22/82 (26%), Positives = 39/82 (47%)

Query: 85  SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
           S +  +  LF+  L+  S E DLE+ F+ YG +  +    D +T   K + F+ +   + 
Sbjct: 3   SGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEH 62

Query: 145 CLAAIRALNRQNFQGSEIIVDF 166
            + A   ++ Q FQG  + V  
Sbjct: 63  AVKAYAEVDGQVFQGRMLHVLP 84

>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 = 50.1 bits (119), Expect = 2e-09
 Identities = 14/74 (18%), Positives = 32/74 (43%), Gaps = 1/74 (1%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           +F+G L+ N+   D++  F ++GKV    ++ D  T   + +GF+ ++ E         +
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-EI 60

Query: 153 NRQNFQGSEIIVDF 166
           +        +    
Sbjct: 61  HFHEINNKMVECKK 74

>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 = 50.5 bits (120), Expect = 3e-09
 Identities = 18/79 (22%), Positives = 35/79 (44%), Gaps = 4/79 (5%)

Query: 92  TLFIGRLNKNSREADLEQAFAEYGKVIS--VRVVRDFVTGHSKRYGFLEYDCEKACLAAI 149
            LFIG + K  +  ++ +  A+  + +   +          ++ + F+EY+  +A   A 
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 150 RALNRQNFQ--GSEIIVDF 166
           R L     Q  G +I VD+
Sbjct: 63  RKLMPGRIQLWGHQIAVDW 81

>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 = 50.1 bits (119), Expect = 4e-09
 Identities = 14/79 (17%), Positives = 35/79 (44%), Gaps = 3/79 (3%)

Query: 88  DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLA 147
           +    +++G L  + R  D+E  F +YG +  + +           + F+E++  +    
Sbjct: 12  NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR---GGPPFAFVEFEDPRDAED 68

Query: 148 AIRALNRQNFQGSEIIVDF 166
           A+   +  ++ G  + V+F
Sbjct: 69  AVYGRDGYDYDGYRLRVEF 87

>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 = 49.7 bits (118), Expect = 5e-09
 Identities = 14/76 (18%), Positives = 33/76 (43%), Gaps = 1/76 (1%)

Query: 91  RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
           + +F+G + +++ E  L   F +YGK+  + ++ D  +G  + + F+ +D   +    + 
Sbjct: 3   KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV- 61

Query: 151 ALNRQNFQGSEIIVDF 166
                   G    V  
Sbjct: 62  IQKYHTVNGHNCEVRK 77

>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 = 50.7 bits (120), Expect = 7e-09
 Identities = 26/96 (27%), Positives = 38/96 (39%)

Query: 88  DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLA 147
           D  R L +  +     E  L Q F  YG + SV++V D  T  S+ YGF+++    +   
Sbjct: 40  DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQ 99

Query: 148 AIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGG 183
           AI  LN  N     + V               +G G
Sbjct: 100 AIAGLNGFNILNKRLKVALAASGHQRPGIAGAVGDG 135

>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 = 49.2 bits (117), Expect = 7e-09
 Identities = 18/76 (23%), Positives = 31/76 (40%), Gaps = 6/76 (7%)

Query: 91  RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
             LF+G L  +  E ++ + F +YGK   V           K +GF+  +       A  
Sbjct: 9   SRLFVGNLPPDITEEEMRKLFEKYGKAGEVF------IHKDKGFGFIRLETRTLAEIAKV 62

Query: 151 ALNRQNFQGSEIIVDF 166
            L+    +G ++ V F
Sbjct: 63  ELDNMPLRGKQLRVRF 78

>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 = 49.0 bits (116), Expect = 1e-08
 Identities = 23/88 (26%), Positives = 40/88 (45%), Gaps = 6/88 (6%)

Query: 85  SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
           S     +T+FI  L+ +S E  L +   ++G +  VRVV    T HSK   F ++  ++A
Sbjct: 3   SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEA 62

Query: 145 CLAAIRALNRQN------FQGSEIIVDF 166
               + A + +         G ++ VD 
Sbjct: 63  AQKCLAAASLEAEGGGLKLDGRQLKVDL 90

>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 = 47.8 bits (113), Expect = 3e-08
 Identities = 30/78 (38%), Positives = 45/78 (57%)

Query: 89  PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAA 148
             R++F+G +   + E  L+  F+E G V+S R+V D  TG  K YGF EY  ++  L+A
Sbjct: 7   SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSA 66

Query: 149 IRALNRQNFQGSEIIVDF 166
           +R LN + F G  + VD 
Sbjct: 67  MRNLNGREFSGRALRVDN 84

>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 = 47.4 bits (112), Expect = 3e-08
 Identities = 27/81 (33%), Positives = 48/81 (59%), Gaps = 1/81 (1%)

Query: 86  STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKAC 145
           ++D    LF+G L+ ++ E  LEQ F++YG++  V VV+D  T  S+ +GF+ ++     
Sbjct: 2   ASDE-GKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDA 60

Query: 146 LAAIRALNRQNFQGSEIIVDF 166
             A+ A+N ++  G +I VD 
Sbjct: 61  KDAMMAMNGKSVDGRQIRVDQ 81

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.0 bits (111), Expect = 4e-08
 Identities = 17/76 (22%), Positives = 29/76 (38%), Gaps = 7/76 (9%)

Query: 92  TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
            L+IG L+      DL Q F +    +               Y F++Y  +   + AI  
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKLPL------AGQVLLKSGYAFVDYPDQNWAIRAIET 56

Query: 152 LNRQ-NFQGSEIIVDF 166
           L+ +    G  + VD+
Sbjct: 57  LSGKVELHGKIMEVDY 72

>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 = 47.7 bits (113), Expect = 5e-08
 Identities = 13/83 (15%), Positives = 31/83 (37%), Gaps = 4/83 (4%)

Query: 85  SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
           +   P   + +  L        L Q F+++G V+ +         +++    L+Y    +
Sbjct: 2   AGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVS 57

Query: 145 CLAAIRALNRQNFQGSEIIVDFE 167
              A  +L+ QN   +   +  +
Sbjct: 58  AQHAKLSLDGQNIYNACCTLRID 80

>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 = 45.1 bits (106), Expect = 1e-07
 Identities = 21/70 (30%), Positives = 33/70 (47%)

Query: 93  LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
           L+I  L   + + DL +    YGK++S + + D  T   K YGF+++D   A   A+ AL
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 153 NRQNFQGSEI 162
                Q    
Sbjct: 61  KASGVQAQMA 70

>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 = 45.5 bits (107), Expect = 2e-07
 Identities = 15/90 (16%), Positives = 28/90 (31%), Gaps = 9/90 (10%)

Query: 85  SSTDPTRTLFI--GRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCE 142
           + +  T++L +  G L        L     + G V ++          +K Y F  Y   
Sbjct: 13  TVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALL------MPPNKPYSFARYRTT 66

Query: 143 KACLAAIRALN-RQNFQGSEIIVDFECGRV 171
           +    A   LN ++        +      V
Sbjct: 67  EESKRAYVTLNGKEVVDDLGQKITLYLNFV 96

>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 = 44.9 bits (106), Expect = 4e-07
 Identities = 10/67 (14%), Positives = 24/67 (35%), Gaps = 4/67 (5%)

Query: 104 EADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEII 163
             DL    +++G++  + +      G       + +   +     I+ L+ + F G +I 
Sbjct: 33  REDLRVECSKFGQIRKLLLFDRHPDG----VASVSFRDPEEADYCIQTLDGRWFGGRQIT 88

Query: 164 VDFECGR 170
                G 
Sbjct: 89  AQAWDGT 95

>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 = 43.9 bits (103), Expect = 6e-07
 Identities = 13/78 (16%), Positives = 30/78 (38%), Gaps = 8/78 (10%)

Query: 89  PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAA 148
              TL++   +       L  AF+ +G +I +           +   F+ Y+  ++   A
Sbjct: 4   KGNTLYVYGEDMT--PTLLRGAFSPFGNIIDLS------MDPPRNCAFVTYEKMESADQA 55

Query: 149 IRALNRQNFQGSEIIVDF 166
           +  LN    +  ++ V+ 
Sbjct: 56  VAELNGTQVESVQLKVNI 73

>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 = 43.9 bits (103), Expect = 7e-07
 Identities = 18/80 (22%), Positives = 34/80 (42%), Gaps = 8/80 (10%)

Query: 89  PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAA 148
           PT  L++G L  N+  A L + F  +G + ++             + +++Y+   A  AA
Sbjct: 16  PTTRLWVGGLGPNTSLAALAREFDRFGSIRTID------HVKGDSFAYIQYESLDAAQAA 69

Query: 149 IRALNRQNFQGSE--IIVDF 166
              +      G +  + VDF
Sbjct: 70  CAKMRGFPLGGPDRRLRVDF 89

>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 = 44.2 bits (104), Expect = 8e-07
 Identities = 16/90 (17%), Positives = 32/90 (35%), Gaps = 12/90 (13%)

Query: 89  PTRTLFIGRL-------NKNSREA---DLEQAFAEYGKVISVRVVRDFVTGHSKRYGF-- 136
           PT  L +  +       +    E    D+    ++YG V S+ + R          G   
Sbjct: 3   PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIF 62

Query: 137 LEYDCEKACLAAIRALNRQNFQGSEIIVDF 166
           +E+     C  A++ L  + F    ++  +
Sbjct: 63  VEFTSVFDCQKAMQGLTGRKFANRVVVTKY 92

>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 = 42.9 bits (100), Expect = 1e-06
 Identities = 13/78 (16%), Positives = 31/78 (39%), Gaps = 6/78 (7%)

Query: 91  RTLFIGRLNKNSREADL---EQAFAEYGKVISVRVVRDFVTGHSKRYGF---LEYDCEKA 144
             +F+  L++   + ++    + F ++GK+  V +        S+       + Y   + 
Sbjct: 9   NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSED 68

Query: 145 CLAAIRALNRQNFQGSEI 162
            L AI+ +N     G  +
Sbjct: 69  ALRAIQCVNNVVVDGRTL 86

>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 = 42.0 bits (98), Expect = 3e-06
 Identities = 14/79 (17%), Positives = 31/79 (39%), Gaps = 5/79 (6%)

Query: 89  PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAA 148
           P+ TL +  +  +  E DL+  F+  G V    V         ++   ++    +  + A
Sbjct: 9   PSATLHLSNIPPSVSEEDLKVLFSSNGGV----VKGFKFFQKDRKMALIQMGSVEEAVQA 64

Query: 149 IRALNRQNF-QGSEIIVDF 166
           +  L+  +  +   + V F
Sbjct: 65  LIDLHNHDLGENHHLRVSF 83

>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 = 42.0 bits (98), Expect = 3e-06
 Identities = 11/77 (14%), Positives = 37/77 (48%), Gaps = 2/77 (2%)

Query: 90  TRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAI 149
            R+++I     ++   D+++   + G+V++   +R  +    K   F+ +D  ++    +
Sbjct: 6   NRSVYIKGFPTDATLDDIKEWLEDKGQVLN-IQMRRTLHKAFKGSIFVVFDSIESAKKFV 64

Query: 150 RALNRQNFQGSEIIVDF 166
                Q ++ +++++ F
Sbjct: 65  -ETPGQKYKETDLLILF 80

>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 = 42.5 bits (99), Expect = 3e-06
 Identities = 14/85 (16%), Positives = 28/85 (32%), Gaps = 11/85 (12%)

Query: 87  TDPTRTLFIGRLN-----KNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDC 141
           +  +  L     N     ++   A  E  F  Y K  + +         S +   + +  
Sbjct: 2   SSGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYF------KSFKRVRINFSN 55

Query: 142 EKACLAAIRALNRQNFQGSEIIVDF 166
             +   A   L++  F G E+ + F
Sbjct: 56  PLSAADARLRLHKTEFLGKEMKLYF 80

>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 = 41.2 bits (96), Expect = 6e-06
 Identities = 11/84 (13%), Positives = 24/84 (28%), Gaps = 9/84 (10%)

