Citrus Sinensis ID: 028027

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-----
Protein Sequence
MGAKQKKALKKNLKKVSSQLPVPSDKKGAADFLPLEGGPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPPEHVHPKLWRGFNPRYKPVDRVQVERKLQNKERTLEEHKKLVEKILKRDQKRRKRIEAAGIEYECPEIVGNVMPAPKKIKFNEG
Secondary Structure (PSIPRED)
ccHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccEEEEccccccccHHHHHHHHHccccEEEEEEEccccccccccEEEEEEccHHHHHHHHHHHcccccccEEEEEEEccccccccccccccccccccccHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHHHHHHcccccccccccccccccHHcHHHHHHHHcccccccccEEEEEcccccccHHHHHHHHHHcccEEEEEEEEcccccccccEEEEEEccHHHHHHHHHHHHHHHHHHcEEEEEEcccHHccHHHHcccccccccccHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHcccccccccHccccccccccEEcccc
Coil and Loop (DISEMBL)
MGAKQKKALKKNLKKvssqlpvpsdkkgaadflpleggpgrklteekplvnkATVLYigriphgfyEKEMQAFFSQFGAIKRLRIARnkktgqskhfgfiefndpEVAEVVADAMHGYLLFEHILQvhlippehvhpklwrgfnprykpvdrVQVERKLQNKERTLEEHKKLVEKILKRDQKRRKRIEAAgieyecpeivgnvmpapkkikfneg
Flexible Loop (DISEMBL)
mgakqkkalkknlkkvssqlpvpsdkkgaadflpleggpgrklteekplvnkATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPPEHVHPKLWRGFNPRYKPVDRVQVErklqnkertleehkklvekilkrdqkRRKRIeaagieyecpeivgnvmpapkkikfneg
Low Complexity Region (SEG)
MGakqkkalkknlkkVSSQLPVPSDKKGAADFLPLEGGPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPPEHVHPKLWRGFNPRYKPVDRVQVERKLQNKERTLEEHKKLVEKILKRDQKRRKRIEAAGIEYECPEIVGNVMPAPKKIKFNEG
Disordered region (IsUnstruct)
************************************************LVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPPEHVHPKLWRGFNPRYKPVDRV*********************************IEAAGIEYECPEIVGNV************
Disordered Region (DISOPRED)
*******************************************************LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQV**************************************************************AGIEYECPEIV***************
Disordered Region (DISEMBL)
************************DKKGAADFLPLEGGPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPPEHVHPKLWRGFNPRYKPVDRVQVERKLQNKERTLEEHKKLVEKILKRDQKRRKRIEAAGIEYECPEIVGNVMPAPKKIKFNEG
Disordered Region (DISPRO)
*****K**********SSQLPVPS*****ADFLPLEGGP*R********VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPPEHVHPKLWRGFNPRYKPVDRVQVERKLQNKERTLEEHKKLVEKILKRDQKRRKRIEAAGIEYECPEIVGNVM***********
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGAKQKKALKKNLKKVSSQLPVPSDKKGAADFLPLEGGPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPPEHVHPKLWRGFNPRYKPVDxxxxxxxxxxxxxxxxxxxxxxxxxxxxDQKRRKRIEAAGIEYECPEIVGNVMPAPKKIKFNEG
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	215	2.2.26 [Sep-21-2011]
Q6GL69	276	MKI67 FHA domain-interact	yes	no	0.655	0.510	0.426	2e-31
Q8JIY8	269	MKI67 FHA domain-interact	yes	no	0.679	0.542	0.427	3e-30
O74978	276	Uncharacterized RNA-bindi	yes	no	0.627	0.489	0.451	5e-30
Q7SYS2	278	MKI67 FHA domain-interact	N/A	no	0.655	0.507	0.412	1e-29
Q3SZM1	296	MKI67 FHA domain-interact	yes	no	0.669	0.486	0.404	1e-24
P53927	220	Ribosome biogenesis prote	yes	no	0.655	0.640	0.370	6e-23
Q9BYG3	293	MKI67 FHA domain-interact	yes	no	0.669	0.491	0.356	2e-22
Q5RJM0	271	MKI67 FHA domain-interact	yes	no	0.697	0.553	0.341	1e-17
Q91VE6	317	MKI67 FHA domain-interact	yes	no	0.702	0.476	0.333	2e-16
Q9LEB3	428	Polyadenylate-binding pro	N/A	no	0.279	0.140	0.363	6e-07

>sp|Q6GL69|MK67I_XENTR MKI67 FHA domain-interacting nucleolar phosphoprotein-like OS=Xenopus tropicalis GN=mki67ipl PE=2 SV=1

 Score =  135 bits (340), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 61/143 (42%), Positives = 95/143 (66%), Gaps = 2/143 (1%)

Query: 55  VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
           V+YIG IP   YE +++ +FSQFG + RLR++R+KKTG SK + ++EF   EVA++VAD 
Sbjct: 42  VIYIGHIPRALYEPQLREYFSQFGTVTRLRLSRSKKTGNSKGYAYVEFECDEVAKIVADT 101

Query: 115 MHGYLLFEHILQVHLIPPEHVHPKLWRGFNPRYKPVDRVQVERKLQNKERTLEEHKKLVE 174
           M+ YL  E +L+   +PPE VHP+L+ G   +++   +  V R   NK R+  E KK+ +
Sbjct: 102 MNNYLFCERLLKCEFVPPEKVHPRLFIGCTAKFRKPTKPAVSR--YNKRRSEAEQKKMTQ 159

Query: 175 KILKRDQKRRKRIEAAGIEYECP 197
           ++L ++ K RKR+   GI+Y+ P
Sbjct: 160 RMLSKENKVRKRLAEKGIDYDFP 182

Xenopus tropicalis (taxid: 8364)

>sp|Q8JIY8|MK67I_DANRE MKI67 FHA domain-interacting nucleolar phosphoprotein OS=Danio rerio GN=mki67ip PE=2 SV=2

 Score =  131 bits (330), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 68/159 (42%), Positives = 102/159 (64%), Gaps = 13/159 (8%)

Query: 55  VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
           VLY+G +P G +E +++++F QFG + RLR++R+KKTG SK +GF+EF   EVA++VA+ 
Sbjct: 46  VLYVGHLPRGLFEPQLKSYFEQFGKVLRLRVSRSKKTGGSKGYGFVEFECDEVAKIVAET 105

Query: 115 MHGYLLFEHILQVHLIPPEHVHPKLWRGF-----NPRYKPVDRVQVERKLQNKERTLEEH 169
           M+ YL+ E I++ H+IPPE VH KL+ G       P+Y  V R        NK  T ++ 
Sbjct: 106 MNNYLMGERIIKCHVIPPEKVHEKLFVGSIAGFKKPKYPAVTRY-------NKTHTEDDV 158

Query: 170 KKLVEKILKRDQKRRKRIEAAGIEYECPEIVGNVMPAPK 208
           KK+  K+L ++ K RKR+ A GI+Y+ P     + PA K
Sbjct: 159 KKVGTKLLSKESKLRKRLAAKGIDYDFPGFAAQI-PAKK 196

Plays an essential role in early embryonic development.

Danio rerio (taxid: 7955)

>sp|O74978|YQL5_SCHPO Uncharacterized RNA-binding protein C1827.05c OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPCC1827.05c PE=4 SV=1

 Score =  130 bits (328), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 61/135 (45%), Positives = 91/135 (67%)

Query: 41  RKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFI 100
           +K++E K L  K  VLY+GR+PHGFYEK+M+ +FSQFG + RLR++RN+KTG SKH+ FI
Sbjct: 92  KKVSENKNLQKKKGVLYVGRLPHGFYEKQMRMYFSQFGPVLRLRMSRNRKTGSSKHYAFI 151

Query: 101 EFNDPEVAEVVADAMHGYLLFEHILQVHLIPPEHVHPKLWRGFNPRYKPVDRVQVERKLQ 160
           EF   +VA VVA+ MH YLL+  +LQ  +IP + VH  +++G +  +K +    + R   
Sbjct: 152 EFESLDVANVVAETMHNYLLYGKLLQCKVIPEDQVHENMFKGADVPFKRIPHATIARLQH 211

Query: 161 NKERTLEEHKKLVEK 175
            K  + E+  KL+ +
Sbjct: 212 EKPLSKEKADKLITR 226

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

>sp|Q7SYS2|MK67I_XENLA MKI67 FHA domain-interacting nucleolar phosphoprotein-like OS=Xenopus laevis GN=mki67ipl PE=2 SV=2

 Score =  129 bits (324), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 59/143 (41%), Positives = 94/143 (65%), Gaps = 2/143 (1%)

Query: 55  VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
           V+YIG IP    E ++Q +F+QFG + RLR++R+KKTG SK + ++E+   EVA++VAD 
Sbjct: 42  VIYIGHIPKSLIEPQLQEYFNQFGTVTRLRLSRSKKTGNSKGYAYVEYECDEVAKIVADT 101

Query: 115 MHGYLLFEHILQVHLIPPEHVHPKLWRGFNPRYKPVDRVQVERKLQNKERTLEEHKKLVE 174
           M+ YL  E +L+   + PE VHP+L+ G N R++   +  V R   N +R  EE KK+ +
Sbjct: 102 MNNYLFCERLLKCEFVTPEKVHPRLFIGCNTRFRKPTKPAVTR--YNSKRNKEEVKKMTQ 159

Query: 175 KILKRDQKRRKRIEAAGIEYECP 197
           +++ ++ K RKR+   GI+Y+ P
Sbjct: 160 RMISKEYKLRKRLAEKGIDYDFP 182

Xenopus laevis (taxid: 8355)

>sp|Q3SZM1|MK67I_BOVIN MKI67 FHA domain-interacting nucleolar phosphoprotein OS=Bos taurus GN=MKI67IP PE=2 SV=1

 Score =  113 bits (282), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 59/146 (40%), Positives = 96/146 (65%), Gaps = 2/146 (1%)

Query: 55  VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
           V+Y+G +P   YE +++A+FSQFG + R R++R+KKTG SK +GF+EF   +VA++ A+ 
Sbjct: 46  VIYVGHLPPTLYETQIRAYFSQFGTVTRFRLSRSKKTGNSKGYGFVEFESEDVAKIAAET 105

Query: 115 MHGYLLFEHILQVHLIPPEHVHPKLWRGFNPRYKPVDRVQVERKLQNKERTLEEHKKLVE 174
           M+ YL  E +L+ H IPPE VH +L+R ++  +K      V+R  QN  R+L +  ++ E
Sbjct: 106 MNNYLFGERLLKCHFIPPEKVHEELFREWHMPFKRPSYPAVKRYNQN--RSLVQKLRMEE 163

Query: 175 KILKRDQKRRKRIEAAGIEYECPEIV 200
           +  K+++  RKR+   GI+Y  P +V
Sbjct: 164 RFKKKEKLLRKRLAKKGIDYNFPSLV 189

Bos taurus (taxid: 9913)

>sp|P53927|NOP15_YEAST Ribosome biogenesis protein 15 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=NOP15 PE=1 SV=1

 Score =  107 bits (267), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 57/154 (37%), Positives = 97/154 (62%), Gaps = 13/154 (8%)

Query: 41  RKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFI 100
           +K  ++K L   + ++Y+ R+PHGF+EKE+  +F+QFG +K +R+ARNKKTG S+H+GF+
Sbjct: 78  KKSKDKKTLEEYSGIIYVSRLPHGFHEKELSKYFAQFGDLKEVRLARNKKTGNSRHYGFL 137

Query: 101 EFNDPEVAEVVADAMHGYLLFEHILQVHLIPPEHVHPKLWRGFNPRYKPVDRVQVERKLQ 160
           EF + E A +  ++M+ YLL  H+LQV ++P      KL       YK   RV VE+ + 
Sbjct: 138 EFVNKEDAMIAQESMNNYLLMGHLLQVRVLPKGAKIEKL-------YKYKKRVLVEKGIT 190

Query: 161 NKERTLEEHKKLVEKILKRDQKRRKRIEAAGIEY 194
              + L+++ K      ++ ++R K++  +GIE+
Sbjct: 191 KPVKQLKDNMK------QKHEERIKKLAKSGIEF 218

Involved in the biogenesis of the 60S ribosomal subunit. Required for pre-rRNA processing and cytokinesis. Associates with the precursors of the 25S and 5.8S rRNAs.

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

>sp|Q9BYG3|MK67I_HUMAN MKI67 FHA domain-interacting nucleolar phosphoprotein OS=Homo sapiens GN=MKI67IP PE=1 SV=1

 Score =  105 bits (263), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 52/146 (35%), Positives = 95/146 (65%), Gaps = 2/146 (1%)

Query: 55  VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
           V+Y+  +P+   E ++ ++FSQFG + R R++R+K+TG SK + F+EF   +VA++VA+ 
Sbjct: 46  VVYVRHLPNLLDETQIFSYFSQFGTVTRFRLSRSKRTGNSKGYAFVEFESEDVAKIVAET 105

Query: 115 MHGYLLFEHILQVHLIPPEHVHPKLWRGFNPRYKPVDRVQVERKLQNKERTLEEHKKLVE 174
           M+ YL  E +L+ H +PPE VH +L++ +N  +K      V+R   N+ RTL +  ++ E
Sbjct: 106 MNNYLFGERLLECHFMPPEKVHKELFKDWNIPFKQPSYPSVKR--YNRNRTLTQKLRMEE 163

Query: 175 KILKRDQKRRKRIEAAGIEYECPEIV 200
           +  K+++  RK++   GI+Y+ P ++
Sbjct: 164 RFKKKERLLRKKLAKKGIDYDFPSLI 189

Homo sapiens (taxid: 9606)

>sp|Q5RJM0|MK67I_RAT MKI67 FHA domain-interacting nucleolar phosphoprotein OS=Rattus norvegicus GN=Mki67ip PE=2 SV=1

 Score = 89.7 bits (221), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 53/155 (34%), Positives = 88/155 (56%), Gaps = 5/155 (3%)

Query: 55  VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
           V+Y+G +P    E  +  + +QFG I+R R++R+K+TG S+ F F+EF   +VA++VA+ 
Sbjct: 45  VVYLGHLPSTLSESHIYDYCAQFGDIRRFRLSRSKRTGNSRGFAFVEFESEDVAKIVAET 104

Query: 115 MHGYLLFEHILQVHLIPPEHVHPKLWRGFNPRYKPVDRVQVERKLQNKERTLEEHKKLVE 174
           M  YL  E +L    +P E VH  L+   N  + P     V+R   N++R   +  K+  
Sbjct: 105 MDNYLFGERLLSCKFMPREKVHKDLFNQCNVPFHPPSFPAVKR--YNQKRGHLQMLKMEY 162

Query: 175 KILKRDQKRRKRIEAAGIEYECPEIVGNVMPAPKK 209
           +  K+++  RK++   GI+Y  P +   V+P PKK
Sbjct: 163 RFKKKEKLLRKKLAKKGIDYSFPSL---VLPKPKK 194

Rattus norvegicus (taxid: 10116)

>sp|Q91VE6|MK67I_MOUSE MKI67 FHA domain-interacting nucleolar phosphoprotein OS=Mus musculus GN=Mki67ip PE=2 SV=1

 Score = 85.5 bits (210), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 52/156 (33%), Positives = 87/156 (55%), Gaps = 5/156 (3%)

Query: 55  VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
           V+Y+G +P    E  +  + +QFG I R R++R+K+TG SK + F+EF   +VA++VA+ 
Sbjct: 48  VVYLGHLPSTLSESHIYNYCAQFGDISRFRLSRSKRTGNSKGYAFVEFESEDVAKIVAET 107

Query: 115 MHGYLLFEHILQVHLIPPEHVHPKLWRGFNPRYKPVDRVQVERKLQNKERTLEEHKKLVE 174
           M  YL  E +L    +P + VH  L+   N  +       V+R   N++R   +  K+  
Sbjct: 108 MDNYLFGERLLSCKFMPRKKVHKDLFSQRNALFHRPSFPAVKR--YNRKRGHLQMLKMEY 165

Query: 175 KILKRDQKRRKRIEAAGIEYECPEIVGNVMPAPKKI 210
           +  K+++  RK++ A GI+Y  P +   V+P PK I
Sbjct: 166 RFKKKEKLLRKKLAAKGIDYSFPSL---VLPKPKNI 198

Mus musculus (taxid: 10090)

>sp|Q9LEB3|RBP47_NICPL Polyadenylate-binding protein RBP47 OS=Nicotiana plumbaginifolia GN=RBP47 PE=1 SV=1

 Score = 54.3 bits (129), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 24/66 (36%), Positives = 40/66 (60%)

Query: 55  VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
            ++IG +     E  + + FSQ G +  ++I RNK+TGQS+ +GF+EFN    AE V  +
Sbjct: 85  TIWIGDLQQWMDESYLHSCFSQAGEVISVKIIRNKQTGQSERYGFVEFNTHAAAEKVLQS 144

Query: 115 MHGYLL 120
            +G ++
Sbjct: 145 YNGTMM 150

Heterogeneous nuclear ribonucleoprotein (hnRNP)-protein binding the poly(A) tail of mRNA and probably involved in some steps of pre-mRNA maturation.

Nicotiana plumbaginifolia (taxid: 4092)

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	215
255580102	216	poly-A binding protein, putative [Ricinu	0.995	0.990	0.744	4e-90
449446269	212	PREDICTED: MKI67 FHA domain-interacting	0.981	0.995	0.719	3e-82
449494170	212	PREDICTED: LOW QUALITY PROTEIN: MKI67 FH	0.981	0.995	0.714	1e-81
359487818	215	PREDICTED: MKI67 FHA domain-interacting	0.897	0.897	0.761	1e-80
297806441	221	RNA recognition motif-containing protein	0.925	0.900	0.705	1e-80
356530697	214	PREDICTED: MKI67 FHA domain-interacting	0.976	0.981	0.706	5e-80
224113503	217	predicted protein [Populus trichocarpa]	0.888	0.880	0.743	7e-80
15238220	222	RNA recognition motif-containing protein	0.920	0.891	0.708	2e-79
357444529	213	MKI67 FHA domain-interacting nucleolar p	0.865	0.873	0.747	1e-74
388514199	213	unknown [Medicago truncatula]	0.865	0.873	0.741	5e-74

>gi|255580102|ref|XP_002530883.1| poly-A binding protein, putative [Ricinus communis] gi|223529536|gb|EEF31489.1| poly-A binding protein, putative [Ricinus communis]

 Score =  336 bits (862), Expect = 4e-90,   Method: Compositional matrix adjust.
 Identities = 160/215 (74%), Positives = 188/215 (87%), Gaps = 1/215 (0%)

Query: 1   MGAKQKKALKKNLKKVSSQLPVPSDKKGAADFLPLEGGPGRKLTEEKPLV-NKATVLYIG 59
           MGAK KKAL KNL+K ++     S++K  ADFLPLEGG GRKL E+K +  + ATVLYIG
Sbjct: 1   MGAKAKKALMKNLRKKAASSAQLSNEKSTADFLPLEGGSGRKLAEQKEVKKSNATVLYIG 60

Query: 60  RIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYL 119
           RIPHGFYEKEMQA+FSQFG IK+LRIARNKKTG+SKH+GFIEF DPEVAEVVAD MH YL
Sbjct: 61  RIPHGFYEKEMQAYFSQFGTIKKLRIARNKKTGKSKHYGFIEFEDPEVAEVVADCMHNYL 120

Query: 120 LFEHILQVHLIPPEHVHPKLWRGFNPRYKPVDRVQVERKLQNKERTLEEHKKLVEKILKR 179
           LFEH+LQV+LIPPE VHPKLW+GFN RYKP+D VQ+ERKLQNK+RTLEEHKKLVEKI+KR
Sbjct: 121 LFEHLLQVYLIPPEQVHPKLWKGFNYRYKPLDWVQIERKLQNKDRTLEEHKKLVEKIMKR 180

Query: 180 DQKRRKRIEAAGIEYECPEIVGNVMPAPKKIKFNE 214
           D+KR+KRIEAAG++YECP +VG + PA K+I+F+E
Sbjct: 181 DKKRQKRIEAAGLDYECPAVVGEIQPAAKRIRFDE 215

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449446269|ref|XP_004140894.1| PREDICTED: MKI67 FHA domain-interacting nucleolar phosphoprotein-like [Cucumis sativus]

 Score =  310 bits (794), Expect = 3e-82,   Method: Compositional matrix adjust.
 Identities = 154/214 (71%), Positives = 185/214 (86%), Gaps = 3/214 (1%)

Query: 1   MGAKQKKALKKNLKKVSSQLPVPSDKKGAADFLPLEGGPGRKLTEEKPLVNKATVLYIGR 60
           MGAK +KA+KK L K +   P+ SDKK +ADFLPLEGGPGRKL+ +KPL + ATVLYIGR
Sbjct: 1   MGAKARKAMKKKLNKAT---PLSSDKKESADFLPLEGGPGRKLSVQKPLESTATVLYIGR 57

Query: 61  IPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLL 120
           IPHGF+EKEM+ FF QFG +KRLRIARNKKTG+SKHFG++EF  PEVA++VAD+MH YLL
Sbjct: 58  IPHGFFEKEMEGFFGQFGKVKRLRIARNKKTGKSKHFGYVEFESPEVAKIVADSMHNYLL 117

Query: 121 FEHILQVHLIPPEHVHPKLWRGFNPRYKPVDRVQVERKLQNKERTLEEHKKLVEKILKRD 180
           +EHIL+VHLI PEHVHPKLW+GFN R++P++  ++ERK  NKERTLEEHKKLV++ILKRD
Sbjct: 118 YEHILKVHLIDPEHVHPKLWKGFNYRHRPLNWSELERKHHNKERTLEEHKKLVDRILKRD 177

Query: 181 QKRRKRIEAAGIEYECPEIVGNVMPAPKKIKFNE 214
           Q R+KRI AAGI+YECPEIVG V P PKKIKF+E
Sbjct: 178 QARQKRIRAAGIDYECPEIVGGVQPTPKKIKFDE 211

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449494170|ref|XP_004159468.1| PREDICTED: LOW QUALITY PROTEIN: MKI67 FHA domain-interacting nucleolar phosphoprotein-like [Cucumis sativus]

 Score =  308 bits (788), Expect = 1e-81,   Method: Compositional matrix adjust.
 Identities = 153/214 (71%), Positives = 184/214 (85%), Gaps = 3/214 (1%)

Query: 1   MGAKQKKALKKNLKKVSSQLPVPSDKKGAADFLPLEGGPGRKLTEEKPLVNKATVLYIGR 60
           MGAK +KA+KK L K +   P+ SDKK +ADFLPLEGGPGRKL+ +KPL + ATVLYIGR
Sbjct: 1   MGAKARKAMKKKLNKAT---PLSSDKKESADFLPLEGGPGRKLSVQKPLESTATVLYIGR 57

Query: 61  IPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLL 120
           IPHGF+EKEM+ FF QFG +K LRIARNKKTG+SKHFG++EF  PEVA++VAD+MH YLL
Sbjct: 58  IPHGFFEKEMEGFFGQFGKVKXLRIARNKKTGKSKHFGYVEFESPEVAKIVADSMHNYLL 117

