Psyllid ID: psy1928

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-----
Protein Sequence
MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVSVLENTVPRPVARGGRGGASGGYRNGTAPTYRPRGGLKKTL
Secondary Structure (PSIPRED)
cHHHHHcccccccEEEEEEccccccccEEEEEEccHHHHHHHHHHHcccccccEEEEEEEEEccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHccHHEEEEEEcccccccccEEEEEccHHHHHHHHHHHcccccccccEEEEEEcccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
MIYELFsefgplksaklhydrsgrslgtADLIYERRSDAIKAMKqyngvpldgrpmQIQLAADVSVlentvprpvarggrggasggyrngtaptyrprgglkktl
Flexible Loop (DISEMBL)
MIYELFSefgplksaklhydrsgrslgTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVSVLentvprpvarggrggasggyrngtaptyrprgglkktl
Low Complexity Region (SEG)
MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVSVLENTVPRPVarggrggasggyrngtaPTYRPRGGLKKTL
Disordered region (IsUnstruct)
*****F**F*******LHY*****SLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVSVL**************************************
Disordered Region (DISOPRED)
MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ**********************************************
Disordered Region (DISEMBL)
MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVSVLENTVPRPVARGGRGGASGGYRNGTAPTYRPRGGLKKTL
Disordered Region (DISPRO)
MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADV*****************************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVSVLENTVPRPVARGGRGGASGGYRNGTAPTYRPRGGLKKTL
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	105	2.2.26 [Sep-21-2011]
O08583	255	THO complex subunit 4 OS=	yes	N/A	0.761	0.313	0.638	5e-23
Q3T0I4	257	THO complex subunit 4 OS=	yes	N/A	0.761	0.311	0.638	5e-23
B5FXN8	254	THO complex subunit 4 OS=	no	N/A	0.761	0.314	0.638	5e-23
Q58EA2	256	THO complex subunit 4-A O	N/A	N/A	0.819	0.335	0.575	6e-23
Q28FB9	260	THO complex subunit 4 OS=	yes	N/A	0.819	0.330	0.575	8e-23
Q86V81	257	THO complex subunit 4 OS=	yes	N/A	0.761	0.311	0.626	2e-22
Q6GLW1	256	THO complex subunit 4-B O	N/A	N/A	0.742	0.304	0.629	1e-21
Q9JJW6	218	RNA and export factor-bin	no	N/A	0.761	0.366	0.626	2e-21
Q6PFR5	281	Transformer-2 protein hom	no	N/A	0.552	0.206	0.423	4e-06
Q13595	282	Transformer-2 protein hom	no	N/A	0.552	0.205	0.423	4e-06

>sp|O08583|THOC4_MOUSE THO complex subunit 4 OS=Mus musculus GN=Alyref PE=1 SV=3

 Score =  106 bits (264), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 53/83 (63%), Positives = 63/83 (75%), Gaps = 3/83 (3%)

Query: 2   IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
           I ELF+EFG LK A +HYDRSGRSLGTAD+ +ER++DA+KAMKQYNGVPLDGRPM IQL 
Sbjct: 121 IQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL- 179

Query: 62  ADVSVLENTVPRPVARGGRGGAS 84
             V+   +T  RP     RGG +
Sbjct: 180 --VTSQIDTQRRPAQSINRGGMT 200

Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Plays a role in mRNA processing and export. Acts as chaperone and promotes the dimerization of transcription factors containing basic leucine zipper (bZIP) domains and thereby promotes transcriptional activation. May function as scaffold that mediates interactions between proteins and/or RNA. Integral part of the THO/TREX complex that is recruited to transcribed genes and travels with the RNA polymerase during elongation. Is part of the exon junction complex that remains associated with spliced mRNA and plays an important role in mRNA export and nonsense-mediated RNA decay.
Mus musculus (taxid: 10090)

>sp|Q3T0I4|THOC4_BOVIN THO complex subunit 4 OS=Bos taurus GN=ALYREF PE=2 SV=1

 Score =  106 bits (264), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 53/83 (63%), Positives = 63/83 (75%), Gaps = 3/83 (3%)

Query: 2   IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
           I ELF+EFG LK A +HYDRSGRSLGTAD+ +ER++DA+KAMKQYNGVPLDGRPM IQL 
Sbjct: 122 IQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL- 180

Query: 62  ADVSVLENTVPRPVARGGRGGAS 84
             V+   +T  RP     RGG +
Sbjct: 181 --VTSQIDTQRRPAQSVNRGGMT 201

Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Acts as chaperone and promotes the dimerization of transcription factors containing basic leucine zipper (bZIP) domains and thereby promotes transcriptional activation. Plays a role in mRNA processing and export. May function as scaffold that mediates interactions between proteins and/or RNA. Integral part of the THO/TREX complex that is recruited to transcribed genes and travels with the RNA polymerase during elongation. Is part of the exon junction complex that remains associated with spliced mRNA and plays an important role in mRNA export and nonsense-mediated RNA decay.

Bos taurus (taxid: 9913)

>sp|B5FXN8|THOC4_TAEGU THO complex subunit 4 OS=Taeniopygia guttata GN=ALYREF PE=2 SV=1

 Score =  106 bits (264), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 53/83 (63%), Positives = 63/83 (75%), Gaps = 3/83 (3%)

Query: 2   IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
           I ELF+EFG LK A +HYDRSGRSLGTAD+ +ER++DA+KAMKQYNGVPLDGRPM IQL 
Sbjct: 119 IQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL- 177

Query: 62  ADVSVLENTVPRPVARGGRGGAS 84
             V+   +T  RP     RGG +
Sbjct: 178 --VTSQIDTQRRPAQSVNRGGMT 198

Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Acts as chaperone and promotes the dimerization of transcription factors containing basic leucine zipper (bZIP) domains and thereby promotes transcriptional activation. Plays a role in mRNA processing and export. May function as scaffold that mediates interactions between proteins and/or RNA. Is part of the exon junction complex that remains associated with spliced mRNA and plays an important role in mRNA export and nonsense-mediated RNA decay.

Taeniopygia guttata (taxid: 59729)

>sp|Q58EA2|THO4A_XENLA THO complex subunit 4-A OS=Xenopus laevis GN=alyref-a PE=2 SV=1

 Score =  105 bits (263), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 57/99 (57%), Positives = 66/99 (66%), Gaps = 13/99 (13%)

Query: 2   IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
           I ELF+EFG LK A +HYDRSGRSLGTAD+ +ER++DA+KAMKQYNGVPLDGRPM IQL 
Sbjct: 122 IQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL- 180

Query: 62  ADVSVLENTVPRPVARGGRGGASGGYRNGTAPTYRPRGG 100
             V+       RP+    RGG             RPRGG
Sbjct: 181 --VTSQIEAQRRPIQSQSRGGG----------VTRPRGG 207

Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Acts as chaperone and promotes the dimerization of transcription factors containing basic leucine zipper (bZIP) domains and thereby promotes transcriptional activation. Plays a role in mRNA processing and export. May function as scaffold that mediates interactions between proteins and/or RNA. Is part of the exon junction complex that remains associated with spliced mRNA and plays an important role in mRNA export and nonsense-mediated RNA decay.

Xenopus laevis (taxid: 8355)

>sp|Q28FB9|THOC4_XENTR THO complex subunit 4 OS=Xenopus tropicalis GN=alyref PE=2 SV=1

 Score =  105 bits (262), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 57/99 (57%), Positives = 66/99 (66%), Gaps = 13/99 (13%)

Query: 2   IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
           I ELF+EFG LK A +HYDRSGRSLGTAD+ +ER++DA+KAMKQYNGVPLDGRPM IQL 
Sbjct: 125 IQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL- 183

Query: 62  ADVSVLENTVPRPVARGGRGGASGGYRNGTAPTYRPRGG 100
             V+       RP+    RGG             RPRGG
Sbjct: 184 --VTSQIEAQRRPIQSQSRGGG----------ITRPRGG 210

Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Acts as chaperone and promotes the dimerization of transcription factors containing basic leucine zipper (bZIP) domains and thereby promotes transcriptional activation. Plays a role in mRNA processing and export. May function as scaffold that mediates interactions between proteins and/or RNA. Is part of the exon junction complex that remains associated with spliced mRNA and plays an important role in mRNA export and nonsense-mediated RNA decay.

Xenopus tropicalis (taxid: 8364)

>sp|Q86V81|THOC4_HUMAN THO complex subunit 4 OS=Homo sapiens GN=ALYREF PE=1 SV=3

 Score =  103 bits (258), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 52/83 (62%), Positives = 62/83 (74%), Gaps = 3/83 (3%)

Query: 2   IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
           I ELF+EFG LK A +HYDRSGRSLGTAD+ +ER++DA+KAMKQYNGVPLDGRPM IQL 
Sbjct: 122 IQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL- 180

Query: 62  ADVSVLENTVPRPVARGGRGGAS 84
             V+   +   RP     RGG +
Sbjct: 181 --VTSQIDAQRRPAQSVNRGGMT 201

Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Acts as chaperone and promotes the dimerization of transcription factors containing basic leucine zipper (bZIP) domains and thereby promotes transcriptional activation. Plays a role in mRNA processing and export. May function as scaffold that mediates interactions between proteins and/or RNA. Is part of the exon junction complex that remains associated with spliced mRNA and plays an important role in mRNA export and nonsense-mediated RNA decay. Directs mRNA derived from Herpes simplex virus intron-less genes to the NXF1-mediated export pathway.

Homo sapiens (taxid: 9606)

>sp|Q6GLW1|THO4B_XENLA THO complex subunit 4-B OS=Xenopus laevis GN=alyref-b PE=2 SV=1

 Score =  102 bits (253), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 51/81 (62%), Positives = 60/81 (74%), Gaps = 3/81 (3%)

Query: 2   IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
           I ELF+EFG LK A +HYDRSGRSLGTAD+ +ER++DA+KAMKQYNGVPLDGR M IQL 
Sbjct: 121 IQELFAEFGSLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRSMNIQL- 179

Query: 62  ADVSVLENTVPRPVARGGRGG 82
             V+       RP+    RGG
Sbjct: 180 --VTSQIEAQRRPIQSQSRGG 198

Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Acts as chaperone and promotes the dimerization of transcription factors containing basic leucine zipper (bZIP) domains and thereby promotes transcriptional activation. Plays a role in mRNA processing and export. May function as scaffold that mediates interactions between proteins and/or RNA. Is part of the exon junction complex that remains associated with spliced mRNA and plays an important role in mRNA export and nonsense-mediated RNA decay.

Xenopus laevis (taxid: 8355)

>sp|Q9JJW6|REFP2_MOUSE RNA and export factor-binding protein 2 OS=Mus musculus GN=Refbp2 PE=1 SV=1

 Score =  100 bits (250), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 52/83 (62%), Positives = 61/83 (73%), Gaps = 3/83 (3%)

Query: 2   IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
           I ELF+EFG LK A + YDRSGRSLGTAD+ +ERR+DA+KAMKQY GVPLDGRPM IQL 
Sbjct: 91  IQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL- 149

Query: 62  ADVSVLENTVPRPVARGGRGGAS 84
             V+   +   RP   G RGG +
Sbjct: 150 --VASQIDPQRRPAQSGNRGGMT 170

Acts as chaperone and promotes the dimerization of transcription factors containing basic leucine zipper (bZIP) domains and thereby promotes transcriptional activation. Plays a role in mRNA processing and export. May function as scaffold that mediates interactions between proteins and/or RNA. Integral part of the THO/TREX complex that is recruited to transcribed genes and travels with the RNA polymerase during elongation (By similarity). Is part of the exon junction complex that remains associated with spliced mRNA and plays an important role in mRNA export and nonsense-mediated RNA decay.

Mus musculus (taxid: 10090)

>sp|Q6PFR5|TRA2A_MOUSE Transformer-2 protein homolog alpha OS=Mus musculus GN=Tra2a PE=1 SV=1

 Score = 50.1 bits (118), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 25/59 (42%), Positives = 40/59 (67%), Gaps = 1/59 (1%)

Query: 4   ELFSEFGPLKSAKLHYD-RSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
           E+FS +GPL    + YD R+GRS G A + +ER  D+ +AM++ NG+ LDGR +++  +
Sbjct: 135 EVFSRYGPLSGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMERANGMELDGRRIRVDYS 193

Sequence-specific RNA-binding protein which participates in the control of pre-mRNA splicing.

Mus musculus (taxid: 10090)

>sp|Q13595|TRA2A_HUMAN Transformer-2 protein homolog alpha OS=Homo sapiens GN=TRA2A PE=1 SV=1

 Score = 50.1 bits (118), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 25/59 (42%), Positives = 40/59 (67%), Gaps = 1/59 (1%)

Query: 4   ELFSEFGPLKSAKLHYD-RSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
           E+FS +GPL    + YD R+GRS G A + +ER  D+ +AM++ NG+ LDGR +++  +
Sbjct: 137 EVFSRYGPLSGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMERANGMELDGRRIRVDYS 195

Sequence-specific RNA-binding protein which participates in the control of pre-mRNA splicing.

Homo sapiens (taxid: 9606)

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	105
312379595	836	hypothetical protein AND_08500 [Anophele	0.695	0.087	0.756	9e-25
158286924	271	AGAP006733-PA [Anopheles gambiae str. PE	0.695	0.269	0.729	6e-24
170043665	290	RNA and export factor binding protein [C	0.771	0.279	0.682	7e-24
112983092	254	ALY [Bombyx mori] gi|95115188|gb|ABF5596	0.866	0.358	0.63	1e-23
91090428	234	PREDICTED: similar to RNA and export fac	0.790	0.354	0.638	1e-23
198455576	284	GA10707 [Drosophila pseudoobscura pseudo	0.695	0.257	0.717	2e-23
195158116	284	GL12678 [Drosophila persimilis] gi|19411	0.695	0.257	0.717	2e-23
21356157	266	RNA and export factor binding protein 1	0.847	0.334	0.627	2e-23
304441001	254	ALY [Bombyx mori]	0.866	0.358	0.62	4e-23
195109702	277	GI23076 [Drosophila mojavensis] gi|19391	0.8	0.303	0.647	4e-23

>gi|312379595|gb|EFR25817.1| hypothetical protein AND_08500 [Anopheles darlingi]

 Score =  117 bits (293), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 56/74 (75%), Positives = 62/74 (83%), Gaps = 1/74 (1%)

Query: 2   IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
           I ELF+EFGPLKSA +HYDRSGRSLGTAD+I+ER+SDAIKAMKQYNGVPLDGRPM IQLA
Sbjct: 704 INELFAEFGPLKSASVHYDRSGRSLGTADVIFERKSDAIKAMKQYNGVPLDGRPMSIQLA 763

Query: 62  ADVSVLENTVPRPV 75
               +     PRPV
Sbjct: 764 TS-EIPSARPPRPV 776

Source: Anopheles darlingi

Species: Anopheles darlingi

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|158286924|ref|XP_309011.3| AGAP006733-PA [Anopheles gambiae str. PEST] gi|157020700|gb|EAA04421.3| AGAP006733-PA [Anopheles gambiae str. PEST]

 Score =  114 bits (286), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 54/74 (72%), Positives = 62/74 (83%), Gaps = 1/74 (1%)

Query: 2   IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
           I ELF+EFGPL+SA +HYDRSGRSLGTAD+++ERRSDAIKAMKQYNGVPLDGRPM IQ+A
Sbjct: 138 INELFAEFGPLRSASVHYDRSGRSLGTADVVFERRSDAIKAMKQYNGVPLDGRPMSIQMA 197

Query: 62  ADVSVLENTVPRPV 75
               +    VPRP 
Sbjct: 198 TS-EIPAPRVPRPA 210

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170043665|ref|XP_001849498.1| RNA and export factor binding protein [Culex quinquefasciatus] gi|167867015|gb|EDS30398.1| RNA and export factor binding protein [Culex quinquefasciatus]

 Score =  114 bits (285), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 58/85 (68%), Positives = 65/85 (76%), Gaps = 4/85 (4%)

Query: 2   IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
           I ELF++FGPLKSA +HYDRSGRSLGTAD+++ERR+DAIKAMKQYNGVPLDGRPM IQLA
Sbjct: 142 INELFADFGPLKSASVHYDRSGRSLGTADVVFERRADAIKAMKQYNGVPLDGRPMSIQLA 201

Query: 62  ADVSVLENTVPRPVARGGRGGASGG 86
                 E  VPR    GG    S G
Sbjct: 202 TS----EIPVPRAPRLGGSSDRSSG 222

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|112983092|ref|NP_001037596.1| ALY [Bombyx mori] gi|95115188|gb|ABF55960.1| ALY [Bombyx mori]

 Score =  114 bits (284), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 63/100 (63%), Positives = 74/100 (74%), Gaps = 9/100 (9%)

Query: 2   IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
           I ELFSEFG LKSA +HYDRSGRSLGTAD+++ER++DA+KAMKQYNGVPLDGR M IQLA
Sbjct: 116 IKELFSEFGILKSASVHYDRSGRSLGTADVVFERKADAVKAMKQYNGVPLDGRAMNIQLA 175

Query: 62  -ADVSVLENTVPRPVARGGRGGASGGYRNGTAPTYRPRGG 100
            ++++ L     RP AR   GGAS G   GT      RGG
Sbjct: 176 TSEINTL-----RPEARNRIGGASVG---GTIRNNPKRGG 207

Source: Bombyx mori

Species: Bombyx mori

Genus: Bombyx

Family: Bombycidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|91090428|ref|XP_971598.1| PREDICTED: similar to RNA and export factor binding protein [Tribolium castaneum] gi|270013379|gb|EFA09827.1| hypothetical protein TcasGA2_TC011974 [Tribolium castaneum]

 Score =  113 bits (283), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 60/94 (63%), Positives = 69/94 (73%), Gaps = 11/94 (11%)

Query: 2   IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
           I ELF+EFGPLKSA +HYDRSGRSLGTAD+I+ERR+DAIKAMKQYNGVPLDGR M IQ  
Sbjct: 111 IQELFAEFGPLKSASVHYDRSGRSLGTADVIFERRTDAIKAMKQYNGVPLDGRAMNIQ-- 168

Query: 62  ADVSVLENTVPRPVAR--GGRGGASGGYRNGTAP 93
               ++ + +P PV R  G R   S   R G AP
Sbjct: 169 ----IITSEIPSPVRRPTGERKFQS---RRGAAP 195

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|198455576|ref|XP_001360055.2| GA10707 [Drosophila pseudoobscura pseudoobscura] gi|198133305|gb|EAL29208.2| GA10707 [Drosophila pseudoobscura pseudoobscura]

 Score =  113 bits (282), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 56/78 (71%), Positives = 66/78 (84%), Gaps = 5/78 (6%)

Query: 2   IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
           I ELF+EFGP+K A +HYDRSGRSLGTAD+I+ERR+DA+KA+KQYNGVPLDGRPM IQLA
Sbjct: 138 IKELFNEFGPIKKAAVHYDRSGRSLGTADVIFERRTDALKAIKQYNGVPLDGRPMTIQLA 197

Query: 62  -ADVSVLENTVPRPVARG 78
            +DV    N + RPVA G
Sbjct: 198 VSDV----NALTRPVASG 211

Source: Drosophila pseudoobscura pseudoobscura

Species: Drosophila pseudoobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195158116|ref|XP_002019940.1| GL12678 [Drosophila persimilis] gi|194116531|gb|EDW38574.1| GL12678 [Drosophila persimilis]

 Score =  113 bits (282), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 56/78 (71%), Positives = 66/78 (84%), Gaps = 5/78 (6%)

Query: 2   IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
           I ELF+EFGP+K A +HYDRSGRSLGTAD+I+ERR+DA+KA+KQYNGVPLDGRPM IQLA
Sbjct: 138 IKELFNEFGPIKKAAVHYDRSGRSLGTADVIFERRTDALKAIKQYNGVPLDGRPMTIQLA 197

Query: 62  -ADVSVLENTVPRPVARG 78
            +DV    N + RPVA G
Sbjct: 198 VSDV----NALTRPVASG 211

Source: Drosophila persimilis

Species: Drosophila persimilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|21356157|ref|NP_651968.1| RNA and export factor binding protein 1 [Drosophila melanogaster] gi|5679350|gb|AAD46930.1|AF172637_1 LD24793p [Drosophila melanogaster] gi|7298863|gb|AAF54070.1| RNA and export factor binding protein 1 [Drosophila melanogaster] gi|220953584|gb|ACL89335.1| Aly-PA [synthetic construct]

 Score =  112 bits (281), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 64/102 (62%), Positives = 77/102 (75%), Gaps = 13/102 (12%)

Query: 2   IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
           I ELF++FGP+K A +HYDRSGRSLGTAD+I+ERR+DA+KA+KQY+GVPLDGRPM IQLA
Sbjct: 125 IKELFNDFGPIKKAAVHYDRSGRSLGTADVIFERRADALKAIKQYHGVPLDGRPMTIQLA 184

Query: 62  -ADVSVLENTVPRPVARGGRGGASGGYR--NGTAPTYRPRGG 100
            +DV+VL     RPVA      A+   R   GTAPT   RGG
Sbjct: 185 VSDVAVLT----RPVA------ATDVKRRVGGTAPTSFKRGG 216

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|304441001|gb|ADM33940.1| ALY [Bombyx mori]

 Score =  112 bits (279), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 62/100 (62%), Positives = 74/100 (74%), Gaps = 9/100 (9%)

Query: 2   IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
           I ELFSEFG L+SA +HYDRSGRSLGTAD+++ER++DA+KAMKQYNGVPLDGR M IQLA
Sbjct: 116 IKELFSEFGILESASVHYDRSGRSLGTADVVFERKADAVKAMKQYNGVPLDGRAMNIQLA 175

Query: 62  -ADVSVLENTVPRPVARGGRGGASGGYRNGTAPTYRPRGG 100
            ++++ L     RP AR   GGAS G   GT      RGG
Sbjct: 176 TSEINTL-----RPEARNRIGGASVG---GTIRNNPKRGG 207

Source: Bombyx mori

Species: Bombyx mori

Genus: Bombyx

Family: Bombycidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195109702|ref|XP_001999422.1| GI23076 [Drosophila mojavensis] gi|193916016|gb|EDW14883.1| GI23076 [Drosophila mojavensis]

 Score =  112 bits (279), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 55/85 (64%), Positives = 68/85 (80%), Gaps = 1/85 (1%)

Query: 2   IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
           I ELF++FGP+K A +HYDRSGRSLGTAD+I+ERRSDA+KA+KQY+GVPLDGRPM IQLA
Sbjct: 135 IKELFNDFGPMKKAAVHYDRSGRSLGTADVIFERRSDALKAIKQYHGVPLDGRPMTIQLA 194

Query: 62  -ADVSVLENTVPRPVARGGRGGASG 85
            +DV+ L   VP    +   G A+G
Sbjct: 195 VSDVAALTRPVPSDDVKRRVGNAAG 219

Source: Drosophila mojavensis

Species: Drosophila mojavensis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

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	105
FB|FBgn0010774	266	Ref1 "RNA and export factor bi	0.666	0.263	0.718	1e-22
UNIPROTKB|E1C2L5	258	THOC4 "Uncharacterized protein	0.561	0.228	0.779	1e-20
UNIPROTKB|Q3T0I4	257	ALYREF "THO complex subunit 4"	0.561	0.229	0.779	1e-20
UNIPROTKB|F1PL92	257	ALYREF "Uncharacterized protei	0.561	0.229	0.779	1e-20
UNIPROTKB|E9PB61	264	ALYREF "THO complex subunit 4"	0.561	0.223	0.779	1e-20
UNIPROTKB|Q86V81	257	ALYREF "THO complex subunit 4"	0.561	0.229	0.779	1e-20
MGI|MGI:1341044	255	Alyref "Aly/REF export factor"	0.561	0.231	0.779	1e-20
ZFIN|ZDB-GENE-070928-29	280	alyref "Aly/REF export factor"	0.561	0.210	0.779	1e-20
MGI|MGI:1913144	218	Alyref2 "Aly/REF export factor	0.580	0.279	0.754	7.2e-20
RGD|1594679	189	Thoc4 "THO complex 4" [Rattus	0.628	0.349	0.632	3.2e-17

FB|FBgn0010774 Ref1 "RNA and export factor binding protein 1" [Drosophila melanogaster (taxid:7227)]

 Score = 263 (97.6 bits), Expect = 1.0e-22, P = 1.0e-22
 Identities = 51/71 (71%), Positives = 63/71 (88%)

Query:     2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
             I ELF++FGP+K A +HYDRSGRSLGTAD+I+ERR+DA+KA+KQY+GVPLDGRPM IQLA
Sbjct:   125 IKELFNDFGPIKKAAVHYDRSGRSLGTADVIFERRADALKAIKQYHGVPLDGRPMTIQLA 184

Query:    62 -ADVSVLENTV 71
              +DV+VL   V
Sbjct:   185 VSDVAVLTRPV 195

GO:0003713 "transcription coactivator activity" evidence=ISS

GO:0003729 "mRNA binding" evidence=ISS

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005654 "nucleoplasm" evidence=IDA

GO:0031965 "nuclear membrane" evidence=IDA

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

GO:0071013 "catalytic step 2 spliceosome" evidence=IDA

GO:0071011 "precatalytic spliceosome" evidence=IDA

UNIPROTKB|E1C2L5 THOC4 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 244 (91.0 bits), Expect = 1.0e-20, P = 1.0e-20
 Identities = 46/59 (77%), Positives = 53/59 (89%)

Query:     2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
             I ELF+EFG LK A +HYDRSGRSLGTAD+ +ER++DA+KAMKQYNGVPLDGRPM IQL
Sbjct:   120 IQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL 178

GO:0000166 "nucleotide binding" evidence=IEA

GO:0000346 "transcription export complex" evidence=IEA

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

GO:0003723 "RNA binding" evidence=IEA

GO:0046784 "intronless viral mRNA export from host nucleus" evidence=IEA

GO:0071013 "catalytic step 2 spliceosome" evidence=IEA

UNIPROTKB|Q3T0I4 ALYREF "THO complex subunit 4" [Bos taurus (taxid:9913)]

 Score = 244 (91.0 bits), Expect = 1.0e-20, P = 1.0e-20
 Identities = 46/59 (77%), Positives = 53/59 (89%)

Query:     2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
             I ELF+EFG LK A +HYDRSGRSLGTAD+ +ER++DA+KAMKQYNGVPLDGRPM IQL
Sbjct:   122 IQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL 180

GO:0016607 "nuclear speck" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0071013 "catalytic step 2 spliceosome" evidence=IEA

GO:0046784 "intronless viral mRNA export from host nucleus" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

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

GO:0000346 "transcription export complex" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|F1PL92 ALYREF "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 244 (91.0 bits), Expect = 1.0e-20, P = 1.0e-20
 Identities = 46/59 (77%), Positives = 53/59 (89%)

Query:     2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
             I ELF+EFG LK A +HYDRSGRSLGTAD+ +ER++DA+KAMKQYNGVPLDGRPM IQL
Sbjct:   122 IQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL 180

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|E9PB61 ALYREF "THO complex subunit 4" [Homo sapiens (taxid:9606)]

 Score = 244 (91.0 bits), Expect = 1.0e-20, P = 1.0e-20
 Identities = 46/59 (77%), Positives = 53/59 (89%)

Query:     2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
             I ELF+EFG LK A +HYDRSGRSLGTAD+ +ER++DA+KAMKQYNGVPLDGRPM IQL
Sbjct:   129 IQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL 187

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

UNIPROTKB|Q86V81 ALYREF "THO complex subunit 4" [Homo sapiens (taxid:9606)]

 Score = 244 (91.0 bits), Expect = 1.0e-20, P = 1.0e-20
 Identities = 46/59 (77%), Positives = 53/59 (89%)

Query:     2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
             I ELF+EFG LK A +HYDRSGRSLGTAD+ +ER++DA+KAMKQYNGVPLDGRPM IQL
Sbjct:   122 IQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL 180

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0016607 "nuclear speck" evidence=IEA

GO:0006406 "mRNA export from nucleus" evidence=IMP;TAS

GO:0005515 "protein binding" evidence=IPI

GO:0000346 "transcription export complex" evidence=IDA

GO:0046784 "intronless viral mRNA export from host nucleus" evidence=IDA

GO:0000398 "mRNA splicing, via spliceosome" evidence=IC;TAS

GO:0071013 "catalytic step 2 spliceosome" evidence=IDA

GO:0005654 "nucleoplasm" evidence=TAS

GO:0005829 "cytosol" evidence=TAS

GO:0006366 "transcription from RNA polymerase II promoter" evidence=TAS

GO:0006369 "termination of RNA polymerase II transcription" evidence=TAS

GO:0008380 "RNA splicing" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0031124 "mRNA 3'-end processing" evidence=TAS

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

MGI|MGI:1341044 Alyref "Aly/REF export factor" [Mus musculus (taxid:10090)]

 Score = 244 (91.0 bits), Expect = 1.0e-20, P = 1.0e-20
 Identities = 46/59 (77%), Positives = 53/59 (89%)

Query:     2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
             I ELF+EFG LK A +HYDRSGRSLGTAD+ +ER++DA+KAMKQYNGVPLDGRPM IQL
Sbjct:   121 IQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL 179

GO:0000166 "nucleotide binding" evidence=IEA

GO:0000346 "transcription export complex" evidence=ISO

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0003723 "RNA binding" evidence=IDA

GO:0005634 "nucleus" evidence=TAS

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0006406 "mRNA export from nucleus" evidence=ISO

GO:0006810 "transport" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0046784 "intronless viral mRNA export from host nucleus" evidence=ISO

GO:0051028 "mRNA transport" evidence=IEA

GO:0071013 "catalytic step 2 spliceosome" evidence=ISO

ZFIN|ZDB-GENE-070928-29 alyref "Aly/REF export factor" [Danio rerio (taxid:7955)]

 Score = 244 (91.0 bits), Expect = 1.0e-20, P = 1.0e-20
 Identities = 46/59 (77%), Positives = 53/59 (89%)

Query:     2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
             I ELF+EFG LK A +HYDRSGRSLGTAD+ +ER++DA+KAMKQYNGVPLDGRPM IQL
Sbjct:   141 IQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL 199

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

MGI|MGI:1913144 Alyref2 "Aly/REF export factor 2" [Mus musculus (taxid:10090)]

 Score = 236 (88.1 bits), Expect = 7.2e-20, P = 7.2e-20
 Identities = 46/61 (75%), Positives = 52/61 (85%)

Query:     2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
             I ELF+EFG LK A + YDRSGRSLGTAD+ +ERR+DA+KAMKQY GVPLDGRPM IQL 
Sbjct:    91 IQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLV 150

Query:    62 A 62
             A
Sbjct:   151 A 151

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0003723 "RNA binding" evidence=IDA

GO:0005575 "cellular_component" evidence=ND

GO:0005634 "nucleus" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0006810 "transport" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0008380 "RNA splicing" evidence=IEA

GO:0051028 "mRNA transport" evidence=IEA

RGD|1594679 Thoc4 "THO complex 4" [Rattus norvegicus (taxid:10116)]

 Score = 211 (79.3 bits), Expect = 3.2e-17, P = 3.2e-17
 Identities = 43/68 (63%), Positives = 53/68 (77%)

Query:     2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGR--PMQIQ 59
             I ELF+EFG LK A +HYDRSGRSLGTAD+ +ER++DA+KAMKQYNGVPLD    P  + 
Sbjct:   122 IQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDASYIPPLLD 181

Query:    60 LAADVSVL 67
             L  + S+L
Sbjct:   182 LLPEDSLL 189

GO:0000166 "nucleotide binding" evidence=IEA

GO:0000346 "transcription export complex" evidence=IEA

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

GO:0003723 "RNA binding" evidence=IEA

GO:0046784 "intronless viral mRNA export from host nucleus" evidence=IEA

GO:0071013 "catalytic step 2 spliceosome" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q86V81	THOC4_HUMAN	No assigned EC number	0.6265	0.7619	0.3112	yes	N/A
O08583	THOC4_MOUSE	No assigned EC number	0.6385	0.7619	0.3137	yes	N/A
Q28FB9	THOC4_XENTR	No assigned EC number	0.5757	0.8190	0.3307	yes	N/A
Q3T0I4	THOC4_BOVIN	No assigned EC number	0.6385	0.7619	0.3112	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	105
cd12680	75	cd12680, RRM_THOC4, RNA recognition motif in THO c	2e-37
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	1e-28
cd12681	69	cd12681, RRM_SKAR, RNA recognition motif in S6K1 A	5e-16
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	3e-14
smart00360	73	smart00360, RRM, RNA recognition motif	9e-14
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	9e-13
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	1e-11
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	7e-10
cd12267	77	cd12267, RRM_YRA1_MLO3, RNA recognition motif in y	4e-09
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	5e-09
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	7e-09
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	8e-09
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	8e-09
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	3e-08
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	3e-08
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	3e-08
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	3e-08
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	5e-08
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	1e-07
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	2e-07
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	2e-07
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	3e-07
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	4e-07
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	4e-07
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	4e-07
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	4e-07
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	4e-07
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	5e-07
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	5e-07
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	8e-07
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	8e-07
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	9e-07
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	1e-06
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	1e-06
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	1e-06
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	3e-06
cd12660	76	cd12660, RRM2_MYEF2, RNA recognition motif 2 in ve	3e-06
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	3e-06
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	3e-06
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	4e-06
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	6e-06
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	7e-06
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	8e-06
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	8e-06
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	1e-05
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	1e-05
cd12478	91	cd12478, RRM1_U2B, RNA recognition motif 1 in U2 s	3e-05
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	4e-05
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	4e-05
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	4e-05
cd12659	76	cd12659, RRM2_hnRNPM, RNA recognition motif 2 in v	5e-05
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	6e-05
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	7e-05
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	1e-04
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	1e-04
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	1e-04
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	2e-04
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	2e-04
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	2e-04
cd12304	93	cd12304, RRM_Set1, RNA recognition motif in the Se	2e-04
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	2e-04
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	2e-04
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	2e-04
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	2e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	4e-04
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	4e-04
cd12498	83	cd12498, RRM3_ACF, RNA recognition motif 3 in vert	4e-04
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	6e-04
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	6e-04
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	7e-04
cd12477	89	cd12477, RRM1_U1A, RNA recognition motif 1 found i	0.001
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	0.001
cd12506	75	cd12506, RRM3_hnRNPH_CRSF1_like, RNA recognition m	0.001
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	0.001
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	0.002
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	0.002
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	0.002
cd12494	72	cd12494, RRM3_hnRNPR, RNA recognition motif 3 in v	0.002
cd12773	84	cd12773, RRM2_HuR, RNA recognition motif 2 in vert	0.002
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	0.002
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	0.003
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	0.003
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	0.003
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	0.003
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	0.003
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	0.003
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	0.003
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	0.004
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	0.004
cd12333	80	cd12333, RRM2_p54nrb_like, RNA recognition motif 2	0.004
cd12476	78	cd12476, RRM1_SNF, RNA recognition motif 1 found i	0.004
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	0.004

>gnl|CDD|241124 cd12680, RRM_THOC4, RNA recognition motif in THO complex subunit 4 (THOC4) and similar proteins

 Score =  120 bits (304), Expect = 2e-37
 Identities = 47/59 (79%), Positives = 55/59 (93%)

Query: 2  IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
          I ELF+EFG LK A +HYDRSGRSLGTAD+++ERR+DA+KAMKQYNGVPLDGRPM+IQL
Sbjct: 17 IKELFAEFGALKKAAVHYDRSGRSLGTADVVFERRADALKAMKQYNGVPLDGRPMKIQL 75

This subgroup corresponds to the RRM of THOC4, also termed transcriptional coactivator Aly/REF, or ally of AML-1 and LEF-1, or bZIP-enhancing factor BEF, an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus. THOC4 was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid. It might be a novel transcription cofactor for erythroid-specific genes. . Length = 75

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

 Score = 98.4 bits (246), Expect = 1e-28
 Identities = 34/57 (59%), Positives = 47/57 (82%)

Query: 4  ELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
          ELF   G +K  K++YDRSGRS GTAD+++E+R DA +A+KQ+NGV LDG+PMQ++L
Sbjct: 19 ELFGRVGEVKKVKINYDRSGRSEGTADVVFEKREDAERAIKQFNGVLLDGQPMQVEL 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|241125 cd12681, RRM_SKAR, RNA recognition motif in S6K1 Aly/REF-like target (SKAR) and similar proteins

 Score = 66.1 bits (162), Expect = 5e-16
 Identities = 25/59 (42%), Positives = 36/59 (61%), Gaps = 6/59 (10%)

Query: 2  IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
          I ELFS  G LK A+L         G A+++Y R+ DA+ A+ +YN   LDG+PM+ +L
Sbjct: 17 IVELFSAIGALKRARL------VRPGVAEVVYVRKDDALTAIDKYNNRELDGQPMKCKL 69

This subgroup corresponds to the RRM of SKAR, also termed polymerase delta-interacting protein 3 (PDIP3), 46 kDa DNA polymerase delta interaction protein (PDIP46), belonging to the Aly/REF family of RNA binding proteins that have been implicated in coupling transcription with pre-mRNA splicing and nucleo-cytoplasmic mRNA transport. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion. SKAR contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Length = 69

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

 Score = 61.9 bits (151), Expect = 3e-14
 Identities = 23/59 (38%), Positives = 38/59 (64%)

Query: 1  MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
           + ELFS+FG ++S ++  D+ G+S G A + +E   DA KA++  NG  LDGR +++ 
Sbjct: 14 DLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALNGKELDGRKLKVS 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|214636 smart00360, RRM, RNA recognition motif

 Score = 60.3 bits (147), Expect = 9e-14
 Identities = 25/59 (42%), Positives = 40/59 (67%), Gaps = 1/59 (1%)

Query: 1  MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
           + ELFS+FG ++S +L  D+ +G+S G A + +E   DA KA++  NG  LDGRP+++
Sbjct: 15 ELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73

Length = 73

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

 Score = 58.0 bits (141), Expect = 9e-13
 Identities = 23/56 (41%), Positives = 36/56 (64%)

Query: 1  MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPM 56
           + +LFS+FGP++S ++  D +GRS G A + +E   DA KA++  NG  L GR +
Sbjct: 14 DLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALNGKELGGREL 69

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

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

 Score = 58.8 bits (141), Expect = 1e-11
 Identities = 31/100 (31%), Positives = 49/100 (49%), Gaps = 5/100 (5%)

Query: 2   IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
           + ELF +FGP+K  +L  DR +G+S G A + +E    A KA+++ NG  L+GRP+++Q 
Sbjct: 132 LRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQK 191

Query: 61  AADV----SVLENTVPRPVARGGRGGASGGYRNGTAPTYR 96
           A       S L N +    A+    G +            
Sbjct: 192 AQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVG 231

Length = 306

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

 Score = 50.6 bits (122), Expect = 7e-10
 Identities = 21/59 (35%), Positives = 37/59 (62%), Gaps = 1/59 (1%)

Query: 1  MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
          M+YE+FS  GP+ S ++  D  + RSLG A + ++  +DA +A+   N   + G+P++I
Sbjct: 15 MLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTLNFDVIKGKPIRI 73

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|240713 cd12267, RRM_YRA1_MLO3, RNA recognition motif in yeast RNA annealing protein YRA1 (Yra1p), yeast mRNA export protein mlo3 and similar proteins

 Score = 48.6 bits (116), Expect = 4e-09
 Identities = 24/61 (39%), Positives = 38/61 (62%), Gaps = 2/61 (3%)

Query: 2  IYELF-SEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDG-RPMQIQ 59
          I E F S+ GP+K   L Y+  G+S G A++ ++R  DA KA  ++NG   DG R M+++
Sbjct: 16 IREYFVSQIGPIKRVLLSYNEGGKSTGIANITFKRAGDATKAYDKFNGRIDDGNRKMKVE 75

Query: 60 L 60
          +
Sbjct: 76 V 76

This subfamily corresponds to the RRM of Yra1p and mlo3. Yra1p is an essential nuclear RNA-binding protein encoded by Saccharomyces cerevisiae YRA1 gene. It belongs to the evolutionarily conserved REF (RNA and export factor binding proteins) family of hnRNP-like proteins. Yra1p possesses potent RNA annealing activity and interacts with a number of proteins involved in nuclear transport and RNA processing. It binds to the mRNA export factor Mex67p/TAP and couples transcription to export in yeast. Yra1p is associated with Pse1p and Kap123p, two members of the beta-importin family, further mediating transport of Yra1p into the nucleus. In addition, the co-transcriptional loading of Yra1p is required for autoregulation. Yra1p consists of two highly conserved N- and C-terminal boxes and a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This subfamily includes RNA-annealing protein mlo3, also termed mRNA export protein mlo3, which has been identified in fission yeast as a protein that causes defects in chromosome segregation when overexpressed. It shows high sequence similarity with Yra1p. . Length = 77

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

 Score = 47.9 bits (115), Expect = 5e-09
 Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 4/60 (6%)

Query: 2  IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
          +Y+LFS FG ++  KL      +  G A + +     A KA++  NGV   GRP+++  +
Sbjct: 1  LYKLFSPFGNVEKIKL----LKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 56

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

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

 Score = 48.0 bits (115), Expect = 7e-09
 Identities = 20/59 (33%), Positives = 33/59 (55%), Gaps = 1/59 (1%)

Query: 1  MIYELFSEFGPLKSAKLHYD-RSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
           +  +F  FG ++  +L  D  +GRS G   + +    DA KA++Q NG  L GRP+++
Sbjct: 14 DLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQLNGFELAGRPIKV 72

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

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

 Score = 48.0 bits (115), Expect = 8e-09
 Identities = 20/61 (32%), Positives = 36/61 (59%), Gaps = 1/61 (1%)

Query: 2  IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
          +++ F+EFG +K+  L+ DR +G   G A + YE + +A  A++  NG  L G+ + +  
Sbjct: 23 VHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGLNGKELLGQTISVDW 82

Query: 61 A 61
          A
Sbjct: 83 A 83

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

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

 Score = 48.0 bits (114), Expect = 8e-09
 Identities = 25/58 (43%), Positives = 39/58 (67%), Gaps = 1/58 (1%)

Query: 2  IYELFSEFGPLKSAKLHYD-RSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
          + E+FS +GPL    + YD R+GRS G A + +ER  D+ +AM+  NG+ LDGR +++
Sbjct: 16 LREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANGMELDGRRIRV 73

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

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

 Score = 46.5 bits (111), Expect = 3e-08
 Identities = 20/59 (33%), Positives = 33/59 (55%), Gaps = 1/59 (1%)

Query: 4  ELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
          +LF +FG + SA++  DR +GRS G   +  E   +A  A+++ NG    GR + +  A
Sbjct: 18 DLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEKLNGTDFGGRTLTVNEA 76

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

 Score = 46.4 bits (111), Expect = 3e-08
 Identities = 23/66 (34%), Positives = 40/66 (60%), Gaps = 6/66 (9%)

Query: 2  IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYN-----GVPLDGRP 55
          + ELFS+FG +K A++  D+ +G S GTA + ++ +  A K ++  +     G+ LDGR 
Sbjct: 17 LKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAADNAEDSGLSLDGRR 76

Query: 56 MQIQLA 61
          + + LA
Sbjct: 77 LIVTLA 82

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

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

 Score = 46.4 bits (111), Expect = 3e-08
 Identities = 20/66 (30%), Positives = 32/66 (48%), Gaps = 14/66 (21%)

Query: 2  IYELFSEFGP------LKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRP 55
          +Y LFS+FGP       K+ K+         G A ++++    A  A++   G P   +P
Sbjct: 20 LYALFSQFGPVLDIVASKTLKMR--------GQAFVVFKDVESATNALRALQGFPFYDKP 71

Query: 56 MQIQLA 61
          M+IQ A
Sbjct: 72 MRIQYA 77

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

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

 Score = 46.1 bits (110), Expect = 3e-08
 Identities = 20/55 (36%), Positives = 36/55 (65%), Gaps = 1/55 (1%)

Query: 2  IYELFSEFGPLKSAKLHYD-RSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRP 55
          + E+FS +GP++  ++ YD ++GRS G   + +E   DA +A ++ NG+ +DGR 
Sbjct: 16 LREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGMEIDGRR 70

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

 Score = 45.7 bits (109), Expect = 5e-08
 Identities = 16/60 (26%), Positives = 29/60 (48%), Gaps = 1/60 (1%)

Query: 4  ELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA 62
          E FSE GP+K   +  D+ S +  G   + +    DA +A+++       GR + ++ A 
Sbjct: 18 EFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEKKKTKFGGRKIHVEFAK 77

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|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 = 44.9 bits (107), Expect = 1e-07
 Identities = 20/61 (32%), Positives = 33/61 (54%), Gaps = 1/61 (1%)

Query: 2  IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
          + E+FSE GP+ S +L  DR +G+  G     +E    A  A++  NG   +GR +++  
Sbjct: 15 LIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLNGYEFNGRALRVDF 74

Query: 61 A 61
          A
Sbjct: 75 A 75

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

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

 Score = 44.5 bits (106), Expect = 2e-07
 Identities = 18/56 (32%), Positives = 33/56 (58%)

Query: 1  MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPM 56
           + ELF ++G + SAK+  D  G+S G   + +E    A KA+++ NG  ++G+ +
Sbjct: 17 KLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEELNGKEVNGKKL 72

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

 Score = 44.3 bits (105), Expect = 2e-07
 Identities = 21/57 (36%), Positives = 34/57 (59%), Gaps = 1/57 (1%)

Query: 6  FSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
          F +FG +  A++  DR +GRS G   + +E   DA KA++  +G  LDGRP+ +  +
Sbjct: 20 FEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEAMDGKELDGRPINVDFS 76

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

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

 Score = 44.1 bits (104), Expect = 3e-07
 Identities = 17/60 (28%), Positives = 34/60 (56%)

Query: 4  ELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD 63
          ++F  +G ++ A +   R G+  G A +  ++R +A  A++  NG+ +DGRP+ +  A  
Sbjct: 20 KIFGRYGKVREATIPRKRGGKLCGFAFVTMKKRKNAEIALENTNGLEIDGRPVAVDWAVQ 79

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

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

 Score = 43.4 bits (103), Expect = 4e-07
 Identities = 19/58 (32%), Positives = 34/58 (58%)

Query: 1  MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
           + +LF E G +  A +  D  GRS G   +++E   DA +A++ +NG  L+GR +++
Sbjct: 14 DLKDLFRECGNVLRADVKTDNDGRSKGFGTVLFESPEDAQRAIEMFNGYDLEGRELEV 71

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

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

 Score = 46.3 bits (110), Expect = 4e-07
 Identities = 21/61 (34%), Positives = 34/61 (55%)

Query: 1   MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
            + ELFSE G + SAK+  D  G S G   + +    +A +A+ + +G  L G+P+ + L
Sbjct: 301 KLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVAL 360

Query: 61  A 61
           A
Sbjct: 361 A 361

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

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

 Score = 43.4 bits (103), Expect = 4e-07
 Identities = 21/63 (33%), Positives = 33/63 (52%), Gaps = 4/63 (6%)

Query: 4  ELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD 63
          +LFS FG +    +     G+  G A + +  ++DA KA+K  NG  + GRP    +A D
Sbjct: 18 KLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGVNGKKIKGRP----VAVD 73

Query: 64 VSV 66
           +V
Sbjct: 74 WAV 76

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|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 = 43.4 bits (103), Expect = 4e-07
 Identities = 20/59 (33%), Positives = 33/59 (55%), Gaps = 1/59 (1%)

Query: 4  ELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
           LFS+FG ++   L  D  +G S G   + +E   DA  A++  NG  L+GR ++++ A
Sbjct: 20 ALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRDLNGKELEGRVIKVEKA 78

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

 Score = 43.3 bits (103), Expect = 4e-07
 Identities = 19/59 (32%), Positives = 32/59 (54%), Gaps = 1/59 (1%)

Query: 2  IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
          + E+FS +G +K   L  DR      G A + +E   DA KA+K  +G  +DG+ + ++
Sbjct: 15 LKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHMDGGQIDGQEVTVE 73

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

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

 Score = 43.2 bits (102), Expect = 5e-07
 Identities = 22/61 (36%), Positives = 34/61 (55%), Gaps = 1/61 (1%)

Query: 2  IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
          I  LFS  G ++S KL  D+ +G+SLG   + Y    DA KA+   NG+ L  + +++  
Sbjct: 18 IRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTLNGLRLQNKTIKVSY 77

Query: 61 A 61
          A
Sbjct: 78 A 78

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

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

 Score = 43.5 bits (102), Expect = 5e-07
 Identities = 22/59 (37%), Positives = 38/59 (64%), Gaps = 1/59 (1%)

Query: 4  ELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
          E+FS++GP+    + YD+ S RS G A + +E   DA +A ++ NG+ LDGR +++  +
Sbjct: 28 EVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFS 86

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

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

 Score = 42.8 bits (101), Expect = 8e-07
 Identities = 17/58 (29%), Positives = 34/58 (58%)

Query: 4  ELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
          +LF + G +KS +L  +RSG+  G A + YE  S A +A+ + +G  +  + + + ++
Sbjct: 21 KLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKMDGTEIKEKTISVAIS 78

This subfamily corresponds to the RRM2 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), is an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 81

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

 Score = 42.7 bits (101), Expect = 8e-07
 Identities = 20/61 (32%), Positives = 34/61 (55%), Gaps = 1/61 (1%)

Query: 2  IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
          +  LF   GP++S K+  DR +G+SLG   + Y   +DA KA+   NG  +  + +++  
Sbjct: 17 LRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLNGFEIRNKRLKVSY 76

Query: 61 A 61
          A
Sbjct: 77 A 77

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

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

 Score = 45.2 bits (107), Expect = 9e-07
 Identities = 20/59 (33%), Positives = 36/59 (61%), Gaps = 1/59 (1%)

Query: 1  MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
           +Y+LF  FGP+ S ++  D  + RSLG   + ++  +DA +A++  N   L G+P++I
Sbjct: 16 KLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRI 74

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

 Score = 42.6 bits (101), Expect = 1e-06
 Identities = 22/58 (37%), Positives = 33/58 (56%)

Query: 4  ELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
          E FS FG + SAK+  D  GRS G   + +    +A KA+ + NG  + G+P+ + LA
Sbjct: 20 EEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAVTEMNGRIIGGKPLYVALA 77

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

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

 Score = 42.3 bits (100), Expect = 1e-06
 Identities = 18/61 (29%), Positives = 31/61 (50%), Gaps = 1/61 (1%)

Query: 2  IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
          + E F E G +   ++  D  GRS G   + +     A KA+++ +G  L GR +++ LA
Sbjct: 16 LEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKALEK-SGEELLGREIRVDLA 74

Query: 62 A 62
           
Sbjct: 75 T 75

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|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 = 41.9 bits (99), Expect = 1e-06
 Identities = 17/56 (30%), Positives = 26/56 (46%), Gaps = 1/56 (1%)

Query: 4  ELFSEFGPLKSAKLHYDRS-GRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
          ELF  FG +    L  D+   RS G A + +     A+KA  + +G    GR + +
Sbjct: 18 ELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSELDGSIFQGRLLHV 73

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

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

 Score = 41.5 bits (98), Expect = 3e-06
 Identities = 23/61 (37%), Positives = 36/61 (59%), Gaps = 7/61 (11%)

Query: 1  MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
           + ELFSE+G ++  K   D        A + +E R DA+KAM++ NG  L+G P+++ L
Sbjct: 17 QLRELFSEYGEVERVKKIKD-------YAFVHFEERDDAVKAMEEMNGKELEGSPIEVSL 69

Query: 61 A 61
          A
Sbjct: 70 A 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|241104 cd12660, RRM2_MYEF2, RNA recognition motif 2 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 41.5 bits (97), Expect = 3e-06
 Identities = 19/57 (33%), Positives = 35/57 (61%)

Query: 4  ELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
          E+FS  G +K A +  D+ G+S G   + +E+  +A++A+  +NG  L  RPM +++
Sbjct: 19 EVFSIAGTVKRADIKEDKDGKSRGMGTVTFEQPIEAVQAISMFNGQFLFDRPMHVKM 75

This subgroup corresponds to the RRM2 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. . Length = 76

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

 Score = 41.1 bits (97), Expect = 3e-06
 Identities = 18/59 (30%), Positives = 34/59 (57%)

Query: 1  MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
          ++YELF + GPL+  K+  D +G+    A + ++       A++  NG+ L GR ++I+
Sbjct: 17 ILYELFLQAGPLEGVKIPKDPNGKPKSFAFVTFKHEVSVPYAIQLLNGIRLFGRELRIK 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|240729 cd12283, RRM1_RBM39_like, RNA recognition motif 1 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins

 Score = 41.1 bits (97), Expect = 3e-06
 Identities = 18/59 (30%), Positives = 30/59 (50%), Gaps = 2/59 (3%)

Query: 2  IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
          +YE FS+ G ++  ++  DR S RS G A + +        A+    G  L G+P+ +Q
Sbjct: 16 LYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLAL-GLTGQRLLGQPIMVQ 73

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

 Score = 41.0 bits (97), Expect = 4e-06
 Identities = 22/58 (37%), Positives = 31/58 (53%), Gaps = 1/58 (1%)

Query: 2  IYELFSEFGPLKSAKLHYDRSGRS-LGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
          IYELFS  G +K   +  DR  ++  G   + Y  R DA  A+K  NG  LD R +++
Sbjct: 15 IYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYLNGTKLDDRIIRV 72

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

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

 Score = 43.0 bits (101), Expect = 6e-06
 Identities = 21/74 (28%), Positives = 39/74 (52%), Gaps = 1/74 (1%)

Query: 1   MIYELFSEFGPLKSAKLHYD-RSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
            + ++F  FG ++  +LH D  +GRS G   + +    +A +A++  NG  L GRP+++ 
Sbjct: 202 ELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVG 261

Query: 60  LAADVSVLENTVPR 73
            A D + L +    
Sbjct: 262 YAQDSTYLLDAANT 275

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

 Score = 40.3 bits (94), Expect = 7e-06
 Identities = 20/59 (33%), Positives = 32/59 (54%)

Query: 1  MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
          +I+ELF + GP+   K+  D+ G+    A + ++       AM   NG+ L GRP+ IQ
Sbjct: 17 LIFELFLQAGPVIKVKIPKDKDGKPKQFAFVNFKHEVSVPYAMNLLNGIKLYGRPLNIQ 75

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

 Score = 40.2 bits (95), Expect = 8e-06
 Identities = 19/63 (30%), Positives = 36/63 (57%), Gaps = 4/63 (6%)

Query: 1  MIYELFSEFGPLKSAKLHYDRS-GRSLGTADLIYERRSDAIKAMKQYNG-VPLDG--RPM 56
           +  LF E+G ++   +  D+  G+S G A + +  R +A KA++  +G V + G  RP+
Sbjct: 15 DVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEALHGKVTMPGASRPL 74

Query: 57 QIQ 59
          Q++
Sbjct: 75 QVK 77

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|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 = 40.2 bits (94), Expect = 8e-06
 Identities = 22/62 (35%), Positives = 37/62 (59%), Gaps = 1/62 (1%)

Query: 1  MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
           + ++FSE GP+ S +L YDR +G+  G     Y+ +  A+ AM+  NG  L+GR +++ 
Sbjct: 14 QLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNLNGYELNGRQLRVD 73

Query: 60 LA 61
           A
Sbjct: 74 NA 75

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

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

 Score = 39.5 bits (93), Expect = 1e-05
 Identities = 18/55 (32%), Positives = 30/55 (54%), Gaps = 1/55 (1%)

Query: 1  MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRP 55
           + E FS +G ++  +L  ++  R  G A + +    DA  A+K+ NG+ LDGR 
Sbjct: 14 DLREFFSPYGKVEGVRLVRNKD-RPRGFAFVEFASPEDAEAALKKLNGLVLDGRT 67

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

>gnl|CDD|240832 cd12386, RRM2_hnRNPM_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 39.3 bits (92), Expect = 1e-05
 Identities = 17/59 (28%), Positives = 34/59 (57%)

Query: 2  IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
          + E+F   G +  A +  D+ G+S G   + +E   +A++A+  +NG  L  RPM++++
Sbjct: 15 LKEVFKLAGKVVRADIKEDKEGKSRGMGVVQFEHPIEAVQAISMFNGQMLFDRPMRVKM 73

This subfamily corresponds to the RRM2 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 74

>gnl|CDD|240922 cd12478, RRM1_U2B, RNA recognition motif 1 in U2 small nuclear ribonucleoprotein B" (U2B") and similar proteins

 Score = 39.2 bits (91), Expect = 3e-05
 Identities = 24/66 (36%), Positives = 35/66 (53%), Gaps = 14/66 (21%)

Query: 2  IYELFSEFG------PLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRP 55
          +Y LFS+FG       LK+ K+         G A +I++  S A  A++Q  G P  G+P
Sbjct: 22 LYALFSQFGHVVDIVALKTMKMR--------GQAFVIFKELSSATNALRQLQGFPFYGKP 73

Query: 56 MQIQLA 61
          M+IQ A
Sbjct: 74 MRIQYA 79

This subgroup corresponds to the RRM1 of U2B" (also termed U2 snRNP B") a unique protein that comprises the U2 snRNP. It was initially identified as binding to stem-loop IV (SLIV) at the 3' end of U2 snRNA. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. U2B" does not require an auxiliary protein for binding to RNA. In addition, the nuclear transport of U2B" is independent of U2 snRNA binding. U2B" contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It also contains a nuclear localization signal (NLS) in the central domain. However, nuclear import of U2B'' does not depend on this NLS. The N-terminal RRM is sufficient to direct U2B" to the nucleus. . Length = 91

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

 Score = 40.6 bits (95), Expect = 4e-05
 Identities = 21/50 (42%), Positives = 32/50 (64%)

Query: 4   ELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDG 53
           ELF++FG + SA +  D SGRS G A + +E+  DA KA+++ NG  +  
Sbjct: 197 ELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGL 246

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

 Score = 38.3 bits (89), Expect = 4e-05
 Identities = 18/58 (31%), Positives = 31/58 (53%), Gaps = 1/58 (1%)

Query: 2  IYELFSEFGPLKSAKLHYD-RSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
          ++  FS F     A++ +D +SGRS G   + +  + DA  A+ + NG  L  RP++ 
Sbjct: 16 LFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEMNGKWLGSRPIRC 73

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|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 = 38.3 bits (89), Expect = 4e-05
 Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 1/63 (1%)

Query: 2  IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
          + ++FS++G +    +  DR + RS G   + +E   DA  AM   NG  +DGR +++  
Sbjct: 17 LEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAMNGKSVDGRQIRVDQ 76

Query: 61 AAD 63
          A  
Sbjct: 77 AGK 79

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|241103 cd12659, RRM2_hnRNPM, RNA recognition motif 2 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 38.1 bits (88), Expect = 5e-05
 Identities = 18/57 (31%), Positives = 34/57 (59%)

Query: 4  ELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
          E+FS  G +  A +  D+ G+S G   + +E+  +A++A+  +NG  L  RPM +++
Sbjct: 19 EVFSMAGMVVRADILEDKDGKSRGIGTVTFEQPIEAVQAISMFNGQLLFDRPMHVKM 75

This subgroup corresponds to the RRM2 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). . Length = 76

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

 Score = 37.9 bits (89), Expect = 6e-05
 Identities = 18/47 (38%), Positives = 28/47 (59%), Gaps = 1/47 (2%)

Query: 3  YELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNG 48
           ELF  FGP+    L  D+ +G+S G A + +  R DA +A+++ NG
Sbjct: 17 RELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNG 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|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA branch site protein p14 (SF3B14) and similar proteins

 Score = 37.6 bits (88), Expect = 7e-05
 Identities = 15/53 (28%), Positives = 28/53 (52%), Gaps = 2/53 (3%)

Query: 2  IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGR 54
          +Y+LF ++G ++  ++   +  R  GTA ++YE   DA  A    +G  +  R
Sbjct: 19 LYDLFGKYGAIRQIRIGNTKETR--GTAFVVYEDIYDAKNACDHLSGFNVANR 69

This subfamily corresponds to the RRM of SF3B14 (also termed p14), a 14 kDa protein subunit of SF3B which is a multiprotein complex that is 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 has been involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B14 associates directly with another SF3B subunit called SF3B155. It is also present in both U2- and U12-dependent spliceosomes and may contribute to branch site positioning in both the major and minor spliceosome. Moreover, SF3B14 interacts directly with the pre-mRNA branch adenosine early in spliceosome assembly and within the fully assembled spliceosome. SF3B14 contains one well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 77

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

 Score = 37.6 bits (88), Expect = 1e-04
 Identities = 16/63 (25%), Positives = 32/63 (50%), Gaps = 6/63 (9%)

Query: 4  ELFSEFGPLKSAKL--HYDRSGR----SLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQ 57
          + F + G ++S  +    D  G     S+G   + ++ +  A KA+K+  G  LDG  ++
Sbjct: 19 KHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQKALKRLQGTVLDGHALE 78

Query: 58 IQL 60
          ++L
Sbjct: 79 LKL 81

This subfamily corresponds to the RRM5 of RBM19 and RRM4 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 82

>gnl|CDD|240669 cd12223, RRM_SR140, RNA recognition motif (RRM) in U2-associated protein SR140 and similar proteins

 Score = 37.2 bits (87), Expect = 1e-04
 Identities = 15/59 (25%), Positives = 31/59 (52%), Gaps = 4/59 (6%)

Query: 4  ELFSEFGPLKSAKLHYDRS----GRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
          + F  FGPL S K+ + R+     R+     + +  R+DA +A+ + +G  + G  +++
Sbjct: 20 QEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERALDELDGKDVMGYELKL 78

This subgroup corresponds to the RRM of SR140 (also termed U2 snRNP-associated SURP motif-containing protein orU2SURP, or 140 kDa Ser/Arg-rich domain protein) which is a putative splicing factor mainly found in higher eukaryotes. Although it is initially identified as one of the 17S U2 snRNP-associated proteins, the molecular and physiological function of SR140 remains unclear. SR140 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a SWAP/SURP domain that is found in a number of pre-mRNA splicing factors in the middle region, and a C-terminal arginine/serine-rich domain (RS domain). Length = 84

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

 Score = 37.1 bits (86), Expect = 1e-04
 Identities = 18/62 (29%), Positives = 30/62 (48%), Gaps = 4/62 (6%)

Query: 2  IYELFSEFGPLKSAKL--HYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
          +  LFS +G LKS ++   +D+S R     +    +  +A+ AM       L GR + +Q
Sbjct: 17 VRTLFSSYGQLKSVRVPKKFDQSARGFAFVEFSTAK--EALNAMNALKDTHLLGRRLVLQ 74

Query: 60 LA 61
           A
Sbjct: 75 YA 76

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

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

 Score = 36.8 bits (86), Expect = 2e-04
 Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 2/50 (4%)

Query: 5  LFSEFGPLKSAKLHY--DRSGRSLGTADLIYERRSDAIKAMKQYNGVPLD 52
          +FS+FG  K   ++   D +G++ G A + +    +A +A+K  NG  LD
Sbjct: 27 IFSKFGVGKIVGIYMPVDETGKTKGYAFVEFATPEEAKEAVKALNGYKLD 76