Query: 86  STDPTRTLFIGRLNKNS-READLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
             +  R + I    +       L Q    +G + +  ++      +     F+E    + 
Sbjct: 4   RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLIL------NKINEAFIEMATTED 57

Query: 145 CLAAIRA--LNRQNFQGSEIIVDF 166
             AA+           G  + V  
Sbjct: 58  AQAAVDYYTTTPALVFGKPVRVHL 81

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 40.9 bits (95), Expect = 7e-06
 Identities = 14/78 (17%), Positives = 30/78 (38%), Gaps = 3/78 (3%)

Query: 91  RTLFIGRLNKN-SREADLEQAFAEYGKVISVRVVRDF-VTGHSKRYGFLEYDCEKACLAA 148
           R + I  L+     E  L ++F  +G +  + +         +    F+ ++ + +   A
Sbjct: 5   REIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERA 64

Query: 149 IRALNRQNFQGSEIIVDF 166
           +  +NR      EI V  
Sbjct: 65  L-QMNRSLLGNREISVSL 81

>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 = 40.8 bits (95), Expect = 7e-06
 Identities = 12/80 (15%), Positives = 34/80 (42%), Gaps = 7/80 (8%)

Query: 87  TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACL 146
           +  +  +F+GR   +  E +L + F++YG V+ V + +       + + F+ +  ++   
Sbjct: 2   SSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK-----PFRAFAFVTFADDQIAQ 56

Query: 147 AAIRALNRQNFQGSEIIVDF 166
           +          +G  + +  
Sbjct: 57  SLCG--EDLIIKGISVHISN 74

>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 = 40.5 bits (94), Expect = 1e-05
 Identities = 17/77 (22%), Positives = 30/77 (38%), Gaps = 2/77 (2%)

Query: 88  DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLA 147
           DPT  L+I  L  +  E +LE    +    +    +    +G S+  GF   +  + C A
Sbjct: 17  DPT-NLYISNLPLSMDEQELEN-MLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEA 74

Query: 148 AIRALNRQNFQGSEIIV 164
            I   N +  +    + 
Sbjct: 75  VIGHFNGKFIKTPPGVS 91

>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 = 40.5 bits (94), Expect = 2e-05
 Identities = 21/112 (18%), Positives = 35/112 (31%), Gaps = 8/112 (7%)

Query: 91  RTLFIGRLN-KNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAI 149
             L +  LN +      L   F  YG V  V+++      + K    ++         A+
Sbjct: 3   SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILF-----NKKENALVQMADGNQAQLAM 57

Query: 150 RALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWGGNRNSGQLRFGGRNKP 201
             LN     G  I +     + +    PR      G  ++ G        KP
Sbjct: 58  SHLNGHKLHGKPIRITLSKHQNVQ--LPREGQEDQGLTKDYGNSPLHRFKKP 107

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.7 bits (92), Expect = 2e-05
 Identities = 12/77 (15%), Positives = 30/77 (38%), Gaps = 7/77 (9%)

Query: 90  TRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAI 149
           +  + +  L ++S   ++     +Y                +KR  F+     +    AI
Sbjct: 5   SSGILVKNLPQDSNCQEVHDLLKDYDLKYCYVD-------RNKRTAFVTLLNGEQAQNAI 57

Query: 150 RALNRQNFQGSEIIVDF 166
           +  ++ +F+G ++IV  
Sbjct: 58  QMFHQYSFRGKDLIVQL 74

>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 = 39.5 bits (91), Expect = 3e-05
 Identities = 24/86 (27%), Positives = 43/86 (50%), Gaps = 2/86 (2%)

Query: 85  SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
           S +     LFIG LN N   A+L+ A +E      + VV    TG ++++G+++++  + 
Sbjct: 8   SESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVDFESAED 66

Query: 145 CLAAIRALNRQNFQGSEIIVDFECGR 170
              A+  L      G+EI ++   GR
Sbjct: 67  LEKALE-LTGLKVFGNEIKLEKPKGR 91

>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 = 38.4 bits (88), Expect = 8e-05
 Identities = 13/95 (13%), Positives = 30/95 (31%), Gaps = 6/95 (6%)

Query: 85  SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
           SS      +    L   +  A++++ F+ +G +  V                +E+     
Sbjct: 5   SSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVL------LPEGGITAIVEFLEPLE 58

Query: 145 CLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRR 179
              A R L    F    + +++    V      ++
Sbjct: 59  ARKAFRHLAYSKFHHVPLYLEWAPIGVFGAAPQKK 93

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 37.9 bits (87), Expect = 1e-04
 Identities = 11/73 (15%), Positives = 27/73 (36%), Gaps = 6/73 (8%)

Query: 86  STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKAC 145
               +  + +  L ++  EADL +A  ++G +  V ++        KR   +E++   + 
Sbjct: 11  KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMM------PFKRQALVEFENIDSA 64

Query: 146 LAAIRALNRQNFQ 158
              +         
Sbjct: 65  KECVTFAADVPVY 77

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.3 bits (83), Expect = 5e-04
 Identities = 14/81 (17%), Positives = 27/81 (33%), Gaps = 7/81 (8%)

Query: 86  STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKAC 145
           +      + +  L  +    DL+    E G V        +        G +EY  ++  
Sbjct: 11  TRRSDFRVLVSGLPPSGSWQDLKDHMREAGDV-------CYADVQKDGMGMVEYLRKEDM 63

Query: 146 LAAIRALNRQNFQGSEIIVDF 166
             A+R L+   F+  E    +
Sbjct: 64  EYALRKLDDTKFRSHEGETSY 84

>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 = 35.2 bits (80), Expect = 0.001
 Identities = 14/80 (17%), Positives = 28/80 (35%), Gaps = 8/80 (10%)

Query: 89  PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAA 148
           P+R L I +L     E ++      +        V + +    K   FLE   E+A +  
Sbjct: 7   PSRVLHIRKLPGEVTETEVIALGLPF------GKVTNILMLKGKNQAFLELATEEAAITM 60

Query: 149 IRA--LNRQNFQGSEIIVDF 166
           +        + +   I + +
Sbjct: 61  VNYYSAVTPHLRNQPIYIQY 80

>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 = 34.5 bits (79), Expect = 0.001
 Identities = 11/72 (15%), Positives = 26/72 (36%), Gaps = 8/72 (11%)

Query: 92  TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
            + +    + S    L   FA+YG ++   +           +  + Y  +     A+ +
Sbjct: 6   WVTVFGFPQASASYIL-LQFAQYGNILKHVMSNT------GNWMHIRYQSKLQARKAL-S 57

Query: 152 LNRQNFQGSEII 163
            + + F  S +I
Sbjct: 58  KDGRIFGESIMI 69

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 33.3 bits (75), Expect = 0.004
 Identities = 15/83 (18%), Positives = 28/83 (33%), Gaps = 6/83 (7%)

Query: 85  SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
           +   P + LF+  L + + E  L   F ++            +  +     F+E+  E  
Sbjct: 3   TEQPPNQILFLTNLPEETNEMMLSMLFNQFPG-----FKEVRLVPNRHDIAFVEFTTELQ 57

Query: 145 CLAAIRALNRQNF-QGSEIIVDF 166
             AA  AL          + + F
Sbjct: 58  SNAAKEALQGFKITPTHAMKITF 80

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	225
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.89
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.89
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.88
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.88
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.88
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.88
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.88
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.88
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.88
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.88
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.87
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.87
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.87
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.87
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.86
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.86
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.86
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.86
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.86
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.86
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.86
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.86
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.86
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.86
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.85
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.85
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.85
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.85
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.85
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.85
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.84
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.84
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.84
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.84
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.84
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.83
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.83
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.83
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.83
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.83
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.83
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.82
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.82
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.82
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.81
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.81
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.8
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.8
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.8
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.8
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.8
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.79
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.79
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.79
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.79
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.79
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.79
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.79
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.79
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.79
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.79
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.79
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.79
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.78
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.78
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.78
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.78
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.78
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.77
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.75
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.75
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.75
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.74
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.74
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.72
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.7
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.69
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.69
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.66
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.66
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	U2	99.6
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.56
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.55
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.55
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.5
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.48
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.41
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.74
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.65
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.48
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	96.41

>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=1.9e-22  Score=149.72  Aligned_cols=85  Identities=28%  Similarity=0.442  Sum_probs=80.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEe
Q psy222           88 DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFE  167 (225)
Q Consensus        88 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a  167 (225)
                      ...++|||+|||+++++++|+++|++||.|..|.|++++.+++++|||||+|.+.++|++||+.||+..|+|+.|+|+++
T Consensus        40 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a  119 (139)
T d1u6fa1          40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALA  119 (139)
T ss_dssp             TTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            34568999999999999999999999999999999999989999999999999999999999999999999999999999


Q ss_pred             eCCCC
Q psy222          168 CGRVL  172 (225)
Q Consensus       168 ~~~~~  172 (225)
                      +++..
T Consensus       120 ~~~~~  124 (139)
T d1u6fa1         120 ASGHQ  124 (139)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            87553

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.89  E-value=1e-22  Score=139.64  Aligned_cols=84  Identities=30%  Similarity=0.527  Sum_probs=79.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF  166 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~  166 (225)
                      ..+.++|||+|||+.+++++|+++|++||.|..|+|++++.+++++|||||+|.+.++|++|+..||+..|+|+.|+|+|
T Consensus         4 s~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~   83 (88)
T d1rk8a_           4 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW   83 (88)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            44678999999999999999999999999999999999998999999999999999999999999999999999999999


Q ss_pred             eeCC
Q psy222          167 ECGR  170 (225)
Q Consensus       167 a~~~  170 (225)
                      |.++
T Consensus        84 a~~k   87 (88)
T d1rk8a_          84 CFVK   87 (88)
T ss_dssp             SEEC
T ss_pred             ecCC
Confidence            9875

>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=99.88  E-value=1.2e-22  Score=142.22  Aligned_cols=84  Identities=25%  Similarity=0.359  Sum_probs=79.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEe
Q psy222           88 DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFE  167 (225)
Q Consensus        88 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a  167 (225)
                      ...++|||+|||+.+++++|+++|.+||.|..|.|+.++.+++++|||||+|.+.++|++||+.||+..|+|+.|+|.++
T Consensus         6 ~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a   85 (99)
T d1whwa_           6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS   85 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            45678999999999999999999999999999999999989999999999999999999999999999999999999999


Q ss_pred             eCCC
Q psy222          168 CGRV  171 (225)
Q Consensus       168 ~~~~  171 (225)
                      ..+.
T Consensus        86 ~~~~   89 (99)
T d1whwa_          86 TIKK   89 (99)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            8754

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.88  E-value=6.1e-23  Score=138.85  Aligned_cols=80  Identities=24%  Similarity=0.446  Sum_probs=77.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEeeC
Q psy222           90 TRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECG  169 (225)
Q Consensus        90 ~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~~  169 (225)
                      .++|||+|||+++++++|+++|++||.|..|+|++++.+++++|||||+|.+.++|++||+.||+..|.|+.|+|++|+|
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            36899999999999999999999999999999999988999999999999999999999999999999999999999975

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.88  E-value=8.7e-23  Score=141.40  Aligned_cols=85  Identities=26%  Similarity=0.434  Sum_probs=80.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF  166 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~  166 (225)
                      ..+.++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||+.||+..|+|+.|+|++
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            34557999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeCCC
Q psy222          167 ECGRV  171 (225)
Q Consensus       167 a~~~~  171 (225)
                      |.++.
T Consensus        86 A~~~~   90 (93)
T d1x5ua1          86 ASAHN   90 (93)
T ss_dssp             TTTTS
T ss_pred             cCCCC
Confidence            98764

