Citrus Sinensis ID: 030632

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170----
Protein Sequence
MANLAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYALPERIKGGEQGWAAQPIWADADTWFERQQQEEEMQRLQAENRAAMQAAEELHRKKMAEDREGEKEEDSEMKDDPMARAEAEVLKQNNSS
Secondary Structure (PSIPRED)
ccccccccccEEEccccccccHHHHHHHccccccEEEEEccccccccccccEEEEEEccHHHHHHHHHHccccccccEEEEEEccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccHHHHHHHHHHHHcccc
Secondary Structure Prediction (SSPRO)
cccccccccEEEEccccccccHHHHHHHHHHcccEEEEEEEEcccccccccEEEEEEccHHHHHHHHHHHccccccccEEEEEccccccccccccccccccEEccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHccccccccHHHHHHHHHHHccccc
Coil and Loop (DISEMBL)
MANLAVQKNTLYVGGLAEEVNEAILHaafipfgdikdvktpldqatqkhrsfgfvtflEKEDAIQAMDNMDGAELYGRVLTvnyalperikggeqgwaaqpiwaDADTWFERQQQEEEMQRLQAENRAAMQAAEELHRKKMAedregekeedsemkddPMARAEAEVLKQNNSS
Flexible Loop (DISEMBL)
manlavqknTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYALPERIKGGEQGWAAQPIWADADTWFERQQQEEEMQRLQAENRAAMQAAEELHrkkmaedregekeedsemkddpmARAEAevlkqnnss
Low Complexity Region (SEG)
MANLAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYALPERIKGGEQGWAAQPIWADADTWFerqqqeeemqrlqaeNRAAMQAAEELHRKkmaedregekeedsemkddpmARAEAEVLKQNNSS
Disordered region (IsUnstruct)
*****VQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYALPERIKGGEQGWAAQPIWADADTWF****************************************************************
Disordered Region (DISOPRED)
************VGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVN*******************************************************************************AE***LK*****
Disordered Region (DISEMBL)
MANLAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYALPERIKGGEQGWAAQPIWADADTWFERQ*******************AEELH********************DPMARAEA*********
Disordered Region (DISPRO)
******QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYALP***********AQPIWADADTWFERQQQEEEMQRLQAENRAAMQAAEEL**KK*AE*******************************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MANLAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYALPERIKGGEQGWAAQPIWADADTWFExxxxxxxxxxxxxxxxxxxxxxxxxxxxKMAEDREGEKEEDSEMKDDPMARAEAEVLKQNNSS
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	174	2.2.26 [Sep-21-2011]
Q9QZH3	301	Peptidyl-prolyl cis-trans	yes	no	0.597	0.345	0.541	5e-28
Q5R723	301	Peptidyl-prolyl cis-trans	yes	no	0.597	0.345	0.541	5e-28
Q9UNP9	301	Peptidyl-prolyl cis-trans	no	no	0.597	0.345	0.541	5e-28
A4FV72	301	Peptidyl-prolyl cis-trans	yes	no	0.597	0.345	0.541	5e-28
Q9V3G3	300	Peptidyl-prolyl cis-trans	yes	no	0.580	0.336	0.5	8e-24
P0C1I2	315	Peptidyl-prolyl cis-trans	N/A	no	0.931	0.514	0.316	7e-17
Q9FNR1	309	Glycine-rich RNA-binding	no	no	0.465	0.262	0.407	4e-13
Q26548	273	Peptidyl-prolyl cis-trans	N/A	no	0.385	0.245	0.458	1e-12
Q99070	168	Glycine-rich RNA-binding	N/A	no	0.431	0.446	0.453	1e-11
Q03878	157	Glycine-rich RNA-binding	N/A	no	0.431	0.477	0.466	6e-11

>sp|Q9QZH3|PPIE_MOUSE Peptidyl-prolyl cis-trans isomerase E OS=Mus musculus GN=Ppie PE=2 SV=2

 Score =  123 bits (309), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 59/109 (54%), Positives = 78/109 (71%), Gaps = 5/109 (4%)

Query: 4   LAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDA 63
           +A  K  LYVGGLAEEV++ +LHAAFIPFGDI D++ PLD  T+KHR F FV F   EDA
Sbjct: 1   MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 60

Query: 64  IQAMDNMDGAELYGRVLTVNYALPERIKGGEQGWAAQPIWADADTWFER 112
             A+DNM+ +EL+GR + VN A P RIK G    +++P+W+D D W ++
Sbjct: 61  AAAIDNMNESELFGRTIRVNLAKPMRIKEG----SSRPVWSD-DDWLKK 104

PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides. Combines RNA-binding and PPIase activities. May be involved in pre-mRNA splicing.
Mus musculus (taxid: 10090)
EC: 5EC: .EC: 2EC: .EC: 1EC: .EC: 8

>sp|Q5R723|PPIE_PONAB Peptidyl-prolyl cis-trans isomerase E OS=Pongo abelii GN=PPIE PE=2 SV=1

 Score =  123 bits (309), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 59/109 (54%), Positives = 78/109 (71%), Gaps = 5/109 (4%)

Query: 4   LAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDA 63
           +A  K  LYVGGLAEEV++ +LHAAFIPFGDI D++ PLD  T+KHR F FV F   EDA
Sbjct: 1   MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 60

Query: 64  IQAMDNMDGAELYGRVLTVNYALPERIKGGEQGWAAQPIWADADTWFER 112
             A+DNM+ +EL+GR + VN A P RIK G    +++P+W+D D W ++
Sbjct: 61  AAAIDNMNESELFGRTIRVNLAKPMRIKEG----SSRPVWSD-DDWLKK 104

PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides. Combines RNA-binding and PPIase activities. May be involved in pre-mRNA splicing.

Pongo abelii (taxid: 9601)

EC: 5

EC: .

EC: 2

EC: .

EC: 1

EC: .

EC: 8

>sp|Q9UNP9|PPIE_HUMAN Peptidyl-prolyl cis-trans isomerase E OS=Homo sapiens GN=PPIE PE=1 SV=1

 Score =  123 bits (309), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 59/109 (54%), Positives = 78/109 (71%), Gaps = 5/109 (4%)

Query: 4   LAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDA 63
           +A  K  LYVGGLAEEV++ +LHAAFIPFGDI D++ PLD  T+KHR F FV F   EDA
Sbjct: 1   MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 60

Query: 64  IQAMDNMDGAELYGRVLTVNYALPERIKGGEQGWAAQPIWADADTWFER 112
             A+DNM+ +EL+GR + VN A P RIK G    +++P+W+D D W ++
Sbjct: 61  AAAIDNMNESELFGRTIRVNLAKPMRIKEG----SSRPVWSD-DDWLKK 104

PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides. Combines RNA-binding and PPIase activities. May be involved in muscle- and brain-specific processes. May be involved in pre-mRNA splicing.

Homo sapiens (taxid: 9606)

EC: 5

EC: .

EC: 2

EC: .

EC: 1

EC: .

EC: 8

>sp|A4FV72|PPIE_BOVIN Peptidyl-prolyl cis-trans isomerase E OS=Bos taurus GN=PPIE PE=2 SV=1

 Score =  123 bits (309), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 59/109 (54%), Positives = 78/109 (71%), Gaps = 5/109 (4%)

Query: 4   LAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDA 63
           +A  K  LYVGGLAEEV++ +LHAAFIPFGDI D++ PLD  T+KHR F FV F   EDA
Sbjct: 1   MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 60

Query: 64  IQAMDNMDGAELYGRVLTVNYALPERIKGGEQGWAAQPIWADADTWFER 112
             A+DNM+ +EL+GR + VN A P RIK G    +++P+W+D D W ++
Sbjct: 61  AAAIDNMNESELFGRTIRVNLAKPMRIKEG----SSRPVWSD-DDWLKK 104

PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides. Combines RNA-binding and PPIase activities. May be involved in pre-mRNA splicing.

Bos taurus (taxid: 9913)

EC: 5

EC: .

EC: 2

EC: .

EC: 1

EC: .

EC: 8

>sp|Q9V3G3|PPIE_DROME Peptidyl-prolyl cis-trans isomerase E OS=Drosophila melanogaster GN=cyp33 PE=1 SV=1

 Score =  109 bits (273), Expect = 8e-24,   Method: Compositional matrix adjust.
 Identities = 53/106 (50%), Positives = 73/106 (68%), Gaps = 5/106 (4%)

Query: 8   KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAM 67
           K T+YVGGLA+EV E +L+ AFIPFGDI D++ P D  +Q+HR F F+ + + EDA  A+
Sbjct: 5   KRTIYVGGLADEVTERLLNNAFIPFGDIADIQMPADYESQRHRGFAFIEYEQSEDAAAAI 64

Query: 68  DNMDGAELYGRVLTVNYALPERIKGGEQGWAAQPIWADADTWFERQ 113
           DNM+ +EL GR + VN A P R+K  E  +  +PIWAD D W ++ 
Sbjct: 65  DNMNDSELCGRTIRVNLAKPVRVK--EDSF--KPIWAD-DDWLQKH 105

PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides. Combines RNA-binding and PPIase activities.

Drosophila melanogaster (taxid: 7227)

EC: 5

EC: .

EC: 2

EC: .

EC: 1

EC: .

EC: 8

>sp|P0C1I2|PPIE_RHIO9 Peptidyl-prolyl cis-trans isomerase E OS=Rhizopus delemar (strain RA 99-880 / ATCC MYA-4621 / FGSC 9543 / NRRL 43880) GN=cyp10 PE=3 SV=1

 Score = 86.7 bits (213), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 57/180 (31%), Positives = 94/180 (52%), Gaps = 18/180 (10%)

Query: 1   MANLAVQKN---TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQ---ATQKHRSFGF 54
           M ++ + KN   TLY+ GL ++VNEA+LHAAFIPFG+I  V+   D    +   HR FGF
Sbjct: 1   MPSVNITKNNKTTLYISGLDQQVNEAVLHAAFIPFGEIIAVQMATDTEIDSNNIHRGFGF 60

Query: 55  VTFLEKEDAIQAMDNMDGAELYGRVLTVNYALPERIKGGEQGWAAQPIWADADTWFERQQ 114
           V +   ED   AMDNM  +ELYG+V+ V  A    +       + + +W D ++W ++  
Sbjct: 61  VEYELAEDCQAAMDNMHLSELYGKVIKVQLAKTINV----TTTSNRAVWTD-ESWLQKYG 115

Query: 115 QEEEMQRLQAE----NRAAMQAAEELHRKKMAEDREGEKEE---DSEMKDDPMARAEAEV 167
             E+++  Q +    N+      +E+     + ++ G+K     D ++ +    R E E+
Sbjct: 116 NVEDVEEKQEDEKENNQETTSEKKEVSSYIPSSEKRGKKSRVYLDIQIGNTLAGRIEIEL 175

PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides. Combines RNA-binding and PPIase activities.

Rhizopus delemar (strain RA 99-880 / ATCC MYA-4621 / FGSC 9543 / NRRL 43880) (taxid: 246409)

EC: 5

EC: .

EC: 2

EC: .

EC: 1

EC: .

EC: 8

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

 Score = 73.9 bits (180), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 33/81 (40%), Positives = 51/81 (62%)

Query: 5   AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
            +  + L++GG+A  ++E  L  AF  +G++ D +  LD+ T + R FGFVTF   E A 
Sbjct: 36  CMSSSKLFIGGMAYSMDEDSLREAFTKYGEVVDTRVILDRETGRSRGFGFVTFTSSEAAS 95

Query: 65  QAMDNMDGAELYGRVLTVNYA 85
            A+  +DG +L+GRV+ VNYA
Sbjct: 96  SAIQALDGRDLHGRVVKVNYA 116

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

Arabidopsis thaliana (taxid: 3702)

>sp|Q26548|PPIE_SCHMA Peptidyl-prolyl cis-trans isomerase E OS=Schistosoma mansoni PE=1 SV=2

 Score = 72.4 bits (176), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 33/72 (45%), Positives = 51/72 (70%), Gaps = 5/72 (6%)

Query: 41  PLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYALPERIKGGEQGWAAQ 100
           P+D  T+KHR F FV F E EDA+ A+DNM+ +E++GR + VN A P RI+   +GW ++
Sbjct: 2   PMDYQTEKHRGFAFVEFEEVEDAMSAIDNMNESEIFGRTIRVNVARPVRIR---EGW-SR 57

Query: 101 PIWADADTWFER 112
           P+W+D + W ++
Sbjct: 58  PVWSD-ENWLKK 68

PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides.

Schistosoma mansoni (taxid: 6183)

EC: 5

EC: .

EC: 2

EC: .

EC: 1

EC: .

EC: 8

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

 Score = 69.3 bits (168), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 34/75 (45%), Positives = 45/75 (60%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
           +VGGLA   N   L  AF  FG + D K   D+ T + R FGFVTF  ++  + A++NM
Sbjct: 10 CFVGGLAWATNNETLEQAFANFGQVIDSKVITDRETGRSRGFGFVTFSSEQSMLDAIENM 69

Query: 71 DGAELYGRVLTVNYA 85
          +G EL GR +TVN A
Sbjct: 70 NGKELDGRNITVNQA 84

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

Sorghum bicolor (taxid: 4558)

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

 Score = 67.0 bits (162), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 35/75 (46%), Positives = 46/75 (61%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
           +VGGLA   N+  L  AF  FGDI D K   D+ T + R FGFVTF +++    A++ M
Sbjct: 8  CFVGGLAWATNDESLEQAFSQFGDITDSKIINDRETGRSRGFGFVTFKDEKSMRDAIEGM 67

Query: 71 DGAELYGRVLTVNYA 85
          +G EL GR +TVN A
Sbjct: 68 NGQELDGRNITVNEA 82

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

Daucus carota (taxid: 4039)

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	174
255541992	176	glycine-rich RNA-binding protein, putati	0.965	0.954	0.875	3e-82
225433902	173	PREDICTED: peptidyl-prolyl cis-trans iso	0.988	0.994	0.906	2e-79
297844272	177	hypothetical protein ARALYDRAFT_471529 [	0.954	0.937	0.825	6e-78
449452837	171	PREDICTED: peptidyl-prolyl cis-trans iso	0.965	0.982	0.904	2e-77
30683419	177	ATPase E1 [Arabidopsis thaliana] gi|1107	0.954	0.937	0.813	9e-77
356499919	172	PREDICTED: peptidyl-prolyl cis-trans iso	0.948	0.959	0.890	2e-75
356498016	172	PREDICTED: peptidyl-prolyl cis-trans iso	0.948	0.959	0.872	1e-73
357487649	170	Peptidyl-prolyl cis-trans isomerase E [M	0.936	0.958	0.865	6e-73
388514621	168	unknown [Medicago truncatula]	0.936	0.970	0.865	7e-73
224101457	174	predicted protein [Populus trichocarpa]	0.965	0.965	0.916	1e-72

>gi|255541992|ref|XP_002512060.1| glycine-rich RNA-binding protein, putative [Ricinus communis] gi|223549240|gb|EEF50729.1| glycine-rich RNA-binding protein, putative [Ricinus communis]

 Score =  309 bits (791), Expect = 3e-82,   Method: Compositional matrix adjust.
 Identities = 147/168 (87%), Positives = 160/168 (95%)

Query: 6   VQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQ 65
           VQKNTLYVGGLA+EVNEAILHAAFIPFGDIKDVKTPLDQATQKHR+FGFVTFLEKEDA  
Sbjct: 9   VQKNTLYVGGLADEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRAFGFVTFLEKEDAAA 68

Query: 66  AMDNMDGAELYGRVLTVNYALPERIKGGEQGWAAQPIWADADTWFERQQQEEEMQRLQAE 125
           AMDNMDGAELYGRVLTVNYALPE+IKGGEQGWAAQPIW DADTWFERQ+ +EEM+R+QAE
Sbjct: 69  AMDNMDGAELYGRVLTVNYALPEKIKGGEQGWAAQPIWKDADTWFERQRHQEEMERIQAE 128

Query: 126 NRAAMQAAEELHRKKMAEDREGEKEEDSEMKDDPMARAEAEVLKQNNS 173
           N+A MQAAEELHRKKMA++REGEKE++ E+KDDPMARAEAEV KQN S
Sbjct: 129 NKATMQAAEELHRKKMAQEREGEKEDEMEVKDDPMARAEAEVSKQNGS 176

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225433902|ref|XP_002265598.1| PREDICTED: peptidyl-prolyl cis-trans isomerase E [Vitis vinifera] gi|297743796|emb|CBI36679.3| unnamed protein product [Vitis vinifera]

 Score =  299 bits (766), Expect = 2e-79,   Method: Compositional matrix adjust.
 Identities = 156/172 (90%), Positives = 164/172 (95%)

Query: 3   NLAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKED 62
           N  VQKNTLYVGGLAEEVNE+ILH+AFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKED
Sbjct: 2   NQPVQKNTLYVGGLAEEVNESILHSAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKED 61

Query: 63  AIQAMDNMDGAELYGRVLTVNYALPERIKGGEQGWAAQPIWADADTWFERQQQEEEMQRL 122
           A  AMDNMDGAELYGRVLTVNYALPERIKGGEQGWAAQPIWADADTWFERQQQEEEMQR+
Sbjct: 62  AAAAMDNMDGAELYGRVLTVNYALPERIKGGEQGWAAQPIWADADTWFERQQQEEEMQRI 121

Query: 123 QAENRAAMQAAEELHRKKMAEDREGEKEEDSEMKDDPMARAEAEVLKQNNSS 174
           QAENRAAMQAAEELHRKKMA++REGEK+E+ E KDDPMAR EAEVL Q+NSS
Sbjct: 122 QAENRAAMQAAEELHRKKMAQEREGEKDEEVEGKDDPMARVEAEVLNQSNSS 173

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297844272|ref|XP_002890017.1| hypothetical protein ARALYDRAFT_471529 [Arabidopsis lyrata subsp. lyrata] gi|297335859|gb|EFH66276.1| hypothetical protein ARALYDRAFT_471529 [Arabidopsis lyrata subsp. lyrata]

 Score =  295 bits (754), Expect = 6e-78,   Method: Compositional matrix adjust.
 Identities = 137/166 (82%), Positives = 155/166 (93%)

Query: 8   KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAM 67
           KNTLYVGGLA+EVNE+ILHAAFIPFGDIKDVKTPLDQA QKHRSFGFVTFLE+EDA  AM
Sbjct: 12  KNTLYVGGLADEVNESILHAAFIPFGDIKDVKTPLDQANQKHRSFGFVTFLEREDASAAM 71

Query: 68  DNMDGAELYGRVLTVNYALPERIKGGEQGWAAQPIWADADTWFERQQQEEEMQRLQAENR 127
           DNMDGAELYGRVLTVNYALPE+IKGGEQGWAA P+WADADTWFERQQQE+EM ++QAEN+
Sbjct: 72  DNMDGAELYGRVLTVNYALPEKIKGGEQGWAAHPLWADADTWFERQQQEKEMLKMQAENK 131

Query: 128 AAMQAAEELHRKKMAEDREGEKEEDSEMKDDPMARAEAEVLKQNNS 173
           AAM+ AEELHRKK+A+DR+GE EED+E KDDPMARAEA+ L  +++
Sbjct: 132 AAMETAEELHRKKLAQDRQGEMEEDTETKDDPMARAEADALSHSDA 177

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449452837|ref|XP_004144165.1| PREDICTED: peptidyl-prolyl cis-trans isomerase E-like [Cucumis sativus] gi|449529401|ref|XP_004171688.1| PREDICTED: peptidyl-prolyl cis-trans isomerase E-like [Cucumis sativus]

 Score =  293 bits (749), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 152/168 (90%), Positives = 163/168 (97%)

Query: 5   AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
           AVQKNTLYVGGLAEEVNE+ILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDA 
Sbjct: 4   AVQKNTLYVGGLAEEVNESILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAS 63

Query: 65  QAMDNMDGAELYGRVLTVNYALPERIKGGEQGWAAQPIWADADTWFERQQQEEEMQRLQA 124
            AMDNMDGAELYGRVLTVNYALPERIKGGEQGWAAQPIWADADTWFERQQQEEEMQRLQA
Sbjct: 64  AAMDNMDGAELYGRVLTVNYALPERIKGGEQGWAAQPIWADADTWFERQQQEEEMQRLQA 123

Query: 125 ENRAAMQAAEELHRKKMAEDREGEKEEDSEMKDDPMARAEAEVLKQNN 172
           ENRAAM+AAEELHRKK+A++REGEK+E+ + K DPMA+AEAEVL+QN+
Sbjct: 124 ENRAAMEAAEELHRKKLAQEREGEKDEEVDTKVDPMAKAEAEVLRQNS 171

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|30683419|ref|NP_563931.2| ATPase E1 [Arabidopsis thaliana] gi|110736770|dbj|BAF00346.1| AtE1 [Arabidopsis thaliana] gi|332190937|gb|AEE29058.1| ATPase E1 [Arabidopsis thaliana]

 Score =  291 bits (744), Expect = 9e-77,   Method: Compositional matrix adjust.
 Identities = 135/166 (81%), Positives = 154/166 (92%)

Query: 8   KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAM 67
           KNTLYVGGLA+EVNE+ILHAAFIPFGDIKDVKTPLDQA QKHRSFGFVTFLE+EDA  AM
Sbjct: 12  KNTLYVGGLADEVNESILHAAFIPFGDIKDVKTPLDQANQKHRSFGFVTFLEREDASAAM 71

Query: 68  DNMDGAELYGRVLTVNYALPERIKGGEQGWAAQPIWADADTWFERQQQEEEMQRLQAENR 127
           DNMDGAELYGRVLTVNYALPE+IKGGEQGWAA P+WADADTWFERQQQE+E+ ++QAEN+
Sbjct: 72  DNMDGAELYGRVLTVNYALPEKIKGGEQGWAAHPLWADADTWFERQQQEKEILKMQAENK 131

Query: 128 AAMQAAEELHRKKMAEDREGEKEEDSEMKDDPMARAEAEVLKQNNS 173
           AAM+ AEELHRKK+AEDR+GE EED++ K+DPMARAEA+ L   ++
Sbjct: 132 AAMETAEELHRKKLAEDRQGEMEEDTDTKNDPMARAEADALSHGDA 177

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356499919|ref|XP_003518783.1| PREDICTED: peptidyl-prolyl cis-trans isomerase E-like [Glycine max]

 Score =  286 bits (732), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 147/165 (89%), Positives = 160/165 (96%)

Query: 5   AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
            VQKNTLYVGGLAEEVNE+ILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLE+EDA 
Sbjct: 6   GVQKNTLYVGGLAEEVNESILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEREDAS 65

Query: 65  QAMDNMDGAELYGRVLTVNYALPERIKGGEQGWAAQPIWADADTWFERQQQEEEMQRLQA 124
            AMDNMDGAELYGRVLTVNYALPERIKGGEQGWAAQP+WADADTWFERQQQEEEM+R++A
Sbjct: 66  AAMDNMDGAELYGRVLTVNYALPERIKGGEQGWAAQPVWADADTWFERQQQEEEMKRIEA 125

Query: 125 ENRAAMQAAEELHRKKMAEDREGEKEEDSEMKDDPMARAEAEVLK 169
           ENRAAMQAAE+LHRK++AE REGEKEE+ E+KDDPMA+AEAEVL+
Sbjct: 126 ENRAAMQAAEDLHRKQVAEQREGEKEEEIEIKDDPMAKAEAEVLQ 170

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356498016|ref|XP_003517851.1| PREDICTED: peptidyl-prolyl cis-trans isomerase E-like [Glycine max]

 Score =  280 bits (717), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 144/165 (87%), Positives = 158/165 (95%)

Query: 5   AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
            VQKNTLYVGGLAEEVNE ILHAAFIPFGDIKDVKTPLDQA+QKHRSFGFVTFLE+EDA 
Sbjct: 6   GVQKNTLYVGGLAEEVNELILHAAFIPFGDIKDVKTPLDQASQKHRSFGFVTFLEREDAS 65

Query: 65  QAMDNMDGAELYGRVLTVNYALPERIKGGEQGWAAQPIWADADTWFERQQQEEEMQRLQA 124
            AMDNMDGAELYGRVLTVNYALPERIKGGEQGWAAQP+WADADTWFERQQQEEEM+R++ 
Sbjct: 66  AAMDNMDGAELYGRVLTVNYALPERIKGGEQGWAAQPVWADADTWFERQQQEEEMKRIEK 125

Query: 125 ENRAAMQAAEELHRKKMAEDREGEKEEDSEMKDDPMARAEAEVLK 169
           ENRAAM+AAE+LHRK++AE REGEKEE+ E+KDDPMA+AEAEVL+
Sbjct: 126 ENRAAMEAAEDLHRKQVAEQREGEKEEEIEIKDDPMAKAEAEVLQ 170

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357487649|ref|XP_003614112.1| Peptidyl-prolyl cis-trans isomerase E [Medicago truncatula] gi|217073180|gb|ACJ84949.1| unknown [Medicago truncatula] gi|355515447|gb|AES97070.1| Peptidyl-prolyl cis-trans isomerase E [Medicago truncatula] gi|388494832|gb|AFK35482.1| unknown [Medicago truncatula]

 Score =  278 bits (711), Expect = 6e-73,   Method: Compositional matrix adjust.
 Identities = 142/164 (86%), Positives = 157/164 (95%), Gaps = 1/164 (0%)

Query: 5   AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
            VQKNTLYVGGLAEEVNE+ILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLE+EDA 
Sbjct: 6   GVQKNTLYVGGLAEEVNESILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEREDAS 65

Query: 65  QAMDNMDGAELYGRVLTVNYALPERIKGGEQGWAAQPIWADADTWFERQQQEEEMQRLQA 124
            AMDNMDGAELYGRVLTVNYALPE+IKGGEQGWAAQPIWADADTWFERQQQEE+M+RL+A
Sbjct: 66  AAMDNMDGAELYGRVLTVNYALPEKIKGGEQGWAAQPIWADADTWFERQQQEEDMRRLEA 125

Query: 125 ENRAAMQAAEELHRKKMAEDREGEKEEDSEMKDDPMARAEAEVL 168
           EN+AAM AAEELHRK++AE+RE  ++E+ E+KDDPMARAEAEV+
Sbjct: 126 ENKAAMLAAEELHRKQVAEERE-GEKEEIEIKDDPMARAEAEVV 168

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388514621|gb|AFK45372.1| unknown [Medicago truncatula]

 Score =  278 bits (710), Expect = 7e-73,   Method: Compositional matrix adjust.
 Identities = 142/164 (86%), Positives = 157/164 (95%), Gaps = 1/164 (0%)

Query: 5   AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
            VQKNTLYVGGLAEEVNE+ILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLE+EDA 
Sbjct: 4   GVQKNTLYVGGLAEEVNESILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEREDAS 63

Query: 65  QAMDNMDGAELYGRVLTVNYALPERIKGGEQGWAAQPIWADADTWFERQQQEEEMQRLQA 124
            AMDNMDGAELYGRVLTVNYALPE+IKGGEQGWAAQPIWADADTWFERQQQEE+M+RL+A
Sbjct: 64  AAMDNMDGAELYGRVLTVNYALPEKIKGGEQGWAAQPIWADADTWFERQQQEEDMRRLEA 123

Query: 125 ENRAAMQAAEELHRKKMAEDREGEKEEDSEMKDDPMARAEAEVL 168
           EN+AAM AAEELHRK++AE+RE  ++E+ E+KDDPMARAEAEV+
Sbjct: 124 ENKAAMLAAEELHRKQVAEERE-GEKEEIEIKDDPMARAEAEVV 166

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224101457|ref|XP_002312289.1| predicted protein [Populus trichocarpa] gi|222852109|gb|EEE89656.1| predicted protein [Populus trichocarpa]

 Score =  277 bits (708), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 154/168 (91%), Positives = 163/168 (97%)

Query: 6   VQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQ 65
           VQKNTLYVGGLAEEVNEAILHA FIPFGDIKDVKTPLDQATQKHRSFGFVTFLE+EDA  
Sbjct: 7   VQKNTLYVGGLAEEVNEAILHATFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEREDAAS 66

Query: 66  AMDNMDGAELYGRVLTVNYALPERIKGGEQGWAAQPIWADADTWFERQQQEEEMQRLQAE 125
           AMDNMDGAELYGRVLTVNYALPE+IKGGEQGWAAQPIWADADTWFERQQQEEEMQR+QAE
Sbjct: 67  AMDNMDGAELYGRVLTVNYALPEKIKGGEQGWAAQPIWADADTWFERQQQEEEMQRMQAE 126

Query: 126 NRAAMQAAEELHRKKMAEDREGEKEEDSEMKDDPMARAEAEVLKQNNS 173
           NRAAM+AAEELHRKKMAE+REGEKE++ ++KDDPMARAEAEVLKQN S
Sbjct: 127 NRAAMEAAEELHRKKMAEEREGEKEDEGQVKDDPMARAEAEVLKQNIS 174

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	174
TAIR|locus:2023903	177	ATE1 "ATPase E1" [Arabidopsis	0.971	0.954	0.668	6.8e-56
UNIPROTKB|E1BUM0	301	PPIE "Uncharacterized protein"	0.580	0.335	0.566	4.5e-27
UNIPROTKB|A4FV72	301	PPIE "Peptidyl-prolyl cis-tran	0.580	0.335	0.556	9.4e-27
UNIPROTKB|G3MZS9	301	PPIE "Peptidyl-prolyl cis-tran	0.580	0.335	0.556	9.4e-27
UNIPROTKB|E2QVB5	301	PPIE "Uncharacterized protein"	0.580	0.335	0.556	9.4e-27
UNIPROTKB|J9P7U8	343	PPIE "Uncharacterized protein"	0.580	0.294	0.556	9.4e-27
UNIPROTKB|E9PK21	208	PPIE "Peptidyl-prolyl cis-tran	0.580	0.485	0.556	9.4e-27
UNIPROTKB|Q5TGA3	314	PPIE "Peptidyl-prolyl cis-tran	0.580	0.321	0.556	9.4e-27
UNIPROTKB|Q9UNP9	301	PPIE "Peptidyl-prolyl cis-tran	0.580	0.335	0.556	9.4e-27
UNIPROTKB|F1SV03	301	PPIE "Uncharacterized protein"	0.580	0.335	0.556	9.4e-27

TAIR|locus:2023903 ATE1 "ATPase E1" [Arabidopsis thaliana (taxid:3702)]

 Score = 576 (207.8 bits), Expect = 6.8e-56, P = 6.8e-56
 Identities = 113/169 (66%), Positives = 124/169 (73%)

Query:     5 AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
             A+QKNTLYVGGLA+EVNE+ILHAAFIPFGDIKDVKTPLDQA QKHRSFGFVTFLE+EDA 
Sbjct:     9 AMQKNTLYVGGLADEVNESILHAAFIPFGDIKDVKTPLDQANQKHRSFGFVTFLEREDAS 68

Query:    65 QAMDNMDGAELYGRVLTVNYALPERIKGGEQGWAAQPIWADADTWFXXXXXXXXXXXXXX 124
              AMDNMDGAELYGRVLTVNYALPE+IKGGEQGWAA P+WADADTWF              
Sbjct:    69 AAMDNMDGAELYGRVLTVNYALPEKIKGGEQGWAAHPLWADADTWFERQQQEKEILKMQA 128

Query:   125 XNRAAMQAAEELHRKXXXXXXXXXXXXXXXXXXXXXARAEAEVLKQNNS 173
              N+AAM+ AEELHRK                     ARAEA+ L   ++
Sbjct:   129 ENKAAMETAEELHRKKLAEDRQGEMEEDTDTKNDPMARAEADALSHGDA 177

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|E1BUM0 PPIE "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 304 (112.1 bits), Expect = 4.5e-27, P = 4.5e-27
 Identities = 60/106 (56%), Positives = 76/106 (71%)

Query:     4 LAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDA 63
             +A  K  LYVGGLAEEV+E +LHAAFIPFGDI D++ PLD  T+KHR F FV F   EDA
Sbjct:     1 MAATKRVLYVGGLAEEVDEKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 60

Query:    64 IQAMDNMDGAELYGRVLTVNYALPERIKGGEQGWAAQPIWADADTW 109
               A+DNM+ +EL+GR + VN A P RIK G    +++P+W+D D W
Sbjct:    61 AAAIDNMNESELFGRTIRVNLAKPMRIKEG----SSRPVWSD-DEW 101

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0003755 "peptidyl-prolyl cis-trans isomerase activity" evidence=IEA

GO:0006457 "protein folding" evidence=IEA

UNIPROTKB|A4FV72 PPIE "Peptidyl-prolyl cis-trans isomerase E" [Bos taurus (taxid:9913)]

 Score = 301 (111.0 bits), Expect = 9.4e-27, P = 9.4e-27
 Identities = 59/106 (55%), Positives = 76/106 (71%)

Query:     4 LAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDA 63
             +A  K  LYVGGLAEEV++ +LHAAFIPFGDI D++ PLD  T+KHR F FV F   EDA
Sbjct:     1 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 60

Query:    64 IQAMDNMDGAELYGRVLTVNYALPERIKGGEQGWAAQPIWADADTW 109
               A+DNM+ +EL+GR + VN A P RIK G    +++P+W+D D W
Sbjct:    61 AAAIDNMNESELFGRTIRVNLAKPMRIKEG----SSRPVWSD-DDW 101

GO:0003755 "peptidyl-prolyl cis-trans isomerase activity" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0006457 "protein folding" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|G3MZS9 PPIE "Peptidyl-prolyl cis-trans isomerase E" [Bos taurus (taxid:9913)]

 Score = 301 (111.0 bits), Expect = 9.4e-27, P = 9.4e-27
 Identities = 59/106 (55%), Positives = 76/106 (71%)

Query:     4 LAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDA 63
             +A  K  LYVGGLAEEV++ +LHAAFIPFGDI D++ PLD  T+KHR F FV F   EDA
Sbjct:     1 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 60

Query:    64 IQAMDNMDGAELYGRVLTVNYALPERIKGGEQGWAAQPIWADADTW 109
               A+DNM+ +EL+GR + VN A P RIK G    +++P+W+D D W
Sbjct:    61 AAAIDNMNESELFGRTIRVNLAKPMRIKEG----SSRPVWSD-DDW 101

GO:0006457 "protein folding" evidence=IEA

GO:0003755 "peptidyl-prolyl cis-trans isomerase activity" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|E2QVB5 PPIE "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 301 (111.0 bits), Expect = 9.4e-27, P = 9.4e-27
 Identities = 59/106 (55%), Positives = 76/106 (71%)

Query:     4 LAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDA 63
             +A  K  LYVGGLAEEV++ +LHAAFIPFGDI D++ PLD  T+KHR F FV F   EDA
Sbjct:     1 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 60

Query:    64 IQAMDNMDGAELYGRVLTVNYALPERIKGGEQGWAAQPIWADADTW 109
               A+DNM+ +EL+GR + VN A P RIK G    +++P+W+D D W
Sbjct:    61 AAAIDNMNESELFGRTIRVNLAKPMRIKEG----SSRPVWSD-DDW 101

GO:0006457 "protein folding" evidence=IEA

GO:0003755 "peptidyl-prolyl cis-trans isomerase activity" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|J9P7U8 PPIE "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 301 (111.0 bits), Expect = 9.4e-27, P = 9.4e-27
 Identities = 59/106 (55%), Positives = 76/106 (71%)

Query:     4 LAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDA 63
             +A  K  LYVGGLAEEV++ +LHAAFIPFGDI D++ PLD  T+KHR F FV F   EDA
Sbjct:     1 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 60

Query:    64 IQAMDNMDGAELYGRVLTVNYALPERIKGGEQGWAAQPIWADADTW 109
               A+DNM+ +EL+GR + VN A P RIK G    +++P+W+D D W
Sbjct:    61 AAAIDNMNESELFGRTIRVNLAKPMRIKEG----SSRPVWSD-DDW 101

GO:0006457 "protein folding" evidence=IEA

GO:0003755 "peptidyl-prolyl cis-trans isomerase activity" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|E9PK21 PPIE "Peptidyl-prolyl cis-trans isomerase E" [Homo sapiens (taxid:9606)]

 Score = 301 (111.0 bits), Expect = 9.4e-27, P = 9.4e-27
 Identities = 59/106 (55%), Positives = 76/106 (71%)

Query:     4 LAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDA 63
             +A  K  LYVGGLAEEV++ +LHAAFIPFGDI D++ PLD  T+KHR F FV F   EDA
Sbjct:     1 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 60

Query:    64 IQAMDNMDGAELYGRVLTVNYALPERIKGGEQGWAAQPIWADADTW 109
               A+DNM+ +EL+GR + VN A P RIK G    +++P+W+D D W
Sbjct:    61 AAAIDNMNESELFGRTIRVNLAKPMRIKEG----SSRPVWSD-DDW 101

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|Q5TGA3 PPIE "Peptidyl-prolyl cis-trans isomerase E" [Homo sapiens (taxid:9606)]

 Score = 301 (111.0 bits), Expect = 9.4e-27, P = 9.4e-27
 Identities = 59/106 (55%), Positives = 76/106 (71%)

Query:     4 LAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDA 63
             +A  K  LYVGGLAEEV++ +LHAAFIPFGDI D++ PLD  T+KHR F FV F   EDA
Sbjct:     1 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 60

Query:    64 IQAMDNMDGAELYGRVLTVNYALPERIKGGEQGWAAQPIWADADTW 109
               A+DNM+ +EL+GR + VN A P RIK G    +++P+W+D D W
Sbjct:    61 AAAIDNMNESELFGRTIRVNLAKPMRIKEG----SSRPVWSD-DDW 101

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0003755 "peptidyl-prolyl cis-trans isomerase activity" evidence=IEA

GO:0006457 "protein folding" evidence=IEA

UNIPROTKB|Q9UNP9 PPIE "Peptidyl-prolyl cis-trans isomerase E" [Homo sapiens (taxid:9606)]

 Score = 301 (111.0 bits), Expect = 9.4e-27, P = 9.4e-27
 Identities = 59/106 (55%), Positives = 76/106 (71%)

Query:     4 LAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDA 63
             +A  K  LYVGGLAEEV++ +LHAAFIPFGDI D++ PLD  T+KHR F FV F   EDA
Sbjct:     1 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 60

Query:    64 IQAMDNMDGAELYGRVLTVNYALPERIKGGEQGWAAQPIWADADTW 109
               A+DNM+ +EL+GR + VN A P RIK G    +++P+W+D D W
Sbjct:    61 AAAIDNMNESELFGRTIRVNLAKPMRIKEG----SSRPVWSD-DDW 101

GO:0000166 "nucleotide binding" evidence=IEA

GO:0006457 "protein folding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0003723 "RNA binding" evidence=TAS

GO:0003755 "peptidyl-prolyl cis-trans isomerase activity" evidence=TAS

GO:0005515 "protein binding" evidence=IPI

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

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

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

GO:0045070 "positive regulation of viral genome replication" evidence=IMP

GO:0016018 "cyclosporin A binding" evidence=TAS

GO:0000413 "protein peptidyl-prolyl isomerization" evidence=TAS

UNIPROTKB|F1SV03 PPIE "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 301 (111.0 bits), Expect = 9.4e-27, P = 9.4e-27
 Identities = 59/106 (55%), Positives = 76/106 (71%)

Query:     4 LAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDA 63
             +A  K  LYVGGLAEEV++ +LHAAFIPFGDI D++ PLD  T+KHR F FV F   EDA
Sbjct:     1 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 60

Query:    64 IQAMDNMDGAELYGRVLTVNYALPERIKGGEQGWAAQPIWADADTW 109
               A+DNM+ +EL+GR + VN A P RIK G    +++P+W+D D W
Sbjct:    61 AAAIDNMNESELFGRTIRVNLAKPMRIKEG----SSRPVWSD-DDW 101

GO:0006457 "protein folding" evidence=IEA

GO:0003755 "peptidyl-prolyl cis-trans isomerase activity" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	174
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	2e-42
smart00360	73	smart00360, RRM, RNA recognition motif	3e-23
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	1e-18
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	4e-18
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	8e-18
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	1e-17
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	3e-17
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	9e-16
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	1e-15
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	2e-15
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	3e-15
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	7e-15
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	8e-15
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	9e-15
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	9e-15
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	3e-14
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	4e-14
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	6e-14
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	8e-14
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	4e-13
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	4e-13
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	4e-13
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	1e-12
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	1e-12
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	2e-12
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	3e-12
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	6e-12
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	6e-12
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	7e-12
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	9e-12
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	1e-11
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	1e-11
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	2e-11
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	2e-11
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	2e-11
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	2e-11
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	3e-11
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	4e-11
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	6e-11
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	7e-11
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	9e-11
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	1e-10
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	1e-10
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	2e-10
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	2e-10
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	2e-10
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	2e-10
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	4e-10
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	4e-10
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	5e-10
cd12305	75	cd12305, RRM_NELFE, RNA recognition motif in negat	5e-10
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	5e-10
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	6e-10
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	6e-10
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	7e-10
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	7e-10
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	7e-10
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	8e-10
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	9e-10
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	1e-09
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	1e-09
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	1e-09
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-09
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	2e-09
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	3e-09
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	3e-09
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	3e-09
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	4e-09
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	5e-09
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	5e-09
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	5e-09
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	7e-09
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	1e-08
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	1e-08
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	1e-08
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	2e-08
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	2e-08
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	2e-08
cd12497	74	cd12497, RRM3_RBM47, RNA recognition motif 3 in ve	3e-08
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	3e-08
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	3e-08
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	4e-08
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	5e-08
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	6e-08
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	7e-08
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	7e-08
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	8e-08
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	1e-07
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	1e-07
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	2e-07
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	2e-07
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	2e-07
cd12615	74	cd12615, RRM1_TIA1, RNA recognition motif 1 in nuc	2e-07
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	2e-07
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	2e-07
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	2e-07
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	3e-07
cd12616	81	cd12616, RRM1_TIAR, RNA recognition motif 1 in nuc	3e-07
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	3e-07
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	3e-07
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	3e-07
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	4e-07
cd12583	75	cd12583, RRM2_hnRNPD, RNA recognition motif 2 in h	4e-07
cd12357	89	cd12357, RRM_PPARGC1A_like, RNA recognition motif	5e-07
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	6e-07
cd12495	72	cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in v	6e-07
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	7e-07
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	8e-07
cd12494	72	cd12494, RRM3_hnRNPR, RNA recognition motif 3 in v	9e-07
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	1e-06
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	1e-06
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	1e-06
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	1e-06
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	1e-06
cd12585	75	cd12585, RRM2_hnRPDL, RNA recognition motif 2 in h	1e-06
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	1e-06
cd12322	71	cd12322, RRM2_TDP43, RNA recognition motif 2 in TA	1e-06
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	2e-06
cd12431	80	cd12431, RRM_ALKBH8, RNA recognition motif in alky	2e-06
cd12358	73	cd12358, RRM1_VICKZ, RNA recognition motif 1 in th	3e-06
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	3e-06
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	3e-06
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	3e-06
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	3e-06
cd12274	71	cd12274, RRM2_NEFsp, RNA recognition motif 2 in ve	3e-06
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	4e-06
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	4e-06
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	4e-06
cd12679	76	cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in	5e-06
cd12584	80	cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in	5e-06
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	5e-06
cd12621	74	cd12621, RRM3_TIA1, RNA recognition motif 3 in nuc	5e-06
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	6e-06
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	6e-06
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	8e-06
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	8e-06
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	8e-06
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	1e-05
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	1e-05
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	1e-05
cd12636	81	cd12636, RRM2_Bruno_like, RNA recognition motif 2	1e-05
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	1e-05
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	1e-05
cd12438	98	cd12438, RRM_CNOT4, RNA recognition motif in Eukar	1e-05
cd12626	77	cd12626, RRM1_IGF2BP2, RNA recognition motif 1 in	1e-05
cd12612	82	cd12612, RRM2_SECp43, RNA recognition motif 2 in t	1e-05
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	1e-05
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	2e-05
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	2e-05
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	3e-05
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	3e-05
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	3e-05
COG5175	480	COG5175, MOT2, Transcriptional repressor [Transcri	3e-05
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	3e-05
cd12627	77	cd12627, RRM1_IGF2BP3, RNA recognition motif 1 in	3e-05
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	4e-05
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	4e-05
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	4e-05
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	4e-05
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	5e-05
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	5e-05
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	5e-05
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	5e-05
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	6e-05
cd12620	73	cd12620, RRM3_TIAR, RNA recognition motif 3 in nuc	6e-05
cd12573	79	cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA	7e-05
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	8e-05
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	9e-05
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	9e-05
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	9e-05
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	1e-04
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	1e-04
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	1e-04
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	1e-04
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	1e-04
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	1e-04
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	2e-04
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	2e-04
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	2e-04
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	2e-04
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	2e-04
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	3e-04
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	3e-04
cd12275	71	cd12275, RRM1_MEI2_EAR1_like, RNA recognition moti	3e-04
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	3e-04
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	3e-04
cd12527	71	cd12527, RRM2_EAR1_like, RNA recognition motif 2 i	4e-04
cd12477	89	cd12477, RRM1_U1A, RNA recognition motif 1 found i	4e-04
cd12773	84	cd12773, RRM2_HuR, RNA recognition motif 2 in vert	4e-04
cd12476	78	cd12476, RRM1_SNF, RNA recognition motif 1 found i	5e-04
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	5e-04
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	5e-04
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	5e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	6e-04
cd12422	85	cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition m	6e-04
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	6e-04
cd12466	70	cd12466, RRM2_AtRSp31_like, RNA recognition motif	7e-04
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	7e-04
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	7e-04
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	8e-04
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	8e-04
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	0.001
cd12496	74	cd12496, RRM3_RBM46, RNA recognition motif 3 in ve	0.001
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	0.001
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	0.001
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	0.001
cd12478	91	cd12478, RRM1_U2B, RNA recognition motif 1 in U2 s	0.001
cd12622	74	cd12622, RRM3_PUB1, RNA recognition motif 3 in yea	0.002
cd12401	76	cd12401, RRM_eIF4H, RNA recognition motif in eukar	0.002
cd12523	78	cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA	0.002
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	0.002
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	0.002
cd12535	86	cd12535, RRM_FUS_TAF15, RNA recognition motif in v	0.002
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	0.002
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	0.002
cd12238	73	cd12238, RRM1_RBM40_like, RNA recognition motif 1	0.002
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	0.003
cd12239	82	cd12239, RRM2_RBM40_like, RNA recognition motif 2	0.003
cd12319	84	cd12319, RRM4_MRD1, RNA recognition motif 4 in yea	0.003
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	0.003
cd12582	80	cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in	0.004
cd12245	79	cd12245, RRM_scw1_like, RNA recognition motif in y	0.004
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	0.004

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

 Score =  135 bits (343), Expect = 2e-42
 Identities = 50/73 (68%), Positives = 59/73 (80%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          LYVGGLAEEV+E +LHAAFIPFGDIKD++ PLD  TQKHR F FV F E EDA  A+DNM
Sbjct: 1  LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 71 DGAELYGRVLTVN 83
          + +EL+GR + VN
Sbjct: 61 NESELFGRTIRVN 73

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

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

 Score = 86.9 bits (216), Expect = 3e-23
 Identities = 29/73 (39%), Positives = 42/73 (57%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
          TL+VG L  +  E  L   F  FG ++ V+   D+ T K + F FV F  +EDA +A++ 
Sbjct: 1  TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 70 MDGAELYGRVLTV 82
          ++G EL GR L V
Sbjct: 61 LNGKELDGRPLKV 73

Length = 73

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

 Score = 74.9 bits (185), Expect = 1e-18
 Identities = 26/71 (36%), Positives = 41/71 (57%), Gaps = 1/71 (1%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          L+VG L  +  E  L   F  FG I+ ++   D+ T + + F FV F ++EDA +A++ +
Sbjct: 1  LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDE-TGRSKGFAFVEFEDEEDAEKALEAL 59

Query: 71 DGAELYGRVLT 81
          +G EL GR L 
Sbjct: 60 NGKELGGRELR 70

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

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

 Score = 73.9 bits (182), Expect = 4e-18
 Identities = 31/74 (41%), Positives = 48/74 (64%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          ++VG L+ E++   L AAF PFG+I D +   D  T K + +GFV+F++KEDA  A+ +M
Sbjct: 2  IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61

Query: 71 DGAELYGRVLTVNY 84
          +G  L GR +  N+
Sbjct: 62 NGQWLGGRAIRTNW 75

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

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

 Score = 73.1 bits (180), Expect = 8e-18
 Identities = 28/73 (38%), Positives = 41/73 (56%), Gaps = 1/73 (1%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          L+VG L  +  E  L   F  FG+I+ V+   D+   K + F FV F   EDA +A++ +
Sbjct: 1  LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDK-DGKSKGFAFVEFESPEDAEKALEAL 59

Query: 71 DGAELYGRVLTVN 83
          +G EL GR L V+
Sbjct: 60 NGKELDGRKLKVS 72

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

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

 Score = 72.7 bits (179), Expect = 1e-17
 Identities = 28/73 (38%), Positives = 43/73 (58%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          LYVG L   + E  L   F PFG+I+ V+   D  T + + +GF+ F + EDA +A++ +
Sbjct: 1  LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60

Query: 71 DGAELYGRVLTVN 83
          +G EL GR + V 
Sbjct: 61 NGFELAGRPIKVG 73

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

>gnl|CDD|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 = 71.9 bits (177), Expect = 3e-17
 Identities = 33/77 (42%), Positives = 44/77 (57%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
          N L+V GL+    E  L A F  FG +++V    D  T + R FGFVTF   EDA  A+ 
Sbjct: 2  NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR 61

Query: 69 NMDGAELYGRVLTVNYA 85
          +++G EL GRV+ V  A
Sbjct: 62 DLNGKELEGRVIKVEKA 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|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2 and similar proteins

 Score = 67.8 bits (166), Expect = 9e-16
 Identities = 30/76 (39%), Positives = 46/76 (60%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
          TL+VG L+  V++  L A F  FG +   +   D+ T + R FG+V F   EDA +A++ 
Sbjct: 1  TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 70 MDGAELYGRVLTVNYA 85
          MDG EL GR + V+++
Sbjct: 61 MDGKELDGRPINVDFS 76

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

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

 Score = 67.6 bits (166), Expect = 1e-15
 Identities = 32/73 (43%), Positives = 46/73 (63%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          +YVG L E+V E +L   FI  G + +V  P D+ TQ H+ +GFV FL +EDA  A+  M
Sbjct: 1  VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 71 DGAELYGRVLTVN 83
          +  +LYG+ + VN
Sbjct: 61 NMIKLYGKPIRVN 73

This subfamily corresponds to the RRM1 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 a component of the multiprotein complex splicing factor 3b (SF3B), an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA, and is involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B4 functions to tether U2 snRNP with pre-mRNA at the branch site during spliceosome assembly. It is an evolutionarily highly conserved protein with orthologs across diverse species. SF3B4 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It binds directly to pre-mRNA and also interacts directly and highly specifically with another SF3B subunit called SAP 145. . Length = 74

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

 Score = 67.3 bits (165), Expect = 2e-15
 Identities = 30/78 (38%), Positives = 41/78 (52%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
           LYVG L   V E  L   F  FG++   +   D+ T + R FGFV     E+A  A++ 
Sbjct: 1  NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 70 MDGAELYGRVLTVNYALP 87
          ++G +  GR LTVN A P
Sbjct: 61 LNGTDFGGRTLTVNEARP 78

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

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

 Score = 66.8 bits (163), Expect = 3e-15
 Identities = 26/74 (35%), Positives = 42/74 (56%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          ++VG L+ EV +A L AAF  F    D +   D  + + R +GFV+F  ++DA  A++ M
Sbjct: 2  IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEM 61

Query: 71 DGAELYGRVLTVNY 84
          +G  L  R +  N+
Sbjct: 62 NGKWLGSRPIRCNW 75

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

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

 Score = 70.4 bits (171), Expect = 7e-15
 Identities = 34/83 (40%), Positives = 46/83 (55%)

Query: 6   VQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQ 65
            + NTL+VG L  +V E  L   F  FG +K V+   D+ T K R F FV F  +E A +
Sbjct: 113 EENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEK 172

Query: 66  AMDNMDGAELYGRVLTVNYALPE 88
           A++ ++G EL GR L V  A P 
Sbjct: 173 AIEELNGKELEGRPLRVQKAQPA 195

Length = 306

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

 Score = 65.4 bits (160), Expect = 8e-15
 Identities = 27/73 (36%), Positives = 40/73 (54%), Gaps = 1/73 (1%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
          TL+VG L   V E IL+  F+  G ++ VK P D   +  +SF FVTF  +     A+  
Sbjct: 3  TLFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGKP-KSFAFVTFKHEVSVPYAIQL 61

Query: 70 MDGAELYGRVLTV 82
          ++G  L+GR L +
Sbjct: 62 LNGIRLFGRELRI 74

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

 Score = 67.4 bits (164), Expect = 9e-15
 Identities = 34/85 (40%), Positives = 50/85 (58%)

Query: 1   MANLAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEK 60
           + +L +    L++GGL+   ++A L  AF  FGD+ D K  +D+ T + R FGFV F ++
Sbjct: 27  LGSLRLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDE 86

Query: 61  EDAIQAMDNMDGAELYGRVLTVNYA 85
             A  A+  MDG EL GR + VN A
Sbjct: 87  GAATAAISEMDGKELNGRHIRVNPA 111

Length = 144

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

 Score = 65.4 bits (160), Expect = 9e-15
 Identities = 27/75 (36%), Positives = 44/75 (58%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
           ++V  L  + +E++L   F PFG + +VK   D  T K + +GFVT    E+A  A+ +
Sbjct: 3  CIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIAS 62

Query: 70 MDGAELYGRVLTVNY 84
          ++G  L GRVL V++
Sbjct: 63 LNGYRLGGRVLQVSF 77

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

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

 Score = 64.0 bits (156), Expect = 3e-14
 Identities = 28/73 (38%), Positives = 40/73 (54%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          +YVG ++ E+ E  +  AF PFG IK +    D  T KH+ F FV +   E A  A++ M
Sbjct: 3  VYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQM 62

Query: 71 DGAELYGRVLTVN 83
          +G  L GR + V 
Sbjct: 63 NGVMLGGRNIKVG 75

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|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 = 63.7 bits (155), Expect = 4e-14
 Identities = 31/75 (41%), Positives = 44/75 (58%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          L++GGL+ + NE  L   F  +G I +V    D+ TQ+ R FGFVTF   +DA  AM  M
Sbjct: 3  LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAM 62

Query: 71 DGAELYGRVLTVNYA 85
          +G  + GR + V+ A
Sbjct: 63 NGKSVDGRQIRVDQA 77

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

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

 Score = 63.1 bits (154), Expect = 6e-14
 Identities = 31/72 (43%), Positives = 38/72 (52%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          L V  L        L   F  +G++ DV  P D+ T++ R F FV F +K DA  AMD M
Sbjct: 1  LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAM 60

Query: 71 DGAELYGRVLTV 82
          DG EL GR L V
Sbjct: 61 DGKELDGRELRV 72

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

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

 Score = 62.6 bits (153), Expect = 8e-14
 Identities = 22/71 (30%), Positives = 35/71 (49%), Gaps = 6/71 (8%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
          T+YVG L   + E  L   F PFG I++V+        K + + FV F   E A  A+  
Sbjct: 2  TVYVGNLPHGLTEEELQRTFSPFGAIEEVR------VFKDKGYAFVRFDTHEAAATAIVA 55

Query: 70 MDGAELYGRVL 80
          ++G  + G+ +
Sbjct: 56 VNGTSINGQTV 66

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

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

 Score = 61.3 bits (148), Expect = 4e-13
 Identities = 31/75 (41%), Positives = 43/75 (57%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          ++VG L+ E+    + AAF PFG I D +   D AT K + +GFV+F  K DA  A+  M
Sbjct: 4  VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 63

Query: 71 DGAELYGRVLTVNYA 85
           G  L GR +  N+A
Sbjct: 64 GGQWLGGRQIRTNWA 78

This subgroup corresponds to the RRM2 of p40-TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1), and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and function as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 80

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

 Score = 60.7 bits (148), Expect = 4e-13
 Identities = 27/77 (35%), Positives = 40/77 (51%), Gaps = 8/77 (10%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          LYV  L     E  L   F  +G+++ VK   D        + FV F E++DA++AM+ M
Sbjct: 4  LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD--------YAFVHFEERDDAVKAMEEM 55

Query: 71 DGAELYGRVLTVNYALP 87
          +G EL G  + V+ A P
Sbjct: 56 NGKELEGSPIEVSLAKP 72

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

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

 Score = 65.7 bits (160), Expect = 4e-13
 Identities = 33/75 (44%), Positives = 46/75 (61%)

Query: 11  LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
           LYVG L   + E  L   F PFGDI+DV+   D  T + + FGF+ F + E+A +A++ M
Sbjct: 189 LYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVM 248

Query: 71  DGAELYGRVLTVNYA 85
           +G EL GR + V YA
Sbjct: 249 NGFELAGRPIKVGYA 263

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

 Score = 59.9 bits (146), Expect = 1e-12
 Identities = 27/72 (37%), Positives = 42/72 (58%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          L+VG L   VN+  L   F  +G +KDV  P+D+     R + +V F   EDA +A+ +M
Sbjct: 1  LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 71 DGAELYGRVLTV 82
          DG ++ G+ +TV
Sbjct: 61 DGGQIDGQEVTV 72

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

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

 Score = 60.0 bits (146), Expect = 1e-12
 Identities = 20/77 (25%), Positives = 42/77 (54%), Gaps = 1/77 (1%)

Query: 10 TLYVGGLAEEVNEAILHAAFIP-FGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
          +++VG LA +V + +L   F   +  ++  K  +D  T + + +GFV F ++++  +A+ 
Sbjct: 3  SIFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRALT 62

Query: 69 NMDGAELYGRVLTVNYA 85
           M+G     R + V+ A
Sbjct: 63 EMNGVYCSSRPMRVSPA 79

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

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

 Score = 59.2 bits (144), Expect = 2e-12
 Identities = 28/77 (36%), Positives = 39/77 (50%), Gaps = 1/77 (1%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
            L V  +  E  +  L   F PFG +K V+ P  +    HR F FV F+ K++A  AM+
Sbjct: 1  TKLIVRNVPFEATKKELRELFSPFGQVKSVRLPK-KFDGSHRGFAFVEFVTKQEAQNAME 59

Query: 69 NMDGAELYGRVLTVNYA 85
           +    LYGR L + YA
Sbjct: 60 ALKSTHLYGRHLVLEYA 76

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

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

 Score = 58.9 bits (142), Expect = 3e-12
 Identities = 30/75 (40%), Positives = 44/75 (58%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          ++VG L+ E+    + +AF PFG I D +   D AT K + +GFV+F  K DA  A+ +M
Sbjct: 4  VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63

Query: 71 DGAELYGRVLTVNYA 85
           G  L GR +  N+A
Sbjct: 64 GGQWLGGRQIRTNWA 78

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

>gnl|CDD|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 = 58.0 bits (141), Expect = 6e-12
 Identities = 23/74 (31%), Positives = 37/74 (50%)

Query: 12 YVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMD 71
          +VG +  +  E  L   F   G +   +   D+ T K + +GF  F + E A  A+ N++
Sbjct: 2  FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLN 61

Query: 72 GAELYGRVLTVNYA 85
          G E  GR L V++A
Sbjct: 62 GYEFNGRALRVDFA 75

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

>gnl|CDD|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 = 58.1 bits (141), Expect = 6e-12
 Identities = 27/72 (37%), Positives = 41/72 (56%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          L+V  L     E  L   F  FG+I +V  PLD+ T++ + F FV+F+  E A++A   +
Sbjct: 2  LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61

Query: 71 DGAELYGRVLTV 82
          DG+   GR+L V
Sbjct: 62 DGSIFQGRLLHV 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|240829 cd12383, RRM_RBM42, RNA recognition motif in RNA-binding protein 42 (RBM42) and similar proteins

 Score = 58.0 bits (141), Expect = 7e-12
 Identities = 21/62 (33%), Positives = 35/62 (56%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          ++VG L  EV + +L  AF  +   +  K   D+ T K + +GFV+F +  D ++AM  M
Sbjct: 9  IFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAMKEM 68

Query: 71 DG 72
          +G
Sbjct: 69 NG 70

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

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

 Score = 57.3 bits (139), Expect = 9e-12
 Identities = 24/71 (33%), Positives = 38/71 (53%), Gaps = 1/71 (1%)

Query: 16 LAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAEL 75
          L  +  EA L   F PFG + +V  P      K + F FV F  K DA +A+  ++G ++
Sbjct: 7  LPFKCTEADLKKLFSPFGFVWEVTIPRK-PDGKKKGFAFVQFTSKADAEKAIKGVNGKKI 65

Query: 76 YGRVLTVNYAL 86
           GR + V++A+
Sbjct: 66 KGRPVAVDWAV 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|240859 cd12413, RRM1_RBM28_like, RNA recognition motif 1 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 57.2 bits (139), Expect = 1e-11
 Identities = 25/76 (32%), Positives = 39/76 (51%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
          TL+V  L  +  +  L   F   G IK      D+ ++K R FG+VTF  +EDA +A++ 
Sbjct: 1  TLFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEE 60

Query: 70 MDGAELYGRVLTVNYA 85
              +  GR + V +A
Sbjct: 61 KKKTKFGGRKIHVEFA 76

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

 Score = 57.0 bits (138), Expect = 1e-11
 Identities = 23/72 (31%), Positives = 39/72 (54%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          L+V  L     E  L   F  FG++ +V   +D+ + K + F +V FL+ EDA++A   +
Sbjct: 5  LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKEL 64

Query: 71 DGAELYGRVLTV 82
          DG    GR++ +
Sbjct: 65 DGKVFQGRLIHI 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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 56.4 bits (137), Expect = 2e-11
 Identities = 25/70 (35%), Positives = 35/70 (50%), Gaps = 2/70 (2%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          LYV  L   V E  L   F P+G ++ V+   ++   + R F FV F   EDA  A+  +
Sbjct: 1  LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNK--DRPRGFAFVEFASPEDAEAALKKL 58

Query: 71 DGAELYGRVL 80
          +G  L GR L
Sbjct: 59 NGLVLDGRTL 68

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

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

 Score = 56.8 bits (138), Expect = 2e-11
 Identities = 32/82 (39%), Positives = 40/82 (48%), Gaps = 5/82 (6%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGD--IKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
          NTL + GL     E  +  A        IKDV+   D+ T   R F FV F   EDA Q 
Sbjct: 3  NTLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQW 62

Query: 67 MD---NMDGAELYGRVLTVNYA 85
          MD   N+D   + GRV+ V+YA
Sbjct: 63 MDALNNLDPFVIDGRVVRVSYA 84

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

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

 Score = 56.6 bits (137), Expect = 2e-11
 Identities = 26/80 (32%), Positives = 40/80 (50%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
          +LYV  +A+      L   F  +G I DV  PLD  T++ R F +V F +  DA  A+  
Sbjct: 2  SLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYY 61

Query: 70 MDGAELYGRVLTVNYALPER 89
          +D     GR + + +A  +R
Sbjct: 62 LDRTRFLGREIEIQFAQGDR 81

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

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

 Score = 56.6 bits (137), Expect = 2e-11
 Identities = 25/78 (32%), Positives = 42/78 (53%)

Query: 8  KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAM 67
          K+T+YV  L   +    LH  F  +G +  V    D+ T+K +   F+ FL++EDA + +
Sbjct: 1  KSTVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCV 60

Query: 68 DNMDGAELYGRVLTVNYA 85
            ++  EL+GR L  + A
Sbjct: 61 KALNNKELFGRTLKCSIA 78

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

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

 Score = 56.1 bits (136), Expect = 3e-11
 Identities = 24/76 (31%), Positives = 42/76 (55%), Gaps = 4/76 (5%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRS---FGFVTFLEKEDAIQAM 67
          +YV  L  +++E  L   F  FG+++ ++ P  Q  ++ R    F FVTF +   A  A+
Sbjct: 3  IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENAL 62

Query: 68 DNMDGAELYGRVLTVN 83
            ++G EL GR ++V+
Sbjct: 63 -QLNGTELGGRKISVS 77

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

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

 Score = 56.1 bits (136), Expect = 4e-11
 Identities = 27/78 (34%), Positives = 44/78 (56%), Gaps = 5/78 (6%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPL---DQATQKHRSFGFVTFLEKEDAIQAM 67
          L++G L  EV+E +L+  F  FG I  ++TP    D  T   + F F+++   E +  A+
Sbjct: 4  LFIGNLDPEVDEKLLYDTFSAFGVI--LQTPKIMRDPDTGNSKGFAFISYDSFEASDAAI 61

Query: 68 DNMDGAELYGRVLTVNYA 85
          + M+G  L  R +TV+YA
Sbjct: 62 EAMNGQYLCNRPITVSYA 79

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

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

 Score = 55.4 bits (134), Expect = 6e-11
 Identities = 26/77 (33%), Positives = 40/77 (51%), Gaps = 1/77 (1%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          ++VGGL   V E  L   F  FG + +V    D   ++ R FGF+TF E ED++  + N 
Sbjct: 5  IFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITF-ESEDSVDQVVNE 63

Query: 71 DGAELYGRVLTVNYALP 87
             ++ G+ + V  A P
Sbjct: 64 HFHDINGKKVEVKRAEP 80

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

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

 Score = 59.3 bits (143), Expect = 7e-11
 Identities = 34/92 (36%), Positives = 47/92 (51%), Gaps = 8/92 (8%)

Query: 11  LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
           +YVG ++ E+ E  +  AF PFG IK +    D AT KH+ F FV +   E A  A++ M
Sbjct: 110 VYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQM 169

Query: 71  DGAELYGRVLTVNYALPERIKGGEQGWAAQPI 102
           +G  L GR + V    P  +        AQPI
Sbjct: 170 NGQMLGGRNIKVG--RPSNMP------QAQPI 193

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

 Score = 55.3 bits (134), Expect = 9e-11
 Identities = 24/75 (32%), Positives = 44/75 (58%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          +Y+GGL  E+ E  +   F  +G+I D+    D+ T K + F F+ + ++   I A+DN+
Sbjct: 12 IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNL 71

Query: 71 DGAELYGRVLTVNYA 85
          +G +L GR + V++ 
Sbjct: 72 NGIKLLGRTIRVDHV 86

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

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

 Score = 54.6 bits (132), Expect = 1e-10
 Identities = 29/76 (38%), Positives = 43/76 (56%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          L V GL+    E  L   F  +G I+ V+   DQ T + R FGFV F   EDA +A + +
Sbjct: 2  LGVFGLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERL 61

Query: 71 DGAELYGRVLTVNYAL 86
          +G E+ GR + V+Y++
Sbjct: 62 NGMEIDGRRIRVDYSI 77

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

 Score = 54.7 bits (132), Expect = 1e-10
 Identities = 24/72 (33%), Positives = 40/72 (55%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          L++  LA    E  L   F  +G + +V  P+D+ T+K + F FVT++  E A++A   +
Sbjct: 5  LFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAEL 64

Query: 71 DGAELYGRVLTV 82
          DG    GR+L +
Sbjct: 65 DGTVFQGRLLHL 76

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

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

 Score = 54.5 bits (132), Expect = 2e-10
 Identities = 21/68 (30%), Positives = 37/68 (54%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          LYVG L  +V EA+L+  F P G +  ++   D  T++   + +V F    DA +A+D +
Sbjct: 2  LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTL 61

Query: 71 DGAELYGR 78
          +   + G+
Sbjct: 62 NFDVIKGK 69

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

 Score = 54.7 bits (131), Expect = 2e-10
 Identities = 28/74 (37%), Positives = 44/74 (59%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          ++V  LA + +E+IL   F PFG + +VK   D  T K + FGFVT    ++A  A+ ++
Sbjct: 6  IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 71 DGAELYGRVLTVNY 84
          +G  L  RVL V++
Sbjct: 66 NGYRLGDRVLQVSF 79

This subgroup corresponds to the RRM3 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 86

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

 Score = 54.1 bits (131), Expect = 2e-10
 Identities = 24/80 (30%), Positives = 37/80 (46%), Gaps = 7/80 (8%)

Query: 10 TLYVGGLAEEVN----EAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQ 65
          TLY+  L E++     +  L+A F  FG + D+       T K R   FV F + E A  
Sbjct: 1  TLYINNLNEKIKKDELKRSLYALFSQFGPVLDIVA---SKTLKMRGQAFVVFKDVESATN 57

Query: 66 AMDNMDGAELYGRVLTVNYA 85
          A+  + G   Y + + + YA
Sbjct: 58 ALRALQGFPFYDKPMRIQYA 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|240682 cd12236, RRM_snRNP70, RNA recognition motif in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins

 Score = 54.2 bits (131), Expect = 2e-10
 Identities = 29/89 (32%), Positives = 41/89 (46%), Gaps = 8/89 (8%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
           TL+V  L  +  E+ L   F  +G IK ++   D+ T K R + F+ F  + D   A  
Sbjct: 2  KTLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYK 61

Query: 69 NMDGAELYG-RVL-------TVNYALPER 89
            DG ++ G RVL       TV   LP R
Sbjct: 62 YADGKKIDGRRVLVDVERGRTVKGWLPRR 90

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

 Score = 53.0 bits (128), Expect = 4e-10
 Identities = 28/80 (35%), Positives = 40/80 (50%), Gaps = 9/80 (11%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
           ++VGGL     +  L   F  FG+I++     D+ T K R +GFVTF +KE A +A  +
Sbjct: 2  KIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKD 61

Query: 70 ----MDGAELYGRVLTVNYA 85
              +D     GR   VN A
Sbjct: 62 PNPIID-----GRKANVNLA 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|241099 cd12655, RRM3_HuC, RNA recognition motif 3 in vertebrate Hu-antigen C (HuC)

 Score = 53.6 bits (128), Expect = 4e-10
 Identities = 28/82 (34%), Positives = 47/82 (57%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          ++V  L+ E +E++L   F PFG + +VK   D  T K + FGFVT    ++A  A+ ++
Sbjct: 4  IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63

Query: 71 DGAELYGRVLTVNYALPERIKG 92
          +G  L  RVL V++   ++ K 
Sbjct: 64 NGYRLGDRVLQVSFKTSKQHKA 85

This subgroup corresponds to the RRM3 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 85

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

 Score = 53.1 bits (128), Expect = 5e-10
 Identities = 23/75 (30%), Positives = 35/75 (46%), Gaps = 3/75 (4%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          LYVG L   V E +L   F   G IK  K   +     +  + FV + +   A  A+  M
Sbjct: 1  LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREH---GNDPYAFVEYYDHRSAAAALQTM 57

Query: 71 DGAELYGRVLTVNYA 85
          +G  + G+ + VN+A
Sbjct: 58 NGRLILGQEIKVNWA 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|240751 cd12305, RRM_NELFE, RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins

 Score = 53.0 bits (128), Expect = 5e-10
 Identities = 29/79 (36%), Positives = 45/79 (56%), Gaps = 8/79 (10%)

Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
          + NTLYV G    + E IL  AF PFG+I ++      + +K ++ GFVTF + E A +A
Sbjct: 3  KGNTLYVHG--YGLTEEILKKAFSPFGNIINI------SMEKEKNCGFVTFEKMESADRA 54

Query: 67 MDNMDGAELYGRVLTVNYA 85
          +  ++G  + G  L V+ A
Sbjct: 55 IAELNGTTVQGVQLKVSLA 73

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

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

 Score = 53.0 bits (128), Expect = 5e-10
 Identities = 27/78 (34%), Positives = 44/78 (56%), Gaps = 3/78 (3%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKT--PLDQAT-QKHRSFGFVTFLEKEDAIQAM 67
          LYVG L  +V E +L   F  FG +  VK   P  +   +++R+ GFV F+ + DA +A+
Sbjct: 4  LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERAL 63

Query: 68 DNMDGAELYGRVLTVNYA 85
          D +DG ++ G  L + + 
Sbjct: 64 DELDGKDVMGYELKLGWG 81

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

 Score = 52.7 bits (127), Expect = 6e-10
 Identities = 23/77 (29%), Positives = 40/77 (51%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
          N +YV  +  +++E  + + F  FG IK      D  T KH+ +GF+ +   + A  A+ 
Sbjct: 1  NRIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIA 60

Query: 69 NMDGAELYGRVLTVNYA 85
          +M+  +L G+ L V  A
Sbjct: 61 SMNLFDLGGQQLRVGKA 77

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

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

 Score = 52.6 bits (127), Expect = 6e-10
 Identities = 25/77 (32%), Positives = 39/77 (50%), Gaps = 1/77 (1%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
            +YV  L E++++  L   F  +G I   K   D    K + FGFV F   E A +A++
Sbjct: 2  TNVYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDD-EGKSKGFGFVNFENHEAAQKAVE 60

Query: 69 NMDGAELYGRVLTVNYA 85
           ++G E+ G+ L V  A
Sbjct: 61 ELNGKEVNGKKLYVGRA 77

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

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

 Score = 52.1 bits (126), Expect = 7e-10
 Identities = 20/61 (32%), Positives = 33/61 (54%), Gaps = 5/61 (8%)

Query: 25 LHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNY 84
          L+  F PFG+++ +K       +K   F FV F  +E A +A+  ++G    GR L V+Y
Sbjct: 1  LYKLFSPFGNVEKIKLL-----KKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDY 55

Query: 85 A 85
          +
Sbjct: 56 S 56

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

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

 Score = 52.5 bits (127), Expect = 7e-10
 Identities = 28/76 (36%), Positives = 43/76 (56%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
          T+ V  L+E+ +E  L   F PFG I  V    D+ T + R F FVTF  +EDA +A++ 
Sbjct: 1  TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEK 60

Query: 70 MDGAELYGRVLTVNYA 85
          ++G      +L+V +A
Sbjct: 61 LNGFGYDNLILSVEWA 76

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|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 = 52.3 bits (126), Expect = 7e-10
 Identities = 23/73 (31%), Positives = 40/73 (54%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          L++  L  E  +  L+  F PFG++   K  +D+ T + + FGFV++   E A  A+  M
Sbjct: 1  LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 71 DGAELYGRVLTVN 83
          +G ++ G+ L V 
Sbjct: 61 NGFQVGGKRLKVQ 73

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

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

 Score = 52.4 bits (126), Expect = 8e-10
 Identities = 24/59 (40%), Positives = 33/59 (55%), Gaps = 2/59 (3%)

Query: 29 FIPFGDIKDVKTPLDQA-TQKHRSFGFVTFLEKEDAIQAMDNM-DGAELYGRVLTVNYA 85
          F  FG++K V+ P     T  HR FGFV F+ K+DA +A   +     LYGR L + +A
Sbjct: 21 FSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAFKALCHSTHLYGRRLVLEWA 79

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

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

 Score = 56.1 bits (135), Expect = 9e-10
 Identities = 23/74 (31%), Positives = 44/74 (59%)

Query: 11  LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
           ++V  L+ + +E +L   F PFG +++VK   D  T + + +GFV+    ++A  A+ ++
Sbjct: 272 IFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSL 331

Query: 71  DGAELYGRVLTVNY 84
           +G  L  RVL V++
Sbjct: 332 NGYTLGNRVLQVSF 345

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

>gnl|CDD|240968 cd12524, RRM1_MEI2_like, RNA recognition motif 1 in plant Mei2-like proteins

 Score = 51.9 bits (125), Expect = 1e-09
 Identities = 26/78 (33%), Positives = 41/78 (52%), Gaps = 5/78 (6%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
          TL+V  +   V +  L A F  FGDI+ + T       KHR F  V++ +   A +A   
Sbjct: 3  TLFVRNINSNVEDEELRALFEQFGDIRTLYT-----ACKHRGFIMVSYYDIRAARRAKRA 57

Query: 70 MDGAELYGRVLTVNYALP 87
          + G EL GR L +++++P
Sbjct: 58 LQGTELGGRKLDIHFSIP 75

This subgroup corresponds to the RRM1 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and it is highly conserved between plants and fungi. Up to date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear. . Length = 77

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

 Score = 52.0 bits (124), Expect = 1e-09
 Identities = 26/74 (35%), Positives = 44/74 (59%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          ++V  L+ + +E++L   F PFG + +VK   D  T K + FGFVT    ++A  A+ ++
Sbjct: 6  IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 71 DGAELYGRVLTVNY 84
          +G  L  RVL V++
Sbjct: 66 NGYRLGDRVLQVSF 79

This subgroup corresponds to the RRM3 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells. And it also regulates the neurite elongation and morphological differentiation. HuD specifically bound poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 86

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

 Score = 52.0 bits (124), Expect = 1e-09
 Identities = 25/74 (33%), Positives = 43/74 (58%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          +++  L ++ +E IL   F PFG + +VK   D  T K + FGFVT    E+A  A+ ++
Sbjct: 4  IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASL 63

Query: 71 DGAELYGRVLTVNY 84
          +G  L  ++L V++
Sbjct: 64 NGYRLGDKILQVSF 77

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

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

 Score = 55.6 bits (134), Expect = 2e-09
 Identities = 25/69 (36%), Positives = 39/69 (56%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
          +LYVG L  +V EA L+  F PFG +  V+   D  T++   +G+V F    DA +A++ 
Sbjct: 2  SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALET 61

Query: 70 MDGAELYGR 78
          M+   L G+
Sbjct: 62 MNFKRLGGK 70

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

 Score = 51.1 bits (123), Expect = 2e-09
 Identities = 21/47 (44%), Positives = 29/47 (61%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTF 57
          L+VGGL E+V E  L   F  +G+++ V+   D+ T K R F FVTF
Sbjct: 2  LFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTF 48

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

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

 Score = 51.0 bits (122), Expect = 3e-09
 Identities = 24/75 (32%), Positives = 37/75 (49%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
           +Y+G L     E  L   F  FG +K+V+    + T   + +GF+ FL  E A  A  +
Sbjct: 1  VIYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKS 60

Query: 70 MDGAELYGRVLTVNY 84
          M+   L G+VL V+ 
Sbjct: 61 MNNYLLMGKVLQVHV 75

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

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

 Score = 50.9 bits (122), Expect = 3e-09
 Identities = 22/54 (40%), Positives = 31/54 (57%), Gaps = 1/54 (1%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
          ++VGGL+    E  +   F  FG ++D     D+ T +HR FGFVTF E ED +
Sbjct: 2  IFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTF-ESEDVV 54

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

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

 Score = 51.1 bits (123), Expect = 3e-09
 Identities = 23/75 (30%), Positives = 46/75 (61%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          ++V G+ EE  E  +H  F  FG+IK++   LD+ T   + +  + +  K++A  A++ +
Sbjct: 9  IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68

Query: 71 DGAELYGRVLTVNYA 85
          +G EL G+ ++V++A
Sbjct: 69 NGKELLGQTISVDWA 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|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 54.0 bits (130), Expect = 4e-09
 Identities = 29/80 (36%), Positives = 36/80 (45%), Gaps = 1/80 (1%)

Query: 7   QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
           Q   LYV  L + V +  L   F   G+I   K  LD      R FGFV F   E+A +A
Sbjct: 284 QGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLD-EKGVSRGFGFVCFSNPEEANRA 342

Query: 67  MDNMDGAELYGRVLTVNYAL 86
           +  M G  L G+ L V  A 
Sbjct: 343 VTEMHGRMLGGKPLYVALAQ 362

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 = 50.3 bits (121), Expect = 5e-09
 Identities = 28/79 (35%), Positives = 42/79 (53%), Gaps = 3/79 (3%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          LYV  L + +++  L   F PFG I   K   D+  +  + FGFV F   E+A +A+  M
Sbjct: 4  LYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRS-KGFGFVCFSSPEEATKAVTEM 62

Query: 71 DGAELYGRVLTVNYALPER 89
          +G  + G+ L V  AL +R
Sbjct: 63 NGRIIGGKPLYV--ALAQR 79

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

 Score = 50.4 bits (121), Expect = 5e-09
 Identities = 22/75 (29%), Positives = 43/75 (57%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          L V  L +++ +  L + F   G I+  K   D+ T +   +GFV ++++ DA +A++ +
Sbjct: 3  LIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTL 62