Query: 121 FEHILQVHLIPPEHVHPKLWRGFNPRYKPVDRVQVERKLQNKERTLEEHKKLVEKILKRD 180
           +EHIL+VHLI PEHVHPKLW+GFN R++P++  ++ERK  NKERTLEEHKKLV++ILKRD
Sbjct: 118 YEHILKVHLIDPEHVHPKLWKGFNYRHRPLNWSELERKHHNKERTLEEHKKLVDRILKRD 177

Query: 181 QKRRKRIEAAGIEYECPEIVGNVMPAPKKIKFNE 214
           Q R+KRI AAGI+YECPEIVG V P PKKIKF+E
Sbjct: 178 QARQKRIRAAGIDYECPEIVGGVQPTPKKIKFDE 211

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359487818|ref|XP_002277092.2| PREDICTED: MKI67 FHA domain-interacting nucleolar phosphoprotein-like [Vitis vinifera] gi|298204899|emb|CBI34206.3| unnamed protein product [Vitis vinifera]

 Score =  304 bits (779), Expect = 1e-80,   Method: Compositional matrix adjust.
 Identities = 147/193 (76%), Positives = 166/193 (86%)

Query: 22  VPSDKKGAADFLPLEGGPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIK 81
           VP  KK AADFLPLEGGPG +L E++P  N  TVLYIGRIPHGFYE EM+ FF QFGA+K
Sbjct: 22  VPGHKKAAADFLPLEGGPGHELPEQEPPKNTGTVLYIGRIPHGFYENEMEGFFKQFGAVK 81

Query: 82  RLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPPEHVHPKLWR 141
           RLRIARNKKTG+SKHFGFIEF  PEVA++VA+ MH +LLFEHILQVH++PPEHVHPKLW+
Sbjct: 82  RLRIARNKKTGKSKHFGFIEFESPEVAKIVAECMHNHLLFEHILQVHVVPPEHVHPKLWK 141

Query: 142 GFNPRYKPVDRVQVERKLQNKERTLEEHKKLVEKILKRDQKRRKRIEAAGIEYECPEIVG 201
           G N  YKP+DRVQ+ERK QNKERTLE+ KKLVE I KRDQKRRKRIEAAGI+YECPEIVG
Sbjct: 142 GVNRLYKPLDRVQIERKRQNKERTLEKQKKLVEGIGKRDQKRRKRIEAAGIDYECPEIVG 201

Query: 202 NVMPAPKKIKFNE 214
              PA KKI+F+E
Sbjct: 202 ISRPASKKIRFDE 214

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297806441|ref|XP_002871104.1| RNA recognition motif-containing protein [Arabidopsis lyrata subsp. lyrata] gi|297316941|gb|EFH47363.1| RNA recognition motif-containing protein [Arabidopsis lyrata subsp. lyrata]

 Score =  304 bits (779), Expect = 1e-80,   Method: Compositional matrix adjust.
 Identities = 141/200 (70%), Positives = 169/200 (84%), Gaps = 1/200 (0%)

Query: 16  VSSQLPVPSDKKGAADFLPLEGGPGRKL-TEEKPLVNKATVLYIGRIPHGFYEKEMQAFF 74
            SSQLP+P + K +ADFLPLEGGP RK     +PL NKATVLYIGRIPHGFYE E++AFF
Sbjct: 21  ASSQLPLPQNPKPSADFLPLEGGPARKAPVTSQPLENKATVLYIGRIPHGFYETEIEAFF 80

Query: 75  SQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPPEH 134
           SQFG +KR+R+ARNKKTG+SKHFGFI+F DPEVAE+ A AM+ YLL EH+L+VH+I PEH
Sbjct: 81  SQFGTVKRVRVARNKKTGKSKHFGFIQFEDPEVAEIAAGAMNDYLLMEHMLKVHVIAPEH 140

Query: 135 VHPKLWRGFNPRYKPVDRVQVERKLQNKERTLEEHKKLVEKILKRDQKRRKRIEAAGIEY 194
           V P LW+GF   YKPVD VQ+ER+  NKERTLEEH+K+++K++KRDQKRRKRI AAGIEY
Sbjct: 141 VKPNLWKGFKCNYKPVDSVQIERRQHNKERTLEEHRKMLQKVVKRDQKRRKRIAAAGIEY 200

Query: 195 ECPEIVGNVMPAPKKIKFNE 214
           ECPE+VGN  P PK+IKF+E
Sbjct: 201 ECPELVGNTQPVPKRIKFSE 220

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356530697|ref|XP_003533917.1| PREDICTED: MKI67 FHA domain-interacting nucleolar phosphoprotein-like [Glycine max]

 Score =  302 bits (774), Expect = 5e-80,   Method: Compositional matrix adjust.
 Identities = 154/218 (70%), Positives = 179/218 (82%), Gaps = 8/218 (3%)

Query: 1   MGAKQKKALKKNLKKVSSQLPVPSDKKGAADFLPLEGGPGRKLTEEK----PLVNKATVL 56
           MG K KKA+KKNLK+ S       D    ADFLPLEGGP RKL  ++    P  N ATVL
Sbjct: 1   MGKKAKKAMKKNLKRASFNKNPSED----ADFLPLEGGPARKLAGQQKPPPPPENTATVL 56

Query: 57  YIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMH 116
           Y+GRIPHGFYEKEM+ +F QFG IKRLRIARNKK+G+S+HFGFIEF  PEVA++VAD MH
Sbjct: 57  YVGRIPHGFYEKEMEGYFGQFGTIKRLRIARNKKSGKSRHFGFIEFESPEVAKIVADTMH 116

Query: 117 GYLLFEHILQVHLIPPEHVHPKLWRGFNPRYKPVDRVQVERKLQNKERTLEEHKKLVEKI 176
            YLLFEH+LQV++IPPEHVHP++WRGFN  YKP+D VQ+ERK  +K+RTLEEHKKLVEK+
Sbjct: 117 NYLLFEHLLQVYVIPPEHVHPRIWRGFNYHYKPLDSVQIERKRHDKDRTLEEHKKLVEKV 176

Query: 177 LKRDQKRRKRIEAAGIEYECPEIVGNVMPAPKKIKFNE 214
           LK DQKRRKRIEAAGI+YECPEIVGN+ PAPKKIKF +
Sbjct: 177 LKHDQKRRKRIEAAGIDYECPEIVGNIQPAPKKIKFED 214

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224113503|ref|XP_002316513.1| predicted protein [Populus trichocarpa] gi|222865553|gb|EEF02684.1| predicted protein [Populus trichocarpa]

 Score =  302 bits (773), Expect = 7e-80,   Method: Compositional matrix adjust.
 Identities = 142/191 (74%), Positives = 168/191 (87%)

Query: 24  SDKKGAADFLPLEGGPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRL 83
           + K+ AADFLPLEGGP RKL E K L  K+ VLYIGRIPHGFYE+EM+A+FSQFG IKRL
Sbjct: 26  NGKQAAADFLPLEGGPARKLPELKELKKKSGVLYIGRIPHGFYEEEMKAYFSQFGTIKRL 85

Query: 84  RIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPPEHVHPKLWRGF 143
           RIARNKKTG+SKHFGF+EF DPEVAEVVA+ MH YLLFEH+LQV++IP EHVHPKLW+GF
Sbjct: 86  RIARNKKTGKSKHFGFMEFEDPEVAEVVAECMHNYLLFEHLLQVYVIPQEHVHPKLWKGF 145

Query: 144 NPRYKPVDRVQVERKLQNKERTLEEHKKLVEKILKRDQKRRKRIEAAGIEYECPEIVGNV 203
           N R+ PVDR+Q ERK QNKERTL+EH++LV +I+KRDQKRRK+IEAAG++YECPE VG+V
Sbjct: 146 NYRFNPVDRLQTERKRQNKERTLDEHRRLVGRIMKRDQKRRKKIEAAGLDYECPEFVGDV 205

Query: 204 MPAPKKIKFNE 214
              PKKIKF++
Sbjct: 206 KCVPKKIKFSQ 216

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15238220|ref|NP_196080.1| RNA recognition motif-containing protein [Arabidopsis thaliana] gi|14190443|gb|AAK55702.1|AF378899_1 AT5g04600/T32M21_200 [Arabidopsis thaliana] gi|7406464|emb|CAB85566.1| rna binding protein-like [Arabidopsis thaliana] gi|15810057|gb|AAL06954.1| AT5g04600/T32M21_200 [Arabidopsis thaliana] gi|17380696|gb|AAL36178.1| putative rna binding protein [Arabidopsis thaliana] gi|21689805|gb|AAM67546.1| putative RNA binding protein [Arabidopsis thaliana] gi|332003380|gb|AED90763.1| RNA recognition motif-containing protein [Arabidopsis thaliana]

 Score =  301 bits (770), Expect = 2e-79,   Method: Compositional matrix adjust.
 Identities = 141/199 (70%), Positives = 169/199 (84%), Gaps = 1/199 (0%)

Query: 17  SSQLPVPSDKKGAADFLPLEGGPGRKL-TEEKPLVNKATVLYIGRIPHGFYEKEMQAFFS 75
           SSQLP+P + K +ADFLPLEGGP RK      PL NKATVLYIGRIPHGFYE E++AFFS
Sbjct: 22  SSQLPLPQNPKPSADFLPLEGGPARKAPVTTPPLQNKATVLYIGRIPHGFYETEIEAFFS 81

Query: 76  QFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPPEHV 135
           QFG +KR+R+ARNKKTG+SKHFGFI+F DPEVAE+ A AM+ YLL EH+L+VH+I PE+V
Sbjct: 82  QFGTVKRVRVARNKKTGKSKHFGFIQFEDPEVAEIAAGAMNDYLLMEHMLKVHVIEPENV 141

Query: 136 HPKLWRGFNPRYKPVDRVQVERKLQNKERTLEEHKKLVEKILKRDQKRRKRIEAAGIEYE 195
            P LWRGF   +KPVD VQ+ER+  NKERTLEEH+K+++KI+K+DQKRRKRIEAAGIEYE
Sbjct: 142 KPNLWRGFKCNFKPVDSVQIERRQLNKERTLEEHRKMLQKIVKKDQKRRKRIEAAGIEYE 201

Query: 196 CPEIVGNVMPAPKKIKFNE 214
           CPE+VGN  P PK+IKF+E
Sbjct: 202 CPELVGNTQPVPKRIKFSE 220

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357444529|ref|XP_003592542.1| MKI67 FHA domain-interacting nucleolar phosphoprotein-like protein [Medicago truncatula] gi|355481590|gb|AES62793.1| MKI67 FHA domain-interacting nucleolar phosphoprotein-like protein [Medicago truncatula] gi|388505268|gb|AFK40700.1| unknown [Medicago truncatula]

 Score =  285 bits (728), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 139/186 (74%), Positives = 166/186 (89%)

Query: 29  AADFLPLEGGPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARN 88
           AADFLPLEGGPGRKL E K L N + VLYIGRIPHGFYEKEM+A+F QFG IKRLRI+RN
Sbjct: 28  AADFLPLEGGPGRKLPELKQLENSSPVLYIGRIPHGFYEKEMEAYFGQFGTIKRLRISRN 87

Query: 89  KKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPPEHVHPKLWRGFNPRYK 148
           KKTG+S+HFGFIEF  PEVA++VAD MH YLLFEH+LQV ++P EHVHP+LW+GFN RYK
Sbjct: 88  KKTGKSRHFGFIEFESPEVAKIVADTMHNYLLFEHLLQVFVVPSEHVHPRLWKGFNYRYK 147

Query: 149 PVDRVQVERKLQNKERTLEEHKKLVEKILKRDQKRRKRIEAAGIEYECPEIVGNVMPAPK 208
           P+D +Q+ER+L +KERTLEEHKKLV++++KRD+KRRK+IEAAGI+YECPEIVGN+  APK
Sbjct: 148 PLDTLQIERELHDKERTLEEHKKLVDRVMKRDKKRRKKIEAAGIDYECPEIVGNLQSAPK 207

Query: 209 KIKFNE 214
           KIKF +
Sbjct: 208 KIKFED 213

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388514199|gb|AFK45161.1| unknown [Medicago truncatula]

 Score =  283 bits (723), Expect = 5e-74,   Method: Compositional matrix adjust.
 Identities = 138/186 (74%), Positives = 165/186 (88%)

Query: 29  AADFLPLEGGPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARN 88
           AADFLPLEGGPGRKL E K L N + VLYIGRIPHGFYEKEM+A+F Q G IKRLRI+RN
Sbjct: 28  AADFLPLEGGPGRKLPELKQLENSSPVLYIGRIPHGFYEKEMEAYFGQLGTIKRLRISRN 87

Query: 89  KKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPPEHVHPKLWRGFNPRYK 148
           KKTG+S+HFGFIEF  PEVA++VAD MH YLLFEH+LQV ++P EHVHP+LW+GFN RYK
Sbjct: 88  KKTGKSRHFGFIEFESPEVAKIVADTMHNYLLFEHLLQVFVVPSEHVHPRLWKGFNYRYK 147

Query: 149 PVDRVQVERKLQNKERTLEEHKKLVEKILKRDQKRRKRIEAAGIEYECPEIVGNVMPAPK 208
           P+D +Q+ER+L +KERTLEEHKKLV++++KRD+KRRK+IEAAGI+YECPEIVGN+  APK
Sbjct: 148 PLDTLQIERELHDKERTLEEHKKLVDRVMKRDKKRRKKIEAAGIDYECPEIVGNLQSAPK 207

Query: 209 KIKFNE 214
           KIKF +
Sbjct: 208 KIKFED 213

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	215
TAIR|locus:2184367	222	AT5G04600 [Arabidopsis thalian	0.920	0.891	0.708	1.9e-76
ASPGD|ASPL0000073265	445	AN4346 [Emericella nidulans (t	0.874	0.422	0.409	1.5e-35
POMBASE|SPCC1827.05c	276	SPCC1827.05c "nucleolar RNA-bi	0.720	0.561	0.412	7.7e-32
ZFIN|ZDB-GENE-021231-4	269	mki67ip "mki67 (FHA domain) in	0.702	0.561	0.435	8.8e-31
UNIPROTKB|Q6GL69	276	mki67ipl "MKI67 FHA domain-int	0.655	0.510	0.426	1.8e-30
UNIPROTKB|F1RXX7	294	MKI67 "Uncharacterized protein	0.734	0.537	0.395	2.3e-30
UNIPROTKB|Q7SYS2	278	mki67ipl "MKI67 FHA domain-int	0.655	0.507	0.412	5.6e-29
CGD|CAL0002077	267	NOP15 [Candida albicans (taxid	0.702	0.565	0.385	2.4e-28
UNIPROTKB|F1NT45	276	MKI67IP "Uncharacterized prote	0.720	0.561	0.379	3.1e-28
UNIPROTKB|Q3SZM1	296	MKI67IP "MKI67 FHA domain-inte	0.730	0.530	0.388	3.1e-28

TAIR|locus:2184367 AT5G04600 [Arabidopsis thaliana (taxid:3702)]

 Score = 770 (276.1 bits), Expect = 1.9e-76, P = 1.9e-76
 Identities = 141/199 (70%), Positives = 169/199 (84%)

Query:    17 SSQLPVPSDKKGAADFLPLEGGPGRKL-TEEKPLVNKATVLYIGRIPHGFYEKEMQAFFS 75
             SSQLP+P + K +ADFLPLEGGP RK      PL NKATVLYIGRIPHGFYE E++AFFS
Sbjct:    22 SSQLPLPQNPKPSADFLPLEGGPARKAPVTTPPLQNKATVLYIGRIPHGFYETEIEAFFS 81

Query:    76 QFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPPEHV 135
             QFG +KR+R+ARNKKTG+SKHFGFI+F DPEVAE+ A AM+ YLL EH+L+VH+I PE+V
Sbjct:    82 QFGTVKRVRVARNKKTGKSKHFGFIQFEDPEVAEIAAGAMNDYLLMEHMLKVHVIEPENV 141

Query:   136 HPKLWRGFNPRYKPVDRVQVERKLQNKERTLEEHKKLVEKILKRDQKRRKRIEAAGIEYE 195
              P LWRGF   +KPVD VQ+ER+  NKERTLEEH+K+++KI+K+DQKRRKRIEAAGIEYE
Sbjct:   142 KPNLWRGFKCNFKPVDSVQIERRQLNKERTLEEHRKMLQKIVKKDQKRRKRIEAAGIEYE 201

Query:   196 CPEIVGNVMPAPKKIKFNE 214
             CPE+VGN  P PK+IKF+E
Sbjct:   202 CPELVGNTQPVPKRIKFSE 220

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0003723 "RNA binding" evidence=ISS

GO:0008150 "biological_process" evidence=ND

GO:0009507 "chloroplast" evidence=ISM

GO:0005730 "nucleolus" evidence=IDA

GO:0001510 "RNA methylation" evidence=RCA

GO:0006333 "chromatin assembly or disassembly" evidence=RCA

GO:0006606 "protein import into nucleus" evidence=RCA

GO:0051604 "protein maturation" evidence=RCA

ASPGD|ASPL0000073265 AN4346 [Emericella nidulans (taxid:162425)]

 Score = 384 (140.2 bits), Expect = 1.5e-35, P = 1.5e-35
 Identities = 81/198 (40%), Positives = 121/198 (61%)

Query:    22 VPSDKKGAADFLPLEGGPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIK 81
             +P  KK     L L+    +  + E+P      V+Y+GRIPHGFYE +M+A+FSQFG I 
Sbjct:   184 IPDSKKAKRKILKLQK-QNKAESSEQP-----GVVYVGRIPHGFYEHQMRAYFSQFGDIT 237

Query:    82 RLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPPEHVHPKLWR 141
             +LR++RN+ TG+SKH+ FIEF    VA++VA  M  YL++ HIL+   +P E +HP+LW+
Sbjct:   238 KLRLSRNRHTGKSKHYAFIEFASESVAKIVAATMDNYLMYGHILKCKYVPSEQLHPELWK 297

Query:   142 GFNPRYKPVDRVQVERKLQNKERTLEEHKKLVEKILKRDQKRRKRIEAAGIEYECPEIVG 201
             G N R+K     ++E+K  NK RT E   K +EK  KR   + ++++  G E E PE+  
Sbjct:   298 GANRRFKATPWNRIEQKRLNKGRTRENWTKNIEKEQKRRLAKAEKLKELGYEIELPELKS 357

Query:   202 -NVMPAPK---KIKFNEG 215
              + +P  K   ++K  EG
Sbjct:   358 VDEVPVQKPDEEVKAIEG 375

GO:0008150 "biological_process" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

POMBASE|SPCC1827.05c SPCC1827.05c "nucleolar RNA-binding protein NIFK (predicted)" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 349 (127.9 bits), Expect = 7.7e-32, P = 7.7e-32
 Identities = 64/155 (41%), Positives = 103/155 (66%)

Query:    41 RKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFI 100
             +K++E K L  K  VLY+GR+PHGFYEK+M+ +FSQFG + RLR++RN+KTG SKH+ FI
Sbjct:    92 KKVSENKNLQKKKGVLYVGRLPHGFYEKQMRMYFSQFGPVLRLRMSRNRKTGSSKHYAFI 151

Query:   101 EFNDPEVAEVVADAMHGYLLFEHILQVHLIPPEHVHPKLWRGFNPRYKPVDRVQVERKLQ 160
             EF   +VA VVA+ MH YLL+  +LQ  +IP + VH  +++G +  +K +    + R   
Sbjct:   152 EFESLDVANVVAETMHNYLLYGKLLQCKVIPEDQVHENMFKGADVPFKRIPHATIARLQH 211

Query:   161 NKERTLEEHKKLVEKILKRDQKRRKRIEAAGIEYE 195
              K  + E+  KL+ +  ++ + ++++++  GI  E
Sbjct:   212 EKPLSKEKADKLITRHNRKLKLKKRKLKELGITLE 246

GO:0003723 "RNA binding" evidence=ISM

GO:0005730 "nucleolus" evidence=ISS;IDA

GO:0042254 "ribosome biogenesis" evidence=ISS

ZFIN|ZDB-GENE-021231-4 mki67ip "mki67 (FHA domain) interacting nucleolar phosphoprotein (human)" [Danio rerio (taxid:7955)]

 Score = 339 (124.4 bits), Expect = 8.8e-31, P = 8.8e-31
 Identities = 67/154 (43%), Positives = 101/154 (65%)

Query:    55 VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
             VLY+G +P G +E +++++F QFG + RLR++R+KKTG SK +GF+EF   EVA++VA+ 
Sbjct:    46 VLYVGHLPRGLFEPQLKSYFEQFGKVLRLRVSRSKKTGGSKGYGFVEFECDEVAKIVAET 105

Query:   115 MHGYLLFEHILQVHLIPPEHVHPKLWRGFNPRYKPVDRVQVERKLQNKERTLEEHKKLVE 174
             M+ YL+ E I++ H+IPPE VH KL+ G    +K      V R   NK  T ++ KK+  
Sbjct:   106 MNNYLMGERIIKCHVIPPEKVHEKLFVGSIAGFKKPKYPAVTR--YNKTHTEDDVKKVGT 163

Query:   175 KILKRDQKRRKRIEAAGIEYECPEIVGNVMPAPK 208
             K+L ++ K RKR+ A GI+Y+ P     + PA K
Sbjct:   164 KLLSKESKLRKRLAAKGIDYDFPGFAAQI-PAKK 196

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0010923 "negative regulation of phosphatase activity" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

UNIPROTKB|Q6GL69 mki67ipl "MKI67 FHA domain-interacting nucleolar phosphoprotein-like" [Xenopus (Silurana) tropicalis (taxid:8364)]

 Score = 336 (123.3 bits), Expect = 1.8e-30, P = 1.8e-30
 Identities = 61/143 (42%), Positives = 95/143 (66%)

Query:    55 VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
             V+YIG IP   YE +++ +FSQFG + RLR++R+KKTG SK + ++EF   EVA++VAD 
Sbjct:    42 VIYIGHIPRALYEPQLREYFSQFGTVTRLRLSRSKKTGNSKGYAYVEFECDEVAKIVADT 101

Query:   115 MHGYLLFEHILQVHLIPPEHVHPKLWRGFNPRYKPVDRVQVERKLQNKERTLEEHKKLVE 174
             M+ YL  E +L+   +PPE VHP+L+ G   +++   +  V R   NK R+  E KK+ +
Sbjct:   102 MNNYLFCERLLKCEFVPPEKVHPRLFIGCTAKFRKPTKPAVSR--YNKRRSEAEQKKMTQ 159

Query:   175 KILKRDQKRRKRIEAAGIEYECP 197
             ++L ++ K RKR+   GI+Y+ P
Sbjct:   160 RMLSKENKVRKRLAEKGIDYDFP 182

GO:0010923 "negative regulation of phosphatase activity" evidence=ISS

UNIPROTKB|F1RXX7 MKI67 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 335 (123.0 bits), Expect = 2.3e-30, P = 2.3e-30
 Identities = 64/162 (39%), Positives = 105/162 (64%)