>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=99.88  E-value=1.7e-22  Score=139.89  Aligned_cols=82  Identities=21%  Similarity=0.366  Sum_probs=78.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEe
Q psy222           88 DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFE  167 (225)
Q Consensus        88 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a  167 (225)
                      ..+++|||+|||+++++++|+++|++||.|.+|.|+.++.++.++|||||+|.+.++|+.||+.||+..|+|+.|+|.|+
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            46789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             eC
Q psy222          168 CG  169 (225)
Q Consensus       168 ~~  169 (225)
                      .+
T Consensus        85 ~~   86 (93)
T d1h2vz_          85 AG   86 (93)
T ss_dssp             SC
T ss_pred             CC
Confidence            65

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.88  E-value=9.7e-23  Score=140.31  Aligned_cols=85  Identities=21%  Similarity=0.428  Sum_probs=80.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF  166 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~  166 (225)
                      ..+.++|||+|||..+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||+.||+..|+|+.|+|++
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            44667999999999999999999999999999999999998999999999999999999999999999999999999999


Q ss_pred             eeCCC
Q psy222          167 ECGRV  171 (225)
Q Consensus       167 a~~~~  171 (225)
                      |+++.
T Consensus        85 akp~~   89 (90)
T d2cq0a1          85 AKPST   89 (90)
T ss_dssp             SSCCC
T ss_pred             eeCCC
Confidence            98753

>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=99.88  E-value=1.7e-22  Score=142.28  Aligned_cols=87  Identities=29%  Similarity=0.383  Sum_probs=81.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q psy222           86 STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD  165 (225)
Q Consensus        86 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~  165 (225)
                      ..++.++|||+|||+++++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|+.||+.||+..|.|+.|+|+
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            34566889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeeCCCC
Q psy222          166 FECGRVL  172 (225)
Q Consensus       166 ~a~~~~~  172 (225)
                      +++++..
T Consensus        94 ~a~~k~~  100 (102)
T d2cpza1          94 LKRSKND  100 (102)
T ss_dssp             CCCCSCC
T ss_pred             EeCCCCC
Confidence            9988654

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.88  E-value=2.1e-22  Score=136.14  Aligned_cols=79  Identities=30%  Similarity=0.472  Sum_probs=76.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEeeC
Q psy222           91 RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECG  169 (225)
Q Consensus        91 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~~  169 (225)
                      .+|||+|||+++++++|+++|++||.|..|+|+.+..++..+|||||+|.+.++|++|++.||+..|+|+.|+|.+|+|
T Consensus         3 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           3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            5799999999999999999999999999999999988999999999999999999999999999999999999999875

>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=99.88  E-value=9.1e-23  Score=140.17  Aligned_cols=83  Identities=23%  Similarity=0.471  Sum_probs=79.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEee
Q psy222           89 PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFEC  168 (225)
Q Consensus        89 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~  168 (225)
                      ..++|||+|||+++++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||..||+..|+|+.|+|++|+
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            45799999999999999999999999999999999999899999999999999999999999999999999999999998


Q ss_pred             CCC
Q psy222          169 GRV  171 (225)
Q Consensus       169 ~~~  171 (225)
                      ++.
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=99.87  E-value=2.8e-22  Score=134.96  Aligned_cols=77  Identities=25%  Similarity=0.483  Sum_probs=75.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEee
Q psy222           92 TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFEC  168 (225)
Q Consensus        92 ~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~  168 (225)
                      +|||+|||+.+++++|+++|++||.|..|+|++++.+++++|||||+|.+.++|..|++.|++..|.|++|+|.+++
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~   78 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999999985

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=1.9e-22  Score=137.37  Aligned_cols=81  Identities=26%  Similarity=0.395  Sum_probs=77.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEeeCC
Q psy222           91 RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECGR  170 (225)
Q Consensus        91 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~~~  170 (225)
                      ++|||+|||+++++++|+++|++||.|..|+|++++.++.++|||||+|.+.++|+.|++.||+..|.|+.|+|.+|.+.
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            57999999999999999999999999999999999999999999999999999999999999999999999999999864


Q ss_pred             C
Q psy222          171 V  171 (225)
Q Consensus       171 ~  171 (225)
                      .
T Consensus        82 ~   82 (85)
T d2u2fa_          82 A   82 (85)
T ss_dssp             C
T ss_pred             C
Confidence            3

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=6e-22  Score=134.23  Aligned_cols=78  Identities=26%  Similarity=0.397  Sum_probs=74.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      ..+.++|||+|||+.+++++|+++|++||.|.+|.|+.++.+++++|||||+|.+.++|++||..||+..|+|+.|+|
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            345679999999999999999999999999999999999989999999999999999999999999999999999987

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=1e-21  Score=138.49  Aligned_cols=82  Identities=24%  Similarity=0.384  Sum_probs=76.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEee
Q psy222           89 PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFEC  168 (225)
Q Consensus        89 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~  168 (225)
                      ..++|||+|||+.+++++|+++|++||.|.+|.|+.++.+++++|||||+|.+.++|++||+.+|+ .|+|+.|+|+++.
T Consensus         9 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a~   87 (103)
T d2cqda1           9 TFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAY   87 (103)
T ss_dssp             SSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEEST
T ss_pred             CCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEEcC
Confidence            456899999999999999999999999999999999999999999999999999999999998775 7999999999987


Q ss_pred             CCC
Q psy222          169 GRV  171 (225)
Q Consensus       169 ~~~  171 (225)
                      ...
T Consensus        88 ~~~   90 (103)
T d2cqda1          88 LGA   90 (103)
T ss_dssp             TTC
T ss_pred             CCC
Confidence            644

>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=99.86  E-value=6.6e-22  Score=136.04  Aligned_cols=84  Identities=31%  Similarity=0.495  Sum_probs=79.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEee
Q psy222           89 PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFEC  168 (225)
Q Consensus        89 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~  168 (225)
                      +.++|||+|||+++++++|+++|++||.|..|.++.+..++.++|||||+|.++++|+.||..||+..|.|+.|+|++|.
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            45689999999999999999999999999999999988899999999999999999999999999999999999999998


Q ss_pred             CCCC
Q psy222          169 GRVL  172 (225)
Q Consensus       169 ~~~~  172 (225)
                      ++..
T Consensus        84 ~~~~   87 (90)
T d1x5sa1          84 KSSD   87 (90)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7653

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=1.1e-21  Score=134.96  Aligned_cols=84  Identities=25%  Similarity=0.418  Sum_probs=77.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF  166 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~  166 (225)
                      .....+|||+|||+++++++|+++|++||.|..|.|++++.++.++|||||+|.+.++|++||+.  .+.|+|+.|.|++
T Consensus         5 ~~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~--~~~l~Gr~i~v~~   82 (90)
T d2cqga1           5 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWCDCKL   82 (90)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTEEEEEEC
T ss_pred             CcCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhc--CCccCCEEeEEEe
Confidence            34567899999999999999999999999999999999999999999999999999999999984  4589999999999


Q ss_pred             eeCCCC
Q psy222          167 ECGRVL  172 (225)
Q Consensus       167 a~~~~~  172 (225)
                      +.++..
T Consensus        83 a~~k~~   88 (90)
T d2cqga1          83 PNSKQS   88 (90)
T ss_dssp             CCTTCC
T ss_pred             CCCCCC
Confidence            987653

>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=99.86  E-value=1.1e-21  Score=133.60  Aligned_cols=79  Identities=35%  Similarity=0.604  Sum_probs=74.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCC--cEEEEEE
Q psy222           89 PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQG--SEIIVDF  166 (225)
Q Consensus        89 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g--~~l~V~~  166 (225)
                      ..++|||+|||+.+++++|+++|++||.|.+|+|++++.++.++|||||+|.+.++|++|++.||+..|.|  ++|+|+|
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            34689999999999999999999999999999999998899999999999999999999999999999987  5599988


Q ss_pred             e
Q psy222          167 E  167 (225)
Q Consensus       167 a  167 (225)
                      |
T Consensus        85 A   85 (85)
T d1fxla2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.86  E-value=1.2e-21  Score=133.24  Aligned_cols=79  Identities=24%  Similarity=0.492  Sum_probs=75.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCC--cEEEEEE
Q psy222           89 PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQG--SEIIVDF  166 (225)
Q Consensus        89 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g--~~l~V~~  166 (225)
                      ...+|||+|||+++++++|+++|++||.|..|+|++++.+++++|||||+|.+.++|++||+.||+..+.|  ++|+|+|
T Consensus         5 ~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~~   84 (85)
T d1b7fa2           5 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRL   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEEE
Confidence            45689999999999999999999999999999999999899999999999999999999999999999976  8899998


Q ss_pred             e
Q psy222          167 E  167 (225)
Q Consensus       167 a  167 (225)
                      |
T Consensus        85 A   85 (85)
T d1b7fa2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.86  E-value=5.1e-22  Score=133.96  Aligned_cols=79  Identities=10%  Similarity=0.235  Sum_probs=69.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEeeC
Q psy222           91 RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECG  169 (225)
Q Consensus        91 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~~  169 (225)
                      ++|||+|||+++++++|+++|++||.|..+.++.+..+++++|||||+|.+.++|++||+.||+..|.|++|+|++++|
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            6999999999999999999999999999998888888899999999999999999999999999999999999999976

>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=99.86  E-value=1.4e-21  Score=135.56  Aligned_cols=85  Identities=16%  Similarity=0.468  Sum_probs=78.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecC-CCCccceEEEEEeCCHHHHHHHHHHh-CCCccCCcEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDF-VTGHSKRYGFLEYDCEKACLAAIRAL-NRQNFQGSEIIV  164 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~-~~g~~kg~afV~F~~~~~a~~Al~~l-~g~~l~g~~l~V  164 (225)
                      .....+|||+|||+++++++|+++|++||.|..|.|+++. .+|.++|||||+|.+.++|++||..| |+..|.|++|+|
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            4466789999999999999999999999999999998875 47899999999999999999999988 899999999999


Q ss_pred             EEeeCCC
Q psy222          165 DFECGRV  171 (225)
Q Consensus       165 ~~a~~~~  171 (225)
                      +||....
T Consensus        85 ~~A~~~~   91 (94)
T d2cpha1          85 EWADSEV   91 (94)
T ss_dssp             EECCCCC
T ss_pred             EEcCCCC
Confidence            9998754

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=1.3e-21  Score=132.81  Aligned_cols=79  Identities=25%  Similarity=0.423  Sum_probs=74.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEee
Q psy222           89 PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFEC  168 (225)
Q Consensus        89 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~  168 (225)
                      ..++|||+|||+++++++|+++|++||.|..|.|++++.+++++|||||+|.+.++|++||+ ++++.|+|+.|+|+.|.
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            34689999999999999999999999999999999999999999999999999999999998 69999999999998874

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=5.9e-22  Score=134.24  Aligned_cols=80  Identities=31%  Similarity=0.505  Sum_probs=75.1

Q ss_pred             EEEcCCCCCCCHHHHHHHHhcCCceeEE-EEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEeeCCC
Q psy222           93 LFIGRLNKNSREADLEQAFAEYGKVISV-RVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECGRV  171 (225)
Q Consensus        93 l~V~nLp~~~te~~L~~~F~~~G~v~~v-~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~~~~  171 (225)
                      |||+|||+++++++|+++|++||.|..+ .|++++.+++++|||||+|.+.++|++||+.|++..|+|++|+|.+|.++.
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            8999999999999999999999998764 788898899999999999999999999999999999999999999998765


Q ss_pred             C
Q psy222          172 L  172 (225)
Q Consensus       172 ~  172 (225)
                      .
T Consensus        81 ~   81 (83)
T d1x5ta1          81 S   81 (83)
T ss_dssp             C
T ss_pred             c
Confidence            3