Query: 71 DGAELYGRVLTVNYA 85
          +G E+  + L V+YA
Sbjct: 63 NGFEIRNKRLKVSYA 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|241057 cd12613, RRM2_NGR1_NAM8_like, RNA recognition motif 2 in yeast negative growth regulatory protein NGR1, yeast protein NAM8 and similar proteins

 Score = 50.2 bits (120), Expect = 5e-09
 Identities = 26/77 (33%), Positives = 40/77 (51%), Gaps = 1/77 (1%)

Query: 10 TLYVGGLAEEVNEAILHAAF-IPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
          +++VG L+ EVNE+ L + F   F   K  K   D  T   R +GFV F ++ D  +A+ 
Sbjct: 3  SIFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRALI 62

Query: 69 NMDGAELYGRVLTVNYA 85
           M G    GR + ++ A
Sbjct: 63 EMQGVYCGGRPMRISTA 79

This subgroup corresponds to the RRM2 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both, RNA and single-stranded DNA (ssDNA), in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs. . Length = 80

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

 Score = 49.7 bits (119), Expect = 7e-09
 Identities = 24/74 (32%), Positives = 35/74 (47%), Gaps = 8/74 (10%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          LYV     + +E+ +   F P+G +K+VK           +F FV F   E AI+A D++
Sbjct: 2  LYVRPFPPDTSESAIREIFSPYGAVKEVKM--------ISNFAFVEFESLESAIRAKDSV 53

Query: 71 DGAELYGRVLTVNY 84
           G  L    L V Y
Sbjct: 54 HGKVLNNNPLYVTY 67

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

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

 Score = 49.2 bits (117), Expect = 1e-08
 Identities = 28/74 (37%), Positives = 39/74 (52%), Gaps = 1/74 (1%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
          TL+VG L   V E IL+  F+  G +  V    D+   K +SFGFV F   E    A+  
Sbjct: 3  TLFVGNLECRVREEILYELFLQAGPLTKVTICKDKEG-KPKSFGFVCFKHSESVPYAIAL 61

Query: 70 MDGAELYGRVLTVN 83
          ++G  LYGR + V+
Sbjct: 62 LNGIRLYGRPIKVH 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|241085 cd12641, RRM_TRA2B, RNA recognition motif in Transformer-2 protein homolog beta (TRA-2 beta) and similar proteins

 Score = 49.6 bits (118), Expect = 1e-08
 Identities = 27/76 (35%), Positives = 41/76 (53%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          L V GL+    E  L   F  +G I DV    DQ +++ R F FV F   +DA +A +  
Sbjct: 12 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 71

Query: 71 DGAELYGRVLTVNYAL 86
          +G EL GR + V++++
Sbjct: 72 NGMELDGRRIRVDFSI 87

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

 Score = 49.2 bits (118), Expect = 1e-08
 Identities = 30/79 (37%), Positives = 42/79 (53%), Gaps = 6/79 (7%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDA--IQA 66
          N ++VGG+  +  E  L   F  FG +KDVK   D+A    + +GFVTF  +EDA  I A
Sbjct: 3  NRIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVS-KGYGFVTFETQEDAEKILA 61

Query: 67 MDNMDGAELYGRVLTVNYA 85
          M N+      G+ L +  A
Sbjct: 62 MGNL---NFRGKKLNIGPA 77

This subfamily corresponds to the RRM domain of two Deleted in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE. BOULE is the founder member of the family and DAZL arose from BOULE in an ancestor of vertebrates. The DAZ gene subsequently originated from a duplication transposition of the DAZL gene. Invertebrates contain a single DAZ homolog, BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. The family members encode closely related RNA-binding proteins that are required for fertility in numerous organisms. These proteins contain an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a varying number of copies of a DAZ motif, believed to mediate protein-protein interactions. DAZL and BOULE contain a single copy of the DAZ motif, while DAZ proteins can contain 8-24 copies of this repeat. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 80

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

 Score = 48.8 bits (117), Expect = 2e-08
 Identities = 23/64 (35%), Positives = 32/64 (50%), Gaps = 6/64 (9%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
          T++VGGL   V E  L + F PFG+I  VK P        +  GFV F+ +  A  A+  
Sbjct: 3  TVFVGGLDPAVTEDELRSLFGPFGEIVYVKIPPG------KGCGFVQFVHRAAAEAAIQQ 56

Query: 70 MDGA 73
          + G 
Sbjct: 57 LQGT 60

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

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

 Score = 48.5 bits (116), Expect = 2e-08
 Identities = 24/68 (35%), Positives = 41/68 (60%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          L+VG L+ + +E  ++ AF  +G+I  V+ P D  + + + FG+V F  +E A  A+D +
Sbjct: 1  LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 71 DGAELYGR 78
           G +L GR
Sbjct: 61 GGTDLLGR 68

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

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

 Score = 48.8 bits (116), Expect = 2e-08
 Identities = 26/74 (35%), Positives = 40/74 (54%)

Query: 13 VGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDG 72
          V GL+    E  L   F  +G +  V    DQ T + R F FV F   +D+ +AM++ +G
Sbjct: 4  VFGLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANG 63

Query: 73 AELYGRVLTVNYAL 86
           EL GR + V+Y++
Sbjct: 64 MELDGRRIRVDYSI 77

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

 Score = 48.1 bits (114), Expect = 3e-08
 Identities = 29/79 (36%), Positives = 40/79 (50%), Gaps = 10/79 (12%)

Query: 11 LYVGGLAEEVNEAILHAAFIPF--GDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
          LYV  L  E +E  +   F  F  G ++ VK        K R + FV F  +EDA+ AM+
Sbjct: 4  LYVRNLMIETSEDTIKKTFGQFNPGCVERVK--------KIRDYAFVHFTSREDAVHAMN 55

Query: 69 NMDGAELYGRVLTVNYALP 87
          N++G EL G  + V  A P
Sbjct: 56 NLNGTELEGSCIEVTLAKP 74

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

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

 Score = 48.0 bits (115), Expect = 3e-08
 Identities = 18/58 (31%), Positives = 29/58 (50%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
          L++GGL+ +  E  L   F  +G++ D     D  T + R FGFVTF +     + + 
Sbjct: 1  LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLA 58

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

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

 Score = 48.2 bits (115), Expect = 3e-08
 Identities = 25/77 (32%), Positives = 36/77 (46%), Gaps = 2/77 (2%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
            L+V  +     +  L   F  FG I DV+   ++   K   FGFVTF    DA +A +
Sbjct: 1  KRLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERGSK--GFGFVTFANSADADRARE 58

Query: 69 NMDGAELYGRVLTVNYA 85
           + G  + GR + VN A
Sbjct: 59 KLHGTVVEGRKIEVNNA 75

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

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

 Score = 48.1 bits (115), Expect = 4e-08
 Identities = 21/59 (35%), Positives = 31/59 (52%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
          L++GGL+ E  +  L   F  +G+I D     D  T++ R FGFVTF    +   AM+ 
Sbjct: 2  LFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNA 60

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

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

 Score = 47.7 bits (114), Expect = 5e-08
 Identities = 24/79 (30%), Positives = 37/79 (46%), Gaps = 3/79 (3%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPL-DQATQKH--RSFGFVTFLEKEDAIQA 66
           L++G L   + E  L   F  +G IK            K   R + FVTF  KE+A +A
Sbjct: 1  RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 67 MDNMDGAELYGRVLTVNYA 85
          + +++G    G+ L V +A
Sbjct: 61 LKSLNGKTALGKKLVVRWA 79

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

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

 Score = 51.0 bits (122), Expect = 6e-08
 Identities = 24/65 (36%), Positives = 34/65 (52%), Gaps = 1/65 (1%)

Query: 11  LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
           LYV  L   VNE  L   F  FG+I       D + +  R F FV F + EDA +A++ M
Sbjct: 181 LYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRS-RGFAFVNFEKHEDAAKAVEEM 239

Query: 71  DGAEL 75
           +G ++
Sbjct: 240 NGKKI 244

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|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 = 47.2 bits (113), Expect = 7e-08
 Identities = 19/62 (30%), Positives = 35/62 (56%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          L+VG L +   E  + A F  +G+I++V    D+ T + +   FV F  +E+A +A++ +
Sbjct: 2  LFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEAL 61

Query: 71 DG 72
           G
Sbjct: 62 HG 63

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

 Score = 47.0 bits (112), Expect = 7e-08
 Identities = 16/75 (21%), Positives = 31/75 (41%), Gaps = 4/75 (5%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
          T+Y G        + +   F   G ++ V       ++  +   F+TF   E A  A++ 
Sbjct: 1  TVYAGPFPTSFCLSDVKRLFETCGPVRKVTML----SRTVQPHAFITFENLEAAQLAIET 56

Query: 70 MDGAELYGRVLTVNY 84
          ++GA + G  + V  
Sbjct: 57 LNGASVDGNCIKVQR 71

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

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

 Score = 46.8 bits (112), Expect = 8e-08
 Identities = 22/77 (28%), Positives = 35/77 (45%), Gaps = 8/77 (10%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          L+VGGL    + A L   F  FG I+ +           R++ ++ +   E A  A + +
Sbjct: 1  LWVGGLGPWTSLAELEREFDRFGAIRRIDYD------PGRNYAYIEYESIEAAQAAKEAL 54

Query: 71 DGAEL--YGRVLTVNYA 85
           G  L   GR L V++A
Sbjct: 55 RGFPLGGPGRRLRVDFA 71

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

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

 Score = 46.8 bits (111), Expect = 1e-07
 Identities = 27/78 (34%), Positives = 39/78 (50%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
          TL+V  LA  V +  L   F     IK      D  T + R +GFVTF   EDA +A+  
Sbjct: 1  TLFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAK 60

Query: 70 MDGAELYGRVLTVNYALP 87
          +   +L+GR+L ++ A  
Sbjct: 61 LKNKKLHGRILRLDIAER 78

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

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

 Score = 46.8 bits (112), Expect = 1e-07
 Identities = 25/72 (34%), Positives = 39/72 (54%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          LYVG L+    E  ++  F   GDIK +   LD+ T+    F FV +  +EDA  A+  +
Sbjct: 1  LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYL 60

Query: 71 DGAELYGRVLTV 82
          +G +L  R++ V
Sbjct: 61 NGTKLDDRIIRV 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|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 49.2 bits (117), Expect = 2e-07
 Identities = 26/87 (29%), Positives = 48/87 (55%), Gaps = 2/87 (2%)

Query: 8  KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAM 67
          K  L V  L + + +  + + F   G+I+  K   D+ T +   +GFV ++  EDA +A+
Sbjct: 3  KTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAV 62

Query: 68 DNMDGAELYGRVLTVNYALP--ERIKG 92
          ++++G  L  + + V+YA P  + IKG
Sbjct: 63 NSLNGLRLQNKTIKVSYARPSSDSIKG 89

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

 Score = 46.5 bits (110), Expect = 2e-07
 Identities = 26/81 (32%), Positives = 44/81 (54%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
          ++L+V  +A++     L   F  +G I DV  PLD  T++ R F +V F +  DA  A+ 
Sbjct: 1  SSLFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALH 60

Query: 69 NMDGAELYGRVLTVNYALPER 89
          N+D   + GR + + +A  +R
Sbjct: 61 NLDRKWICGRQIEIQFAQGDR 81

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

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

 Score = 46.0 bits (110), Expect = 2e-07
 Identities = 21/76 (27%), Positives = 35/76 (46%), Gaps = 1/76 (1%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI-QAMDN 69
          L+VGGL+  V E+ L   F  FG + DV+    +     R F ++     E  + +    
Sbjct: 2  LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKST 61

Query: 70 MDGAELYGRVLTVNYA 85
          ++G +  G VL +  A
Sbjct: 62 LNGTKWKGSVLKIEEA 77

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

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

 Score = 46.2 bits (109), Expect = 2e-07
 Identities = 26/76 (34%), Positives = 41/76 (53%), Gaps = 2/76 (2%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
          TLYVG L+ +V EA++   F   G  K  K  +D  T  +  + FV F E   A  ++  
Sbjct: 1  TLYVGNLSRDVTEALILQLFSQIGPCKSCKMIMD--TAGNDPYCFVEFFEHRHAAASLAA 58

Query: 70 MDGAELYGRVLTVNYA 85
          M+G ++ G+ + VN+A
Sbjct: 59 MNGRKIMGKEVKVNWA 74

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

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

 Score = 46.2 bits (110), Expect = 2e-07
 Identities = 26/75 (34%), Positives = 39/75 (52%), Gaps = 1/75 (1%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          ++VGGL  +V E      F  FG + D +   D  T + R FGFVTF + E A++ + + 
Sbjct: 2  IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTF-DSESAVERVFSA 60

Query: 71 DGAELYGRVLTVNYA 85
             EL G+ + V  A
Sbjct: 61 GMLELGGKQVEVKRA 75

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

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

 Score = 46.4 bits (110), Expect = 2e-07
 Identities = 23/61 (37%), Positives = 37/61 (60%), Gaps = 3/61 (4%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTF---LEKEDAIQAM 67
          L++  L +E  +A L   F+PFG++   K  +D+AT + + FGFV+F      + AIQAM
Sbjct: 7  LFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAM 66

Query: 68 D 68
          +
Sbjct: 67 N 67

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

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

 Score = 46.0 bits (109), Expect = 2e-07
 Identities = 26/73 (35%), Positives = 40/73 (54%), Gaps = 1/73 (1%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
          TL+VG L  +V E ++   F+  G +  VK P D+   K + F FV F  +     AM+ 
Sbjct: 3  TLFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDK-DGKPKQFAFVNFKHEVSVPYAMNL 61

Query: 70 MDGAELYGRVLTV 82
          ++G +LYGR L +
Sbjct: 62 LNGIKLYGRPLNI 74

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

 Score = 45.6 bits (108), Expect = 3e-07
 Identities = 25/75 (33%), Positives = 40/75 (53%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          ++VG +  E  E  L   F   G +   +   D+ T K + +GF  + ++E A+ AM N+
Sbjct: 1  VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 71 DGAELYGRVLTVNYA 85
          +G EL GR L V+ A
Sbjct: 61 NGYELNGRQLRVDNA 75

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

>gnl|CDD|241060 cd12616, RRM1_TIAR, RNA recognition motif 1 in nucleolysin TIAR and similar proteins

 Score = 45.9 bits (108), Expect = 3e-07
 Identities = 25/76 (32%), Positives = 39/76 (51%), Gaps = 2/76 (2%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
          TLYVG L+ +V E ++   F   G  K  K   +  +     + FV F E  DA  A+  
Sbjct: 1  TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSND--PYCFVEFYEHRDAAAALAA 58

Query: 70 MDGAELYGRVLTVNYA 85
          M+G ++ G+ + VN+A
Sbjct: 59 MNGRKILGKEVKVNWA 74

This subgroup corresponds to the RRM1 of nucleolysin TIAR, also termed TIA-1-related protein, and a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 81

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

 Score = 45.4 bits (108), Expect = 3e-07
 Identities = 20/54 (37%), Positives = 34/54 (62%), Gaps = 1/54 (1%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
          ++VGGL+ E  E  +   F  FG+I +++ P+D+ T K R F F+TF + E+ +
Sbjct: 2  IFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITF-DSEEPV 54

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

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

 Score = 48.8 bits (116), Expect = 3e-07
 Identities = 29/79 (36%), Positives = 41/79 (51%), Gaps = 10/79 (12%)

Query: 11  LYVGGLAEEVNEAILHAAFIPF--GDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
           LYV  L     E I+  +F  F  G ++ VK        K R + FV F ++EDA++AMD
Sbjct: 236 LYVRNLMTTTTEEIIEKSFSEFKPGKVERVK--------KIRDYAFVHFEDREDAVKAMD 287

Query: 69  NMDGAELYGRVLTVNYALP 87
            ++G EL G  + V  A P
Sbjct: 288 ELNGKELEGSEIEVTLAKP 306

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

 Score = 45.7 bits (109), Expect = 3e-07
 Identities = 21/85 (24%), Positives = 40/85 (47%)

Query: 8  KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAM 67
            TL+VG L+ +  E  L   F  +GDI+ ++   D  T   + + FV +  + DA++A 
Sbjct: 3  YLTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAY 62

Query: 68 DNMDGAELYGRVLTVNYALPERIKG 92
           +     + G  + V++     + G
Sbjct: 63 RDAHKLVIDGSEIFVDFERERTLPG 87

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

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

 Score = 45.2 bits (107), Expect = 4e-07
 Identities = 25/75 (33%), Positives = 40/75 (53%), Gaps = 1/75 (1%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          LYVG L   V E IL   F   G +++VK   D+   K  ++GFV + +  DA  A+  +
Sbjct: 1  LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDK-NNKGVNYGFVEYHQSHDAEIALQTL 59

Query: 71 DGAELYGRVLTVNYA 85
          +G ++    + VN+A
Sbjct: 60 NGRQIENNEIRVNWA 74

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

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

 Score = 45.4 bits (107), Expect = 4e-07
 Identities = 20/60 (33%), Positives = 35/60 (58%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          ++VGGL+ +  E  +   F  FG+++ ++ P+D  T K R F F+TF E+E   + M+  
Sbjct: 2  IFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61

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

>gnl|CDD|240803 cd12357, RRM_PPARGC1A_like, RNA recognition motif in the peroxisome proliferator-activated receptor gamma coactivator 1A (PGC-1alpha) family of regulated coactivators

 Score = 45.4 bits (108), Expect = 5e-07
 Identities = 16/63 (25%), Positives = 33/63 (52%), Gaps = 3/63 (4%)

Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
          ++  +YVG +  +   + L   F PFG+I+++            ++GFVT+    DA +A
Sbjct: 1  ERRVIYVGKIPIDTTRSELRQRFQPFGEIEEITLHF---RDDGDNYGFVTYRYACDAFRA 57

Query: 67 MDN 69
          +++
Sbjct: 58 IEH 60

This subfamily corresponds to the RRM of PGC-1alpha, PGC-1beta, and PGC-1-related coactivator (PRC), which serve as mediators between environmental or endogenous signals and the transcriptional machinery governing mitochondrial biogenesis. They play an important integrative role in the control of respiratory gene expression through interacting with a number of transcription factors, such as NRF-1, NRF-2, ERR, CREB and YY1. All family members are multi-domain proteins containing the N-terminal activation domain, an LXXLL coactivator signature, a tetrapeptide motif (DHDY) responsible for HCF binding, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In contrast to PGC-1alpha and PRC, PGC-1beta possesses two glutamic/aspartic acid-rich acidic domains, but lacks most of the arginine/serine (SR)-rich domain that is responsible for the regulation of RNA processing. . Length = 89

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

 Score = 45.0 bits (107), Expect = 6e-07
 Identities = 21/59 (35%), Positives = 33/59 (55%)

Query: 20 VNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGR 78
          V E  L  AF PFG+I+D+    D+ T++ +   +V F +   A +AM+ M+G  L G 
Sbjct: 14 VTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNGKCLGGD 72

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

 Score = 44.6 bits (105), Expect = 6e-07
 Identities = 28/77 (36%), Positives = 43/77 (55%), Gaps = 8/77 (10%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          L+V  LA  V E IL  AF  FG ++ VK        K + + F+ F E++ A++AM+ M
Sbjct: 4  LFVRNLANTVTEEILEKAFGQFGKLERVK--------KLKDYAFIHFDERDGAVKAMEEM 55

Query: 71 DGAELYGRVLTVNYALP 87
          +G EL G  + + +A P
Sbjct: 56 NGKELEGENIEIVFAKP 72

This subgroup corresponds to the RRM3 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP that is a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains. . Length = 72

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

 Score = 44.5 bits (106), Expect = 7e-07
 Identities = 20/76 (26%), Positives = 30/76 (39%), Gaps = 13/76 (17%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDV----KTPLDQATQKHRSFGFVTFLEKEDAIQA 66
          +YVG L     +  L   F  +G ++ V      P          F FV F +  DA  A
Sbjct: 2  VYVGNLGPRATKRELEDEFEKYGPLRSVWVARNPP---------GFAFVEFEDPRDAEDA 52

Query: 67 MDNMDGAELYGRVLTV 82
          +  +DG  + G  + V
Sbjct: 53 VRALDGRRICGNRVRV 68

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

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

 Score = 44.5 bits (106), Expect = 8e-07
 Identities = 26/81 (32%), Positives = 37/81 (45%), Gaps = 5/81 (6%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDA---IQA 66
          T+++  L  +  E  L   F  FG++K  +   D+ T   +   FV F  KE A   ++A
Sbjct: 2  TVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEA 61

Query: 67 MDN--MDGAELYGRVLTVNYA 85
           DN    G  L GR L V  A
Sbjct: 62 ADNAEDSGLSLDGRRLIVTLA 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|240938 cd12494, RRM3_hnRNPR, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 44.2 bits (104), Expect = 9e-07
 Identities = 28/77 (36%), Positives = 42/77 (54%), Gaps = 8/77 (10%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          L+V  LA  V E IL  +F  FG ++ VK        K + + FV F E++ A++AMD M
Sbjct: 4  LFVRNLATTVTEEILEKSFSEFGKLERVK--------KLKDYAFVHFEERDAAVRAMDEM 55

Query: 71 DGAELYGRVLTVNYALP 87
          +G E+ G  + +  A P
Sbjct: 56 NGKEIEGEEIEIVLAKP 72

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

 Score = 44.3 bits (104), Expect = 1e-06
 Identities = 23/80 (28%), Positives = 44/80 (55%)

Query: 8  KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAM 67
          K  L V  L + + +  L + F   G+I+  K   D+ T +   +GFV +++ +DA +A+
Sbjct: 4  KTNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 63

Query: 68 DNMDGAELYGRVLTVNYALP 87
          + ++G  L  + + V+YA P
Sbjct: 64 NTLNGLRLQTKTIKVSYARP 83

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

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

 Score = 44.3 bits (104), Expect = 1e-06
 Identities = 22/80 (27%), Positives = 43/80 (53%)

Query: 8  KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAM 67
          K  L V  L + + +    + F   G+I+  K   D+ T +   +GFV +++ +DA +A+
Sbjct: 2  KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61

Query: 68 DNMDGAELYGRVLTVNYALP 87
          + ++G  L  + + V+YA P
Sbjct: 62 NTLNGLRLQTKTIKVSYARP 81

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

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

 Score = 43.7 bits (104), Expect = 1e-06
 Identities = 22/73 (30%), Positives = 36/73 (49%), Gaps = 5/73 (6%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
          TL V  L   +++  L + F  FG++KD++    + +QK     FV F +   A  A+D 
Sbjct: 3  TLLVFNLDSPISDQELRSLFSQFGEVKDIRETPLRPSQK-----FVEFYDIRAAEAALDA 57

Query: 70 MDGAELYGRVLTV 82
          ++G    G  L V
Sbjct: 58 LNGRPFLGGRLKV 70

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

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

 Score = 44.2 bits (105), Expect = 1e-06
 Identities = 22/63 (34%), Positives = 38/63 (60%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
          TL++G L   ++EA +++AF   G++  VK   ++ T K   +GFV F   E A QA+ +
Sbjct: 1  TLWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQS 60

Query: 70 MDG 72
          ++G
Sbjct: 61 LNG 63

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

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

 Score = 44.3 bits (104), Expect = 1e-06
 Identities = 22/80 (27%), Positives = 43/80 (53%)

Query: 8  KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAM 67
          K  L V  L + + +    + F   G+I+  K   D+ T +   +GFV +++  DA +A+
Sbjct: 3  KTNLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAI 62

Query: 68 DNMDGAELYGRVLTVNYALP 87
          + ++G +L  + + V+YA P
Sbjct: 63 NTLNGLKLQTKTIKVSYARP 82

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

 Score = 43.9 bits (103), Expect = 1e-06
 Identities = 18/59 (30%), Positives = 37/59 (62%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
          ++VGGL+ +  E  +   F  FG+I++++ P+D  T + R F FVT+ ++E   + +++
Sbjct: 2  VFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQKLLES 60

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

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

 Score = 43.8 bits (103), Expect = 1e-06
 Identities = 20/61 (32%), Positives = 34/61 (55%), Gaps = 3/61 (4%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTF---LEKEDAIQAM 67
          L++  L +E  +  L   F+PFG++   K  +D+ T   + FGFV++      + AIQAM
Sbjct: 7  LFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAAIQAM 66

Query: 68 D 68
          +
Sbjct: 67 N 67

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

>gnl|CDD|240768 cd12322, RRM2_TDP43, RNA recognition motif 2 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 43.4 bits (103), Expect = 1e-06
 Identities = 20/53 (37%), Positives = 28/53 (52%), Gaps = 5/53 (9%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDA 63
          ++VG L E++ E  L   F  FG++ DV  P        R+F FVTF + E A
Sbjct: 3  VFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKP-----FRAFAFVTFADPEVA 50

This subfamily corresponds to the RRM2 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity. . Length = 71

>gnl|CDD|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE

 Score = 43.3 bits (102), Expect = 2e-06
 Identities = 22/63 (34%), Positives = 36/63 (57%), Gaps = 1/63 (1%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
          N ++VGG+  + NE  L   F  +G +K+VK   D+A    + +GFVTF  +EDA + + 
Sbjct: 3  NRIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDRAGVS-KGYGFVTFETQEDAQKILQ 61

Query: 69 NMD 71
            +
Sbjct: 62 EAN 64

This subgroup corresponds to the RRM of BOULE, the founder member of the human DAZ gene family. Invertebrates contain a single BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. BOULE encodes an RNA-binding protein containing an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a single copy of the DAZ motif. Although its specific biochemical functions remains to be investigated, BOULE protein may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 81

>gnl|CDD|240877 cd12431, RRM_ALKBH8, RNA recognition motif in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and similar proteins

 Score = 43.0 bits (102), Expect = 2e-06
 Identities = 21/75 (28%), Positives = 35/75 (46%), Gaps = 10/75 (13%)

Query: 14 GGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGA 73
          GGL   V+   L   F  +G ++D+  P        + + FV++   EDA  A D ++G 
Sbjct: 9  GGLGNGVSREELLRVFEKYGTVEDLVMP------PGKPYCFVSYSSIEDAAAAYDALNGK 62

Query: 74 ELY----GRVLTVNY 84
          EL      + L ++Y
Sbjct: 63 ELELPQQNKPLYLSY 77

This subfamily corresponds to the RRM of ALKBH8, also termed alpha-ketoglutarate-dependent dioxygenase ABH8, or S-adenosyl-L-methionine-dependent tRNA methyltransferase ABH8, expressed in various types of human cancers. It is essential in urothelial carcinoma cell survival mediated by NOX-1-dependent ROS signals. ALKBH8 has also been identified as a tRNA methyltransferase that catalyzes methylation of tRNA to yield 5-methylcarboxymethyl uridine (mcm5U) at the wobble position of the anticodon loop. Thus, ALKBH8 plays a crucial role in the DNA damage survival pathway through a distinct mechanism involving the regulation of tRNA modification. ALKBH8 localizes to the cytoplasm. It contains the characteristic AlkB domain that is composed of a tRNA methyltransferase motif, a motif homologous to the bacterial AlkB DNA/RNA repair enzyme, and a dioxygenase catalytic core domain encompassing cofactor-binding sites for iron and 2-oxoglutarate. In addition, unlike other AlkB homologs, ALKBH8 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal S-adenosylmethionine (SAM)-dependent methyltransferase (MT) domain. . Length = 80

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

 Score = 43.1 bits (102), Expect = 3e-06
 Identities = 22/79 (27%), Positives = 44/79 (55%), Gaps = 6/79 (7%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          LY+G L+ +VNE+ L   F      ++ K P+     K   + FV   ++  A +A++ +
Sbjct: 1  LYIGNLSSDVNESDLRQLF------EEHKIPVSSVLVKKGGYAFVDCPDQSWADKAIEKL 54

Query: 71 DGAELYGRVLTVNYALPER 89
          +G  L G+V+ V +++P++
Sbjct: 55 NGKILQGKVIEVEHSVPKK 73

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

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

 Score = 43.2 bits (102), Expect = 3e-06
 Identities = 21/76 (27%), Positives = 39/76 (51%), Gaps = 1/76 (1%)

Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
          +K+ L+V GL   V +  L   F   G +K V+   +++  K +   +V +  +  A QA
Sbjct: 1  EKHKLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSG-KPKGLAYVEYENESSASQA 59

Query: 67 MDNMDGAELYGRVLTV 82
          +  MDG E+  + ++V
Sbjct: 60 VLKMDGTEIKEKTISV 75

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

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

 Score = 43.1 bits (102), Expect = 3e-06
 Identities = 19/79 (24%), Positives = 41/79 (51%), Gaps = 2/79 (2%)

Query: 6  VQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQ 65
          + K +++VG L+ +V +  L+  F   G I +V   L +      +F F+ F  ++ A +
Sbjct: 1  IDKYSIFVGQLSPDVTKEELNERFSRHGKILEVN--LIKRANHTNAFAFIKFEREQAAAR 58

Query: 66 AMDNMDGAELYGRVLTVNY 84
          A+++ + + L  + + V Y
Sbjct: 59 AVESENHSMLKNKTMHVQY 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|240671 cd12225, RRM1_2_CID8_like, RNA recognition motif 1 and 2 (RRM1, RRM2) in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins

 Score = 42.7 bits (101), Expect = 3e-06
 Identities = 24/74 (32%), Positives = 36/74 (48%), Gaps = 3/74 (4%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
          T++VGG+   ++E  L   F   G++  V   L    Q    F FV F + E A+ A+ N
Sbjct: 2  TIHVGGIDGSLSEDDLKEFFSNCGEVTRV--RLCGDRQHSARFAFVEFADAESALSAL-N 58

Query: 70 MDGAELYGRVLTVN 83
          + G  L G  L V+
Sbjct: 59 LSGTLLGGHPLRVS 72

This subgroup corresponds to the RRM domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 77

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

 Score = 42.8 bits (101), Expect = 3e-06
 Identities = 22/78 (28%), Positives = 43/78 (55%)

Query: 8  KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAM 67
          K  L V  L + + +  + + F   G+I+  K   D+ T +   +GFV +++ EDA +A+
Sbjct: 1  KTNLIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAI 60

Query: 68 DNMDGAELYGRVLTVNYA 85
          + ++G  L  + + V+YA
Sbjct: 61 NTLNGLRLQNKTIKVSYA 78

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

>gnl|CDD|240720 cd12274, RRM2_NEFsp, RNA recognition motif 2 in vertebrate putative RNA exonuclease NEF-sp

 Score = 42.6 bits (100), Expect = 3e-06
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 1/69 (1%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          +YV G  + + E  L   F    D++ +  P D  + K   + F+ F + + A  A+D++
Sbjct: 1  IYVSGFTKSLTEEFLQERFGQLSDLEAIFLPKDLLSGKPAKYCFLKFRQSQSATAALDHI 60

Query: 71 DGA-ELYGR 78
           G  EL GR
Sbjct: 61 TGEWELKGR 69

This subfamily corresponds to the RRM2 of NEF-sp., including uncharacterized putative RNA exonuclease NEF-sp found in vertebrates. Although its cellular functions remains unclear, NEF-sp contains an exonuclease domain and two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), suggesting it may possess both exonuclease and RNA-binding activities. . Length = 71

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

 Score = 42.5 bits (100), Expect = 4e-06
 Identities = 20/64 (31%), Positives = 36/64 (56%)

Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
          Q   L+VGGL  + +++ L   F  +G + +    +D  T++ R FGF+TF   ++A +A
Sbjct: 1  QLCKLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEA 60

Query: 67 MDNM 70
          M+  
Sbjct: 61 MEAQ 64

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

>gnl|CDD|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins

 Score = 42.2 bits (100), Expect = 4e-06
 Identities = 23/60 (38%), Positives = 29/60 (48%), Gaps = 6/60 (10%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
          TLYVGGL E V E  L   F  FG+I+ +     Q         FVTF  +E A +A + 
Sbjct: 3  TLYVGGLGERVTEKDLRDHFYQFGEIRSITVVPRQQC------AFVTFTTREAAEKAAER 56

This subgroup corresponds to the RRM of RBM22 (also known as RNA-binding motif protein 22, or Zinc finger CCCH domain-containing protein 16), a newly discovered RNA-binding motif protein which belongs to the SLT11 gene family. SLT11 gene encoding protein (Slt11p) is a splicing factor in yeast, which is required for spliceosome assembly. Slt11p has two distinct biochemical properties: RNA-annealing and RNA-binding activities. RBM22 is the homolog of SLT11 in vertebrate. It has been reported to be involved in pre-splicesome assembly and to interact with the Ca2+-signaling protein ALG-2. It also plays an important role in embryogenesis. RBM22 contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a zinc finger of the unusual type C-x8-C-x5-C-x3-H, and a C-terminus that is unusually rich in the amino acids Gly and Pro, including sequences of tetraprolines. Length = 74

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

 Score = 42.3 bits (99), Expect = 4e-06
 Identities = 21/55 (38%), Positives = 30/55 (54%), Gaps = 1/55 (1%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQ 65
          ++VGGL+       +   F  FG + D     D+ T +HR FGFVTF E ED ++
Sbjct: 2  IFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTF-ESEDIVE 55

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

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

 Score = 42.4 bits (99), Expect = 5e-06
 Identities = 20/72 (27%), Positives = 37/72 (51%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          L+V GL+       L   F  +G +   K   +  +   R +GFVT    E+A + ++++
Sbjct: 4  LWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSEEATKCINHL 63

Query: 71 DGAELYGRVLTV 82
             EL+GR+++V
Sbjct: 64 HRTELHGRMISV 75

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

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

 Score = 42.7 bits (100), Expect = 5e-06
 Identities = 20/51 (39%), Positives = 31/51 (60%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKE 61
          ++VGGL  E  E  +   F  FG+I+ ++ P+D  T K R F F+TF E++
Sbjct: 7  IFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEED 57

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

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

 Score = 42.3 bits (100), Expect = 5e-06
 Identities = 23/72 (31%), Positives = 37/72 (51%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          L+V GL+     A L   F  +G +   K   +  +   R FGFVT    E+A + + ++
Sbjct: 2  LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQHL 61

Query: 71 DGAELYGRVLTV 82
             EL+GRV++V
Sbjct: 62 HRTELHGRVISV 73

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

>gnl|CDD|241065 cd12621, RRM3_TIA1, RNA recognition motif 3 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 42.4 bits (99), Expect = 5e-06
 Identities = 21/71 (29%), Positives = 36/71 (50%), Gaps = 6/71 (8%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
          T+Y GG+   + E ++   F PFG I +V+   D      + + FV F   E A  A+ +
Sbjct: 2  TVYCGGVTSGLTEQLMRQTFSPFGQIMEVRVFPD------KGYSFVRFNSHESAAHAIVS 55

Query: 70 MDGAELYGRVL 80
          ++G  + G V+
Sbjct: 56 VNGTTIEGHVV 66

This subgroup corresponds to the RRM3 of p40-TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1) and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and function as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 74

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

 Score = 42.1 bits (99), Expect = 6e-06
 Identities = 18/47 (38%), Positives = 26/47 (55%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTF 57
          L+VGGL+ E  +  L   F  +G++ D     D+ T + R FGFV F
Sbjct: 2  LFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKF 48

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

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

 Score = 42.2 bits (100), Expect = 6e-06
 Identities = 18/74 (24%), Positives = 37/74 (50%), Gaps = 1/74 (1%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          +++  L + ++   L+  F  FG+I   K   D      + +GFV F  +E A++A++ +
Sbjct: 5  IFIKNLDKSIDNKALYDTFSAFGNILSCKVATD-ENGGSKGYGFVHFETEEAAVRAIEKV 63

Query: 71 DGAELYGRVLTVNY 84
          +G  L  + + V  
Sbjct: 64 NGMLLNDKKVFVGP 77

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|241203 cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 41.9 bits (98), Expect = 8e-06
 Identities = 17/50 (34%), Positives = 31/50 (62%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEK 60
          +++GGL+ +  +  L   F  FG++K+     D  T++ R FGFVTF+++
Sbjct: 3  MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQ 52

This subgroup corresponds to the RRM1 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells and associated with asymmetric divisions in neural progenitor cells. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). Musashi-1 has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, it represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 77

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

 Score = 41.7 bits (98), Expect = 8e-06
 Identities = 18/57 (31%), Positives = 34/57 (59%), Gaps = 1/57 (1%)

Query: 6  VQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKED 62
          +  NT++VGG+   ++E  + + F  +G +K+VK   D+ T   + +GFV+F +  D
Sbjct: 3  IMPNTVFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDR-TGVSKGYGFVSFYDDVD 58

This subgroup corresponds to the RRM of DAZL, also termed SPGY-like-autosomal, encoded by the autosomal homolog of DAZ gene, DAZL. It is ancestral to the deleted in azoospermia (DAZ) protein. DAZL is germ-cell-specific RNA-binding protein that contains a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a DAZ motif, a protein-protein interaction domain. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 82

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

 Score = 41.5 bits (97), Expect = 8e-06
 Identities = 24/70 (34%), Positives = 38/70 (54%), Gaps = 1/70 (1%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          +++GGL+ +  +  L   F  FG++ D    LD  T + R FGFV F E E   + MD  
Sbjct: 1  MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60

Query: 71 DGAELYGRVL 80
          +  +L G+V+
Sbjct: 61 E-HKLNGKVI 69

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

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

 Score = 41.5 bits (97), Expect = 1e-05
 Identities = 28/79 (35%), Positives = 44/79 (55%), Gaps = 3/79 (3%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
          TL+V GL+E+  E  L  +F   G I   +   D+ T   + FGFV F  +EDA  A + 
Sbjct: 2  TLFVKGLSEDTTEETLKESFD--GSIA-ARIVTDRDTGSSKGFGFVDFSSEEDAKAAKEA 58

Query: 70 MDGAELYGRVLTVNYALPE 88
          M+  E+ G  +T+++A P+
Sbjct: 59 MEDGEIDGNKVTLDFAKPK 77

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

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

 Score = 41.6 bits (98), Expect = 1e-05
 Identities = 22/78 (28%), Positives = 39/78 (50%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
           L +  L + + +    + F+  G +K+ K   D+ T     FGFV +   EDA +A+  
Sbjct: 2  NLIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRT 61

Query: 70 MDGAELYGRVLTVNYALP 87
          ++G +L  + + V YA P
Sbjct: 62 LNGLQLQNKRIKVAYARP 79

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

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

 Score = 41.2 bits (97), Expect = 1e-05
 Identities = 19/57 (33%), Positives = 29/57 (50%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAM 67
          L V GL  +  E  L   F  FG++  V+   D  T + + FGFV F + ED ++ +
Sbjct: 2  LIVLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVL 58

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

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

 Score = 41.3 bits (97), Expect = 1e-05
 Identities = 21/60 (35%), Positives = 33/60 (55%), Gaps = 1/60 (1%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          L+VG L+++ NE  +   F PFG I++  T L     + R   FVTF  ++ A+ A+  M
Sbjct: 4  LFVGMLSKKCNENDVRIMFAPFGSIEEC-TVLRDQNGQSRGCAFVTFASRQCALNAIKAM 62

This subgroup corresponds to the RRM2 of Bruno, a Drosophila RNA recognition motif (RRM)-containing protein that plays a central role in regulation of Oskar (Osk) expression. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. . Length = 81

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

 Score = 41.6 bits (97), Expect = 1e-05
 Identities = 21/62 (33%), Positives = 33/62 (53%)

Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
          Q   L++GGL+ E  +  L + F  +G + D     D  T++ R FGFVT+   E+   A
Sbjct: 1  QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAA 60

Query: 67 MD 68
          M+
Sbjct: 61 MN 62

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

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

 Score = 41.5 bits (97), Expect = 1e-05
 Identities = 24/80 (30%), Positives = 42/80 (52%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
          +L+V  +A+      L   F  +G I DV  PLD  T++ R F ++ F +  DA  A+ N
Sbjct: 2  SLFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYN 61

Query: 70 MDGAELYGRVLTVNYALPER 89
          ++   + GR + + +A  +R
Sbjct: 62 LNRKWVCGRQIEIQFAQGDR 81

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

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

 Score = 41.8 bits (99), Expect = 1e-05
 Identities = 25/86 (29%), Positives = 44/86 (51%), Gaps = 6/86 (6%)

Query: 6  VQKNTLYVGGLA-EEVNEAIL--HAAFIPFGDIKDV---KTPLDQATQKHRSFGFVTFLE 59
          +Q+N +YV GL     +E +L     F  +G IK +   +      +Q   +  +VT+  
Sbjct: 3  IQRNLVYVVGLPPRLADEEVLKKPEYFGQYGKIKKIVINRNTSYNGSQGPSASAYVTYSR 62

Query: 60 KEDAIQAMDNMDGAELYGRVLTVNYA 85
          KEDA++ +  +DG  L GR+L  ++ 
Sbjct: 63 KEDALRCIQAVDGFYLDGRLLKASFG 88

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

>gnl|CDD|241070 cd12626, RRM1_IGF2BP2, RNA recognition motif 1 in vertebrate insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2)

 Score = 41.1 bits (96), Expect = 1e-05
 Identities = 25/82 (30%), Positives = 43/82 (52%), Gaps = 7/82 (8%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
          N LY+G L+  V    L   F       D K PL         + FV + ++  AI+A++
Sbjct: 2  NKLYIGNLSPAVTAEDLRQLF------GDRKLPLTGQVLLKSGYAFVDYPDQNWAIRAIE 55

Query: 69 NMDG-AELYGRVLTVNYALPER 89
           + G  EL+G+V+ V+Y++P++
Sbjct: 56 TLSGKVELHGKVMEVDYSVPKK 77

This subgroup corresponds to the RRM1 of IGF2BP2 (IGF2 mRNA-binding protein 2 or IMP-2), also termed hepatocellular carcinoma autoantigen p62, or VICKZ family member 2, which is a ubiquitously expressed RNA-binding protein involved in the stimulation of insulin action. It is predominantly nuclear. SNPs in IGF2BP2 gene are implicated in susceptibility to type 2 diabetes. IGF2BP2 plays an important role in cellular motility; it regulates the expression of PINCH-2, an important mediator of cell adhesion and motility, and MURF-3, a microtubule-stabilizing protein, through direct binding to their mRNAs. IGF2BP2 may be involved in the regulation of mRNA stability through the interaction with the AU-rich element-binding factor AUF1. IGF2BP2 binds initially to nascent beta-actin transcripts and facilitates the subsequent binding of the shuttling IGF2BP1. IGF2BP2 contains four hnRNP K-homology (KH) domains, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a RGG RNA-binding domain. . Length = 77

>gnl|CDD|241056 cd12612, RRM2_SECp43, RNA recognition motif 2 in tRNA selenocysteine-associated protein 1 (SECp43)

 Score = 41.1 bits (97), Expect = 1e-05
 Identities = 26/80 (32%), Positives = 43/80 (53%), Gaps = 3/80 (3%)

Query: 10 TLYVGGLAEEVNEAILHAAFIP-FGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
          +L+VG L  +V++  L+  F   +   K  K  LDQ     R +GFV F ++ +  +A+ 
Sbjct: 3  SLFVGDLTPDVDDYQLYEFFSKRYPSCKGAKVVLDQNG-NSRGYGFVRFSDESEQKRALT 61

Query: 69 NMDGAE-LYGRVLTVNYALP 87
           M GA  L G+ + V+ A+P
Sbjct: 62 EMQGASGLGGKPIRVSLAIP 81

This subgroup corresponds to the RRM2 of SECp43, an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. . Length = 82

>gnl|CDD|241023 cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 41.0 bits (96), Expect = 1e-05
 Identities = 22/56 (39%), Positives = 30/56 (53%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
          L+VGGL  +V E  L   F  FG ++  +   D+ T K R FGFV F   + A +A
Sbjct: 2  LFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKA 57

This subgroup corresponds to the RRM2 of hnRNP A0, a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

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

 Score = 41.2 bits (96), Expect = 2e-05
 Identities = 20/80 (25%), Positives = 41/80 (51%)

Query: 8  KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAM 67
          +  L V  L + + +  L + F   G+++  K   D+       +GFV ++  +DA +A+
Sbjct: 1  RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAI 60

Query: 68 DNMDGAELYGRVLTVNYALP 87
          + ++G  L  + + V+YA P
Sbjct: 61 NTLNGLRLQSKTIKVSYARP 80

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

 Score = 40.6 bits (95), Expect = 2e-05
 Identities = 22/70 (31%), Positives = 37/70 (52%), Gaps = 1/70 (1%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          ++VGGL+ +  +  L   F  FG++ D    +D  T + R FGFV F +     + +D  
Sbjct: 1  MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQK 60

Query: 71 DGAELYGRVL 80
          +  +L GRV+
Sbjct: 61 E-HKLDGRVI 69

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

>gnl|CDD|241076 cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 40.5 bits (95), Expect = 3e-05
 Identities = 17/58 (29%), Positives = 29/58 (50%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
          L+VG +   + E  L   F  FG I ++    D+ T  H+   F+T+  +E A++A  
Sbjct: 8  LFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALKAQS 65

This subfamily corresponds to the RRM1 of CELF-3, CELF-4, CELF-5, CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein.The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in an muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In additiona to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 87

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

 Score = 40.7 bits (96), Expect = 3e-05
 Identities = 22/81 (27%), Positives = 35/81 (43%), Gaps = 2/81 (2%)

Query: 10 TLYVGGLAEE-VNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
           L+V  L +   + +IL   F   G     +  +    Q  R F FV +   EDA +A  
Sbjct: 4  CLFVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIAPNGQ-PRGFAFVEYATAEDAEEAQQ 62

Query: 69 NMDGAELYGRVLTVNYALPER 89
           ++G  L G  + V++  P R
Sbjct: 63 ALNGHSLQGSPIRVSFGNPGR 83

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

 Score = 40.1 bits (94), Expect = 3e-05
 Identities = 18/47 (38%), Positives = 27/47 (57%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTF 57
          +++GGL+ +     L   F  FG+IK+     D  T++ R FGFVTF
Sbjct: 1  MFIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTF 47

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

>gnl|CDD|227502 COG5175, MOT2, Transcriptional repressor [Transcription]

 Score = 42.7 bits (100), Expect = 3e-05
 Identities = 32/89 (35%), Positives = 46/89 (51%), Gaps = 11/89 (12%)

Query: 6   VQKNTLYVGGL----AEEVNEAIL--HAAFIPFGDIKDV----KTPLDQATQKHRSFGFV 55
           VQKN +YV G+    A+E    +L  H  F  +G IK +    KT    +T  H    ++
Sbjct: 112 VQKNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGV-YI 170

Query: 56  TFLEKEDAIQAMDNMDGAELYGRVLTVNY 84
           T+  KEDA + +  +DG+ L GRVL   Y
Sbjct: 171 TYSTKEDAARCIAEVDGSLLDGRVLKATY 199

Length = 480

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

 Score = 40.0 bits (94), Expect = 3e-05
 Identities = 20/72 (27%), Positives = 33/72 (45%), Gaps = 6/72 (8%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          L+VG L  ++ E      F  +G++ +V         K + FGF+    + +A +A   +
Sbjct: 4  LFVGNLPNDITEEEFKELFSKYGEVSEVFLN------KEKGFGFIRLDTRTNAEKAKAEL 57

Query: 71 DGAELYGRVLTV 82
          DG    GR L V
Sbjct: 58 DGIMRKGRQLRV 69

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

>gnl|CDD|241071 cd12627, RRM1_IGF2BP3, RNA recognition motif 1 in vertebrate insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3)

 Score = 40.0 bits (93), Expect = 3e-05
 Identities = 25/82 (30%), Positives = 43/82 (52%), Gaps = 7/82 (8%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
          N LY+G L+E  +   L + F      KD K P          + FV   ++  A++A+D
Sbjct: 2  NKLYIGNLSENASPLDLESIF------KDSKIPFSGPFLVKSGYAFVDCPDESWAMKAID 55

Query: 69 NMDG-AELYGRVLTVNYALPER 89
           + G  EL+G+V+ V +++P+R
Sbjct: 56 TLSGKVELHGKVIEVEHSVPKR 77

This subgroup corresponds to the RRM1 of IGF2BP3 (IGF2 mRNA-binding protein 3 or IMP-3), also termed KH domain-containing protein overexpressed in cancer (KOC), or VICKZ family member 3, an RNA-binding protein that plays an important role in the differentiation process during early embryogenesis. It is known to bind to and repress the translation of IGF2 leader 3 mRNA. IGF2BP3 also acts as a Glioblastoma-specific proproliferative and proinvasive marker acting through IGF2 resulting in the activation of oncogenic phosphatidylinositol 3-kinase/mitogen-activated protein kinase (PI3K/MAPK) pathways. IGF2BP3 contains four hnRNP K-homology (KH) domains, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a RGG RNA-binding domain. . Length = 77

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

 Score = 39.7 bits (93), Expect = 4e-05
 Identities = 23/78 (29%), Positives = 36/78 (46%), Gaps = 9/78 (11%)

Query: 10 TLYVGGLAEE-VNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
          TL+V G       E  +   F PFG +              ++F FV F + EDA +A++
Sbjct: 1  TLFVVGFDPGTTREEDIEKLFEPFGPLVRCDIR--------KTFAFVEFEDSEDATKALE 52

Query: 69 NMDGAELYGRVLTVNYAL 86
           + G+ + G VLTV +  
Sbjct: 53 ALHGSRIDGSVLTVEFVK 70

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

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

 Score = 39.8 bits (94), Expect = 4e-05
 Identities = 22/73 (30%), Positives = 39/73 (53%), Gaps = 1/73 (1%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
          +++VG L  ++ E  L   F   GD++ V+   D+ T   + FG+V F  K+    A+  
Sbjct: 1  SVFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALAL-K 59

Query: 70 MDGAELYGRVLTV 82
          ++G +L GR + V
Sbjct: 60 LNGIKLKGRKIRV 72

This subfamily corresponds to the RRM2 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein. . Length = 73

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

 Score = 39.9 bits (94), Expect = 4e-05
 Identities = 22/63 (34%), Positives = 30/63 (47%), Gaps = 1/63 (1%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          + V  L + V E  L   F   G++ DVK  +     K R FGFV F  +EDA QA+   
Sbjct: 3  IIVKNLPKYVTEDRLREHFESKGEVTDVKV-MRTRDGKSRRFGFVGFKSEEDAQQAVKYF 61

Query: 71 DGA 73
          +  
Sbjct: 62 NKT 64

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

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

 Score = 39.8 bits (93), Expect = 4e-05
 Identities = 19/62 (30%), Positives = 32/62 (51%), Gaps = 1/62 (1%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          L+VG L ++  E  +   F P+G ++D+    D+  Q  R   FV +  KE A  A+  +
Sbjct: 2  LFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMKQS-RGCAFVKYSSKEMAQAAIKAL 60

Query: 71 DG 72
          +G
Sbjct: 61 NG 62

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

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

 Score = 39.4 bits (92), Expect = 5e-05
 Identities = 24/77 (31%), Positives = 37/77 (48%), Gaps = 5/77 (6%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTP--LDQATQKHRSFGFVTFLEKEDAIQAMD 68
          + V  L  E  +  +   F  +G +K V+ P   DQ+    R F FV F   ++A+ AM+
Sbjct: 3  ILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSA---RGFAFVEFSTAKEALNAMN 59

Query: 69 NMDGAELYGRVLTVNYA 85
           +    L GR L + YA
Sbjct: 60 ALKDTHLLGRRLVLQYA 76

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

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

 Score = 39.5 bits (92), Expect = 5e-05
 Identities = 18/47 (38%), Positives = 26/47 (55%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTF 57
          +++GGL  E  +  L   F  FG++ D     D AT + R FGF+TF
Sbjct: 1  MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTF 47

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

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

 Score = 39.2 bits (92), Expect = 5e-05
 Identities = 21/62 (33%), Positives = 33/62 (53%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          +Y+ GL     +  L     PFG I   K  LD+ T K + +GFV F   E A++A++ +
Sbjct: 3  VYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIEGL 62

Query: 71 DG 72
          +G
Sbjct: 63 NG 64

This subfamily corresponds to the RRM1 of c-myc gene single-strand binding proteins (MSSP) family, including single-stranded DNA-binding protein MSSP-1 (also termed RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3). All MSSP family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity. Both, MSSP-1 and -2, have been identified as protein factors binding to a putative DNA replication origin/transcriptional enhancer sequence present upstream from the human c-myc gene in both single- and double-stranded forms. Thus, they have been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with c-MYC, the product of protooncogene c-myc. Moreover, the family includes a new member termed RNA-binding motif, single-stranded-interacting protein 3 (RBMS3), which is not a transcriptional regulator. RBMS3 binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. In addition, a putative meiosis-specific RNA-binding protein termed sporulation-specific protein 5 (SPO5, or meiotic RNA-binding protein 1, or meiotically up-regulated gene 12 protein), encoded by Schizosaccharomyces pombe Spo5/Mug12 gene, is also included in this family. SPO5 is a novel meiosis I regulator that may function in the vicinity of the Mei2 dot. . Length = 71

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

 Score = 39.5 bits (92), Expect = 5e-05
 Identities = 23/77 (29%), Positives = 38/77 (49%), Gaps = 2/77 (2%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          LYV  L  ++ E  L   F  +G+I       D++T   R   FV + ++E+A  A+ ++
Sbjct: 3  LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSL 62

Query: 71 DGAELYGRV--LTVNYA 85
          +G    G    L+V YA
Sbjct: 63 NGTIPPGSTMPLSVRYA 79

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

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

 Score = 39.2 bits (92), Expect = 6e-05
 Identities = 22/73 (30%), Positives = 30/73 (41%), Gaps = 1/73 (1%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
           L+VG L   V    L   F  FG +K    P D+ T   + +GFV+F    D ++    
Sbjct: 1  KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSF-SSRDGLENALQ 59

Query: 70 MDGAELYGRVLTV 82
               L G  L V
Sbjct: 60 KQKHILEGNKLQV 72

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

>gnl|CDD|241064 cd12620, RRM3_TIAR, RNA recognition motif 3 in nucleolysin TIAR and similar proteins

 Score = 39.2 bits (91), Expect = 6e-05
 Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 8/72 (11%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKT-PLDQATQKHRSFGFVTFLEKEDAIQAMD 68
          T+Y GG+A  + E ++   F PFG I +++  P        + + F+ F   E A  A+ 
Sbjct: 2  TVYCGGIASGLTEQLMRQTFSPFGQIMEIRVFP-------EKGYSFIRFSTHESAAHAIV 54

Query: 69 NMDGAELYGRVL 80
          +++G  + G V+
Sbjct: 55 SVNGTTIEGHVV 66

This subgroup corresponds to the RRM3 of nucleolysin TIAR, also termed TIA-1-related protein, a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 73

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

 Score = 39.3 bits (91), Expect = 7e-05
 Identities = 21/55 (38%), Positives = 31/55 (56%), Gaps = 1/55 (1%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQ 65
          ++VGGL+       +   F  FG ++D     D+ T +HR FGFVTF E ED ++
Sbjct: 6  IFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTF-ENEDVVE 59

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 79

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

 Score = 38.8 bits (91), Expect = 8e-05
 Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 2/77 (2%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          LYV GL + + +  L A F P+G I   +   D  T   R  GF+ F ++ +A +A+  +
Sbjct: 3  LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL 62

Query: 71 DGAELYG--RVLTVNYA 85
          +G    G    +TV +A
Sbjct: 63 NGTIPPGATEPITVKFA 79

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

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

 Score = 38.8 bits (91), Expect = 9e-05
 Identities = 19/69 (27%), Positives = 32/69 (46%), Gaps = 2/69 (2%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
          T++V  L   V E  L   F   G+I DV+   +    K + + +V F  +E   +A+  
Sbjct: 1  TVFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYK-GKSKGYAYVEFENEESVQEAL-K 58

Query: 70 MDGAELYGR 78
          +D   + GR
Sbjct: 59 LDRELIKGR 67

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

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

 Score = 38.8 bits (90), Expect = 9e-05
 Identities = 19/70 (27%), Positives = 37/70 (52%), Gaps = 1/70 (1%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          ++VGGL+ + ++  L   F  FG++ D    +D  T + R FGF+ F +     + ++  
Sbjct: 2  MFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQK 61

Query: 71 DGAELYGRVL 80
          +   L GR++
Sbjct: 62 E-HRLDGRLI 70

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

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

 Score = 38.9 bits (90), Expect = 9e-05
 Identities = 17/49 (34%), Positives = 29/49 (59%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLE 59
          +++GGL+ + +   L   F  FG+I++     D  T++ R FGFVTF +
Sbjct: 2  MFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFAD 50

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

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

 Score = 41.1 bits (96), Expect = 1e-04
 Identities = 19/71 (26%), Positives = 39/71 (54%)

Query: 2   ANLAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKE 61
           ++ +++   LYV GL + + +  L + F PFG I   +   D  T   +  GF+ F +++
Sbjct: 83  SSDSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRD 142

Query: 62  DAIQAMDNMDG 72
           +A +A+  ++G
Sbjct: 143 EADRAIKTLNG 153

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

 Score = 41.4 bits (97), Expect = 1e-04
 Identities = 18/78 (23%), Positives = 32/78 (41%)

Query: 8   KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAM 67
           K+ +Y+G L   + E  +      FGD+K      D AT   + + F  + +      A+
Sbjct: 295 KDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAI 354

Query: 68  DNMDGAELYGRVLTVNYA 85
             ++G +     L V  A
Sbjct: 355 AALNGKDTGDNKLHVQRA 372

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

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

 Score = 38.6 bits (90), Expect = 1e-04
 Identities = 27/75 (36%), Positives = 36/75 (48%), Gaps = 3/75 (4%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          L+VG L+ E  E  L A F   G I+ V+    + + K + F FV F E E    A + +
Sbjct: 1  LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIE---FATNAL 57

Query: 71 DGAELYGRVLTVNYA 85
           G  L GR L V Y 
Sbjct: 58 KGKHLNGRALRVEYG 72

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

>gnl|CDD|240892 cd12446, RRM_RBM25, RNA recognition motif in eukaryotic RNA-binding protein 25 and similar proteins

 Score = 38.7 bits (91), Expect = 1e-04
 Identities = 24/78 (30%), Positives = 41/78 (52%), Gaps = 8/78 (10%)

Query: 10 TLYVGGLAEEVNEA----ILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQ 65
          T++VG + E V++     +L       G +   K   D +T K ++FGF  F + E A++
Sbjct: 2  TVFVGNIPEGVSDDFIRKLLEK----CGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALR 57

Query: 66 AMDNMDGAELYGRVLTVN 83
          A+  ++G EL G+ L V 
Sbjct: 58 ALRLLNGLELGGKKLLVK 75

This subfamily corresponds to the RRM of RBM25, also termed Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein S164, or RNA-binding region-containing protein 7, an evolutionary-conserved splicing coactivator SRm160 (SR-related nuclear matrix protein of 160 kDa, )-interacting protein. RBM25 belongs to a family of RNA-binding proteins containing a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminus, a RE/RD-rich (ER) central region, and a C-terminal proline-tryptophan-isoleucine (PWI) motif. It localizes to the nuclear speckles and associates with multiple splicing components, including splicing cofactors SRm160/300, U snRNAs, assembled splicing complexes, and spliced mRNAs. It may play an important role in pre-mRNA processing by coupling splicing with mRNA 3'-end formation. Additional research indicates that RBM25 is one of the RNA-binding regulators that direct the alternative splicing of apoptotic factors. It can activate proapoptotic Bcl-xS 5'ss by binding to the exonic splicing enhancer, CGGGCA, and stabilize the pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1 snRNP-associated factor. . Length = 84

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

 Score = 38.7 bits (90), Expect = 1e-04
 Identities = 18/62 (29%), Positives = 35/62 (56%), Gaps = 1/62 (1%)

Query: 25 LHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNY 84
          L   F  +G +++   P  +   K   F FVT  ++++A  A++N +G E+ GR + V++
Sbjct: 18 LKKIFGRYGKVREATIPRKRGG-KLCGFAFVTMKKRKNAEIALENTNGLEIDGRPVAVDW 76

Query: 85 AL 86
          A+
Sbjct: 77 AV 78

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

 Score = 38.0 bits (89), Expect = 1e-04
 Identities = 22/75 (29%), Positives = 35/75 (46%), Gaps = 14/75 (18%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKD---VKTPLDQATQKHRSFGFVTFLEKEDAIQAM 67
          L+VG L +      L A F  +G + +   VK           ++GFV   E+EDA  A+
Sbjct: 2  LFVGNLPDATTSEELRALFEKYGTVTECDVVK-----------NYGFVHMEEEEDAEDAI 50

Query: 68 DNMDGAELYGRVLTV 82
            ++G E  G+ + V
Sbjct: 51 KALNGYEFMGKRINV 65

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

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

 Score = 38.5 bits (89), Expect = 2e-04
 Identities = 21/78 (26%), Positives = 39/78 (50%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          L++  L +E  +  L   F+PFG++   K  +D+ T   + FGFV++     A  A+  M
Sbjct: 10 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQAM 69

Query: 71 DGAELYGRVLTVNYALPE 88
          +G ++  + L V     +
Sbjct: 70 NGFQIGMKRLKVQLKRSK 87

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

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

 Score = 37.9 bits (89), Expect = 2e-04
 Identities = 19/73 (26%), Positives = 31/73 (42%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
           +Y+G L     E  L   F  FG +  ++    + T K + + FV F   E A    + 
Sbjct: 1  VVYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAET 60

Query: 70 MDGAELYGRVLTV 82
          M+   L+ R+L  
Sbjct: 61 MNNYLLFERLLKC 73

This subgroup corresponds to the RRM of NIFK and Nop15p. NIFK, also termed MKI67 FHA domain-interacting nucleolar phosphoprotein, or nucleolar phosphoprotein Nopp34, is a putative RNA-binding protein interacting with the forkhead associated (FHA) domain of pKi-67 antigen in a mitosis-specific and phosphorylation-dependent manner. It is nucleolar in interphase but associates with condensed mitotic chromosomes. This family also includes Saccharomyces cerevisiae YNL110C gene encoding ribosome biogenesis protein 15 (Nop15p), also termed nucleolar protein 15. Both, NIFK and Nop15p, contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 74

>gnl|CDD|240743 cd12297, RRM2_Prp24, RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 37.9 bits (89), Expect = 2e-04
 Identities = 20/79 (25%), Positives = 35/79 (44%), Gaps = 1/79 (1%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
          +TL+V       +++ +   F  +G+I  ++ P      K R F +V F   E A  A+ 
Sbjct: 1  STLWVTNFPPSFDQSDIRDLFEQYGEILSIRFP-SLRFNKTRRFCYVQFTSPESAAAAVA 59

Query: 69 NMDGAELYGRVLTVNYALP 87
           ++G    G  L V  + P
Sbjct: 60 LLNGKLGEGYKLVVKISDP 78

This subfamily corresponds to the RRM2 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 78

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

 Score = 37.7 bits (88), Expect = 2e-04
 Identities = 21/75 (28%), Positives = 34/75 (45%), Gaps = 8/75 (10%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          +Y+G L     E  +   F  +G I+++             FGFV F +  DA  A+  +
Sbjct: 2  VYIGRLPYRARERDVERFFKGYGRIREINL--------KNGFGFVEFEDPRDADDAVYEL 53

Query: 71 DGAELYGRVLTVNYA 85
          +G EL G  + V +A
Sbjct: 54 NGKELCGERVIVEHA 68

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

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

 Score = 37.7 bits (88), Expect = 2e-04
 Identities = 24/74 (32%), Positives = 39/74 (52%), Gaps = 5/74 (6%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIK--DVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
          +YVGG+     E  + + F   G+I+  D+ T  D  T + R   F+TF + E+A +   
Sbjct: 1  VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPD--TGRFRGIAFITF-KTEEAAKRAL 57

Query: 69 NMDGAELYGRVLTV 82
           +DG ++ GR L V
Sbjct: 58 ALDGEDMGGRFLKV 71

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

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

 Score = 37.6 bits (88), Expect = 3e-04
 Identities = 20/65 (30%), Positives = 27/65 (41%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
          N L+V  L     +  L   F  FG IK  +   D+ T     + F+ F  KED  +A  
Sbjct: 4  NVLFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYF 63

Query: 69 NMDGA 73
           MD  
Sbjct: 64 KMDNV 68

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

 Score = 37.8 bits (87), Expect = 3e-04
 Identities = 21/61 (34%), Positives = 31/61 (50%)

Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
          Q   L++GGL+ E  E  L   +  +G + D     D A+++ R FGFVTF    +   A
Sbjct: 1  QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAA 60

Query: 67 M 67
          M
Sbjct: 61 M 61

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

>gnl|CDD|240721 cd12275, RRM1_MEI2_EAR1_like, RNA recognition motif 1 in Mei2-like proteins and terminal EAR1-like proteins

 Score = 37.2 bits (86), Expect = 3e-04
 Identities = 17/71 (23%), Positives = 33/71 (46%), Gaps = 5/71 (7%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
          +L+V  +  +V E+ L   F  +GD++ V+T      +       V F +  DA +A+  
Sbjct: 3  SLFVINVPRDVTESTLRRLFEVYGDVRGVQT-----ERISEGIVTVHFYDIRDAKRAVRE 57

Query: 70 MDGAELYGRVL 80
          + G  +  + L
Sbjct: 58 LCGRHMQQQAL 68

This subfamily corresponds to the RRM1 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding protein family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins. . Length = 71

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

 Score = 39.6 bits (92), Expect = 3e-04
 Identities = 25/85 (29%), Positives = 41/85 (48%), Gaps = 4/85 (4%)

Query: 11  LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
           L V  L +++ +  L+A F   G I   +   D  T     + FV F  + D+ +A+ N+
Sbjct: 110 LIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNL 169

Query: 71  DGAELYGRVLTVNYALPERIKGGEQ 95
           +G  +  + L V+YA P    GGE 
Sbjct: 170 NGITVRNKRLKVSYARP----GGES 190

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

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

 Score = 37.4 bits (86), Expect = 3e-04
 Identities = 21/61 (34%), Positives = 31/61 (50%)

Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
          Q   L++GGL+ E  +  L   F  +G + D     D  T++ R FGFVT+   E+   A
Sbjct: 1  QLRKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAA 60

Query: 67 M 67
          M
Sbjct: 61 M 61

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

>gnl|CDD|240971 cd12527, RRM2_EAR1_like, RNA recognition motif 2 in terminal EAR1-like proteins

 Score = 37.1 bits (86), Expect = 4e-04
 Identities = 22/70 (31%), Positives = 38/70 (54%), Gaps = 7/70 (10%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVK-TPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
          TL +  L   V+   L + F  +GD+K+++ TP     ++ R   FV F +  DA +A+ 
Sbjct: 3  TLVIFNLDPTVSSETLRSIFQVYGDVKELRETP---CKREQR---FVEFFDVRDAAKALR 56

Query: 69 NMDGAELYGR 78
           M+G E+ G+
Sbjct: 57 AMNGKEISGK 66

This subgroup corresponds to the RRM2 of terminal EAR1-like proteins, including terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land plants. They may play a role in the regulation of leaf initiation. The terminal EAR1-like proteins are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and TEL characteristic motifs that allow sequence and putative functional discrimination between the terminal EAR1-like proteins and Mei2-like proteins. . Length = 71

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

 Score = 37.3 bits (86), Expect = 4e-04
 Identities = 26/81 (32%), Positives = 39/81 (48%), Gaps = 7/81 (8%)

Query: 9  NTLYVGGLAEEVNE----AILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
          +T+Y+  L E++ +      LHA F  FG I D+   L   + K R   FV F E   A 
Sbjct: 4  HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDI---LVSRSLKMRGQAFVIFKEVSSAT 60

Query: 65 QAMDNMDGAELYGRVLTVNYA 85
           A+ +M G   Y + + + YA
Sbjct: 61 NALRSMQGFPFYDKPMRIQYA 81

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

 Score = 37.3 bits (86), Expect = 4e-04
 Identities = 22/77 (28%), Positives = 40/77 (51%), Gaps = 2/77 (2%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          LY+ GL   + +  +   F  FG I + +  +DQAT   R   F+ F ++ +A +A+ + 
Sbjct: 3  LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITSF 62

Query: 71 DGAELYGRV--LTVNYA 85
          +G +  G    +TV +A
Sbjct: 63 NGHKPPGSSEPITVKFA 79

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

 Score = 36.8 bits (85), Expect = 5e-04
 Identities = 24/80 (30%), Positives = 38/80 (47%), Gaps = 7/80 (8%)

Query: 10 TLYVGGLAEEVNE----AILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQ 65
          T+Y+  L E+V +      L+A F  FG I D+   +   T K R   FV F +   A  
Sbjct: 1  TIYINNLNEKVKKEELKKSLYAIFSQFGQILDI---VALKTLKMRGQAFVVFKDISSATN 57

Query: 66 AMDNMDGAELYGRVLTVNYA 85
          A+ +M G   Y + + + Y+
Sbjct: 58 ALRSMQGFPFYDKPMRIAYS 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|240822 cd12376, RRM2_Hu_like, RNA recognition motif 2 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 36.8 bits (85), Expect = 5e-04
 Identities = 23/77 (29%), Positives = 39/77 (50%), Gaps = 2/77 (2%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          LYV GL + + +  L   F  +G I   +   DQ T   R  GF+ F ++ +A +A+  +
Sbjct: 3  LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKGL 62

Query: 71 DGAELYG--RVLTVNYA 85
          +G +  G    +TV +A
Sbjct: 63 NGQKPEGASEPITVKFA 79

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

>gnl|CDD|241024 cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 36.9 bits (85), Expect = 5e-04
 Identities = 17/47 (36%), Positives = 27/47 (57%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTF 57
          ++VGG+ E+  E  L   F  +G I+ ++   D+ + K R F FVTF
Sbjct: 3  IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 49

This subgroup corresponds to the RRM2 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A1 has been characterized as a splicing silencer, often acting in opposition to an activating hnRNP H. It silences exons when bound to exonic elements in the alternatively spliced transcripts of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle between the nucleus and the cytoplasm. Thus, it may be involved in transport of cellular RNAs, including the packaging of pre-mRNA into hnRNP particles and transport of poly A+ mRNA from the nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has high affinity with AU-rich elements, whereas the nuclear hnRNP A1 has high affinity with a polypyrimidine stretch bordered by AG at the 3' ends of introns. hnRNP A1 is also involved in the replication of an RNA virus, such as mouse hepatitis virus (MHV), through an interaction with the transcription-regulatory region of viral RNA. Moreover, hnRNP A1, together with the scaffold protein septin 6, serves as host proteins to form a complex with NS5b and viral RNA, and further play important roles in the replication of Hepatitis C virus (HCV). hnRNP A1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The RRMs of hnRNP A1 play an important role in silencing the exon and the glycine-rich domain is responsible for protein-protein interactions. . Length = 77

>gnl|CDD|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like proteins mainly from plants

 Score = 36.6 bits (85), Expect = 5e-04
 Identities = 24/83 (28%), Positives = 38/83 (45%), Gaps = 11/83 (13%)

Query: 10 TLYVGG----LAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLE---KED 62
          T++V G    L E+     L   F   G+I  V  P D+ T   + F ++ F      E 
Sbjct: 1  TIFVKGFDSSLGEDDIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEK 60

Query: 63 AIQAMDNMDGAELYGRVLTVNYA 85
          A++    +DG++L G  L V+ A
Sbjct: 61 ALE----LDGSDLGGGNLVVDEA 79

This subfamily corresponds to the RRM2 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 39.0 bits (91), Expect = 6e-04
 Identities = 22/72 (30%), Positives = 36/72 (50%), Gaps = 1/72 (1%)

Query: 11  LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
           ++V  L + V+   L   F  FG+I   K   D+   K R +GFV F ++E A  A+  +
Sbjct: 91  IFVKNLDKSVDNKALFDTFSKFGNILSCKVATDE-NGKSRGYGFVHFEKEESAKAAIQKV 149

Query: 71  DGAELYGRVLTV 82
           +G  L  + + V
Sbjct: 150 NGMLLNDKEVYV 161

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

>gnl|CDD|240868 cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition motif in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins

 Score = 36.8 bits (86), Expect = 6e-04
 Identities = 19/72 (26%), Positives = 27/72 (37%), Gaps = 18/72 (25%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDV----KTPLDQATQKHRSFGFVTFLEKEDAI 64
          N LY       V   +LH  F P+G ++ +    K    QA         V F   E A 
Sbjct: 8  NLLYP------VTVDVLHQVFSPYGAVEKILIFEKNTGVQA--------LVQFDSVESAE 53

Query: 65 QAMDNMDGAELY 76
           A   ++G  +Y
Sbjct: 54 NAKKALNGRNIY 65

This subfamily corresponds to the RRM2 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), polypyrimidine tract-binding protein homolog 3 (PTBPH3), polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2), and similar proteins, and RRM3 of PTBPH1 and PTBPH2. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. Rod1 is a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL protein plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. This family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to other family members, all of which contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although their biological roles remain unclear, both PTBPH1 and PTBPH2 show significant sequence similarity to PTB. However, in contrast to PTB, they have three RRMs. . Length = 85

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

 Score = 36.8 bits (86), Expect = 6e-04
 Identities = 23/76 (30%), Positives = 31/76 (40%), Gaps = 5/76 (6%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDV-----KTPLDQATQKHRSFGFVTFLEKEDAI 64
          TL+V  L  +  E  L   F   G ++ V     K P          +GFV F  KE A 
Sbjct: 2  TLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQ 61

Query: 65 QAMDNMDGAELYGRVL 80
          +A+  + G  L G  L
Sbjct: 62 KALKRLQGTVLDGHAL 77

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

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

 Score = 36.4 bits (84), Expect = 7e-04
 Identities = 17/58 (29%), Positives = 34/58 (58%), Gaps = 8/58 (13%)

Query: 29 FIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYAL 86
          F P+G + +V        +  R+F FV +  +EDA +A+++ + +++  RV++V YA 
Sbjct: 21 FEPYGKLVNV--------RIRRNFAFVQYETQEDATKALESTNMSKVLDRVISVEYAA 70

This subgroup corresponds to the RRM2 in a family that represents a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at their N-terminus, and an RS domain at their C-terminus. Length = 70

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

 Score = 36.0 bits (84), Expect = 7e-04
 Identities = 22/74 (29%), Positives = 38/74 (51%), Gaps = 9/74 (12%)

Query: 11 LYVGGLA-EEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
          ++VG L  ++V++  L   F  +G I  +          H+ +GFV F  +EDA  A+  
Sbjct: 3  VFVGNLNTDKVSKEDLEEIFSKYGKILGISL--------HKGYGFVQFDNEEDARAAVAG 54

Query: 70 MDGAELYGRVLTVN 83
           +G E+ G+ L +N
Sbjct: 55 ENGREIAGQKLDIN 68

This subfamily corresponds to the RRM in the hnRNP C-related protein family, including hnRNP C proteins, Raly, and Raly-like protein (RALYL). hnRNP C proteins, C1 and C2, are produced by a single coding sequence. They are the major constituents of the heterogeneous nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in vertebrates. They bind hnRNA tightly, suggesting a central role in the formation of the ubiquitous hnRNP complex; they are involved in the packaging of the hnRNA in the nucleus and in processing of pre-mRNA such as splicing and 3'-end formation. Raly, also termed autoantigen p542, is an RNA-binding protein that may play a critical role in embryonic development. The biological role of RALYL remains unclear. It shows high sequence homology with hnRNP C proteins and Raly. Members of this family are characterized by an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain. The Raly proteins contain a glycine/serine-rich stretch within the C-terminal regions, which is absent in the hnRNP C proteins. Thus, the Raly proteins represent a newly identified class of evolutionarily conserved autoepitopes. . Length = 68

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

 Score = 36.4 bits (85), Expect = 7e-04
 Identities = 25/76 (32%), Positives = 37/76 (48%), Gaps = 5/76 (6%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFG--FVTFLEKEDAIQAM 67
           L V  L  +V E  L   F   G++K VK   D++    RS G   V F ++EDA +A+
Sbjct: 2  RLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDRSG---RSEGTADVVFEKREDAERAI 58

Query: 68 DNMDGAELYGRVLTVN 83
             +G  L G+ + V 
Sbjct: 59 KQFNGVLLDGQPMQVE 74

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

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

 Score = 38.9 bits (90), Expect = 8e-04
 Identities = 17/78 (21%), Positives = 39/78 (50%)

Query: 9   NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
           N +YV  +  +++E  + + F  FG+I   +       + H+ +GF+ +   +   +A+ 
Sbjct: 205 NRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIA 264

Query: 69  NMDGAELYGRVLTVNYAL 86
           +M+  +L G+ L V   +
Sbjct: 265 SMNLFDLGGQYLRVGKCV 282

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

 Score = 36.5 bits (84), Expect = 8e-04
 Identities = 22/77 (28%), Positives = 41/77 (53%), Gaps = 2/77 (2%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          LYV GL + +++  +   F  +G I   +  +DQ T   R  GF+ F ++ +A +A+  +
Sbjct: 4  LYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIKGL 63

Query: 71 DGAELYGRV--LTVNYA 85
          +G +  G    +TV +A
Sbjct: 64 NGQKPLGAAEPITVKFA 80

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

>gnl|CDD|240761 cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1 in RNA-binding protein 19 (RBM19), yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 36.1 bits (84), Expect = 0.001
 Identities = 14/55 (25%), Positives = 26/55 (47%), Gaps = 1/55 (1%)

Query: 31 PFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYA 85
            G+I DVK    +   K R   F+ +  +E+A +A D  +   +    ++V +A
Sbjct: 24 HGGEITDVKLLRTE-DGKSRRIAFIGYKTEEEAQKAKDYFNNTYINTSKISVEFA 77

This subfamily corresponds to the RRM1 of RBM19 and MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 77

>gnl|CDD|240940 cd12496, RRM3_RBM46, RNA recognition motif 3 in vertebrate RNA-binding protein 46 (RBM46)

 Score = 35.8 bits (82), Expect = 0.001
 Identities = 25/77 (32%), Positives = 35/77 (45%), Gaps = 6/77 (7%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          LYV  L     E  + A F  F      K  + +  +K R + FV F  +EDA+ AM  M
Sbjct: 4  LYVRNLMISTTEETIKAEFNKF------KPGVVERVKKLRDYAFVHFFNREDAVAAMSVM 57

Query: 71 DGAELYGRVLTVNYALP 87
          +G  + G  + V  A P
Sbjct: 58 NGKCIDGASIEVTLAKP 74

This subgroup corresponds to the RRM3 of RBM46, also termed cancer/testis antigen 68 (CT68), is a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM46 contains two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 74

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

 Score = 35.8 bits (83), Expect = 0.001
 Identities = 21/65 (32%), Positives = 32/65 (49%), Gaps = 5/65 (7%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIK--DVKTPLDQATQKHRSFGFVTFLEKEDAIQAM 67
          TL+VG L   + E  L  AF  +G ++  D+K P      +  ++ FV FL  + A +A 
Sbjct: 4  TLFVGNLEITITEEELRRAFERYGVVEDVDIKRP---PRGQGNAYAFVKFLNLDMAHRAK 60

Query: 68 DNMDG 72
            M G
Sbjct: 61 VAMSG 65

This subfamily corresponds to the RRM2 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B), and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which share a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 79

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

 Score = 35.9 bits (82), Expect = 0.001
 Identities = 23/83 (27%), Positives = 43/83 (51%), Gaps = 2/83 (2%)

Query: 5  AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
          +++   LYV GL + + +  L   F  +G I   +  +DQ T   R  GF+ F ++ +A 
Sbjct: 2  SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAE 61

Query: 65 QAMDNMDGAELYGRV--LTVNYA 85
          +A+  ++G +  G    +TV +A
Sbjct: 62 EAIKGLNGQKPPGATEPITVKFA 84

This subgroup corresponds to the RRM2 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 90

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

 Score = 35.9 bits (82), Expect = 0.001
 Identities = 23/77 (29%), Positives = 40/77 (51%), Gaps = 2/77 (2%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          LYV GL + + +  L   F  +G I   +  +DQ T   R  GF+ F ++ +A +A+  +
Sbjct: 5  LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 64

Query: 71 DGAELYGRV--LTVNYA 85
          +G +  G    +TV +A
Sbjct: 65 NGQKPSGAAEPITVKFA 81

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

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

 Score = 36.2 bits (83), Expect = 0.001
 Identities = 23/81 (28%), Positives = 39/81 (48%), Gaps = 7/81 (8%)