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

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

 Score = 36.5 bits (85), Expect = 2e-04
 Identities = 18/57 (31%), Positives = 31/57 (54%), Gaps = 2/57 (3%)

Query: 4  ELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
          E FS+FG +KS  + +D+ +G S G   + +  R D ++   Q     L+G  +Q+Q
Sbjct: 18 EYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSR-DGLENALQKQKHILEGNKLQVQ 73

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

 Score = 38.8 bits (90), Expect = 2e-04
 Identities = 22/61 (36%), Positives = 34/61 (55%), Gaps = 1/61 (1%)

Query: 2  IYELFSEFGPLKSAKLHYDRS-GRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
          I  LF+  G ++S KL  D+  G+SLG   + Y R  DA KA+   NG+ L  + +++  
Sbjct: 20 IRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSY 79

Query: 61 A 61
          A
Sbjct: 80 A 80

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|240750 cd12304, RRM_Set1, RNA recognition motif in the Set1-like family of histone-lysine N-methyltransferases

 Score = 36.9 bits (86), Expect = 2e-04
 Identities = 9/58 (15%), Positives = 34/58 (58%), Gaps = 1/58 (1%)

Query: 4  ELFSEFGPLKSAKLHYD-RSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
          ++  ++G ++  K+++  ++ + LG A ++++    A + +++ N   + G+ +++ L
Sbjct: 21 DMCKKYGEVEEVKIYFHPKTNKHLGLARVVFDSVKSAKRCVEKLNQTSVMGKIIKVFL 78

This subfamily corresponds to the RRM of the Set1-like family of histone-lysine N-methyltransferases which includes Set1A and Set1B that are ubiquitously expressed vertebrates histone methyltransferases exhibiting high homology to yeast Set1. Set1A and Set1B proteins exhibit a largely non-overlapping subnuclear distribution in euchromatic nuclear speckles, strongly suggesting that they bind to a unique set of target genes and thus make non-redundant contributions to the epigenetic control of chromatin structure and gene expression. With the exception of the catalytic component, the subunit composition of the Set1A and Set1B histone methyltransferase complexes are identical. Each complex contains six human homologs of the yeast Set1/COMPASS complex, including Set1A or Set1B, Ash2 (homologous to yeast Bre2), CXXC finger protein 1 (CFP1; homologous to yeast Spp1), Rbbp5 (homologous to yeast Swd1), Wdr5 (homologous to yeast Swd3), and Wdr82 (homologous to yeast Swd2). The genomic targeting of these complexes is determined by the identity of the catalytic subunit present in each histone methyltransferase complex. Thus, the Set1A and Set1B complexes may exhibit both overlapping and non-redundant properties. Both Set1A and Set1B contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), an N- SET domain, and a C-terminal catalytic SET domain followed by a post-SET domain. In contrast to Set1B, Set1A additionally contains an HCF-1 binding motif that interacts with HCF-1 in vivo. . Length = 93

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

 Score = 36.6 bits (85), Expect = 2e-04
 Identities = 22/59 (37%), Positives = 34/59 (57%), Gaps = 1/59 (1%)

Query: 1  MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
           I + FS FGP+KS  + +D  + +  G A + YE    A  A++Q NGV L GR +++
Sbjct: 16 TIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQMNGVMLGGRNIKV 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|240830 cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins

 Score = 36.4 bits (85), Expect = 2e-04
 Identities = 19/61 (31%), Positives = 35/61 (57%), Gaps = 2/61 (3%)

Query: 2  IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
          + + FS+FG ++ A +  DR +G+S G   + ++ +  A +A K  N + +DGR   + L
Sbjct: 17 LRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKDPNPI-IDGRKANVNL 75

Query: 61 A 61
          A
Sbjct: 76 A 76

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

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

 Score = 36.3 bits (84), Expect = 2e-04
 Identities = 15/57 (26%), Positives = 26/57 (45%), Gaps = 7/57 (12%)

Query: 2  IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
          I E+FS +G +K  K+           A + +E    AI+A    +G  L+  P+ +
Sbjct: 16 IREIFSPYGAVKEVKMIS-------NFAFVEFESLESAIRAKDSVHGKVLNNNPLYV 65

This subfamily corresponds to the RRM1 of Npl3p, also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. Npl3p is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein containing two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues. . Length = 67

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

 Score = 38.1 bits (88), Expect = 2e-04
 Identities = 31/97 (31%), Positives = 45/97 (46%), Gaps = 6/97 (6%)

Query: 1   MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
           +I + FSEF P K      +R  +    A + +E R DA+KAM + NG  L+G  +++ L
Sbjct: 249 IIEKSFSEFKPGK-----VERVKKIRDYAFVHFEDREDAVKAMDELNGKELEGSEIEVTL 303

Query: 61  AADVSVLENTVPRPVARGGRGGASGGYRNGTAPTYRP 97
           A  V   ++ V      GGRG      R      Y P
Sbjct: 304 AKPVDK-KSYVRYTRGTGGRGKERQAARQSLGQVYDP 339

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

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

 Score = 37.5 bits (87), Expect = 4e-04
 Identities = 16/53 (30%), Positives = 33/53 (62%)

Query: 2   IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGR 54
           +++ FS+FG + S K+  D +G+S G   + +E+   A  A+++ NG+ L+ +
Sbjct: 105 LFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDK 157

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

 Score = 36.1 bits (84), Expect = 4e-04
 Identities = 17/50 (34%), Positives = 29/50 (58%), Gaps = 1/50 (2%)

Query: 6  FSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGR 54
          FS FG +KS ++  D+ +G SL  A + +E + D  +A  + + V +D R
Sbjct: 24 FSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFKMDNVLIDDR 73

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

 Score = 35.8 bits (82), Expect = 4e-04
 Identities = 13/32 (40%), Positives = 19/32 (59%)

Query: 33 YERRSDAIKAMKQYNGVPLDGRPMQIQLAADV 64
          +  R DA+ AM   NG  +DG P+++ LA  V
Sbjct: 51 FSNREDAVDAMNALNGKVIDGSPIEVTLAKPV 82

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

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

 Score = 35.7 bits (83), Expect = 6e-04
 Identities = 18/50 (36%), Positives = 28/50 (56%), Gaps = 1/50 (2%)

Query: 6  FSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGR 54
          F E+GP+K  +L  D+ +G+  G A + +E   D   A K  +G  +DGR
Sbjct: 22 FEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYADGKKIDGR 71

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

 Score = 35.3 bits (81), Expect = 6e-04
 Identities = 16/59 (27%), Positives = 30/59 (50%)

Query: 1  MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
          ++YELF + GPL    +  D+ G+      + ++       A+   NG+ L GRP+++ 
Sbjct: 17 ILYELFLQAGPLTKVTICKDKEGKPKSFGFVCFKHSESVPYAIALLNGIRLYGRPIKVH 75

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

 Score = 35.3 bits (82), Expect = 7e-04
 Identities = 19/64 (29%), Positives = 32/64 (50%), Gaps = 2/64 (3%)

Query: 1  MIYELFSEFGP-LKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
          M+ E F    P ++ AK+  D  +GRS G   + +    +  +A+ + NGV    RPM++
Sbjct: 17 MLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRALTEMNGVYCSSRPMRV 76

Query: 59 QLAA 62
            A 
Sbjct: 77 SPAT 80

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|240921 cd12477, RRM1_U1A, RNA recognition motif 1 found in vertebrate U1 small nuclear ribonucleoprotein A (U1A)

 Score = 35.0 bits (80), Expect = 0.001
 Identities = 18/58 (31%), Positives = 31/58 (53%), Gaps = 2/58 (3%)

Query: 2  IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
          ++ +FS FG +    +   RS +  G A +I++  S A  A++   G P   +PM+IQ
Sbjct: 24 LHAIFSRFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQ 79

This subgroup corresponds to the RRM1 of U1A (also termed U1 snRNP A or U1-A), an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein and it also shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins, including polypyrimidine tract binding protein (PTB), polypyrimidine-tract binding protein-associated factor (PSF), and non-POU-domain-containing, octamer-binding (NONO), DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5). It also binds to a flavivirus NS5 protein and plays an important role in virus replication. U1A contains two RNA recognition motifs (RRMs); the N-terminal RRM (RRM1) binds tightly and specifically to the U1 snRNA SLII and its own 3'-UTR, while in contrast, the C-terminal RRM (RRM2) does not appear to associate with any RNA and may be free to bind other proteins. U1A also contains a proline-rich region, and a nuclear localization signal (NLS) in the central domain that is responsible for its nuclear import. . Length = 89

>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 = 34.5 bits (80), Expect = 0.001
 Identities = 19/58 (32%), Positives = 34/58 (58%), Gaps = 1/58 (1%)

Query: 3  YELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
          Y+LF+ FG + SAK+  D+ +G+S     + Y+    A  A+K  NG  + G+ +++Q
Sbjct: 16 YQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAMNGFQVGGKRLKVQ 73

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

>gnl|CDD|240950 cd12506, RRM3_hnRNPH_CRSF1_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein hnRNP H protein family, G-rich sequence factor 1 (GRSF-1) and similar proteins

 Score = 34.6 bits (80), Expect = 0.001
 Identities = 14/44 (31%), Positives = 23/44 (52%), Gaps = 2/44 (4%)

Query: 4  ELFSEFGPLKSAKLH--YDRSGRSLGTADLIYERRSDAIKAMKQ 45
          ++F  F PL    +   Y+  GR+ G AD+ +    DA+ AM +
Sbjct: 16 DIFEFFSPLNPVNVRIEYNADGRATGEADVEFATHEDAVAAMSK 59

This subfamily corresponds to the RRM3 of hnRNP H proteins and GRSF-1. The hnRNP H protein family includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9), which represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing. These proteins have similar RNA binding affinities and specifically recognize the sequence GGGA. They can either stimulate or repress splicing upon binding to a GGG motif. hnRNP H binds to the RNA substrate in the presence or absence of these proteins, whereas hnRNP F binds to the nuclear mRNA only in the presence of cap-binding proteins. hnRNP H and hnRNP H2 are almost identical; both have been found to bind nuclear-matrix proteins. hnRNP H activates exon inclusion by binding G-rich intronic elements downstream of the 5' splice site in the transcripts of c-src, human immunodeficiency virus type 1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences exons when bound to exonic elements in the transcripts of beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP H2 has been implicated in pre-mRNA 3' end formation. hnRNP H3 may be involved in the splicing arrest induced by heat shock. Most family members contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), except for hnRNP H3, in which the RRM1 is absent. RRM1 and RRM2 are responsible for the binding to the RNA at DGGGD motifs, and they play an important role in efficiently silencing the exon. For instance, members in this family can regulate the alternative splicing of the fibroblast growth factor receptor 2 (FGFR2) transcripts, and function as silencers of FGFR2 exon IIIc through an interaction with the exonic GGG motifs. The lack of RRM1 could account for the reduced silencing activity within hnRNP H3. In addition, the family members have an extensive glycine-rich region near the C-terminus, which may allow them to homo- or heterodimerize. The family also includes a cytoplasmic poly(A)+ mRNA binding protein, GRSF-1, which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. GRSF-1 also contains three potential RRMs responsible for the RNA binding, and two auxiliary domains (an acidic alpha-helical domain and an N-terminal alanine-rich region) that may play a role in protein-protein interactions and provide binding specificity. . Length = 75

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

 Score = 34.2 bits (79), Expect = 0.001
 Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 2/60 (3%)

Query: 2  IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
          + ELFS+ GP+KS KL  +         +  Y     A  A++  NG  + G+ +++  A
Sbjct: 15 LAELFSQIGPIKSCKLIREHGNDPYAFVE--YYDHRSAAAALQTMNGRLILGQEIKVNWA 72

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

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

 Score = 34.2 bits (79), Expect = 0.002
 Identities = 14/59 (23%), Positives = 25/59 (42%), Gaps = 1/59 (1%)

Query: 2  IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
          + E FS  G +    L    +  +   A + +ER   A +A++  N   L  + M +Q 
Sbjct: 20 LNERFSRHGKILEVNLIKRANHTN-AFAFIKFEREQAAARAVESENHSMLKNKTMHVQY 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|240894 cd12448, RRM2_gar2, RNA recognition motif 2 in yeast protein gar2 and similar proteins

 Score = 33.9 bits (78), Expect = 0.002
 Identities = 20/58 (34%), Positives = 30/58 (51%), Gaps = 1/58 (1%)

Query: 2  IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
          IYE F E+G + S +L  D  SGR  G   + +  +  A  A+    G  L GRP+++
Sbjct: 15 IYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDALGGTDLLGRPVRL 72

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

 Score = 34.3 bits (79), Expect = 0.002
 Identities = 21/55 (38%), Positives = 32/55 (58%), Gaps = 1/55 (1%)

Query: 5  LFSEFGPLKSAKLHYD-RSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
          LFS+FG L    +  D +SG+S G A +++    DA+KA K+ +G    GR + I
Sbjct: 22 LFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKELDGKVFQGRLIHI 76

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

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

 Score = 33.8 bits (77), Expect = 0.002
 Identities = 20/56 (35%), Positives = 30/56 (53%), Gaps = 7/56 (12%)

Query: 6  FSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
          FSEFG L+  K   D        A + +E R  A++AM + NG  ++G  ++I LA
Sbjct: 22 FSEFGKLERVKKLKD-------YAFVHFEERDAAVRAMDEMNGKEIEGEEIEIVLA 70

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

 Score = 34.2 bits (78), Expect = 0.002
 Identities = 19/65 (29%), Positives = 41/65 (63%), Gaps = 3/65 (4%)

Query: 2  IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNG--VPLDGRPMQI 58
          + ++FS FG + ++++  D+ +G S G A + +++RS+A +A+  +NG   P    P+ +
Sbjct: 17 VEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITSFNGHKPPGSSEPITV 76

Query: 59 QLAAD 63
          + AA+
Sbjct: 77 KFAAN 81

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

 Score = 33.9 bits (77), Expect = 0.002
 Identities = 21/58 (36%), Positives = 33/58 (56%), Gaps = 1/58 (1%)

Query: 5  LFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
          LFS  G ++SAKL  D+ +G SLG   + Y    DA +A+   NG+ L  + +++  A
Sbjct: 21 LFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINTLNGLRLQSKTIKVSYA 78

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

 Score = 35.3 bits (81), Expect = 0.003
 Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 2/61 (3%)

Query: 2   IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
           +YE FS+ G ++  +   DR S RS G A + +      IKA+    G  L GRP+ +Q 
Sbjct: 106 LYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKAL-ALTGQMLLGRPIIVQS 164

Query: 61  A 61
           +
Sbjct: 165 S 165

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

 Score = 33.5 bits (77), Expect = 0.003
 Identities = 19/60 (31%), Positives = 33/60 (55%), Gaps = 1/60 (1%)

Query: 3  YELFSEFGPLKSAKLHYD-RSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
            LF   GP+K+ K+  D R+G S G   + Y+   DA +A++  NG+ L  + +++  A
Sbjct: 18 RSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTLNGLQLQNKRIKVAYA 77

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

 Score = 33.4 bits (77), Expect = 0.003
 Identities = 14/58 (24%), Positives = 29/58 (50%)

Query: 4  ELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
          +LF  FG +   +L Y + G+      + Y+   +A KA+K +N   +D   + +++ 
Sbjct: 19 KLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALKHFNNSFIDTSKITVEIC 76

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

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

 Score = 33.5 bits (77), Expect = 0.003
 Identities = 18/61 (29%), Positives = 35/61 (57%), Gaps = 3/61 (4%)

Query: 4  ELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPL--DGRPMQIQL 60
          E F+ FG ++   +  D+ +  S G A + + + S A +AM++ NG  L  D +P+++ +
Sbjct: 21 EAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNGKCLGGDTKPLKVLI 80

Query: 61 A 61
          A
Sbjct: 81 A 81

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

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

 Score = 33.6 bits (76), Expect = 0.003
 Identities = 20/58 (34%), Positives = 33/58 (56%), Gaps = 1/58 (1%)

Query: 5  LFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
          LF   G ++S KL  D+ +G+SLG   + Y   +DA KA+   NG+ L  + +++  A
Sbjct: 23 LFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINTLNGLKLQTKTIKVSYA 80

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

 Score = 34.6 bits (79), Expect = 0.003
 Identities = 24/82 (29%), Positives = 37/82 (45%), Gaps = 1/82 (1%)

Query: 6   FSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADV 64
           F+ FG +  AK+  DR +GRS G   + +     A  A+ + +G  L+GR +++  A D 
Sbjct: 55  FAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPANDR 114

Query: 65  SVLENTVPRPVARGGRGGASGG 86
                         G GG  GG
Sbjct: 115 PSAPRAYGGGGGYSGGGGGYGG 136

Length = 144

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

 Score = 33.3 bits (77), Expect = 0.003
 Identities = 17/53 (32%), Positives = 32/53 (60%)

Query: 2  IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGR 54
          +Y+ FS FG + S K+  D +G S G   + +E    A++A+++ NG+ L+ +
Sbjct: 19 LYDTFSAFGNILSCKVATDENGGSKGYGFVHFETEEAAVRAIEKVNGMLLNDK 71

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

 Score = 33.4 bits (77), Expect = 0.004
 Identities = 17/55 (30%), Positives = 28/55 (50%)

Query: 4  ELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
          +LFS+ G     +L    +G+  G A + Y    DA +A +  NG  L G P+++
Sbjct: 22 KLFSQVGKPTFCQLAIAPNGQPRGFAFVEYATAEDAEEAQQALNGHSLQGSPIRV 76

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

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

 Score = 34.7 bits (79), Expect = 0.004
 Identities = 21/65 (32%), Positives = 35/65 (53%), Gaps = 1/65 (1%)

Query: 1   MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
            I   F  FGP+KS  + +D  +G+  G A + YE    A  A++Q NG  L GR +++ 
Sbjct: 123 TIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVG 182

Query: 60  LAADV 64
             +++
Sbjct: 183 RPSNM 187

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|240779 cd12333, RRM2_p54nrb_like, RNA recognition motif 2 in the p54nrb/PSF/PSP1 family

 Score = 33.0 bits (76), Expect = 0.004
 Identities = 14/45 (31%), Positives = 26/45 (57%)

Query: 1  MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQ 45
          ++ + FS+FG ++ A +  D  GRS G   + + R+  A  A+K+
Sbjct: 15 LLEQAFSQFGEVERAVVIVDDRGRSTGEGIVEFSRKPGAQAAIKR 59

This subfamily corresponds to the RRM2 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. The family 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 contains 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 = 80

>gnl|CDD|240920 cd12476, RRM1_SNF, RNA recognition motif 1 found in Drosophila melanogaster sex determination protein SNF and similar proteins

 Score = 33.4 bits (76), Expect = 0.004
 Identities = 18/66 (27%), Positives = 32/66 (48%), Gaps = 14/66 (21%)

Query: 2  IYELFSEFGP------LKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRP 55
          +Y +FS+FG       LK+ K+         G A ++++  S A  A++   G P   +P
Sbjct: 20 LYAIFSQFGQILDIVALKTLKMR--------GQAFVVFKDISSATNALRSMQGFPFYDKP 71

Query: 56 MQIQLA 61
          M+I  +
Sbjct: 72 MRIAYS 77

This subgroup corresponds to the RRM1 of SNF (Sans fille), also termed U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A), an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila. It is essential in Drosophila sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). SNF contains two RNA recognition motifs (RRMs); it can self-associate through RRM1, and each RRM can recognize poly(U) RNA binding independently. . Length = 78

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

 Score = 33.3 bits (76), Expect = 0.004
 Identities = 16/59 (27%), Positives = 30/59 (50%), Gaps = 1/59 (1%)

Query: 4  ELFSEFGPLKSAKLHYD-RSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
          + FS+  P+K A +  D  +G S G   + +    DA +A+ +     L GR +++ +A
Sbjct: 18 DFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKLKNKKLHGRILRLDIA 76

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	105
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.77
KOG4207|consensus	256		99.64
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.57
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.5
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.5
KOG0122|consensus	270		99.48
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.41
smart00361	70	RRM_1 RNA recognition motif.	99.4
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.4
KOG0148|consensus	321		99.37
KOG0145|consensus	360		99.36
KOG0107|consensus	195		99.36
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.36
KOG0105|consensus	241		99.34
KOG0125|consensus	376		99.29
KOG0113|consensus	335		99.28
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.27
smart00360	71	RRM RNA recognition motif.	99.25
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.25
KOG0130|consensus	170		99.25
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.24
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.23
KOG0121|consensus	153		99.21
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.21
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.19
KOG4212|consensus	608		99.19
PLN03120	260	nucleic acid binding protein; Provisional	99.17
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.17
KOG0144|consensus	510		99.17
smart00362	72	RRM_2 RNA recognition motif.	99.15
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.15
KOG0117|consensus	506		99.14
KOG0146|consensus	371		99.13
KOG0126|consensus	219		99.12
KOG0149|consensus	247		99.1
KOG0144|consensus	510		99.1
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.07
KOG0148|consensus	321		99.04
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.03
PLN03121	243	nucleic acid binding protein; Provisional	99.03
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.03
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.02
KOG0127|consensus	678		99.02
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.01
KOG0108|consensus	435		99.0
KOG0145|consensus	360		99.0
KOG0146|consensus	371		98.99
KOG0111|consensus	298		98.98
KOG0124|consensus	544		98.97
PLN03213	759	repressor of silencing 3; Provisional	98.96
KOG0415|consensus	479		98.96
KOG0116|consensus	419		98.94
KOG4661|consensus	940		98.93
COG0724	306	RNA-binding proteins (RRM domain) [General functio	98.92
KOG0117|consensus	506		98.88
KOG0131|consensus	203		98.86
KOG0123|consensus	369		98.83
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	98.83
KOG0123|consensus	369		98.82
KOG0109|consensus	346		98.79
KOG4208|consensus	214		98.74
KOG0147|consensus	549		98.71
KOG0131|consensus	203		98.69
KOG4206|consensus	221		98.6
KOG0114|consensus	124		98.6
KOG0124|consensus	544		98.59
KOG0127|consensus	678		98.55
KOG0109|consensus	346		98.55
KOG0533|consensus	243		98.5
KOG0110|consensus	725		98.5
KOG0110|consensus	725		98.49
KOG0153|consensus	377		98.43
KOG4209|consensus	231		98.37
KOG0132|consensus	894		98.35
KOG0226|consensus	290		98.26
KOG1190|consensus	492		98.21
KOG2314|consensus	698		98.15
KOG0106|consensus	216		98.09
KOG0147|consensus	549		98.04
KOG4205|consensus	311		98.02
KOG4205|consensus	311		97.95
KOG0120|consensus	500		97.91
KOG1995|consensus	351		97.89
KOG4660|consensus	549		97.79
KOG4212|consensus	608		97.61
KOG4454|consensus	267		97.59
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.59
KOG1548|consensus	382		97.51
KOG4211|consensus	510		97.5
KOG2202|consensus	260		97.47
KOG0120|consensus	500		97.39
KOG1457|consensus	284		97.37
KOG1548|consensus	382		97.33
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	97.29
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.29
KOG0151|consensus	877		97.2
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.18
KOG4211|consensus	510		97.16
KOG1456|consensus	494		97.15
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	97.1
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.1
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.07
KOG0106|consensus	216		97.07
KOG1456|consensus	494		96.85
KOG4210|consensus	285		96.83
KOG4307|consensus	944		96.78
KOG1855|consensus	484		96.67
KOG1996|consensus	378		96.21
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	95.87
KOG4849|consensus	498		95.77
KOG1190|consensus	492		95.7
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	95.51
KOG1365|consensus	508		95.42
KOG4206|consensus	221		95.34
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	95.02
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	95.02
KOG4285|consensus	350		94.78
KOG2068|consensus	327		94.59
KOG2135|consensus	526		94.25
KOG0105|consensus	241		93.93
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	93.93
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	93.9
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	91.7
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	91.51
KOG0112|consensus	975		91.13
KOG1457|consensus	284		90.66
KOG3152|consensus	278		90.23
KOG0128|consensus	881		90.12
KOG4676|consensus	479		89.53
KOG0128|consensus	881		87.83
KOG4574|consensus	1007		87.83
KOG1365|consensus	508		87.68
KOG0129|consensus	520		87.03
KOG4660|consensus	549		87.0
KOG4307|consensus	944		86.19
smart00596	69	PRE_C2HC PRE_C2HC domain.	86.14
KOG2193|consensus	584		86.08
KOG2416|consensus	718		85.53
PF15513	62	DUF4651: Domain of unknown function (DUF4651)	81.19
PF07530	68	PRE_C2HC: Associated with zinc fingers; InterPro:	80.62
KOG0115|consensus	275		80.13

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

Probab=99.77  E-value=1.8e-17  Score=102.85  Aligned_cols=68  Identities=28%  Similarity=0.461  Sum_probs=62.7

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccCCCC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVSVLE   68 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~~~~   68 (105)
                      +|+++|++||.|.++.|+.++ ++++++||||+|.+.++|++||+.||+..|.++.|+|+++..++..+
T Consensus        50 ~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~a~~~~~~~  118 (144)
T PLN03134         50 SLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPANDRPSAP  118 (144)
T ss_pred             HHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEeCCcCCCCC
Confidence            589999999999999999998 99999999999999999999999999999999999999988555443

>KOG4207|consensus

Probab=99.64  E-value=7.3e-16  Score=99.11  Aligned_cols=62  Identities=27%  Similarity=0.489  Sum_probs=60.3

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+.+|++||.|-.|.|++|+ +..+++|+||-|.+..+|+.|+++|++.+|+++.|.|+.+.
T Consensus        29 ~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~ar   91 (256)
T KOG4207|consen   29 DLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMAR   91 (256)
T ss_pred             HHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehhhh
Confidence            589999999999999999999 99999999999999999999999999999999999999998

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.57  E-value=4.9e-14  Score=98.22  Aligned_cols=63  Identities=24%  Similarity=0.532  Sum_probs=57.7

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCC--eeEEEEEeec
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDG--RPMQIQLAAD   63 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~--~~i~V~~~~~   63 (105)
                      +|+++|++||.|+.+.|+.++ ++++++|+||+|.+.++|++||+.||+..+.+  +.|+|.++..
T Consensus       209 ~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~a~~  274 (346)
T TIGR01659       209 QLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRLAEE  274 (346)
T ss_pred             HHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCc
Confidence            589999999999999999998 99999999999999999999999999998865  6888888873

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).

>PF13893 RRM_5: RNA recognition motif

Probab=99.50  E-value=3.1e-13  Score=71.04  Aligned_cols=56  Identities=38%  Similarity=0.663  Sum_probs=50.4

Q ss_pred             HHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEe
Q psy1928           2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA   61 (105)
Q Consensus         2 l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~   61 (105)
                      |.++|++||.|..+.+..++    .+++||+|.+.++|+.|++.||+..+.+++|+|+++
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            67899999999999887653    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 ....

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.50  E-value=1e-13  Score=96.29  Aligned_cols=65  Identities=22%  Similarity=0.411  Sum_probs=61.5

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|.++|++||.|.+++|+.++ ++.++||+||+|.+.++|.+||..||+..|+++.|+|.+...++
T Consensus       285 ~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~~~~  350 (352)
T TIGR01661       285 VLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKTNKA  350 (352)
T ss_pred             HHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEccCCC
Confidence            488999999999999999998 99999999999999999999999999999999999999988554

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

>KOG0122|consensus

Probab=99.48  E-value=1.7e-13  Score=89.95  Aligned_cols=64  Identities=31%  Similarity=0.494  Sum_probs=61.0

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeecc
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADV   64 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~   64 (105)
                      +|+++|.+||.|..+++.+|+ +|.++|||||+|.+.++|++||+.||+.-+++-.|.|+|+++.
T Consensus       205 dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEwskP~  269 (270)
T KOG0122|consen  205 DLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEWSKPS  269 (270)
T ss_pred             HHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEecCCC
Confidence            589999999999999999999 9999999999999999999999999999999999999999854

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.41  E-value=9.2e-13  Score=91.51  Aligned_cols=64  Identities=34%  Similarity=0.535  Sum_probs=60.1

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeecc
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADV   64 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~   64 (105)
                      +|+++|+.||.|.+|.|+.++ ++++++||||+|.+.++|++||+.||+..|.++.|+|+++.+.
T Consensus        19 ~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a~~~   83 (352)
T TIGR01661        19 EIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYARPS   83 (352)
T ss_pred             HHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeeccc
Confidence            589999999999999999998 8999999999999999999999999999999999999988633

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

>smart00361 RRM_1 RNA recognition motif

Probab=99.40  E-value=2.3e-12  Score=70.77  Aligned_cols=58  Identities=28%  Similarity=0.440  Sum_probs=51.9

Q ss_pred             CHHHHhc----cCCCeeEEE-EEeCC-C--CCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEE
Q psy1928           1 MIYELFS----EFGPLKSAK-LHYDR-S--GRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI   58 (105)
Q Consensus         1 ~l~~~f~----~~G~i~~~~-i~~~~-~--~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V   58 (105)
                      +|+++|+    +||.|.++. ++.++ +  +++++++||.|.+.++|++|+..||+..+.++.|++
T Consensus         4 ~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~   69 (70)
T smart00361        4 DFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKA   69 (70)
T ss_pred             hHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence            5788888    999999985 66665 5  889999999999999999999999999999998876

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.40  E-value=1.1e-12  Score=91.57  Aligned_cols=62  Identities=26%  Similarity=0.561  Sum_probs=58.4

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|+.||.|++|+|+.++ ++++++||||+|.+.++|++||+.|++..+.++.|+|.+++
T Consensus       123 ~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~~a~  185 (346)
T TIGR01659       123 ELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYAR  185 (346)
T ss_pred             HHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeeeccc
Confidence            589999999999999999997 99999999999999999999999999999999999998765

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).

>KOG0148|consensus

Probab=99.37  E-value=1.4e-12  Score=86.89  Aligned_cols=65  Identities=29%  Similarity=0.420  Sum_probs=61.6

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|++.|.+||+|.+++|++|. +++++||+||.|.+.++|++||..||+.=|..+.|+-.|++-++
T Consensus        78 ~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATRKp  143 (321)
T KOG0148|consen   78 KLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATRKP  143 (321)
T ss_pred             HHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeeccccccCc
Confidence            488999999999999999998 99999999999999999999999999999999999999998555

>KOG0145|consensus

Probab=99.36  E-value=1.7e-12  Score=86.38  Aligned_cols=65  Identities=34%  Similarity=0.524  Sum_probs=61.3

Q ss_pred             HHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccCC
Q psy1928           2 IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVSV   66 (105)
Q Consensus         2 l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~~   66 (105)
                      ++.+|..+|+|++|++++|+ +|++.||+||.|.++.+|++||..||+..+..+.|+|.++++...
T Consensus        58 ~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSyARPSs~  123 (360)
T KOG0145|consen   58 LRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSYARPSSD  123 (360)
T ss_pred             HHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEeccCChh
Confidence            68899999999999999999 999999999999999999999999999999999999999984443

>KOG0107|consensus

Probab=99.36  E-value=5.8e-12  Score=79.29  Aligned_cols=65  Identities=23%  Similarity=0.356  Sum_probs=57.2

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccCCCCC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVSVLEN   69 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~~~~~   69 (105)
                      +|+.+|.+||.|..|-|..+    +.+||||+|.+..+|+.|+..|++..|.+..|.|++++..+...+
T Consensus        26 eLE~~F~~yG~lrsvWvArn----PPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G~~r~~r   90 (195)
T KOG0107|consen   26 ELERAFSKYGPLRSVWVARN----PPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTGRPRGSR   90 (195)
T ss_pred             HHHHHHHhcCcceeEEEeec----CCCceEEeccCcccHHHHHhhcCCccccCceEEEEeecCCccccc
Confidence            58999999999999877665    479999999999999999999999999999999999995555443

>PF00076 RRM_1: RNA recognition motif

Probab=99.36  E-value=4.6e-12  Score=68.68  Aligned_cols=57  Identities=35%  Similarity=0.602  Sum_probs=52.7

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEE
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQ   57 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~   57 (105)
                      +|+++|+.||.|..+.+..+.++..+++|||+|.+.++|++|++.|++..+.++.|+
T Consensus        14 ~l~~~f~~~g~i~~~~~~~~~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen   14 ELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             HHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             HHHHHHHHhhhcccccccccccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            478999999999999998877888899999999999999999999999999998874

(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 ....

>KOG0105|consensus

Probab=99.34  E-value=9.4e-12  Score=79.22  Aligned_cols=61  Identities=21%  Similarity=0.324  Sum_probs=53.5

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeec
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD   63 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~   63 (105)
                      +|+++|.+||.|..|++...  -.+..||||+|.+..+|+.||..-++..+++..|.|++..-
T Consensus        22 eieDlFyKyg~i~~ieLK~r--~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfprg   82 (241)
T KOG0105|consen   22 EIEDLFYKYGRIREIELKNR--PGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPRG   82 (241)
T ss_pred             cHHHHHhhhcceEEEEeccC--CCCCCeeEEEecCccchhhhhhcccccccCcceEEEEeccC
Confidence            58999999999999887432  23468999999999999999999999999999999999873

>KOG0125|consensus

Probab=99.29  E-value=8.2e-12  Score=85.11  Aligned_cols=63  Identities=21%  Similarity=0.374  Sum_probs=57.7

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeecc
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADV   64 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~   64 (105)
                      ||+.+|.+||.|.+|+|+.+. .-+|||+||+|++.++|++|-+.||+..+.|++|+|..++.+
T Consensus       112 DL~aMF~kfG~VldVEIIfNE-RGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~ATar  174 (376)
T KOG0125|consen  112 DLRAMFEKFGKVLDVEIIFNE-RGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNATAR  174 (376)
T ss_pred             cHHHHHHhhCceeeEEEEecc-CCCCccceEEecChhhHHHHHHHhhcceeeceEEEEeccchh
Confidence            799999999999999999874 335899999999999999999999999999999999998743

>KOG0113|consensus

Probab=99.28  E-value=6.4e-11  Score=79.93  Aligned_cols=62  Identities=31%  Similarity=0.575  Sum_probs=58.9

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      .|+..|++||.|+.|.|+.++ +++++|||||+|.+..+...|.+..++..|+++.|.|.+..
T Consensus       117 kLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDvER  179 (335)
T KOG0113|consen  117 KLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDVER  179 (335)
T ss_pred             HHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEecc
Confidence            378999999999999999998 99999999999999999999999999999999999998876

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

Probab=99.27  E-value=2.1e-11  Score=89.97  Aligned_cols=63  Identities=17%  Similarity=0.242  Sum_probs=59.6

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeec
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD   63 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~   63 (105)
                      +|+++|+.||.|.++.|..++ +++++||+||+|.+.++|.+||+.||+..|+|+.|+|.++..
T Consensus       220 dLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi~  283 (612)
T TIGR01645       220 DIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVT  283 (612)
T ss_pred             HHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecCC
Confidence            488999999999999999998 888999999999999999999999999999999999998873

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.

>smart00360 RRM RNA recognition motif

Probab=99.25  E-value=4.4e-11  Score=64.02  Aligned_cols=59  Identities=42%  Similarity=0.715  Sum_probs=53.5

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEE
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ   59 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~   59 (105)
                      +|+++|+.||.|..+.+..++ ++.++++|||+|.+.++|..|+..+++..+.++.|.|+
T Consensus        12 ~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360       12 ELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             HHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            478999999999999998887 78889999999999999999999999999999888763

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

Probab=99.25  E-value=2.1e-11  Score=89.94  Aligned_cols=62  Identities=34%  Similarity=0.536  Sum_probs=58.3

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|++||.|.+|.|++++ +++++|||||+|.+.++|++||+.||+..+.++.|+|....
T Consensus       123 ~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp~  185 (612)
T TIGR01645       123 TIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS  185 (612)
T ss_pred             HHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeecccc
Confidence            488999999999999999998 99999999999999999999999999999999999998654

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=99.25  E-value=2.1e-11  Score=74.10  Aligned_cols=65  Identities=28%  Similarity=0.419  Sum_probs=60.9

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      ||.+.|..||.|+.+.+..|. ++..+||++|+|....+|++||..+|+..|.+..|.|.|+-.+.
T Consensus        88 di~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~Fv~g  153 (170)
T KOG0130|consen   88 DIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWCFVKG  153 (170)
T ss_pred             HHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEEEecC
Confidence            578899999999999999998 99999999999999999999999999999999999999987444

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

Probab=99.24  E-value=1.3e-10  Score=85.57  Aligned_cols=58  Identities=38%  Similarity=0.560  Sum_probs=52.6

Q ss_pred             CHHHHhccC--CCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEF--GPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~--G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|++|  |.|++|.+++       +|+||+|.+.++|++|++.||+..|.++.|+|.++++.+
T Consensus       249 ~L~~~F~~f~~G~I~rV~~~r-------gfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~Akp~~  308 (578)
T TIGR01648       249 IIEKSFSEFKPGKVERVKKIR-------DYAFVHFEDREDAVKAMDELNGKELEGSEIEVTLAKPVD  308 (578)
T ss_pred             HHHHHHHhcCCCceEEEEeec-------CeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEccCCC
Confidence            488999999  9999998764       599999999999999999999999999999999998543

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.

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

Probab=99.23  E-value=4e-11  Score=88.12  Aligned_cols=62  Identities=32%  Similarity=0.588  Sum_probs=58.9

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|++||.|.+|.|++++ +++++|||||+|.+.++|++||+.||...+.++.|+|.++.
T Consensus        16 ~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~   78 (562)
T TIGR01628        16 KLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQ   78 (562)
T ss_pred             HHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeeccc
Confidence            588999999999999999998 89999999999999999999999999999999999999876

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

>KOG0121|consensus

Probab=99.21  E-value=3.1e-11  Score=72.67  Aligned_cols=62  Identities=35%  Similarity=0.553  Sum_probs=57.6

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|++.|.|..|-|=.|+ +..++|||||+|.+.++|+.|+.-+++..+++++|.|.+..
T Consensus        52 qiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D~  114 (153)
T KOG0121|consen   52 QIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWDA  114 (153)
T ss_pred             HHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeeccc
Confidence            488999999999999888888 78899999999999999999999999999999999998765

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

Probab=99.21  E-value=5.4e-11  Score=87.48  Aligned_cols=63  Identities=33%  Similarity=0.515  Sum_probs=59.5

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeec
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD   63 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~   63 (105)
                      +|+++|+.||.|.++.++.+.++.+++|+||+|.+.++|++|+..||+..+.++.|.|.++..
T Consensus       301 ~L~~~F~~~G~i~~~~i~~d~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a~~  363 (562)
T TIGR01628       301 KLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQR  363 (562)
T ss_pred             HHHHHHHhcCCeEEEEEEECCCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEeccC
Confidence            488999999999999999988899999999999999999999999999999999999998873

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

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

Probab=99.19  E-value=8.7e-11  Score=84.29  Aligned_cols=62  Identities=31%  Similarity=0.592  Sum_probs=58.7

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|++||.|..|.++.++ ++++++||||+|.+.++|++|+..||+..|.++.|+|.++.
T Consensus       202 ~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~  264 (457)
T TIGR01622       202 ELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQ  264 (457)
T ss_pred             HHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEcc
Confidence            478999999999999999988 78999999999999999999999999999999999999976

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.

>KOG4212|consensus

Probab=99.19  E-value=1.1e-10  Score=82.44  Aligned_cols=69  Identities=20%  Similarity=0.356  Sum_probs=62.0

Q ss_pred             CHHHHhc-cCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccCCCCC
Q psy1928           1 MIYELFS-EFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVSVLEN   69 (105)
Q Consensus         1 ~l~~~f~-~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~~~~~   69 (105)
                      ||+++|. +.|+|.+|+++.|.++++++|+.|+|.+++.+++|++.||.+.+.+++|+|+.....+...+
T Consensus        60 dLKdLvrekvGev~yveLl~D~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd~d~q~~~~  129 (608)
T KOG4212|consen   60 DLKDLVREKVGEVEYVELLFDESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKEDHDEQRDQY  129 (608)
T ss_pred             hHHHHHHHhcCceEeeeeecccCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEeccCchhhhhh
Confidence            5888885 78999999999999999999999999999999999999999999999999998875544443

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.17  E-value=1.5e-10  Score=77.46  Aligned_cols=62  Identities=19%  Similarity=0.250  Sum_probs=55.3

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|+.||.|.+|.|+.++  ..++||||+|.+.++++.||. |++..|.++.|.|..+.+.+
T Consensus        20 dLrefFS~~G~I~~V~I~~d~--~~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~~~   81 (260)
T PLN03120         20 DIKEFFSFSGDIEYVEMQSEN--ERSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAEDYQ   81 (260)
T ss_pred             HHHHHHHhcCCeEEEEEeecC--CCCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccCCC
Confidence            589999999999999998875  246899999999999999996 99999999999999987443

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.17  E-value=2.3e-10  Score=62.33  Aligned_cols=57  Identities=32%  Similarity=0.592  Sum_probs=52.0

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEE
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQ   57 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~   57 (105)
                      +|.++|+.+|.|..+.+..++.+.++++|||+|.+.++|++|+..+++..+.++.|+
T Consensus        14 ~l~~~f~~~g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen   14 DLRNFFSRFGPVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             HHHHHCTTSSBEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             HHHHHHHhcCCcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            478999999999999999987788899999999999999999999998999998764

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 ....

>KOG0144|consensus

Probab=99.17  E-value=3.6e-11  Score=84.54  Aligned_cols=65  Identities=26%  Similarity=0.468  Sum_probs=58.1

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCccc-C--CeeEEEEEee-ccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPL-D--GRPMQIQLAA-DVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i-~--~~~i~V~~~~-~~~   65 (105)
                      +++++|++||.|++|+|+++..+.++||+||.|...+.|..||+.||+... .  ..+|.|+++. .++
T Consensus       140 evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVkFADtqkd  208 (510)
T KOG0144|consen  140 EVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVKFADTQKD  208 (510)
T ss_pred             HHHHHHHhhCccchhhheecccccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEEecccCCC
Confidence            478999999999999999999999999999999999999999999999743 3  4689999998 444

>smart00362 RRM_2 RNA recognition motif

Probab=99.15  E-value=2.6e-10  Score=61.21  Aligned_cols=58  Identities=43%  Similarity=0.723  Sum_probs=51.7

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEE
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ   59 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~   59 (105)
                      +|+++|..||.+..+.+..++ +.+.+++||+|.+.++|+.|+..+++..+.++.|.|+
T Consensus        15 ~l~~~~~~~g~v~~~~~~~~~-~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362       15 DLKELFSKFGPIESVKIPKDT-GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             HHHHHHHhcCCEEEEEEecCC-CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            478999999999999888776 6678999999999999999999999999999888763

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

Probab=99.15  E-value=2.2e-10  Score=83.17  Aligned_cols=62  Identities=32%  Similarity=0.327  Sum_probs=58.8

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|+.||.|..+.++.++ ++.++|||||+|.+.++|+.||..||+..|.++.|.|+++.
T Consensus       311 ~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~  373 (509)
T TIGR01642       311 QIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRAC  373 (509)
T ss_pred             HHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECc
Confidence            478999999999999999987 89999999999999999999999999999999999999986

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

>KOG0117|consensus

Probab=99.14  E-value=2.2e-10  Score=80.91  Aligned_cols=62  Identities=23%  Similarity=0.404  Sum_probs=57.2

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccC-CeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLD-GRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~-~~~i~V~~~~   62 (105)
                      +|.-+|.+.|.|-+++++.|+ +|.++|||||.|.+.++|+.||+.||..+|. ++.|.|..+.
T Consensus        99 eLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~Sv  162 (506)
T KOG0117|consen   99 ELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCVSV  162 (506)
T ss_pred             hhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEEee
Confidence            477899999999999999998 9999999999999999999999999999986 8888888665

>KOG0146|consensus

Probab=99.13  E-value=4.1e-11  Score=80.15  Aligned_cols=64  Identities=23%  Similarity=0.393  Sum_probs=59.9

Q ss_pred             HHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           2 IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         2 l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      |.++|-.||.|.+.++..|+ +..++||+||.|++..+++.||.+||++.|..++|+|++.++++
T Consensus       302 liQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQLKRPkd  366 (371)
T KOG0146|consen  302 LIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQLKRPKD  366 (371)
T ss_pred             HHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhhhcCccc
Confidence            67889999999999999999 99999999999999999999999999999999999999887555

>KOG0126|consensus

Probab=99.12  E-value=1.5e-11  Score=77.94  Aligned_cols=63  Identities=30%  Similarity=0.531  Sum_probs=58.0

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeec
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD   63 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~   63 (105)
                      ||..+|+.||.|+.|-+++|+ ||+++||||+.|.++.+..-|+..||+..|.++.|+|.....
T Consensus        51 Dil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv~~  114 (219)
T KOG0126|consen   51 DILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHVSN  114 (219)
T ss_pred             cEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeeccc
Confidence            466789999999999999999 999999999999999998889999999999999999997663

>KOG0149|consensus

Probab=99.10  E-value=1.3e-10  Score=76.21  Aligned_cols=61  Identities=28%  Similarity=0.437  Sum_probs=54.3

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|++.|+.||+|++..|+.|+ +++++||+||+|.+.+.|++|++. ..-.|+|++-.|.++.
T Consensus        28 ~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNcnlA~   89 (247)
T KOG0149|consen   28 TLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKANCNLAS   89 (247)
T ss_pred             HHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC-CCCcccccccccchhh
Confidence            378999999999999999999 999999999999999999999874 4457899988888765

>KOG0144|consensus

Probab=99.10  E-value=1.8e-10  Score=81.11  Aligned_cols=66  Identities=26%  Similarity=0.411  Sum_probs=57.7

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCc-ccC--CeeEEEEEee-ccCC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGV-PLD--GRPMQIQLAA-DVSV   66 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~-~i~--~~~i~V~~~~-~~~~   66 (105)
                      ||+++|++||.|.+|-|++|+ ++.+++||||.|.+.++|.+|+.+||.. +|.  ..+|.|+++. +++.
T Consensus        50 dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqvk~Ad~E~er  120 (510)
T KOG0144|consen   50 DLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQVKYADGERER  120 (510)
T ss_pred             HHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceeecccchhhhc
Confidence            589999999999999999999 9999999999999999999999999774 454  4688898887 4443

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

Probab=99.07  E-value=6e-10  Score=80.01  Aligned_cols=61  Identities=34%  Similarity=0.500  Sum_probs=57.1

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|++||.|..|.|+.++ ++++++||||+|.+.++|++||. |++..+.++.|.|..+.
T Consensus       105 ~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~~~~  166 (457)
T TIGR01622       105 DLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQSSQ  166 (457)
T ss_pred             HHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEeecc
Confidence            488999999999999999998 89999999999999999999997 89999999999998765

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.

>KOG0148|consensus

Probab=99.04  E-value=5.8e-10  Score=74.60  Aligned_cols=57  Identities=25%  Similarity=0.462  Sum_probs=53.9

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|++.|+.||.|.+|++..+     ++|+||.|.+++.|..||..+|+.+|.++.++|.|-+
T Consensus       180 ~mr~~Fs~fG~I~EVRvFk~-----qGYaFVrF~tkEaAahAIv~mNntei~G~~VkCsWGK  236 (321)
T KOG0148|consen  180 LMRQTFSPFGPIQEVRVFKD-----QGYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCSWGK  236 (321)
T ss_pred             HHHHhcccCCcceEEEEecc-----cceEEEEecchhhHHHHHHHhcCceeCceEEEEeccc
Confidence            37899999999999999987     6999999999999999999999999999999999987

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

Probab=99.03  E-value=9.6e-10  Score=79.83  Aligned_cols=62  Identities=26%  Similarity=0.326  Sum_probs=55.5

Q ss_pred             CHHHHhccCCCeeEEEEEeCC----CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR----SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~----~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|++||.|..|.|+++.    ++...|++||+|.+.++|++||..||+..+.++.|.|.+..
T Consensus       435 dl~~~f~~~G~v~~v~i~~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnGr~~~gr~v~~~~~~  500 (509)
T TIGR01642       435 DVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGRKFNDRVVVAAFYG  500 (509)
T ss_pred             HHHHHHHhcCCeeEEEeeccCcCCCcCCCcceEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEeC
Confidence            367889999999999998763    34567999999999999999999999999999999999876

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

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.03  E-value=1.3e-09  Score=72.07  Aligned_cols=60  Identities=15%  Similarity=0.217  Sum_probs=53.1

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeec
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD   63 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~   63 (105)
                      +|+++|+.||.|.+|+|+.+.  ...+++||+|.+.+.++.|+. |++..|.++.|.|.....
T Consensus        21 dLrefFS~~G~I~~V~I~~D~--et~gfAfVtF~d~~aaetAll-LnGa~l~d~~I~It~~~~   80 (243)
T PLN03121         21 DVYDFFSHCGAIEHVEIIRSG--EYACTAYVTFKDAYALETAVL-LSGATIVDQRVCITRWGQ   80 (243)
T ss_pred             HHHHHHHhcCCeEEEEEecCC--CcceEEEEEECCHHHHHHHHh-cCCCeeCCceEEEEeCcc
Confidence            589999999999999999874  334799999999999999996 999999999999887663

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

Probab=99.03  E-value=5.9e-10  Score=82.13  Aligned_cols=61  Identities=26%  Similarity=0.422  Sum_probs=54.0

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccC-CeeEEEEEe
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLD-GRPMQIQLA   61 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~-~~~i~V~~~   61 (105)
                      +|.++|++||.|.+++|++|.++++++||||+|.+.++|++||+.||+..+. ++.|.|..+
T Consensus        74 ~L~~~F~~~G~I~~vrl~~D~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~S  135 (578)
T TIGR01648        74 ELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCIS  135 (578)
T ss_pred             HHHHHHHhhCCEEEEEEEECCCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCcccccccc
Confidence            4889999999999999999989999999999999999999999999998885 666655543

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.

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

Probab=99.02  E-value=1.3e-09  Score=79.19  Aligned_cols=58  Identities=24%  Similarity=0.405  Sum_probs=54.1

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|+.||.|..|+++.++    +++|||+|.+.++|+.||..||+..|.++.|+|.+++
T Consensus       292 ~L~~lF~~yG~V~~vki~~~~----~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~  349 (481)
T TIGR01649       292 RLFNLFCVYGNVERVKFMKNK----KETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSK  349 (481)
T ss_pred             HHHHHHHhcCCeEEEEEEeCC----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEcc
Confidence            488999999999999998863    6899999999999999999999999999999999986

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).

>KOG0127|consensus

Probab=99.02  E-value=8.8e-10  Score=79.64  Aligned_cols=65  Identities=29%  Similarity=0.531  Sum_probs=60.3

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      ||..+|+.||.+.+|.|++.+.++.+||+||.|....+|..|++.+|+..|.+++|.|.|+.++.
T Consensus       133 dLk~vFs~~G~V~Ei~IP~k~dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd  197 (678)
T KOG0127|consen  133 DLKNVFSNFGKVVEIVIPRKKDGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDKD  197 (678)
T ss_pred             HHHHHHhhcceEEEEEcccCCCCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeecccc
Confidence            58899999999999999977788888999999999999999999999999999999999997444

>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=99.01  E-value=3.7e-09  Score=56.86  Aligned_cols=60  Identities=37%  Similarity=0.623  Sum_probs=53.5

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEE
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL   60 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~   60 (105)
                      +|+++|..+|.|..+.+..++...+.+++||+|.+.++|+.|+..+++..+.++.+.|.+
T Consensus        15 ~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590          15 DLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             HHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            478899999999999999877557789999999999999999999999999999888763

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).

>KOG0108|consensus

Probab=99.00  E-value=6.9e-10  Score=79.27  Aligned_cols=69  Identities=28%  Similarity=0.521  Sum_probs=63.1

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccCCCCC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVSVLEN   69 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~~~~~   69 (105)
                      +|..+|+..|.|.+++++.|+ +|+++||+|++|.+.++++.|++.||+.++.++.|+|.++.......+
T Consensus        34 ~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~~~~~~~  103 (435)
T KOG0108|consen   34 QLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASNRKNAER  103 (435)
T ss_pred             HHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeecccccchhHH
Confidence            378899999999999999999 999999999999999999999999999999999999999885554443

>KOG0145|consensus

Probab=99.00  E-value=3.4e-09  Score=70.85  Aligned_cols=63  Identities=22%  Similarity=0.405  Sum_probs=58.8

Q ss_pred             HHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeecc
Q psy1928           2 IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADV   64 (105)
Q Consensus         2 l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~   64 (105)
                      |+++|..||.|..+++++|. +.+=+||+||++.+.++|.-||..||+..+.++.|.|.+.+.+
T Consensus       295 LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsFKtnk  358 (360)
T KOG0145|consen  295 LWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTNK  358 (360)
T ss_pred             HHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccceEEEEEEecCC
Confidence            78999999999999999998 7888899999999999999999999999999999999987644

>KOG0146|consensus

Probab=98.99  E-value=5.7e-10  Score=74.75  Aligned_cols=68  Identities=19%  Similarity=0.298  Sum_probs=59.2

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccC---CeeEEEEEee-ccCCCC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLD---GRPMQIQLAA-DVSVLE   68 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~---~~~i~V~~~~-~~~~~~   68 (105)
                      |++.+|..||.|.+|.+.+.+++.++||+||.|.+..+|+.||..||+....   ...|.|+++. +++...
T Consensus        35 dvrrlf~pfG~~~e~tvlrg~dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK~ADTdkER~l  106 (371)
T KOG0146|consen   35 DVRRLFQPFGNIEECTVLRGPDGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVKFADTDKERTL  106 (371)
T ss_pred             HHHHHhcccCCcceeEEecCCCCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEEeccchHHHHH
Confidence            4788999999999999999889999999999999999999999999997554   5679999987 555443

>KOG0111|consensus

Probab=98.98  E-value=5.4e-10  Score=73.00  Aligned_cols=67  Identities=27%  Similarity=0.392  Sum_probs=60.4

Q ss_pred             HHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccCCCC
Q psy1928           2 IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVSVLE   68 (105)
Q Consensus         2 l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~~~~   68 (105)
                      |...|=.||.|..|.++.|. +.+.++|+||+|...++|..||..||..+|-++.|+|.++++...+.
T Consensus        27 LhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~AkP~kike   94 (298)
T KOG0111|consen   27 LHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAKPEKIKE   94 (298)
T ss_pred             HHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeecCCccccC
Confidence            45667899999999999998 99999999999999999999999999999999999999998555443

>KOG0124|consensus

Probab=98.97  E-value=8e-10  Score=76.82  Aligned_cols=65  Identities=32%  Similarity=0.533  Sum_probs=59.5

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      .|+..|..||.|++|.+.||+ +++.++|+||+|.-++.|+-|++.||+..++++.|+|..-.+.+
T Consensus       129 tiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPsNmp  194 (544)
T KOG0124|consen  129 TIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSNMP  194 (544)
T ss_pred             HHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCCCCc
Confidence            378899999999999999999 99999999999999999999999999999999999998655444

>PLN03213 repressor of silencing 3; Provisional

Probab=98.96  E-value=1.8e-09  Score=77.56  Aligned_cols=59  Identities=19%  Similarity=0.352  Sum_probs=53.4

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCH--HHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERR--SDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~--~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      ||..+|+.||.|..+.|++. ++  ++|+||+|...  .++.+||..||+..+.|+.|+|..++
T Consensus        26 DLravFSeFGsVkdVEIpRE-TG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKAK   86 (759)
T PLN03213         26 DLLKIFSPMGTVDAVEFVRT-KG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKAK   86 (759)
T ss_pred             HHHHHHHhcCCeeEEEEecc-cC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeecc
Confidence            58999999999999999943 55  89999999976  68999999999999999999999776

>KOG0415|consensus

Probab=98.96  E-value=1.1e-09  Score=75.72  Aligned_cols=62  Identities=26%  Similarity=0.424  Sum_probs=59.5

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      ||+-+|+.||.|.+|.|+++. ++.+..||||+|.+.+++++|.=.|+...|+++.|.|.++.
T Consensus       255 DLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDFSQ  317 (479)
T KOG0415|consen  255 DLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDFSQ  317 (479)
T ss_pred             chhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeehhh
Confidence            688899999999999999998 99999999999999999999999999999999999999886

>KOG0116|consensus

Probab=98.94  E-value=8.6e-09  Score=73.40  Aligned_cols=62  Identities=18%  Similarity=0.393  Sum_probs=53.0

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeec
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD   63 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~   63 (105)
                      +|+++|+.||.|+...|.... .++..+|+||+|.+.++++.+|.+ +...|+++++.|+..+.
T Consensus       304 ~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek~~  366 (419)
T KOG0116|consen  304 ELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEKRP  366 (419)
T ss_pred             HHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEeccc
Confidence            478999999999998876654 556569999999999999999997 67888999999998763

>KOG4661|consensus

Probab=98.93  E-value=2.4e-09  Score=78.03  Aligned_cols=65  Identities=20%  Similarity=0.291  Sum_probs=59.4

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      ||..+|++||.|+-.+|+.+. +.-.+||+||++.+.++|.+||+.|+..+|+++.|-|+.+++.+
T Consensus       421 DLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaKNEp  486 (940)
T KOG4661|consen  421 DLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAKNEP  486 (940)
T ss_pred             HHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeecccCc
Confidence            689999999999999998886 77778999999999999999999999999999999999887444

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

Probab=98.92  E-value=4.6e-09  Score=69.19  Aligned_cols=62  Identities=42%  Similarity=0.693  Sum_probs=58.7

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|..||.|..+.+..++ ++.++++|||+|.+.+++..|+..+++..+.++.|.|.+..
T Consensus       131 ~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~  193 (306)
T COG0724         131 DLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQ  193 (306)
T ss_pred             HHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeeccc
Confidence            488999999999999999997 99999999999999999999999999999999999999864

>KOG0117|consensus

Probab=98.88  E-value=5.1e-09  Score=74.11  Aligned_cols=57  Identities=42%  Similarity=0.659  Sum_probs=52.6

Q ss_pred             HHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         2 l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      |+++|+.||.|..|+.++|       |+||.|.+.++|.+|++.+|+++|++..|.|.++++.+
T Consensus       276 lk~~F~~~G~veRVkk~rD-------YaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAKP~~  332 (506)
T KOG0117|consen  276 LKKLFNEFGKVERVKKPRD-------YAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAKPVD  332 (506)
T ss_pred             HHHHHHhccceEEeecccc-------eeEEeecchHHHHHHHHHhcCceecCceEEEEecCChh
Confidence            7899999999999987765       99999999999999999999999999999999998433

>KOG0131|consensus

Probab=98.86  E-value=4.2e-09  Score=66.89  Aligned_cols=61  Identities=33%  Similarity=0.494  Sum_probs=57.6

Q ss_pred             HHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           2 IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         2 l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      |+++|-..|.|..+++++++ +...+||||++|.+.++|+=|++.||...+.+++|+|..+.
T Consensus        26 l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~kas   87 (203)
T KOG0131|consen   26 LYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKAS   87 (203)
T ss_pred             HHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEecc
Confidence            67888899999999999999 88899999999999999999999999999999999999887

>KOG0123|consensus

Probab=98.83  E-value=1.4e-08  Score=71.61  Aligned_cols=60  Identities=35%  Similarity=0.581  Sum_probs=55.6

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|+.||+|.+|++..+.++ +++| ||+|.+.++|++||..||+..+.++.|.|....
T Consensus        92 ~~~d~f~~~g~ilS~kv~~~~~g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~  151 (369)
T KOG0123|consen   92 SLYDTFSEFGNILSCKVATDENG-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFE  151 (369)
T ss_pred             HHHHHHHhhcCeeEEEEEEcCCC-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeecc
Confidence            47899999999999999998877 8999 999999999999999999999999999987765

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

Probab=98.83  E-value=1.8e-08  Score=73.26  Aligned_cols=59  Identities=19%  Similarity=0.308  Sum_probs=51.2

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCC--eeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDG--RPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~--~~i~V~~~~   62 (105)
                      +|+++|++||.|.+|.++.++.   .++|||+|.+.++|++|++.||+..|.+  ..|+|++++
T Consensus       112 ~L~~~F~~~G~V~~v~i~~~~~---~~~afVef~~~~~A~~A~~~Lng~~i~~~~~~l~v~~sk  172 (481)
T TIGR01649       112 VLYQIFNPYGKVLRIVTFTKNN---VFQALVEFESVNSAQHAKAALNGADIYNGCCTLKIEYAK  172 (481)
T ss_pred             HHHHHHhccCCEEEEEEEecCC---ceEEEEEECCHHHHHHHHHHhcCCcccCCceEEEEEEec
Confidence            4889999999999999877542   3689999999999999999999999964  478888876

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).