>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=99.86  E-value=7.5e-22  Score=139.07  Aligned_cols=82  Identities=24%  Similarity=0.416  Sum_probs=77.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEeeCC
Q psy222           91 RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECGR  170 (225)
Q Consensus        91 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~~~  170 (225)
                      ++|||+|||+++++++|+++|++||.|..+.|++++.++.++|||||+|.+.++|++||+ ++++.|+|+.|.|++|.++
T Consensus        21 ~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~~k   99 (103)
T d1x4ba1          21 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVAR   99 (103)
T ss_dssp             TEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCSSC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECccc
Confidence            689999999999999999999999999999999999899999999999999999999997 7999999999999999887


Q ss_pred             CCC
Q psy222          171 VLP  173 (225)
Q Consensus       171 ~~~  173 (225)
                      ..+
T Consensus       100 e~~  102 (103)
T d1x4ba1         100 EES  102 (103)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            643

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.86  E-value=1.5e-21  Score=130.63  Aligned_cols=76  Identities=21%  Similarity=0.379  Sum_probs=73.5

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEee
Q psy222           92 TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFEC  168 (225)
Q Consensus        92 ~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~  168 (225)
                      +|||+|||+++++++|+++|++||.|..|+|+.++ +++++|||||+|.+.++|++|++.||+..|.|+.|+|+++.
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~   77 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEee-ccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            69999999999999999999999999999999986 89999999999999999999999999999999999999985

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=4.1e-21  Score=132.81  Aligned_cols=85  Identities=25%  Similarity=0.446  Sum_probs=77.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q psy222           86 STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD  165 (225)
Q Consensus        86 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~  165 (225)
                      .....++|||+|||+.+++++|+++|++||.|..|.|+.++  +..+|||||+|.+.++|++||..||+..|+|+.|+|+
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            34456789999999999999999999999999999999885  3468999999999999999999999999999999999


Q ss_pred             EeeCCCC
Q psy222          166 FECGRVL  172 (225)
Q Consensus       166 ~a~~~~~  172 (225)
                      +|+++..
T Consensus        85 ~A~~r~~   91 (93)
T d2cq3a1          85 NATARVM   91 (93)
T ss_dssp             ECCSSCC
T ss_pred             ecCcCCC
Confidence            9998754

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.85  E-value=2.8e-22  Score=133.92  Aligned_cols=76  Identities=22%  Similarity=0.411  Sum_probs=73.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEe
Q psy222           91 RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFE  167 (225)
Q Consensus        91 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a  167 (225)
                      |+|||+|||+++++++|+++|++||.|..+.|++++.+++++|||||+|.++++|++||+ ++++.|+|+.|.|+.|
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            589999999999999999999999999999999999999999999999999999999998 7999999999999986

>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=99.85  E-value=1.1e-21  Score=138.55  Aligned_cols=81  Identities=37%  Similarity=0.648  Sum_probs=77.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEeeC
Q psy222           90 TRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECG  169 (225)
Q Consensus        90 ~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~~  169 (225)
                      .++|||+|||+++++++|+++|++||.|..|.|++++.+++++|||||+|.+.++|++||+.||+..|.|+.|+|+++.+
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            36899999999999999999999999999999999998999999999999999999999999999999999999999875


Q ss_pred             C
Q psy222          170 R  170 (225)
Q Consensus       170 ~  170 (225)
                      .
T Consensus        88 ~   88 (104)
T d1p1ta_          88 E   88 (104)
T ss_dssp             T
T ss_pred             C
Confidence            3

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.85  E-value=1.9e-21  Score=132.31  Aligned_cols=78  Identities=24%  Similarity=0.405  Sum_probs=72.7

Q ss_pred             EEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCC---ccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEeeC
Q psy222           93 LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTG---HSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECG  169 (225)
Q Consensus        93 l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g---~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~~  169 (225)
                      |||+|||+++++++|+++|++||.|..|.|++++.++   .++|||||+|.+.++|++|++.||+..|+|+.|+|+++..
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            8999999999999999999999999999999887554   4689999999999999999999999999999999999865


Q ss_pred             C
Q psy222          170 R  170 (225)
Q Consensus       170 ~  170 (225)
                      .
T Consensus        81 ~   81 (85)
T d2cpfa1          81 A   81 (85)
T ss_dssp             S
T ss_pred             C
Confidence            3

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=4.3e-21  Score=131.91  Aligned_cols=83  Identities=24%  Similarity=0.466  Sum_probs=75.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF  166 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~  166 (225)
                      ..+.++|||+|||..+++++|+++|++||.|..|.|+.++.++  ++||||+|.+.++|+.|+..||+..|.|+.|+|.+
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            4456799999999999999999999999999999999886443  78999999999999999999999999999999999


Q ss_pred             eeCCC
Q psy222          167 ECGRV  171 (225)
Q Consensus       167 a~~~~  171 (225)
                      |++..
T Consensus        83 a~~~~   87 (90)
T d2cqia1          83 ATTPS   87 (90)
T ss_dssp             CCCTT
T ss_pred             cCCCC
Confidence            98643

>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=99.85  E-value=1.9e-21  Score=129.23  Aligned_cols=75  Identities=23%  Similarity=0.462  Sum_probs=71.4

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEe
Q psy222           92 TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFE  167 (225)
Q Consensus        92 ~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a  167 (225)
                      +|||+|||+++++++|+++|++||.|..|.|++++.+++++|||||+|.+.++|++||+ +++..|+|+.|.|+.|
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            59999999999999999999999999999999999999999999999999999999998 7999999999998653

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=7.5e-21  Score=127.48  Aligned_cols=77  Identities=18%  Similarity=0.436  Sum_probs=73.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEe
Q psy222           90 TRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFE  167 (225)
Q Consensus        90 ~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a  167 (225)
                      .++|||+|||+++|+++|+++|++||.|..+.++.++.++..+|||||+|.+.+++++|++ |+++.|+|+.|+|+.|
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            3689999999999999999999999999999999999999999999999999999999997 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=99.84  E-value=8.4e-21  Score=132.34  Aligned_cols=85  Identities=27%  Similarity=0.396  Sum_probs=78.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhC------CCccCCc
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALN------RQNFQGS  160 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~------g~~l~g~  160 (225)
                      ..+.++|||+|||+++++++|+++|.+||.|..+.++.+..++.++|||||+|.+.++|.+||+.|+      +..|.|+
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            4456899999999999999999999999999999999998899999999999999999999999887      5678999


Q ss_pred             EEEEEEeeCCC
Q psy222          161 EIIVDFECGRV  171 (225)
Q Consensus       161 ~l~V~~a~~~~  171 (225)
                      .|+|+++.++.
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

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=1.5e-21  Score=137.05  Aligned_cols=79  Identities=33%  Similarity=0.416  Sum_probs=75.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEeeC
Q psy222           90 TRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECG  169 (225)
Q Consensus        90 ~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~~  169 (225)
                      .++|||+|||+.+++++|+++|+.||.|..|.|++++.+++++|||||+|.+.++|++||. ||+..|.|+.|+|.++.+
T Consensus        18 ~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a~~   96 (101)
T d2cq4a1          18 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQA   96 (101)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECCC
Confidence            4689999999999999999999999999999999999899999999999999999999996 999999999999999865

>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=99.84  E-value=3.3e-21  Score=132.23  Aligned_cols=80  Identities=28%  Similarity=0.460  Sum_probs=74.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEeeC
Q psy222           90 TRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECG  169 (225)
Q Consensus        90 ~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~~  169 (225)
                      ..+|||+|||+++++++|+++|++||.|..|+|+.+.  +.++|||||+|.+.++|++||+.||+..|+|+.|+|.++++
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            4589999999999999999999999999999999885  44689999999999999999999999999999999999987


Q ss_pred             CC
Q psy222          170 RV  171 (225)
Q Consensus       170 ~~  171 (225)
                      +.
T Consensus        86 ~~   87 (89)
T d1cvja2          86 RK   87 (89)
T ss_dssp             TT
T ss_pred             CC
Confidence            64

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=1.5e-21  Score=129.58  Aligned_cols=75  Identities=19%  Similarity=0.364  Sum_probs=71.3

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEe
Q psy222           92 TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFE  167 (225)
Q Consensus        92 ~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a  167 (225)
                      +|||+|||+++++++|+++|++||.|..|.|+.++.+++++|||||+|.+.++|++||+ ++++.|+|+.|.|+.|
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            59999999999999999999999999999999999999999999999999999999998 5778999999999875

>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=99.83  E-value=1.1e-20  Score=132.52  Aligned_cols=85  Identities=22%  Similarity=0.346  Sum_probs=77.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCcee--------EEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccC
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVI--------SVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQ  158 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~--------~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~  158 (225)
                      ..+..+|||+|||+.+++++|+++|.+||.|.        .+.+..++.+++.++||||+|.++++|.+||+.||+..|+
T Consensus         5 ~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~   84 (101)
T d2cpea1           5 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQ   84 (101)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEET
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEEC
Confidence            45678999999999999999999999999874        5677778888999999999999999999999999999999


Q ss_pred             CcEEEEEEeeCCC
Q psy222          159 GSEIIVDFECGRV  171 (225)
Q Consensus       159 g~~l~V~~a~~~~  171 (225)
                      |+.|+|++|+++.
T Consensus        85 gr~i~V~~a~~~~   97 (101)
T d2cpea1          85 GSKLKVSLARKKP   97 (101)
T ss_dssp             TEECEEECSSCCC
T ss_pred             CEEEEEEEcCCCC
Confidence            9999999998754

>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=99.83  E-value=4.2e-21  Score=130.86  Aligned_cols=82  Identities=17%  Similarity=0.304  Sum_probs=71.7

Q ss_pred             CCCeEEEcCCCCCCC-HHHHHHHHhcCCceeEEEEeec-CCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEE
Q psy222           89 PTRTLFIGRLNKNSR-EADLEQAFAEYGKVISVRVVRD-FVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF  166 (225)
Q Consensus        89 ~~~~l~V~nLp~~~t-e~~L~~~F~~~G~v~~v~i~~~-~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~  166 (225)
                      +.++|||+|||++++ +++|+++|++||.|..|.|+.+ ..+++++|||||+|.+.++|++||+ ||++.|+|+.|+|.+
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            467999999999976 5669999999999999998764 5688999999999999999999996 999999999999999


Q ss_pred             eeCCC
Q psy222          167 ECGRV  171 (225)
Q Consensus       167 a~~~~  171 (225)
                      +.+++
T Consensus        82 a~~kP   86 (86)
T d2ghpa3          82 ADKKP   86 (86)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            98753

>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=99.83  E-value=1.6e-20  Score=132.42  Aligned_cols=85  Identities=24%  Similarity=0.373  Sum_probs=74.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecC-CCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDF-VTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD  165 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~-~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~  165 (225)
                      ..+.++|||+|||+.+++++|+++|+.|| +..+.++.+. .+++++|||||+|.+.++|++|++ ||+..|+|+.|+|.
T Consensus        12 ~~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~-~~~~~~~gr~l~V~   89 (104)
T d1wi8a_          12 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLGNKRIRVD   89 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHG-GGTCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHH-cCCCEECCEEEEEE
Confidence            44668999999999999999999999999 7788777665 478899999999999999987775 99999999999999


Q ss_pred             EeeCCCCC
Q psy222          166 FECGRVLP  173 (225)
Q Consensus       166 ~a~~~~~~  173 (225)
                      ++.++...
T Consensus        90 ~a~~~~~~   97 (104)
T d1wi8a_          90 VADQAQDK   97 (104)
T ss_dssp             ECCCCCCC
T ss_pred             ECCCCCCC
Confidence            99876543

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.83  E-value=7.6e-21  Score=126.12  Aligned_cols=75  Identities=19%  Similarity=0.396  Sum_probs=72.2

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEe
Q psy222           92 TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFE  167 (225)
Q Consensus        92 ~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a  167 (225)
                      +|||+|||+++++++|+++|++||.|..+.++.++.++..++||||+|.+.++|++||+ ||++.|+|+.|+|++|
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            59999999999999999999999999999999999899999999999999999999997 9999999999999876