Query: 9  NTLYVGGLAEEVNEA----ILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
          +T+Y+  L +++ +      L+A F  FG + D+   +   T K R   FV F E   A 
Sbjct: 2  HTIYINNLNDKIKKEELKRSLYALFSQFGHVVDI---VALKTMKMRGQAFVIFKELSSAT 58

Query: 65 QAMDNMDGAELYGRVLTVNYA 85
           A+  + G   YG+ + + YA
Sbjct: 59 NALRQLQGFPFYGKPMRIQYA 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|241066 cd12622, RRM3_PUB1, RNA recognition motif 3 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 35.5 bits (82), Expect = 0.002
 Identities = 22/71 (30%), Positives = 31/71 (43%), Gaps = 6/71 (8%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
          T+YVG +     +A L   F  FG I + +   D      R F FV     E A  A+  
Sbjct: 2  TVYVGNIPPYTTQADLIPLFQNFGYILEFRHQPD------RGFAFVKLDTHEQAAMAIVQ 55

Query: 70 MDGAELYGRVL 80
          + G  ++GR L
Sbjct: 56 LQGFPVHGRPL 66

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

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

 Score = 35.4 bits (82), Expect = 0.002
 Identities = 24/76 (31%), Positives = 36/76 (47%), Gaps = 2/76 (2%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
          T +VG L     +  L A F     +K V+   D+ T K + F +V F + E   +A++ 
Sbjct: 3  TAFVGNLPFNTVQGDLDAIFKDL-SVKSVRLVRDKETDKFKGFCYVEFEDVESLKEALE- 60

Query: 70 MDGAELYGRVLTVNYA 85
           DGA    R L V+ A
Sbjct: 61 YDGALFDDRSLRVDIA 76

This subfamily corresponds to the RRM of eIF-4H, also termed Williams-Beuren syndrome chromosomal region 1 protein, which, together with elf-4B/eIF-4G, serves as the accessory protein of RNA helicase eIF-4A. eIF-4H contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It stimulates protein synthesis by enhancing the helicase activity of eIF-4A in the initiation step of mRNA translation. . Length = 76

>gnl|CDD|240967 cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA-binding protein MRN1 and similar proteins

 Score = 35.5 bits (82), Expect = 0.002
 Identities = 17/60 (28%), Positives = 27/60 (45%), Gaps = 6/60 (10%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          +Y+G L E  +E  L      FG I  +K        K ++  FV FL   +AI+ +  +
Sbjct: 6  VYIGNLPESYSEEELREDLEKFGPIDQIK------IVKEKNIAFVHFLSIANAIKVVTTL 59

This subgroup corresponds to the RRM2 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 78

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

 Score = 35.3 bits (82), Expect = 0.002
 Identities = 17/71 (23%), Positives = 31/71 (43%), Gaps = 1/71 (1%)

Query: 12 YVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMD 71
          +VG +        L   F   G I  +    D+ T + + F ++ FL+K     A+  ++
Sbjct: 3  FVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALL-LN 61

Query: 72 GAELYGRVLTV 82
           +E  GR + V
Sbjct: 62 ESEFRGRQIKV 72

This subfamily corresponds to the RRM of type II polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 2 (PABP-2 or PABPN1), embryonic polyadenylate-binding protein 2 (ePABP-2 or PABPN1L) and similar proteins. PABPs are highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. ePABP-2 is predominantly located in the cytoplasm and PABP-2 is located in the nucleus. In contrast to the type I PABPs containing four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), the type II PABPs contains a single highly-conserved RRM. This subfamily also includes Saccharomyces cerevisiae RBP29 (SGN1, YIR001C) gene encoding cytoplasmic mRNA-binding protein Rbp29 that binds preferentially to poly(A). Although not essential for cell viability, Rbp29 plays a role in modulating the expression of cytoplasmic mRNA. Like other type II PABPs, Rbp29 contains one RRM only. . Length = 73

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

 Score = 35.4 bits (81), Expect = 0.002
 Identities = 19/47 (40%), Positives = 27/47 (57%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTF 57
          L+VGG+ E+  E  L   F  +G I  ++   D+ + K R FGFVTF
Sbjct: 3  LFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTF 49

This subgroup corresponds to the RRM2 of hnRNP A2/B1, an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

>gnl|CDD|240979 cd12535, RRM_FUS_TAF15, RNA recognition motif in vertebrate fused in Ewing's sarcoma protein (FUS), TATA-binding protein-associated factor 15 (TAF15) and similar proteins

 Score = 35.3 bits (81), Expect = 0.002
 Identities = 26/84 (30%), Positives = 39/84 (46%), Gaps = 8/84 (9%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKT---PL-----DQATQKHRSFGFVTFLEK 60
          NT++V GL E+V    +   F   G IK  K    P+     D+ T K +    V+F + 
Sbjct: 3  NTIFVQGLGEDVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 62

Query: 61 EDAIQAMDNMDGAELYGRVLTVNY 84
            A  A+D  DG E  G  + V++
Sbjct: 63 PSAKAAIDWFDGKEFSGNPIKVSF 86

This subgroup corresponds to the RRM of FUS and TAF15. FUS (TLS or Pigpen or hnRNP P2), also termed 75 kDa DNA-pairing protein (POMp75), or oncoprotein TLS (Translocated in liposarcoma), is a member of the FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA- and DNA-binding proteins whose expression is altered in cancer. It is a multi-functional protein and has been implicated in pre-mRNA splicing, chromosome stability, cell spreading, and transcription. FUS was originally identified in human myxoid and round cell liposarcomas as an oncogenic fusion with the stress-induced DNA-binding transcription factor CHOP (CCAAT enhancer-binding homologous protein) and later as hnRNP P2, a component of hnRNP H complex assembled on pre-mRNA. It can form ternary complexes with hnRNP A1 and hnRNP C1/C2. Additional research indicates that FUS binds preferentially to GGUG-containing RNAs. In the presence of Mg2+, it can bind both single- and double-stranded DNA (ssDNA/dsDNA) and promote ATP-independent annealing of complementary ssDNA and D-loop formation in superhelical dsDNA. FUS has been shown to be recruited by single stranded noncoding RNAs to the regulatory regions of target genes such as cyclin D1, where it represses transcription by disrupting complex formation. TAF15 (TAFII68), also termed TATA-binding protein-associated factor 2N (TAF2N), or RNA-binding protein 56 (RBP56), originally identified as a TAF in the general transcription initiation TFIID complex, is a novel RNA/ssDNA-binding protein with homology to the proto-oncoproteins FUS and EWS (also termed EWSR1), belonging to the FET family as well. TAF15 likely functions in RNA polymerase II (RNAP II) transcription by interacting with TFIID and subunits of RNAP II itself. TAF15 is also associated with U1 snRNA, chromatin and RNA, in a complex distinct from the Sm-containing U1 snRNP that functions in splicing. Like other members in the FET family, both FUS and TAF15 contain an N-terminal Ser, Gly, Gln and Tyr-rich region composed of multiple copies of a degenerate hexapeptide repeat motif. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a C2/C2 zinc-finger motif, a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and at least 1 arginine-glycine-glycine (RGG)-repeat region. . Length = 86

>gnl|CDD|240818 cd12372, RRM_CFIm68_CFIm59, RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6), pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7), and similar proteins

 Score = 35.0 bits (81), Expect = 0.002
 Identities = 22/76 (28%), Positives = 33/76 (43%), Gaps = 2/76 (2%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFG--DIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
          LYVG L     +  L  A    G  D+K +K    +A  K + F +V F  +  A    +
Sbjct: 1  LYVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKE 60

Query: 69 NMDGAELYGRVLTVNY 84
           ++G E  G+   V Y
Sbjct: 61 KLEGREFNGKKCVVTY 76

This subfamily corresponds to the RRM of cleavage factor Im (CFIm) subunits. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the regulation of alternative poly(A) site selection, mRNA export, and mRNA splicing. It is a complex composed of a small 25 kDa (CFIm25) subunit and a larger 59/68/72 kDa subunit. Two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. Structurally related CFIm68 and CFIm59, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF7), or cleavage and polyadenylation specificity factor 59 kDa subunit (CPSF59), are functionally redundant. Both contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a central proline-rich region, and a C-terminal RS-like domain. Their N-terminal RRM mediates the interaction with CFIm25, and also serves to enhance RNA binding and facilitate RNA looping. . Length = 76

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

 Score = 34.9 bits (81), Expect = 0.002
 Identities = 22/76 (28%), Positives = 39/76 (51%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
           L VG L  E  +        PFG ++       ++T + + +GFV +  K  A++A + 
Sbjct: 1  LLCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQ 60

Query: 70 MDGAELYGRVLTVNYA 85
          +DG ++ GR L V++A
Sbjct: 61 LDGKQIGGRKLQVDWA 76

This subfamily corresponds to the RRM2 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only. . Length = 77

>gnl|CDD|240684 cd12238, RRM1_RBM40_like, RNA recognition motif 1 in RNA-binding protein 40 (RBM40) and similar proteins

 Score = 34.9 bits (81), Expect = 0.002
 Identities = 21/76 (27%), Positives = 34/76 (44%), Gaps = 3/76 (3%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
          TL V  L  E++E         FG    V+    +   K+ +F   TF  ++ A QA+  
Sbjct: 1  TLLVRHLPPELSEDDKEDLLKHFG-ASSVRVMSRRGKLKNTAF--ATFDNEQAASQALSR 57

Query: 70 MDGAELYGRVLTVNYA 85
          +   ++ G+ L V YA
Sbjct: 58 LHQLKILGKRLVVEYA 73

This subfamily corresponds to the RRM1 of RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein), It serves as a bridging factor between the U11 and U12 snRNPs. It contains two repeats of RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions. . Length = 73

>gnl|CDD|240736 cd12290, RRM1_LARP7, RNA recognition motif 1 in La-related protein 7 (LARP7) and similar proteins

 Score = 35.0 bits (81), Expect = 0.003
 Identities = 17/57 (29%), Positives = 26/57 (45%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
          T+YV  L +      L A F  +G +  V  P  + T   + F F+ F   E+A +A
Sbjct: 1  TVYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKA 57

This subfamily corresponds to the RRM1 of LARP7, also termed La ribonucleoprotein domain family member 7, or P-TEFb-interaction protein for 7SK stability (PIP7S), an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. LARP7 is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP). It intimately associates with all the nuclear 7SK and is required for 7SK stability. LARP7 also acts as a negative transcriptional regulator of cellular and viral polymerase II genes, acting by means of the 7SK snRNP system. It plays an essential role in the inhibition of positive transcription elongation factor b (P-TEFb)-dependent transcription, which has been linked to the global control of cell growth and tumorigenesis. LARP7 contains a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminal region, which mediates binding to the U-rich 3' terminus of 7SK RNA. LARP7 also carries another putative RRM domain at its C-terminus. . Length = 80

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

 Score = 34.8 bits (81), Expect = 0.003
 Identities = 24/89 (26%), Positives = 36/89 (40%), Gaps = 20/89 (22%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDV-KTPLD-----------QATQKHRSFGFVT 56
            LYV  L++ V E  L   F  F D     K   D           QA        FVT
Sbjct: 2  KRLYVKNLSKRVTEEDLVYIFGRFVDSSSEEKNMFDIRLMTEGRMKGQA--------FVT 53

Query: 57 FLEKEDAIQAMDNMDGAELYGRVLTVNYA 85
          F  +E A +A++ ++G  L G+ + + + 
Sbjct: 54 FPSEEIATKALNLVNGYVLKGKPMVIQFG 82

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

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

 Score = 34.8 bits (80), Expect = 0.003
 Identities = 27/81 (33%), Positives = 31/81 (38%), Gaps = 5/81 (6%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGD--IKDVKTPLDQATQKHR---SFGFVTFLEKEDAI 64
          TL+V  L        L  AF          VKT  D           FGFV F  KE A 
Sbjct: 2  TLFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQAQ 61

Query: 65 QAMDNMDGAELYGRVLTVNYA 85
           A+  MDG  L G  L V ++
Sbjct: 62 AALKAMDGFVLDGHTLVVKFS 82

This subfamily corresponds to the RRM4 of MRD1which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 84

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

 Score = 34.5 bits (80), Expect = 0.003
 Identities = 25/74 (33%), Positives = 36/74 (48%), Gaps = 5/74 (6%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDI--KDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
          ++V  L   V    L   F   G++   DVKT  D    + + FG V F   EDA +A++
Sbjct: 1  IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDG---RSKGFGTVLFESPEDAQRAIE 57

Query: 69 NMDGAELYGRVLTV 82
            +G +L GR L V
Sbjct: 58 MFNGYDLEGRELEV 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|241026 cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 34.6 bits (79), Expect = 0.004
 Identities = 17/47 (36%), Positives = 27/47 (57%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTF 57
          ++VGG+ E+  E  L   F  +G I+ ++   D+ + K R F FVTF
Sbjct: 3  IFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTF 49

This subgroup corresponds to the RRM2 of hnRNP A3, a novel RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE) independently of hnRNP A2 and participates in the trafficking of A2RE-containing RNA. hnRNP A3 can shuttle between the nucleus and the cytoplasm. It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

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

 Score = 34.5 bits (80), Expect = 0.004
 Identities = 22/85 (25%), Positives = 32/85 (37%), Gaps = 15/85 (17%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
          NTL+V  L     E  L   F      + +K         ++  G V F+E ED   A  
Sbjct: 3  NTLFVANLGPNTTEEELRQLFSRQPGFRRLKM-------HNKGGGPVCFVEFEDVSFATQ 55

Query: 69 NMDGAELYGRVLTVNYALPERIKGG 93
           +    L G VL+ +       +GG
Sbjct: 56 AL--NSLQGAVLSSS------DRGG 72

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

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

 Score = 34.3 bits (79), Expect = 0.004
 Identities = 17/56 (30%), Positives = 29/56 (51%), Gaps = 1/56 (1%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
          L+VG L  ++ E  L   F  FG++ +V+        +  +FGFV F +  +A+Q 
Sbjct: 6  LFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVF-DDPEAVQK 60

This subfamily corresponds to the RRM domain in the G3BP family of RNA-binding and SH3 domain-binding proteins. G3BP acts at the level of RNA metabolism in response to cell signaling, possibly as RNA transcript stabilizing factors or an RNase. Members include G3BP1, G3BP2 and similar proteins. These proteins associate directly with the SH3 domain of GTPase-activating protein (GAP), which functions as an inhibitor of Ras. They all contain an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing PXXP motif(s), an RNA recognition motif (RRM), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). Length = 81

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	174
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.85
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.84
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.79
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.77
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.75
KOG0122	270	consensus Translation initiation factor 3, subunit	99.74
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.73
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.73
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.71
PLN03213	759	repressor of silencing 3; Provisional	99.69
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.66
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.66
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.66
PLN03120	260	nucleic acid binding protein; Provisional	99.65
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.64
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.64
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.64
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.63
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.63
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.62
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.62
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.61
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.6
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.6
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.6
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.59
smart00362	72	RRM_2 RNA recognition motif.	99.59
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.59
PLN03121	243	nucleic acid binding protein; Provisional	99.58
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.58
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.57
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.57
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.57
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.57
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.57
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.55
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.55
smart00360	71	RRM RNA recognition motif.	99.53
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.53
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.51
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.51
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.51
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.5
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.5
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	99.48
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.46
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.46
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.46
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.44
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.44
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.42
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.39
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.38
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.38
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.37
smart00361	70	RRM_1 RNA recognition motif.	99.37
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	99.32
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	99.31
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.28
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.28
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	99.27
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.26
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.26
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.24
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	99.2
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.19
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.17
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.14
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.12
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.08
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.05
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.04
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.0
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.99
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	98.98
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.96
KOG0226	290	consensus RNA-binding proteins [General function p	98.94
KOG1548	382	consensus Transcription elongation factor TAT-SF1	98.94
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.94
KOG0151	877	consensus Predicted splicing regulator, contains R	98.93
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.91
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.91
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.9
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.9
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.75
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.61
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	98.52
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	98.41
KOG3152	278	consensus TBP-binding protein, activator of basal	98.35
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.3
KOG1995	351	consensus Conserved Zn-finger protein [General fun	98.28
KOG4210	285	consensus Nuclear localization sequence binding pr	98.21
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	98.19
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.18
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.18
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	98.17
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	98.05
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.03
COG5175	480	MOT2 Transcriptional repressor [Transcription]	98.01
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.0
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	97.93
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.9
KOG2314	698	consensus Translation initiation factor 3, subunit	97.88
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	97.83
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	97.72
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	97.71
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.7
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.69
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	97.63
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	97.55
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	97.54
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	97.5
KOG1855	484	consensus Predicted RNA-binding protein [General f	97.46
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	97.45
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	97.42
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	97.42
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	97.41
KOG1548	382	consensus Transcription elongation factor TAT-SF1	97.41
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	97.28
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.25
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	97.11
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	97.05
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	96.77
KOG1996	378	consensus mRNA splicing factor [RNA processing and	96.76
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	96.74
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	96.62
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	96.59
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	96.52
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	96.47
KOG2135	526	consensus Proteins containing the RNA recognition	96.22
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	96.08
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	95.98
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	95.88
KOG4660	549	consensus Protein Mei2, essential for commitment t	95.81
KOG2068	327	consensus MOT2 transcription factor [Transcription	95.65
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	95.54
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	95.25
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	95.25
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	95.02
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	94.59
KOG2318	650	consensus Uncharacterized conserved protein [Funct	92.13
KOG2591	684	consensus c-Mpl binding protein, contains La domai	91.74
KOG4210	285	consensus Nuclear localization sequence binding pr	91.72
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	91.3
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	88.85
KOG4008	261	consensus rRNA processing protein RRP7 [RNA proces	85.4
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	83.61
KOG4410	396	consensus 5-formyltetrahydrofolate cyclo-ligase [C	82.46
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	81.75
KOG4019	193	consensus Calcineurin-mediated signaling pathway i	80.32

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

Probab=99.85  E-value=2e-21  Score=143.12  Aligned_cols=159  Identities=51%  Similarity=0.842  Sum_probs=123.8

Q ss_pred             CCCCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEe
Q 030632            5 AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNY   84 (174)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~   84 (174)
                      ....+|||||+|...+++..|...|-+||.|..|.++.+..++++||||||+|...++|..||..||+..+.||+|+|.+
T Consensus         7 a~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~   86 (298)
T KOG0111|consen    7 ANQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNL   86 (298)
T ss_pred             cccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEee
Confidence            35689999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCCCCCCCCCCCCccccchhHHHHHHHHHHH------HHHHHHHHH-HHHHHHHHHHhhhhhhcccCcccccCCCCC
Q 030632           85 ALPERIKGGEQGWAAQPIWADADTWFERQQQEEE------MQRLQAENR-AAMQAAEELHRKKMAEDREGEKEEDSEMKD  157 (174)
Q Consensus        85 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~e~e~~~~~~~  157 (174)
                      ++|.+-+.+    +..|.|.+ +.|++++.-+..      ..+.+.+.. ..+...............-+.-...-.-+-
T Consensus        87 AkP~kikeg----sqkPvWAD-DdWlkk~~g~~q~E~e~eaeK~et~s~kaa~~~pqv~~~ikig~~~~Gri~~~lrtdv  161 (298)
T KOG0111|consen   87 AKPEKIKEG----SQKPVWAD-DDWLKKQQGEAQAEKEIEAEKAETESKKAAMENPQVYHDIKIGEDRAGRIVMLLRTDV  161 (298)
T ss_pred             cCCccccCC----CCCCcccC-cHHHHHhccccccccccchhhhcCccchhhhhChHhhhheeecccccceEEEeecccC
Confidence            999877654    45999999 999999872111      112222222 222233333334444444455555666677


Q ss_pred             ChhhHHHHHHh
Q 030632          158 DPMARAEAEVL  168 (174)
Q Consensus       158 ~~~~~~~~~~~  168 (174)
                      .||.......|
T Consensus       162 ~Pmtaenfr~L  172 (298)
T KOG0111|consen  162 VPMTAENFRCL  172 (298)
T ss_pred             Chhhhhhhhhh
Confidence            88888777665

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

Probab=99.84  E-value=9e-20  Score=129.91  Aligned_cols=86  Identities=38%  Similarity=0.616  Sum_probs=80.7

Q ss_pred             CCCCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEe
Q 030632            5 AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNY   84 (174)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~   84 (174)
                      ...+++|||+|||+.+++.+|+.+|.+||.|..|.++.++.++.++|||||+|.+.++|..||..||+..|.|++|+|.+
T Consensus        31 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~  110 (144)
T PLN03134         31 RLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNP  110 (144)
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            34578999999999999999999999999999999999998999999999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 030632           85 ALPERI   90 (174)
Q Consensus        85 a~~~~~   90 (174)
                      +.++..
T Consensus       111 a~~~~~  116 (144)
T PLN03134        111 ANDRPS  116 (144)
T ss_pred             CCcCCC
Confidence            976543

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.79  E-value=1.3e-18  Score=140.38  Aligned_cols=83  Identities=28%  Similarity=0.500  Sum_probs=78.6

Q ss_pred             CCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEeec
Q 030632            7 QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYAL   86 (174)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a~   86 (174)
                      .+.+|||+|||+.+++.+|+.+|++||.|..|+|++++.+|.++|||||.|.+.++|..||..|||..|.|+.|+|.|+.
T Consensus       268 ~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~  347 (352)
T TIGR01661       268 AGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKT  347 (352)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcc
Confidence            34579999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             CCC
Q 030632           87 PER   89 (174)
Q Consensus        87 ~~~   89 (174)
                      .+.
T Consensus       348 ~~~  350 (352)
T TIGR01661       348 NKA  350 (352)
T ss_pred             CCC
Confidence            653

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

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

Probab=99.77  E-value=7.3e-19  Score=143.79  Aligned_cols=85  Identities=27%  Similarity=0.458  Sum_probs=78.9

Q ss_pred             CCCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEee
Q 030632            6 VQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYA   85 (174)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a   85 (174)
                      .+.++|+|+|||+.|...+|+.+|+.||.|..|.|++.+ .|+.+|||||.|....+|..|++.||+..|.||+|.|.||
T Consensus       115 ~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~-dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWA  193 (678)
T KOG0127|consen  115 LPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKK-DGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWA  193 (678)
T ss_pred             CccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCC-CCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeee
Confidence            357899999999999999999999999999999999888 6667799999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 030632           86 LPERIK   91 (174)
Q Consensus        86 ~~~~~~   91 (174)
                      .++..+
T Consensus       194 V~Kd~y  199 (678)
T KOG0127|consen  194 VDKDTY  199 (678)
T ss_pred             cccccc
Confidence            877554

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.75  E-value=5.9e-18  Score=136.66  Aligned_cols=84  Identities=27%  Similarity=0.504  Sum_probs=80.2

Q ss_pred             CCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEeec
Q 030632            7 QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYAL   86 (174)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a~   86 (174)
                      +.++|||+|||+.+++.+|+.+|+.||+|..|.|++++.+|.++|||||+|.+.++|.+||..|||..|.|++|.|.++.
T Consensus         2 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a~   81 (352)
T TIGR01661         2 SKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYAR   81 (352)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeec
Confidence            57899999999999999999999999999999999998899999999999999999999999999999999999999998


Q ss_pred             CCCC
Q 030632           87 PERI   90 (174)
Q Consensus        87 ~~~~   90 (174)
                      |...
T Consensus        82 ~~~~   85 (352)
T TIGR01661        82 PSSD   85 (352)
T ss_pred             cccc
Confidence            7654

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

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

Probab=99.74  E-value=1.6e-17  Score=124.16  Aligned_cols=83  Identities=31%  Similarity=0.509  Sum_probs=80.0

Q ss_pred             CCCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEee
Q 030632            6 VQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYA   85 (174)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a   85 (174)
                      ...++|-|.|||..+++.+|..+|.+||.|..|.|.+++.||.++|||||.|.++++|.+||..|||+-+.+-.|+|.|+
T Consensus       187 ~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEws  266 (270)
T KOG0122|consen  187 DDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEWS  266 (270)
T ss_pred             CccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEec
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCC
Q 030632           86 LPE   88 (174)
Q Consensus        86 ~~~   88 (174)
                      +|+
T Consensus       267 kP~  269 (270)
T KOG0122|consen  267 KPS  269 (270)
T ss_pred             CCC
Confidence            986

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.73  E-value=2.3e-17  Score=132.83  Aligned_cols=85  Identities=26%  Similarity=0.375  Sum_probs=80.2

Q ss_pred             CCCCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEe
Q 030632            5 AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNY   84 (174)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~   84 (174)
                      ....++|||+|||+.+++++|+.+|..||.|..|.|++++.+++++|||||+|.+.++|.+||..||+..|.+++|+|.+
T Consensus       104 ~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~~  183 (346)
T TIGR01659       104 NNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSY  183 (346)
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeeec
Confidence            34678999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ecCCC
Q 030632           85 ALPER   89 (174)
Q Consensus        85 a~~~~   89 (174)
                      +.+..
T Consensus       184 a~p~~  188 (346)
T TIGR01659       184 ARPGG  188 (346)
T ss_pred             ccccc
Confidence            87643

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).

>PF00076 RRM_1: RNA recognition motif

Probab=99.73  E-value=2.7e-17  Score=102.48  Aligned_cols=70  Identities=34%  Similarity=0.656  Sum_probs=66.8

Q ss_pred             EEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEE
Q 030632           11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLT   81 (174)
Q Consensus        11 l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~   81 (174)
                      |||+|||+.+++.+|+.+|+.||.|..+.+..+ .++..+|+|||.|.+.++|..|+..|+|..+.|++|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~-~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRN-SSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEE-TTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhccccccccc-ccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            799999999999999999999999999999887 4889999999999999999999999999999999986

(a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....

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

Probab=99.71  E-value=2.4e-17  Score=112.08  Aligned_cols=81  Identities=26%  Similarity=0.443  Sum_probs=76.8

Q ss_pred             CCCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEee
Q 030632            6 VQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYA   85 (174)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a   85 (174)
                      ..++|||||||++.++++.|.++|+.+|.|..|.+-.++.+..+.|||||.|.+.++|..|++.++|+.+..++|+|.|-
T Consensus        34 r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D  113 (153)
T KOG0121|consen   34 RKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWD  113 (153)
T ss_pred             hhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeecc
Confidence            35789999999999999999999999999999999888888889999999999999999999999999999999999985


Q ss_pred             c
Q 030632           86 L   86 (174)
Q Consensus        86 ~   86 (174)
                      -
T Consensus       114 ~  114 (153)
T KOG0121|consen  114 A  114 (153)
T ss_pred             c
Confidence            4

>PLN03213 repressor of silencing 3; Provisional

Probab=99.69  E-value=2.5e-16  Score=128.01  Aligned_cols=91  Identities=25%  Similarity=0.370  Sum_probs=80.1

Q ss_pred             CCCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCH--HHHHHHHHhcCCceecCeEEEEE
Q 030632            6 VQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEK--EDAIQAMDNMDGAELYGRVLTVN   83 (174)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~--~~a~~al~~l~g~~~~g~~l~V~   83 (174)
                      ..+.+||||||++.+++.+|+.+|+.||.|..|.|++.  +|  ||||||+|...  ..+.+||..|||..+.|+.|+|.
T Consensus         8 ~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRE--TG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVN   83 (759)
T PLN03213          8 GGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRT--KG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLE   83 (759)
T ss_pred             CcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecc--cC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEe
Confidence            45679999999999999999999999999999999944  66  99999999987  78999999999999999999999


Q ss_pred             eecCCCCCCCCCCCCCCccccchhHHHHHHHHHHHHH
Q 030632           84 YALPERIKGGEQGWAAQPIWADADTWFERQQQEEEMQ  120 (174)
Q Consensus        84 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  120 (174)
                      .|+                    ..|+.+.+++....
T Consensus        84 KAK--------------------P~YLeRLkrEReea  100 (759)
T PLN03213         84 KAK--------------------EHYLARLKREWEAA  100 (759)
T ss_pred             ecc--------------------HHHHHHHHHHHHHh
Confidence            986                    56777776655443

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

Probab=99.66  E-value=5e-16  Score=131.93  Aligned_cols=82  Identities=21%  Similarity=0.428  Sum_probs=78.0

Q ss_pred             CCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEeec
Q 030632            7 QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYAL   86 (174)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a~   86 (174)
                      ..++|||+|||+.+++++|+.+|+.||.|..|.|++++.++.++|||||.|.+.++|..||..||+..|+|+.|+|.++.
T Consensus       203 ~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi  282 (612)
T TIGR01645       203 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCV  282 (612)
T ss_pred             ccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecC
Confidence            35799999999999999999999999999999999999889999999999999999999999999999999999999987


Q ss_pred             CC
Q 030632           87 PE   88 (174)
Q Consensus        87 ~~   88 (174)
                      +.
T Consensus       283 ~p  284 (612)
T TIGR01645       283 TP  284 (612)
T ss_pred             CC
Confidence            53

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.

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.66  E-value=9.6e-16  Score=95.89  Aligned_cols=70  Identities=31%  Similarity=0.563  Sum_probs=64.8

Q ss_pred             EEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEE
Q 030632           11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLT   81 (174)
Q Consensus        11 l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~   81 (174)
                      |||+|||+.++..+|..+|..||.|..+.+..++. +..+|+|||+|.+.++|..|+..+++..|+|+.|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~-~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKD-GQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTT-SSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeec-cccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            79999999999999999999999999999999885 88999999999999999999999999999999874

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 ....

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

Probab=99.66  E-value=5e-16  Score=110.94  Aligned_cols=80  Identities=25%  Similarity=0.441  Sum_probs=73.4

Q ss_pred             CCCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEee
Q 030632            6 VQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYA   85 (174)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a   85 (174)
                      +-.++||||||+..++..+|..+|..||.|..|.|-.+     +.|||||+|.++.+|..|+..|+|..|.|..|+|..+
T Consensus         8 ~~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn-----PPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S   82 (195)
T KOG0107|consen    8 NGNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARN-----PPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELS   82 (195)
T ss_pred             CCCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeec-----CCCceEEeccCcccHHHHHhhcCCccccCceEEEEee
Confidence            34789999999999999999999999999999988665     4799999999999999999999999999999999998


Q ss_pred             cCCCC
Q 030632           86 LPERI   90 (174)
Q Consensus        86 ~~~~~   90 (174)
                      .....
T Consensus        83 ~G~~r   87 (195)
T KOG0107|consen   83 TGRPR   87 (195)
T ss_pred             cCCcc
Confidence            76544

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.65  E-value=8.3e-16  Score=117.54  Aligned_cols=76  Identities=22%  Similarity=0.295  Sum_probs=70.6

Q ss_pred             CCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEeecC
Q 030632            8 KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYALP   87 (174)
Q Consensus         8 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a~~   87 (174)
                      .++|||+|||+.+++.+|+.+|+.||.|..|.|+.++   ..+|||||+|.+...|..||. |||..|.|+.|.|.++..
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~---~~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~   79 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSEN---ERSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAED   79 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecC---CCCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccC
Confidence            5799999999999999999999999999999998875   357999999999999999995 999999999999999863

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

Probab=99.64  E-value=7.1e-16  Score=130.98  Aligned_cols=81  Identities=36%  Similarity=0.556  Sum_probs=76.7

Q ss_pred             CCCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEee
Q 030632            6 VQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYA   85 (174)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a   85 (174)
                      ...++|||||||+.+++.+|+.+|.+||.|.+|.++.++.+|+++|||||+|.+.+.|.+|+..|||..|.|+.|+|.+.
T Consensus       105 ~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp  184 (612)
T TIGR01645       105 AIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRP  184 (612)
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeeccc
Confidence            34679999999999999999999999999999999999999999999999999999999999999999999999999864


Q ss_pred             c
Q 030632           86 L   86 (174)
Q Consensus        86 ~   86 (174)
                      .
T Consensus       185 ~  185 (612)
T TIGR01645       185 S  185 (612)
T ss_pred             c
Confidence            3

In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.64  E-value=1.7e-15  Score=122.05  Aligned_cols=82  Identities=27%  Similarity=0.403  Sum_probs=76.3

Q ss_pred             CCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecC--eEEEEEe
Q 030632            7 QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYG--RVLTVNY   84 (174)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g--~~l~V~~   84 (174)
                      ..++|||+|||+.+++++|+.+|++||.|..|.|++++.++.++|||||+|.+.++|.+||..||+..+.+  ++|+|.+
T Consensus       192 ~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~  271 (346)
T TIGR01659       192 KDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRL  271 (346)
T ss_pred             ccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEE
Confidence            46789999999999999999999999999999999998899999999999999999999999999998865  7899999


Q ss_pred             ecCC
Q 030632           85 ALPE   88 (174)
Q Consensus        85 a~~~   88 (174)
                      +...
T Consensus       272 a~~~  275 (346)
T TIGR01659       272 AEEH  275 (346)
T ss_pred             CCcc
Confidence            8753

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).

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

Probab=99.64  E-value=4.2e-17  Score=117.12  Aligned_cols=80  Identities=29%  Similarity=0.590  Sum_probs=75.9

Q ss_pred             CCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEeec
Q 030632            7 QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYAL   86 (174)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a~   86 (174)
                      .+.-|||||||+..|+.+|.-+|++||.|..|.++++..||+++||||+.|.+..+...|+..|||..|.||.|+|....
T Consensus        34 dsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv~  113 (219)
T KOG0126|consen   34 DSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHVS  113 (219)
T ss_pred             cceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeecc
Confidence            35679999999999999999999999999999999999999999999999999999999999999999999999998753

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

Probab=99.63  E-value=2.9e-15  Score=116.24  Aligned_cols=80  Identities=29%  Similarity=0.430  Sum_probs=74.5

Q ss_pred             CCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEeec
Q 030632            7 QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYAL   86 (174)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a~   86 (174)
                      -.++|+|.|||+.+.+-||+.+|.+||.|.+|.|+.+  ...++|||||+|.+.++|.+|-..|||..+.||+|.|..+.
T Consensus        95 ~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfN--ERGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~AT  172 (376)
T KOG0125|consen   95 TPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFN--ERGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNAT  172 (376)
T ss_pred             CCceeEeecCCccccCccHHHHHHhhCceeeEEEEec--cCCCCccceEEecChhhHHHHHHHhhcceeeceEEEEeccc
Confidence            3579999999999999999999999999999998877  45689999999999999999999999999999999999987


Q ss_pred             CC
Q 030632           87 PE   88 (174)
Q Consensus        87 ~~   88 (174)
                      ++
T Consensus       173 ar  174 (376)
T KOG0125|consen  173 AR  174 (376)
T ss_pred             hh
Confidence            65

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

Probab=99.63  E-value=6.8e-16  Score=114.97  Aligned_cols=78  Identities=32%  Similarity=0.500  Sum_probs=71.3

Q ss_pred             CCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEeec
Q 030632            8 KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYAL   86 (174)
Q Consensus         8 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a~   86 (174)
                      -++||||||+|.+..+.|+.+|.+||.|.+..|+.++.+|+++|||||+|.+.+.|.+|++- ..-.|.||+..+..|.
T Consensus        12 ~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNcnlA~   89 (247)
T KOG0149|consen   12 FTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKANCNLAS   89 (247)
T ss_pred             EEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC-CCCcccccccccchhh
Confidence            45899999999999999999999999999999999999999999999999999999999986 4467899998777653

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

Probab=99.62  E-value=4.3e-15  Score=125.49  Aligned_cols=82  Identities=22%  Similarity=0.338  Sum_probs=77.6

Q ss_pred             CCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEeec
Q 030632            7 QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYAL   86 (174)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a~   86 (174)
                      +.++|||+|||+.+++.+|+.+|..||.|..+.|+.++.+|.++|||||+|.+...|..||..|||..|.|+.|.|.++.
T Consensus       294 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~  373 (509)
T TIGR01642       294 SKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRAC  373 (509)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECc
Confidence            45799999999999999999999999999999999998899999999999999999999999999999999999999986


Q ss_pred             CC
Q 030632           87 PE   88 (174)
Q Consensus        87 ~~   88 (174)
                      ..
T Consensus       374 ~~  375 (509)
T TIGR01642       374 VG  375 (509)
T ss_pred             cC
Confidence            43

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

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

Probab=99.62  E-value=3.4e-15  Score=124.56  Aligned_cols=80  Identities=41%  Similarity=0.679  Sum_probs=76.8

Q ss_pred             CCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEeec
Q 030632            7 QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYAL   86 (174)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a~   86 (174)
                      ..++|||+|||+.+++.+|+.+|+.||.|..|.++.++.+|.++|||||+|.+.+.|..|+..|||..|.|++|.|.|+.
T Consensus       185 ~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~  264 (457)
T TIGR01622       185 NFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQ  264 (457)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEcc
Confidence            36899999999999999999999999999999999998888999999999999999999999999999999999999976

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

Probab=99.61  E-value=3.9e-15  Score=112.99  Aligned_cols=79  Identities=28%  Similarity=0.565  Sum_probs=73.8

Q ss_pred             CCCCCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEE
Q 030632            4 LAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVN   83 (174)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~   83 (174)
                      +++.+++||||||+.-++++.|+..|++||.|.+|++..+      +||+||.|.+.+.|..||..+|+..|.|..+++.
T Consensus       160 ssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~------qGYaFVrF~tkEaAahAIv~mNntei~G~~VkCs  233 (321)
T KOG0148|consen  160 SSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD------QGYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCS  233 (321)
T ss_pred             CCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc------cceEEEEecchhhHHHHHHHhcCceeCceEEEEe
Confidence            4677899999999999999999999999999999999866      5899999999999999999999999999999999


Q ss_pred             eecCC
Q 030632           84 YALPE   88 (174)
Q Consensus        84 ~a~~~   88 (174)
                      |.+..
T Consensus       234 WGKe~  238 (321)
T KOG0148|consen  234 WGKEG  238 (321)
T ss_pred             ccccC
Confidence            98743

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

Probab=99.60  E-value=4.9e-15  Score=113.72  Aligned_cols=82  Identities=26%  Similarity=0.433  Sum_probs=78.3

Q ss_pred             CCCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEee
Q 030632            6 VQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYA   85 (174)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a   85 (174)
                      .|-+||||+.|+..+++..|+..|..||.|..|.|+++..||+++|||||+|....+...|.+..+|..|.|+.|.|.+-
T Consensus        99 DPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDvE  178 (335)
T KOG0113|consen   99 DPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDVE  178 (335)
T ss_pred             CccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEec
Confidence            56789999999999999999999999999999999999999999999999999999999999999999999999999886


Q ss_pred             cC
Q 030632           86 LP   87 (174)
Q Consensus        86 ~~   87 (174)
                      ..
T Consensus       179 Rg  180 (335)
T KOG0113|consen  179 RG  180 (335)
T ss_pred             cc
Confidence            43

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

Probab=99.60  E-value=5.8e-15  Score=126.25  Aligned_cols=78  Identities=32%  Similarity=0.558  Sum_probs=75.3

Q ss_pred             EEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEeecC
Q 030632           10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYALP   87 (174)
Q Consensus        10 ~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a~~   87 (174)
                      +|||||||+++++.+|+.+|+.||.|..|+|.++..+++++|||||+|.+.++|.+|+..||+..|.|+.|+|.|+..
T Consensus         2 sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~   79 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQR   79 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeecccc
Confidence            799999999999999999999999999999999998899999999999999999999999999999999999999864

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

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

Probab=99.60  E-value=7.2e-15  Score=111.16  Aligned_cols=116  Identities=22%  Similarity=0.335  Sum_probs=95.1

Q ss_pred             CCCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEee
Q 030632            6 VQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYA   85 (174)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a   85 (174)
                      ...++|+|.-||..+|.++|+.+|...|+|.+|.+++++.+|.+.||+||.|..+.+|++|+..|||..+..++|+|.|+
T Consensus        39 ~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSyA  118 (360)
T KOG0145|consen   39 ESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSYA  118 (360)
T ss_pred             cccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEec
Confidence            34578999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCCCC-----CCCCCCccccchhHHHHHHHHHHHHHH
Q 030632           86 LPERIKGGE-----QGWAAQPIWADADTWFERQQQEEEMQR  121 (174)
Q Consensus        86 ~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~  121 (174)
                      +|....-..     .+........+.+..+..+.+--..+-
T Consensus       119 RPSs~~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRi  159 (360)
T KOG0145|consen  119 RPSSDSIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRI  159 (360)
T ss_pred             cCChhhhcccceEEecCCccchHHHHHHHHHHhhhhhhhhh
Confidence            987653222     223333344455566666665544333

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

Probab=99.59  E-value=2.4e-15  Score=108.12  Aligned_cols=83  Identities=41%  Similarity=0.620  Sum_probs=79.5

Q ss_pred             CCCCCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEE
Q 030632            4 LAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVN   83 (174)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~   83 (174)
                      ..+...|||||||+..+++..|.++|-+.|+|..+.+++++.+...+||||++|.+.++|.-|++.||...+.|++|+|.
T Consensus         5 ~rnqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~   84 (203)
T KOG0131|consen    5 ERNQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVN   84 (203)
T ss_pred             ccCCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEE
Confidence            45677899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eec
Q 030632           84 YAL   86 (174)
Q Consensus        84 ~a~   86 (174)
                      .+.
T Consensus        85 kas   87 (203)
T KOG0131|consen   85 KAS   87 (203)
T ss_pred             ecc
Confidence            886

>smart00362 RRM_2 RNA recognition motif

Probab=99.59  E-value=1.4e-14  Score=89.66  Aligned_cols=72  Identities=43%  Similarity=0.701  Sum_probs=67.2

Q ss_pred             EEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEE
Q 030632           10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVN   83 (174)
Q Consensus        10 ~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~   83 (174)
                      +|||+|||+.++..+|+.+|..||.|..+.+..++  +.++|+|||+|.+...|..|+..+++..+.|++|.|.
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT--GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC--CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            58999999999999999999999999999988775  6788999999999999999999999999999998873

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

Probab=99.59  E-value=4.1e-15  Score=102.18  Aligned_cols=84  Identities=27%  Similarity=0.533  Sum_probs=79.4

Q ss_pred             CCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEeec
Q 030632            7 QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYAL   86 (174)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a~   86 (174)
                      .++.|||.++...+++++|...|..||.|+.+.+..++.||..+|||+|+|.+...|+.|+..|||..|.|.+|.|.|+.
T Consensus        71 EGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~F  150 (170)
T KOG0130|consen   71 EGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWCF  150 (170)
T ss_pred             eeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEEE
Confidence            46889999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             CCCC
Q 030632           87 PERI   90 (174)
Q Consensus        87 ~~~~   90 (174)
                      .+.+
T Consensus       151 v~gp  154 (170)
T KOG0130|consen  151 VKGP  154 (170)
T ss_pred             ecCC
Confidence            5443

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.58  E-value=1.5e-14  Score=109.24  Aligned_cols=77  Identities=18%  Similarity=0.134  Sum_probs=69.9

Q ss_pred             CCCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEee
Q 030632            6 VQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYA   85 (174)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a   85 (174)
                      +.+++|||+||++.+++.+|+.+|+.||.|..|.|+++.   ...|||||+|.+...+..|+ .|+|..|.+++|.|...
T Consensus         3 ~~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~---et~gfAfVtF~d~~aaetAl-lLnGa~l~d~~I~It~~   78 (243)
T PLN03121          3 PGGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG---EYACTAYVTFKDAYALETAV-LLSGATIVDQRVCITRW   78 (243)
T ss_pred             CCceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC---CcceEEEEEECCHHHHHHHH-hcCCCeeCCceEEEEeC
Confidence            457899999999999999999999999999999999874   45589999999999999999 58999999999999764


Q ss_pred             c
Q 030632           86 L   86 (174)
Q Consensus        86 ~   86 (174)
                      .
T Consensus        79 ~   79 (243)
T PLN03121         79 G   79 (243)
T ss_pred             c
Confidence            3

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

Probab=99.58  E-value=1.1e-14  Score=124.62  Aligned_cols=82  Identities=35%  Similarity=0.503  Sum_probs=77.1

Q ss_pred             CCCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEee
Q 030632            6 VQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYA   85 (174)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a   85 (174)
                      ..+++|||+||++.+++++|+.+|+.||.|..|.++.+. +|.++|||||.|.+.++|.+|+..|||..|.|++|.|.++
T Consensus       283 ~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d~-~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a  361 (562)
T TIGR01628       283 AQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDE-KGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALA  361 (562)
T ss_pred             cCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEECC-CCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEec
Confidence            456789999999999999999999999999999999984 8999999999999999999999999999999999999998


Q ss_pred             cCC
Q 030632           86 LPE   88 (174)
Q Consensus        86 ~~~   88 (174)
                      ..+
T Consensus       362 ~~k  364 (562)
T TIGR01628       362 QRK  364 (562)
T ss_pred             cCc
Confidence            754

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

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

Probab=99.57  E-value=8.4e-15  Score=111.18  Aligned_cols=82  Identities=37%  Similarity=0.618  Sum_probs=78.2

Q ss_pred             CCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEeecC
Q 030632            8 KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYALP   87 (174)
Q Consensus         8 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a~~   87 (174)
                      ...+||+-|.+.++-+.|+..|.+||.|..++|+++..|++++||+||.|....+|+.||..|||.-|++|.|+-.||..
T Consensus        62 hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATR  141 (321)
T KOG0148|consen   62 HFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATR  141 (321)
T ss_pred             ceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeecccccc
Confidence            44799999999999999999999999999999999999999999999999999999999999999999999999999975


Q ss_pred             CC
Q 030632           88 ER   89 (174)
Q Consensus        88 ~~   89 (174)
                      +.
T Consensus       142 Kp  143 (321)
T KOG0148|consen  142 KP  143 (321)
T ss_pred             Cc
Confidence            54

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

Probab=99.57  E-value=5e-14  Score=92.62  Aligned_cols=78  Identities=26%  Similarity=0.423  Sum_probs=71.2

Q ss_pred             CCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEeecC
Q 030632            8 KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYALP   87 (174)
Q Consensus         8 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a~~   87 (174)
                      ++-|||+|||+++|.++...+|.+||.|..|+|-..+   ..+|-|||+|.+..+|.+|+.+|+|..+.++.|.|-+..|
T Consensus        18 nriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k---~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq~   94 (124)
T KOG0114|consen   18 NRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTK---ETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQP   94 (124)
T ss_pred             heeEEEecCCccccHHHHHHHhhcccceEEEEecCcc---CcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecCH
Confidence            5789999999999999999999999999999985543   5689999999999999999999999999999999998754


Q ss_pred             C
Q 030632           88 E   88 (174)
Q Consensus        88 ~   88 (174)
                      .
T Consensus        95 ~   95 (124)
T KOG0114|consen   95 E   95 (124)
T ss_pred             H
Confidence            3

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

Probab=99.57  E-value=1.8e-14  Score=120.25  Aligned_cols=80  Identities=26%  Similarity=0.443  Sum_probs=75.5

Q ss_pred             CCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEeec
Q 030632            7 QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYAL   86 (174)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a~   86 (174)
                      +.++|||+|||+.+++.+|+.+|+.||.|..|.|+.++.++.++|||||+|.+.++|.+||. |+|..|.|++|.|.++.
T Consensus        88 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~~~~  166 (457)
T TIGR01622        88 DDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQSSQ  166 (457)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEeecc
Confidence            46799999999999999999999999999999999998899999999999999999999996 89999999999998865


Q ss_pred             C
Q 030632           87 P   87 (174)
Q Consensus        87 ~   87 (174)
                      .
T Consensus       167 ~  167 (457)
T TIGR01622       167 A  167 (457)
T ss_pred             h
Confidence            4

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.

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

Probab=99.57  E-value=1.3e-14  Score=116.55  Aligned_cols=84  Identities=26%  Similarity=0.460  Sum_probs=78.9

Q ss_pred             CCCCCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceec-CeEEEE
Q 030632            4 LAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELY-GRVLTV   82 (174)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~-g~~l~V   82 (174)
                      .++.++-||||.||..+.+.+|.-+|.+.|.|-.++|+.++.+|.+||||||+|.+.+.|+.||+.||++.|. |+.|.|
T Consensus        79 ~p~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igv  158 (506)
T KOG0117|consen   79 PPPRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGV  158 (506)
T ss_pred             CCCCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEE
Confidence            4567899999999999999999999999999999999999999999999999999999999999999999987 899999


Q ss_pred             EeecC
Q 030632           83 NYALP   87 (174)
Q Consensus        83 ~~a~~   87 (174)
                      +.+..
T Consensus       159 c~Sva  163 (506)
T KOG0117|consen  159 CVSVA  163 (506)
T ss_pred             EEeee
Confidence            88753

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

Probab=99.57  E-value=3.8e-15  Score=109.11  Aligned_cols=78  Identities=40%  Similarity=0.562  Sum_probs=75.6

Q ss_pred             CEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEeec
Q 030632            9 NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYAL   86 (174)
Q Consensus         9 ~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a~   86 (174)
                      .+|-|-||.+-++.++|+.+|.+||.|-.|.|++++.|+.++|||||.|....+|+.|+..|+|..|.|+.|+|.+|+
T Consensus        14 ~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~ar   91 (256)
T KOG4207|consen   14 TSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMAR   91 (256)
T ss_pred             eeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehhhh
Confidence            578999999999999999999999999999999999999999999999999999999999999999999999998876

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

Probab=99.55  E-value=1.7e-14  Score=122.39  Aligned_cols=81  Identities=27%  Similarity=0.452  Sum_probs=73.9

Q ss_pred             CCCCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceec-CeEEEEE
Q 030632            5 AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELY-GRVLTVN   83 (174)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~-g~~l~V~   83 (174)
                      +...++|||+|||+.+++++|+.+|++||.|..|+|+++ .+|.++|||||+|.+.++|.+||..||+..|. |+.|.|.
T Consensus        55 p~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~  133 (578)
T TIGR01648        55 PGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVC  133 (578)
T ss_pred             CCCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC-CCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCcccccc
Confidence            344689999999999999999999999999999999999 59999999999999999999999999999886 7888777


Q ss_pred             eec
Q 030632           84 YAL   86 (174)
Q Consensus        84 ~a~   86 (174)
                      ++.
T Consensus       134 ~S~  136 (578)
T TIGR01648       134 ISV  136 (578)
T ss_pred             ccc
Confidence            654

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.

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

Probab=99.55  E-value=2.9e-14  Score=109.52  Aligned_cols=80  Identities=43%  Similarity=0.645  Sum_probs=76.7

Q ss_pred             CCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEeecC
Q 030632            8 KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYALP   87 (174)
Q Consensus         8 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a~~   87 (174)
                      .++|||+|||+.+++.+|+.+|..||.|..+.+..++.++.++|||||.|.+...|..|+..++|..|.|++|.|.++.+
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~~  194 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQP  194 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeecccc
Confidence            59999999999999999999999999999999999988999999999999999999999999999999999999999653

>smart00360 RRM RNA recognition motif

Probab=99.53  E-value=5.1e-14  Score=86.68  Aligned_cols=71  Identities=41%  Similarity=0.649  Sum_probs=66.5

Q ss_pred             EcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEE
Q 030632           13 VGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVN   83 (174)
Q Consensus        13 V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~   83 (174)
                      |+|||..++..+|+.+|..||.|..+.+..++.++.++|+|||+|.+.+.|..|+..|++..+.|+.|.|.
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            68999999999999999999999999998887778899999999999999999999999999999998873

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

Probab=99.53  E-value=5.9e-15  Score=118.14  Aligned_cols=86  Identities=29%  Similarity=0.476  Sum_probs=78.3

Q ss_pred             CCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCce-ec--CeEEEEE
Q 030632            7 QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAE-LY--GRVLTVN   83 (174)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~-~~--g~~l~V~   83 (174)
                      ..++||||.|+..+++.+++.+|++||.|..|.|.+++ .+.+||||||.|.+++.|..||+.|||.. +.  ..+|.|+
T Consensus       123 ~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~-~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVk  201 (510)
T KOG0144|consen  123 EERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDP-DGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVK  201 (510)
T ss_pred             cchhhhhhhccccccHHHHHHHHHhhCccchhhheecc-cccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEE
Confidence            46789999999999999999999999999999999998 88999999999999999999999999964 44  5789999


Q ss_pred             eecCCCCCCC
Q 030632           84 YALPERIKGG   93 (174)
Q Consensus        84 ~a~~~~~~~~   93 (174)
                      ||.+++.+..
T Consensus       202 FADtqkdk~~  211 (510)
T KOG0144|consen  202 FADTQKDKDG  211 (510)
T ss_pred             ecccCCCchH
Confidence            9998876643

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

Probab=99.51  E-value=6e-14  Score=101.34  Aligned_cols=80  Identities=25%  Similarity=0.440  Sum_probs=72.2

Q ss_pred             CCCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEee
Q 030632            6 VQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYA   85 (174)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a   85 (174)
                      ...++|||||||..+.+.+|..+|.+||.|..|.|...+   ...+||||+|.+..+|+.||..-+|+.+.|.+|+|.++
T Consensus         4 r~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~---g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfp   80 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRP---GPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFP   80 (241)
T ss_pred             cccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCC---CCCCeeEEEecCccchhhhhhcccccccCcceEEEEec
Confidence            457899999999999999999999999999999886543   35679999999999999999999999999999999998


Q ss_pred             cCC
Q 030632           86 LPE   88 (174)
Q Consensus        86 ~~~   88 (174)
                      ..-
T Consensus        81 rgg   83 (241)
T KOG0105|consen   81 RGG   83 (241)
T ss_pred             cCC
Confidence            643

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

Probab=99.51  E-value=1.4e-13  Score=104.21  Aligned_cols=82  Identities=33%  Similarity=0.517  Sum_probs=78.0

Q ss_pred             CCCCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEe
Q 030632            5 AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNY   84 (174)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~   84 (174)
                      +..++.|||-||.+.+.+.-|..+|.+||.|..|.++++..+.+.+||+||++.+.++|..||..|||+.+.++.|.|.+
T Consensus       275 ~~~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsF  354 (360)
T KOG0145|consen  275 PGGGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSF  354 (360)
T ss_pred             CCCeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccceEEEEEE
Confidence            44578999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             ec
Q 030632           85 AL   86 (174)
Q Consensus        85 a~   86 (174)
                      ..
T Consensus       355 Kt  356 (360)
T KOG0145|consen  355 KT  356 (360)
T ss_pred             ec
Confidence            64

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

Probab=99.51  E-value=1.2e-13  Score=116.21  Aligned_cols=78  Identities=23%  Similarity=0.388  Sum_probs=71.9

Q ss_pred             CCCCEEEEcCCCC-CChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEe
Q 030632            6 VQKNTLYVGGLAE-EVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNY   84 (174)
Q Consensus         6 ~~~~~l~V~nLp~-~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~   84 (174)
                      +++++|||+|||+ .+++.+|+.+|+.||.|..|.++.++     +|||||+|.+.++|..|+..|||..|.|++|+|.+
T Consensus       273 ~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~-----~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~  347 (481)
T TIGR01649       273 GPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNK-----KETALIEMADPYQAQLALTHLNGVKLFGKPLRVCP  347 (481)
T ss_pred             CCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEE
Confidence            4678999999998 69999999999999999999998753     69999999999999999999999999999999999


Q ss_pred             ecCC
Q 030632           85 ALPE   88 (174)
Q Consensus        85 a~~~   88 (174)
                      ++..
T Consensus       348 s~~~  351 (481)
T TIGR01649       348 SKQQ  351 (481)
T ss_pred             cccc
Confidence            8653

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability

Probab=99.50  E-value=2.3e-13  Score=84.51  Aligned_cols=74  Identities=39%  Similarity=0.690  Sum_probs=68.3

Q ss_pred             EEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEe
Q 030632           10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNY   84 (174)
Q Consensus        10 ~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~   84 (174)
                      +|||+|||+.++..+|+.+|..||.|..+.+..++. +..+|+|||.|.+.+.|..|+..+++..+.|+.|.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~-~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKD-TKSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCC-CCcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            589999999999999999999999999999988763 36789999999999999999999999999999999864

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

Probab=99.50  E-value=4e-14  Score=116.15  Aligned_cols=82  Identities=34%  Similarity=0.564  Sum_probs=78.5

Q ss_pred             CEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEeecCC
Q 030632            9 NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYALPE   88 (174)
Q Consensus         9 ~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a~~~   88 (174)
                      +.|||||+|+.++++.|..+|+..|.|..++++.++.+|+.+||||++|.+.+.|..|++.|||..+.|++|+|.|+.-.
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~~   98 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASNR   98 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeeccccc
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999998644


Q ss_pred             CC
Q 030632           89 RI   90 (174)
Q Consensus        89 ~~   90 (174)
                      ..
T Consensus        99 ~~  100 (435)
T KOG0108|consen   99 KN  100 (435)
T ss_pred             ch
Confidence            33

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

Probab=99.48  E-value=5.2e-14  Score=110.50  Aligned_cols=86  Identities=26%  Similarity=0.368  Sum_probs=81.8

Q ss_pred             CCCCCCCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEE
Q 030632            2 ANLAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLT   81 (174)
Q Consensus         2 ~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~   81 (174)
                      |...||.+.|||+.|.|-++.++|.-+|+.||.|.+|.+++++.||.+..||||+|.+.++|++|.-.|.+..|..++|+
T Consensus       233 Ad~~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIH  312 (479)
T KOG0415|consen  233 ADVKPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIH  312 (479)
T ss_pred             cccCCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEE
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeecC
Q 030632           82 VNYALP   87 (174)
Q Consensus        82 V~~a~~   87 (174)
                      |.++..
T Consensus       313 VDFSQS  318 (479)
T KOG0415|consen  313 VDFSQS  318 (479)
T ss_pred             eehhhh
Confidence            998753

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

Probab=99.46  E-value=3.3e-13  Score=113.50  Aligned_cols=76  Identities=25%  Similarity=0.301  Sum_probs=69.5

Q ss_pred             CCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhc--CCceecCeEEEEEe
Q 030632            7 QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM--DGAELYGRVLTVNY   84 (174)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l--~g~~~~g~~l~V~~   84 (174)
                      |+++|||+|||+.+++.+|+.+|++||.|..|.++.      .+|||||+|.+.++|.+|+..|  ++..|.|++|.|.|
T Consensus         1 ps~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~------~k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~   74 (481)
T TIGR01649         1 PSPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLP------GKRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNY   74 (481)
T ss_pred             CccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEEC------CCCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEe
Confidence            578999999999999999999999999999999874      3589999999999999999864  78899999999999


Q ss_pred             ecCC
Q 030632           85 ALPE   88 (174)
Q Consensus        85 a~~~   88 (174)
                      +.++
T Consensus        75 s~~~   78 (481)
T TIGR01649        75 STSQ   78 (481)
T ss_pred             cCCc
Confidence            8754

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).

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

Probab=99.46  E-value=3.9e-13  Score=114.08  Aligned_cols=76  Identities=37%  Similarity=0.639  Sum_probs=70.1

Q ss_pred             CCCEEEEcCCCCCChHHHHHHhcccC--CCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEe
Q 030632            7 QKNTLYVGGLAEEVNEAILHAAFIPF--GDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNY   84 (174)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~L~~~F~~~--G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~   84 (174)
                      ..++|||+|||+.+++++|+.+|+.|  |.|..|.++        ++||||+|.+.++|.+|+..||+..|.|+.|+|.|
T Consensus       232 ~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~--------rgfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~  303 (578)
T TIGR01648       232 KVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI--------RDYAFVHFEDREDAVKAMDELNGKELEGSEIEVTL  303 (578)
T ss_pred             cccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee--------cCeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            35789999999999999999999999  999998764        46999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 030632           85 ALPERI   90 (174)
Q Consensus        85 a~~~~~   90 (174)
                      ++|...
T Consensus       304 Akp~~~  309 (578)
T TIGR01648       304 AKPVDK  309 (578)
T ss_pred             ccCCCc
Confidence            988644

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

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

Probab=99.46  E-value=5.9e-14  Score=110.67  Aligned_cols=75  Identities=39%  Similarity=0.631  Sum_probs=73.5

Q ss_pred             CEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEE
Q 030632            9 NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVN   83 (174)
Q Consensus         9 ~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~   83 (174)
                      ++||||.|.+.+.++.|+..|.+||+|++|.+..++.|++++|||||+|.-++.|+.|++.|||..++||.|+|.
T Consensus       114 cRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVg  188 (544)
T KOG0124|consen  114 CRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVG  188 (544)
T ss_pred             HheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCcccccc
Confidence            689999999999999999999999999999999999999999999999999999999999999999999999997

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

Probab=99.44  E-value=1.1e-13  Score=105.11  Aligned_cols=86  Identities=30%  Similarity=0.491  Sum_probs=81.7

Q ss_pred             CCCCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEe
Q 030632            5 AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNY   84 (174)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~   84 (174)
                      .+.+|+|||-.||..+...+|..+|-+||.|.+.++..++.|+.+++|+||.|.++.+++.||..|||..|+-++|+|..
T Consensus       282 GPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQL  361 (371)
T KOG0146|consen  282 GPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQL  361 (371)
T ss_pred             CCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhhh
Confidence            46799999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 030632           85 ALPERI   90 (174)
Q Consensus        85 a~~~~~   90 (174)
                      .+|+..
T Consensus       362 KRPkda  367 (371)
T KOG0146|consen  362 KRPKDA  367 (371)
T ss_pred             cCcccc
Confidence            887753

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

Probab=99.44  E-value=2.5e-13  Score=111.66  Aligned_cols=83  Identities=29%  Similarity=0.424  Sum_probs=78.5

Q ss_pred             CCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEeec
Q 030632            7 QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYAL   86 (174)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a~   86 (174)
                      .+.||||++||+.++..+|..+|+.+|+|..|.++.++.++.+|||+||+|...++++.|+..+++..|.|+.|+|..+.
T Consensus         4 ~g~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A~   83 (678)
T KOG0127|consen    4 SGATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDPAK   83 (678)
T ss_pred             CCceEEEecCCCccchhHHHHhhhcccCcceeEEecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceeccccccc
Confidence            34899999999999999999999999999999999999899999999999999999999999999999999999999987


Q ss_pred             CCC
Q 030632           87 PER   89 (174)
Q Consensus        87 ~~~   89 (174)
                      ++.
T Consensus        84 ~R~   86 (678)
T KOG0127|consen   84 KRA   86 (678)
T ss_pred             ccc
Confidence            643

>PF13893 RRM_5: RNA recognition motif

Probab=99.42  E-value=1.4e-12  Score=78.05  Aligned_cols=56  Identities=39%  Similarity=0.696  Sum_probs=50.7

Q ss_pred             HHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEee
Q 030632           25 LHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYA   85 (174)
Q Consensus        25 L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a   85 (174)
                      |..+|++||.|..+.+..+.     +++|||+|.+.++|..|+..|||..+.|++|+|.|+
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            67899999999999987553     689999999999999999999999999999999986

(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 ....

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

Probab=99.39  E-value=1.3e-12  Score=97.15  Aligned_cols=83  Identities=31%  Similarity=0.511  Sum_probs=74.1

Q ss_pred             CCCCCEEEEcCCCCCChHHHHHH----hcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEE
Q 030632            5 AVQKNTLYVGGLAEEVNEAILHA----AFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVL   80 (174)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~L~~----~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l   80 (174)
                      .++..||||.||+..+..++|+.    +|++||.|..|....   +.+.+|-|||.|.+...|-.|+..|+|..+.|+++
T Consensus         6 ~~pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~k---t~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~m   82 (221)
T KOG4206|consen    6 VNPNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFK---TPKMRGQAFVVFKETEAASAALRALQGFPFYGKPM   82 (221)
T ss_pred             cCCCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecC---CCCccCceEEEecChhHHHHHHHHhcCCcccCchh
Confidence            35566999999999999988777    999999999987754   56899999999999999999999999999999999


Q ss_pred             EEEeecCCCC
Q 030632           81 TVNYALPERI   90 (174)
Q Consensus        81 ~V~~a~~~~~   90 (174)
                      +|.||+....
T Consensus        83 riqyA~s~sd   92 (221)
T KOG4206|consen   83 RIQYAKSDSD   92 (221)
T ss_pred             heecccCccc
Confidence            9999986544

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

Probab=99.38  E-value=7.2e-13  Score=108.99  Aligned_cols=79  Identities=39%  Similarity=0.730  Sum_probs=74.8

Q ss_pred             CEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEeecC
Q 030632            9 NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYALP   87 (174)
Q Consensus         9 ~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a~~   87 (174)
                      .+||||||.+++++..|+.+|.+||.|..|.++.+..+|.++|||||+|.+.+.|.+|+..|||..|-|+.|+|.....
T Consensus       279 ~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~  357 (549)
T KOG0147|consen  279 RRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTE  357 (549)
T ss_pred             hhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeee
Confidence            3499999999999999999999999999999999988999999999999999999999999999999999999987653

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

Probab=99.38  E-value=8.3e-13  Score=105.97  Aligned_cols=84  Identities=21%  Similarity=0.403  Sum_probs=75.6

Q ss_pred             CCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceec---CeEEEEEe
Q 030632            8 KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELY---GRVLTVNY   84 (174)
Q Consensus         8 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~---g~~l~V~~   84 (174)
                      .-++|||-||..+++.+|+.+|.+||.|.+|.|++++.++.++|||||.|.++.+|.+|+..||....-   ..+|.|++
T Consensus        34 ~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqvk~  113 (510)
T KOG0144|consen   34 AVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQVKY  113 (510)
T ss_pred             hhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceeecc
Confidence            347999999999999999999999999999999999999999999999999999999999999886543   47789999


Q ss_pred             ecCCCCC
Q 030632           85 ALPERIK   91 (174)
Q Consensus        85 a~~~~~~   91 (174)
                      +...+.+
T Consensus       114 Ad~E~er  120 (510)
T KOG0144|consen  114 ADGERER  120 (510)
T ss_pred             cchhhhc
Confidence            8766554

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

Probab=99.37  E-value=1.1e-12  Score=94.39  Aligned_cols=89  Identities=33%  Similarity=0.510  Sum_probs=80.5

Q ss_pred             CCCCEEEEcCCCCCChHHHHHHhcccCCCeeEE-EEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEe
Q 030632            6 VQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDV-KTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNY   84 (174)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v-~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~   84 (174)
                      ..+.+|||+||.+.+.+..|...|+.||.+... .+++++.+|.++|||||.|.+.+.+.+|+..|||..+.+++|+|.+
T Consensus        94 ~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~y  173 (203)
T KOG0131|consen   94 DVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPITVSY  173 (203)
T ss_pred             cccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCceEEEE
Confidence            346799999999999999999999999988664 7888888999999999999999999999999999999999999999


Q ss_pred             ecCCCCCCCC
Q 030632           85 ALPERIKGGE   94 (174)
Q Consensus        85 a~~~~~~~~~   94 (174)
                      +..+..++.+
T Consensus       174 a~k~~~kg~~  183 (203)
T KOG0131|consen  174 AFKKDTKGER  183 (203)
T ss_pred             EEecCCCccc
Confidence            9877666543

>smart00361 RRM_1 RNA recognition motif

Probab=99.37  E-value=2.9e-12  Score=80.28  Aligned_cols=61  Identities=23%  Similarity=0.446  Sum_probs=54.2

Q ss_pred             HHHHHHhcc----cCCCeeEEE-EecCCCC--CCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEE
Q 030632           22 EAILHAAFI----PFGDIKDVK-TPLDQAT--QKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTV   82 (174)
Q Consensus        22 ~~~L~~~F~----~~G~i~~v~-~~~~~~~--~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V   82 (174)
                      +.+|+.+|+    .||.|..+. ++.++.+  +.++|||||.|.+.++|.+|+..|||..+.|++|++
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence            457888888    999999995 6665545  889999999999999999999999999999999986

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

Probab=99.32  E-value=7.4e-12  Score=91.89  Aligned_cols=82  Identities=22%  Similarity=0.346  Sum_probs=75.9

Q ss_pred             CCCEEEEcCCCCCChHHHHHHhcccC-CCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEee
Q 030632            7 QKNTLYVGGLAEEVNEAILHAAFIPF-GDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYA   85 (174)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~L~~~F~~~-G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a   85 (174)
                      ...-+||+.+|.-+.+..+..+|.+| |.+..+++.+++.||.++|||||+|.+.+.|..|.+.||++.|.++.|.|.+-
T Consensus        48 ~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~vm  127 (214)
T KOG4208|consen   48 IEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHVM  127 (214)
T ss_pred             CccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEEe
Confidence            45678999999999999999999998 78888888899999999999999999999999999999999999999999987


Q ss_pred             cCC
Q 030632           86 LPE   88 (174)
Q Consensus        86 ~~~   88 (174)
                      .|.
T Consensus       128 ppe  130 (214)
T KOG4208|consen  128 PPE  130 (214)
T ss_pred             Cch
Confidence            765

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

Probab=99.31  E-value=3.5e-12  Score=105.70  Aligned_cols=81  Identities=25%  Similarity=0.458  Sum_probs=76.0

Q ss_pred             CCCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEee
Q 030632            6 VQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYA   85 (174)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a   85 (174)
                      .-+++|||.+|+..+...+|+.+|++||.|....++++-.+...+||+||++.+...|.+||..||.+.|+|+.|.|..+
T Consensus       403 ~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEka  482 (940)
T KOG4661|consen  403 TLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKA  482 (940)
T ss_pred             ccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeec
Confidence            34689999999999999999999999999999999998878888999999999999999999999999999999999887


Q ss_pred             c
Q 030632           86 L   86 (174)
Q Consensus        86 ~   86 (174)
                      +
T Consensus       483 K  483 (940)
T KOG4661|consen  483 K  483 (940)
T ss_pred             c
Confidence            5

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

Probab=99.28  E-value=8.3e-12  Score=95.90  Aligned_cols=74  Identities=26%  Similarity=0.448  Sum_probs=68.7

Q ss_pred             CEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEeecCC
Q 030632            9 NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYALPE   88 (174)
Q Consensus         9 ~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a~~~   88 (174)
                      ..|||||||..+++..|+.+|.+||+|..|.|+++        ||||-..+...+..||..|||..|+|..|.|+-++.+
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN--------YgFVHiEdktaaedairNLhgYtLhg~nInVeaSksK   74 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVKN--------YGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSK   74 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeecc--------cceEEeecccccHHHHhhcccceecceEEEEEecccc
Confidence            46999999999999999999999999999999855        9999999999999999999999999999999988876


Q ss_pred             CC
Q 030632           89 RI   90 (174)
Q Consensus        89 ~~   90 (174)
                      ..
T Consensus        75 sk   76 (346)
T KOG0109|consen   75 SK   76 (346)
T ss_pred             CC
Confidence            43

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

Probab=99.28  E-value=1.4e-11  Score=99.37  Aligned_cols=82  Identities=20%  Similarity=0.337  Sum_probs=74.8

Q ss_pred             CCCCCCEEEEcCCCCCChHHHHHHhcc-cCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEE
Q 030632            4 LAVQKNTLYVGGLAEEVNEAILHAAFI-PFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTV   82 (174)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~L~~~F~-~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V   82 (174)
                      +....+.+||.|||+.+.+.+|+.+|. +.|.|..|.++.+. +|+++|||.|+|++++.+++|++.||.+.+.||+|.|
T Consensus        40 ~~~r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~-~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~v  118 (608)
T KOG4212|consen   40 VAARDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDE-SGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVV  118 (608)
T ss_pred             cccccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeeccc-CCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEE
Confidence            344566799999999999999999997 58999999999887 8999999999999999999999999999999999999


Q ss_pred             Eeec
Q 030632           83 NYAL   86 (174)
Q Consensus        83 ~~a~   86 (174)
                      +--.
T Consensus       119 KEd~  122 (608)
T KOG4212|consen  119 KEDH  122 (608)
T ss_pred             eccC
Confidence            7643

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

Probab=99.27  E-value=1.2e-11  Score=105.41  Aligned_cols=79  Identities=24%  Similarity=0.485  Sum_probs=72.6

Q ss_pred             CCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEeecC
Q 030632            8 KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYALP   87 (174)
Q Consensus         8 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a~~   87 (174)
                      ++|||||+|+.++++.+|..+|..||.|.+|.++.      .+|||||.+..+.+|.+|+..|+.+.+.++.|+|.|+..
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~------~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g  494 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIP------PRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVG  494 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEeecc------CCceeEEEEeehhHHHHHHHHHhcccccceeeEEeeecc
Confidence            58999999999999999999999999999998863      479999999999999999999999999999999999986


Q ss_pred             CCCCC
Q 030632           88 ERIKG   92 (174)
Q Consensus        88 ~~~~~   92 (174)
                      ...+.
T Consensus       495 ~G~ks  499 (894)
T KOG0132|consen  495 KGPKS  499 (894)
T ss_pred             CCcch
Confidence            65544

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

Probab=99.26  E-value=1.3e-11  Score=99.65  Aligned_cols=74  Identities=41%  Similarity=0.659  Sum_probs=68.9

Q ss_pred             CEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEeecCC
Q 030632            9 NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYALPE   88 (174)
Q Consensus         9 ~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a~~~   88 (174)
                      ..|||+||+.++|++.|+.+|..||.|..|..+++        ||||-|..+++|.+|++.+||..|.|..|.|.+|+|.
T Consensus       260 KvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD--------YaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAKP~  331 (506)
T KOG0117|consen  260 KVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD--------YAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAKPV  331 (506)
T ss_pred             eeeeeeccchhhhHHHHHHHHHhccceEEeecccc--------eeEEeecchHHHHHHHHHhcCceecCceEEEEecCCh
Confidence            47999999999999999999999999999977644        9999999999999999999999999999999999986


Q ss_pred             CC
Q 030632           89 RI   90 (174)
Q Consensus        89 ~~   90 (174)
                      ..
T Consensus       332 ~k  333 (506)
T KOG0117|consen  332 DK  333 (506)
T ss_pred             hh
Confidence            43

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

Probab=99.26  E-value=5e-12  Score=106.75  Aligned_cols=80  Identities=31%  Similarity=0.579  Sum_probs=75.5

Q ss_pred             CCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEeec
Q 030632            7 QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYAL   86 (174)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a~   86 (174)
                      ..+.|+|.|||+.++-.+++.+|..||.+..|+|+.....+.++|||||.|-++.+|.+|+..|..+-++||+|.+.|+.
T Consensus       612 ~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEwA~  691 (725)
T KOG0110|consen  612 KGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEWAK  691 (725)
T ss_pred             ccceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhcccceechhhheehhc
Confidence            35789999999999999999999999999999999886677889999999999999999999999999999999999996

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

Probab=99.24  E-value=1.2e-11  Score=94.18  Aligned_cols=83  Identities=23%  Similarity=0.437  Sum_probs=74.9

Q ss_pred             CCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceec---CeEEEEE
Q 030632            7 QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELY---GRVLTVN   83 (174)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~---g~~l~V~   83 (174)
                      ..++||||.|...-.+++++.+|..||.|.+|.+.+.+ .|.++||+||.|.+..+|+.||..|||....   ..-|.|+
T Consensus        18 ~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~-dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK   96 (371)
T KOG0146|consen   18 DDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGP-DGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVK   96 (371)
T ss_pred             cchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCC-CCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEE
Confidence            56899999999999999999999999999999999988 8999999999999999999999999997654   4669999


Q ss_pred             eecCCCC
Q 030632           84 YALPERI   90 (174)
Q Consensus        84 ~a~~~~~   90 (174)
                      ++...+.
T Consensus        97 ~ADTdkE  103 (371)
T KOG0146|consen   97 FADTDKE  103 (371)
T ss_pred             eccchHH
Confidence            9875544

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

Probab=99.20  E-value=7.2e-11  Score=92.66  Aligned_cols=74  Identities=30%  Similarity=0.558  Sum_probs=66.1

Q ss_pred             CCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHH-hcCCceecCeEEEEEeec
Q 030632            8 KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD-NMDGAELYGRVLTVNYAL   86 (174)
Q Consensus         8 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~-~l~g~~~~g~~l~V~~a~   86 (174)
                      -.+|||++|...+++.+|+.+|.+||.|.++.+...      +++|||+|.++..|+.|.. .+|...|.|++|+|.|+.
T Consensus       228 I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~------~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg~  301 (377)
T KOG0153|consen  228 IKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR------KGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWGR  301 (377)
T ss_pred             eeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc------cccceeeehhhHHHHHHHHhhcceeeecceEEEEEeCC
Confidence            469999999999999999999999999999988643      4699999999999998766 456677899999999999


Q ss_pred             C
Q 030632           87 P   87 (174)
Q Consensus        87 ~   87 (174)
                      |
T Consensus       302 ~  302 (377)
T KOG0153|consen  302 P  302 (377)
T ss_pred             C
Confidence            8

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

Probab=99.19  E-value=4.3e-11  Score=92.00  Aligned_cols=78  Identities=23%  Similarity=0.415  Sum_probs=71.6

Q ss_pred             CCCCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEe
Q 030632            5 AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNY   84 (174)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~   84 (174)
                      ...+++|+||||.+.|+..+|+..|.+||+|..|.|++        +|+||-|...++|..|++.|++..|.|++++|..
T Consensus        75 sk~stkl~vgNis~tctn~ElRa~fe~ygpviecdivk--------dy~fvh~d~~eda~~air~l~~~~~~gk~m~vq~  146 (346)
T KOG0109|consen   75 SKASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVK--------DYAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQL  146 (346)
T ss_pred             CCCccccccCCCCccccCHHHhhhhcccCCceeeeeec--------ceeEEEEeeccchHHHHhcccccccccceeeeee
Confidence            34678999999999999999999999999999999974        5999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 030632           85 ALPERI   90 (174)
Q Consensus        85 a~~~~~   90 (174)
                      +..+-.
T Consensus       147 stsrlr  152 (346)
T KOG0109|consen  147 STSRLR  152 (346)
T ss_pred             eccccc
Confidence            876544

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

Probab=99.17  E-value=9.9e-11  Score=95.15  Aligned_cols=79  Identities=24%  Similarity=0.463  Sum_probs=72.7

Q ss_pred             EEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEeecCCC
Q 030632           10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYALPER   89 (174)
Q Consensus        10 ~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a~~~~   89 (174)
                      .|||.||++.++...|..+|+.||.|.+|.+.++. .| ++|| ||.|.+.+.|.+|+..|||..+.|+.|.|.....+.
T Consensus        78 ~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~-~g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~  154 (369)
T KOG0123|consen   78 LVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDE-NG-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERKE  154 (369)
T ss_pred             eeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcC-CC-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccchh
Confidence            39999999999999999999999999999999987 55 8999 999999999999999999999999999998876554


Q ss_pred             CC
Q 030632           90 IK   91 (174)
Q Consensus        90 ~~   91 (174)
                      .+
T Consensus       155 er  156 (369)
T KOG0123|consen  155 ER  156 (369)
T ss_pred             hh
Confidence            43

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

Probab=99.14  E-value=2.6e-10  Score=96.42  Aligned_cols=81  Identities=15%  Similarity=0.245  Sum_probs=68.2

Q ss_pred             CCCCEEEEcCCCCC----------ChHHHHHHhcccCCCeeEEEEecCC---CCCCcccEEEEEEcCHHHHHHHHHhcCC
Q 030632            6 VQKNTLYVGGLAEE----------VNEAILHAAFIPFGDIKDVKTPLDQ---ATQKHRSFGFVTFLEKEDAIQAMDNMDG   72 (174)
Q Consensus         6 ~~~~~l~V~nLp~~----------~t~~~L~~~F~~~G~i~~v~~~~~~---~~~~~~g~afV~f~~~~~a~~al~~l~g   72 (174)
                      .++.+|+|.||...          ...++|+.+|.+||.|..|.|++..   .++...|++||.|.+.+.|.+|+..|||
T Consensus       407 ~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnG  486 (509)
T TIGR01642       407 KPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNG  486 (509)
T ss_pred             CCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEeeccCcCCCcCCCcceEEEEECCHHHHHHHHHHcCC
Confidence            35678999999642          1236799999999999999998752   2456689999999999999999999999