Query:    41 RKLTEEKPLVNKAT--VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFG 98
             R+   ++P   K T  V+Y+G +P   YE +++A+FSQFG + RLR++R+KKTG SK +G
Sbjct:    30 RRRATKQPEKQKLTPGVIYVGHLPPSLYETQIRAYFSQFGTVTRLRLSRSKKTGNSKGYG 89

Query:    99 FIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPPEHVHPKLWRGFNPRYKPVDRVQVERK 158
             F+EF   +VA + A+ M+ YL  E +L+ H+IPPE VH +L+R ++  +K      V+R 
Sbjct:    90 FVEFESEDVARIAAETMNNYLFGERLLKCHIIPPEKVHEELFREWHMPFKRPSFPAVKR- 148

Query:   159 LQNKERTLEEHKKLVEKILKRDQKRRKRIEAAGIEYECPEIV 200
               N++RTL +  ++ E+  K+++  RKR+   GI+Y  P +V
Sbjct:   149 -YNQKRTLRQKLRMEERFKKKEKSLRKRLAKKGIDYNFPSLV 189

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|Q7SYS2 mki67ipl "MKI67 FHA domain-interacting nucleolar phosphoprotein-like" [Xenopus laevis (taxid:8355)]

 Score = 322 (118.4 bits), Expect = 5.6e-29, P = 5.6e-29
 Identities = 59/143 (41%), Positives = 94/143 (65%)

Query:    55 VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
             V+YIG IP    E ++Q +F+QFG + RLR++R+KKTG SK + ++E+   EVA++VAD 
Sbjct:    42 VIYIGHIPKSLIEPQLQEYFNQFGTVTRLRLSRSKKTGNSKGYAYVEYECDEVAKIVADT 101

Query:   115 MHGYLLFEHILQVHLIPPEHVHPKLWRGFNPRYKPVDRVQVERKLQNKERTLEEHKKLVE 174
             M+ YL  E +L+   + PE VHP+L+ G N R++   +  V R   N +R  EE KK+ +
Sbjct:   102 MNNYLFCERLLKCEFVTPEKVHPRLFIGCNTRFRKPTKPAVTR--YNSKRNKEEVKKMTQ 159

Query:   175 KILKRDQKRRKRIEAAGIEYECP 197
             +++ ++ K RKR+   GI+Y+ P
Sbjct:   160 RMISKEYKLRKRLAEKGIDYDFP 182

GO:0010923 "negative regulation of phosphatase activity" evidence=ISS

CGD|CAL0002077 NOP15 [Candida albicans (taxid:5476)]

 Score = 316 (116.3 bits), Expect = 2.4e-28, P = 2.4e-28
 Identities = 59/153 (38%), Positives = 102/153 (66%)

Query:    47 KPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPE 106
             K   +K+ V+YIGR+P GF E E++ +FSQFG +  +++ARNKKTG +KH+GFIEF+  E
Sbjct:   117 KSTKSKSGVIYIGRLPSGFQESELKTYFSQFGDVINVKLARNKKTGNTKHYGFIEFDSIE 176

Query:   107 VAEVVADAMHGYLLFEHILQVHLIPPEHVHPKLWRGFNPRYKPVDRVQVERKLQNKERTL 166
             VA+V A+ M+ YLLF H+++  ++  E+ H   ++  N ++K +   ++ ++   K RT 
Sbjct:   177 VAKVAAETMNNYLLFGHLIKCEVV--ENPHEDTFKHGNRKFKVIPWKKIAKEKHEKSRTE 234

Query:   167 EEHKKLVEKILKRDQKRRKRIEAAGIEYECPEI 199
             EE K L+ K  +  QK+++ +++ GI+++   I
Sbjct:   235 EEWKVLIAKFEESKQKKQEELKSKGIDFDVSAI 267

GO:0005730 "nucleolus" evidence=IEA

GO:0030687 "preribosome, large subunit precursor" evidence=IEA

GO:0000915 "cytokinesis, actomyosin contractile ring assembly" evidence=IEA

GO:0042273 "ribosomal large subunit biogenesis" evidence=IEA

UNIPROTKB|F1NT45 MKI67IP "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 315 (115.9 bits), Expect = 3.1e-28, P = 3.1e-28
 Identities = 60/158 (37%), Positives = 98/158 (62%)

Query:    55 VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
             V+Y+G +P G  E +++ +F QFG ++RLR++R+KKTG SK + FIEF   +VA++VAD 
Sbjct:    45 VVYVGHLPRGLCEPQLRQYFEQFGTVRRLRLSRSKKTGGSKGYAFIEFESDDVAKIVADT 104

Query:   115 MHGYLLFEHILQVHLIPPEHVHPKLWRGFNPRYKPVDRVQVERKLQNKERTLEEHKKLVE 174
             M+ YL  E +L+   +PPE VH  L++     ++   +  V+R   NK R+L E  K+ +
Sbjct:   105 MNNYLFSERLLKCQFMPPERVHANLFKNSERMFQKPSQPAVKR--YNKVRSLVEKAKMAK 162

Query:   175 KILKRDQKRRKRIEAAGIEYECPEIVGNVMPAP-KKIK 211
             ++L+++   RKR+   GI+Y  P      +P   KK+K
Sbjct:   163 RLLRKENCLRKRLAEKGIKYSFPGFAAQGLPVKRKKVK 200

GO:0000166 "nucleotide binding" evidence=IEA

GO:0000794 "condensed nuclear chromosome" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005654 "nucleoplasm" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0010923 "negative regulation of phosphatase activity" evidence=IEA

UNIPROTKB|Q3SZM1 MKI67IP "MKI67 FHA domain-interacting nucleolar phosphoprotein" [Bos taurus (taxid:9913)]

 Score = 315 (115.9 bits), Expect = 3.1e-28, P = 3.1e-28
 Identities = 63/162 (38%), Positives = 104/162 (64%)

Query:    41 RKLTEEKPLVNKAT--VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFG 98
             R+ T+++    K T  V+Y+G +P   YE +++A+FSQFG + R R++R+KKTG SK +G
Sbjct:    31 RRATKQQEK-QKPTPGVIYVGHLPPTLYETQIRAYFSQFGTVTRFRLSRSKKTGNSKGYG 89

Query:    99 FIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPPEHVHPKLWRGFNPRYKPVDRVQVERK 158
             F+EF   +VA++ A+ M+ YL  E +L+ H IPPE VH +L+R ++  +K      V+R 
Sbjct:    90 FVEFESEDVAKIAAETMNNYLFGERLLKCHFIPPEKVHEELFREWHMPFKRPSYPAVKRY 149

Query:   159 LQNKERTLEEHKKLVEKILKRDQKRRKRIEAAGIEYECPEIV 200
              QN  R+L +  ++ E+  K+++  RKR+   GI+Y  P +V
Sbjct:   150 NQN--RSLVQKLRMEERFKKKEKLLRKRLAKKGIDYNFPSLV 189

GO:0010923 "negative regulation of phosphatase activity" evidence=ISS

GO:0005730 "nucleolus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005654 "nucleoplasm" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000794 "condensed nuclear chromosome" 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	215
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	7e-40
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	1e-36
smart00360	73	smart00360, RRM, RNA recognition motif	7e-18
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	2e-15
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	2e-13
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	4e-13
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	4e-13
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	9e-13
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	2e-12
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	3e-12
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	6e-12
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	8e-12
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	7e-11
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	2e-10
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	2e-10
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	3e-10
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	4e-10
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	9e-10
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	2e-09
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	2e-09
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	2e-09
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	3e-09
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	3e-09
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	5e-09
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	5e-09
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	9e-09
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	9e-09
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	1e-08
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	2e-08
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	2e-08
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	2e-08
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	2e-08
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	3e-08
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	3e-08
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	3e-08
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	3e-08
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	3e-08
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	3e-08
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	4e-08
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	4e-08
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	5e-08
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	5e-08
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	5e-08
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	5e-08
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	6e-08
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	7e-08
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	7e-08
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	8e-08
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	8e-08
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	9e-08
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	1e-07
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	1e-07
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	1e-07
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	1e-07
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	2e-07
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	3e-07
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	4e-07
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	4e-07
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	5e-07
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	6e-07
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	8e-07
cd12230	82	cd12230, RRM1_U2AF65, RNA recognition motif 1 foun	8e-07
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	1e-06
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	1e-06
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	1e-06
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	1e-06
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	1e-06
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	2e-06
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	2e-06
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	2e-06
cd12244	79	cd12244, RRM2_MSSP, RNA recognition motif 2 in the	2e-06
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	2e-06
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	3e-06
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	3e-06
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	4e-06
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	4e-06
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	4e-06
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	5e-06
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	5e-06
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	5e-06
cd12464	83	cd12464, RRM_G3BP2, RNA recognition motif in ras G	5e-06
cd12322	71	cd12322, RRM2_TDP43, RNA recognition motif 2 in TA	5e-06
cd12263	98	cd12263, RRM_ABT1_like, RNA recognition motif foun	6e-06
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	6e-06
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	7e-06
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	7e-06
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	7e-06
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	7e-06
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	7e-06
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	8e-06
cd12482	79	cd12482, RRM1_hnRNPR, RNA recognition motif 1 in v	8e-06
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	8e-06
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	8e-06
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	9e-06
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	9e-06
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	1e-05
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	1e-05
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	1e-05
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	1e-05
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	1e-05
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	1e-05
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-05
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	2e-05
cd12550	76	cd12550, RRM_II_PABPN1, RNA recognition motif in t	2e-05
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	2e-05
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	3e-05
cd12631	84	cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif	3e-05
cd12463	80	cd12463, RRM_G3BP1, RNA recognition motif found in	3e-05
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	3e-05
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	3e-05
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	3e-05
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	4e-05
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	4e-05
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	4e-05
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	4e-05
cd12551	77	cd12551, RRM_II_PABPN1L, RNA recognition motif in	5e-05
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	5e-05
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	5e-05
cd12452	88	cd12452, RRM_ARP_like, RNA recognition motif in ye	6e-05
cd12634	81	cd12634, RRM2_CELF1_2, RNA recognition motif 2 in	6e-05
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	7e-05
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	7e-05
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	8e-05
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	9e-05
cd12665	77	cd12665, RRM2_RAVER1, RNA recognition motif 2 foun	9e-05
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	1e-04
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	1e-04
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	1e-04
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	1e-04
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	1e-04
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	2e-04
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	2e-04
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	2e-04
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	2e-04
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	2e-04
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	2e-04
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	2e-04
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	2e-04
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	2e-04
cd12758	76	cd12758, RRM1_hnRPDL, RNA recognition motif 1 in h	2e-04
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	2e-04
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	2e-04
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	3e-04
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	3e-04
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	3e-04
cd12238	73	cd12238, RRM1_RBM40_like, RNA recognition motif 1	3e-04
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	3e-04
cd12598	72	cd12598, RRM1_SRSF9, RNA recognition motif 1 in ve	3e-04
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	3e-04
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	3e-04
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	3e-04
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	3e-04
cd12610	84	cd12610, RRM1_SECp43, RNA recognition motif 1 in t	4e-04
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	4e-04
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	4e-04
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	4e-04
cd12483	79	cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in v	4e-04
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	5e-04
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	5e-04
cd12245	79	cd12245, RRM_scw1_like, RNA recognition motif in y	5e-04
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	6e-04
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	7e-04
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	7e-04
cd12487	78	cd12487, RRM1_DND1, RNA recognition motif 1 found	8e-04
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	8e-04
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	9e-04
cd12773	84	cd12773, RRM2_HuR, RNA recognition motif 2 in vert	0.001
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	0.001
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	0.001
cd12595	70	cd12595, RRM1_SRSF5, RNA recognition motif 1 in ve	0.001
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	0.001
cd12458	70	cd12458, RRM_AtC3H46_like, RNA recognition motif i	0.001
cd12597	73	cd12597, RRM1_SRSF1, RNA recognition motif 1 in se	0.001
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	0.001
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	0.002
cd12472	80	cd12472, RRM1_RBMS3, RNA recognition motif 1 found	0.002
cd12646	77	cd12646, RRM_SRSF7, RNA recognition motif in verte	0.002
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	0.002
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	0.002
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	0.002
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	0.002
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	0.002
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	0.002
cd12666	77	cd12666, RRM2_RAVER2, RNA recognition motif 2 in v	0.002
cd12621	74	cd12621, RRM3_TIA1, RNA recognition motif 3 in nuc	0.003
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	0.003
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	0.003
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	0.003
cd12401	76	cd12401, RRM_eIF4H, RNA recognition motif in eukar	0.004
cd12556	85	cd12556, RRM2_RBM15B, RNA recognition motif 2 in p	0.004
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	0.004
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	0.004
cd12555	87	cd12555, RRM2_RBM15, RNA recognition motif 2 in ve	0.004

>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 =  130 bits (330), Expect = 7e-40
 Identities = 42/74 (56%), Positives = 60/74 (81%)

Query: 55  VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
           V+YIG +PHGFYE E++ +FSQFG + RLR++R+KKTG+SK + F+EF  PEVA++VA+ 
Sbjct: 1   VVYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAET 60

Query: 115 MHGYLLFEHILQVH 128
           M+ YLLFE +L+  
Sbjct: 61  MNNYLLFERLLKCK 74

This subgroup corresponds to the RRM of NIFK and Nop15p. NIFK, also termed MKI67 FHA domain-interacting nucleolar phosphoprotein, or nucleolar phosphoprotein Nopp34, is a putative RNA-binding protein interacting with the forkhead associated (FHA) domain of pKi-67 antigen in a mitosis-specific and phosphorylation-dependent manner. It is nucleolar in interphase but associates with condensed mitotic chromosomes. This family also includes Saccharomyces cerevisiae YNL110C gene encoding ribosome biogenesis protein 15 (Nop15p), also termed nucleolar protein 15. Both, NIFK and Nop15p, contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 74

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

 Score =  122 bits (309), Expect = 1e-36
 Identities = 45/77 (58%), Positives = 63/77 (81%)

Query: 55  VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
           V+YIG +PHGF EKE++ +FSQFG +K +R+AR+KKTG SKH+GFI+F +PEVA + A +
Sbjct: 1   VIYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKS 60

Query: 115 MHGYLLFEHILQVHLIP 131
           M+ YLL   +LQVH++P
Sbjct: 61  MNNYLLMGKVLQVHVLP 77

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

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

 Score = 74.2 bits (183), Expect = 7e-18
 Identities = 28/73 (38%), Positives = 47/73 (64%)

Query: 55  VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
            L++G +P    E+E++  FS+FG ++ +R+ R+K+TG+SK F F+EF   E AE   +A
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 115 MHGYLLFEHILQV 127
           ++G  L    L+V
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

>gnl|CDD|240835 cd12389, RRM2_RAVER, RNA recognition motif 2 in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins

 Score = 68.1 bits (167), Expect = 2e-15
 Identities = 21/77 (27%), Positives = 40/77 (51%)

Query: 55  VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
           +L +G +P  F +++ +   S FGA++R  +  ++ TG+SK +GF+E+     A    + 
Sbjct: 1   LLCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQ 60

Query: 115 MHGYLLFEHILQVHLIP 131
           + G  +    LQV    
Sbjct: 61  LDGKQIGGRKLQVDWAD 77

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

 Score = 62.3 bits (152), Expect = 2e-13
 Identities = 29/73 (39%), Positives = 46/73 (63%), Gaps = 1/73 (1%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L++G +P    E++++  FS+FG I+ +RI R+K  G+SK F F+EF  PE AE   +A+
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKD-GKSKGFAFVEFESPEDAEKALEAL 59

Query: 116 HGYLLFEHILQVH 128
           +G  L    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|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins

 Score = 61.9 bits (151), Expect = 4e-13
 Identities = 20/63 (31%), Positives = 38/63 (60%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           LY+G +P+   E++++  F QFG +   R+  +++TG+S+ FGF+E    E A    + +
Sbjct: 2   LYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEKL 61

Query: 116 HGY 118
           +G 
Sbjct: 62  NGT 64

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

 Score = 62.0 bits (151), Expect = 4e-13
 Identities = 18/65 (27%), Positives = 38/65 (58%)

Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
           T L +  +P    ++E+++ F   G I+  +I R++ TGQS  +GF+++ D   A+   +
Sbjct: 1   TNLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAIN 60

Query: 114 AMHGY 118
            ++G+
Sbjct: 61  TLNGF 65

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

 Score = 65.4 bits (158), Expect = 9e-13
 Identities = 26/80 (32%), Positives = 48/80 (60%)

Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
             L++G +P+   E++++  F +FG +KR+R+ R+++TG+S+ F F+EF   E AE   +
Sbjct: 116 NTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIE 175

Query: 114 AMHGYLLFEHILQVHLIPPE 133
            ++G  L    L+V    P 
Sbjct: 176 ELNGKELEGRPLRVQKAQPA 195

Length = 306

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

 Score = 59.9 bits (146), Expect = 2e-12
 Identities = 28/70 (40%), Positives = 45/70 (64%), Gaps = 1/70 (1%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L++G +P    E++++  FS+FG I+ +RI R++ TG+SK F F+EF D E AE   +A+
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDE-TGRSKGFAFVEFEDEEDAEKALEAL 59

Query: 116 HGYLLFEHIL 125
           +G  L    L
Sbjct: 60  NGKELGGREL 69

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

>gnl|CDD|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 = 59.6 bits (145), Expect = 3e-12
 Identities = 22/65 (33%), Positives = 42/65 (64%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L+I  +P+ F ++++   F+ FG +   ++  +K TGQSK FGF+ +++PE A+    AM
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 116 HGYLL 120
           +G+ +
Sbjct: 61  NGFQV 65

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|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 = 58.8 bits (143), Expect = 6e-12
 Identities = 19/62 (30%), Positives = 38/62 (61%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L++  +     EKE++A FS+FG ++ + + ++ +TG+S+ FGF+ F   E A+     +
Sbjct: 4   LFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRDL 63

Query: 116 HG 117
           +G
Sbjct: 64  NG 65

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

>gnl|CDD|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 = 58.4 bits (142), Expect = 8e-12
 Identities = 22/71 (30%), Positives = 38/71 (53%)

Query: 57  YIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMH 116
           ++G IP+   E+++   FS+ G +   R+  ++ TG+ K +GF EF D E A      ++
Sbjct: 2   FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLN 61

Query: 117 GYLLFEHILQV 127
           GY      L+V
Sbjct: 62  GYEFNGRALRV 72

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

 Score = 56.0 bits (136), Expect = 7e-11
 Identities = 19/52 (36%), Positives = 34/52 (65%)

Query: 67  EKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGY 118
           E +++  F  FG I R+ +A++K+TGQS+ F F+ F+  E AE   + ++G+
Sbjct: 13  EDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNGF 64

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

 Score = 54.9 bits (133), Expect = 2e-10
 Identities = 25/72 (34%), Positives = 39/72 (54%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           LY+G +     EK + A F  FG IK ++I  + +T + + F F+EF +PE A    D M
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 116 HGYLLFEHILQV 127
           +   LF   ++V
Sbjct: 61  NESELFGRTIRV 72

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

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

 Score = 54.6 bits (132), Expect = 2e-10
 Identities = 22/65 (33%), Positives = 35/65 (53%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           LY+  +P    ++E++A FS +G I   RI  +  TG S+  GFI F+    AE    A+
Sbjct: 3   LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL 62

Query: 116 HGYLL 120
           +G + 
Sbjct: 63  NGTIP 67

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|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 = 54.1 bits (131), Expect = 3e-10
 Identities = 23/62 (37%), Positives = 42/62 (67%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L++G++P    E++++A F ++G I+ + I R+K TGQSK   F++F+  E A+   +A+
Sbjct: 2   LFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEAL 61

Query: 116 HG 117
           HG
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|240675 cd12229, RRM_G3BP, RNA recognition motif (RRM) in ras GTPase-activating protein-binding protein G3BP1, G3BP2 and similar proteins

 Score = 54.3 bits (131), Expect = 4e-10
 Identities = 24/72 (33%), Positives = 39/72 (54%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L++G +PH   E E++ FF +FG +  +RI      G+  +FGF+ F+DPE  + +    
Sbjct: 6   LFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILANK 65

Query: 116 HGYLLFEHILQV 127
             Y   +H L V
Sbjct: 66  PIYFRGDHRLNV 77

This subfamily corresponds to the RRM domain in the G3BP family of RNA-binding and SH3 domain-binding proteins. G3BP acts at the level of RNA metabolism in response to cell signaling, possibly as RNA transcript stabilizing factors or an RNase. Members include G3BP1, G3BP2 and similar proteins. These proteins associate directly with the SH3 domain of GTPase-activating protein (GAP), which functions as an inhibitor of Ras. They all contain an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing PXXP motif(s), an RNA recognition motif (RRM), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). Length = 81

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

 Score = 53.2 bits (128), Expect = 9e-10
 Identities = 22/74 (29%), Positives = 39/74 (52%)

Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
           T L I  +P    ++E ++ F   G +K  +I R+K+TG S  FGF+++   E A+    
Sbjct: 1   TNLIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIR 60

Query: 114 AMHGYLLFEHILQV 127
            ++G  L    ++V
Sbjct: 61  TLNGLQLQNKRIKV 74

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|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 = 52.2 bits (126), Expect = 2e-09
 Identities = 23/64 (35%), Positives = 38/64 (59%), Gaps = 6/64 (9%)

Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
           T +Y+G +PHG  E+E+Q  FS FGAI+ +R+ ++      K + F+ F+  E A     
Sbjct: 1   TTVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD------KGYAFVRFDTHEAAATAIV 54

Query: 114 AMHG 117
           A++G
Sbjct: 55  AVNG 58

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

 Score = 51.9 bits (125), Expect = 2e-09
 Identities = 19/52 (36%), Positives = 33/52 (63%)

Query: 55  VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPE 106
            L++G +P     KE++ +FSQFG +K   +  +K+TG SK +GF+ F+  +
Sbjct: 1   KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRD 52

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

 Score = 52.2 bits (126), Expect = 2e-09
 Identities = 24/74 (32%), Positives = 39/74 (52%), Gaps = 4/74 (5%)

Query: 56  LYIGRIPHGFYEKEMQAF--FSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
           LY+G +   FY  E Q +  FS+ G IKR+ +  ++ T     F F+E+   E AE    
Sbjct: 1   LYVGNLS--FYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVK 58

Query: 114 AMHGYLLFEHILQV 127
            ++G  L + I++V
Sbjct: 59  YLNGTKLDDRIIRV 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|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family

 Score = 51.9 bits (125), Expect = 3e-09
 Identities = 26/80 (32%), Positives = 44/80 (55%), Gaps = 5/80 (6%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           +YIG +P+   E ++   FSQ+G I  + + R+KKTG+SK F F+ + D     +  D +
Sbjct: 12  IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNL 71