>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=99.83  E-value=2.7e-20  Score=129.11  Aligned_cols=81  Identities=17%  Similarity=0.422  Sum_probs=73.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF  166 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~  166 (225)
                      ..+.++|||+|||+.+++++|+++|++||.|..+.+..+   ...++||||+|.+.++|+.||+.||++.|.|++|+|++
T Consensus        11 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~---~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~   87 (95)
T d1x4aa1          11 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEF   87 (95)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc---ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            456679999999999999999999999999999887654   45689999999999999999999999999999999999


Q ss_pred             eeCC
Q psy222          167 ECGR  170 (225)
Q Consensus       167 a~~~  170 (225)
                      |++.
T Consensus        88 a~~~   91 (95)
T d1x4aa1          88 PRSG   91 (95)
T ss_dssp             CCCC
T ss_pred             ccCC
Confidence            8753

>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=99.83  E-value=2.6e-21  Score=135.99  Aligned_cols=86  Identities=17%  Similarity=0.380  Sum_probs=80.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q psy222           86 STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD  165 (225)
Q Consensus        86 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~  165 (225)
                      ...++++|||+|||.++++++|+++|.+||.|..+.++.+..++++++||||+|.+.++|++||+.||+..|.|++|+|+
T Consensus        14 ~~~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   93 (102)
T d2cpxa1          14 PGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIE   93 (102)
T ss_dssp             CCSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999998887789999999999999999999999999999999999999


Q ss_pred             EeeCCC
Q psy222          166 FECGRV  171 (225)
Q Consensus       166 ~a~~~~  171 (225)
                      |++++.
T Consensus        94 ~ak~k~   99 (102)
T d2cpxa1          94 FGKNKK   99 (102)
T ss_dssp             ECCCCS
T ss_pred             eCCCcc
Confidence            998764

>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=99.82  E-value=4.3e-20  Score=132.27  Aligned_cols=80  Identities=18%  Similarity=0.268  Sum_probs=73.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF  166 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~  166 (225)
                      ...+++|||+|||+.+++++|+++|++||.|..|.+..+   +..+|||||+|.+.++|..||+.|||+.|.|+.|+|.+
T Consensus         4 p~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~---~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~   80 (114)
T d2f9da1           4 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLY   80 (114)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc---CCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            345689999999999999999999999999999998754   55689999999999999999999999999999999999


Q ss_pred             eeC
Q psy222          167 ECG  169 (225)
Q Consensus       167 a~~  169 (225)
                      +..
T Consensus        81 a~~   83 (114)
T d2f9da1          81 YNA   83 (114)
T ss_dssp             CCH
T ss_pred             cCC
Confidence            864

>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=99.82  E-value=5.4e-20  Score=124.42  Aligned_cols=78  Identities=23%  Similarity=0.347  Sum_probs=71.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCcc-CCcEEEE
Q psy222           86 STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNF-QGSEIIV  164 (225)
Q Consensus        86 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l-~g~~l~V  164 (225)
                      ..+|+++|||+|||..+++++|+.+|++||.|..|++++++     +|||||+|.+.++|..|++.|||..| +++.|+|
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            45678899999999999999999999999999999998653     78999999999999999999999988 4689999


Q ss_pred             EEee
Q psy222          165 DFEC  168 (225)
Q Consensus       165 ~~a~  168 (225)
                      .||+
T Consensus        79 ~~ak   82 (83)
T d2b0ga1          79 TFAK   82 (83)
T ss_dssp             EECC
T ss_pred             EEec
Confidence            9986

>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=99.82  E-value=4.1e-20  Score=128.46  Aligned_cols=78  Identities=18%  Similarity=0.409  Sum_probs=72.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEe
Q psy222           88 DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFE  167 (225)
Q Consensus        88 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a  167 (225)
                      +..++|||+|||..+++++|+++|++||.|.+|+|+.+      +|||||+|.+.++|++||..||+..|+|+.|+|.|+
T Consensus        16 ~~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~a   89 (96)
T d1x4ga1          16 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWG   89 (96)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            34578999999999999999999999999999999876      789999999999999999999999999999999998


Q ss_pred             eCCC
Q psy222          168 CGRV  171 (225)
Q Consensus       168 ~~~~  171 (225)
                      ++++
T Consensus        90 k~~p   93 (96)
T d1x4ga1          90 KESP   93 (96)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7643

>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=99.81  E-value=4.2e-21  Score=132.25  Aligned_cols=82  Identities=28%  Similarity=0.442  Sum_probs=75.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF  166 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~  166 (225)
                      ....++|||+|||+.+++++|+++|+.||.|..+.|+.+ .+++++|||||+|.+.++|++||+ ||+..|+|+.|+|++
T Consensus        10 ~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~   87 (91)
T d1fjeb1          10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEK   87 (91)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEEC
T ss_pred             CCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEe
Confidence            445679999999999999999999999999998888755 489999999999999999999997 999999999999999


Q ss_pred             eeCC
Q psy222          167 ECGR  170 (225)
Q Consensus       167 a~~~  170 (225)
                      |+.|
T Consensus        88 ak~k   91 (91)
T d1fjeb1          88 PKGR   91 (91)
T ss_dssp             CCCS
T ss_pred             cCCC
Confidence            8764

>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=99.81  E-value=3.7e-20  Score=129.86  Aligned_cols=84  Identities=25%  Similarity=0.406  Sum_probs=76.0

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      ....+.++|||+|||+++++++|+++|++||.|..+.++.+. ++.++|||||+|.+.++|++||+.|||..|.|+++.|
T Consensus        13 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~-~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v   91 (101)
T d1x5oa1          13 QQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVS   91 (101)
T ss_dssp             CCCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSC
T ss_pred             cccCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeeccc-ccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCcc
Confidence            334556799999999999999999999999999999998885 8889999999999999999999999999999998888


Q ss_pred             EEeeC
Q psy222          165 DFECG  169 (225)
Q Consensus       165 ~~a~~  169 (225)
                      ..++|
T Consensus        92 ~~~~P   96 (101)
T d1x5oa1          92 APTEP   96 (101)
T ss_dssp             CCSSC
T ss_pred             CCCCC
Confidence            76654

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=1.3e-19  Score=123.11  Aligned_cols=77  Identities=14%  Similarity=0.342  Sum_probs=72.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEee
Q psy222           90 TRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFEC  168 (225)
Q Consensus        90 ~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~  168 (225)
                      .++|||+|||+++++++|+++|+.||.|..|.|..+. +++++|||||+|.+.++|++||+ +++..|.|+.|.|.++.
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            4689999999999999999999999999999998875 89999999999999999999997 79999999999999864

>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=99.80  E-value=1.5e-19  Score=123.59  Aligned_cols=79  Identities=16%  Similarity=0.328  Sum_probs=71.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCcc-CCcEEEEEE
Q psy222           88 DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNF-QGSEIIVDF  166 (225)
Q Consensus        88 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l-~g~~l~V~~  166 (225)
                      +|+++|||+|||+++++++|+++|++||.|..+.+...    +.++||||+|.+.++|.+|+..||+..| +|+.|+|.|
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 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSF   83 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS----SSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeee----cccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEe
Confidence            56789999999999999999999999999988877644    3578999999999999999999999988 589999999


Q ss_pred             eeCC
Q psy222          167 ECGR  170 (225)
Q Consensus       167 a~~~  170 (225)
                      ++++
T Consensus        84 sk~~   87 (88)
T d2adca2          84 SKST   87 (88)
T ss_dssp             CSSC
T ss_pred             CCCC
Confidence            8764

>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=9.6e-20  Score=127.94  Aligned_cols=83  Identities=13%  Similarity=0.163  Sum_probs=74.6

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q psy222           86 STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD  165 (225)
Q Consensus        86 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~  165 (225)
                      .....++|||+|||+++|+++|+++|..|+ +..|.++.+. ++..+|||||+|.+.++|++||+ ||++.|+|+.|+|.
T Consensus        11 ~~~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~~-~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~   87 (102)
T d1weza_          11 QSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELF   87 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEec-CCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEE
Confidence            345668999999999999999999999998 5578888775 68899999999999999999997 89999999999999


Q ss_pred             EeeCCC
Q psy222          166 FECGRV  171 (225)
Q Consensus       166 ~a~~~~  171 (225)
                      ++..+.
T Consensus        88 ~s~~~~   93 (102)
T d1weza_          88 LNSTAG   93 (102)
T ss_dssp             EECCCC
T ss_pred             EcCCCC
Confidence            988754

>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=99.80  E-value=1.1e-19  Score=126.61  Aligned_cols=76  Identities=25%  Similarity=0.488  Sum_probs=68.9

Q ss_pred             CCCCCeEEEcCCC-CCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q psy222           87 TDPTRTLFIGRLN-KNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD  165 (225)
Q Consensus        87 ~~~~~~l~V~nLp-~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~  165 (225)
                      ....++|||+||+ ..+++++|+++|++||.|..|.|.        +|||||+|.+.++|++||+.||++.|.|+.|+|+
T Consensus        12 ~~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~--------rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~   83 (98)
T d1wf2a_          12 RSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH--------KGFAFVQYVNERNARAAVAGEDGRMIAGQVLDIN   83 (98)
T ss_dssp             SSCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE--------TEEEEEEESSHHHHHHHHHTTTTCEETTEECEEE
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe--------CCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            3455689999997 578899999999999999999983        7899999999999999999999999999999999


Q ss_pred             EeeCC
Q psy222          166 FECGR  170 (225)
Q Consensus       166 ~a~~~  170 (225)
                      ++++.
T Consensus        84 ~a~~~   88 (98)
T d1wf2a_          84 LAAEP   88 (98)
T ss_dssp             ETTSC
T ss_pred             ECCCC
Confidence            99754

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.80  E-value=1.9e-19  Score=125.42  Aligned_cols=79  Identities=19%  Similarity=0.209  Sum_probs=72.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF  166 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~  166 (225)
                      ....++|||+|||+.+++++|+++|++||.|+.|.|..       +|||||+|.+.++|++||+.||+..|.|+.|+|.+
T Consensus        12 ~~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~   84 (98)
T d1wg4a_          12 RRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSY   84 (98)
T ss_dssp             CSCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEE
Confidence            34567899999999999999999999999999999863       57999999999999999999999999999999999


Q ss_pred             eeCCCC
Q psy222          167 ECGRVL  172 (225)
Q Consensus       167 a~~~~~  172 (225)
                      ++.+..
T Consensus        85 ~~~~~~   90 (98)
T d1wg4a_          85 IRVYPE   90 (98)
T ss_dssp             EEEECC
T ss_pred             EecCCC
Confidence            987653

>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=99.79  E-value=9.9e-20  Score=123.94  Aligned_cols=76  Identities=26%  Similarity=0.530  Sum_probs=71.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEee
Q psy222           89 PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFEC  168 (225)
Q Consensus        89 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~  168 (225)
                      ..++|||+|||+++++++|+++|++||.|.+|.++.+      ++||||+|.+.++|++|++.||+..|+|+.|+|++|.
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~------k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~   80 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFAC   80 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc------cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            4468999999999999999999999999999999865      6899999999999999999999999999999999987


Q ss_pred             CC
Q psy222          169 GR  170 (225)
Q Consensus       169 ~~  170 (225)
                      ..
T Consensus        81 ~~   82 (86)
T d2cpja1          81 HS   82 (86)
T ss_dssp             CC
T ss_pred             Cc
Confidence            64

>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=99.79  E-value=4.7e-20  Score=126.10  Aligned_cols=78  Identities=15%  Similarity=0.338  Sum_probs=69.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEe
Q psy222           88 DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFE  167 (225)
Q Consensus        88 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a  167 (225)
                      ...++|||+|||+.+++++|+++|++||.|..|++..+     .++||||+|.+.++|++||.  +++.|+|+.|+|+++
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 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNA   75 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEeec-----cCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeC
Confidence            35689999999999999999999999999999987543     58899999999999999985  788999999999999