Q ss_pred             ceecCeEEEEEeec
Q 030632           73 AELYGRVLTVNYAL   86 (174)
Q Consensus        73 ~~~~g~~l~V~~a~   86 (174)
                      ..|.|+.|.|.|..
T Consensus       487 r~~~gr~v~~~~~~  500 (509)
T TIGR01642       487 RKFNDRVVVAAFYG  500 (509)
T ss_pred             CEECCeEEEEEEeC
Confidence            99999999999974

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

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

Probab=99.12  E-value=1.4e-10  Score=91.86  Aligned_cols=79  Identities=22%  Similarity=0.439  Sum_probs=74.8

Q ss_pred             CCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEeec
Q 030632            8 KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYAL   86 (174)
Q Consensus         8 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a~   86 (174)
                      -++|||..+.+..++.+|+..|..||+|..|.+-+.+..+.++||+|++|.+......||..||-..++|..|+|..+.
T Consensus       210 fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~v  288 (544)
T KOG0124|consen  210 FNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCV  288 (544)
T ss_pred             hheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEeccccc
Confidence            4699999999999999999999999999999999999888899999999999999999999999999999999997664

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

Probab=99.08  E-value=1.6e-10  Score=91.40  Aligned_cols=85  Identities=29%  Similarity=0.479  Sum_probs=76.6

Q ss_pred             CCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEeec
Q 030632            7 QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYAL   86 (174)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a~   86 (174)
                      ..++||||+|+|.++++.|+..|.+||.|..|.+++++.+++++||+||+|.+......++.. .-+.|.|+.|.+..+.
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~-~~h~~dgr~ve~k~av   83 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNA-RTHKLDGRSVEPKRAV   83 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecc-cccccCCccccceecc
Confidence            678999999999999999999999999999999999999999999999999988888888764 4578999999999988


Q ss_pred             CCCCCC
Q 030632           87 PERIKG   92 (174)
Q Consensus        87 ~~~~~~   92 (174)
                      |+....
T Consensus        84 ~r~~~~   89 (311)
T KOG4205|consen   84 SREDQT   89 (311)
T ss_pred             Cccccc
Confidence            876543

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

Probab=99.05  E-value=1.9e-09  Score=80.32  Aligned_cols=82  Identities=23%  Similarity=0.378  Sum_probs=67.7

Q ss_pred             CCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEec-CCCCCCcccEEEEEEcCHHHHHHHHHhcCCceec---CeEEEEE
Q 030632            8 KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPL-DQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELY---GRVLTVN   83 (174)
Q Consensus         8 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~-~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~---g~~l~V~   83 (174)
                      -+||||.|||..+...+|..+|..|.....+.+.. .+.....+-+||++|.+...|..|++.|||..|.   +.+|++.
T Consensus        34 VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLhiE  113 (284)
T KOG1457|consen   34 VRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLHIE  113 (284)
T ss_pred             cceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeEee
Confidence            58999999999999999999999997666665533 2222234579999999999999999999999987   7889999


Q ss_pred             eecCCC
Q 030632           84 YALPER   89 (174)
Q Consensus        84 ~a~~~~   89 (174)
                      +++...
T Consensus       114 lAKSNt  119 (284)
T KOG1457|consen  114 LAKSNT  119 (284)
T ss_pred             ehhcCc
Confidence            987543

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

Probab=99.04  E-value=7e-10  Score=90.23  Aligned_cols=75  Identities=29%  Similarity=0.526  Sum_probs=70.0

Q ss_pred             CEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEeecCC
Q 030632            9 NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYALPE   88 (174)
Q Consensus         9 ~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a~~~   88 (174)
                      ..||||   +.+|+..|..+|+++|+|.++++.++. +  +.|||||.|.++.+|.+|+..||...+.|++|+|-|+...
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~-t--slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd   75 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDA-T--SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRD   75 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecC-C--ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccC
Confidence            468999   899999999999999999999999997 5  9999999999999999999999999999999999998654


Q ss_pred             C
Q 030632           89 R   89 (174)
Q Consensus        89 ~   89 (174)
                      .
T Consensus        76 ~   76 (369)
T KOG0123|consen   76 P   76 (369)
T ss_pred             C
Confidence            3

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

Probab=99.00  E-value=1.1e-09  Score=92.83  Aligned_cols=78  Identities=23%  Similarity=0.351  Sum_probs=69.9

Q ss_pred             CEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCC---CcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEee
Q 030632            9 NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQ---KHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYA   85 (174)
Q Consensus         9 ~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~---~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a   85 (174)
                      ++|||.||++.++...|..+|..+|.|..+.|...+...   .+.|||||.|.+.++|+.|++.|+|+.|.|+.|.|.++
T Consensus       516 t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S  595 (725)
T KOG0110|consen  516 TKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKIS  595 (725)
T ss_pred             hhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEec
Confidence            349999999999999999999999999999887665221   24599999999999999999999999999999999998


Q ss_pred             c
Q 030632           86 L   86 (174)
Q Consensus        86 ~   86 (174)
                      .
T Consensus       596 ~  596 (725)
T KOG0110|consen  596 E  596 (725)
T ss_pred             c
Confidence            7

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

Probab=98.99  E-value=2.1e-09  Score=82.19  Aligned_cols=80  Identities=25%  Similarity=0.384  Sum_probs=74.3

Q ss_pred             CCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEeec
Q 030632            7 QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYAL   86 (174)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a~   86 (174)
                      ...+|+|.|||+.++..+|+++|..||.+..+.+..++ +|.+.|.|-|.|....+|..|+..|||..+.|++|++....
T Consensus        82 ~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~-~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~  160 (243)
T KOG0533|consen   82 RSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDR-AGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIIS  160 (243)
T ss_pred             CcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCC-CCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEec
Confidence            34789999999999999999999999999999998888 89999999999999999999999999999999999988765


Q ss_pred             C
Q 030632           87 P   87 (174)
Q Consensus        87 ~   87 (174)
                      +
T Consensus       161 ~  161 (243)
T KOG0533|consen  161 S  161 (243)
T ss_pred             C
Confidence            4

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

Probab=98.98  E-value=9.8e-10  Score=88.83  Aligned_cols=76  Identities=25%  Similarity=0.341  Sum_probs=68.4

Q ss_pred             CCCCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEe
Q 030632            5 AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNY   84 (174)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~   84 (174)
                      .+..++|||.|||+.+|+.-|+.-|..||.|....|+.   .|+++|  .|.|.++++|++|+..|+|..+.|+.|.|.+
T Consensus       533 arKa~qIiirNlP~dfTWqmlrDKfre~G~v~yadime---~GkskG--VVrF~s~edAEra~a~Mngs~l~Gr~I~V~y  607 (608)
T KOG4212|consen  533 ARKACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIME---NGKSKG--VVRFFSPEDAERACALMNGSRLDGRNIKVTY  607 (608)
T ss_pred             cccccEEEEecCCccccHHHHHHHHHhccceehhhhhc---cCCccc--eEEecCHHHHHHHHHHhccCcccCceeeeee
Confidence            34568899999999999999999999999999988854   466776  8999999999999999999999999999987


Q ss_pred             e
Q 030632           85 A   85 (174)
Q Consensus        85 a   85 (174)
                      .
T Consensus       608 ~  608 (608)
T KOG4212|consen  608 F  608 (608)
T ss_pred             C
Confidence            3

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

Probab=98.96  E-value=1.5e-09  Score=85.92  Aligned_cols=84  Identities=27%  Similarity=0.499  Sum_probs=76.7

Q ss_pred             CCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEeecC
Q 030632            8 KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYALP   87 (174)
Q Consensus         8 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a~~   87 (174)
                      ...||||+||..+++.+++..|.+||.|..+.++.+..+.+.+||+||.|.+.+.+.+++.. .-+.|.|+.+.|..|.|
T Consensus        97 tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~~-~f~~~~gk~vevkrA~p  175 (311)
T KOG4205|consen   97 TKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTLQ-KFHDFNGKKVEVKRAIP  175 (311)
T ss_pred             eeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceeccc-ceeeecCceeeEeeccc
Confidence            45899999999999999999999999999999999999999999999999999999988764 77899999999999998


Q ss_pred             CCCCC
Q 030632           88 ERIKG   92 (174)
Q Consensus        88 ~~~~~   92 (174)
                      +....
T Consensus       176 k~~~~  180 (311)
T KOG4205|consen  176 KEVMQ  180 (311)
T ss_pred             hhhcc
Confidence            76543

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

Probab=98.94  E-value=1.9e-09  Score=81.58  Aligned_cols=81  Identities=28%  Similarity=0.503  Sum_probs=74.7

Q ss_pred             CCCCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEe
Q 030632            5 AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNY   84 (174)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~   84 (174)
                      +....+||+|.|...++...|-..|.+|-......++++..+|+++||+||.|.+..++..|+..|+|..++.++|+++.
T Consensus       187 ~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRk  266 (290)
T KOG0226|consen  187 DEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRK  266 (290)
T ss_pred             ccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhh
Confidence            34467999999999999999999999998888888999999999999999999999999999999999999999998865


Q ss_pred             e
Q 030632           85 A   85 (174)
Q Consensus        85 a   85 (174)
                      +
T Consensus       267 S  267 (290)
T KOG0226|consen  267 S  267 (290)
T ss_pred             h
Confidence            4

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

Probab=98.94  E-value=9.1e-09  Score=80.99  Aligned_cols=81  Identities=23%  Similarity=0.308  Sum_probs=73.1

Q ss_pred             CCEEEEcCCCCCChHHHHHHhcccCCCee--------EEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeE
Q 030632            8 KNTLYVGGLAEEVNEAILHAAFIPFGDIK--------DVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRV   79 (174)
Q Consensus         8 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~--------~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~   79 (174)
                      ++.|||.|||..+|...+..+|++||-|.        .|.|.++. .|..+|=|++.|...++...|+..|++..|.|+.
T Consensus       134 Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~-~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~~  212 (382)
T KOG1548|consen  134 NTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDN-QGKLKGDALCCYIKRESVELAIKILDEDELRGKK  212 (382)
T ss_pred             CceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecC-CCCccCceEEEeecccHHHHHHHHhCcccccCcE
Confidence            56799999999999999999999999875        47777776 6999999999999999999999999999999999


Q ss_pred             EEEEeecCCC
Q 030632           80 LTVNYALPER   89 (174)
Q Consensus        80 l~V~~a~~~~   89 (174)
                      |+|..|+-..
T Consensus       213 ~rVerAkfq~  222 (382)
T KOG1548|consen  213 LRVERAKFQM  222 (382)
T ss_pred             EEEehhhhhh
Confidence            9999987443

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

Probab=98.94  E-value=3.5e-09  Score=86.82  Aligned_cols=79  Identities=28%  Similarity=0.412  Sum_probs=67.4

Q ss_pred             CCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEeecC
Q 030632            8 KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYALP   87 (174)
Q Consensus         8 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a~~   87 (174)
                      ..+|||+|||++++...|+.+|..||.|....|......++..+||||+|.+...++.||.. +-..|++++|.|.-.++
T Consensus       288 ~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek~~  366 (419)
T KOG0116|consen  288 GLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEKRP  366 (419)
T ss_pred             ccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEeccc
Confidence            45699999999999999999999999999887754322344459999999999999999987 67889999999987765

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

Probab=98.93  E-value=2e-09  Score=91.39  Aligned_cols=81  Identities=28%  Similarity=0.518  Sum_probs=72.7

Q ss_pred             CCCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCC---CCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEE
Q 030632            6 VQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQA---TQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTV   82 (174)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~---~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V   82 (174)
                      |-+++|||+||++++++..|-..|..||+|..+.|+..+.   ....+.|+||.|-+..++++|++.|+|..+.++.+++
T Consensus       172 P~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K~  251 (877)
T KOG0151|consen  172 PQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMKL  251 (877)
T ss_pred             CcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeeee
Confidence            4578999999999999999999999999999998876542   2345789999999999999999999999999999999


Q ss_pred             Eeec
Q 030632           83 NYAL   86 (174)
Q Consensus        83 ~~a~   86 (174)
                      .|++
T Consensus       252 gWgk  255 (877)
T KOG0151|consen  252 GWGK  255 (877)
T ss_pred             cccc
Confidence            9984

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

Probab=98.91  E-value=1.7e-09  Score=81.00  Aligned_cols=72  Identities=33%  Similarity=0.533  Sum_probs=66.4

Q ss_pred             CEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEeecCC
Q 030632            9 NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYALPE   88 (174)
Q Consensus         9 ~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a~~~   88 (174)
                      ..+|||+||+.+.+.+|..+|..||.+..+.+.        .||+||.|.+..+|..|+.-||+..|.|..+.|.|+...
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk--------~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~   73 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMK--------NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGK   73 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceee--------cccceeccCchhhhhcccchhcCceecceeeeeeccccc
Confidence            479999999999999999999999999998763        579999999999999999999999999999999999853

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

Probab=98.91  E-value=1e-08  Score=67.87  Aligned_cols=79  Identities=18%  Similarity=0.319  Sum_probs=69.5

Q ss_pred             CCEEEEcCCCCCChHHHHHHhccc--CCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceec----CeEEE
Q 030632            8 KNTLYVGGLAEEVNEAILHAAFIP--FGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELY----GRVLT   81 (174)
Q Consensus         8 ~~~l~V~nLp~~~t~~~L~~~F~~--~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~----g~~l~   81 (174)
                      .+||.|+|||...+...|..++..  .|....+.++.+..++.+.|||||.|.++..|..-...++|..+.    .+.+.
T Consensus         1 RTTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~   80 (97)
T PF04059_consen    1 RTTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCE   80 (97)
T ss_pred             CeeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEE
Confidence            379999999999999998888865  377788899999889999999999999999999999999998775    57788


Q ss_pred             EEeec
Q 030632           82 VNYAL   86 (174)
Q Consensus        82 V~~a~   86 (174)
                      |.||+
T Consensus        81 i~yAr   85 (97)
T PF04059_consen   81 ISYAR   85 (97)
T ss_pred             EehhH
Confidence            88875

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

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

Probab=98.90  E-value=6.5e-09  Score=79.40  Aligned_cols=82  Identities=24%  Similarity=0.389  Sum_probs=75.7

Q ss_pred             CCCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEee
Q 030632            6 VQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYA   85 (174)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a   85 (174)
                      ...+.+||+|+.+.++...+..+|..||.|..+.++.+..++.++||+||.|.+...+..++. |+|..|.|+.|.|.+.
T Consensus        99 ~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt~~  177 (231)
T KOG4209|consen   99 VDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVTLK  177 (231)
T ss_pred             cCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceeeee
Confidence            356789999999999999999999999999999999999888999999999999999999999 9999999999999887


Q ss_pred             cCC
Q 030632           86 LPE   88 (174)
Q Consensus        86 ~~~   88 (174)
                      +-.
T Consensus       178 r~~  180 (231)
T KOG4209|consen  178 RTN  180 (231)
T ss_pred             eee
Confidence            543

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

Probab=98.90  E-value=1.2e-09  Score=90.53  Aligned_cols=72  Identities=26%  Similarity=0.484  Sum_probs=66.3

Q ss_pred             CCCCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEE
Q 030632            5 AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLT   81 (174)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~   81 (174)
                      ..+.++|+|-|||..++..+|+.+|+.||.|..|+.     +...+|..||.|.+...|+.|++.||+..|.|+.|+
T Consensus        72 ~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~-----t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   72 DMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRE-----TPNKRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             cCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhc-----ccccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            346789999999999999999999999999999766     556789999999999999999999999999999988

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

Probab=98.75  E-value=4e-09  Score=78.37  Aligned_cols=81  Identities=25%  Similarity=0.302  Sum_probs=72.3

Q ss_pred             CCCCCCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEE
Q 030632            3 NLAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTV   82 (174)
Q Consensus         3 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V   82 (174)
                      ..++..+||||+||...++++-|.++|-+.|+|..|.|+..+ .+..+ ||||.|.+.....-|+..+||..+.+..|.|
T Consensus         4 aaae~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~-d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~   81 (267)
T KOG4454|consen    4 AAAEMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQ-DQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQR   81 (267)
T ss_pred             CCcchhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCc-cCCCc-eeeeecccccchhhhhhhcccchhccchhhc
Confidence            345568999999999999999999999999999999998877 55666 9999999999999999999999999988887


Q ss_pred             Eee
Q 030632           83 NYA   85 (174)
Q Consensus        83 ~~a   85 (174)
                      .+-
T Consensus        82 ~~r   84 (267)
T KOG4454|consen   82 TLR   84 (267)
T ss_pred             ccc
Confidence            654

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

Probab=98.61  E-value=2.1e-07  Score=76.42  Aligned_cols=79  Identities=20%  Similarity=0.244  Sum_probs=66.8

Q ss_pred             CCCCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEe
Q 030632            5 AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNY   84 (174)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~   84 (174)
                      .....-|-+.+|||+||+++|..||+.++ |..+.+++.  +|+..|-|||+|.+.+++.+|++. +...+..+.|.|-.
T Consensus         7 ~~~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r~--~Gr~sGeA~Ve~~seedv~~Alkk-dR~~mg~RYIEVf~   82 (510)
T KOG4211|consen    7 GSTAFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPRR--NGRPSGEAYVEFTSEEDVEKALKK-DRESMGHRYIEVFT   82 (510)
T ss_pred             CCcceEEEecCCCccccHHHHHHHHhcCc-eeEEEEecc--CCCcCcceEEEeechHHHHHHHHh-hHHHhCCceEEEEc
Confidence            34455677889999999999999999995 666555544  799999999999999999999986 88889999999987


Q ss_pred             ecC
Q 030632           85 ALP   87 (174)
Q Consensus        85 a~~   87 (174)
                      +.+
T Consensus        83 ~~~   85 (510)
T KOG4211|consen   83 AGG   85 (510)
T ss_pred             cCC
Confidence            754

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

Probab=98.52  E-value=8.9e-08  Score=79.80  Aligned_cols=84  Identities=25%  Similarity=0.398  Sum_probs=77.8

Q ss_pred             CCCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEee
Q 030632            6 VQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYA   85 (174)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a   85 (174)
                      .....+||++||..+++..+.+++..||.+....++.+..+|-++||||.+|.+......|+..|||..+++++|.|..+
T Consensus       287 ~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A  366 (500)
T KOG0120|consen  287 DSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRA  366 (500)
T ss_pred             cccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehh
Confidence            34568999999999999999999999999999999999988999999999999999999999999999999999999887


Q ss_pred             cCCC
Q 030632           86 LPER   89 (174)
Q Consensus        86 ~~~~   89 (174)
                      -+..
T Consensus       367 ~~g~  370 (500)
T KOG0120|consen  367 IVGA  370 (500)
T ss_pred             hccc
Confidence            6543

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

Probab=98.41  E-value=2.1e-06  Score=69.34  Aligned_cols=76  Identities=26%  Similarity=0.478  Sum_probs=68.2

Q ss_pred             CCEEEEcCCCC-CChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEeec
Q 030632            8 KNTLYVGGLAE-EVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYAL   86 (174)
Q Consensus         8 ~~~l~V~nLp~-~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a~   86 (174)
                      +..|.|.||.. .+|...|..+|+.||.|.+|.|..++     +-.|+|.|.+...|.-|+..|+|+.+.|++|+|.+++
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nk-----kd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SK  371 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNK-----KDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSK  371 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecC-----CcceeeeecchhHHHHHHHHhhcceecCceEEEeecc
Confidence            56788888865 69999999999999999999998774     3689999999999999999999999999999999987


Q ss_pred             CC
Q 030632           87 PE   88 (174)
Q Consensus        87 ~~   88 (174)
                      -.
T Consensus       372 H~  373 (492)
T KOG1190|consen  372 HT  373 (492)
T ss_pred             Cc
Confidence            43

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

Probab=98.35  E-value=4e-07  Score=69.19  Aligned_cols=73  Identities=15%  Similarity=0.317  Sum_probs=60.8

Q ss_pred             CCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCC--------CCcc----cEEEEEEcCHHHHHHHHHhcCCce
Q 030632            7 QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQAT--------QKHR----SFGFVTFLEKEDAIQAMDNMDGAE   74 (174)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~--------~~~~----g~afV~f~~~~~a~~al~~l~g~~   74 (174)
                      ....||+++||+.+...-|+.+|+.||.|-.|.|-....+        |..+    .-|+|+|.+...|..+...||+..
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~  152 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTP  152 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCc
Confidence            4578999999999999999999999999999987543322        2222    238899999999999999999999


Q ss_pred             ecCeE
Q 030632           75 LYGRV   79 (174)
Q Consensus        75 ~~g~~   79 (174)
                      |+|+.
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99875

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

Probab=98.30  E-value=2.3e-06  Score=70.42  Aligned_cols=77  Identities=21%  Similarity=0.260  Sum_probs=65.1

Q ss_pred             CCCEEEEcCCCCCChHHHHHHhcccCCCeeE-EEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEee
Q 030632            7 QKNTLYVGGLAEEVNEAILHAAFIPFGDIKD-VKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYA   85 (174)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~-v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a   85 (174)
                      ....|-+++||+.|++.+|.+||+..-.+.. |.++.++ .+++.|-|||.|.+.+.|++||.. |...|..+.|.|..+
T Consensus       102 ~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~-rgR~tGEAfVqF~sqe~ae~Al~r-hre~iGhRYIEvF~S  179 (510)
T KOG4211|consen  102 NDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQ-RGRPTGEAFVQFESQESAEIALGR-HRENIGHRYIEVFRS  179 (510)
T ss_pred             CCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccC-CCCcccceEEEecCHHHHHHHHHH-HHHhhccceEEeehh
Confidence            3457888999999999999999998755544 5666666 677999999999999999999986 778899999998765

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

Probab=98.28  E-value=5.8e-07  Score=71.29  Aligned_cols=83  Identities=23%  Similarity=0.311  Sum_probs=74.5

Q ss_pred             CCCCEEEEcCCCCCChHHHHHHhcccCCCee--------EEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecC
Q 030632            6 VQKNTLYVGGLAEEVNEAILHAAFIPFGDIK--------DVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYG   77 (174)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~--------~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g   77 (174)
                      ...-+|||-+||.+++..+|..+|.++|.|.        .|.|.+++.|+..+|-|.|+|.+...|+.|+.-+++..|.+
T Consensus        64 s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~g  143 (351)
T KOG1995|consen   64 SDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFCG  143 (351)
T ss_pred             cccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccccC
Confidence            3456899999999999999999999999875        36677888899999999999999999999999999999999


Q ss_pred             eEEEEEeecCC
Q 030632           78 RVLTVNYALPE   88 (174)
Q Consensus        78 ~~l~V~~a~~~   88 (174)
                      .+|+|..+..+
T Consensus       144 n~ikvs~a~~r  154 (351)
T KOG1995|consen  144 NTIKVSLAERR  154 (351)
T ss_pred             CCchhhhhhhc
Confidence            99999887544

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.21  E-value=1.4e-06  Score=68.69  Aligned_cols=84  Identities=23%  Similarity=0.427  Sum_probs=75.7

Q ss_pred             CCCEEE-EcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEee
Q 030632            7 QKNTLY-VGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYA   85 (174)
Q Consensus         7 ~~~~l~-V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a   85 (174)
                      +..++| |++|+..++..+|+.+|..+|.|..++++..+.++...||++|.|.....+..++.. ....+.++++.+...
T Consensus       183 ~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~  261 (285)
T KOG4210|consen  183 PSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEED  261 (285)
T ss_pred             ccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCcccccccC
Confidence            445666 999999999999999999999999999999999999999999999999999999887 788999999999998


Q ss_pred             cCCCCC
Q 030632           86 LPERIK   91 (174)
Q Consensus        86 ~~~~~~   91 (174)
                      .+....
T Consensus       262 ~~~~~~  267 (285)
T KOG4210|consen  262 EPRPKS  267 (285)
T ss_pred             CCCccc
Confidence            776443

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

Probab=98.19  E-value=2e-06  Score=68.25  Aligned_cols=77  Identities=19%  Similarity=0.222  Sum_probs=67.2

Q ss_pred             CEEEEcCCCCCChHHHHHHhcccCC--CeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEee
Q 030632            9 NTLYVGGLAEEVNEAILHAAFIPFG--DIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYA   85 (174)
Q Consensus         9 ~~l~V~nLp~~~t~~~L~~~F~~~G--~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a   85 (174)
                      -.+|||||-|++|.++|.+.+...|  .+..++++.++.+|.++|||+|...+....++.+..|.-..|+|..-.|-..
T Consensus        81 ~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~~~  159 (498)
T KOG4849|consen   81 YCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVLSY  159 (498)
T ss_pred             EEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeeecc
Confidence            4689999999999999999998876  5667788899989999999999999999999999999999999877666443

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes

Probab=98.18  E-value=5.1e-06  Score=53.01  Aligned_cols=68  Identities=22%  Similarity=0.381  Sum_probs=47.1

Q ss_pred             CEEEEcCCCCCChHHH----HHHhcccCC-CeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEE
Q 030632            9 NTLYVGGLAEEVNEAI----LHAAFIPFG-DIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVN   83 (174)
Q Consensus         9 ~~l~V~nLp~~~t~~~----L~~~F~~~G-~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~   83 (174)
                      +.|||.|||.......    |+.++..|| .|..|          ..+-|+|.|.+.+.|.+|.+.|+|-.+.|++|.|.
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v----------~~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~   72 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV----------SGGTAILRFPNQEFAERAQKRMEGEDVFGNKISVS   72 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEE
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE----------eCCEEEEEeCCHHHHHHHHHhhcccccccceEEEE
Confidence            4689999999877654    566666775 55554          23689999999999999999999999999999999


Q ss_pred             eec
Q 030632           84 YAL   86 (174)
Q Consensus        84 ~a~   86 (174)
                      +..
T Consensus        73 ~~~   75 (90)
T PF11608_consen   73 FSP   75 (90)
T ss_dssp             SS-
T ss_pred             EcC
Confidence            874

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

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

Probab=98.18  E-value=1.8e-06  Score=64.68  Aligned_cols=67  Identities=22%  Similarity=0.298  Sum_probs=55.4

Q ss_pred             CCCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceec
Q 030632            6 VQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELY   76 (174)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~   76 (174)
                      ..+.||||.||.++|+++.|+.+|+.|.....++|...    ..-+.||+.|...+.|..|+..|.|..|.
T Consensus       208 ~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~----~g~~vaf~~~~~~~~at~am~~lqg~~~s  274 (284)
T KOG1457|consen  208 RACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRAR----GGMPVAFADFEEIEQATDAMNHLQGNLLS  274 (284)
T ss_pred             hhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecC----CCcceEeecHHHHHHHHHHHHHhhcceec
Confidence            34679999999999999999999999987766665322    23468999999999999999999887653

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

Probab=98.17  E-value=6.7e-07  Score=74.34  Aligned_cols=80  Identities=21%  Similarity=0.367  Sum_probs=73.0

Q ss_pred             CCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEeecC
Q 030632            8 KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYALP   87 (174)
Q Consensus         8 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a~~   87 (174)
                      .+|+|+--|+..++..+|..||+.+|.|..|.++.++.++.++|.+||+|.+......|| .|.|..+.|.+|.|.....
T Consensus       179 ~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~ai-aLsGqrllg~pv~vq~sEa  257 (549)
T KOG0147|consen  179 QRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAI-ALSGQRLLGVPVIVQLSEA  257 (549)
T ss_pred             HHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHh-hhcCCcccCceeEecccHH
Confidence            468888888888999999999999999999999999999999999999999999999998 5899999999999987644


Q ss_pred             C
Q 030632           88 E   88 (174)
Q Consensus        88 ~   88 (174)
                      .
T Consensus       258 e  258 (549)
T KOG0147|consen  258 E  258 (549)
T ss_pred             H
Confidence            3

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

Probab=98.05  E-value=2.2e-06  Score=69.54  Aligned_cols=110  Identities=20%  Similarity=0.338  Sum_probs=82.8

Q ss_pred             CEEEEcCCCCCChHHHHHHhcccCC-CeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCc-eecCeEEEEEeec
Q 030632            9 NTLYVGGLAEEVNEAILHAAFIPFG-DIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGA-ELYGRVLTVNYAL   86 (174)
Q Consensus         9 ~~l~V~nLp~~~t~~~L~~~F~~~G-~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~-~~~g~~l~V~~a~   86 (174)
                      ..+|++||.+.++..+|+.+|...- ....-++       ...||+||.+.+...|.+|+..++|. .+.|+++.|.++.
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl-------~k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv   74 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFL-------VKSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSV   74 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCccee-------eecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchh
Confidence            4689999999999999999998641 1111122       23589999999999999999999996 7899999999999


Q ss_pred             CCCCCCCCCCCCCCcc---ccchhHHHHHHHHHHHHHHHHHH
Q 030632           87 PERIKGGEQGWAAQPI---WADADTWFERQQQEEEMQRLQAE  125 (174)
Q Consensus        87 ~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~  125 (174)
                      ++..+.+.....+.|.   |+....++.++.-.+..++...+
T Consensus        75 ~kkqrsrk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~  116 (584)
T KOG2193|consen   75 PKKQRSRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTD  116 (584)
T ss_pred             hHHHHhhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccc
Confidence            9888877766666655   66666666666555544443333

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

Probab=98.03  E-value=2.3e-05  Score=52.79  Aligned_cols=71  Identities=25%  Similarity=0.415  Sum_probs=42.8

Q ss_pred             CCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCc-----eecCeEEEE
Q 030632            8 KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGA-----ELYGRVLTV   82 (174)
Q Consensus         8 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~-----~~~g~~l~V   82 (174)
                      ++.|.|.+++..++..+|+.+|+.||.|..|.+...      ...|||.|.+.+.|+.|+..+...     .|.+..+.+
T Consensus         1 G~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G------~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~   74 (105)
T PF08777_consen    1 GCILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRG------DTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTL   74 (105)
T ss_dssp             --EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-------SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEE
T ss_pred             CeEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCC------CCEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEE
Confidence            356889999999999999999999999999988532      348999999999999998876433     444544444


Q ss_pred             Ee
Q 030632           83 NY   84 (174)
Q Consensus        83 ~~   84 (174)
                      ..
T Consensus        75 ~v   76 (105)
T PF08777_consen   75 EV   76 (105)
T ss_dssp             E-
T ss_pred             EE
Confidence            43

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

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=98.01  E-value=1.4e-05  Score=63.28  Aligned_cols=80  Identities=31%  Similarity=0.499  Sum_probs=62.1

Q ss_pred             CCEEEEcCCCCCChHHH------HHHhcccCCCeeEEEEecCCC-CCCcccE--EEEEEcCHHHHHHHHHhcCCceecCe
Q 030632            8 KNTLYVGGLAEEVNEAI------LHAAFIPFGDIKDVKTPLDQA-TQKHRSF--GFVTFLEKEDAIQAMDNMDGAELYGR   78 (174)
Q Consensus         8 ~~~l~V~nLp~~~t~~~------L~~~F~~~G~i~~v~~~~~~~-~~~~~g~--afV~f~~~~~a~~al~~l~g~~~~g~   78 (174)
                      ..-+||-+||+.+..+.      -..+|.+||.|..|.+-+.-. .....++  .||+|.+.++|.+||....|..+.||
T Consensus       114 KNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr  193 (480)
T COG5175         114 KNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGR  193 (480)
T ss_pred             cceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCc
Confidence            34589999998866544      247899999999998754421 1122233  49999999999999999999999999


Q ss_pred             EEEEEeecC
Q 030632           79 VLTVNYALP   87 (174)
Q Consensus        79 ~l~V~~a~~   87 (174)
                      .|+..|...
T Consensus       194 ~lkatYGTT  202 (480)
T COG5175         194 VLKATYGTT  202 (480)
T ss_pred             eEeeecCch
Confidence            999988754

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

Probab=98.00  E-value=3.4e-05  Score=57.82  Aligned_cols=77  Identities=21%  Similarity=0.395  Sum_probs=67.5

Q ss_pred             CCCCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceec-CeEEEEE
Q 030632            5 AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELY-GRVLTVN   83 (174)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~-g~~l~V~   83 (174)
                      .++...+|+.|||..++...|..+|.+|+....++++..     ..+.|||+|.+...+..|...+.+..|. ...+.|.
T Consensus       143 ~ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~-----~~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~  217 (221)
T KOG4206|consen  143 APPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPP-----RSGIAFVEFLSDRQASAAQQALQGFKITKKNTMQIT  217 (221)
T ss_pred             CCCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccC-----CCceeEEecchhhhhHHHhhhhccceeccCceEEec
Confidence            577889999999999999999999999999999988654     3689999999999999999999998887 7788887


Q ss_pred             eec
Q 030632           84 YAL   86 (174)
Q Consensus        84 ~a~   86 (174)
                      ++.
T Consensus       218 ~a~  220 (221)
T KOG4206|consen  218 FAK  220 (221)
T ss_pred             ccC
Confidence            763

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

Probab=97.93  E-value=8.3e-06  Score=61.38  Aligned_cols=71  Identities=35%  Similarity=0.533  Sum_probs=62.1

Q ss_pred             CCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEeec
Q 030632            8 KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYAL   86 (174)
Q Consensus         8 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a~   86 (174)
                      .+.++|.+++..+.+.+|..+|.++|.+....+        .++++||.|....++..|+..|++..+.++.|.+....
T Consensus        99 ~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~--------~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~~~~~  169 (216)
T KOG0106|consen   99 HFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA--------RRNFAFVEFSEQEDAKRALEKLDGKKLNGRRISVEKNS  169 (216)
T ss_pred             cceeeeccchhhhhHHHHhhhhcccCCCchhhh--------hccccceeehhhhhhhhcchhccchhhcCceeeecccC
Confidence            567889999999999999999999999844332        46799999999999999999999999999999995543

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

Probab=97.90  E-value=5.2e-05  Score=62.99  Aligned_cols=64  Identities=25%  Similarity=0.355  Sum_probs=59.8

Q ss_pred             CCCCEEEEcCCCCCChHHHHHHhcc-cCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHh
Q 030632            6 VQKNTLYVGGLAEEVNEAILHAAFI-PFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN   69 (174)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~L~~~F~-~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~   69 (174)
                      .+.+|||||+||.-++..+|..+|. -||.|..+.|-+++.-+.++|-|=|+|.+...-.+||..
T Consensus       368 DprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  368 DPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             CccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            6789999999999999999999999 699999999999988889999999999999999999874

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

Probab=97.88  E-value=6e-05  Score=63.34  Aligned_cols=77  Identities=21%  Similarity=0.350  Sum_probs=63.7

Q ss_pred             CCEEEEcCCCCCCh------HHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceec-CeEE
Q 030632            8 KNTLYVGGLAEEVN------EAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELY-GRVL   80 (174)
Q Consensus         8 ~~~l~V~nLp~~~t------~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~-g~~l   80 (174)
                      ...|+|.|+|---.      ...|..+|+++|+|....++.+.. |..+||.|++|.+...|..|++.|||+.|. .++.
T Consensus        58 D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~-ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHtf  136 (698)
T KOG2314|consen   58 DSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEE-GGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHTF  136 (698)
T ss_pred             ceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCcc-CCeeeEEEEEecChhhHHHHHHhcccceecccceE
Confidence            45788889986322      246789999999999999998874 459999999999999999999999999876 6777


Q ss_pred             EEEee
Q 030632           81 TVNYA   85 (174)
Q Consensus        81 ~V~~a   85 (174)
                      .|...
T Consensus       137 ~v~~f  141 (698)
T KOG2314|consen  137 FVRLF  141 (698)
T ss_pred             Eeehh
Confidence            77654

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

Probab=97.83  E-value=6.5e-05  Score=64.56  Aligned_cols=79  Identities=15%  Similarity=0.182  Sum_probs=66.3

Q ss_pred             CCCCC-EEEEcCCCCCChHHHHHHhcccCCCee-EEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEE
Q 030632            5 AVQKN-TLYVGGLAEEVNEAILHAAFIPFGDIK-DVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTV   82 (174)
Q Consensus         5 ~~~~~-~l~V~nLp~~~t~~~L~~~F~~~G~i~-~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V   82 (174)
                      ..+++ .|-+.|+|+.++.++|.+||..|-.+- +|.+.++ ..|+..|-|.|-|.+.++|..|...|++..|.++++.+
T Consensus       863 ~~pGp~V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~n-d~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~V~l  941 (944)
T KOG4307|consen  863 KSPGPRVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRN-DDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSL  941 (944)
T ss_pred             CCCCCeEEEecCCCccccHHHHHHHhcccccCCCceeEeec-CCCCcccceeEeecCHHHHHhhhhccccCcccceeEEE
Confidence            34555 566789999999999999999997654 4444444 37999999999999999999999999999999999887


Q ss_pred             Ee
Q 030632           83 NY   84 (174)
Q Consensus        83 ~~   84 (174)
                      ..
T Consensus       942 ~i  943 (944)
T KOG4307|consen  942 RI  943 (944)
T ss_pred             Ee
Confidence            64

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

Probab=97.72  E-value=0.00028  Score=49.90  Aligned_cols=76  Identities=21%  Similarity=0.329  Sum_probs=53.7

Q ss_pred             CCCCCCCCEEEEcCCCC------CChH---HHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCC
Q 030632            2 ANLAVQKNTLYVGGLAE------EVNE---AILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDG   72 (174)
Q Consensus         2 ~~~~~~~~~l~V~nLp~------~~t~---~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g   72 (174)
                      +...||..||.|.-+.+      .+.+   ..|...|..||.+.-++++.        +.-+|+|.+-..|.+|+. |+|
T Consensus        21 ~~~GPpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~--------~~mwVTF~dg~sALaals-~dg   91 (146)
T PF08952_consen   21 SSQGPPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVG--------DTMWVTFRDGQSALAALS-LDG   91 (146)
T ss_dssp             -----TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEET--------TCEEEEESSCHHHHHHHH-GCC
T ss_pred             HhcCCCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeC--------CeEEEEECccHHHHHHHc-cCC
Confidence            34567888988875551      2222   46888899999998888863        367999999999999997 699


Q ss_pred             ceecCeEEEEEeec
Q 030632           73 AELYGRVLTVNYAL   86 (174)
Q Consensus        73 ~~~~g~~l~V~~a~   86 (174)
                      ..+.|+.|+|+...
T Consensus        92 ~~v~g~~l~i~LKt  105 (146)
T PF08952_consen   92 IQVNGRTLKIRLKT  105 (146)
T ss_dssp             SEETTEEEEEEE--
T ss_pred             cEECCEEEEEEeCC
Confidence            99999999999865

; PDB: 1UFW_A 2DNR_A.

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

Probab=97.71  E-value=0.00015  Score=60.84  Aligned_cols=64  Identities=22%  Similarity=0.379  Sum_probs=55.0

Q ss_pred             HHHHHhcccCCCeeEEEEecC-C--CCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEeec
Q 030632           23 AILHAAFIPFGDIKDVKTPLD-Q--ATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYAL   86 (174)
Q Consensus        23 ~~L~~~F~~~G~i~~v~~~~~-~--~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a~   86 (174)
                      ++++.-+++||.|..|.+++. .  ......|..||+|.+.++|++|...|+|..|.|+++...|..
T Consensus       424 Edvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYyd  490 (500)
T KOG0120|consen  424 EDVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYD  490 (500)
T ss_pred             HHHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecC
Confidence            567788899999999999887 2  123356889999999999999999999999999999998873

>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=97.70  E-value=0.00031  Score=46.77  Aligned_cols=78  Identities=15%  Similarity=0.178  Sum_probs=52.2

Q ss_pred             CCCEEEEcCCCCCChHHHHHHhcccCCCeeEEE-EecCC------CCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeE
Q 030632            7 QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVK-TPLDQ------ATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRV   79 (174)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~-~~~~~------~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~   79 (174)
                      ..+-|.|-|.|+..+ ..+...|++||.|.... +.++.      .......+..|+|.++.+|.+||.. ||..|.|..
T Consensus         5 ~~~wVtVFGfp~~~~-~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~-NG~i~~g~~   82 (100)
T PF05172_consen    5 SETWVTVFGFPPSAS-NQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQK-NGTIFSGSL   82 (100)
T ss_dssp             GCCEEEEE---GGGH-HHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTT-TTEEETTCE
T ss_pred             CCeEEEEEccCHHHH-HHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHh-CCeEEcCcE
Confidence            456688889999855 55788999999998764 11110      0123456899999999999999986 999998864


Q ss_pred             -EEEEeec
Q 030632           80 -LTVNYAL   86 (174)
Q Consensus        80 -l~V~~a~   86 (174)
                       +-|.+.+
T Consensus        83 mvGV~~~~   90 (100)
T PF05172_consen   83 MVGVKPCD   90 (100)
T ss_dssp             EEEEEE-H
T ss_pred             EEEEEEcH
Confidence             4466664

This family also includes Q05166 from SWISSPROT a suppressor of thermosensitive mutations in the DNA polymerase delta gene, Pol III []. The conserved central region appears to be distantly related to the RNA-binding region RNP-1 (RNA recognition motif, IPR000504 from INTERPRO), suggesting an RNA binding function for this protein.; PDB: 1WWH_C 3P3D_A.

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

Probab=97.69  E-value=0.00012  Score=43.00  Aligned_cols=52  Identities=23%  Similarity=0.530  Sum_probs=42.5

Q ss_pred             CEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHH
Q 030632            9 NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAM   67 (174)
Q Consensus         9 ~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al   67 (174)
                      +.|-|.|.++..... +..+|..||.|..+.+.      ....+.+|.|.+..+|++||
T Consensus         2 ~wI~V~Gf~~~~~~~-vl~~F~~fGeI~~~~~~------~~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAEE-VLEHFASFGEIVDIYVP------ESTNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHHH-HHHHHHhcCCEEEEEcC------CCCcEEEEEECCHHHHHhhC
Confidence            568899999887755 55588899999998885      23469999999999999885

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

Probab=97.63  E-value=0.0004  Score=55.92  Aligned_cols=81  Identities=22%  Similarity=0.308  Sum_probs=65.3

Q ss_pred             CCCCEEEEcCCC--CCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecC--eEEE
Q 030632            6 VQKNTLYVGGLA--EEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYG--RVLT   81 (174)
Q Consensus         6 ~~~~~l~V~nLp--~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g--~~l~   81 (174)
                      .++..|.+.=|.  +-+|.+.|..+.-..|+|.+|.|++.  +|   -.|.|+|.+.+.|++|...|||..|+.  -+|+
T Consensus       118 ~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkk--ng---VQAmVEFdsv~~AqrAk~alNGADIYsGCCTLK  192 (494)
T KOG1456|consen  118 TPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKK--NG---VQAMVEFDSVEVAQRAKAALNGADIYSGCCTLK  192 (494)
T ss_pred             CCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEec--cc---eeeEEeechhHHHHHHHhhcccccccccceeEE
Confidence            445556655554  45888999999999999999988765  33   369999999999999999999998874  5688


Q ss_pred             EEeecCCCCC
Q 030632           82 VNYALPERIK   91 (174)
Q Consensus        82 V~~a~~~~~~   91 (174)
                      |.||+|.+.+
T Consensus       193 IeyAkP~rln  202 (494)
T KOG1456|consen  193 IEYAKPTRLN  202 (494)
T ss_pred             EEecCcceee
Confidence            9999987553

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

Probab=97.55  E-value=0.00027  Score=57.40  Aligned_cols=78  Identities=23%  Similarity=0.217  Sum_probs=65.0

Q ss_pred             CCCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCe-EEEEEe
Q 030632            6 VQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGR-VLTVNY   84 (174)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~-~l~V~~   84 (174)
                      ||+.+|.+.|+|+.+++++|+.+|..-|........    .++.+-++++.+.+.+.|..|+..++.+.+++. .|+|.+
T Consensus       412 PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkf----f~kd~kmal~q~~sveeA~~ali~~hnh~lgen~hlRvSF  487 (492)
T KOG1190|consen  412 PPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKF----FQKDRKMALPQLESVEEAIQALIDLHNHYLGENHHLRVSF  487 (492)
T ss_pred             CchhheeeccCCcccchhHHHHhhhcCCceEEeeee----cCCCcceeecccCChhHhhhhccccccccCCCCceEEEEe
Confidence            677899999999999999999999988766444322    344567999999999999999999999998854 899999


Q ss_pred             ecC
Q 030632           85 ALP   87 (174)
Q Consensus        85 a~~   87 (174)
                      ++.
T Consensus       488 Sks  490 (492)
T KOG1190|consen  488 SKS  490 (492)
T ss_pred             ecc
Confidence            863

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

Probab=97.54  E-value=0.00035  Score=51.21  Aligned_cols=63  Identities=24%  Similarity=0.289  Sum_probs=56.4

Q ss_pred             CCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceec
Q 030632            7 QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELY   76 (174)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~   76 (174)
                      +..+|.|.+||++.++.+|+.+....|.|+...+.++       |.+.|.|...++.+-|+..|....+.
T Consensus       114 Se~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD-------g~GvV~~~r~eDMkYAvr~ld~~~~~  176 (241)
T KOG0105|consen  114 SEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD-------GVGVVEYLRKEDMKYAVRKLDDQKFR  176 (241)
T ss_pred             cceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc-------cceeeeeeehhhHHHHHHhhcccccc
Confidence            4568999999999999999999999999999888665       58999999999999999999877665

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

Probab=97.50  E-value=0.00059  Score=54.96  Aligned_cols=76  Identities=20%  Similarity=0.266  Sum_probs=67.3

Q ss_pred             CCCCEEEEcCCCC-CChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEe
Q 030632            6 VQKNTLYVGGLAE-EVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNY   84 (174)
Q Consensus         6 ~~~~~l~V~nLp~-~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~   84 (174)
                      .+++.++|-+|.. +++-+-|..+|-.||.|..|.+++.+     .|-|.|++.+....++|+..||+..+.|.+|.|.+
T Consensus       285 ~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk-----~gtamVemgd~~aver~v~hLnn~~lfG~kl~v~~  359 (494)
T KOG1456|consen  285 APGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK-----PGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVCV  359 (494)
T ss_pred             CCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc-----cceeEEEcCcHHHHHHHHHHhccCccccceEEEee
Confidence            4578899999985 46667899999999999999998654     57899999999999999999999999999999998


Q ss_pred             ec
Q 030632           85 AL   86 (174)
Q Consensus        85 a~   86 (174)
                      ++
T Consensus       360 Sk  361 (494)
T KOG1456|consen  360 SK  361 (494)
T ss_pred             cc
Confidence            75

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

Probab=97.46  E-value=0.0001  Score=60.00  Aligned_cols=66  Identities=18%  Similarity=0.216  Sum_probs=55.1

Q ss_pred             CCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecC---CCCCC----------cccEEEEEEcCHHHHHHHHHhcCC
Q 030632            7 QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLD---QATQK----------HRSFGFVTFLEKEDAIQAMDNMDG   72 (174)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~---~~~~~----------~~g~afV~f~~~~~a~~al~~l~g   72 (174)
                      ++++|.+.|||..-.-+-|..+|+.+|.|+.|+|...   +.+.+          .+-||||+|.....|.+|.+.|+.
T Consensus       230 ~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~~  308 (484)
T KOG1855|consen  230 PSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLNP  308 (484)
T ss_pred             ccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhch
Confidence            6889999999998777889999999999999998665   32211          146899999999999999998854

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

Probab=97.45  E-value=0.0012  Score=42.23  Aligned_cols=56  Identities=21%  Similarity=0.361  Sum_probs=41.7

Q ss_pred             CCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcC
Q 030632            7 QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMD   71 (174)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~   71 (174)
                      +....||+ +|..+...+|..+|+.||.|. |.++.+       .-|||.....+.+..++..+.
T Consensus         8 RdHVFhlt-FPkeWK~~DI~qlFspfG~I~-VsWi~d-------TSAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen    8 RDHVFHLT-FPKEWKTSDIYQLFSPFGQIY-VSWIND-------TSAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             GCCEEEEE---TT--HHHHHHHCCCCCCEE-EEEECT-------TEEEEEECCCHHHHHHHHHHT
T ss_pred             cceEEEEe-CchHhhhhhHHHHhccCCcEE-EEEEcC-------CcEEEEeecHHHHHHHHHHhc
Confidence            34455565 999999999999999999984 555544       379999999999999888775

; 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.

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

Probab=97.42  E-value=0.00022  Score=57.48  Aligned_cols=79  Identities=18%  Similarity=0.175  Sum_probs=66.2

Q ss_pred             CCCEEEEcCCCCCChHHHHHHhcccCCC-ee--EEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEE
Q 030632            7 QKNTLYVGGLAEEVNEAILHAAFIPFGD-IK--DVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVN   83 (174)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~-i~--~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~   83 (174)
                      +...|-+++||+.++.++|..||..|.. |.  .|.++.+. .|+..|-|||.|.+.+.|..|....+.+.+.+|.|.|-
T Consensus       279 ~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~-qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvf  357 (508)
T KOG1365|consen  279 SKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNG-QGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVF  357 (508)
T ss_pred             CCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcC-CCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEe
Confidence            3557889999999999999999998863 32  36666665 78999999999999999999999888888889999987


Q ss_pred             eec
Q 030632           84 YAL   86 (174)
Q Consensus        84 ~a~   86 (174)
                      .+.
T Consensus       358 p~S  360 (508)
T KOG1365|consen  358 PCS  360 (508)
T ss_pred             ecc
Confidence            654

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

Probab=97.42  E-value=0.00026  Score=62.44  Aligned_cols=80  Identities=26%  Similarity=0.382  Sum_probs=69.5

Q ss_pred             CCCCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecC--eEEEE
Q 030632            5 AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYG--RVLTV   82 (174)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g--~~l~V   82 (174)
                      ..+.+.+||++|++++....|...|..||.|..|.+-      ...-|++|.|.+...++.|+..|-|..|+|  ++|+|
T Consensus       452 st~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~------hgq~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rv  525 (975)
T KOG0112|consen  452 STPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYR------HGQPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRV  525 (975)
T ss_pred             cccceeeccCCCCCCChHHHHHHHhhccCcceeeecc------cCCcceeeecccCccchhhHHHHhcCcCCCCCccccc
Confidence            4567899999999999999999999999999988763      345699999999999999999999999985  77999


Q ss_pred             EeecCCCC
Q 030632           83 NYALPERI   90 (174)
Q Consensus        83 ~~a~~~~~   90 (174)
                      .++.+...
T Consensus       526 dla~~~~~  533 (975)
T KOG0112|consen  526 DLASPPGA  533 (975)
T ss_pred             ccccCCCC
Confidence            99875443

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

Probab=97.41  E-value=5.8e-05  Score=66.37  Aligned_cols=99  Identities=16%  Similarity=0.287  Sum_probs=76.4

Q ss_pred             CCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEeec
Q 030632            7 QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYAL   86 (174)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a~   86 (174)
                      .++|||+|||+..+++.+|+..|..+|.|..|.|.+.+ -+...-|+||.|.+...+..|+..+.+..|....+++.+..
T Consensus       371 atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~-~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~glG~  449 (975)
T KOG0112|consen  371 ATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPH-IKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGLGQ  449 (975)
T ss_pred             hhhhhhhcCcccchhhhhhhhhhhhhccccccccccCC-CCcccchhhhhhhccccCcccchhhcCCccccCcccccccc
Confidence            46899999999999999999999999999999886654 44556699999999999999999999988887777777776


Q ss_pred             CCCCCCCCCCCCCCccccch
Q 030632           87 PERIKGGEQGWAAQPIWADA  106 (174)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~  106 (174)
                      +......+.+....+.|...
T Consensus       450 ~kst~ttr~~sgglg~w~p~  469 (975)
T KOG0112|consen  450 PKSTPTTRLQSGGLGPWSPV  469 (975)
T ss_pred             cccccceeeccCCCCCCChH
Confidence            53333323333334445553

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

Probab=97.41  E-value=0.00062  Score=54.23  Aligned_cols=77  Identities=25%  Similarity=0.253  Sum_probs=61.5

Q ss_pred             CCCCEEEEcCCCC----CCh-------HHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCce
Q 030632            6 VQKNTLYVGGLAE----EVN-------EAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAE   74 (174)
Q Consensus         6 ~~~~~l~V~nLp~----~~t-------~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~   74 (174)
                      ...++|+|.||=.    ..+       .++|+.-..+||.|..|.|.-.    .+.|.+.|.|.+...|..||..|+|..
T Consensus       263 r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d~----hPdGvvtV~f~n~eeA~~ciq~m~GR~  338 (382)
T KOG1548|consen  263 RADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYDR----HPDGVVTVSFRNNEEADQCIQTMDGRW  338 (382)
T ss_pred             cCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEecc----CCCceeEEEeCChHHHHHHHHHhcCee
Confidence            3467888888721    122       2566777889999999988633    467999999999999999999999999


Q ss_pred             ecCeEEEEEeec
Q 030632           75 LYGRVLTVNYAL   86 (174)
Q Consensus        75 ~~g~~l~V~~a~   86 (174)
                      |.||.|......
T Consensus       339 fdgRql~A~i~D  350 (382)
T KOG1548|consen  339 FDGRQLTASIWD  350 (382)
T ss_pred             ecceEEEEEEeC
Confidence            999999987654

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

Probab=97.28  E-value=0.00015  Score=63.57  Aligned_cols=80  Identities=16%  Similarity=0.134  Sum_probs=71.0

Q ss_pred             CCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEeecC
Q 030632            8 KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYALP   87 (174)
Q Consensus         8 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a~~   87 (174)
                      ...|||.|+|+.+|.+.|+.+++.+|.+..++++..+ .|+++|.+||.|.+..++.+++..+....+.-+.+.|..+.|
T Consensus       736 K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r-~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsnp  814 (881)
T KOG0128|consen  736 KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVR-AGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNP  814 (881)
T ss_pred             hhhhheeCCCCCCchHHHHhhccccCCccccchhhhh-ccccccceeccCCCcchhhhhcccchhhhhhhcCccccccCC
Confidence            3468999999999999999999999999999988887 899999999999999999999988888777777777777665


Q ss_pred             C
Q 030632           88 E   88 (174)
Q Consensus        88 ~   88 (174)
                      .
T Consensus       815 ~  815 (881)
T KOG0128|consen  815 E  815 (881)
T ss_pred             c
Confidence            3

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

Probab=97.25  E-value=0.0016  Score=54.33  Aligned_cols=62  Identities=23%  Similarity=0.469  Sum_probs=47.2

Q ss_pred             CCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCC---CCccc---EEEEEEcCHHHHHHHHHhc
Q 030632            8 KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQAT---QKHRS---FGFVTFLEKEDAIQAMDNM   70 (174)
Q Consensus         8 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~---~~~~g---~afV~f~~~~~a~~al~~l   70 (174)
                      .+.||||+||+.+++..|...|..||.+ .|.++.....   ..++|   |+|+.|.+......-+..+
T Consensus       259 S~KVFvGGlp~dise~~i~~~F~~FGs~-~VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC  326 (520)
T KOG0129|consen  259 SRKVFVGGLPWDITEAQINASFGQFGSV-KVDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSAC  326 (520)
T ss_pred             ccceeecCCCccccHHHHHhhcccccce-EeecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHH
Confidence            5789999999999999999999999986 4555532211   12456   9999999888777665543

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

Probab=97.11  E-value=0.00065  Score=54.90  Aligned_cols=67  Identities=21%  Similarity=0.185  Sum_probs=52.6

Q ss_pred             EEcCCCCCChHHHHHHhcccC----CCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEE
Q 030632           12 YVGGLAEEVNEAILHAAFIPF----GDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVL   80 (174)
Q Consensus        12 ~V~nLp~~~t~~~L~~~F~~~----G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l   80 (174)
                      -.++||+.++..++..||.+-    |....|.+++.+ .|+..|-|||.|...+.|+.||.+ |...|+-|.|
T Consensus       165 RmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rp-dgrpTGdAFvlfa~ee~aq~aL~k-hrq~iGqRYI  235 (508)
T KOG1365|consen  165 RMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRP-DGRPTGDAFVLFACEEDAQFALRK-HRQNIGQRYI  235 (508)
T ss_pred             EecCCCCCcchHHHHHhcCCCCcccCCccceEEEECC-CCCcccceEEEecCHHHHHHHHHH-HHHHHhHHHH
Confidence            346999999999999999732    355667777766 789999999999999999999986 5544544333

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

Probab=97.05  E-value=0.0012  Score=57.06  Aligned_cols=78  Identities=18%  Similarity=0.143  Sum_probs=65.0

Q ss_pred             CCCEEEEcCCCCCChHHHHHHhcccCCCeeE-EEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEee
Q 030632            7 QKNTLYVGGLAEEVNEAILHAAFIPFGDIKD-VKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYA   85 (174)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~-v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a   85 (174)
                      .+..|||..||..++..++-.+|+..-.|.. |.|.+.+ ++..++.|||.|.....+..|+..-+.+.++.+.|+|...
T Consensus       433 ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~P-~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~si  511 (944)
T KOG4307|consen  433 AGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRLP-TDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDSI  511 (944)
T ss_pred             ccceEEeccCCccccccchhhhhhhhhhhhheeEeccCC-cccccchhhheeccccccchhhhcccccccCceEEEeech
Confidence            3678999999999999999999998777766 7776666 7888999999999988888877655666777888999865

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=96.77  E-value=0.0079  Score=42.38  Aligned_cols=74  Identities=18%  Similarity=0.230  Sum_probs=56.0

Q ss_pred             CCCCCEEEEcCCCCCChH----HHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEE
Q 030632            5 AVQKNTLYVGGLAEEVNE----AILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVL   80 (174)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~----~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l   80 (174)
                      .+|=.||.|+=|..++..    ..+...++.||+|.+|.+       .++.-|.|+|.+..+|=+|+..+.. ..-|..+
T Consensus        83 epPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~-------cGrqsavVvF~d~~SAC~Av~Af~s-~~pgtm~  154 (166)
T PF15023_consen   83 EPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTL-------CGRQSAVVVFKDITSACKAVSAFQS-RAPGTMF  154 (166)
T ss_pred             CCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeee-------cCCceEEEEehhhHHHHHHHHhhcC-CCCCceE
Confidence            356678888866555443    456667788999999966       3466899999999999999998764 5567778


Q ss_pred             EEEeec
Q 030632           81 TVNYAL   86 (174)
Q Consensus        81 ~V~~a~   86 (174)
                      .+.|-.
T Consensus       155 qCsWqq  160 (166)
T PF15023_consen  155 QCSWQQ  160 (166)
T ss_pred             Eeeccc
Confidence            887754

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=96.76  E-value=0.005  Score=48.25  Aligned_cols=64  Identities=20%  Similarity=0.241  Sum_probs=52.6

Q ss_pred             HHHHHhcccCCCeeEEEEecCCCCCCccc-EEEEEEcCHHHHHHHHHhcCCceecCeEEEEEeec
Q 030632           23 AILHAAFIPFGDIKDVKTPLDQATQKHRS-FGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYAL   86 (174)
Q Consensus        23 ~~L~~~F~~~G~i~~v~~~~~~~~~~~~g-~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a~   86 (174)
                      ..+..-..+||.|..|.|...+....... -.||+|...++|.+|+--|||..|+|+.+...+..
T Consensus       301 de~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn  365 (378)
T KOG1996|consen  301 DETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYN  365 (378)
T ss_pred             HHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheecc
Confidence            45667788999999998877764333332 37999999999999999999999999999988864

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

Probab=96.74  E-value=0.0013  Score=55.91  Aligned_cols=75  Identities=16%  Similarity=0.240  Sum_probs=60.5

Q ss_pred             CCCCEEEEcCCCCCChHHHHHHhcc-cCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCcee---cCeEEE
Q 030632            6 VQKNTLYVGGLAEEVNEAILHAAFI-PFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAEL---YGRVLT   81 (174)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~L~~~F~-~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~---~g~~l~   81 (174)
                      ..++.|||.||-.-+|.-.|+.++. .+|.|... |+ +    +-+.+|||.|.+.+.|......|||..+   +++.|-
T Consensus       442 ~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~-Wm-D----kIKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~  515 (718)
T KOG2416|consen  442 EPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEF-WM-D----KIKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLI  515 (718)
T ss_pred             CccceEeeecccccchHHHHHHHHhhccCchHHH-HH-H----HhhcceeEecccHHHHHHHHHHHhccccCCCCCceeE
Confidence            3467899999999999999999999 46666665 33 2    3567999999999999999999999765   467787


Q ss_pred             EEeec
Q 030632           82 VNYAL   86 (174)
Q Consensus        82 V~~a~   86 (174)
                      +.|..
T Consensus       516 adf~~  520 (718)
T KOG2416|consen  516 ADFVR  520 (718)
T ss_pred             eeecc
Confidence            77763

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

Probab=96.62  E-value=0.00013  Score=63.91  Aligned_cols=68  Identities=25%  Similarity=0.360  Sum_probs=57.7

Q ss_pred             CEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceec
Q 030632            9 NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELY   76 (174)
Q Consensus         9 ~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~   76 (174)
                      .++||.||++.+.+.+|...|..+|.+..+++......+..+|.|++.|.....+.+||....+..++
T Consensus       668 ~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~g  735 (881)
T KOG0128|consen  668 IKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFG  735 (881)
T ss_pred             HHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhh
Confidence            47899999999999999999999999988877655557899999999999999999998865444433

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

Probab=96.59  E-value=0.0055  Score=49.75  Aligned_cols=76  Identities=14%  Similarity=0.233  Sum_probs=59.6

Q ss_pred             CEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCC---CCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEee
Q 030632            9 NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQA---TQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYA   85 (174)
Q Consensus         9 ~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~---~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a   85 (174)
                      ..|-|.||.+.++.++++.+|...|.|..+.|+-+..   .......|||.|.+...+..|- .|..+.|-++.|.|-.+
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQ-hLtntvfvdraliv~p~   86 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQ-HLTNTVFVDRALIVRPY   86 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHh-hhccceeeeeeEEEEec
Confidence            4899999999999999999999999999998865331   2234568999999888777665 46777777777776543

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=96.52  E-value=0.0025  Score=48.95  Aligned_cols=74  Identities=28%  Similarity=0.382  Sum_probs=59.0

Q ss_pred             CEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCc----eecCeEEEEE
Q 030632            9 NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGA----ELYGRVLTVN   83 (174)
Q Consensus         9 ~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~----~~~g~~l~V~   83 (174)
                      ..|||.||+..++.+.|...|+.||+|....+..+- .++..+-++|.|...-.+.+|+..++..    ...+++.-|.
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~-r~k~t~eg~v~~~~k~~a~~a~rr~~~~g~~~~~~~~p~~Ve  109 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDD-RGKPTREGIVEFAKKPNARKAARRCREGGFGGTTGGRPVGVE  109 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeecc-cccccccchhhhhcchhHHHHHHHhccCccccCCCCCccCCC
Confidence            579999999999999999999999999876655554 6778889999999999999998877432    3334554443

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

Probab=96.47  E-value=0.0089  Score=43.99  Aligned_cols=82  Identities=16%  Similarity=0.197  Sum_probs=50.6

Q ss_pred             CCCCCEEEEcCCCCCChHHHHHHhccc-CCCe---eEEE--EecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecC-
Q 030632            5 AVQKNTLYVGGLAEEVNEAILHAAFIP-FGDI---KDVK--TPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYG-   77 (174)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~L~~~F~~-~G~i---~~v~--~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g-   77 (174)
                      ......|.|++||+++|++++...++. ++.-   ..+.  ............-|||.|.+.+.+......++|+.|.+ 
T Consensus         4 ~~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~   83 (176)
T PF03467_consen    4 EKEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDS   83 (176)
T ss_dssp             -----EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-T
T ss_pred             cccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECC
Confidence            345679999999999999999988887 6655   2332  11111111123459999999999999999999987752 


Q ss_pred             ----eEEEEEeec
Q 030632           78 ----RVLTVNYAL   86 (174)
Q Consensus        78 ----~~l~V~~a~   86 (174)
                          .+..|.+|-
T Consensus        84 kg~~~~~~VE~Ap   96 (176)
T PF03467_consen   84 KGNEYPAVVEFAP   96 (176)
T ss_dssp             TS-EEEEEEEE-S
T ss_pred             CCCCcceeEEEcc
Confidence                345566664

Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=96.22  E-value=0.0028  Score=52.49  Aligned_cols=74  Identities=23%  Similarity=0.335  Sum_probs=58.1

Q ss_pred             CEEEEcCCCCCC-hHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEeecC
Q 030632            9 NTLYVGGLAEEV-NEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYALP   87 (174)
Q Consensus         9 ~~l~V~nLp~~~-t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a~~   87 (174)
                      +.|-+.-.|+.. +..+|..+|.+||.|..|.+-..      .-.|.|+|.+...|-.|... ++..|.++.|+|.|-+|
T Consensus       373 s~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~------~~~a~vTF~t~aeag~a~~s-~~avlnnr~iKl~whnp  445 (526)
T KOG2135|consen  373 SPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYS------SLHAVVTFKTRAEAGEAYAS-HGAVLNNRFIKLFWHNP  445 (526)
T ss_pred             chhhhhccCCCCchHhhhhhhhhhcCccccccccCc------hhhheeeeeccccccchhcc-ccceecCceeEEEEecC
Confidence            344444455543 45789999999999999987433      45799999999999777764 89999999999999987


Q ss_pred             CC
Q 030632           88 ER   89 (174)
Q Consensus        88 ~~   89 (174)
                      ..
T Consensus       446 s~  447 (526)
T KOG2135|consen  446 SP  447 (526)
T ss_pred             Cc
Confidence            54

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

Probab=96.08  E-value=0.0022  Score=49.21  Aligned_cols=63  Identities=16%  Similarity=0.265  Sum_probs=51.6

Q ss_pred             HHHHHhcc-cCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEeec
Q 030632           23 AILHAAFI-PFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYAL   86 (174)
Q Consensus        23 ~~L~~~F~-~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a~   86 (174)
                      +++...|. +||.|..+.|-.+. .-..+|-++|.|...++|++|+..||+..+.|++|...+..
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl-~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~p  146 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNL-GDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSP  146 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhccc-chhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecC
Confidence            44555555 89999988665443 44567889999999999999999999999999999988764

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

Probab=95.98  E-value=0.041  Score=33.26  Aligned_cols=56  Identities=18%  Similarity=0.213  Sum_probs=44.3

Q ss_pred             CCCEEEEcCCCCCChHHHHHHhcccC---CCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhc
Q 030632            7 QKNTLYVGGLAEEVNEAILHAAFIPF---GDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM   70 (174)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~L~~~F~~~---G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l   70 (174)
                      ....|+|.|+.. ++..+|+.+|..|   .....|.++-+.       -|-|.|.+...|.+||..|
T Consensus         4 rpeavhirGvd~-lsT~dI~~y~~~y~~~~~~~~IEWIdDt-------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    4 RPEAVHIRGVDE-LSTDDIKAYFSEYFDEEGPFRIEWIDDT-------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eeceEEEEcCCC-CCHHHHHHHHHHhcccCCCceEEEecCC-------cEEEEECCHHHHHHHHHcC
Confidence            456899999854 7778899999988   235578887664       5779999999999999764

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

Probab=95.88  E-value=0.16  Score=34.39  Aligned_cols=76  Identities=18%  Similarity=0.286  Sum_probs=53.1

Q ss_pred             CCCEEEEcCCCCCChH-HHHHHhcccC-CCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecC---eEEE
Q 030632            7 QKNTLYVGGLAEEVNE-AILHAAFIPF-GDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYG---RVLT   81 (174)
Q Consensus         7 ~~~~l~V~nLp~~~t~-~~L~~~F~~~-G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g---~~l~   81 (174)
                      ++.+|.|-.+|+..+. .+|..+...+ ..|..++|+++.  ...+-.+++.|.+...|..-...+||..+..   ..++
T Consensus        11 ~~~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~--~pnrymVLikF~~~~~Ad~Fy~~fNGk~FnslEpE~Ch   88 (110)
T PF07576_consen   11 RRSTLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDG--TPNRYMVLIKFRDQESADEFYEEFNGKPFNSLEPETCH   88 (110)
T ss_pred             CCceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCC--CCceEEEEEEECCHHHHHHHHHHhCCCccCCCCCceeE
Confidence            4455666556665555 5566555555 467788888874  3356679999999999999999999988763   4454


Q ss_pred             EEe
Q 030632           82 VNY   84 (174)
Q Consensus        82 V~~   84 (174)
                      |-+
T Consensus        89 vvf   91 (110)
T PF07576_consen   89 VVF   91 (110)
T ss_pred             EEE
Confidence            444

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

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

Probab=95.81  E-value=0.016  Score=48.95  Aligned_cols=80  Identities=18%  Similarity=0.301  Sum_probs=59.3

Q ss_pred             CCCEEEEcCCCCCChHHHHHHhcc-cCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceec----CeEEE
Q 030632            7 QKNTLYVGGLAEEVNEAILHAAFI-PFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELY----GRVLT   81 (174)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~L~~~F~-~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~----g~~l~   81 (174)
                      +.+++.|.|+|.+.|-.-|...-. ..|.-..+.++.+..+....|||||.|.+...+..+.+.+||..+.    .+.+.
T Consensus       387 ~rtt~~iknipNK~T~~ml~~~d~~~~gtYDFlYLPiDF~nkcNvGYAFINm~sp~ai~~F~kAFnGk~W~~FnS~Kia~  466 (549)
T KOG4660|consen  387 PRTTLMIKNIPNKYTSKMLLAADEKNKGTYDFLYLPIDFKNKCNVGYAFINMTSPEAIIRFYKAFNGKKWEKFNSEKIAS  466 (549)
T ss_pred             chhhhHhhccCchhhHHhhhhhhccccCccceEEeccccccccccceeEEeecCHHHHHHHHHHHcCCchhhhcceeeee
Confidence            445677777777666555444432 3677778888888878888999999999999999999999997543    34556


Q ss_pred             EEeec
Q 030632           82 VNYAL   86 (174)
Q Consensus        82 V~~a~   86 (174)
                      +.||+
T Consensus       467 itYAr  471 (549)
T KOG4660|consen  467 ITYAR  471 (549)
T ss_pred             eehhh
Confidence            66664

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=95.65  E-value=0.005  Score=48.98  Aligned_cols=80  Identities=26%  Similarity=0.418  Sum_probs=60.3

Q ss_pred             CEEEEcCCCCCChHHH-H--HHhcccCCCeeEEEEecCCC--CCC-cccEEEEEEcCHHHHHHHHHhcCCceecCeEEEE
Q 030632            9 NTLYVGGLAEEVNEAI-L--HAAFIPFGDIKDVKTPLDQA--TQK-HRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTV   82 (174)
Q Consensus         9 ~~l~V~nLp~~~t~~~-L--~~~F~~~G~i~~v~~~~~~~--~~~-~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V   82 (174)
                      .-+||-+|+.....+. |  ...|.+||.|..|.+..++.  .+. ...-++|+|...++|..||...+|..+.|+.|+.
T Consensus        78 nlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lka  157 (327)
T KOG2068|consen   78 NLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALKA  157 (327)
T ss_pred             hhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhHH
Confidence            4578888887765543 3  25788999999998877652  111 1224899999999999999999999999998887


Q ss_pred             EeecCC
Q 030632           83 NYALPE   88 (174)
Q Consensus        83 ~~a~~~   88 (174)
                      .+..++
T Consensus       158 ~~gttk  163 (327)
T KOG2068|consen  158 SLGTTK  163 (327)
T ss_pred             hhCCCc
Confidence            776543

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

Probab=95.54  E-value=0.0077  Score=51.83  Aligned_cols=72  Identities=19%  Similarity=0.306  Sum_probs=62.0

Q ss_pred             CCCCCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEE
Q 030632            4 LAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVN   83 (174)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~   83 (174)
                      +.++.-++||+|+...+....+..++..||.|..+...         -|||..|..+.....|+..++-..+.|..+.+.
T Consensus        36 ~~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~---------~fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~~  106 (668)
T KOG2253|consen   36 PLPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRD---------KFGFCEFLKHIGDLRASRLLTELNIDDQKLIEN  106 (668)
T ss_pred             CCCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhh---------hhcccchhhHHHHHHHHHHhcccCCCcchhhcc
Confidence            44677899999999999999999999999998876442         299999999999999999999888888877765


Q ss_pred             e
Q 030632           84 Y   84 (174)
Q Consensus        84 ~   84 (174)
                      .
T Consensus       107 ~  107 (668)
T KOG2253|consen  107 V  107 (668)
T ss_pred             c
Confidence            4

>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=95.25  E-value=0.097  Score=32.71  Aligned_cols=67  Identities=21%  Similarity=0.355  Sum_probs=39.2

Q ss_pred             EEEEc-CCCCCChHHHHHHhcccCCCe-----eEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEE
Q 030632           10 TLYVG-GLAEEVNEAILHAAFIPFGDI-----KDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVN   83 (174)
Q Consensus        10 ~l~V~-nLp~~~t~~~L~~~F~~~G~i-----~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~   83 (174)
                      ++||. |--..++..+|..++...+.|     -.|.+.        ..|+||.... ..+..++..|++..+.|++++|.
T Consensus         2 rl~in~Gr~dg~~~~~iv~~i~~~~gi~~~~IG~I~I~--------~~~S~vev~~-~~a~~v~~~l~~~~~~gk~v~ve   72 (74)
T PF03880_consen    2 RLFINVGRKDGLTPRDIVGAICNEAGIPGRDIGRIDIF--------DNFSFVEVPE-EVAEKVLEALNGKKIKGKKVRVE   72 (74)
T ss_dssp             EEEES-SGGGT--HHHHHHHHHTCTTB-GGGEEEEEE---------SS-EEEEE-T-T-HHHHHHHHTT--SSS----EE
T ss_pred             EEEEEcccccCCCHHHHHHHHHhccCCCHHhEEEEEEe--------eeEEEEEECH-HHHHHHHHHhcCCCCCCeeEEEE
Confidence            55663 334567888888888876544     456663        2489998854 57888999999999999999998


Q ss_pred             ee
Q 030632           84 YA   85 (174)
Q Consensus        84 ~a   85 (174)
                      .|
T Consensus        73 ~A   74 (74)
T PF03880_consen   73 RA   74 (74)
T ss_dssp             E-
T ss_pred             EC
Confidence            64

; PDB: 2G0C_A 3MOJ_B.

>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=95.25  E-value=0.081  Score=39.19  Aligned_cols=62  Identities=21%  Similarity=0.195  Sum_probs=45.6

Q ss_pred             HHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcC--CceecCeEEEEEeecCCC
Q 030632           22 EAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMD--GAELYGRVLTVNYALPER   89 (174)
Q Consensus        22 ~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~--g~~~~g~~l~V~~a~~~~   89 (174)
                      ...|+.+|..|+.+..+..+...      +=..|.|.+.+.|..|...|+  +..+.|..|+|.++.+..
T Consensus         9 ~~~l~~l~~~~~~~~~~~~L~sF------rRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~~   72 (184)
T PF04847_consen    9 LAELEELFSTYDPPVQFSPLKSF------RRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPTP   72 (184)
T ss_dssp             HHHHHHHHHTT-SS-EEEEETTT------TEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----SS
T ss_pred             HHHHHHHHHhcCCceEEEEcCCC------CEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEccccc
Confidence            46799999999998888766442      357899999999999999999  899999999999886543

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.