Query: 116 HGYLLFEHILQVHLIPPEHV 135
           +G  L    ++V     +HV
Sbjct: 72  NGIKLLGRTIRV-----DHV 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|240681 cd12235, RRM_PPIL4, RNA recognition motif in peptidyl-prolyl cis-trans isomerase-like 4 (PPIase) and similar proteins

 Score = 51.5 bits (124), Expect = 3e-09
 Identities = 18/43 (41%), Positives = 27/43 (62%)

Query: 67  EKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAE 109
           +++++  FS+FG IK   + R+KKTG S  + FIEF   E  E
Sbjct: 17  DEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCE 59

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

 Score = 51.1 bits (123), Expect = 5e-09
 Identities = 22/65 (33%), Positives = 41/65 (63%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           LY+G +     E +++  F  FG I+ +++ R+ +TG+SK +GFI+F D E A+   + +
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60

Query: 116 HGYLL 120
           +G+ L
Sbjct: 61  NGFEL 65

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

 Score = 51.1 bits (123), Expect = 5e-09
 Identities = 23/90 (25%), Positives = 39/90 (43%), Gaps = 6/90 (6%)

Query: 56  LYIGRIPHGFYEKEMQAF---FSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVA 112
           L++ R+P  F  +++      FSQ G     ++A     GQ + F F+E+   E AE   
Sbjct: 5   LFVDRLPKTF--RDVSILRKLFSQVGKPTFCQLAIAP-NGQPRGFAFVEYATAEDAEEAQ 61

Query: 113 DAMHGYLLFEHILQVHLIPPEHVHPKLWRG 142
            A++G+ L    ++V    P      L   
Sbjct: 62  QALNGHSLQGSPIRVSFGNPGRPGASLLNA 91

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|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score = 54.5 bits (131), Expect = 9e-09
 Identities = 22/72 (30%), Positives = 38/72 (52%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           +YIG +P    E +++     FG +K   + ++  TG SK + F E+ DP V +V   A+
Sbjct: 298 IYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAAL 357

Query: 116 HGYLLFEHILQV 127
           +G    ++ L V
Sbjct: 358 NGKDTGDNKLHV 369

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|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 = 50.2 bits (120), Expect = 9e-09
 Identities = 21/63 (33%), Positives = 36/63 (57%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L+I  +P  F + E+   F  FG +   ++  ++ T QSK FGF+ F++P  A+    AM
Sbjct: 7   LFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAM 66

Query: 116 HGY 118
           +G+
Sbjct: 67  NGF 69

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

 Score = 49.6 bits (119), Expect = 1e-08
 Identities = 20/53 (37%), Positives = 29/53 (54%)

Query: 57  YIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAE 109
           ++G + +G   +E+Q  F   G I R+ I  +K TGQ K F +IEF D    E
Sbjct: 3   FVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVE 55

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

 Score = 49.6 bits (119), Expect = 2e-08
 Identities = 20/62 (32%), Positives = 37/62 (59%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L++G +     E  + + F++ G +  ++I RNK+TG+S  +GF+EF   E AE    ++
Sbjct: 2   LWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSL 61

Query: 116 HG 117
           +G
Sbjct: 62  NG 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|240767 cd12321, RRM1_TDP43, RNA recognition motif 1 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 49.3 bits (118), Expect = 2e-08
 Identities = 20/56 (35%), Positives = 33/56 (58%)

Query: 61  IPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMH 116
           +P    E++++ +FS FG +  +++ ++ KTGQSK FGF+ F D E    V    H
Sbjct: 7   LPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVLSQRH 62

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

 Score = 49.1 bits (118), Expect = 2e-08
 Identities = 14/62 (22%), Positives = 32/62 (51%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L++G++     +  ++  FS +G +K + +  +++    + + ++EF  PE AE     M
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 116 HG 117
            G
Sbjct: 61  DG 62

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

 Score = 48.9 bits (117), Expect = 2e-08
 Identities = 19/65 (29%), Positives = 35/65 (53%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L++G +     E  +   F ++G I  +R+  +  +G+ K FG++EF+  E A+   DA+
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 116 HGYLL 120
            G  L
Sbjct: 61  GGTDL 65

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

 Score = 49.2 bits (118), Expect = 3e-08
 Identities = 19/65 (29%), Positives = 38/65 (58%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           +Y+  +     E ++++ F  FG IK   +A + +TG+ K +GFIE+ +P+ A+    +M
Sbjct: 3   IYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIASM 62

Query: 116 HGYLL 120
           + + L
Sbjct: 63  NLFDL 67

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

 Score = 49.6 bits (119), Expect = 3e-08
 Identities = 20/65 (30%), Positives = 36/65 (55%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L++GR+     E+ ++  FS++G I+RLR+ R+  TG SK + F+E+     A       
Sbjct: 6   LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRDA 65

Query: 116 HGYLL 120
           H  ++
Sbjct: 66  HKLVI 70

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

 Score = 49.1 bits (117), Expect = 3e-08
 Identities = 23/83 (27%), Positives = 41/83 (49%), Gaps = 7/83 (8%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           ++IG +     +  ++ +F QFG +    + R+  TG+S+ FGF+ F  P+    V    
Sbjct: 1   MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEV---- 56

Query: 116 HGYLLFEHILQVHLIPPEHVHPK 138
              +  EHIL   +I P+   P+
Sbjct: 57  ---MKKEHILDGKIIDPKRAIPR 76

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

 Score = 49.2 bits (118), Expect = 3e-08
 Identities = 18/51 (35%), Positives = 33/51 (64%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPE 106
           L++ R+ +   E +++  F ++G IKR+R+ R+KKTG+ + + FIEF    
Sbjct: 4   LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHER 54

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

 Score = 48.8 bits (117), Expect = 3e-08
 Identities = 20/72 (27%), Positives = 37/72 (51%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           ++IG +P+   E +++     FG +K   + ++  TG SK + F E+ DP V +     +
Sbjct: 3   IFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAGL 62

Query: 116 HGYLLFEHILQV 127
           +G  L +  L V
Sbjct: 63  NGMQLGDKKLTV 74

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

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

 Score = 48.8 bits (117), Expect = 3e-08
 Identities = 24/66 (36%), Positives = 36/66 (54%), Gaps = 1/66 (1%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAI-KRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
           L+IG +     EK +   FS FG I +  +I R+  TG SK F FI ++  E ++   +A
Sbjct: 4   LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEA 63

Query: 115 MHGYLL 120
           M+G  L
Sbjct: 64  MNGQYL 69

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

 Score = 49.0 bits (116), Expect = 4e-08
 Identities = 23/82 (28%), Positives = 44/82 (53%)

Query: 51  NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEV 110
           +  T L +  +P    ++E+++ F   G I+  ++ R+K TGQS  +GF+ + DP+ AE 
Sbjct: 2   DSKTNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEK 61

Query: 111 VADAMHGYLLFEHILQVHLIPP 132
             + ++G  L    ++V    P
Sbjct: 62  AINTLNGLRLQTKTIKVSYARP 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|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 51.9 bits (124), Expect = 4e-08
 Identities = 22/66 (33%), Positives = 34/66 (51%)

Query: 52  KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVV 111
           K   LY+  +P    + E+++ FS FG I   RI  +  TG SK  GFI F+  + A+  
Sbjct: 88  KGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRA 147

Query: 112 ADAMHG 117
              ++G
Sbjct: 148 IKTLNG 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|240861 cd12415, RRM3_RBM28_like, RNA recognition motif 3 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 48.4 bits (116), Expect = 5e-08
 Identities = 25/68 (36%), Positives = 35/68 (51%), Gaps = 5/68 (7%)

Query: 67  EKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA-----MHGYLLF 121
           E+E++  FSQFG +K  RI ++K TG SK   F++F   E A+   +A       G  L 
Sbjct: 14  EEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAADNAEDSGLSLD 73

Query: 122 EHILQVHL 129
              L V L
Sbjct: 74  GRRLIVTL 81

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

 Score = 48.4 bits (116), Expect = 5e-08
 Identities = 19/56 (33%), Positives = 37/56 (66%)

Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAE 109
           T +++G +P+   +  ++ +FSQFG I+   +  +++TG+S+ +GF+ F D E AE
Sbjct: 1   TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAE 56

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

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

 Score = 48.0 bits (115), Expect = 5e-08
 Identities = 17/51 (33%), Positives = 31/51 (60%), Gaps = 1/51 (1%)

Query: 67  EKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAE-VVADAMH 116
           E+ ++ +FS++G +    I ++  TG+S+ FGF+ F DP   + V+A   H
Sbjct: 12  EESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAKPH 62

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

 Score = 48.6 bits (115), Expect = 5e-08
 Identities = 22/82 (26%), Positives = 42/82 (51%)

Query: 51  NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEV 110
           +  T L +  +P    ++E ++ F   G I+  ++ R+K TGQS  +GF+ + DP  A+ 
Sbjct: 1   DSKTNLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADK 60

Query: 111 VADAMHGYLLFEHILQVHLIPP 132
             + ++G  L    ++V    P
Sbjct: 61  AINTLNGLKLQTKTIKVSYARP 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|240816 cd12370, RRM1_PUF60, RNA recognition motif 1 in (U)-binding-splicing factor PUF60 and similar proteins

 Score = 48.2 bits (115), Expect = 6e-08
 Identities = 21/65 (32%), Positives = 37/65 (56%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           +Y+G I     E  ++  FS FG IK + ++ +  T + K F F+E+  PE A++  + M
Sbjct: 3   VYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQM 62

Query: 116 HGYLL 120
           +G +L
Sbjct: 63  NGVML 67

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|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 = 48.2 bits (115), Expect = 7e-08
 Identities = 22/65 (33%), Positives = 34/65 (52%)

Query: 53  ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVA 112
           A  L++G+IP    EK+++  F QFG I  L + ++K TG  K   F+ +   E A    
Sbjct: 5   AIKLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALKAQ 64

Query: 113 DAMHG 117
            A+H 
Sbjct: 65  SALHE 69

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

 Score = 47.8 bits (114), Expect = 7e-08
 Identities = 22/64 (34%), Positives = 38/64 (59%)

Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
           T L +  +P    + E+++ FS  G I+  ++ R+K TGQS  +GF+ + DPE AE   +
Sbjct: 2   TNLIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAIN 61

Query: 114 AMHG 117
            ++G
Sbjct: 62  TLNG 65

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

 Score = 48.0 bits (114), Expect = 8e-08
 Identities = 23/64 (35%), Positives = 35/64 (54%)

Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
             LY+  +P    +KE++  FSQ+G I   RI R++ TG S+  GFI F+    AE    
Sbjct: 1   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIK 60

Query: 114 AMHG 117
            ++G
Sbjct: 61  GLNG 64

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

 Score = 48.2 bits (114), Expect = 8e-08
 Identities = 23/79 (29%), Positives = 42/79 (53%)

Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
           T L +  +P    ++E ++ F   G I+  ++ R+K TGQS  +GF+ + DP+ AE   +
Sbjct: 3   TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62

Query: 114 AMHGYLLFEHILQVHLIPP 132
            ++G  L    ++V    P
Sbjct: 63  TLNGLRLQTKTIKVSYARP 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|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2 and similar proteins

 Score = 47.4 bits (113), Expect = 9e-08
 Identities = 20/65 (30%), Positives = 40/65 (61%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L++G +     ++ ++A F +FG +   R+  +++TG+S+ FG+++F  PE A+   +AM
Sbjct: 2   LFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEAM 61

Query: 116 HGYLL 120
            G  L
Sbjct: 62  DGKEL 66

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

 Score = 50.7 bits (121), Expect = 1e-07
 Identities = 23/79 (29%), Positives = 44/79 (55%)

Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
           T L +  +P    ++E+++ F+  G I+  ++ R+K TGQS  +GF+ +  PE AE   +
Sbjct: 4   TNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVN 63

Query: 114 AMHGYLLFEHILQVHLIPP 132
           +++G  L    ++V    P
Sbjct: 64  SLNGLRLQNKTIKVSYARP 82

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

 Score = 47.7 bits (113), Expect = 1e-07
 Identities = 21/73 (28%), Positives = 41/73 (56%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L+I  +P  F + ++   F  FG +   ++  +K+T  SK FGF+ +++P+ A+    AM
Sbjct: 7   LFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAAIQAM 66

Query: 116 HGYLLFEHILQVH 128
           +G+ +    L+V 
Sbjct: 67  NGFQIGTKRLKVQ 79

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

 Score = 46.9 bits (112), Expect = 1e-07
 Identities = 17/63 (26%), Positives = 34/63 (53%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           +YI  +P    +++++     FG I   +   +KKT + K +GF++F+ PE A    + +
Sbjct: 3   VYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIEGL 62

Query: 116 HGY 118
           +G 
Sbjct: 63  NGR 65

This subfamily corresponds to the RRM1 of c-myc gene single-strand binding proteins (MSSP) family, including single-stranded DNA-binding protein MSSP-1 (also termed RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3). All MSSP family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity. Both, MSSP-1 and -2, have been identified as protein factors binding to a putative DNA replication origin/transcriptional enhancer sequence present upstream from the human c-myc gene in both single- and double-stranded forms. Thus, they have been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with c-MYC, the product of protooncogene c-myc. Moreover, the family includes a new member termed RNA-binding motif, single-stranded-interacting protein 3 (RBMS3), which is not a transcriptional regulator. RBMS3 binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. In addition, a putative meiosis-specific RNA-binding protein termed sporulation-specific protein 5 (SPO5, or meiotic RNA-binding protein 1, or meiotically up-regulated gene 12 protein), encoded by Schizosaccharomyces pombe Spo5/Mug12 gene, is also included in this family. SPO5 is a novel meiosis I regulator that may function in the vicinity of the Mei2 dot. . Length = 71

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

 Score = 47.1 bits (112), Expect = 1e-07
 Identities = 17/72 (23%), Positives = 35/72 (48%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L++  +     ++++  FFS    IK   +  + +TG+S+ +GF+ F   E A+     +
Sbjct: 2   LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61

Query: 116 HGYLLFEHILQV 127
               L   IL++
Sbjct: 62  KNKKLHGRILRL 73

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

 Score = 47.2 bits (113), Expect = 2e-07
 Identities = 15/65 (23%), Positives = 37/65 (56%), Gaps = 1/65 (1%)

Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
           T +Y+  +     +++++  F ++G I   ++ ++ + G+SK FGF+ F + E A+   +
Sbjct: 2   TNVYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDE-GKSKGFGFVNFENHEAAQKAVE 60

Query: 114 AMHGY 118
            ++G 
Sbjct: 61  ELNGK 65

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

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

 Score = 46.2 bits (110), Expect = 3e-07
 Identities = 19/62 (30%), Positives = 36/62 (58%), Gaps = 1/62 (1%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAE-VVADA 114
           +++G +P    E+E + +FSQFG +   ++ ++  TG+S+ FGF+ F+     E V +  
Sbjct: 2   IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSAG 61

Query: 115 MH 116
           M 
Sbjct: 62  ML 63

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

 Score = 46.1 bits (109), Expect = 4e-07
 Identities = 23/62 (37%), Positives = 34/62 (54%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           LY+  +P    +KEM+  FSQ+G I   RI  ++ TG S+  GFI F+    AE     +
Sbjct: 4   LYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIKGL 63

Query: 116 HG 117
           +G
Sbjct: 64  NG 65

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

 Score = 49.4 bits (118), Expect = 4e-07
 Identities = 29/131 (22%), Positives = 52/131 (39%), Gaps = 14/131 (10%)

Query: 41  RKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFI 100
           +K   E   + K T LY+  +     E +++  F++FG I    + ++   G+S+ F F+
Sbjct: 166 KKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGS-GRSRGFAFV 224

Query: 101 EFNDPEVAEVVADAMHGYLLFEHILQVHLIPPEHVHPKLWRGFNPRYKPVDRVQVERKLQ 160
            F   E A    + M+G            I       KL+ G   R +     + E + +
Sbjct: 225 NFEKHEDAAKAVEEMNG----------KKIGLAKEGKKLYVG---RAQKRAEREAELRRK 271

Query: 161 NKERTLEEHKK 171
            +E   E   K
Sbjct: 272 FEELQQERKMK 282

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

 Score = 49.1 bits (117), Expect = 5e-07
 Identities = 24/63 (38%), Positives = 42/63 (66%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           LY+G +     E+E++  F  FG I+ +++ R+ +TG+SK FGFI+F+D E A+   + M
Sbjct: 189 LYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVM 248

Query: 116 HGY 118
           +G+
Sbjct: 249 NGF 251

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|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 = 45.2 bits (107), Expect = 6e-07
 Identities = 19/62 (30%), Positives = 39/62 (62%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L+IG +     E+ ++  FS++G I  + + ++++T +S+ FGF+ F +P+ A+    AM
Sbjct: 3   LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAM 62

Query: 116 HG 117
           +G
Sbjct: 63  NG 64

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

 Score = 44.8 bits (107), Expect = 8e-07
 Identities = 16/53 (30%), Positives = 30/53 (56%)

Query: 57  YIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAE 109
           ++G +P    E+E++  F   G ++ +RI R++KTG  K FG++ F   +   
Sbjct: 3   FVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVA 55

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|240676 cd12230, RRM1_U2AF65, RNA recognition motif 1 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 45.2 bits (108), Expect = 8e-07
 Identities = 20/63 (31%), Positives = 30/63 (47%), Gaps = 13/63 (20%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQS---------KHFGFIEFNDPE 106
           LY+G +P G  E+E+  FF+Q  A+    +  N+  G           K+F F+EF   E
Sbjct: 4   LYVGNLPPGITEEELVDFFNQ--AMLAAGL--NQAPGNPVLSVQINPEKNFAFVEFRTVE 59

Query: 107 VAE 109
            A 
Sbjct: 60  EAT 62

The subfamily corresponds to the RRM1 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs. Length = 82

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

 Score = 44.7 bits (106), Expect = 1e-06
 Identities = 19/53 (35%), Positives = 35/53 (66%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVA 108
           L++  +P+   E +++  FS+FG +  + +A +KK+G+SK F ++ F DPE A
Sbjct: 5   LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDA 57

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

 Score = 44.6 bits (106), Expect = 1e-06
 Identities = 18/66 (27%), Positives = 30/66 (45%), Gaps = 6/66 (9%)

Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
           T LY+G +     EK+++  F QFG I+ + +         +   F+ F   E AE  A+
Sbjct: 2   TTLYVGGLGERVTEKDLRDHFYQFGEIRSITVV------PRQQCAFVTFTTREAAEKAAE 55

Query: 114 AMHGYL 119
            +   L
Sbjct: 56  RLFNKL 61

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

 Score = 44.5 bits (106), Expect = 1e-06
 Identities = 16/72 (22%), Positives = 37/72 (51%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L++  +P+   +++++ FFS+ G IKR  + ++K + + + FG++ F   E A+   +  
Sbjct: 2   LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 116 HGYLLFEHILQV 127
                    + V
Sbjct: 62  KKTKFGGRKIHV 73

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

 Score = 44.7 bits (106), Expect = 1e-06
 Identities = 21/73 (28%), Positives = 40/73 (54%), Gaps = 2/73 (2%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L++  IP  F + +++  F QFG I  + I  N++   SK FGF+ F +   A+   + +
Sbjct: 3   LHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERG--SKGFGFVTFANSADADRAREKL 60

Query: 116 HGYLLFEHILQVH 128
           HG ++    ++V+
Sbjct: 61  HGTVVEGRKIEVN 73

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

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

 Score = 44.8 bits (106), Expect = 1e-06
 Identities = 20/62 (32%), Positives = 37/62 (59%), Gaps = 1/62 (1%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPE-VAEVVADA 114
           L++G +     ++ ++ +FSQ+G +    I ++K T +S+ FGF++F DP  V  V+A  
Sbjct: 2   LFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLAGG 61

Query: 115 MH 116
            H
Sbjct: 62  PH 63

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

 Score = 43.8 bits (104), Expect = 2e-06
 Identities = 23/76 (30%), Positives = 40/76 (52%), Gaps = 1/76 (1%)

Query: 52  KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVV 111
           K+TV Y+  +P      ++   FS++G + ++ I ++K+T +SK   FI F D E A   
Sbjct: 1   KSTV-YVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKC 59

Query: 112 ADAMHGYLLFEHILQV 127
             A++   LF   L+ 
Sbjct: 60  VKALNNKELFGRTLKC 75

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|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 = 43.8 bits (104), Expect = 2e-06
 Identities = 21/72 (29%), Positives = 36/72 (50%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L++  +P    E+E++  F  FG I  + +  +K+T +SK F F+ F  PE A      +
Sbjct: 2   LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61

Query: 116 HGYLLFEHILQV 127
            G +    +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|240786 cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in yeast nucleolar protein 3 (Npl3p) and similar proteins

 Score = 43.6 bits (103), Expect = 2e-06
 Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 8/72 (11%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           LY+   P    E  ++  FS +GA+K +++  N        F F+EF   E A    D++
Sbjct: 2   LYVRPFPPDTSESAIREIFSPYGAVKEVKMISN--------FAFVEFESLESAIRAKDSV 53

Query: 116 HGYLLFEHILQV 127
           HG +L  + L V
Sbjct: 54  HGKVLNNNPLYV 65

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

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

 Score = 43.9 bits (104), Expect = 2e-06
 Identities = 20/67 (29%), Positives = 31/67 (46%), Gaps = 1/67 (1%)

Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
           T LYI  +P    E++++     +G +   RI R+ K GQS+  GF      E  E +  
Sbjct: 1   TNLYISNLPLHMDEQDLETMLKPYGQVISTRILRDSK-GQSRGVGFARMESREKCEDIIS 59

Query: 114 AMHGYLL 120
             +G  L
Sbjct: 60  KFNGKYL 66

This subfamily corresponds to the RRM2 of c-myc gene single-strand binding proteins (MSSP) family, including single-stranded DNA-binding protein MSSP-1 (also termed RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3). All MSSP family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity. Both, MSSP-1 and -2, have been identified as protein factors binding to a putative DNA replication origin/transcriptional enhancer sequence present upstream from the human c-myc gene in both single- and double-stranded forms. Thus they have been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. Moreover, they family includes a new member termed RNA-binding motif, single-stranded-interacting protein 3 (RBMS3), which is not a transcriptional regulator. RBMS3 binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. In addition, a putative meiosis-specific RNA-binding protein termed sporulation-specific protein 5 (SPO5, or meiotic RNA-binding protein 1, or meiotically up-regulated gene 12 protein), encoded by Schizosaccharomyces pombe Spo5/Mug12 gene, is also included in this family. SPO5 is a novel meiosis I regulator that may function in the vicinity of the Mei2 dot. . Length = 79

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

 Score = 44.3 bits (104), Expect = 2e-06
 Identities = 22/78 (28%), Positives = 43/78 (55%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L+I  +P  F ++++   F  FG +   ++  +K+T  SK FGF+ +++P  A+    AM
Sbjct: 10  LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQAM 69

Query: 116 HGYLLFEHILQVHLIPPE 133
           +G+ +    L+V L   +
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|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 = 43.6 bits (103), Expect = 3e-06
 Identities = 22/72 (30%), Positives = 42/72 (58%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           +++G IP+   E++++  FS+ G +   R+  +++TG+ K +GF E+ D E A      +
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 116 HGYLLFEHILQV 127
           +GY L    L+V
Sbjct: 61  NGYELNGRQLRV 72