Q ss_pred             eCCCC
Q psy222          168 CGRVL  172 (225)
Q Consensus       168 ~~~~~  172 (225)
                      +++..
T Consensus        76 ~~k~~   80 (88)
T d1wf0a_          76 EPKHN   80 (88)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87653

>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=99.79  E-value=6.8e-20  Score=123.08  Aligned_cols=75  Identities=24%  Similarity=0.456  Sum_probs=68.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCC-ccCCcEEEEEEeeC
Q psy222           91 RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQ-NFQGSEIIVDFECG  169 (225)
Q Consensus        91 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~-~l~g~~l~V~~a~~  169 (225)
                      ++|||+|||+++++++|+++|++||.|..+.++..      +|||||+|.+.++|++|++.|||. .|.|+.|+|+++.+
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            47999999999999999999999999887777654      789999999999999999999996 69999999999997


Q ss_pred             CC
Q psy222          170 RV  171 (225)
Q Consensus       170 ~~  171 (225)
                      +.
T Consensus        76 k~   77 (80)
T d2cqha1          76 KK   77 (80)
T ss_dssp             CC
T ss_pred             cC
Confidence            64

>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=99.79  E-value=1.5e-19  Score=125.58  Aligned_cols=80  Identities=19%  Similarity=0.308  Sum_probs=72.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF  166 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~  166 (225)
                      ..+.++|||+|||+++++++|+++|.+||.|..+..     ++..++||||+|.+.++|++||+.||+..|+|+.|+|.+
T Consensus        13 ~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~-----~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~   87 (96)
T d1fjca_          13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ-----DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY   87 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE-----TTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee-----cCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            445689999999999999999999999998766542     677899999999999999999999999999999999999


Q ss_pred             eeCCC
Q psy222          167 ECGRV  171 (225)
Q Consensus       167 a~~~~  171 (225)
                      +.++.
T Consensus        88 a~~k~   92 (96)
T d1fjca_          88 TGEKG   92 (96)
T ss_dssp             CSSSC
T ss_pred             eCCCC
Confidence            98764

>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=99.79  E-value=2e-19  Score=120.42  Aligned_cols=76  Identities=17%  Similarity=0.305  Sum_probs=69.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEe
Q psy222           88 DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFE  167 (225)
Q Consensus        88 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a  167 (225)
                      ..+++|||+||+  +|+++|+++|++||.|.+|.+..+      ++||||+|.+.++|.+|+..||+..|+|+.|+|.|+
T Consensus         3 ~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a   74 (79)
T d2bz2a1           3 RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA   74 (79)
T ss_dssp             CCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT------TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC------CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            456899999996  899999999999999999998754      679999999999999999999999999999999999


Q ss_pred             eCCC
Q psy222          168 CGRV  171 (225)
Q Consensus       168 ~~~~  171 (225)
                      ++++
T Consensus        75 ~~~P   78 (79)
T d2bz2a1          75 RKQP   78 (79)
T ss_dssp             CSSC
T ss_pred             cCCC
Confidence            8754

>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=99.79  E-value=4.7e-19  Score=124.78  Aligned_cols=85  Identities=12%  Similarity=0.085  Sum_probs=76.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF  166 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~  166 (225)
                      ......|||+|||+++++++|+++|..||.|..+.++.+..+++.+|||||+|.++++|++||+ ||+..|+++.|.|.+
T Consensus        12 ~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~   90 (104)
T d1wg5a_          12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFK   90 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEE
Confidence            3455689999999999999999999999998887677776789999999999999999999997 899999999999999


Q ss_pred             eeCCCC
Q psy222          167 ECGRVL  172 (225)
Q Consensus       167 a~~~~~  172 (225)
                      +.++..
T Consensus        91 ~~~~~~   96 (104)
T d1wg5a_          91 SSRAEV   96 (104)
T ss_dssp             ECTTTS
T ss_pred             CCHHHh
Confidence            987643

>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=99.79  E-value=1e-19  Score=123.84  Aligned_cols=81  Identities=9%  Similarity=0.121  Sum_probs=71.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF  166 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~  166 (225)
                      .+...+|||+|||+.+++++|+++|..||.+....++....+++++|||||+|.+.++|++||+.||++.|.|++|+|.+
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            34456799999999999999999999999987643344445899999999999999999999999999999999999987


Q ss_pred             e
Q psy222          167 E  167 (225)
Q Consensus       167 a  167 (225)
                      +
T Consensus        86 ~   86 (86)
T d2cqpa1          86 G   86 (86)
T ss_dssp             S
T ss_pred             C
Confidence            5

>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=99.79  E-value=3.8e-20  Score=126.31  Aligned_cols=74  Identities=22%  Similarity=0.284  Sum_probs=68.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEeeCC
Q psy222           91 RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECGR  170 (225)
Q Consensus        91 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~~~  170 (225)
                      ++|||+|||+.+++++|+++|++||.|..|.|+.       .|||||+|.+.++|++||..||+..|.|+.|+|.+++.+
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~   73 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR-------DGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   73 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECT-------TSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEE
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhcccccccccc-------cceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecC
Confidence            4799999999999999999999999999999874       379999999999999999999999999999999887754


Q ss_pred             C
Q psy222          171 V  171 (225)
Q Consensus       171 ~  171 (225)
                      .
T Consensus        74 ~   74 (87)
T d3begb1          74 V   74 (87)
T ss_dssp             E
T ss_pred             c
Confidence            3

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=4.2e-19  Score=120.75  Aligned_cols=77  Identities=22%  Similarity=0.356  Sum_probs=70.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEee
Q psy222           89 PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFEC  168 (225)
Q Consensus        89 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~  168 (225)
                      ..++|||+|||+++++++|+++|++||.|..+.+..      .+|||||+|.+.++|.+||..||+..|.|+.|+|.|++
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            457999999999999999999999999988877654      47899999999999999999999999999999999998


Q ss_pred             CCC
Q psy222          169 GRV  171 (225)
Q Consensus       169 ~~~  171 (225)
                      |+.
T Consensus        81 P~~   83 (86)
T d2cpda1          81 PVD   83 (86)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            754

>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=99.79  E-value=2.8e-19  Score=127.25  Aligned_cols=77  Identities=14%  Similarity=0.229  Sum_probs=70.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEee
Q psy222           89 PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFEC  168 (225)
Q Consensus        89 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~  168 (225)
                      ..++|||+|||+.+++++|+++|++||.|..|.|..      .++||||+|.+.++|++||+.||+..|.|++|+|+++.
T Consensus         9 ~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~------~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~   82 (111)
T d1whxa_           9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAP   82 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeec------cCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECC
Confidence            446899999999999999999999999999998853      37899999999999999999999999999999999997


Q ss_pred             CCC
Q psy222          169 GRV  171 (225)
Q Consensus       169 ~~~  171 (225)
                      ...
T Consensus        83 ~~~   85 (111)
T d1whxa_          83 IGV   85 (111)
T ss_dssp             TTT
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=99.79  E-value=3.9e-19  Score=126.15  Aligned_cols=77  Identities=19%  Similarity=0.295  Sum_probs=71.0

Q ss_pred             CCeEEEcCCCC-CCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEee
Q psy222           90 TRTLFIGRLNK-NSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFEC  168 (225)
Q Consensus        90 ~~~l~V~nLp~-~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~  168 (225)
                      ..+|||+||++ .+++++|+++|+.||.|..|.|++++     +|||||+|.+.++|.+||+.||+..|.|+.|+|.+++
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            46899999965 59999999999999999999999875     7899999999999999999999999999999999987


Q ss_pred             CCC
Q psy222          169 GRV  171 (225)
Q Consensus       169 ~~~  171 (225)
                      .+.
T Consensus        77 ~~~   79 (109)
T d2adca1          77 HQN   79 (109)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.79  E-value=1.1e-19  Score=124.56  Aligned_cols=77  Identities=17%  Similarity=0.312  Sum_probs=70.0

Q ss_pred             CCCeEEEcCCCCCCCHHHH---HHHHhcCCceeEEEEeecCCCCcc---ceEEEEEeCCHHHHHHHHHHhCCCccCCcEE
Q psy222           89 PTRTLFIGRLNKNSREADL---EQAFAEYGKVISVRVVRDFVTGHS---KRYGFLEYDCEKACLAAIRALNRQNFQGSEI  162 (225)
Q Consensus        89 ~~~~l~V~nLp~~~te~~L---~~~F~~~G~v~~v~i~~~~~~g~~---kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l  162 (225)
                      ..++|||+|||+.+++++|   +++|++||.|..|.|++++.++..   +|||||+|.+.++|++|++.|||..|+|+.|
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~l   86 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTL   86 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEE
Confidence            4568999999999999999   678999999999999998766544   4899999999999999999999999999999


Q ss_pred             EEE
Q psy222          163 IVD  165 (225)
Q Consensus       163 ~V~  165 (225)
                      +|.
T Consensus        87 kvS   89 (89)
T d2cpia1          87 KAS   89 (89)
T ss_dssp             EEE
T ss_pred             EEC
Confidence            984

>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=99.78  E-value=3.5e-19  Score=121.69  Aligned_cols=76  Identities=17%  Similarity=0.340  Sum_probs=66.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEee
Q psy222           89 PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFEC  168 (225)
Q Consensus        89 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~  168 (225)
                      ...+|||+|||+++++++|+++|.+|| +..+.+      +..++||||+|.+.++|++||+.||+..|.|+.|+|++++
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            356899999999999999999999999 333433      2358999999999999999999999999999999999997


Q ss_pred             CCC
Q psy222          169 GRV  171 (225)
Q Consensus       169 ~~~  171 (225)
                      .+.
T Consensus        77 ~~~   79 (88)
T d1wg1a_          77 TDA   79 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            644

>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=99.78  E-value=6.2e-19  Score=122.62  Aligned_cols=79  Identities=24%  Similarity=0.487  Sum_probs=71.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCC--cEEEE
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQG--SEIIV  164 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g--~~l~V  164 (225)
                      ..|.++|||+|||+++++++|+++|++||.|..|++.++      ++||||+|.+.++|++|++.||+..|.+  ++|+|
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 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRV   87 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEE
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEE
Confidence            456789999999999999999999999999999998755      6799999999999999999999999986  58999


Q ss_pred             EEeeCCC
Q psy222          165 DFECGRV  171 (225)
Q Consensus       165 ~~a~~~~  171 (225)
                      +|+++.+
T Consensus        88 ~~ak~~~   94 (97)
T d1whya_          88 DFAKSGP   94 (97)
T ss_dssp             EECCCCC
T ss_pred             EeCCCCC
Confidence            9988643

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=2.5e-19  Score=124.42  Aligned_cols=84  Identities=24%  Similarity=0.358  Sum_probs=74.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCc-eeEEEEeecC-CCCccceEEEEEeCCHHHHHHHHHHhCCC--ccCCcEEEEEE
Q psy222           91 RTLFIGRLNKNSREADLEQAFAEYGK-VISVRVVRDF-VTGHSKRYGFLEYDCEKACLAAIRALNRQ--NFQGSEIIVDF  166 (225)
Q Consensus        91 ~~l~V~nLp~~~te~~L~~~F~~~G~-v~~v~i~~~~-~~g~~kg~afV~F~~~~~a~~Al~~l~g~--~l~g~~l~V~~  166 (225)
                      ++|||+|||..+++++|+++|++||. |..+.|+.+. .+++++|||||+|.+.++|..|++.|++.  .+.|+.|+|.|
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~~   81 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDW   81 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEE
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEEE
Confidence            68999999999999999999999995 8999998875 46889999999999999999999998654  46799999999


Q ss_pred             eeCCCCCC
Q psy222          167 ECGRVLPG  174 (225)
Q Consensus       167 a~~~~~~~  174 (225)
                      |+++..+.
T Consensus        82 A~p~~~~~   89 (96)
T d2disa1          82 AEPEIDVD   89 (96)
T ss_dssp             SCSSCSTT
T ss_pred             cCCCCCCC
Confidence            98866543