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=95.02  E-value=0.098  Score=41.33  Aligned_cols=66  Identities=20%  Similarity=0.328  Sum_probs=49.3

Q ss_pred             EEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeE-EEEEe
Q 030632           11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRV-LTVNY   84 (174)
Q Consensus        11 l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~-l~V~~   84 (174)
                      |-|-++|+.-. .-|..+|.+||.|......      ..-.+-+|.|.++..|++||.. ||..|.|.. |-|..
T Consensus       200 VTVfGFppg~~-s~vL~~F~~cG~Vvkhv~~------~ngNwMhirYssr~~A~KALsk-ng~ii~g~vmiGVkp  266 (350)
T KOG4285|consen  200 VTVFGFPPGQV-SIVLNLFSRCGEVVKHVTP------SNGNWMHIRYSSRTHAQKALSK-NGTIIDGDVMIGVKP  266 (350)
T ss_pred             EEEeccCccch-hHHHHHHHhhCeeeeeecC------CCCceEEEEecchhHHHHhhhh-cCeeeccceEEeeee
Confidence            44557877643 4578899999999876543      2335899999999999999986 899888755 33444

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=94.59  E-value=0.12  Score=42.89  Aligned_cols=68  Identities=16%  Similarity=0.239  Sum_probs=57.8

Q ss_pred             CCCEEEEcCCCCCChHHHHHHhcccC-CCeeEEEEecCCCCCCc-ccEEEEEEcCHHHHHHHHHhcCCceecC
Q 030632            7 QKNTLYVGGLAEEVNEAILHAAFIPF-GDIKDVKTPLDQATQKH-RSFGFVTFLEKEDAIQAMDNMDGAELYG   77 (174)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~L~~~F~~~-G~i~~v~~~~~~~~~~~-~g~afV~f~~~~~a~~al~~l~g~~~~g   77 (174)
                      +++.|+|-.+|-.++-.+|-.|...| ..|..++++++.   .+ +-..+|.|.+..+|......+||..|..
T Consensus        73 ~~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~---~pnrymvLIkFr~q~da~~Fy~efNGk~Fn~  142 (493)
T KOG0804|consen   73 SSTMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDG---MPNRYMVLIKFRDQADADTFYEEFNGKQFNS  142 (493)
T ss_pred             CCcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecC---CCceEEEEEEeccchhHHHHHHHcCCCcCCC
Confidence            47889999999999999999998875 578899999863   33 4458899999999999999999988763

>KOG2318 consensus Uncharacterized conserved protein [Function unknown]

Probab=92.13  E-value=1  Score=38.79  Aligned_cols=79  Identities=22%  Similarity=0.245  Sum_probs=59.2

Q ss_pred             CCCCEEEEcCCCCC-ChHHHHHHhcccC----CCeeEEEEecCC----------CCCC----------------------
Q 030632            6 VQKNTLYVGGLAEE-VNEAILHAAFIPF----GDIKDVKTPLDQ----------ATQK----------------------   48 (174)
Q Consensus         6 ~~~~~l~V~nLp~~-~t~~~L~~~F~~~----G~i~~v~~~~~~----------~~~~----------------------   48 (174)
                      .++++|-|.||.|. +...+|..+|..|    |.|.+|.|....          .+|.                      
T Consensus       172 ~~T~RLAVvNMDWd~v~AkDL~v~~nSFlP~gGsilSV~IYpSeFGkeRM~eEeV~GP~~el~~~~e~~~~s~sD~ee~~  251 (650)
T KOG2318|consen  172 EETKRLAVVNMDWDRVKAKDLFVLFNSFLPKGGSILSVKIYPSEFGKERMKEEEVHGPPKELFKPVEEYKESESDDEEEE  251 (650)
T ss_pred             cccceeeEeccccccccHHHHHHHHHhhcCCCCceeEEEechhhhhHHHhhhhcccCChhhhccccccCcccccchhhhh
Confidence            46789999999985 7778999998876    688888764321          1122                      


Q ss_pred             ---------------cccEEEEEEcCHHHHHHHHHhcCCceecC--eEEEEEe
Q 030632           49 ---------------HRSFGFVTFLEKEDAIQAMDNMDGAELYG--RVLTVNY   84 (174)
Q Consensus        49 ---------------~~g~afV~f~~~~~a~~al~~l~g~~~~g--~~l~V~~   84 (174)
                                     ..-||.|+|.+...|......+.|..|..  ..|-++|
T Consensus       252 ~~~~~kLR~Yq~~rLkYYyAVvecDsi~tA~~vYe~CDG~EfEsS~~~~DLRF  304 (650)
T KOG2318|consen  252 DVDREKLRQYQLNRLKYYYAVVECDSIETAKAVYEECDGIEFESSANKLDLRF  304 (650)
T ss_pred             hHHHHHHHHHHhhhheeEEEEEEecCchHHHHHHHhcCcceeccccceeeeee
Confidence                           12479999999999999999999998874  4444444

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=91.74  E-value=0.32  Score=41.58  Aligned_cols=70  Identities=14%  Similarity=0.217  Sum_probs=53.9

Q ss_pred             CCCEEEEcCCCCCChHHHHHHhccc--CCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCC--ceecCeEEEE
Q 030632            7 QKNTLYVGGLAEEVNEAILHAAFIP--FGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDG--AELYGRVLTV   82 (174)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~L~~~F~~--~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g--~~~~g~~l~V   82 (174)
                      ..+.|+|+-||..+-.++++.+|..  |-.+.+|.+-.+-       -=||+|.+..+|+.|.+.|..  ..|.|++|..
T Consensus       174 kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~-------nWyITfesd~DAQqAykylreevk~fqgKpImA  246 (684)
T KOG2591|consen  174 KRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND-------NWYITFESDTDAQQAYKYLREEVKTFQGKPIMA  246 (684)
T ss_pred             ceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC-------ceEEEeecchhHHHHHHHHHHHHHhhcCcchhh
Confidence            4567788999999999999999985  7788888775442       348999999999999887743  3566666544


Q ss_pred             E
Q 030632           83 N   83 (174)
Q Consensus        83 ~   83 (174)
                      +
T Consensus       247 R  247 (684)
T KOG2591|consen  247 R  247 (684)
T ss_pred             h
Confidence            3

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=91.72  E-value=0.1  Score=41.42  Aligned_cols=78  Identities=18%  Similarity=0.150  Sum_probs=61.4

Q ss_pred             CCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEe
Q 030632            7 QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNY   84 (174)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~   84 (174)
                      ..+++|++++.+.+.+..+..++..+|.+..+.+........++|++.+.|...+.+..|+...-...+.+..+....
T Consensus        87 ~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl  164 (285)
T KOG4210|consen   87 SSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDL  164 (285)
T ss_pred             ccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCcc
Confidence            367899999999999998889999999887777766556788999999999999999999976433455554444433

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=91.30  E-value=0.15  Score=45.50  Aligned_cols=75  Identities=23%  Similarity=0.286  Sum_probs=60.0

Q ss_pred             EEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCcee--cCeEEEEEeecCC
Q 030632           11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAEL--YGRVLTVNYALPE   88 (174)
Q Consensus        11 l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~--~g~~l~V~~a~~~   88 (174)
                      .++.|.+-..+-..|..+|+.||.|.+.+..++.      ..|.|.|...+.|-.|+..|+|..+  .|-+.+|.++++-
T Consensus       301 ~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~------N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~~  374 (1007)
T KOG4574|consen  301 QSLENNAVNLTSSSLATLCSDYGSVASAWTLRDL------NMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKTL  374 (1007)
T ss_pred             hhhhcccccchHHHHHHHHHhhcchhhheecccc------cchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEecccc
Confidence            3444555567778899999999999998776553      5899999999999999999999865  4888999998865


Q ss_pred             CCC
Q 030632           89 RIK   91 (174)
Q Consensus        89 ~~~   91 (174)
                      ...
T Consensus       375 ~~~  377 (1007)
T KOG4574|consen  375 PMY  377 (1007)
T ss_pred             ccc
Confidence            443

>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes

Probab=88.85  E-value=3.7  Score=25.08  Aligned_cols=55  Identities=11%  Similarity=0.217  Sum_probs=42.2

Q ss_pred             CChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEE
Q 030632           19 EVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTV   82 (174)
Q Consensus        19 ~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V   82 (174)
                      .++-.+++..+..|+- ..|..  ++      ---||.|.+..+|.+|....+|..+.+.+|.+
T Consensus        11 ~~~v~d~K~~Lr~y~~-~~I~~--d~------tGfYIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYRW-DRIRD--DR------TGFYIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCCc-ceEEe--cC------CEEEEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            4567899999999964 33332  22      23489999999999999999999988887764

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

>KOG4008 consensus rRNA processing protein RRP7 [RNA processing and modification]

Probab=85.40  E-value=0.44  Score=36.44  Aligned_cols=35  Identities=14%  Similarity=0.256  Sum_probs=30.1

Q ss_pred             CCCCCEEEEcCCCCCChHHHHHHhcccCCCeeEEE
Q 030632            5 AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVK   39 (174)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~   39 (174)
                      .+...+||+-|+|..++++.|..+.+.+|-+..+.
T Consensus        37 ~~eKd~lfl~Nvp~~~tee~lkr~vsqlg~vq~~~   71 (261)
T KOG4008|consen   37 SNEKDCLFLVNVPLLSTEEHLKRFVSQLGHVQELL   71 (261)
T ss_pred             cccccceeeecccccccHHHHHHHHHHhhhhhhee
Confidence            35678999999999999999999999999666554

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

Probab=83.61  E-value=0.04  Score=45.44  Aligned_cols=76  Identities=16%  Similarity=0.343  Sum_probs=61.6

Q ss_pred             CCCEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEee
Q 030632            7 QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYA   85 (174)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a   85 (174)
                      .++.+-|.|+|+...++.|..++..||.+..|..+.   +..-....-|+|...+.+..||..|+|..+....++|.|-
T Consensus        79 rsrk~Qirnippql~wevld~Ll~qyg~ve~~eqvn---t~~etavvnvty~~~~~~~~ai~kl~g~Q~en~~~k~~Yi  154 (584)
T KOG2193|consen   79 RSRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVN---TDSETAVVNVTYSAQQQHRQAIHKLNGPQLENQHLKVGYI  154 (584)
T ss_pred             HhhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhc---cchHHHHHHHHHHHHHHHHHHHHhhcchHhhhhhhhcccC
Confidence            356788999999999999999999999999886532   1122234457888999999999999999999988888774

>KOG4410 consensus 5-formyltetrahydrofolate cyclo-ligase [Coenzyme transport and metabolism]

Probab=82.46  E-value=3.8  Score=32.43  Aligned_cols=58  Identities=12%  Similarity=0.194  Sum_probs=41.4

Q ss_pred             CCEEEEcCCCCCChHHHHHHhcccCCCe-eEEEEecCCCCCCcccEEEEEEcCH-------HHHHHHHHhcC
Q 030632            8 KNTLYVGGLAEEVNEAILHAAFIPFGDI-KDVKTPLDQATQKHRSFGFVTFLEK-------EDAIQAMDNMD   71 (174)
Q Consensus         8 ~~~l~V~nLp~~~t~~~L~~~F~~~G~i-~~v~~~~~~~~~~~~g~afV~f~~~-------~~a~~al~~l~   71 (174)
                      .+-||++|||..+.-.+|+..+.+.|.+ .++.|      ..+.|-||+-|.+.       .++.+++..+|
T Consensus       330 ~~di~~~nl~rd~rv~dlk~~lr~~~~~pm~isw------kg~~~k~flh~~~~~~~~~~~~~~~~~~~s~~  395 (396)
T KOG4410|consen  330 KTDIKLTNLSRDIRVKDLKSELRKRECTPMSISW------KGHFGKCFLHFGNRKGVPSTQDDMDKVLKSLN  395 (396)
T ss_pred             ccceeeccCccccchHHHHHHHHhcCCCceeEee------ecCCcceeEecCCccCCCCCchHHHHHhccCC
Confidence            4569999999999999999999987754 34444      23467799999654       44555555443

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

Probab=81.75  E-value=0.17  Score=41.45  Aligned_cols=74  Identities=16%  Similarity=0.102  Sum_probs=54.7

Q ss_pred             CEEEEcCCCCCChHHHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCeEEEEEeecC
Q 030632            9 NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYALP   87 (174)
Q Consensus         9 ~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~~l~V~~a~~   87 (174)
                      +|++|++|+..+...++-.+|..+|.|....+-    .+....+|.+.|........|+.. +|..+.-+...+...+|
T Consensus       152 Rt~~v~sl~~~~~l~e~~e~f~r~Gev~ya~~a----sk~~s~~c~~sf~~qts~~halr~-~gre~k~qhsr~ai~kP  225 (479)
T KOG4676|consen  152 RTREVQSLISAAILPESGESFERKGEVSYAHTA----SKSRSSSCSHSFRKQTSSKHALRS-HGRERKRQHSRRAIIKP  225 (479)
T ss_pred             hhhhhhcchhhhcchhhhhhhhhcchhhhhhhh----ccCCCcchhhhHhhhhhHHHHHHh-cchhhhhhhhhhhhcCc
Confidence            689999999999999999999999999877664    334455677999888888888875 66666533333333333

>KOG4019 consensus Calcineurin-mediated signaling pathway inhibitor DSCR1 [Signal transduction mechanisms; General function prediction only]

Probab=80.32  E-value=1.8  Score=31.91  Aligned_cols=78  Identities=17%  Similarity=0.183  Sum_probs=55.1

Q ss_pred             CCEEEEcCCCCCChH-----HHHHHhcccCCCeeEEEEecCCCCCCcccEEEEEEcCHHHHHHHHHhcCCceecCe-EEE
Q 030632            8 KNTLYVGGLAEEVNE-----AILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGR-VLT   81 (174)
Q Consensus         8 ~~~l~V~nLp~~~t~-----~~L~~~F~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~a~~al~~l~g~~~~g~-~l~   81 (174)
                      .+++++++++..+-.     .....+|.+|-......+++      +.++.-|.|.+...|..|...++...|.|+ .++
T Consensus        10 p~~~~~c~i~~~VF~~~~~k~~~~~lFrq~n~~~~fq~lr------sfrrvRi~f~~p~~a~~a~i~~~~~~f~~~~~~k   83 (193)
T KOG4019|consen   10 PTAIIACDIHEEVFVNREDKALFENLFRQINEDATFQLLR------SFRRVRINFSNPEAAADARIKLHSTSFNGKNELK   83 (193)
T ss_pred             cceeeeecccHHhhccHHHHHHHHhHHhhhCcchHHHHHH------hhceeEEeccChhHHHHHHHHhhhcccCCCceEE
Confidence            456788888765332     34556677776665555543      234566899999999999999999999988 777


Q ss_pred             EEeecCCCCC
Q 030632           82 VNYALPERIK   91 (174)
Q Consensus        82 V~~a~~~~~~   91 (174)
                      .-++.+....
T Consensus        84 ~yfaQ~~~~~   93 (193)
T KOG4019|consen   84 LYFAQPGHPE   93 (193)
T ss_pred             EEEccCCCcc
Confidence            7777654443

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	174
2cqb_A	102	Solution Structure Of The Rna Recognition Motif In		2e-26
3mdf_A	85	Crystal Structure Of The Rrm Domain Of Cyclophilin		4e-24
2ku7_A	140	Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric		6e-24
2kyx_A	83	Solution Structure Of The Rrm Domain Of Cyp33 Lengt		2e-23
3lpy_A	79	Crystal Structure Of The Rrm Domain Of Cyp33 Length		2e-23
1x5u_A	105	Solution Structure Of Rrm Domain In Splicing Factor		3e-12
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		7e-11
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		1e-10
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		5e-10
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		6e-10
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		6e-10
2kn4_A	158	The Structure Of The Rrm Domain Of Sc35 Length = 15		8e-09
2lea_A	135	Solution Structure Of Human Srsf2 (Sc35) Rrm Length		8e-09
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		1e-08
3bs9_A	87	X-Ray Structure Of Human Tia-1 Rrm2 Length = 87		4e-08
3md1_A	83	Crystal Structure Of The Second Rrm Domain Of Yeast		5e-08
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		5e-08
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		9e-08
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		1e-07
1whw_A	99	Solution Structure Of The N-Terminal Rna Binding Do		1e-07
2rra_A	99	Solution Structure Of Rna Binding Domain In Human T		3e-07
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		4e-07
2kxn_B	129	Nmr Structure Of Human Tra2beta1 Rrm In Complex Wit		4e-07
2rrb_A	96	Refinement Of Rna Binding Domain In Human Tra2 Beta		5e-07
2cq0_A	103	Solution Structure Of Rna Binding Domain In Eukaryo		8e-07
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		8e-07
2dgu_A	103	Solution Structure Of The Rna Binding Domain In Het		1e-06
2dnm_A	103	Solution Structure Of Rna Binding Domain In Srp46 S		1e-06
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		2e-06
1wtb_A	79	Complex Structure Of The C-Terminal Rna-Binding Dom		2e-06
1iqt_A	75	Solution Structure Of The C-Terminal Rna-Binding Do		2e-06
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		2e-06
1hl6_A	165	A Novel Mode Of Rbd-Protein Recognition In The Y14-		3e-06
2fc8_A	102	Solution Structure Of The Rrm_1 Domain Of Ncl Prote		3e-06
2j0s_D	89	The Crystal Structure Of The Exon Junction Complex		4e-06
2xb2_D	90	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		4e-06
2hyi_B	91	Structure Of The Human Exon Junction Complex With A		4e-06
2j0q_D	109	The Crystal Structure Of The Exon Junction Complex		4e-06
1p27_B	106	Crystal Structure Of The Human Y14MAGOH COMPLEX Len		4e-06
3ex7_B	126	The Crystal Structure Of Ejc In Its Transition Stat		4e-06
2ywk_A	95	Crystal Structure Of Rrm-Domain Derived From Human		5e-06
2dgs_A	99	Solution Structure Of The Second Rna Binding Domain		6e-06
2cqc_A	95	Solution Structure Of The Rna Recognition Motif In		8e-06
2e5h_A	94	Solution Structure Of Rna Binding Domain In Zinc Fi		8e-06
2cph_A	107	Solution Structure Of The C-Terminal Rna Recognitio		9e-06
1hd0_A	75	Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D		1e-05
1x5p_A	97	Solution Structure Of Rrm Domain In Parp14 Length =		2e-05
2jx2_A	121	Solution Structure Of Nelf E Rrm Length = 121		2e-05
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		2e-05
2ki2_A	90	Solution Structure Of Ss-Dna Binding Protein 12rnp2		2e-05
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		2e-05
1d8z_A	89	Solution Structure Of The First Rna-Binding Domain		3e-05
2khc_A	118	Bruno Rrm3+ Length = 118		3e-05
1h2t_Z	156	Structure Of The Human Nuclear Cap-Binding-Complex		3e-05
2cqi_A	103	Solution Structure Of The Rna Binding Domain Of Nuc		3e-05
1oo0_B	110	Crystal Structure Of The Drosophila Mago Nashi-Y14		3e-05
1x5t_A	96	Solution Structure Of The Second Rrm Domain In Spli		4e-05
4fxv_A	99	Crystal Structure Of An Elav-Like Protein 1 (Elavl1		4e-05
2cpx_A	115	Solution Structure Of Rna Binding Domain In Hypothe		5e-05
2d9p_A	103	Solution Structure Of Rna Binding Domain 4 In Polya		6e-05
2mss_A	75	Musashi1 Rbd2, Nmr Length = 75		8e-05
2rs2_A	109	1h, 13c, And 15n Chemical Shift Assignments For Mus		9e-05
1urn_A	97	U1a MutantRNA COMPLEX + GLYCEROL Length = 97		2e-04
1u6b_A	98	Crystal Structure Of A Self-Splicing Group I Intron		2e-04
3bo2_A	95	A Relaxed Active Site Following Exon Ligation By A		2e-04
1m5k_C	100	Crystal Structure Of A Hairpin Ribozyme In The Cata		2e-04
3k0j_A	96	Crystal Structure Of The E. Coli Thim Riboswitch In		2e-04
2nz4_A	94	Structural Investigation Of The Glms Ribozyme Bound		2e-04
2cqd_A	116	Solution Structure Of The Rna Recognition Motif In		2e-04
3l3c_A	90	Crystal Structure Of The Bacillus Anthracis Glms Ri		2e-04
1aud_A	101	U1a-Utrrna, Nmr, 31 Structures Length = 101		2e-04
1x4g_A	109	Solution Structure Of Rrm Domain In Nucleolysin Tia		2e-04
3iwn_C	91	Co-Crystal Structure Of A Bacterial C-Di-Gmp Ribosw		2e-04
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		2e-04
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		2e-04
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		2e-04
3hi9_A	84	The X-Ray Crystal Structure Of The First Rna Recogn		2e-04
1uaw_A	77	Solution Structure Of The N-Terminal Rna-Binding Do		3e-04
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		3e-04
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		3e-04
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		3e-04
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		3e-04
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		3e-04
1d9a_A	85	Solution Structure Of The Second Rna-Binding Domain		3e-04
2cpz_A	115	Solution Structure Of Rna Binding Domain 3 In Cug T		5e-04
1h6k_Z	98	Nuclear Cap Binding Complex Length = 98		5e-04
1fht_A	116	Rna-Binding Domain Of The U1a Spliceosomal Protein		6e-04
1x4b_A	116	Solution Structure Of Rrm Domain In Heterogeneous N		7e-04
3pgw_A	282	Crystal Structure Of Human U1 Snrnp Length = 282		7e-04

>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In Peptidyl- Prolyl Cis-Trans Isomerase E Length = 102

Iteration: 1
 Score =  115 bits (287), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 53/90 (58%), Positives = 66/90 (73%)
Query: 2  ANLAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKE 61
          + +A  K  LYVGGLAEEV++ +LHAAFIPFGDI D++ PLD  T+KHR F FV F   E
Sbjct: 6  SGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 65
Query: 62 DAIQAMDNMDGAELYGRVLTVNYALPERIK 91
          DA  A+DNM+ +EL+GR + VN A P RIK
Sbjct: 66 DAAAAIDNMNESELFGRTIRVNLAKPMRIK 95

>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33 Length = 85

Iteration: 1
 Score =  107 bits (266), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 49/83 (59%), Positives = 62/83 (74%)
Query: 3  NLAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKED 62
          ++A  K  LYVGGLAEEV++ +LHAAFIPFGDI D++ PLD  T+KHR F FV F   ED
Sbjct: 2  SMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAED 61
Query: 63 AIQAMDNMDGAELYGRVLTVNYA 85
          A  A+DNM+ +EL+GR + VN A
Sbjct: 62 AAAAIDNMNESELFGRTIRVNLA 84

>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein Length = 140

Iteration: 1
 Score =  106 bits (265), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 49/81 (60%), Positives = 60/81 (74%)
Query: 5   AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
           A  K  LYVGGLAEEV++ +LHAAFIPFGDI D++ PLD  T+KHR F FV F   EDA 
Sbjct: 60  ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 119
Query: 65  QAMDNMDGAELYGRVLTVNYA 85
            A+DNM+ +EL+GR + VN A
Sbjct: 120 AAIDNMNESELFGRTIRVNLA 140

>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33 Length = 83

Iteration: 1
 Score =  104 bits (260), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 48/81 (59%), Positives = 60/81 (74%)
Query: 5  AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
          +  K  LYVGGLAEEV++ +LHAAFIPFGDI D++ PLD  T+KHR F FV F   EDA 
Sbjct: 2  STTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 61
Query: 65 QAMDNMDGAELYGRVLTVNYA 85
           A+DNM+ +EL+GR + VN A
Sbjct: 62 AAIDNMNESELFGRTIRVNLA 82

>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33 Length = 79

Iteration: 1
 Score =  104 bits (260), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 48/79 (60%), Positives = 59/79 (74%)
Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
           K  LYVGGLAEEV++ +LHAAFIPFGDI D++ PLD  T+KHR F FV F   EDA  A
Sbjct: 1  SKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 60
Query: 67 MDNMDGAELYGRVLTVNYA 85
          +DNM+ +EL+GR + VN A
Sbjct: 61 IDNMNESELFGRTIRVNLA 79

>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b Length = 105

Iteration: 1
 Score = 67.4 bits (163), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 34/79 (43%), Positives = 50/79 (63%)
Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
          Q  T+YVGGL E+V+E +L   F+  G + +   P D+ T +H+ +GFV FL +EDA  A
Sbjct: 14 QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA 73
Query: 67 MDNMDGAELYGRVLTVNYA 85
          +  MD  +LYG+ + VN A
Sbjct: 74 IKIMDMIKLYGKPIRVNKA 92

>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In Cytotoxic Granule-Associated Rna Binding Protein 1 Length = 115

Iteration: 1
 Score = 63.2 bits (152), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 31/75 (41%), Positives = 43/75 (57%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          ++VG L+ E+    + AAF PFG I D +   D AT K + +GFV+F  K DA  A+  M
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 71 DGAELYGRVLTVNYA 85
           G  L GR +  N+A
Sbjct: 78 GGQWLGGRQIRTNWA 92

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 62.4 bits (150), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 33/82 (40%), Positives = 47/82 (57%)
Query: 4  LAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDA 63
          +A  +  L+VGGL+ + NE  L   F  +G I +V    D+ TQ+ R FGFVTF   +DA
Sbjct: 8  MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDA 67
Query: 64 IQAMDNMDGAELYGRVLTVNYA 85
            AM  M+G  + GR + V+ A
Sbjct: 68 KDAMMAMNGKSVDGRQIRVDQA 89

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 60.5 bits (145), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 30/75 (40%), Positives = 44/75 (58%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          ++VG L+ E+    + +AF PFG I D +   D AT K + +GFV+F  K DA  A+ +M
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 71 DGAELYGRVLTVNYA 85
           G  L GR +  N+A
Sbjct: 78 GGQWLGGRQIRTNWA 92

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 60.1 bits (144), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 31/84 (36%), Positives = 49/84 (58%), Gaps = 1/84 (1%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          LYVG L   + E +L   F PFG I ++    D  T + + +GF+TF + E A +A++ +
Sbjct: 8  LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 71 DGAELYGRVLTVNYALPERIKGGE 94
          +G EL GR + V + + ER+ GG 
Sbjct: 68 NGFELAGRPMRVGH-VTERLDGGS 90

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 60.1 bits (144), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 27/75 (36%), Positives = 45/75 (60%)
Query: 11  LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
           LYVG L   + E +L   F PFG I+ ++  +D  T + + +GF+TF + E A +A++ +
Sbjct: 29  LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 71  DGAELYGRVLTVNYA 85
           +G EL GR + V + 
Sbjct: 89  NGFELAGRPMKVGHV 103

>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35 Length = 158

Iteration: 1
 Score = 56.2 bits (134), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 32/77 (41%), Positives = 40/77 (51%)
Query: 9   NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
            +L V  L    +   L   F  +G + DV  P D+ T++ R F FV F +K DA  AMD
Sbjct: 71  TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 130
Query: 69  NMDGAELYGRVLTVNYA 85
            MDGA L GR L V  A
Sbjct: 131 AMDGAVLDGRELRVQMA 147

>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm Length = 135

Iteration: 1
 Score = 56.2 bits (134), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 32/77 (41%), Positives = 40/77 (51%)
Query: 9   NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
            +L V  L    +   L   F  +G + DV  P D+ T++ R F FV F +K DA  AMD
Sbjct: 48  TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 107
Query: 69  NMDGAELYGRVLTVNYA 85
            MDGA L GR L V  A
Sbjct: 108 AMDGAVLDGRELRVQMA 124

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 55.8 bits (133), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 30/75 (40%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          L++GGL  E NE +L A F   G I +V    D+ T K R F F+TF    DA  A  +M
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDM 68
Query: 71 DGAELYGRVLTVNYA 85
          +G  L+G+ + V  A
Sbjct: 69 NGKSLHGKAIKVEQA 83

>pdb|3BS9|A Chain A, X-Ray Structure Of Human Tia-1 Rrm2 Length = 87

Iteration: 1
 Score = 53.9 bits (128), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 32/75 (42%), Positives = 44/75 (58%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          ++VG L+ E+  A + AAF PFG I D +   D AT K + +GFV+F  K DA  A+  M
Sbjct: 9  VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68
Query: 71 DGAELYGRVLTVNYA 85
           G  L GR +  N+A
Sbjct: 69 GGQWLGGRQIRTNWA 83

>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast Poly(U)-Binding Protein (Pub1) Length = 83

Iteration: 1
 Score = 53.9 bits (128), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 29/75 (38%), Positives = 40/75 (53%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          L+VG L   V++  L  AF  F          D  T   R +GFV+F  ++DA  AMD+M
Sbjct: 4  LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 71 DGAELYGRVLTVNYA 85
           G +L GR L +N+A
Sbjct: 64 QGQDLNGRPLRINWA 78

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score = 53.5 bits (127), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 29/76 (38%), Positives = 40/76 (52%)
Query: 10  TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
            L+VG L   V++  L  AF  F          D  T   R +GFV+F  ++DA  AMD+
Sbjct: 89  NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 148
Query: 70  MDGAELYGRVLTVNYA 85
           M G +L GR L +N+A
Sbjct: 149 MQGQDLNGRPLRINWA 164

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 43.1 bits (100), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 21/78 (26%), Positives = 43/78 (55%)
Query: 9   NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
           N +YV  + +++++  + + F  FG IK      D  T KH+ +GF+ + + + +  A+ 
Sbjct: 111 NRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVS 170
Query: 69  NMDGAELYGRVLTVNYAL 86
           +M+  +L G+ L V  A+
Sbjct: 171 SMNLFDLGGQYLRVGKAV 188

>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To Ssdna From A Portion Of Fuse Length = 216

Iteration: 1
 Score = 42.7 bits (99), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/78 (26%), Positives = 43/78 (55%)
Query: 9   NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
           N +YV  + +++++  + + F  FG IK      D  T KH+ +GF+ + + + +  A+ 
Sbjct: 126 NRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVS 185
Query: 69  NMDGAELYGRVLTVNYAL 86
           +M+  +L G+ L V  A+
Sbjct: 186 SMNLFDLGGQYLRVGKAV 203

>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain From Hypothetical Protein Bab23448 Length = 99

Iteration: 1
 Score = 52.4 bits (124), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 29/81 (35%), Positives = 44/81 (54%), Gaps = 3/81 (3%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          L+V  L+   +E  L   F  +G + ++  P+D  T+K + F FVTF+  E A++A   +
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 71 DGAELYGRVLTVNYALPERIK 91
          DG    GR+L V   LP  IK
Sbjct: 71 DGQVFQGRMLHV---LPSTIK 88

>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 = 51.2 bits (121), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 28/80 (35%), Positives = 43/80 (53%)
Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
           L V GL+    E  L   F  +G I DV    DQ +++ R F FV F   +DA +A + 
Sbjct: 17 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 76
Query: 70 MDGAELYGRVLTVNYALPER 89
           +G EL GR + V++++ +R
Sbjct: 77 ANGMELDGRRIRVDFSITKR 96

>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U Binding Splicing Factor 60kda (Puf60) From Homo Sapiens At 2.50 A Resolution Length = 200

Iteration: 1
 Score = 40.8 bits (94), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 20/78 (25%), Positives = 42/78 (53%)
Query: 9   NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
           N +YV  + +++++  + + F  FG IK      D  T KH+ +GF+ + + + +  A+ 
Sbjct: 110 NRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVS 169
Query: 69  NMDGAELYGRVLTVNYAL 86
           + +  +L G+ L V  A+
Sbjct: 170 SXNLFDLGGQYLRVGKAV 187

>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With Aagaac Rna Length = 129

Iteration: 1
 Score = 50.8 bits (120), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 28/80 (35%), Positives = 43/80 (53%)
Query: 10  TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
            L V GL+    E  L   F  +G I DV    DQ +++ R F FV F   +DA +A + 
Sbjct: 48  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 107
Query: 70  MDGAELYGRVLTVNYALPER 89
            +G EL GR + V++++ +R
Sbjct: 108 ANGMELDGRRIRVDFSITKR 127

>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta Protein Length = 96

Iteration: 1
 Score = 50.4 bits (119), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 28/80 (35%), Positives = 43/80 (53%)
Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
           L V GL+    E  L   F  +G I DV    DQ +++ R F FV F   +DA +A + 
Sbjct: 14 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 73
Query: 70 MDGAELYGRVLTVNYALPER 89
           +G EL GR + V++++ +R
Sbjct: 74 ANGMELDGRRIRVDFSITKR 93

>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic Translation Initiation Factor 3 Subunit 4 Length = 103

Iteration: 1
 Score = 49.7 bits (117), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 27/87 (31%), Positives = 42/87 (48%)
Query: 10  TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
           T+ V  L+E+  E  L   F PFG I  +    D+ T + + F F++F  +EDA +A+  
Sbjct: 17  TIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAG 76
Query: 70  MDGAELYGRVLTVNYALPERIKGGEQG 96
           + G      +L V +A P    G   G
Sbjct: 77  VSGFGYDHLILNVEWAKPSTNSGPSSG 103

>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage Stimulation Factor 64 Kda Subunit Length = 104

Iteration: 1
 Score = 49.7 bits (117), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 26/82 (31%), Positives = 43/82 (52%)
Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
          +++VG +  E  E  L   F   G +   +   D+ T K + +GF  + ++E A+ AM N
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 70 MDGAELYGRVLTVNYALPERIK 91
          ++G E  GR L V+ A  E+ K
Sbjct: 70 LNGREFSGRALRVDNAASEKNK 91

>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In Heterogeneous Nuclear Ribonucleoprotein Q Length = 103

Iteration: 1
 Score = 49.3 bits (116), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 27/78 (34%), Positives = 43/78 (55%), Gaps = 8/78 (10%)
Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
           L+V  LA  V E IL  AF  FG ++ VK        K + + F+ F E++ A++AM+ 
Sbjct: 13 VLFVRNLANTVTEEILEKAFSQFGKLERVK--------KLKDYAFIHFDERDGAVKAMEE 64
Query: 70 MDGAELYGRVLTVNYALP 87
          M+G +L G  + + +A P
Sbjct: 65 MNGKDLEGENIEIVFAKP 82

>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing Factor Length = 103

Iteration: 1
 Score = 48.9 bits (115), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 30/76 (39%), Positives = 37/76 (48%)
Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
          TL V  L    +   L   F  +G + DV  P +  T+  R F FV F ++ DA  A   
Sbjct: 15 TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA 74
Query: 70 MDGAELYGRVLTVNYA 85
          MDGAEL GR L V  A
Sbjct: 75 MDGAELDGRELRVQVA 90

>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In Complex With Polyadenylate Rna Length = 190

Iteration: 1
 Score = 48.5 bits (114), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 23/73 (31%), Positives = 41/73 (56%)
Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
          +LYVG L  +V EA+L+  F P G I  ++   D  T++   + +V F +  DA +A+D 
Sbjct: 12 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 71
Query: 70 MDGAELYGRVLTV 82
          M+   + G+ + +
Sbjct: 72 MNFDVIKGKPVRI 84

>pdb|1WTB|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of Hnrnp D (Auf1) With Telomere Dna Length = 79

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 20/58 (34%), Positives = 35/58 (60%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
          ++VGGL+ +  E  +   F  FG+++ ++ P+D  T K R F F+TF E+E   + M+
Sbjct: 4  IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 61

>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1) Length = 75

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 20/58 (34%), Positives = 35/58 (60%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
          ++VGGL+ +  E  +   F  FG+++ ++ P+D  T K R F F+TF E+E   + M+
Sbjct: 2  IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 59

>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In Complex With Rrm1-2 Of Pabp And Poly(A) Length = 213

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 23/73 (31%), Positives = 41/73 (56%)
Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
          +LYVG L  +V EA+L+  F P G I  ++   D  T++   + +V F +  DA +A+D 
Sbjct: 17 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 76
Query: 70 MDGAELYGRVLTV 82
          M+   + G+ + +
Sbjct: 77 MNFDVIKGKPVRI 89

>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago Complex Length = 165

Iteration: 1
 Score = 48.1 bits (113), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 24/88 (27%), Positives = 48/88 (54%), Gaps = 3/88 (3%)
Query: 11  LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
           L+V  + EE  E  +   F  +G+IK++   LD+ T   + +  V +   + A+ A + +
Sbjct: 75  LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 71  DGAELYGRVLTVNYAL---PERIKGGEQ 95
           +GAE+ G+ + V++     P+R+K  E+
Sbjct: 135 NGAEIMGQTIQVDWCFVKGPKRVKKSEK 162

>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein Length = 102

Iteration: 1
 Score = 47.8 bits (112), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 27/79 (34%), Positives = 45/79 (56%), Gaps = 3/79 (3%)
Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
          TL+V GL+E+  E  L  +F   G ++  +   D+ T   + FGFV F  +EDA  A + 
Sbjct: 17 TLFVKGLSEDTTEETLKESFD--GSVR-ARIVTDRETGSSKGFGFVDFNSEEDAKAAKEA 73
Query: 70 MDGAELYGRVLTVNYALPE 88
          M+  E+ G  +T+++A P+
Sbjct: 74 MEDGEIDGNKVTLDWAKPK 92

>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2 A Resolution Length = 89

Iteration: 1
 Score = 47.8 bits (112), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 23/82 (28%), Positives = 47/82 (57%)
Query: 5  AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
          +V+   L+V G+ EE  E  +H  F  +G+IK++   LD+ T   + +  V +   ++A 
Sbjct: 4  SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 63
Query: 65 QAMDNMDGAELYGRVLTVNYAL 86
           AM+ ++G +L G+ ++V++  
Sbjct: 64 AAMEGLNGQDLMGQPISVDWCF 85

>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd Machinery Length = 90

Iteration: 1
 Score = 47.8 bits (112), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 23/82 (28%), Positives = 47/82 (57%)
Query: 5  AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
          +V+   L+V G+ EE  E  +H  F  +G+IK++   LD+ T   + +  V +   ++A 
Sbjct: 4  SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 63
Query: 65 QAMDNMDGAELYGRVLTVNYAL 86
           AM+ ++G +L G+ ++V++  
Sbjct: 64 AAMEGLNGQDLMGQPISVDWCF 85

>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A Trapped Dead-Box Helicase Bound To Rna Length = 91

Iteration: 1
 Score = 47.4 bits (111), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 23/82 (28%), Positives = 47/82 (57%)
Query: 5  AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
          +V+   L+V G+ EE  E  +H  F  +G+IK++   LD+ T   + +  V +   ++A 
Sbjct: 6  SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 65
Query: 65 QAMDNMDGAELYGRVLTVNYAL 86
           AM+ ++G +L G+ ++V++  
Sbjct: 66 AAMEGLNGQDLMGQPISVDWCF 87

>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 109

Iteration: 1
 Score = 47.4 bits (111), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 23/82 (28%), Positives = 47/82 (57%)
Query: 5  AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
          +V+   L+V G+ EE  E  +H  F  +G+IK++   LD+ T   + +  V +   ++A 
Sbjct: 4  SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 63
Query: 65 QAMDNMDGAELYGRVLTVNYAL 86
           AM+ ++G +L G+ ++V++  
Sbjct: 64 AAMEGLNGQDLMGQPISVDWCF 85

>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX Length = 106

Iteration: 1
 Score = 47.4 bits (111), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 23/82 (28%), Positives = 47/82 (57%)
Query: 5   AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
           +V+   L+V G+ EE  E  +H  F  +G+IK++   LD+ T   + +  V +   ++A 
Sbjct: 20  SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 79
Query: 65  QAMDNMDGAELYGRVLTVNYAL 86
            AM+ ++G +L G+ ++V++  
Sbjct: 80  AAMEGLNGQDLMGQPISVDWCF 101

>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State Length = 126

Iteration: 1
 Score = 47.4 bits (111), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 23/82 (28%), Positives = 47/82 (57%)
Query: 5   AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
           +V+   L+V G+ EE  E  +H  F  +G+IK++   LD+ T   + +  V +   ++A 
Sbjct: 19  SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 78
Query: 65  QAMDNMDGAELYGRVLTVNYAL 86
            AM+ ++G +L G+ ++V++  
Sbjct: 79  AAMEGLNGQDLMGQPISVDWCF 100

>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human Putative Rna-Binding Protein 11 Length = 95

Iteration: 1
 Score = 47.4 bits (111), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 27/74 (36%), Positives = 39/74 (52%), Gaps = 1/74 (1%)
Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
          T++VG L   V E IL+  F+  G +  V    D+   K +SFGFV F   E    A+  
Sbjct: 18 TVFVGNLEARVREEILYELFLQAGPLTKVTICKDREG-KPKSFGFVCFKHPESVSYAIAL 76
Query: 70 MDGAELYGRVLTVN 83
          ++G  LYGR + V+
Sbjct: 77 LNGIRLYGRPINVS 90

>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In Daz- Associated Protein 1 Length = 99

Iteration: 1
 Score = 47.0 bits (110), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 26/79 (32%), Positives = 41/79 (51%), Gaps = 1/79 (1%)
Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
          N ++VGG+     E  L   F  FG + +V    D   Q+ R FGF+TF +++   QA+ 
Sbjct: 11 NKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV- 69
Query: 69 NMDGAELYGRVLTVNYALP 87
          NM   ++ G+ + V  A P
Sbjct: 70 NMHFHDIMGKKVEVKRAEP 88

>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In ArginineSERINE-Rich Splicing Factor 10 Length = 95

Iteration: 1
 Score = 46.6 bits (109), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 27/74 (36%), Positives = 38/74 (51%)
Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
           L V GL+    E  L   F  +G I DV    DQ +++ R F FV F   +DA +A + 
Sbjct: 17 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 76
Query: 70 MDGAELYGRVLTVN 83
           +G EL GR + V+
Sbjct: 77 ANGMELDGRRIRVS 90

>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger Cchc-Type And Rna Binding Motif 1 Length = 94

Iteration: 1
 Score = 46.6 bits (109), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 24/83 (28%), Positives = 43/83 (51%)
Query: 4  LAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDA 63
          LA  K+T+YV  L   +    L+  F  +G +  V    D+ T+K +   F+ FL+K+ A
Sbjct: 12 LAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSA 71
Query: 64 IQAMDNMDGAELYGRVLTVNYAL 86
                ++  +L+GRV+  + A+
Sbjct: 72 QNCTRAINNKQLFGRVIKASIAI 94

>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif Of Hypothetical Rna-Binding Protein Rbm19 Length = 107

Iteration: 1
 Score = 46.2 bits (108), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 25/69 (36%), Positives = 38/69 (55%), Gaps = 2/69 (2%)
Query: 19 EVNEAILHAAFIPFGDIKDVKTPLDQ-ATQKHRSFGFVTFLEKEDAIQAMDNM-DGAELY 76
          + N+  +   F  FG++K V+ P     T  HR FGFV F+ K+DA +A + +     LY
Sbjct: 26 QANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLY 85
Query: 77 GRVLTVNYA 85
          GR L + +A
Sbjct: 86 GRRLVLEWA 94

>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0 Rbd1), Nmr Length = 75

Iteration: 1
 Score = 45.8 bits (107), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 24/70 (34%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          +++GGL+ +  +  L   F  FG++ D    LD  T + R FGFV F E E   + MD  
Sbjct: 2  MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 71 DGAELYGRVL 80
          +  +L G+V+
Sbjct: 62 E-HKLNGKVI 70

>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14 Length = 97

Iteration: 1
 Score = 45.4 bits (106), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 28/77 (36%), Positives = 42/77 (54%), Gaps = 8/77 (10%)
Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
          NTLYV G  E++   +L  AF PFG+I      +D +    R+  FVT+ + E A QA+ 
Sbjct: 16 NTLYVYG--EDMTPTLLRGAFSPFGNI------IDLSMDPPRNCAFVTYEKMESADQAVA 67
Query: 69 NMDGAELYGRVLTVNYA 85
           ++G ++    L VN A
Sbjct: 68 ELNGTQVESVQLKVNIA 84

>pdb|2JX2|A Chain A, Solution Conformation Of Rna-Bound Nelf-E Rrm Length = 121

Iteration: 1
 Score = 45.4 bits (106), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 28/77 (36%), Positives = 42/77 (54%), Gaps = 8/77 (10%)
Query: 9   NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
           NTLYV G  E++   +L  AF PFG+I      +D +    R+  FVT+ + E A QA+ 
Sbjct: 40  NTLYVYG--EDMTPTLLRGAFSPFGNI------IDLSMDPPRNCAFVTYEKMESADQAVA 91
Query: 69  NMDGAELYGRVLTVNYA 85
            ++G ++    L VN A
Sbjct: 92  ELNGTQVESVQLKVNIA 108

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 45.1 bits (105), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 22/80 (27%), Positives = 43/80 (53%)
Query: 8  KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAM 67
          K  L V  L + + +    + F   G+I+  K   D+ T +   +GFV +++ +DA +A+
Sbjct: 2  KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61
Query: 68 DNMDGAELYGRVLTVNYALP 87
          + ++G  L  + + V+YA P
Sbjct: 62 NTLNGLRLQTKTIKVSYARP 81

>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2 Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori Length = 90

Iteration: 1
 Score = 45.1 bits (105), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 24/79 (30%), Positives = 41/79 (51%), Gaps = 1/79 (1%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          +YVG L        +   F  FG + +VK   D+ T+K + FGFV  +++E   +A+  +
Sbjct: 4  IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVE-MQEESVSEAIAKL 62
Query: 71 DGAELYGRVLTVNYALPER 89
          D  +  GR + V  A P++
Sbjct: 63 DNTDFMGRTIRVTEANPKK 81

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 45.1 bits (105), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 23/81 (28%), Positives = 42/81 (51%)
Query: 8  KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAM 67
          K  L V  L + + +    + F   GDI+  K   D+ T +   +GFV + +  DA +A+
Sbjct: 4  KTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAI 63
Query: 68 DNMDGAELYGRVLTVNYALPE 88
          + ++G +L  + + V+YA P 
Sbjct: 64 NTLNGLKLQTKTIKVSYARPS 84

>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1) Of Hu Antigen C (Huc) Length = 89

Iteration: 1
 Score = 44.7 bits (104), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 23/81 (28%), Positives = 42/81 (51%)
Query: 8  KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAM 67
          K  L V  L + + +    + F   GDI+  K   D+ T +   +GFV + +  DA +A+
Sbjct: 4  KTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAI 63
Query: 68 DNMDGAELYGRVLTVNYALPE 88
          + ++G +L  + + V+YA P 
Sbjct: 64 NTLNGLKLQTKTIKVSYARPS 84

>pdb|2KHC|A Chain A, Bruno Rrm3+ Length = 118

Iteration: 1
 Score = 44.7 bits (104), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 22/72 (30%), Positives = 40/72 (55%)
Query: 11  LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
           L++  L +E  +  L + F+PFG++   K  +D+ T   + FGFV+F   + A  A+  M
Sbjct: 43  LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 71  DGAELYGRVLTV 82
           +G ++  + L V
Sbjct: 103 NGFQVGTKRLKV 114

>pdb|1H2T|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc) In Complex With A Cap Analogue M7gpppg Length = 156

Iteration: 1
 Score = 44.3 bits (103), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 25/80 (31%), Positives = 39/80 (48%)
Query: 4   LAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDA 63
           L  +  TLYVG L+    E  ++  F   GDIK +   LD+  +    F FV +  + DA
Sbjct: 35  LLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADA 94
Query: 64  IQAMDNMDGAELYGRVLTVN 83
             AM  ++G  L  R++  +
Sbjct: 95  ENAMRYINGTRLDDRIIRTD 114

>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of Nucleolysin Tiar Length = 103

Iteration: 1
 Score = 44.3 bits (103), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 29/88 (32%), Positives = 43/88 (48%), Gaps = 3/88 (3%)
Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
          Q  TLYVG L+ +V E ++   F   G  K  K   +  +     + FV F E  DA  A
Sbjct: 14 QPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSND--PYCFVEFYEHRDAAAA 71
Query: 67 MDNMDGAELYGRVLTVNYA-LPERIKGG 93
          +  M+G ++ G+ + VN+A  P   K G
Sbjct: 72 LAAMNGRKILGKEVKVNWATTPSSQKSG 99

>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex Length = 110

Iteration: 1
 Score = 44.3 bits (103), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 23/88 (26%), Positives = 47/88 (53%), Gaps = 3/88 (3%)
Query: 5   AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
           +V+   L+V  + EE  E  +   F  +G+IK++   LD+ T   + +  V +   + A+
Sbjct: 23  SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQAL 82
Query: 65  QAMDNMDGAELYGRVLTVNYAL---PER 89
            A + ++GAE+ G+ + V++     P+R
Sbjct: 83  AAKEALNGAEIMGQTIQVDWCFVKGPKR 110

>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing Factor 3b Length = 96

Iteration: 1
 Score = 44.3 bits (103), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 26/85 (30%), Positives = 46/85 (54%), Gaps = 5/85 (5%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTP---LDQATQKHRSFGFVTFLEKEDAIQAM 67
          +++G L  E++E +L+  F  FG I  ++TP    D  T   + + F+ F   + +  A+
Sbjct: 8  IFIGNLDPEIDEKLLYDTFSAFGVI--LQTPKIMRDPDTGNSKGYAFINFASFDASDAAI 65
Query: 68 DNMDGAELYGRVLTVNYALPERIKG 92
          + M+G  L  R +TV+YA  +  KG
Sbjct: 66 EAMNGQYLCNRPITVSYAFKKDSKG 90

>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From Homo Sapiens At 1.90 A Resolution Length = 99

Iteration: 1
 Score = 43.9 bits (102), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 23/85 (27%), Positives = 42/85 (49%)
Query: 3  NLAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKED 62
          NL  Q   L V  L +   +  L + F   G+++  K   D+       +GFV ++  +D
Sbjct: 14 NLYFQGTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKD 73
Query: 63 AIQAMDNMDGAELYGRVLTVNYALP 87
          A +A++ ++G  L  + + V+YA P
Sbjct: 74 AERAINTLNGLRLQSKTIKVSYARP 98

>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical Protein Flj11016 Length = 115

Iteration: 1
 Score = 43.9 bits (102), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 24/76 (31%), Positives = 38/76 (50%)
Query: 10  TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
            LY+  L+  V E  L + F  F + K         T + R   F+TF  KE A QA+  
Sbjct: 27  VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 86
Query: 70  MDGAELYGRVLTVNYA 85
           ++G +LYG++L + + 
Sbjct: 87  VNGYKLYGKILVIEFG 102

>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In Polyadenylation Binding Protein 3 Length = 103

Iteration: 1
 Score = 43.5 bits (101), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 22/62 (35%), Positives = 34/62 (54%), Gaps = 2/62 (3%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          LYV  L + +++  L  AF PFG I   K  ++    + + FGFV F   E+A +A+  M
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGG--RSKGFGFVCFSSPEEATKAVTEM 75
Query: 71 DG 72
          +G
Sbjct: 76 NG 77

>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr Length = 75

Iteration: 1
 Score = 43.1 bits (100), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 22/70 (31%), Positives = 37/70 (52%), Gaps = 1/70 (1%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          ++VGGL+       +   F  FG + D     D+ T +HR FGFVTF E ED ++ +  +
Sbjct: 2  IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTF-ESEDIVEKVCEI 60
Query: 71 DGAELYGRVL 80
             E+  +++
Sbjct: 61 HFHEINNKMV 70

>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1 Rbd1:r(Guagu) Complex Length = 109

Iteration: 1
 Score = 42.7 bits (99), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 24/90 (26%), Positives = 44/90 (48%), Gaps = 5/90 (5%)
Query: 2   ANLAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKE 61
           +++      +++GGL+ +  +  L   F  FG++K+     D  T++ R FGFVTF+++ 
Sbjct: 19  SHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQA 78
Query: 62  --DAIQAMDNMDGAELYGRVLTVNYALPER 89
             D + A       EL  + +    A P R
Sbjct: 79  GVDKVLAQSR---HELDSKTIDPKVAFPRR 105

>pdb|1URN|A Chain A, U1a MutantRNA COMPLEX + GLYCEROL Length = 97

Iteration: 1
 Score = 42.0 bits (97), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 26/81 (32%), Positives = 39/81 (48%), Gaps = 7/81 (8%)
Query: 9  NTLYVGGLAEEVNE----AILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
          +T+Y+  L E++ +      LHA F  FG I D+   L   + K R   FV F E   A 
Sbjct: 9  HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDI---LVSRSLKMRGQAFVIFKEVSSAT 65
Query: 65 QAMDNMDGAELYGRVLTVNYA 85
           A+ +M G   Y + + + YA
Sbjct: 66 NALRSMQGFPFYDKPMRIQYA 86

>pdb|1U6B|A Chain A, Crystal Structure Of A Self-Splicing Group I Intron With Both Exons Length = 98

Iteration: 1
 Score = 42.0 bits (97), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 26/81 (32%), Positives = 39/81 (48%), Gaps = 7/81 (8%)
Query: 9  NTLYVGGLAEEVNE----AILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
          +T+Y+  L E++ +      LHA F  FG I D+   L   + K R   FV F E   A 
Sbjct: 10 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDI---LVSRSLKMRGQAFVIFKEVSSAT 66
Query: 65 QAMDNMDGAELYGRVLTVNYA 85
           A+ +M G   Y + + + YA
Sbjct: 67 NALRSMQGFPFYDKPMRIQYA 87

>pdb|3BO2|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I Intron Length = 95

Iteration: 1
 Score = 42.0 bits (97), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 26/81 (32%), Positives = 39/81 (48%), Gaps = 7/81 (8%)
Query: 9  NTLYVGGLAEEVNE----AILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
          +T+Y+  L E++ +      LHA F  FG I D+   L   + K R   FV F E   A 
Sbjct: 7  HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDI---LVSRSLKMRGQAFVIFKEVSSAT 63
Query: 65 QAMDNMDGAELYGRVLTVNYA 85
           A+ +M G   Y + + + YA
Sbjct: 64 NALRSMQGFPFYDKPMRIQYA 84

>pdb|1M5K|C Chain C, Crystal Structure Of A Hairpin Ribozyme In The Catalytically-Active Conformation Length = 100

Iteration: 1
 Score = 42.0 bits (97), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 26/81 (32%), Positives = 39/81 (48%), Gaps = 7/81 (8%)
Query: 9  NTLYVGGLAEEVNE----AILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
          +T+Y+  L E++ +      LHA F  FG I D+   L   + K R   FV F E   A 
Sbjct: 10 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDI---LVSRSLKMRGQAFVIFKEVSSAT 66
Query: 65 QAMDNMDGAELYGRVLTVNYA 85
           A+ +M G   Y + + + YA
Sbjct: 67 NALRSMQGFPFYDKPMRIQYA 87

>pdb|3K0J|A Chain A, Crystal Structure Of The E. Coli Thim Riboswitch In Complex With Thiamine Pyrophosphate And The U1a Crystallization Module Length = 96

Iteration: 1
 Score = 42.0 bits (97), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 26/81 (32%), Positives = 39/81 (48%), Gaps = 7/81 (8%)
Query: 9  NTLYVGGLAEEVNE----AILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
          +T+Y+  L E++ +      LHA F  FG I D+   L   + K R   FV F E   A 
Sbjct: 9  HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDI---LVSRSLKMRGQAFVIFKEVSSAT 65
Query: 65 QAMDNMDGAELYGRVLTVNYA 85
           A+ +M G   Y + + + YA
Sbjct: 66 NALRSMQGFPFYDKPMRIQYA 86

>pdb|2NZ4|A Chain A, Structural Investigation Of The Glms Ribozyme Bound To Its Catalytic Cofactor Length = 94

Iteration: 1
 Score = 42.0 bits (97), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 26/81 (32%), Positives = 39/81 (48%), Gaps = 7/81 (8%)
Query: 9  NTLYVGGLAEEVNE----AILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
          +T+Y+  L E++ +      LHA F  FG I D+   L   + K R   FV F E   A 
Sbjct: 6  HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDI---LVSRSLKMRGQAFVIFKEVSSAT 62
Query: 65 QAMDNMDGAELYGRVLTVNYA 85
           A+ +M G   Y + + + YA
Sbjct: 63 NALRSMQGFPFYDKPMRIQYA 83

>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna- Binding Region Containing Protein 1 Length = 116

Iteration: 1
 Score = 42.0 bits (97), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 29/83 (34%), Positives = 43/83 (51%), Gaps = 5/83 (6%)
Query: 7  QKNT----LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKED 62
          QK+T    ++VGGL     +A L   F  FGDI++     D+ T K R +GFVT  ++  
Sbjct: 12 QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAA 71
Query: 63 AIQAMDNMDGAELYGRVLTVNYA 85
          A +A  + +   + GR   VN A
Sbjct: 72 AERACKDPN-PIIDGRKANVNLA 93

>pdb|3L3C|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme Bound To Glc6p Length = 90

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 26/81 (32%), Positives = 39/81 (48%), Gaps = 7/81 (8%)
Query: 9  NTLYVGGLAEEVNE----AILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
          +T+Y+  L E++ +      LHA F  FG I D+   L   + K R   FV F E   A 
Sbjct: 4  HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDI---LVSRSLKMRGQAFVIFKEVSSAT 60
Query: 65 QAMDNMDGAELYGRVLTVNYA 85
           A+ +M G   Y + + + YA
Sbjct: 61 NALRSMQGFPFYDKPMRIQYA 81

>pdb|1AUD|A Chain A, U1a-Utrrna, Nmr, 31 Structures Length = 101

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 26/81 (32%), Positives = 39/81 (48%), Gaps = 7/81 (8%)
Query: 9  NTLYVGGLAEEVNE----AILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
          +T+Y+  L E++ +      LHA F  FG I D+   L   + K R   FV F E   A 
Sbjct: 9  HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDI---LVSRSLKMRGQAFVIFKEVSSAT 65
Query: 65 QAMDNMDGAELYGRVLTVNYA 85
           A+ +M G   Y + + + YA
Sbjct: 66 NALRSMQGFPFYDKPMRIQYA 86

>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar Length = 109

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/81 (27%), Positives = 41/81 (50%), Gaps = 7/81 (8%)
Query: 1  MANLAVQKN-TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLE 59
          + N +  KN T+Y GG+A  + + ++   F PFG I +++          + + FV F  
Sbjct: 17 VVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIR------VFPEKGYSFVRFST 70
Query: 60 KEDAIQAMDNMDGAELYGRVL 80
           E A  A+ +++G  + G V+
Sbjct: 71 HESAAHAIVSVNGTTIEGHVV 91

>pdb|3IWN|C Chain C, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch Length = 91

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 26/81 (32%), Positives = 39/81 (48%), Gaps = 7/81 (8%)
Query: 9  NTLYVGGLAEEVNE----AILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
          +T+Y+  L E++ +      LHA F  FG I D+   L   + K R   FV F E   A 
Sbjct: 5  HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDI---LVSRSLKMRGQAFVIFKEVSSAT 61
Query: 65 QAMDNMDGAELYGRVLTVNYA 85
           A+ +M G   Y + + + YA
Sbjct: 62 NALRSMQGFPFYDKPMRIQYA 82

>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi) G); A Human Telomeric Repeat Containing 6-Methyl-8-(2- Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi) Length = 195

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 26/80 (32%), Positives = 41/80 (51%), Gaps = 1/80 (1%)
Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
          Q   L++GGL+ E  +  L + F  +G + D     D  T++ R FGFVT+   E+   A
Sbjct: 11 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 70
Query: 67 MDNMDGAELYGRVLTVNYAL 86
          M N    ++ GRV+    A+
Sbjct: 71 M-NARPHKVDGRVVEPKRAV 89

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 26/80 (32%), Positives = 41/80 (51%), Gaps = 1/80 (1%)
Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
          Q   L++GGL+ E  +  L + F  +G + D     D  T++ R FGFVT+   E+   A
Sbjct: 12 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 71
Query: 67 MDNMDGAELYGRVLTVNYAL 86
          M N    ++ GRV+    A+
Sbjct: 72 M-NARPHKVDGRVVEPKRAV 90

>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1 (up1) Using Segmental Isotope Labeling Length = 197

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 26/80 (32%), Positives = 41/80 (51%), Gaps = 1/80 (1%)
Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
          Q   L++GGL+ E  +  L + F  +G + D     D  T++ R FGFVT+   E+   A
Sbjct: 13 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 72
Query: 67 MDNMDGAELYGRVLTVNYAL 86
          M N    ++ GRV+    A+
Sbjct: 73 M-NARPHKVDGRVVEPKRAV 91

>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition Motif (Rrm1) Of The Au-Rich Element (Are) Binding Protein Hur At 2.0 Angstrom Resolution Length = 84

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 20/81 (24%), Positives = 41/81 (50%)
Query: 8  KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAM 67
          +  L V  L + + +  L + F   G+++  K   D+       +GFV ++  +DA +A+
Sbjct: 4  RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 63
Query: 68 DNMDGAELYGRVLTVNYALPE 88
          + ++G  L  + + V+YA P 
Sbjct: 64 NTLNGLRLQSKTIKVSYARPS 84

>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of Mouse Musashi1 Length = 77

Iteration: 1
 Score = 41.2 bits (95), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 17/50 (34%), Positives = 31/50 (62%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEK 60
          +++GGL+ +  +  L   F  FG++K+     D  T++ R FGFVTF+++
Sbjct: 3  MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQ 52

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 41.2 bits (95), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 20/80 (25%), Positives = 41/80 (51%)
Query: 8  KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAM 67
          +  L V  L + + +  L + F   G+++  K   D+       +GFV ++  +DA +A+
Sbjct: 2  RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 61
Query: 68 DNMDGAELYGRVLTVNYALP 87
          + ++G  L  + + V+YA P
Sbjct: 62 NTLNGLRLQSKTIKVSYARP 81

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 41.2 bits (95), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 20/80 (25%), Positives = 41/80 (51%)
Query: 8  KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAM 67
          +  L V  L + + +  L + F   G+++  K   D+       +GFV ++  +DA +A+
Sbjct: 2  RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 61
Query: 68 DNMDGAELYGRVLTVNYALP 87
          + ++G  L  + + V+YA P
Sbjct: 62 NTLNGLRLQSKTIKVSYARP 81

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 41.2 bits (95), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 26/80 (32%), Positives = 41/80 (51%), Gaps = 1/80 (1%)
Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
          Q   L++GGL+ E  +  L + F  +G + D     D  T++ R FGFVT+   E+   A
Sbjct: 10 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 69
Query: 67 MDNMDGAELYGRVLTVNYAL 86
          M N    ++ GRV+    A+
Sbjct: 70 M-NARPHKVDGRVVEPKRAV 88

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 41.2 bits (95), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 26/80 (32%), Positives = 41/80 (51%), Gaps = 1/80 (1%)
Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
          Q   L++GGL+ E  +  L + F  +G + D     D  T++ R FGFVT+   E+   A
Sbjct: 5  QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 64
Query: 67 MDNMDGAELYGRVLTVNYAL 86
          M N    ++ GRV+    A+
Sbjct: 65 M-NARPHKVDGRVVEPKRAV 83

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 41.2 bits (95), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 26/80 (32%), Positives = 41/80 (51%), Gaps = 1/80 (1%)
Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
          Q   L++GGL+ E  +  L + F  +G + D     D  T++ R FGFVT+   E+   A
Sbjct: 12 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 71
Query: 67 MDNMDGAELYGRVLTVNYAL 86
          M N    ++ GRV+    A+
Sbjct: 72 M-NARPHKVDGRVVEPKRAV 90

>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2) Of Hu Antigen C (Huc) Length = 85

Iteration: 1
 Score = 41.2 bits (95), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 24/77 (31%), Positives = 42/77 (54%), Gaps = 2/77 (2%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          LYV GL + +++  +   F  +G I   +  LDQAT   R  GF+ F ++ +A +A+  +
Sbjct: 4  LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 71 DGAELYG--RVLTVNYA 85
          +G +  G    +TV +A
Sbjct: 64 NGQKPLGAAEPITVKFA 80

>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet Repeat Rna-Binding Protein 1 Length = 115

Iteration: 1
 Score = 40.4 bits (93), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 21/72 (29%), Positives = 39/72 (54%)
Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          L++  L +E  +  L   F+PFG++   K  +D+ T   + FGFV++     A  A+ +M
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87
Query: 71 DGAELYGRVLTV 82
          +G ++  + L V
Sbjct: 88 NGFQIGMKRLKV 99

>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex Length = 98

Iteration: 1
 Score = 40.4 bits (93), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 25/81 (30%), Positives = 40/81 (49%), Gaps = 1/81 (1%)
Query: 4  LAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDA 63
          L  +  TLYVG L+    E  ++  F   GDIK +   LD+  +    F FV +  + DA
Sbjct: 14 LLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKM-KTACGFCFVEYYSRADA 72
Query: 64 IQAMDNMDGAELYGRVLTVNY 84
            AM  ++G  L  R++  ++
Sbjct: 73 ENAMRYINGTRLDDRIIRTDW 93

>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117, Nmr, 43 Structures Length = 116

Iteration: 1
 Score = 40.0 bits (92), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 25/81 (30%), Positives = 39/81 (48%), Gaps = 7/81 (8%)
Query: 9  NTLYVGGLAEEVNE----AILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
          +T+Y+  L E++ +      L+A F  FG I D+   L   + K R   FV F E   A 
Sbjct: 9  HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDI---LVSRSLKMRGQAFVIFKEVSSAT 65
Query: 65 QAMDNMDGAELYGRVLTVNYA 85
           A+ +M G   Y + + + YA
Sbjct: 66 NALRSMQGFPFYDKPMRIQYA 86

>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear Ribonucleaoproteins A2B1 Length = 116

Iteration: 1
 Score = 40.0 bits (92), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 19/51 (37%), Positives = 28/51 (54%)
Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTF 57
          Q   L++GGL+ E  E  L   +  +G + D     D A+++ R FGFVTF
Sbjct: 26 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTF 76

>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp Length = 282

Iteration: 1
 Score = 40.0 bits (92), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 25/81 (30%), Positives = 39/81 (48%), Gaps = 7/81 (8%)
Query: 9  NTLYVGGLAEEVNE----AILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
          +T+Y+  L E++ +      L+A F  FG I D+   L   + K R   FV F E   A 
Sbjct: 10 HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDI---LVSRSLKMRGQAFVIFKEVSSAT 66
Query: 65 QAMDNMDGAELYGRVLTVNYA 85
           A+ +M G   Y + + + YA
Sbjct: 67 NALRSMQGFPFYDKPMRIQYA 87

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	174
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	1e-36
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	2e-36
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	2e-35
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	5e-34
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	7e-29
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	4e-28
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	1e-27
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	1e-27
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	1e-27
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	2e-27
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	8e-27
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	9e-27
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	9e-27
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	1e-26
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	1e-26
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	1e-26
1x5p_A	97	Negative elongation factor E; structure genomics,	1e-26
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	2e-26
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	2e-26
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	3e-26
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	6e-26
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	6e-26
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	7e-26
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	8e-26
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-25
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	4e-25
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	5e-25
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	6e-25
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	7e-25
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	9e-25
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	2e-24
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	2e-24
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	3e-24
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	3e-24
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	3e-24
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	4e-20
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	3e-24
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	1e-18
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	4e-24
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	4e-17
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	4e-24
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-18
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	4e-24
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	4e-24
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	2e-21
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	7e-24
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	4e-18
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-15
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	7e-24
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	1e-23
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	1e-23
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	1e-23
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	1e-23
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	2e-23
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	2e-23
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	2e-23
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	3e-23
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	8e-23
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-22
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	1e-22
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-22
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	2e-22
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	4e-22
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	7e-22
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	9e-22
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	1e-21
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	1e-21
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	1e-21
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	3e-21
1x4e_A	85	RNA binding motif, single-stranded interacting pro	5e-21
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	5e-21
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	5e-21
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	7e-21
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	7e-21
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	8e-21
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	9e-21
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	2e-20
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	2e-20
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	3e-20
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	5e-20
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	3e-17
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	8e-14
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	7e-20
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	8e-20
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-19
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	8e-19
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	1e-19
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	1e-19
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	2e-19
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	4e-19
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	4e-19
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	5e-19
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	5e-19
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	7e-19
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	7e-19
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	9e-17
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	2e-18
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-18
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	2e-18
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	2e-18
2div_A	99	TRNA selenocysteine associated protein; structural	3e-18
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	4e-18
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	4e-18
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	4e-18
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	5e-18
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	6e-18
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	6e-18
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	7e-18
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	8e-18
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	2e-17
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	2e-17
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	2e-17
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	3e-17
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	4e-17
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-16
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	5e-17
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	6e-17
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	6e-17
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	8e-17
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	8e-17
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	3e-15
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-16
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	7e-13
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	1e-16
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	1e-16
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	1e-16
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	4e-16
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	2e-16
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	2e-16
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	5e-16
1x5o_A	114	RNA binding motif, single-stranded interacting pro	5e-16
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	5e-16
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	6e-16
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	6e-16
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	1e-12
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	7e-16
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	7e-16
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	8e-16
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	9e-16
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	3e-09
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	1e-15
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	1e-15
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	7e-12
2dis_A	109	Unnamed protein product; structural genomics, RRM	1e-15
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	2e-15
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	2e-15
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	3e-15
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	6e-15
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	6e-15
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	2e-14
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	2e-14
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	6e-14
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	7e-14
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	1e-13
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	1e-13
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-13
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	2e-13
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	5e-13
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	8e-13
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	9e-13
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	9e-13
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	3e-12
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	3e-12
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	8e-12
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	1e-11
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	2e-11
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	2e-11
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	4e-11
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	4e-11
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	1e-10
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	4e-10
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	8e-10
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	4e-09
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	7e-09
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	9e-09
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	1e-08
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	2e-08
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	3e-08
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	4e-08
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	2e-07
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	4e-07
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	6e-07
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	6e-07
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	6e-07
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	2e-06
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	2e-06
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	2e-05
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	3e-05
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	3e-05
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	3e-04
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	4e-04

>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 =  121 bits (306), Expect = 1e-36
 Identities = 52/90 (57%), Positives = 63/90 (70%)

Query: 7   QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
            K  LYVGGLAEEV++ +LHAAFIPFGDI D++ PLD  T+KHR F FV F   EDA  A
Sbjct: 11  TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 70

Query: 67  MDNMDGAELYGRVLTVNYALPERIKGGEQG 96
           +DNM+ +EL+GR + VN A P RIK     
Sbjct: 71  IDNMNESELFGRTIRVNLAKPMRIKESGPS 100

>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 =  120 bits (303), Expect = 2e-36
 Identities = 49/84 (58%), Positives = 62/84 (73%)

Query: 2  ANLAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKE 61
           ++A  K  LYVGGLAEEV++ +LHAAFIPFGDI D++ PLD  T+KHR F FV F   E
Sbjct: 1  GSMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 60

Query: 62 DAIQAMDNMDGAELYGRVLTVNYA 85
          DA  A+DNM+ +EL+GR + VN A
Sbjct: 61 DAAAAIDNMNESELFGRTIRVNLA 84

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score =  119 bits (301), Expect = 2e-35
 Identities = 48/79 (60%), Positives = 59/79 (74%)

Query: 7   QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
            K  LYVGGLAEEV++ +LHAAFIPFGDI D++ PLD  T+KHR F FV F   EDA  A
Sbjct: 62  TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 121

Query: 67  MDNMDGAELYGRVLTVNYA 85
           +DNM+ +EL+GR + VN A
Sbjct: 122 IDNMNESELFGRTIRVNLA 140

>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 =  115 bits (289), Expect = 5e-34
 Identities = 36/92 (39%), Positives = 54/92 (58%), Gaps = 2/92 (2%)

Query: 7   QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
           Q  T+YVGGL E+V+E +L   F+  G + +   P D+ T +H+ +GFV FL +EDA  A
Sbjct: 14  QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA 73

Query: 67  MDNMDGAELYGRVLTVNYALP--ERIKGGEQG 96
           +  MD  +LYG+ + VN A    + + G   G
Sbjct: 74  IKIMDMIKLYGKPIRVNKASAHNKNLSGPSSG 105

>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 =  101 bits (254), Expect = 7e-29
 Identities = 27/88 (30%), Positives = 42/88 (47%)

Query: 9   NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
            T+ V  L+E+  E  L   F PFG I  +    D+ T + + F F++F  +EDA +A+ 
Sbjct: 16  ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIA 75

Query: 69  NMDGAELYGRVLTVNYALPERIKGGEQG 96
            + G      +L V +A P    G   G
Sbjct: 76  GVSGFGYDHLILNVEWAKPSTNSGPSSG 103

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score =  100 bits (250), Expect = 4e-28
 Identities = 23/84 (27%), Positives = 46/84 (54%)

Query: 6   VQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQ 65
           V+   L+V G+ EE  E  +H  F  +G+IK++   LD+ T   + +  V +   ++A  
Sbjct: 21  VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQA 80

Query: 66  AMDNMDGAELYGRVLTVNYALPER 89
           AM+ ++G +L G+ ++V++     
Sbjct: 81  AMEGLNGQDLMGQPISVDWCFVRG 104

>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 = 99.3 bits (248), Expect = 1e-27
 Identities = 31/90 (34%), Positives = 44/90 (48%), Gaps = 1/90 (1%)

Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
              L++GGL  E NE +L A F   G I +V    D+ T K R F F+TF    DA  A
Sbjct: 6  HPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNA 64

Query: 67 MDNMDGAELYGRVLTVNYALPERIKGGEQG 96
            +M+G  L+G+ + V  A     + G + 
Sbjct: 65 AKDMNGKSLHGKAIKVEQAKKPSFQSGGRR 94

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A Length = 129

 Score = 99.4 bits (248), Expect = 1e-27
 Identities = 28/81 (34%), Positives = 43/81 (53%)

Query: 9   NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
             L V GL+    E  L   F  +G I DV    DQ +++ R F FV F   +DA +A +
Sbjct: 47  CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 106

Query: 69  NMDGAELYGRVLTVNYALPER 89
             +G EL GR + V++++ +R
Sbjct: 107 RANGMELDGRRIRVDFSITKR 127

>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 = 98.5 bits (246), Expect = 1e-27
 Identities = 26/85 (30%), Positives = 42/85 (49%), Gaps = 2/85 (2%)

Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
          Q  TLYVG L+ +V E ++   F   G  K  K   +  +  +  + FV F E  DA  A
Sbjct: 14 QPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAA 71

Query: 67 MDNMDGAELYGRVLTVNYALPERIK 91
          +  M+G ++ G+ + VN+A     +
Sbjct: 72 LAAMNGRKILGKEVKVNWATTPSSQ 96

>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 = 98.1 bits (245), Expect = 2e-27
 Identities = 24/85 (28%), Positives = 43/85 (50%)

Query: 2  ANLAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKE 61
            LA  K+T+YV  L   +    L+  F  +G +  V    D+ T+K +   F+ FL+K+
Sbjct: 10 GGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKD 69

Query: 62 DAIQAMDNMDGAELYGRVLTVNYAL 86
           A      ++  +L+GRV+  + A+
Sbjct: 70 SAQNCTRAINNKQLFGRVIKASIAI 94

>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 = 96.1 bits (240), Expect = 8e-27
 Identities = 27/77 (35%), Positives = 38/77 (49%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
            L V GL+    E  L   F  +G I DV    DQ +++ R F FV F   +DA +A +
Sbjct: 16 CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 75

Query: 69 NMDGAELYGRVLTVNYA 85
            +G EL GR + V+  
Sbjct: 76 RANGMELDGRRIRVSGP 92

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 97.5 bits (243), Expect = 9e-27
 Identities = 33/81 (40%), Positives = 41/81 (50%)

Query: 9   NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
            +L V  L    +   L   F  +G + DV  P D+ T++ R F FV F +K DA  AMD
Sbjct: 48  TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 107

Query: 69  NMDGAELYGRVLTVNYALPER 89
            MDGA L GR L V  A   R
Sbjct: 108 AMDGAVLDGRELRVQMARYGR 128

>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 = 96.5 bits (241), Expect = 9e-27
 Identities = 31/80 (38%), Positives = 38/80 (47%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
          TL V  L    +   L   F  +G + DV  P +  T+  R F FV F ++ DA  A   
Sbjct: 15 TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA 74

Query: 70 MDGAELYGRVLTVNYALPER 89
          MDGAEL GR L V  A   R
Sbjct: 75 MDGAELDGRELRVQVARYGR 94

>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 = 97.1 bits (242), Expect = 1e-26
 Identities = 23/88 (26%), Positives = 47/88 (53%)

Query: 9   NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
             L+V G+ EE  E  +H  F  +G+IK++   LD+ T   + +  V +   ++A  AM+
Sbjct: 23  WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 82

Query: 69  NMDGAELYGRVLTVNYALPERIKGGEQG 96
            ++G +L G+ ++V++        G++ 
Sbjct: 83  GLNGQDLMGQPISVDWCFVRGPPKGKRR 110

>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 = 95.7 bits (239), Expect = 1e-26
 Identities = 18/82 (21%), Positives = 39/82 (47%), Gaps = 1/82 (1%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLD-QATQKHRSFGFVTFLEKEDAIQAM 67
            +++G L   V +  +   F  +G IK +  P++       + + +V F   ++A +A+
Sbjct: 5  TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64

Query: 68 DNMDGAELYGRVLTVNYALPER 89
           +MDG ++ G+ +T    L   
Sbjct: 65 KHMDGGQIDGQEITATAVLAPW 86

>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 = 95.8 bits (239), Expect = 1e-26
 Identities = 30/92 (32%), Positives = 44/92 (47%), Gaps = 10/92 (10%)

Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
          + NTLYV G   ++   +L  AF PFG+I D+           R+  FVT+ + E A QA
Sbjct: 14 KGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQA 65

Query: 67 MDNMDGAELYGRVLTVNYA--LPERIKGGEQG 96
          +  ++G ++    L VN A   P    G   G
Sbjct: 66 VAELNGTQVESVQLKVNIARKQPMLDSGPSSG 97

>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 = 95.4 bits (238), Expect = 2e-26
 Identities = 34/90 (37%), Positives = 47/90 (52%), Gaps = 2/90 (2%)

Query: 9   NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
             L+VGGL+ + NE  L   F  +G I +V    D+ TQ+ R FGFVTF   +DA  AM 
Sbjct: 13  GKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMM 72

Query: 69  NMDGAELYGRVLTVNYALP--ERIKGGEQG 96
            M+G  + GR + V+ A    +   G   G
Sbjct: 73  AMNGKSVDGRQIRVDQAGKSSDNRSGPSSG 102

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 94.9 bits (237), Expect = 2e-26
 Identities = 29/90 (32%), Positives = 47/90 (52%), Gaps = 2/90 (2%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
          + LYVG L   + E +L   F PFG I ++    D  T + + +GF+TF + E A +A++
Sbjct: 6  SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65

Query: 69 NMDGAELYGRVLTVNYALP--ERIKGGEQG 96
           ++G EL GR + V +     +   G   G
Sbjct: 66 QLNGFELAGRPMRVGHVTERLDGGSGPSSG 95

>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 = 95.8 bits (239), Expect = 3e-26
 Identities = 24/81 (29%), Positives = 40/81 (49%)

Query: 9   NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
             LY+  L+  V E  L + F  F + K         T + R   F+TF  KE A QA+ 
Sbjct: 26  KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 85

Query: 69  NMDGAELYGRVLTVNYALPER 89
            ++G +LYG++L + +   ++
Sbjct: 86  LVNGYKLYGKILVIEFGKNKK 106

>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 = 94.2 bits (235), Expect = 6e-26
 Identities = 19/91 (20%), Positives = 38/91 (41%)

Query: 10  TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
            +Y+G +  +  E  +       G + ++K   D  T + + + F+ F + E +  A+ N
Sbjct: 4   VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 63

Query: 70  MDGAELYGRVLTVNYALPERIKGGEQGWAAQ 100
           ++G +L  R L   Y+    I G        
Sbjct: 64  LNGYQLGSRFLKCGYSSNSDISGVSLEHHHH 94

>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 = 93.8 bits (234), Expect = 6e-26
 Identities = 32/77 (41%), Positives = 44/77 (57%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          ++VG L+ E+  A + AAF PFG I D +   D AT K + +GFV+F  K DA  A+  M
Sbjct: 9  VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68

Query: 71 DGAELYGRVLTVNYALP 87
           G  L GR +  N+A  
Sbjct: 69 GGQWLGGRQIRTNWATR 85

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 94.4 bits (235), Expect = 7e-26
 Identities = 15/78 (19%), Positives = 30/78 (38%)

Query: 8  KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAM 67
             +    L + V E  L      +G++++V+  L   T+KH     V F     A + +
Sbjct: 6  LKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETV 65

Query: 68 DNMDGAELYGRVLTVNYA 85
           N+    + G ++     
Sbjct: 66 KNLHLTSVMGNIIHAQLD 83

>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 = 93.3 bits (233), Expect = 8e-26
 Identities = 29/79 (36%), Positives = 40/79 (50%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
            L+VG L   V++  L  AF  F          D  T   R +GFV+F  ++DA  AMD
Sbjct: 2  FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61

Query: 69 NMDGAELYGRVLTVNYALP 87
          +M G +L GR L +N+A  
Sbjct: 62 SMQGQDLNGRPLRINWAAK 80

>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 = 93.8 bits (234), Expect = 1e-25
 Identities = 25/90 (27%), Positives = 44/90 (48%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
            L+V  L+   +E  L   F  +G + ++  P+D  T+K + F FVTF+  E A++A  
Sbjct: 9  GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

Query: 69 NMDGAELYGRVLTVNYALPERIKGGEQGWA 98
           +DG    GR+L V  +  ++        +
Sbjct: 69 EVDGQVFQGRMLHVLPSTIKKEASQSGPSS 98

>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 = 91.9 bits (229), Expect = 4e-25
 Identities = 27/79 (34%), Positives = 39/79 (49%), Gaps = 1/79 (1%)

Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
             T++VG L   V E IL+  F+  G +  V    D+   K +SFGFV F   E    A
Sbjct: 15 ADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREG-KPKSFGFVCFKHPESVSYA 73

Query: 67 MDNMDGAELYGRVLTVNYA 85
          +  ++G  LYGR + V+  
Sbjct: 74 IALLNGIRLYGRPINVSGP 92

>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 = 92.4 bits (230), Expect = 5e-25
 Identities = 31/78 (39%), Positives = 43/78 (55%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
           ++VG L+ E+    + AAF PFG I D +   D AT K + +GFV+F  K DA  A+  
Sbjct: 17 HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76

Query: 70 MDGAELYGRVLTVNYALP 87
          M G  L GR +  N+A  
Sbjct: 77 MGGQWLGGRQIRTNWATR 94

>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 = 93.7 bits (233), Expect = 6e-25
 Identities = 22/92 (23%), Positives = 48/92 (52%)

Query: 5   AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
           +V+   L+V  + EE  E  +   F  +G+IK++   LD+ T   + +  V +   + A+
Sbjct: 69  SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQAL 128

Query: 65  QAMDNMDGAELYGRVLTVNYALPERIKGGEQG 96
            A + ++GAE+ G+ + V++   +  K  ++ 
Sbjct: 129 AAKEALNGAEIMGQTIQVDWCFVKGPKRVKKS 160

>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 = 91.6 bits (228), Expect = 7e-25
 Identities = 21/84 (25%), Positives = 44/84 (52%)

Query: 6   VQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQ 65
           V+   L+V  + EE  E  +   F  +G+IK++   LD+ T   + +  V +   + A+ 
Sbjct: 24  VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALA 83

Query: 66  AMDNMDGAELYGRVLTVNYALPER 89
           A + ++GAE+ G+ + V++   + 
Sbjct: 84  AKEALNGAEIMGQTIQVDWCFVKG 107

>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 = 91.2 bits (227), Expect = 9e-25
 Identities = 21/86 (24%), Positives = 42/86 (48%), Gaps = 7/86 (8%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
          N LY+G L+  V    L   F           PL         + FV + ++  AI+A++
Sbjct: 9  NKLYIGNLSPAVTADDLRQLFGDRK------LPLAGQVLLKSGYAFVDYPDQNWAIRAIE 62

Query: 69 NMDG-AELYGRVLTVNYALPERIKGG 93
           + G  EL+G+++ V+Y++ ++++  
Sbjct: 63 TLSGKVELHGKIMEVDYSVSKKLRSS 88

>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 = 92.2 bits (229), Expect = 2e-24
 Identities = 24/81 (29%), Positives = 39/81 (48%)

Query: 9   NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
            TLYVG L+    E  ++  F   GDIK +   LD+  +    F FV +  + DA  AM 
Sbjct: 40  CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 99

Query: 69  NMDGAELYGRVLTVNYALPER 89
            ++G  L  R++  ++    +
Sbjct: 100 YINGTRLDDRIIRTDWDAGFK 120

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 93.9 bits (234), Expect = 2e-24
 Identities = 21/79 (26%), Positives = 43/79 (54%)

Query: 9   NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
           N +YV  + +++++  + + F  FG IK      D  T KH+ +GF+ + + + +  A+ 
Sbjct: 126 NRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVS 185