>KOG0123|consensus

Probab=98.82  E-value=1.5e-08  Score=71.50  Aligned_cols=61  Identities=31%  Similarity=0.502  Sum_probs=57.5

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeec
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD   63 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~   63 (105)
                      +|.+.|+.+|.+.++++++|. + +.+|+||.|.+..+|++||..||...+.+++|+|.|+..
T Consensus        14 ~l~~~f~~~~~v~s~rvc~d~-t-slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~r   74 (369)
T KOG0123|consen   14 MLFDKFSPAGPVLSIRVCRDA-T-SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQR   74 (369)
T ss_pred             HHHHHhcccCCceeEEEeecC-C-ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhcc
Confidence            488999999999999999998 6 999999999999999999999999999999999998873

>KOG0109|consensus

Probab=98.79  E-value=1.1e-08  Score=69.26  Aligned_cols=56  Identities=16%  Similarity=0.340  Sum_probs=52.7

Q ss_pred             HHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeecc
Q psy1928           2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADV   64 (105)
Q Consensus         2 l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~   64 (105)
                      |+.+|++||+|.+|+|+.+       |+||...+...++.||..||+.+|++..|+|+.++++
T Consensus        19 lr~lFe~ygkVlECDIvKN-------YgFVHiEdktaaedairNLhgYtLhg~nInVeaSksK   74 (346)
T KOG0109|consen   19 LRSLFEQYGKVLECDIVKN-------YGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSK   74 (346)
T ss_pred             HHHHHHhhCceEeeeeecc-------cceEEeecccccHHHHhhcccceecceEEEEEecccc
Confidence            7889999999999999865       9999999999999999999999999999999998866

>KOG4208|consensus

Probab=98.74  E-value=3.3e-08  Score=63.89  Aligned_cols=62  Identities=23%  Similarity=0.313  Sum_probs=53.6

Q ss_pred             HHHHhccC-CCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeec
Q psy1928           2 IYELFSEF-GPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD   63 (105)
Q Consensus         2 l~~~f~~~-G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~   63 (105)
                      |...|..+ |.+..+++-+++ ||.+++||||+|.+.+.|+-|.+.||+..+.++.|.|.+..+
T Consensus        66 ~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~vmpp  129 (214)
T KOG4208|consen   66 ILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHVMPP  129 (214)
T ss_pred             HhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEEeCc
Confidence            45566666 677788888888 999999999999999999999999999999999998887663

>KOG0147|consensus

Probab=98.71  E-value=3.5e-08  Score=71.28  Aligned_cols=62  Identities=32%  Similarity=0.597  Sum_probs=58.1

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+.+|..||.|..|.++.+. +|..++|+|++|.+.+.|.+|++.||+.+|-|+.|+|....
T Consensus       294 ~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~  356 (549)
T KOG0147|consen  294 MLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVT  356 (549)
T ss_pred             HHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEee
Confidence            478899999999999999998 99999999999999999999999999999999999988765

>KOG0131|consensus

Probab=98.69  E-value=4.7e-08  Score=62.20  Aligned_cols=64  Identities=30%  Similarity=0.421  Sum_probs=57.6

Q ss_pred             HHHHhccCCCeeE-EEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           2 IYELFSEFGPLKS-AKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         2 l~~~f~~~G~i~~-~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      |.+.|++||.|.. .++++++ ++.+++|+|+.|.+.+.+.+||+.+|+..+..++|.|.++..+.
T Consensus       113 L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~ya~k~~  178 (203)
T KOG0131|consen  113 LYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPITVSYAFKKD  178 (203)
T ss_pred             HHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCceEEEEEEecC
Confidence            6889999998854 5788888 89999999999999999999999999999999999999987444

>KOG4206|consensus

Probab=98.60  E-value=1.2e-07  Score=62.03  Aligned_cols=59  Identities=31%  Similarity=0.572  Sum_probs=53.6

Q ss_pred             HHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         2 l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      |+.+|+.||.|..|....  +.+.+|-|||.|.+.+.|-.|+..|++..+.|+.++|+++.
T Consensus        30 L~~LFsqfG~ildI~a~k--t~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriqyA~   88 (221)
T KOG4206|consen   30 LYLLFSQFGKILDISAFK--TPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQYAK   88 (221)
T ss_pred             HHHHHHhhCCeEEEEecC--CCCccCceEEEecChhHHHHHHHHhcCCcccCchhheeccc
Confidence            677999999999886653  66778999999999999999999999999999999999987

>KOG0114|consensus

Probab=98.60  E-value=2.6e-07  Score=53.99  Aligned_cols=59  Identities=27%  Similarity=0.515  Sum_probs=51.5

Q ss_pred             HHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         2 l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      ..++|.+||.|..|+|=..+  ..+|-|||.|.+..+|.+|+.+|++..+.++.+.|-+-.
T Consensus        35 mydlFGkyg~IrQIRiG~~k--~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq   93 (124)
T KOG0114|consen   35 MYDLFGKYGTIRQIRIGNTK--ETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQ   93 (124)
T ss_pred             HHHHhhcccceEEEEecCcc--CcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecC
Confidence            57899999999999885543  346899999999999999999999999999999888765

>KOG0124|consensus

Probab=98.59  E-value=7.9e-08  Score=67.10  Aligned_cols=62  Identities=18%  Similarity=0.246  Sum_probs=57.8

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      ||+.+|..||.|.+|.+.+++ ....+||+|++|.+......||..||-+.+++..|+|-.+.
T Consensus       226 DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~v  288 (544)
T KOG0124|consen  226 DIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCV  288 (544)
T ss_pred             HHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEeccccc
Confidence            688999999999999999998 66789999999999999999999999999999999998875

>KOG0127|consensus

Probab=98.55  E-value=1.2e-07  Score=68.88  Aligned_cols=65  Identities=22%  Similarity=0.360  Sum_probs=59.7

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|.++|+.+|.|..+.++.++ +...+||+||+|...+++++|++..+...+.++.|.|..+..++
T Consensus        21 qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A~~R~   86 (678)
T KOG0127|consen   21 QLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDPAKKRA   86 (678)
T ss_pred             HHHHhhhcccCcceeEEecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceecccccccccc
Confidence            578999999999999999998 88899999999999999999999999999999999999887433

>KOG0109|consensus

Probab=98.55  E-value=1.2e-07  Score=64.23  Aligned_cols=56  Identities=23%  Similarity=0.510  Sum_probs=52.2

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeec
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD   63 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~   63 (105)
                      .|+..|.+||.+.+|+|+++       |+||.|+-.++|..||..|++.++.+++++|+.++.
T Consensus        94 ElRa~fe~ygpviecdivkd-------y~fvh~d~~eda~~air~l~~~~~~gk~m~vq~sts  149 (346)
T KOG0109|consen   94 ELRAKFEKYGPVIECDIVKD-------YAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLSTS  149 (346)
T ss_pred             HHhhhhcccCCceeeeeecc-------eeEEEEeeccchHHHHhcccccccccceeeeeeecc
Confidence            36789999999999999875       999999999999999999999999999999999883

>KOG0533|consensus

Probab=98.50  E-value=4.9e-07  Score=60.36  Aligned_cols=62  Identities=60%  Similarity=1.033  Sum_probs=58.0

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      ||+++|..|+.+..+.+.+++.+.+.+.|-|.|...++|..|++.+++..++++.+++....
T Consensus        99 Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~  160 (243)
T KOG0533|consen   99 DLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIIS  160 (243)
T ss_pred             HHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEec
Confidence            68999999998999999999999999999999999999999999999999999999888765

>KOG0110|consensus

Probab=98.50  E-value=5.6e-07  Score=66.93  Aligned_cols=64  Identities=22%  Similarity=0.394  Sum_probs=55.1

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCC----CcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeecc
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSG----RSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADV   64 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~----~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~   64 (105)
                      +|...|.+.|.|..+.|...++.    .+.||+||+|.+.++|++|++.|+++.|+++.|.|+++...
T Consensus       531 ~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~~k  598 (725)
T KOG0110|consen  531 DLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISENK  598 (725)
T ss_pred             HHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEeccCc
Confidence            46788999999999888765532    24599999999999999999999999999999999998833

>KOG0110|consensus

Probab=98.49  E-value=8.8e-08  Score=71.05  Aligned_cols=63  Identities=25%  Similarity=0.359  Sum_probs=57.0

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeec
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD   63 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~   63 (105)
                      +++++|..||++..|+|+... .+..+|||||+|.++.+|.+|+.+|....+.++.|+++|+.+
T Consensus       629 EVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEwA~~  692 (725)
T KOG0110|consen  629 EVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEWAKS  692 (725)
T ss_pred             HHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhcccceechhhheehhcc
Confidence            378999999999999998764 566789999999999999999999999999999999999873

>KOG0153|consensus

Probab=98.43  E-value=5.4e-07  Score=62.32  Aligned_cols=58  Identities=22%  Similarity=0.355  Sum_probs=50.2

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHh-CCcccCCeeEEEEEeec
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQY-NGVPLDGRPMQIQLAAD   63 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l-~~~~i~~~~i~V~~~~~   63 (105)
                      +|+++|.+||+|+++.+...     ++||||+|.+...|+.|.+.+ +...|++.+|+|.|...
T Consensus       244 dIrdhFyqyGeirsi~~~~~-----~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg~~  302 (377)
T KOG0153|consen  244 DIRDHFYQYGEIRSIRILPR-----KGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWGRP  302 (377)
T ss_pred             HHHHHHhhcCCeeeEEeecc-----cccceeeehhhHHHHHHHHhhcceeeecceEEEEEeCCC
Confidence            58999999999999987764     579999999999999988755 65678999999999885

>KOG4209|consensus

Probab=98.37  E-value=2.6e-06  Score=56.72  Aligned_cols=60  Identities=20%  Similarity=0.309  Sum_probs=56.0

Q ss_pred             HHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           2 IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         2 l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      ++..|+.+|.|..+.|+.++ .+++++++||+|.+.+.++.++. |++..|.++.++|.+..
T Consensus       118 ~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt~~r  178 (231)
T KOG4209|consen  118 IELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVTLKR  178 (231)
T ss_pred             hhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceeeeee
Confidence            56788999999999999998 88899999999999999999999 99999999999999887

>KOG0132|consensus

Probab=98.35  E-value=1e-06  Score=66.29  Aligned_cols=57  Identities=32%  Similarity=0.422  Sum_probs=53.0

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      ||..+|+.||+|.+|.++-.     ++||||.+.+..+|++|+..|....+.++.|+|.|+.
T Consensus       437 dL~~~feefGeiqSi~li~~-----R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~  493 (894)
T KOG0132|consen  437 DLANLFEEFGEIQSIILIPP-----RGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAV  493 (894)
T ss_pred             HHHHHHHhcccceeEeeccC-----CceeEEEEeehhHHHHHHHHHhcccccceeeEEeeec
Confidence            58899999999999988764     7999999999999999999999999999999999987

>KOG0226|consensus

Probab=98.26  E-value=4.1e-07  Score=60.68  Aligned_cols=64  Identities=23%  Similarity=0.445  Sum_probs=54.4

Q ss_pred             HHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           2 IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         2 l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      |-..|.+|-.-....+++++ ++++++|.||.|.+..++..|+..|++..++.+.|++..+.+++
T Consensus       207 l~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRkS~wke  271 (290)
T KOG0226|consen  207 LARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRKSEWKE  271 (290)
T ss_pred             HHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhhhhHHh
Confidence            34567776655556788998 99999999999999999999999999999999999988776444

>KOG1190|consensus

Probab=98.21  E-value=9.2e-06  Score=57.54  Aligned_cols=57  Identities=23%  Similarity=0.471  Sum_probs=52.9

Q ss_pred             HHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         2 l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      |..+|..||+|..|+|+.++    +.-|+|.|.+...|+-|+++|++..+.++.|+|.+++
T Consensus       315 LftlFgvYGdVqRVkil~nk----kd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SK  371 (492)
T KOG1190|consen  315 LFTLFGVYGDVQRVKILYNK----KDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSK  371 (492)
T ss_pred             HHHHHhhhcceEEEEeeecC----CcceeeeecchhHHHHHHHHhhcceecCceEEEeecc
Confidence            67889999999999999875    3679999999999999999999999999999999998

>KOG2314|consensus

Probab=98.15  E-value=3.5e-06  Score=61.67  Aligned_cols=61  Identities=28%  Similarity=0.371  Sum_probs=54.2

Q ss_pred             HHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccC-CeeEEEEEee
Q psy1928           2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLD-GRPMQIQLAA   62 (105)
Q Consensus         2 l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~-~~~i~V~~~~   62 (105)
                      |.++|+++|.|..+.++-+..+..+||.|++|.+..+|+.|++.|||+.|+ .+.+.|...+
T Consensus        81 l~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHtf~v~~f~  142 (698)
T KOG2314|consen   81 LTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHTFFVRLFK  142 (698)
T ss_pred             HHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceecccceEEeehhh
Confidence            578999999999999988875668999999999999999999999999987 6788887665

>KOG0106|consensus

Probab=98.09  E-value=2e-06  Score=56.51  Aligned_cols=55  Identities=22%  Similarity=0.367  Sum_probs=48.6

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      ||+.+|..||+|..+.+..       +|+||+|.+..+|..||..||+..+.+..+.|+++.
T Consensus        17 d~E~~f~~yg~~~d~~mk~-------gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r   71 (216)
T KOG0106|consen   17 DVERFFKGYGKIPDADMKN-------GFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHAR   71 (216)
T ss_pred             HHHHHHhhccccccceeec-------ccceeccCchhhhhcccchhcCceecceeeeeeccc
Confidence            5889999999999987753       689999999999999999999999998777777666

>KOG0147|consensus

Probab=98.04  E-value=7.3e-06  Score=59.61  Aligned_cols=61  Identities=30%  Similarity=0.386  Sum_probs=56.5

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      ||+++|+.+|.|..|.++.|. +..+++.+||+|.+.+...-||. |.|..+.+.+|.|+...
T Consensus       195 dL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aia-LsGqrllg~pv~vq~sE  256 (549)
T KOG0147|consen  195 DLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIA-LSGQRLLGVPVIVQLSE  256 (549)
T ss_pred             hHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhh-hcCCcccCceeEecccH
Confidence            689999999999999999998 99999999999999999998885 89999999999998765

>KOG4205|consensus

Probab=98.02  E-value=5.9e-06  Score=57.16  Aligned_cols=68  Identities=22%  Similarity=0.319  Sum_probs=56.5

Q ss_pred             HHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccCCCCCC
Q psy1928           2 IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVSVLENT   70 (105)
Q Consensus         2 l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~~~~~~   70 (105)
                      |++.|..||+|..|.+++++ ++.+++|+||+|.+.+.+.+++.. ..+.|+++.|.++.+.++..+...
T Consensus        23 Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~-~~h~~dgr~ve~k~av~r~~~~~~   91 (311)
T KOG4205|consen   23 LREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNA-RTHKLDGRSVEPKRAVSREDQTKV   91 (311)
T ss_pred             HHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecc-cccccCCccccceeccCccccccc
Confidence            78889999999999999999 999999999999988888877763 566788998888887755544433

>KOG4205|consensus

Probab=97.95  E-value=2e-05  Score=54.54  Aligned_cols=67  Identities=16%  Similarity=0.334  Sum_probs=57.8

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccCCCC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVSVLE   68 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~~~~   68 (105)
                      ++++.|.+||.|..+.++.|. +..+++|+||+|.+.+.+++++. ..-+.|.++.+.|..+.+++...
T Consensus       113 ~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~-~~f~~~~gk~vevkrA~pk~~~~  180 (311)
T KOG4205|consen  113 DFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL-QKFHDFNGKKVEVKRAIPKEVMQ  180 (311)
T ss_pred             HHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecc-cceeeecCceeeEeeccchhhcc
Confidence            467889999999999999998 88899999999999999998876 47778999999999998666554

>KOG0120|consensus

Probab=97.91  E-value=4e-05  Score=55.90  Aligned_cols=62  Identities=15%  Similarity=0.254  Sum_probs=53.2

Q ss_pred             CHHHHhccCCCeeEEEEEeC-CCCC---cccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYD-RSGR---SLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~-~~~~---~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      |++....+||.|..|.++++ ....   ..|..||+|.+.+++++|.++|+|..+.++.++..|-.
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            35667789999999999888 3322   45899999999999999999999999999999988865

>KOG1995|consensus

Probab=97.89  E-value=4.2e-05  Score=53.26  Aligned_cols=64  Identities=25%  Similarity=0.399  Sum_probs=54.1

Q ss_pred             CHHHHhccCCCee--------EEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeecc
Q psy1928           1 MIYELFSEFGPLK--------SAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADV   64 (105)
Q Consensus         1 ~l~~~f~~~G~i~--------~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~   64 (105)
                      +|.++|.+++.|.        .|.|.+++ ++.+++.|.|+|.+...|+.||..++++.+.+..|+|..+...
T Consensus        82 ~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~gn~ikvs~a~~r  154 (351)
T KOG1995|consen   82 DNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFCGNTIKVSLAERR  154 (351)
T ss_pred             HHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccccCCCchhhhhhhc
Confidence            4678888888774        25566677 9999999999999999999999999999999999998887633

>KOG4660|consensus

Probab=97.79  E-value=7.9e-06  Score=59.51  Aligned_cols=53  Identities=17%  Similarity=0.345  Sum_probs=45.9

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEE
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQ   57 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~   57 (105)
                      +|+.+|+.||+|+.|..-.    ...+.+||+|.|..+|++|+++|+..++.++.|+
T Consensus        91 ~L~~~f~~yGeir~ir~t~----~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   91 TLLRIFGAYGEIREIRETP----NKRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             HHHHHHHhhcchhhhhccc----ccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            4789999999999865433    3468999999999999999999999999988877

>KOG4212|consensus

Probab=97.61  E-value=0.00011  Score=52.85  Aligned_cols=56  Identities=29%  Similarity=0.421  Sum_probs=48.5

Q ss_pred             HHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEe
Q psy1928           2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA   61 (105)
Q Consensus         2 l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~   61 (105)
                      |++-|..||.+.+.+|+.  .+++++  .|.|.++++|+.|+..|++..++++.|+|.++
T Consensus       553 lrDKfre~G~v~yadime--~GkskG--VVrF~s~edAEra~a~Mngs~l~Gr~I~V~y~  608 (608)
T KOG4212|consen  553 LRDKFREIGHVLYADIME--NGKSKG--VVRFFSPEDAERACALMNGSRLDGRNIKVTYF  608 (608)
T ss_pred             HHHHHHhccceehhhhhc--cCCccc--eEEecCHHHHHHHHHHhccCcccCceeeeeeC
Confidence            678899999999888843  455555  89999999999999999999999999999873

>KOG4454|consensus

Probab=97.59  E-value=8.5e-05  Score=48.94  Aligned_cols=60  Identities=20%  Similarity=0.217  Sum_probs=52.3

Q ss_pred             HHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         2 l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      |.++|-.-|.|..+.|+.+++++.+ |+||.|.+...+.-|++-+|+..+.+..+.|++..
T Consensus        26 L~ElfiqaGPV~kv~ip~~~d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r~   85 (267)
T KOG4454|consen   26 LSELFIQAGPVYKVGIPSGQDQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLRC   85 (267)
T ss_pred             HHHHhhccCceEEEeCCCCccCCCc-eeeeecccccchhhhhhhcccchhccchhhccccc
Confidence            6778888899999988877777777 99999999999999999999999998888777654

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.59  E-value=0.00022  Score=49.76  Aligned_cols=60  Identities=22%  Similarity=0.410  Sum_probs=47.4

Q ss_pred             HHHhccCCCeeEEEEEeCC-CCC--cc-cEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           3 YELFSEFGPLKSAKLHYDR-SGR--SL-GTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         3 ~~~f~~~G~i~~~~i~~~~-~~~--~~-g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      .++|..||.|..|.|.+.. +-.  .. --++|+|...++|.+||..+++..++|+.|+..+.+
T Consensus       138 ~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr~lkatYGT  201 (480)
T COG5175         138 HEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGRVLKATYGT  201 (480)
T ss_pred             hhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCceEeeecCc
Confidence            4689999999998775532 111  11 234999999999999999999999999999988654

>KOG1548|consensus

Probab=97.51  E-value=0.00031  Score=48.96  Aligned_cols=61  Identities=26%  Similarity=0.351  Sum_probs=54.8

Q ss_pred             HHHHhccCCCee--------EEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           2 IYELFSEFGPLK--------SAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         2 l~~~f~~~G~i~--------~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +.++|+++|-|.        .|++.+++.|+.+|=+++.|...++++-|+..|+...+.++.|.|+.+.
T Consensus       151 ~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~~~rVerAk  219 (382)
T KOG1548|consen  151 FAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDELRGKKLRVERAK  219 (382)
T ss_pred             HHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCcccccCcEEEEehhh
Confidence            457889999775        3788888899999999999999999999999999999999999999887

>KOG4211|consensus

Probab=97.50  E-value=0.00031  Score=50.86  Aligned_cols=61  Identities=23%  Similarity=0.379  Sum_probs=49.7

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeecc
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADV   64 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~   64 (105)
                      +|.++|+.++ |..+.+.+. ++++.+.|||+|.+.+++++|++ .+...+..+-|.|..+...
T Consensus        26 ei~~Ff~~~~-I~~~~~~r~-~Gr~sGeA~Ve~~seedv~~Alk-kdR~~mg~RYIEVf~~~~~   86 (510)
T KOG4211|consen   26 EILDFFSNCG-IENLEIPRR-NGRPSGEAYVEFTSEEDVEKALK-KDRESMGHRYIEVFTAGGA   86 (510)
T ss_pred             HHHHHHhcCc-eeEEEEecc-CCCcCcceEEEeechHHHHHHHH-hhHHHhCCceEEEEccCCc
Confidence            4788888876 777544432 79999999999999999999999 4888888999999887633

>KOG2202|consensus

Probab=97.47  E-value=4e-05  Score=51.27  Aligned_cols=61  Identities=16%  Similarity=0.394  Sum_probs=50.9

Q ss_pred             HHHHhc-cCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           2 IYELFS-EFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         2 l~~~f~-~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +...|. +||+|+++.|..+-..+..+-++|.|...++|++|++.||+.-+.+++|.++++.
T Consensus        85 ~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~p  146 (260)
T KOG2202|consen   85 VFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSP  146 (260)
T ss_pred             HHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecC
Confidence            445555 8999998866554466678899999999999999999999999999999888765

>KOG0120|consensus

Probab=97.39  E-value=0.00012  Score=53.42  Aligned_cols=61  Identities=34%  Similarity=0.446  Sum_probs=55.7

Q ss_pred             HHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           2 IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         2 l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +.+++..||.+....++.+. ++-+++|+|.+|.+......|++.||+..+.++.|.|+.+.
T Consensus       306 ~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~  367 (500)
T KOG0120|consen  306 VKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAI  367 (500)
T ss_pred             HHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhh
Confidence            56788889999888888887 88999999999999999999999999999999999999876

>KOG1457|consensus

Probab=97.37  E-value=0.0015  Score=43.33  Aligned_cols=61  Identities=31%  Similarity=0.484  Sum_probs=43.4

Q ss_pred             HHHHhccCCCeeEEEEEeC-CC-CCcccEEEEEeCCHHHHHHHHHHhCCcccC---CeeEEEEEee
Q psy1928           2 IYELFSEFGPLKSAKLHYD-RS-GRSLGTADLIYERRSDAIKAMKQYNGVPLD---GRPMQIQLAA   62 (105)
Q Consensus         2 l~~~f~~~G~i~~~~i~~~-~~-~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~---~~~i~V~~~~   62 (105)
                      |+.+|..|---+.+.+... +. ..-+-++|++|.+..+|++|++.|||..++   ...|.|++++
T Consensus        51 iynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLhiElAK  116 (284)
T KOG1457|consen   51 IYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLHIELAK  116 (284)
T ss_pred             HHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeEeeehh
Confidence            5566665532333333222 22 223479999999999999999999999887   6789999987

>KOG1548|consensus

Probab=97.33  E-value=0.0011  Score=46.27  Aligned_cols=58  Identities=16%  Similarity=0.302  Sum_probs=48.4

Q ss_pred             HHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         2 l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      |.+.=.+||.|.+|.|.-   .++.|.+-|.|.+.++|+.||..|+|.-+.++.|..+...
T Consensus       293 l~eec~K~G~v~~vvv~d---~hPdGvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i~D  350 (382)
T KOG1548|consen  293 LTEECEKFGQVRKVVVYD---RHPDGVVTVSFRNNEEADQCIQTMDGRWFDGRQLTASIWD  350 (382)
T ss_pred             HHHHHHHhCCcceEEEec---cCCCceeEEEeCChHHHHHHHHHhcCeeecceEEEEEEeC
Confidence            344457899999987653   3567899999999999999999999999999999888664

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

Probab=97.29  E-value=0.0016  Score=37.85  Aligned_cols=54  Identities=24%  Similarity=0.221  Sum_probs=45.3

Q ss_pred             CCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccC----CeeEEEEEee
Q psy1928           9 FGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLD----GRPMQIQLAA   62 (105)
Q Consensus         9 ~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~----~~~i~V~~~~   62 (105)
                      .|....++++.|- +.-+.|||||.|.+++.+.+-.+.+++..+.    .+.+.|.+|+
T Consensus        27 ~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~i~yAr   85 (97)
T PF04059_consen   27 KGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCEISYAR   85 (97)
T ss_pred             cCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEEEehhH
Confidence            3566778888887 7888999999999999999999999998775    4667777776

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

>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=97.29  E-value=0.0014  Score=37.12  Aligned_cols=52  Identities=25%  Similarity=0.308  Sum_probs=36.3

Q ss_pred             HHHHhccCC-CeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           2 IYELFSEFG-PLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         2 l~~~f~~~G-~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      |++++..+| .|.+|         +.+.|++.|.+++.|++|.+.|++..+.+..|.|++..
T Consensus        23 L~qLsdNCGGkVl~v---------~~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~~~   75 (90)
T PF11608_consen   23 LRQLSDNCGGKVLSV---------SGGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSFSP   75 (90)
T ss_dssp             HHHHHHTTT--EEE-----------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEESS-
T ss_pred             HHHHhhccCCEEEEE---------eCCEEEEEeCCHHHHHHHHHhhcccccccceEEEEEcC
Confidence            456666765 44443         24689999999999999999999999999999999875

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

>KOG0151|consensus

Probab=97.20  E-value=0.00062  Score=51.51  Aligned_cols=64  Identities=27%  Similarity=0.463  Sum_probs=55.0

Q ss_pred             HHHHhccCCCeeEEEEEeCC----CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           2 IYELFSEFGPLKSAKLHYDR----SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         2 l~~~f~~~G~i~~~~i~~~~----~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      |...|..||.|..++|++..    ......|+||.|-+..++++|++.|++..+....+++-|.+..+
T Consensus       191 ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K~gWgk~V~  258 (877)
T KOG0151|consen  191 LLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMKLGWGKAVP  258 (877)
T ss_pred             HHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeeeeccccccc
Confidence            55678889999999998875    34467899999999999999999999999999999999987333

>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=97.18  E-value=0.0017  Score=37.90  Aligned_cols=60  Identities=17%  Similarity=0.265  Sum_probs=41.5

Q ss_pred             HHHHhccCCCeeEEE-EEeC-------CCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCe-eEEEEEee
Q psy1928           2 IYELFSEFGPLKSAK-LHYD-------RSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGR-PMQIQLAA   62 (105)
Q Consensus         2 l~~~f~~~G~i~~~~-i~~~-------~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~-~i~V~~~~   62 (105)
                      |.+.|++||.|.+.. +..+       +.-....+..|.|++..+|++||.. ||..+.+. .+-|.+++
T Consensus        22 Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~-NG~i~~g~~mvGV~~~~   90 (100)
T PF05172_consen   22 VLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQK-NGTIFSGSLMVGVKPCD   90 (100)
T ss_dssp             HHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTT-TTEEETTCEEEEEEE-H
T ss_pred             HHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHh-CCeEEcCcEEEEEEEcH
Confidence            567899999997653 1111       1112357899999999999999985 99999875 45577764

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.

>KOG4211|consensus

Probab=97.16  E-value=0.00071  Score=49.08  Aligned_cols=61  Identities=21%  Similarity=0.289  Sum_probs=48.5

Q ss_pred             CHHHHhccCCCee-EEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLK-SAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~-~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      ||.++|+..-.+. .|-++.+..+++.+.|||.|.+.+.|++|+.. |...|..+-|.|..+.
T Consensus       119 dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al~r-hre~iGhRYIEvF~Ss  180 (510)
T KOG4211|consen  119 DIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEIALGR-HRENIGHRYIEVFRSS  180 (510)
T ss_pred             HHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHHHHHH-HHHhhccceEEeehhH
Confidence            5788887654332 24566666778999999999999999999985 8888999999998776

>KOG1456|consensus

Probab=97.15  E-value=0.0023  Score=45.39  Aligned_cols=57  Identities=21%  Similarity=0.399  Sum_probs=50.5

Q ss_pred             HHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         2 l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      |..+|=.||.|..|++++.+    .+-+.|++-+..+.++|+..||+..+-+.+|.|..++
T Consensus       305 lFNl~ClYGNV~rvkFmkTk----~gtamVemgd~~aver~v~hLnn~~lfG~kl~v~~Sk  361 (494)
T KOG1456|consen  305 LFNLFCLYGNVERVKFMKTK----PGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVCVSK  361 (494)
T ss_pred             hhhhhhhcCceeeEEEeecc----cceeEEEcCcHHHHHHHHHHhccCccccceEEEeecc
Confidence            45667789999999999875    4679999999999999999999999999999988887

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

Probab=97.10  E-value=0.0037  Score=38.86  Aligned_cols=56  Identities=20%  Similarity=0.429  Sum_probs=43.8

Q ss_pred             HHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         2 l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      |.+.|..||.+.-+++..+       .-.|+|.+-..|-+|+. +++..+.++.|+|+..++.+
T Consensus        53 ll~~~~~~GevvLvRfv~~-------~mwVTF~dg~sALaals-~dg~~v~g~~l~i~LKtpdW  108 (146)
T PF08952_consen   53 LLQKFAQYGEVVLVRFVGD-------TMWVTFRDGQSALAALS-LDGIQVNGRTLKIRLKTPDW  108 (146)
T ss_dssp             HHHHHHCCS-ECEEEEETT-------CEEEEESSCHHHHHHHH-GCCSEETTEEEEEEE-----
T ss_pred             HHHHHHhCCceEEEEEeCC-------eEEEEECccHHHHHHHc-cCCcEECCEEEEEEeCCccH
Confidence            5677889999988887754       67899999999999998 79999999999999877444

; PDB: 1UFW_A 2DNR_A.

>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation

Probab=97.10  E-value=0.0011  Score=39.01  Aligned_cols=55  Identities=18%  Similarity=0.326  Sum_probs=33.8

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCc-----ccCCeeEEEEE
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGV-----PLDGRPMQIQL   60 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~-----~i~~~~i~V~~   60 (105)
                      +|.++|+.||.|.+|.+...     ...++|-|.+.+.|+.|+..+...     .|.+..+.++.
T Consensus        17 ~iK~~f~~~g~V~yVD~~~G-----~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~v   76 (105)
T PF08777_consen   17 DIKEAFSQFGEVAYVDFSRG-----DTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLEV   76 (105)
T ss_dssp             HHHHHT-SS--EEEEE--TT------SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE-
T ss_pred             HHHHHHHhcCCcceEEecCC-----CCEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEEE
Confidence            47899999999999988654     358999999999999999876433     45555555553

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

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

Probab=97.07  E-value=0.00096  Score=34.47  Aligned_cols=37  Identities=32%  Similarity=0.411  Sum_probs=30.8

Q ss_pred             HHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHH
Q psy1928           2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAM   43 (105)
Q Consensus         2 l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai   43 (105)
                      +...|..||+|..+.+..     ...+.++.|.+..+|++|+
T Consensus        17 vl~~F~~fGeI~~~~~~~-----~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen   17 VLEHFASFGEIVDIYVPE-----STNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             HHHHHHhcCCEEEEEcCC-----CCcEEEEEECCHHHHHhhC
Confidence            567899999999987762     2468999999999999885

>KOG0106|consensus

Probab=97.07  E-value=0.0003  Score=46.35  Aligned_cols=54  Identities=19%  Similarity=0.327  Sum_probs=45.0

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEe
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA   61 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~   61 (105)
                      +|.+.|.++|.+.+..+.       .+++||+|...+++.+||..|++..+.++.|.+...
T Consensus       115 dl~d~~~~~g~~~~~~~~-------~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~~~~  168 (216)
T KOG0106|consen  115 DLKDHFRPAGEVTYVDAR-------RNFAFVEFSEQEDAKRALEKLDGKKLNGRRISVEKN  168 (216)
T ss_pred             HHhhhhcccCCCchhhhh-------ccccceeehhhhhhhhcchhccchhhcCceeeeccc
Confidence            477889999988544332       469999999999999999999999999999988443

>KOG1456|consensus

Probab=96.85  E-value=0.0057  Score=43.47  Aligned_cols=56  Identities=18%  Similarity=0.245  Sum_probs=44.9

Q ss_pred             HHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCC--eeEEEEEee
Q psy1928           3 YELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDG--RPMQIQLAA   62 (105)
Q Consensus         3 ~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~--~~i~V~~~~   62 (105)
                      +.+-...|+|..|.|+.. ++   --|.|+|++.+.|++|.+.||+..|..  ..|+|++++
T Consensus       140 y~Icnp~GkVlRIvIfkk-ng---VQAmVEFdsv~~AqrAk~alNGADIYsGCCTLKIeyAk  197 (494)
T KOG1456|consen  140 YTICNPQGKVLRIVIFKK-NG---VQAMVEFDSVEVAQRAKAALNGADIYSGCCTLKIEYAK  197 (494)
T ss_pred             hhhcCCCCceEEEEEEec-cc---eeeEEeechhHHHHHHHhhcccccccccceeEEEEecC
Confidence            344456788988877764 33   368899999999999999999999874  578888887

>KOG4210|consensus

Probab=96.83  E-value=0.0011  Score=45.65  Aligned_cols=63  Identities=24%  Similarity=0.356  Sum_probs=53.2

Q ss_pred             HHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           2 IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         2 l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      |+..|..+|.|..++++.++ ++..++++++.|.+......++.. +...+.++++.|.+....+
T Consensus       202 ~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~  265 (285)
T KOG4210|consen  202 LKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEEDEPRP  265 (285)
T ss_pred             HhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCcccccccCCCCc
Confidence            45577888999999988887 999999999999999999999886 7788889888888776443

>KOG4307|consensus

Probab=96.78  E-value=0.0039  Score=47.38  Aligned_cols=60  Identities=20%  Similarity=0.440  Sum_probs=49.7

Q ss_pred             CHHHHhccCCCe-eEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEE
Q psy1928           1 MIYELFSEFGPL-KSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL   60 (105)
Q Consensus         1 ~l~~~f~~~G~i-~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~   60 (105)
                      ||.++|.-|--+ .+|.+-++..|+..|.|-|-|.+.++|.+|...|++..|..+.+.+.+
T Consensus       883 dI~~FF~dY~~~p~sI~~r~nd~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~V~l~i  943 (944)
T KOG4307|consen  883 DIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             HHHHHhcccccCCCceeEeecCCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            467888877644 455555555899999999999999999999999999999999887754

>KOG1855|consensus

Probab=96.67  E-value=0.0015  Score=46.78  Aligned_cols=48  Identities=25%  Similarity=0.281  Sum_probs=39.4

Q ss_pred             HHHHhccCCCeeEEEEEeC---C-C--CC--------cccEEEEEeCCHHHHHHHHHHhCCc
Q psy1928           2 IYELFSEFGPLKSAKLHYD---R-S--GR--------SLGTADLIYERRSDAIKAMKQYNGV   49 (105)
Q Consensus         2 l~~~f~~~G~i~~~~i~~~---~-~--~~--------~~g~~fv~f~~~~~a~~ai~~l~~~   49 (105)
                      |.++|+.+|.|..|+|+..   + +  +.        .+-||+|+|...+.|.+|.+.|+..
T Consensus       248 l~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~~e  309 (484)
T KOG1855|consen  248 LSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLNPE  309 (484)
T ss_pred             HHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhchh
Confidence            7899999999999999876   3 2  11        2578999999999999999987543

>KOG1996|consensus

Probab=96.21  E-value=0.023  Score=39.31  Aligned_cols=60  Identities=20%  Similarity=0.190  Sum_probs=47.5

Q ss_pred             HHHhccCCCeeEEEEEeCC--CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           3 YELFSEFGPLKSAKLHYDR--SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         3 ~~~f~~~G~i~~~~i~~~~--~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      .+...+||.|..|-|..++  --.-.--.||+|...++|.+|+-.||+..++++.+...+-.
T Consensus       304 keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn  365 (378)
T KOG1996|consen  304 KEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYN  365 (378)
T ss_pred             HHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheecc
Confidence            4456799999988777765  22234568999999999999999999999999987766543

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

Probab=95.87  E-value=0.036  Score=31.35  Aligned_cols=41  Identities=29%  Similarity=0.389  Sum_probs=33.6

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNG   48 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~   48 (105)
                      ||.++|+.||.| .|.++.+      ..|||...+.+.+..++..+.-
T Consensus        24 DI~qlFspfG~I-~VsWi~d------TSAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen   24 DIYQLFSPFGQI-YVSWIND------TSAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             HHHHHCCCCCCE-EEEEECT------TEEEEEECCCHHHHHHHHHHTT
T ss_pred             hHHHHhccCCcE-EEEEEcC------CcEEEEeecHHHHHHHHHHhcc
Confidence            589999999975 4566665      4899999999999999888763

; 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.

>KOG4849|consensus

Probab=95.77  E-value=0.03  Score=39.60  Aligned_cols=49  Identities=18%  Similarity=0.287  Sum_probs=41.4

Q ss_pred             CeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEE
Q psy1928          11 PLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ   59 (105)
Q Consensus        11 ~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~   59 (105)
                      ++.++++..+. ++.++||+++...+...+++.++.|..++|++..-.|.
T Consensus       108 ~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~  157 (498)
T KOG4849|consen  108 QFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVL  157 (498)
T ss_pred             HHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeee
Confidence            56677777777 99999999999999999999999999999998754443

>KOG1190|consensus

Probab=95.70  E-value=0.022  Score=40.96  Aligned_cols=58  Identities=19%  Similarity=0.237  Sum_probs=43.6

Q ss_pred             HHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCC--eeEEEEEee
Q psy1928           2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDG--RPMQIQLAA   62 (105)
Q Consensus         2 l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~--~~i~V~~~~   62 (105)
                      |..+|++||.|..|.-.....+   =-|+|.|.+.+.|+.|...|++..|..  ..|+|.+++
T Consensus       167 LHqvFS~fG~VlKIiTF~Knn~---FQALvQy~d~~sAq~AK~aLdGqnIyngcCtLrId~Sk  226 (492)
T KOG1190|consen  167 LHQVFSKFGFVLKIITFTKNNG---FQALVQYTDAVSAQAAKLALDGQNIYNGCCTLRIDFSK  226 (492)
T ss_pred             HHHHHhhcceeEEEEEEecccc---hhhhhhccchhhHHHHHHhccCCcccCceeEEEeehhh
Confidence            6789999999988744332221   237899999999999999999998864  456666654

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells

Probab=95.51  E-value=0.058  Score=34.92  Aligned_cols=56  Identities=18%  Similarity=0.378  Sum_probs=41.7

Q ss_pred             HHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhC--CcccCCeeEEEEEee
Q psy1928           2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYN--GVPLDGRPMQIQLAA   62 (105)
Q Consensus         2 l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~--~~~i~~~~i~V~~~~   62 (105)
                      |+++|..++.+....++..     -.-..|.|.+.+.|..|...|+  +..+.+..++|.++.
T Consensus        12 l~~l~~~~~~~~~~~~L~s-----FrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~   69 (184)
T PF04847_consen   12 LEELFSTYDPPVQFSPLKS-----FRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQ   69 (184)
T ss_dssp             HHHHHHTT-SS-EEEEETT-----TTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE---
T ss_pred             HHHHHHhcCCceEEEEcCC-----CCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEcc
Confidence            6788999998887765542     4678899999999999999998  889999999999885

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.

>KOG1365|consensus

Probab=95.42  E-value=0.014  Score=41.66  Aligned_cols=62  Identities=15%  Similarity=0.255  Sum_probs=48.6

Q ss_pred             CHHHHhccCC-CeeE--EEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFG-PLKS--AKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G-~i~~--~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      ||.++|..|- .|..  ++|+.+..|++.|.|||+|.+.+.|..|....+.+....+.|.|.-+.
T Consensus       296 dIL~FlgdFa~~i~f~gVHmv~N~qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp~S  360 (508)
T KOG1365|consen  296 DILDFLGDFATDIRFQGVHMVLNGQGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFPCS  360 (508)
T ss_pred             HHHHHHHHHhhhcccceeEEEEcCCCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEeecc
Confidence            3566666655 3444  778887789999999999999999999988777766668888888766

>KOG4206|consensus

Probab=95.34  E-value=0.058  Score=35.73  Aligned_cols=57  Identities=26%  Similarity=0.355  Sum_probs=44.9

Q ss_pred             HHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccC-CeeEEEEEee
Q psy1928           2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLD-GRPMQIQLAA   62 (105)
Q Consensus         2 l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~-~~~i~V~~~~   62 (105)
                      +..+|..|..-..++++...    .+.+||+|.+...+..|...+++..|. ...+.|.++.
T Consensus       163 l~~lf~qf~g~keir~i~~~----~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~~a~  220 (221)
T KOG4206|consen  163 LSDLFEQFPGFKEIRLIPPR----SGIAFVEFLSDRQASAAQQALQGFKITKKNTMQITFAK  220 (221)
T ss_pred             HHHHHhhCcccceeEeccCC----CceeEEecchhhhhHHHhhhhccceeccCceEEecccC
Confidence            56677778777777776542    579999999999999999999998887 6777777653

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=95.02  E-value=0.3  Score=37.30  Aligned_cols=35  Identities=11%  Similarity=0.289  Sum_probs=29.5

Q ss_pred             cEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928          27 GTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus        27 g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      .|.||+.. ...+...+..|+...+.++.+.|+.+.
T Consensus       527 ~~s~v~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~  561 (629)
T PRK11634        527 SHSTIELP-KGMPGEVLQHFTRTRILNKPMNMQLLG  561 (629)
T ss_pred             CceEEEcC-hhhHHHHHHHhccccccCCceEEEECC
Confidence            48899987 456788899999999999999999875

>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=95.02  E-value=0.085  Score=28.88  Aligned_cols=42  Identities=14%  Similarity=0.209  Sum_probs=24.4

Q ss_pred             eeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEe
Q psy1928          12 LKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA   61 (105)
Q Consensus        12 i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~   61 (105)
                      |-.|.+..       .|+||+.+. +.++.++..|++..+.++.++|+.+
T Consensus        33 IG~I~I~~-------~~S~vev~~-~~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen   33 IGRIDIFD-------NFSFVEVPE-EVAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             EEEEEE-S-------S-EEEEE-T-T-HHHHHHHHTT--SSS----EEE-
T ss_pred             EEEEEEee-------eEEEEEECH-HHHHHHHHHhcCCCCCCeeEEEEEC
Confidence            44566654       489999884 5788899999999999999999864

; PDB: 2G0C_A 3MOJ_B.

>KOG4285|consensus

Probab=94.78  E-value=0.071  Score=37.00  Aligned_cols=55  Identities=24%  Similarity=0.336  Sum_probs=42.2

Q ss_pred             HHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCe-eEEEEEee
Q psy1928           2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGR-PMQIQLAA   62 (105)
Q Consensus         2 l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~-~i~V~~~~   62 (105)
                      |..+|++||.|++.....     .-.+-+|-|.+..+|++||. .|+..|++. .|-|..+.
T Consensus       213 vL~~F~~cG~Vvkhv~~~-----ngNwMhirYssr~~A~KALs-kng~ii~g~vmiGVkpCt  268 (350)
T KOG4285|consen  213 VLNLFSRCGEVVKHVTPS-----NGNWMHIRYSSRTHAQKALS-KNGTIIDGDVMIGVKPCT  268 (350)
T ss_pred             HHHHHHhhCeeeeeecCC-----CCceEEEEecchhHHHHhhh-hcCeeeccceEEeeeecC
Confidence            567899999998764432     24688999999999999998 499988865 45566554

>KOG2068|consensus

Probab=94.59  E-value=0.016  Score=40.40  Aligned_cols=59  Identities=24%  Similarity=0.427  Sum_probs=45.2

Q ss_pred             HHhccCCCeeEEEEEeCCC----CCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           4 ELFSEFGPLKSAKLHYDRS----GRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         4 ~~f~~~G~i~~~~i~~~~~----~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +.|..||.|..|.+..+.+    .-....++|+|...++|..||..+++..++++.+++.+.+
T Consensus        99 eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lka~~gt  161 (327)
T KOG2068|consen   99 EYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALKASLGT  161 (327)
T ss_pred             ccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhHHhhCC
Confidence            4577889999987776542    1123558999999999999999999998888776665443

>KOG2135|consensus

Probab=94.25  E-value=0.021  Score=41.61  Aligned_cols=57  Identities=19%  Similarity=0.339  Sum_probs=46.6

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeec
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD   63 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~   63 (105)
                      +|...|.+||.|..|.+-+.     .-.+.|+|....+|-.|.. .++..|+++.|+|.|-.+
T Consensus       389 ~ln~hfA~fG~i~n~qv~~~-----~~~a~vTF~t~aeag~a~~-s~~avlnnr~iKl~whnp  445 (526)
T KOG2135|consen  389 DLNPHFAQFGEIENIQVDYS-----SLHAVVTFKTRAEAGEAYA-SHGAVLNNRFIKLFWHNP  445 (526)
T ss_pred             hhhhhhhhcCccccccccCc-----hhhheeeeeccccccchhc-cccceecCceeEEEEecC
Confidence            46778999999998876543     4578999999999866655 488999999999998775

>KOG0105|consensus

Probab=93.93  E-value=0.56  Score=30.65  Aligned_cols=46  Identities=20%  Similarity=0.276  Sum_probs=40.1

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLD   52 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~   52 (105)
                      ||++++.+-|.++...+.+|      +++.|+|...++.+=|+..|....+.
T Consensus       131 DLKDHmReaGdvCfadv~rD------g~GvV~~~r~eDMkYAvr~ld~~~~~  176 (241)
T KOG0105|consen  131 DLKDHMREAGDVCFADVQRD------GVGVVEYLRKEDMKYAVRKLDDQKFR  176 (241)
T ss_pred             HHHHHHHhhCCeeeeeeecc------cceeeeeeehhhHHHHHHhhcccccc
Confidence            58888999999999988886      58899999999999999998876655

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

Probab=93.93  E-value=0.17  Score=26.97  Aligned_cols=40  Identities=18%  Similarity=0.261  Sum_probs=30.4

Q ss_pred             CHHHHhccC---CCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHh
Q psy1928           1 MIYELFSEF---GPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQY   46 (105)
Q Consensus         1 ~l~~~f~~~---G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l   46 (105)
                      ||+.+|..|   .....|+++.|.      .|-|.|.+.+.|.+|+.+|
T Consensus        20 dI~~y~~~y~~~~~~~~IEWIdDt------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen   20 DIKAYFSEYFDEEGPFRIEWIDDT------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             HHHHHHHHhcccCCCceEEEecCC------cEEEEECCHHHHHHHHHcC
Confidence            466777776   235678888774      6779999999999998764

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=93.90  E-value=0.24  Score=30.94  Aligned_cols=52  Identities=23%  Similarity=0.370  Sum_probs=39.1

Q ss_pred             HHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEE
Q psy1928           2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL   60 (105)
Q Consensus         2 l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~   60 (105)
                      +...++.||.|.+|.+.-      +-.|+|.|.+...|=+|+.+++. ...+..+.+.|
T Consensus       107 V~~~Ls~fGpI~SVT~cG------rqsavVvF~d~~SAC~Av~Af~s-~~pgtm~qCsW  158 (166)
T PF15023_consen  107 VIQRLSVFGPIQSVTLCG------RQSAVVVFKDITSACKAVSAFQS-RAPGTMFQCSW  158 (166)
T ss_pred             HHHHHHhcCCcceeeecC------CceEEEEehhhHHHHHHHHhhcC-CCCCceEEeec
Confidence            345568999999987654      35799999999999999998775 44455566554

>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=91.70  E-value=1.3  Score=26.35  Aligned_cols=42  Identities=12%  Similarity=0.260  Sum_probs=34.4

Q ss_pred             CeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCC
Q psy1928          11 PLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDG   53 (105)
Q Consensus        11 ~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~   53 (105)
                      .|..++|+++.. -++-.+++.|.+...|..-...+||+.++.
T Consensus        40 ~i~~~riird~~-pnrymVLikF~~~~~Ad~Fy~~fNGk~Fns   81 (110)
T PF07576_consen   40 DIEHIRIIRDGT-PNRYMVLIKFRDQESADEFYEEFNGKPFNS   81 (110)
T ss_pred             cEEEEEEeeCCC-CceEEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            466778887642 356789999999999999999999998874

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

>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=91.51  E-value=0.98  Score=24.34  Aligned_cols=49  Identities=12%  Similarity=0.261  Sum_probs=33.0

Q ss_pred             HHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEE
Q psy1928           2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI   58 (105)
Q Consensus         2 l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V   58 (105)
                      ++..+.+|. ...  |..+++     --||.|.+..+|++|....++..+....+.+
T Consensus        17 ~K~~Lr~y~-~~~--I~~d~t-----GfYIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   17 FKKRLRKYR-WDR--IRDDRT-----GFYIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             HHHHHhcCC-cce--EEecCC-----EEEEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            455556664 233  233332     3479999999999999999988776655543

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>KOG0112|consensus

Probab=91.13  E-value=0.23  Score=39.11  Aligned_cols=56  Identities=29%  Similarity=0.502  Sum_probs=47.3

Q ss_pred             HHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCC--eeEEEEEee
Q psy1928           2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDG--RPMQIQLAA   62 (105)
Q Consensus         2 l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~--~~i~V~~~~   62 (105)
                      |..+|..||.|..|.+-.     ...|++|.|.+...++.|++.|.+..|++  +.+.|.++.
T Consensus       472 l~r~fd~fGpir~Idy~h-----gq~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvdla~  529 (975)
T KOG0112|consen  472 LNREFDRFGPIRIIDYRH-----GQPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVDLAS  529 (975)
T ss_pred             HHHHhhccCcceeeeccc-----CCcceeeecccCccchhhHHHHhcCcCCCCCccccccccc
Confidence            567899999999876643     35799999999999999999999999984  568888776

>KOG1457|consensus

Probab=90.66  E-value=0.53  Score=31.62  Aligned_cols=48  Identities=23%  Similarity=0.310  Sum_probs=34.1

Q ss_pred             HHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccC
Q psy1928           2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLD   52 (105)
Q Consensus         2 l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~   52 (105)
                      |+.+|+.|-.-..++|. .+.  .-+.+|++|.+.+.|..|+..|++..|.
T Consensus       227 l~~~~~~~~gf~~l~~~-~~~--g~~vaf~~~~~~~~at~am~~lqg~~~s  274 (284)
T KOG1457|consen  227 LKQLLSRYPGFHILKIR-ARG--GMPVAFADFEEIEQATDAMNHLQGNLLS  274 (284)
T ss_pred             HHHHHHhCCCceEEEEe-cCC--CcceEeecHHHHHHHHHHHHHhhcceec
Confidence            67778777543333332 222  2368999999999999999999987765

>KOG3152|consensus

Probab=90.23  E-value=0.19  Score=34.10  Aligned_cols=54  Identities=19%  Similarity=0.354  Sum_probs=41.7

Q ss_pred             HHHHhccCCCeeEEEEEeCC-C--------CCcc----cEEEEEeCCHHHHHHHHHHhCCcccCCee
Q psy1928           2 IYELFSEFGPLKSAKLHYDR-S--------GRSL----GTADLIYERRSDAIKAMKQYNGVPLDGRP   55 (105)
Q Consensus         2 l~~~f~~~G~i~~~~i~~~~-~--------~~~~----g~~fv~f~~~~~a~~ai~~l~~~~i~~~~   55 (105)
                      |+++|+.||.|-.|.+.... +        +.+.    ..+.|+|.+...|..+...||+.+|+++.
T Consensus        91 lReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~Iggkk  157 (278)
T KOG3152|consen   91 LREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTPIGGKK  157 (278)
T ss_pred             HHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCccCCCC
Confidence            67899999999888775443 3        2222    34558999999999999999999999753

>KOG0128|consensus

Probab=90.12  E-value=0.14  Score=40.01  Aligned_cols=62  Identities=21%  Similarity=0.270  Sum_probs=51.8

Q ss_pred             HHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeec
Q psy1928           2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD   63 (105)
Q Consensus         2 l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~   63 (105)
                      ++.++++.|.+..+.++..+.+++++.+++.|.+..++.+++...+...+....+.|..+.+
T Consensus       753 ~k~l~~~~gn~~~~~~vt~r~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsnp  814 (881)
T KOG0128|consen  753 LKSLASKTGNVTSLRLVTVRAGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNP  814 (881)
T ss_pred             HHhhccccCCccccchhhhhccccccceeccCCCcchhhhhcccchhhhhhhcCccccccCC
Confidence            56778899999888887777999999999999999999999887777777777777777653

>KOG4676|consensus

Probab=89.53  E-value=0.36  Score=34.79  Aligned_cols=59  Identities=12%  Similarity=0.122  Sum_probs=40.8

Q ss_pred             CHHHHhccCCCeeEEEEEeCC----CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEE
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR----SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL   60 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~----~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~   60 (105)
                      +++.+|...|.|..+.++-+.    -....-.|||.|.+...+..|-. |-.+++-++.|.|..
T Consensus        23 qm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQh-Ltntvfvdraliv~p   85 (479)
T KOG4676|consen   23 QMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQH-LTNTVFVDRALIVRP   85 (479)
T ss_pred             HHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhh-hccceeeeeeEEEEe
Confidence            367899999999988765432    12345789999999888877654 655555555554443

>KOG0128|consensus

Probab=87.83  E-value=0.089  Score=40.97  Aligned_cols=52  Identities=17%  Similarity=0.170  Sum_probs=39.1

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLD   52 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~   52 (105)
                      ||...|..++.|..+.+.... .+..+|.|++.|.+.+++.+||.......+.
T Consensus       683 dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~g  735 (881)
T KOG0128|consen  683 DLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFG  735 (881)
T ss_pred             hhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhh
Confidence            466778888877666554334 7788999999999999999999865554443

>KOG4574|consensus

Probab=87.83  E-value=0.53  Score=37.05  Aligned_cols=59  Identities=25%  Similarity=0.393  Sum_probs=48.3

Q ss_pred             HHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccC--CeeEEEEEeeccC
Q psy1928           2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLD--GRPMQIQLAADVS   65 (105)
Q Consensus         2 l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~--~~~i~V~~~~~~~   65 (105)
                      |..+++.||.+.+...+++     -..+.|+|...+.|..|+.+|+++++.  +-+.+|.+++..+
T Consensus       315 L~~l~s~yg~v~s~wtlr~-----~N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~~~  375 (1007)
T KOG4574|consen  315 LATLCSDYGSVASAWTLRD-----LNMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKTLP  375 (1007)
T ss_pred             HHHHHHhhcchhhheeccc-----ccchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEeccccc
Confidence            5668899999988877665     468999999999999999999998765  6678888887333

>KOG1365|consensus

Probab=87.68  E-value=0.2  Score=36.02  Aligned_cols=61  Identities=18%  Similarity=0.272  Sum_probs=44.6

Q ss_pred             CHHHHhcc----CCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSE----FGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~----~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      |+.++|..    -+..+.|-++..++++..|-|||.|...++|+.|+.. |...|+.+.|.+..++
T Consensus       177 dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~ee~aq~aL~k-hrq~iGqRYIElFRST  241 (508)
T KOG1365|consen  177 DVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACEEDAQFALRK-HRQNIGQRYIELFRST  241 (508)
T ss_pred             HHHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCHHHHHHHHHH-HHHHHhHHHHHHHHHh
Confidence            35566641    1234566666666899999999999999999999985 7777777777666554

>KOG0129|consensus

Probab=87.03  E-value=1.6  Score=32.54  Aligned_cols=44  Identities=16%  Similarity=0.252  Sum_probs=38.4

Q ss_pred             HHHHhc-cCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHH
Q psy1928           2 IYELFS-EFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQ   45 (105)
Q Consensus         2 l~~~f~-~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~   45 (105)
                      |-.+|. -||.|+.+.|-.|+ -..++|-+-|+|.+.....+||.+
T Consensus       387 LA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  387 LAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             HHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            455666 69999999999996 888999999999999999999974

>KOG4660|consensus

Probab=87.00  E-value=2.2  Score=32.04  Aligned_cols=54  Identities=20%  Similarity=0.182  Sum_probs=40.6

Q ss_pred             CCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccC----CeeEEEEEee
Q psy1928           9 FGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLD----GRPMQIQLAA   62 (105)
Q Consensus         9 ~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~----~~~i~V~~~~   62 (105)
                      .|.=..++++.|- +....|||||.|.+.+.+....++.|++...    .+.+.|.|++
T Consensus       413 ~gtYDFlYLPiDF~nkcNvGYAFINm~sp~ai~~F~kAFnGk~W~~FnS~Kia~itYAr  471 (549)
T KOG4660|consen  413 KGTYDFLYLPIDFKNKCNVGYAFINMTSPEAIIRFYKAFNGKKWEKFNSEKIASITYAR  471 (549)
T ss_pred             cCccceEEeccccccccccceeEEeecCHHHHHHHHHHHcCCchhhhcceeeeeeehhh
Confidence            4444566777765 6667899999999999999999999998643    3455666555

>KOG4307|consensus

Probab=86.19  E-value=0.37  Score=37.21  Aligned_cols=61  Identities=10%  Similarity=-0.005  Sum_probs=44.6

Q ss_pred             HHHHhccCCCeeE-EEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           2 IYELFSEFGPLKS-AKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         2 l~~~f~~~G~i~~-~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +.++|++.-.|++ |+|-+.++++....+||.|.+.+++.+|+..-+.+.+..+.|.|.-..
T Consensus       451 ~v~~f~~~~~Ved~I~lt~~P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~si~  512 (944)
T KOG4307|consen  451 PVNKFMGAAAVEDFIELTRLPTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDSIA  512 (944)
T ss_pred             hhhhhhhhhhhhheeEeccCCcccccchhhheeccccccchhhhcccccccCceEEEeechh
Confidence            4566766555654 777666688889999999999888888877556666667777777444

>smart00596 PRE_C2HC PRE_C2HC domain

Probab=86.14  E-value=0.95  Score=24.62  Aligned_cols=59  Identities=14%  Similarity=0.178  Sum_probs=41.7

Q ss_pred             CHHHHhccCC-CeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFG-PLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G-~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|.+.|.+.| ++..++.+... +..+...-+|+.....+...   .|+-+.|.+..+.|+...
T Consensus         3 ~I~~~L~~~G~~v~~i~~m~~~~~r~P~nmf~vel~~~~~~~~---Il~ik~Lg~~~V~VEr~~   63 (69)
T smart00596        3 QIEEALKDIGFPVLFIHNMLNRDTKNPQNMFEVELVPAANGKE---ILNIKTLGGQRVTVERPH   63 (69)
T ss_pred             HHHHHHHHcCCceeEEEcccccCCCCcceeEEEEeeecCCCcc---eEeehhhCCeeEEEecCc
Confidence            4778888888 66788877776 56677888888875544333   456667778888877543

>KOG2193|consensus

Probab=86.08  E-value=0.49  Score=34.59  Aligned_cols=40  Identities=20%  Similarity=0.199  Sum_probs=33.9

Q ss_pred             ccEEEEEeCCHHHHHHHHHHhCCc-ccCCeeEEEEEeeccC
Q psy1928          26 LGTADLIYERRSDAIKAMKQYNGV-PLDGRPMQIQLAADVS   65 (105)
Q Consensus        26 ~g~~fv~f~~~~~a~~ai~~l~~~-~i~~~~i~V~~~~~~~   65 (105)
                      .+|+|+.+.+...+.+|++.++++ ++.++.+.|..+.++.
T Consensus        37 ~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~kk   77 (584)
T KOG2193|consen   37 SGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVPKK   77 (584)
T ss_pred             cceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhhHH
Confidence            589999999999999999999986 5778888888776433

>KOG2416|consensus

Probab=85.53  E-value=1.3  Score=33.72  Aligned_cols=56  Identities=11%  Similarity=0.135  Sum_probs=39.3

Q ss_pred             HHHHhc-cCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccC---CeeEEEEEee
Q psy1928           2 IYELFS-EFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLD---GRPMQIQLAA   62 (105)
Q Consensus         2 l~~~f~-~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~---~~~i~V~~~~   62 (105)
                      |+.++. ..|.|... +|    .+.+..|||.|.+.++|...+.+||+..+-   .+-|.|.|..
T Consensus       461 LkelL~rtgg~Vee~-Wm----DkIKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~adf~~  520 (718)
T KOG2416|consen  461 LKELLGRTGGNVEEF-WM----DKIKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLIADFVR  520 (718)
T ss_pred             HHHHHhhccCchHHH-HH----HHhhcceeEecccHHHHHHHHHHHhccccCCCCCceeEeeecc
Confidence            556665 34444443 22    134679999999999999999999998654   4567777765

>PF15513 DUF4651: Domain of unknown function (DUF4651)

Probab=81.19  E-value=2.9  Score=22.23  Aligned_cols=18  Identities=22%  Similarity=0.445  Sum_probs=14.5

Q ss_pred             CHHHHhccCCCeeEEEEE
Q psy1928           1 MIYELFSEFGPLKSAKLH   18 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~   18 (105)
                      +|+++|+..|.|.-+.+.
T Consensus        10 ~iR~~fs~lG~I~vLYvn   27 (62)
T PF15513_consen   10 EIRQFFSQLGEIAVLYVN   27 (62)
T ss_pred             HHHHHHHhcCcEEEEEEc
Confidence            488999999999766553

>PF07530 PRE_C2HC: Associated with zinc fingers; InterPro: IPR006579 This domain is present in proteins found exclusively in the arthropods, including a number of Drosophila species, the silk moth and the gypsy moth

Probab=80.62  E-value=2.7  Score=22.68  Aligned_cols=59  Identities=17%  Similarity=0.236  Sum_probs=40.8

Q ss_pred             CHHHHhccCC-CeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFG-PLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G-~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|.+.|...| .+.++.-+..+ +..+....||+.....+..   +.|+-..+.+..++|+...
T Consensus         3 ~I~~~L~~~G~~v~~i~~~~~~~~k~pl~mf~veL~p~~~~k---~i~~Ik~l~~~~V~vE~~~   63 (68)
T PF07530_consen    3 EIKEELKDQGHPVRNIHNMHSRNTKKPLNMFFVELEPKPNNK---EIYKIKTLCGQRVKVERPR   63 (68)
T ss_pred             HHHHHHHHcCCceEEEEccccCCCCCCceEEEEeeccCcccc---ceeehHhhCCeEEEEecCC
Confidence            4667777777 66777766666 6777788899987654422   3456667778788877544

These proteins are possibly involved in RNA binding or single strand DNA binding.