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

 Score = 43.4 bits (103), Expect = 3e-06
 Identities = 21/53 (39%), Positives = 35/53 (66%), Gaps = 1/53 (1%)

Query: 57  YIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAE 109
           ++G IP    E+E++ FFS+FG++K ++I  + + G SK +GF+ F   E AE
Sbjct: 6   FVGGIPPDTTEEELRDFFSRFGSVKDVKIITD-RAGVSKGYGFVTFETQEDAE 57

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|240813 cd12367, RRM2_RBM45, RNA recognition motif 2 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 43.2 bits (102), Expect = 4e-06
 Identities = 19/50 (38%), Positives = 34/50 (68%)

Query: 61  IPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEV 110
           IP  + E++++  F +FG I+ + I ++K TG+SK FG+++F+ P  A V
Sbjct: 8   IPKSYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAV 57

This subfamily corresponds to the RRM2 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 74

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

 Score = 43.1 bits (102), Expect = 4e-06
 Identities = 17/54 (31%), Positives = 29/54 (53%)

Query: 67  EKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLL 120
             +++  F ++G +  + I R++ T +S+ F F+ F D   AE   DAM G  L
Sbjct: 12  PDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDGKEL 65

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

 Score = 44.6 bits (105), Expect = 4e-06
 Identities = 20/65 (30%), Positives = 36/65 (55%)

Query: 53  ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVA 112
           +T L+IG +  G  +  ++  F+ FG +   ++  +++TG+S+ FGF+ FND   A    
Sbjct: 34  STKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAI 93

Query: 113 DAMHG 117
             M G
Sbjct: 94  SEMDG 98

Length = 144

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

 Score = 43.4 bits (103), Expect = 5e-06
 Identities = 16/62 (25%), Positives = 33/62 (53%)

Query: 67  EKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQ 126
           E+++   F++FG IK L +  +++TG  K +  IE+   + A+   + ++G  L    + 
Sbjct: 20  EEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGLNGKELLGQTIS 79

Query: 127 VH 128
           V 
Sbjct: 80  VD 81

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

 Score = 43.1 bits (102), Expect = 5e-06
 Identities = 18/55 (32%), Positives = 31/55 (56%)

Query: 73  FFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQV 127
            FS FGA+  +++ R+  T + K +GF+   + E A     +++GY L   +LQV
Sbjct: 21  LFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIASLNGYRLGGRVLQV 75

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

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

 Score = 43.0 bits (102), Expect = 5e-06
 Identities = 18/68 (26%), Positives = 33/68 (48%), Gaps = 5/68 (7%)

Query: 67  EKEMQAFFSQFGAIKRLRIARNK-----KTGQSKHFGFIEFNDPEVAEVVADAMHGYLLF 121
           E+ ++  F + G ++ + IA+ K         S  +GF+EF   E A+     + G +L 
Sbjct: 14  EETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQKALKRLQGTVLD 73

Query: 122 EHILQVHL 129
            H L++ L
Sbjct: 74  GHALELKL 81

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

>gnl|CDD|240910 cd12464, RRM_G3BP2, RNA recognition motif in ras GTPase-activating protein-binding protein 2 (G3BP2) and similar proteins

 Score = 43.0 bits (101), Expect = 5e-06
 Identities = 20/51 (39%), Positives = 30/51 (58%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPE 106
           L++G +PH   E E++ FF  FG +  LRI      G+  +FGF+ F+D E
Sbjct: 8   LFVGNLPHDIDESELKEFFMSFGNVVELRINTKGVGGKLPNFGFVVFDDSE 58

This subgroup corresponds to the RRM of G3BP2, also termed GAP SH3 domain-binding protein 2, a cytoplasmic protein that interacts with both IkappaBalpha and IkappaBalpha/NF-kappaB complexes, indicating that G3BP2 may play a role in the control of nucleocytoplasmic distribution of IkappaBalpha and cytoplasmic anchoring of the IkappaBalpha/NF-kappaB complex. G3BP2 contains an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing five PXXP motifs, an RNA recognition motif (RRM domain), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). It binds to the SH3 domain of RasGAP, a multi-functional protein controlling Ras activity, through its N-terminal NTF2-like domain. The acidic domain is sufficient for the interaction of G3BP2 with the IkappaBalpha cytoplasmic retention sequence. Furthermore, G3BP2 might influence stability or translational efficiency of particular mRNAs by binding to RNA-containing structures within the cytoplasm through its RNA-binding domain. Length = 83

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

 Score = 42.6 bits (101), Expect = 5e-06
 Identities = 17/54 (31%), Positives = 32/54 (59%), Gaps = 5/54 (9%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAE 109
           +++GR+     E++++ +FSQFG +  + I +       + F F+ F DPEVA+
Sbjct: 3   VFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKP-----FRAFAFVTFADPEVAQ 51

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|240709 cd12263, RRM_ABT1_like, RNA recognition motif found in activator of basal transcription 1 (ABT1) and similar proteins

 Score = 43.3 bits (103), Expect = 6e-06
 Identities = 23/76 (30%), Positives = 41/76 (53%), Gaps = 12/76 (15%)

Query: 55  VLYIGRIPHGFYEKEMQAFFSQFGAIKRL---------RIARNKKTG-QSKHF--GFIEF 102
           ++Y+ RIP      +++   SQ+G + R+         R  R KK G + K F  G++EF
Sbjct: 2   IVYLSRIPPRMNPAKLRQLLSQYGEVGRIYLQPEDPAKRKRRKKKGGNKKKKFTEGWVEF 61

Query: 103 NDPEVAEVVADAMHGY 118
            D +VA+ VA++++  
Sbjct: 62  EDKKVAKRVAESLNNT 77

This subfamily corresponds to the RRM of novel nuclear proteins termed ABT1 and its homologous counterpart, pre-rRNA-processing protein ESF2 (eighteen S factor 2), from yeast. ABT1 associates with the TATA-binding protein (TBP) and enhances basal transcription activity of class II promoters. Meanwhile, ABT1 could be a transcription cofactor that can bind to DNA in a sequence-independent manner. The yeast ABT1 homolog, ESF2, is a component of 90S preribosomes and 5' ETS-based RNPs. It is previously identified as a putative partner of the TATA-element binding protein. However, it is primarily localized to the nucleolus and physically associates with pre-rRNA processing factors. ESF2 may play a role in ribosome biogenesis. It is required for normal pre-rRNA processing, as well as for SSU processome assembly and function. Both ABT1 and ESF2 contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 98

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

 Score = 42.7 bits (100), Expect = 6e-06
 Identities = 19/55 (34%), Positives = 32/55 (58%)

Query: 73  FFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQV 127
            F  FGA+  +++ R+  T + K FGF+   + E A +   +++GY L + ILQV
Sbjct: 21  MFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASLNGYRLGDKILQV 75

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

 Score = 42.3 bits (100), Expect = 7e-06
 Identities = 19/72 (26%), Positives = 32/72 (44%), Gaps = 3/72 (4%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           LY+G +     E  +   FSQ G IK  ++ R      +  + F+E+ D   A      M
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHG---NDPYAFVEYYDHRSAAAALQTM 57

Query: 116 HGYLLFEHILQV 127
           +G L+    ++V
Sbjct: 58  NGRLILGQEIKV 69

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

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

 Score = 42.4 bits (100), Expect = 7e-06
 Identities = 17/77 (22%), Positives = 38/77 (49%), Gaps = 1/77 (1%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L++  +P    ++E++  F + G +K +R+  N ++G+ K   ++E+ +   A      M
Sbjct: 5   LFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTN-RSGKPKGLAYVEYENESSASQAVLKM 63

Query: 116 HGYLLFEHILQVHLIPP 132
            G  + E  + V +  P
Sbjct: 64  DGTEIKEKTISVAISNP 80

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

 Score = 42.8 bits (100), Expect = 7e-06
 Identities = 18/61 (29%), Positives = 34/61 (55%)

Query: 67  EKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQ 126
           E  +   F  FGA+  +++ R+  T + K FGF+   + + A +   +++GY L + +LQ
Sbjct: 15  ESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQ 74

Query: 127 V 127
           V
Sbjct: 75  V 75

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

 Score = 42.2 bits (100), Expect = 7e-06
 Identities = 20/65 (30%), Positives = 36/65 (55%), Gaps = 1/65 (1%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           LY+  +     ++ ++  FS FG I   ++  ++K G+SK FGF+ F+ PE A      M
Sbjct: 4   LYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEK-GRSKGFGFVCFSSPEEATKAVTEM 62

Query: 116 HGYLL 120
           +G ++
Sbjct: 63  NGRII 67

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

 Score = 42.2 bits (100), Expect = 7e-06
 Identities = 19/66 (28%), Positives = 35/66 (53%), Gaps = 5/66 (7%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           +Y+G +     ++E++  F ++G ++ + +ARN   G    F F+EF DP  AE    A+
Sbjct: 2   VYVGNLGPRATKRELEDEFEKYGPLRSVWVARN-PPG----FAFVEFEDPRDAEDAVRAL 56

Query: 116 HGYLLF 121
            G  + 
Sbjct: 57  DGRRIC 62

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

 Score = 41.9 bits (99), Expect = 8e-06
 Identities = 23/61 (37%), Positives = 37/61 (60%), Gaps = 11/61 (18%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           +YIGR+P+   E++++ FF  +G I+ +    N K G    FGF+EF DP  A+   DA+
Sbjct: 2   VYIGRLPYRARERDVERFFKGYGRIREI----NLKNG----FGFVEFEDPRDAD---DAV 50

Query: 116 H 116
           +
Sbjct: 51  Y 51

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|240926 cd12482, RRM1_hnRNPR, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 42.3 bits (99), Expect = 8e-06
 Identities = 19/57 (33%), Positives = 32/57 (56%)

Query: 53  ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAE 109
            T +++G+IP   YE E+   F + G I  LR+  +  +GQ++ + FI F   E A+
Sbjct: 1   GTEVFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQ 57

This subgroup corresponds to the RRM1 of hnRNP R, which is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. It is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, and in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; it binds RNA through its RRM domains. . Length = 79

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

 Score = 41.7 bits (99), Expect = 8e-06
 Identities = 16/58 (27%), Positives = 28/58 (48%), Gaps = 5/58 (8%)

Query: 72  AFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL 129
             FS FG ++++++ + K       F F+EF+  E AE     ++G L     L+V  
Sbjct: 3   KLFSPFGNVEKIKLLKKKP-----GFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDY 55

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

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

 Score = 45.4 bits (107), Expect = 8e-06
 Identities = 35/124 (28%), Positives = 60/124 (48%), Gaps = 12/124 (9%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           +Y+G I     E  ++  F  FG IK + ++ +  TG+ K F F+E+  PE A++  + M
Sbjct: 110 VYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQM 169

Query: 116 HGYLLFEHILQVHLIPPEHVHPKLWRGFNPRYKPV-DRVQVERKLQNKERTLEEHKKLVE 174
           +G +L    ++V    P ++         P+ +P+ D VQ E K  N+      H  L E
Sbjct: 170 NGQMLGGRNIKVGR--PSNM---------PQAQPIIDMVQEEAKKFNRIYVASVHPDLSE 218

Query: 175 KILK 178
             +K
Sbjct: 219 TDIK 222

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

 Score = 43.0 bits (101), Expect = 9e-06
 Identities = 15/56 (26%), Positives = 29/56 (51%)

Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAE 109
             L++  +P+   E+ +   FS+FG+++      +K TG++K  GF+ F D     
Sbjct: 2   FTLFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYN 57

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

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

 Score = 41.8 bits (99), Expect = 9e-06
 Identities = 14/40 (35%), Positives = 27/40 (67%)

Query: 67  EKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPE 106
           E+++  FFS+ G ++ +RI R++ + +SK   ++EF D E
Sbjct: 13  ERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEE 52

This subfamily corresponds to the RRM1 of RNA-binding protein 39 (RBM39), RNA-binding protein 23 (RBM23) and similar proteins. RBM39 (also termed HCC1) is a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor. . Length = 73

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

 Score = 42.4 bits (99), Expect = 1e-05
 Identities = 18/61 (29%), Positives = 34/61 (55%)

Query: 67  EKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQ 126
           E  +   F  FGA+  +++ R+  T + K FGF+   + + A +   +++GY L + +LQ
Sbjct: 17  ESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQ 76

Query: 127 V 127
           V
Sbjct: 77  V 77

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

 Score = 42.2 bits (99), Expect = 1e-05
 Identities = 17/64 (26%), Positives = 33/64 (51%)

Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
           T LY+  +P    E E++  F  +G I +  + R+K TG  +   F+ ++  E A+    
Sbjct: 1   TNLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAIS 60

Query: 114 AMHG 117
           +++G
Sbjct: 61  SLNG 64

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|241023 cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 42.2 bits (99), Expect = 1e-05
 Identities = 17/57 (29%), Positives = 34/57 (59%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVA 112
           L++G +     E ++   FSQFG +++  +  +K+TG+ + FGF+ F + + A+  A
Sbjct: 2   LFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAA 58

This subgroup corresponds to the RRM2 of hnRNP A0, a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

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

 Score = 42.2 bits (100), Expect = 1e-05
 Identities = 18/50 (36%), Positives = 27/50 (54%), Gaps = 2/50 (4%)

Query: 67  EKEMQAFFSQFGA--IKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
           E+++    S   +  IK +R+ R+K TG S+ F F+EF   E A    DA
Sbjct: 16  EEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMDA 65

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

 Score = 42.0 bits (98), Expect = 1e-05
 Identities = 19/79 (24%), Positives = 40/79 (50%)

Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
           T L +  +P    + E+++ FS  G ++  ++ R+K  G S  +GF+ + + + AE   +
Sbjct: 2   TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAIN 61

Query: 114 AMHGYLLFEHILQVHLIPP 132
            ++G  L    ++V    P
Sbjct: 62  TLNGLRLQSKTIKVSYARP 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|241098 cd12654, RRM3_HuB, RNA recognition motif 3 in vertebrate Hu-antigen B (HuB)

 Score = 42.0 bits (98), Expect = 1e-05
 Identities = 18/61 (29%), Positives = 34/61 (55%)

Query: 67  EKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQ 126
           E  +   F  FGA+  +++ R+  T + K FGF+   + + A +   +++GY L + +LQ
Sbjct: 17  ESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQ 76

Query: 127 V 127
           V
Sbjct: 77  V 77

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

 Score = 44.8 bits (106), Expect = 2e-05
 Identities = 22/80 (27%), Positives = 44/80 (55%), Gaps = 1/80 (1%)

Query: 41  RKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFI 100
            +L +E+ +  +   LY+  +     +++++  FS+ G I   ++  ++K G S+ FGF+
Sbjct: 273 EELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEK-GVSRGFGFV 331

Query: 101 EFNDPEVAEVVADAMHGYLL 120
            F++PE A      MHG +L
Sbjct: 332 CFSNPEEANRAVTEMHGRML 351

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

 Score = 41.5 bits (97), Expect = 2e-05
 Identities = 23/78 (29%), Positives = 40/78 (51%), Gaps = 6/78 (7%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           +++G +     +K+++ +F++FG +    I  +  TG+S+ FGFI F D    E V +  
Sbjct: 2   MFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQK 61

Query: 116 HGYLLFEHILQVHLIPPE 133
                 EH L   LI P+
Sbjct: 62  ------EHRLDGRLIDPK 73

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|240994 cd12550, RRM_II_PABPN1, RNA recognition motif in type II polyadenylate-binding protein 2 (PABP-2) and similar proteins

 Score = 41.3 bits (97), Expect = 2e-05
 Identities = 18/51 (35%), Positives = 32/51 (62%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPE 106
           +Y+G + +G   +E++A F   G++ R+ I  +K +G  K F +IEF+D E
Sbjct: 2   VYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKE 52

This subgroup corresponds to the RRM of PABP-2, also termed poly(A)-binding protein 2, or nuclear poly(A)-binding protein 1 (PABPN1), or poly(A)-binding protein II (PABII), which is a ubiquitously expressed type II nuclear poly(A)-binding protein that directs the elongation of mRNA poly(A) tails during pre-mRNA processing. Although PABP-2 binds poly(A) with high affinity and specificity as type I poly(A)-binding proteins, it contains only one highly conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, PABP-2 possesses an acidic N-terminal domain that is essential for the stimulation of PAP, and an arginine-rich C-terminal domain. . Length = 76

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

 Score = 41.2 bits (96), Expect = 2e-05
 Identities = 22/62 (35%), Positives = 34/62 (54%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           LY+  +P    +KE++  FSQ+G I   RI  ++ TG S+  GFI F+    AE     +
Sbjct: 5   LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 64

Query: 116 HG 117
           +G
Sbjct: 65  NG 66

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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 40.6 bits (96), Expect = 3e-05
 Identities = 21/62 (33%), Positives = 37/62 (59%), Gaps = 2/62 (3%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           LY+  +P    E++++ FFS +G ++ +R+ RNK   + + F F+EF  PE AE     +
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKD--RPRGFAFVEFASPEDAEAALKKL 58

Query: 116 HG 117
           +G
Sbjct: 59  NG 60

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

>gnl|CDD|241075 cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif 1 in CUGBP Elav-like family member CELF-1, CELF-2, Drosophila melanogaster Bruno protein and similar proteins

 Score = 40.9 bits (96), Expect = 3e-05
 Identities = 19/66 (28%), Positives = 38/66 (57%), Gaps = 2/66 (3%)

Query: 53  ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTG--QSKHFGFIEFNDPEVAEV 110
           A  +++G+IP  + EK+++  F Q+GA+ ++ + R++     QSK   F+ F   + A  
Sbjct: 1   AIKMFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTRKAALE 60

Query: 111 VADAMH 116
             +A+H
Sbjct: 61  AQNALH 66

This subgroup corresponds to the RRM1 of CELF-1, CELF-2 and Bruno protein. CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR) belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in regulation of pre-mRNA splicing, and control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. The human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It binds specifically to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it binds preferentially to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contains three highly conserved RRMs. It binds to RNA via the first two RRMs, which are also important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. This subgroup also includes Drosophila melanogaster Bruno protein, which plays a central role in regulation of Oskar (Osk) expression in flies. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. . Length = 84

>gnl|CDD|240909 cd12463, RRM_G3BP1, RNA recognition motif found in ras GTPase-activating protein-binding protein 1 (G3BP1) and similar proteins

 Score = 41.1 bits (96), Expect = 3e-05
 Identities = 19/51 (37%), Positives = 31/51 (60%), Gaps = 3/51 (5%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPE 106
           L++G +PH   + E++ FF Q+G +  LRI      G+  +FGF+ F+D E
Sbjct: 6   LFVGNLPHDVDKSELKEFFQQYGNVVELRI---NSGGKLPNFGFVVFDDSE 53

This subgroup corresponds to the RRM of G3BP1, also termed ATP-dependent DNA helicase VIII (DH VIII), or GAP SH3 domain-binding protein 1, which has been identified as a phosphorylation-dependent endoribonuclease that interacts with the SH3 domain of RasGAP, a multi-functional protein controlling Ras activity. The acidic RasGAP binding domain of G3BP1 harbors an arsenite-regulated phosphorylation site and dominantly inhibits stress granule (SG) formation. G3BP1 also contains an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an RNA recognition motif (RRM domain), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). The RRM domain and RGG-rich region are canonically associated with RNA binding. G3BP1 co-immunoprecipitates with mRNAs. It binds to and cleaves the 3'-untranslated region (3'-UTR) of the c-myc mRNA in a phosphorylation-dependent manner. Thus, G3BP1 may play a role in coupling extra-cellular stimuli to mRNA stability. It has been shown that G3BP1 is a novel Dishevelled-associated protein that is methylated upon Wnt3a stimulation and that arginine methylation of G3BP1 regulates both Ctnnb1 mRNA and canonical Wnt/beta-catenin signaling. Furthermore, G3BP1 can be associated with the 3'-UTR of beta-F1 mRNA in cytoplasmic RNA-granules, demonstrating that G3BP1 may specifically repress the translation of the transcript. Length = 80

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

 Score = 40.7 bits (96), Expect = 3e-05
 Identities = 13/34 (38%), Positives = 26/34 (76%)

Query: 73  FFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPE 106
            FS++ + ++ ++ R+K+TG+SK +GF+ F+DP 
Sbjct: 26  AFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPN 59

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

 Score = 40.4 bits (95), Expect = 3e-05
 Identities = 18/54 (33%), Positives = 30/54 (55%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAE 109
           +Y+G IP+   E E++++FS  G I+ L +     TG+ +   FI F   E A+
Sbjct: 1   VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAK 54

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

 Score = 40.6 bits (96), Expect = 3e-05
 Identities = 15/54 (27%), Positives = 27/54 (50%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAE 109
           LY+G +     E  +   FS  G +  +R+ R+  T +S  + ++ F +P  AE
Sbjct: 2   LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAE 55

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

 Score = 43.4 bits (102), Expect = 4e-05
 Identities = 18/54 (33%), Positives = 32/54 (59%)

Query: 74  FSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQV 127
           F  FGA++ ++I R+  T Q K +GF+   + + A +   +++GY L   +LQV
Sbjct: 290 FGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQV 343

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

 Score = 40.4 bits (95), Expect = 4e-05
 Identities = 18/48 (37%), Positives = 30/48 (62%)

Query: 70  MQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHG 117
           ++A F+ FG I   R+ ++ +TG+SK +GF+ F   E AE    +M+G
Sbjct: 16  LRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSMNG 63

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|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 = 40.3 bits (95), Expect = 4e-05
 Identities = 19/64 (29%), Positives = 33/64 (51%), Gaps = 5/64 (7%)

Query: 68  KEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQV 127
           KE++  FS FG +K +R+ + K  G  + F F+EF   + A+   +A+       H+   
Sbjct: 15  KELRELFSPFGQVKSVRLPK-KFDGSHRGFAFVEFVTKQEAQNAMEALKS----THLYGR 69

Query: 128 HLIP 131
           HL+ 
Sbjct: 70  HLVL 73

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|240736 cd12290, RRM1_LARP7, RNA recognition motif 1 in La-related protein 7 (LARP7) and similar proteins

 Score = 40.4 bits (95), Expect = 4e-05
 Identities = 19/54 (35%), Positives = 31/54 (57%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAE 109
           +Y+  +P     + ++A FS++G +  + + R K TG  K F FIEF  PE A+
Sbjct: 2   VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQ 55

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

 Score = 40.2 bits (94), Expect = 5e-05
 Identities = 17/47 (36%), Positives = 29/47 (61%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEF 102
           +Y+G + +G   +E++A FS  G I R+ I  +K +G  K + +IEF
Sbjct: 2   VYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEF 48