Query: 69  NMDGAELYGRVLTVNYALP 87
           +M+  +L G+ L V  A+ 
Sbjct: 186 SMNLFDLGGQYLRVGKAVT 204

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 93.1 bits (232), Expect = 3e-24
 Identities = 27/83 (32%), Positives = 39/83 (46%)

Query: 7   QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
             + +YVG +  E+ E  +  AF PFG IK +    D  T KH+ F FV +   E A  A
Sbjct: 27  IMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLA 86

Query: 67  MDNMDGAELYGRVLTVNYALPER 89
           ++ M+   L GR + V       
Sbjct: 87  LEQMNSVMLGGRNIKVGRPSNIG 109

>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 = 90.1 bits (224), Expect = 3e-24
 Identities = 27/85 (31%), Positives = 43/85 (50%), Gaps = 2/85 (2%)

Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQ-ATQKHRSFGFVTFLEKEDAIQ 65
            + + V  +  + N+  +   F  FG++K V+ P     T  HR FGFV F+ K+DA +
Sbjct: 14 TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKK 73

Query: 66 AMDNM-DGAELYGRVLTVNYALPER 89
          A + +     LYGR L + +A  E 
Sbjct: 74 AFNALCHSTHLYGRRLVLEWADSEV 98

>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 = 91.9 bits (229), Expect = 3e-24
 Identities = 24/86 (27%), Positives = 40/86 (46%), Gaps = 2/86 (2%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
           L V  L +++ +  L+A F   G I   +   D  T     + FV F  + D+ +A+  
Sbjct: 5  NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64

Query: 70 MDGAELYGRVLTVNYALP--ERIKGG 93
          ++G  +  + L V+YA P  E IK  
Sbjct: 65 LNGITVRNKRLKVSYARPGGESIKDT 90

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 81.1 bits (201), Expect = 4e-20
 Identities = 20/77 (25%), Positives = 35/77 (45%), Gaps = 2/77 (2%)

Query: 11  LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
           LYV  L   + +  L   F  +G I       D+ T + R   FV + ++E+A +A+  +
Sbjct: 92  LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 151

Query: 71  DGAELYG--RVLTVNYA 85
           +     G  + L+V  A
Sbjct: 152 NNVIPEGGSQPLSVRLA 168

>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 = 91.5 bits (228), Expect = 3e-24
 Identities = 23/88 (26%), Positives = 45/88 (51%), Gaps = 2/88 (2%)

Query: 8  KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAM 67
          K  L V  L + + +    + F   G+I+  K   D+ T +   +GFV +++ +DA +A+
Sbjct: 2  KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61

Query: 68 DNMDGAELYGRVLTVNYALP--ERIKGG 93
          + ++G  L  + + V+YA P    I+  
Sbjct: 62 NTLNGLRLQTKTIKVSYARPSSASIRDA 89

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 77.6 bits (192), Expect = 1e-18
 Identities = 23/77 (29%), Positives = 40/77 (51%), Gaps = 2/77 (2%)

Query: 11  LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
           LYV GL + + +  L   F  +G I   +  +DQ T   R  GF+ F ++ +A +A+  +
Sbjct: 91  LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150

Query: 71  DGAELYG--RVLTVNYA 85
           +G +  G    +TV +A
Sbjct: 151 NGQKPSGATEPITVKFA 167

>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 = 92.4 bits (230), Expect = 4e-24
 Identities = 19/77 (24%), Positives = 36/77 (46%)

Query: 9   NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
           + L++GGL   +N+  +      FG +K      D AT   + + F  +++     QA+ 
Sbjct: 115 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 174

Query: 69  NMDGAELYGRVLTVNYA 85
            ++G +L  + L V  A
Sbjct: 175 GLNGMQLGDKKLLVQRA 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 = 73.9 bits (182), Expect = 4e-17
 Identities = 18/100 (18%), Positives = 33/100 (33%), Gaps = 6/100 (6%)

Query: 7   QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTP-----LDQATQKHRSFGFVTFLEKE 61
               LYVG +   + E  +   F     +  +        L     + ++F F+ F   +
Sbjct: 3   MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 62

Query: 62  DAIQAMDNMDGAELYGRVLTVNYALPERIKGGEQGWAAQP 101
           +  QAM   DG    G+ L +      +   G     +  
Sbjct: 63  ETTQAM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVY 101

>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 = 91.9 bits (229), Expect = 4e-24
 Identities = 19/77 (24%), Positives = 36/77 (46%)

Query: 9   NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
           + L++GGL   +N+  +      FG +K      D AT   + + F  +++     QA+ 
Sbjct: 95  HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 154

Query: 69  NMDGAELYGRVLTVNYA 85
            ++G +L  + L V  A
Sbjct: 155 GLNGMQLGDKKLLVQRA 171

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 76.5 bits (189), Expect = 2e-18
 Identities = 17/84 (20%), Positives = 30/84 (35%), Gaps = 6/84 (7%)

Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTP-----LDQATQKHRSFGFVTFLEKE 61
              LYVG +   + E  +   F     +  +        L     + ++F F+ F   +
Sbjct: 3  SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 62

Query: 62 DAIQAMDNMDGAELYGRVLTVNYA 85
          +  QAM   DG    G+ L +   
Sbjct: 63 ETTQAM-AFDGIIFQGQSLKIRRP 85

>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 = 89.6 bits (223), Expect = 4e-24
 Identities = 25/88 (28%), Positives = 44/88 (50%), Gaps = 1/88 (1%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDI-KDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
           +++G L  E++E +L+  F  FG I +  K   D  T   + + F+ F   + +  A++
Sbjct: 7  GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66

Query: 69 NMDGAELYGRVLTVNYALPERIKGGEQG 96
           M+G  L  R +TV+YA  +  KG    
Sbjct: 67 AMNGQYLCNRPITVSYAFKKDSKGSGPS 94

>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 = 92.7 bits (231), Expect = 4e-24
 Identities = 23/79 (29%), Positives = 43/79 (54%)

Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
             +LYVG L  +V EA+L+  F P G I  ++   D  T++   + +V F +  DA +A
Sbjct: 14 PMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERA 73

Query: 67 MDNMDGAELYGRVLTVNYA 85
          +D M+   + G+ + + ++
Sbjct: 74 LDTMNFDVIKGKPVRIMWS 92

>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 = 85.8 bits (213), Expect = 2e-21
 Identities = 22/88 (25%), Positives = 40/88 (45%), Gaps = 2/88 (2%)

Query: 9   NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
             +++  L + ++   L+  F  FG+I   K   D      + +GFV F  +E A +A++
Sbjct: 104 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIE 161

Query: 69  NMDGAELYGRVLTVNYALPERIKGGEQG 96
            M+G  L  R + V      + +  E G
Sbjct: 162 KMNGMLLNDRKVFVGRFKSRKEREAELG 189

>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 = 93.9 bits (234), Expect = 7e-24
 Identities = 18/85 (21%), Positives = 35/85 (41%)

Query: 3   NLAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKED 62
            L      L V  L   + +        PFG ++       + T + + +GF  +++K+ 
Sbjct: 90  QLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDS 149

Query: 63  AIQAMDNMDGAELYGRVLTVNYALP 87
           A +A  ++ G  L  R L V++   
Sbjct: 150 AARAKSDLLGKPLGPRTLYVHWTDA 174

>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 = 78.1 bits (193), Expect = 4e-18
 Identities = 21/99 (21%), Positives = 31/99 (31%), Gaps = 4/99 (4%)

Query: 5   AVQKNTLYVGGLAEEVNEA-ILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDA 63
            +    L V  L    N+   L  A          +    Q   + + F  + +   E A
Sbjct: 181 LLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEMA 239

Query: 64  IQAMDNMDGAELYGRVLTVNYALP--ERIKGGEQGWAAQ 100
            +A    DG  L G  L V++  P            AAQ
Sbjct: 240 EEAQQQADGLSLGGSHLRVSFCAPGPPGRSMLAALIAAQ 278

>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 = 71.6 bits (176), Expect = 1e-15
 Identities = 17/79 (21%), Positives = 30/79 (37%), Gaps = 7/79 (8%)

Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
           +  + + GL  +V    +H     +  +K           K++   FVT L  E A  A
Sbjct: 21 NRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAA 73

Query: 67 MDNMDGAELYGRVLTVNYA 85
          ++    + L  R L+V   
Sbjct: 74 INAFHQSRLRERELSVQLQ 92

>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 = 90.7 bits (225), Expect = 7e-24
 Identities = 33/81 (40%), Positives = 41/81 (50%)

Query: 9   NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
            +L V  L    +   L   F  +G + DV  P D+ T++ R F FV F +K DA  AMD
Sbjct: 71  TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 130

Query: 69  NMDGAELYGRVLTVNYALPER 89
            MDGA L GR L V  A   R
Sbjct: 131 AMDGAVLDGRELRVQMARYGR 151

>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 = 88.1 bits (219), Expect = 1e-23
 Identities = 22/81 (27%), Positives = 34/81 (41%), Gaps = 6/81 (7%)

Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
              LYV  L    +E ++   F         +       +K R + FV F  +EDA++A
Sbjct: 14 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV------KKIRDYAFVHFSNREDAVEA 67

Query: 67 MDNMDGAELYGRVLTVNYALP 87
          M  ++G  L G  + V  A P
Sbjct: 68 MKALNGKVLDGSPIEVTLAKP 88

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 88.5 bits (220), Expect = 1e-23
 Identities = 22/92 (23%), Positives = 42/92 (45%), Gaps = 8/92 (8%)

Query: 7   QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
           +  T+Y GG+A  + + ++   F PFG I +++          + + FV F   E A  A
Sbjct: 24  KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVF------PEKGYSFVRFSTHESAAHA 77

Query: 67  MDNMDGAELYGRVLTVNYA--LPERIKGGEQG 96
           + +++G  + G V+   +    P+   G   G
Sbjct: 78  IVSVNGTTIEGHVVKCYWGKESPDMTSGPSSG 109

>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 = 88.4 bits (219), Expect = 1e-23
 Identities = 22/86 (25%), Positives = 41/86 (47%), Gaps = 6/86 (6%)

Query: 6  VQKNTLYVGGLAEEVNEAIL---HAAFIPFGDIKDVKTPLDQAT---QKHRSFGFVTFLE 59
          VQKN ++V GL++ + +  +      F  FG I  V      +    Q   +  +VT++ 
Sbjct: 13 VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIR 72

Query: 60 KEDAIQAMDNMDGAELYGRVLTVNYA 85
           EDA++A+  ++   + GR L  +  
Sbjct: 73 SEDALRAIQCVNNVVVDGRTLKASLG 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 = 88.1 bits (219), Expect = 1e-23
 Identities = 26/90 (28%), Positives = 38/90 (42%), Gaps = 4/90 (4%)

Query: 9   NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
             L+V  +     +  L   F  FG I DV+   +   +  + FGFVTF    DA +A +
Sbjct: 16  KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGFVTFENSADADRARE 73

Query: 69  NMDGAELYGRVLTVNYALP--ERIKGGEQG 96
            + G  + GR + VN A        G   G
Sbjct: 74  KLHGTVVEGRKIEVNNATARVMTNSGPSSG 103

>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 = 88.1 bits (219), Expect = 2e-23
 Identities = 27/78 (34%), Positives = 45/78 (57%)

Query: 10  TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
            LYVG L   + E +L   F PFG I+ ++  +D  T + + +GF+TF + E A +A++ 
Sbjct: 28  RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87

Query: 70  MDGAELYGRVLTVNYALP 87
           ++G EL GR + V +   
Sbjct: 88  LNGFELAGRPMKVGHVTE 105

>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 = 87.7 bits (218), Expect = 2e-23
 Identities = 27/96 (28%), Positives = 45/96 (46%), Gaps = 2/96 (2%)

Query: 9   NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
            +++VG +  E  E  L   F   G +   +   D+ T K + +GF  + ++E A+ AM 
Sbjct: 9   RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 68

Query: 69  NMDGAELYGRVLTVNYALP--ERIKGGEQGWAAQPI 102
           N++G E  GR L V+ A     + +    G  A  I
Sbjct: 69  NLNGREFSGRALRVDNAASEKNKEELKSLGTGAPVI 104

>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 = 87.8 bits (218), Expect = 2e-23
 Identities = 25/98 (25%), Positives = 42/98 (42%), Gaps = 8/98 (8%)

Query: 7   QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
           +  T+++  L+ +  E  L      FGD+K V+  L   T+  +   F  F+ +E A + 
Sbjct: 14  EGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKC 73

Query: 67  MDNMD------GAELYGRVLTVNYALP--ERIKGGEQG 96
           +          G +L GR L V+ A+   E   G   G
Sbjct: 74  LAAASLEAEGGGLKLDGRQLKVDLAVTRDEAASGPSSG 111

>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 = 87.3 bits (217), Expect = 3e-23
 Identities = 26/79 (32%), Positives = 41/79 (51%), Gaps = 3/79 (3%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
           TL+V GL+E+  E  L  +F         +   D+ T   + FGFV F  +EDA  A +
Sbjct: 16 KTLFVKGLSEDTTEETLKESF---DGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKE 72

Query: 69 NMDGAELYGRVLTVNYALP 87
           M+  E+ G  +T+++A P
Sbjct: 73 AMEDGEIDGNKVTLDWAKP 91

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 88.0 bits (219), Expect = 8e-23
 Identities = 29/76 (38%), Positives = 40/76 (52%)

Query: 10  TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
            L+VG L   V++  L  AF  F          D  T   R +GFV+F  ++DA  AMD+
Sbjct: 89  NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 148

Query: 70  MDGAELYGRVLTVNYA 85
           M G +L GR L +N+A
Sbjct: 149 MQGQDLNGRPLRINWA 164

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 86.8 bits (216), Expect = 3e-22
 Identities = 22/80 (27%), Positives = 42/80 (52%), Gaps = 1/80 (1%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
           LYVG L + + E IL   F   G I ++K  +D    K+ ++ FV + +  DA  A+  
Sbjct: 2  VLYVGNLDKAITEDILKQYFQVGGPIANIKIMID-KNNKNVNYAFVEYHQSHDANIALQT 60

Query: 70 MDGAELYGRVLTVNYALPER 89
          ++G ++   ++ +N+A   +
Sbjct: 61 LNGKQIENNIVKINWAFQSQ 80

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 85.8 bits (213), Expect = 1e-22
 Identities = 18/87 (20%), Positives = 38/87 (43%), Gaps = 1/87 (1%)

Query: 6   VQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQ 65
           ++K+ L++ GL     +  L       G +KD++   ++   K +   +V +  +  A Q
Sbjct: 15  LEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQ 73

Query: 66  AMDNMDGAELYGRVLTVNYALPERIKG 92
           A+  MDG  +   ++ V  +      G
Sbjct: 74  AVMKMDGMTIKENIIKVAISNSGPSSG 100

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 85.4 bits (212), Expect = 1e-22
 Identities = 18/76 (23%), Positives = 26/76 (34%), Gaps = 6/76 (7%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
          T Y+G +     EA L   F  FG I D K          +   F+ +   E A   +  
Sbjct: 29 TAYIGNIPHFATEADLIPLFQNFGFILDFKHY------PEKGCCFIKYDTHEQAAVCIVA 82

Query: 70 MDGAELYGRVLTVNYA 85
          +      GR L   + 
Sbjct: 83 LANFPFQGRNLRTGWG 98

>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 = 86.3 bits (214), Expect = 2e-22
 Identities = 26/89 (29%), Positives = 40/89 (44%)

Query: 8   KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAM 67
              L V  +   V+E  L   F  +G I+ VK   D+ T++ R +GFV F     A QA+
Sbjct: 42  LRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAI 101

Query: 68  DNMDGAELYGRVLTVNYALPERIKGGEQG 96
             ++G  +  + L V  A     + G  G
Sbjct: 102 AGLNGFNILNKRLKVALAASGHQRPGIAG 130

>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 = 84.2 bits (209), Expect = 4e-22
 Identities = 25/82 (30%), Positives = 38/82 (46%), Gaps = 7/82 (8%)

Query: 8  KNTLYVGGLAEEVNE----AILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDA 63
           +T+Y+  L E++ +      LHA F  FG I D+       + K R   FV F E   A
Sbjct: 8  NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVS---RSLKMRGQAFVIFKEVSSA 64

Query: 64 IQAMDNMDGAELYGRVLTVNYA 85
            A+ +M G   Y + + + YA
Sbjct: 65 TNALRSMQGFPFYDKPMRIQYA 86

>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 = 83.8 bits (208), Expect = 7e-22
 Identities = 25/86 (29%), Positives = 35/86 (40%), Gaps = 8/86 (9%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
            L+VGGL    + A L   F  FG I+ +         K  SF ++ +   + A  A  
Sbjct: 18 TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHV------KGDSFAYIQYESLDAAQAACA 71

Query: 69 NMDGAELYG--RVLTVNYALPERIKG 92
           M G  L G  R L V++A      G
Sbjct: 72 KMRGFPLGGPDRRLRVDFAKSGPSSG 97

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 83.5 bits (207), Expect = 9e-22
 Identities = 21/81 (25%), Positives = 35/81 (43%), Gaps = 6/81 (7%)

Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
          Q++ L+VG L  ++ E  +   F  +G   +V         K + FGF+    +  A  A
Sbjct: 14 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIH------KDKGFGFIRLETRTLAEIA 67

Query: 67 MDNMDGAELYGRVLTVNYALP 87
             +D   L G+ L V +A  
Sbjct: 68 KVELDNMPLRGKQLRVRFACH 88

>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 = 83.9 bits (208), Expect = 1e-21
 Identities = 23/88 (26%), Positives = 42/88 (47%), Gaps = 2/88 (2%)

Query: 11  LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
           L++  L +E  +  L   F+PFG++   K  +D+ T   + FGFV++     A  A+ +M
Sbjct: 28  LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87

Query: 71  DGAELYGRVLTVNYALP--ERIKGGEQG 96
           +G ++  + L V       +   G   G
Sbjct: 88  NGFQIGMKRLKVQLKRSKNDSKSGPSSG 115

>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 = 83.1 bits (206), Expect = 1e-21
 Identities = 27/81 (33%), Positives = 44/81 (54%), Gaps = 8/81 (9%)

Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
          +   L+V  LA  V E IL  AF  FG ++ VK        K + + F+ F E++ A++A
Sbjct: 10 KVKVLFVRNLANTVTEEILEKAFSQFGKLERVK--------KLKDYAFIHFDERDGAVKA 61

Query: 67 MDNMDGAELYGRVLTVNYALP 87
          M+ M+G +L G  + + +A P
Sbjct: 62 MEEMNGKDLEGENIEIVFAKP 82

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 83.0 bits (206), Expect = 1e-21
 Identities = 29/88 (32%), Positives = 43/88 (48%), Gaps = 4/88 (4%)

Query: 11  LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
           LYV  L + +++  L  AF PFG I   K  ++    + + FGFV F   E+A +A+  M
Sbjct: 18  LYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEM 75

Query: 71  DGAELYGRVLTVNYALP--ERIKGGEQG 96
           +G  +  + L V  A    ER  G   G
Sbjct: 76  NGRIVATKPLYVALAQRKEERQSGPSSG 103

>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 = 81.8 bits (203), Expect = 3e-21
 Identities = 24/80 (30%), Positives = 40/80 (50%), Gaps = 1/80 (1%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
           +YVG L        +   F  FG + +VK   D+ T+K + FGFV   ++E   +A+  
Sbjct: 3  NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEM-QEESVSEAIAK 61

Query: 70 MDGAELYGRVLTVNYALPER 89
          +D  +  GR + V  A P++
Sbjct: 62 LDNTDFMGRTIRVTEANPKK 81

>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 = 81.0 bits (201), Expect = 5e-21
 Identities = 19/73 (26%), Positives = 33/73 (45%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          LY+ GL     +  L     P+G I   K  LD+ T K + +GFV F     A +A+  +
Sbjct: 8  LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67

Query: 71 DGAELYGRVLTVN 83
            + +  ++   +
Sbjct: 68 KASGVQAQMAKQS 80

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 81.6 bits (202), Expect = 5e-21
 Identities = 17/83 (20%), Positives = 37/83 (44%), Gaps = 6/83 (7%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFG--DIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
          +T+ +  +A       +  A  P+    + +++   D+ TQ++R F FV      DA Q 
Sbjct: 10 DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQL 69

Query: 67 MDNMDGAE----LYGRVLTVNYA 85
          +  +        + G+ + V++A
Sbjct: 70 LQILQSLHPPLKIDGKTIGVDFA 92

>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 = 81.1 bits (201), Expect = 5e-21
 Identities = 19/82 (23%), Positives = 35/82 (42%), Gaps = 2/82 (2%)

Query: 8  KNTLYVGGLAEEVNEAILHAAFIPFG--DIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQ 65
          +  LY+G L     +  L  A    G  DI ++K   ++A  + + F  V    +  + +
Sbjct: 1  RIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKK 60

Query: 66 AMDNMDGAELYGRVLTVNYALP 87
           MD +   EL+G+   V  +  
Sbjct: 61 LMDLLPKRELHGQNPVVTPSNK 82

>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 = 81.6 bits (202), Expect = 7e-21
 Identities = 22/86 (25%), Positives = 39/86 (45%), Gaps = 3/86 (3%)

Query: 11  LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
           L++G +   ++E  L   F  FG I ++    D+ T  H+   F+T+ E+E A++A   +
Sbjct: 16  LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSAL 75

Query: 71  DGAELY---GRVLTVNYALPERIKGG 93
              +      R + V  A  E   G 
Sbjct: 76  HEQKTLPGMNRPIQVKPADSESRGGS 101

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 81.1 bits (201), Expect = 7e-21
 Identities = 27/88 (30%), Positives = 41/88 (46%), Gaps = 3/88 (3%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          ++VGG+     E  L   F  FG + +V    D   Q+ R FGF+TF E E ++    NM
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITF-EDEQSVDQAVNM 71

Query: 71 DGAELYGRVLTVNYALP--ERIKGGEQG 96
             ++ G+ + V  A P   +  G   G
Sbjct: 72 HFHDIMGKKVEVKRAEPRDSKSSGPSSG 99

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 81.2 bits (201), Expect = 8e-21
 Identities = 24/79 (30%), Positives = 37/79 (46%), Gaps = 2/79 (2%)

Query: 9   NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
             L+V  +     +  L   F  FG I DV+   ++  +  + FGFVTF    DA +A +
Sbjct: 30  KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRARE 87

Query: 69  NMDGAELYGRVLTVNYALP 87
            + G  + GR + VN A  
Sbjct: 88  KLHGTVVEGRKIEVNNATA 106

>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 = 81.5 bits (202), Expect = 9e-21
 Identities = 22/88 (25%), Positives = 40/88 (45%), Gaps = 2/88 (2%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
            +++  L + ++   L+  F  FG+I   K   D      + +GFV F  +E A +A++
Sbjct: 6  GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIE 63

Query: 69 NMDGAELYGRVLTVNYALPERIKGGEQG 96
           M+G  L  R + V      + +  E G
Sbjct: 64 KMNGMLLNDRKVFVGRFKSRKEREAELG 91

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 81.9 bits (202), Expect = 2e-20
 Identities = 15/96 (15%), Positives = 36/96 (37%), Gaps = 2/96 (2%)

Query: 8   KNTLYVGGLAEEVNEAILHAAFIPFG--DIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQ 65
           +  +YVG  +    +  L       G  D+ ++K   ++A  + + +  V    +    +
Sbjct: 55  RAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHK 114

Query: 66  AMDNMDGAELYGRVLTVNYALPERIKGGEQGWAAQP 101
            ++ + G  L G  + V  A  + +   E     + 
Sbjct: 115 LLELLPGKVLNGEKVDVRPATRQNLSQFEAQARKRE 150

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 80.5 bits (199), Expect = 2e-20
 Identities = 22/75 (29%), Positives = 40/75 (53%)

Query: 11  LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
           L++  L +E  +  L + F+PFG++   K  +D+ T   + FGFV+F   + A  A+  M
Sbjct: 43  LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102

Query: 71  DGAELYGRVLTVNYA 85
           +G ++  + L V   
Sbjct: 103 NGFQVGTKRLKVQLK 117

>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 = 79.6 bits (197), Expect = 3e-20
 Identities = 20/82 (24%), Positives = 31/82 (37%), Gaps = 3/82 (3%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQAT-QKHRS--FGFVTFLEKEDAIQ 65
          + L++  L     E  L   F   G IK       +       S  FGFV + + E A +
Sbjct: 6  SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65

Query: 66 AMDNMDGAELYGRVLTVNYALP 87
          A+  + G  + G  L V  +  
Sbjct: 66 ALKQLQGHTVDGHKLEVRISER 87

>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 = 83.5 bits (207), Expect = 5e-20
 Identities = 13/96 (13%), Positives = 33/96 (34%), Gaps = 2/96 (2%)

Query: 6   VQKNTLYVGGLAEEVNEAILHAAFIPFGDIK-DVKTPLDQATQKHRSFGFVTFLEKEDAI 64
           + + TL++        +  +         +   ++ P  +     R F ++    KEDA 
Sbjct: 115 LTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLR-FNTSRRFAYIDVTSKEDAR 173

Query: 65  QAMDNMDGAELYGRVLTVNYALPERIKGGEQGWAAQ 100
             ++ ++G ++ G  L    + P            +
Sbjct: 174 YCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLE 209

>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 = 75.8 bits (187), Expect = 3e-17
 Identities = 20/83 (24%), Positives = 40/83 (48%), Gaps = 3/83 (3%)

Query: 7   QKNTLYVGGLAEEV-NEAILHAAFIPFGDIKDVKTPLDQ-ATQKHRSFGFVTFLEKEDAI 64
           +   + +  L+ E+ +E +L  +F  FG I+ +  P  Q     +    F+ F  K+ A 
Sbjct: 209 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAE 268

Query: 65  QAMDNMDGAELYGRVLTVNYALP 87
           +A+  M+ + L  R ++V+ A  
Sbjct: 269 RAL-QMNRSLLGNREISVSLADK 290

>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 = 66.5 bits (163), Expect = 8e-14
 Identities = 14/74 (18%), Positives = 28/74 (37%), Gaps = 3/74 (4%)

Query: 10  TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
           T+ V  L +  N+  ++  F   G I  V        +K+  F  + F   + A+ A+  
Sbjct: 43  TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS--LKKNFRFARIEFARYDGALAAITK 100

Query: 70  MDGAELYGRVLTVN 83
                +    + V+
Sbjct: 101 THK-VVGQNEIIVS 113

>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 = 78.5 bits (194), Expect = 7e-20
 Identities = 22/88 (25%), Positives = 38/88 (43%), Gaps = 8/88 (9%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
           TL    L+  + E  L   F    +I+     L     K +   ++ F  + DA + ++
Sbjct: 17 RTLLAKNLSFNITEDELKEVFEDALEIR-----LVSQDGKSKGIAYIEFKSEADAEKNLE 71

Query: 69 NMDGAELYGRVLTVNYALPERIKGGEQG 96
             GAE+ GR +++ Y      KGG +G
Sbjct: 72 EKQGAEIDGRSVSLYYTGE---KGGTRG 96

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 79.0 bits (195), Expect = 8e-20
 Identities = 28/100 (28%), Positives = 42/100 (42%), Gaps = 10/100 (10%)

Query: 7   QKNTLYVGGLAEEVNEAILHAAFIPFGDIK--------DVKTPLDQATQKHRSFGFVTFL 58
             NT++V GL E V    +   F   G IK         +    D+ T K +    V+F 
Sbjct: 6   DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFD 65

Query: 59  EKEDAIQAMDNMDGAELYGRVLTVNYALP--ERIKGGEQG 96
           +   A  A+D  DG E  G  + V++A    +  +GG  G
Sbjct: 66  DPPSAKAAIDWFDGKEFSGNPIKVSFATRRADFNRGGGNG 105

>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 = 80.3 bits (199), Expect = 1e-19
 Identities = 18/81 (22%), Positives = 33/81 (40%), Gaps = 5/81 (6%)

Query: 7   QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
              TL    L+  + E  L   F    +I+     L     K +   ++ F  + DA + 
Sbjct: 98  AARTLLAKNLSFNITEDELKEVFEDALEIR-----LVSQDGKSKGIAYIEFKSEADAEKN 152

Query: 67  MDNMDGAELYGRVLTVNYALP 87
           ++   GAE+ GR +++ Y   
Sbjct: 153 LEEKQGAEIDGRSVSLYYTGE 173

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 78.0 bits (193), Expect = 8e-19
 Identities = 20/90 (22%), Positives = 35/90 (38%), Gaps = 2/90 (2%)

Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
              L++G L    + A L  A        D+    D  T  +R FG+V F   ED  +A
Sbjct: 12 TPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESAEDLEKA 70

Query: 67 MDNMDGAELYGRVLTVNYALPERIKGGEQG 96
          ++ + G +++G  + +        K     
Sbjct: 71 LE-LTGLKVFGNEIKLEKPKGRDSKKVRAA 99

>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 = 81.3 bits (200), Expect = 1e-19
 Identities = 20/92 (21%), Positives = 38/92 (41%), Gaps = 2/92 (2%)

Query: 7   QKNTLYVGGLAEEVNEAILHAAFIPFG--DIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
           ++  LY+G L     +  L  A    G  DI ++K   ++A  + + F  V    +  + 
Sbjct: 67  KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSK 126

Query: 65  QAMDNMDGAELYGRVLTVNYALPERIKGGEQG 96
           + MD +   EL+G+   V     + +   E  
Sbjct: 127 KLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQ 158

>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 = 77.7 bits (192), Expect = 1e-19
 Identities = 19/81 (23%), Positives = 33/81 (40%), Gaps = 4/81 (4%)

Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
          +  TL +  L+    E  L   F     IK           K + + F+ F   EDA +A
Sbjct: 14 ESKTLVLSNLSYSATEETLQEVFEKATFIKVP----QNQNGKSKGYAFIEFASFEDAKEA 69

Query: 67 MDNMDGAELYGRVLTVNYALP 87
          +++ +  E+ GR + +    P
Sbjct: 70 LNSCNKREIEGRAIRLELQGP 90

>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 = 77.3 bits (191), Expect = 2e-19
 Identities = 20/84 (23%), Positives = 38/84 (45%), Gaps = 3/84 (3%)

Query: 10  TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
            L++G L    + A L  A        D+   +D  T  +R FG+V F   ED  +A++ 
Sbjct: 19  NLFIGNLNPNKSVAELKVAISELFAKNDLAV-VDVRTGTNRKFGYVDFESAEDLEKALE- 76

Query: 70  MDGAELYGRVLTVNYALP-ERIKG 92
           + G +++G  + +      +  +G
Sbjct: 77  LTGLKVFGNEIKLEKPKGRDGTRG 100

>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 = 77.0 bits (190), Expect = 4e-19
 Identities = 22/85 (25%), Positives = 34/85 (40%), Gaps = 3/85 (3%)

Query: 9   NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
             +YVG L  ++    +   F  +G I+D+     +       F FV F +  DA  A+ 
Sbjct: 23  CRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR---GGPPFAFVEFEDPRDAEDAVY 79

Query: 69  NMDGAELYGRVLTVNYALPERIKGG 93
             DG +  G  L V +    R  G 
Sbjct: 80  GRDGYDYDGYRLRVEFPRSGRGTGS 104

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 76.5 bits (189), Expect = 4e-19
 Identities = 16/84 (19%), Positives = 35/84 (41%), Gaps = 8/84 (9%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
           ++VG ++       L + F   G + +            + + FV   ++ DA  A+  
Sbjct: 11 KIFVGNVSAACTSQELRSLFERRGRVIECD--------VVKDYAFVHMEKEADAKAAIAQ 62

Query: 70 MDGAELYGRVLTVNYALPERIKGG 93
          ++G E+ G+ + V  +   + K G
Sbjct: 63 LNGKEVKGKRINVELSTKGQKKSG 86

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score = 76.0 bits (188), Expect = 5e-19
 Identities = 18/84 (21%), Positives = 33/84 (39%), Gaps = 1/84 (1%)

Query: 6  VQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQ 65
              ++YVG +        L A F   G +  V    D+ +   + F ++ F +KE    
Sbjct: 4  ADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRT 63

Query: 66 AMDNMDGAELYGRVLTVNYALPER 89
          ++  +D +   GR + V      R
Sbjct: 64 SLA-LDESLFRGRQIKVIPKRTNR 86

>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 = 76.9 bits (190), Expect = 5e-19
 Identities = 26/77 (33%), Positives = 39/77 (50%), Gaps = 1/77 (1%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          ++VGGL     +A L   F  FGDI++     D+ T K R +GFVT  ++  A +A  + 
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDP 79

Query: 71 DGAELYGRVLTVNYALP 87
          +   + GR   VN A  
Sbjct: 80 NP-IIDGRKANVNLAYL 95

>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 = 75.8 bits (187), Expect = 7e-19
 Identities = 21/77 (27%), Positives = 35/77 (45%), Gaps = 7/77 (9%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
          TLYVGGL + + E  L   F  FG+I+ +         + +   F+ F  ++ A  A + 
Sbjct: 14 TLYVGGLGDTITETDLRNHFYQFGEIRTITVV------QRQQCAFIQFATRQAAEVAAEK 67

Query: 70 M-DGAELYGRVLTVNYA 85
            +   + GR L V + 
Sbjct: 68 SFNKLIVNGRRLNVKWG 84

>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 = 78.0 bits (193), Expect = 7e-19
 Identities = 22/81 (27%), Positives = 38/81 (46%), Gaps = 1/81 (1%)

Query: 7   QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
           +   ++VGG+  +V        F  +G I D +  LD+ T + R FGFVT+ +  DA+  
Sbjct: 86  KTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTY-DSADAVDR 144

Query: 67  MDNMDGAELYGRVLTVNYALP 87
           +      +   R + +  A P
Sbjct: 145 VCQNKFIDFKDRKIEIKRAEP 165

>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 = 72.2 bits (178), Expect = 9e-17
 Identities = 22/81 (27%), Positives = 39/81 (48%), Gaps = 2/81 (2%)

Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
          +   +++GGL  +  E  L   F  +G + D+K   D AT + R FGF++F +     + 
Sbjct: 2  ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV 61

Query: 67 MDNMDGAELYGRVLTVNYALP 87
          +       L G+V+    A+P
Sbjct: 62 VKTQ--HILDGKVIDPKRAIP 80

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 76.1 bits (187), Expect = 2e-18
 Identities = 16/81 (19%), Positives = 33/81 (40%), Gaps = 7/81 (8%)

Query: 9   NTLYVGGLAEEVNE----AILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
             + +  +  EV +    A+L+A     GDI D+   L   +  +    ++ F  +E A 
Sbjct: 30  QVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQ 86

Query: 65  QAMDNMDGAELYGRVLTVNYA 85
             ++   G    G  L + ++
Sbjct: 87  AFVEAFQGYPFQGNPLVITFS 107

>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 = 75.4 bits (186), Expect = 2e-18
 Identities = 21/77 (27%), Positives = 33/77 (42%), Gaps = 1/77 (1%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
          +T++V  L  +V    L   F   G +       D    K R  G VTF +  +A+QA+ 
Sbjct: 16 STVFVANLDYKVGWKKLKEVFSMAGVVVRADILED-KDGKSRGIGTVTFEQSIEAVQAIS 74

Query: 69 NMDGAELYGRVLTVNYA 85
            +G  L+ R + V   
Sbjct: 75 MFNGQLLFDRPMHVKMD 91

>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 = 75.0 bits (185), Expect = 2e-18
 Identities = 21/79 (26%), Positives = 43/79 (54%), Gaps = 3/79 (3%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
          NT++VGG+   ++E  + + F  +G +K+VK   D+ T   + +GFV+F    D  + ++
Sbjct: 10 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE 68

Query: 69 NMDGAELYGRVLTVNYALP 87
          +      +G+ L +  A+ 
Sbjct: 69 S--QINFHGKKLKLGPAIR 85

>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 = 75.0 bits (185), Expect = 2e-18
 Identities = 21/79 (26%), Positives = 33/79 (41%), Gaps = 1/79 (1%)

Query: 7   QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
               L V  L   V++A +   F  FG +K      D+ + +      V F  K DA++A
Sbjct: 28  TGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKA 86

Query: 67  MDNMDGAELYGRVLTVNYA 85
           M   +G  L GR + +   
Sbjct: 87  MKQYNGVPLDGRPMNIQLV 105

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 74.3 bits (183), Expect = 3e-18
 Identities = 20/84 (23%), Positives = 37/84 (44%), Gaps = 5/84 (5%)

Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFG-DIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQ 65
             +L++G L   ++E  +  AF   G  +  VK   ++ T     + FV F +   A +
Sbjct: 8  MAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEK 67

Query: 66 AMDNMDGAELYG----RVLTVNYA 85
           +  ++G  L G    +   +NYA
Sbjct: 68 CLHKINGKPLPGATPAKRFKLNYA 91

>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 = 74.3 bits (183), Expect = 4e-18
 Identities = 25/87 (28%), Positives = 37/87 (42%), Gaps = 8/87 (9%)

Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKD--------VKTPLDQATQKHRSFGFVTFL 58
            NT++V GL E V    +   F   G IK         +    D+ T K +    V+F 
Sbjct: 12 DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFD 71

Query: 59 EKEDAIQAMDNMDGAELYGRVLTVNYA 85
          +   A  A+D  DG E  G  + V++A
Sbjct: 72 DPPSAKAAIDWFDGKEFSGNPIKVSFA 98

>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 = 74.7 bits (184), Expect = 4e-18
 Identities = 18/82 (21%), Positives = 36/82 (43%), Gaps = 1/82 (1%)

Query: 8   KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAM 67
             T++   LA  +    L   F   G ++DV+   D+ +++ +   +V F E +    A+
Sbjct: 25  ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI 84

Query: 68  DNMDGAELYGRVLTVNYALPER 89
             + G  L G  + V  +  E+
Sbjct: 85  -GLTGQRLLGVPIIVQASQAEK 105

>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 = 73.8 bits (182), Expect = 4e-18
 Identities = 19/90 (21%), Positives = 34/90 (37%), Gaps = 10/90 (11%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
            L+VG ++       L A F  +G + +            + + FV     EDA++A+ 
Sbjct: 11 TKLHVGNISPTCTNQELRAKFEEYGPVIECD--------IVKDYAFVHMERAEDAVEAIR 62

Query: 69 NMDGAELYGRVLTVNYALP--ERIKGGEQG 96
           +D  E  G+ + V  +        G   G
Sbjct: 63 GLDNTEFQGKRMHVQLSTSRLRTASGPSSG 92

>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 = 74.3 bits (183), Expect = 5e-18
 Identities = 23/114 (20%), Positives = 48/114 (42%), Gaps = 19/114 (16%)

Query: 10  TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
            LY+  L  ++    ++  F  +G I+ ++      T + R   +V + +  DA  A+D+
Sbjct: 10  ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVG---NTPETRGTAYVVYEDIFDAKNAVDH 66

Query: 70  MDGAELYGRVLTVNYALPERIKGGEQGWAAQPIWADADTWFERQQQEEEMQRLQ 123
           + G  +  R L V Y    R                A    + +++EE+++ L+
Sbjct: 67  LSGFNVSNRYLVVLYYNANR----------------AFQKMDTKKKEEQLKLLK 104

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 73.9 bits (182), Expect = 6e-18
 Identities = 24/85 (28%), Positives = 37/85 (43%), Gaps = 8/85 (9%)

Query: 5   AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
            +    L+V     +V E+ L+  F PFG +K+VK            F FV F E E A 
Sbjct: 28  ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAA 79

Query: 65  QAMDNMDGAELYGRVLTVNYALPER 89
           +A++ + G     + L V Y+    
Sbjct: 80  KAIEEVHGKSFANQPLEVVYSKLPA 104

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 73.8 bits (182), Expect = 6e-18
 Identities = 27/90 (30%), Positives = 39/90 (43%), Gaps = 4/90 (4%)

Query: 9   NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
            T YVG L     +  + A F     I+ V+   D+ T K + F +V F E +   +A+ 
Sbjct: 16  YTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL- 73

Query: 69  NMDGAELYGRVLTVNYALP--ERIKGGEQG 96
             DGA L  R L V+ A    +   G   G
Sbjct: 74  TYDGALLGDRSLRVDIAEGRKQDKSGPSSG 103

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 73.6 bits (181), Expect = 7e-18
 Identities = 18/84 (21%), Positives = 33/84 (39%), Gaps = 1/84 (1%)

Query: 3  NLAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKED 62
             V      +      V +  L + F   G + +++ P+D+AT K + F FV      D
Sbjct: 7  QYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMND 66

Query: 63 AIQAMDNMDGAELYGR-VLTVNYA 85
          A + + +  G  L  +  L +   
Sbjct: 67 AKKIIKSFHGKRLDLKHRLFLYTM 90

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 73.5 bits (181), Expect = 8e-18
 Identities = 26/91 (28%), Positives = 49/91 (53%), Gaps = 5/91 (5%)

Query: 10  TLYVGGLAEEVNEAILHAAFI-PFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
           +L+VG L  +V++ +L+  F+  +   +  K  LDQ T   + +GFV F ++ +  +A+ 
Sbjct: 11  SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALT 69

Query: 69  NMDGA-ELYGRVLTVNYALP--ERIKGGEQG 96
              GA  L  + + ++ A+P   R+K  E G
Sbjct: 70  ECQGAVGLGSKPVRLSVAIPKASRVKPVESG 100

>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 = 73.2 bits (180), Expect = 2e-17
 Identities = 20/81 (24%), Positives = 33/81 (40%), Gaps = 1/81 (1%)

Query: 9   NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
             L V  L   V++A +   F  FG +K      D+ + +      V F  + DA++AM 
Sbjct: 36  AKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMK 94

Query: 69  NMDGAELYGRVLTVNYALPER 89
              G  L GR + +     + 
Sbjct: 95  QYKGVPLDGRPMDIQLVASQI 115

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 71.8 bits (177), Expect = 2e-17
 Identities = 20/76 (26%), Positives = 38/76 (50%), Gaps = 1/76 (1%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          +++GGL+ +  +  L   F  FG++K+     D  T++ R FGFVTF+++    + +   
Sbjct: 3  MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-AQ 61

Query: 71 DGAELYGRVLTVNYAL 86
             EL  + +    A 
Sbjct: 62 SRHELDSKTIDPKVAF 77

>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 = 72.3 bits (178), Expect = 2e-17
 Identities = 21/89 (23%), Positives = 36/89 (40%), Gaps = 4/89 (4%)

Query: 11  LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
           L+VG L ++ +E  +   F PFG I +            +   FV F    +A  A+  +
Sbjct: 18  LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHAL 76

Query: 71  DGAELY---GRVLTVNYALPERIKGGEQG 96
            G++        L V +A  ++  G   G
Sbjct: 77  HGSQTMPGASSSLVVKFADTDKESGPSSG 105

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 71.0 bits (175), Expect = 3e-17
 Identities = 20/75 (26%), Positives = 35/75 (46%), Gaps = 1/75 (1%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          ++VGGL+       +   F  FG + D     D+ T +HR FGFVTF  ++   +    +
Sbjct: 2  IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-EI 60

Query: 71 DGAELYGRVLTVNYA 85
             E+  +++    A
Sbjct: 61 HFHEINNKMVECKKA 75

>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 = 75.1 bits (185), Expect = 4e-17
 Identities = 22/79 (27%), Positives = 34/79 (43%), Gaps = 6/79 (7%)

Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
          Q+  L+VG L  ++ E      F  +G+  +V    D      R FGF+    +  A  A
Sbjct: 21 QRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIA 74

Query: 67 MDNMDGAELYGRVLTVNYA 85
             +DG  L  R L + +A
Sbjct: 75 KAELDGTILKSRPLRIRFA 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 = 73.2 bits (180), Expect = 2e-16
 Identities = 36/157 (22%), Positives = 61/157 (38%), Gaps = 6/157 (3%)

Query: 3   NLAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKED 62
             A     L V  L+  V+  +L  AF  FG ++     +D    +    GFV F  K  
Sbjct: 91  RFATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDD-RGRATGKGFVEFAAKPP 149

Query: 63  AIQAMDNM-DGAELYGRVLTVNYALPERIKGGEQGWAAQPIWADADTWFERQQ--QEEEM 119
           A +A++   DGA L           P      E G   + +        ER+Q  +  + 
Sbjct: 150 ARKALERCGDGAFLLTTTPRPVIVEPMEQFDDEDGLPEKLMQKTQQYHKEREQPPRFAQP 209

Query: 120 QRLQAENRAAMQAAEELHRKKMAE-DRE-GEKEEDSE 154
              + E  +  +A +E+ +++  + DR   E +E  E
Sbjct: 210 GTFEFEYASRWKALDEMEKQQREQVDRNIREAKEKLE 246

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score = 71.5 bits (176), Expect = 5e-17
 Identities = 21/77 (27%), Positives = 39/77 (50%), Gaps = 1/77 (1%)

Query: 11  LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
           +++GGL+ +  +  L   F  FG++K+     D  T++ R FGFVTF+++    + +   
Sbjct: 28  MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-AQ 86

Query: 71  DGAELYGRVLTVNYALP 87
              EL  + +    A P
Sbjct: 87  SRHELDSKTIDPKVAFP 103

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 71.1 bits (175), Expect = 6e-17
 Identities = 18/77 (23%), Positives = 30/77 (38%), Gaps = 2/77 (2%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
            ++V  L  +    +L   F   G +      ++    K +  G V F   E A +A  
Sbjct: 9  CQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACR 66

Query: 69 NMDGAELYGRVLTVNYA 85
           M+G +L GR + V   
Sbjct: 67 MMNGMKLSGREIDVRID 83

>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 = 70.7 bits (174), Expect = 6e-17
 Identities = 17/79 (21%), Positives = 35/79 (44%), Gaps = 8/79 (10%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          L++G L  E  E  + + F  +G + +            +++GFV   +K  A  A+ N+
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECD--------IIKNYGFVHIEDKTAAEDAIRNL 62

Query: 71 DGAELYGRVLTVNYALPER 89
             +L+G  + V  +  + 
Sbjct: 63 HHYKLHGVNINVEASKNKS 81

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 70.8 bits (174), Expect = 8e-17
 Identities = 20/79 (25%), Positives = 32/79 (40%), Gaps = 5/79 (6%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          +YVG L     +  L  AF  +G ++ V    +        F FV F +  DA  A+  +
Sbjct: 3  VYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGL 57

Query: 71 DGAELYGRVLTVNYALPER 89
          DG  + G  + V  +    
Sbjct: 58 DGKVICGSRVRVELSTGMP 76

>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 = 73.1 bits (180), Expect = 8e-17
 Identities = 21/79 (26%), Positives = 36/79 (45%), Gaps = 1/79 (1%)

Query: 9   NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
             ++VGG+ E+  E  L   F  +G I+ ++   D+ + K R F FVTF + +   + + 
Sbjct: 105 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV- 163

Query: 69  NMDGAELYGRVLTVNYALP 87
                 + G    V  AL 
Sbjct: 164 IQKYHTVNGHNCEVRKALS 182

>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 = 68.9 bits (169), Expect = 3e-15
 Identities = 26/81 (32%), Positives = 41/81 (50%), Gaps = 1/81 (1%)

Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
          Q   L++GGL+ E  +  L + F  +G + D     D  T++ R FGFVT+   E+   A
Sbjct: 12 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 71

Query: 67 MDNMDGAELYGRVLTVNYALP 87
          M N    ++ GRV+    A+ 
Sbjct: 72 M-NARPHKVDGRVVEPKRAVS 91

>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 = 73.5 bits (180), Expect = 1e-16
 Identities = 20/94 (21%), Positives = 39/94 (41%), Gaps = 6/94 (6%)

Query: 9   NTLYVGGLAEE-VNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAM 67
           + L V  L  E V    L   F  +GD++ VK          +    V   +   A  AM
Sbjct: 35  SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKI-----LFNKKENALVQMADGNQAQLAM 89

Query: 68  DNMDGAELYGRVLTVNYALPERIKGGEQGWAAQP 101
            +++G +L+G+ + +  +  + ++   +G   Q 
Sbjct: 90  SHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQG 123

>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 = 63.1 bits (153), Expect = 7e-13
 Identities = 18/86 (20%), Positives = 35/86 (40%), Gaps = 5/86 (5%)

Query: 1   MANLAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEK 60
             N+     TL++  +   V+E  L   F   G +        +  QK R    +     
Sbjct: 144 FQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGF----KFFQKDRKMALIQMGSV 199

Query: 61  EDAIQAMDNMDGAELY-GRVLTVNYA 85
           E+A+QA+ ++   +L     L V+++
Sbjct: 200 EEAVQALIDLHNHDLGENHHLRVSFS 225

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 70.8 bits (174), Expect = 1e-16
 Identities = 27/88 (30%), Positives = 40/88 (45%), Gaps = 3/88 (3%)

Query: 11  LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
           L++GGL+ E  E  L   +  +G + D     D A+++ R FGFVTF    +   AM   
Sbjct: 30  LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM-AA 88

Query: 71  DGAELYGRVLTVNYALP--ERIKGGEQG 96
               + GRV+    A+   E   G   G
Sbjct: 89  RPHSIDGRVVEPKRAVAREESGSGPSSG 116

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score = 70.3 bits (173), Expect = 1e-16
 Identities = 23/88 (26%), Positives = 35/88 (39%), Gaps = 3/88 (3%)

Query: 11  LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
           L+VGGL     +  L + F  +G++ D     D+ T + R FGFV F +       +   
Sbjct: 19  LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVL-AS 77

Query: 71  DGAELYGRVLTVNYALP--ERIKGGEQG 96
               L GR +      P   +  G   G
Sbjct: 78  RPHTLDGRNIDPKPCTPRGMQPSGPSSG 105

>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 = 72.3 bits (178), Expect = 1e-16
 Identities = 17/90 (18%), Positives = 39/90 (43%), Gaps = 5/90 (5%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRS--FGFVTFLEKEDAIQAM 67
           ++VG +    +E  L   F  +G + ++    D++    +S    FVTF  ++ A++A 
Sbjct: 5  KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64

Query: 68 DNMDGAEL---YGRVLTVNYALPERIKGGE 94
          + +   ++       + +  A  E+    E
Sbjct: 65 NALHNMKVLPGMHHPIQMKPADSEKNNAVE 94

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 71.1 bits (175), Expect = 4e-16
 Identities = 18/78 (23%), Positives = 33/78 (42%), Gaps = 4/78 (5%)

Query: 11  LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
           L++G ++++  E  +   F  FG I++ +          R   FVTF  +  A  A+  M
Sbjct: 98  LFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAM 156

Query: 71  DGAELY---GRVLTVNYA 85
             A+        + V +A
Sbjct: 157 HQAQTMEGCSSPMVVKFA 174

>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 = 70.5 bits (173), Expect = 2e-16
 Identities = 22/90 (24%), Positives = 36/90 (40%), Gaps = 8/90 (8%)

Query: 6   VQKNTLYVGGLAEEVNEAILHAAFIPFGDIK--------DVKTPLDQATQKHRSFGFVTF 57
              + +YV GL + V    L   F   G +K         +   LD+ T K +    V++
Sbjct: 13  SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSY 72

Query: 58  LEKEDAIQAMDNMDGAELYGRVLTVNYALP 87
            +   A  A++  DG +  G  L V+ A  
Sbjct: 73  EDPPTAKAAVEWFDGKDFQGSKLKVSLARK 102

>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 = 71.1 bits (174), Expect = 2e-16
 Identities = 23/80 (28%), Positives = 35/80 (43%), Gaps = 5/80 (6%)

Query: 10  TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
            +YVG L    N+  L  AF  +G ++ V    +        F FV F +  DA  A+  
Sbjct: 75  KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRE 129

Query: 70  MDGAELYGRVLTVNYALPER 89
           +DG  L G  + V  +  E+
Sbjct: 130 LDGRTLCGCRVRVELSNGEK 149

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 68.8 bits (169), Expect = 5e-16
 Identities = 17/85 (20%), Positives = 39/85 (45%), Gaps = 3/85 (3%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQA-TQKHRSFGFVTFLEKEDAIQAMD 68
          T ++G L  +V E  +   F     I  V+ P + +  ++ + FG+  F + +  + A+ 
Sbjct: 17 TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL- 74

Query: 69 NMDGAELYGRVLTVNYALPERIKGG 93
          +++   L  + + V+ A   + K  
Sbjct: 75 SLNEESLGNKRIRVDVADQAQDKDS 99

>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 = 69.2 bits (170), Expect = 5e-16
 Identities = 16/81 (19%), Positives = 26/81 (32%), Gaps = 1/81 (1%)

Query: 11  LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
           LY+  L   ++E  L     PFG +   +   D  +   R  GF      E     + + 
Sbjct: 28  LYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHF 86

Query: 71  DGAELYGRVLTVNYALPERIK 91
           +G  +           P   K
Sbjct: 87  NGKFIKTPPGVSAPTEPLLCK 107

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 68.8 bits (169), Expect = 5e-16
 Identities = 22/77 (28%), Positives = 30/77 (38%), Gaps = 2/77 (2%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          L V GL  +  E  L   F  FG++  V+   D  T   + FGFV F E E  ++ M   
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR 77

Query: 71 DGAELYGRVLTVNYALP 87
              + GR         
Sbjct: 78 H--MIDGRWCDCKLPNS 92

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score = 67.9 bits (167), Expect = 6e-16
 Identities = 21/75 (28%), Positives = 38/75 (50%), Gaps = 1/75 (1%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          ++VGGL+ +  E  +   F  FG+++ ++ P+D  T K R F F+TF E+E   + M+  
Sbjct: 2  IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-K 60

Query: 71 DGAELYGRVLTVNYA 85
              +      +  A
Sbjct: 61 KYHNVGLSKCEIKVA 75

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 71.1 bits (174), Expect = 6e-16
 Identities = 18/77 (23%), Positives = 32/77 (41%), Gaps = 6/77 (7%)

Query: 10 TLYVGGLAEE-VNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
           L V  L  E V    L   F  +GD++ VK          +    V   +   A  AM 
Sbjct: 5  VLLVSNLNPERVTPQSLFILFGVYGDVQRVK-----ILFNKKENALVQMADGNQAQLAMS 59

Query: 69 NMDGAELYGRVLTVNYA 85
          +++G +L+G+ + +  +
Sbjct: 60 HLNGHKLHGKPIRITLS 76

>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 = 62.2 bits (151), Expect = 1e-12
 Identities = 18/85 (21%), Positives = 34/85 (40%), Gaps = 5/85 (5%)

Query: 2   ANLAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKE 61
            N+     TL++  +   V+E  L   F   G +           QK R    +     E
Sbjct: 114 QNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKF----FQKDRKMALIQMGSVE 169

Query: 62  DAIQAMDNMDGAELY-GRVLTVNYA 85
           +A+QA+ ++   +L     L V+++
Sbjct: 170 EAVQALIDLHNHDLGENHHLRVSFS 194

>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 = 69.0 bits (169), Expect = 7e-16
 Identities = 17/82 (20%), Positives = 33/82 (40%), Gaps = 1/82 (1%)

Query: 6   VQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQ 65
           + K ++YVG +        L A F   G I  +    D+ +   + + ++ F  + +++ 
Sbjct: 34  IDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEF-AERNSVD 92

Query: 66  AMDNMDGAELYGRVLTVNYALP 87
           A   MD     GR + V     
Sbjct: 93  AAVAMDETVFRGRTIKVLPKRT 114

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 70.3 bits (172), Expect = 7e-16
 Identities = 20/83 (24%), Positives = 33/83 (39%), Gaps = 1/83 (1%)

Query: 7   QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
               L V  L   V++A +   F  FG +K      D+ + +      V F  + DA++A
Sbjct: 87  TGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKA 145

Query: 67  MDNMDGAELYGRVLTVNYALPER 89
           M    G  L GR + +     + 
Sbjct: 146 MKQYKGVPLDGRPMDIQLVASQI 168

>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 = 69.5 bits (170), Expect = 8e-16
 Identities = 18/88 (20%), Positives = 34/88 (38%), Gaps = 5/88 (5%)

Query: 7   QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPL-----DQATQKHRSFGFVTFLEKE 61
               +YV  LA+ V E  L   F  + D       +          + +   F+    ++
Sbjct: 44  PNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEK 103

Query: 62  DAIQAMDNMDGAELYGRVLTVNYALPER 89
            A +A+   +G  L+G+ + V +A   R
Sbjct: 104 AAAKALKEANGYVLFGKPMVVQFARSAR 131

>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 = 71.8 bits (175), Expect = 9e-16
 Identities = 26/90 (28%), Positives = 41/90 (45%), Gaps = 8/90 (8%)

Query: 1  MANLAVQ-KNTLYVGGLAEEVNEA----ILHAAFIPFGDIKDVKTPLDQATQKHRSFGFV 55
          MA    +  +T+Y+  L E++ +      L+A F  FG I D+       + K R   FV
Sbjct: 1  MAVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVS---RSLKMRGQAFV 57

Query: 56 TFLEKEDAIQAMDNMDGAELYGRVLTVNYA 85
           F E   A  A+ +M G   Y + + + YA
Sbjct: 58 IFKEVSSATNALRSMQGFPFYDKPMRIQYA 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 = 53.7 bits (128), Expect = 3e-09
 Identities = 19/80 (23%), Positives = 33/80 (41%), Gaps = 6/80 (7%)

Query: 7   QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
             + L++  L EE NE +L   F  F   K+V+              FV F  +  A  A
Sbjct: 206 PNHILFLTNLPEETNELMLSMLFNQFPGFKEVRL-----VPGRHDIAFVEFDNEVQAGAA 260

Query: 67  MDNMDGAELY-GRVLTVNYA 85
            D + G ++     + +++A
Sbjct: 261 RDALQGFKITQNNAMKISFA 280

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 67.9 bits (166), Expect = 1e-15
 Identities = 22/83 (26%), Positives = 32/83 (38%), Gaps = 5/83 (6%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
            +YVG L  +   + L  A    G +     PL    Q  R   F+ + +   A QA+ 
Sbjct: 20 ADVYVGNLPRDARVSDLKRALRELGSV-----PLRLTWQGPRRRAFLHYPDSAAAQQAVS 74

Query: 69 NMDGAELYGRVLTVNYALPERIK 91
           + G  L    L V  A  +R K
Sbjct: 75 CLQGLRLGTDTLRVALARQQRDK 97

>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 = 70.1 bits (171), Expect = 1e-15
 Identities = 13/84 (15%), Positives = 27/84 (32%)

Query: 3   NLAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKED 62
            +    N L+      EV E          G  +     +     +  S G + +  K D
Sbjct: 118 RIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSD 177

Query: 63  AIQAMDNMDGAELYGRVLTVNYAL 86
           A++ +  ++  ++        Y L
Sbjct: 178 ALETLGFLNHYQMKNPNGPYPYTL 201

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 60.1 bits (145), Expect = 7e-12
 Identities = 13/78 (16%), Positives = 31/78 (39%), Gaps = 6/78 (7%)

Query: 9  NTLYVGGLAEE-VNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAM 67
            L V GL +  +N   +   F  +G+++ VK               V   +     +A+
Sbjct: 5  PVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS-----KPGAAMVEMADGYAVDRAI 59

Query: 68 DNMDGAELYGRVLTVNYA 85
           +++   ++G+ + V  +
Sbjct: 60 THLNNNFMFGQKMNVCVS 77

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 67.9 bits (166), Expect = 1e-15
 Identities = 18/88 (20%), Positives = 33/88 (37%), Gaps = 4/88 (4%)

Query: 6  VQKNTLYVGGLAEEVNEAILHAAFIPFGD-IKDVKTPLD-QATQKHRSFGFVTFLEKEDA 63
               L++GG+ +      +        + + DV          K+R F FV +     A
Sbjct: 6  SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAA 65

Query: 64 IQAMDNM--DGAELYGRVLTVNYALPER 89
            A   +     +L+G  + V++A PE 
Sbjct: 66 AMARRKLMPGRIQLWGHQIAVDWAEPEI 93

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A Length = 87

 Score = 66.8 bits (164), Expect = 2e-15
 Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 1/75 (1%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          ++VGGL+ + ++  L   F  FG++ D    +D  T + R FGF+ F +     + +D  
Sbjct: 14 MFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQK 73

Query: 71 DGAELYGRVLTVNYA 85
          +   L GRV+    A
Sbjct: 74 EH-RLDGRVIDPKKA 87

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 66.9 bits (164), Expect = 2e-15
 Identities = 18/90 (20%), Positives = 36/90 (40%), Gaps = 9/90 (10%)

Query: 8  KNTLYVGGL-AEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
          K+ L++G L  + V++  L   F P+G I  +            +FGF+ F   +    A
Sbjct: 10 KSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDA 61

Query: 67 MDNMDGAELYGRVLTVNYALPERIKGGEQG 96
          ++       +G+ L +  +        + G
Sbjct: 62 IECESQEMNFGKKLILEVSSSNARPQFDHG 91

>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 = 66.6 bits (163), Expect = 3e-15
 Identities = 16/83 (19%), Positives = 34/83 (40%), Gaps = 9/83 (10%)

Query: 8   KNTLYVGGL-AEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
            + +++G L    V ++ +   F  +G +             H+ + FV +  +  A  A
Sbjct: 27  NSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAA 78

Query: 67  MDNMDGAELYGRVLTVNYALPER 89
           +   +G  L G+ L +N A   +
Sbjct: 79  VLGENGRVLAGQTLDINMAGEPK 101

>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 = 65.7 bits (161), Expect = 6e-15
 Identities = 17/81 (20%), Positives = 37/81 (45%), Gaps = 3/81 (3%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQ-KHRSFGFVTFLEKEDAIQAMD 68
          T ++G L  +V E  +   F     I  V+ P + +   + + FG+  F + +  + A+ 
Sbjct: 21 TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL- 78

Query: 69 NMDGAELYGRVLTVNYALPER 89
          +++   L  R + V+ A   +
Sbjct: 79 SLNEESLGNRRIRVDVADQAQ 99

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 65.9 bits (161), Expect = 6e-15
 Identities = 16/82 (19%), Positives = 34/82 (41%), Gaps = 3/82 (3%)

Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
          +   L +  +   +   +L +  + +G ++  +     +         VT+  K+ A QA
Sbjct: 14 RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETA---VVNVTYSSKDQARQA 70

Query: 67 MDNMDGAELYGRVLTVNYALPE 88
          +D ++G +L    L V Y   E
Sbjct: 71 LDKLNGFQLENFTLKVAYIPDE 92

>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 = 64.6 bits (158), Expect = 2e-14
 Identities = 17/90 (18%), Positives = 36/90 (40%), Gaps = 9/90 (10%)

Query: 1  MANLAVQKNTLYVGGL-AEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLE 59
          +   +  K+ L++G L  + V++  L   F P+G I  +            +FGF+ F  
Sbjct: 15 VPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDN 66

Query: 60 KEDAIQAMDNMDGAELYGRVLTVNYALPER 89
           +    A++       +G+ L +  +    
Sbjct: 67 PQSVRDAIEXESQEMNFGKKLILEVSSSNA 96

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 64.8 bits (158), Expect = 2e-14
 Identities = 21/85 (24%), Positives = 31/85 (36%), Gaps = 8/85 (9%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
            ++V GL E V EA L  A   FG I  V           +    V F   + A + + 
Sbjct: 16 PVVHVRGLCESVVEADLVEALEKFGTICYVM------MMPFKRQALVEFENIDSAKECVT 69

Query: 69 --NMDGAELYGRVLTVNYALPERIK 91
                  + G+    NY+  +RI 
Sbjct: 70 FAADVPVYIAGQQAFFNYSTSKRIT 94

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 63.8 bits (155), Expect = 6e-14
 Identities = 18/95 (18%), Positives = 35/95 (36%), Gaps = 13/95 (13%)

Query: 9   NTLYV--GGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
            +L V  GGL   V+   L       G +  +  P       ++ + F  +   E++ +A
Sbjct: 26  QSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMP------PNKPYSFARYRTTEESKRA 79

Query: 67  MDNMDGAELYGR-----VLTVNYALPERIKGGEQG 96
              ++G E+         L +N+    +  G   G
Sbjct: 80  YVTLNGKEVVDDLGQKITLYLNFVEKVQWSGPSSG 114

>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 = 62.8 bits (153), Expect = 7e-14
 Identities = 15/79 (18%), Positives = 27/79 (34%), Gaps = 7/79 (8%)

Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
            + + V  L ++ N   +H     +  +K           +++   FVT L  E A  A
Sbjct: 4  GSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVD------RNKRTAFVTLLNGEQAQNA 56

Query: 67 MDNMDGAELYGRVLTVNYA 85
          +         G+ L V   
Sbjct: 57 IQMFHQYSFRGKDLIVQLQ 75

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 88

 Score = 62.2 bits (152), Expect = 1e-13
 Identities = 20/77 (25%), Positives = 35/77 (45%), Gaps = 7/77 (9%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          ++VG    ++ E  L   F  +GD+ DV  P     +  R+F FVTF + + A       
Sbjct: 8  VFVGRCTGDMTEDELREFFSQYGDVMDVFIP-----KPFRAFAFVTFADDQIAQSLC--G 60

Query: 71 DGAELYGRVLTVNYALP 87
          +   + G  + ++ A P
Sbjct: 61 EDLIIKGISVHISNAEP 77

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 66.8 bits (162), Expect = 1e-13
 Identities = 30/154 (19%), Positives = 55/154 (35%), Gaps = 2/154 (1%)

Query: 9   NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
            TL+V  +  +  E+ L   F  +G IK +     + + K R + F+ +  + D   A  
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162

Query: 69  NMDGAELYGRVLTVNYALPERIKGGEQGWAAQPIWADADTWFERQQQEEEMQRLQAENRA 128
           + DG ++ GR + V+      +KG         +        +   +          +  
Sbjct: 163 HADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRDDTSRYDE- 221

Query: 129 AMQAAEELHRKKMAEDREGEKEEDSEMKDDPMAR 162
                  L  +    DRE E+ E S  +D    R
Sbjct: 222 -RPGPSPLPHRDRDRDRERERRERSRERDKERER 254

>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 = 62.5 bits (152), Expect = 2e-13
 Identities = 18/94 (19%), Positives = 32/94 (34%), Gaps = 6/94 (6%)

Query: 8   KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAM 67
           K  +    L      A +   F  FG +  V  P      +      V FLE  +A +A 
Sbjct: 10  KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP------EGGITAIVEFLEPLEARKAF 63

Query: 68  DNMDGAELYGRVLTVNYALPERIKGGEQGWAAQP 101
            ++  ++ +   L + +A         Q   +Q 
Sbjct: 64  RHLAYSKFHHVPLYLEWAPIGVFGAAPQKKDSQH 97

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 62.1 bits (151), Expect = 2e-13
 Identities = 20/84 (23%), Positives = 33/84 (39%), Gaps = 8/84 (9%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
            +++ GL + V EA L  A   FG I  V           +    V F +   A  A++
Sbjct: 22 PVVHIRGLIDGVVEADLVEALQEFGPISYVVVM------PKKRQALVEFEDVLGACNAVN 75

Query: 69 --NMDGAELYGRVLTVNYALPERI 90
              +   + G    VNY+  ++I
Sbjct: 76 YAADNQIYIAGHPAFVNYSTSQKI 99

>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 = 61.5 bits (149), Expect = 5e-13
 Identities = 13/85 (15%), Positives = 36/85 (42%), Gaps = 8/85 (9%)

Query: 9   NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
             +++  L  +V E  + +  +PFG + ++         K ++  F+    +E A   ++
Sbjct: 32  RVIHIRKLPIDVTEGEVISLGLPFGKVTNLL------MLKGKNQAFIEMNTEEAANTMVN 85

Query: 69  --NMDGAELYGRVLTVNYALPERIK 91
                   L G+ + + ++  + +K
Sbjct: 86  YYTSVTPVLRGQPIYIQFSNHKELK 110

>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 = 60.6 bits (147), Expect = 8e-13
 Identities = 17/85 (20%), Positives = 37/85 (43%), Gaps = 8/85 (9%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
            L++  L  EV E  + A  +PFG + ++         K ++  F+    +E AI  ++
Sbjct: 16 RVLHIRKLPGEVTETEVIALGLPFGKVTNILML------KGKNQAFLELATEEAAITMVN 69

Query: 69 --NMDGAELYGRVLTVNYALPERIK 91
            +     L  + + + Y+  + +K
Sbjct: 70 YYSAVTPHLRNQPIYIQYSNHKELK 94

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 60.3 bits (146), Expect = 9e-13
 Identities = 13/85 (15%), Positives = 36/85 (42%), Gaps = 8/85 (9%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
            +++  L  +V E  + +  +PFG + ++         K ++  F+    +E A   ++
Sbjct: 17 RVIHIRKLPIDVTEGEVISLGLPFGKVTNLL------MLKGKNQAFIEMNTEEAANTMVN 70

Query: 69 --NMDGAELYGRVLTVNYALPERIK 91
                  L G+ + + ++  + +K
Sbjct: 71 YYTSVTPVLRGQPIYIQFSNHKELK 95

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 108

 Score = 60.6 bits (147), Expect = 9e-13
 Identities = 17/83 (20%), Positives = 26/83 (31%), Gaps = 7/83 (8%)

Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
           +N + V GL    +   L       GD+       D         G V F+ KED   A
Sbjct: 14 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYA 66

Query: 67 MDNMDGAELYGRVLTVNYALPER 89
          +  +D  +         Y   + 
Sbjct: 67 VRKLDNTKFRSHEGETAYIRVKV 89

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89

 Score = 58.8 bits (143), Expect = 3e-12
 Identities = 19/77 (24%), Positives = 34/77 (44%), Gaps = 7/77 (9%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          ++VG   E++    L   F  +G++ DV  P        R+F FVTF + + A       
Sbjct: 14 VFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQSLC--G 66

Query: 71 DGAELYGRVLTVNYALP 87
          +   + G  + ++ A P
Sbjct: 67 EDLIIKGISVHISNAEP 83

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 58.6 bits (142), Expect = 3e-12
 Identities = 17/78 (21%), Positives = 30/78 (38%), Gaps = 6/78 (7%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTP-----LDQATQKHRSFGFVTFLEKEDAIQ 65
          LYVG +   + E  +   F     +  +        L     + ++F F+ F   ++  Q
Sbjct: 9  LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68

Query: 66 AMDNMDGAELYGRVLTVN 83
          AM   DG    G+ L + 
Sbjct: 69 AM-AFDGIIFQGQSLKIR 85

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 57.0 bits (138), Expect = 8e-12
 Identities = 18/82 (21%), Positives = 34/82 (41%), Gaps = 9/82 (10%)

Query: 9  NTLYVGGL------AEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKED 62
          + + V  +        E  + ++H  F  FG I +   P +    K + + F+ +     
Sbjct: 2  SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAH 59

Query: 63 AIQAMDNMDGAELYGR-VLTVN 83
          A+ A+ N DG +L  +    VN
Sbjct: 60 AVDAVKNADGYKLDKQHTFRVN 81

>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 = 57.3 bits (139), Expect = 1e-11
 Identities = 9/77 (11%), Positives = 25/77 (32%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
            + V  +   V+   +   F  +  I                   V F  +++A  A+ 
Sbjct: 16 TVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 75

Query: 69 NMDGAELYGRVLTVNYA 85
          +++   +  R + ++  
Sbjct: 76 DLNDRPIGSRKVKLSGP 92

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 57.0 bits (138), Expect = 2e-11
 Identities = 18/84 (21%), Positives = 34/84 (40%), Gaps = 9/84 (10%)

Query: 9  NTLYVGGL------AEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKED 62
          + + V  +        E  + ++H  F  FG I +   P +    K + + F+ +     
Sbjct: 16 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAH 73

Query: 63 AIQAMDNMDGAELYGR-VLTVNYA 85
          A+ A+ N DG +L  +    VN  
Sbjct: 74 AVDAVKNADGYKLDKQHTFRVNLF 97

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 56.6 bits (137), Expect = 2e-11
 Identities = 18/87 (20%), Positives = 29/87 (33%), Gaps = 6/87 (6%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
          +++V G    V+ A L   F+ FG +  V    D        F  V       A +A+ +
Sbjct: 10 SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKD-----KGVFAIVEM-GDVGAREAVLS 63

Query: 70 MDGAELYGRVLTVNYALPERIKGGEQG 96
               L G  L V     +  +     
Sbjct: 64 QSQHSLGGHRLRVRPREQKEFQSPASK 90

>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 = 55.8 bits (135), Expect = 4e-11
 Identities = 9/80 (11%), Positives = 24/80 (30%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
            + V  +   V+   +   F  +  I                   V F  +++A  A+ 
Sbjct: 16 TIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 75

Query: 69 NMDGAELYGRVLTVNYALPE 88
          +++   +  R + +      
Sbjct: 76 DLNDRPIGSRKVKLVLGSGP 95

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115

 Score = 56.4 bits (136), Expect = 4e-11
 Identities = 17/82 (20%), Positives = 26/82 (31%), Gaps = 7/82 (8%)

Query: 8  KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAM 67
          +N + V GL    +   L       GD+       D         G V F+ KED   A+
Sbjct: 16 ENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAV 68

Query: 68 DNMDGAELYGRVLTVNYALPER 89
            +D  +         Y   + 
Sbjct: 69 RKLDNTKFRSHEGETAYIRVKV 90

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 102

 Score = 54.5 bits (131), Expect = 1e-10
 Identities = 15/84 (17%), Positives = 29/84 (34%), Gaps = 9/84 (10%)

Query: 10 TLYVGGLAEEVN-EAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
           +++       N    L     PFG I +             +  F+     EDA  A+D
Sbjct: 17 VVHIMDFQRGKNLRYQLLQLVEPFGVISNHL------ILNKINEAFIEMATTEDAQAAVD 70

Query: 69 --NMDGAELYGRVLTVNYALPERI 90
                A ++G+ + V+ +   + 
Sbjct: 71 YYTTTPALVFGKPVRVHLSQKYKR 94

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 53.3 bits (128), Expect = 4e-10
 Identities = 14/75 (18%), Positives = 28/75 (37%), Gaps = 3/75 (4%)

Query: 8  KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAM 67
          +  + +  L E  +   L              T     T+     G + F  +E  ++A+
Sbjct: 28 RYRITMKNLPEGCSWQDLKDLARENSL---ETTFSSVNTRDFDGTGALEFPSEEILVEAL 84

Query: 68 DNMDGAELYGRVLTV 82
          + ++  E  G V+TV
Sbjct: 85 ERLNNIEFRGSVITV 99

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 55.2 bits (132), Expect = 8e-10
 Identities = 26/118 (22%), Positives = 43/118 (36%), Gaps = 22/118 (18%)

Query: 10  TLYVGGLAEEVN---------EAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEK 60
           TLYVGG+   +N         E+ +   F   GDI  ++        + ++ GFV F  +
Sbjct: 136 TLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYV------ESKNCGFVKFKYQ 189

Query: 61  EDAIQAMDNMDGAELYGRVLTVNYALPERIKGGEQGWAAQPIWADADTWFERQQQEEE 118
            +A  A + M    L                   +G      WA+ D     Q++ +E
Sbjct: 190 ANAEFAKEAMSNQTLLLPSDKEWD-------DRREGTGLLVKWANEDPDPAAQKRLQE 240

>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 = 50.9 bits (122), Expect = 4e-09
 Identities = 11/84 (13%), Positives = 29/84 (34%), Gaps = 1/84 (1%)

Query: 8  KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAM 67
          K   ++  +   + +  +          ++    L     +      V F  ++DA ++ 
Sbjct: 15 KVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSE 74

Query: 68 DNMDGAELYGRVLTVNYALPERIK 91
            +   +L GR   V+    E ++
Sbjct: 75 -RLHRKKLNGREAFVHVVTLEDMR 97

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 50.8 bits (121), Expect = 7e-09
 Identities = 16/82 (19%), Positives = 33/82 (40%), Gaps = 7/82 (8%)

Query: 11  LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
           L +      +   +L+    P G ++ +        +++     V F     A +A   +
Sbjct: 28  LSIQNPLYPITVDVLYTVCNPVGKVQRIVI-----FKRNGIQAMVEFESVLCAQKAKAAL 82

Query: 71  DGAELYGR--VLTVNYALPERI 90
           +GA++Y     L + YA P R+
Sbjct: 83  NGADIYAGCCTLKIEYARPTRL 104

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 49.7 bits (119), Expect = 9e-09
 Identities = 11/77 (14%), Positives = 28/77 (36%), Gaps = 2/77 (2%)

Query: 6  VQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQ 65
          V+  ++Y+ G   +     +       G + +++       +  +   FV F   E A +
Sbjct: 9  VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKK 67

Query: 66 AMDNMDGAELYGRVLTV 82
           ++   G +     L +
Sbjct: 68 FVE-TPGQKYKETDLLI 83

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 50.0 bits (119), Expect = 1e-08
 Identities = 15/82 (18%), Positives = 33/82 (40%), Gaps = 6/82 (7%)

Query: 11  LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
           + V  L   V   +LH  F  FG +  +       T+ ++    + + +   A  A  ++
Sbjct: 31  IIVENLFYPVTLDVLHQIFSKFGTVLKII----TFTKNNQFQALLQYADPVSAQHAKLSL 86

Query: 71  DGAELY--GRVLTVNYALPERI 90
           DG  +Y     L ++++    +
Sbjct: 87  DGQNIYNACCTLRIDFSKLTSL 108

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A Length = 164

 Score = 50.1 bits (119), Expect = 2e-08
 Identities = 15/82 (18%), Positives = 33/82 (40%), Gaps = 6/82 (7%)

Query: 11  LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
           + V  L   V   +LH  F  FG +  +       T+ ++    + + +   A  A  ++
Sbjct: 49  IIVENLFYPVTLDVLHQIFSKFGTVLKII----TFTKNNQFQALLQYADPVSAQHAKLSL 104

Query: 71  DGAELY--GRVLTVNYALPERI 90
           DG  +Y     L ++++    +
Sbjct: 105 DGQNIYNACCTLRIDFSKLTSL 126

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 112

 Score = 48.4 bits (115), Expect = 3e-08
 Identities = 14/79 (17%), Positives = 32/79 (40%), Gaps = 9/79 (11%)

Query: 10 TLYVGGLAEE-VNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
           +++  L     +++ +     P+G IK+          + +S  F+    +EDA+  +D
Sbjct: 27 VIHLSNLPHSGYSDSAVLKLAEPYGKIKNYI------LMRMKSQAFIEMETREDAMAMVD 80

Query: 69 --NMDGAELYGRVLTVNYA 85
                    GR + V+ +
Sbjct: 81 HCLKKALWFQGRCVKVDLS 99

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 48.4 bits (115), Expect = 4e-08
 Identities = 13/63 (20%), Positives = 27/63 (42%), Gaps = 2/63 (3%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRS--FGFVTFLEKEDAIQA 66
            ++VGGL  +++E  + A+F  FG +        ++        + F+ F E+      
Sbjct: 9  RKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQAL 68

Query: 67 MDN 69
          +D 
Sbjct: 69 IDA 71

>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 = 46.8 bits (111), Expect = 2e-07
 Identities = 15/82 (18%), Positives = 26/82 (31%), Gaps = 1/82 (1%)

Query: 7   QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
               +Y+ GL  E     +   F     ++D          K    GFV F  + D   A
Sbjct: 24  AGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAA 83

Query: 67  MDNMDGAELYGRVLTVNYALPE 88
           +       +  R + V+    +
Sbjct: 84  LC-RHKQYMGNRFIQVHPITKK 104

>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 = 45.0 bits (107), Expect = 4e-07
 Identities = 14/76 (18%), Positives = 28/76 (36%), Gaps = 3/76 (3%)

Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
            +T+ + G    V E  +     P      ++   +        + FV F  +E+  QA
Sbjct: 9  TCHTVKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNA-HGNKTGYIFVDFSNEEEVKQA 66

Query: 67 MDNMDGAELYGRVLTV 82
          +   +   + GR + V
Sbjct: 67 LK-CNREYMGGRYIEV 81

>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 = 45.6 bits (108), Expect = 6e-07
 Identities = 14/82 (17%), Positives = 26/82 (31%), Gaps = 1/82 (1%)