>KOG0115|consensus

Probab=80.13  E-value=1.8  Score=29.54  Aligned_cols=46  Identities=22%  Similarity=0.444  Sum_probs=38.3

Q ss_pred             HHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhC
Q psy1928           2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYN   47 (105)
Q Consensus         2 l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~   47 (105)
                      +++.|+.||.|....++.|..++..+..+|.|.....+.+|+..++
T Consensus        48 l~~~f~~fg~~e~av~~vD~r~k~t~eg~v~~~~k~~a~~a~rr~~   93 (275)
T KOG0115|consen   48 LEQAFRRFGPIERAVAKVDDRGKPTREGIVEFAKKPNARKAARRCR   93 (275)
T ss_pred             HHHhhhhcCccchheeeecccccccccchhhhhcchhHHHHHHHhc
Confidence            5677899999987666666677888899999999999999988774

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	105
1no8_A	106	Solution Structure Of The Nuclear Factor Aly Rbd Do		6e-23
2kt5_A	124	Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To H		5e-22
2yka_A	124	Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To H		5e-22
2f3j_A	177	The Solution Structure Of The Ref2-I Mrna Export Fa		9e-22
3ulh_A	107	Crystal Structure Of A Rna Binding Domain Of Tho Co		2e-21
2rra_A	99	Solution Structure Of Rna Binding Domain In Human T		3e-05
2rrb_A	96	Refinement Of Rna Binding Domain In Human Tra2 Beta		3e-05
2kxn_B	129	Nmr Structure Of Human Tra2beta1 Rrm In Complex Wit		4e-05
2cqc_A	95	Solution Structure Of The Rna Recognition Motif In		6e-05
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		8e-05
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		1e-04
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		2e-04
2do0_A	114	Solution Structure Of The Rna Binding Domain Of Het		4e-04
1h6k_Z	98	Nuclear Cap Binding Complex Length = 98		5e-04

>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain Length = 106

Iteration: 1
 Score =  102 bits (254), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 46/59 (77%), Positives = 53/59 (89%)
Query: 2   IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
           I ELF+EFG LK A +HYDRSGRSLGTAD+ +ER++DA+KAMKQYNGVPLDGRPM IQL
Sbjct: 45  IQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL 103

>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1 Icp27 Peptide Length = 124

Iteration: 1
 Score = 99.4 bits (246), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 48/67 (71%), Positives = 54/67 (80%)
Query: 2   IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
           I ELF+EFG LK A + YDRSGRSLGTAD+ +ERR+DA+KAMKQY GVPLDGRPM IQL 
Sbjct: 52  IQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLV 111
Query: 62  ADVSVLE 68
           A    LE
Sbjct: 112 ASQIDLE 118

>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs Orf57 Peptide Length = 124

Iteration: 1
 Score = 99.4 bits (246), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 48/67 (71%), Positives = 54/67 (80%)
Query: 2   IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
           I ELF+EFG LK A + YDRSGRSLGTAD+ +ERR+DA+KAMKQY GVPLDGRPM IQL 
Sbjct: 52  IQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLV 111
Query: 62  ADVSVLE 68
           A    LE
Sbjct: 112 ASQIDLE 118

>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor (Residues 1-155) Length = 177

Iteration: 1
 Score = 98.2 bits (243), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 48/67 (71%), Positives = 54/67 (80%)
Query: 2   IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
           I ELF+EFG LK A + YDRSGRSLGTAD+ +ERR+DA+KAMKQY GVPLDGRPM IQL 
Sbjct: 105 IQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLV 164
Query: 62  ADVSVLE 68
           A    LE
Sbjct: 165 ASQIDLE 171

>pdb|3ULH|A Chain A, Crystal Structure Of A Rna Binding Domain Of Tho Complex Subunit 4 Protein (Thoc4) From Homo Sapiens At 2.54 A Resolution Length = 107

Iteration: 1
 Score = 97.1 bits (240), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 44/59 (74%), Positives = 51/59 (86%)
Query: 2   IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
           I ELF+EFG LK A +HYDRSGRSLGTAD+ +ER++DA+KA KQYNGVPLDGRP  IQL
Sbjct: 46  IQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQYNGVPLDGRPXNIQL 104

>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2 Beta Protein In Complex With Rna (Gaagaa) Length = 99

Iteration: 1
 Score = 43.9 bits (102), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 22/59 (37%), Positives = 38/59 (64%), Gaps = 1/59 (1%)
Query: 4  ELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
          E+FS++GP+    + YD+ S RS G A + +E   DA +A ++ NG+ LDGR +++  +
Sbjct: 34 EVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFS 92

>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta Protein Length = 96

Iteration: 1
 Score = 43.9 bits (102), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 22/59 (37%), Positives = 38/59 (64%), Gaps = 1/59 (1%)
Query: 4  ELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
          E+FS++GP+    + YD+ S RS G A + +E   DA +A ++ NG+ LDGR +++  +
Sbjct: 31 EVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFS 89

>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With Aagaac Rna Length = 129

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 22/59 (37%), Positives = 38/59 (64%), Gaps = 1/59 (1%)
Query: 4   ELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
           E+FS++GP+    + YD+ S RS G A + +E   DA +A ++ NG+ LDGR +++  +
Sbjct: 65  EVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFS 123

>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In ArginineSERINE-Rich Splicing Factor 10 Length = 95

Iteration: 1
 Score = 42.4 bits (98), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 22/57 (38%), Positives = 37/57 (64%), Gaps = 1/57 (1%)
Query: 4  ELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
          E+FS++GP+    + YD+ S RS G A + +E   DA +A ++ NG+ LDGR +++ 
Sbjct: 34 EVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVS 90

>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 = 42.0 bits (97), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 22/60 (36%), Positives = 35/60 (58%), Gaps = 1/60 (1%)
Query: 4  ELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA 62
          ++FSE GP+ S +L YDR +G+  G     Y+ +  A+ AM+  NG    GR +++  AA
Sbjct: 27 DIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAA 86

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 41.6 bits (96), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/74 (31%), Positives = 37/74 (50%)
Query: 1  MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
          M+  +F + GP+    L  DR+ +S G A + +E  +DA  A K  NG  L G+ ++++ 
Sbjct: 23 MLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQ 82
Query: 61 AADVSVLENTVPRP 74
          A   S       RP
Sbjct: 83 AKKPSFQSGGRRRP 96

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 40.8 bits (94), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/59 (37%), Positives = 34/59 (57%), Gaps = 1/59 (1%)
Query: 1   MIYELFSEFGPLKSAKLHYD-RSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
           M+  +F  FG ++S +L  D  +GRS G   + +     A KA++Q NG  L GRPM++
Sbjct: 42  MLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKV 100

>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of Heterogeneous Nuclear Ribonucleoprotein M Length = 114

Iteration: 1
 Score = 40.0 bits (92), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 18/59 (30%), Positives = 35/59 (59%)
Query: 2  IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
          + E+FS  G +  A +  D+ G+S G   + +E+  +A++A+  +NG  L  RPM +++
Sbjct: 32 LKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKM 90

>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex Length = 98

Iteration: 1
 Score = 39.3 bits (90), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 22/61 (36%), Positives = 32/61 (52%)
Query: 2  IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
          IYELFS+ G +K   +  D+   + G   + Y  R+DA  AM+  NG  LD R ++    
Sbjct: 35 IYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD 94
Query: 62 A 62
          A
Sbjct: 95 A 95

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	105
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	7e-26
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	1e-25
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	1e-23
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	8e-20
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-14
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-11
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	6e-14
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	2e-13
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	3e-13
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	3e-13
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	3e-09
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	3e-13
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	1e-10
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	3e-13
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	1e-09
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	4e-13
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	4e-13
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	1e-05
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	5e-13
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	6e-13
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	8e-13
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	9e-13
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	2e-12
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	2e-12
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	7e-06
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	2e-12
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	4e-12
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	4e-12
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	5e-12
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	8e-12
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	8e-12
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	8e-12
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	9e-12
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	1e-11
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	1e-11
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-11
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	4e-11
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	8e-08
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	2e-11
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	2e-11
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	2e-11
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	2e-11
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	3e-11
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	3e-11
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	3e-11
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	3e-11
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	3e-11
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	4e-11
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	4e-11
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	4e-11
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	4e-11
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	9e-11
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	2e-09
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	9e-11
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	1e-05
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-10
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	1e-10
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	2e-10
1x5o_A	114	RNA binding motif, single-stranded interacting pro	2e-10
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	3e-10
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	7e-04
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	3e-10
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	4e-10
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	4e-10
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	5e-10
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	5e-10
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	7e-10
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	7e-10
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	4e-07
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	8e-10
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	8e-10
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	1e-09
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	1e-09
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	2e-09
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	2e-09
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	2e-09
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	2e-09
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	3e-09
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	3e-09
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	4e-09
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	5e-09
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	5e-09
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	5e-09
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	5e-09
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	3e-07
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	6e-09
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	6e-09
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	3e-08
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	8e-07
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	1e-08
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	1e-08
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	2e-08
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	2e-08
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	3e-08
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	5e-08
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-05
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	5e-08
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	7e-08
1x4e_A	85	RNA binding motif, single-stranded interacting pro	7e-08
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	9e-08
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	1e-07
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	1e-07
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	2e-07
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	2e-07
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-07
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	4e-06
2div_A	99	TRNA selenocysteine associated protein; structural	2e-07
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	3e-07
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	3e-07
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	3e-07
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	4e-07
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	4e-07
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	4e-07
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	4e-07
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	5e-07
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	6e-07
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	7e-07
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	9e-07
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	9e-07
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	1e-06
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	1e-06
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	2e-06
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	2e-06
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	3e-06
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	3e-06
1x5p_A	97	Negative elongation factor E; structure genomics,	3e-06
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	3e-06
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	3e-06
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	4e-06
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	5e-06
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	5e-06
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	5e-06
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	8e-06
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	8e-06
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	8e-06
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	9e-06
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	9e-06
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	1e-05
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	2e-05
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	3e-05
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	5e-05
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	6e-05
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	3e-04
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	7e-05
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	1e-04
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-04
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	1e-04
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	1e-04
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	1e-04
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	2e-04
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	2e-04
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	2e-04
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	2e-04
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	3e-04
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	3e-04
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	3e-04
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	3e-04
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	4e-04
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	5e-04

>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 = 92.1 bits (229), Expect = 7e-26
 Identities = 46/63 (73%), Positives = 52/63 (82%)

Query: 1   MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
            I ELF+EFG LK A + YDRSGRSLGTAD+ +ERR+DA+KAMKQY GVPLDGRPM IQL
Sbjct: 51  DIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL 110

Query: 61  AAD 63
            A 
Sbjct: 111 VAS 113

>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 = 90.8 bits (226), Expect = 1e-25
 Identities = 46/61 (75%), Positives = 53/61 (86%)

Query: 1   MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
            I ELF+EFG LK A +HYDRSGRSLGTAD+ +ER++DA+KAMKQYNGVPLDGRPM IQL
Sbjct: 45  DIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL 104

Query: 61  A 61
            
Sbjct: 105 V 105

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 88.4 bits (219), Expect = 1e-23
 Identities = 46/63 (73%), Positives = 52/63 (82%)

Query: 1   MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
            I ELF+EFG LK A + YDRSGRSLGTAD+ +ERR+DA+KAMKQY GVPLDGRPM IQL
Sbjct: 104 DIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL 163

Query: 61  AAD 63
            A 
Sbjct: 164 VAS 166

>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 = 76.6 bits (189), Expect = 8e-20
 Identities = 23/85 (27%), Positives = 42/85 (49%), Gaps = 2/85 (2%)

Query: 2   IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
           + E+FS  G +  A +  D+ G+S G   + +E+  +A++A+  +NG  L  RPM +++ 
Sbjct: 32  LKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMD 91

Query: 62  ADVSVLENTVPRPVARGGRGGASGG 86
                  +  P    R  + G S G
Sbjct: 92  ERALPKGDFFPPE--RPQQSGPSSG 114

>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 = 63.3 bits (155), Expect = 3e-14
 Identities = 13/58 (22%), Positives = 32/58 (55%)

Query: 1  MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
          ++ + F   GP+ + K+  D++ +++  A + Y +  DA  A++  NG  ++   ++I
Sbjct: 16 ILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKI 73

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 56.4 bits (137), Expect = 1e-11
 Identities = 19/63 (30%), Positives = 30/63 (47%), Gaps = 1/63 (1%)

Query: 1   MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
            +   F +F    S  + +D  +G S G   + +  + DA  AM    G  L+GRP++I 
Sbjct: 103 TLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRIN 162

Query: 60  LAA 62
            AA
Sbjct: 163 WAA 165

>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 = 62.5 bits (152), Expect = 6e-14
 Identities = 32/106 (30%), Positives = 46/106 (43%), Gaps = 10/106 (9%)

Query: 1   MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
            IYELFS+ G +K   +  D+    + G   + Y  R+DA  AM+  NG  LD R ++  
Sbjct: 55  QIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTD 114

Query: 60  LAADVSVLENTVPRPVARGGRGGASGGYRNGTAPTY-RPRGGLKKT 104
             A          +   + GRG + G  R+     Y   RGG  K 
Sbjct: 115 WDAG--------FKEGRQYGRGRSGGQVRDEYRQDYDAGRGGYGKL 152

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 60.1 bits (146), Expect = 2e-13
 Identities = 9/64 (14%), Positives = 28/64 (43%), Gaps = 1/64 (1%)

Query: 1  MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
           + ++  ++G ++  ++     + + LG A +++     A + +K  +   + G  +  Q
Sbjct: 22 FLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQ 81

Query: 60 LAAD 63
          L   
Sbjct: 82 LDIK 85

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 60.3 bits (146), Expect = 3e-13
 Identities = 13/60 (21%), Positives = 26/60 (43%), Gaps = 2/60 (3%)

Query: 2   IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
           +Y L S  G +    +    S  + G A +++  +  A   ++ + G P  G P+ I  +
Sbjct: 50  LYALASSQGDILDIVVD--LSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFS 107

>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 = 61.0 bits (149), Expect = 3e-13
 Identities = 20/62 (32%), Positives = 32/62 (51%), Gaps = 1/62 (1%)

Query: 1  MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
              LF   G ++S KL  D+ +G+SLG   + Y    DA KA+   NG+ L  + +++ 
Sbjct: 18 EFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVS 77

Query: 60 LA 61
           A
Sbjct: 78 YA 79

>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 = 50.3 bits (121), Expect = 3e-09
 Identities = 17/64 (26%), Positives = 38/64 (59%), Gaps = 3/64 (4%)

Query: 1   MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDG--RPMQ 57
            + +LFS++G + ++++  D+ +G S G   + +++R +A +A+K  NG    G   P+ 
Sbjct: 104 ELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPIT 163

Query: 58  IQLA 61
           ++ A
Sbjct: 164 VKFA 167

>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 = 61.5 bits (150), Expect = 3e-13
 Identities = 21/59 (35%), Positives = 37/59 (62%), Gaps = 1/59 (1%)

Query: 1  MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
          M+YE FS  GP+ S ++  D  + RSLG A + +++ +DA +A+   N   + G+P++I
Sbjct: 31 MLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRI 89

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 54.6 bits (132), Expect = 1e-10
 Identities = 22/100 (22%), Positives = 39/100 (39%), Gaps = 10/100 (10%)

Query: 1   MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
            +Y+ FS FG + S K+  D    S G   + +E +  A +A+++ NG+ L+ R + +  
Sbjct: 119 ALYDTFSAFGNILSCKVVCD-ENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGR 177

Query: 61  AADVSVLENTVPRPVARGGRGGASGGYRNGTAPTYRPRGG 100
                       R       G  +  +     P Y    G
Sbjct: 178 FK---------SRKEREAELGARAKEFYPYDVPDYAGSSG 208

>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 = 60.7 bits (148), Expect = 3e-13
 Identities = 16/62 (25%), Positives = 33/62 (53%), Gaps = 1/62 (1%)

Query: 1  MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
           +Y LF   GP+ + ++  D  +G S G A + +    D+ +A+K  NG+ +  + +++ 
Sbjct: 19 ELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVS 78

Query: 60 LA 61
           A
Sbjct: 79 YA 80

>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 = 51.4 bits (124), Expect = 1e-09
 Identities = 17/64 (26%), Positives = 35/64 (54%), Gaps = 3/64 (4%)

Query: 1   MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDG--RPMQ 57
            +  +F ++G +    +  D+ +GR  G A + Y +R +A +A+   N V  +G  +P+ 
Sbjct: 105 QLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLS 164

Query: 58  IQLA 61
           ++LA
Sbjct: 165 VRLA 168

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Length = 95

 Score = 58.8 bits (143), Expect = 4e-13
 Identities = 17/62 (27%), Positives = 30/62 (48%)

Query: 1  MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
          ++YELF + GPL    +  DR G+      + ++       A+   NG+ L GRP+ +  
Sbjct: 32 ILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSG 91

Query: 61 AA 62
           +
Sbjct: 92 PS 93

>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 = 60.7 bits (148), Expect = 4e-13
 Identities = 20/63 (31%), Positives = 32/63 (50%), Gaps = 1/63 (1%)

Query: 1   MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
            + EL + FGPLK+  L  D  +G S G A   Y   +   +A+   NG+ L  + + +Q
Sbjct: 110 QVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQ 169

Query: 60  LAA 62
            A+
Sbjct: 170 RAS 172

>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 = 40.7 bits (96), Expect = 1e-05
 Identities = 11/76 (14%), Positives = 25/76 (32%), Gaps = 7/76 (9%)

Query: 1  MIYELFSEFGPLKSAKLHYDR------SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGR 54
           + + F+    L                 +    A L +    +  +AM  ++G+   G+
Sbjct: 20 AMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQ 78

Query: 55 PMQIQLAADVSVLENT 70
           ++I+   D   L   
Sbjct: 79 SLKIRRPHDYQPLPGA 94

>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 = 58.4 bits (142), Expect = 5e-13
 Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 2/60 (3%)

Query: 2  IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
          ++ +FS FG +    +   RS +  G A +I++  S A  A++   G P   +PM+IQ A
Sbjct: 29 LHAIFSRFGQILDILVS--RSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA 86

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 57.9 bits (141), Expect = 6e-13
 Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 1/62 (1%)

Query: 1  MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
           I   F+ FG +  A++  D  +G+S G   + +  + DA  A++Q  G  L GR ++  
Sbjct: 22 AIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTN 81

Query: 60 LA 61
           A
Sbjct: 82 WA 83

>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 = 57.9 bits (141), Expect = 8e-13
 Identities = 18/63 (28%), Positives = 31/63 (49%), Gaps = 2/63 (3%)

Query: 1  MIYELFSEFGPLKSAKLHYDR--SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
           I E+FS +G +K   +  +R     S G A + +E   +A KA+K  +G  +DG+ +  
Sbjct: 20 HIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITA 79

Query: 59 QLA 61
             
Sbjct: 80 TAV 82

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 115

 Score = 58.5 bits (142), Expect = 9e-13
 Identities = 15/62 (24%), Positives = 28/62 (45%), Gaps = 1/62 (1%)

Query: 1   MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
            +  LF+ F   K   + +   +GR  G A + +  +  A +A+   NG  L G+ + I+
Sbjct: 41  DLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIE 100

Query: 60  LA 61
             
Sbjct: 101 FG 102

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 57.3 bits (139), Expect = 2e-12
 Identities = 14/60 (23%), Positives = 32/60 (53%)

Query: 4  ELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD 63
          E+    G +K  +L  +R+G+  G A + YE  S A +A+ + +G+ +    +++ ++  
Sbjct: 36 EICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAISNS 95

>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 = 59.3 bits (144), Expect = 2e-12
 Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 1/62 (1%)

Query: 1   MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
            + EL + FGPLK+  L  D  +G S G A   Y   +   +A+   NG+ L  + + +Q
Sbjct: 130 QVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQ 189

Query: 60  LA 61
            A
Sbjct: 190 RA 191

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 41.6 bits (98), Expect = 7e-06
 Identities = 12/83 (14%), Positives = 26/83 (31%), Gaps = 7/83 (8%)

Query: 1   MIYELFSEFGPLKSAKLHYDR------SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGR 54
            + + F+    L                 +    A L +    +  +AM  ++G+   G+
Sbjct: 20  AMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQ 78

Query: 55  PMQIQLAADVSVLENTVPRPVAR 77
            ++I+   D   L      P   
Sbjct: 79  SLKIRRPHDYQPLPGMSENPSVY 101

>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 = 56.9 bits (138), Expect = 2e-12
 Identities = 17/64 (26%), Positives = 33/64 (51%), Gaps = 1/64 (1%)

Query: 1  MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
           I +L S  GP+ + K+ +D  +GRS G A + +     +  A++  NG  L  R ++  
Sbjct: 18 QILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCG 77

Query: 60 LAAD 63
           +++
Sbjct: 78 YSSN 81

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Length = 116

 Score = 57.0 bits (138), Expect = 4e-12
 Identities = 25/85 (29%), Positives = 38/85 (44%)

Query: 4   ELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD 63
            +F + GP+    L  DR+ +S G A + +E  +DA  A K  NG  L G+ ++++ A  
Sbjct: 26  AVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKK 85

Query: 64  VSVLENTVPRPVARGGRGGASGGYR 88
            S       RP A       SG   
Sbjct: 86  PSFQSGGRRRPPASSRNRSPSGSLE 110

>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 = 57.4 bits (139), Expect = 4e-12
 Identities = 23/86 (26%), Positives = 42/86 (48%), Gaps = 7/86 (8%)

Query: 1   MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
            + +LF  +GP++S K+  DR + +S G   + ++  S A +A+   NG  +  + +++ 
Sbjct: 58  QLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVA 117

Query: 60  LAADVSVLENTVPRPVARGGRGGASG 85
           LAA          RP   G  G  +G
Sbjct: 118 LAASGH------QRPGIAGAVGDGNG 137

>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 = 56.5 bits (137), Expect = 5e-12
 Identities = 17/62 (27%), Positives = 35/62 (56%), Gaps = 1/62 (1%)

Query: 1  MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
          +++ELF + GP+ +  +  DR +G+  G   + +    DA  A+K  + + L G+P+++ 
Sbjct: 31 LLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVN 90

Query: 60 LA 61
           A
Sbjct: 91 KA 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 = 56.2 bits (136), Expect = 8e-12
 Identities = 29/99 (29%), Positives = 45/99 (45%), Gaps = 13/99 (13%)

Query: 2   IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
           I++ F+E+G +K+  L+ DR +G   G   + YE   +A  AM+  NG  L G+P+ +  
Sbjct: 39  IHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 98

Query: 61  AADVSVLENTVPRPVARGGRGGASGGYRNGTAPTYRPRG 99
                       R   +G R    GG R   +P  R R 
Sbjct: 99  CF---------VRGPPKGKRR---GGRRRSRSPDRRRRL 125

>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 = 56.2 bits (136), Expect = 8e-12
 Identities = 22/91 (24%), Positives = 37/91 (40%), Gaps = 7/91 (7%)

Query: 1   MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
            I   F+ FG +  A++  D  +G+S G   + +  + DA  A++Q  G  L GR ++  
Sbjct: 31  DIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTN 90

Query: 60  LAADVSVLENTVPRPVARGGRGGASGGYRNG 90
            A          P P +         G  +G
Sbjct: 91  WATRKP------PAPKSTYESNTKQSGPSSG 115

>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 = 55.4 bits (134), Expect = 8e-12
 Identities = 15/61 (24%), Positives = 28/61 (45%), Gaps = 1/61 (1%)

Query: 2  IYELFSEFGPLKSA-KLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
          I + F  +  +  +  L Y+  G   G A + +E R +A  A+   N  P+  R +++ L
Sbjct: 32 ILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVL 91

Query: 61 A 61
           
Sbjct: 92 G 92

>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 = 55.8 bits (135), Expect = 9e-12
 Identities = 20/62 (32%), Positives = 33/62 (53%), Gaps = 1/62 (1%)

Query: 1   MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
            I E F ++G +K+  L+ DR +G S G A + YE    A+ A +  NG  + G+ +Q+ 
Sbjct: 42  EIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD 101

Query: 60  LA 61
             
Sbjct: 102 WC 103

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 55.3 bits (134), Expect = 1e-11
 Identities = 20/62 (32%), Positives = 34/62 (54%), Gaps = 1/62 (1%)

Query: 1   MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
            I++ F+E+G +K+  L+ DR +G   G   + YE   +A  AM+  NG  L G+P+ + 
Sbjct: 39  DIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD 98

Query: 60  LA 61
             
Sbjct: 99  WC 100

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108

 Score = 55.0 bits (133), Expect = 1e-11
 Identities = 22/62 (35%), Positives = 34/62 (54%), Gaps = 1/62 (1%)

Query: 1   MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
           M+  +F  FG ++S +L  D  +GRS G   + +     A KA++Q NG  L GRPM++ 
Sbjct: 42  MLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVG 101

Query: 60  LA 61
             
Sbjct: 102 HV 103

>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 = 57.7 bits (140), Expect = 1e-11
 Identities = 17/62 (27%), Positives = 25/62 (40%), Gaps = 1/62 (1%)

Query: 1   MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
              EL   FG L+   L Y   +G+S G     Y ++  A +A     G PL  R + + 
Sbjct: 111 QFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVH 170

Query: 60  LA 61
             
Sbjct: 171 WT 172

>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 = 56.5 bits (137), Expect = 4e-11
 Identities = 14/60 (23%), Positives = 25/60 (41%)

Query: 2   IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
           +    S        +L   + G+  G A L YE    A +A +Q +G+ L G  +++   
Sbjct: 202 LCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFC 261

>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 = 47.3 bits (113), Expect = 8e-08
 Identities = 12/62 (19%), Positives = 24/62 (38%), Gaps = 6/62 (9%)

Query: 1  MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
           +++L S++         Y    +  GTA +       A  A+  ++   L  R + +QL
Sbjct: 38 EVHDLLSDYELK------YCFVDKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQL 91

Query: 61 AA 62
            
Sbjct: 92 QP 93

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 95

 Score = 54.5 bits (132), Expect = 2e-11
 Identities = 22/63 (34%), Positives = 39/63 (61%), Gaps = 1/63 (1%)

Query: 1  MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
           + E+FS++GP+    + YD+ S RS G A + +E   DA +A ++ NG+ LDGR +++ 
Sbjct: 31 DLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVS 90

Query: 60 LAA 62
            +
Sbjct: 91 GPS 93

>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 = 54.6 bits (132), Expect = 2e-11
 Identities = 24/84 (28%), Positives = 38/84 (45%), Gaps = 16/84 (19%)

Query: 2  IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
          I + F+   P    ++   R       A + +  R DA++AMK  NG  LDG P+++ LA
Sbjct: 32 IEKEFNNIKPGAVERVKKIR-----DYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLA 86

Query: 62 ADVSVLENTVPRPVARGGRGGASG 85
                     +PV +   G +SG
Sbjct: 87 -----------KPVDKDSSGPSSG 99

>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 = 55.6 bits (134), Expect = 2e-11
 Identities = 18/67 (26%), Positives = 27/67 (40%), Gaps = 6/67 (8%)

Query: 1   MIYELFSEFGPLKSAKLH------YDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGR 54
            +  +F  +    S            + GR  G A +       A KA+K+ NG  L G+
Sbjct: 61  DLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGK 120

Query: 55  PMQIQLA 61
           PM +Q A
Sbjct: 121 PMVVQFA 127

>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 = 55.1 bits (133), Expect = 2e-11
 Identities = 14/61 (22%), Positives = 31/61 (50%), Gaps = 2/61 (3%)

Query: 2  IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
          +Y++F ++GP++  ++       + GTA ++YE   DA  A+   +G  +  R + +   
Sbjct: 25 MYDIFGKYGPIRQIRVGNT--PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYY 82

Query: 62 A 62
           
Sbjct: 83 N 83

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 54.1 bits (131), Expect = 3e-11
 Identities = 16/61 (26%), Positives = 33/61 (54%), Gaps = 1/61 (1%)

Query: 1  MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
          M+ + F+E G +  A +  + +G+S G   + +E    A +A +  NG+ L GR + +++
Sbjct: 24 MLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRI 82

Query: 61 A 61
           
Sbjct: 83 D 83

>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 = 54.1 bits (131), Expect = 3e-11
 Identities = 25/86 (29%), Positives = 38/86 (44%), Gaps = 12/86 (13%)

Query: 1  MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
          M+  +F  FG + +  L  D  +GRS G   + +     A +A++Q NG  L GRPM++ 
Sbjct: 21 MLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVG 80

Query: 60 LAADVSVLENTVPRPVARGGRGGASG 85
                            GG G +SG
Sbjct: 81 HV-----------TERLDGGSGPSSG 95

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 55.2 bits (133), Expect = 3e-11
 Identities = 16/62 (25%), Positives = 30/62 (48%), Gaps = 1/62 (1%)

Query: 1   MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
           +++  F  FG +   ++  D  + +  G A + +E   DA  A+   N   L GR +++ 
Sbjct: 79  VLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN 138

Query: 60  LA 61
           LA
Sbjct: 139 LA 140

>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 = 55.6 bits (134), Expect = 3e-11
 Identities = 20/61 (32%), Positives = 33/61 (54%), Gaps = 1/61 (1%)

Query: 2   IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
           I E F ++G +K+  L+ DR +G S G A + YE    A+ A +  NG  + G+ +Q+  
Sbjct: 89  IQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW 148

Query: 61  A 61
            
Sbjct: 149 C 149

>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 = 53.8 bits (130), Expect = 3e-11
 Identities = 14/62 (22%), Positives = 31/62 (50%), Gaps = 1/62 (1%)

Query: 1  MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
           +Y +FS++G +    +  D+ + +S G A +++  +  A    +  N   L GR ++  
Sbjct: 32 DLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKAS 91

Query: 60 LA 61
          +A
Sbjct: 92 IA 93

>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 = 54.2 bits (131), Expect = 4e-11
 Identities = 17/64 (26%), Positives = 30/64 (46%), Gaps = 3/64 (4%)

Query: 1  MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
          +I +LFS+ GP KS K+  +  S       +  +    DA  A+   NG  + G+ +++ 
Sbjct: 31 LILQLFSQIGPCKSCKMITEHTSNDPYCFVE--FYEHRDAAAALAAMNGRKILGKEVKVN 88

Query: 60 LAAD 63
           A  
Sbjct: 89 WATT 92

>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 = 53.3 bits (129), Expect = 4e-11
 Identities = 16/62 (25%), Positives = 30/62 (48%), Gaps = 1/62 (1%)

Query: 1  MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
          +++  F  FG +   ++  D  + +  G A + +E   DA  A+   N   L GR +++ 
Sbjct: 23 VLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN 82

Query: 60 LA 61
          LA
Sbjct: 83 LA 84

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 54.0 bits (130), Expect = 4e-11
 Identities = 14/55 (25%), Positives = 28/55 (50%), Gaps = 1/55 (1%)

Query: 1  MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGR 54
           +  LFS+ G + + +   D  +G++ G   +     +DA K +K ++G  LD +
Sbjct: 28 ALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLK 82

>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 = 53.8 bits (130), Expect = 4e-11
 Identities = 18/83 (21%), Positives = 32/83 (38%), Gaps = 11/83 (13%)

Query: 4  ELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA 62
          +LFS +GPL       D  + +  G A + +     A+KA  + +G    GR + +  + 
Sbjct: 27 KLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPST 86

Query: 63 DVSVLENTVPRPVARGGRGGASG 85
                    +       G +SG
Sbjct: 87 ---------IKK-EASQSGPSSG 99

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 55.0 bits (133), Expect = 9e-11
 Identities = 25/97 (25%), Positives = 36/97 (37%), Gaps = 14/97 (14%)

Query: 1   MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
            I + F+ FGP+KS  + +D  + +  G A + YE    A  A++Q N V L GR +   
Sbjct: 44  TIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNI--- 100

Query: 60  LAADVSVLENTVPRPVARGGRGGASGGYRNGTAPTYR 96
                      V RP   G                 R
Sbjct: 101 ----------KVGRPSNIGQAQPIIDQLAEEARAFNR 127

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 51.5 bits (124), Expect = 2e-09
 Identities = 18/62 (29%), Positives = 30/62 (48%), Gaps = 1/62 (1%)

Query: 1   MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
            I  +F  FG +KSA L  D  +G+  G   + YE+   +  A+   N   L G+ +++ 
Sbjct: 141 DIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVG 200

Query: 60  LA 61
            A
Sbjct: 201 KA 202

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 55.7 bits (133), Expect = 9e-11
 Identities = 20/61 (32%), Positives = 33/61 (54%), Gaps = 2/61 (3%)

Query: 1  MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
           +Y +FS+FG +    +   RS +  G A +I++  S A  A++   G P   +PM+IQ 
Sbjct: 29 SLYAIFSQFGQILDILVS--RSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY 86

Query: 61 A 61
          A
Sbjct: 87 A 87

>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 = 41.4 bits (96), Expect = 1e-05
 Identities = 14/62 (22%), Positives = 23/62 (37%), Gaps = 5/62 (8%)

Query: 1   MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPL-DGRPMQIQ 59
           M+  LF++F   K  +L   R       A + ++    A  A     G  +     M+I 
Sbjct: 223 MLSMLFNQFPGFKEVRLVPGRH----DIAFVEFDNEVQAGAARDALQGFKITQNNAMKIS 278

Query: 60  LA 61
            A
Sbjct: 279 FA 280

>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 = 52.5 bits (127), Expect = 1e-10
 Identities = 18/62 (29%), Positives = 29/62 (46%), Gaps = 1/62 (1%)

Query: 1  MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
           +   F +F    S  + +D  +G S G   + +  + DA  AM    G  L+GRP++I 
Sbjct: 17 TLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRIN 76

Query: 60 LA 61
           A
Sbjct: 77 WA 78

>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 = 52.3 bits (126), Expect = 1e-10
 Identities = 14/61 (22%), Positives = 27/61 (44%), Gaps = 1/61 (1%)

Query: 2  IYELFSEFGPLKSA-KLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
          I + F  +  +  +  L Y+  G   G A + +E R +A  A+   N  P+  R +++  
Sbjct: 32 ILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSG 91

Query: 61 A 61
           
Sbjct: 92 P 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 = 52.2 bits (126), Expect = 2e-10
 Identities = 19/62 (30%), Positives = 32/62 (51%), Gaps = 1/62 (1%)

Query: 1  MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
           + ELF  FG +    L  D+ +G+S G A + + RR DA +A+   +G   D   + ++
Sbjct: 31 DLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVE 90

Query: 60 LA 61
           A
Sbjct: 91 WA 92

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 52.3 bits (126), Expect = 2e-10
 Identities = 12/61 (19%), Positives = 20/61 (32%)

Query: 1   MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
            +  +   FG + S ++  D SG S G      E        +  +NG  +   P     
Sbjct: 41  ELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAP 100

Query: 61  A 61
            
Sbjct: 101 T 101

>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 = 53.4 bits (128), Expect = 3e-10
 Identities = 21/100 (21%), Positives = 39/100 (39%), Gaps = 9/100 (9%)

Query: 1   MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
            ++ LF  +G ++  K+ +++       A +     + A  AM   NG  L G+P++I L
Sbjct: 20  SLFILFGVYGDVQRVKILFNKKE----NALVQMADGNQAQLAMSHLNGHKLHGKPIRITL 75

Query: 61  AADVSVLENTVPRPVARGGRGGASGGYRNGTAPTYRPRGG 100
           +         V  P       G +  Y N     ++  G 
Sbjct: 76  SK-----HQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGS 110

>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 = 36.0 bits (83), Expect = 7e-04
 Identities = 8/62 (12%), Positives = 23/62 (37%), Gaps = 4/62 (6%)

Query: 1   MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPL-DGRPMQIQ 59
            +  LFS  G +      + +       A +      +A++A+   +   L +   +++ 
Sbjct: 136 DLKVLFSSNGGVVKGFKFFQKDR---KMALIQMGSVEEAVQALIDLHNHDLGENHHLRVS 192

Query: 60  LA 61
            +
Sbjct: 193 FS 194

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 51.3 bits (123), Expect = 3e-10
 Identities = 11/63 (17%), Positives = 29/63 (46%), Gaps = 4/63 (6%)

Query: 2  IYELFSEFGPLKSAK-LHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
          +  L  ++G ++S + ++ D     +    + Y  +  A +A+ + NG  L+   +++  
Sbjct: 32 LDSLLVQYGVVESCEQVNTDSETAVVN---VTYSSKDQARQALDKLNGFQLENFTLKVAY 88

Query: 61 AAD 63
            D
Sbjct: 89 IPD 91

>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 = 51.7 bits (124), Expect = 4e-10
 Identities = 19/85 (22%), Positives = 38/85 (44%), Gaps = 3/85 (3%)

Query: 2   IYELFSEFGPLKSA-KLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
           + +        ++A  +  D +G+ LG A + ++   DA K+ +  +   L+GR   + +
Sbjct: 32  VLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHV 90

Query: 61  AADVSVLENTVPRPVARGGRGGASG 85
                + E     P A+G  G +SG
Sbjct: 91  VTLEDMRE-IEKNPPAQGKSGPSSG 114

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 51.6 bits (124), Expect = 4e-10
 Identities = 15/60 (25%), Positives = 28/60 (46%), Gaps = 1/60 (1%)

Query: 3   YELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
              F  FG + SAK+  D+ +  S     + ++    A  A+K  NG  +  + +++QL 
Sbjct: 58  ASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLK 117

>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 = 51.2 bits (123), Expect = 5e-10
 Identities = 22/92 (23%), Positives = 37/92 (40%), Gaps = 18/92 (19%)

Query: 1   MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYN------GVPLDG 53
            + E+  +FG LK  ++     +  S G A   +  +  A K +   +      G+ LDG
Sbjct: 31  ALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDG 90

Query: 54  RPMQIQLAADVSVLENTVPRPVARGGRGGASG 85
           R +++ LA         V R       G +SG
Sbjct: 91  RQLKVDLA---------VTRD--EAASGPSSG 111

>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 = 51.7 bits (124), Expect = 5e-10
 Identities = 22/61 (36%), Positives = 39/61 (63%), Gaps = 1/61 (1%)

Query: 2   IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
           + E+FS++GP+    + YD+ S RS G A + +E   DA +A ++ NG+ LDGR +++  
Sbjct: 63  LREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDF 122

Query: 61  A 61
           +
Sbjct: 123 S 123

>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 = 50.7 bits (122), Expect = 7e-10
 Identities = 19/86 (22%), Positives = 39/86 (45%), Gaps = 15/86 (17%)

Query: 4  ELFSEFGPLKSAKLHYDRSG----RSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
           +FS+ G +KS  +   ++      S+G   + Y++   A KA+KQ  G  +DG  ++++
Sbjct: 24 GVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVR 83

Query: 60 LAADVSVLENTVPRPVARGGRGGASG 85
          ++               +   G +SG
Sbjct: 84 IS-----------ERATKPASGPSSG 98

>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 = 52.2 bits (126), Expect = 7e-10
 Identities = 10/61 (16%), Positives = 24/61 (39%), Gaps = 1/61 (1%)

Query: 1  MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
           +    SE        +   R+G +     + +E   D  KA+ +  G+ + G  ++++ 
Sbjct: 29 ELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEK 87

Query: 61 A 61
           
Sbjct: 88 P 88

>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 = 44.5 bits (106), Expect = 4e-07
 Identities = 13/61 (21%), Positives = 30/61 (49%), Gaps = 4/61 (6%)

Query: 1   MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
            + E+F +   ++       + G+S G A + ++  +DA K +++  G  +DGR + +  
Sbjct: 115 ELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY 170

Query: 61  A 61
            
Sbjct: 171 T 171

>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 = 50.7 bits (122), Expect = 8e-10
 Identities = 18/80 (22%), Positives = 32/80 (40%), Gaps = 9/80 (11%)

Query: 4   ELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA 62
            +F ++G +    +  +  +    G A + +  R DA  A    +G  LDGR +++Q+A 
Sbjct: 32  RVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVAR 91

Query: 63  DVSVLENTVPRPVARGGRGG 82
                     R    G   G
Sbjct: 92  Y--------GRRDLSGPSSG 103

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Length = 105

 Score = 50.4 bits (121), Expect = 8e-10
 Identities = 13/63 (20%), Positives = 26/63 (41%), Gaps = 3/63 (4%)

Query: 2  IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNG---VPLDGRPMQI 58
          +  LF  FG +    +     G S G A + +   ++A  A+   +G   +P     + +
Sbjct: 32 VLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVV 91

Query: 59 QLA 61
          + A
Sbjct: 92 KFA 94

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 49.9 bits (120), Expect = 1e-09
 Identities = 20/86 (23%), Positives = 37/86 (43%), Gaps = 12/86 (13%)

Query: 1   MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
           +++  F  FG +   ++  D  + +  G A + +E   DA  A+   N   L GR +++ 
Sbjct: 28  VLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN 87

Query: 60  LAADVSVLENTVPRPVARGGRGGASG 85
           LA           +P+     G +SG
Sbjct: 88  LA-----------KPMRIKESGPSSG 102

>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 = 49.9 bits (120), Expect = 1e-09
 Identities = 22/83 (26%), Positives = 37/83 (44%), Gaps = 12/83 (14%)

Query: 4   ELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA 62
           ++FS++G +    +  DR + RS G   + +E   DA  AM   NG  +DGR +++  A 
Sbjct: 31  QVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQA- 89

Query: 63  DVSVLENTVPRPVARGGRGGASG 85
                        +    G +SG
Sbjct: 90  ----------GKSSDNRSGPSSG 102

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 50.1 bits (120), Expect = 2e-09
 Identities = 20/98 (20%), Positives = 38/98 (38%), Gaps = 18/98 (18%)

Query: 1   MIYELFSEFGPLKSA--------KLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPL 51
            + + F + G +K+          L+ DR +G+  G A + ++    A  A+  ++G   
Sbjct: 23  SVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEF 82

Query: 52  DGRPMQIQLAADVSVLENTVPRPVARGGRGGASGGYRN 89
            G P+++  A           R     G G   GG  +
Sbjct: 83  SGNPIKVSFA---------TRRADFNRGGGNGRGGLEH 111

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 49.6 bits (119), Expect = 2e-09
 Identities = 24/83 (28%), Positives = 40/83 (48%), Gaps = 7/83 (8%)

Query: 2   IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
           + ++FSE GP+ S +L YDR +G+  G     Y+ +  A+ AM+  NG    GR +++  
Sbjct: 25  LKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDN 84

Query: 61  AADVSVLENTVPRPVARGGRGGA 83
           AA          +   +    GA
Sbjct: 85  AASEK------NKEELKSLGTGA 101

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 48.9 bits (117), Expect = 2e-09
 Identities = 15/54 (27%), Positives = 30/54 (55%), Gaps = 1/54 (1%)

Query: 1  MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGR 54
          +I+++FS+FG + +     +  G++ G   L Y   + A+ A+K  +G  LD +
Sbjct: 23 VIHKIFSKFGKITNDFYPEE-DGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ 75

>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 = 49.2 bits (118), Expect = 2e-09
 Identities = 15/69 (21%), Positives = 32/69 (46%), Gaps = 9/69 (13%)

Query: 2  IYELFSEFGPLKSA--------KLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLD 52
          + + F + G +K+          L+ DR +G+  G A + ++    A  A+  ++G    
Sbjct: 30 VADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFS 89

Query: 53 GRPMQIQLA 61
          G P+++  A
Sbjct: 90 GNPIKVSFA 98

>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 = 49.2 bits (118), Expect = 3e-09
 Identities = 13/58 (22%), Positives = 33/58 (56%), Gaps = 1/58 (1%)

Query: 4  ELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
          ++F +FG +   ++ ++    S G   + +E  +DA +A ++ +G  ++GR +++  A
Sbjct: 34 QMFGQFGKILDVEIIFNE-RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA 90

>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 = 50.2 bits (120), Expect = 3e-09
 Identities = 18/61 (29%), Positives = 33/61 (54%), Gaps = 1/61 (1%)

Query: 2   IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
           +  +F ++G +    +  DR +  S G A + +  + DA  AM   +G  LDGR +++Q+
Sbjct: 87  LRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQM 146

Query: 61  A 61
           A
Sbjct: 147 A 147

>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 = 48.9 bits (117), Expect = 4e-09
 Identities = 15/60 (25%), Positives = 30/60 (50%), Gaps = 1/60 (1%)

Query: 3   YELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
            ++F  FG + SAK+  D+ +  S     + Y+    A  A++  NG  +  + +++QL 
Sbjct: 43  LQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK 102

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 48.9 bits (117), Expect = 5e-09
 Identities = 13/58 (22%), Positives = 33/58 (56%), Gaps = 1/58 (1%)

Query: 4   ELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
           ++F +FG +   ++ ++    S G   + +E  +DA +A ++ +G  ++GR +++  A
Sbjct: 48  QMFGQFGKILDVEIIFNE-RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA 104

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 48.5 bits (116), Expect = 5e-09
 Identities = 20/65 (30%), Positives = 30/65 (46%), Gaps = 3/65 (4%)

Query: 2  IYELFSEFGPLKSAKLHYDR--SGRSLGTADLIYERRSDAIKAMKQ-YNGVPLDGRPMQI 58
          I ELFS FG LK+ +L      +G   G   + +  + DA KA     +   L GR + +
Sbjct: 32 IRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVL 91

Query: 59 QLAAD 63
          + A  
Sbjct: 92 EWADS 96

>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 = 50.5 bits (120), Expect = 5e-09
 Identities = 18/105 (17%), Positives = 35/105 (33%), Gaps = 6/105 (5%)

Query: 2   IYELFSEFGP--LKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
           + E     G   +   K   +R +G+S G A +     + + K M       L G+   +
Sbjct: 85  LTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVV 144

Query: 59  QLAADVSVLENTV---PRPVARGGRGGASGGYRNGTAPTYRPRGG 100
                  + +  +       +    G    G   G++    P+GG
Sbjct: 145 TPVNKQFLSQFEMQSRKTTQSGQMSGEGKAGPPGGSSRAAFPQGG 189

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 49.9 bits (120), Expect = 5e-09
 Identities = 16/64 (25%), Positives = 29/64 (45%), Gaps = 3/64 (4%)

Query: 1   MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNG---VPLDGRPMQ 57
            I  +FS FG ++  ++     G S G A + +  R+ A  A+K  +    +     PM 
Sbjct: 111 DIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMV 170

Query: 58  IQLA 61
           ++ A
Sbjct: 171 VKFA 174

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 45.3 bits (108), Expect = 3e-07
 Identities = 15/66 (22%), Positives = 31/66 (46%), Gaps = 6/66 (9%)

Query: 2  IYELFSEFGPLKSAKLHYDRSG---RSLGTADLIYERRSDAIKAMKQYNGVPLDG---RP 55
          + ELF ++G +    +  DRS    +S G   + +  R  A++A    + + +      P
Sbjct: 20 LRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHP 79

Query: 56 MQIQLA 61
          +Q++ A
Sbjct: 80 IQMKPA 85

>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 = 48.5 bits (116), Expect = 6e-09
 Identities = 21/65 (32%), Positives = 31/65 (47%), Gaps = 4/65 (6%)

Query: 1  MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNG---VPLDGRPM 56
           +  LF EFG +    +  DR +G   G A L Y  R  A+KA    +    +P   RP+
Sbjct: 29 DLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPI 88

Query: 57 QIQLA 61
          Q++ A
Sbjct: 89 QVKPA 93

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 50.4 bits (121), Expect = 6e-09
 Identities = 11/62 (17%), Positives = 28/62 (45%), Gaps = 1/62 (1%)

Query: 1   MIYELFSEFGPLKSA-KLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
            I +L  +   +  + +L   R   S   A +    + DA   +++ NG+ ++G  +  +
Sbjct: 133 NIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTK 192

Query: 60  LA 61
           ++
Sbjct: 193 VS 194

>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 = 48.8 bits (117), Expect = 3e-08
 Identities = 14/63 (22%), Positives = 29/63 (46%), Gaps = 3/63 (4%)

Query: 1   MIYELFSEFGPLKSAKLHYDR--SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
           ++ E F  FG ++   +   +     +   A +++E +  A +A+ Q N   L  R + +
Sbjct: 227 LLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISV 285

Query: 59  QLA 61
            LA
Sbjct: 286 SLA 288

>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 = 44.6 bits (106), Expect = 8e-07
 Identities = 9/63 (14%), Positives = 25/63 (39%), Gaps = 2/63 (3%)

Query: 1   MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
            +Y+ F   GP+    +      ++   A + + R   A+ A+ + + V +    + +  
Sbjct: 57  KVYKYFKHCGPIIHVDVADS-LKKNFRFARIEFARYDGALAAITKTHKV-VGQNEIIVSH 114

Query: 61  AAD 63
             +
Sbjct: 115 LTE 117

>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 = 47.6 bits (114), Expect = 1e-08
 Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 2/63 (3%)

Query: 1  MIYELFSEFGP-LKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
          ++Y+ FS FG  L++ K+  D  +G S G A + +     +  A++  NG  L  RP+ +
Sbjct: 21 LLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITV 80

Query: 59 QLA 61
            A
Sbjct: 81 SYA 83

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 48.2 bits (115), Expect = 1e-08
 Identities = 18/59 (30%), Positives = 32/59 (54%), Gaps = 1/59 (1%)

Query: 4   ELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
            +F ++G +    +  DR +  S G A + +  + DA  AM   +G  LDGR +++Q+A
Sbjct: 66  RVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA 124

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 47.4 bits (113), Expect = 2e-08
 Identities = 15/54 (27%), Positives = 30/54 (55%), Gaps = 1/54 (1%)

Query: 1  MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGR 54
          +I+++FS+FG + +     +  G++ G   L Y   + A+ A+K  +G  LD +
Sbjct: 37 VIHKIFSKFGKITNDFYPEE-DGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ 89

>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 = 47.2 bits (113), Expect = 2e-08
 Identities = 20/87 (22%), Positives = 36/87 (41%), Gaps = 10/87 (11%)

Query: 3  YELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA 62
          Y+ FS FG + S K+  D    S G   + +E +  A +A+++ NG+ L+ R + +    
Sbjct: 23 YDTFSAFGNILSCKVVCDE-NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRF- 80

Query: 63 DVSVLENTVPRPVARGGRGGASGGYRN 89
                    R       G  +  + N
Sbjct: 81 --------KSRKEREAELGARAKEFTN 99

>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 = 46.6 bits (111), Expect = 3e-08
 Identities = 19/93 (20%), Positives = 37/93 (39%), Gaps = 20/93 (21%)

Query: 2   IYELFSEFGPLKS--------AKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLD 52
           + + F + G +K           ++ D+ +G+  G A + YE    A  A++ ++G    
Sbjct: 32  LADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQ 91

Query: 53  GRPMQIQLAADVSVLENTVPRPVARGGRGGASG 85
           G  +++ LA           R       G +SG
Sbjct: 92  GSKLKVSLA-----------RKKPPMNSGPSSG 113

>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 = 47.8 bits (113), Expect = 5e-08
 Identities = 9/61 (14%), Positives = 24/61 (39%), Gaps = 4/61 (6%)

Query: 1  MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
           ++ +F  +G ++  K    + G     A +         +A+   N   + G+ M + +
Sbjct: 21 RVFNVFCLYGNVEKVKFMKSKPG----AAMVEMADGYAVDRAITHLNNNFMFGQKMNVCV 76

Query: 61 A 61
          +
Sbjct: 77 S 77

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 40.5 bits (94), Expect = 2e-05
 Identities = 8/59 (13%), Positives = 20/59 (33%), Gaps = 1/59 (1%)

Query: 1   MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
             +E+  E G  +   +           +  L ++ +SDA++ +   N   +       
Sbjct: 139 NFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPY 197

>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 = 45.7 bits (109), Expect = 5e-08
 Identities = 19/59 (32%), Positives = 32/59 (54%), Gaps = 1/59 (1%)

Query: 3  YELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
           + FS FG + SAK+  +  GRS G   + +    +A KA+ + NG  +  +P+ + LA
Sbjct: 33 RKAFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALA 90

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 45.4 bits (108), Expect = 7e-08
 Identities = 11/61 (18%), Positives = 21/61 (34%), Gaps = 5/61 (8%)

Query: 1  MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
           +  LF  FG +   K + ++     G   + Y+    A   +      P  GR ++   
Sbjct: 43 DLIPLFQNFGFILDFKHYPEK-----GCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGW 97

Query: 61 A 61
           
Sbjct: 98 G 98

>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 = 45.2 bits (108), Expect = 7e-08
 Identities = 10/58 (17%), Positives = 24/58 (41%), Gaps = 1/58 (1%)

Query: 1  MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQ 57
           + +L   +G + S K   D+ + +  G   + ++  S A KA+       +  +  +
Sbjct: 21 DLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK 78

>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 = 46.9 bits (111), Expect = 9e-08
 Identities = 16/66 (24%), Positives = 32/66 (48%), Gaps = 4/66 (6%)

Query: 1   MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
            ++ LF  +G ++  K+ +++       A +     + A  AM   NG  L G+P++I L
Sbjct: 51  SLFILFGVYGDVQRVKILFNKKE----NALVQMADGNQAQLAMSHLNGHKLHGKPIRITL 106

Query: 61  AADVSV 66
           +   +V
Sbjct: 107 SKHQNV 112

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 45.1 bits (107), Expect = 1e-07
 Identities = 11/60 (18%), Positives = 20/60 (33%), Gaps = 7/60 (11%)

Query: 2  IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVP--LDGRPMQIQ 59
          + E   EFGP+    +   +       A + +E    A  A+         + G P  + 
Sbjct: 38 LVEALQEFGPISYVVVMPKK-----RQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVN 92

>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 = 44.6 bits (106), Expect = 1e-07
 Identities = 15/79 (18%), Positives = 32/79 (40%), Gaps = 15/79 (18%)

Query: 1  MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
           + E+F +   ++          G+S G A + ++  +DA K +++  G  +DGR + + 
Sbjct: 32 ELKEVFEDALEIR-----LVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLY 86

Query: 60 LAADVSVLENTVPRPVARG 78
                       +   RG
Sbjct: 87 YTG---------EKGGTRG 96

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score = 44.1 bits (105), Expect = 2e-07
 Identities = 13/58 (22%), Positives = 28/58 (48%), Gaps = 2/58 (3%)

Query: 4  ELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
            F+ +G +K  K+  DR+G S G   + +    D  K ++  + +   G+ +++  A
Sbjct: 28 SFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPA 83

>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 = 44.2 bits (105), Expect = 2e-07
 Identities = 13/85 (15%), Positives = 31/85 (36%), Gaps = 16/85 (18%)

Query: 1   MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
           ++ + FS FG +   ++  ++     G + + +     A  A+   NG  ++G  ++   
Sbjct: 41  LMRQTFSPFGQIMEIRVFPEK-----GYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYW 95

Query: 61  AADVSVLENTVPRPVARGGRGGASG 85
                       +       G +SG
Sbjct: 96  G-----------KESPDMTSGPSSG 109

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score = 46.2 bits (110), Expect = 2e-07
 Identities = 16/61 (26%), Positives = 26/61 (42%), Gaps = 5/61 (8%)

Query: 1  MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
              LF  +G      ++ DR     G   +  E R+ A  A  + +G  L  RP++I+ 
Sbjct: 38 DFKRLFERYGEPSEVFINRDR-----GFGFIRLESRTLAEIAKAELDGTILKSRPLRIRF 92

Query: 61 A 61
          A
Sbjct: 93 A 93

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score = 42.8 bits (101), Expect = 4e-06
 Identities = 15/63 (23%), Positives = 32/63 (50%), Gaps = 1/63 (1%)

Query: 1   MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQ-YNGVPLDGRPMQIQ 59
           ++ + FS+FGP++ A +  D  GR+ G   + +  +  A KA+++  +G  L     +  
Sbjct: 112 LLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPV 171

Query: 60  LAA 62
           +  
Sbjct: 172 IVE 174

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 44.2 bits (105), Expect = 2e-07
 Identities = 15/62 (24%), Positives = 26/62 (41%), Gaps = 2/62 (3%)

Query: 1  MIYELFSEFG-PLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
           I   F+  G  + S K+  +R +G   G   + +   + A K + + NG PL G     
Sbjct: 25 FISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAK 84

Query: 59 QL 60
          + 
Sbjct: 85 RF 86

>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 = 43.7 bits (104), Expect = 3e-07
 Identities = 12/61 (19%), Positives = 22/61 (36%), Gaps = 3/61 (4%)

Query: 4  ELFSEFGP--LKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
          E     G   +   K   +R +G+S G A +     + + K M       L G+   +  
Sbjct: 20 EAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTP 79

Query: 61 A 61
          +
Sbjct: 80 S 80

>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 = 43.8 bits (104), Expect = 3e-07
 Identities = 10/61 (16%), Positives = 24/61 (39%), Gaps = 1/61 (1%)

Query: 1  MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
           +    SE        +   R+G +     + +E   D  KA+ +  G+ + G  ++++ 
Sbjct: 33 ELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEK 91

Query: 61 A 61
           
Sbjct: 92 P 92

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 43.6 bits (103), Expect = 4e-07
 Identities = 9/62 (14%), Positives = 22/62 (35%), Gaps = 1/62 (1%)

Query: 2  IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
          I E   + G + + ++         G+  ++++    A K ++   G       + I   
Sbjct: 28 IKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVET-PGQKYKETDLLILFK 86

Query: 62 AD 63
           D
Sbjct: 87 DD 88

>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 = 43.3 bits (103), Expect = 4e-07
 Identities = 16/59 (27%), Positives = 30/59 (50%), Gaps = 2/59 (3%)

Query: 4  ELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
          ELFS+FG + + KL YDR + +  G   +  +      +A+ + +     GR +++  A
Sbjct: 20 ELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQ-EESVSEAIAKLDNTDFMGRTIRVTEA 77

>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 = 43.4 bits (103), Expect = 4e-07
 Identities = 19/61 (31%), Positives = 33/61 (54%), Gaps = 7/61 (11%)

Query: 1  MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
          ++ + FS+FG L+  K   D        A + ++ R  A+KAM++ NG  L+G  ++I  
Sbjct: 27 ILEKAFSQFGKLERVKKLKD-------YAFIHFDERDGAVKAMEEMNGKDLEGENIEIVF 79

Query: 61 A 61
          A
Sbjct: 80 A 80

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 44.5 bits (105), Expect = 4e-07
 Identities = 12/64 (18%), Positives = 29/64 (45%), Gaps = 3/64 (4%)

Query: 1   MIYELFSEFGP--LKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQ 57
            + ++    G   +   K   +R +G+S G A+++    +   K ++   G  L+G  + 
Sbjct: 71  QLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVD 130

Query: 58  IQLA 61
           ++ A
Sbjct: 131 VRPA 134

>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 = 43.4 bits (103), Expect = 5e-07
 Identities = 18/82 (21%), Positives = 34/82 (41%), Gaps = 16/82 (19%)

Query: 4  ELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD 63
          +LF ++G      +H D+     G   +  E R+ A  A  + + +PL G+ ++++ A  
Sbjct: 34 KLFEKYGKAGEVFIHKDK-----GFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFA-- 86

Query: 64 VSVLENTVPRPVARGGRGGASG 85
                      A    G +SG
Sbjct: 87 ---------CHSASLTSGPSSG 99

>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 = 43.0 bits (102), Expect = 6e-07
 Identities = 20/83 (24%), Positives = 31/83 (37%), Gaps = 12/83 (14%)

Query: 4   ELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA 62
            L   F     A++  DR +G S G   + +    DA  A +      +DG  + +  A 
Sbjct: 31  TLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWA- 89

Query: 63  DVSVLENTVPRPVARGGRGGASG 85
                     +P   GG G +SG
Sbjct: 90  ----------KPKGEGGSGPSSG 102

>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 = 42.9 bits (101), Expect = 7e-07
 Identities = 9/62 (14%), Positives = 21/62 (33%), Gaps = 7/62 (11%)

Query: 2  IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVP--LDGRPMQIQ 59
          + E   +FG +    +   +       A + +E    A + +     VP  + G+     
Sbjct: 32 LVEALEKFGTICYVMMMPFK-----RQALVEFENIDSAKECVTFAADVPVYIAGQQAFFN 86

Query: 60 LA 61
           +
Sbjct: 87 YS 88

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score = 42.7 bits (101), Expect = 9e-07
 Identities = 14/63 (22%), Positives = 33/63 (52%), Gaps = 3/63 (4%)

Query: 1  MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
           + E+F +   +K   +  +++G+S G A + +    DA +A+   N   ++GR ++++L
Sbjct: 31 TLQEVFEKATFIK---VPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLEL 87

Query: 61 AAD 63
             
Sbjct: 88 QGP 90

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 124

 Score = 42.9 bits (101), Expect = 9e-07
 Identities = 13/86 (15%), Positives = 35/86 (40%), Gaps = 4/86 (4%)

Query: 2   IYELFSEFGPLKSA-KLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
           + + F +   ++ +  + Y  +G++ G   + +   +D   A+   +   +  R +Q+  
Sbjct: 42  VIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHP 100

Query: 61  AADVSVLENTVPRPVARGGRGGASGG 86
                +LE      + +  + G S G
Sbjct: 101 ITKKGMLE--KIDMIRKRLQSGPSSG 124

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 42.7 bits (101), Expect = 1e-06
 Identities = 15/61 (24%), Positives = 30/61 (49%), Gaps = 7/61 (11%)

Query: 1   MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
            + E+F  FGP+K  K+         G A + +E    A KA+++ +G     +P+++  
Sbjct: 47  ELNEIFGPFGPMKEVKI-------LNGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVY 99

Query: 61  A 61
           +
Sbjct: 100 S 100

>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 = 42.0 bits (99), Expect = 1e-06
 Identities = 11/60 (18%), Positives = 25/60 (41%), Gaps = 6/60 (10%)

Query: 2  IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
          +++L  ++       L Y    R+  TA +       A  A++ ++     G+ + +QL 
Sbjct: 22 VHDLLKDYD------LKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQ 75

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 41.5 bits (98), Expect = 2e-06
 Identities = 10/60 (16%), Positives = 28/60 (46%), Gaps = 6/60 (10%)

Query: 1  MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQ-YNGVPLDGRPMQIQ 59
           +   F +FG +++  +   +       A + +  R  A  A ++ +N + ++GR + ++
Sbjct: 28 DLRNHFYQFGEIRTITVVQRQ-----QCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVK 82

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 41.5 bits (98), Expect = 2e-06
 Identities = 18/82 (21%), Positives = 31/82 (37%), Gaps = 18/82 (21%)

Query: 4  ELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD 63
            F E+GP+    +           A +  ER  DA++A++  +     G+ M +QL+  
Sbjct: 29 AKFEEYGPVIECDIVK-------DYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLS-- 79

Query: 64 VSVLENTVPRPVARGGRGGASG 85
                       R   G +SG
Sbjct: 80 ---------TSRLRTASGPSSG 92

>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 = 41.5 bits (98), Expect = 3e-06
 Identities = 17/81 (20%), Positives = 31/81 (38%), Gaps = 10/81 (12%)

Query: 2   IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
           I ++F ++G ++   L   R G     A + +E   DA  A+   +G   DG  ++++  
Sbjct: 39  IEDVFYKYGAIRDIDLKNRRGGP--PFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFP 96

Query: 62  ADVSVLENTVPRPVARGGRGG 82
                      R    G   G
Sbjct: 97  --------RSGRGTGSGPSSG 109

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 41.7 bits (98), Expect = 3e-06
 Identities = 15/85 (17%), Positives = 30/85 (35%), Gaps = 8/85 (9%)

Query: 2   IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
           + + F       +  L  D  GR+ G   + +    D  +A+K  N + +  R +++  A
Sbjct: 33  VRDFFHGLRV-DAVHLLKDHVGRNNGNGLVKFLSPQDTFEALK-RNRMLMIQRYVEVSPA 90

Query: 62  ADVSVLENTVPRPVARGGRGGASGG 86
            +   +              G S G
Sbjct: 91  TERQWVA------AGGHITSGPSSG 109

>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 = 41.1 bits (97), Expect = 3e-06
 Identities = 13/61 (21%), Positives = 28/61 (45%), Gaps = 5/61 (8%)

Query: 1  MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
          ++   FS FG +    +   R       A + YE+   A +A+ + NG  ++   +++ +
Sbjct: 29 LLRGAFSPFGNIIDLSMDPPR-----NCAFVTYEKMESADQAVAELNGTQVESVQLKVNI 83

Query: 61 A 61
          A
Sbjct: 84 A 84

>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 = 41.5 bits (98), Expect = 3e-06
 Identities = 16/61 (26%), Positives = 28/61 (45%), Gaps = 2/61 (3%)

Query: 2   IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
           + + FS  G ++  ++  DR S RS G A + +        A+    G  L G P+ +Q 
Sbjct: 42  LEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGL-TGQRLLGVPIIVQA 100

Query: 61  A 61
           +
Sbjct: 101 S 101

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 41.2 bits (97), Expect = 3e-06
 Identities = 11/69 (15%), Positives = 28/69 (40%), Gaps = 7/69 (10%)