This subgroup corresponds to the RRM of ePABP-2, also termed embryonic poly(A)-binding protein 2, or poly(A)-binding protein nuclear-like 1 (PABPN1L). ePABP-2 is a novel embryonic-specific cytoplasmic type II poly(A)-binding protein that is expressed during the early stages of vertebrate development and in adult ovarian tissue. It may play an important role in the poly(A) metabolism of stored mRNAs during early vertebrate development. ePABP-2 shows significant sequence similarity to the ubiquitously expressed nuclear polyadenylate-binding protein 2 (PABP-2 or PABPN1). Like PABP-2, ePABP-2 contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, it possesses an acidic N-terminal domain predicted to form a coiled-coil and an arginine-rich C-terminal domain. . Length = 77

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

 Score = 39.9 bits (94), Expect = 5e-05
 Identities = 15/54 (27%), Positives = 35/54 (64%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAE 109
           L++G +     E++++ +FSQ+G ++ + I  +K+TG+ + F F+ F+D +  +
Sbjct: 2   LFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVD 55

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

 Score = 40.5 bits (94), Expect = 5e-05
 Identities = 22/62 (35%), Positives = 34/62 (54%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           LY+  +P    +KE++  FSQ+G I   RI  ++ TG S+  GFI F+    AE     +
Sbjct: 8   LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 67

Query: 116 HG 117
           +G
Sbjct: 68  NG 69

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|240898 cd12452, RRM_ARP_like, RNA recognition motif in yeast asparagine-rich protein (ARP) and similar proteins

 Score = 40.2 bits (94), Expect = 6e-05
 Identities = 24/79 (30%), Positives = 37/79 (46%), Gaps = 7/79 (8%)

Query: 55  VLYIGRIPHGFYEKEMQAFFSQFG----AIKRLRIARNKKTGQSKH--FGFIEFNDPEVA 108
           VLYI  +P    + E++++F+Q+G    A   L+         SK    GF  F   E A
Sbjct: 2   VLYISNLPPDTTQLELESWFTQYGVRPVAFWTLKTPDEDAYVSSKDSISGFAVFQSHEEA 61

Query: 109 EVVADAMHGYLLFEHILQV 127
              A A++G  L E  ++V
Sbjct: 62  M-EALALNGRCLGERAIEV 79

This subfamily corresponds to the RRM of ARP, also termed NRP1, encoded by Saccharomyces cerevisiae YDL167C. Although its exact biological function remains unclear, ARP contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), two Ran-binding protein zinc fingers (zf-RanBP), and an asparagine-rich region. It may possess RNA-binding and zinc ion binding activities. Additional research had indicated that ARP may function as a factor involved in the stress response. . Length = 88

>gnl|CDD|241078 cd12634, RRM2_CELF1_2, RNA recognition motif 2 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins

 Score = 40.0 bits (93), Expect = 6e-05
 Identities = 20/61 (32%), Positives = 30/61 (49%), Gaps = 1/61 (1%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L+IG +     E +++  FS FG I+  RI R    G S+   F+ F    +A+    AM
Sbjct: 4   LFIGMVSKKCNENDIRVMFSPFGQIEECRILRGPD-GLSRGCAFVTFTTRAMAQTAIKAM 62

Query: 116 H 116
           H
Sbjct: 63  H 63

This subgroup corresponds to the RRM2 of CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. Human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It binds specifically to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it preferentially binds to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contains three highly conserved RRMs. It binds to RNA via the first two RRMs, which are also important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. . Length = 81

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

 Score = 39.7 bits (93), Expect = 7e-05
 Identities = 19/62 (30%), Positives = 36/62 (58%), Gaps = 3/62 (4%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L++G +     E E++A F + G I+R+R+   + +G+ K F F++F + E A    +A+
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFAT---NAL 57

Query: 116 HG 117
            G
Sbjct: 58  KG 59

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

 Score = 39.5 bits (93), Expect = 7e-05
 Identities = 17/57 (29%), Positives = 30/57 (52%), Gaps = 4/57 (7%)

Query: 67  EKEMQAFFSQFGAIKRLRIARNKKTGQSKH---FGFIEFNDPEVAEVVADAMHGYLL 120
           E +++  FS+FG ++ +RI + +   Q +    F F+ F D   AE  A  ++G  L
Sbjct: 14  EDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAE-NALQLNGTEL 69

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

 Score = 39.5 bits (93), Expect = 8e-05
 Identities = 16/51 (31%), Positives = 36/51 (70%)

Query: 67  EKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHG 117
           E++++  FS++G I+++++  ++KTG+S+ FGF+ F   E A+   + ++G
Sbjct: 13  ERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNG 63

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|240892 cd12446, RRM_RBM25, RNA recognition motif in eukaryotic RNA-binding protein 25 and similar proteins

 Score = 39.5 bits (93), Expect = 9e-05
 Identities = 17/53 (32%), Positives = 29/53 (54%)

Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPE 106
           T +++G IP G  +  ++    + G +   +  ++  TG+ K FGF EF DPE
Sbjct: 1   TTVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPE 53

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|241109 cd12665, RRM2_RAVER1, RNA recognition motif 2 found in vertebrate ribonucleoprotein PTB-binding 1 (raver-1)

 Score = 39.2 bits (91), Expect = 9e-05
 Identities = 19/74 (25%), Positives = 36/74 (48%)

Query: 55  VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
           +L I  +P  + +++ +     FG ++R  +  ++ TG SK +GF+E+   + A      
Sbjct: 1   LLCIANLPPTYTQQQFEELVRPFGNLERCFLVYSETTGHSKGYGFVEYMKKDSAARAKSD 60

Query: 115 MHGYLLFEHILQVH 128
           + G  L    L VH
Sbjct: 61  LLGKQLGSRTLYVH 74

This subgroup corresponds to the RRM2 of raver-1, 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-1 contains 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 PTB-binding [SG][IL]LGxxP motifs. Raver1 binds to PTB through the PTB-binding motifs at its C-terminal half, and binds to other partners, such as RNA having the sequence UCAUGCAGUCUG, through its N-terminal RRMs. Interestingly, the 12-nucleotide RNA having the sequence UCAUGCAGUCUG with micromolar affinity is found in vinculin mRNA. Additional research indicates that the RRM1 of raver-1 directs its interaction with the tail domain of activated vinculin. Then the raver1/vinculin tail (Vt) complex binds to vinculin mRNA, which is permissive for vinculin binding to F-actin. . Length = 77

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

 Score = 39.4 bits (92), Expect = 1e-04
 Identities = 19/54 (35%), Positives = 33/54 (61%), Gaps = 1/54 (1%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAE 109
           +++G I     E +++ FFSQ+G +K ++I  N + G SK +GF+ F   E A+
Sbjct: 5   IFVGGIDFKTNENDLRKFFSQYGTVKEVKIV-NDRAGVSKGYGFVTFETQEDAQ 57

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|240718 cd12272, RRM2_PHIP1, RNA recognition motif 2 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 38.9 bits (91), Expect = 1e-04
 Identities = 18/55 (32%), Positives = 31/55 (56%), Gaps = 1/55 (1%)

Query: 55  VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAE 109
            +YIG +     E +++ FF     I  +R+A +K+TG+ K FG ++F D E  +
Sbjct: 1   TVYIGNLAWDITEDDVREFFKG-CEITSVRLATDKETGEFKGFGHVDFADEESLD 54

The CD corresponds to the RRM2 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA. . Length = 72

>gnl|CDD|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 = 38.8 bits (91), Expect = 1e-04
 Identities = 16/67 (23%), Positives = 30/67 (44%), Gaps = 6/67 (8%)

Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
           T +++G +     E E+++ F  FG I  ++I         K  GF++F     AE    
Sbjct: 2   TTVFVGGLDPAVTEDELRSLFGPFGEIVYVKIP------PGKGCGFVQFVHRAAAEAAIQ 55

Query: 114 AMHGYLL 120
            + G ++
Sbjct: 56  QLQGTII 62

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|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 = 1e-04
 Identities = 18/61 (29%), Positives = 32/61 (52%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           ++IG +        ++ +FS+FG I+   + R+  T +S+ FGF+ F DP   + V    
Sbjct: 2   MFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVLAQP 61

Query: 116 H 116
           H
Sbjct: 62  H 62

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

 Score = 38.7 bits (90), Expect = 1e-04
 Identities = 23/78 (29%), Positives = 40/78 (51%), Gaps = 6/78 (7%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           +++G +     +K+++ +FS+FG +    I  +  TG+S+ FGF+ F D    E V D  
Sbjct: 1   MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLD-- 58

Query: 116 HGYLLFEHILQVHLIPPE 133
                 EH L   +I P+
Sbjct: 59  ----QKEHKLDGRVIDPK 72

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

 Score = 38.7 bits (91), Expect = 2e-04
 Identities = 15/74 (20%), Positives = 32/74 (43%), Gaps = 1/74 (1%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           + +  +P    E  ++  F   G +  +++ R +  G+S+ FGF+ F   E A+      
Sbjct: 3   IIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTR-DGKSRRFGFVGFKSEEDAQQAVKYF 61

Query: 116 HGYLLFEHILQVHL 129
           +   +    + V L
Sbjct: 62  NKTFIDTSKISVEL 75

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

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

 Score = 38.6 bits (90), Expect = 2e-04
 Identities = 19/45 (42%), Positives = 29/45 (64%), Gaps = 1/45 (2%)

Query: 73  FFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPE-VAEVVADAMH 116
           +FS+FG IK   + R+  T +S+ FGF+ F+DP  V +V+A   H
Sbjct: 18  YFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVLAQGPH 62

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

 Score = 38.4 bits (90), Expect = 2e-04
 Identities = 20/75 (26%), Positives = 33/75 (44%), Gaps = 3/75 (4%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNK---KTGQSKHFGFIEFNDPEVAEVVA 112
           L+IG +     E  +   FS++G IK+     +K     GQ + + F+ F   E AE   
Sbjct: 2   LWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKAL 61

Query: 113 DAMHGYLLFEHILQV 127
            +++G       L V
Sbjct: 62  KSLNGKTALGKKLVV 76

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|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 = 38.5 bits (90), Expect = 2e-04
 Identities = 17/52 (32%), Positives = 27/52 (51%), Gaps = 2/52 (3%)

Query: 57  YIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVA 108
           ++G I     E +++ FFS  G + R+R+  +     S  F F+EF D E A
Sbjct: 4   HVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGD--RQHSARFAFVEFADAESA 53

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

 Score = 38.4 bits (90), Expect = 2e-04
 Identities = 20/65 (30%), Positives = 35/65 (53%), Gaps = 2/65 (3%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L++G +     + +++ FF + G +  +RIA++   G+SK FG +EF   E A+  A   
Sbjct: 2   LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDD-GRSKGFGHVEFATEEGAQ-KALEK 59

Query: 116 HGYLL 120
            G  L
Sbjct: 60  SGEEL 64

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

>gnl|CDD|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 = 38.4 bits (90), Expect = 2e-04
 Identities = 12/54 (22%), Positives = 28/54 (51%), Gaps = 2/54 (3%)

Query: 67  EKEMQAFFSQFGAI--KRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGY 118
           +++++   ++ G +  K ++   +K  G+SK F ++EF     A  V + + G 
Sbjct: 12  DEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKEKLEGR 65

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|240784 cd12338, RRM1_SRSF1_like, RNA recognition motif 1 in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins

 Score = 38.1 bits (89), Expect = 2e-04
 Identities = 22/74 (29%), Positives = 39/74 (52%), Gaps = 3/74 (4%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           +Y+G +P    E++++  F ++G IK + + +N++ G    F F+EF DP  AE      
Sbjct: 2   IYVGNLPGDIRERDIEDLFYKYGPIKAIDL-KNRRRGPP--FAFVEFEDPRDAEDAVRGR 58

Query: 116 HGYLLFEHILQVHL 129
            GY    + L+V  
Sbjct: 59  DGYDFDGYRLRVEF 72

This subgroup corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C), and plant pre-mRNA-splicing factor SF2 (SR1). SRSF1 is a shuttling SR protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF9 has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. It can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. Both, SRSF1 and SRSF9, contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RS domains rich in serine-arginine dipeptides. In contrast, SF2 contains two N-terminal RRMs and a C-terminal PSK domain rich in proline, serine and lysine residues. . Length = 72

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

 Score = 38.3 bits (90), Expect = 2e-04
 Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 5/72 (6%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L +  +     ++E+++ FSQFG +K +R    +         F+EF D   AE   DA+
Sbjct: 4   LLVFNLDSPISDQELRSLFSQFGEVKDIRETPLR-----PSQKFVEFYDIRAAEAALDAL 58

Query: 116 HGYLLFEHILQV 127
           +G       L+V
Sbjct: 59  NGRPFLGGRLKV 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|240846 cd12400, RRM_Nop6, RNA recognition motif in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and similar proteins

 Score = 38.1 bits (89), Expect = 2e-04
 Identities = 22/66 (33%), Positives = 37/66 (56%), Gaps = 1/66 (1%)

Query: 55  VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
           +L++G +P+    +++ A F   GA   +R+  +KKTG+SK   F+EF+  E     A  
Sbjct: 2   ILFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMT-KALK 60

Query: 115 MHGYLL 120
           +H  LL
Sbjct: 61  LHHTLL 66

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

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

 Score = 38.4 bits (89), Expect = 2e-04
 Identities = 23/78 (29%), Positives = 39/78 (50%), Gaps = 6/78 (7%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           ++IG +     +K++  + S+FG +    I  +  TG+S+ FGF+ F D    + V +  
Sbjct: 2   MFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLE-- 59

Query: 116 HGYLLFEHILQVHLIPPE 133
               L EH L   LI P+
Sbjct: 60  ----LKEHKLDGKLIDPK 73

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

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

 Score = 38.3 bits (90), Expect = 2e-04
 Identities = 13/51 (25%), Positives = 26/51 (50%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPE 106
           L++G +     E +++  FS+FG +  + I + K  G  + F +I+    E
Sbjct: 2   LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSE 52

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

 Score = 38.0 bits (88), Expect = 2e-04
 Identities = 16/38 (42%), Positives = 24/38 (63%), Gaps = 1/38 (2%)

Query: 78  GAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           G+I   RI  ++ TG SK FGF++F+  E A+   +AM
Sbjct: 23  GSI-AARIVTDRDTGSSKGFGFVDFSSEEDAKAAKEAM 59

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

 Score = 38.0 bits (89), Expect = 3e-04
 Identities = 15/54 (27%), Positives = 32/54 (59%), Gaps = 1/54 (1%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAE 109
           +++  + +   E E++  FS+ G I  +R+ +N K G+SK + ++EF + E  +
Sbjct: 2   VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYK-GKSKGYAYVEFENEESVQ 54

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

 Score = 37.9 bits (89), Expect = 3e-04
 Identities = 18/53 (33%), Positives = 28/53 (52%), Gaps = 1/53 (1%)

Query: 68  KEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLL 120
           K +   FS FG I   ++A ++  G SK +GF+ F   E A    + ++G LL
Sbjct: 17  KALYDTFSAFGNILSCKVATDEN-GGSKGYGFVHFETEEAAVRAIEKVNGMLL 68

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

 Score = 38.1 bits (89), Expect = 3e-04
 Identities = 14/57 (24%), Positives = 30/57 (52%)

Query: 67  EKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEH 123
           E +++  F+ FG I+ + + ++K+T +SK   +++F     A    + M+G  L   
Sbjct: 16  EDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNGKCLGGD 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|240684 cd12238, RRM1_RBM40_like, RNA recognition motif 1 in RNA-binding protein 40 (RBM40) and similar proteins

 Score = 38.0 bits (89), Expect = 3e-04
 Identities = 15/72 (20%), Positives = 28/72 (38%), Gaps = 3/72 (4%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L +  +P    E + +     FGA     ++R    G+ K+  F  F++ + A      +
Sbjct: 2   LLVRHLPPELSEDDKEDLLKHFGASSVRVMSRR---GKLKNTAFATFDNEQAASQALSRL 58

Query: 116 HGYLLFEHILQV 127
           H   +    L V
Sbjct: 59  HQLKILGKRLVV 70

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

 Score = 37.8 bits (88), Expect = 3e-04
 Identities = 15/58 (25%), Positives = 34/58 (58%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
           +++G +     E +++ +FSQFG ++   +  +K+T + + FGF+ F   +V + V +
Sbjct: 2   IFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCE 59

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

>gnl|CDD|241042 cd12598, RRM1_SRSF9, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 9 (SRSF9)

 Score = 37.9 bits (88), Expect = 3e-04
 Identities = 19/62 (30%), Positives = 32/62 (51%), Gaps = 6/62 (9%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           +Y+G +P    EK+++  F ++G I+ + +   K       F F+ F DP  AE   DA+
Sbjct: 2   IYVGNLPSDVREKDLEDLFYKYGRIRDIEL---KNRRGLVPFAFVRFEDPRDAE---DAV 55

Query: 116 HG 117
            G
Sbjct: 56  FG 57

This subgroup corresponds to the RRM1 of SRSF9, also termed pre-mRNA-splicing factor SRp30C. SRSF9 is an essential splicing regulatory serine/arginine (SR) protein that has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. SRSF9 can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. SRSF9 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by an unusually short C-terminal RS domains rich in serine-arginine dipeptides. . Length = 72

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

 Score = 38.1 bits (89), Expect = 3e-04
 Identities = 16/72 (22%), Positives = 33/72 (45%), Gaps = 1/72 (1%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L++G +     E+ +   F Q G ++ ++I ++   G+ K F F+ F            +
Sbjct: 4   LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPN-GKPKSFAFVTFKHEVSVPYAIQLL 62

Query: 116 HGYLLFEHILQV 127
           +G  LF   L++
Sbjct: 63  NGIRLFGRELRI 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|241063 cd12619, RRM2_PUB1, RNA recognition motif 2 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 37.9 bits (88), Expect = 3e-04
 Identities = 14/44 (31%), Positives = 25/44 (56%)

Query: 74  FSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHG 117
           FS F +    R+  + K+G+S+ +GF+ F   + AE   + M+G
Sbjct: 20  FSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEMNG 63

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

 Score = 38.1 bits (89), Expect = 3e-04
 Identities = 15/64 (23%), Positives = 31/64 (48%), Gaps = 3/64 (4%)

Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
           T LY+  +       +++  F ++G I  + I  +  T + + F +++F D   AE   D
Sbjct: 1   TSLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAE---D 57

Query: 114 AMHG 117
           A++ 
Sbjct: 58  ALYY 61

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

 Score = 38.0 bits (88), Expect = 3e-04
 Identities = 15/61 (24%), Positives = 35/61 (57%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L++G +P    E+E++  F + G +  + I ++K+TG  +   F++++  + A+    A+
Sbjct: 2   LFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRAL 61

Query: 116 H 116
           H
Sbjct: 62  H 62

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

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

 Score = 37.7 bits (88), Expect = 4e-04
 Identities = 16/47 (34%), Positives = 23/47 (48%), Gaps = 3/47 (6%)

Query: 70  MQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMH 116
            +AF S    +  ++I RNK TG    + F+EF D   AE     +H
Sbjct: 17  KRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAE---RCLH 60

This subgroup corresponds to the RRM1 of SECp43, an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. . Length = 84

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

 Score = 37.4 bits (87), Expect = 4e-04
 Identities = 18/44 (40%), Positives = 26/44 (59%), Gaps = 3/44 (6%)

Query: 61  IPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKH--FGFIEF 102
           IP     KE++  FS FG +K +R+ + K TG   H  FGF++F
Sbjct: 8   IPFEATVKELRELFSTFGELKTVRLPK-KMTGTGSHRGFGFVDF 50

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

 Score = 37.3 bits (87), Expect = 4e-04
 Identities = 14/56 (25%), Positives = 31/56 (55%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVV 111
           +++G +P    E +++ +FSQFG +  + +  + +  + + FGFI F   +  + V
Sbjct: 5   IFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQV 60

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|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor

 Score = 40.0 bits (93), Expect = 4e-04
 Identities = 19/65 (29%), Positives = 33/65 (50%)

Query: 52  KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVV 111
           K T LY+  +P    + ++   F ++G I +  I R+K TG  +   F+ FN  E A+  
Sbjct: 192 KDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEA 251

Query: 112 ADAMH 116
             A++
Sbjct: 252 ISALN 256

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|240927 cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 37.7 bits (87), Expect = 4e-04
 Identities = 17/57 (29%), Positives = 31/57 (54%)

Query: 53  ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAE 109
            T +++G+IP   +E E+   F + G I  LR+  +  TG ++ + F+ F   E A+
Sbjct: 1   GTEIFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQ 57

This subgroup corresponds to the RRM1 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP, a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains. Length = 79

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

 Score = 37.5 bits (87), Expect = 5e-04
 Identities = 18/77 (23%), Positives = 39/77 (50%), Gaps = 5/77 (6%)

Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
           T + +  +P    +K+++  FS +G +K +R+ + K    ++ F F+EF+  + A    +
Sbjct: 1   TKILVKNLPFEATKKDVRTLFSSYGQLKSVRVPK-KFDQSARGFAFVEFSTAKEALNAMN 59

Query: 114 AMHGYLLFEHILQVHLI 130
           A+       H+L   L+
Sbjct: 60  ALKD----THLLGRRLV 72

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

 Score = 37.4 bits (87), Expect = 5e-04
 Identities = 18/60 (30%), Positives = 32/60 (53%), Gaps = 3/60 (5%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L+IG + +   +  ++ +FSQ+G I    + ++  T +S+ FGF+ F     A  V  AM
Sbjct: 2   LFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFAS---ASEVDAAM 58

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

 Score = 37.2 bits (87), Expect = 5e-04
 Identities = 17/65 (26%), Positives = 32/65 (49%), Gaps = 4/65 (6%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L++  +     E+E++  FS+    +RL++  NK  G      F+EF D   A    +++
Sbjct: 5   LFVANLGPNTTEEELRQLFSRQPGFRRLKM-HNKGGGPV---CFVEFEDVSFATQALNSL 60

Query: 116 HGYLL 120
            G +L
Sbjct: 61  QGAVL 65

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

 Score = 37.0 bits (85), Expect = 6e-04
 Identities = 18/65 (27%), Positives = 35/65 (53%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           +++G +      +++++ F+ FG I   R+ ++  TG+SK +GF+ F +   AE     M
Sbjct: 4   VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63

Query: 116 HGYLL 120
            G  L
Sbjct: 64  GGQWL 68

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|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor

 Score = 39.6 bits (92), Expect = 7e-04
 Identities = 18/52 (34%), Positives = 27/52 (51%)

Query: 51  NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEF 102
           N  T L +  +P    ++E+ A F   G I   RI R+ KTG S  + F++F
Sbjct: 105 NSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDF 156

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

 Score = 37.0 bits (85), Expect = 7e-04
 Identities = 19/65 (29%), Positives = 34/65 (52%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           +++G +       +++A F+ FG I   R+ ++  TG+SK +GF+ F +   AE     M
Sbjct: 4   VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 63

Query: 116 HGYLL 120
            G  L
Sbjct: 64  GGQWL 68

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|240931 cd12487, RRM1_DND1, RNA recognition motif 1 found in vertebrate dead end protein homolog 1 (DND1)