>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=99.78  E-value=5.8e-20  Score=120.89  Aligned_cols=71  Identities=30%  Similarity=0.514  Sum_probs=68.2

Q ss_pred             EEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEE
Q psy222           93 LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEII  163 (225)
Q Consensus        93 l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~  163 (225)
                      |||+|||+++++++|+++|++||.|..+++++++.++..+|||||+|.+.++|++|++.|||..|.|+.|+
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

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=3e-19  Score=122.82  Aligned_cols=80  Identities=18%  Similarity=0.422  Sum_probs=72.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHH----HHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           89 PTRTLFIGRLNKNSREADLE----QAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        89 ~~~~l~V~nLp~~~te~~L~----~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      |.++|||+|||+.+++++|+    .+|++||.|..|.+..   +++.+|||||+|.+.++|.+|++.||+..|.|+.|+|
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            57899999999999999886    4689999999998764   4667999999999999999999999999999999999


Q ss_pred             EEeeCCC
Q psy222          165 DFECGRV  171 (225)
Q Consensus       165 ~~a~~~~  171 (225)
                      .+|+++.
T Consensus        79 ~~ak~~~   85 (91)
T d1nu4a_          79 QYAKTDS   85 (91)
T ss_dssp             EECSSCC
T ss_pred             EEeCCCc
Confidence            9998653

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.77  E-value=7.9e-19  Score=116.31  Aligned_cols=74  Identities=24%  Similarity=0.343  Sum_probs=67.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEe
Q psy222           91 RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFE  167 (225)
Q Consensus        91 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a  167 (225)
                      .+|||+|||+.+++++|+++|+.||.|..|.|+.++..  .++||||+|.++++|++||. ||++.|+|+.|.|..+
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 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK--NFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS--SSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccc--cceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            48999999999999999999999999999999988633  35799999999999999996 8999999999999865

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=2.8e-18  Score=121.59  Aligned_cols=80  Identities=19%  Similarity=0.244  Sum_probs=71.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCcc--CCcEEEEE
Q psy222           88 DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNF--QGSEIIVD  165 (225)
Q Consensus        88 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l--~g~~l~V~  165 (225)
                      .+..+|||+|||+.+|+++|+++|++||.|..|.|+.++    .+|||||+|.+.++|++||..||+..|  .++.|+|.
T Consensus         5 s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~   80 (108)
T d2adba1           5 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID   80 (108)
T ss_dssp             CCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEE
T ss_pred             CCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEE
Confidence            355689999999999999999999999999999998774    489999999999999999999999998  46789999


Q ss_pred             EeeCCC
Q psy222          166 FECGRV  171 (225)
Q Consensus       166 ~a~~~~  171 (225)
                      +++++.
T Consensus        81 ~s~~~~   86 (108)
T d2adba1          81 FSKLTS   86 (108)
T ss_dssp             ECSSCS
T ss_pred             ecCCcc
Confidence            887644

>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=99.75  E-value=1.1e-17  Score=117.65  Aligned_cols=81  Identities=15%  Similarity=0.264  Sum_probs=72.1

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHh--CCCccCCcEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL--NRQNFQGSEI  162 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l--~g~~l~g~~l  162 (225)
                      ....++++|||+|||+.+++++|+++|++||.|..|.+.++      ++||||+|.+.++|+.||..|  ++..+.|++|
T Consensus        10 ~~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l   83 (104)
T d1wexa_          10 HKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQA   83 (104)
T ss_dssp             CCCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBC
T ss_pred             CcCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec------ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEE
Confidence            34567889999999999999999999999999999998754      689999999999999999987  4567899999


Q ss_pred             EEEEeeCCC
Q psy222          163 IVDFECGRV  171 (225)
Q Consensus       163 ~V~~a~~~~  171 (225)
                      +|.|++.+.
T Consensus        84 ~v~~s~~~~   92 (104)
T d1wexa_          84 FFNYSTSKR   92 (104)
T ss_dssp             EEEECSSSS
T ss_pred             EEEEcCCCc
Confidence            999997644

>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=99.75  E-value=5.8e-18  Score=115.49  Aligned_cols=80  Identities=20%  Similarity=0.367  Sum_probs=72.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHh--CCCccCCcEEE
Q psy222           86 STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL--NRQNFQGSEII  163 (225)
Q Consensus        86 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l--~g~~l~g~~l~  163 (225)
                      ...|+++|||+|||+.+++++|+++|++||.|..+.++.+      ++||||+|.+.++|++|++.|  ++..|.|+.|+
T Consensus         4 ~~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~   77 (88)
T d2cq1a1           4 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIY   77 (88)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc------ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEE
Confidence            4568899999999999999999999999999999998855      579999999999999999865  56789999999


Q ss_pred             EEEeeCCC
Q psy222          164 VDFECGRV  171 (225)
Q Consensus       164 V~~a~~~~  171 (225)
                      |.|++.+.
T Consensus        78 v~~sk~~~   85 (88)
T d2cq1a1          78 IQYSNHKE   85 (88)
T ss_dssp             EEECSCSS
T ss_pred             EEECCCCC
Confidence            99997654

>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=99.74  E-value=6e-18  Score=111.95  Aligned_cols=71  Identities=15%  Similarity=0.231  Sum_probs=64.0

Q ss_pred             EEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEeeCC
Q psy222           93 LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECGR  170 (225)
Q Consensus        93 l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~~~  170 (225)
                      |||+|||+++++++|+++|.+|| +..+.+.      +.+|||||+|.+.++|++|+..||+..|.|++|+|++++..
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-LKYCFVD------KYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEEE------TTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceeec------ccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            79999999999999999999999 5555543      35899999999999999999999999999999999999754

>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=99.74  E-value=1.6e-18  Score=121.74  Aligned_cols=80  Identities=15%  Similarity=0.097  Sum_probs=71.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEee
Q psy222           89 PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFEC  168 (225)
Q Consensus        89 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~  168 (225)
                      ...+|||+|||+++++++|+++|..||.|..+.++....+|.++|||||+|.+.++|++||. ||++.|+|+.|.|.++.
T Consensus         7 ~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~~   85 (103)
T d2cpya1           7 AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVVT   85 (103)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEEC
T ss_pred             CceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEECC
Confidence            44679999999999999999999999998875555555689999999999999999999997 89999999999999986


Q ss_pred             C
Q psy222          169 G  169 (225)
Q Consensus       169 ~  169 (225)
                      .
T Consensus        86 ~   86 (103)
T d2cpya1          86 L   86 (103)
T ss_dssp             H
T ss_pred             H
Confidence            4

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=3.6e-18  Score=121.77  Aligned_cols=84  Identities=17%  Similarity=0.140  Sum_probs=74.7

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      ......++|||+|||+.+++++|+++|+.||.+..+.++.+..+|..+|||||+|.+.++|++||+ ||+..|+|+.|.|
T Consensus        13 ~~~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V   91 (112)
T d1wela1          13 SPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQV   91 (112)
T ss_dssp             SCCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEE
T ss_pred             CCCCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEE
Confidence            344567799999999999999999999999998776666666689999999999999999999997 8999999999999


Q ss_pred             EEeeC
Q psy222          165 DFECG  169 (225)
Q Consensus       165 ~~a~~  169 (225)
                      ..+..
T Consensus        92 ~~~~~   96 (112)
T d1wela1          92 HPITK   96 (112)
T ss_dssp             EEECH
T ss_pred             EEcCh
Confidence            98764

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.70  E-value=2.5e-17  Score=114.77  Aligned_cols=79  Identities=19%  Similarity=0.299  Sum_probs=70.4

Q ss_pred             CCCCCCeEEEcCCCCC-CCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHH--HhCCCccCCcEE
Q psy222           86 STDPTRTLFIGRLNKN-SREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR--ALNRQNFQGSEI  162 (225)
Q Consensus        86 ~~~~~~~l~V~nLp~~-~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~--~l~g~~l~g~~l  162 (225)
                      ...++++|||+|||.. +++++|.++|++||.|..|.++.+      ++||||+|.+.++|.+|++  .+++..|.|+.|
T Consensus        14 ~~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l   87 (99)
T d1x4fa1          14 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCV   87 (99)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCC
T ss_pred             CCCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCCceECCEEE
Confidence            3456789999999985 899999999999999999999865      6899999999999999997  468889999999


Q ss_pred             EEEEeeCC
Q psy222          163 IVDFECGR  170 (225)
Q Consensus       163 ~V~~a~~~  170 (225)
                      +|.+++.+
T Consensus        88 ~V~~s~~~   95 (99)
T d1x4fa1          88 KVDLSEKY   95 (99)
T ss_dssp             EEEEECSC
T ss_pred             EEEEcCCc
Confidence            99999754

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=7.2e-17  Score=124.04  Aligned_cols=85  Identities=16%  Similarity=0.391  Sum_probs=78.7

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q psy222           85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV  164 (225)
Q Consensus        85 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V  164 (225)
                      ......++|||+|||+.+++++|+++|+.||.|..+.|+.+..++.++|||||+|.+.++|.+||+ ++++.|.|+.|+|
T Consensus        92 ~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V  170 (183)
T d1u1qa_          92 GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEV  170 (183)
T ss_dssp             TTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEE
T ss_pred             ccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeECCEEEEE
Confidence            335566899999999999999999999999999999999998899999999999999999999998 7899999999999


Q ss_pred             EEeeCC
Q psy222          165 DFECGR  170 (225)
Q Consensus       165 ~~a~~~  170 (225)
                      .+|.++
T Consensus       171 ~~A~~k  176 (183)
T d1u1qa_         171 RKALSK  176 (183)
T ss_dssp             EECCCH
T ss_pred             EecCCc
Confidence            998764

>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=99.69  E-value=5.1e-17  Score=110.94  Aligned_cols=77  Identities=14%  Similarity=0.199  Sum_probs=69.5

Q ss_pred             CCCCCeEEEcCCCCC-CCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHh--CCCccCCcEEE
Q psy222           87 TDPTRTLFIGRLNKN-SREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL--NRQNFQGSEII  163 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~-~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l--~g~~l~g~~l~  163 (225)
                      ..++++|||+|||.. +|+++|.++|++||.|..|.++.+      +++|||+|.+.++|..|+..|  ++..+.|++|+
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~------k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~   78 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVR   78 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc------ceEEEEEEcchhhHHHHHHHHhhCCCccCCceEE
Confidence            567789999999986 789999999999999999999865      468999999999999999966  67789999999


Q ss_pred             EEEeeC
Q psy222          164 VDFECG  169 (225)
Q Consensus       164 V~~a~~  169 (225)
                      |.|++.
T Consensus        79 V~~s~~   84 (89)
T d1x4da1          79 VHLSQK   84 (89)
T ss_dssp             EEEECC
T ss_pred             EEECCC
Confidence            999975

>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=99.66  E-value=8.7e-19  Score=120.15  Aligned_cols=76  Identities=17%  Similarity=0.298  Sum_probs=66.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEe-----ecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q psy222           91 RTLFIGRLNKNSREADLEQAFAEYGKVISVRVV-----RDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVD  165 (225)
Q Consensus        91 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~-----~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~  165 (225)
                      ++|||+|||+.+++++|+++|++||.|..+.+.     .+..+++.+|||||+|.+.++|++|++ ||+..|.|+.|+|.
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            689999999999999999999999987765543     344567789999999999999999996 99999999999996


Q ss_pred             Ee
Q psy222          166 FE  167 (225)
Q Consensus       166 ~a  167 (225)
                      .+
T Consensus        81 r~   82 (90)
T d1u2fa_          81 RP   82 (90)
T ss_dssp             CT
T ss_pred             CC
Confidence            43

>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=99.66  E-value=5.3e-17  Score=114.00  Aligned_cols=78  Identities=18%  Similarity=0.216  Sum_probs=69.3