Query: 7   QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
               + + GL     +  +   F     + +  T       K     FV F  +E A +A
Sbjct: 41  NDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKA 100

Query: 67  MDNMDGAELYGRVLTVNYALPE 88
           +       +  R + V  +  E
Sbjct: 101 LG-KHKERIGHRYIEVFKSSQE 121

>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 = 45.1 bits (107), Expect = 6e-07
 Identities = 16/95 (16%), Positives = 31/95 (32%), Gaps = 3/95 (3%)

Query: 7   QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
               + V G+     E  +   F     +  V    D    ++   G V FL  +D  +A
Sbjct: 15  DDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDH-VGRNNGNGLVKFLSPQDTFEA 72

Query: 67  MDNMDGAELYGRVLTVNYALPERIKGGEQGWAAQP 101
           +   +   +  R + V+ A   +         + P
Sbjct: 73  LK-RNRMLMIQRYVEVSPATERQWVAAGGHITSGP 106

>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 = 44.7 bits (106), Expect = 6e-07
 Identities = 11/85 (12%), Positives = 28/85 (32%), Gaps = 1/85 (1%)

Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
              + + GL    ++  +   F     + +  T       +     FV F  +E A +A
Sbjct: 14 NDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKA 73

Query: 67 MDNMDGAELYGRVLTVNYALPERIK 91
          +       +  R + +  +    ++
Sbjct: 74 LK-KHKERIGHRYIEIFKSSRAEVR 97

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 43.2 bits (102), Expect = 2e-06
 Identities = 16/70 (22%), Positives = 26/70 (37%), Gaps = 3/70 (4%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
          + +++ GL     E  ++  F P      V   +     +      V F   EDA+ AM 
Sbjct: 16 HCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA 73

Query: 69 NMDGAELYGR 78
            D A +  R
Sbjct: 74 -KDKANMQHR 82

>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A* Length = 345

 Score = 45.5 bits (107), Expect = 2e-06
 Identities = 20/132 (15%), Positives = 49/132 (37%), Gaps = 18/132 (13%)

Query: 9   NTLYV--GGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
            +L V  GGL   V+   L       G +  +  P       ++ + F  +   E++ +A
Sbjct: 19  QSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMP------PNKPYSFARYRTTEESKRA 72

Query: 67  MDNMDG---AELYGRVLTVNYALPERIKGGEQGWAAQP----IWADADTWFERQQQEEEM 119
              ++G    +  G+ +T+     E+++  E    A P    +  +       ++++  +
Sbjct: 73  YVTLNGKEVVDDLGQKITLYLNFVEKVQWKELRPQALPPGLMVVEE---IISSEEEKMLL 129

Query: 120 QRLQAENRAAMQ 131
           + +        Q
Sbjct: 130 ESVDWTEDTDNQ 141

>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 = 42.5 bits (99), Expect = 2e-05
 Identities = 10/76 (13%), Positives = 27/76 (35%), Gaps = 2/76 (2%)

Query: 7   QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
           +  ++Y+ G   +     +       G + +++       +  +   FV F   E A + 
Sbjct: 108 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKF 166

Query: 67  MDNMDGAELYGRVLTV 82
           ++   G +     L +
Sbjct: 167 VETP-GQKYKETDLLI 181

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 41.0 bits (96), Expect = 3e-05
 Identities = 15/70 (21%), Positives = 27/70 (38%), Gaps = 3/70 (4%)

Query: 9   NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
           + +++ GL  +  E  ++  F P      V   +     +      V F   E+A+ AM 
Sbjct: 47  HCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGP-DGRVTGEADVEFATHEEAVAAMS 104

Query: 69  NMDGAELYGR 78
             D A +  R
Sbjct: 105 -KDRANMQHR 113

>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 = 40.0 bits (93), Expect = 3e-05
 Identities = 14/82 (17%), Positives = 33/82 (40%), Gaps = 7/82 (8%)

Query: 10 TLYVGGLAEEVNEA----ILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQ 65
           + V  +   ++      +L  AF   G +K V+         ++    V     +DAI 
Sbjct: 11 DVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVEL---SPHTDYQLKAVVQMENLQDAIG 67

Query: 66 AMDNMDGAELYGRVLTVNYALP 87
          A++++   ++  + + V+ A  
Sbjct: 68 AVNSLHRYKIGSKKILVSLATG 89

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 37.6 bits (87), Expect = 3e-04
 Identities = 21/85 (24%), Positives = 32/85 (37%), Gaps = 14/85 (16%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPF-----GDIKDVKTPLDQATQKHRSFGFVTFLEKEDA 63
            + V GL   V + +L   F        G +           Q+    G +TF E  DA
Sbjct: 9  VAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSW--------QRLGCGGVLTFREPADA 60

Query: 64 IQAMDNMDGAELYGRVLTVNYALPE 88
           + +   D  EL+G  L++  A P 
Sbjct: 61 ERVLAQAD-HELHGAQLSLRPAPPR 84

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 118

 Score = 37.6 bits (87), Expect = 4e-04
 Identities = 10/76 (13%), Positives = 22/76 (28%), Gaps = 5/76 (6%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPF---GDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
           + + GL    +   +            +  V     +   +     FV    ++D   A
Sbjct: 19 VVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTR-EGRQSGEAFVELESEDDVKLA 77

Query: 67 MDNMDGAELYGRVLTV 82
          +   D   +  R + V
Sbjct: 78 LK-KDRESMGHRYIEV 92

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

No hit with probability above 80.00

---

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	174
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	4e-20
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	2e-18
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	3e-18
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	9e-18
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	4e-17
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	6e-17
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	8e-17
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	9e-17
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	9e-17
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	2e-16
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	3e-16
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	3e-16
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	5e-16
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	9e-16
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	1e-15
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	1e-15
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	1e-15
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	2e-15
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	2e-15
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	4e-15
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	4e-15
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	6e-15
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	6e-15
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	7e-15
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	1e-14
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	2e-14
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	2e-14
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	5e-14
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	5e-14
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	5e-14
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	6e-14
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	6e-14
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	2e-13
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	2e-13
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	2e-13
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	2e-13
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	3e-13
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	3e-13
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	6e-13
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	6e-13
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	7e-13
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	8e-13
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	9e-13
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	1e-12
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	1e-12
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	2e-12
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	2e-12
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:) 3e-12
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	5e-12
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	6e-12
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	6e-12
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	6e-12
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	1e-11
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	2e-11
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	2e-11
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	3e-11
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	4e-11
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	7e-11
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	1e-10
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	2e-10
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	5e-10
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	6e-10
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	1e-07
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	2e-09
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	2e-09
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-09
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	3e-09
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-08
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	3e-08
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	3e-08
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	4e-08
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	5e-08
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	7e-08
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	1e-07
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	2e-07
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	3e-07
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	4e-07
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	4e-07
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	5e-07
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	6e-07
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	4e-06
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	2e-05
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	3e-05
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	5e-05
d1ufwa_	95	d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens)	0.003

>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 = 77.8 bits (191), Expect = 4e-20
 Identities = 53/88 (60%), Positives = 65/88 (73%)

Query: 4  LAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDA 63
          +A  K  LYVGGLAEEV++ +LHAAFIPFGDI D++ PLD  T+KHR F FV F   EDA
Sbjct: 1  MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 60

Query: 64 IQAMDNMDGAELYGRVLTVNYALPERIK 91
            A+DNM+ +EL+GR + VN A P RIK
Sbjct: 61 AAAIDNMNESELFGRTIRVNLAKPMRIK 88

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 73.0 bits (179), Expect = 2e-18
 Identities = 23/76 (30%), Positives = 43/76 (56%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
          +LYVG L  +V EA+L+  F P G I  ++   D  T++   + +V F +  DA +A+D 
Sbjct: 2  SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 70 MDGAELYGRVLTVNYA 85
          M+   + G+ + + ++
Sbjct: 62 MNFDVIKGKPVRIMWS 77

>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 = 73.1 bits (179), Expect = 3e-18
 Identities = 24/83 (28%), Positives = 40/83 (48%)

Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
          +  TLYVG L+    E  ++  F   GDIK +   LD+  +    F FV +  + DA  A
Sbjct: 6  KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENA 65

Query: 67 MDNMDGAELYGRVLTVNYALPER 89
          M  ++G  L  R++  ++    +
Sbjct: 66 MRYINGTRLDDRIIRTDWDAGFK 88

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 72.0 bits (176), Expect = 9e-18
 Identities = 34/83 (40%), Positives = 50/83 (60%)

Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
          Q  T+YVGGL E+V+E +L   F+  G + +   P D+ T +H+ +GFV FL +EDA  A
Sbjct: 8  QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA 67

Query: 67 MDNMDGAELYGRVLTVNYALPER 89
          +  MD  +LYG+ + VN A    
Sbjct: 68 IKIMDMIKLYGKPIRVNKASAHN 90

>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 = 70.8 bits (173), Expect = 4e-17
 Identities = 23/117 (19%), Positives = 48/117 (41%), Gaps = 19/117 (16%)

Query: 9   NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
             LY+  L  ++    ++  F  +G I+ ++      T + R   +V + +  DA  A D
Sbjct: 8   RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVG---NTPETRGTAYVVYEDIFDAKNACD 64

Query: 69  NMDGAELYGRVLTVNYALPERIKGGEQGWAAQPIWADADTWFERQQQEEEMQRLQAE 125
           ++ G  +  R L V Y    R                A    + +++EE+++ L+ +
Sbjct: 65  HLSGFNVCNRYLVVLYYNANR----------------AFQKMDTKKKEEQLKLLKEK 105

>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 = 69.6 bits (170), Expect = 6e-17
 Identities = 20/82 (24%), Positives = 37/82 (45%), Gaps = 2/82 (2%)

Query: 6  VQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQ 65
          ++   LYV  L   + +  L   F  +G I       D+ T + R   FV + ++E+A +
Sbjct: 4  IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQE 63

Query: 66 AMDNMDGAELYG--RVLTVNYA 85
          A+  ++     G  + L+V  A
Sbjct: 64 AISALNNVIPEGGSQPLSVRLA 85

>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 = 69.4 bits (169), Expect = 8e-17
 Identities = 22/80 (27%), Positives = 43/80 (53%)

Query: 8  KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAM 67
          K  L V  L + + +    + F   G+I+  K   D+ T +   +GFV +++ +DA +A+
Sbjct: 2  KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61

Query: 68 DNMDGAELYGRVLTVNYALP 87
          + ++G  L  + + V+YA P
Sbjct: 62 NTLNGLRLQTKTIKVSYARP 81

>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 = 69.5 bits (170), Expect = 9e-17
 Identities = 20/84 (23%), Positives = 38/84 (45%), Gaps = 9/84 (10%)

Query: 7  QKNTLYVGGLA-EEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQ 65
            + +++G L    V ++ + A F  +G I             H+ F FV ++ + +A  
Sbjct: 14 MNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCS--------VHKGFAFVQYVNERNARA 65

Query: 66 AMDNMDGAELYGRVLTVNYALPER 89
          A+   DG  + G+VL +N A   +
Sbjct: 66 AVAGEDGRMIAGQVLDINLAAEPK 89

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 68.9 bits (168), Expect = 9e-17
 Identities = 21/80 (26%), Positives = 37/80 (46%)

Query: 8  KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAM 67
             L V  L +++ +  L+A F   G I   +   D  T     + FV F  + D+ +A+
Sbjct: 2  NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 61

Query: 68 DNMDGAELYGRVLTVNYALP 87
            ++G  +  + L V+YA P
Sbjct: 62 KVLNGITVRNKRLKVSYARP 81

>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 = 68.4 bits (167), Expect = 2e-16
 Identities = 27/84 (32%), Positives = 43/84 (51%), Gaps = 2/84 (2%)

Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQ-ATQKHRSFGFVTFLEKEDAIQ 65
            + + V  +  + N+  +   F  FG++K V+ P     T  HR FGFV F+ K+DA +
Sbjct: 7  TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKK 66

Query: 66 AMDNM-DGAELYGRVLTVNYALPE 88
          A + +     LYGR L + +A  E
Sbjct: 67 AFNALCHSTHLYGRRLVLEWADSE 90

>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 = 67.7 bits (165), Expect = 3e-16
 Identities = 19/79 (24%), Positives = 36/79 (45%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
          + L++GGL   +N+  +      FG +K      D AT   + + F  +++     QA+ 
Sbjct: 2  HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 61

Query: 69 NMDGAELYGRVLTVNYALP 87
           ++G +L  + L V  A  
Sbjct: 62 GLNGMQLGDKKLLVQRASV 80

>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 = 67.8 bits (165), Expect = 3e-16
 Identities = 27/74 (36%), Positives = 37/74 (50%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
            L V GL+    E  L   F  +G I DV    DQ +++ R F FV F   +DA +A +
Sbjct: 10 CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 69

Query: 69 NMDGAELYGRVLTV 82
            +G EL GR + V
Sbjct: 70 RANGMELDGRRIRV 83

>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 = 67.4 bits (164), Expect = 5e-16
 Identities = 25/81 (30%), Positives = 43/81 (53%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
            L+V  L+   +E  L   F  +G + ++  P+D  T+K + F FVTF+  E A++A  
Sbjct: 9  GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

Query: 69 NMDGAELYGRVLTVNYALPER 89
           +DG    GR+L V  +  ++
Sbjct: 69 EVDGQVFQGRMLHVLPSTIKK 89

>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 = 66.5 bits (162), Expect = 9e-16
 Identities = 21/75 (28%), Positives = 33/75 (44%), Gaps = 1/75 (1%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          L V  L   V++A +   F  FG +K      D+ + +      V F  K DA++AM   
Sbjct: 3  LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQY 61

Query: 71 DGAELYGRVLTVNYA 85
          +G  L GR + +   
Sbjct: 62 NGVPLDGRPMNIQLV 76

>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 = 67.0 bits (163), Expect = 1e-15
 Identities = 17/83 (20%), Positives = 34/83 (40%), Gaps = 1/83 (1%)

Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
             T++   LA  +    L   F   G ++DV+   D+ +++ +   +V F E +     
Sbjct: 17 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSV-PL 75

Query: 67 MDNMDGAELYGRVLTVNYALPER 89
             + G  L G  + V  +  E+
Sbjct: 76 AIGLTGQRLLGVPIIVQASQAEK 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 = 66.2 bits (161), Expect = 1e-15
 Identities = 20/75 (26%), Positives = 38/75 (50%), Gaps = 1/75 (1%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          +++GGL+ +  +  L   F  FG++K+     D  T++ R FGFVTF+++    + +   
Sbjct: 3  MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-AQ 61

Query: 71 DGAELYGRVLTVNYA 85
             EL  + +    A
Sbjct: 62 SRHELDSKTIDPKVA 76

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 66.3 bits (161), Expect = 1e-15
 Identities = 21/83 (25%), Positives = 44/83 (53%)

Query: 5  AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
          +V+   L+V  + EE  E  +   F  +G+IK++   LD+ T   + +  V +   + A+
Sbjct: 4  SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQAL 63

Query: 65 QAMDNMDGAELYGRVLTVNYALP 87
           A + ++GAE+ G+ + V++   
Sbjct: 64 AAKEALNGAEIMGQTIQVDWCFV 86

>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 = 65.8 bits (160), Expect = 2e-15
 Identities = 23/83 (27%), Positives = 43/83 (51%), Gaps = 2/83 (2%)

Query: 5  AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAI 64
          +++   LYV GL + + +  L   F  +G I   +  +DQ T   R  GF+ F ++ +A 
Sbjct: 3  SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAE 62

Query: 65 QAMDNMDGAELYGRV--LTVNYA 85
          +A+  ++G +  G    +TV +A
Sbjct: 63 EAIKGLNGQKPSGATEPITVKFA 85

>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 = 65.8 bits (160), Expect = 2e-15
 Identities = 19/83 (22%), Positives = 38/83 (45%), Gaps = 6/83 (7%)

Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
          +  T+Y GG+A  + + ++   F PFG I +++          + + FV F   E A  A
Sbjct: 17 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVF------PEKGYSFVRFSTHESAAHA 70

Query: 67 MDNMDGAELYGRVLTVNYALPER 89
          + +++G  + G V+   +     
Sbjct: 71 IVSVNGTTIEGHVVKCYWGKESP 93

>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 = 65.1 bits (158), Expect = 4e-15
 Identities = 20/78 (25%), Positives = 29/78 (37%), Gaps = 3/78 (3%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKD---VKTPLDQATQKHRSFGFVTFLEKEDAIQAM 67
          L++  L     E  L   F   G IK     K            FGFV + + E A +A+
Sbjct: 1  LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 68 DNMDGAELYGRVLTVNYA 85
            + G  + G  L V  +
Sbjct: 61 KQLQGHTVDGHKLEVRIS 78

>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 = 65.1 bits (158), Expect = 4e-15
 Identities = 25/79 (31%), Positives = 40/79 (50%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
           T+ V  L+E+  E  L   F PFG I  +    D+ T + + F F++F  +EDA +A+ 
Sbjct: 9  ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIA 68

Query: 69 NMDGAELYGRVLTVNYALP 87
           + G      +L V +A P
Sbjct: 69 GVSGFGYDHLILNVEWAKP 87

>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 = 64.4 bits (156), Expect = 6e-15
 Identities = 25/83 (30%), Positives = 43/83 (51%), Gaps = 1/83 (1%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDV-KTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
          +++G L  E++E +L+  F  FG I    K   D  T   + + F+ F   + +  A++ 
Sbjct: 1  IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 70 MDGAELYGRVLTVNYALPERIKG 92
          M+G  L  R +TV+YA  +  KG
Sbjct: 61 MNGQYLCNRPITVSYAFKKDSKG 83

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 64.6 bits (157), Expect = 6e-15
 Identities = 22/81 (27%), Positives = 32/81 (39%), Gaps = 2/81 (2%)

Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
          + + L V GL  +  E  L   F  FG++  V+   D  T   + FGFV F E E  ++ 
Sbjct: 7  KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKV 66

Query: 67 MDNMDGAELYGRVLTVNYALP 87
          M       + GR         
Sbjct: 67 MSQRH--MIDGRWCDCKLPNS 85

>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 = 64.2 bits (156), Expect = 7e-15
 Identities = 21/81 (25%), Positives = 35/81 (43%), Gaps = 6/81 (7%)

Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
          Q++ L+VG L  ++ E  +   F  +G   +V         K + FGF+    +  A  A
Sbjct: 7  QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFI------HKDKGFGFIRLETRTLAEIA 60

Query: 67 MDNMDGAELYGRVLTVNYALP 87
             +D   L G+ L V +A  
Sbjct: 61 KVELDNMPLRGKQLRVRFACH 81

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.5 bits (154), Expect = 1e-14
 Identities = 26/80 (32%), Positives = 41/80 (51%), Gaps = 1/80 (1%)

Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
          Q   L++GGL+ E  +  L + F  +G + D     D  T++ R FGFVT+   E+   A
Sbjct: 5  QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 64

Query: 67 MDNMDGAELYGRVLTVNYAL 86
          M N    ++ GRV+    A+
Sbjct: 65 M-NARPHKVDGRVVEPKRAV 83

>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 = 63.3 bits (153), Expect = 2e-14
 Identities = 12/78 (15%), Positives = 26/78 (33%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
          TL++        +  +         +              R F ++    KEDA   ++ 
Sbjct: 3  TLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEK 62

Query: 70 MDGAELYGRVLTVNYALP 87
          ++G ++ G  L    + P
Sbjct: 63 LNGLKIEGYTLVTKVSNP 80

>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 = 63.3 bits (153), Expect = 2e-14
 Identities = 22/89 (24%), Positives = 36/89 (40%), Gaps = 8/89 (8%)

Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKD--------VKTPLDQATQKHRSFGFVTFL 58
            + +YV GL + V    L   F   G +K         +   LD+ T K +    V++ 
Sbjct: 7  DNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYE 66

Query: 59 EKEDAIQAMDNMDGAELYGRVLTVNYALP 87
          +   A  A++  DG +  G  L V+ A  
Sbjct: 67 DPPTAKAAVEWFDGKDFQGSKLKVSLARK 95

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.9 bits (150), Expect = 5e-14
 Identities = 25/75 (33%), Positives = 38/75 (50%), Gaps = 1/75 (1%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          +++GGL+ +  +  L   F  FG++ D    LD  T + R FGFV F E E   + MD  
Sbjct: 2  MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-Q 60

Query: 71 DGAELYGRVLTVNYA 85
             +L G+V+    A
Sbjct: 61 KEHKLNGKVIDPKRA 75

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.4 bits (151), Expect = 5e-14
 Identities = 22/84 (26%), Positives = 34/84 (40%), Gaps = 3/84 (3%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
            +YVG L  ++    +   F  +G I+D+     +       F FV F +  DA  A+ 
Sbjct: 15 CRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR---GGPPFAFVEFEDPRDAEDAVY 71

Query: 69 NMDGAELYGRVLTVNYALPERIKG 92
            DG +  G  L V +    R  G
Sbjct: 72 GRDGYDYDGYRLRVEFPRSGRGTG 95

>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 = 62.0 bits (150), Expect = 5e-14
 Identities = 26/85 (30%), Positives = 41/85 (48%), Gaps = 2/85 (2%)

Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
          Q  TLYVG L+ +V E ++   F   G  K  K   +     +  + FV F E  DA  A
Sbjct: 7  QPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEH--TSNDPYCFVEFYEHRDAAAA 64

Query: 67 MDNMDGAELYGRVLTVNYALPERIK 91
          +  M+G ++ G+ + VN+A     +
Sbjct: 65 LAAMNGRKILGKEVKVNWATTPSSQ 89

>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 = 62.0 bits (150), Expect = 6e-14
 Identities = 22/90 (24%), Positives = 38/90 (42%), Gaps = 8/90 (8%)

Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
             TL    L+  + E  L   F    +I+ V         K +   ++ F  + DA + 
Sbjct: 15 AARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKN 69

Query: 67 MDNMDGAELYGRVLTVNYALPERIKGGEQG 96
          ++   GAE+ GR +++ Y      KGG +G
Sbjct: 70 LEEKQGAEIDGRSVSLYYTGE---KGGTRG 96

>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 = 61.5 bits (149), Expect = 6e-14
 Identities = 21/75 (28%), Positives = 38/75 (50%), Gaps = 1/75 (1%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          ++VGGL+ +  E  +   F  FG+++ ++ P+D  T K R F F+TF E+E   + M+  
Sbjct: 2  IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61

Query: 71 DGAELYGRVLTVNYA 85
              +      +  A
Sbjct: 62 -YHNVGLSKCEIKVA 75

>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 = 60.8 bits (147), Expect = 2e-13
 Identities = 21/81 (25%), Positives = 38/81 (46%), Gaps = 2/81 (2%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
            +++  L + ++   L+  F  FG+I   K   D+   K   +GFV F  +E A +A++
Sbjct: 9  GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKG--YGFVHFETQEAAERAIE 66

Query: 69 NMDGAELYGRVLTVNYALPER 89
           M+G  L  R + V      +
Sbjct: 67 KMNGMLLNDRKVFVGRFKSRK 87

>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 = 60.9 bits (147), Expect = 2e-13
 Identities = 21/81 (25%), Positives = 40/81 (49%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
            L++  L +E  +  L   F+PFG++   K  +D+ T   + FGFV++     A  A+ 
Sbjct: 19 ANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQ 78

Query: 69 NMDGAELYGRVLTVNYALPER 89
          +M+G ++  + L V     + 
Sbjct: 79 SMNGFQIGMKRLKVQLKRSKN 99

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.8 bits (147), Expect = 2e-13
 Identities = 25/81 (30%), Positives = 38/81 (46%), Gaps = 1/81 (1%)

Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
          Q   L++GGL+ E  E  L   +  +G + D     D A+++ R FGFVTF    +   A
Sbjct: 19 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAA 78

Query: 67 MDNMDGAELYGRVLTVNYALP 87
          M       + GRV+    A+ 
Sbjct: 79 M-AARPHSIDGRVVEPKRAVA 98

>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 = 60.5 bits (146), Expect = 2e-13
 Identities = 24/81 (29%), Positives = 36/81 (44%), Gaps = 2/81 (2%)

Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
              L+V  +     +  L   F  FG I DV+   +   +  + FGFVTF    DA +A
Sbjct: 10 TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGFVTFENSADADRA 67

Query: 67 MDNMDGAELYGRVLTVNYALP 87
           + + G  + GR + VN A  
Sbjct: 68 REKLHGTVVEGRKIEVNNATA 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 = 60.0 bits (145), Expect = 3e-13
 Identities = 22/81 (27%), Positives = 34/81 (41%), Gaps = 6/81 (7%)

Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
              LYV  L    +E ++   F         +       +K R + FV F  +EDA++A
Sbjct: 7  SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV------KKIRDYAFVHFSNREDAVEA 60

Query: 67 MDNMDGAELYGRVLTVNYALP 87
          M  ++G  L G  + V  A P
Sbjct: 61 MKALNGKVLDGSPIEVTLAKP 81

>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 = 60.1 bits (145), Expect = 3e-13
 Identities = 20/79 (25%), Positives = 34/79 (43%), Gaps = 1/79 (1%)

Query: 8  KNTLYVGGLAEEVNEAILHAAFIP-FGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
           +T+Y+  L E++ +  L  +    F     +   L   + K R   FV F E   A  A
Sbjct: 3  NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 62

Query: 67 MDNMDGAELYGRVLTVNYA 85
          + +M G   Y + + + YA
Sbjct: 63 LRSMQGFPFYDKPMRIQYA 81

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.9 bits (142), Expect = 6e-13
 Identities = 20/82 (24%), Positives = 39/82 (47%), Gaps = 7/82 (8%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
          N LY+G L+  V    L   F            L         + FV + ++  AI+A++
Sbjct: 2  NKLYIGNLSPAVTADDLRQLFGDRKLP------LAGQVLLKSGYAFVDYPDQNWAIRAIE 55

Query: 69 NMDGA-ELYGRVLTVNYALPER 89
           + G  EL+G+++ V+Y++ ++
Sbjct: 56 TLSGKVELHGKIMEVDYSVSKK 77

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 59.1 bits (142), Expect = 6e-13
 Identities = 18/83 (21%), Positives = 35/83 (42%), Gaps = 6/83 (7%)

Query: 6  VQKNTLYVGGLAEEVNEAILHAAFI---PFGDIKDVKTPLDQATQKHRSFGFVTFLE--- 59
          VQKN ++V GL++ + +  +         FG I  V      +    +      ++    
Sbjct: 6  VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIR 65

Query: 60 KEDAIQAMDNMDGAELYGRVLTV 82
           EDA++A+  ++   + GR L  
Sbjct: 66 SEDALRAIQCVNNVVVDGRTLKA 88

>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 = 58.6 bits (141), Expect = 7e-13
 Identities = 20/75 (26%), Positives = 35/75 (46%), Gaps = 1/75 (1%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          ++VGGL+       +   F  FG + D     D+ T +HR FGFVTF  ++   +    +
Sbjct: 2  IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-EI 60

Query: 71 DGAELYGRVLTVNYA 85
             E+  +++    A
Sbjct: 61 HFHEINNKMVECKKA 75

>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 = 58.9 bits (142), Expect = 8e-13
 Identities = 20/79 (25%), Positives = 36/79 (45%), Gaps = 7/79 (8%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
          + ++VG    ++ E  L   F  +GD+ DV  P     +  R+F FVTF + + A     
Sbjct: 6  SGVFVGRCTGDMTEDELREFFSQYGDVMDVFIP-----KPFRAFAFVTFADDQIAQSLC- 59

Query: 69 NMDGAELYGRVLTVNYALP 87
            +   + G  + ++ A P
Sbjct: 60 -GEDLIIKGISVHISNAEP 77

>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 = 59.0 bits (142), Expect = 9e-13
 Identities = 33/86 (38%), Positives = 47/86 (54%)

Query: 4  LAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDA 63
          +A  +  L+VGGL+ + NE  L   F  +G I +V    D+ TQ+ R FGFVTF   +DA
Sbjct: 1  MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDA 60

Query: 64 IQAMDNMDGAELYGRVLTVNYALPER 89
            AM  M+G  + GR + V+ A    
Sbjct: 61 KDAMMAMNGKSVDGRQIRVDQAGKSS 86

>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 = 58.5 bits (141), Expect = 1e-12
 Identities = 9/78 (11%), Positives = 24/78 (30%)

Query: 8  KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAM 67
             + V  +   V+   +   F  +  I                   V F  +++A  A+
Sbjct: 9  PTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAV 68

Query: 68 DNMDGAELYGRVLTVNYA 85
           +++   +  R + +   
Sbjct: 69 IDLNDRPIGSRKVKLVLG 86

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.6 bits (141), Expect = 1e-12
 Identities = 24/81 (29%), Positives = 40/81 (49%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
            LY+  L+  V E  L + F  F + K         T + R   F+TF  KE A QA+ 
Sbjct: 19 KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 78

Query: 69 NMDGAELYGRVLTVNYALPER 89
           ++G +LYG++L + +   ++
Sbjct: 79 LVNGYKLYGKILVIEFGKNKK 99

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.8 bits (139), Expect = 2e-12
 Identities = 22/77 (28%), Positives = 37/77 (48%), Gaps = 1/77 (1%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
           ++VGG+ E+  E  L   F  +G I+ ++   D+ + K R F FVTF +  D++  +  
Sbjct: 4  KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF-DDHDSVDKIVI 62

Query: 70 MDGAELYGRVLTVNYAL 86
               + G    V  AL
Sbjct: 63 QKYHTVNGHNCEVRKAL 79

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.2 bits (140), Expect = 2e-12
 Identities = 13/85 (15%), Positives = 31/85 (36%), Gaps = 1/85 (1%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
           T ++G L  +V E  +   F                 ++ + FG+  F + +    +  
Sbjct: 16 YTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSL-LSAL 74

Query: 69 NMDGAELYGRVLTVNYALPERIKGG 93
          +++   L  + + V+ A   + K  
Sbjct: 75 SLNEESLGNKRIRVDVADQAQDKDS 99

>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 = 58.1 bits (140), Expect = 3e-12
 Identities = 12/82 (14%), Positives = 32/82 (39%), Gaps = 1/82 (1%)

Query: 3   NLAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKED 62
            L    + + +    +E  E +       +G+++++    D          +V F  +ED
Sbjct: 22  GLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVC-DNLGDHLVGNVYVKFRREED 80

Query: 63  AIQAMDNMDGAELYGRVLTVNY 84
           A +A+ +++     G+ +    
Sbjct: 81  AEKAVIDLNNRWFNGQPIHAEL 102

>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 = 57.1 bits (137), Expect = 5e-12
 Identities = 26/82 (31%), Positives = 43/82 (52%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
          +++VG +  E  E  L   F   G +   +   D+ T K + +GF  + ++E A+ AM N
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

Query: 70 MDGAELYGRVLTVNYALPERIK 91
          ++G E  GR L V+ A  E+ K
Sbjct: 70 LNGREFSGRALRVDNAASEKNK 91

>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 = 56.6 bits (136), Expect = 6e-12
 Identities = 26/82 (31%), Positives = 42/82 (51%), Gaps = 8/82 (9%)

Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
          + NTLYV G   ++   +L  AF PFG+I D+     +      +  FVT+ + E A QA
Sbjct: 4  KGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPPR------NCAFVTYEKMESADQA 55

Query: 67 MDNMDGAELYGRVLTVNYALPE 88
          +  ++G ++    L VN A  +
Sbjct: 56 VAELNGTQVESVQLKVNIARKQ 77

>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 = 57.3 bits (138), Expect = 6e-12
 Identities = 16/83 (19%), Positives = 34/83 (40%), Gaps = 6/83 (7%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          + V  L   V   +LH  F  FG +  + T     T+ ++    + + +   A  A  ++
Sbjct: 10 IIVENLFYPVTLDVLHQIFSKFGTVLKIITF----TKNNQFQALLQYADPVSAQHAKLSL 65

Query: 71 DGAELY--GRVLTVNYALPERIK 91
          DG  +Y     L ++++    + 
Sbjct: 66 DGQNIYNACCTLRIDFSKLTSLN 88

>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 = 56.7 bits (136), Expect = 6e-12
 Identities = 17/79 (21%), Positives = 30/79 (37%), Gaps = 6/79 (7%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTP-----LDQATQKHRSFGFVTFLEKEDAI 64
           LYVG +   + E  +   F     +  +        L     + ++F F+ F   ++  
Sbjct: 3  RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 65 QAMDNMDGAELYGRVLTVN 83
          QAM   DG    G+ L + 
Sbjct: 63 QAM-AFDGIIFQGQSLKIR 80

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.3 bits (135), Expect = 1e-11
 Identities = 28/90 (31%), Positives = 45/90 (50%), Gaps = 2/90 (2%)

Query: 10  TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
            ++VGGL     +A L   F  FGDI++     D+ T K R +GFVT  ++  A +A  +
Sbjct: 12  KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 71

Query: 70  MDGAELYGRVLTVNYALPE-RIKGGEQGWA 98
            +   + GR   VN A    + +  + G+A
Sbjct: 72  PNP-IIDGRKANVNLAYLGAKPRSLQTGFA 100

>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 = 55.9 bits (134), Expect = 2e-11
 Identities = 16/84 (19%), Positives = 31/84 (36%), Gaps = 4/84 (4%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKD--VKTPLDQATQKHRSFGFVTFLEKEDAIQAM 67
           L++GG+ +      +        +     +         K+R F FV +     A  A 
Sbjct: 3  RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 68 DNMDGA--ELYGRVLTVNYALPER 89
            +     +L+G  + V++A PE 
Sbjct: 63 RKLMPGRIQLWGHQIAVDWAEPEI 86

>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 = 56.5 bits (135), Expect = 2e-11
 Identities = 26/88 (29%), Positives = 40/88 (45%)

Query: 9   NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
             L V  +   V+E  L   F  +G I+ VK   D+ T++ R +GFV F     A QA+ 
Sbjct: 43  RNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIA 102

Query: 69  NMDGAELYGRVLTVNYALPERIKGGEQG 96
            ++G  +  + L V  A     + G  G
Sbjct: 103 GLNGFNILNKRLKVALAASGHQRPGIAG 130

>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 = 54.8 bits (131), Expect = 3e-11
 Identities = 22/87 (25%), Positives = 39/87 (44%), Gaps = 6/87 (6%)

Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
          +  T+++  L+ +  E  L      FGD+K V+  L   T+  +   F  F+ +E A + 
Sbjct: 7  EGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKC 66

Query: 67 MDNM------DGAELYGRVLTVNYALP 87
          +          G +L GR L V+ A+ 
Sbjct: 67 LAAASLEAEGGGLKLDGRQLKVDLAVT 93

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 54.7 bits (131), Expect = 4e-11
 Identities = 25/86 (29%), Positives = 35/86 (40%), Gaps = 8/86 (9%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
            L+VGGL    + A L   F  FG I+ +         K  SF ++ +   + A  A  
Sbjct: 18 TRLWVGGLGPNTSLAALAREFDRFGSIRTIDH------VKGDSFAYIQYESLDAAQAACA 71

Query: 69 NMDGAELYG--RVLTVNYALPERIKG 92
           M G  L G  R L V++A      G
Sbjct: 72 KMRGFPLGGPDRRLRVDFAKSGPSSG 97

>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 = 54.4 bits (130), Expect = 7e-11
 Identities = 21/98 (21%), Positives = 41/98 (41%), Gaps = 6/98 (6%)

Query: 9   NTLYVGGLAEE-VNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAM 67
           + L V  L  E V    L   F  +GD++ VK          +    V   +   A  AM
Sbjct: 3   SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKIL-----FNKKENALVQMADGNQAQLAM 57

Query: 68  DNMDGAELYGRVLTVNYALPERIKGGEQGWAAQPIWAD 105
            +++G +L+G+ + +  +  + ++   +G   Q +  D
Sbjct: 58  SHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKD 95

>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 = 53.2 bits (127), Expect = 1e-10
 Identities = 14/77 (18%), Positives = 25/77 (32%), Gaps = 7/77 (9%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
          + + V  L ++ N   +H     +               +++   FVT L  E A  A+ 
Sbjct: 6  SGILVKNLPQDSNCQEVHDLLKDYDLK-------YCYVDRNKRTAFVTLLNGEQAQNAIQ 58

Query: 69 NMDGAELYGRVLTVNYA 85
                  G+ L V   
Sbjct: 59 MFHQYSFRGKDLIVQLQ 75

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 52.4 bits (125), Expect = 2e-10
 Identities = 20/84 (23%), Positives = 41/84 (48%), Gaps = 3/84 (3%)

Query: 6  VQKNTLYVGGLAEEV-NEAILHAAFIPFGDIKDVKTPLDQ-ATQKHRSFGFVTFLEKEDA 63
          ++   + +  L+ E+ +E +L  +F  FG I+ +  P  Q     +    F+ F  K+ A
Sbjct: 2  LEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSA 61

Query: 64 IQAMDNMDGAELYGRVLTVNYALP 87
           +A+  M+ + L  R ++V+ A  
Sbjct: 62 ERALQ-MNRSLLGNREISVSLADK 84

>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 = 52.1 bits (124), Expect = 5e-10
 Identities = 12/88 (13%), Positives = 24/88 (27%), Gaps = 11/88 (12%)

Query: 9  NTLYVGGLAEEVNE-----AILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDA 63
          + L      ++V       A   + F  +      +        K      + F     A
Sbjct: 6  SGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYF------KSFKRVRINFSNPLSA 59

Query: 64 IQAMDNMDGAELYGRVLTVNYALPERIK 91
            A   +   E  G+ + + +A    I 
Sbjct: 60 ADARLRLHKTEFLGKEMKLYFAQTLHIG 87

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.5 bits (127), Expect = 6e-10
 Identities = 21/83 (25%), Positives = 38/83 (45%), Gaps = 1/83 (1%)

Query: 7   QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
               ++VGG+ E+  E  L   F  +G I+ ++   D+ + K R F FVTF + +   + 
Sbjct: 96  TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 155

Query: 67  MDNMDGAELYGRVLTVNYALPER 89
           +       + G    V  AL ++
Sbjct: 156 VI-QKYHTVNGHNCEVRKALSKQ 177

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.9 bits (110), Expect = 1e-07
 Identities = 21/66 (31%), Positives = 33/66 (50%)

Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
          Q   L++GGL+ E  +  L + F  +G + D     D  T++ R FGFVT+   E+   A
Sbjct: 5  QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 64

Query: 67 MDNMDG 72
          M+    
Sbjct: 65 MNARPH 70

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 50.5 bits (120), Expect = 2e-09
 Identities = 16/83 (19%), Positives = 25/83 (30%), Gaps = 7/83 (8%)

Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
              + V GL    +   L       GD+         A  +    G V +L KED   A
Sbjct: 14 SDFRVLVSGLPPSGSWQDLKDHMREAGDV-------CYADVQKDGMGMVEYLRKEDMEYA 66

Query: 67 MDNMDGAELYGRVLTVNYALPER 89
          +  +D  +        +Y     
Sbjct: 67 LRKLDDTKFRSHEGETSYIRVYP 89

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.1 bits (119), Expect = 2e-09
 Identities = 17/78 (21%), Positives = 32/78 (41%), Gaps = 5/78 (6%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
           TL++  +   V+E  L   F   G +           QK R    +     E+A+QA+ 
Sbjct: 11 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKF----FQKDRKMALIQMGSVEEAVQALI 66

Query: 69 NMDGAELY-GRVLTVNYA 85
          ++   +L     L V+++
Sbjct: 67 DLHNHDLGENHHLRVSFS 84

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 50.2 bits (119), Expect = 2e-09
 Identities = 21/85 (24%), Positives = 31/85 (36%), Gaps = 8/85 (9%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
            ++V GL E V EA L  A   FG I  V           +    V F   + A + + 
Sbjct: 16 PVVHVRGLCESVVEADLVEALEKFGTICYVM------MMPFKRQALVEFENIDSAKECVT 69

Query: 69 --NMDGAELYGRVLTVNYALPERIK 91
                  + G+    NY+  +RI 
Sbjct: 70 FAADVPVYIAGQQAFFNYSTSKRIT 94

>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 = 49.0 bits (116), Expect = 3e-09
 Identities = 19/70 (27%), Positives = 32/70 (45%)

Query: 11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM 70
          LY+ GL     +  L     P+G I   K  LD+ T K + +GFV F     A +A+  +
Sbjct: 1  LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 71 DGAELYGRVL 80
            + +  ++ 
Sbjct: 61 KASGVQAQMA 70

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.2 bits (114), Expect = 1e-08
 Identities = 16/87 (18%), Positives = 29/87 (33%), Gaps = 3/87 (3%)

Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
            + +++ GL     E  ++  F P   ++           +      V F   EDA+ A
Sbjct: 14 TGHCVHMRGLPYRATENDIYNFFSPLNPMRVH--IEIGPDGRVTGEADVEFATHEDAVAA 71

Query: 67 MDNMDGAELYGRVLTVNYALPERIKGG 93
          M   D A +  R + +         G 
Sbjct: 72 M-AKDKANMQHRYVELFLNSTAGTSGS 97

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.5 bits (112), Expect = 3e-08
 Identities = 12/89 (13%), Positives = 31/89 (34%), Gaps = 1/89 (1%)

Query: 8  KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAM 67
          K   ++  +   + +  +          ++    L     +      V F  ++DA ++ 
Sbjct: 8  KVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSE 67

Query: 68 DNMDGAELYGRVLTVNYALPERIKGGEQG 96
            +   +L GR   V+    E ++  E+ 
Sbjct: 68 R-LHRKKLNGREAFVHVVTLEDMREIEKN 95

>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 = 47.5 bits (112), Expect = 3e-08
 Identities = 15/85 (17%), Positives = 26/85 (30%), Gaps = 1/85 (1%)

Query: 7   QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
               LY+  L   ++E  L     PFG +   +     ++   R  GF      E     
Sbjct: 17  DPTNLYISNLPLSMDEQELENMLKPFGQVISTRIL-RDSSGTSRGVGFARMESTEKCEAV 75

Query: 67  MDNMDGAELYGRVLTVNYALPERIK 91
           + + +G  +           P   K
Sbjct: 76  IGHFNGKFIKTPPGVSAPTEPLLCK 100

>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 = 46.5 bits (109), Expect = 4e-08
 Identities = 18/81 (22%), Positives = 33/81 (40%), Gaps = 2/81 (2%)

Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
              L++G L    + A L  A        D+     + T  +R FG+V F   ED  +A
Sbjct: 12 TPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVDFESAEDLEKA 70

Query: 67 MDNMDGAELYGRVLTVNYALP 87
          +  + G +++G  + +     
Sbjct: 71 L-ELTGLKVFGNEIKLEKPKG 90

>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 = 46.5 bits (110), Expect = 5e-08
 Identities = 12/54 (22%), Positives = 20/54 (37%), Gaps = 4/54 (7%)

Query: 32 FGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYA 85
          FG I+ +                V+F + E+A   +  +DG    GR +T    
Sbjct: 43 FGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAW 92

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 111

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 46.5 bits (109), Expect = 7e-08
 Identities = 18/94 (19%), Positives = 32/94 (34%), Gaps = 6/94 (6%)

Query: 8   KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAM 67
           K  +    L      A +   F  FG +  V  P      +      V FLE  +A +A 
Sbjct: 10  KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP------EGGITAIVEFLEPLEARKAF 63

Query: 68  DNMDGAELYGRVLTVNYALPERIKGGEQGWAAQP 101
            ++  ++ +   L + +A         Q   +Q 
Sbjct: 64  RHLAYSKFHHVPLYLEWAPIGVFGAAPQKKDSQH 97

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.3 bits (106), Expect = 1e-07
 Identities = 17/81 (20%), Positives = 25/81 (30%), Gaps = 7/81 (8%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
          N + V GL    +   L       GD+         A       G V F+ KED   A+ 
Sbjct: 1  NRVVVSGLPPSGSWQDLKDHMREAGDV-------CYADVYRDGTGVVEFVRKEDMTYAVR 53

Query: 69 NMDGAELYGRVLTVNYALPER 89
           +D  +         Y   + 
Sbjct: 54 KLDNTKFRSHEGETAYIRVKV 74

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.7 bits (105), Expect = 2e-07
 Identities = 11/80 (13%), Positives = 28/80 (35%), Gaps = 2/80 (2%)

Query: 6  VQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQ 65
          V+  ++Y+ G   +     +       G + +++       +  +   FV F   E A +
Sbjct: 4  VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMR-RTLHKAFKGSIFVVFDSIESAKK 62

Query: 66 AMDNMDGAELYGRVLTVNYA 85
           +    G +     L + + 
Sbjct: 63 FV-ETPGQKYKETDLLILFK 81

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.3 bits (104), Expect = 3e-07
 Identities = 15/84 (17%), Positives = 31/84 (36%), Gaps = 13/84 (15%)

Query: 9  NTLYV--GGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
           +L V  GGL   V+   L       G +  +          ++ + F  +   E++ +A
Sbjct: 19 QSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLM------PPNKPYSFARYRTTEESKRA 72

Query: 67 MDNMDGAELYGR-----VLTVNYA 85
             ++G E+         L +N+ 
Sbjct: 73 YVTLNGKEVVDDLGQKITLYLNFV 96

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.2 bits (104), Expect = 4e-07
 Identities = 14/67 (20%), Positives = 25/67 (37%), Gaps = 2/67 (2%)

Query: 25 LHAAFIPFGDIKDVKTPLDQATQKHRSFGF--VTFLEKEDAIQAMDNMDGAELYGRVLTV 82
          +      +G +K ++ P      +    G   V F    D  +AM  + G +   RV+  
Sbjct: 31 VRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVT 90

Query: 83 NYALPER 89
           Y  P+ 
Sbjct: 91 KYCDPDS 97

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.4 bits (102), Expect = 4e-07
 Identities = 12/72 (16%), Positives = 25/72 (34%), Gaps = 8/72 (11%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
            + V G  +     IL   F  +G+I               ++  + +  K  A +A+ 
Sbjct: 5  TWVTVFGFPQASASYILLQ-FAQYGNILKHVM------SNTGNWMHIRYQSKLQARKAL- 56

Query: 69 NMDGAELYGRVL 80
          + DG      ++
Sbjct: 57 SKDGRIFGESIM 68

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 43.3 bits (101), Expect = 5e-07
 Identities = 13/76 (17%), Positives = 26/76 (34%), Gaps = 3/76 (3%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDN 69
          T+ V  L +  N+  ++  F   G I  V        +K+  F  + F   +    A   
Sbjct: 2  TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSL--KKNFRFARIEFARYDG-ALAAIT 58

Query: 70 MDGAELYGRVLTVNYA 85
               +    + V++ 
Sbjct: 59 KTHKVVGQNEIIVSHL 74

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 43.3 bits (101), Expect = 6e-07
 Identities = 16/78 (20%), Positives = 30/78 (38%), Gaps = 6/78 (7%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
            L++  L EE NE +L   F  F   K+      +         FV F  +  +  A +
Sbjct: 9  QILFLTNLPEETNEMMLSMLFNQFPGFKE-----VRLVPNRHDIAFVEFTTELQSNAAKE 63

Query: 69 NMDGAELY-GRVLTVNYA 85
           + G ++     + + +A
Sbjct: 64 ALQGFKITPTHAMKITFA 81

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.4 bits (96), Expect = 4e-06
 Identities = 17/85 (20%), Positives = 36/85 (42%), Gaps = 8/85 (9%)

Query: 9  NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
            L++  L  EV E  + A  +PFG + +          K ++  F+    +E AI  ++
Sbjct: 9  RVLHIRKLPGEVTETEVIALGLPFGKVTN------ILMLKGKNQAFLELATEEAAITMVN 62

Query: 69 --NMDGAELYGRVLTVNYALPERIK 91
            +     L  + + + Y+  + +K
Sbjct: 63 YYSAVTPHLRNQPIYIQYSNHKELK 87

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.3 bits (91), Expect = 2e-05
 Identities = 17/86 (19%), Positives = 32/86 (37%), Gaps = 10/86 (11%)

Query: 10 TLYVGGLAE-EVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD 68
           +++      +     L     PFG I +             +  F+     EDA  A+D
Sbjct: 10 VVHIMDFQRGKNLRYQLLQLVEPFGVISNHLI------LNKINEAFIEMATTEDAQAAVD 63

Query: 69 --NMDGAELYGRVLTVNYA-LPERIK 91
                A ++G+ + V+ +   +RIK
Sbjct: 64 YYTTTPALVFGKPVRVHLSQKYKRIK 89

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 113

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.4 bits (91), Expect = 3e-05
 Identities = 17/80 (21%), Positives = 31/80 (38%), Gaps = 7/80 (8%)

Query: 10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEK-EDAIQAMD 68
            + G L ++     LH  F   G+IK +         +    G + F EK ++A+    
Sbjct: 13 LKFSGDLDDQTCREDLHILFSNHGEIKWIDFV------RGAKEGIILFKEKAKEALGKAK 66

Query: 69 NMDGAELYGRVLTVNYALPE 88
          + +   L  R   V + + E
Sbjct: 67 DANNGNLQLRNKEVTWEVLE 86

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 112

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.7 bits (89), Expect = 5e-05
 Identities = 15/82 (18%), Positives = 26/82 (31%), Gaps = 1/82 (1%)

Query: 7  QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQA 66
              +Y+ GL  E     +   F     ++D          K    GFV F  + D   A
Sbjct: 17 AGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAA 76

Query: 67 MDNMDGAELYGRVLTVNYALPE 88
          +       +  R + V+    +
Sbjct: 77 LC-RHKQYMGNRFIQVHPITKK 97

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {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: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 33.3 bits (76), Expect = 0.003
 Identities = 13/61 (21%), Positives = 25/61 (40%), Gaps = 9/61 (14%)

Query: 23 AILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTV 82
            L      +G I  V+    Q          VTF +   A+  + ++DG ++ GR + +
Sbjct: 39 TELMQTLGSYGTIVLVRINQGQM--------LVTFADSHSALSVL-DVDGMKVKGRAVKI 89

Query: 83 N 83
          +
Sbjct: 90 S 90

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	174
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.81
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.8
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.79
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.79
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.79
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.79
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.79
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.78
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.77
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.77
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.76
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.76
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.76
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.76
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.76
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.76
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.75
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.74
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.74
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.74
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.74
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.74
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.74
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.74
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.74
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.73
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.73
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.73
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.73
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.72
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.72
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.71
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.71
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.7
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.7
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.7
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.69
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.69
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.68
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.67
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.67
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.67
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.67
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.67
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.66
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.66
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.66
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.66
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.65
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.65
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.65
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.64
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.64
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.64
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.64
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.63
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.63
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.63
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.63
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.62
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.62
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.62
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.62
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.62
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.61
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.6
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.59
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.59
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.59
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.58
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.58
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.58
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.57
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.56
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.55
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.53
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.53
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.51
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.51
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.46
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.41
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	99.38
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.37
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.3
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.29
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.16
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.08
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	96.99
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	96.81
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	96.57
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	93.51

>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=99.81  E-value=6e-20  Score=125.41  Aligned_cols=88  Identities=28%  Similarity=0.436  Sum_probs=81.0

Q ss_pred             CCCCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEEE
Q ss_conf             99997998299998829999983144998469997117999995208999970779899999823995124859799853
Q 030632            6 VQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYA   85 (174)
Q Consensus         6 ~~~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~a   85 (174)
                      ...++|||+|||+.+++.+|+.+|++||.|..+.+++++.++.++|||||+|.+.++|..||..|||..|.|++|+|.+|
T Consensus        40 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a  119 (139)
T d1u6fa1          40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALA  119 (139)
T ss_dssp             TTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEECCHHHHHHHHHHHCCCEECCEEEEEEEC
T ss_conf             99988999697988999999999976500322111122111112220368979999999999984898889988899876


Q ss_pred             CCCCCCCC
Q ss_conf             17888899
Q 030632           86 LPERIKGG   93 (174)
Q Consensus        86 ~~~~~~~~   93 (174)
                      .+...+..
T Consensus       120 ~~~~~~p~  127 (139)
T d1u6fa1         120 ASGHQRPG  127 (139)
T ss_dssp             SCCCCCCC
T ss_pred             CCCCCCCC
T ss_conf             88888989

>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=99.80  E-value=3.6e-19  Score=121.14  Aligned_cols=90  Identities=28%  Similarity=0.444  Sum_probs=82.1

Q ss_pred             CCCCCCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEE
Q ss_conf             89999979982999988299999831449984699971179999952089999707798999998239951248597998
Q 030632            4 LAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVN   83 (174)
Q Consensus         4 ~~~~~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~   83 (174)
                      -....++|||+|||+.+++.+|+.+|.+||.|..+.+++++.++.++|||||+|.+.+.|..|+..||+..|.|++|+|.
T Consensus         4 ~~~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~   83 (99)
T d1whwa_           4 GSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVL   83 (99)
T ss_dssp             CCCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCEEEEECCHHHHHHHHHHCCCCEECCEEEEEE
T ss_conf             98999889997999869899999999764975065310244434667504999889999999999829998999987999


Q ss_pred             EECCCCCCCC
Q ss_conf             5317888899
Q 030632           84 YALPERIKGG   93 (174)
Q Consensus        84 ~a~~~~~~~~   93 (174)
                      ++.++.....
T Consensus        84 ~a~~~~~~~~   93 (99)
T d1whwa_          84 PSTIKKEASQ   93 (99)
T ss_dssp             ECCCCSTTCC
T ss_pred             ECCCCCCCCC
T ss_conf             8888876677

>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=99.79  E-value=2.3e-19  Score=122.24  Aligned_cols=86  Identities=24%  Similarity=0.419  Sum_probs=80.8

Q ss_pred             CCCCCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEE
Q ss_conf             99999799829999882999998314499846999711799999520899997077989999982399512485979985
Q 030632            5 AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNY   84 (174)
Q Consensus         5 ~~~~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~   84 (174)
                      .+++++|||+|||+.+++.+|+.+|++||.+..+.++.++.++.++|||||+|.+.++|..||..|||..|.|++|+|.|
T Consensus        15 ~p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~   94 (102)
T d2cpza1          15 GPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQL   94 (102)
T ss_dssp             CSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCCCEEEECCCCCCCCCEEEEECCHHHHHHHHHHHCCCEECCEEEEEEE
T ss_conf             99999999959999999999999997633454321000013698765338874899999999998589988999889987


Q ss_pred             ECCCCC
Q ss_conf             317888
Q 030632           85 ALPERI   90 (174)
Q Consensus        85 a~~~~~   90 (174)
                      ++++..
T Consensus        95 a~~k~~  100 (102)
T d2cpza1          95 KRSKND  100 (102)
T ss_dssp             CCCSCC
T ss_pred             ECCCCC
T ss_conf             078889

>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=99.79  E-value=2.4e-19  Score=122.07  Aligned_cols=87  Identities=39%  Similarity=0.618  Sum_probs=81.1

Q ss_pred             CCCCCCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEE
Q ss_conf             89999979982999988299999831449984699971179999952089999707798999998239951248597998
Q 030632            4 LAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVN   83 (174)
Q Consensus         4 ~~~~~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~   83 (174)
                      ..++.++|||+|||+.+++.+|+.+|++||.|..+.+++++.++.++|||||+|.+.++|..|+..||+..+.|+.|+|.
T Consensus         5 ~~~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   84 (93)
T d1x5ua1           5 ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVN   84 (93)
T ss_dssp             CCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCCCEEECCCCCCCCCCEEEEECCHHHHHHHHHHCCCCEECCEEEEEE
T ss_conf             67999899990899858899999999984976542121012543566520799899999999999859998999887998


Q ss_pred             EECCCCC
Q ss_conf             5317888
Q 030632           84 YALPERI   90 (174)
Q Consensus        84 ~a~~~~~   90 (174)
                      ||.++..
T Consensus        85 ~A~~~~~   91 (93)
T d1x5ua1          85 KASAHNK   91 (93)
T ss_dssp             ETTTTSC
T ss_pred             ECCCCCC
T ss_conf             7289899

>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=99.79  E-value=4.2e-19  Score=120.75  Aligned_cols=86  Identities=30%  Similarity=0.499  Sum_probs=80.9

Q ss_pred             CCCCCCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEE
Q ss_conf             89999979982999988299999831449984699971179999952089999707798999998239951248597998
Q 030632            4 LAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVN   83 (174)
Q Consensus         4 ~~~~~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~   83 (174)
                      ...+.++|||+|||+.+++.+|+.+|++||.|..+.++.++.++.++|||||+|.+.++|..|+..|||..+.|+.|+|.
T Consensus         4 ~~~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~   83 (90)
T d2cq0a1           4 RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVE   83 (90)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHCCCEECCEEEEEE
T ss_conf             88899999997999879899999999875623321111135544666320589899999999999828998999898998


Q ss_pred             EECCCC
Q ss_conf             531788
Q 030632           84 YALPER   89 (174)
Q Consensus        84 ~a~~~~   89 (174)
                      ||+|+.
T Consensus        84 ~akp~~   89 (90)
T d2cq0a1          84 WAKPST   89 (90)
T ss_dssp             ESSCCC
T ss_pred             EEECCC
T ss_conf             634889

>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=99.79  E-value=1.8e-19  Score=122.79  Aligned_cols=86  Identities=60%  Similarity=0.985  Sum_probs=80.5

Q ss_pred             CCCCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEEE
Q ss_conf             99997998299998829999983144998469997117999995208999970779899999823995124859799853
Q 030632            6 VQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYA   85 (174)
Q Consensus         6 ~~~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~a   85 (174)
                      ..+++|||+|||+.+++.+|+.+|++||.|..+.+++++.++.++|||||+|.+.++|..|+..||+..+.|++|+|.||
T Consensus         3 ~~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a   82 (89)
T d2cqba1           3 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   82 (89)
T ss_dssp             CCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHCCEEEECCCCCCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEEE
T ss_conf             89829999699986889999998864783886110245565455630499988999999999985999999999899982


Q ss_pred             CCCCCC
Q ss_conf             178888
Q 030632           86 LPERIK   91 (174)
Q Consensus        86 ~~~~~~   91 (174)
                      +|+..+
T Consensus        83 ~p~~~k   88 (89)
T d2cqba1          83 KPMRIK   88 (89)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
T ss_conf             798989

>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=99.79  E-value=6.4e-19  Score=119.76  Aligned_cols=84  Identities=29%  Similarity=0.424  Sum_probs=79.6

Q ss_pred             CCCCCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEE
Q ss_conf             99999799829999882999998314499846999711799999520899997077989999982399512485979985
Q 030632            5 AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNY   84 (174)
Q Consensus         5 ~~~~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~   84 (174)
                      ...+++|||+|||+++++.+|+.+|++||.|..+.++.++.++.++|||||+|.+.++|..|+..|||..+.|++|+|.|
T Consensus         4 ~~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~   83 (93)
T d1h2vz_           4 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDW   83 (93)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCEECCCCCCCCCCCCCEEEEEECCHHHHHHHHHHHCCCEECCEEEEEEE
T ss_conf             67999999959999798999999999878862001024655322241579998899999999998089989998889998


Q ss_pred             ECCC
Q ss_conf             3178
Q 030632           85 ALPE   88 (174)
Q Consensus        85 a~~~   88 (174)
                      +.+.
T Consensus        84 a~~~   87 (93)
T d1h2vz_          84 DAGF   87 (93)
T ss_dssp             ESCC
T ss_pred             CCCC
T ss_conf             4898

>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=99.78  E-value=4.3e-19  Score=120.70  Aligned_cols=81  Identities=26%  Similarity=0.406  Sum_probs=77.4

Q ss_pred             CCCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEEEC
Q ss_conf             99979982999988299999831449984699971179999952089999707798999998239951248597998531
Q 030632            7 QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYAL   86 (174)
Q Consensus         7 ~~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~a~   86 (174)
                      .+++|||+|||+.+++.+|+.+|++||.|..+.+++++.++.++|||||+|.+.++|.+|+..|||..+.|++|+|.||+
T Consensus         1 s~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~   80 (82)
T d1b7fa1           1 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYAR   80 (82)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHHCCCCEEEEEEECCCCCCCCCCEEEECCHHHHHHHHHHHCCCEECCEEEEEEECC
T ss_conf             99999996979979899999999985981466466320368864224379899999999999868998999998999718


Q ss_pred             C
Q ss_conf             7
Q 030632           87 P   87 (174)
Q Consensus        87 ~   87 (174)
                      |
T Consensus        81 p   81 (82)
T d1b7fa1          81 P   81 (82)
T ss_dssp             C
T ss_pred             C
T ss_conf             9

>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=99.77  E-value=7.7e-19  Score=119.33  Aligned_cols=84  Identities=25%  Similarity=0.536  Sum_probs=79.5

Q ss_pred             CCCCCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEE
Q ss_conf             99999799829999882999998314499846999711799999520899997077989999982399512485979985
Q 030632            5 AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNY   84 (174)
Q Consensus         5 ~~~~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~   84 (174)
                      ...+++|||+|||+.+++.+|+.+|++||.|..+.+++++.+|.++|||||+|.+.++|..|+..|||..+.|++|+|.|
T Consensus         4 s~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~   83 (88)
T d1rk8a_           4 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW   83 (88)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHCCCCEECCEEEEEEE
T ss_conf             78998999948999898999999998729864100012343225564116898999999999998199989999899998


Q ss_pred             ECCC
Q ss_conf             3178
Q 030632           85 ALPE   88 (174)
Q Consensus        85 a~~~   88 (174)
                      |.++
T Consensus        84 a~~k   87 (88)
T d1rk8a_          84 CFVK   87 (88)
T ss_dssp             SEEC
T ss_pred             ECCC
T ss_conf             5589

>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=99.77  E-value=9.8e-19  Score=118.75  Aligned_cols=80  Identities=28%  Similarity=0.525  Sum_probs=77.0

Q ss_pred             CCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEEECC
Q ss_conf             99799829999882999998314499846999711799999520899997077989999982399512485979985317
Q 030632            8 KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYALP   87 (174)
Q Consensus         8 ~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~a~~   87 (174)
                      .++|||+|||+.+++.+|+.+|++||.|..+.+++++.++.++|||||+|.+.++|..|+..|||..+.|++|+|.||+|
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHHCCCCCCCCEEECCCCCCEEEEEEEECCHHHHHHHHHHHCCCEECCEEEEEEEEEC
T ss_conf             88899989898798999999999969764101000025787302589998999999999998289999999999998548

>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=99.76  E-value=2.7e-18  Score=116.29  Aligned_cols=88  Identities=31%  Similarity=0.509  Sum_probs=78.4

Q ss_pred             CCCCCCCCCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEE
Q ss_conf             99989999979982999988299999831449984699971179999952089999707798999998239951248597
Q 030632            1 MANLAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVL   80 (174)
Q Consensus         1 ~~~~~~~~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l   80 (174)
                      |-....+.++|||+|||+.+++.+|+.+|+.||.|..+.++.++.+  .+|||||+|.+.++|..|+..|||..+.|+.|
T Consensus         1 mm~d~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~--~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i   78 (90)
T d2cqia1           1 MMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAMNGRKILGKEV   78 (90)
T ss_dssp             CCCCSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS--SCCEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCCCCCCCCEEEEECCCCCCCHHHHHHHHHHCCCCEEEEEECCCCC--CCEEEEEEECCHHHHHHHHHHCCCCEECCEEE
T ss_conf             9877899999999899997989999999976399436644126676--41002888889999999999819998999988


Q ss_pred             EEEEECCCCC
Q ss_conf             9985317888
Q 030632           81 TVNYALPERI   90 (174)
Q Consensus        81 ~v~~a~~~~~   90 (174)
                      +|.||+++..
T Consensus        79 ~v~~a~~~~~   88 (90)
T d2cqia1          79 KVNWATTPSS   88 (90)
T ss_dssp             EEEECCCTTC
T ss_pred             EEEECCCCCC
T ss_conf             9997689778

>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=99.76  E-value=1.6e-18  Score=117.58  Aligned_cols=86  Identities=31%  Similarity=0.567  Sum_probs=78.6

Q ss_pred             CCCCCCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCC-CCCCCCEEEEEECCHHHHHHHHHHC-CCCEECCEEEE
Q ss_conf             899999799829999882999998314499846999711799-9995208999970779899999823-99512485979
Q 030632            4 LAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQA-TQKHRSFGFVTFLEKEDAIQAMDNM-DGAELYGRVLT   81 (174)
Q Consensus         4 ~~~~~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~-~g~~~g~afv~f~~~~~a~~ai~~l-~g~~~~g~~l~   81 (174)
                      ...++++|||+|||+.+++.+|+.+|++||.|..+.+++++. +|.++|||||+|.+.++|..|+..| |+..+.|++|+
T Consensus         4 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~   83 (94)
T d2cpha1           4 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLV   83 (94)
T ss_dssp             CSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCCEECCEEEE
T ss_conf             88899899996999989999999999985996488988536667983668999989999999999972399488999989


Q ss_pred             EEEECCCC
Q ss_conf             98531788
Q 030632           82 VNYALPER   89 (174)
Q Consensus        82 v~~a~~~~   89 (174)
                      |.||.+..
T Consensus        84 V~~A~~~~   91 (94)
T d2cpha1          84 LEWADSEV   91 (94)
T ss_dssp             EEECCCCC
T ss_pred             EEECCCCC
T ss_conf             99829977

>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=99.76  E-value=2e-18  Score=117.10  Aligned_cols=84  Identities=30%  Similarity=0.471  Sum_probs=77.9

Q ss_pred             CCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEEECC
Q ss_conf             99799829999882999998314499846999711799999520899997077989999982399512485979985317
Q 030632            8 KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYALP   87 (174)
Q Consensus         8 ~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~a~~   87 (174)
                      .++|||+|||+.+++.+|+.+|++||.|..+.|++++.++.++|||||+|.+..+|..|+. +++..|.|++|.|.+|.+
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~~   98 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVA   98 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCSS
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEECCCCCCCCCCCEEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECCC
T ss_conf             9889995999858899999999761866300001235677755769999787999999998-498959997979887740


Q ss_pred             CCCCC
Q ss_conf             88889
Q 030632           88 ERIKG   92 (174)
Q Consensus        88 ~~~~~   92 (174)
                      +...|
T Consensus        99 ke~~g  103 (103)
T d1x4ba1          99 REESG  103 (103)
T ss_dssp             CCCCC
T ss_pred             CCCCC
T ss_conf             68896

>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=99.76  E-value=3.1e-18  Score=116.02  Aligned_cols=88  Identities=25%  Similarity=0.346  Sum_probs=79.4

Q ss_pred             CCCCCCCCCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEE
Q ss_conf             99989999979982999988299999831449984699971179999952089999707798999998239951248597
Q 030632            1 MANLAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVL   80 (174)
Q Consensus         1 ~~~~~~~~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l   80 (174)
                      |......+++|||+|||+.+++.+|+.+|++||.|..+.+++++.+|.++|||||+|.+.++|.+||..  ...|.|+.|
T Consensus         1 vk~~~~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~--~~~l~Gr~i   78 (90)
T d2cqga1           1 VKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWC   78 (90)
T ss_dssp             CSCCCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTEEE
T ss_pred             CCCCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCEEEECCCCCCCCCCCEEEEEECCHHHHHHHHHC--CCCCCCEEE
T ss_conf             977776898699979999899999999997626330000024788766677799997999999999866--983499896


Q ss_pred             EEEEECCCCC
Q ss_conf             9985317888
Q 030632           81 TVNYALPERI   90 (174)
Q Consensus        81 ~v~~a~~~~~   90 (174)
                      .|.++.++..
T Consensus        79 ~v~~a~~k~~   88 (90)
T d2cqga1          79 DCKLPNSKQS   88 (90)
T ss_dssp             EEECCCTTCC
T ss_pred             EEEECCCCCC
T ss_conf             9986899778

>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=99.76  E-value=6e-18  Score=114.42  Aligned_cols=84  Identities=31%  Similarity=0.447  Sum_probs=76.6

Q ss_pred             CCCCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEEE
Q ss_conf             99997998299998829999983144998469997117999995208999970779899999823995124859799853
Q 030632            6 VQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYA   85 (174)
Q Consensus         6 ~~~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~a   85 (174)
                      ...++|||+|||+.+++.+|+.+|++||.|..+.+++++.++.++|||||+|.+.++|..||..+|+ .|.|++|+|.++
T Consensus         8 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a   86 (103)
T d2cqda1           8 TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLA   86 (103)
T ss_dssp             CSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHCCCCCCEECCCCCCCCCCCCEEEEEECCHHHHHHHHHHCCC-CCCCEEEEEEEC
T ss_conf             9976899969999695999998776144321100023344455687699997899999999997899-199989799872


Q ss_pred             CCCCC
Q ss_conf             17888
Q 030632           86 LPERI   90 (174)
Q Consensus        86 ~~~~~   90 (174)
                      .+...
T Consensus        87 ~~~~~   91 (103)
T d2cqda1          87 YLGAK   91 (103)
T ss_dssp             TTTCC
T ss_pred             CCCCC
T ss_conf             78899

>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=99.76  E-value=1.4e-18  Score=117.88  Aligned_cols=82  Identities=23%  Similarity=0.401  Sum_probs=77.8

Q ss_pred             CEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEEECCC
Q ss_conf             97998299998829999983144998469997117999995208999970779899999823995124859799853178
Q 030632            9 NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYALPE   88 (174)
Q Consensus         9 ~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~a~~~   88 (174)
                      .+|||+|||+.+++.+|+.+|++||+|..+.+++++.+|.++|||||+|.+.++|..|+..||+..|.|++|.|.||.+.
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~   81 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG   81 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHCCCCCEEEEECCCCCCCCCEEEEEEECCHHHHHHHHHHHCCCEECCEEEEEEECCCC
T ss_conf             88999899998999999999974576524776024566565405999988999999999971998899998799988898


Q ss_pred             CC
Q ss_conf             88
Q 030632           89 RI   90 (174)
Q Consensus        89 ~~   90 (174)
                      ..
T Consensus        82 ~~   83 (85)
T d2u2fa_          82 AK   83 (85)
T ss_dssp             CC
T ss_pred             CC
T ss_conf             88

>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=99.75  E-value=4e-18  Score=115.40  Aligned_cols=82  Identities=21%  Similarity=0.331  Sum_probs=74.4

Q ss_pred             CCCCCCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEE
Q ss_conf             89999979982999988299999831449984699971179999952089999707798999998239951248597998
Q 030632            4 LAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVN   83 (174)
Q Consensus         4 ~~~~~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~   83 (174)
                      ++..+++|||+|||..+++.+|+.+|++||.|..|.+..+   +.++|||||+|.+.++|..|+..|||..|.|++|+|.
T Consensus         3 pp~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~---~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~   79 (114)
T d2f9da1           3 PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVL   79 (114)
T ss_dssp             CTTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHCCCEEEECCCCC---CCCCCEEEEEECCHHHHHHHHHHHCCCEECCEEEEEE
T ss_conf             6679999999799998989999999852698676012346---7767769999788999999999828998899888999


Q ss_pred             EECCC
Q ss_conf             53178
Q 030632           84 YALPE   88 (174)
Q Consensus        84 ~a~~~   88 (174)
                      ++.+.
T Consensus        80 ~a~~~   84 (114)
T d2f9da1          80 YYNAN   84 (114)
T ss_dssp             ECCHH
T ss_pred             ECCCC
T ss_conf             84787

>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=99.74  E-value=2.9e-18  Score=116.12  Aligned_cols=82  Identities=28%  Similarity=0.525  Sum_probs=76.1

Q ss_pred             CCCCCCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECC--EEEE
Q ss_conf             89999979982999988299999831449984699971179999952089999707798999998239951248--5979
Q 030632            4 LAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYG--RVLT   81 (174)
Q Consensus         4 ~~~~~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g--~~l~   81 (174)
                      ....+++|||+|||+.+++.+|+.+|++||.|..+.+++++.++.++|||||+|.+.++|..|+..|||..+.|  ++|+
T Consensus         2 ~s~k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~   81 (85)
T d1fxla2           2 ASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPIT   81 (85)
T ss_dssp             GGGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEECCHHHHHHHHHHHCCCEECCCCEEEE
T ss_conf             98889999995989989899999999984976310301245443578716999858999999999838999589987899


Q ss_pred             EEEE
Q ss_conf             9853
Q 030632           82 VNYA   85 (174)
Q Consensus        82 v~~a   85 (174)
                      |.||
T Consensus        82 V~~A   85 (85)
T d1fxla2          82 VKFA   85 (85)
T ss_dssp             EEEC
T ss_pred             EEEC
T ss_conf             9849

>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=99.74  E-value=5.2e-18  Score=114.75  Aligned_cols=77  Identities=30%  Similarity=0.521  Sum_probs=74.8

Q ss_pred             EEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEEEC
Q ss_conf             79982999988299999831449984699971179999952089999707798999998239951248597998531
Q 030632           10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYAL   86 (174)
Q Consensus        10 ~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~a~   86 (174)
                      .|||+|||+.+++.+|+.+|++||.|..+.+++++.++.++|||||+|.+.++|..|+..|||..+.|++|+|.||+
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~   78 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHHCCEEEEEEEECCCCCCCCCCEEEEECCHHHHHHHHHHCCCCEECCEEEEEEEEC
T ss_conf             99994798848799999999976988599998404544778836999889999999999819998999998999827

>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=99.74  E-value=5.2e-18  Score=114.79  Aligned_cols=81  Identities=25%  Similarity=0.434  Sum_probs=76.2

Q ss_pred             CCCCCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECC--EEEEE
Q ss_conf             9999979982999988299999831449984699971179999952089999707798999998239951248--59799
Q 030632            5 AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYG--RVLTV   82 (174)
Q Consensus         5 ~~~~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g--~~l~v   82 (174)
                      ...+++|||+|||+.+++.+|+.+|++||.|..+.+++++.++.++|||||+|.+.++|..|+..||+..+.|  ++|+|
T Consensus         3 ~~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V   82 (85)
T d1b7fa2           3 SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSV   82 (85)
T ss_dssp             TTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHHCCEEEEEEECCCCCCCCCEEEEEEECCHHHHHHHHHHHCCCEECCCCEEEEE
T ss_conf             88899999949899799999999999659874643101235556760699998999999999999788885799817999


Q ss_pred             EEE
Q ss_conf             853
Q 030632           83 NYA   85 (174)
Q Consensus        83 ~~a   85 (174)
                      .||
T Consensus        83 ~~A   85 (85)
T d1b7fa2          83 RLA   85 (85)
T ss_dssp             EEC
T ss_pred             EEC
T ss_conf             979

>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=99.74  E-value=2.7e-18  Score=116.30  Aligned_cols=85  Identities=38%  Similarity=0.569  Sum_probs=79.1

Q ss_pred             CCCCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEEE
Q ss_conf             99997998299998829999983144998469997117999995208999970779899999823995124859799853
Q 030632            6 VQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYA   85 (174)
Q Consensus         6 ~~~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~a   85 (174)
                      ...++|||+|||+.+++.+|+.+|++||.|..+.++..+.++.++|||||+|.+.++|..|+..||++.|.|++|+|.||
T Consensus         3 ~~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a   82 (90)
T d1x5sa1           3 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQA   82 (90)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHCCCCCCCEEECCCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEEC
T ss_conf             89989999799986879999875640222211011000033334663899987899999999980998999999899981


Q ss_pred             CCCCC
Q ss_conf             17888
Q 030632           86 LPERI   90 (174)
Q Consensus        86 ~~~~~   90 (174)
                      .++..
T Consensus        83 ~~~~~   87 (90)
T d1x5sa1          83 GKSSD   87 (90)
T ss_dssp             ECCCC
T ss_pred             CCCCC
T ss_conf             89999

>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=99.74  E-value=1.5e-17  Score=112.32  Aligned_cols=84  Identities=29%  Similarity=0.419  Sum_probs=76.8

Q ss_pred             CCCCCCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEE
Q ss_conf             89999979982999988299999831449984699971179999952089999707798999998239951248597998
Q 030632            4 LAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVN   83 (174)
Q Consensus         4 ~~~~~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~   83 (174)
                      .....++|||+|||+.+++.+|+.+|++||.|..+.++.++  +.++|||||+|.+.+.|.+|+..||+..+.|++|+|.
T Consensus         7 ~~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~--~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~   84 (93)
T d2cq3a1           7 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN   84 (93)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT--TTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHCCEEEECCCCCCC--CCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEE
T ss_conf             89999989997989989999999998634433000112566--6774023789889999999999819998999888998


Q ss_pred             EECCCC
Q ss_conf             531788
Q 030632           84 YALPER   89 (174)
Q Consensus        84 ~a~~~~   89 (174)
                      ||+++.
T Consensus        85 ~A~~r~   90 (93)
T d2cq3a1          85 NATARV   90 (93)
T ss_dssp             ECCSSC
T ss_pred             ECCCCC
T ss_conf             657579

>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=99.74  E-value=1.7e-18  Score=117.42  Aligned_cols=82  Identities=30%  Similarity=0.558  Sum_probs=77.3

Q ss_pred             CCCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEEEC
Q ss_conf             99979982999988299999831449984699971179999952089999707798999998239951248597998531
Q 030632            7 QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYAL   86 (174)
Q Consensus         7 ~~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~a~   86 (174)
                      ..++|||+|||+.+++.+|+.+|++||.|..+.+++++.+|.++|||||+|.+.++|..|+..||+..|.|++|+|.||.
T Consensus         7 ~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~   86 (104)
T d1p1ta_           7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAA   86 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETT
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCEECCCCCEEEEECCHHHHHHHHHHCCCCEECCEEEEEEECC
T ss_conf             87889997999869899999766403322221101110001147846789899999999999809998899987998899


Q ss_pred             CC
Q ss_conf             78
Q 030632           87 PE   88 (174)
Q Consensus        87 ~~   88 (174)
                      +.
T Consensus        87 ~~   88 (104)
T d1p1ta_          87 SE   88 (104)
T ss_dssp             CT
T ss_pred             CC
T ss_conf             98

>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=99.74  E-value=4.7e-18  Score=115.00  Aligned_cols=79  Identities=34%  Similarity=0.442  Sum_probs=74.9

Q ss_pred             CCCCCCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEE
Q ss_conf             8999997998299998829999983144998469997117999995208999970779899999823995124859799
Q 030632            4 LAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTV   82 (174)
Q Consensus         4 ~~~~~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v   82 (174)
                      .+.++++|||+|||+.+++.+|+.+|++||.|..+.+++++.++.++|||||+|.+.++|..|+..||+..|.|++|+|
T Consensus         5 ~p~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           5 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             SCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHCCCCEECCEEEEC
T ss_conf             8999989999399998989999999998597730011136666555530289988999999999980999989999379

>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=99.74  E-value=1.7e-18  Score=117.39  Aligned_cols=80  Identities=23%  Similarity=0.394  Sum_probs=75.4

Q ss_pred             CCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEEECC
Q ss_conf             99799829999882999998314499846999711799999520899997077989999982399512485979985317
Q 030632            8 KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYALP   87 (174)
Q Consensus         8 ~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~a~~   87 (174)
                      .++|||+|||+.+++.+|+.+|+.||.|..+.+++++.+|.++|||||+|.+.++|..|+. |||..|.|++|+|.++.+
T Consensus        18 ~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a~~   96 (101)
T d2cq4a1          18 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQA   96 (101)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHCCCCEEEEEEEEECCCCCCCCCEEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECCC
T ss_conf             9899998999989999999997189749998865448876434148999899999999998-799888999989997888


Q ss_pred             C
Q ss_conf             8
Q 030632           88 E   88 (174)
Q Consensus        88 ~   88 (174)
                      +
T Consensus        97 ~   97 (101)
T d2cq4a1          97 E   97 (101)
T ss_dssp             H
T ss_pred             C
T ss_conf             7

>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=99.73  E-value=4.7e-18  Score=114.99  Aligned_cols=82  Identities=30%  Similarity=0.559  Sum_probs=75.6

Q ss_pred             EEECCCCCCCHHHHHHHHCCCCCCEEEE-EEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEEECCCC
Q ss_conf             9982999988299999831449984699-971179999952089999707798999998239951248597998531788
Q 030632           11 LYVGGLAEEVNEAILHAAFIPFGDIKDV-KTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYALPER   89 (174)
Q Consensus        11 i~V~~Lp~~~~~~~l~~~F~~~G~i~~~-~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~a~~~~   89 (174)
                      |||+|||+.+++.+|+.+|++||.|..+ .+++++.++.++|||||+|.+.++|..|+..|||..+.|++|+|.||.++.
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k~   80 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKD   80 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCC
T ss_pred             CEECCCCCCCCHHHHHHHHHHHCCEEEEEEEEEECCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEEECCCC
T ss_conf             99938989486999999998729450467997611332447539999899999999998579929899999999965879