Query: 2  IYELFSEFG--PLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVP----LDGR 54
          I    S +    + + +L  D+ + ++ G A +      DA + ++    +     +DG+
Sbjct: 26 IMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGK 85

Query: 55 PMQIQLAAD 63
           + +  A  
Sbjct: 86 TIGVDFAKS 94

>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 = 41.0 bits (96), Expect = 4e-06
 Identities = 15/60 (25%), Positives = 22/60 (36%), Gaps = 5/60 (8%)

Query: 2  IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
          I E FS FG L    L          TA + +    +A KA +          P+ ++ A
Sbjct: 27 IQETFSRFGSLGRVLLPEGG-----ITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWA 81

>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 = 41.0 bits (96), Expect = 5e-06
 Identities = 17/63 (26%), Positives = 30/63 (47%), Gaps = 4/63 (6%)

Query: 3  YELFSEFGPLKSAKLHYDR----SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
           E F +FG +    ++       S     +A + Y R  DA++A++  N V +DGR ++ 
Sbjct: 36 PEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKA 95

Query: 59 QLA 61
           L 
Sbjct: 96 SLG 98

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 40.4 bits (95), Expect = 5e-06
 Identities = 9/60 (15%), Positives = 24/60 (40%), Gaps = 2/60 (3%)

Query: 2  IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
          + E  +   P  + ++  +  G   G   + +    +  +A+K  N   + GR +++   
Sbjct: 27 VMEFLAPLKP-VAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFRE 84

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 41.0 bits (96), Expect = 5e-06
 Identities = 11/62 (17%), Positives = 21/62 (33%), Gaps = 7/62 (11%)

Query: 2  IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQY--NGVPLDGRPMQIQ 59
          +  L   FG + +  +   +       A +       A   +  Y      L G+P+ IQ
Sbjct: 33 VISLGLPFGKVTNLLMLKGK-----NQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQ 87

Query: 60 LA 61
           +
Sbjct: 88 FS 89

>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 = 41.4 bits (96), Expect = 8e-06
 Identities = 9/62 (14%), Positives = 22/62 (35%), Gaps = 1/62 (1%)

Query: 2   IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
           I E   + G + + ++         G+  ++++    A K ++   G       + I   
Sbjct: 126 IKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFK 184

Query: 62  AD 63
            D
Sbjct: 185 DD 186

>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 = 40.7 bits (95), Expect = 8e-06
 Identities = 12/62 (19%), Positives = 22/62 (35%), Gaps = 7/62 (11%)

Query: 2   IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVP--LDGRPMQIQ 59
           +  L   FG + +  +   +       A +       A   +  Y  V   L G+P+ IQ
Sbjct: 48  VISLGLPFGKVTNLLMLKGK-----NQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQ 102

Query: 60  LA 61
            +
Sbjct: 103 FS 104

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 40.3 bits (95), Expect = 8e-06
 Identities = 16/63 (25%), Positives = 33/63 (52%), Gaps = 2/63 (3%)

Query: 1  MIYELFSEFGP-LKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNG-VPLDGRPMQI 58
          M+YE F +  P  +  K+  D++G S G   + +    +  +A+ +  G V L  +P+++
Sbjct: 25 MLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRL 84

Query: 59 QLA 61
           +A
Sbjct: 85 SVA 87

>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 = 39.9 bits (94), Expect = 9e-06
 Identities = 12/58 (20%), Positives = 21/58 (36%), Gaps = 5/58 (8%)

Query: 2  IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
          +   F  FG +++              A + YE    A  A  +  G PL G   +++
Sbjct: 34 LAREFDRFGSIRTIDHVKGD-----SFAYIQYESLDAAQAACAKMRGFPLGGPDRRLR 86

>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 = 40.1 bits (94), Expect = 9e-06
 Identities = 16/60 (26%), Positives = 25/60 (41%), Gaps = 2/60 (3%)

Query: 2  IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
          IY  FS   P     +     GR  G AD+ +    DA+ AM   +   +  R +++ L 
Sbjct: 32 IYNFFSPLNP-MRVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLN 89

>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 = 39.8 bits (93), Expect = 1e-05
 Identities = 13/62 (20%), Positives = 23/62 (37%), Gaps = 7/62 (11%)

Query: 2  IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVP--LDGRPMQIQ 59
          +  L   FG + +  +   +       A L       AI  +  Y+ V   L  +P+ IQ
Sbjct: 32 VIALGLPFGKVTNILMLKGK-----NQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQ 86

Query: 60 LA 61
           +
Sbjct: 87 YS 88

>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 = 39.2 bits (92), Expect = 2e-05
 Identities = 23/84 (27%), Positives = 38/84 (45%), Gaps = 4/84 (4%)

Query: 4   ELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA 62
           + F  FG ++ A +  DR +G+S G   +    R+ A +A K  N + +DGR   + LA 
Sbjct: 36  KYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNPI-IDGRKANVNLAY 94

Query: 63  DVSVLENTVPRPVARGGRGGASGG 86
             +   +   +     G  G S G
Sbjct: 95  LGAKPRS--LQTGFAIGVSGPSSG 116

>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 = 38.7 bits (91), Expect = 3e-05
 Identities = 12/84 (14%), Positives = 30/84 (35%), Gaps = 18/84 (21%)

Query: 2  IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
          I  LF ++G +    +             +  E ++ A  A++  +   L G  + ++ +
Sbjct: 25 IRSLFEQYGKVLECDIIK-------NYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEAS 77

Query: 62 ADVSVLENTVPRPVARGGRGGASG 85
                     +  ++   G +SG
Sbjct: 78 -----------KNKSKASSGPSSG 90

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 38.3 bits (89), Expect = 5e-05
 Identities = 15/88 (17%), Positives = 30/88 (34%), Gaps = 8/88 (9%)

Query: 2   IYELFSEFGPLKSAK----LHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQ 57
           +   F +  P+   K          GR  G A +++     A  A+ + +   L  R ++
Sbjct: 40  VVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNAL-RKHKDLLGKRYIE 98

Query: 58  IQLAADVSVLENTVPRPVARGGRGGASG 85
           +  +   +  E            G +SG
Sbjct: 99  LFRS---TAAEVQQVLNRFSSASGPSSG 123

>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 = 38.7 bits (91), Expect = 6e-05
 Identities = 14/62 (22%), Positives = 29/62 (46%), Gaps = 2/62 (3%)

Query: 1   MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
              E FS++G +  A+L  D+ +G+S G   + Y+      +  +    +    R ++I+
Sbjct: 103 EFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQN-KFIDFKDRKIEIK 161

Query: 60  LA 61
            A
Sbjct: 162 RA 163

>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 = 36.7 bits (86), Expect = 3e-04
 Identities = 17/59 (28%), Positives = 30/59 (50%), Gaps = 3/59 (5%)

Query: 4  ELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
          E F ++G +   K+  D  +GRS G   L +E+ S   + +K  +   LDG+ +  + A
Sbjct: 22 EYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQHI--LDGKVIDPKRA 78

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 37.7 bits (88), Expect = 7e-05
 Identities = 17/87 (19%), Positives = 35/87 (40%), Gaps = 15/87 (17%)

Query: 2  IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
          +   FS +GPL++  +    +    G A + +E   DA  A++  +G  + G  ++++L+
Sbjct: 17 LERAFSYYGPLRTVWI----ARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELS 72

Query: 62 ADVSVLENTVPRPVARGGRGGASGGYR 88
                       + R  R       R
Sbjct: 73 -----------TGMPRRSRFDRPPARR 88

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 37.4 bits (87), Expect = 1e-04
 Identities = 16/61 (26%), Positives = 28/61 (45%), Gaps = 2/61 (3%)

Query: 2  IYELFSEFGPLKSA-KLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
          I + FS    + +   L  D  GRS G A + +  +  A KA+K  +   +  R ++I  
Sbjct: 32 IVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFK 90

Query: 61 A 61
          +
Sbjct: 91 S 91

>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 = 38.4 bits (90), Expect = 1e-04
 Identities = 13/86 (15%), Positives = 33/86 (38%), Gaps = 11/86 (12%)

Query: 1   MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
            + + F ++G ++  ++  DR SG+  G A + ++      K + Q     ++G   +++
Sbjct: 120 HLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVR 178

Query: 60  LAADVSVLENTVPRPVARGGRGGASG 85
            A         + +           G
Sbjct: 179 KA---------LSKQEMASASSSQRG 195

>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 = 36.8 bits (86), Expect = 1e-04
 Identities = 15/79 (18%), Positives = 27/79 (34%), Gaps = 16/79 (20%)

Query: 4  ELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD 63
           LF   G +    +           A +  E+ +DA  A+ Q NG  + G+ + ++L+  
Sbjct: 28 SLFERRGRVIECDVVK-------DYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELST- 79

Query: 64 VSVLENTVPRPVARGGRGG 82
                        G   G
Sbjct: 80 --------KGQKKSGPSSG 90

>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 = 36.8 bits (86), Expect = 1e-04
 Identities = 16/86 (18%), Positives = 33/86 (38%), Gaps = 17/86 (19%)

Query: 1  MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNG-VPLDGRPMQIQ 59
           + +LF +     +      +     G A + Y  ++ AI+A++  +G V L G+ M++ 
Sbjct: 24 DLRQLFGDRKLPLAG-----QVLLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVD 78

Query: 60 LAADVSVLENTVPRPVARGGRGGASG 85
           +                   G +SG
Sbjct: 79 YS-----------VSKKLRSSGPSSG 93

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 36.9 bits (85), Expect = 1e-04
 Identities = 15/65 (23%), Positives = 28/65 (43%), Gaps = 2/65 (3%)

Query: 1  MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
          ++ E F+  G +KS +L      +    A +  E   DAI A+   +   +  + + + L
Sbjct: 29 LLQEAFARHGKVKSVELSPHTDYQ--LKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSL 86

Query: 61 AADVS 65
          A   S
Sbjct: 87 ATGAS 91

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 36.5 bits (85), Expect = 2e-04
 Identities = 14/82 (17%), Positives = 33/82 (40%), Gaps = 12/82 (14%)

Query: 2   IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
           I  +F +   ++S +L  D+ + +  G   + ++      +A+  Y+G  L  R +++ +
Sbjct: 32  IDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT-YDGALLGDRSLRVDI 89

Query: 61  AADVSVLENTVPRPVARGGRGG 82
           A           R   + G   
Sbjct: 90  AE---------GRKQDKSGPSS 102

>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 = 36.0 bits (84), Expect = 2e-04
 Identities = 9/61 (14%), Positives = 22/61 (36%), Gaps = 2/61 (3%)

Query: 2  IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
          +   F   G +    +  D+ SG   G A + +  +     ++   +     GR +++  
Sbjct: 23 LEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA-LDESLFRGRQIKVIP 81

Query: 61 A 61
           
Sbjct: 82 K 82

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 36.7 bits (85), Expect = 2e-04
 Identities = 15/60 (25%), Positives = 25/60 (41%), Gaps = 2/60 (3%)

Query: 2   IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
           IY  FS   P     +     GR  G AD+ +    +A+ AM   +   +  R +++ L 
Sbjct: 63  IYNFFSPLNP-VRVHIEIGPDGRVTGEADVEFATHEEAVAAMS-KDRANMQHRYIELFLN 120

>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 = 36.1 bits (84), Expect = 2e-04
 Identities = 5/60 (8%), Positives = 23/60 (38%), Gaps = 7/60 (11%)

Query: 2  IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
          ++ +FS +G +    +             + ++       A++  +     G+ + ++++
Sbjct: 40 LFRIFSPYGHIMQINIKN-------AFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVS 92

>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 = 36.6 bits (85), Expect = 3e-04
 Identities = 12/61 (19%), Positives = 24/61 (39%), Gaps = 2/61 (3%)

Query: 2   IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
           +   FS  G +    +  D+ SG   G A + +  R+    A+   +     GR +++  
Sbjct: 53  LEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLP 111

Query: 61  A 61
            
Sbjct: 112 K 112

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A Length = 126

 Score = 36.4 bits (84), Expect = 3e-04
 Identities = 12/61 (19%), Positives = 26/61 (42%), Gaps = 2/61 (3%)

Query: 2   IYELFSEFGPLKSA-KLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
           I + FS    + +   L  D  G+  G A + +  +  A KA+   +   +  R +++  
Sbjct: 59  IVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKALG-KHKERIGHRYIEVFK 117

Query: 61  A 61
           +
Sbjct: 118 S 118

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A Length = 110

 Score = 36.2 bits (84), Expect = 3e-04
 Identities = 19/81 (23%), Positives = 32/81 (39%), Gaps = 15/81 (18%)

Query: 2   IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
           +  +FS++G +    +H        G A + Y     A  A+   NG  L G+ + I +A
Sbjct: 45  VETIFSKYGRVAGCSVHK-------GYAFVQYSNERHARAAVLGENGRVLAGQTLDINMA 97

Query: 62  ADVSVLENTVPRPVARGGRGG 82
            +        P+P   G   G
Sbjct: 98  GE--------PKPDRSGPSSG 110

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 35.6 bits (83), Expect = 3e-04
 Identities = 9/83 (10%), Positives = 30/83 (36%), Gaps = 14/83 (16%)

Query: 2  IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
          ++ +FS +G +    +             + ++       A++  +     G+ + ++++
Sbjct: 28 LFRIFSPYGHIMQINIKN-------AFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVS 80

Query: 62 ADVSVLENTVPRPVARGGRGGAS 84
                 ++  RP    G  G +
Sbjct: 81 -------SSNARPQFDHGDHGTN 96

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A Length = 150

 Score = 36.4 bits (84), Expect = 4e-04
 Identities = 15/60 (25%), Positives = 31/60 (51%), Gaps = 4/60 (6%)

Query: 2   IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
           +   F  +GPL+S  +    +    G A + +E   DA  A+++ +G  L G  ++++L+
Sbjct: 90  LERAFGYYGPLRSVWV----ARNPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELS 145

>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 = 35.3 bits (82), Expect = 5e-04
 Identities = 12/63 (19%), Positives = 22/63 (34%), Gaps = 4/63 (6%)

Query: 2  IYELFSEFGPLKSAKLHYDR--SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
          I E F       + +L  +     R  G     +E     + A+   N   L  R +++ 
Sbjct: 36 IKEFFRGLNI-SAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLGNRRIRVD 93

Query: 60 LAA 62
          +A 
Sbjct: 94 VAD 96

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	105
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.74
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.71
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.68
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.66
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.66
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.65
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.65
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.65
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.65
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.65
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.64
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.64
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.64
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.63
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.63
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.63
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.63
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.63
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.63
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.63
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.62
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.62
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.62
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.62
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.61
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.61
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.61
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.61
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.6
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.6
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.6
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.6
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.6
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.6
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.6
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.59
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.59
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.59
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.59
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.59
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.59
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.59
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.59
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.58
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.58
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.58
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.58
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.58
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.58
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.57
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.57
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.57
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.57
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.56
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.56
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.56
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.56
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.56
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.56
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.56
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.56
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.56
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.56
2div_A	99	TRNA selenocysteine associated protein; structural	99.56
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.55
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.55
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.55
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.55
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.54
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.54
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.54
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.54
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.54
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.54
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.53
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.53
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.53
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.53
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.52
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.52
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.52
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.52
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.52
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.51
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.51
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.51
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.51
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.51
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.5
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.5
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.25
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.5
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.5
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.49
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.49
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.49
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.48
1x5p_A	97	Negative elongation factor E; structure genomics,	99.48
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.48
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.48
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.48
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.48
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.47
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.47
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.47
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.47
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.47
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.47
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.47
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.47
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.46
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.46
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.46
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.45
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.45
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.45
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.45
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.45
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.44
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.44
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.44
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.44
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.44
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.44
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.43
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.43
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.43
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.43
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.42
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.42
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.42
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.42
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.41
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.41
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.41
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.4
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.4
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.4
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.4
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.4
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.4
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.39
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.39
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.39
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.39
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.39
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.39
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.38
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.38
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.38
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.38
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.38
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.38
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.38
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.37
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.37
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.37
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.37
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.37
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.37
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.36
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.36
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.36
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.35
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.35
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.35
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.35
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.35
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.34
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.34
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.34
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.34
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.34
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.32
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.32
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.3
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.3
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.29
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.28
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.28
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.28
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.27
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.26
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.24
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.23
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.18
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.18
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.17
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.16
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.15
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.13
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.12
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.11
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	99.11
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.11
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.09
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.08
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.08
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.04
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.03
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.03
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.0
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.89
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	98.88
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	98.86
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	98.82
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	98.79
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.55
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	97.69
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.17
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	96.94
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	96.59
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	96.17
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	96.0
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	95.9
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	95.76
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	89.2
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	89.18
2g0c_A	76	ATP-dependent RNA helicase DBPA; RNA recognition m	83.16
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	80.32

>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=99.74  E-value=1.1e-17  Score=103.65  Aligned_cols=65  Identities=34%  Similarity=0.468  Sum_probs=60.9

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|++||.|..|.|+.++ ++.+++||||+|.+.++|++||+.||+..|.++.|+|+++....
T Consensus        55 ~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~  120 (156)
T 1h2v_Z           55 QIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFK  120 (156)
T ss_dssp             HHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEESCCC
T ss_pred             HHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCC
Confidence            488999999999999999998 89999999999999999999999999999999999999998443

>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=99.71  E-value=5.5e-17  Score=93.88  Aligned_cols=62  Identities=34%  Similarity=0.531  Sum_probs=59.4

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|++||.|.++.++.++ ++.+++||||+|.+.++|++|++.||+..+.++.|+|++++
T Consensus        35 ~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~Ak   97 (99)
T 4fxv_A           35 ELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYAR   97 (99)
T ss_dssp             HHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             HHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            488999999999999999998 89999999999999999999999999999999999999986

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.68  E-value=2e-16  Score=93.19  Aligned_cols=62  Identities=15%  Similarity=0.345  Sum_probs=59.5

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|++||.|.++.|++++ +++++|||||+|.+.++|++||+.||+..+.++.|+|+++.
T Consensus        22 ~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a~   84 (110)
T 3s8s_A           22 FLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLDI   84 (110)
T ss_dssp             HHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             HHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            488999999999999999998 89999999999999999999999999999999999999986

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.66  E-value=2e-15  Score=88.95  Aligned_cols=68  Identities=26%  Similarity=0.348  Sum_probs=62.4

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccCCCC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVSVLE   68 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~~~~   68 (105)
                      +|+++|+.||.|..|.|+.++ ++.+++||||+|.+.++|++||+.||+..+.++.|.|+++.......
T Consensus        31 ~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~~   99 (115)
T 2dgo_A           31 DIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAP   99 (115)
T ss_dssp             HHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESSCCCCCS
T ss_pred             HHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccCCCCCC
Confidence            488999999999999999997 89999999999999999999999999999999999999998555443

>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=99.66  E-value=9.8e-16  Score=108.60  Aligned_cols=66  Identities=29%  Similarity=0.519  Sum_probs=61.3

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccCC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVSV   66 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~~   66 (105)
                      +|.++|++||.|..|.|+.++ ++++++||||+|.+.++|++||..||+..|.++.|.|.++.....
T Consensus       118 ~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a~~~~~  184 (437)
T 3pgw_S          118 KLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERGRTV  184 (437)
T ss_pred             HHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEeCCCCC
Confidence            488999999999999999997 999999999999999999999999999999999999999985443

>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=99.65  E-value=7.2e-16  Score=88.65  Aligned_cols=67  Identities=22%  Similarity=0.332  Sum_probs=61.8

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccCCC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVSVL   67 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~~~   67 (105)
                      +|+++|+.||.|..|.++.++ ++.+++||||+|.+.++|++|++.||+..+.++.|.|+++...+..
T Consensus        24 ~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~   91 (99)
T 1whw_A           24 DLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKEA   91 (99)
T ss_dssp             HHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECCCCSTT
T ss_pred             HHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCCccc
Confidence            488999999999999999998 9999999999999999999999999999999999999999855443

>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=99.65  E-value=8.4e-16  Score=86.31  Aligned_cols=64  Identities=28%  Similarity=0.398  Sum_probs=59.4

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeecc
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADV   64 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~   64 (105)
                      +|+++|+.||.|..+.++.++ ++.+++||||+|.+.++|++|++.||+..+.++.|.|+++..+
T Consensus        22 ~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~k   86 (87)
T 3bs9_A           22 AIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRK   86 (87)
T ss_dssp             HHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC--
T ss_pred             HHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEecCCC
Confidence            488999999999999999997 9999999999999999999999999999999999999998754

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.65  E-value=1.1e-15  Score=87.13  Aligned_cols=65  Identities=31%  Similarity=0.519  Sum_probs=60.4

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|++||.|..+.++.++ ++++++||||+|.+.++|++|++.||+..+.++.|+|+++.++.
T Consensus        21 ~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   86 (95)
T 2dnz_A           21 MLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHVTERL   86 (95)
T ss_dssp             HHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEESSCCC
T ss_pred             HHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEccccc
Confidence            488999999999999999988 89999999999999999999999999999999999999987433

>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=99.65  E-value=1.2e-15  Score=85.04  Aligned_cols=65  Identities=29%  Similarity=0.508  Sum_probs=60.7

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|+.||.|..+.++.++ ++.+++||||+|.+.++|++|++.||+..+.++.|.|+++.+++
T Consensus        17 ~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~~   82 (83)
T 3md1_A           17 TLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKLE   82 (83)
T ss_dssp             HHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCCCC
T ss_pred             HHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCcCC
Confidence            478999999999999999997 89999999999999999999999999999999999999988543

>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=99.65  E-value=4.2e-16  Score=93.30  Aligned_cols=66  Identities=30%  Similarity=0.446  Sum_probs=61.2

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccCC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVSV   66 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~~   66 (105)
                      +|+++|++||.|..|.|+.++ ++.+++||||+|.+.++|++||+.||+..|.++.|.|+++.....
T Consensus        38 ~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  104 (126)
T 3ex7_B           38 DIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGP  104 (126)
T ss_dssp             HHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEESEESSS
T ss_pred             HHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEecCCCC
Confidence            488999999999999999998 999999999999999999999999999999999999999985443

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=1.1e-15  Score=90.24  Aligned_cols=63  Identities=30%  Similarity=0.389  Sum_probs=58.6

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeecc
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADV   64 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~   64 (105)
                      +|+++|+.||.|..|.|+.++ ++++++||||+|.+.++|++||+.+++ .+.++.|+|+++...
T Consensus        33 ~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V~~a~~~   96 (116)
T 2cqd_A           33 SLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAYLG   96 (116)
T ss_dssp             HHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEESTTT
T ss_pred             HHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEEEEcccC
Confidence            488999999999999999988 899999999999999999999999998 899999999998743

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.64  E-value=9.2e-16  Score=93.20  Aligned_cols=64  Identities=28%  Similarity=0.479  Sum_probs=60.0

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeecc
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADV   64 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~   64 (105)
                      +|+++|+.||.|..|.|+.++ ++++++||||+|.+.++|++||+.||+..+.++.|+|+++...
T Consensus        58 ~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  122 (139)
T 1u6f_A           58 QLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASG  122 (139)
T ss_dssp             HHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESSCC
T ss_pred             HHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCC
Confidence            488999999999999999988 8899999999999999999999999999999999999998844

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=1.8e-15  Score=87.01  Aligned_cols=65  Identities=18%  Similarity=0.304  Sum_probs=59.9

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccCC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVSV   66 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~~   66 (105)
                      +|+++|+.||.|..|.|+.++ ++.+++||||+|.+.++|++||+ |++..+.++.|.|+++.+...
T Consensus        26 ~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V~~a~~~~~   91 (99)
T 2dgs_A           26 ELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVKRAEPRDS   91 (99)
T ss_dssp             HHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEEEECCCCCC
T ss_pred             HHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEEEECCCCcc
Confidence            488999999999999999988 89999999999999999999999 999999999999999885443

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.63  E-value=1.6e-15  Score=87.85  Aligned_cols=65  Identities=29%  Similarity=0.451  Sum_probs=60.5

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|+.||.|..|.|+.++ ++.+++||||+|.+.++|++||+.||+..+.++.|+|+++....
T Consensus        31 ~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~   96 (103)
T 2cq0_A           31 DLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPST   96 (103)
T ss_dssp             HHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESSCCC
T ss_pred             HHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEECCCCC
Confidence            478999999999999999997 89999999999999999999999999999999999999987443

>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=99.63  E-value=1.9e-15  Score=89.58  Aligned_cols=65  Identities=32%  Similarity=0.527  Sum_probs=60.4

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|++||.|..|.|+.++++.+++||||+|.+.++|++|++.||+..+.++.|+|+++....
T Consensus        23 ~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~   87 (116)
T 2fy1_A           23 MLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKKPS   87 (116)
T ss_dssp             HHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEECCCSS
T ss_pred             HHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCC
Confidence            48899999999999999998888999999999999999999999999999999999999988443

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.63  E-value=1.1e-15  Score=88.33  Aligned_cols=66  Identities=30%  Similarity=0.465  Sum_probs=61.0

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccCC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVSV   66 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~~   66 (105)
                      +|+++|+.||.|..+.|+.++ ++.+++||||+|.+.++|++|++.||+..+.++.|+|+++.....
T Consensus        28 ~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~   94 (102)
T 1x5s_A           28 SLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSD   94 (102)
T ss_dssp             HHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEECCCC
T ss_pred             HHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCC
Confidence            488999999999999999987 888999999999999999999999999999999999999985443

>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=99.63  E-value=1.8e-15  Score=89.23  Aligned_cols=65  Identities=23%  Similarity=0.361  Sum_probs=60.9

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|+.||.|..|.|+.++ ++.+++||||+|.+.++|++||+.||+..|.++.|+|+++.+..
T Consensus        41 ~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~  106 (115)
T 2cpz_A           41 DLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKN  106 (115)
T ss_dssp             HHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCCCSC
T ss_pred             HHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCCC
Confidence            488999999999999999998 89999999999999999999999999999999999999988444

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.63  E-value=8.2e-16  Score=88.86  Aligned_cols=67  Identities=24%  Similarity=0.377  Sum_probs=61.3

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccCCC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVSVL   67 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~~~   67 (105)
                      +|+++|+.||.|..|.|+.++ ++.+++||||+|.+.++|++|++.||+..+.++.|.|+++.+....
T Consensus        28 ~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~   95 (102)
T 2cqb_A           28 VLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPMRIK   95 (102)
T ss_dssp             HHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECCCCCCC
T ss_pred             HHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEeCCCCCCC
Confidence            488999999999999999987 8999999999999999999999999999999999999998854433

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.63  E-value=7.5e-15  Score=86.32  Aligned_cols=62  Identities=29%  Similarity=0.530  Sum_probs=59.2

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|+.||.|..|.|+.++++++++||||+|.+.++|++||+.||+..+.++.|.|+++.
T Consensus        31 ~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   92 (114)
T 2do0_A           31 KLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDE   92 (114)
T ss_dssp             HHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             HHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEcc
Confidence            48899999999999999998888899999999999999999999999999999999999987

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.63  E-value=2.7e-16  Score=90.96  Aligned_cols=64  Identities=25%  Similarity=0.343  Sum_probs=59.9

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCC-eeEEEEEeecc
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDG-RPMQIQLAADV   64 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~-~~i~V~~~~~~   64 (105)
                      +|+++|++||.|.+|.|+.++ +++++|||||+|.+.++|++||+.||+..+.+ +.|+|.++.+.
T Consensus        28 ~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~l~V~~a~~~   93 (100)
T 3ns6_A           28 ALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRLFLYTMKDV   93 (100)
T ss_dssp             HHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEESHHH
T ss_pred             HHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCeEEEEEECchh
Confidence            478999999999999999998 79999999999999999999999999999999 99999998743

>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=99.62  E-value=2.8e-16  Score=89.17  Aligned_cols=65  Identities=18%  Similarity=0.198  Sum_probs=57.6

Q ss_pred             CHHHHhccCC--CeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFG--PLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G--~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|+.||  .|.++.++.++ +++++|||||+|.+.++|++|++.||+..+.++.|+|+++.+.+
T Consensus        17 ~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~~~~   84 (90)
T 3p5t_L           17 DLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSNKLE   84 (90)
T ss_dssp             HHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC----
T ss_pred             HHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECCCCc
Confidence            4889999999  99999999998 99999999999999999999999999999999999999988443

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.62  E-value=3.4e-15  Score=86.02  Aligned_cols=65  Identities=22%  Similarity=0.397  Sum_probs=60.5

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|+.||.|..+.++.++++++++||||+|.+.++|++|++.||+..+.++.|+|+++.+.+
T Consensus        33 ~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   97 (100)
T 2do4_A           33 ELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAISNSGP   97 (100)
T ss_dssp             HHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCCCS
T ss_pred             HHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCC
Confidence            48899999999999999998888999999999999999999999999999999999999987443

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.62  E-value=2.8e-15  Score=87.14  Aligned_cols=65  Identities=31%  Similarity=0.462  Sum_probs=60.7

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|+.||.|..|.++.++ ++.+++||||+|.+.++|++|++.||+..+.++.|.|+++...+
T Consensus        39 ~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~  104 (106)
T 1p27_B           39 DIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRG  104 (106)
T ss_dssp             HHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEESEESS
T ss_pred             HHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEeecCCC
Confidence            488999999999999999998 89999999999999999999999999999999999999988543

>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=99.62  E-value=5.8e-16  Score=101.57  Aligned_cols=62  Identities=19%  Similarity=0.189  Sum_probs=59.4

Q ss_pred             CHHHHhccCC--CeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFG--PLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G--~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|++||  .|..|.|+.++ ++++++||||+|.+.++|++||+.||+..|.++.|+|.++.
T Consensus        84 ~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~a~  148 (229)
T 3q2s_C           84 DLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVN  148 (229)
T ss_dssp             HHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEECC
T ss_pred             HHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEECC
Confidence            4899999999  99999999998 99999999999999999999999999999999999999986

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.61  E-value=1.5e-15  Score=87.90  Aligned_cols=64  Identities=23%  Similarity=0.377  Sum_probs=60.0

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeecc
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADV   64 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~   64 (105)
                      +|+++|+.||.|..|.|+.++ ++.+++||||+|.+.++|++||+.||+..+.++.|.|+++...
T Consensus        29 ~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~   93 (103)
T 2dnm_A           29 SLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVARYG   93 (103)
T ss_dssp             HHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEEECSSC
T ss_pred             HHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEECCcC
Confidence            488999999999999999988 8999999999999999999999999999999999999999843

>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=99.61  E-value=4.1e-15  Score=86.30  Aligned_cols=65  Identities=18%  Similarity=0.301  Sum_probs=60.1

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCC---eeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDG---RPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~---~~i~V~~~~~~~   65 (105)
                      +|+++|+.||.|..|.|+.++++.+++||||+|.+.++|++||+.||+..+.+   +.|.|+++....
T Consensus        31 ~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V~~a~~~~   98 (105)
T 2dnh_A           31 DVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVVKFADTDK   98 (105)
T ss_dssp             HHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEEEESCSSC
T ss_pred             HHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEEEECccCc
Confidence            48899999999999999998888999999999999999999999999999988   999999998443

>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=99.61  E-value=2e-15  Score=87.66  Aligned_cols=65  Identities=26%  Similarity=0.471  Sum_probs=60.6

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|++||.|..|.++.++ ++.+++||||+|.+.++|++|++.||+..+.++.|+|+++....
T Consensus        31 ~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   96 (105)
T 1x5u_A           31 LLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHN   96 (105)
T ss_dssp             HHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETTTTS
T ss_pred             HHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCCCC
Confidence            488999999999999999998 89999999999999999999999999999999999999987443

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.61  E-value=1.9e-15  Score=86.33  Aligned_cols=65  Identities=28%  Similarity=0.432  Sum_probs=60.2

Q ss_pred             CHHHHhccCCCeeEE-EEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSA-KLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~-~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|+.||.|..+ .++.++ ++.+++||||+|.+.++|++|++.||+..+.++.|.|+++.+.+
T Consensus        21 ~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~   87 (96)
T 1x5t_A           21 LLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKD   87 (96)
T ss_dssp             HHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCC
T ss_pred             HHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEecccC
Confidence            488999999999999 999986 89999999999999999999999999999999999999987443

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.60  E-value=2.9e-16  Score=89.45  Aligned_cols=66  Identities=18%  Similarity=0.263  Sum_probs=59.0

Q ss_pred             CHHHHhccCC-CeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhC-CcccCCeeEEEEEeeccCC
Q psy1928           1 MIYELFSEFG-PLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYN-GVPLDGRPMQIQLAADVSV   66 (105)
Q Consensus         1 ~l~~~f~~~G-~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~-~~~i~~~~i~V~~~~~~~~   66 (105)
                      +|+++|++|| .|.+|.|++++ ++.+++||||+|.+.++|++||+.++ +..+.++.|.|+++.+++.
T Consensus        17 ~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a~~~~~   85 (91)
T 2lxi_A           17 DIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYSDPKPK   85 (91)
T ss_dssp             HHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECCCSCCC
T ss_pred             HHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEcCCCCC
Confidence            5889999999 79999999998 89999999999999999999999874 5679999999999885543

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.60  E-value=6.6e-15  Score=85.19  Aligned_cols=64  Identities=30%  Similarity=0.474  Sum_probs=59.6

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|+.||.|..|.|+.+ ++.+++||||+|.+.++|++|++.||+..+.++.|.|+++....
T Consensus        31 ~l~~~F~~~G~i~~v~i~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~   94 (103)
T 2d9p_A           31 RLRKAFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKE   94 (103)
T ss_dssp             HHHHTTTTTSCEEEEEEEEC-SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECSSCC
T ss_pred             HHHHHHHhcCCEEEEEEEcC-CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEecccc
Confidence            48899999999999999998 88899999999999999999999999999999999999998443

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.60  E-value=3.6e-15  Score=84.97  Aligned_cols=62  Identities=35%  Similarity=0.594  Sum_probs=58.8

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|++||.|..+.++.++ ++.+++||||+|.+.++|++|++.||+..+.++.|+|++++
T Consensus        31 ~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   93 (95)
T 2cqc_A           31 DLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSGPS   93 (95)
T ss_dssp             HHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCS
T ss_pred             HHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEecC
Confidence            488999999999999999998 88999999999999999999999999999999999999876

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.60  E-value=3.2e-15  Score=85.11  Aligned_cols=62  Identities=23%  Similarity=0.435  Sum_probs=58.3

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|++||.|..+.++.++ ++.+++||||+|.+.++|++|++.||+..+.++.|+|++++
T Consensus        32 ~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~ak   94 (94)
T 2e5h_A           32 DLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASIAI   94 (94)
T ss_dssp             HHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEECC
T ss_pred             HHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEecC
Confidence            488999999999999999988 78999999999999999999999999999999999999874

>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=99.60  E-value=1.8e-15  Score=84.58  Aligned_cols=62  Identities=26%  Similarity=0.398  Sum_probs=58.1

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|++||.|..+.++.++ ++.+++||||+|.+.++|++|++.||+..+.++.|+|++++
T Consensus        23 ~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~ak   85 (85)
T 3mdf_A           23 VLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK   85 (85)
T ss_dssp             HHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             HHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcC
Confidence            488999999999999999886 88899999999999999999999999999999999999874

>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=99.60  E-value=5e-15  Score=86.20  Aligned_cols=62  Identities=74%  Similarity=1.172  Sum_probs=58.9

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|++||.|..|.|+.++++.+++||||+|.+.++|++|++.||+..+.++.|+|++++
T Consensus        45 ~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~  106 (107)
T 3ulh_A           45 DIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT  106 (107)
T ss_dssp             HHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             HHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEeC
Confidence            48899999999999999998889999999999999999999999999999999999999875

>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=99.60  E-value=5.3e-15  Score=86.53  Aligned_cols=65  Identities=26%  Similarity=0.413  Sum_probs=60.5

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhC------CcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYN------GVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~------~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|+.||.|..|.|+.++ ++.+++||||+|.+.++|++||..||      +..+.++.|.|+++.+..
T Consensus        31 ~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g~~l~v~~a~~~~  102 (111)
T 1x4h_A           31 ALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRD  102 (111)
T ss_dssp             HHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCEEEEECCCCCC
T ss_pred             HHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcCEEEEEEECCCCc
Confidence            488999999999999999998 89999999999999999999999999      999999999999988544

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.59  E-value=8.7e-15  Score=84.73  Aligned_cols=63  Identities=19%  Similarity=0.412  Sum_probs=58.2

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|+.|| |..|.|+.++ ++++++||||+|.+.++|++|| .||+..|.++.|.|+++....
T Consensus        31 ~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~~~   94 (103)
T 2dng_A           31 DIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDIAEGRK   94 (103)
T ss_dssp             HHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEEECCCCC
T ss_pred             HHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEEEecCCC
Confidence            4889999997 9999999998 8999999999999999999999 899999999999999988444

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.59  E-value=5.6e-15  Score=85.91  Aligned_cols=65  Identities=31%  Similarity=0.416  Sum_probs=60.4

Q ss_pred             CHHHHhccCCCeeEEEEEeC-C-CCCcccEEEEEeCCHHHHHHHHHHh-CCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYD-R-SGRSLGTADLIYERRSDAIKAMKQY-NGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~-~-~~~~~g~~fv~f~~~~~a~~ai~~l-~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|+.||.|..|.|+.+ + ++.+++||||+|.+.++|++||+.| |+..+.++.|+|+++....
T Consensus        31 ~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~v~~a~~~~   98 (107)
T 2cph_A           31 EIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEV   98 (107)
T ss_dssp             HHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEEECCCCC
T ss_pred             HHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEEEEeCCCCC
Confidence            48899999999999999998 5 8999999999999999999999999 9999999999999998544

>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=99.59  E-value=3.9e-15  Score=85.22  Aligned_cols=65  Identities=26%  Similarity=0.447  Sum_probs=60.4

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|+.||.|..+.++.++ ++.+++||||+|.+.++|++|++.||+..+.++.|.|+++.+..
T Consensus        18 ~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~   83 (96)
T 2x1f_A           18 QILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSNSD   83 (96)
T ss_dssp             HHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCSS
T ss_pred             HHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcCCCC
Confidence            488999999999999999987 89999999999999999999999999999999999999988443

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.59  E-value=4.7e-15  Score=85.90  Aligned_cols=65  Identities=22%  Similarity=0.466  Sum_probs=60.1

Q ss_pred             CHHHHhcc-CCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcc-cCCeeEEEEEeeccC
Q psy1928           1 MIYELFSE-FGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVP-LDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~-~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~-i~~~~i~V~~~~~~~   65 (105)
                      +|+++|+. ||.|..|.|+.++++.+++||||+|.+.++|++||+.||+.. +.++.|.|+++....
T Consensus        25 ~l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v~~a~~~~   91 (104)
T 2dhg_A           25 MLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLSVAIPKA   91 (104)
T ss_dssp             HHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCCCBCCCCC
T ss_pred             HHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEEEEccCCC
Confidence            48899999 999999999998888899999999999999999999999999 999999999987444

>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=99.59  E-value=5.2e-15  Score=85.82  Aligned_cols=64  Identities=17%  Similarity=0.290  Sum_probs=58.6

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-C-CCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccCC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-S-GRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVSV   66 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~-~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~~   66 (105)
                      +|+++|+.|| |..|.|+.++ + +.+++||||+|.+.++|++|| .||+..+.++.|.|+++.....
T Consensus        31 ~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~~~~   96 (104)
T 1wi8_A           31 SIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVADQAQD   96 (104)
T ss_dssp             HHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEECCCCCC
T ss_pred             HHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEEEEccCCCC
Confidence            4889999999 9999999988 5 899999999999999999999 8999999999999999885443

>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=99.59  E-value=5e-15  Score=84.42  Aligned_cols=62  Identities=27%  Similarity=0.523  Sum_probs=58.7

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|+.||.|..|.|+.++++.+++||||+|.+.++|++|++.||+..+.++.|.|++++
T Consensus        32 ~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   93 (95)
T 2ywk_A           32 ILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSGPS   93 (95)
T ss_dssp             HHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             HHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEEcC
Confidence            48899999999999999998888899999999999999999999999999999999999876

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.59  E-value=5.4e-15  Score=85.05  Aligned_cols=62  Identities=24%  Similarity=0.535  Sum_probs=58.4

Q ss_pred             CHHHHhccCCCeeE--------EEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKS--------AKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~--------~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|++||.|..        +.++.++ ++.+++||||+|.+.++|++|++.||+..+.++.|+|++++
T Consensus        29 ~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~A~   99 (99)
T 2la6_A           29 SVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFAT   99 (99)
T ss_dssp             HHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBSSSSBCEEEECC
T ss_pred             HHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEecC
Confidence            48899999999999        9999997 89999999999999999999999999999999999999874

>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=99.59  E-value=3.7e-15  Score=86.64  Aligned_cols=65  Identities=32%  Similarity=0.416  Sum_probs=59.8

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCccc---CCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPL---DGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i---~~~~i~V~~~~~~~   65 (105)
                      +|+++|++||.|..|.|+.++ ++++++||||+|.+.++|++|++.||+..+   .++.|.|+++....
T Consensus        29 ~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l~v~~a~~~~   97 (106)
T 2dgp_A           29 DLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQVKPADSES   97 (106)
T ss_dssp             HHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCEEEECCCCS
T ss_pred             HHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceEEEEECCccc
Confidence            488999999999999999988 899999999999999999999999999887   88999999988444

>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=99.58  E-value=6.2e-15  Score=86.23  Aligned_cols=65  Identities=31%  Similarity=0.470  Sum_probs=60.6

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|+.||.|..+.++.++ ++.+++||||+|.+.++|++|+..||+..+.++.|.|+++....
T Consensus        42 ~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~  107 (110)
T 1oo0_B           42 EIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKG  107 (110)
T ss_dssp             HHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEESS
T ss_pred             HHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEcccCC
Confidence            488999999999999999987 89999999999999999999999999999999999999988543

>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=99.58  E-value=3.7e-15  Score=89.93  Aligned_cols=64  Identities=34%  Similarity=0.598  Sum_probs=60.0

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeecc
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADV   64 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~   64 (105)
                      +|+++|++||.|..|.|+.++ ++.+++||||+|.+.++|++||+.||+..|.++.|+|+++..+
T Consensus        62 ~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~~a~~~  126 (129)
T 2kxn_B           62 DLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITK  126 (129)
T ss_dssp             HHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEESCCSSS
T ss_pred             HHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCC
Confidence            488999999999999999998 8899999999999999999999999999999999999998743

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.58  E-value=1e-15  Score=87.97  Aligned_cols=62  Identities=18%  Similarity=0.329  Sum_probs=56.7

Q ss_pred             CHHHHhccCCC--eeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCc----ccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGP--LKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGV----PLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~--i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~----~i~~~~i~V~~~~   62 (105)
                      +|+++|++||.  +.+|.+++|+ +++++|||||+|.+.++|++||+.||+.    .|++++|.|++++
T Consensus        25 ~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~i~V~~Ak   93 (95)
T 2lkz_A           25 SIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGVDFAK   93 (95)
T ss_dssp             HHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEEEEEEECC
T ss_pred             HHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEEEEEEEcc
Confidence            48899999995  5789999998 8999999999999999999999999986    4889999999986

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.58  E-value=1e-14  Score=85.24  Aligned_cols=62  Identities=21%  Similarity=0.193  Sum_probs=58.0

Q ss_pred             CHHHHhccCCCeeEEEEEeCC--CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR--SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~--~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|++||.|.++.|+.++  ++.++|++||+|.+.++|++|+..||+..+.++.|.|.++.
T Consensus        29 dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~i~v~~a~   92 (105)
T 2pe8_A           29 ETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVVKACFYN   92 (105)
T ss_dssp             HHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             HHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcEEEEEEcC
Confidence            478999999999999999986  46889999999999999999999999999999999999987

>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=99.58  E-value=2.1e-14  Score=83.06  Aligned_cols=66  Identities=21%  Similarity=0.451  Sum_probs=59.1

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccCCC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVSVL   67 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~~~   67 (105)
                      +|+++|+.||.|..|.|+.++.. +++||||+|.+.++|++|+..||+..+.++.|.|+++......
T Consensus        31 ~l~~~f~~~G~v~~v~i~~~~~~-~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~   96 (103)
T 2cq3_A           31 DLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARVMT   96 (103)
T ss_dssp             HHHHHGGGTSCEEEEEEECCTTT-TCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCSSCCC
T ss_pred             HHHHHHHhcCCeEEEEEEecCCC-CcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcccCCCC
Confidence            48899999999999999987643 7899999999999999999999999999999999999855433

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.58  E-value=5.7e-15  Score=86.78  Aligned_cols=65  Identities=23%  Similarity=0.465  Sum_probs=59.8

Q ss_pred             CHHHHhccCCCee--------EEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLK--------SAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~--------~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|+.||.|.        .|.|+.++ ++.+++||||+|.+.++|++||+.||+..+.++.|+|+++....
T Consensus        31 ~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~  104 (113)
T 2cpe_A           31 DLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKP  104 (113)
T ss_dssp             HHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETTEECEEECSSCCC
T ss_pred             HHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCccCCCEEEEEECCCCC
Confidence            4889999999998        69999987 89999999999999999999999999999999999999988444

>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=99.57  E-value=7.2e-15  Score=86.87  Aligned_cols=62  Identities=27%  Similarity=0.434  Sum_probs=56.9

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeec
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD   63 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~   63 (105)
                      +|+++|+.||.|.+|.|+.++ +.+++||||+|.+.++|++||+.|++..|.++.|.|.++..
T Consensus        21 ~L~~~F~~~G~v~~v~i~~d~-~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~   82 (115)
T 4f25_A           21 ALYDTFSAFGNILSCKVVCDE-NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   82 (115)
T ss_dssp             HHHHHHGGGSCEEEEEEEEET-TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSC
T ss_pred             HHHHHHhccCCEEEEEEeecC-CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            589999999999999999875 33789999999999999999999999999999999998874

>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=99.57  E-value=1.2e-14  Score=90.78  Aligned_cols=65  Identities=31%  Similarity=0.470  Sum_probs=60.9

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|+.||.|..|.|+.++ ++.+++||||+|.+.++|++||..||+..|.++.|.|.++....
T Consensus        88 ~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~  153 (165)
T 1rk8_A           88 EIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKG  153 (165)
T ss_dssp             HHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEECC
T ss_pred             HHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCCC
Confidence            488999999999999999997 99999999999999999999999999999999999999998544

>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=99.57  E-value=9e-15  Score=82.36  Aligned_cols=62  Identities=15%  Similarity=0.288  Sum_probs=58.3

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeec
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD   63 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~   63 (105)
                      +|+++|+.||.|..+.++.++ ++.+++||||+|.+.++|++|+ .||+..+.++.|+|+++++
T Consensus        22 ~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~~   84 (89)
T 3ucg_A           22 ELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKRT   84 (89)
T ss_dssp             HHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETTT
T ss_pred             HHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEccC
Confidence            488999999999999999998 8999999999999999999999 8999999999999998863

>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=99.57  E-value=6.7e-15  Score=86.22  Aligned_cols=64  Identities=34%  Similarity=0.578  Sum_probs=59.8

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeecc
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADV   64 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~   64 (105)
                      +|+++|+.||.|..+.++.++ ++.+++||||+|.+.++|++|++.|++..+.++.|.|+++.++
T Consensus        42 ~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~k  106 (108)
T 2jrs_A           42 MLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTER  106 (108)
T ss_dssp             HHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEECSCSS
T ss_pred             HHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcccC
Confidence            478999999999999999987 8899999999999999999999999999999999999998743

>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=99.56  E-value=6.2e-15  Score=85.99  Aligned_cols=61  Identities=18%  Similarity=0.391  Sum_probs=56.2

Q ss_pred             CHHHHh-ccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEe
Q psy1928           1 MIYELF-SEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA   61 (105)
Q Consensus         1 ~l~~~f-~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~   61 (105)
                      +|+++| ++||.|.+|.|+.+.+++++||+||+|.+.++|++|+..||+..+.++.|.|.++
T Consensus        42 dl~~~f~~~~G~V~~v~i~~~~~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i~v~~s  103 (104)
T 1jmt_A           42 EVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             HHHHHhhccCCceEEEEEEeCCCCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEEEEEEc
Confidence            366777 9999999999998777789999999999999999999999999999999999876

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.56  E-value=9.8e-15  Score=90.71  Aligned_cols=62  Identities=19%  Similarity=0.374  Sum_probs=59.4

Q ss_pred             CHHHHhccCC--CeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFG--PLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G--~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|+.||  .|..|.|+.++ +++++|||||+|.+.++|++||+.||+..|.++.|.|.++.
T Consensus        71 ~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~a~  135 (156)
T 3n9u_C           71 QLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPAT  135 (156)
T ss_dssp             HHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEECC
T ss_pred             HHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEEcC
Confidence            4889999999  99999999998 99999999999999999999999999999999999999986

>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=99.56  E-value=2.3e-14  Score=82.86  Aligned_cols=64  Identities=27%  Similarity=0.403  Sum_probs=57.7

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|+.||.|..|.|+.++.. +++||||+|.+.++|++|+..||+..+.++.|+|+++....
T Consensus        31 ~l~~~F~~~G~i~~v~i~~~~~~-~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   94 (103)
T 2cqi_A           31 LILQLFSQIGPCKSCKMITEHTS-NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPS   94 (103)
T ss_dssp             HHHHHHHHHSCEEEEEEECCCCS-SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCTT
T ss_pred             HHHHHHHhcCCEeEEEEEecCCC-CCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEECCCCc
Confidence            48899999999999999988633 58999999999999999999999999999999999998543

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.56  E-value=4.5e-15  Score=87.82  Aligned_cols=62  Identities=24%  Similarity=0.335  Sum_probs=58.0

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|++||.|..+.++.++ ++++++|+||+|.+.++|++|++.||+..+.++.|+|++++
T Consensus        56 ~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~ak  118 (118)
T 2khc_A           56 DLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLKK  118 (118)
T ss_dssp             HHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEEEC-
T ss_pred             HHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEecC
Confidence            488999999999999999987 89999999999999999999999999999999999999864

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.56  E-value=1.6e-14  Score=86.16  Aligned_cols=61  Identities=20%  Similarity=0.326  Sum_probs=57.9

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|+.||.|..|.++.++ ++.+++||||+|.+.++|++|+ .||+..+.++.|.|+++.
T Consensus        52 ~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~  113 (124)
T 2jwn_A           52 DLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKR  113 (124)
T ss_dssp             HHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESS
T ss_pred             HHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECC
Confidence            488999999999999999987 8999999999999999999999 799999999999999987

>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=99.56  E-value=2.3e-14  Score=84.16  Aligned_cols=62  Identities=26%  Similarity=0.447  Sum_probs=56.3

Q ss_pred             HHhccCCCeeEEEEEeCC-CC---CcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           4 ELFSEFGPLKSAKLHYDR-SG---RSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         4 ~~f~~~G~i~~~~i~~~~-~~---~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      ++|++||.|..|.|+.++ ++   .+++||||+|.+.++|++||+.||+..+.++.|+|+++..++
T Consensus        37 ~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~~k~  102 (111)
T 2cpi_A           37 EYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKASLGTTKY  102 (111)
T ss_dssp             TTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEESCCCCS
T ss_pred             HHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCEEEEEEeccccc
Confidence            899999999999998876 43   456999999999999999999999999999999999998555

>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=99.56  E-value=1e-14  Score=90.19  Aligned_cols=64  Identities=28%  Similarity=0.456  Sum_probs=60.4

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeecc
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADV   64 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~   64 (105)
                      +|+++|+.||.|..|.|+.++ ++.+++||||+|.+.++|++||..||+..+.++.|.|+++.+.
T Consensus        86 ~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  150 (158)
T 2kn4_A           86 TLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYG  150 (158)
T ss_dssp             HHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEECCS
T ss_pred             HHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCC
Confidence            488999999999999999997 8999999999999999999999999999999999999999844

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.56  E-value=1e-14  Score=84.69  Aligned_cols=65  Identities=15%  Similarity=0.257  Sum_probs=59.8

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccCC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVSV   66 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~~   66 (105)
                      +|+++|+.||.|..|.|+.++ ++.+++||||+|.+.++|++||+. ++..|.++.|.|+++.++..
T Consensus        32 ~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V~~a~~~~~   97 (105)
T 2dh8_A           32 TLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPKPCTPRGM   97 (105)
T ss_dssp             HHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBCCCSCCSSC
T ss_pred             HHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEEccCCCC
Confidence            488999999999999999997 899999999999999999999998 99999999999999875443

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.56  E-value=1.3e-14  Score=85.61  Aligned_cols=64  Identities=20%  Similarity=0.283  Sum_probs=59.2

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|+.||.|..|.|+.++ ++.+++||||+|.+.++|++||+. ++..|.++.|.|+++.++.
T Consensus        43 ~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a~~~~  107 (116)
T 1x4b_A           43 SLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAVARE  107 (116)
T ss_dssp             HHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECCSSCC
T ss_pred             HHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEECCCCc
Confidence            488999999999999999997 899999999999999999999997 9999999999999987544

>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=99.56  E-value=5.2e-15  Score=87.54  Aligned_cols=56  Identities=16%  Similarity=0.215  Sum_probs=49.0

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|++||.|..|.|+.+      +||||+|.+.++|++||+.||+..|.++.|+|.+..
T Consensus        32 ~l~~~F~~~G~v~~~~i~~~------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~   87 (115)
T 3beg_B           32 DLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIR   87 (115)
T ss_dssp             HHHHHHGGGSCEEEEEECTT------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCE
T ss_pred             HHHHHHHhcCCeEEEEEecC------CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEE
Confidence            58899999999999998764      899999999999999999999999999985444443

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.56  E-value=6.8e-15  Score=84.51  Aligned_cols=62  Identities=26%  Similarity=0.421  Sum_probs=58.6

Q ss_pred             CHHHHhccCCCee-EEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCee----EEEEEee
Q psy1928           1 MIYELFSEFGPLK-SAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRP----MQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~-~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~----i~V~~~~   62 (105)
                      +|+++|+.||.|. .+.++.++ ++.+++||||+|.+.++|++|++.||+..+.++.    |+|.+++
T Consensus        25 ~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~l~v~~a~   92 (99)
T 2div_A           25 FISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKRFKLNYAT   92 (99)
T ss_dssp             HHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEECCEEETT
T ss_pred             HHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcceeEEEeecC
Confidence            4889999999999 99999998 8999999999999999999999999999999998    9999887

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.55  E-value=1.6e-14  Score=82.85  Aligned_cols=65  Identities=26%  Similarity=0.515  Sum_probs=58.3

Q ss_pred             CHHHHhccCCCeeEEEEEeCCC--C--CcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRS--G--RSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~--~--~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|++||.|..|.++.++.  +  .+++||||+|.+.++|++|++.||+..+.++.|.|+++....
T Consensus        21 ~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   89 (98)
T 2cpf_A           21 TLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISERAT   89 (98)
T ss_dssp             HHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSCSS
T ss_pred             HHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEccCCC
Confidence            4889999999999999988652  3  788999999999999999999999999999999999987444

>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=99.55  E-value=2.3e-14  Score=82.09  Aligned_cols=62  Identities=24%  Similarity=0.278  Sum_probs=55.9

Q ss_pred             HHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         2 l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      |+++|++||.|.+|.|+.++..  ++||||+|.+.++|++||+.||+..+.++.|+|+++.+..
T Consensus        30 l~~~F~~~G~v~~v~i~~~~~~--rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~~~   91 (96)
T 2dgx_A           30 LQEAFARHGKVKSVELSPHTDY--QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATGAS   91 (96)
T ss_dssp             HHHHHHHHSCEEEEEECSCCST--TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCSS
T ss_pred             HHHhccccCcEEEEEEEeCCCC--CeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcCCCC
Confidence            3499999999999999988733  7899999999999999999999999999999999997443

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.55  E-value=3.3e-14  Score=84.83  Aligned_cols=64  Identities=72%  Similarity=1.106  Sum_probs=60.0

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeecc
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADV   64 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~   64 (105)
                      +|+++|+.||.|..|.++.++++.+++||||+|.+.++|++|++.||+..+.++.|+|+++...
T Consensus        51 ~l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  114 (124)
T 2kt5_A           51 DIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQ  114 (124)
T ss_dssp             HHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEECCT
T ss_pred             HHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEeCCC
Confidence            4889999999999999999888889999999999999999999999999999999999999843

>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=99.55  E-value=4.2e-14  Score=81.87  Aligned_cols=60  Identities=30%  Similarity=0.462  Sum_probs=53.7

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccCCC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVSVL   67 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~~~   67 (105)
                      +|+++|++||.|..|.+++       +||||+|.+.++|++||+.||+..+.++.|.|+++.+....
T Consensus        27 ~l~~~F~~~G~i~~v~~~~-------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~   86 (103)
T 2dgu_A           27 ILEKAFSQFGKLERVKKLK-------DYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPPDQK   86 (103)
T ss_dssp             HHHHHHHHHSCEEEEEECS-------SCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCCCCC
T ss_pred             HHHHHHHhcCCEEEEEEEC-------CEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEcCCCccc
Confidence            4889999999999998864       59999999999999999999999999999999999854433

>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=99.54  E-value=5.3e-14  Score=81.35  Aligned_cols=65  Identities=23%  Similarity=0.305  Sum_probs=58.6

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccCCC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVSVL   67 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~~~   67 (105)
                      +|+++|+.||.|..|.|+.++ ++.+++||||+|.+.++|++||.  ++..+.++.|.|+++.+++..
T Consensus        31 ~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~v~~a~~~~~~   96 (103)
T 2cqg_A           31 DLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCKLPNSKQSQ   96 (103)
T ss_dssp             HHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEECCCTTCCC
T ss_pred             HHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEEEEecCCCCcC
Confidence            488999999999999999998 89999999999999999999998  467899999999999855543

>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=99.54  E-value=8.7e-15  Score=84.69  Aligned_cols=64  Identities=34%  Similarity=0.609  Sum_probs=59.8

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeecc
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADV   64 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~   64 (105)
                      +|+++|+.||.|..+.++.++ ++.+++||||+|.+.++|++|++.||+..+.++.|.|+++...
T Consensus        24 ~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~   88 (104)
T 1p1t_A           24 QLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASE   88 (104)
T ss_dssp             HHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTCT
T ss_pred             HHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeCCCc
Confidence            488999999999999999987 8999999999999999999999999999999999999998743

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.54  E-value=3.6e-14  Score=80.35  Aligned_cols=63  Identities=13%  Similarity=0.201  Sum_probs=58.6

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|+.| .|..+.|+.+.++++++||||+|.+.++|++||. ||+..+.++.|.|.++.+.+
T Consensus        26 ~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~a~~~~   88 (91)
T 2dgw_A           26 NVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFREKSGP   88 (91)
T ss_dssp             HHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEEESSCC
T ss_pred             HHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEECCcCC
Confidence            488999999 9999999998889999999999999999999999 99999999999999988553

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.54  E-value=2.6e-14  Score=83.76  Aligned_cols=65  Identities=22%  Similarity=0.286  Sum_probs=58.9

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccCC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVSV   66 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~~   66 (105)
                      +|+++|+.||.|..|.++.++ ++.+++||||+|.+.++|++||..++ ..+.++.|.|+++.+++.
T Consensus        41 ~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~~-~~l~g~~l~V~~a~~~~~  106 (109)
T 2rs2_A           41 GLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVAFPRRA  106 (109)
T ss_dssp             HHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSSC-EEETTEEEEEEECCCCCC
T ss_pred             HHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHCC-CcCCCEEEEEEEccCCCC
Confidence            488999999999999999988 89999999999999999999999764 899999999999885543

>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=99.54  E-value=7.5e-15  Score=84.19  Aligned_cols=62  Identities=21%  Similarity=0.355  Sum_probs=57.6

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|+.||.|..+.++.++ ++.+++||||+|.+.++|++||+.||+..+.++.|+|+++.
T Consensus        31 ~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~   93 (98)
T 2cqp_A           31 EILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLGS   93 (98)
T ss_dssp             HHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEESS
T ss_pred             HHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEcC
Confidence            488999999999888777776 89999999999999999999999999999999999999987

>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=99.54  E-value=1.2e-14  Score=81.69  Aligned_cols=62  Identities=29%  Similarity=0.469  Sum_probs=57.1

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCC-cccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGR-SLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~-~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|++||.|..+.++.++ ++. +++||||+|.+.++|++|++.||+..+.++.|.|+++.
T Consensus        20 ~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   83 (88)
T 4a8x_A           20 HIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAVL   83 (88)
T ss_dssp             HHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             HHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEECC
Confidence            478999999999999998877 444 88999999999999999999999999999999999987

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.53  E-value=2.9e-14  Score=80.75  Aligned_cols=64  Identities=27%  Similarity=0.488  Sum_probs=58.3

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|+.||.|..+.++.+ ++.+++||||+|.+.++|++|++.||+..+.++.|.|+++....
T Consensus        24 ~l~~~f~~~G~v~~~~i~~~-~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~~   87 (92)
T 2dgv_A           24 MLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDRNAS   87 (92)
T ss_dssp             HHHHHHHTTSCEEEEEEEES-SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEECSCCS
T ss_pred             HHHHHHHhcCCEEEEEEEcc-CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCCC
Confidence            48899999999999999874 78889999999999999999999999999999999999987433

>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=99.53  E-value=6e-14  Score=81.96  Aligned_cols=59  Identities=17%  Similarity=0.263  Sum_probs=53.9

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCC-----eeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDG-----RPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~-----~~i~V~~~~~~~   65 (105)
                      +|+++|++||.|..|.|+.+      +||||+|.+.++|++||+.||+..|.+     +.|+|+++.++.
T Consensus        31 ~l~~~F~~~G~i~~~~i~~~------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i~V~~a~~~~   94 (108)
T 1x4c_A           31 DLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRS   94 (108)
T ss_dssp             HHHHHHGGGSCEEEEEEETT------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEEEEEESSCCS
T ss_pred             HHHHHHHhcCCEeEEEEecC------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEEEEEeCCCCC
Confidence            58899999999999999875      899999999999999999999999999     999999988533

>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=99.53  E-value=8.5e-15  Score=83.46  Aligned_cols=62  Identities=19%  Similarity=0.318  Sum_probs=57.4

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|+.||.|..+.++.++ ++.+++||||+|.+.++|++||+.||+..+.++.|+|+++.
T Consensus        31 ~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a~   93 (95)
T 2ek1_A           31 EILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGPS   93 (95)
T ss_dssp             HHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             HHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEecc
Confidence            488999999999888888877 88999999999999999999999999999999999999875

>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=99.53  E-value=1.4e-14  Score=85.26  Aligned_cols=62  Identities=26%  Similarity=0.359  Sum_probs=58.4

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeec
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD   63 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~   63 (105)
                      +|+++|+.||.|..|.|+.++ ++.+++||||+|.+.++|++|| .||+..|.++.|.|+++..
T Consensus        41 ~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~  103 (114)
T 2cq4_A           41 DLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQA  103 (114)
T ss_dssp             HHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEHHH
T ss_pred             HHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEecCC
Confidence            488999999999999999988 7899999999999999999999 8999999999999999873