 Score = 36.7 bits (85), Expect = 8e-04
 Identities = 17/67 (25%), Positives = 31/67 (46%), Gaps = 1/67 (1%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           ++IG+IP   YE  +   F   G +   R+     +G ++ F + +++D   A      +
Sbjct: 4   VFIGKIPQDVYEDRLIPLFQSVGTLYEFRLMMT-FSGLNRGFAYAKYSDRRGASAAIATL 62

Query: 116 HGYLLFE 122
           H Y L E
Sbjct: 63  HNYELPE 69

This subgroup corresponds to the RRM1 of DND1, also termed RNA-binding motif, single-stranded-interacting protein 4, an RNA-binding protein that is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. For instance, DND1 binds cell cycle inhibitor, P27 (p27Kip1, CDKN1B), and cell cycle regulator and tumor suppressor, LATS2 (large tumor suppressor, homolog 2 of Drosophila). It helps maintain their protein expression through blocking the inhibitory function of microRNAs (miRNA) from these transcripts. DND1 may also impose another level of translational regulation to modulate expression of critical factors in embryonic stem (ES) cells. DND1 interacts specifically with apolipoprotein B editing complex 3 (APOBEC3), a multi-functional protein inhibiting retroviral replication. The DND1-APOBEC3 interaction may play a role in maintaining viability of germ cells and for preventing germ cell tumor development. DND1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 78

>gnl|CDD|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like proteins mainly from plants

 Score = 36.6 bits (85), Expect = 8e-04
 Identities = 14/37 (37%), Positives = 21/37 (56%)

Query: 68  KEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFND 104
           + +   FS  G I R+ I  +++TG SK F +IEF  
Sbjct: 18  RSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKS 54

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

 Score = 36.5 bits (84), Expect = 9e-04
 Identities = 19/62 (30%), Positives = 36/62 (58%), Gaps = 1/62 (1%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPE-VAEVVADA 114
           ++IG +     ++ ++ +F QFG +K   + R+  T +S+ FGF+ F D   V +V+A +
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62

Query: 115 MH 116
            H
Sbjct: 63  RH 64

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

 Score = 36.9 bits (85), Expect = 0.001
 Identities = 20/63 (31%), Positives = 34/63 (53%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           LYI  +P    +K+++  FS+FG I   R+  ++ TG S+   FI F+    AE    + 
Sbjct: 3   LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITSF 62

Query: 116 HGY 118
           +G+
Sbjct: 63  NGH 65

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

 Score = 36.0 bits (83), Expect = 0.001
 Identities = 17/65 (26%), Positives = 32/65 (49%), Gaps = 8/65 (12%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L++G +P    E+E+++ F Q+G +    I +N        +GF+  +D   A+     +
Sbjct: 3   LFVGNLPPEATEQEIRSLFEQYGKVLECDIIKN--------YGFVHMDDKTAADEAIRNL 54

Query: 116 HGYLL 120
           H Y L
Sbjct: 55  HHYKL 59

This subgroup corresponds to the RRM1 of RBM4, a ubiquitously expressed splicing factor that has two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may function as a translational regulator of stress-associated mRNAs and also plays a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. The C-terminal region may be crucial for nuclear localization and protein-protein interaction. The RRMs, in combination with the C-terminal region, are responsible for the splicing function of RBM4. . Length = 67

>gnl|CDD|241081 cd12637, RRM2_FCA, RNA recognition motif 2 in plant flowering time control protein FCA and similar proteins

 Score = 36.4 bits (84), Expect = 0.001
 Identities = 16/62 (25%), Positives = 37/62 (59%), Gaps = 1/62 (1%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L++G +     EKE++  FS +G ++ + + R++   QS+   F++++  E+A+    A+
Sbjct: 2   LFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMK-QSRGCAFVKYSSKEMAQAAIKAL 60

Query: 116 HG 117
           +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|241039 cd12595, RRM1_SRSF5, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 5 (SRSF5)

 Score = 36.1 bits (83), Expect = 0.001
 Identities = 18/54 (33%), Positives = 31/54 (57%), Gaps = 8/54 (14%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAE 109
           ++IGR+     EK+++ FF  +G I+ + + R         FGF+EF+DP  A+
Sbjct: 2   VFIGRLNPAAREKDVERFFKGYGRIRDIDLKRG--------FGFVEFDDPRDAD 47

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

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

 Score = 36.3 bits (84), Expect = 0.001
 Identities = 19/57 (33%), Positives = 40/57 (70%), Gaps = 2/57 (3%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEF-NDPEVAEVV 111
           +++G I     E E+++FF+++G++K ++I  + +TG SK +GF+ F +D +V ++V
Sbjct: 8   VFVGGIDIRMDETEIRSFFAKYGSVKEVKIITD-RTGVSKGYGFVSFYDDVDVQKIV 63

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|240904 cd12458, RRM_AtC3H46_like, RNA recognition motif in Arabidopsis thaliana zinc finger CCCH domain-containing protein 46 (AtC3H46) and similar proteins

 Score = 36.3 bits (84), Expect = 0.001
 Identities = 14/59 (23%), Positives = 29/59 (49%), Gaps = 4/59 (6%)

Query: 64  GFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFE 122
            F E+++  +F QFG +  +RI   +K    + FGF+ F + E  + +    + + +  
Sbjct: 10  RFTEEDVSEYFGQFGPVLDVRIPYQQK----RMFGFVTFENAETVKRILSKGNPHFICG 64

This subfamily corresponds to the RRM domain in AtC3H46, a putative RNA-binding protein that contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCCH class of zinc finger, typically C-X8-C-X5-C-X3-H. It may possess ribonuclease activity. . Length = 70

>gnl|CDD|241041 cd12597, RRM1_SRSF1, RNA recognition motif 1 in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins

 Score = 35.9 bits (83), Expect = 0.001
 Identities = 20/62 (32%), Positives = 37/62 (59%), Gaps = 7/62 (11%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           +Y+G +P     K+++  F ++GAI+ + + +N++      F F+EF DP  AE   DA+
Sbjct: 2   IYVGNLPPDIRTKDIEDLFYKYGAIRDIDL-KNRRGPP---FAFVEFEDPRDAE---DAV 54

Query: 116 HG 117
           +G
Sbjct: 55  YG 56

This subgroup corresponds to the RRM1 of SRSF1, also termed alternative-splicing factor 1 (ASF-1), or pre-mRNA-splicing factor SF2, P33 subunit. SRSF1 is a splicing regulatory serine/arginine (SR) protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF1 is a shuttling SR protein and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a long glycine-rich spacer, and a C-terminal RS domains rich in serine-arginine dipeptides. . Length = 73

>gnl|CDD|241024 cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 36.1 bits (83), Expect = 0.001
 Identities = 16/62 (25%), Positives = 35/62 (56%), Gaps = 1/62 (1%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPE-VAEVVADA 114
           +++G I     E  ++ +F Q+G I+ + I  ++ +G+ + F F+ F+D + V ++V   
Sbjct: 3   IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQK 62

Query: 115 MH 116
            H
Sbjct: 63  YH 64

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

 Score = 38.5 bits (89), Expect = 0.002
 Identities = 17/67 (25%), Positives = 35/67 (52%), Gaps = 3/67 (4%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           +Y+  +     E ++++ F  FG I + ++AR       K +GFIE+N+    +  ++A+
Sbjct: 207 IYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNN---LQSQSEAI 263

Query: 116 HGYLLFE 122
               LF+
Sbjct: 264 ASMNLFD 270

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

 Score = 36.0 bits (82), Expect = 0.002
 Identities = 17/56 (30%), Positives = 30/56 (53%)

Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAE 109
           T LYI  +P G  ++++      +G I   +   +K T Q K +GF++F+ P  A+
Sbjct: 5   TNLYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQ 60

This subgroup corresponds to the RRM1 of RBMS3, a new member of the c-myc gene single-strand binding proteins (MSSP) family of DNA regulators. Unlike other MSSP proteins, RBMS3 is not a transcriptional regulator. It binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. RBMS3 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and its C-terminal region is acidic and enriched in prolines, glutamines and threonines. . Length = 80

>gnl|CDD|241090 cd12646, RRM_SRSF7, RNA recognition motif in vertebrate serine/arginine-rich splicing factor 7 (SRSF7)

 Score = 35.8 bits (82), Expect = 0.002
 Identities = 20/65 (30%), Positives = 34/65 (52%), Gaps = 5/65 (7%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           +Y+G +  G  + E++  FS +G ++ + IARN        F F+EF DP  AE     +
Sbjct: 2   VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPG-----FAFVEFEDPRDAEDAVRGL 56

Query: 116 HGYLL 120
            G ++
Sbjct: 57  DGKVI 61

This subgroup corresponds to the RRM of SRSF7, also termed splicing factor 9G8, is a splicing regulatory serine/arginine (SR) protein that plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. SRSF7 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a CCHC-type zinc knuckle motif in its median region, and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions. . Length = 77

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

 Score = 35.6 bits (82), Expect = 0.002
 Identities = 15/73 (20%), Positives = 38/73 (52%), Gaps = 1/73 (1%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           LY+G +     E  ++  F   G ++ ++I  +K   +  ++GF+E++    AE+    +
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNN-KGVNYGFVEYHQSHDAEIALQTL 59

Query: 116 HGYLLFEHILQVH 128
           +G  +  + ++V+
Sbjct: 60  NGRQIENNEIRVN 72

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

 Score = 35.5 bits (82), Expect = 0.002
 Identities = 13/60 (21%), Positives = 31/60 (51%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L++G +     +  ++  F+++G +    +  +  T +S+ FGFI F+  + A+   +A 
Sbjct: 5   LFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAMEAQ 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|241043 cd12599, RRM1_SF2_plant_like, RNA recognition motif 1 in plant pre-mRNA-splicing factor SF2 and similar proteins

 Score = 35.5 bits (82), Expect = 0.002
 Identities = 21/74 (28%), Positives = 34/74 (45%), Gaps = 3/74 (4%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           +Y+G +P    E+E++  F ++G I  + +   K   +   + FIEF D   AE      
Sbjct: 2   VYVGNLPGDIREREVEDLFYKYGPIVDIDL---KLPPRPPGYAFIEFEDARDAEDAIRGR 58

Query: 116 HGYLLFEHILQVHL 129
            GY      L+V L
Sbjct: 59  DGYDFDGQRLRVEL 72

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

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

 Score = 35.3 bits (82), Expect = 0.002
 Identities = 18/72 (25%), Positives = 36/72 (50%), Gaps = 1/72 (1%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           +++  +P     ++++  F + G + R  +  +   G+SK FG + F  PE A+   +  
Sbjct: 1   IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDND-GRSKGFGTVLFESPEDAQRAIEMF 59

Query: 116 HGYLLFEHILQV 127
           +GY L    L+V
Sbjct: 60  NGYDLEGRELEV 71

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

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

 Score = 35.5 bits (82), Expect = 0.002
 Identities = 20/75 (26%), Positives = 38/75 (50%), Gaps = 7/75 (9%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPE-----VAEV 110
           L+I  + +   E++++  FS++G +  + +  +K T + K F F+ +  PE      AE+
Sbjct: 5   LFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAEL 64

Query: 111 VADAMHGYLLFEHIL 125
                 G LL  H+L
Sbjct: 65  DGTVFQGRLL--HLL 77

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

 Score = 35.1 bits (81), Expect = 0.002
 Identities = 13/73 (17%), Positives = 32/73 (43%), Gaps = 4/73 (5%)

Query: 55  VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
            +Y G  P  F   +++  F   G ++++ +             FI F + E A++  + 
Sbjct: 1   TVYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRTVQP----HAFITFENLEAAQLAIET 56

Query: 115 MHGYLLFEHILQV 127
           ++G  +  + ++V
Sbjct: 57  LNGASVDGNCIKV 69

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

>gnl|CDD|241110 cd12666, RRM2_RAVER2, RNA recognition motif 2 in vertebrate ribonucleoprotein PTB-binding 2 (raver-2)

 Score = 35.3 bits (81), Expect = 0.002
 Identities = 18/72 (25%), Positives = 35/72 (48%), Gaps = 5/72 (6%)

Query: 55  VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVA-----E 109
           +L +  +P  F  +E +     +G I+R  +  ++ TG SK +GF+E+   + A     E
Sbjct: 1   LLCVTNLPISFTLEEFEELVRAYGNIERCFLVYSEVTGHSKGYGFVEYMKKDSASKARLE 60

Query: 110 VVADAMHGYLLF 121
           ++   +    LF
Sbjct: 61  LLGKQLGESTLF 72

This subgroup corresponds to the RRM2 of raver-2, a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It is present in vertebrates and shows high sequence homology to raver-1, a ubiquitously expressed co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. In contrast, raver-2 exerts a distinct 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. Raver-2 contains 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. Raver-2 binds to PTB through the SLLGEPP motif only, and binds to RNA through its RRMs. . Length = 77

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

 Score = 35.4 bits (81), Expect = 0.003
 Identities = 19/73 (26%), Positives = 36/73 (49%), Gaps = 6/73 (8%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           +Y G +  G  E+ M+  FS FG I  +R+  +K       + F+ FN  E A     ++
Sbjct: 3   VYCGGVTSGLTEQLMRQTFSPFGQIMEVRVFPDKG------YSFVRFNSHESAAHAIVSV 56

Query: 116 HGYLLFEHILQVH 128
           +G  +  H+++ +
Sbjct: 57  NGTTIEGHVVKCY 69

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

 Score = 35.3 bits (81), Expect = 0.003
 Identities = 19/73 (26%), Positives = 37/73 (50%), Gaps = 1/73 (1%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L++G +     E+ +   F Q G + ++ I ++K+ G+ K FGF+ F   E        +
Sbjct: 4   LFVGNLECRVREEILYELFLQAGPLTKVTICKDKE-GKPKSFGFVCFKHSESVPYAIALL 62

Query: 116 HGYLLFEHILQVH 128
           +G  L+   ++VH
Sbjct: 63  NGIRLYGRPIKVH 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|240968 cd12524, RRM1_MEI2_like, RNA recognition motif 1 in plant Mei2-like proteins

 Score = 34.9 bits (81), Expect = 0.003
 Identities = 24/82 (29%), Positives = 35/82 (42%), Gaps = 10/82 (12%)

Query: 55  VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFI--EFNDPEVAEVVA 112
            L++  I     ++E++A F QFG I+ L           KH GFI   + D   A    
Sbjct: 3   TLFVRNINSNVEDEELRALFEQFGDIRTL-------YTACKHRGFIMVSYYDIRAARRAK 55

Query: 113 DAMHGYLLFEHILQVH-LIPPE 133
            A+ G  L    L +H  IP +
Sbjct: 56  RALQGTELGGRKLDIHFSIPKD 77

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|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA branch site protein p14 (SF3B14) and similar proteins

 Score = 34.9 bits (81), Expect = 0.003
 Identities = 17/64 (26%), Positives = 34/64 (53%), Gaps = 3/64 (4%)

Query: 55  VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
           +LY+  +P     +E+   F ++GAI+++RI   K+T   +   F+ + D   A+   D 
Sbjct: 4   ILYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKET---RGTAFVVYEDIYDAKNACDH 60

Query: 115 MHGY 118
           + G+
Sbjct: 61  LSGF 64

This subfamily corresponds to the RRM of SF3B14 (also termed p14), a 14 kDa protein subunit of SF3B which is a multiprotein complex that is an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA and has been involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B14 associates directly with another SF3B subunit called SF3B155. It is also present in both U2- and U12-dependent spliceosomes and may contribute to branch site positioning in both the major and minor spliceosome. Moreover, SF3B14 interacts directly with the pre-mRNA branch adenosine early in spliceosome assembly and within the fully assembled spliceosome. SF3B14 contains one well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 77

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

 Score = 35.0 bits (81), Expect = 0.004
 Identities = 15/50 (30%), Positives = 30/50 (60%), Gaps = 1/50 (2%)

Query: 57  YIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPE 106
           ++G +P    + ++ A F    ++K +R+ R+K+T + K F ++EF D E
Sbjct: 5   FVGNLPFNTVQGDLDAIFKDL-SVKSVRLVRDKETDKFKGFCYVEFEDVE 53

This subfamily corresponds to the RRM of eIF-4H, also termed Williams-Beuren syndrome chromosomal region 1 protein, which, together with elf-4B/eIF-4G, serves as the accessory protein of RNA helicase eIF-4A. eIF-4H contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It stimulates protein synthesis by enhancing the helicase activity of eIF-4A in the initiation step of mRNA translation. . Length = 76

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

 Score = 34.9 bits (80), Expect = 0.004
 Identities = 19/65 (29%), Positives = 36/65 (55%), Gaps = 1/65 (1%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L+IG + H   E E++  F ++G I+ + I R  + GQ   + F++F + ++A     AM
Sbjct: 11  LFIGNLDHNVSEVELRRAFDKYGIIEEVVIKRPAR-GQGGAYAFLKFQNLDMAHRAKVAM 69

Query: 116 HGYLL 120
            G ++
Sbjct: 70  SGRVI 74

This subgroup corresponds to the RRM2 of RBM15B, also termed one twenty-two 3 (OTT3), a paralog of RNA binding motif protein 15 (RBM15), also known as One-twenty two protein 1 (OTT1). Like RBM15, RBM15B has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. RBM15B belongs to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 85

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

 Score = 35.1 bits (80), Expect = 0.004
 Identities = 17/62 (27%), Positives = 36/62 (58%), Gaps = 1/62 (1%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPE-VAEVVADA 114
           L++G I     E  ++ +F ++G I  + I  ++++G+ + FGF+ F+D + V ++V   
Sbjct: 3   LFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIVLQK 62

Query: 115 MH 116
            H
Sbjct: 63  YH 64

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

 Score = 34.8 bits (81), Expect = 0.004
 Identities = 16/63 (25%), Positives = 34/63 (53%), Gaps = 1/63 (1%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           +++G+IP   +E E+   F + G I  LR+  +  +G ++ + F+ + + E A+     +
Sbjct: 4   VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMD-FSGLNRGYAFVTYTNKEAAQRAVKQL 62

Query: 116 HGY 118
           H Y
Sbjct: 63  HNY 65

This subfamily corresponds to the RRM1 in hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF), and dead end protein homolog 1 (DND1). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. It has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. DND1 is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members in this family, except for DND1, contain three conserved RNA recognition motifs (RRMs); DND1 harbors only two RRMs. . Length = 78

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

 Score = 34.9 bits (80), Expect = 0.004
 Identities = 19/72 (26%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L++G +     E +++  F +FG I  + I R  + GQ+  +GF++F + ++A     AM
Sbjct: 10  LFLGNLDITVTETDLRRAFDRFGVITEVDIKRPGR-GQTSTYGFLKFENLDMAHRAKLAM 68

Query: 116 HGYLLFEHILQV 127
            G +L  + +++
Sbjct: 69  SGKVLRRNPIKI 80

This subgroup corresponds to the RRM2 of RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contain three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. This family also includes a RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is N-terminally fused to megakaryoblastic leukemia 1 protein (MKL1) at the C-terminus in a translocation involving chromosome 1 and 22, resulting in acute megakaryoblastic leukemia. The fusion protein could interact with the mRNA export machinery. Although it maintains the specific transactivator function of MKL1, the fusion protein cannot activate RTE-mediated mRNA expression and has lost the post-transcriptional activator function of RBM15. However, it has transdominant suppressor function contributing to its oncogenic properties. . Length = 87

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	215
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	99.85
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.83
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.75
KOG0122	270	consensus Translation initiation factor 3, subunit	99.73
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	99.72
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.71
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.67
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.66
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.65
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.65
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.65
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.64
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.64
PLN03120	260	nucleic acid binding protein; Provisional	99.61
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.61
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.61
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.6
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.6
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.59
PLN03213	759	repressor of silencing 3; Provisional	99.57
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.57
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.57
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.56
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.56
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.56
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.55
PLN03121	243	nucleic acid binding protein; Provisional	99.55
smart00362	72	RRM_2 RNA recognition motif.	99.55
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.55
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.54
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.54
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.53
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.53
smart00360	71	RRM RNA recognition motif.	99.53
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.52
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.52
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.51
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.5
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.5
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.5
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.48
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.47
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.43
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.43
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.41
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.41
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.39
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.39
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.39
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.37
smart00361	70	RRM_1 RNA recognition motif.	99.37
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.36
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.35
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.35
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.34
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	99.33
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.31
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.31
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.28
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.22
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.21
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.2
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.19
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.14
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.14
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	99.12
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.11
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	99.1
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	99.08
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.07
KOG0533	243	consensus RRM motif-containing protein [RNA proces	99.02
KOG1548	382	consensus Transcription elongation factor TAT-SF1	99.0
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.0
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	98.98
KOG0151	877	consensus Predicted splicing regulator, contains R	98.94
KOG0226	290	consensus RNA-binding proteins [General function p	98.91
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	98.89
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.86
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.81
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.77
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.63
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.61
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.59
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.52
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.5
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	98.43
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	98.36
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	98.31
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.24
KOG1995	351	consensus Conserved Zn-finger protein [General fun	98.2
KOG3152	278	consensus TBP-binding protein, activator of basal	98.14
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.14
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.09
KOG4210	285	consensus Nuclear localization sequence binding pr	98.06
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.98
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	97.97
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	97.91
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	97.9
KOG1457	284	consensus RNA binding protein (contains RRM repeat	97.84
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	97.77
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	97.75
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.69
KOG2314	698	consensus Translation initiation factor 3, subunit	97.63
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	97.52
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.49
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	97.47
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.45
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	97.44
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	97.44
KOG1548	382	consensus Transcription elongation factor TAT-SF1	97.28
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.26
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	97.18
KOG1855	484	consensus Predicted RNA-binding protein [General f	97.11
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	97.04
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	97.03
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	97.0
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	96.98
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	96.79
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	96.74
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	96.71
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	96.62
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	96.62
KOG2068	327	consensus MOT2 transcription factor [Transcription	96.58
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	96.46
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	96.45
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	96.4
KOG1996	378	consensus mRNA splicing factor [RNA processing and	96.3
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	96.22
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	96.16
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	96.09
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	96.02
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	96.0
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	95.1
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	95.02
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	94.42
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	94.39
KOG2135	526	consensus Proteins containing the RNA recognition	94.14
KOG4210	285	consensus Nuclear localization sequence binding pr	91.94
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	91.86
KOG2591	684	consensus c-Mpl binding protein, contains La domai	91.26
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	91.02
KOG4660	549	consensus Protein Mei2, essential for commitment t	90.65
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	89.72
KOG2891	445	consensus Surface glycoprotein [General function p	89.17
KOG2318	650	consensus Uncharacterized conserved protein [Funct	88.66
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	84.96
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	83.84

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

Probab=99.85  E-value=3.1e-21  Score=150.01  Aligned_cols=167  Identities=41%  Similarity=0.704  Sum_probs=154.5