Q ss_pred             CCC
Q ss_conf             889
Q 030632           90 IKG   92 (174)
Q Consensus        90 ~~~   92 (174)
                      .+|
T Consensus        81 ~kG   83 (83)
T d1x5ta1          81 SKG   83 (83)
T ss_dssp             CCC
T ss_pred             CCC
T ss_conf             697

>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=99.73  E-value=1e-17  Score=113.10  Aligned_cols=88  Identities=25%  Similarity=0.308  Sum_probs=78.3

Q ss_pred             CCCCCCEEEECCCCCCCHHHHHHHHCCCCCCEE--------EEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEE
Q ss_conf             899999799829999882999998314499846--------999711799999520899997077989999982399512
Q 030632            4 LAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIK--------DVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAEL   75 (174)
Q Consensus         4 ~~~~~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~--------~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~   75 (174)
                      .....++|||+|||+.+++.+|+.+|+.||.|.        .+.+..++.++.++|||||+|.+.++|..|+..|||..|
T Consensus         4 ~~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~   83 (101)
T d2cpea1           4 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   83 (101)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHCCEEEEEEECCCCEEEEEECCCCCCCCCEEEEEECCHHHHHHHHHHHCCCEE
T ss_conf             89989999997999868899999878877437875632530367754266444341235876699999999998399989


Q ss_pred             CCEEEEEEEECCCCCC
Q ss_conf             4859799853178888
Q 030632           76 YGRVLTVNYALPERIK   91 (174)
Q Consensus        76 ~g~~l~v~~a~~~~~~   91 (174)
                      .|++|+|.+|+++.++
T Consensus        84 ~gr~i~V~~a~~~~p~   99 (101)
T d2cpea1          84 QGSKLKVSLARKKPPM   99 (101)
T ss_dssp             TTEECEEECSSCCCCS
T ss_pred             CCEEEEEEECCCCCCC
T ss_conf             9998799975789888

>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=99.73  E-value=1.8e-17  Score=111.85  Aligned_cols=87  Identities=25%  Similarity=0.439  Sum_probs=79.0

Q ss_pred             CCCCCCCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCC------CCEEC
Q ss_conf             989999979982999988299999831449984699971179999952089999707798999998239------95124
Q 030632            3 NLAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMD------GAELY   76 (174)
Q Consensus         3 ~~~~~~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~------g~~~~   76 (174)
                      +....+++|||+|||+.+++.+|+.+|.+||.+..+.++.++.++.++|||||+|.+.++|..|+..||      |..+.
T Consensus         3 ~~~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~   82 (98)
T d1x4ha1           3 SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLD   82 (98)
T ss_dssp             CCCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESS
T ss_pred             CCCCCCCEEEECCCCCCCCHHHHHHHHHCCCCCEEEEECCCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCCCCCCCEEC
T ss_conf             48989989999189996889999987751242203332036655456625899986999999999873522346990889


Q ss_pred             CEEEEEEEECCCC
Q ss_conf             8597998531788
Q 030632           77 GRVLTVNYALPER   89 (174)
Q Consensus        77 g~~l~v~~a~~~~   89 (174)
                      |++|+|.||.++.
T Consensus        83 gr~l~v~~a~~k~   95 (98)
T d1x4ha1          83 GRQLKVDLAVTRD   95 (98)
T ss_dssp             SCEEEEECCCCCC
T ss_pred             CEEEEEEECCCCC
T ss_conf             9988999898878

>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=99.73  E-value=8.7e-19  Score=119.03  Aligned_cols=87  Identities=28%  Similarity=0.449  Sum_probs=79.6

Q ss_pred             CCCCCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEE
Q ss_conf             99999799829999882999998314499846999711799999520899997077989999982399512485979985
Q 030632            5 AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNY   84 (174)
Q Consensus         5 ~~~~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~   84 (174)
                      ..++++|||+|||..+++.+|+.+|++||.+..+.++.+..+|.++|||||.|.+.++|..|+..|||..|.|++|+|.|
T Consensus        15 ~~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   94 (102)
T d2cpxa1          15 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF   94 (102)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHCCCEEEEEEECCCCCCCCCCCCEEEECCHHHHHHHHHHHCCCEECCEEEEEEE
T ss_conf             78998999969999898999999785345424677530466555553214774337899999998589988999889996


Q ss_pred             ECCCCCC
Q ss_conf             3178888
Q 030632           85 ALPERIK   91 (174)
Q Consensus        85 a~~~~~~   91 (174)
                      |+++..+
T Consensus        95 ak~k~~r  101 (102)
T d2cpxa1          95 GKNKKQR  101 (102)
T ss_dssp             CCCCSCC
T ss_pred             CCCCCCC
T ss_conf             7780309

>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=99.72  E-value=6.7e-18  Score=114.16  Aligned_cols=80  Identities=15%  Similarity=0.245  Sum_probs=75.3

Q ss_pred             CCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEEECC
Q ss_conf             99799829999882999998314499846999711799999520899997077989999982399512485979985317
Q 030632            8 KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYALP   87 (174)
Q Consensus         8 ~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~a~~   87 (174)
                      .++|||+|||+++++.+|+.+|++||.|..+.++.+..++.++|||||+|.+.++|..|+..|||..+.|++|+|.+++|
T Consensus         1 d~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           1 ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHHCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHHCCCEECCEEEEEEECCC
T ss_conf             96999979798698999999999829687642200011234552158998999999999998699788999999997408

>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=99.72  E-value=2.7e-17  Score=110.84  Aligned_cols=84  Identities=25%  Similarity=0.413  Sum_probs=74.9

Q ss_pred             CCCCCCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEE
Q ss_conf             89999979982999988299999831449984699971179999952089999707798999998239951248597998
Q 030632            4 LAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVN   83 (174)
Q Consensus         4 ~~~~~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~   83 (174)
                      ...+.++|||+|||+.+++.+|+.+|+.||.|..+.+...   ...+|||||+|.+.++|..||..||++.|.|++|+|.
T Consensus        10 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~---~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~   86 (95)
T d1x4aa1          10 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVE   86 (95)
T ss_dssp             CCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEECCC---CCCCCEEEEEECCHHHHHHHHHHHCCCEECCEEEEEE
T ss_conf             9999989999798988989999998842786699884156---5546539999889999999999819998999897998


Q ss_pred             EECCCCC
Q ss_conf             5317888
Q 030632           84 YALPERI   90 (174)
Q Consensus        84 ~a~~~~~   90 (174)
                      ||++.+.
T Consensus        87 ~a~~~r~   93 (95)
T d1x4aa1          87 FPRSGRG   93 (95)
T ss_dssp             CCCCCCC
T ss_pred             ECCCCCC
T ss_conf             2569797

>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=99.71  E-value=1.4e-17  Score=112.35  Aligned_cols=82  Identities=24%  Similarity=0.435  Sum_probs=75.3

Q ss_pred             CCCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEEEC
Q ss_conf             99979982999988299999831449984699971179999952089999707798999998239951248597998531
Q 030632            7 QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYAL   86 (174)
Q Consensus         7 ~~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~a~   86 (174)
                      ...+|||+|||+.+++.+|+.+|++||.|..+.++.++  +.++|||||+|.+.++|..|+..|||..|.|++|.|.+++
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~   84 (89)
T d1cvja2           7 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK   84 (89)
T ss_dssp             TTTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBT--TBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHCCCCEEEEEEEEC--CCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEECC
T ss_conf             99889992899999999999999863996079998504--7874033799899999999999809999999988998898


Q ss_pred             CCCC
Q ss_conf             7888
Q 030632           87 PERI   90 (174)
Q Consensus        87 ~~~~   90 (174)
                      ++..
T Consensus        85 ~~~~   88 (89)
T d1cvja2          85 SRKE   88 (89)
T ss_dssp             CTTT
T ss_pred             CCCC
T ss_conf             8788

>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=99.71  E-value=2.6e-17  Score=110.90  Aligned_cols=81  Identities=31%  Similarity=0.502  Sum_probs=75.3

Q ss_pred             CCCCCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEE
Q ss_conf             99999799829999882999998314499846999711799999520899997077989999982399512485979985
Q 030632            5 AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNY   84 (174)
Q Consensus         5 ~~~~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~   84 (174)
                      +...++|||+|||+.+++.+|+.+|++||.|..+.+++++.+|.++|||||+|.+.+.|.+|+. +++..|.|+.|+|..
T Consensus         3 pe~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~   81 (84)
T d1l3ka1           3 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKR   81 (84)
T ss_dssp             CGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEECCCCCCCCCCCEEEEEECCHHHHHHHHH-HCCCEECCEEEEEEE
T ss_conf             8888679997999979899999999750645210001146679962289999868999999998-499979999989995


Q ss_pred             EC
Q ss_conf             31
Q 030632           85 AL   86 (174)
Q Consensus        85 a~   86 (174)
                      |.
T Consensus        82 A~   83 (84)
T d1l3ka1          82 AV   83 (84)
T ss_dssp             CC
T ss_pred             EE
T ss_conf             14

>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=99.70  E-value=3.2e-17  Score=110.40  Aligned_cols=77  Identities=27%  Similarity=0.420  Sum_probs=73.7

Q ss_pred             CEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEEEC
Q ss_conf             979982999988299999831449984699971179999952089999707798999998239951248597998531
Q 030632            9 NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYAL   86 (174)
Q Consensus         9 ~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~a~   86 (174)
                      .+|||+|||+.+++.+|+.+|++||.|..+.++.++ ++.++|||||+|.+.++|..|+..|||..+.|++|+|.++.
T Consensus         1 grl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~   77 (78)
T d1no8a_           1 GKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHHCCCEEEEEEEEE-CCCCCEEEEEEECCHHHHHHHHHHHCCCEECCEEEEEEEEE
T ss_conf             999998899879899999999985997289999860-12454368999989999999999838999999999999931

>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=99.70  E-value=3.2e-17  Score=110.41  Aligned_cols=78  Identities=24%  Similarity=0.400  Sum_probs=71.7

Q ss_pred             EEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCC---CCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEEECC
Q ss_conf             9982999988299999831449984699971179999---9520899997077989999982399512485979985317
Q 030632           11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQ---KHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYALP   87 (174)
Q Consensus        11 i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g---~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~a~~   87 (174)
                      |||+|||+.+++.+|+.+|++||.|..+.+++++.++   .++|||||+|.+.++|..|+..||+..+.|++|+|.|+.+
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~~   80 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISER   80 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSC
T ss_pred             CEECCCCCCCCHHHHHHHHHHHCCCCCCCEECCCCCCCCCCCCEEEEEEECCHHHHHHHHHHHCCCEECCEEEEEEECCC
T ss_conf             98838999798999999999839803221000233235453313789998999999999998299889999979998888


Q ss_pred             C
Q ss_conf             8
Q 030632           88 E   88 (174)
Q Consensus        88 ~   88 (174)
                      .
T Consensus        81 ~   81 (85)
T d2cpfa1          81 A   81 (85)
T ss_dssp             S
T ss_pred             C
T ss_conf             9

>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=99.70  E-value=4.1e-17  Score=109.86  Aligned_cols=79  Identities=24%  Similarity=0.564  Sum_probs=72.8

Q ss_pred             CCCCCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEE
Q ss_conf             99999799829999882999998314499846999711799999520899997077989999982399512485979985
Q 030632            5 AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNY   84 (174)
Q Consensus         5 ~~~~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~   84 (174)
                      .++.++|||+|||..+++.+|+.+|++||.|..+.++.+      +|||||+|.+.++|..|+..|||..|.|++|+|.|
T Consensus        15 ~~~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~   88 (96)
T d1x4ga1          15 SPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYW   88 (96)
T ss_dssp             CSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEECCCCCCCCHHHHHHHHHHHCCCEEEEEEEC------CEEEEEEECCHHHHHHHHHHHCCCEECCEEEEEEE
T ss_conf             999999999089998999999999998299669999701------30899998999999999998199999999989997


Q ss_pred             ECCCC
Q ss_conf             31788
Q 030632           85 ALPER   89 (174)
Q Consensus        85 a~~~~   89 (174)
                      +++.+
T Consensus        89 ak~~p   93 (96)
T d1x4ga1          89 GKESP   93 (96)
T ss_dssp             CCCCC
T ss_pred             CCCCC
T ss_conf             57897

>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=99.69  E-value=1.6e-17  Score=112.02  Aligned_cols=81  Identities=19%  Similarity=0.308  Sum_probs=74.8

Q ss_pred             CCCCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEEE
Q ss_conf             99997998299998829999983144998469997117999995208999970779899999823995124859799853
Q 030632            6 VQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYA   85 (174)
Q Consensus         6 ~~~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~a   85 (174)
                      ...++|||+|||+.+++.+|+.+|++||.|..+.+..+. ++.++|||||+|.+.++|..|+..|||..|.|+++.|.++
T Consensus        16 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~-~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~   94 (101)
T d1x5oa1          16 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPT   94 (101)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHCCCCCCEEEECCC-CCCCCCCEEEEECCHHHHHHHHHHHCCCEECCCCCCCCCC
T ss_conf             899989996999989899999888613664210110011-2356631047768999999999984899889839866789


Q ss_pred             CC
Q ss_conf             17
Q 030632           86 LP   87 (174)
Q Consensus        86 ~~   87 (174)
                      .|
T Consensus        95 ~P   96 (101)
T d1x5oa1          95 EP   96 (101)
T ss_dssp             SC
T ss_pred             CC
T ss_conf             88

>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=99.69  E-value=2.9e-17  Score=110.70  Aligned_cols=82  Identities=22%  Similarity=0.322  Sum_probs=73.9

Q ss_pred             CCCCCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEE
Q ss_conf             99999799829999882999998314499846999711799999520899997077989999982399512485979985
Q 030632            5 AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNY   84 (174)
Q Consensus         5 ~~~~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~   84 (174)
                      ..+.++|||+|||+.+++.+|+.+|.+||.+..+..     ++.++|||||+|.+.+.|..|+..||+..|.|++|+|.|
T Consensus        13 ~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~-----~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~   87 (96)
T d1fjca_          13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ-----DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY   87 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE-----TTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHCCCCEEEEE-----CCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEE
T ss_conf             778999999189987989999999975165605634-----375066888986899999999998299999999979998


Q ss_pred             ECCCCCC
Q ss_conf             3178888
Q 030632           85 ALPERIK   91 (174)
Q Consensus        85 a~~~~~~   91 (174)
                      +.++...
T Consensus        88 a~~k~~~   94 (96)
T d1fjca_          88 TGEKGGT   94 (96)
T ss_dssp             CSSSCCC
T ss_pred             ECCCCCC
T ss_conf             0789998

>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=99.68  E-value=4.4e-17  Score=109.66  Aligned_cols=82  Identities=23%  Similarity=0.410  Sum_probs=73.3

Q ss_pred             CCCCEEEECCCCCCCH-HHHHHHHCCCCCCEEEEEEECC-CCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEE
Q ss_conf             9999799829999882-9999983144998469997117-9999952089999707798999998239951248597998
Q 030632            6 VQKNTLYVGGLAEEVN-EAILHAAFIPFGDIKDVKTPLD-QATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVN   83 (174)
Q Consensus         6 ~~~~~i~V~~Lp~~~~-~~~l~~~F~~~G~i~~~~~~~~-~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~   83 (174)
                      ..+++|||+|||+.++ ++.|+.+|++||.|..+.++.+ ..++.++|||||+|.+.++|..|+. ||+..+.|++|+|.
T Consensus         2 ~e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~   80 (86)
T d2ghpa3           2 LEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVS   80 (86)
T ss_dssp             CTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEE
T ss_pred             CCCCEEEEECCCCCCCCHHHHHHHHHHHHHCCCEEEECCCCCCCCCCEEEEEEECCHHHHHHHHH-CCCCEECCEEEEEE
T ss_conf             88889999799977434999999977531211100000257765552265689889999999996-29998999998999


Q ss_pred             EECCC
Q ss_conf             53178
Q 030632           84 YALPE   88 (174)
Q Consensus        84 ~a~~~   88 (174)
                      +|+++
T Consensus        81 ~a~~k   85 (86)
T d2ghpa3          81 LADKK   85 (86)
T ss_dssp             ECCCC
T ss_pred             ECCCC
T ss_conf             74789

>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=99.67  E-value=1.7e-16  Score=106.42  Aligned_cols=85  Identities=20%  Similarity=0.381  Sum_probs=72.8

Q ss_pred             CCCCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCC-CCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEE
Q ss_conf             999979982999988299999831449984699971179-9999520899997077989999982399512485979985
Q 030632            6 VQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQ-ATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNY   84 (174)
Q Consensus         6 ~~~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~-~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~   84 (174)
                      .+.++|||+|||+.+++.+|+.+|+.|| +..+.++..+ .++.++|||||+|.+.++|.+|+ .||+..|.|+.|+|.+
T Consensus        13 ~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~~~gr~l~V~~   90 (104)
T d1wi8a_          13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDV   90 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHHC-CCCCEEEEEECCCCCCCEEEEEEECCHHHHHHHH-HCCCCEECCEEEEEEE
T ss_conf             9997899809998698999999999832-1531023431147886135457877999999999-8099989999889997


Q ss_pred             ECCCCCCC
Q ss_conf             31788889
Q 030632           85 ALPERIKG   92 (174)
Q Consensus        85 a~~~~~~~   92 (174)
                      |.++..+.
T Consensus        91 a~~~~~~~   98 (104)
T d1wi8a_          91 ADQAQDKD   98 (104)
T ss_dssp             CCCCCCCC
T ss_pred             CCCCCCCC
T ss_conf             89988899

>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=99.67  E-value=1.9e-16  Score=106.25  Aligned_cols=77  Identities=26%  Similarity=0.424  Sum_probs=72.8

Q ss_pred             CCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEEE
Q ss_conf             997998299998829999983144998469997117999995208999970779899999823995124859799853
Q 030632            8 KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYA   85 (174)
Q Consensus         8 ~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~a   85 (174)
                      -++|||+|||+.+++++|+.+|++||.+..+.++.++.++.++|||||+|.+.+++.+|+. +|+..|.|++|+|..|
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             CCEEEECCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEECCHHHHHHHHH-HCCCEECCEEEEEEEC
T ss_conf             8789987989858799999999975513322103578875544189999938999999999-6998799979899978

>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=99.67  E-value=4.5e-17  Score=109.60  Aligned_cols=80  Identities=20%  Similarity=0.208  Sum_probs=71.8

Q ss_pred             CCCCCCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEE
Q ss_conf             89999979982999988299999831449984699971179999952089999707798999998239951248597998
Q 030632            4 LAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVN   83 (174)
Q Consensus         4 ~~~~~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~   83 (174)
                      ....+++|||+|||+.+++.+|+.+|++||.|..+.+..      .+|||||+|.+.++|.+|+..|||..|.|++|.|.
T Consensus         6 ~~r~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~------~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~   79 (111)
T d1whxa_           6 SGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLE   79 (111)
T ss_dssp             TSEEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHCCCCCCEEEEEC------CCCEEEEEECCHHHHHHHHHHHCCCCCCCCEEEEE
T ss_conf             898899999979899888999976640268861899604------68638999847789999999976983589758999


Q ss_pred             EECCCC
Q ss_conf             531788
Q 030632           84 YALPER   89 (174)
Q Consensus        84 ~a~~~~   89 (174)
                      |+....
T Consensus        80 ~a~~~~   85 (111)
T d1whxa_          80 WAPIGV   85 (111)
T ss_dssp             EEETTT
T ss_pred             ECCCCC
T ss_conf             787776

>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=99.67  E-value=5.5e-18  Score=114.63  Aligned_cols=84  Identities=21%  Similarity=0.341  Sum_probs=74.8

Q ss_pred             CCCCCCCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEE
Q ss_conf             98999997998299998829999983144998469997117999995208999970779899999823995124859799
Q 030632            3 NLAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTV   82 (174)
Q Consensus         3 ~~~~~~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v   82 (174)
                      ..+...++|||+|||+.+++.+|+.+|+.||.|..+.++... +|.++|||||+|.+.++|.+|+. ||+..+.|++|+|
T Consensus         8 ~~~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~-~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V   85 (91)
T d1fjeb1           8 SESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKL   85 (91)
T ss_dssp             SSCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEE-EETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEE
T ss_pred             CCCCCCCEEEEECCCCCCHHHHHHHHHHCCCCEEEEEEEECC-CCCCCEEEEEEECCHHHHHHHHH-CCCCEECCEEEEE
T ss_conf             889998389995765761288999998637847875410068-99853776786389999999982-3994889999899


Q ss_pred             EEECCC
Q ss_conf             853178
Q 030632           83 NYALPE   88 (174)
Q Consensus        83 ~~a~~~   88 (174)
                      .+|+++
T Consensus        86 ~~ak~k   91 (91)
T d1fjeb1          86 EKPKGR   91 (91)
T ss_dssp             ECCCCS
T ss_pred             EECCCC
T ss_conf             855889

>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=99.67  E-value=2.5e-17  Score=111.01  Aligned_cols=76  Identities=26%  Similarity=0.486  Sum_probs=72.8

Q ss_pred             CEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEEE
Q ss_conf             97998299998829999983144998469997117999995208999970779899999823995124859799853
Q 030632            9 NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYA   85 (174)
Q Consensus         9 ~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~a   85 (174)
                      ++|||+|||+.+++.+|+.+|++||.|..+.+++++.++.++|||||+|.+.++|.+|+. +|++.+.|++|.|.+|
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHHCCCCEEEEECCCCCCCCCCEEEEEECCHHHHHHHHH-CCCCEECCEEEEEEEC
T ss_conf             999991899969899999999986986202441136788866639999889999999997-1989899949899979

>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=99.66  E-value=3.2e-16  Score=104.94  Aligned_cols=77  Identities=26%  Similarity=0.518  Sum_probs=68.9

Q ss_pred             CCCCEEEECCCC-CCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEE
Q ss_conf             999979982999-9882999998314499846999711799999520899997077989999982399512485979985
Q 030632            6 VQKNTLYVGGLA-EEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNY   84 (174)
Q Consensus         6 ~~~~~i~V~~Lp-~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~   84 (174)
                      ...++|||+||| ..+++.+|+.+|++||.|..+.+        ++|||||+|.+.++|.+||..|||..|.|++|+|.|
T Consensus        13 ~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i--------~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~   84 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINL   84 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE--------ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCCEEEEECCCCCCCCHHHHHHHHHHCCCEEEEEE--------ECCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEE
T ss_conf             997589993889021999999999862698799997--------088689997999999999998199989998879997


Q ss_pred             ECCCCC
Q ss_conf             317888
Q 030632           85 ALPERI   90 (174)
Q Consensus        85 a~~~~~   90 (174)
                      ++++..
T Consensus        85 a~~~~~   90 (98)
T d1wf2a_          85 AAEPKV   90 (98)
T ss_dssp             TTSCCC
T ss_pred             CCCCCC
T ss_conf             789999

>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=99.66  E-value=8.7e-17  Score=108.04  Aligned_cols=75  Identities=33%  Similarity=0.572  Sum_probs=70.9

Q ss_pred             EEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEEE
Q ss_conf             7998299998829999983144998469997117999995208999970779899999823995124859799853
Q 030632           10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYA   85 (174)
Q Consensus        10 ~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~a   85 (174)
                      +|||+|||+++++.+|+.+|++||.|..+.+++++.+++++|||||+|.+.++|..|+. +++..|.|+.|.|..|
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECCC
T ss_pred             CEEEECCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEECCHHHHHHHHH-CCCCEECCCEEEEEEC
T ss_conf             98991899859899999999754503333213588877767659999898999999996-2989799979785679

>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=99.66  E-value=1.4e-16  Score=106.89  Aligned_cols=85  Identities=21%  Similarity=0.349  Sum_probs=74.2

Q ss_pred             CCEEEECCCCCCCHHHHHHHHCCCCCC-EEEEEEECCC-CCCCCCCEEEEEECCHHHHHHHHHHCCC--CEECCEEEEEE
Q ss_conf             997998299998829999983144998-4699971179-9999520899997077989999982399--51248597998
Q 030632            8 KNTLYVGGLAEEVNEAILHAAFIPFGD-IKDVKTPLDQ-ATQKHRSFGFVTFLEKEDAIQAMDNMDG--AELYGRVLTVN   83 (174)
Q Consensus         8 ~~~i~V~~Lp~~~~~~~l~~~F~~~G~-i~~~~~~~~~-~~g~~~g~afv~f~~~~~a~~ai~~l~g--~~~~g~~l~v~   83 (174)
                      +++|||+|||..+++.+|+.+|++||. +..+.+++++ .++.++|||||+|.+...|..|+..|++  ..+.|++|+|.
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~   80 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVD   80 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEE
T ss_pred             CCEEEECCCCCCCCHHHHHHHHHHHCCCCEEEEEEEECCCCCCCCCEEEEEECCHHHHHHHHHHHCCCCEEECCEEEEEE
T ss_conf             97999949898688999999999869750589986411232367875999983999999999997689827899888999


Q ss_pred             EECCCCCCC
Q ss_conf             531788889
Q 030632           84 YALPERIKG   92 (174)
Q Consensus        84 ~a~~~~~~~   92 (174)
                      ||+|+....
T Consensus        81 ~A~p~~~~~   89 (96)
T d2disa1          81 WAEPEIDVD   89 (96)
T ss_dssp             ESCSSCSTT
T ss_pred             ECCCCCCCC
T ss_conf             718988989

>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=99.66  E-value=2e-16  Score=106.03  Aligned_cols=79  Identities=22%  Similarity=0.381  Sum_probs=71.8

Q ss_pred             CCCCCCCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEEC-CEEEE
Q ss_conf             98999997998299998829999983144998469997117999995208999970779899999823995124-85979
Q 030632            3 NLAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELY-GRVLT   81 (174)
Q Consensus         3 ~~~~~~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~-g~~l~   81 (174)
                      ...+|+++|||+|||+.+++.+|..+|+.||.|..+.++++     .+|||||+|.+.++|..|+..|||..+. |++|+
T Consensus         3 ~~~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~   77 (83)
T d2b0ga1           3 TEQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN-----RHDIAFVEFTTELQSNAAKEALQGFKITPTHAMK   77 (83)
T ss_dssp             CCCSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT-----TCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHCCCCCEEEEEEECC-----CCEEEEEECCCHHHHHHHHHHHCCCEECCCCEEE
T ss_conf             88999889999889987779999754235764787431011-----2114899519999999999983994968992899


Q ss_pred             EEEEC
Q ss_conf             98531
Q 030632           82 VNYAL   86 (174)
Q Consensus        82 v~~a~   86 (174)
                      |.||+
T Consensus        78 v~~ak   82 (83)
T d2b0ga1          78 ITFAK   82 (83)
T ss_dssp             EEECC
T ss_pred             EEEEC
T ss_conf             99841

>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=99.65  E-value=2.2e-16  Score=105.89  Aligned_cols=78  Identities=22%  Similarity=0.403  Sum_probs=70.8

Q ss_pred             CCEEEECCCCC-CCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEEEC
Q ss_conf             99799829999-88299999831449984699971179999952089999707798999998239951248597998531
Q 030632            8 KNTLYVGGLAE-EVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYAL   86 (174)
Q Consensus         8 ~~~i~V~~Lp~-~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~a~   86 (174)
                      +++|||+|||+ .+++++|+.+|+.||.|..+.++++     .+|||||+|.+.++|.+|+..|||..|.|++|+|.|++
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~-----~kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~   76 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   76 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCT-----TSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCS
T ss_pred             CCEEEEECCCCCCCCHHHHHHHHHHCCCCCEEEEEEC-----CCCEEEEEECCHHHHHHHHHHHCCCEECCEEEEEEECC
T ss_conf             9999996799252999999998750356404999760-----34258999778799999999839978799888999887


Q ss_pred             CCCC
Q ss_conf             7888
Q 030632           87 PERI   90 (174)
Q Consensus        87 ~~~~   90 (174)
                      ....
T Consensus        77 ~~~~   80 (109)
T d2adca1          77 HQNV   80 (109)
T ss_dssp             CCCC
T ss_pred             CCCC
T ss_conf             8878

>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=99.65  E-value=5.7e-16  Score=103.56  Aligned_cols=78  Identities=13%  Similarity=0.197  Sum_probs=72.9

Q ss_pred             CCCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEEEC
Q ss_conf             99979982999988299999831449984699971179999952089999707798999998239951248597998531
Q 030632            7 QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYAL   86 (174)
Q Consensus         7 ~~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~a~   86 (174)
                      ..++|||+|||+.+++.+|+.+|+.||.|..+.++.++ ++.++|||||+|.+.++|.+|+. +++..+.|+.|.|.|+.
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~-~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHHCCCCCCEEEEEC-CCCCCEEEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECC
T ss_conf             86789997979879799999989875524230032102-58863578999848999999999-78997999898999737

>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=99.65  E-value=3e-16  Score=105.10  Aligned_cols=80  Identities=21%  Similarity=0.271  Sum_probs=71.3

Q ss_pred             CCCCCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEEC-CEEEEEE
Q ss_conf             999997998299998829999983144998469997117999995208999970779899999823995124-8597998
Q 030632            5 AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELY-GRVLTVN   83 (174)
Q Consensus         5 ~~~~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~-g~~l~v~   83 (174)
                      .+|+++|||+|||+.+++++|+.+|++||.+..+.+..    ++.+|||||+|.+.++|..|+..|||..+. |++|+|.
T Consensus         7 ~pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~----~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~   82 (88)
T d2adca2           7 FPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFF----QKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVS   82 (88)
T ss_dssp             CCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEEC----SSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEEE----ECCCCEEEEEECCHHHHHHHHHHCCCCEECCCCEEEEE
T ss_conf             99978899979998889999999853369788888753----02440069998999999999975169792699889999


Q ss_pred             EECCC
Q ss_conf             53178
Q 030632           84 YALPE   88 (174)
Q Consensus        84 ~a~~~   88 (174)
                      |+++.
T Consensus        83 ~sk~~   87 (88)
T d2adca2          83 FSKST   87 (88)
T ss_dssp             ECSSC
T ss_pred             ECCCC
T ss_conf             37988

>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=99.64  E-value=1e-15  Score=102.12  Aligned_cols=87  Identities=13%  Similarity=0.100  Sum_probs=76.1

Q ss_pred             CCCCCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEE
Q ss_conf             99999799829999882999998314499846999711799999520899997077989999982399512485979985
Q 030632            5 AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNY   84 (174)
Q Consensus         5 ~~~~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~   84 (174)
                      .....+|||+|||+.+++.+|+.+|..+|.+....++....++.++|||||+|.+.++|.+|+. +|+..|+||.|.|.+
T Consensus        12 ~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~   90 (104)
T d1wg5a_          12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFK   90 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHCCCCEEEEEEEECCCCCCCEEEEEEECCHHHHHHHHH-HCCCEECCEEEEEEE
T ss_conf             8998589985899989899999988753872478897768999723688997489999999874-489889335999998


Q ss_pred             ECCCCCCC
Q ss_conf             31788889
Q 030632           85 ALPERIKG   92 (174)
Q Consensus        85 a~~~~~~~   92 (174)
                      +.+...+.
T Consensus        91 ~~~~~~~~   98 (104)
T d1wg5a_          91 SSRAEVRT   98 (104)
T ss_dssp             ECTTTSCC
T ss_pred             CCHHHHCC
T ss_conf             89778344

>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=99.64  E-value=1.5e-16  Score=106.69  Aligned_cols=81  Identities=30%  Similarity=0.517  Sum_probs=72.1

Q ss_pred             CCCCEEEECCCCCCCHHHHHH----HHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEE
Q ss_conf             999979982999988299999----8314499846999711799999520899997077989999982399512485979
Q 030632            6 VQKNTLYVGGLAEEVNEAILH----AAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLT   81 (174)
Q Consensus         6 ~~~~~i~V~~Lp~~~~~~~l~----~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~   81 (174)
                      .|+++|||+|||+.+++++|+    .+|++||.|..+.+..   ++.++|||||+|.+.++|..|+..|||..+.|++|+
T Consensus         1 ~P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~---~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~   77 (91)
T d1nu4a_           1 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMR   77 (91)
T ss_dssp             CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEE---ECCCCCCEEEEECCHHHHHHHHHHHCCCEECCEEEE
T ss_conf             98999999599999999999999998703123255328854---306898157888999999999998499889998889


Q ss_pred             EEEECCCC
Q ss_conf             98531788
Q 030632           82 VNYALPER   89 (174)
Q Consensus        82 v~~a~~~~   89 (174)
                      |.||+++.
T Consensus        78 v~~ak~~~   85 (91)
T d1nu4a_          78 IQYAKTDS   85 (91)
T ss_dssp             EEECSSCC
T ss_pred             EEEECCCC
T ss_conf             99807975

>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=99.64  E-value=7.1e-16  Score=103.05  Aligned_cols=80  Identities=26%  Similarity=0.375  Sum_probs=71.7

Q ss_pred             CCCCCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEE
Q ss_conf             99999799829999882999998314499846999711799999520899997077989999982399512485979985
Q 030632            5 AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNY   84 (174)
Q Consensus         5 ~~~~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~   84 (174)
                      ....++|||+|||+.+++.+|+.+|++||.+..+.+..      ++|||||+|.+...|..|+..|||..|.|+.|+|.|
T Consensus         5 ~~~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~------~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~   78 (86)
T d2cpda1           5 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK------IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTL   78 (86)
T ss_dssp             SSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE------CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEEC
T ss_pred             CCCCCEEEECCCCCCCCHHHHHHHHCCCCEEEEEEECC------CCEEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEE
T ss_conf             65899999929899788999998620653265579755------427999986999999999998099899998989996


Q ss_pred             ECCCCC
Q ss_conf             317888
Q 030632           85 ALPERI   90 (174)
Q Consensus        85 a~~~~~   90 (174)
                      |+|+..
T Consensus        79 akP~~~   84 (86)
T d2cpda1          79 AKPVDK   84 (86)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
T ss_conf             607898

>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=99.64  E-value=5.8e-16  Score=103.51  Aligned_cols=85  Identities=19%  Similarity=0.219  Sum_probs=73.7

Q ss_pred             CCCCCCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEE
Q ss_conf             89999979982999988299999831449984699971179999952089999707798999998239951248597998
Q 030632            4 LAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVN   83 (174)
Q Consensus         4 ~~~~~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~   83 (174)
                      ..+.+.+|||+|||+.+++.+|+.+|..||.+ .+.++.+. ++..+|||||+|.+.++|..|+. +|+..|.||.|+|.
T Consensus        11 ~~~~~~~v~v~nLp~~~te~dl~~~F~~~~~~-~v~~~~~~-~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~   87 (102)
T d1weza_          11 QSTTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELF   87 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHCCCCC-EEEEEEEC-CCCCEEEEEEEECCHHHHHHHHH-CCCCEECCEEEEEE
T ss_conf             68999889980899868899998787424752-24667724-78604777899879999999997-29998999999999


Q ss_pred             EECCCCCC
Q ss_conf             53178888
Q 030632           84 YALPERIK   91 (174)
Q Consensus        84 ~a~~~~~~   91 (174)
                      ++.+....
T Consensus        88 ~s~~~~~~   95 (102)
T d1weza_          88 LNSTAGTS   95 (102)
T ss_dssp             EECCCCCC
T ss_pred             ECCCCCCC
T ss_conf             75889878

>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=99.63  E-value=3.1e-16  Score=105.04  Aligned_cols=78  Identities=27%  Similarity=0.443  Sum_probs=70.0

Q ss_pred             CCCCEEEECCCCCCCHHHHH---HHHCCCCCCEEEEEEECCCCCCC---CCCEEEEEECCHHHHHHHHHHCCCCEECCEE
Q ss_conf             99997998299998829999---98314499846999711799999---5208999970779899999823995124859
Q 030632            6 VQKNTLYVGGLAEEVNEAIL---HAAFIPFGDIKDVKTPLDQATQK---HRSFGFVTFLEKEDAIQAMDNMDGAELYGRV   79 (174)
Q Consensus         6 ~~~~~i~V~~Lp~~~~~~~l---~~~F~~~G~i~~~~~~~~~~~g~---~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~   79 (174)
                      ...++|||+|||+.+++++|   ..+|++||.|..+.+++++.++.   .+|||||+|.+.++|..|+..|||..+.|++
T Consensus         6 iq~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~   85 (89)
T d2cpia1           6 VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRT   85 (89)
T ss_dssp             CCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             EECCEEEEECCCCCCCHHHHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCCEEEEEECCCCHHHHHHHHHHCCCEECCEE
T ss_conf             82688999798976387899988987635588258777202676877776537998515412299999985899999978


Q ss_pred             EEEE
Q ss_conf             7998
Q 030632           80 LTVN   83 (174)
Q Consensus        80 l~v~   83 (174)
                      |+|.
T Consensus        86 lkvS   89 (89)
T d2cpia1          86 LKAS   89 (89)
T ss_dssp             EEEE
T ss_pred             EEEC
T ss_conf             8879

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.63  E-value=1.2e-15  Score=101.80  Aligned_cols=83  Identities=25%  Similarity=0.420  Sum_probs=68.1

Q ss_pred             CCCCCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEE
Q ss_conf             99999799829999882999998314499846999711799999520899997077989999982399512485979985
Q 030632            5 AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNY   84 (174)
Q Consensus         5 ~~~~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~   84 (174)
                      ....++|||+|||+.+++.+|+.+|+.||.|..+.++.++.++.++|||||+|.+.+.|.+|+. +++..+.|++|+|.+
T Consensus        94 ~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~~  172 (183)
T d1u1qa_          94 HLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRK  172 (183)
T ss_dssp             TCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEEEE
T ss_pred             CCCCCEEEECCCCCCCCHHHHHHHHCCCCCEEEEEEECCCCCCCCCEEEEEEECCHHHHHHHHH-HCCCEECCEEEEEEE
T ss_conf             4564235881677767899996543158865322330026668501059999789999999998-599909997979996


Q ss_pred             ECCC
Q ss_conf             3178
Q 030632           85 ALPE   88 (174)
Q Consensus        85 a~~~   88 (174)
                      |.++
T Consensus       173 A~~k  176 (183)
T d1u1qa_         173 ALSK  176 (183)
T ss_dssp             CCCH
T ss_pred             CCCC
T ss_conf             6884

>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=99.63  E-value=5.7e-16  Score=103.56  Aligned_cols=78  Identities=27%  Similarity=0.454  Sum_probs=71.8

Q ss_pred             CCCCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEEE
Q ss_conf             99997998299998829999983144998469997117999995208999970779899999823995124859799853
Q 030632            6 VQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYA   85 (174)
Q Consensus         6 ~~~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~a   85 (174)
                      ...++|||+|||+.+++.+|+.+|++||.|..+.+.++      +|||||+|.+.++|..|+..|||..|.|++|+|.||
T Consensus         6 ~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~------k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A   79 (86)
T d2cpja1           6 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFA   79 (86)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHHCCCEEEEEECC------CCEEEEEECCHHHHHHHHHHHCCCEECCEEEEEEEC
T ss_conf             69989999799987989999999998698607634213------536999988999999999981998899988899978


Q ss_pred             CCCC
Q ss_conf             1788
Q 030632           86 LPER   89 (174)
Q Consensus        86 ~~~~   89 (174)
                      .+..
T Consensus        80 ~~~~   83 (86)
T d2cpja1          80 CHSA   83 (86)
T ss_dssp             SCCS
T ss_pred             CCCC
T ss_conf             9857

>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=99.63  E-value=2.4e-16  Score=105.61  Aligned_cols=75  Identities=27%  Similarity=0.496  Sum_probs=71.6

Q ss_pred             EEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEEE
Q ss_conf             7998299998829999983144998469997117999995208999970779899999823995124859799853
Q 030632           10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYA   85 (174)
Q Consensus        10 ~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~a   85 (174)
                      +|||+|||+.+++.+|+.+|++||.+..+.++.++.++.++|||||+|.+.++|..|+. +|+..|.|++|+|.+|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             CEEEECCCCCCCHHHHHHHHHHHCCCCEEEEEEECCCCCCCCEEEEEECCHHHHHHHHH-CCCCEECCEEEEEEEC
T ss_conf             98990899988899999999986874022332103433567336999989999999995-2999899949899889

>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=99.62  E-value=1.8e-16  Score=106.28  Aligned_cols=75  Identities=28%  Similarity=0.510  Sum_probs=70.4

Q ss_pred             EEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEEE
Q ss_conf             7998299998829999983144998469997117999995208999970779899999823995124859799853
Q 030632           10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYA   85 (174)
Q Consensus        10 ~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~a   85 (174)
                      +|||+|||+.+++++|+.+|++||.|..+.++.++.++.++|||||+|.+.++|.+||.. ++..+.|+.|.|..|
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~~-~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTTC-SSCCBTTBCCEEECC
T ss_pred             CEEECCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEECCHHHHHHHHHH-CCCEECCEEEEEEEC
T ss_conf             989918999898999999999858765212244655456652899997889999999830-998799978599889

>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=99.62  E-value=3.8e-16  Score=104.54  Aligned_cols=82  Identities=11%  Similarity=0.090  Sum_probs=71.6

Q ss_pred             CCCCCCCEEEECCCCCCCHHHHHHHHCCCCCCEEEE-EEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEE
Q ss_conf             989999979982999988299999831449984699-9711799999520899997077989999982399512485979
Q 030632            3 NLAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDV-KTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLT   81 (174)
Q Consensus         3 ~~~~~~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~-~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~   81 (174)
                      +..+..++|||+|||+.+++++|+.+|..||.+... .+..+ .++.++|+|||+|.+.++|.+|+..||+..+.|++|+
T Consensus         4 ~g~p~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~-~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~   82 (86)
T d2cqpa1           4 SGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYN-EKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVK   82 (86)
T ss_dssp             CCCCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEEC-SSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHHCCCCEEEEEEEEC-CCCCCCEEEEEEECCCHHHHHHHHHCCCCEECCEEEE
T ss_conf             988999889997989989899999877512464269999768-9999660899998285799999998089999999999


Q ss_pred             EEEE
Q ss_conf             9853
Q 030632           82 VNYA   85 (174)
Q Consensus        82 v~~a   85 (174)
                      |.++
T Consensus        83 v~l~   86 (86)
T d2cqpa1          83 LVLG   86 (86)
T ss_dssp             EEES
T ss_pred             EEEC
T ss_conf             9979

>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=99.62  E-value=5.8e-16  Score=103.53  Aligned_cols=80  Identities=25%  Similarity=0.407  Sum_probs=70.8

Q ss_pred             CCCCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEEE
Q ss_conf             99997998299998829999983144998469997117999995208999970779899999823995124859799853
Q 030632            6 VQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYA   85 (174)
Q Consensus         6 ~~~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~a   85 (174)
                      ..+++|||+|||+.+++.+|+.+|++||.|..+.++.     .++|||||+|.+.+.|..|+.  +++.|.|++|.|.++
T Consensus         3 ~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~-----~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a   75 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK-----PFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNA   75 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCS-----SCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHCCCCEEEEEEE-----CCCCEEEEEECCHHHHHHHHH--CCCEECCEEEEEEEC
T ss_conf             8998999928998898999988899829844999942-----137658999889999999972--989899999699867


Q ss_pred             CCCCCCC
Q ss_conf             1788889
Q 030632           86 LPERIKG   92 (174)
Q Consensus        86 ~~~~~~~   92 (174)
                      .++....
T Consensus        76 ~~k~~~~   82 (88)
T d1wf0a_          76 EPKHNSN   82 (88)
T ss_dssp             CCCCCCC
T ss_pred             CCCCCCC
T ss_conf             7888798

>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=99.62  E-value=1.1e-15  Score=101.95  Aligned_cols=80  Identities=30%  Similarity=0.443  Sum_probs=72.0

Q ss_pred             CCCCCCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECC--EEEE
Q ss_conf             89999979982999988299999831449984699971179999952089999707798999998239951248--5979
Q 030632            4 LAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYG--RVLT   81 (174)
Q Consensus         4 ~~~~~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g--~~l~   81 (174)
                      ..+|+++|||+|||+.+++++|+.+|++||.|..+.+.++      ++||||+|.+.++|..|+..||+..|.|  ++|+
T Consensus        13 ~~~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~   86 (97)
T d1whya_          13 KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLR   86 (97)
T ss_dssp             CCCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCE
T ss_pred             CCCCCCEEEECCCCCCCCHHHHHHHHHHHCCCCEEEEECC------CCEEEECCCCHHHHHHHHHHHCCCEECCCCEEEE
T ss_conf             8999999998489998989999999975345624764022------2178761499999999999858889699965899


Q ss_pred             EEEECCCC
Q ss_conf             98531788
Q 030632           82 VNYALPER   89 (174)
Q Consensus        82 v~~a~~~~   89 (174)
                      |.||++.+
T Consensus        87 v~~ak~~~   94 (97)
T d1whya_          87 VDFAKSGP   94 (97)
T ss_dssp             EEECCCCC
T ss_pred             EEECCCCC
T ss_conf             98688989

>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=99.62  E-value=9.2e-16  Score=102.43  Aligned_cols=82  Identities=18%  Similarity=0.286  Sum_probs=73.2

Q ss_pred             CCCCCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEEC--CEEEEE
Q ss_conf             999997998299998829999983144998469997117999995208999970779899999823995124--859799
Q 030632            5 AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELY--GRVLTV   82 (174)
Q Consensus         5 ~~~~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~--g~~l~v   82 (174)
                      +.+..+|||+|||+.+++.+|+.+|++||.|..+.+...+    .+|||||+|.+.++|..|+..||+..|.  +++|+|
T Consensus         4 ~s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v   79 (108)
T d2adba1           4 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRI   79 (108)
T ss_dssp             CCCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEE
T ss_pred             CCCEEEEEEECCCCCCCHHHHHHHHCCCCCEEEEEEEEEC----CCCEEEEEECCHHHHHHHHHHHCCCEECCCCCEEEE
T ss_conf             9980899993929999899998887039758997998508----998189998999999999999778870469808999


Q ss_pred             EEECCCCC
Q ss_conf             85317888
Q 030632           83 NYALPERI   90 (174)
Q Consensus        83 ~~a~~~~~   90 (174)
                      .|+++...
T Consensus        80 ~~s~~~~~   87 (108)
T d2adba1          80 DFSKLTSL   87 (108)
T ss_dssp             EECSSCSC
T ss_pred             EECCCCCC
T ss_conf             94577655

>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=99.61  E-value=7.6e-16  Score=102.87  Aligned_cols=78  Identities=35%  Similarity=0.492  Sum_probs=70.8

Q ss_pred             CCCCCCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEE
Q ss_conf             89999979982999988299999831449984699971179999952089999707798999998239951248597998
Q 030632            4 LAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVN   83 (174)
Q Consensus         4 ~~~~~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~   83 (174)
                      .|..+++|||+||+  +++.+|+.+|++||.|..+.+.++      +|||||+|.+.++|..|+..|||..+.|++|+|.
T Consensus         1 ap~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~   72 (79)
T d2bz2a1           1 APRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAELNGTQVESVQLKVN   72 (79)
T ss_dssp             CCCCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT------TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEE
T ss_pred             CCCCCCEEEEECCC--CCHHHHHHHHHCCCCCCEEEECCC------CCEEEEEECCCHHHHHHHHHHCCCEECCEEEEEE
T ss_conf             99899899997897--999999999855075643520268------9889999924189999999859999999998999


Q ss_pred             EECCCC
Q ss_conf             531788
Q 030632           84 YALPER   89 (174)
Q Consensus        84 ~a~~~~   89 (174)
                      |+++++
T Consensus        73 ~a~~~P   78 (79)
T d2bz2a1          73 IARKQP   78 (79)
T ss_dssp             ECCSSC
T ss_pred             EECCCC
T ss_conf             705898

>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=99.60  E-value=1.2e-15  Score=101.77  Aligned_cols=84  Identities=12%  Similarity=0.086  Sum_probs=72.9

Q ss_pred             CCCCCCCCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEE
Q ss_conf             99899999799829999882999998314499846999711799999520899997077989999982399512485979
Q 030632            2 ANLAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLT   81 (174)
Q Consensus         2 ~~~~~~~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~   81 (174)
                      ++-.....+|||+|||+.+++.+|+.+|..||.+..+.++....+|.++|||||+|.+.++|.+|+. +|+..|.|+.|.
T Consensus         2 ~dv~~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~   80 (103)
T d2cpya1           2 GDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAF   80 (103)
T ss_dssp             CSCCSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEE
T ss_pred             CCCCCCCEEEEEECCCCCCCHHHHHHHHCCCCEEEEEEEEEECCCCCCCCCEEEEECCHHHHHHHHH-CCCCEECCCEEE
T ss_conf             9877882089995989888889986421022237778888768989857637899889999999996-398749991899


Q ss_pred             EEEEC
Q ss_conf             98531
Q 030632           82 VNYAL   86 (174)
Q Consensus        82 v~~a~   86 (174)
                      |.++.
T Consensus        81 V~~~~   85 (103)
T d2cpya1          81 VHVVT   85 (103)
T ss_dssp             EEEEC
T ss_pred             EEECC
T ss_conf             99899

>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=99.59  E-value=5.4e-16  Score=103.68  Aligned_cols=77  Identities=26%  Similarity=0.492  Sum_probs=68.3

Q ss_pred             CEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCC-EECCEEEEEEEECC
Q ss_conf             97998299998829999983144998469997117999995208999970779899999823995-12485979985317
Q 030632            9 NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGA-ELYGRVLTVNYALP   87 (174)
Q Consensus         9 ~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~-~~~g~~l~v~~a~~   87 (174)
                      ++|||+|||+.+++.+|+.+|++||.+..+.+..      .+|||||+|.+.++|..|+..|||. .+.|++|+|.||.|
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~------~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~   75 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVS   75 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHHCCEEEEEEEC------CCCEEEEEECCHHHHHHHHHHHCCCEEECCEEEEEEECCC
T ss_conf             8899979999899999999999809689737861------2664999988878799999981799699998989997588


Q ss_pred             CCCC
Q ss_conf             8888
Q 030632           88 ERIK   91 (174)
Q Consensus        88 ~~~~   91 (174)
                      +..+
T Consensus        76 k~~r   79 (80)
T d2cqha1          76 KKLR   79 (80)
T ss_dssp             CCCC
T ss_pred             CCCC
T ss_conf             5769

>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=99.59  E-value=2.4e-15  Score=100.16  Aligned_cols=79  Identities=19%  Similarity=0.211  Sum_probs=71.3

Q ss_pred             CCCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEEEC
Q ss_conf             99979982999988299999831449984699971179999952089999707798999998239951248597998531
Q 030632            7 QKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYAL   86 (174)
Q Consensus         7 ~~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~a~   86 (174)
                      ..++|||+|||+.+++.+|+.+|++||.|..+.+..       +|||||+|.+.++|..||..||+..|.|+.|+|.+++
T Consensus        14 ~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~   86 (98)
T d1wg4a_          14 SDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIR   86 (98)
T ss_dssp             CSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHHCCCCCCCCCC-------CCEEEEEECCHHHHHHHHHHHCCCEECCEEEEEEEEE
T ss_conf             888899977999998999999997522343200133-------4469999789999999999968899689088999971


Q ss_pred             CCCCCC
Q ss_conf             788889
Q 030632           87 PERIKG   92 (174)
Q Consensus        87 ~~~~~~   92 (174)
                      +...+.
T Consensus        87 ~~~~~~   92 (98)
T d1wg4a_          87 VYPERS   92 (98)
T ss_dssp             EECCCS
T ss_pred             CCCCCC
T ss_conf             378889

>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=99.59  E-value=3.9e-15  Score=99.00  Aligned_cols=78  Identities=19%  Similarity=0.301  Sum_probs=67.3

Q ss_pred             CCCCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEEE
Q ss_conf             99997998299998829999983144998469997117999995208999970779899999823995124859799853
Q 030632            6 VQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYA   85 (174)
Q Consensus         6 ~~~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~a   85 (174)
                      ..+++|||+|||+.+++.+|+.+|.+|| +..+.+      +..+|||||+|.+.++|..|+..||+..|.|++|+|.++
T Consensus         3 s~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~------~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a   75 (88)
T d1wg1a_           3 SGSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV------DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQ   75 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE------EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHCC-CEEEEE------ECCCCCEEEEECCHHHHHHHHHHHCCCEECCEEEEEEEC
T ss_conf             9998999969998637578877788609-603530------115771489988999999999985899899989899983


Q ss_pred             CCCCC
Q ss_conf             17888
Q 030632           86 LPERI   90 (174)
Q Consensus        86 ~~~~~   90 (174)
                      +++..
T Consensus        76 ~~~~~   80 (88)
T d1wg1a_          76 PTDAL   80 (88)
T ss_dssp             CCCCC
T ss_pred             CCCCC
T ss_conf             89988

>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=99.58  E-value=9.3e-15  Score=96.91  Aligned_cols=80  Identities=19%  Similarity=0.309  Sum_probs=71.4

Q ss_pred             CCCCCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHC--CCCEECCEEEEE
Q ss_conf             999997998299998829999983144998469997117999995208999970779899999823--995124859799
Q 030632            5 AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM--DGAELYGRVLTV   82 (174)
Q Consensus         5 ~~~~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l--~g~~~~g~~l~v   82 (174)
                      .+|+++|||+|||+.+++.+|+.+|++||.|..+.+..+      +|||||+|.+.++|..|+..+  ++..+.|++|+|
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v   78 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYI   78 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHCCCCCCCCCCCCC------CEEEEEEECCHHHHHHHHHHHCCCCCCCCCCEEEE
T ss_conf             999999999679988889999988750242222000234------41799984899999999999805997459977999


Q ss_pred             EEECCCCC
Q ss_conf             85317888
Q 030632           83 NYALPERI   90 (174)
Q Consensus        83 ~~a~~~~~   90 (174)
                      .|++.+..
T Consensus        79 ~~sk~~~l   86 (88)
T d2cq1a1          79 QYSNHKEL   86 (88)
T ss_dssp             EECSCSSC
T ss_pred             EECCCCCC
T ss_conf             97888777

>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=99.58  E-value=1.4e-14  Score=95.98  Aligned_cols=82  Identities=26%  Similarity=0.235  Sum_probs=71.6

Q ss_pred             CCCCCCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHC--CCCEECCEEEE
Q ss_conf             8999997998299998829999983144998469997117999995208999970779899999823--99512485979
Q 030632            4 LAVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM--DGAELYGRVLT   81 (174)
Q Consensus         4 ~~~~~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l--~g~~~~g~~l~   81 (174)
                      ...++++|||+|||+.+++.+|..+|.+||.|..+.+.+      .+|+|||+|.+.++|..|+..|  ++..+.|++|+
T Consensus        11 ~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~------~k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~   84 (104)
T d1wexa_          11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMP------FKRQALVEFENIDSAKECVTFAADVPVYIAGQQAF   84 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHCCCCEEEEEEE------CCEEEEEEECCHHHHHHHHHHHCCCCCEEEEEEEE
T ss_conf             699998999918999997999997660256534999973------11037998689999999999874799487037889


Q ss_pred             EEEECCCCCC
Q ss_conf             9853178888
Q 030632           82 VNYALPERIK   91 (174)
Q Consensus        82 v~~a~~~~~~   91 (174)
                      |.|++.++..
T Consensus        85 v~~s~~~~~~   94 (104)
T d1wexa_          85 FNYSTSKRIT   94 (104)
T ss_dssp             EEECSSSSCC
T ss_pred             EEECCCCCCC
T ss_conf             9974788667

>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=99.58  E-value=5.1e-16  Score=103.81  Aligned_cols=76  Identities=21%  Similarity=0.193  Sum_probs=68.4

Q ss_pred             CEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEEECCC
Q ss_conf             97998299998829999983144998469997117999995208999970779899999823995124859799853178
Q 030632            9 NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYALPE   88 (174)
Q Consensus         9 ~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~a~~~   88 (174)
                      ++|||+|||+.+++.+|+.+|++||.|..+.++.       .|||||+|.+.++|..||..|||..|.|+.|+|.+++++
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~   73 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR-------DGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   73 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECT-------TSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEE
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHHCCCCCCCCCC-------CCEEEEEECCHHHHHHHHHHHCCCEECCCEEEEEEEECC
T ss_conf             9699979998588999999875221232110022-------321357748889999999996879979967587577617


Q ss_pred             CCC
Q ss_conf             888
Q 030632           89 RIK   91 (174)
Q Consensus        89 ~~~   91 (174)
                      ...
T Consensus        74 ~~~   76 (87)
T d3begb1          74 VDG   76 (87)
T ss_dssp             ECC
T ss_pred             CCC
T ss_conf             677

>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=99.57  E-value=2.8e-15  Score=99.76  Aligned_cols=81  Identities=19%  Similarity=0.142  Sum_probs=71.2

Q ss_pred             CCCCCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEE
Q ss_conf             99999799829999882999998314499846999711799999520899997077989999982399512485979985
Q 030632            5 AVQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNY   84 (174)
Q Consensus         5 ~~~~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~   84 (174)
                      ....++|||+|||+.+++.+|..+|+.||.+..+.++....+|.++|||||+|.+.++|.+|+. ||+..|+|+.|.|..
T Consensus        15 ~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~   93 (112)
T d1wela1          15 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHP   93 (112)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEE
T ss_pred             CCCCEEEEEECCCCCCCHHHHHHHHHHCCCCCCCEEEECCCCCCEEEEEEEEECCHHHHHHHHH-CCCCCCCCEEEEEEE
T ss_conf             8897699994699757599996677533444321022107654300478999889999999997-189847998989998


Q ss_pred             EC
Q ss_conf             31
Q 030632           85 AL   86 (174)
Q Consensus        85 a~   86 (174)
                      +.
T Consensus        94 ~~   95 (112)
T d1wela1          94 IT   95 (112)
T ss_dssp             EC
T ss_pred             CC
T ss_conf             69

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.56  E-value=1.2e-15  Score=101.89  Aligned_cols=71  Identities=27%  Similarity=0.469  Sum_probs=67.8

Q ss_pred             EEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEE
Q ss_conf             99829999882999998314499846999711799999520899997077989999982399512485979
Q 030632           11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLT   81 (174)
Q Consensus        11 i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~   81 (174)
                      |||+|||+.+++.+|+.+|++||.|..+.+++++.++.++|||||+|.+.++|.+|+..|||..|.|+.|+
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             CEEECCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEECCHHHHHHHHHHHCCCEECCEECC
T ss_conf             99947998588999999886323332211100023322341159998899999999998389987888886

>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=99.55  E-value=1.2e-14  Score=96.40  Aligned_cols=74  Identities=19%  Similarity=0.184  Sum_probs=67.5

Q ss_pred             CEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEEE
Q ss_conf             97998299998829999983144998469997117999995208999970779899999823995124859799853
Q 030632            9 NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYA   85 (174)
Q Consensus         9 ~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~a   85 (174)
                      ++|||+|||+.+++.+|+.+|+.||.|..+.++.++.  ..++||||+|.+.++|.+|+. +|+..|+|++|.|..+
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~--~~~~~afV~F~~~~~a~~Al~-~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK--KNFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTT--SSSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEEEECC--CCCEEEEEEECCHHHHHHHHH-HCCCEECCEEEEEEEC
T ss_conf             9999989999998899999871288169999975023--331699999832677688887-3696999999999989

>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=99.53  E-value=4.2e-14  Score=93.30  Aligned_cols=80  Identities=18%  Similarity=0.170  Sum_probs=70.8

Q ss_pred             CCCCCCCEEEECCCCCC-CHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHC--CCCEECCEE
Q ss_conf             98999997998299998-829999983144998469997117999995208999970779899999823--995124859
Q 030632            3 NLAVQKNTLYVGGLAEE-VNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNM--DGAELYGRV   79 (174)
Q Consensus         3 ~~~~~~~~i~V~~Lp~~-~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l--~g~~~~g~~   79 (174)
                      ....++++|||+|||.. +++.+|..+|++||.|..+.++.+      +++|||.|.+.++|..|+..|  ++..+.|++
T Consensus         3 ~~~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~------k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~   76 (89)
T d1x4da1           3 GRVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKP   76 (89)
T ss_dssp             CCCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEE
T ss_pred             CCCCCCCEEEEECCCCCCCCHHHHHHHHHHHCCEEEEEEECC------CEEEEEEECCHHHHHHHHHHHHHCCCCCCCCE
T ss_conf             888999689997899876789999999986387278876044------22899997460557999998750888669924


Q ss_pred             EEEEEECCC
Q ss_conf             799853178
Q 030632           80 LTVNYALPE   88 (174)
Q Consensus        80 l~v~~a~~~   88 (174)
                      |+|.||++.
T Consensus        77 l~V~~s~~~   85 (89)
T d1x4da1          77 VRVHLSQKY   85 (89)
T ss_dssp             CEEEEECCC
T ss_pred             EEEEECCCC
T ss_conf             899978885

>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=99.53  E-value=1.7e-14  Score=95.44  Aligned_cols=80  Identities=18%  Similarity=0.233  Sum_probs=69.8

Q ss_pred             CCCCCCEEEECCCCCC-CHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHH--HCCCCEECCEEE
Q ss_conf             8999997998299998-8299999831449984699971179999952089999707798999998--239951248597
Q 030632            4 LAVQKNTLYVGGLAEE-VNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMD--NMDGAELYGRVL   80 (174)
Q Consensus         4 ~~~~~~~i~V~~Lp~~-~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~--~l~g~~~~g~~l   80 (174)
                      ...++++|||+|||.. +++.+|..+|++||.|..+.++++      +|+|||+|.+.++|..|+.  .+++..+.|++|
T Consensus        14 ~~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l   87 (99)
T d1x4fa1          14 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCV   87 (99)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCC
T ss_pred             CCCCCCEEEEECCCCCCCCHHHHHHHHCCCCCEEEEEEEEC------CCCEEEEECCHHHHHHHHHHHHCCCCEECCEEE
T ss_conf             77888789993786775389999866534453048987604------772799963568999999997368964899788


Q ss_pred             EEEEECCCC
Q ss_conf             998531788
Q 030632           81 TVNYALPER   89 (174)
Q Consensus        81 ~v~~a~~~~   89 (174)
                      +|.+|+.+.
T Consensus        88 ~V~~s~~~~   96 (99)
T d1x4fa1          88 KVDLSEKYK   96 (99)
T ss_dssp             EEEEECSCS
T ss_pred             EEEECCCCC
T ss_conf             999828704

>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=99.51  E-value=2.5e-14  Score=94.60  Aligned_cols=81  Identities=14%  Similarity=0.096  Sum_probs=70.8

Q ss_pred             CCCCEEEECCCCCCCH-----HHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEE
Q ss_conf             9999799829999882-----99999831449984699971179999952089999707798999998239951248597
Q 030632            6 VQKNTLYVGGLAEEVN-----EAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVL   80 (174)
Q Consensus         6 ~~~~~i~V~~Lp~~~~-----~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l   80 (174)
                      ..+++|||+||+..+.     ...|+.+|++||.|..+.+++      +++||||+|.+.++|..|+..|||..|.|++|
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k------~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l   76 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK------SFKRVRINFSNPLSAADARLRLHKTEFLGKEM   76 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET------TTTEEEEECSSTTHHHHHHHTSTTSEETTEEC
T ss_pred             CCCCEEEEEECCCHHCCCHHHHHHHHHHHCCCCCCEEEEEEC------CCCEEEEEECCHHHHHHHHHHHCCCCCCCCEE
T ss_conf             987608999589011371888999998720355526899966------88789999899999999999855013389876


Q ss_pred             EEEEECCCCCCC
Q ss_conf             998531788889
Q 030632           81 TVNYALPERIKG   92 (174)
Q Consensus        81 ~v~~a~~~~~~~   92 (174)
                      +|.|+++.....
T Consensus        77 ~v~~a~~~~~~~   88 (104)
T d1weya_          77 KLYFAQTLHIGS   88 (104)
T ss_dssp             EEECCCCSSCCS
T ss_pred             EEEECCCCCCCC
T ss_conf             885344689888

>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=99.51  E-value=4.9e-14  Score=92.97  Aligned_cols=72  Identities=24%  Similarity=0.368  Sum_probs=64.0

Q ss_pred             EEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEEECCCC
Q ss_conf             9982999988299999831449984699971179999952089999707798999998239951248597998531788
Q 030632           11 LYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYALPER   89 (174)
Q Consensus        11 i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~a~~~~   89 (174)
                      |||+|||+.+++.+|+.+|++|| +..+.+      +..+|||||+|.+.++|.+|+..|||..+.|++|+|.|++...
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~------~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d~   72 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTDA   72 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCSTT
T ss_pred             CEEECCCCCCCHHHHHHHHHCCC-CCCEEE------CCCCEEEEEEECCHHHHHHHHHHHCCCCCCCCEEEEEEECCCC
T ss_conf             99969999678999999874325-221155------4632169999877788888889857966799899999967987

>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=99.46  E-value=3.1e-13  Score=88.52  Aligned_cols=82  Identities=29%  Similarity=0.483  Sum_probs=73.1

Q ss_pred             CCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEEECC
Q ss_conf             99799829999882999998314499846999711799999520899997077989999982399512485979985317
Q 030632            8 KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYALP   87 (174)
Q Consensus         8 ~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~a~~   87 (174)
                      .++|||+|||+.+++.+|+.+|++||.|..+.+++++.++.++|||||.|.+...|..|+.. ++..+.++.+.+.+..+
T Consensus         6 ~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~-~~~~~~~~~~~~~~~~~   84 (183)
T d1u1qa_           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAVS   84 (183)
T ss_dssp             HHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHCCCEEEEEEEECCCCCCCCCCEECCCCCHHHHHHHHHH-CCCCCCCCCHHHHHHHH
T ss_conf             97899979899898999999998739878998641124788557432204888999999984-57764111023333221


Q ss_pred             CCC
Q ss_conf             888
Q 030632           88 ERI   90 (174)
Q Consensus        88 ~~~   90 (174)
                      ...
T Consensus        85 ~~~   87 (183)
T d1u1qa_          85 RED   87 (183)
T ss_dssp             TTG
T ss_pred             CCC
T ss_conf             123

>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=99.41  E-value=2.1e-15  Score=100.43  Aligned_cols=77  Identities=22%  Similarity=0.393  Sum_probs=66.1

Q ss_pred             CEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEE-----CCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEE
Q ss_conf             979982999988299999831449984699971-----179999952089999707798999998239951248597998
Q 030632            9 NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTP-----LDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVN   83 (174)
Q Consensus         9 ~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~-----~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~   83 (174)
                      ++|||+|||+.+++.+|+.+|++||.+..+.+.     .+..++.++|||||+|.+.++|..|+. |||..+.|++|+|.
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~Gr~l~V~   80 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIR   80 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSSSSCCCCB
T ss_pred             CEEEECCCCCCCCHHHHHHHHHHHCCEEEEEEECCCEEEECCCCCCCEEEEEEECCHHHHHHHHH-HCCCEECCEEEEEC
T ss_conf             99999699976245898888986085779999425605664469976289998389999999986-19958899888978


Q ss_pred             EEC
Q ss_conf             531
Q 030632           84 YAL   86 (174)
Q Consensus        84 ~a~   86 (174)
                      .++
T Consensus        81 r~k   83 (90)
T d1u2fa_          81 RPH   83 (90)
T ss_dssp             CTT
T ss_pred             CCC
T ss_conf             888

>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=99.38  E-value=4.2e-14  Score=93.31  Aligned_cols=75  Identities=13%  Similarity=0.203  Sum_probs=68.4

Q ss_pred             EEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEEE
Q ss_conf             7998299998829999983144998469997117999995208999970779899999823995124859799853
Q 030632           10 TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYA   85 (174)
Q Consensus        10 ~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~a   85 (174)
                      .++|++++..++++.|+.+|++||.|..+.++++. ++.++|||||+|.+.++|.+|+..|||..+.|++|+|.++
T Consensus        29 ~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~-~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          29 DVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEECCC-CCCEEEEEEEEEECHHHHHHHHHHHCCCEECCEEEEEEEC
T ss_conf             68866301665699999985057878999962189-9988417999995403799999997898899999999977

>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=99.37  E-value=3.6e-12  Score=82.71  Aligned_cols=76  Identities=21%  Similarity=0.266  Sum_probs=65.2

Q ss_pred             CCCC-EEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCH-HHHHHHHHHCCCCEECCEEEEEE
Q ss_conf             9999-799829999882999998314499846999711799999520899997077-98999998239951248597998
Q 030632            6 VQKN-TLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEK-EDAIQAMDNMDGAELYGRVLTVN   83 (174)
Q Consensus         6 ~~~~-~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~-~~a~~ai~~l~g~~~~g~~l~v~   83 (174)
                      +.++ .+||||||+.+++.+|+.+|++||+|..+.++++      +|||||.|.+. ++|..|+..+|+..+.++.+.|.
T Consensus         8 ~~g~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~   81 (113)
T d1owxa_           8 KIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVT   81 (113)
T ss_dssp             CCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEE
T ss_pred             CCCCEEEEECCCCCCCCHHHHHHHHHHCCCHHEEEEECC------CCEEEEEECCCHHHHHHHHHHHCCCCEECCCEEEE
T ss_conf             889769998799987879999999983577414887458------86689996682789999999834883315742898


Q ss_pred             EECC
Q ss_conf             5317
Q 030632           84 YALP   87 (174)
Q Consensus        84 ~a~~   87 (174)
                      |+..
T Consensus        82 ~~~~   85 (113)
T d1owxa_          82 WEVL   85 (113)
T ss_dssp             EEEC
T ss_pred             EEEC
T ss_conf             7634

>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=99.30  E-value=3.1e-12  Score=83.10  Aligned_cols=68  Identities=19%  Similarity=0.385  Sum_probs=60.0

Q ss_pred             CCCCCCCEEEEC--CCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEEC
Q ss_conf             989999979982--99998829999983144998469997117999995208999970779899999823995124
Q 030632            3 NLAVQKNTLYVG--GLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELY   76 (174)
Q Consensus         3 ~~~~~~~~i~V~--~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~   76 (174)
                      ....|++++||.  |||+.+++++|+.+|++||.|..+.++.+      ++||||+|.+.++|..|+..|||..+.
T Consensus        13 ~~~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i~   82 (101)
T d2cq2a1          13 TVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEVV   82 (101)
T ss_dssp             CCSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEEE
T ss_pred             CCCCCCCEEEEECCCCCCCCCHHHHHHHHHHHCCCCEEEECCC------CCEEEEEECCHHHHHHHHHHHCCCCCC
T ss_conf             6789976599977789998789999999975276617863267------508999989989999999983898977

>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=99.29  E-value=1.2e-11  Score=79.90  Aligned_cols=83  Identities=16%  Similarity=0.169  Sum_probs=70.2

Q ss_pred             CCCCCCCEEEECCC--CCCC---------HHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCC
Q ss_conf             98999997998299--9988---------299999831449984699971179999952089999707798999998239
Q 030632            3 NLAVQKNTLYVGGL--AEEV---------NEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMD   71 (174)
Q Consensus         3 ~~~~~~~~i~V~~L--p~~~---------~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~   71 (174)
                      +....+++|+|.||  |..+         ..++|+..|++||.|..+.+..+    ..+|++||.|.+.++|.+|+..||
T Consensus         3 ~~~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~ln   78 (99)
T d2dita1           3 SRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLD   78 (99)
T ss_dssp             CCCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHHST
T ss_pred             CCCCCCCEEEECCCCCHHHHHCCHHHHHHHHHHHHHHHCCCCCEEEEECCCC----CCCCEEEEEECCHHHHHHHHHHHC
T ss_conf             8877761999956999788434467789999999987267660799963477----886479999898999999999868


Q ss_pred             CCEECCEEEEEEEECCCC
Q ss_conf             951248597998531788
Q 030632           72 GAELYGRVLTVNYALPER   89 (174)
Q Consensus        72 g~~~~g~~l~v~~a~~~~   89 (174)
                      |..+.|++|+|.++.++.
T Consensus        79 g~~~~gr~i~v~~~~g~~   96 (99)
T d2dita1          79 GRWFGGRQITAQAWDGTT   96 (99)
T ss_dssp             TCEETTEECEEEECCSCC
T ss_pred             CCEECCEEEEEEEECCCC
T ss_conf             969899799999837967

>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=99.16  E-value=2.8e-11  Score=77.78  Aligned_cols=81  Identities=20%  Similarity=0.245  Sum_probs=68.8

Q ss_pred             CCCCEEEECCC--CCCC--------HHHHHHHHCCCCCCEEEEEEECCCCC--CCCCCEEEEEECCHHHHHHHHHHCCCC
Q ss_conf             99997998299--9988--------29999983144998469997117999--995208999970779899999823995
Q 030632            6 VQKNTLYVGGL--AEEV--------NEAILHAAFIPFGDIKDVKTPLDQAT--QKHRSFGFVTFLEKEDAIQAMDNMDGA   73 (174)
Q Consensus         6 ~~~~~i~V~~L--p~~~--------~~~~l~~~F~~~G~i~~~~~~~~~~~--g~~~g~afv~f~~~~~a~~ai~~l~g~   73 (174)
                      +|++.|.+.||  |..+        ..++|+..|.+||.|..+.+++++.+  ....|++||.|.+.++|.+|+..|||.
T Consensus         2 ~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr   81 (104)
T d1o0pa_           2 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   81 (104)
T ss_dssp             CCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSC
T ss_pred             CCCCEEEEECCCCHHHCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCCEEEEEEECCHHHHHHHHHHHCCC
T ss_conf             98759999688987773783148889999999961668257789752377776577328999989999999999997899


Q ss_pred             EECCEEEEEEEEC
Q ss_conf             1248597998531
Q 030632           74 ELYGRVLTVNYAL   86 (174)
Q Consensus        74 ~~~g~~l~v~~a~   86 (174)
                      .+.||+|.+.++.
T Consensus        82 ~f~gR~v~v~f~~   94 (104)
T d1o0pa_          82 KFANRVVVTKYCD   94 (104)
T ss_dssp             CSSSSCCEEEEEC
T ss_pred             EECCEEEEEEECC
T ss_conf             9899189999858

>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=99.08  E-value=1.4e-10  Score=73.92  Aligned_cols=71  Identities=18%  Similarity=0.248  Sum_probs=59.7

Q ss_pred             CCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEE-EEEEEEC
Q ss_conf             997998299998829999983144998469997117999995208999970779899999823995124859-7998531
Q 030632            8 KNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRV-LTVNYAL   86 (174)
Q Consensus         8 ~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~-l~v~~a~   86 (174)
                      .+.|+|.|+|+.++...| .+|++||.|..+.+.+      .+||+||.|.+..+|.+|+. +||..|.|+. +.|..+.
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~------~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~   75 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSN------TGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCI   75 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECS------SSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECC
T ss_pred             CCEEEEECCCHHHHHHHH-HHHHHHHHHHEEEECC------CCCEEEEEECCCHHHHHHHH-CCCCEECCCEEEEEEECC
T ss_conf             409999898857779999-9997420110689548------99889999763279999986-078757995799999688

>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=96.99  E-value=0.0012  Score=35.88  Aligned_cols=74  Identities=20%  Similarity=0.273  Sum_probs=59.0

Q ss_pred             CCCCCCCEEEECCCCCCCH---------HHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCC
Q ss_conf             9899999799829999882---------9999983144998469997117999995208999970779899999823995
Q 030632            3 NLAVQKNTLYVGGLAEEVN---------EAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGA   73 (174)
Q Consensus         3 ~~~~~~~~i~V~~Lp~~~~---------~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~   73 (174)
                      -+-++..||.|.-..+...         -..|...|..||.|.-++++.+        --+|+|.+-.+|.+|+. +++.
T Consensus        10 ~qGPpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al~-l~g~   80 (95)
T d1ufwa_          10 FQGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVLD-VDGM   80 (95)
T ss_dssp             CCCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHHH-GGGS
T ss_pred             CCCCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHCCEEEEEEEECC--------EEEEEECCCHHHHHHHC-CCCE
T ss_conf             34899867999961688311565888999999999863781999999588--------29999878687998752-5781


Q ss_pred             EECCEEEEEEEE
Q ss_conf             124859799853
Q 030632           74 ELYGRVLTVNYA   85 (174)
Q Consensus        74 ~~~g~~l~v~~a   85 (174)
                      .+.|+.|+|...
T Consensus        81 ~v~G~~l~It~~   92 (95)
T d1ufwa_          81 KVKGRAVKISGP   92 (95)
T ss_dssp             EETTEEEEEECC
T ss_pred             EECCEEEEEECC
T ss_conf             971569999657

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.81  E-value=0.0027  Score=34.01  Aligned_cols=77  Identities=16%  Similarity=0.229  Sum_probs=59.8

Q ss_pred             CEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCC--CCCEEEEEECCHHHHHHHHHHCCCCEECC-----EEEE
Q ss_conf             9799829999882999998314499846999711799999--52089999707798999998239951248-----5979
Q 030632            9 NTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQK--HRSFGFVTFLEKEDAIQAMDNMDGAELYG-----RVLT   81 (174)
Q Consensus         9 ~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~--~~g~afv~f~~~~~a~~ai~~l~g~~~~g-----~~l~   81 (174)
                      ++|.|+.||+..+++.+...+...|.+..........+.+  ...-|+|.|.+.+........++|+.+.+     .+-.
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D~~g~~~~a~   81 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPAI   81 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEECE
T ss_pred             CEEEEECCCCCCCHHHHHHHHCCCCCEEEEEEECCCCCCCCCCCEEEEEEECCHHHHHHHHHHCCCCEEECCCCCEEEEE
T ss_conf             66999369798999999998577674589988589867899744589998689999999998729818982999990257


Q ss_pred             EEEE
Q ss_conf             9853
Q 030632           82 VNYA   85 (174)
Q Consensus        82 v~~a   85 (174)
                      |.+|
T Consensus        82 VE~A   85 (91)
T d1uw4a_          82 VEFA   85 (91)
T ss_dssp             EEEC
T ss_pred             EEEC
T ss_conf             9975

>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=96.57  E-value=0.0022  Score=34.47  Aligned_cols=62  Identities=21%  Similarity=0.303  Sum_probs=52.0

Q ss_pred             HHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEEEC
Q ss_conf             99999831449984699971179999952089999707798999998239951248597998531
Q 030632           22 EAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMDGAELYGRVLTVNYAL   86 (174)
Q Consensus        22 ~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~a~   86 (174)
                      ...|...|.++|.|..+.+....   ...-.|-|...+..+|.-|+..||...|++++|.|.++.
T Consensus        10 qq~L~~~f~~h~~V~sv~l~~~~---dg~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          10 QQLLQEAFARHGKVKSVELSPHT---DYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHHHSCEEEEEECSCC---STTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHHHHHEEEEEEEEEECC---CCCEEEEEECCCHHHHHHHHHHHHHHHCCCEEEEEEEEC
T ss_conf             99999998852158999998636---896899998487788999999987874287079999842

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=93.51  E-value=0.11  Score=25.20  Aligned_cols=58  Identities=19%  Similarity=0.231  Sum_probs=45.7

Q ss_pred             CCCCEEEECCCCCCCHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHCC
Q ss_conf             999979982999988299999831449984699971179999952089999707798999998239
Q 030632            6 VQKNTLYVGGLAEEVNEAILHAAFIPFGDIKDVKTPLDQATQKHRSFGFVTFLEKEDAIQAMDNMD   71 (174)
Q Consensus         6 ~~~~~i~V~~Lp~~~~~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~ai~~l~   71 (174)
                      +....+|.-..|..+...+|..+|++||.|.-..| .+       --|||.....+.+..++..+.
T Consensus        13 p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswI-dd-------TSa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          13 PKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWI-DD-------TSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCCSEEEEECCTTCCHHHHHHHHTTTCSCCCEEE-ET-------TEEEEECSCHHHHHHHHHHHH
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHCCCCCEEEEEE-CC-------CEEEEEECCHHHHHHHHHHHC
T ss_conf             77440688717764515679987157775588886-58-------607999527889999999860