Q ss_pred             CCCCeEEEcCCCCCC-CH----HHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEE
Q psy222           88 DPTRTLFIGRLNKNS-RE----ADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEI  162 (225)
Q Consensus        88 ~~~~~l~V~nLp~~~-te----~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l  162 (225)
                      ....+|||+||+..+ ++    ++|+.+|++||.|..+++++.      ++||||+|.+.++|.+|+..|||..|.|+.|
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            356799999999986 43    569999999999999999853      6799999999999999999999999999999


Q ss_pred             EEEEeeCCC
Q psy222          163 IVDFECGRV  171 (225)
Q Consensus       163 ~V~~a~~~~  171 (225)
                      +|.|++++.
T Consensus        77 ~v~~a~~~~   85 (104)
T d1weya_          77 KLYFAQTLH   85 (104)
T ss_dssp             EEECCCCSS
T ss_pred             EEeecccCC
Confidence            999998654

>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=99.60  E-value=7.7e-17  Score=113.17  Aligned_cols=75  Identities=17%  Similarity=0.251  Sum_probs=70.2

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEe
Q psy222           92 TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFE  167 (225)
Q Consensus        92 ~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a  167 (225)
                      .++|.+++..++|++|+++|++||.|.+|.|+++. +++.+|||||+|.+.++|.+|+..|||..|+|++|+|++.
T Consensus        29 ~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~-~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          29 DVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             hHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCC-CCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            47788888889999999999999999999998774 8999999999999999999999999999999999999985

>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=99.56  E-value=4.8e-15  Score=103.28  Aligned_cols=67  Identities=19%  Similarity=0.300  Sum_probs=60.1

Q ss_pred             CCCCCCCeEEEcC--CCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCcc
Q psy222           85 SSTDPTRTLFIGR--LNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNF  157 (225)
Q Consensus        85 ~~~~~~~~l~V~n--Lp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l  157 (225)
                      ....++.+|||.|  ||..+|+++|+++|++||.|..|.++.+      ++||||+|.+.++|++|+..|||+.|
T Consensus        13 ~~~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          13 TVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             CCSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             cCCCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            3456778999955  9999999999999999999999988755      57999999999999999999999986

>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=99.55  E-value=4.7e-15  Score=105.44  Aligned_cols=74  Identities=23%  Similarity=0.319  Sum_probs=64.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCH-HHHHHHHHHhCCCccCCcEEEEEEee
Q psy222           90 TRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCE-KACLAAIRALNRQNFQGSEIIVDFEC  168 (225)
Q Consensus        90 ~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~-~~a~~Al~~l~g~~l~g~~l~V~~a~  168 (225)
                      ...+||+|||+.+|+++|+++|++||.|..|.|+.+      ++||||.|.+. ++|..|+..|++..|.++.+.|.++.
T Consensus        11 ~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~   84 (113)
T d1owxa_          11 CLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEV   84 (113)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEE
T ss_pred             CeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEee
Confidence            445699999999999999999999999999999854      78999999985 78999999999999888777777765


Q ss_pred             C
Q psy222          169 G  169 (225)
Q Consensus       169 ~  169 (225)
                      .
T Consensus        85 ~   85 (113)
T d1owxa_          85 L   85 (113)
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=99.55  E-value=1.4e-14  Score=111.02  Aligned_cols=79  Identities=27%  Similarity=0.451  Sum_probs=72.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEeeCC
Q psy222           91 RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECGR  170 (225)
Q Consensus        91 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~~~  170 (225)
                      ++|||+|||+.+++++|+++|++||.|..+.++++..++..+|||||+|.+.++|++|+. +++..+..+.+.+......
T Consensus         7 r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~-~~~~~~~~~~~~~~~~~~~   85 (183)
T d1u1qa_           7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAVSR   85 (183)
T ss_dssp             HEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECCCT
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHH-hcCCcccccchhhhhhhhc
Confidence            689999999999999999999999999999999998899999999999999999999999 5677788888888776543

>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=99.50  E-value=4.6e-14  Score=97.85  Aligned_cols=81  Identities=15%  Similarity=0.245  Sum_probs=69.3

Q ss_pred             CCCCCeEEEcCC--CCCCC---------HHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCC
Q psy222           87 TDPTRTLFIGRL--NKNSR---------EADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQ  155 (225)
Q Consensus        87 ~~~~~~l~V~nL--p~~~t---------e~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~  155 (225)
                      ....++|+|.||  |.++.         +++|++.|++||.|..|.+..+    ..+|||||+|.+.++|.+|+..|||.
T Consensus         5 ~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~lng~   80 (99)
T d2dita1           5 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLDGR   80 (99)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHHSTTC
T ss_pred             CCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC----CCccEEEEEECCHHHHHHHHHHhCCc
Confidence            456789999999  54321         3678899999999999998754    35799999999999999999999999


Q ss_pred             ccCCcEEEEEEeeCCC
Q psy222          156 NFQGSEIIVDFECGRV  171 (225)
Q Consensus       156 ~l~g~~l~V~~a~~~~  171 (225)
                      .|+|++|+|.+..++.
T Consensus        81 ~~~gr~i~v~~~~g~~   96 (99)
T d2dita1          81 WFGGRQITAQAWDGTT   96 (99)
T ss_dssp             EETTEECEEEECCSCC
T ss_pred             EECCEEEEEEEeCCcC
Confidence            9999999999987654

>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=99.48  E-value=3.7e-14  Score=94.61  Aligned_cols=72  Identities=17%  Similarity=0.159  Sum_probs=61.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcE-EEEEEee
Q psy222           90 TRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSE-IIVDFEC  168 (225)
Q Consensus        90 ~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~-l~V~~a~  168 (225)
                      .+.|+|.+||++++++.| ++|++||.|.++++..+      ++||||+|.++++|++||. |||..|+|+. |.|..+.
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~~------~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~   75 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSNT------GNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCI   75 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECSS------SSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECC
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEecCC------CCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCC
Confidence            357999999999987655 57999999999987543      7899999999999999997 8999999985 5677665


Q ss_pred             C
Q psy222          169 G  169 (225)
Q Consensus       169 ~  169 (225)
                      .
T Consensus        76 ~   76 (81)
T d1wwha1          76 D   76 (81)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.41  E-value=2e-13  Score=95.42  Aligned_cols=82  Identities=18%  Similarity=0.288  Sum_probs=69.5

Q ss_pred             CCCCeEEEcCC--CCCCC--------HHHHHHHHhcCCceeEEEEeecCCC--CccceEEEEEeCCHHHHHHHHHHhCCC
Q psy222           88 DPTRTLFIGRL--NKNSR--------EADLEQAFAEYGKVISVRVVRDFVT--GHSKRYGFLEYDCEKACLAAIRALNRQ  155 (225)
Q Consensus        88 ~~~~~l~V~nL--p~~~t--------e~~L~~~F~~~G~v~~v~i~~~~~~--g~~kg~afV~F~~~~~a~~Al~~l~g~  155 (225)
                      +|++.|.|.||  +..+.        .++|++.|++||.|.+|.|+++..+  ....|++||+|.+.++|.+|+..|||.
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            46889999999  55432        3468999999999999999876543  334689999999999999999999999


Q ss_pred             ccCCcEEEEEEeeC
Q psy222          156 NFQGSEIIVDFECG  169 (225)
Q Consensus       156 ~l~g~~l~V~~a~~  169 (225)
                      .++|+.|.|.+..+
T Consensus        82 ~f~gR~v~v~f~~~   95 (104)
T d1o0pa_          82 KFANRVVVTKYCDP   95 (104)
T ss_dssp             CSSSSCCEEEEECH
T ss_pred             EECCeEEEEEEcCH
Confidence            99999999999764

>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=97.74  E-value=9.2e-05  Score=48.83  Aligned_cols=78  Identities=10%  Similarity=0.122  Sum_probs=61.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCc--cceEEEEEeCCHHHHHHHHHHhCCCccCCc-----EEE
Q psy222           91 RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGH--SKRYGFLEYDCEKACLAAIRALNRQNFQGS-----EII  163 (225)
Q Consensus        91 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~--~kg~afV~F~~~~~a~~Al~~l~g~~l~g~-----~l~  163 (225)
                      .+|.|+.||+.+||+++.+.+...+.+........+.+-+  .-.-|||.|.+.+++....+.++|+.|.+.     +-.
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            4789999999999999999999988887777666544332  234689999999999999999999987542     455


Q ss_pred             EEEee
Q psy222          164 VDFEC  168 (225)
Q Consensus       164 V~~a~  168 (225)
                      |++|-
T Consensus        82 VE~AP   86 (91)
T d1uw4a_          82 VEFAP   86 (91)
T ss_dssp             EEECS
T ss_pred             EEEcC
Confidence            66653

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.65  E-value=4.2e-05  Score=49.93  Aligned_cols=72  Identities=14%  Similarity=0.285  Sum_probs=56.7

Q ss_pred             CCCCCeEEEcCCCCCC------CH---HHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCcc
Q psy222           87 TDPTRTLFIGRLNKNS------RE---ADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNF  157 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~------te---~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l  157 (225)
                      .++--||.|.-+.+..      .|   .+|.+.|..||+|.-|+++.+        -..|+|.+-..|.+|+. |++..+
T Consensus        12 GPpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al~-l~g~~v   82 (95)
T d1ufwa_          12 GPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVLD-VDGMKV   82 (95)
T ss_dssp             CCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHHH-GGGSEE
T ss_pred             CCCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHhc-cCCeEE
Confidence            3455577775444322      22   357788899999999999866        37899999999999999 799999


Q ss_pred             CCcEEEEEEe
Q psy222          158 QGSEIIVDFE  167 (225)
Q Consensus       158 ~g~~l~V~~a  167 (225)
                      .|+.|.|...
T Consensus        83 ~G~~l~It~~   92 (95)
T d1ufwa_          83 KGRAVKISGP   92 (95)
T ss_dssp             TTEEEEEECC
T ss_pred             cceEEEEecC
Confidence            9999999764

>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=97.48  E-value=0.00037  Score=43.13  Aligned_cols=61  Identities=25%  Similarity=0.358  Sum_probs=51.4

Q ss_pred             HHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEEeeC
Q psy222          106 DLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECG  169 (225)
Q Consensus       106 ~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~g~~l~g~~l~V~~a~~  169 (225)
                      .|...|.+++.|..+.|.... .+  .-.|-|...+..+|.-|+..|+...|+.++|.|.++..
T Consensus        12 ~L~~~f~~h~~V~sv~l~~~~-dg--~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~~   72 (73)
T d2dgxa1          12 LLQEAFARHGKVKSVELSPHT-DY--QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATG   72 (73)
T ss_dssp             HHHHHHHHHSCEEEEEECSCC-ST--TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             HHHHHHHhheeEEEEEEEecc-CC--cEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEecC
Confidence            455778899999999987553 23  33689999999999999999999999999999999763

>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=96.41  E-value=0.0068  Score=39.81  Aligned_cols=59  Identities=15%  Similarity=0.270  Sum_probs=48.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhcCCceeEEEEeecCCCCccceEEEEEeCCHHHHHHHHHHhC
Q psy222           87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALN  153 (225)
Q Consensus        87 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~~g~~kg~afV~F~~~~~a~~Al~~l~  153 (225)
                      .+....||.-.+|..+...+|.++|+.||.| .|.++.+.       -|||...+.+.|..++..+.
T Consensus        12 ~p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V-~VswIddT-------Sa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          12 QPKRDHVLHVTFPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCCCSEEEEECCTTCCHHHHHHHHTTTCSC-CCEEEETT-------EEEEECSCHHHHHHHHHHHH
T ss_pred             CCCcceeEEEeCCcccchhHHHHHhcCCCce-EEEEecCc-------eEEEEecCHHHHHHHHHHhc
Confidence            4455678888999999999999999999976 56666553       69999999999999887654