>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=99.52  E-value=6.8e-14  Score=81.69  Aligned_cols=62  Identities=19%  Similarity=0.292  Sum_probs=55.5

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeecc
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADV   64 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~   64 (105)
                      +|+++|++||.|..|.|+.  +..+++||||+|.+.++|++||+.||+..|.++.|+|+++...
T Consensus        38 ~l~~~F~~~G~v~~~~i~~--~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~   99 (109)
T 1x4a_A           38 DIEDVFYKYGAIRDIDLKN--RRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSG   99 (109)
T ss_dssp             HHHHHHGGGSCEEEEEECC--SSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCCC
T ss_pred             HHHHHHHhcCCeEEEEEEE--CCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcccC
Confidence            4889999999999998854  4457899999999999999999999999999999999998743

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.52  E-value=7.4e-15  Score=80.40  Aligned_cols=60  Identities=18%  Similarity=0.303  Sum_probs=56.0

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEe
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA   61 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~   61 (105)
                      +|+++|++||.|..+.++.++ ++.+++||||+|.+.++|++|++ |++..+.++.|.|+++
T Consensus        15 ~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A           15 DVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             HHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSSCCCEEECC
T ss_pred             HHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECCEEEEEEeC
Confidence            478999999999999999988 89999999999999999999998 8999999999999864

>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=99.52  E-value=4.3e-14  Score=82.02  Aligned_cols=60  Identities=25%  Similarity=0.422  Sum_probs=55.3

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|+.|| +..|.|+.++++++++||||+|.+.++|++||+ +|+..|.++.|+|..+.
T Consensus        31 ~l~~~F~~~G-~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~~~   90 (102)
T 1wez_A           31 DIYNFFSPLN-PMRVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLNS   90 (102)
T ss_dssp             HHHHSSCSCC-CSEEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEEC
T ss_pred             HHHHHHHHcC-ceEEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEECC
Confidence            5889999999 559999998899999999999999999999995 79999999999999877

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.52  E-value=2.6e-14  Score=80.80  Aligned_cols=57  Identities=25%  Similarity=0.239  Sum_probs=53.4

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|.+||.|.++.+..     ++|||||+|.+.++|++|++.||+..+.+++|+|++++
T Consensus        23 ~L~~lF~q~G~V~~~~l~~-----~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~   79 (89)
T 2wbr_A           23 TLRTLCMQHGPLVSFHPYL-----NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             HHHHHHHHHSCEEEEEEET-----TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             HHHHHHHhhCCEEEEEEcC-----CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            4889999999999999876     48999999999999999999999999999999999886

>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=99.52  E-value=3.5e-14  Score=82.90  Aligned_cols=62  Identities=18%  Similarity=0.190  Sum_probs=57.1

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-C--CCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-S--GRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~--~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      ||+++|++||.|.++.|++++ +  ..++|++||+|.+.++|++|+..||+..+.++.|.|.+..
T Consensus        31 dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~~f~GR~i~v~~~~   95 (105)
T 3v4m_A           31 DVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCD   95 (105)
T ss_dssp             HHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             HHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEeC
Confidence            478999999999999998876 3  3678999999999999999999999999999999999986

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.51  E-value=2.1e-14  Score=83.59  Aligned_cols=63  Identities=27%  Similarity=0.488  Sum_probs=57.4

Q ss_pred             HHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCe-eEEEEEeeccC
Q psy1928           2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGR-PMQIQLAADVS   65 (105)
Q Consensus         2 l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~-~i~V~~~~~~~   65 (105)
                      |+++|++||.|..|.|+ ..++.+++||||+|.+.++|++||..||+..+.++ .|+|.++.+.+
T Consensus        38 l~~~F~~~G~v~~v~i~-~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~~l~V~~a~~~~  101 (105)
T 2nlw_A           38 IHKIFSKFGKITNDFYP-EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRVNLFTDFD  101 (105)
T ss_dssp             HHHHHGGGSCEEEEECC-CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTCEEEEECSCCCC
T ss_pred             HHHHHhcCCCEEEEEee-CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCceEEEEEcchHh
Confidence            88999999999999887 34888999999999999999999999999999998 99999987443

>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=99.51  E-value=6.6e-14  Score=78.57  Aligned_cols=60  Identities=23%  Similarity=0.431  Sum_probs=55.4

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEe
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA   61 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~   61 (105)
                      +|+++|++||.|..+.++.++ ++.+++||||+|.+.++|++|++ +++..+.++.|.|+++
T Consensus        27 ~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v~~A   87 (87)
T 3s7r_A           27 DLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDPKKA   87 (87)
T ss_dssp             HHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEEEEC
T ss_pred             HHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEEEeC
Confidence            488999999999999999998 89999999999999999999997 4888899999999874

>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=99.51  E-value=6.1e-15  Score=83.37  Aligned_cols=64  Identities=27%  Similarity=0.420  Sum_probs=57.0

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|+.||.|..+.++.++ ++.+++||||+|.+.+ |++|+..||+..+.++.|.|+++....
T Consensus        17 ~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~~~   81 (90)
T 2ki2_A           17 QVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANPKK   81 (90)
T ss_dssp             HHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC----
T ss_pred             HHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCCCC
Confidence            478899999999999999988 8999999999999999 999999999999999999999988443

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.51  E-value=1.8e-14  Score=87.44  Aligned_cols=64  Identities=28%  Similarity=0.456  Sum_probs=60.0

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeecc
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADV   64 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~   64 (105)
                      +|+++|+.||.|..|.|+.++ ++.+++||||+|.+.++|++||..||+..+.++.|+|+++...
T Consensus        63 ~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~~  127 (135)
T 2lea_A           63 TLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYG  127 (135)
T ss_dssp             HHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEECCCC
T ss_pred             HHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            488999999999999999987 8999999999999999999999999999999999999999843

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.51  E-value=3.4e-14  Score=82.69  Aligned_cols=61  Identities=13%  Similarity=0.148  Sum_probs=57.3

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|+.||.|.+|.|+.++.+.++|||||+|.+.++|++||. +++..+.++.|.|.++.
T Consensus        27 ~L~~~F~~~G~v~~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~~~   87 (103)
T 1s79_A           27 DIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   87 (103)
T ss_dssp             HHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEHH
T ss_pred             HHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEch
Confidence            48899999999999999998888899999999999999999999 89999999999999876

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.50  E-value=3.3e-14  Score=86.10  Aligned_cols=61  Identities=26%  Similarity=0.407  Sum_probs=57.0

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEe
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA   61 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~   61 (105)
                      +|+++|++||.|..+.++.++ ++.+++||||+|.+.++|++|++.||+..+.++.|+|+++
T Consensus        79 ~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~A  140 (140)
T 2ku7_A           79 VLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA  140 (140)
T ss_dssp             HHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEEC-
T ss_pred             HHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            488999999999999999987 8999999999999999999999999999999999999875

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.50  E-value=2e-14  Score=78.86  Aligned_cols=60  Identities=23%  Similarity=0.338  Sum_probs=56.3

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEe
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA   61 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~   61 (105)
                      +|+++|++||.|..+.++.++ ++.+++||||+|.+.++|++|++.++ ..+.++.|.|+++
T Consensus        16 ~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a   76 (77)
T 1uaw_A           16 GLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             HHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             HHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            478999999999999999988 89999999999999999999999999 9999999999875

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.25  E-value=1.6e-15  Score=89.68  Aligned_cols=65  Identities=23%  Similarity=0.504  Sum_probs=59.8

Q ss_pred             CHHHHhccCCCeeE--------EEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKS--------AKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~--------~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|+.||.|..        +.++.++ ++.+++||||+|.+.++|++|++.||+..+.++.|.|+++...+
T Consensus        23 ~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~   96 (116)
T 2lcw_A           23 SVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRA   96 (116)
Confidence            58899999999988        8899887 88999999999999999999999999999999999999988544

>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=99.50  E-value=8.1e-14  Score=81.90  Aligned_cols=62  Identities=19%  Similarity=0.330  Sum_probs=57.3

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCccc--------CCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPL--------DGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i--------~~~~i~V~~~~   62 (105)
                      +|+++|+.||.|..+.|+.++++.+++||||+|.+.++|++|++.||+..+        .+++|.|.++.
T Consensus        41 ~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~~~~l~v~~a~  110 (114)
T 1x5o_A           41 ELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEPLLCKFSG  110 (114)
T ss_dssp             HHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSSCBEEEECC
T ss_pred             HHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCCCCceeEEccC
Confidence            478999999999999999988889999999999999999999999999999        57779999887

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.50  E-value=7.2e-14  Score=80.50  Aligned_cols=62  Identities=23%  Similarity=0.380  Sum_probs=54.7

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|++||.|   .++.+.++++++||||+|.+.++|++||+.||+..+.++.|+|+++....
T Consensus        31 ~l~~~F~~~g~v---~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~   92 (101)
T 2fc9_A           31 TLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQGPRG   92 (101)
T ss_dssp             HHHHHCSSCSEE---ECCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEECSSCC
T ss_pred             HHHHHHHhCCEE---EEEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEcCCCC
Confidence            488999999977   45665688899999999999999999999999999999999999988443

>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=99.49  E-value=3.3e-14  Score=82.02  Aligned_cols=62  Identities=19%  Similarity=0.321  Sum_probs=57.2

Q ss_pred             CHHHHhccCCCeeEEEEEeCC--CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeecc
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR--SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADV   64 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~--~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~   64 (105)
                      +|+++|+.|| |.++.|+.++  ++++++||||+|.+.++|++|+ .||+..+.++.|.|+++.+.
T Consensus        35 ~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V~~a~~~   98 (100)
T 2j76_E           35 SIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRVDVADQA   98 (100)
T ss_dssp             HHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCCEECCCS
T ss_pred             HHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEEEEeccCC
Confidence            4889999999 9999999886  7889999999999999999999 89999999999999998743

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.49  E-value=7.1e-15  Score=82.27  Aligned_cols=61  Identities=16%  Similarity=0.212  Sum_probs=55.7

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEe
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA   61 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~   61 (105)
                      +|+++|+.||.|..+.++.++ ++.+++||||+|.+.++|++|++.||+..+.++.|++.+.
T Consensus        21 ~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~   82 (85)
T 1x4e_A           21 DLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGP   82 (85)
T ss_dssp             HHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCC
T ss_pred             HHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCC
Confidence            478899999999999999997 8999999999999999999999999999999988776543

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.49  E-value=4.5e-14  Score=82.70  Aligned_cols=63  Identities=21%  Similarity=0.435  Sum_probs=57.1

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeecc
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADV   64 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~   64 (105)
                      +|+++|++||.|..+.++.++. .+++||||+|.+.++|++|++.||+..+.++.|.|+++..+
T Consensus        45 ~l~~~F~~~G~i~~v~i~~~~~-~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  107 (109)
T 2err_A           45 DLRQMFGQFGKILDVEIIFNER-GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR  107 (109)
T ss_dssp             HHHHHGGGTCCCSCEEECCBTT-BCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEEECCCS
T ss_pred             HHHHHHHhcCCEEEEEEEECCC-CCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            4889999999999999988753 37899999999999999999999999999999999998743

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.48  E-value=2.3e-14  Score=86.42  Aligned_cols=63  Identities=16%  Similarity=0.303  Sum_probs=58.5

Q ss_pred             CHHHHhccCCCeeE--EEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCc----ccCCeeEEEEEeecc
Q psy1928           1 MIYELFSEFGPLKS--AKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGV----PLDGRPMQIQLAADV   64 (105)
Q Consensus         1 ~l~~~f~~~G~i~~--~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~----~i~~~~i~V~~~~~~   64 (105)
                      +|+++|++||.|..  |.|+.++ +++++|||||+|.+. +|++||..||+.    .+.++.|.|+++...
T Consensus        39 ~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr~l~V~~a~~~  108 (131)
T 2m2b_A           39 SILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGKTINVEFAKGS  108 (131)
T ss_dssp             HHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGCCCCCEECCCS
T ss_pred             HHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCEEEEEEECCCC
Confidence            48899999999976  9999998 999999999999999 999999999999    999999999998743

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.48  E-value=2.3e-13  Score=77.92  Aligned_cols=60  Identities=20%  Similarity=0.370  Sum_probs=54.1

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|++||.|..|.|.     .+++||||+|.+.++|++||..||+..+.++.|+|+++....
T Consensus        29 ~l~~~F~~~G~i~~v~i~-----~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~~~   88 (97)
T 1x5p_A           29 LLRGAFSPFGNIIDLSMD-----PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQP   88 (97)
T ss_dssp             HHHHHHTTTSCEEEEEEE-----TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECCSSCC
T ss_pred             HHHHHHhhCCCEEEEEec-----CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCCCC
Confidence            488999999999999885     357899999999999999999999999999999999987444

>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=99.48  E-value=4.8e-14  Score=83.13  Aligned_cols=63  Identities=17%  Similarity=0.275  Sum_probs=58.2

Q ss_pred             CHHHHhccCCCe-eEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeecc
Q psy1928           1 MIYELFSEFGPL-KSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADV   64 (105)
Q Consensus         1 ~l~~~f~~~G~i-~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~   64 (105)
                      +|+++|+.||.| ..|.|+.++++++++||||+|.+.++|++||+. |+..|.++.|.|.++...
T Consensus        31 ~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~~a~~~   94 (114)
T 2cpy_A           31 DVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVHVVTLE   94 (114)
T ss_dssp             HHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEEEECHH
T ss_pred             HHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEEECCHH
Confidence            488999999999 889999988899999999999999999999997 999999999999999843

>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=99.48  E-value=9.3e-15  Score=89.32  Aligned_cols=63  Identities=22%  Similarity=0.400  Sum_probs=56.9

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|+.|| |..|.|+.++++++++||||+|.+.++|++|| .+|+..|.++.|+|..+...+
T Consensus        62 dL~~~F~~~G-i~~v~i~~d~~g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~a~~~~  124 (139)
T 2hgn_A           62 DIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLNSTTG  124 (139)
T ss_dssp             HHHHHHCSCC-CSEEECCCSSSSCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEECCCSC
T ss_pred             HHHHHHHhcC-CeEEEEEECCCCCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEECCCCC
Confidence            5899999999 77999998888899999999999999999999 689999999999998877443

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.48  E-value=2.3e-13  Score=76.88  Aligned_cols=59  Identities=17%  Similarity=0.271  Sum_probs=53.5

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccCC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVSV   66 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~~   66 (105)
                      +|+++|++||.|..+.++       ++||||+|.+.++|++|++.||+..+.++.|+|+++.....
T Consensus        24 ~l~~~F~~~G~i~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~   82 (90)
T 2dnq_A           24 EIRSLFEQYGKVLECDII-------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNKSK   82 (90)
T ss_dssp             HHHHHHHTSSCEEEEEEE-------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECSSCCCC
T ss_pred             HHHHHHHhCCCEEEEEEE-------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEECCCCCC
Confidence            488999999999999887       47999999999999999999999999999999999885443

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.48  E-value=2.4e-13  Score=87.17  Aligned_cols=65  Identities=28%  Similarity=0.399  Sum_probs=60.9

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|++||.|..+.++.++ ++.+++||||+|.+.++|++|++.||+..|.++.|.|.++...+
T Consensus       141 ~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a~~~~  206 (216)
T 2qfj_A          141 DIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPP  206 (216)
T ss_dssp             HHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEECSSCS
T ss_pred             HHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEecCCC
Confidence            488999999999999999997 89999999999999999999999999999999999999998443

>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=99.47  E-value=1.5e-13  Score=79.82  Aligned_cols=64  Identities=25%  Similarity=0.287  Sum_probs=57.8

Q ss_pred             CHHHHhccCCCeeE-EEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKS-AKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~-~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|+.||.|.. |.|+.+.++++++||||+|.+.++|++||.. ++..+.++.|.|.++...+
T Consensus        31 ~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~~~~~~~   95 (104)
T 1wg5_A           31 EIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIFKSSRAE   95 (104)
T ss_dssp             HHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEEEECTTT
T ss_pred             HHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEEECCHHH
Confidence            58899999999987 8888888899999999999999999999997 9999999999999887443

>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=99.47  E-value=1.5e-13  Score=80.08  Aligned_cols=65  Identities=17%  Similarity=0.128  Sum_probs=58.1

Q ss_pred             CHHHHhccCCC-eeEEEEE-eCC-CCCcccEEEEEeCCHHHHHHHHHHhC--CcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGP-LKSAKLH-YDR-SGRSLGTADLIYERRSDAIKAMKQYN--GVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~-i~~~~i~-~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~--~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|+.||. |..+.++ .++ ++.+++||||+|.+.++|++|+..|+  +..+.++.|+|+++.+..
T Consensus        24 ~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~V~~a~~~~   93 (109)
T 2dis_A           24 EILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEI   93 (109)
T ss_dssp             HHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEESCSSC
T ss_pred             HHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEEEEEcCCCC
Confidence            47899999998 9999988 666 78899999999999999999999996  589999999999998444

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.47  E-value=7.9e-14  Score=80.32  Aligned_cols=61  Identities=23%  Similarity=0.404  Sum_probs=55.9

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|++||.|..+.++.+    +++||||+|.+.++|++|++.||+..+.++.|.|+++...+
T Consensus        16 ~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   76 (101)
T 2hvz_A           16 ELERAFSYYGPLRTVWIARN----PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMP   76 (101)
T ss_dssp             HHHHHHHHHCCCSEEEEESS----SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSCC
T ss_pred             HHHHHHHhcCCeEEEEEeeC----CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCCC
Confidence            48899999999999999876    67999999999999999999999999999999999998544

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.47  E-value=7.7e-14  Score=82.83  Aligned_cols=62  Identities=19%  Similarity=0.261  Sum_probs=57.9

Q ss_pred             CHHHHhccCCC---eeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeec
Q psy1928           1 MIYELFSEFGP---LKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD   63 (105)
Q Consensus         1 ~l~~~f~~~G~---i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~   63 (105)
                      +|+++|+.||.   |..|.|+.++.+++++||||+|.+.++|++||+ +|+..|.++.|+|.++..
T Consensus        33 ~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~a~~   97 (118)
T 2db1_A           33 DVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK-KDRESMGHRYIEVFKSHR   97 (118)
T ss_dssp             HHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEEEEEECH
T ss_pred             HHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEEEEECCH
Confidence            48899999998   899999998889999999999999999999999 999999999999999873

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.47  E-value=3.2e-13  Score=77.80  Aligned_cols=62  Identities=23%  Similarity=0.280  Sum_probs=54.3

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|+.|   ..+.++.++ ++.+++||||+|.+.++|++||+.||+..|.++.|+|+++.+..
T Consensus        31 ~l~~~F~~~---~~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~   93 (102)
T 2fc8_A           31 TLKESFDGS---VRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPKG   93 (102)
T ss_dssp             HHHHTSTTC---SEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCCC
T ss_pred             HHHHHhcCC---eEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEecCCC
Confidence            477888866   467788887 89999999999999999999999999999999999999988433

>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=99.47  E-value=1.5e-13  Score=81.84  Aligned_cols=62  Identities=16%  Similarity=0.235  Sum_probs=56.7

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-C----CCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-S----GRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~----~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      ||++.|++||.|.+|.|+.++ +    ++++|++||+|.+.++|++|+..||+..+.++.|.|.++.
T Consensus        41 dl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~GR~i~v~~~~  107 (118)
T 3ue2_A           41 EVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYD  107 (118)
T ss_dssp             HHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             HHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECCcEEEEEEcC
Confidence            478999999999999998875 2    4577999999999999999999999999999999999986

>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=99.47  E-value=2e-13  Score=79.68  Aligned_cols=61  Identities=16%  Similarity=0.333  Sum_probs=55.6

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccCC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVSV   66 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~~   66 (105)
                      +|+++|+.||.|..|.++.+     ++||||+|.+.++|++|+..|++..+.++.|+|.++...+.
T Consensus        41 ~l~~~F~~~G~i~~v~i~~~-----~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  101 (109)
T 1x4g_A           41 LMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPD  101 (109)
T ss_dssp             HHHHHHHHHSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCCCS
T ss_pred             HHHHHHHhcCCeEEEEEeCC-----CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEecCCCCC
Confidence            47899999999999999875     78999999999999999999999999999999999985443

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.47  E-value=1.1e-13  Score=83.29  Aligned_cols=60  Identities=22%  Similarity=0.456  Sum_probs=54.1

Q ss_pred             HHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeec
Q psy1928           2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD   63 (105)
Q Consensus         2 l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~   63 (105)
                      |+++|++||.|..|.+.  .++.++|||||+|.+.++|+.|+..||+..+.++.|+|.++..
T Consensus        50 L~~~F~~~G~I~~v~i~--~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~V~~a~~  109 (127)
T 2a3j_A           50 LYALASSQGDILDIVVD--LSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSET  109 (127)
T ss_dssp             HHHHHHHHSCEEEEEEC--CCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCEEEECCC
T ss_pred             HHHHhccCCCeEEEEec--cCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEEEEEccC
Confidence            56799999999988764  3677899999999999999999999999999999999999873

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.46  E-value=2.7e-13  Score=83.43  Aligned_cols=62  Identities=31%  Similarity=0.519  Sum_probs=58.8

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|+.||.|..+.++.++ ++.++++|||+|.+.++|++|+..||+..+.++.|.|.+++
T Consensus       103 ~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~  165 (166)
T 3md3_A          103 TLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAA  165 (166)
T ss_dssp             HHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESC
T ss_pred             HHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEecC
Confidence            478999999999999999997 89999999999999999999999999999999999999875

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.46  E-value=3.2e-14  Score=79.03  Aligned_cols=57  Identities=26%  Similarity=0.500  Sum_probs=51.6

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCe-eEEE
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGR-PMQI   58 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~-~i~V   58 (105)
                      +|+++|++||.|..+.++ ..++++++||||+|.+.++|++|++.||+..+.++ .|+|
T Consensus        23 ~l~~~F~~~G~i~~v~i~-~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~V   80 (81)
T 2krb_A           23 VIHKIFSKFGKITNDFYP-EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRV   80 (81)
T ss_dssp             HHHHHHHTTCCEEEEECC-CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCCC
T ss_pred             HHHHHHhhcCCeEEEEec-CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEEe
Confidence            478999999999999877 34888999999999999999999999999999998 8765

>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=99.46  E-value=2.7e-13  Score=77.87  Aligned_cols=62  Identities=24%  Similarity=0.401  Sum_probs=55.6

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccCCC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVSVL   67 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~~~   67 (105)
                      +|+++|++||.|..+.++.+     ++||||+|.+.++|++|++.||+..+.++.|.|+++.+....
T Consensus        31 ~l~~~F~~~G~i~~v~~~~~-----kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~~~~   92 (99)
T 2cpj_A           31 EMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSASL   92 (99)
T ss_dssp             HHHHHTSTTCCCSEEEEETT-----TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCSCC
T ss_pred             HHHHHHhhcCCeEEEEEecC-----CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEcCCCCCC
Confidence            48899999999999998864     689999999999999999999999999999999998854433

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.45  E-value=1.1e-13  Score=87.49  Aligned_cols=62  Identities=74%  Similarity=1.147  Sum_probs=59.0

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|+.||.|..|.|+.++++.+++||||+|.+.++|++||+.||+..|.++.|+|+++.
T Consensus       104 ~L~~~F~~~G~I~~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~a~  165 (177)
T 2f3j_A          104 DIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVA  165 (177)
T ss_dssp             HHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEEES
T ss_pred             HHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEec
Confidence            48899999999999999988888899999999999999999999999999999999999987

>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=99.45  E-value=1.4e-13  Score=80.03  Aligned_cols=60  Identities=18%  Similarity=0.330  Sum_probs=52.9

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCc--ccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGV--PLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~--~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|++||.|.+|.|+.+     ++||||+|.+.++|++||+.|++.  .+.+++|.|+++....
T Consensus        32 dL~~lF~~fG~V~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~~~   93 (102)
T 1x4d_A           32 QLLQLVEPFGVISNHLILNK-----INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKYK   93 (102)
T ss_dssp             HHHTTTGGGSCEEEEEECSS-----SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECCCT
T ss_pred             HHHHHHHhcCCEEEEEEEcC-----CCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEEECCCCC
Confidence            48899999999999998865     589999999999999999998864  5899999999998433

>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=99.45  E-value=2.7e-13  Score=85.73  Aligned_cols=66  Identities=18%  Similarity=0.341  Sum_probs=57.6

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccCCC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVSVL   67 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~~~   67 (105)
                      +|+++|+.||.|..+.++.++ ++.+++||||+|.+.++|++|+.. ++..+.++.|.|.++.+++..
T Consensus       120 ~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~a~~k~~~  186 (196)
T 1l3k_A          120 HLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKALSKQEM  186 (196)
T ss_dssp             HHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEECC-----
T ss_pred             HHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEecCChhHh
Confidence            488999999999999999998 899999999999999999999986 899999999999998855543

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.45  E-value=1.2e-13  Score=80.72  Aligned_cols=63  Identities=17%  Similarity=0.204  Sum_probs=55.2

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCC--cccCCeeEEEEEeeccCCCC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNG--VPLDGRPMQIQLAADVSVLE   68 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~--~~i~~~~i~V~~~~~~~~~~   68 (105)
                      +|+++|++||.|.+|.|+.+     ++||||+|.+.++|++||+.|++  ..+.+++|.|.++..++...
T Consensus        32 dL~~lF~~fG~V~~v~i~~~-----kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~A~~~~~~~   96 (105)
T 1sjq_A           32 EVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKT   96 (105)
T ss_dssp             HHHHHHHHHCCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBCCCSSSSCCC
T ss_pred             HHHHHHHhcCCEEEEEEEcC-----CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEcCCCCCCc
Confidence            58899999999999999875     69999999999999999998864  68999999999998555443

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.45  E-value=4.2e-13  Score=76.07  Aligned_cols=58  Identities=24%  Similarity=0.431  Sum_probs=52.8

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|++||.|..+.+++       +||||+|.+.++|++|++.||+..+.++.|+|+++....
T Consensus        26 ~l~~~F~~~G~v~~v~~~~-------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   83 (92)
T 2dgt_A           26 ELRAKFEEYGPVIECDIVK-------DYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTSRL   83 (92)
T ss_dssp             HHHHHHHTTSCCCEEEECS-------SEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEESSCCC
T ss_pred             HHHHHHHhcCCeEEEEEEC-------CEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEccCCC
Confidence            4889999999999998874       499999999999999999999999999999999998443

>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=99.44  E-value=6.4e-13  Score=78.08  Aligned_cols=62  Identities=21%  Similarity=0.328  Sum_probs=54.6

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|++||.|..|.| .++  .+++|+||+|.+.++|++|+..||+..+.++.|.|.++.+..
T Consensus        42 ~l~~~f~~~G~v~~v~i-~~~--~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~l~v~~a~~~~  103 (112)
T 2dit_A           42 DLRVECSKFGQIRKLLL-FDR--HPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGTT  103 (112)
T ss_dssp             HHHHHGGGTSCCSEEEE-ETT--CTTCEEEEECSCHHHHHHHHHHSTTCEETTEECEEEECCSCC
T ss_pred             HHHHHHHccCCEeEEEE-ecC--CCCEEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEeCCCC
Confidence            47889999999999965 443  378999999999999999999999999999999999987544

>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=99.44  E-value=2.9e-13  Score=84.03  Aligned_cols=62  Identities=32%  Similarity=0.418  Sum_probs=58.7

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|++||.|..+.++.++ ++.++++|||+|.+.++|++|++.||+..+.++.|.|+++.
T Consensus       110 ~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~As  172 (172)
T 2g4b_A          110 QVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS  172 (172)
T ss_dssp             HHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             HHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeCC
Confidence            478999999999999999997 99999999999999999999999999999999999999873

>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=99.44  E-value=2.9e-13  Score=77.48  Aligned_cols=59  Identities=22%  Similarity=0.333  Sum_probs=53.8

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccC--CeeEEEEEeecc
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLD--GRPMQIQLAADV   64 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~--~~~i~V~~~~~~   64 (105)
                      +|+++|++||.|..+.++.+     ++||||+|.+.++|++|++.||+..+.  ++.|.|+++.+.
T Consensus        33 ~l~~~F~~~G~v~~v~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~~a~~~   93 (97)
T 1why_A           33 ALAREFDRFGSIRTIDHVKG-----DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSG   93 (97)
T ss_dssp             HHHHHHHTTSCEEEEEECSS-----SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCC
T ss_pred             HHHHHHHhcCCeeEEEEeCC-----CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEEECCCC
Confidence            48899999999999988754     689999999999999999999999999  999999998854

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.44  E-value=9.5e-14  Score=81.84  Aligned_cols=62  Identities=13%  Similarity=0.187  Sum_probs=53.8

Q ss_pred             CHHHHhccCC-CeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFG-PLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G-~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|+.|| .|..+.++..   .+++||||+|.+.++|++||+.||+..+.++.|+|+++...+
T Consensus        44 dL~~~F~~~G~~v~~v~i~~~---~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a~~~p  106 (111)
T 2jvr_A           44 DLKDLARENSLETTFSSVNTR---DFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDDNPP  106 (111)
T ss_dssp             HHHHHHHHHTCCCSEEECSSC---SSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEESCC--
T ss_pred             HHHHHHHHhCCeeEEEEEEcC---CCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCCCC
Confidence            5889999999 8999887532   468999999999999999999999999999999999987443

>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=99.44  E-value=1.1e-13  Score=84.32  Aligned_cols=62  Identities=18%  Similarity=0.225  Sum_probs=57.9

Q ss_pred             CHHHHhccCCC---eeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeec
Q psy1928           1 MIYELFSEFGP---LKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD   63 (105)
Q Consensus         1 ~l~~~f~~~G~---i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~   63 (105)
                      +|+++|+.||.   |..|.|+.++.++++|||||+|.+.++|++||+ ||+..|.++.|+|.++..
T Consensus        60 dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~V~~a~~  124 (136)
T 2hgl_A           60 DVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIEVFKSHR  124 (136)
T ss_dssp             HHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEEEEECCH
T ss_pred             HHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEEEEECCh
Confidence            58899999999   889999998889999999999999999999999 999999999999998863

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.44  E-value=3.2e-13  Score=79.34  Aligned_cols=61  Identities=18%  Similarity=0.310  Sum_probs=56.2

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeec
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD   63 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~   63 (105)
                      ||+++|+.| .|..|.|+.+++++++|||||+|.+.++|++|| .+|+..|.++.|.|..+..
T Consensus        32 dl~~~F~~~-~v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a~~   92 (109)
T 2dnn_A           32 DVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPATE   92 (109)
T ss_dssp             HHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECCH
T ss_pred             HHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCc
Confidence            589999999 899999999888899999999999999999999 5899999999999988763

>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=99.43  E-value=4.8e-14  Score=82.95  Aligned_cols=65  Identities=23%  Similarity=0.394  Sum_probs=54.4

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|+.||.|..+.+..+. ++.+++||||+|.+.++|++||+.||+..+.++.|.|+++....
T Consensus        41 ~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~~~  106 (115)
T 2cpx_A           41 DLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKK  106 (115)
T ss_dssp             HHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEECCCCS
T ss_pred             HHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEccCCC
Confidence            478999999998443322222 77889999999999999999999999999999999999998444

>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=99.43  E-value=5.7e-13  Score=77.61  Aligned_cols=61  Identities=13%  Similarity=0.123  Sum_probs=53.1

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCc--ccCCeeEEEEEeeccCC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGV--PLDGRPMQIQLAADVSV   66 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~--~i~~~~i~V~~~~~~~~   66 (105)
                      +|+++|++||.|..|.++.+     ++||||+|.+.++|++|++.|++.  .+.++.|.|+++..+..
T Consensus        31 ~L~~~F~~fG~V~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~~a~~~~~   93 (104)
T 1wex_A           31 DLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRI   93 (104)
T ss_dssp             HHHHHHTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSSSSC
T ss_pred             HHHHHHHhCCCEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEccCccc
Confidence            48899999999999988764     689999999999999999988654  58999999999985443

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.43  E-value=4.7e-13  Score=84.75  Aligned_cols=65  Identities=31%  Similarity=0.373  Sum_probs=60.7

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|++||.|..+.++.++ ++.+++||||+|.+.++|++|++.||+..+.++.|.|+++.+..
T Consensus       130 ~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  195 (198)
T 2yh0_A          130 QVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA  195 (198)
T ss_dssp             HHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEESCCCC
T ss_pred             HHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            478999999999999999998 99999999999999999999999999999999999999988543

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.43  E-value=2e-13  Score=82.15  Aligned_cols=62  Identities=21%  Similarity=0.305  Sum_probs=54.6

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCC----HHH----HHHHHH--HhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYER----RSD----AIKAMK--QYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~----~~~----a~~ai~--~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+.+|+.||+|.++.++.|+ |+.++||+||+|.+    .++    |.+|+.  .|++..|+++.|+|.+.+
T Consensus        22 ~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~I~Gr~irV~ln~   94 (136)
T 2j8a_A           22 SIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCFIMGFKFEVILNK   94 (136)
T ss_dssp             HHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEEETTEEEEEEECC
T ss_pred             HHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCeecCcEEEEEECc
Confidence            478999999999999999999 99999999999996    333    788888  789999999999999765

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.42  E-value=4.3e-13  Score=77.64  Aligned_cols=60  Identities=18%  Similarity=0.242  Sum_probs=53.2

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcc--cCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVP--LDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~--i~~~~i~V~~~~~~~   65 (105)
                      +|+++|++||.|.++.++..     +++|||+|.+.++|++|++.|++..  +.+++|.|++++.++
T Consensus        37 ~L~~lF~~fG~V~~v~i~~~-----kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~~S~~k~   98 (100)
T 3r27_A           37 DLVEALQEFGPISYVVVMPK-----KRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTSQK   98 (100)
T ss_dssp             HHHHHHGGGSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEEECSCSC
T ss_pred             HHHHHHhccCCEEEEEEEcC-----CCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEEeccccc
Confidence            48899999999999988753     6899999999999999999999875  789999999998543

>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=99.42  E-value=6.7e-14  Score=83.60  Aligned_cols=62  Identities=11%  Similarity=0.188  Sum_probs=55.2

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeec
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD   63 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~   63 (105)
                      +|+++|+.||.|..+.++.+. ++++++||||+|.+.++|++||. ||+..|.++.|.|.++..
T Consensus        41 ~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~a~~  103 (124)
T 1wel_A           41 HVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPITK  103 (124)
T ss_dssp             HHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEECH
T ss_pred             HHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEECCH
Confidence            488999999999875444444 99999999999999999999999 999999999999999874

>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=99.42  E-value=5e-13  Score=78.13  Aligned_cols=55  Identities=25%  Similarity=0.395  Sum_probs=51.5

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|++||.|..|.+       +++||||+|.+.++|++|++.||+..+.++.|+|+++.
T Consensus        44 ~l~~~F~~~G~v~~v~i-------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~   98 (110)
T 1wf1_A           44 DVETIFSKYGRVAGCSV-------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAG   98 (110)
T ss_dssp             HHHHHHGGGSCCSEEEE-------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEESC
T ss_pred             HHHHHHHhCCCeEEEEE-------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECC
Confidence            48899999999999988       36899999999999999999999999999999999987

>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=99.42  E-value=5.2e-13  Score=79.57  Aligned_cols=63  Identities=17%  Similarity=0.204  Sum_probs=55.4

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCC--cccCCeeEEEEEeeccCCCC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNG--VPLDGRPMQIQLAADVSVLE   68 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~--~~i~~~~i~V~~~~~~~~~~   68 (105)
                      +|+++|++||.|.+|.|+.+     ++||||+|.+.++|++|++.|++  ..+.+++|.|.++..++...
T Consensus        47 dL~~lF~~fG~V~~v~i~~~-----kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~k~~~~  111 (119)
T 2ad9_A           47 EVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKT  111 (119)
T ss_dssp             HHHHHHTTTSCCCEEEEEGG-----GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEEECSSSSCCC
T ss_pred             HHHHHHHhcCCEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEEEccCCCCCc
Confidence            48899999999999999875     79999999999999999998874  67999999999998555443

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.41  E-value=6e-13  Score=76.09  Aligned_cols=58  Identities=9%  Similarity=0.216  Sum_probs=52.9

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|++||.|..+.+.       ++||||+|.+.++|++|++.||+..+.++.|.|+++....
T Consensus        27 ~l~~~F~~~G~v~~v~i~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~   84 (96)
T 2kvi_A           27 DLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSNA   84 (96)
T ss_dssp             HHHHHHTTTCCCCEEEEE-------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEEEECCC
T ss_pred             HHHHHHHhcCCEEEEEEe-------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEcCcCC
Confidence            488999999999999884       5899999999999999999999999999999999998443

>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=99.41  E-value=1.5e-12  Score=75.46  Aligned_cols=62  Identities=19%  Similarity=0.186  Sum_probs=53.9

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHh--CCcccCCeeEEEEEeeccCCC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQY--NGVPLDGRPMQIQLAADVSVL   67 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l--~~~~i~~~~i~V~~~~~~~~~   67 (105)
                      +|+++|+.||.|..+.++.+     ++||||+|.+.++|++|++.|  ++..+.+++|.|.++...+..
T Consensus        31 ~L~~~F~~fG~v~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~~~~~   94 (101)
T 2cq1_A           31 EVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHKELK   94 (101)
T ss_dssp             HHHHTTTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSCSSCC
T ss_pred             HHHHHHHhcCCEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEEEcCcccCc
Confidence            48899999999999988764     799999999999999999977  467799999999999855443

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.41  E-value=8.3e-13  Score=74.56  Aligned_cols=58  Identities=22%  Similarity=0.329  Sum_probs=52.7

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|+.||.|..+.+++       +||||+|.+.++|++|++.||+..+.++.|.|+++....
T Consensus        25 ~l~~~F~~~G~v~~~~~~~-------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   82 (90)
T 2dnp_A           25 ELRSLFERRGRVIECDVVK-------DYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTKGQ   82 (90)
T ss_dssp             HHHHHHHHHSCEEEEEECS-------SCEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCCCC
T ss_pred             HHHHHHHcCCCEEEEEEEC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEECCCCC
Confidence            4889999999999998874       499999999999999999999999999999999988443

>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=99.40  E-value=6.8e-14  Score=76.42  Aligned_cols=60  Identities=22%  Similarity=0.320  Sum_probs=55.0

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEe
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA   61 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~   61 (105)
                      +|+++|+.||.|..+.++.++ ++.+++||||+|.+.++|++|++. ++..+.++.|.|+++
T Consensus        15 ~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A           15 KIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIKVA   75 (75)
T ss_dssp             HHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTT-SSCCBTTBCCCEEEC
T ss_pred             HHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEEC
Confidence            478999999999999999887 899999999999999999999994 889999999998864

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.40  E-value=6e-13  Score=77.84  Aligned_cols=58  Identities=26%  Similarity=0.479  Sum_probs=53.1

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|+.||.|..+.++       ++||||+|.+.++|++|++.||+..+.++.|.|+++....
T Consensus        47 ~L~~~F~~~G~i~~v~i~-------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~  104 (108)
T 2jvo_A           47 ELNEIFGPFGPMKEVKIL-------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPA  104 (108)
T ss_dssp             HHHHHHTTTSCCCEEEEE-------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEESCSCCC
T ss_pred             HHHHHHHhcCCEEEEEEE-------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecCCC
Confidence            488999999999999887       5899999999999999999999999999999999987443

>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=99.40  E-value=1.3e-12  Score=80.39  Aligned_cols=63  Identities=32%  Similarity=0.491  Sum_probs=59.6

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeec
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD   63 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~   63 (105)
                      +|+++|+.||.|..+.++.++ ++.++++|||+|.+.++|++|++.|++..+.++.|.|.++.+
T Consensus        18 ~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~   81 (167)
T 1fxl_A           18 EFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (167)
T ss_dssp             HHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             HHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecCC
Confidence            478999999999999999998 999999999999999999999999999999999999998873

>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=99.40  E-value=2.9e-13  Score=83.61  Aligned_cols=63  Identities=22%  Similarity=0.369  Sum_probs=58.5

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeecc
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADV   64 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~   64 (105)
                      +|+++|+.||.|..+.++.++ ++.++++|||+|.+.++|++|++ +++..+.++.|.|.++.++
T Consensus       103 ~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a~pk  166 (167)
T 2cjk_A          103 EFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAEPR  166 (167)
T ss_dssp             HHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEECCCC
T ss_pred             HHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeecCCC
Confidence            478999999999999999987 89999999999999999999998 8999999999999998754

>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=99.40  E-value=9e-13  Score=77.40  Aligned_cols=58  Identities=26%  Similarity=0.213  Sum_probs=53.2

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeec
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD   63 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~   63 (105)
                      +|+++|++||.|..|.|+.     .++||||+|.+.++|++||..||+..+.++.|.|+++..
T Consensus        26 ~L~~~F~~~G~i~~v~i~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   83 (111)
T 1whx_A           26 EIQETFSRFGSLGRVLLPE-----GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPI   83 (111)
T ss_dssp             HHHHHHHTTSCEEEEECCS-----SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEET
T ss_pred             HHHHHHHhcCCEEEEEEeC-----CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCC
Confidence            4889999999999998764     468999999999999999999999999999999999984

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.39  E-value=2.4e-12  Score=79.15  Aligned_cols=64  Identities=22%  Similarity=0.380  Sum_probs=58.7

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeecc
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADV   64 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~   64 (105)
                      +|+++|++||.|.++.++.++++.+++||||+|.+.++|++|++.|++..+.++.|.|.++...
T Consensus        16 ~l~~~f~~~G~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~   79 (166)
T 3md3_A           16 ILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQS   79 (166)
T ss_dssp             HHHHHHGGGSCEEEEEEECCCC-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             HHHHHHHhcCCeEEEEEEECCCCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCC
Confidence            4889999999999999999888889999999999999999999999999999999999998743

>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=99.39  E-value=1.4e-12  Score=80.54  Aligned_cols=61  Identities=28%  Similarity=0.580  Sum_probs=57.1

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCC--eeEEEEEe
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDG--RPMQIQLA   61 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~--~~i~V~~~   61 (105)
                      +|+++|++||.|..+.++.++ ++.++++|||+|.+.++|++|+..||+..+.+  ++|.|+++
T Consensus       105 ~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A          105 QLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA  168 (168)
T ss_dssp             HHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             HHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEEEeC
Confidence            478999999999999999998 89999999999999999999999999999977  89999875

>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=99.39  E-value=6.5e-13  Score=74.09  Aligned_cols=57  Identities=18%  Similarity=0.296  Sum_probs=52.3

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHh-CCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQY-NGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l-~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|++||.|..+.++.+     ++||||+|.+.++|++|++.| ++..+.++.|+|++++
T Consensus        28 ~l~~~f~~~G~i~~~~~~~~-----kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~ak   85 (85)
T 2ytc_A           28 DLRNHFYQFGEIRTITVVQR-----QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWGR   85 (85)
T ss_dssp             HHHHHHHTTSCEEEEEEEGG-----GTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEECC
T ss_pred             HHHHHHHhCCCEeEEEEECC-----CCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEecC
Confidence            47899999999999998864     799999999999999999999 9999999999999864

>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=99.39  E-value=6.8e-13  Score=78.53  Aligned_cols=59  Identities=14%  Similarity=0.159  Sum_probs=53.8

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      ||+++|++||.|.+|.|+++.   ++|++||+|.+.++|++|+..||+..+.++.|.|.++.
T Consensus        33 dl~~~f~kfG~V~~v~i~~~~---~~G~~fV~f~~~e~A~~Ai~~lnG~~f~GR~i~v~~~~   91 (114)
T 3s6e_A           33 DVIEECNKHGGVIHIYVDKNS---AQGNVYVKCPSIAAAIAAVNALHGRWFAGKMITAAYVP   91 (114)
T ss_dssp             HHHHHHTTTTCCSEEEECTTC---TTCCEEEECSSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             HHHHHHhccCCEEEEEEecCC---CcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEEc
Confidence            578999999999999886542   58999999999999999999999999999999999986

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.39  E-value=6.9e-13  Score=85.58  Aligned_cols=62  Identities=27%  Similarity=0.434  Sum_probs=56.7

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeec
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD   63 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~   63 (105)
                      +|+++|++||.|..+.|+.++ +.+++||||+|.+.++|++||+.||+..|.++.|.|.++..
T Consensus       119 ~l~~~F~~~G~i~~~~i~~d~-~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~~  180 (213)
T 4f02_A          119 ALYDTFSAFGNILSCKVVCDE-NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS  180 (213)
T ss_dssp             HHHHHHGGGSCEEEEEEEEET-TEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             HHHHHHhhcCCeEEEEeeccC-CCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            488999999999999999875 33689999999999999999999999999999999999873

>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=99.39  E-value=1.1e-12  Score=77.18  Aligned_cols=61  Identities=23%  Similarity=0.484  Sum_probs=55.5

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeec
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD   63 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~   63 (105)
                      +|+++|+.||.|..|.++.+  +.+++||||+|.+.++|++|+..||+..+.++.|.|.++.+
T Consensus        24 ~l~~~F~~~G~v~~v~i~~~--~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~   84 (115)
T 3lqv_A           24 EMYDIFGKYGPIRQIRVGNT--PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYNA   84 (115)
T ss_dssp             HHHHHHHTTSCEEEEEEECS--TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECCH
T ss_pred             HHHHHHHhcCCeEEEEEeeC--CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecC
Confidence            47899999999999999865  34589999999999999999999999999999999999873

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.38  E-value=1.9e-12  Score=83.54  Aligned_cols=62  Identities=34%  Similarity=0.537  Sum_probs=58.8

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|++||.|.+|.|++++ ++++++||||+|.+.++|++||+.+++..+.++.|++.++.
T Consensus        31 ~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~~   93 (213)
T 4f02_A           31 MLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   93 (213)
T ss_dssp             HHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             HHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCccccccccc
Confidence            488999999999999999998 89999999999999999999999999999999999998876

>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=99.38  E-value=1.6e-12  Score=80.63  Aligned_cols=61  Identities=26%  Similarity=0.384  Sum_probs=56.3

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccC---CeeEEEEEe
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLD---GRPMQIQLA   61 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~---~~~i~V~~~   61 (105)
                      +|+++|++||.|..+.++.++++.+++||||+|.+.++|++|++.||+..+.   +++|.|.++
T Consensus       111 ~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V~~a  174 (175)
T 3nmr_A          111 DIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFA  174 (175)
T ss_dssp             HHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEEEEC
T ss_pred             HHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEEEec
Confidence            4789999999999999999888899999999999999999999999998776   389999986

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.38  E-value=6.9e-13  Score=76.47  Aligned_cols=62  Identities=23%  Similarity=0.392  Sum_probs=57.2

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeecc
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADV   64 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~   64 (105)
                      +|+++|+.||.|..+.++.++++.+++||||+|.+.++|++|+.  ++..++++.|.|.++..+
T Consensus        25 ~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~a~~~   86 (102)
T 2xs2_A           25 EIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPAIRK   86 (102)
T ss_dssp             HHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEEEEEC
T ss_pred             HHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEECCcC
Confidence            47899999999999999998888999999999999999999998  889999999999988743

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.38  E-value=7.7e-13  Score=75.72  Aligned_cols=60  Identities=20%  Similarity=0.297  Sum_probs=52.9

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeecc
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADV   64 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~   64 (105)
                      +|+++|+.||.|. +.++.+   .+++||||+|.+.++|++|++.||+..+.++.|.|+++.+.
T Consensus        35 ~l~~~F~~~G~v~-~~~~~~---~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   94 (97)
T 2e5j_A           35 DLKRALRELGSVP-LRLTWQ---GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQ   94 (97)
T ss_dssp             HHHHHHHHTTCCC-SEEEEE---TTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEECCCC
T ss_pred             HHHHHHHhcCCEE-EEEEcC---CCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCC
Confidence            4889999999986 666653   56899999999999999999999999999999999998744

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.38  E-value=1.8e-12  Score=78.31  Aligned_cols=60  Identities=18%  Similarity=0.218  Sum_probs=53.2

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccE-EEEEeCCHHHHHHHHHHhCCcccCC--eeEEEEEeecc
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGT-ADLIYERRSDAIKAMKQYNGVPLDG--RPMQIQLAADV   64 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~-~fv~f~~~~~a~~ai~~l~~~~i~~--~~i~V~~~~~~   64 (105)
                      +|+++|++||.|.+|.++..    .+++ |||+|.+.++|++|++.||+..|.+  +.|+|++++..
T Consensus        44 ~L~~lFs~yG~V~~V~i~~~----~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~ak~~  106 (130)
T 3zzy_A           44 VLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLT  106 (130)
T ss_dssp             HHHHHHTTSSCEEEEEEEEE----TTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEECSCS
T ss_pred             HHHHHHhCcCCEEEEEEEcC----CCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEecCCC
Confidence            48899999999999988763    2577 9999999999999999999999988  89999999843

>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=99.38  E-value=1.2e-12  Score=81.82  Aligned_cols=61  Identities=18%  Similarity=0.213  Sum_probs=53.9

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCC--eeEEEEEeecc
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDG--RPMQIQLAADV   64 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~--~~i~V~~~~~~   64 (105)
                      +|+++|++||.|.+|.|+...   +++|+||+|.+.++|++|++.||+..|.+  +.|+|++++..
T Consensus        62 ~L~~~Fs~fG~V~~V~i~~k~---~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~Ak~~  124 (164)
T 1sjr_A           62 VLHQIFSKFGTVLKIITFTKN---NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLT  124 (164)
T ss_dssp             HHHHHHHHHSCEEEEEEEESS---SCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEECSSS
T ss_pred             HHHHHHHhcCCEEEEEEEeCC---CCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEecCC
Confidence            488999999999999987542   46899999999999999999999999965  99999999844

>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=99.38  E-value=7e-13  Score=78.42  Aligned_cols=60  Identities=10%  Similarity=0.166  Sum_probs=52.2

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCccc-----CCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPL-----DGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i-----~~~~i~V~~~~~~~   65 (105)
                      +|+++|++||.|..|.|+.+     ++||||+|.+.++|++|++.||+.++     .+++|.|.++...+
T Consensus        43 ~L~~~F~~fG~v~~v~i~~~-----rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~l~v~~a~~~p  107 (114)
T 2cq2_A           43 QLLPVLEKCGLVDALLMPPN-----KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVEKVQ  107 (114)
T ss_dssp             HHHHHHHHHSCEEEEECCTT-----CSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEEEESCCC
T ss_pred             HHHHHHHhcCCeEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcEEEEEecccCc
Confidence            48999999999999877542     68999999999999999999999988     57889999987433

>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=99.37  E-value=8.5e-13  Score=77.86  Aligned_cols=59  Identities=20%  Similarity=0.271  Sum_probs=51.9

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCC--cccCCeeEEEEEeecc
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNG--VPLDGRPMQIQLAADV   64 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~--~~i~~~~i~V~~~~~~   64 (105)
                      +|+++|++||.|.+|.|+..     ++||||+|.+.++|++||+.|++  ..+.++.|.|.++...
T Consensus        42 ~L~~lF~~fG~V~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~~  102 (112)
T 1x4f_A           42 AVLKLAEPYGKIKNYILMRM-----KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKY  102 (112)
T ss_dssp             HHHTTTTTTSCCSEEEEETT-----TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECSC
T ss_pred             HHHHHHHhcCCEEEEEEecC-----CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEECccc
Confidence            48899999999999998753     79999999999999999998864  5689999999999833

>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=99.37  E-value=1.8e-13  Score=79.77  Aligned_cols=62  Identities=18%  Similarity=0.258  Sum_probs=57.1

Q ss_pred             CHHHHhccCCC---eeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeec
Q psy1928           1 MIYELFSEFGP---LKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD   63 (105)
Q Consensus         1 ~l~~~f~~~G~---i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~   63 (105)
                      +|+++|+.||.   |..|.|+.++.++++|||||+|.+.++|++||. +|+..+.++.|+|.++..
T Consensus        27 ~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~a~~   91 (107)
T 2lmi_A           27 DVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVEVYEINN   91 (107)
T ss_dssp             HHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCCCEECCH
T ss_pred             HHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEEEEECCH
Confidence            48899999887   889999988888999999999999999999999 999999999999998873

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.37  E-value=5.6e-13  Score=76.71  Aligned_cols=58  Identities=19%  Similarity=0.319  Sum_probs=52.9

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeec
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD   63 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~   63 (105)
                      +|+++|+.||.|.++.+..     +++||||+|.+.++|++|+..||+..+.++.|+|+++++
T Consensus        43 ~l~~~f~~~G~i~~~~~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~  100 (101)
T 2la4_A           43 DLIPLFQNFGFILDFKHYP-----EKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKE  100 (101)
T ss_dssp             HHHHHHHTTSCCSEEEEET-----TTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCCC
T ss_pred             HHHHHHHhCCCEEEEEEec-----CCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEeccC
Confidence            4789999999999998874     479999999999999999999999999999999998763

>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=99.37  E-value=9.7e-13  Score=80.75  Aligned_cols=60  Identities=25%  Similarity=0.403  Sum_probs=55.0

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeecc
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADV   64 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~   64 (105)
                      +|+++|+.||.|.+|.++.+    +++||||+|.+.++|++|+..||+..+.++.|+|+++.+.
T Consensus        89 ~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  148 (150)
T 2i2y_A           89 ELERAFGYYGPLRSVWVARN----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGE  148 (150)
T ss_dssp             HHHHHHHHHSCEEEEEECSS----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECCCC
T ss_pred             HHHHHHHhhCCEEEEEEeeC----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcCCC
Confidence            48899999999999999876    5799999999999999999999999999999999998743

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.37  E-value=3.2e-12  Score=73.30  Aligned_cols=58  Identities=36%  Similarity=0.539  Sum_probs=52.1

Q ss_pred             CHHHHhccC--CCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEF--GPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~--G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|+.|  |.|..+.++       ++||||+|.+.++|++|+..||+..+.++.|.|+++.+..
T Consensus        31 ~l~~~F~~~g~g~v~~~~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~   90 (99)
T 2cpd_A           31 MIEKEFNNIKPGAVERVKKI-------RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVD   90 (99)
T ss_dssp             HHHHHHHTTSTTCEEEEEEC-------SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCCC
T ss_pred             HHHHHHHhcCCcceEEEEEe-------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEECCCCC
Confidence            488999999  999988765       4699999999999999999999999999999999988444

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.37  E-value=1.8e-12  Score=73.79  Aligned_cols=59  Identities=19%  Similarity=0.268  Sum_probs=51.0

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|+.||.|.+|  +.++ ++.   ||||+|.+.++|++||+ ||+..+.++.|.|+++..+.
T Consensus        24 ~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a~~~~   83 (94)
T 2e5g_A           24 QLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPREQKE   83 (94)
T ss_dssp             HHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECCCBCSCCSC
T ss_pred             HHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEECCcCC
Confidence            488999999999987  5555 555   99999999999999999 99999999999999776443

>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=99.36  E-value=2.7e-12  Score=73.63  Aligned_cols=56  Identities=9%  Similarity=0.244  Sum_probs=51.7

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeec
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD   63 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~   63 (105)
                      +|+++|+.||.|..+.+.       ++||||+|.+.++|++|+..||+..+.++.|+|++++.
T Consensus        39 ~L~~~F~~~G~v~~v~i~-------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   94 (97)
T 2xnq_A           39 DLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSS   94 (97)
T ss_dssp             HHHHHHGGGSCEEEEEEC-------SSEEEEEESSHHHHHHHHHHHTTSEETTEECEEEECCC
T ss_pred             HHHHHHHhcCCEEEEEEe-------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCC
Confidence            488999999999999883       68999999999999999999999999999999999873

>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=99.36  E-value=2.7e-12  Score=78.97  Aligned_cols=61  Identities=26%  Similarity=0.519  Sum_probs=55.8

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCee--EEEEEe
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRP--MQIQLA   61 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~--i~V~~~   61 (105)
                      +|+++|++||.|..+.++.++ ++.++++|||+|.+.++|++|++.||+..+.++.  |.|.++
T Consensus       104 ~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v~~A  167 (167)
T 1fxl_A          104 ELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA  167 (167)
T ss_dssp             HHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             HHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEEEeC
Confidence            478999999999999999988 8999999999999999999999999999999865  777764

>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=99.36  E-value=1.3e-12  Score=80.73  Aligned_cols=64  Identities=25%  Similarity=0.492  Sum_probs=59.5

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeecc
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADV   64 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~   64 (105)
                      +|+++|+.||.|.++.++.++ ++.+++||||+|.+.++|++|++.|++..+.++.|.|.++.+.
T Consensus        19 ~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~   83 (168)
T 1b7f_A           19 ELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARPG   83 (168)
T ss_dssp             HHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             HHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecCCC
Confidence            488999999999999999887 8899999999999999999999999999999999999998743

>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=99.35  E-value=1.7e-12  Score=73.59  Aligned_cols=59  Identities=25%  Similarity=0.346  Sum_probs=51.0

Q ss_pred             CHHHHhccCCC-eeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCC-cccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGP-LKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNG-VPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~-i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~-~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|++||. |..+.+.      +++||||+|.+.++|++|++.||+ ..+.++.|+|+++.+..
T Consensus        24 ~l~~~F~~~G~vv~~~~~~------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~~   84 (93)
T 2cqh_A           24 DLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKK   84 (93)
T ss_dssp             HHHHHHHHTTCCCSSCEEE------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCC
T ss_pred             HHHHHHHHcCCceEEEEEc------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEEEccCcc
Confidence            48899999999 5555553      368999999999999999999999 99999999999988443

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.35  E-value=4.6e-14  Score=81.31  Aligned_cols=62  Identities=16%  Similarity=0.157  Sum_probs=54.4

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeecc
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADV   64 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~   64 (105)
                      +|+++|+.||.|.. .++.++ ++.+++||||+|.+.++|++||+ ||+..+.++.|+|+++..+
T Consensus        33 ~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~a~~~   95 (101)
T 1fj7_A           33 ELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKGR   95 (101)
T ss_dssp             HHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEECCSCC
T ss_pred             HHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEEcCCC
Confidence            47899999998876 455555 78899999999999999999999 9999999999999998743

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.35  E-value=1.5e-12  Score=74.21  Aligned_cols=61  Identities=18%  Similarity=0.437  Sum_probs=53.5

Q ss_pred             CHHHHhccCCCeeEE-EEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSA-KLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~-~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|+.||.|..+ .++.++ ++    .|||+|.+.++|++|+..||+..+.++.|.|+++.+.+
T Consensus        31 ~l~~~F~~~G~v~~~~~i~~~~~~~----~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~~   93 (96)
T 2e44_A           31 VLDSLLVQYGVVESCEQVNTDSETA----VVNVTYSSKDQARQALDKLNGFQLENFTLKVAYIPDEM   93 (96)
T ss_dssp             HHHHHHHHHSCEEEEEEECCSSSSE----EEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEECCCCC
T ss_pred             HHHHHHHhcCCeEEEEEeecCCCCC----EEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCccc
Confidence            488999999999999 477765 32    29999999999999999999999999999999998553

>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=99.35  E-value=5.1e-13  Score=76.25  Aligned_cols=61  Identities=30%  Similarity=0.470  Sum_probs=54.1

Q ss_pred             HHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeecc
Q psy1928           2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADV   64 (105)
Q Consensus         2 l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~   64 (105)
                      |+++|++||.|..|.++.  ++.+++||||+|.+.++|++|++.||+..+.++.|.|+++...
T Consensus        29 l~~~f~~~G~i~~v~i~~--~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~   89 (97)
T 1nu4_A           29 LHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTD   89 (97)
T ss_dssp             HHHHHGGGSCEEEEECCH--HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSSC
T ss_pred             HHHHHHhCCCEEEEEEEc--CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEEEEEccCC
Confidence            349999999999988763  5567899999999999999999999999999999999998743

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.35  E-value=3.9e-12  Score=76.28  Aligned_cols=59  Identities=20%  Similarity=0.265  Sum_probs=51.9

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccE-EEEEeCCHHHHHHHHHHhCCcccCC--eeEEEEEeecc
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGT-ADLIYERRSDAIKAMKQYNGVPLDG--RPMQIQLAADV   64 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~-~fv~f~~~~~a~~ai~~l~~~~i~~--~~i~V~~~~~~   64 (105)
                      +|+++|++||.|.+|.|+..     .++ |||+|.+.++|+.|++.||+..|.+  +.|+|++++..
T Consensus        41 ~L~~~Fs~yG~V~~v~i~~~-----~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~Ak~~  102 (124)
T 2e5i_A           41 VLYTVCNPVGKVQRIVIFKR-----NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPT  102 (124)
T ss_dssp             HHHHHHTTTSCEEEEEEEES-----SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCSCS
T ss_pred             HHHHHHHhcCCEEEEEEEeC-----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEecCC
Confidence            48899999999999988652     275 9999999999999999999999987  58999998744

>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=99.34  E-value=3.2e-12  Score=85.26  Aligned_cols=65  Identities=23%  Similarity=0.291  Sum_probs=60.8

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|+.||.|..+.++.++++.++++|||+|.+.++|++|+..||+..+.++.|.|.++.+.+
T Consensus       201 ~l~~~f~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~  265 (284)
T 3smz_A          201 ALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGP  265 (284)
T ss_dssp             HHHHHTCSSSCCSEEEEEECSSCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCSSS
T ss_pred             HHHHHhhCCCCeEEEEEEECCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEEecCCC
Confidence            48899999999999999998899999999999999999999999999999999999999997544

>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=99.34  E-value=8.5e-13  Score=80.42  Aligned_cols=64  Identities=28%  Similarity=0.392  Sum_probs=54.3

Q ss_pred             CHHHHhccCCCeeEE------EEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeecc
Q psy1928           1 MIYELFSEFGPLKSA------KLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADV   64 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~------~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~   64 (105)
                      +|+++|+.||.|..+      .+....++.+++||||+|.+.++|++||..||+..+.++.|.|+++...
T Consensus        61 ~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~  130 (143)
T 3egn_A           61 DLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFARSA  130 (143)
T ss_dssp             HHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEECEEEECCCS
T ss_pred             HHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEECCCC
Confidence            488999999998764      2222237888999999999999999999999999999999999999743

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.34  E-value=5.6e-12  Score=72.95  Aligned_cols=59  Identities=19%  Similarity=0.261  Sum_probs=50.5

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|++||.|..|.|+.    .+++||||+|.+.++|+.||+.++  .+.++.|+|+++...+
T Consensus        33 ~L~~~F~~~G~V~~v~i~~----~~rGfaFVeF~~~~~A~~Ai~~~~--~~~g~~l~V~~a~~~~   91 (100)
T 2d9o_A           33 VLLRLLQKYGEVLNLVLSS----KKPGTAVVEFATVKAAELAVQNEV--GLVDNPLKISWLEGQP   91 (100)
T ss_dssp             HHHHHHHTTSCEEEEEEES----SSSSEEEEEESCHHHHHHHHHTCC--BCSSSBCEEECSSCCC
T ss_pred             HHHHHHHhcCCEEEEEEcc----CCCCEEEEEECCHHHHHHHHHhcC--CCCCCeEEEEEccCCC
Confidence            4889999999999999873    568999999999999999999754  4678999999987443

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.34  E-value=6.7e-13  Score=79.50  Aligned_cols=62  Identities=16%  Similarity=0.254  Sum_probs=56.0

Q ss_pred             CHHHHhccCCCe----eEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeec
Q psy1928           1 MIYELFSEFGPL----KSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD   63 (105)
Q Consensus         1 ~l~~~f~~~G~i----~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~   63 (105)
                      +|+++|+.||.|    ..|.|+.+++++++|||||+|.+.++|++||+. |+..+.++.|.|..+..
T Consensus        39 dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~V~~a~~  104 (123)
T 2dha_A           39 EVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIELFRSTA  104 (123)
T ss_dssp             HHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEECCEEECH
T ss_pred             HHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEEEEECCH
Confidence            589999999875    689999888999999999999999999999996 99999999999988863

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.34  E-value=8.1e-13  Score=75.31  Aligned_cols=60  Identities=22%  Similarity=0.432  Sum_probs=52.8

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeecc
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADV   64 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~   64 (105)
                      +|+++|+.||.|..+    ..++.+++||||+|.+.++|++|+..|++..+.++.|.|+++.++
T Consensus        32 ~l~~~F~~~g~v~~~----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~   91 (96)
T 1fjc_A           32 ELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK   91 (96)
T ss_dssp             HHHHHHCSEEEECCE----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSS
T ss_pred             HHHHHHhhCCcEEEe----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcCCC
Confidence            478999999987665    237788999999999999999999999999999999999998743

>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=99.32  E-value=4.7e-12  Score=81.63  Aligned_cols=59  Identities=15%  Similarity=0.272  Sum_probs=54.4

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeec
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD   63 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~   63 (105)
                      +|+++|++||.|.+|.++.+    .++||||+|.+.++|++||+.||+..+.++.|.|.+++.
T Consensus        21 ~L~~~F~~~G~v~~v~i~~~----~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s~~   79 (205)
T 3tyt_A           21 RVFNVFCLYGNVEKVKFMKS----KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQ   79 (205)
T ss_dssp             HHHHHHTTTSCEEEEEECTT----STTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSC
T ss_pred             HHHHHHHhcCCeEEEEEecC----CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEccC
Confidence            48899999999999998765    379999999999999999999999999999999999873

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.32  E-value=3.4e-12  Score=81.73  Aligned_cols=62  Identities=32%  Similarity=0.487  Sum_probs=55.6

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|+.||.|.+|.++.++ ++.+++||||+|.+.++|++|++.|++..+.++.|.|.++.
T Consensus        44 ~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~  106 (216)
T 2qfj_A           44 TIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPS  106 (216)
T ss_dssp             HHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCS
T ss_pred             HHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCC
Confidence            488999999999999999988 89999999999999999999999999999999999998765

>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=99.30  E-value=9e-12  Score=78.66  Aligned_cols=63  Identities=22%  Similarity=0.290  Sum_probs=57.6

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeecc
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADV   64 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~   64 (105)
                      +|+++|+.||.|.+|.++.++ ++.+++||||+|.+.++|++||+. ++..+.++.|.|.++...
T Consensus        29 ~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v~~~~~~   92 (196)
T 1l3k_A           29 SLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAVSR   92 (196)
T ss_dssp             HHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEECCC-
T ss_pred             HHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeeeecccCc
Confidence            488999999999999999998 899999999999999999999986 889999999999988743

>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=99.30  E-value=4.3e-12  Score=84.96  Aligned_cols=63  Identities=22%  Similarity=0.368  Sum_probs=57.6

Q ss_pred             CHHHHhccCCCeeEEEEEeCCC--CCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeecc
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRS--GRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADV   64 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~--~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~   64 (105)
                      +|+++|+.||.|..+.++.+..  +.+++||||+|.+.++|++|+ .||+..+.++.|.|.++.++
T Consensus       227 ~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~~i~V~~a~~k  291 (292)
T 2ghp_A          227 LLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISVSLADKK  291 (292)
T ss_dssp             HHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEEEEEECCCC
T ss_pred             HHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-HhcCCEECCcEEEEEEecCC
Confidence            4789999999999999988875  899999999999999999999 99999999999999998854

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.29  E-value=4.9e-12  Score=83.43  Aligned_cols=60  Identities=17%  Similarity=0.214  Sum_probs=53.1

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCccc------------CCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPL------------DGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i------------~~~~i~V~~~~~~~   65 (105)
                      +|+++|++||.|.+|.|+.     +++||||+|.+.++|+.|++.|++..|            .++.|.|.++...+
T Consensus       159 ~L~~~F~~fG~I~~v~v~~-----~kG~AFV~F~~~~~Ae~A~~am~g~~l~~~~~~e~~~~~~gr~L~V~wA~~~p  230 (240)
T 3u1l_A          159 RIRFVFSRLGDIDRIRYVE-----SKNCGFVKFKYQANAEFAKEAMSNQTLLLPSDKEWDDRREGTGLLVKWANEDP  230 (240)
T ss_dssp             HHHHHHHTTSCEEEEEEEG-----GGTEEEEEESSHHHHHHHHHHHTTCCCCCTTSTTGGGGGGSCCCEEEECC---
T ss_pred             HHHHHHHccCCEEEEEEEC-----CCCEEEEEeCCHHHHHHHHHHhCCCEEeccccccccccCCCCEEEEEEccCCC
Confidence            4789999999999999986     379999999999999999999999999            78999999998443

>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=99.28  E-value=1e-11  Score=79.43  Aligned_cols=62  Identities=13%  Similarity=0.136  Sum_probs=56.1

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeec
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD   63 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~   63 (105)
                      +|+++|+.||.|..|.|+++.++.++|||||+|.+.++|++|++.++ ..+.|+.|.|.++.+
T Consensus       125 ~L~~~F~~~G~v~~v~i~~~~~~~~kG~aFVeF~~~e~A~~A~~~~~-~~~~Gr~l~V~~~~~  186 (193)
T 2voo_A          125 DIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPG-QKYKETDLLILFKDD  186 (193)
T ss_dssp             HHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESSHHHHHHHHHCTT-CEETTEECEEEETTT
T ss_pred             HHHHHHhcCCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHhCC-CeECCEEEEEEEhHH
Confidence            47899999999999999998888899999999999999999998655 589999999998764

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.28  E-value=6.3e-12  Score=71.74  Aligned_cols=53  Identities=19%  Similarity=0.259  Sum_probs=48.6

Q ss_pred             HHHHhccC-CCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeec
Q psy1928           2 IYELFSEF-GPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD   63 (105)
Q Consensus         2 l~~~f~~~-G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~   63 (105)
                      |+++|++| |.|.+|      ++   |+|||.|.+.++|++|++.|++.++.+++|+|.+++.
T Consensus        30 L~~lF~~yGG~Vl~V------tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v~~A~~   83 (96)
T 2diu_A           30 LRRLSDNCGGKVLSI------TG---CSAILRFINQDSAERAQKRMENEDVFGNRIIVSFTPK   83 (96)
T ss_dssp             HHHHHHTTTCCEEEC------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSCCEEESSCC
T ss_pred             HHHHHHHcCCeeEEE------ec---CEEEEEECCHHHHHHHHHHhcCCccCCceEEEEecCC
Confidence            77899999 599987      22   9999999999999999999999999999999999983

>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=99.28  E-value=1.7e-12  Score=78.07  Aligned_cols=61  Identities=20%  Similarity=0.268  Sum_probs=54.9

Q ss_pred             CHHHHhccCCCee--EEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeec
Q psy1928           1 MIYELFSEFGPLK--SAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD   63 (105)
Q Consensus         1 ~l~~~f~~~G~i~--~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~   63 (105)
                      +|+++|+.| .|.  .|.|+.++.++++|||||+|.+.++|++||+. ++..|.++.|.|..+..
T Consensus        58 dL~~~F~~~-~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~~-~~~~l~gR~I~V~~a~~  120 (126)
T 2hgm_A           58 EIVQFFSGL-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGK-HKERIGHRYIEVFKSSQ  120 (126)
T ss_dssp             HHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHTT-TTCCBTTBCCCCEEECH
T ss_pred             HHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHHH-CCCEECCEEEEEEECCH
Confidence            589999999 677  89999888889999999999999999999985 77999999999998873

>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=99.27  E-value=7.6e-12  Score=70.35  Aligned_cols=58  Identities=19%  Similarity=0.300  Sum_probs=52.5

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeecc
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADV   64 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~   64 (105)
                      +|+++|++| .|.++.+.     ++++||||+|.+.++|++|++.||+..+.++.|+|+++...
T Consensus        21 ~l~~~F~~~-~v~~~~i~-----~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~   78 (88)
T 1wg1_A           21 EVHDLLKDY-DLKYCYVD-----RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTD   78 (88)
T ss_dssp             HHHHHTCSS-CCCCEEEE-----GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCC
T ss_pred             HHHHHHhhC-CeEEEEEe-----CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcCCC
Confidence            478999999 99998885     46899999999999999999999999999999999998743

>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=99.26  E-value=1.1e-11  Score=77.12  Aligned_cols=60  Identities=22%  Similarity=0.432  Sum_probs=53.6

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeecc
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADV   64 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~   64 (105)
                      +|+++|+.||.|..+    ..++.++++|||+|.+.++|++|+..||+..+.++.|.|+++.++
T Consensus       115 ~l~~~F~~~g~v~~~----~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~k  174 (175)
T 1fje_B          115 ELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK  174 (175)
T ss_dssp             HHHHHCTTCSEEEEE----CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEECSSC
T ss_pred             HHHHHHHhcCeEEEe----cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEecCCC
Confidence            478999999987765    448889999999999999999999999999999999999998754

>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=99.24  E-value=3.9e-11  Score=79.98  Aligned_cols=65  Identities=26%  Similarity=0.384  Sum_probs=60.4

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|+.||.|..+.++.++ ++.+++||||+|.+.++|++|+..|++..+.++.|.|.++....
T Consensus       111 ~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a~~~~  176 (284)
T 3smz_A          111 QFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQ  176 (284)
T ss_dssp             HHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCGGG
T ss_pred             HHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCC
Confidence            478999999999999999988 99999999999999999999999999999999999999987433

>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=99.23  E-value=3.9e-11  Score=79.93  Aligned_cols=60  Identities=32%  Similarity=0.556  Sum_probs=54.9

Q ss_pred             HHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeec
Q psy1928           2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD   63 (105)
Q Consensus         2 l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~   63 (105)
                      |.++|+.||.|.+|.++.  ++++++||||+|.+.++|++||+.||+..+.++.|+|+++..
T Consensus        30 L~~~F~~~G~i~~v~~~~--~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~   89 (282)
T 3pgw_A           30 LYAIFSQFGQILDILVSR--SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKT   89 (282)
T ss_pred             HHHHHhccCCeEEEEEcC--CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEEecc
Confidence            558999999999998775  677899999999999999999999999999999999999873

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.18  E-value=5.3e-11  Score=67.34  Aligned_cols=59  Identities=20%  Similarity=0.294  Sum_probs=52.7

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccCCC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVSVL   67 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~~~   67 (105)
                      +|.+.|+.||.|..++++.+       .+||+|.+.++|.+||+ ||+..+.++.|+|+++++.+..
T Consensus        31 ~L~~~F~~~G~Vi~vr~~~d-------~~fVtF~d~~sAlaAi~-mnG~~v~Gr~LkV~lkt~dW~~   89 (91)
T 2dnr_A           31 ELLQQFASFGEVILIRFVED-------KMWVTFLEGSSALNVLS-LNGKELLNRTITIALKSPSGPS   89 (91)
T ss_dssp             HHHHHHHTTCCEEEEEECSS-------SEEEEESSHHHHHHGGG-GTTCEETTEEEEEEECCCSSCS
T ss_pred             HHHHHHHhCCCeEEEEEecC-------CEEEEECChHHHHHHHh-cCCeEeCCeEEEEEeCCCCccc
Confidence            37889999999999999886       38999999999999998 9999999999999999865543

>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=99.18  E-value=7.2e-11  Score=73.09  Aligned_cols=62  Identities=23%  Similarity=0.381  Sum_probs=54.3

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CC--CcccEEEEEeCCHHHHHHHHHHhCCcccC---CeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SG--RSLGTADLIYERRSDAIKAMKQYNGVPLD---GRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~--~~~g~~fv~f~~~~~a~~ai~~l~~~~i~---~~~i~V~~~~   62 (105)
                      +|+++|++||.|.++.++.++ ++  .+++||||+|.+.++|++|++.|++..+.   .+.+.+..+.
T Consensus        19 ~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~~~~~~   86 (175)
T 3nmr_A           19 DLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMKPAD   86 (175)
T ss_dssp             HHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCEEEECG
T ss_pred             HHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceEEcccc
Confidence            488999999999999999988 54  78999999999999999999999998775   5667777665

>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=99.17  E-value=7.4e-11  Score=78.55  Aligned_cols=58  Identities=24%  Similarity=0.338  Sum_probs=53.3

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccC-CeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLD-GRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~-~~~i~V~~~~   62 (105)
                      +|+++|++||.|.++.++.++    ++++||+|.+.++|++|++.||+..+. ++.|+|++++
T Consensus       223 ~l~~~F~~~G~i~~v~~~~~~----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          223 MLSMLFNQFPGFKEVRLVPGR----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             HHHHHHHhcCCeEEEEEecCC----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence            588999999999999988653    589999999999999999999999999 9999999975

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.16  E-value=8.3e-11  Score=69.09  Aligned_cols=56  Identities=23%  Similarity=0.235  Sum_probs=45.7

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-C---CCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEE
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-S---GRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ   59 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~---~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~   59 (105)
                      +|+++|++||.|. +.++.++ +   +++++||||+|.+.++|++||+.|+  .++++.|.+.
T Consensus        24 ~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~~~   83 (114)
T 2dnl_A           24 EITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYLCV   83 (114)
T ss_dssp             HHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEEEE
T ss_pred             HHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEEec
Confidence            4889999999999 7777766 5   7899999999999999999999883  3455555444

>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=99.15  E-value=5.4e-11  Score=66.38  Aligned_cols=54  Identities=20%  Similarity=0.485  Sum_probs=48.5

Q ss_pred             CHHHHhccC----C-------CeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEE
Q psy1928           1 MIYELFSEF----G-------PLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL   60 (105)
Q Consensus         1 ~l~~~f~~~----G-------~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~   60 (105)
                      +|+++|+.|    |       .|.++.+..+     ++||||+|.+.++|++|+ .||+..+.++.|+|+.
T Consensus        22 ~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~-----kg~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~r   86 (87)
T 2hzc_A           22 AMMDFFNAQMRLGGLTQAPGNPVLAVQINQD-----KNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIRR   86 (87)
T ss_dssp             HHHHHHHHHHHHTTCCSSSSCSEEEEEECSS-----SSEEEEEESSHHHHHHHG-GGTTCEETTEECEEEC
T ss_pred             HHHHHHHHHhhhcccccCCCCcceEEEecCC-----CcEEEEEcCCHHHHHHHH-hcCCCEECCeEEEEeC
Confidence            478899999    8       8999888754     799999999999999999 8999999999999873

>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=99.13  E-value=6.3e-11  Score=79.24  Aligned_cols=65  Identities=18%  Similarity=0.225  Sum_probs=53.3

Q ss_pred             CHHHHhccCC-CeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFG-PLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G-~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|+.|| .|..+.++.++.+.+++||||+|.+.++|++|+..|++..+.++.|.|.++.+..
T Consensus       133 ~l~~~f~~~G~~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  198 (292)
T 2ghp_A          133 NIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLE  198 (292)
T ss_dssp             HHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCC-
T ss_pred             HHHHHHHHhCCCeEEEEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCc
Confidence            4789999999 9999999888777889999999999999999999999999999999999987443

>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=99.12  E-value=7e-11  Score=76.89  Aligned_cols=59  Identities=25%  Similarity=0.489  Sum_probs=54.5

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeec
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD   63 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~   63 (105)
                      +|+++|+.||.|..|.++.++    ++||||+|.+.++|++|++.|++..+.++.|.|.++..
T Consensus        51 ~L~~~F~~~G~i~~v~i~~~~----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  109 (229)
T 2adc_A           51 SLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKH  109 (229)
T ss_dssp             HHHHHHHHHTCEEEEEECCTT----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSC
T ss_pred             HHHHHHHhCCCeEEEEEEECC----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEecC
Confidence            488999999999999998764    68999999999999999999999999999999999873

>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=99.11  E-value=1.6e-10  Score=76.58  Aligned_cols=64  Identities=27%  Similarity=0.465  Sum_probs=56.3

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhC-CcccC---CeeEEEEEeecc
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYN-GVPLD---GRPMQIQLAADV   64 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~-~~~i~---~~~i~V~~~~~~   64 (105)
                      +|+++|+.||.|..|.++.++++.+++||||+|.+.++|.+|+..|| +..+.   +++|.|.++...
T Consensus       112 ~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v~~~~~~  179 (261)
T 3sde_A          112 LLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQF  179 (261)
T ss_dssp             HHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEEEECCCE
T ss_pred             HHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEEeecccc
Confidence            47899999999999999998899999999999999999999999995 44444   889999988743

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=99.11  E-value=1.9e-10  Score=74.46  Aligned_cols=62  Identities=16%  Similarity=0.236  Sum_probs=56.2

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-----CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-----SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-----~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|.+.|++||.|.++.|+.+.     ++.++|++||+|.+.++|++|+..||+..+.|+.|.|.+..
T Consensus       145 dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~  211 (222)
T 3dxb_A          145 EVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYD  211 (222)
T ss_dssp             HHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECC
T ss_pred             HHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcC
Confidence            477889999999999998654     44889999999999999999999999999999999999976

>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=99.11  E-value=8e-11  Score=72.53  Aligned_cols=60  Identities=28%  Similarity=0.411  Sum_probs=53.4

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|+.||.|.++.++.++ ++.+++||||+|.+.++|++|++.  ...+.++.|.|.++.
T Consensus        19 ~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g~~i~v~~~~   79 (167)
T 2cjk_A           19 NLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT--QHILDGKVIDPKRAI   79 (167)
T ss_dssp             HHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS--CCEETTEECCCEECC
T ss_pred             HHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc--ccccCCeEccccccc
Confidence            488999999999999999997 899999999999999999999984  567888888877665

>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=99.09  E-value=2.1e-10  Score=64.72  Aligned_cols=57  Identities=16%  Similarity=0.171  Sum_probs=45.2

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCccc--CCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPL--DGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i--~~~~i~V~~~~~~~   65 (105)
                      +|+++|++||.|.+|.|+.+    ++|||||+|.+.++|++    +++..+  .++.|.|.++.++.
T Consensus        27 ~L~~~F~~~G~i~~v~i~~~----srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v~~a~~k~   85 (89)
T 3d2w_A           27 ELQQFFCQYGEVVDVFIPKP----FRAFAFVTFADDKVAQS----LCGEDLIIKGISVHISNAEPKH   85 (89)
T ss_dssp             HHHHHHTTTSCEEEEECCSS----CCSEEEEEESCHHHHHH----HTTCEEEETTEEEEEEECC---
T ss_pred             HHHHHHhccCCEEEEEEeeC----CCCEEEEEECCHHHHHH----HcCCCcccCCEEEEEEEcCCCC
Confidence            48899999999999998874    68999999999999883    455544  58889988887443

>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=99.08  E-value=5.3e-11  Score=66.73  Aligned_cols=59  Identities=15%  Similarity=0.147  Sum_probs=46.3

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|++||.|..+.++.+    +++||||+|.+.++|++++.  ....+.++.|.|.++.++.
T Consensus        21 ~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~~~~~--~~~~~~g~~l~v~~a~~~~   79 (88)
T 1wf0_A           21 ELREFFSQYGDVMDVFIPKP----FRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAEPKH   79 (88)
T ss_dssp             HHHHHSTTTSCCCEEECCSS----CCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCCCCC
T ss_pred             HHHHHHHHcCCeeEEEEecC----CCCEEEEEECCHHHHHHHhc--CCceeCCEEEEEEecCCCC
Confidence            48899999999999988764    67999999999999976432  1234578888888877443

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.08  E-value=9.4e-11  Score=74.33  Aligned_cols=59  Identities=25%  Similarity=0.489  Sum_probs=54.2

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeec
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD   63 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~   63 (105)
                      +|+++|+.||.|.+|.++.++    ++||||+|.+.++|++|++.||+..+.++.|.|.++..
T Consensus        20 ~l~~~F~~~G~i~~v~i~~~~----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~~   78 (198)
T 1qm9_A           20 SLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKH   78 (198)
T ss_dssp             HHHHHHHTTCCCSEEECSTTC----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECCC
T ss_pred             HHHHHHHhcCCEEEEEEEeCC----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEecC
Confidence            478999999999999988764    68999999999999999999999999999999999873

>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=99.04  E-value=4.2e-10  Score=73.18  Aligned_cols=59  Identities=17%  Similarity=0.218  Sum_probs=52.9

Q ss_pred             CHHHHhccCC-CeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccC-CeeEEEEEeec
Q psy1928           1 MIYELFSEFG-PLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLD-GRPMQIQLAAD   63 (105)
Q Consensus         1 ~l~~~f~~~G-~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~-~~~i~V~~~~~   63 (105)
                      +|+++|+.|| .|..+.++.+    .+++|||+|.+.++|++|+..||+..+. ++.|.|.++++
T Consensus       167 ~l~~~f~~~G~~i~~v~i~~~----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~  227 (229)
T 2adc_A          167 DLKVLFSSNGGVVKGFKFFQK----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS  227 (229)
T ss_dssp             HHHHHHHTTSCCEEEEEECSS----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSS
T ss_pred             HHHHHHHHcCCCeeEEEEEEC----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecC
Confidence            4789999999 9999988543    3689999999999999999999999999 99999999873

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.03  E-value=2.5e-10  Score=72.35  Aligned_cols=59  Identities=17%  Similarity=0.218  Sum_probs=53.0

Q ss_pred             CHHHHhccCC-CeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccC-CeeEEEEEeec
Q psy1928           1 MIYELFSEFG-PLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLD-GRPMQIQLAAD   63 (105)
Q Consensus         1 ~l~~~f~~~G-~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~-~~~i~V~~~~~   63 (105)
                      +|+++|+.|| .|..+.++.+    .+++|||+|.+.++|++|+..||+..+. ++.|.|.++++
T Consensus       136 ~l~~~f~~~G~~v~~v~i~~~----~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~  196 (198)
T 1qm9_A          136 DLKVLFSSNGGVVKGFKFFQK----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS  196 (198)
T ss_dssp             HHHHHHHHTTSCCCEEEESST----TSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECC
T ss_pred             HHHHHHHHcCCCceEEEEEeC----CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeecc
Confidence            4789999999 9999988653    2689999999999999999999999999 99999999873

>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=99.03  E-value=3.3e-10  Score=72.94  Aligned_cols=60  Identities=20%  Similarity=0.374  Sum_probs=50.8

Q ss_pred             CHHHHhccCCCe--eEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCe----eEEEEEe
Q psy1928           1 MIYELFSEFGPL--KSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGR----PMQIQLA   61 (105)
Q Consensus         1 ~l~~~f~~~G~i--~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~----~i~V~~~   61 (105)
                      +|+++|++||.|  ..+.++.++ +..++++||+|.+.++|.+||..||+..|.+.    ++.|+++
T Consensus       139 ~L~~~F~~~G~v~~~~v~~~~~~-~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~vk~~  204 (205)
T 3tyt_A          139 NFFEICDELGVKRPTSVKVFSGK-SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKLC  204 (205)
T ss_dssp             HHHHHHHHHTCCCCSEEEECSCC-SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEECEEE
T ss_pred             HHHHHHHhcCCcceEEEEEEcCC-CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceEEEec
Confidence            489999999999  888887765 44569999999999999999999999999865    5666654

>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=99.00  E-value=7.6e-10  Score=73.28  Aligned_cols=57  Identities=26%  Similarity=0.370  Sum_probs=52.6

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|+.||.|..|.+..+     ++||||+|.+.++|++|+..|++..+.++.|.|.++.
T Consensus        38 ~l~~~F~~~G~i~~v~i~~~-----kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~a~   94 (261)
T 3sde_A           38 DFKRLFERYGEPSEVFINRD-----RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFAT   94 (261)
T ss_dssp             HHHHHTGGGCCCSEEEEETT-----TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             HHHHHHHhcCCEEEEEEeCC-----CcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeecc
Confidence            48899999999999988754     6999999999999999999999999999999999876

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.89  E-value=1.8e-09  Score=61.37  Aligned_cols=53  Identities=11%  Similarity=0.370  Sum_probs=48.6

Q ss_pred             HHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         2 l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      |.+.|+.||.|..++++.+       -+||+|.+.++|.+||+ ||+..+.++.|+|++..
T Consensus        41 L~~~F~~~G~Vilvr~v~d-------~~fVtF~d~~sAl~AI~-ldG~~v~Gr~L~V~~k~   93 (95)
T 1ufw_A           41 LMQTLGSYGTIVLVRINQG-------QMLVTFADSHSALSVLD-VDGMKVKGRAVKISGPS   93 (95)
T ss_dssp             HHHHHHHHSCCSEEEEETT-------EEEEECSCSHHHHHHHH-GGGSEETTEEEEEECCC
T ss_pred             HHHHHHHCCCEEEEEEecC-------cEEEEEcChHHHHHHHh-cCCeeeCCeEEEEeccC
Confidence            7788999999999999987       39999999999999999 99999999999998654

>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*

Probab=98.88  E-value=2.3e-09  Score=73.94  Aligned_cols=56  Identities=11%  Similarity=0.192  Sum_probs=46.4

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccC---Ce--eEEEEEe
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLD---GR--PMQIQLA   61 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~---~~--~i~V~~~   61 (105)
                      +|+++|++||+|..|.++.     +++||||+|.+.++|++||+.||+.++.   ++  .|.|.+.
T Consensus        36 ~L~~~F~~~G~V~~v~~~~-----~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~~ly~~~~   96 (345)
T 3tht_A           36 QLLPVLEKCGLVDALLMPP-----NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFV   96 (345)
T ss_dssp             HHHHHHHTTSCEEEEECCT-----TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEEEC
T ss_pred             HHHHHHHhcCCeEEEEEeC-----CCCEEEEEECCHHHHHHHHHHhCCCccccccCCceEEEEEEe
Confidence            4899999999999887643     4699999999999999999999999873   33  4566655

>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=98.86  E-value=2e-10  Score=71.40  Aligned_cols=62  Identities=16%  Similarity=0.162  Sum_probs=50.6

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeecc
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADV   64 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~   64 (105)
                      +|+++|+.||.+..+ ++.+. ++.+++||||+|.+.++|++|++ ||+..+.++.|.|.++...
T Consensus        29 ~l~~~f~~~g~~~~~-~~~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~v~~~~~~   91 (175)
T 1fje_B           29 ELKVAISELFAKNDL-AVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKGR   91 (175)
T ss_dssp             HHHHHHHHHHHHHTC-CCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECCCCS
T ss_pred             HHHHHHHHhCCcceE-EEEECCCCccccEEEEEECCHHHHHHHHh-cCCCEeCCeEEEEecCCCc
Confidence            467888888876552 22333 77889999999999999999995 9999999999999988743

>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=98.82  E-value=7.3e-09  Score=63.92  Aligned_cols=57  Identities=19%  Similarity=0.459  Sum_probs=48.7

Q ss_pred             CHHHHhccC----C-------CeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeec
Q psy1928           1 MIYELFSEF----G-------PLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD   63 (105)
Q Consensus         1 ~l~~~f~~~----G-------~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~   63 (105)
                      +|+++|++|    |       .|..+.+..     +++||||+|.+.++|++|+ .||+..+.++.|.|.++..
T Consensus        20 ~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~-----~~g~afV~f~~~~~A~~A~-~~~~~~~~g~~i~v~~~~~   87 (172)
T 2g4b_A           20 AMMDFFNAQMRLGGLTQAPGNPVLAVQINQ-----DKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIRRPHD   87 (172)
T ss_dssp             HHHHHHHHHHHHTTCCSSSSCSEEEEEEET-----TTTEEEEEESSHHHHHHHG-GGTTCEETTEECEEECCSS
T ss_pred             HHHHHHHHHhhhcccccCCCCceeeeEecC-----CCCEEEEEeCCHHHHHHHH-HhCCcEecCceeeecCCcc
Confidence            478899999    6       666666654     3799999999999999999 7999999999999998763

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=98.79  E-value=9.4e-09  Score=64.73  Aligned_cols=58  Identities=19%  Similarity=0.464  Sum_probs=48.4

Q ss_pred             CHHHHhccC----C-------CeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeecc
Q psy1928           1 MIYELFSEF----G-------PLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADV   64 (105)
Q Consensus         1 ~l~~~f~~~----G-------~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~   64 (105)
                      +|+++|+.|    |       .|..+.+.     .+++||||+|.+.++|++|+ .||+..+.++.|.|.++...
T Consensus        20 ~l~~~F~~~g~i~g~~~~~~~~v~~~~~~-----~~~g~afV~F~~~~~A~~Al-~l~g~~~~g~~i~v~~~~~~   88 (198)
T 2yh0_A           20 AMMDFFNAQMRLGGLTQAPGNPVLAVQIN-----QDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIRRPHDY   88 (198)
T ss_dssp             HHHHHHHHHHHHHTCCSSSSCSEEEEEEE-----TTTTEEEEEESCSHHHHHHG-GGTTEEETTEEEEEECCCCC
T ss_pred             HHHHHHHHHHhhcccccCCCCceEEeEec-----CCCCEEEEEeCCHHHHHHHH-HhcCCEEcCceEEEeCCCCC
Confidence            478999999    4       55555543     34799999999999999999 79999999999999988743

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.55  E-value=2e-07  Score=55.43  Aligned_cols=57  Identities=16%  Similarity=0.260  Sum_probs=48.7

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCC-HHHHHHHHHHhC--CcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYER-RSDAIKAMKQYN--GVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~-~~~a~~ai~~l~--~~~i~~~~i~V~~~~   62 (105)
                      +|+++|++||.|.+|.+..+.     ..+||.|.+ ..+|..|+..|+  +..|.+..++++...
T Consensus        35 dLke~F~~~G~V~~Vd~~~g~-----~tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~~evL~   94 (121)
T 1owx_A           35 DLHILFSNHGEIKWIDFVRGA-----KEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVLE   94 (121)
T ss_dssp             HHHHHTCSSCCEEEEECCTTC-----SEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEECC
T ss_pred             HHHHHHHhcCCEEEEEEecCC-----CEEEEEECCChHHHHHHHHHhhcCCcEEeCcEEEEEECC
Confidence            488999999999999998764     359999999 899999999995  678888888887655

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=97.69  E-value=0.00013  Score=42.53  Aligned_cols=54  Identities=20%  Similarity=0.281  Sum_probs=46.2

Q ss_pred             HHHHhccC-----CCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEE
Q psy1928           2 IYELFSEF-----GPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL   60 (105)
Q Consensus         2 l~~~f~~~-----G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~   60 (105)
                      |+.++.++     |.|..+.+..|     -+-|+|+|.+...|-+|.-.|++.++.++.|+|.-
T Consensus        38 Ir~lve~~~~i~~g~i~KI~L~pD-----H~GAivef~d~~~AgKasLaL~G~ef~gr~Lr~gT   96 (117)
T 2l9w_A           38 ICQFLQEEIHINEKDIRKILLVSD-----FNGAIIIFRDSKFAAKMLMILNGSQFQGKVIRSGT   96 (117)
T ss_dssp             HHHHHHHHTCCCTTTCSEEEEETT-----TTEEEEECSCHHHHHHHHHHHSSEEETTEEEEEEC
T ss_pred             HHHHHhhhhccCccceeEEEEecC-----CCceEEEEccchhhHHHHhhcCCeeecCeEEEecC
Confidence            56677777     89999887765     46799999999999999989999999999998864

>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=97.17  E-value=0.0016  Score=38.34  Aligned_cols=54  Identities=15%  Similarity=0.224  Sum_probs=43.2

Q ss_pred             HHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCC-eeEEEEEe
Q psy1928           2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDG-RPMQIQLA   61 (105)
Q Consensus         2 l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~-~~i~V~~~   61 (105)
                      |...|++||.|.+.....     ...+-+|.|.+..+|++||. .|+..+.+ -.|-|...
T Consensus        40 VL~~F~~~G~Iv~~~~~~-----~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~p~   94 (119)
T 1wwh_A           40 ILLQFAQYGNILKHVMSN-----TGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPC   94 (119)
T ss_dssp             HHHHHHTTSCEEEEEECS-----SSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEEC
T ss_pred             HHHHHHhhCcEEEeccCC-----CCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEEC
Confidence            567899999998876521     24699999999999999998 49999984 56677664

>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=96.94  E-value=0.0024  Score=36.70  Aligned_cols=57  Identities=12%  Similarity=0.190  Sum_probs=48.3

Q ss_pred             HHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeec
Q psy1928           2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD   63 (105)
Q Consensus         2 l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~   63 (105)
                      ++++|..|+.+....+...     -.-..|.|.+.++|.+|-..|++..+.++.|+|-++.+
T Consensus        27 ~e~Lf~~~~~~~tF~~lkS-----FRRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~YFgq~   83 (104)
T 1wey_A           27 FESLFRTYDKDTTFQYFKS-----FKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQT   83 (104)
T ss_dssp             HHHHHHTTCSSCEEEEETT-----TTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCCC
T ss_pred             HHHHHHhhCcCcceeecCc-----ceEEEEEeCChHHHHHHHHHhccceecCceeEEEecCC
Confidence            5788999998877665542     34678999999999999999999999999999999873

>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=96.59  E-value=0.0032  Score=38.04  Aligned_cols=34  Identities=24%  Similarity=0.143  Sum_probs=27.2

Q ss_pred             EEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCc
Q psy1928          15 AKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGV   49 (105)
Q Consensus        15 ~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~   49 (105)
                      +.++.+.. .++||+||+|.+.++|++|+..+++.
T Consensus         3 ~kl~ln~~-~~~G~~fV~f~~~~~A~~al~~~~~~   36 (158)
T 2kn4_A            3 YKLILNGK-TLKGETTTEAVDAATAEKVFKQYAND   36 (158)
T ss_dssp             EEEEEECS-SCEEEEEEECSSHHHHHHHHHHHHHH
T ss_pred             EEEEecCc-cccchhHHHHHHHHhHHHHHHhhccc
Confidence            45555533 57899999999999999999887754

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=96.17  E-value=0.0078  Score=34.21  Aligned_cols=39  Identities=23%  Similarity=0.265  Sum_probs=32.9

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHh
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQY   46 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l   46 (105)
                      ||+++|+.||. ..|.++.|      -.|||.|.+.+.|..|+..+
T Consensus        31 DI~~lFs~fgg-v~I~WidD------TsAlvvf~~~~~a~~al~~i   69 (100)
T 1whv_A           31 DLYQLFSAFGN-IQISWIDD------TSAFVSLSQPEQVQIAVNTS   69 (100)
T ss_dssp             HHHHHHTTTCS-CCCEEEET------TEEEEECSCHHHHHHHHHHH
T ss_pred             HHHHHhhccCC-EEEEEEcC------CeEEEEecCHHHHHHHHHhc
Confidence            68999999994 55677776      48999999999999999876

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=96.00  E-value=0.0086  Score=34.12  Aligned_cols=40  Identities=23%  Similarity=0.246  Sum_probs=33.7

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYN   47 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~   47 (105)
                      ||+++|+.|| -..|.++.|      -.|||.|.+.+.|..|+..+.
T Consensus        21 Di~~lFs~fg-gv~I~WidD------TsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A           21 DLYQLFSAFG-NIQISWIDD------TSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             HHHHHTTTSE-EEEEEEEET------TEEEEEEEEECHHHHHHHHHT
T ss_pred             HHHHHHhccC-CEEEEEEcC------CeEEEEecCHHHHHHHHHhcc
Confidence            6899999998 456777776      489999999999999999764

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=95.90  E-value=0.0062  Score=36.41  Aligned_cols=60  Identities=17%  Similarity=0.300  Sum_probs=43.3

Q ss_pred             HHHHhccCCCeeE-EEEEe---------CCCC-----CcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           2 IYELFSEFGPLKS-AKLHY---------DRSG-----RSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         2 l~~~f~~~G~i~~-~~i~~---------~~~~-----~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +.+.|++||.|.+ +.+..         .+..     ....+..|.|++..+|++||. .|+..+.+..|-|....
T Consensus        23 VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG~ii~G~mIGV~Py~   97 (132)
T 3p3d_A           23 VIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENGAVFNGVLLGVIPYT   97 (132)
T ss_dssp             HHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTTCEETTEECEEEECC
T ss_pred             HHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCCeEeCcEEEEEEECC
Confidence            4678999999865 22111         0001     135788999999999999998 49999999888777655

>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=95.76  E-value=0.0029  Score=38.03  Aligned_cols=39  Identities=26%  Similarity=0.198  Sum_probs=34.7

Q ss_pred             CCcccEEEEEeCCHHHHHHHHHHh-CCcccCCeeEEEEEee
Q psy1928          23 GRSLGTADLIYERRSDAIKAMKQY-NGVPLDGRPMQIQLAA   62 (105)
Q Consensus        23 ~~~~g~~fv~f~~~~~a~~ai~~l-~~~~i~~~~i~V~~~~   62 (105)
                      ...+|+++++|.+.++|++|++.+ |+..+++ .|.+.++.
T Consensus        10 ~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~   49 (150)
T 2i2y_A           10 KTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDAT   49 (150)
T ss_dssp             SSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTT
T ss_pred             ccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceeccccc
Confidence            356799999999999999999999 9999999 88888765

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=89.20  E-value=0.17  Score=36.23  Aligned_cols=40  Identities=13%  Similarity=0.094  Sum_probs=29.2

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHH
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMK   44 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~   44 (105)
                      +|.+.|+.||.|.++.+..++    ..|++|+|.+.+++++++.
T Consensus        68 ~l~~y~~~~g~i~~~~~~~~~----g~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           68 KFLKYLSQFGPINNHFFYESF----GLYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             HHHHHHGGGSCCCCEEEECSS----SEEEEEECC---CCHHHHS
T ss_pred             HHHHHHHhcCCcceEEEEccC----CeEEEEEeCCHHHHHHHHh
Confidence            367889999999998766542    3799999999988887654

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=89.18  E-value=2  Score=24.51  Aligned_cols=53  Identities=21%  Similarity=0.243  Sum_probs=38.2

Q ss_pred             HHHHhcc-----CCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           2 IYELFSE-----FGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         2 l~~~f~~-----~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      |+-.|++     -|.|..+....       .-|+|+|.+...|++.++. ..+.|++..|.|.-..
T Consensus        25 L~LYFEn~rrsGGG~V~~v~~~~-------~~AvItF~d~~va~rVL~k-~~H~L~~~~LsV~P~~   82 (104)
T 2dhx_A           25 LTLYFENRRRSGGGPVLSWQRLG-------CGGVLTFREPADAERVLAQ-ADHELHGAQLSLRPAP   82 (104)
T ss_dssp             HHHHHHCTTTTCCCCEEEEEEET-------TEEEEEESSHHHHHHHHTC-SCCBSSSSBCEEEECC
T ss_pred             heEEEeCCCcCCCceeeEEEEcC-------CcEEEEEcChHHHHHHhcC-CcceecCeEEEEEcCC
Confidence            4455654     25777776542       5799999999999999873 3668888888887544

>2g0c_A ATP-dependent RNA helicase DBPA; RNA recognition motif, hydrolase; 1.70A {Bacillus subtilis} PDB: 3moj_B

Probab=83.16  E-value=1.4  Score=23.12  Aligned_cols=34  Identities=9%  Similarity=0.199  Sum_probs=24.7

Q ss_pred             cEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEe
Q psy1928          27 GTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA   61 (105)
Q Consensus        27 g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~   61 (105)
                      .|.||+... ..++.++..|+...+.++.+.|+.+
T Consensus        41 ~~s~v~v~~-~~~~~~~~~l~~~~i~g~~~~v~~~   74 (76)
T 2g0c_A           41 NASYVEILN-GKGPHVLKVMKNTTVKGKQLKVNKA   74 (76)
T ss_dssp             SCEEEEECT-TCHHHHHHHHTTCCC---CCCEEEC
T ss_pred             CcEEEEECH-HHHHHHHHHhccccCcCceEEEEEC
Confidence            488888874 5577888999999999999888765

>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=80.32  E-value=2.9  Score=30.22  Aligned_cols=40  Identities=23%  Similarity=0.265  Sum_probs=32.1

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYN   47 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~   47 (105)
                      +|.++|+.||. ..|.++.+      ..+||.|.+.+.|..++.++.
T Consensus       455 ~i~~~fs~fg~-v~V~widd------t~a~V~~~~~~~a~~~l~~~~  494 (507)
T 3d45_A          455 DLYQLFSAFGN-IQISWIDD------TSAFVSLSQPEQVQIAVNTSK  494 (507)
T ss_dssp             HHHHHGGGGCC-CEEEECSS------SEEEEECSCHHHHHHHHHHHT
T ss_pred             HHHHHHHhcCC-EEEEEEcC------CeEEEEECCHHHHHHHHHHHH
Confidence            47889999994 45555544      479999999999999999885

---

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	105
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	2e-13
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	4e-12
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	9e-12
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	1e-10
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	2e-10
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 4e-10
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	6e-10
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	9e-10
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	1e-09
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	2e-09
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	4e-09
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	7e-09
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	7e-09
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	9e-09
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	9e-09
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	1e-08
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	1e-08
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	2e-08
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-08
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	2e-08
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	3e-08
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	3e-08
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	4e-08
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	5e-08
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	6e-08
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	6e-08
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	3e-07
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	5e-07
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	7e-07
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	1e-06
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	1e-06
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	2e-06
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	2e-06
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	2e-06
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	2e-06
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	2e-06
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	3e-06
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	3e-06
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	3e-06
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	9e-06
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	1e-05
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	1e-05
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	3e-05
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	3e-05
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	4e-05
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	4e-05
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	5e-05
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	8e-05
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	8e-05
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-04
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	2e-04
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	3e-04
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	4e-04
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	4e-04
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	4e-04
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	8e-04
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	0.001
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	0.001

>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 = 58.0 bits (140), Expect = 2e-13
 Identities = 46/61 (75%), Positives = 53/61 (86%)

Query: 1  MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
           I ELF+EFG LK A +HYDRSGRSLGTAD+ +ER++DA+KAMKQYNGVPLDGRPM IQL
Sbjct: 16 DIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL 75

Query: 61 A 61
           
Sbjct: 76 V 76

>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 = 54.5 bits (131), Expect = 4e-12
 Identities = 20/62 (32%), Positives = 37/62 (59%), Gaps = 1/62 (1%)

Query: 1  MIYELFSEFGPLKSAKL-HYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
          M+YE FS  GP+ S ++     + RSLG A + +++ +DA +A+   N   + G+P++I 
Sbjct: 16 MLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIM 75

Query: 60 LA 61
           +
Sbjct: 76 WS 77

>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 = 54.2 bits (130), Expect = 9e-12
 Identities = 20/64 (31%), Positives = 30/64 (46%), Gaps = 3/64 (4%)

Query: 1  MIYELFSEFGPLKSAKLHYDR--SGRSLGTADLIYERRSDAIKAMKQ-YNGVPLDGRPMQ 57
           I ELFS FG LK+ +L      +G   G   + +  + DA KA     +   L GR + 
Sbjct: 24 EIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLV 83

Query: 58 IQLA 61
          ++ A
Sbjct: 84 LEWA 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 = 51.2 bits (122), Expect = 1e-10
 Identities = 15/62 (24%), Positives = 33/62 (53%), Gaps = 1/62 (1%)

Query: 1  MIYELFSEFGPLKSAK-LHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
           +Y LF   GP+ + + +   ++G S G A + +    D+ +A+K  NG+ +  + +++ 
Sbjct: 18 ELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVS 77

Query: 60 LA 61
           A
Sbjct: 78 YA 79

>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 = 50.4 bits (120), Expect = 2e-10
 Identities = 16/65 (24%), Positives = 34/65 (52%), Gaps = 4/65 (6%)

Query: 1  MIYELFSEFGPLKSAKLHYDR----SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPM 56
           +  +FS+ G +KS  +   +       S+G   + Y++   A KA+KQ  G  +DG  +
Sbjct: 14 TLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKL 73

Query: 57 QIQLA 61
          +++++
Sbjct: 74 EVRIS 78

>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 = 50.4 bits (120), Expect = 4e-10
 Identities = 12/60 (20%), Positives = 28/60 (46%)

Query: 1   MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
           +  E+  ++G ++   +  +     +G   + + R  DA KA+   N    +G+P+  +L
Sbjct: 43  VFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAEL 102

>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 = 49.6 bits (118), Expect = 6e-10
 Identities = 21/63 (33%), Positives = 32/63 (50%), Gaps = 1/63 (1%)

Query: 1  MIYELFSEFGPLKSAKLHYDRSGRSLGTADLI-YERRSDAIKAMKQYNGVPLDGRPMQIQ 59
           IYELFS+ G +K   +  D+  ++      + Y  R+DA  AM+  NG  LD R ++  
Sbjct: 23 QIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTD 82

Query: 60 LAA 62
            A
Sbjct: 83 WDA 85

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.1 bits (117), Expect = 9e-10
 Identities = 17/84 (20%), Positives = 31/84 (36%), Gaps = 18/84 (21%)

Query: 2  IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
          +  +FS++G +    +H        G A + Y    +A  A+   +G  + G+ + I LA
Sbjct: 33 VEAIFSKYGKIVGCSVHK-------GFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLA 85

Query: 62 ADVSVLENTVPRPVARGGRGGASG 85
                             G +SG
Sbjct: 86 -----------AEPKVNRSGPSSG 98

>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 = 48.4 bits (115), Expect = 1e-09
 Identities = 14/62 (22%), Positives = 29/62 (46%), Gaps = 2/62 (3%)

Query: 1  MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
           + E F +FG +K   +  D  + RS G   + +  ++   K + Q +   LD + +  +
Sbjct: 16 GLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ-SRHELDSKTIDPK 74

Query: 60 LA 61
          +A
Sbjct: 75 VA 76

>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 = 48.9 bits (116), Expect = 2e-09
 Identities = 14/61 (22%), Positives = 29/61 (47%), Gaps = 2/61 (3%)

Query: 1  MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
           +Y++F ++GP++        +  + GTA ++YE   DA  A    +G  +  R + +  
Sbjct: 23 EMYDIFGKYGPIRQI--RVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLY 80

Query: 61 A 61
           
Sbjct: 81 Y 81

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 47.3 bits (112), Expect = 4e-09
 Identities = 17/64 (26%), Positives = 34/64 (53%), Gaps = 3/64 (4%)

Query: 1  MIYELFSEFGPLKSAKLHYD-RSGRSLGTADLIYERRSDAIKAMKQYNGVPLDG--RPMQ 57
           +  +F ++G +    +  D  +GR  G A + Y +R +A +A+   N V  +G  +P+ 
Sbjct: 22 QLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLS 81

Query: 58 IQLA 61
          ++LA
Sbjct: 82 VRLA 85

>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 = 46.6 bits (110), Expect = 7e-09
 Identities = 18/61 (29%), Positives = 30/61 (49%), Gaps = 2/61 (3%)

Query: 1  MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
           ++ +FS FG +    +      R  G A +I++  S A  A++   G P   +PM+IQ 
Sbjct: 23 SLHAIFSRFGQILDILVSRSLKMR--GQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY 80

Query: 61 A 61
          A
Sbjct: 81 A 81

>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 = 46.9 bits (111), Expect = 7e-09
 Identities = 10/61 (16%), Positives = 24/61 (39%), Gaps = 5/61 (8%)

Query: 1  MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
          ++ + FS FG +   ++         G + + +     A  A+   NG  ++G  ++   
Sbjct: 34 LMRQTFSPFGQIMEIRVF-----PEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYW 88

Query: 61 A 61
           
Sbjct: 89 G 89

>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 = 46.2 bits (109), Expect = 9e-09
 Identities = 22/59 (37%), Positives = 38/59 (64%), Gaps = 1/59 (1%)

Query: 1  MIYELFSEFGPLKSAKLHYD-RSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
           + E+FS++GP+    + YD +S RS G A + +E   DA +A ++ NG+ LDGR +++
Sbjct: 25 DLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 83

>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 = 46.6 bits (110), Expect = 9e-09
 Identities = 16/61 (26%), Positives = 30/61 (49%), Gaps = 1/61 (1%)

Query: 1  MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
          +I +LFS+ GP KS K+  +    +     + +    DA  A+   NG  + G+ +++  
Sbjct: 24 LILQLFSQIGPCKSCKMITEH-TSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNW 82

Query: 61 A 61
          A
Sbjct: 83 A 83

>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 = 46.2 bits (109), Expect = 1e-08
 Identities = 16/62 (25%), Positives = 30/62 (48%), Gaps = 1/62 (1%)

Query: 1  MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
          +++  F  FG +   ++  D  + +  G A + +E   DA  A+   N   L GR +++ 
Sbjct: 21 VLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN 80

Query: 60 LA 61
          LA
Sbjct: 81 LA 82

>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 = 46.2 bits (109), Expect = 1e-08
 Identities = 16/62 (25%), Positives = 34/62 (54%), Gaps = 1/62 (1%)

Query: 1  MIYELFSEFGPLKSAKLHYD-RSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
          +++ELF + GP+ +  +  D  +G+  G   + +    DA  A+K  + + L G+P+++ 
Sbjct: 25 LLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVN 84

Query: 60 LA 61
           A
Sbjct: 85 KA 86

>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 = 45.5 bits (107), Expect = 2e-08
 Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 1/62 (1%)

Query: 1  MIYELFSEFGPLKSAKLHYD-RSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
              LF   G ++S KL  D  +G+SLG   + Y    DA KA+   NG+ L  + +++ 
Sbjct: 18 EFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVS 77

Query: 60 LA 61
           A
Sbjct: 78 YA 79

>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 = 45.4 bits (107), Expect = 2e-08
 Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 1/62 (1%)

Query: 1  MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
           + EL + FGPLK+  L  D  +G S G A   Y   +   +A+   NG+ L  + + +Q
Sbjct: 17 QVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQ 76

Query: 60 LA 61
           A
Sbjct: 77 RA 78

>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 = 45.1 bits (106), Expect = 2e-08
 Identities = 16/63 (25%), Positives = 28/63 (44%), Gaps = 2/63 (3%)

Query: 1  MIYELFSEFGPLKSAKL--HYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
          ++Y+ FS FG +           +G S G A + +     +  A++  NG  L  RP+ +
Sbjct: 14 LLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITV 73

Query: 59 QLA 61
            A
Sbjct: 74 SYA 76

>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 = 45.3 bits (107), Expect = 3e-08
 Identities = 13/61 (21%), Positives = 29/61 (47%), Gaps = 5/61 (8%)

Query: 1  MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
           + +LF ++G      +H D+         +  E R+ A  A  + + +PL G+ ++++ 
Sbjct: 24 EMRKLFEKYGKAGEVFIHKDKG-----FGFIRLETRTLAEIAKVELDNMPLRGKQLRVRF 78

Query: 61 A 61
          A
Sbjct: 79 A 79

>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 = 45.0 bits (106), Expect = 3e-08
 Identities = 18/61 (29%), Positives = 34/61 (55%), Gaps = 1/61 (1%)

Query: 1  MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
           +Y+ FS FG + S K+  D +G S G   + +E +  A +A+++ NG+ L+ R + +  
Sbjct: 24 ALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGR 82

Query: 61 A 61
           
Sbjct: 83 F 83

>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 = 45.1 bits (106), Expect = 4e-08
 Identities = 13/61 (21%), Positives = 34/61 (55%), Gaps = 1/61 (1%)

Query: 1  MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
           + ++F +FG +   ++ ++    S G   + +E  +DA +A ++ +G  ++GR +++  
Sbjct: 27 DLRQMFGQFGKILDVEIIFNER-GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN 85

Query: 61 A 61
          A
Sbjct: 86 A 86

>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 = 44.7 bits (105), Expect = 5e-08
 Identities = 19/62 (30%), Positives = 32/62 (51%), Gaps = 1/62 (1%)

Query: 1  MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
           + ELF  FG +    L  D+ +G+S G A + + RR DA +A+   +G   D   + ++
Sbjct: 24 DLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVE 83

Query: 60 LA 61
           A
Sbjct: 84 WA 85

>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 = 44.3 bits (104), Expect = 6e-08
 Identities = 15/61 (24%), Positives = 33/61 (54%), Gaps = 1/61 (1%)

Query: 1  MIYELFSEFGPLKSAKLHYDRSGR-SLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
           + +LFS++G + ++++  D+    S G   + +++R +A +A+K  NG    G    I 
Sbjct: 22 ELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPIT 81

Query: 60 L 60
          +
Sbjct: 82 V 82

>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 = 44.3 bits (104), Expect = 6e-08
 Identities = 13/63 (20%), Positives = 31/63 (49%), Gaps = 4/63 (6%)

Query: 1  MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
           + E+F +   ++       + G+S G A + ++  +DA K +++  G  +DGR + +  
Sbjct: 32 ELKEVFEDALEIR----LVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY 87

Query: 61 AAD 63
            +
Sbjct: 88 TGE 90

>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 = 42.7 bits (100), Expect = 3e-07
 Identities = 16/61 (26%), Positives = 28/61 (45%), Gaps = 2/61 (3%)

Query: 2  IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
          + + FS  G ++  ++  DR S RS G A + +        A+    G  L G P+ +Q 
Sbjct: 35 LEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGL-TGQRLLGVPIIVQA 93

Query: 61 A 61
          +
Sbjct: 94 S 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 = 41.7 bits (97), Expect = 5e-07
 Identities = 9/62 (14%), Positives = 25/62 (40%), Gaps = 1/62 (1%)

Query: 1  MIYELFSEFGPLKSAKLHYDRSG-RSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
           I +L  +   +  +          S   A +    + DA   +++ NG+ ++G  +  +
Sbjct: 17 NIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTK 76

Query: 60 LA 61
          ++
Sbjct: 77 VS 78

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.6 bits (97), Expect = 7e-07
 Identities = 13/46 (28%), Positives = 22/46 (47%)

Query: 16 KLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
           L Y+  G   G A + +E R +A  A+   N  P+  R +++ L 
Sbjct: 41 CLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG 86

>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 = 40.8 bits (95), Expect = 1e-06
 Identities = 13/61 (21%), Positives = 28/61 (45%), Gaps = 5/61 (8%)

Query: 1  MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
          ++   FS FG +    +   R       A + YE+   A +A+ + NG  ++   +++ +
Sbjct: 19 LLRGAFSPFGNIIDLSMDPPR-----NCAFVTYEKMESADQAVAELNGTQVESVQLKVNI 73

Query: 61 A 61
          A
Sbjct: 74 A 74

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 40.9 bits (95), Expect = 1e-06
 Identities = 19/62 (30%), Positives = 31/62 (50%), Gaps = 1/62 (1%)

Query: 1  MIYELFSEFGPLKSAKLHYDRSGR-SLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
           I E F ++G +K+  L+ DR    S G A + YE    A+ A +  NG  + G+ +Q+ 
Sbjct: 23 EIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD 82

Query: 60 LA 61
            
Sbjct: 83 WC 84

>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 = 40.3 bits (94), Expect = 2e-06
 Identities = 13/62 (20%), Positives = 27/62 (43%), Gaps = 2/62 (3%)

Query: 1  MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
           I E F  FG ++S +L  D  + +  G   + ++      K M++     +     +I+
Sbjct: 15 KIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIK 73

Query: 60 LA 61
          +A
Sbjct: 74 VA 75

>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 = 40.5 bits (94), Expect = 2e-06
 Identities = 15/70 (21%), Positives = 29/70 (41%), Gaps = 9/70 (12%)

Query: 1  MIYELFSEFGPLKSAKLHYD---------RSGRSLGTADLIYERRSDAIKAMKQYNGVPL 51
           + + F + G +K  K              +G+  G A + YE    A  A++ ++G   
Sbjct: 24 DLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF 83

Query: 52 DGRPMQIQLA 61
           G  +++ LA
Sbjct: 84 QGSKLKVSLA 93

>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 = 40.5 bits (94), Expect = 2e-06
 Identities = 15/62 (24%), Positives = 30/62 (48%), Gaps = 1/62 (1%)

Query: 1  MIYELFSEFGPLKSAKLHYDRS-GRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
           + ++F  FG + SAK+  D+    S     + Y+    A  A++  NG  +  + +++Q
Sbjct: 34 DLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQ 93

Query: 60 LA 61
          L 
Sbjct: 94 LK 95

>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 = 40.3 bits (93), Expect = 2e-06
 Identities = 10/61 (16%), Positives = 24/61 (39%), Gaps = 1/61 (1%)

Query: 1  MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
           +    SE        +   R+G +     + +E   D  KA+ +  G+ + G  ++++ 
Sbjct: 29 ELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEK 87

Query: 61 A 61
           
Sbjct: 88 P 88

>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 = 40.0 bits (93), Expect = 2e-06
 Identities = 20/61 (32%), Positives = 31/61 (50%), Gaps = 5/61 (8%)

Query: 1  MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
          MI + F+   P        +R  +    A + +  R DA++AMK  NG  LDG P+++ L
Sbjct: 24 MIEKEFNNIKPGA-----VERVKKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTL 78

Query: 61 A 61
          A
Sbjct: 79 A 79

>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 = 40.5 bits (94), Expect = 3e-06
 Identities = 18/87 (20%), Positives = 31/87 (35%), Gaps = 12/87 (13%)

Query: 1  MIYELFSEFGPLKSAKLHYDRSGR-SLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
           + +LFS +GPL       D   +   G A + +     A+KA  + +G    GR + + 
Sbjct: 24 DLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVL 83

Query: 60 LAADVSVLENTVPRPVARGGRGGASGG 86
           +                  + G S G
Sbjct: 84 PS-----------TIKKEASQSGPSSG 99

>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 = 39.8 bits (92), Expect = 3e-06
 Identities = 16/59 (27%), Positives = 28/59 (47%), Gaps = 4/59 (6%)

Query: 2  IYELFSEFGPLKSAKLHYDR----SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPM 56
            E F +FG +    ++       S     +A + Y R  DA++A++  N V +DGR +
Sbjct: 28 RPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTL 86

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.1 bits (93), Expect = 3e-06
 Identities = 11/66 (16%), Positives = 21/66 (31%), Gaps = 5/66 (7%)

Query: 1  MIYELFSEFGPLKSA---KLHYDRSGRSLGTADLIYERRSDAIKAMKQYNG--VPLDGRP 55
           I E  ++                  ++ G A + YE    A  A ++     + L G  
Sbjct: 17 EILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQ 76

Query: 56 MQIQLA 61
          + +  A
Sbjct: 77 IAVDWA 82

>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 = 39.5 bits (91), Expect = 9e-06
 Identities = 13/53 (24%), Positives = 23/53 (43%), Gaps = 6/53 (11%)

Query: 33  YERRSDAIKAMKQYNGVPLDGRPMQIQLAADVSVLENTVPRPVARGGRGGASG 85
           ++  S A +A+   NG  +  + +++ LAA          RP   G  G  +G
Sbjct: 91  FQSGSSAQQAIAGLNGFNILNKRLKVALAASGH------QRPGIAGAVGDGNG 137

>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 = 38.5 bits (89), Expect = 1e-05
 Identities = 14/61 (22%), Positives = 28/61 (45%), Gaps = 2/61 (3%)

Query: 1  MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
           I ++F ++G ++   L   R G     A + +E   DA  A+   +G   DG  ++++ 
Sbjct: 30 DIEDVFYKYGAIRDIDLKNRRGGP--PFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEF 87

Query: 61 A 61
           
Sbjct: 88 P 88

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.2 bits (88), Expect = 1e-05
 Identities = 14/44 (31%), Positives = 21/44 (47%)

Query: 18 HYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
              + RS G   + +E   DA  AM   NG  +DGR +++  A
Sbjct: 39 KDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQA 82

>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 = 37.0 bits (85), Expect = 3e-05
 Identities = 10/62 (16%), Positives = 24/62 (38%), Gaps = 2/62 (3%)

Query: 1  MIYELFSEFGPLKSAKLH-YDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
           +   F +FG +  A L     + R  G   + +E      K  +  +   ++ + ++ +
Sbjct: 15 DVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI-HFHEINNKMVECK 73

Query: 60 LA 61
           A
Sbjct: 74 KA 75

>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 = 37.7 bits (87), Expect = 3e-05
 Identities = 11/63 (17%), Positives = 24/63 (38%), Gaps = 5/63 (7%)

Query: 1  MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPL--DGRPMQI 58
          +++++FS+FG +         +      A L Y     A  A    +G  +      ++I
Sbjct: 23 VLHQIFSKFGTVLKIITFTKNNQ---FQALLQYADPVSAQHAKLSLDGQNIYNACCTLRI 79

Query: 59 QLA 61
            +
Sbjct: 80 DFS 82

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.4 bits (86), Expect = 4e-05
 Identities = 10/35 (28%), Positives = 17/35 (48%)

Query: 27 GTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
          G     Y+ +  A+ AM+  NG    GR +++  A
Sbjct: 51 GYGFCEYQDQETALSAMRNLNGREFSGRALRVDNA 85

>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 = 37.0 bits (85), Expect = 4e-05
 Identities = 10/61 (16%), Positives = 24/61 (39%), Gaps = 6/61 (9%)

Query: 1  MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
           +++L  ++         Y    R+  TA +       A  A++ ++     G+ + +QL
Sbjct: 21 EVHDLLKDYDL------KYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQL 74

Query: 61 A 61
           
Sbjct: 75 Q 75

>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 = 37.1 bits (85), Expect = 5e-05
 Identities = 12/66 (18%), Positives = 21/66 (31%)

Query: 1  MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
           +  +   FG + S ++  D SG S G      E        +  +NG  +   P     
Sbjct: 34 ELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAP 93

Query: 61 AADVSV 66
             +  
Sbjct: 94 TEPLLC 99

>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 = 36.4 bits (84), Expect = 8e-05
 Identities = 11/64 (17%), Positives = 23/64 (35%), Gaps = 3/64 (4%)

Query: 2  IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
          +    S+FG ++   L         G A + +    +A   ++  +G    GR +  Q  
Sbjct: 36 LRVECSKFGQIRKLLLFDRHPD---GVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAW 92

Query: 62 ADVS 65
             +
Sbjct: 93 DGTT 96

>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 = 36.3 bits (83), Expect = 8e-05
 Identities = 10/69 (14%), Positives = 25/69 (36%), Gaps = 7/69 (10%)

Query: 1  MIYELFSEFGPLKSAKL------HYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGR 54
           + + F+    L              +  +    A L +    +  +AM  ++G+   G+
Sbjct: 17 AMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQ 75

Query: 55 PMQIQLAAD 63
           ++I+   D
Sbjct: 76 SLKIRRPHD 84

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.7 bits (82), Expect = 2e-04
 Identities = 11/63 (17%), Positives = 23/63 (36%), Gaps = 3/63 (4%)

Query: 2  IYELFSEFGPLKSAKLHYD---RSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
          + +  S++G +KS ++            G   + +    D  KAM+   G     R +  
Sbjct: 31 VRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVT 90

Query: 59 QLA 61
          +  
Sbjct: 91 KYC 93

>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 = 35.1 bits (80), Expect = 2e-04
 Identities = 11/62 (17%), Positives = 25/62 (40%), Gaps = 7/62 (11%)

Query: 2  IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQY--NGVPLDGRPMQIQ 59
          + +L   FG + +  +    +      A +      DA  A+  Y      + G+P+++ 
Sbjct: 26 LLQLVEPFGVISNHLILNKIN-----EAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVH 80

Query: 60 LA 61
          L+
Sbjct: 81 LS 82

>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 = 35.1 bits (80), Expect = 3e-04
 Identities = 15/62 (24%), Positives = 28/62 (45%), Gaps = 1/62 (1%)

Query: 1  MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
           +  LF+ F   K   + +   +GR  G A + +  +  A +A+   NG  L G+ + I+
Sbjct: 34 DLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIE 93

Query: 60 LA 61
            
Sbjct: 94 FG 95

>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 = 34.3 bits (78), Expect = 4e-04
 Identities = 9/44 (20%), Positives = 19/44 (43%), Gaps = 1/44 (2%)

Query: 18 HYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
                 +   A +++E +  A +A++  N   L  R + + LA
Sbjct: 40 GQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSLA 82

>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 = 34.7 bits (79), Expect = 4e-04
 Identities = 20/89 (22%), Positives = 36/89 (40%), Gaps = 9/89 (10%)

Query: 1  MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
           ++ LF  +G ++  K+ +++       A +     + A  AM   NG  L G+P++I L
Sbjct: 19 SLFILFGVYGDVQRVKILFNKKEN----ALVQMADGNQAQLAMSHLNGHKLHGKPIRITL 74

Query: 61 AADVSVLENTVPRPVARGGRGGASGGYRN 89
          +         V  P       G +  Y N
Sbjct: 75 SKH-----QNVQLPREGQEDQGLTKDYGN 98

>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 = 34.8 bits (79), Expect = 4e-04
 Identities = 9/74 (12%), Positives = 24/74 (32%), Gaps = 5/74 (6%)

Query: 1  MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
              LF  +    + +       +S     + +     A  A  + +     G+ M++  
Sbjct: 26 KFESLFRTYDKDTTFQYF-----KSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYF 80

Query: 61 AADVSVLENTVPRP 74
          A  + +  + +  P
Sbjct: 81 AQTLHIGSSHLAPP 94

>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 = 33.6 bits (76), Expect = 8e-04
 Identities = 17/68 (25%), Positives = 30/68 (44%), Gaps = 7/68 (10%)

Query: 1  MIYELFSEFGPLKSAKLHYDRSGR-SLGTADLIYERRSDAIKAMKQYN------GVPLDG 53
           + E+  +FG LK  ++        S G A   +  +  A K +   +      G+ LDG
Sbjct: 24 ALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDG 83

Query: 54 RPMQIQLA 61
          R +++ LA
Sbjct: 84 RQLKVDLA 91

>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 = 33.1 bits (75), Expect = 0.001
 Identities = 13/85 (15%), Positives = 24/85 (28%), Gaps = 17/85 (20%)

Query: 1  MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
           + E FS++G +    +       +  T    +     A         + + G  + I  
Sbjct: 21 ELREFFSQYGDVMDVFIPKPFRAFAFVT----FADDQIAQSLCG--EDLIIKGISVHISN 74

Query: 61 AADVSVLENTVPRPVARGGRGGASG 85
          A            P      G +SG
Sbjct: 75 A-----------EPKHNSNSGPSSG 88

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 32.8 bits (74), Expect = 0.001
 Identities = 4/25 (16%), Positives = 10/25 (40%)

Query: 33 YERRSDAIKAMKQYNGVPLDGRPMQ 57
          ++  S A KA+       +  +  +
Sbjct: 47 FDSPSAAQKAVTALKASGVQAQMAK 71

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	105
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.71
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.7
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.69
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.68
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.68
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.68
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.68
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.67
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.67
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.67
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.67
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.67
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.65
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.64
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.64
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.63
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.63
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	99.62
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.62
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.61
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.61
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.61
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.61
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.61
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.6
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.6
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.6
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.59
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.59
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.58
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.58
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.57
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.56
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.56
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.55
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.55
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.54
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.54
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.54
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.53
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.53
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.52
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.52
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.51
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.51
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.51
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.51
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.51
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.5
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.48
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.48
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.47
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.47
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.46
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.45
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.45
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.45
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.44
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.44
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.44
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.43
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.41
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.4
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.4
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.39
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.39
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.38
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.37
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.37
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.36
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.36
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.35
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.35
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.35
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.34
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.34
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.32
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.32
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.31
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.31
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.28
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.24
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.1
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.03
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.03
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.01
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	98.83
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.83
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.49
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	92.69

>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=99.71  E-value=2.2e-17  Score=94.20  Aligned_cols=67  Identities=22%  Similarity=0.332  Sum_probs=61.7

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccCCC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVSVL   67 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~~~   67 (105)
                      +|+++|++||.|..+.|+.++ ++.+++||||+|.+.++|++||+.||+..+.++.|+|+++..+...
T Consensus        24 ~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a~~~~~~   91 (99)
T d1whwa_          24 DLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKEA   91 (99)
T ss_dssp             HHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECCCCSTT
T ss_pred             HHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCcc
Confidence            588999999999999999988 8999999999999999999999999999999999999998855433

>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=99.70  E-value=4.4e-17  Score=91.15  Aligned_cols=63  Identities=32%  Similarity=0.491  Sum_probs=59.8

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeec
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD   63 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~   63 (105)
                      +|.++|+.||.|.++.++.++ ++++++||||+|.+.++|++|+..||+..+.++.|.|+++.+
T Consensus        23 ~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~a~~   86 (88)
T d1rk8a_          23 EIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFV   86 (88)
T ss_dssp             HHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEE
T ss_pred             HHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEecC
Confidence            488999999999999999998 899999999999999999999999999999999999999874

>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=99.69  E-value=5.2e-17  Score=91.14  Aligned_cols=64  Identities=30%  Similarity=0.450  Sum_probs=60.1

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeecc
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADV   64 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~   64 (105)
                      +|+++|+.||.|..+.|+.++ ++.++|||||+|.+.++|++||+.||+..+.++.|+|++++++
T Consensus        24 ~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~akp~   88 (90)
T d2cq0a1          24 DLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPS   88 (90)
T ss_dssp             HHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESSCC
T ss_pred             HHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEeeeCC
Confidence            478999999999999999998 8999999999999999999999999999999999999998743

>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=99.68  E-value=6e-17  Score=89.06  Aligned_cols=62  Identities=34%  Similarity=0.537  Sum_probs=59.1

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|+.||.|.++.|++++ ++.+++||||+|.+.++|+.|++.||+..+.++.|+|.++.
T Consensus        16 ~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~   78 (80)
T d1cvja1          16 MLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             HHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             HHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            488999999999999999998 89999999999999999999999999999999999999885

>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=99.68  E-value=7.3e-17  Score=89.68  Aligned_cols=64  Identities=31%  Similarity=0.373  Sum_probs=60.4

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeecc
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADV   64 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~   64 (105)
                      +|+++|++||.|..+.|+.++ ++.+++||||+|.+.++|+.|+..||+..+.++.|.|+++.+.
T Consensus        17 ~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~   81 (85)
T d2u2fa_          17 QVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG   81 (85)
T ss_dssp             HHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCC
T ss_pred             HHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            488999999999999999998 8999999999999999999999999999999999999999743

>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=99.68  E-value=3.5e-17  Score=90.27  Aligned_cols=63  Identities=25%  Similarity=0.517  Sum_probs=59.4

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeec
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD   63 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~   63 (105)
                      +|+++|++||.|..+.+++++ ++.+++||||+|.+.++|++||..||+..+.++.|+|+++++
T Consensus        18 ~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~p   81 (82)
T d1b7fa1          18 ELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   81 (82)
T ss_dssp             HHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             HHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            488999999999999999987 899999999999999999999999999999999999999863

>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=99.68  E-value=4e-17  Score=92.18  Aligned_cols=65  Identities=26%  Similarity=0.471  Sum_probs=60.8

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|++||.|.++.++.++ ++.+++||||+|.+.++|++|++.||+..+.++.|+|+++.+..
T Consensus        25 ~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A~~~~   90 (93)
T d1x5ua1          25 LLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHN   90 (93)
T ss_dssp             HHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETTTTS
T ss_pred             HHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCCC
Confidence            588999999999999999988 89999999999999999999999999999999999999987443

>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=99.67  E-value=6.9e-17  Score=88.43  Aligned_cols=62  Identities=74%  Similarity=1.172  Sum_probs=58.9

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|++||.|.++.++.++++++++||||+|.+.++|++|++.||+..+.+++|+|++++
T Consensus        16 ~l~~~F~~~G~v~~~~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~   77 (78)
T d1no8a_          16 DIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             HHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             HHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            58899999999999999988899999999999999999999999999999999999999875

>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=99.67  E-value=1.4e-16  Score=87.74  Aligned_cols=62  Identities=32%  Similarity=0.503  Sum_probs=59.0

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|++||.|.++.++.+. ++.+++||||+|.+.++|++|++.||+..+.++.|+|++++
T Consensus        18 ~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~Ak   80 (82)
T d1fxla1          18 EFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYAR   80 (82)
T ss_dssp             HHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             HHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            588999999999999999987 88999999999999999999999999999999999999986

>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=99.67  E-value=4.8e-17  Score=91.13  Aligned_cols=64  Identities=25%  Similarity=0.390  Sum_probs=60.0

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeecc
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADV   64 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~   64 (105)
                      +|+++|++||.|.++.++.++ ++.++|||||+|.+.++|++|+..||+..+.++.|.|+++.+.
T Consensus        21 ~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~p~   85 (89)
T d2cqba1          21 VLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPM   85 (89)
T ss_dssp             HHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECCCC
T ss_pred             HHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCCC
Confidence            488999999999999999988 8999999999999999999999999999999999999998743

>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=99.67  E-value=2.8e-16  Score=88.60  Aligned_cols=62  Identities=35%  Similarity=0.489  Sum_probs=59.2

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|++||.|.+|.++.++ ++.+++||||+|.+.++|+.|++.||+..++++.|+|+++.
T Consensus        23 ~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a~   85 (93)
T d1h2vz_          23 QIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDA   85 (93)
T ss_dssp             HHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEES
T ss_pred             HHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            488999999999999999998 89999999999999999999999999999999999999986

>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=99.67  E-value=1.5e-16  Score=95.62  Aligned_cols=64  Identities=28%  Similarity=0.479  Sum_probs=60.1

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeecc
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADV   64 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~   64 (105)
                      +|+++|+.||.|.+|.|+.++ ++.++|||||+|.+.++|+.||+.||+..|.++.|+|+++...
T Consensus        58 ~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~~~  122 (139)
T d1u6fa1          58 QLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASG  122 (139)
T ss_dssp             HHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESSCC
T ss_pred             HHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            588999999999999999988 8999999999999999999999999999999999999998733

>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=99.65  E-value=2.2e-16  Score=90.45  Aligned_cols=65  Identities=23%  Similarity=0.361  Sum_probs=60.7

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|+.||.|.++.++.++ ++.++|||||+|.+.++|+.||+.||+..|.++.|+|+++.++.
T Consensus        34 ~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a~~k~   99 (102)
T d2cpza1          34 DLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKN   99 (102)
T ss_dssp             HHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCCCSC
T ss_pred             HHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEeCCCC
Confidence            588999999999999999988 89999999999999999999999999999999999999987544

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.64  E-value=4.6e-16  Score=86.31  Aligned_cols=61  Identities=28%  Similarity=0.580  Sum_probs=56.8

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCC--eeEEEEEe
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDG--RPMQIQLA   61 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~--~~i~V~~~   61 (105)
                      +|+++|++||.|..+.++.++ ++.+++||||+|.+.++|++||+.||+..+.+  ++|.|++|
T Consensus        22 ~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~~A   85 (85)
T d1b7fa2          22 QLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA   85 (85)
T ss_dssp             HHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             HHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEEEC
Confidence            488999999999999999998 89999999999999999999999999998875  78999875

>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=99.64  E-value=3.2e-16  Score=88.55  Aligned_cols=65  Identities=31%  Similarity=0.408  Sum_probs=59.3

Q ss_pred             CHHHHhccCCCeeEEEEEeCC--CCCcccEEEEEeCCHHHHHHHHHHh-CCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR--SGRSLGTADLIYERRSDAIKAMKQY-NGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~--~~~~~g~~fv~f~~~~~a~~ai~~l-~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|++||.|..+.|+.+.  ++.+++||||+|.+.++|++||+.| |+..+.++.|.|+++....
T Consensus        24 ~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~~A~~~~   91 (94)
T d2cpha1          24 EIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEV   91 (94)
T ss_dssp             HHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEEECCCCC
T ss_pred             HHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEEEcCCCC
Confidence            488999999999999998875  7899999999999999999999998 8999999999999998443

>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=99.63  E-value=6.5e-16  Score=85.73  Aligned_cols=61  Identities=28%  Similarity=0.565  Sum_probs=56.3

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCC--eeEEEEEe
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDG--RPMQIQLA   61 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~--~~i~V~~~   61 (105)
                      +|+++|++||.|.++.++.++ ++.+++||||+|.+.++|++|++.||+..+.+  ++|.|.++
T Consensus        22 ~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~A   85 (85)
T d1fxla2          22 ELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA   85 (85)
T ss_dssp             HHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             HHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEeC
Confidence            488999999999999999998 89999999999999999999999999999986  55888875

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.63  E-value=7.4e-16  Score=85.08  Aligned_cols=58  Identities=38%  Similarity=0.651  Sum_probs=55.2

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEE
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI   58 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V   58 (105)
                      +|+++|++||.|.++.++.++ ++.+++||||+|.+.++|+.|+..||+..+.++.|+|
T Consensus        25 ~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1          25 DLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             HHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             HHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            488999999999999999998 8999999999999999999999999999999999987

>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=99.62  E-value=4e-16  Score=89.71  Aligned_cols=60  Identities=20%  Similarity=0.380  Sum_probs=56.6

Q ss_pred             HHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEe
Q psy1928           2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA   61 (105)
Q Consensus         2 l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~   61 (105)
                      |+++|++||.|.+|.|+.+.+++++|++||+|.+.++|++|+..||+..++++.|+|+++
T Consensus        44 l~e~f~k~G~I~~v~I~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          44 FTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             HHHHhccCCCEEEEEeecCCCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            678899999999999987779999999999999999999999999999999999999986

>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=99.62  E-value=3.7e-16  Score=86.27  Aligned_cols=65  Identities=28%  Similarity=0.432  Sum_probs=58.4

Q ss_pred             CHHHHhccCCCeeEE-EEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSA-KLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~-~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|++||.|.++ .++.++ ++++++||||+|.+.++|++||+.|++..+.++.|+|+++.+++
T Consensus        14 ~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k~   80 (83)
T d1x5ta1          14 LLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKD   80 (83)
T ss_dssp             HHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCC
T ss_pred             HHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCCC
Confidence            588999999998664 678877 89999999999999999999999999999999999999987443

>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=99.61  E-value=3.4e-16  Score=89.84  Aligned_cols=62  Identities=35%  Similarity=0.636  Sum_probs=58.9

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|+.||.|.++.|+.++ ++.+++||||+|.+.++|++|++.||+..+.++.|+|+++.
T Consensus        24 ~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~   86 (104)
T d1p1ta_          24 QLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAA   86 (104)
T ss_dssp             HHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETT
T ss_pred             HHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            488999999999999999988 89999999999999999999999999999999999999976

>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=99.61  E-value=6.9e-16  Score=85.81  Aligned_cols=63  Identities=21%  Similarity=0.347  Sum_probs=55.4

Q ss_pred             HHHHhccCCCeeEEEEEeCC--CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           2 IYELFSEFGPLKSAKLHYDR--SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         2 l~~~f~~~G~i~~~~i~~~~--~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      |+++|++||.|.++.|+.+.  +++++|||||+|.+.++|++|++ ||+..+.++.|+|+++.++|
T Consensus        22 l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~~a~~kP   86 (86)
T d2ghpa3          22 LRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSLADKKP   86 (86)
T ss_dssp             HHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEEECCCCC
T ss_pred             HHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEEEcCCCC
Confidence            78999999999999987753  88899999999999999999996 99999999999999987543

>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=99.61  E-value=1e-15  Score=87.72  Aligned_cols=62  Identities=31%  Similarity=0.412  Sum_probs=57.4

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeec
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD   63 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~   63 (105)
                      +|+++|++||.|.++.|+.++ ++.+++||||+|.+.++|++||+.+|+ .|.++.|.|+++..
T Consensus        26 ~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a~~   88 (103)
T d2cqda1          26 SLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAYL   88 (103)
T ss_dssp             HHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEESTT
T ss_pred             HHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEEcCC
Confidence            588999999999999999998 899999999999999999999998875 79999999998873

>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=99.61  E-value=7e-16  Score=85.50  Aligned_cols=62  Identities=26%  Similarity=0.496  Sum_probs=56.2

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CC---CcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SG---RSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~---~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|++||.|.++.|+.++ ++   .++|||||+|.+.++|++|++.||+..+.++.|.|+++.
T Consensus        14 ~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~   79 (85)
T d2cpfa1          14 TLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISE   79 (85)
T ss_dssp             HHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSS
T ss_pred             HHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            488999999999999998876 33   368999999999999999999999999999999999876

>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=99.61  E-value=8.9e-16  Score=85.90  Aligned_cols=64  Identities=30%  Similarity=0.483  Sum_probs=59.6

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeecc
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADV   64 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~   64 (105)
                      +|+++|+.||.|..+.++.++ ++.+++||||+|.+.++|+.||..||+..+.++.|+|+++...
T Consensus        21 ~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a~~~   85 (90)
T d1x5sa1          21 SLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKS   85 (90)
T ss_dssp             HHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEECC
T ss_pred             HHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCC
Confidence            588999999999999988887 8999999999999999999999999999999999999998743

>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=99.60  E-value=1.9e-15  Score=83.65  Aligned_cols=61  Identities=23%  Similarity=0.297  Sum_probs=56.8

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|++||.|..+.|+.++ ++.++|||||+|.+.++|++||+ +++..|.|+.|+|+.|.
T Consensus        22 ~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1          22 SLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             HHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             HHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEeee
Confidence            588999999999999999998 89999999999999999999998 58899999999998763

>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=99.60  E-value=1.4e-15  Score=85.22  Aligned_cols=63  Identities=25%  Similarity=0.338  Sum_probs=56.8

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|+.||.|..+.|+.++ ++.++|||||+|.+.++|++||+.  ...|+++.|.|+++.++.
T Consensus        24 ~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~--~~~l~Gr~i~v~~a~~k~   87 (90)
T d2cqga1          24 DLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWCDCKLPNSKQ   87 (90)
T ss_dssp             HHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTEEEEEECCCTTC
T ss_pred             HHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhc--CCccCCEEeEEEeCCCCC
Confidence            488999999999999999998 899999999999999999999984  448899999999887544

>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=99.60  E-value=3e-15  Score=84.30  Aligned_cols=64  Identities=22%  Similarity=0.463  Sum_probs=58.1

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|+.||.|..|.++.++.+ +++||||+|.+.++|++||..||+..+.++.|+|+++.++.
T Consensus        27 ~L~~~F~~~G~v~~v~~~~~~~~-~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A~~r~   90 (93)
T d2cq3a1          27 DLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARV   90 (93)
T ss_dssp             HHHHHGGGTSCEEEEEEECCTTT-TCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCSSC
T ss_pred             HHHHHHhhcceeeeccccccccC-CcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCcCC
Confidence            48899999999999999987633 58999999999999999999999999999999999998654

>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=99.59  E-value=5.9e-16  Score=84.50  Aligned_cols=60  Identities=22%  Similarity=0.322  Sum_probs=56.2

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEe
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA   61 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~   61 (105)
                      +|+++|++||.|.++.++.++ ++++++||||+|.+.++|++||+ +++..++++.|.|+.+
T Consensus        16 ~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_          16 GLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             HHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             HHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            488999999999999999998 89999999999999999999998 6999999999999875

>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=99.59  E-value=1.5e-15  Score=87.18  Aligned_cols=64  Identities=20%  Similarity=0.273  Sum_probs=58.7

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|++||.|..+.|+.++ ++.+++||||+|.+.++|++||+ +++..|.++.|.|.++.+++
T Consensus        36 ~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~~ke  100 (103)
T d1x4ba1          36 SLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVARE  100 (103)
T ss_dssp             HHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCSSCC
T ss_pred             HHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECcccC
Confidence            589999999999999999998 88999999999999999999997 79999999999999877544

>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=99.58  E-value=1e-15  Score=84.08  Aligned_cols=63  Identities=14%  Similarity=0.152  Sum_probs=52.9

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeec
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD   63 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~   63 (105)
                      +|+++|+.||.|..+.++.+. ++++++||||+|.+.++|++|++.||+..+.++.|.|+++++
T Consensus        17 ~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1          17 NIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             HHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             HHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            488999999999888777666 888999999999999999999999999999999999999874

>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=99.58  E-value=1.5e-15  Score=86.82  Aligned_cols=61  Identities=26%  Similarity=0.366  Sum_probs=57.5

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|+.||.|..+.|+.++ +++++|||||+|.+.++|++|++ ||+..+.++.|.|+++.
T Consensus        34 ~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a~   95 (101)
T d2cq4a1          34 DLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQ   95 (101)
T ss_dssp             HHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHH
T ss_pred             HHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECC
Confidence            488999999999999999988 89999999999999999999996 99999999999999875

>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=99.57  E-value=1.4e-15  Score=82.57  Aligned_cols=59  Identities=24%  Similarity=0.410  Sum_probs=54.8

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEE
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL   60 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~   60 (105)
                      +|+++|++||.|..+.++.++ ++++++||||+|.+.++|++||+ +++..|.|+.|.|+.
T Consensus        15 ~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~r   74 (75)
T d1hd0a_          15 DLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKR   74 (75)
T ss_dssp             HHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECC
T ss_pred             HHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeE
Confidence            488999999999999999988 89999999999999999999998 799999999998864

>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=99.56  E-value=3.3e-15  Score=81.75  Aligned_cols=60  Identities=20%  Similarity=0.351  Sum_probs=54.6

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|++||.|.++.+..+     ++||||+|.+.++|++|+..||+..+.++.|+|+++++.|
T Consensus        19 ~L~~~F~~~G~I~~v~~~~~-----~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~P   78 (79)
T d2bz2a1          19 LLRGAFSPFGNIIDLSMDPP-----RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQP   78 (79)
T ss_dssp             HHHHHHSTTCCCSCEEEETT-----TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECCSSC
T ss_pred             HHHHHHhccCccceeeeccC-----CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEecCCC
Confidence            48899999999999988754     6899999999999999999999999999999999997543

>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=99.56  E-value=1.5e-15  Score=84.89  Aligned_cols=63  Identities=27%  Similarity=0.419  Sum_probs=56.7

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeecc
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADV   64 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~   64 (105)
                      +|+++|+.||.|..+.++.++. .+++||||+|.+.++|++||+.||+..+.++.|.|+++..+
T Consensus        24 ~l~~~F~~~G~v~~~~i~~~~~-~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~~   86 (89)
T d1cvja2          24 ALYDTFSAFGNILSCKVVCDEN-GSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR   86 (89)
T ss_dssp             HHHHHHHTTSCEEEEEECCBTT-BCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCCT
T ss_pred             HHHHHHHhcCCceEEEEEeecC-CCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            4889999999999999988763 36799999999999999999999999999999999998743

>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=99.55  E-value=9.7e-15  Score=81.66  Aligned_cols=62  Identities=26%  Similarity=0.413  Sum_probs=56.1

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeec
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD   63 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~   63 (105)
                      +|+++|+.||.|..+.++.++.. .++||||+|.+.++|+.|+..||+..+.++.|+|.++..
T Consensus        24 ~l~~~F~~~G~i~~v~i~~d~~~-~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~   85 (90)
T d2cqia1          24 LILQLFSQIGPCKSCKMITEHTS-NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATT   85 (90)
T ss_dssp             HHHHHHHHHSCEEEEEEECCCCS-SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             HHHHHHHhcCCceeeeeecccCc-cceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCC
Confidence            48899999999999999988632 378999999999999999999999999999999999873

>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=99.55  E-value=6.3e-15  Score=83.44  Aligned_cols=60  Identities=17%  Similarity=0.354  Sum_probs=55.2

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|+.||.|.++.++.+     ++||||+|.+.++|++||..||+..|.++.|+|.|++..+
T Consensus        34 ~L~~~F~~fG~i~~v~i~~~-----kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak~~p   93 (96)
T d1x4ga1          34 LMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESP   93 (96)
T ss_dssp             HHHHHHHHHSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCCC
T ss_pred             HHHHHHHHhCCceEEEEEec-----ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            48899999999999999876     6899999999999999999999999999999999987544

>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=99.54  E-value=1e-14  Score=82.82  Aligned_cols=56  Identities=27%  Similarity=0.435  Sum_probs=51.9

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeec
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD   63 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~   63 (105)
                      +|+++|++||.|..+.|.       ++||||+|.+.++|++||+.||+..+.++.|+|+++.+
T Consensus        32 ~L~~~F~~~G~i~~~~i~-------rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~   87 (98)
T d1wf2a_          32 DVEAIFSKYGKIVGCSVH-------KGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAE   87 (98)
T ss_dssp             HHHHSSTTSSCEEEEEEE-------TEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEETTS
T ss_pred             HHHHHHhhcCCEEEEEEe-------CCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            488999999999999884       58999999999999999999999999999999999873

>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=99.54  E-value=1.4e-15  Score=82.63  Aligned_cols=60  Identities=22%  Similarity=0.320  Sum_probs=54.7

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEe
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA   61 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~   61 (105)
                      +|+++|++||.|..+.|+.++ +++++|||||+|.+.++|++||+. +...|+++.|.|+.|
T Consensus        15 ~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~~-~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1          15 KIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIKVA   75 (75)
T ss_dssp             HHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTTC-SSCCBTTBCCEEECC
T ss_pred             HHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHhh-CCCEECCEEeEEEEC
Confidence            488999999999999999998 899999999999999999999974 777899999998764

>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=99.54  E-value=1.9e-14  Score=78.52  Aligned_cols=60  Identities=18%  Similarity=0.358  Sum_probs=55.6

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEe
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA   61 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~   61 (105)
                      +|+++|++||.|..+.++.++ ++.++++|||+|.+.+++++|++ +++..|+++.|+|+.|
T Consensus        18 ~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2          18 HLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             HHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             HHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEEC
Confidence            488999999999999999988 89999999999999999999986 8999999999999875

>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=99.53  E-value=4.6e-15  Score=80.18  Aligned_cols=60  Identities=18%  Similarity=0.303  Sum_probs=55.9

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEe
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA   61 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~   61 (105)
                      +|+++|+.||.|..+.++.++ ++.++++|||+|.+.++|++|++ +|+..++++.|+|++|
T Consensus        15 ~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_          15 DVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             HHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             HHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECCeEEEEEEC
Confidence            588999999999999988888 88999999999999999999997 8999999999999875

>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=99.53  E-value=4.9e-15  Score=82.42  Aligned_cols=61  Identities=15%  Similarity=0.128  Sum_probs=53.7

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccCCC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVSVL   67 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~~~   67 (105)
                      +|+++|++||.|.++.++.+      +||||+|.+.++|++||..||+..+.++.|+|.++...+..
T Consensus        16 ~l~~~F~~~G~v~~~~i~~~------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~~~~   76 (87)
T d3begb1          16 DLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDG   76 (87)
T ss_dssp             HHHHHHGGGSCEEEEEECTT------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEECC
T ss_pred             HHHHHHhhhccccccccccc------ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecCcCC
Confidence            58999999999999988653      79999999999999999999999999999999887744433

>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=99.52  E-value=2e-14  Score=81.30  Aligned_cols=65  Identities=26%  Similarity=0.413  Sum_probs=57.9

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhC------CcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYN------GVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~------~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|++||.|..+.++.++ ++.+++||||+|.+.++|++||+.||      +..+.++.|+|+++.+++
T Consensus        24 ~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr~l~v~~a~~k~   95 (98)
T d1x4ha1          24 ALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRD   95 (98)
T ss_dssp             HHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCEEEEECCCCCC
T ss_pred             HHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCEEEEEEECCCCC
Confidence            488999999999999998887 88899999999999999999999886      566889999999987544

>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=99.52  E-value=1.9e-14  Score=80.39  Aligned_cols=57  Identities=26%  Similarity=0.459  Sum_probs=51.0

Q ss_pred             HHHhccCCCeeEEEEEeCC-CCC---cccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEE
Q psy1928           3 YELFSEFGPLKSAKLHYDR-SGR---SLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ   59 (105)
Q Consensus         3 ~~~f~~~G~i~~~~i~~~~-~~~---~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~   59 (105)
                      .++|++||.|..|.++.++ ++.   ..+||||+|.+.++|++||+.||+..+.++.|+|.
T Consensus        29 ~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~lkvS   89 (89)
T d2cpia1          29 PEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKAS   89 (89)
T ss_dssp             TTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             HHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEEEEC
Confidence            5679999999999999887 443   35899999999999999999999999999999874

>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=99.51  E-value=1.2e-14  Score=83.79  Aligned_cols=58  Identities=26%  Similarity=0.495  Sum_probs=54.2

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|+.||.|.+|.|+.++    +++|||+|.+.++|++|++.||+..|.++.|+|+++.
T Consensus        19 ~L~~~F~~fG~I~~v~i~~~~----kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~   76 (109)
T d2adca1          19 SLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   76 (109)
T ss_dssp             HHHHHHHHHTCEEEEEECCTT----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCS
T ss_pred             HHHHHHhhccccceEEEEecc----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            488999999999999998764    6899999999999999999999999999999999987

>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=99.51  E-value=2.9e-14  Score=78.96  Aligned_cols=61  Identities=13%  Similarity=0.148  Sum_probs=56.6

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|+.||.|..+.|..++++.++|||||+|.+.++|++||+ +++..+.++.|.|++..
T Consensus        22 ~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2          22 DIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             HHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             HHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            58899999999999999888899999999999999999999997 69999999999999765

>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=99.51  E-value=1.4e-14  Score=82.32  Aligned_cols=65  Identities=23%  Similarity=0.465  Sum_probs=57.0

Q ss_pred             CHHHHhccCCCee--------EEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLK--------SAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~--------~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|+.||.|.        .+.+..++ ++++++||||+|.+.++|++||+.||+..+.++.|+|++++.++
T Consensus        24 ~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~a~~~~   97 (101)
T d2cpea1          24 DLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKP   97 (101)
T ss_dssp             HHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETTEECEEECSSCCC
T ss_pred             HHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            4889999999874        45566666 78999999999999999999999999999999999999988544

>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=99.51  E-value=3e-14  Score=82.67  Aligned_cols=60  Identities=23%  Similarity=0.459  Sum_probs=54.9

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|++||.|.+|.+..+  +.++|||||+|.+.++|..||+.||+..|.++.|.|.++.
T Consensus        23 ~l~~~F~~~G~v~~i~~~~~--~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~   82 (114)
T d2f9da1          23 EMYDIFGKYGPIRQIRVGNT--PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYN   82 (114)
T ss_dssp             HHHHHHHTTSCEEEEEEECS--TTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             HHHHHHhhcCCeEeeccccc--CCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            48899999999999988754  4568999999999999999999999999999999999986

>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=99.51  E-value=2.2e-14  Score=79.58  Aligned_cols=60  Identities=23%  Similarity=0.397  Sum_probs=54.8

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|+.||.|.++.+..+     ++||||+|.+.++|++|++.||+..+.++.|+|+++....
T Consensus        24 ~l~~~F~~~G~i~~i~~~~~-----k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~~~   83 (86)
T d2cpja1          24 EMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSA   83 (86)
T ss_dssp             HHHHHTSTTCCCSEEEEETT-----TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCS
T ss_pred             HHHHHHHHhCCceEeeeecc-----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCcC
Confidence            48899999999999998865     6899999999999999999999999999999999988443

>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=99.50  E-value=2.3e-15  Score=85.90  Aligned_cols=65  Identities=23%  Similarity=0.394  Sum_probs=59.4

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|.++|+.||.|..+.++.+. ++.+++||||+|.+.++|++||+.||+..+.++.|+|+++++++
T Consensus        34 ~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~ak~k~   99 (102)
T d2cpxa1          34 DLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKK   99 (102)
T ss_dssp             HHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEECCCCS
T ss_pred             HHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeCCCcc
Confidence            488999999999988888776 88999999999999999999999999999999999999998543

>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=99.48  E-value=6.4e-14  Score=80.07  Aligned_cols=63  Identities=17%  Similarity=0.306  Sum_probs=54.5

Q ss_pred             CHHHHhccCCCeeEEEEEeCC--CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR--SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~--~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|+.|| |..+.++.++  ++.+++||||+|.+.++|++|++ ||+..|.++.|+|.++....
T Consensus        31 ~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~-~~~~~~~gr~l~V~~a~~~~   95 (104)
T d1wi8a_          31 SIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLGNKRIRVDVADQAQ   95 (104)
T ss_dssp             HHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHG-GGTCEETTEECEEEECCCCC
T ss_pred             HHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHH-cCCCEECCEEEEEEECCCCC
Confidence            5889999998 7788777765  78899999999999999987775 99999999999999987443

>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=99.48  E-value=9e-16  Score=86.22  Aligned_cols=62  Identities=16%  Similarity=0.173  Sum_probs=56.0

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeec
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD   63 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~   63 (105)
                      +|+++|+.||.|..+.++.+.++++++||||+|.+.++|++||+ ||+..+.++.|+|++++.
T Consensus        29 ~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~ak~   90 (91)
T d1fjeb1          29 ELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKG   90 (91)
T ss_dssp             HHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECCCC
T ss_pred             HHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEecCC
Confidence            48899999999988877665588999999999999999999996 999999999999998863

>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=99.47  E-value=1.6e-14  Score=82.35  Aligned_cols=62  Identities=19%  Similarity=0.255  Sum_probs=55.9

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|+.||.|..+.+..+.++.+++||||+|.+.++|++||+.||+..|.++++.|..+.
T Consensus        34 ~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~~   95 (101)
T d1x5oa1          34 ELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTE   95 (101)
T ss_dssp             HHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSS
T ss_pred             HHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCCC
Confidence            48899999999999998888888999999999999999999999999999999887765443

>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=99.47  E-value=1.3e-14  Score=77.92  Aligned_cols=57  Identities=18%  Similarity=0.261  Sum_probs=52.7

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEE
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQ   57 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~   57 (105)
                      +|+++|++||.|..+.++.++ ++.++++|||+|.+.++|++|++.||+..+.++.++
T Consensus        14 ~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1          14 DLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             HHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             HHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEECc
Confidence            478999999999999999988 899999999999999999999999999999988753

>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=99.46  E-value=9.7e-14  Score=78.19  Aligned_cols=60  Identities=20%  Similarity=0.317  Sum_probs=53.8

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|+.||.|..+.+..  +...++||||+|.+.++|+.||+.||+..+.++.|+|++++
T Consensus        30 ~l~~~F~~~G~v~~~~~~~--~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a~   89 (95)
T d1x4aa1          30 DIEDVFYKYGAIRDIDLKN--RRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPR   89 (95)
T ss_dssp             HHHHHHGGGSCEEEEEECC--SSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             HHHHHHhcCCceEEEEecc--cccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEecc
Confidence            5889999999999887654  34567999999999999999999999999999999999987

>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=99.45  E-value=1.1e-13  Score=79.68  Aligned_cols=59  Identities=25%  Similarity=0.191  Sum_probs=53.2

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeecc
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADV   64 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~   64 (105)
                      +|+++|+.||.|..|.|..     .++||||+|.+.++|++||+.||+..+.++.|.|+++...
T Consensus        26 ~L~~~F~~fG~I~~v~l~~-----~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~~   84 (111)
T d1whxa_          26 EIQETFSRFGSLGRVLLPE-----GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIG   84 (111)
T ss_dssp             HHHHHHHTTSCEEEEECCS-----SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETT
T ss_pred             HHHhhhhccCCccEEEeec-----cCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCCC
Confidence            4899999999999987743     3689999999999999999999999999999999998743

>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=99.45  E-value=2.1e-13  Score=78.07  Aligned_cols=58  Identities=14%  Similarity=0.207  Sum_probs=53.1

Q ss_pred             HHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeecc
Q psy1928           2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADV   64 (105)
Q Consensus         2 l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~   64 (105)
                      |+++|+.||.|.++.++.     +++||||+|.+.++|++|+..||+..|.++.|+|.++...
T Consensus        27 l~~lF~~~G~i~~~~~~k-----~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~~   84 (104)
T d1weya_          27 FESLFRTYDKDTTFQYFK-----SFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQTL   84 (104)
T ss_dssp             HHHHHHTTCSSCEEEEET-----TTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCCCS
T ss_pred             HHHHhcccccceEEEEec-----CCCEEEEEECCHHHHHHHHHHhcccccCCCEeEEeecccC
Confidence            778999999999998875     3689999999999999999999999999999999999733

>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=99.45  E-value=1.4e-13  Score=78.02  Aligned_cols=59  Identities=14%  Similarity=0.140  Sum_probs=53.8

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|+.||.|.++.+..      ++||||+|.+.++|++||+.||+..+.++.|+|.+.+..+
T Consensus        31 ~L~~~F~~~G~v~~~~i~~------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~~~~   89 (98)
T d1wg4a_          31 DLKDHMREAGDVCYADVQK------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRVYP   89 (98)
T ss_dssp             HHHHHHTTSSCEEEEEEET------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEEEEC
T ss_pred             HHHHHHHhhcccccccccc------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEecCC
Confidence            5899999999999998864      4899999999999999999999999999999999988544

>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=99.44  E-value=1.5e-13  Score=78.40  Aligned_cols=63  Identities=24%  Similarity=0.404  Sum_probs=56.0

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      ||+++|..++ +..+.++.+.++..++||||+|.+.++|++|++ ||+..|.++.|+|.++...+
T Consensus        31 dl~~~F~~~~-~~~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~s~~~~   93 (102)
T d1weza_          31 DIYNFFSPLN-PMRVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLNSTAG   93 (102)
T ss_dssp             HHHHSSCSCC-CSEEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEECCCC
T ss_pred             HHHHHHhccC-cceeeeEEecCCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEcCCCC
Confidence            5889999997 567888888888999999999999999999987 89999999999999988443

>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=99.44  E-value=4.9e-14  Score=77.98  Aligned_cols=61  Identities=25%  Similarity=0.469  Sum_probs=54.4

Q ss_pred             CHHHHhccCCCeeE-EEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEe
Q psy1928           1 MIYELFSEFGPLKS-AKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA   61 (105)
Q Consensus         1 ~l~~~f~~~G~i~~-~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~   61 (105)
                      ||+++|+.|+.+.. +.+..+.++.++++|||+|.+.++|++||+.||+..+.+++|+|+++
T Consensus        25 di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1          25 EILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             HHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             HHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            58999999998865 45666669999999999999999999999999999999999999864

>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=99.44  E-value=2.8e-13  Score=73.25  Aligned_cols=59  Identities=14%  Similarity=0.244  Sum_probs=52.5

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEe
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA   61 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~   61 (105)
                      +|+++|+.||.|..+.++.++.+. +++|||+|.+.++|++|+. +|+..|+++.|.|+.+
T Consensus        16 ~l~~~F~~~G~I~~v~~~~~~~~~-~~~afV~F~~~~~a~~Al~-~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2          16 KVYKYFKHCGPIIHVDVADSLKKN-FRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             HHHHHHGGGSCEEEEEEEECTTSS-SEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             HHHHHHhcCCceEEEEEEeecccc-ceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            488999999999999999887443 4699999999999999996 8999999999999865

>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=99.43  E-value=2.7e-13  Score=74.99  Aligned_cols=60  Identities=33%  Similarity=0.484  Sum_probs=53.1

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|.++|+.||.|..+.+..     +++||||+|.+.++|+.|+..||+..|.++.|.|+++.+.+
T Consensus        24 ~l~~~F~~~g~i~~~~~~~-----~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP~~   83 (86)
T d2cpda1          24 MIEKEFNNIKPGAVERVKK-----IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVD   83 (86)
T ss_dssp             HHHHHHHTTSTTCEEEEEE-----CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCCC
T ss_pred             HHHHhhcccceeeeEEEcc-----ccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccCCC
Confidence            4789999999988777654     36899999999999999999999999999999999987544

>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=99.41  E-value=9.3e-14  Score=76.02  Aligned_cols=60  Identities=20%  Similarity=0.281  Sum_probs=51.9

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCc-ccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGV-PLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~-~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|++||.|..+.+..     .++||||+|.+.++|++|++.||+. .+.++.|+|+++.++.
T Consensus        17 ~L~~~F~~~G~i~~~~~~~-----~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k~   77 (80)
T d2cqha1          17 DLRQLFGDRKLPLAGQVLL-----KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKK   77 (80)
T ss_dssp             HHHHHHHHTTCCCSSCEEE-----ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCC
T ss_pred             HHHHHHHHhCcEEEeEEec-----ccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCcC
Confidence            5889999999987766554     3689999999999999999999986 6999999999988543

>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=99.40  E-value=2.3e-13  Score=76.74  Aligned_cols=65  Identities=17%  Similarity=0.095  Sum_probs=55.7

Q ss_pred             CHHHHhccCCC-eeEEEEEeCC--CCCcccEEEEEeCCHHHHHHHHHHhCCc--ccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGP-LKSAKLHYDR--SGRSLGTADLIYERRSDAIKAMKQYNGV--PLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~-i~~~~i~~~~--~~~~~g~~fv~f~~~~~a~~ai~~l~~~--~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|+.||. |..+.++.+.  ++.+++||||+|.+.++|..|++.|+..  .+.++.|+|.++.+.+
T Consensus        17 ~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~~A~p~~   86 (96)
T d2disa1          17 EILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEI   86 (96)
T ss_dssp             HHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEESCSSC
T ss_pred             HHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEEEcCCCC
Confidence            48899999995 8899988875  6788999999999999999999998654  5568999999998444

>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=99.40  E-value=4.4e-13  Score=74.50  Aligned_cols=59  Identities=19%  Similarity=0.305  Sum_probs=49.6

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|++|| +..+.+.     ..++||||+|.+.++|++||+.||+..+.++.|.|++++...
T Consensus        21 ~l~~lF~~~G-~~~~~~~-----~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~~~   79 (88)
T d1wg1a_          21 EVHDLLKDYD-LKYCYVD-----RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDA   79 (88)
T ss_dssp             HHHHHTCSSC-CCCEEEE-----GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCCC
T ss_pred             HHHHHHHhcC-ceeeeee-----ccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            5899999999 3333333     347899999999999999999999999999999999987443

>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=99.39  E-value=4.3e-13  Score=73.70  Aligned_cols=58  Identities=21%  Similarity=0.297  Sum_probs=51.5

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccC-CeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLD-GRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~-~~~i~V~~~~   62 (105)
                      +|.++|+.||.|..+.++.+    .++||||+|.+.++|+.|+..||+..+. ++.|+|.|++
T Consensus        24 ~l~~~f~~~G~i~~v~~~~~----~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~ak   82 (83)
T d2b0ga1          24 MLSMLFNQFPGFKEVRLVPN----RHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFAK   82 (83)
T ss_dssp             HHHHHHTTSTTEEEEEECTT----TCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEECC
T ss_pred             HHHhhhccCccEEEeeeecc----cceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEec
Confidence            47899999999999998764    2579999999999999999999999885 6899999986

>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=99.39  E-value=7.8e-13  Score=75.53  Aligned_cols=64  Identities=22%  Similarity=0.200  Sum_probs=55.1

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|+.+|.|....++.++ ++.++++|||+|.+.++|++|++ +|+..|.++.|.|..++..+
T Consensus        31 dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~~~~~~   95 (104)
T d1wg5a_          31 EIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFKSSRAE   95 (104)
T ss_dssp             HHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEEECTTT
T ss_pred             HHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEECCHHH
Confidence            589999999988765444444 88999999999999999999996 89999999999999988444

>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=99.38  E-value=6.4e-13  Score=76.38  Aligned_cols=60  Identities=18%  Similarity=0.203  Sum_probs=52.6

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccC--CeeEEEEEeec
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLD--GRPMQIQLAAD   63 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~--~~~i~V~~~~~   63 (105)
                      +|+++|++||.|..+.++.++   .+++|||+|.+.++|++||..||+..|.  +..|.|.+++.
T Consensus        23 ~L~~~F~~~G~i~~~~i~~~~---~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s~~   84 (108)
T d2adba1          23 VLHQIFSKFGTVLKIITFTKN---NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKL   84 (108)
T ss_dssp             HHHHHHTTTSCEEEEEEEEET---TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEECSS
T ss_pred             HHHHHHccCCcEEEEEEEeeC---CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEecCC
Confidence            589999999999999988764   4789999999999999999999999885  67788888763

>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=99.37  E-value=2.4e-13  Score=75.98  Aligned_cols=60  Identities=30%  Similarity=0.494  Sum_probs=52.7

Q ss_pred             HHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeec
Q psy1928           2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD   63 (105)
Q Consensus         2 l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~   63 (105)
                      |.++|++||.|.+|.+..  ++++++||||+|.+.++|++|++.||+..+.++.|.|++++.
T Consensus        24 l~~~f~~~G~i~~i~~~~--~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~~ak~   83 (91)
T d1nu4a_          24 LHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKT   83 (91)
T ss_dssp             HHHHHGGGSCEEEEECCH--HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSS
T ss_pred             HHHHhcccccccceEEee--eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeCC
Confidence            356789999999987643  566789999999999999999999999999999999999874

>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=99.37  E-value=8.8e-14  Score=79.38  Aligned_cols=61  Identities=20%  Similarity=0.338  Sum_probs=53.6

Q ss_pred             CHHHHhccCCCeeEE-EEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSA-KLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~-~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|+.||.|..+ .+..+.++.++|+|||+|.+.++|++||. ||+..|+++.|.|..+.
T Consensus        24 ~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~~   85 (103)
T d2cpya1          24 DVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVVT   85 (103)
T ss_dssp             HHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEEC
T ss_pred             HHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEECC
Confidence            588999999988764 44444589999999999999999999996 89999999999999876

>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=99.36  E-value=9.2e-13  Score=74.36  Aligned_cols=60  Identities=23%  Similarity=0.366  Sum_probs=52.6

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCC--eeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDG--RPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~--~~i~V~~~~~~~   65 (105)
                      +|+++|++||.|..+.+..+     ++||||+|.+.++|+.|++.||+..|.+  +.|+|++++..+
T Consensus        33 ~l~~~f~~~G~i~~~~~~~~-----~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~ak~~~   94 (97)
T d1whya_          33 ALAREFDRFGSIRTIDHVKG-----DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSGP   94 (97)
T ss_dssp             HHHHHHHTTSCEEEEEECSS-----SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCCC
T ss_pred             HHHHHHHhhcccceEeeecc-----ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEeCCCCC
Confidence            48899999999999988764     5799999999999999999999999975  579999987433

>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=99.36  E-value=3.2e-12  Score=72.94  Aligned_cols=60  Identities=13%  Similarity=0.088  Sum_probs=52.1

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHh--CCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQY--NGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l--~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|.++|+.||.|.++.+..+     +++|||+|.+.++|+.|+..|  +...+.+++|+|++++..+
T Consensus        31 ~l~~~F~~fG~I~~~~~~~~-----k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~~s~~~~   92 (104)
T d1wexa_          31 DLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKR   92 (104)
T ss_dssp             HHHHHHTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSSSS
T ss_pred             HHHHhhhhcccceEEEEEec-----ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEEEcCCCc
Confidence            58899999999999988764     689999999999999999987  4567789999999997433

>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=99.35  E-value=5.1e-13  Score=75.29  Aligned_cols=61  Identities=21%  Similarity=0.408  Sum_probs=52.8

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|+.||.|..+..    ++.+++||||+|.+.++|++|++.||+..+.++.|+|+++.++.
T Consensus        32 ~l~~~F~~~g~v~~~~~----~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a~~k~   92 (96)
T d1fjca_          32 ELKEVFEDALEIRLVSQ----DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKG   92 (96)
T ss_dssp             HHHHHHCSEEEECCEEE----TTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSSC
T ss_pred             HHHHHHHhcccceeeee----cCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEeCCCC
Confidence            58899999998765432    56788999999999999999999999999999999999988443

>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=99.35  E-value=1.1e-12  Score=73.00  Aligned_cols=57  Identities=19%  Similarity=0.348  Sum_probs=51.3

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHh--CCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQY--NGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l--~~~~i~~~~i~V~~~~   62 (105)
                      ||.++|++||.|.++.++.+     +++|||+|.+.++|+.|+..|  ++..+.+++|+|.+++
T Consensus        25 eL~~lF~~fG~I~~i~i~~~-----k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V~~s~   83 (89)
T d1x4da1          25 QLLQLVEPFGVISNHLILNK-----INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQ   83 (89)
T ss_dssp             HHHTTTGGGSCEEEEEECSS-----SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEEC
T ss_pred             HHHHHHHhhCCeEEEEeecc-----ceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEEEECC
Confidence            58899999999999998765     469999999999999999966  6778999999999997

>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=99.35  E-value=2.3e-12  Score=69.50  Aligned_cols=57  Identities=23%  Similarity=0.320  Sum_probs=49.5

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeec
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD   63 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~   63 (105)
                      +|+++|++|| +..+.+.     +++++|||+|.+.++|++|+..||+..+.+++|.|++++.
T Consensus        14 ~l~~~F~~~g-~~~~~~~-----~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~   70 (75)
T d1wi6a1          14 EVHDLLSDYE-LKYCFVD-----KYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPT   70 (75)
T ss_dssp             HHHHHTTTSC-EEEEEEE-----TTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCS
T ss_pred             HHHHHHhccc-ccceeec-----ccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCC
Confidence            4889999999 5555443     3579999999999999999999999999999999999873

>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=99.34  E-value=1.5e-12  Score=74.35  Aligned_cols=62  Identities=18%  Similarity=0.190  Sum_probs=55.5

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-C--CCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-S--GRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~--~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      ||++.|++||.|.+|.|++++ +  ....+++||+|.+.++|.+|+..||+..++++.|.|.+..
T Consensus        30 di~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~f~gR~v~v~f~~   94 (104)
T d1o0pa_          30 DVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCD   94 (104)
T ss_dssp             HHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCCSSSSCCEEEEEC
T ss_pred             HHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCEECCeEEEEEEcC
Confidence            478889999999999998866 2  3346899999999999999999999999999999999986

>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=99.34  E-value=1.7e-12  Score=71.93  Aligned_cols=59  Identities=14%  Similarity=0.213  Sum_probs=51.1

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCccc-CCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPL-DGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i-~~~~i~V~~~~   62 (105)
                      +|+++|+.||.|..+.+..+   +.+++|||+|.+.++|.+|+..||+..+ +++.|+|++++
T Consensus        26 ~l~~~F~~~G~v~~~~~~~~---~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~sk   85 (88)
T d2adca2          26 DLKVLFSSNGGVVKGFKFFQ---KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSK   85 (88)
T ss_dssp             HHHHHHHTTSCCEEEEEECS---SSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECS
T ss_pred             HHHHHhhccCCEEEEEEeee---cccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeCC
Confidence            47899999999988766543   3467999999999999999999999988 47999999986

>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=99.32  E-value=4.4e-13  Score=74.47  Aligned_cols=59  Identities=15%  Similarity=0.146  Sum_probs=50.6

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|++||.|..+.+..    .+++||||+|.+.++|++||.  ++..|.++.|.|+++.++.
T Consensus        21 ~L~~~F~~~G~v~~v~~~~----~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~~k~   79 (88)
T d1wf0a_          21 ELREFFSQYGDVMDVFIPK----PFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAEPKH   79 (88)
T ss_dssp             HHHHHSTTTSCCCEEECCS----SCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCCCCC
T ss_pred             HHHHHHHHcCCceEEEEee----ccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCCCCC
Confidence            5899999999999987644    357899999999999999985  7789999999999987544

>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=99.32  E-value=2.8e-12  Score=72.65  Aligned_cols=60  Identities=18%  Similarity=0.232  Sum_probs=53.5

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeec
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD   63 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~   63 (105)
                      ||++.|++||.|..+.++.+   +++|++||+|.+.++|++|+..||+..++++.|.|++...
T Consensus        35 dv~~~~~~~G~V~~v~~~~~---~~~G~~fV~f~~~e~A~~A~~~lng~~~~gr~i~v~~~~g   94 (99)
T d2dita1          35 DLRVECSKFGQIRKLLLFDR---HPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDG   94 (99)
T ss_dssp             HHHHHGGGTSCCSEEEEETT---CTTCEEEEECSCHHHHHHHHHHSTTCEETTEECEEEECCS
T ss_pred             HHHHHhcCcccEEEEeccCC---CCccEEEEEECCHHHHHHHHHHhCCcEECCEEEEEEEeCC
Confidence            47788999999999987654   4568999999999999999999999999999999998763

>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=99.31  E-value=4.5e-12  Score=70.20  Aligned_cols=60  Identities=20%  Similarity=0.193  Sum_probs=52.3

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHh--CCcccCCeeEEEEEeeccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQY--NGVPLDGRPMQIQLAADVS   65 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l--~~~~i~~~~i~V~~~~~~~   65 (105)
                      +|+++|+.||.|.++.+..+     +++|||+|.+.++|++|++.+  ++..+.+++|.|++++.+.
T Consensus        24 ~L~~~f~~~G~i~~v~~~~~-----~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~~sk~~~   85 (88)
T d2cq1a1          24 EVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHKE   85 (88)
T ss_dssp             HHHHTTTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSCSS
T ss_pred             HHHHHHhccccccccccccc-----ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEEECCCCC
Confidence            48899999999999988764     589999999999999999865  5678999999999997444

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.31  E-value=2.2e-12  Score=73.10  Aligned_cols=59  Identities=20%  Similarity=0.277  Sum_probs=52.2

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHH--HhCCcccCCeeEEEEEeecc
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMK--QYNGVPLDGRPMQIQLAADV   64 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~--~l~~~~i~~~~i~V~~~~~~   64 (105)
                      +|.++|+.||.|.++.++.+     +++|||+|.+.++|.+|++  .+++..+.++.|+|.+++..
T Consensus        35 ~l~~~F~~fG~V~~v~~~~~-----k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V~~s~~~   95 (99)
T d1x4fa1          35 AVLKLAEPYGKIKNYILMRM-----KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKY   95 (99)
T ss_dssp             HHHTTTTTTSCCSEEEEETT-----TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECSC
T ss_pred             HHHhhhccccceeEEEEeec-----CCcEEEEecchHHHHHHHHHHhcCCceECCEEEEEEEcCCc
Confidence            47899999999999998865     5899999999999999997  46788899999999999743

>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=99.28  E-value=4.9e-12  Score=78.09  Aligned_cols=62  Identities=18%  Similarity=0.343  Sum_probs=57.0

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEeec
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD   63 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~~   63 (105)
                      +|+++|+.||.|..+.++.+. ++.+++||||+|.+.++|++||+ +++..+.|+.|.|.++.+
T Consensus       113 ~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~~A~~  175 (183)
T d1u1qa_         113 HLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKALS  175 (183)
T ss_dssp             HHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEEEECCC
T ss_pred             HHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEecCC
Confidence            488999999999999999987 89999999999999999999997 688899999999998763

>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=99.24  E-value=1.8e-12  Score=74.95  Aligned_cols=61  Identities=13%  Similarity=0.267  Sum_probs=53.0

Q ss_pred             CHHHHhccCCCeeEEEE-EeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKL-HYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i-~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|.++|+.+|.+..+.+ ..+.++.++|+|||+|.+.++|++|++ ||+..|+++.|.|..+.
T Consensus        34 di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~~~   95 (112)
T d1wela1          34 HVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPIT   95 (112)
T ss_dssp             HHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEEC
T ss_pred             HHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEEcC
Confidence            58899999998866444 444599999999999999999999996 89999999999999876

>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=99.10  E-value=5.4e-11  Score=64.96  Aligned_cols=56  Identities=16%  Similarity=0.242  Sum_probs=46.9

Q ss_pred             HHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCee-EEEEEeec
Q psy1928           2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRP-MQIQLAAD   63 (105)
Q Consensus         2 l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~-i~V~~~~~   63 (105)
                      +.+.|++||.|.++.+..+     ++|+||+|.+.++|++||. +|+..++++. |.|..+.+
T Consensus        20 il~~F~~~G~I~~~~~~~~-----~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~~   76 (81)
T d1wwha1          20 ILLQFAQYGNILKHVMSNT-----GNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCID   76 (81)
T ss_dssp             HHHHHHTTSCEEEEEECSS-----SSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECCC
T ss_pred             HHHHHHhhhhhheEEecCC-----CCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCCC
Confidence            4568999999999887543     6899999999999999996 8999999874 56776653

>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=99.03  E-value=1.3e-10  Score=65.89  Aligned_cols=47  Identities=11%  Similarity=0.132  Sum_probs=42.2

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLD   52 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~   52 (105)
                      +|+++|++||.|..+.++.+     ++||||+|.+.++|++|+..||+..+.
T Consensus        36 ~L~~~F~~~G~i~~i~~~~~-----k~~aFV~f~~~e~A~~A~~~lng~~i~   82 (101)
T d2cq2a1          36 QLLPVLEKCGLVDALLMPPN-----KPYSFARYRTTEESKRAYVTLNGKEVV   82 (101)
T ss_dssp             HHHHHHHHHSCEEEEECCTT-----CSCEEEEESSHHHHHHHHHHTTTCEEE
T ss_pred             HHHHHHHhhCcccEEeeccC-----ccEEEEEECCHHHHHHHHHHhCCCCCC
Confidence            48899999999999887654     579999999999999999999998874

>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=99.03  E-value=8.6e-13  Score=73.45  Aligned_cols=61  Identities=15%  Similarity=0.263  Sum_probs=49.2

Q ss_pred             CHHHHhccCCCeeEEEEE-----eCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLH-----YDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~-----~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|+.||.+..+.+.     .+. ++.+++||||+|.+.++|++|++ ||+..+.++.|+|+..+
T Consensus        17 ~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~Gr~l~V~r~k   83 (90)
T d1u2fa_          17 AMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIRRPH   83 (90)
T ss_dssp             HHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSSSSCCCCBCTT
T ss_pred             HHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEECCEEEEECCCC
Confidence            588999999877654332     223 66788999999999999999986 99999999999997544

>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=99.01  E-value=1.6e-10  Score=66.63  Aligned_cols=57  Identities=18%  Similarity=0.234  Sum_probs=48.0

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCH-HHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERR-SDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~-~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|++||.|.+|.|+.+     ++||||.|.+. ++|..|+..+++..+..+.+.|.+..
T Consensus        27 ~Lk~~F~~fG~V~~v~i~~~-----kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~   84 (113)
T d1owxa_          27 DLHILFSNHGEIKWIDFVRG-----AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEV   84 (113)
T ss_dssp             HHHHHTCSSCCEEEEECCTT-----CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEE
T ss_pred             HHHHHHHhcCChheEEEecC-----CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEee
Confidence            48899999999999999864     68999999885 67889999999998887666666654

>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=98.83  E-value=1e-08  Score=62.80  Aligned_cols=61  Identities=23%  Similarity=0.308  Sum_probs=53.1

Q ss_pred             CHHHHhccCCCeeEEEEEeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~-~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      +|+++|++||.|..+.++.+. ++.++++|||+|.+.++|++|+.. +...+..+.+.+....
T Consensus        22 ~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~-~~~~~~~~~~~~~~~~   83 (183)
T d1u1qa_          22 SLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAV   83 (183)
T ss_dssp             HHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEECC
T ss_pred             HHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHh-cCCcccccchhhhhhh
Confidence            488999999999999999988 899999999999999999999985 6667777777776654

>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=97.83  E-value=6.1e-05  Score=38.98  Aligned_cols=59  Identities=24%  Similarity=0.279  Sum_probs=50.0

Q ss_pred             HHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEEee
Q psy1928           2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA   62 (105)
Q Consensus         2 l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~~~   62 (105)
                      |...|++++.|.++.+.....+  .-.|-|...+..+|.-|+..|+...|+.++|.|.+++
T Consensus        13 L~~~f~~h~~V~sv~l~~~~dg--~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          13 LQEAFARHGKVKSVELSPHTDY--QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHSCEEEEEECSCCST--TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHhheeEEEEEEEeccCC--cEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            5678999999999887543322  3468899999999999999999999999999999875

>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=97.49  E-value=0.00012  Score=39.76  Aligned_cols=51  Identities=12%  Similarity=0.375  Sum_probs=45.3

Q ss_pred             HHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcccCCeeEEEEE
Q psy1928           2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL   60 (105)
Q Consensus         2 l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~~~~i~~~~i~V~~   60 (105)
                      |.+.|..||+|.-++++.+       --.|+|.+-..|-+|+. +++.++.++.|+|..
T Consensus        41 Llq~l~~~GeViLvRFv~d-------~mwVTF~dG~SAL~al~-l~g~~v~G~~l~It~   91 (95)
T d1ufwa_          41 LMQTLGSYGTIVLVRINQG-------QMLVTFADSHSALSVLD-VDGMKVKGRAVKISG   91 (95)
T ss_dssp             HHHHHHHHSCCSEEEEETT-------EEEEECSCSHHHHHHHH-GGGSEETTEEEEEEC
T ss_pred             HHHHHhhCCeEEEEEEeCC-------eEEEEECCcHHHHHHhc-cCCeEEcceEEEEec
Confidence            5678899999999998875       68899999999999988 799999999999874

>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=92.69  E-value=0.11  Score=28.05  Aligned_cols=40  Identities=23%  Similarity=0.306  Sum_probs=30.9

Q ss_pred             CHHHHhccCCCeeEEEEEeCCCCCcccEEEEEeCCHHHHHHHHHHhC
Q psy1928           1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYN   47 (105)
Q Consensus         1 ~l~~~f~~~G~i~~~~i~~~~~~~~~g~~fv~f~~~~~a~~ai~~l~   47 (105)
                      ||.++|+.||.| +|.++.+      --|||...+.+.++.++..+.
T Consensus        31 dI~~lFSpfG~V-~VswIdd------TSa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          31 DLYQLFSAFGNI-QISWIDD------TSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             HHHHHHTTTCSC-CCEEEET------TEEEEECSCHHHHHHHHHHHH
T ss_pred             HHHHHhcCCCce-EEEEecC------ceEEEEecCHHHHHHHHHHhc
Confidence            588999999975 3445554      379999999999998887654