Q ss_pred             CCCCCCCCCcEEEEcCCCCCCcHHHHHHHhccC-CCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCe
Q 028027           45 EEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQF-GAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEH  123 (215)
Q Consensus        45 ~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~-G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~  123 (215)
                      +..+.......+||..+|..+.+..|..+|.+| |.|..+++.+++.||.++|||||+|++.+.|..|.+.||++.|.|+
T Consensus        41 ~~~p~~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~  120 (214)
T KOG4208|consen   41 REKPEQEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEH  120 (214)
T ss_pred             ccCCccCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhh
Confidence            445667788899999999999999999999998 7889999999999999999999999999999999999999999999


Q ss_pred             EEEEEEeCCC-CCCCCCcCCCCCCCCCCChHHHHHHHhhhhcCHHHHHHHHHHHHHHHHHHHHHHHHhCCcccCCccccC
Q 028027          124 ILQVHLIPPE-HVHPKLWRGFNPRYKPVDRVQVERKLQNKERTLEEHKKLVEKILKRDQKRRKRIEAAGIEYECPEIVGN  202 (215)
Q Consensus       124 ~l~V~~a~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~e~~~~~~~~~~~~~~~~~kl~~~gi~~~~~~~~~~  202 (215)
                      .|.|.+..|. ..+...|.+++..+.+.....+.+...++..+.+++.....+.........+.+.+.||.+.++..++.
T Consensus       121 lL~c~vmppe~~v~~~~~k~~~~~~~~~~~~~~k~~~~~~~~t~~e~~k~~~k~~~~~~~~~~~~~~~~i~~~~~e~~~~  200 (214)
T KOG4208|consen  121 LLECHVMPPEQKVEKNLKKVSGTPFKPGKTVPIKRLQDNKDLTHEERRKKLVKENKKDAKDDKAVTEAGIEPEVSEPVTK  200 (214)
T ss_pred             eeeeEEeCchhhhhhhhhhhcCCcCCCCCcccccccCcccccchHHhhHHHHhhhhhhhcccchhcccCccccccccccc
Confidence            9999999998 788899999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             CCCCCcccc
Q 028027          203 VMPAPKKIK  211 (215)
Q Consensus       203 ~~~~~~~~~  211 (215)
                      ..+.+..+.
T Consensus       201 ~~~~~~~kk  209 (214)
T KOG4208|consen  201 KVPIKTRKK  209 (214)
T ss_pred             cCCCccccc
Confidence            777765544

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

Probab=99.83  E-value=2e-19  Score=136.67  Aligned_cols=94  Identities=26%  Similarity=0.470  Sum_probs=85.7

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEE
Q 028027           48 PLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQV  127 (215)
Q Consensus        48 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V  127 (215)
                      .....+++|||+|||+.+++++|+++|.+||.|.+|.++.++.|+.++|||||+|.+.++|+.|+..||+..|+|+.|+|
T Consensus        29 ~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V  108 (144)
T PLN03134         29 SLRLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRV  108 (144)
T ss_pred             cccCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            33467789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeCCCCCCCCCcC
Q 028027          128 HLIPPEHVHPKLWR  141 (215)
Q Consensus       128 ~~a~~~~~~~~~~~  141 (215)
                      .++.++...+..+.
T Consensus       109 ~~a~~~~~~~~~~~  122 (144)
T PLN03134        109 NPANDRPSAPRAYG  122 (144)
T ss_pred             EeCCcCCCCCCCCC
Confidence            99987766554443

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.75  E-value=1.2e-17  Score=144.09  Aligned_cols=82  Identities=23%  Similarity=0.445  Sum_probs=78.4

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeCC
Q 028027           53 ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPP  132 (215)
Q Consensus        53 ~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~~  132 (215)
                      +.+|||+|||+.+++++|+++|++||.|.+|+|++++.||.++|||||+|.+.++|..||..|||..|+|+.|+|.|+..
T Consensus       269 ~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~~  348 (352)
T TIGR01661       269 GYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKTN  348 (352)
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEccC
Confidence            44799999999999999999999999999999999998999999999999999999999999999999999999999876


Q ss_pred             CC
Q 028027          133 EH  134 (215)
Q Consensus       133 ~~  134 (215)
                      +.
T Consensus       349 ~~  350 (352)
T TIGR01661       349 KA  350 (352)
T ss_pred             CC
Confidence            54

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=99.73  E-value=3.3e-17  Score=130.51  Aligned_cols=85  Identities=27%  Similarity=0.492  Sum_probs=81.7

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 028027           49 LVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVH  128 (215)
Q Consensus        49 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~  128 (215)
                      ...+..+|.|.||+.+++|++|+++|..||.|..|.|.+|+.||.++|||||.|.+.++|.+||..|||+-++.-.|+|+
T Consensus       185 ~R~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvE  264 (270)
T KOG0122|consen  185 ERDDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVE  264 (270)
T ss_pred             cCCccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEE
Confidence            44678899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeCCC
Q 028027          129 LIPPE  133 (215)
Q Consensus       129 ~a~~~  133 (215)
                      |++|+
T Consensus       265 wskP~  269 (270)
T KOG0122|consen  265 WSKPS  269 (270)
T ss_pred             ecCCC
Confidence            99885

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.73  E-value=4.6e-17  Score=140.05  Aligned_cols=86  Identities=26%  Similarity=0.441  Sum_probs=81.1

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEE
Q 028027           48 PLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQV  127 (215)
Q Consensus        48 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V  127 (215)
                      ......++|||+|||+++++++|+++|+.||.|.+|+|+.+..+++++|||||+|.+.++|..||..||+..|.++.|+|
T Consensus       102 ~~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V  181 (346)
T TIGR01659       102 DTNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKV  181 (346)
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeee
Confidence            34567889999999999999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             EEeCCC
Q 028027          128 HLIPPE  133 (215)
Q Consensus       128 ~~a~~~  133 (215)
                      .++.+.
T Consensus       182 ~~a~p~  187 (346)
T TIGR01659       182 SYARPG  187 (346)
T ss_pred             eccccc
Confidence            998764

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=99.72  E-value=7e-17  Score=106.93  Aligned_cols=70  Identities=36%  Similarity=0.719  Sum_probs=67.3

Q ss_pred             EEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEE
Q 028027           56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQ  126 (215)
Q Consensus        56 l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~  126 (215)
                      |||+|||+.+++++|+++|++||.|..+.+..+ .++..+|||||+|.+.++|+.|+..|+|..++|+.|+
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            799999999999999999999999999999998 5899999999999999999999999999999999885

(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 ....

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.71  E-value=5.7e-17  Score=139.82  Aligned_cols=83  Identities=28%  Similarity=0.557  Sum_probs=79.2

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeC
Q 028027           52 KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIP  131 (215)
Q Consensus        52 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~  131 (215)
                      +.++|||+|||+.+++++|+++|+.||+|.+|+|++++.+|+++|||||+|.+.++|..||..|||..|.|+.|.|.++.
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            35789999999999999999999999999999999999899999999999999999999999999999999999999997


Q ss_pred             CCC
Q 028027          132 PEH  134 (215)
Q Consensus       132 ~~~  134 (215)
                      +..
T Consensus        82 ~~~   84 (352)
T TIGR01661        82 PSS   84 (352)
T ss_pred             ccc
Confidence            654

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

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

Probab=99.67  E-value=4.5e-16  Score=141.28  Aligned_cols=83  Identities=23%  Similarity=0.383  Sum_probs=78.9

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeC
Q 028027           52 KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIP  131 (215)
Q Consensus        52 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~  131 (215)
                      ..++|||+|||+.+++++|+++|+.||.|.+|+|.+++.+|.++|||||+|.+.++|..|+..||++.|+|+.|+|.++.
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            45799999999999999999999999999999999999899999999999999999999999999999999999999987


Q ss_pred             CCC
Q 028027          132 PEH  134 (215)
Q Consensus       132 ~~~  134 (215)
                      +.+
T Consensus       283 ~pP  285 (612)
T TIGR01645       283 TPP  285 (612)
T ss_pred             CCc
Confidence            654

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=99.66  E-value=7.6e-16  Score=132.53  Aligned_cols=105  Identities=21%  Similarity=0.318  Sum_probs=89.2

Q ss_pred             CCCCcccCCCCCCCCCCCC-CCCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHH
Q 028027           29 AADFLPLEGGPGRKLTEEK-PLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEV  107 (215)
Q Consensus        29 ~~d~~~~~g~p~r~~~~~~-~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~  107 (215)
                      .+++..+.++++++..... ......++|||+|||+.+++++|+++|++||.|..|.|++++.+|.++|||||+|.+.++
T Consensus       168 ~LnG~~l~gr~i~V~~a~p~~~~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~  247 (346)
T TIGR01659       168 NLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREE  247 (346)
T ss_pred             HcCCCccCCceeeeecccccccccccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHH
Confidence            4566777777776543321 223456789999999999999999999999999999999998899999999999999999


Q ss_pred             HHHHHHHhCCceeCC--eEEEEEEeCCC
Q 028027          108 AEVVADAMHGYLLFE--HILQVHLIPPE  133 (215)
Q Consensus       108 a~~ai~~l~g~~l~g--~~l~V~~a~~~  133 (215)
                      |+.||..||+..+.+  +.|.|.++...
T Consensus       248 A~~Ai~~lng~~~~g~~~~l~V~~a~~~  275 (346)
T TIGR01659       248 AQEAISALNNVIPEGGSQPLTVRLAEEH  275 (346)
T ss_pred             HHHHHHHhCCCccCCCceeEEEEECCcc
Confidence            999999999998876  68999998764

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

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

Probab=99.65  E-value=3.2e-16  Score=113.53  Aligned_cols=86  Identities=19%  Similarity=0.296  Sum_probs=80.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ...+++||||||+..++|++|.++|+.+|+|..|.+-.|+.+-.+.|||||+|.+.++|..|+.-++|+.|+.+.|++.|
T Consensus        33 ~r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~  112 (153)
T KOG0121|consen   33 LRKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDW  112 (153)
T ss_pred             HhhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeec
Confidence            35689999999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             eCCCCC
Q 028027          130 IPPEHV  135 (215)
Q Consensus       130 a~~~~~  135 (215)
                      ...-..
T Consensus       113 D~GF~e  118 (153)
T KOG0121|consen  113 DAGFVE  118 (153)
T ss_pred             cccchh
Confidence            765433

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

Probab=99.65  E-value=2.2e-16  Score=125.32  Aligned_cols=80  Identities=24%  Similarity=0.451  Sum_probs=73.4

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ..-++||||||+|.++.+.|+.+|++||+|.+..++.|+.||+++|||||+|.+.++|.+|+.. ..-.|+||+..|.+|
T Consensus        10 T~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNcnlA   88 (247)
T KOG0149|consen   10 TTFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKANCNLA   88 (247)
T ss_pred             ceEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC-CCCcccccccccchh
Confidence            3457899999999999999999999999999999999999999999999999999999999965 456799999999886


Q ss_pred             C
Q 028027          131 P  131 (215)
Q Consensus       131 ~  131 (215)
                      .
T Consensus        89 ~   89 (247)
T KOG0149|consen   89 S   89 (247)
T ss_pred             h
Confidence            4

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

Probab=99.65  E-value=9.3e-16  Score=126.81  Aligned_cols=102  Identities=23%  Similarity=0.426  Sum_probs=88.1

Q ss_pred             CCCcccCCCCCCCCCCCC-CCCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHH
Q 028027           30 ADFLPLEGGPGRKLTEEK-PLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVA  108 (215)
Q Consensus        30 ~d~~~~~g~p~r~~~~~~-~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a  108 (215)
                      .++..++|-|+...+.+. +....+.+|+|+|||+.+.+-||+.+|.+||.|.+|.|+.+  ...++|||||+|++.++|
T Consensus        72 ~~~~~t~g~~~~~~~st~s~s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfN--ERGSKGFGFVTmen~~da  149 (376)
T KOG0125|consen   72 SNGAPTDGQPIQTQPSTNSSSKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFN--ERGSKGFGFVTMENPADA  149 (376)
T ss_pred             cCCCCCCCCccccCCCCcCCCCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEec--cCCCCccceEEecChhhH
Confidence            344566666765555443 33566789999999999999999999999999999999998  456899999999999999


Q ss_pred             HHHHHHhCCceeCCeEEEEEEeCCC
Q 028027          109 EVVADAMHGYLLFEHILQVHLIPPE  133 (215)
Q Consensus       109 ~~ai~~l~g~~l~g~~l~V~~a~~~  133 (215)
                      ++|-..|||..+.||+|.|..++++
T Consensus       150 dRARa~LHgt~VEGRkIEVn~ATar  174 (376)
T KOG0125|consen  150 DRARAELHGTVVEGRKIEVNNATAR  174 (376)
T ss_pred             HHHHHHhhcceeeceEEEEeccchh
Confidence            9999999999999999999999876

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.64  E-value=2e-15  Score=100.39  Aligned_cols=70  Identities=33%  Similarity=0.669  Sum_probs=65.0

Q ss_pred             EEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEE
Q 028027           56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQ  126 (215)
Q Consensus        56 l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~  126 (215)
                      |||+|||+++++++|+++|+.||.|..+.+..++. |.++|+|||+|.+.++|..|+..+++..++|+.|+
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            79999999999999999999999999999999975 99999999999999999999999999999999874

k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....

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

Probab=99.64  E-value=4.2e-17  Score=124.71  Aligned_cols=83  Identities=28%  Similarity=0.574  Sum_probs=78.2

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      -.++.-|||||||+.+||.||..+|++||+|..|.+++|+.||+++||||+.|++..+.-.|++.|||..|.||.|+|..
T Consensus        32 YkdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDH  111 (219)
T KOG0126|consen   32 YKDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDH  111 (219)
T ss_pred             cccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeee
Confidence            35678899999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             eCC
Q 028027          130 IPP  132 (215)
Q Consensus       130 a~~  132 (215)
                      ...
T Consensus       112 v~~  114 (219)
T KOG0126|consen  112 VSN  114 (219)
T ss_pred             ccc
Confidence            543

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.61  E-value=4.6e-15  Score=121.08  Aligned_cols=78  Identities=15%  Similarity=0.355  Sum_probs=71.6

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeCC
Q 028027           53 ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPP  132 (215)
Q Consensus        53 ~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~~  132 (215)
                      .++|||+|||+.+++++|+++|+.||.|.+|.|+.+..   ++|||||+|.+.++|+.|| .|||..|.|+.|.|.++..
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~Al-lLnG~~l~gr~V~Vt~a~~   79 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETAL-LLSGATIVDQSVTITPAED   79 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHH-HhcCCeeCCceEEEEeccC
Confidence            57999999999999999999999999999999998853   4689999999999999999 5999999999999999875


Q ss_pred             CC
Q 028027          133 EH  134 (215)
Q Consensus       133 ~~  134 (215)
                      -.
T Consensus        80 ~~   81 (260)
T PLN03120         80 YQ   81 (260)
T ss_pred             CC
Confidence            43

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

Probab=99.61  E-value=8.8e-16  Score=119.75  Aligned_cols=83  Identities=28%  Similarity=0.423  Sum_probs=78.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      .....+|.|.||.+.++.++|+.+|+.||.|-+|.|++|+.|+.++|||||.|....+|+.|++.|+|..|+|+.|+|++
T Consensus        10 v~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~   89 (256)
T KOG4207|consen   10 VEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQM   89 (256)
T ss_pred             cccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehh
Confidence            35567899999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             eCC
Q 028027          130 IPP  132 (215)
Q Consensus       130 a~~  132 (215)
                      |.-
T Consensus        90 ary   92 (256)
T KOG4207|consen   90 ARY   92 (256)
T ss_pred             hhc
Confidence            853

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

Probab=99.61  E-value=8e-16  Score=121.05  Aligned_cols=90  Identities=31%  Similarity=0.555  Sum_probs=84.1

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ...-++||||+|...++|..|...|-.||.|..|.++.|.+++++||||||+|...++|.+||+.||+..|.|+.|+|.+
T Consensus         7 a~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~   86 (298)
T KOG0111|consen    7 ANQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNL   86 (298)
T ss_pred             cccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEee
Confidence            45668999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eCCCCCCCCC
Q 028027          130 IPPEHVHPKL  139 (215)
Q Consensus       130 a~~~~~~~~~  139 (215)
                      +.|.......
T Consensus        87 AkP~kikegs   96 (298)
T KOG0111|consen   87 AKPEKIKEGS   96 (298)
T ss_pred             cCCccccCCC
Confidence            9987665433

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

Probab=99.60  E-value=3.7e-15  Score=135.36  Aligned_cols=81  Identities=27%  Similarity=0.506  Sum_probs=76.8

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ...++|||+|||+.+++++|+++|..||.|.+|.++.++.+|+++|||||+|.+.++|+.|+..|||..|+|+.|+|.+.
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            45689999999999999999999999999999999999999999999999999999999999999999999999999864


Q ss_pred             C
Q 028027          131 P  131 (215)
Q Consensus       131 ~  131 (215)
                      .
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.

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

Probab=99.60  E-value=6.4e-15  Score=133.45  Aligned_cols=98  Identities=23%  Similarity=0.442  Sum_probs=83.6

Q ss_pred             CCcccCCCCCCCCCCCCCCCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHH
Q 028027           31 DFLPLEGGPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEV  110 (215)
Q Consensus        31 d~~~~~g~p~r~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~  110 (215)
                      ++...+|+|....  +..+....++|||+|||++++|++|+.+|++||.|.+|+|++| .+|.++|||||+|.+.++|+.
T Consensus        38 ~g~r~~g~Pp~~~--~~~~p~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D-~sG~sRGfaFV~F~~~e~A~~  114 (578)
T TIGR01648        38 NGQRKYGGPPPGW--SGVQPGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKE  114 (578)
T ss_pred             CCcccCCCCCCcc--cCCCCCCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC-CCCCccceEEEEeCCHHHHHH
Confidence            4456677766542  3344456799999999999999999999999999999999999 699999999999999999999


Q ss_pred             HHHHhCCceeC-CeEEEEEEeC
Q 028027          111 VADAMHGYLLF-EHILQVHLIP  131 (215)
Q Consensus       111 ai~~l~g~~l~-g~~l~V~~a~  131 (215)
                      ||..||+..|. |+.|.|.++.
T Consensus       115 Ai~~lng~~i~~Gr~l~V~~S~  136 (578)
T TIGR01648       115 AVKLLNNYEIRPGRLLGVCISV  136 (578)
T ss_pred             HHHHcCCCeecCCccccccccc
Confidence            99999999885 7887777653

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.

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

Probab=99.59  E-value=6.4e-15  Score=120.50  Aligned_cols=84  Identities=24%  Similarity=0.424  Sum_probs=79.7

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      .+-+||||+.|+++++|..|+..|+.||+|..|+|+.+..||+++|||||+|.+..++..|.+..+|..|+|+.|.|.+-
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            56789999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             CCCC
Q 028027          131 PPEH  134 (215)
Q Consensus       131 ~~~~  134 (215)
                      ..+.
T Consensus       179 RgRT  182 (335)
T KOG0113|consen  179 RGRT  182 (335)
T ss_pred             cccc
Confidence            6543

>PLN03213 repressor of silencing 3; Provisional

Probab=99.57  E-value=1e-14  Score=126.38  Aligned_cols=79  Identities=15%  Similarity=0.318  Sum_probs=72.4

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCH--HHHHHHHHHhCCceeCCeEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDP--EVAEVVADAMHGYLLFEHILQV  127 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~--~~a~~ai~~l~g~~l~g~~l~V  127 (215)
                      .....+||||||++.+++++|+.+|+.||.|.+|.|++  ++|  ||||||+|.+.  .++..||..|||..+.|+.|+|
T Consensus         7 ~~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpR--ETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKV   82 (759)
T PLN03213          7 GGGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVR--TKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRL   82 (759)
T ss_pred             CCcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEec--ccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEE
Confidence            34567899999999999999999999999999999994  477  89999999987  6899999999999999999999


Q ss_pred             EEeCC
Q 028027          128 HLIPP  132 (215)
Q Consensus       128 ~~a~~  132 (215)
                      ..|++
T Consensus        83 NKAKP   87 (759)
T PLN03213         83 EKAKE   87 (759)
T ss_pred             eeccH
Confidence            98865

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

Probab=99.57  E-value=1.6e-14  Score=132.12  Aligned_cols=79  Identities=23%  Similarity=0.441  Sum_probs=75.8

Q ss_pred             EEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeCCC
Q 028027           55 VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPPE  133 (215)
Q Consensus        55 ~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~~~  133 (215)
                      +|||+|||+++||++|+++|+.||.|.+|+|+++..|++++|||||+|.+.++|+.|+..||+..|.|+.|+|.|+...
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~~~   80 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQRD   80 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeeccccc
Confidence            7999999999999999999999999999999999989999999999999999999999999999999999999997643

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

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

Probab=99.57  E-value=6e-15  Score=107.91  Aligned_cols=83  Identities=18%  Similarity=0.392  Sum_probs=79.5

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ..+..|||.++...++|++|.+.|..||+|..+++..|+.||-.+|||+|+|++...|+.|+..|||..|.|..|.|.|+
T Consensus        70 VEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~  149 (170)
T KOG0130|consen   70 VEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWC  149 (170)
T ss_pred             eeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEE
Confidence            67899999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCC
Q 028027          131 PPE  133 (215)
Q Consensus       131 ~~~  133 (215)
                      --.
T Consensus       150 Fv~  152 (170)
T KOG0130|consen  150 FVK  152 (170)
T ss_pred             Eec
Confidence            543

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

Probab=99.56  E-value=2.9e-14  Score=128.75  Aligned_cols=83  Identities=27%  Similarity=0.486  Sum_probs=78.5

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ...++|||+|||+.+++++|+++|+.||.|..+.++.+..+|.++|||||+|.+.+.|..||..|||..|+|+.|.|.++
T Consensus       293 ~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a  372 (509)
T TIGR01642       293 DSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRA  372 (509)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            34679999999999999999999999999999999999889999999999999999999999999999999999999998


Q ss_pred             CCC
Q 028027          131 PPE  133 (215)
Q Consensus       131 ~~~  133 (215)
                      ...
T Consensus       373 ~~~  375 (509)
T TIGR01642       373 CVG  375 (509)
T ss_pred             ccC
Confidence            654

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

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

Probab=99.56  E-value=2.2e-14  Score=122.89  Aligned_cols=88  Identities=23%  Similarity=0.477  Sum_probs=81.6

Q ss_pred             CCCCCCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeC-Ce
Q 028027           45 EEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLF-EH  123 (215)
Q Consensus        45 ~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~-g~  123 (215)
                      .+.++...++.||||.||.++.|++|.-+|...|.|..++|+.|+.+|.+||||||+|.+.+.|+.||+.||+++|. |+
T Consensus        75 weg~~p~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK  154 (506)
T KOG0117|consen   75 WEGPPPPRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGK  154 (506)
T ss_pred             ccCCCCCCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCC
Confidence            55566678899999999999999999999999999999999999999999999999999999999999999999875 89


Q ss_pred             EEEEEEeCC
Q 028027          124 ILQVHLIPP  132 (215)
Q Consensus       124 ~l~V~~a~~  132 (215)
                      .|.|+.+..
T Consensus       155 ~igvc~Sva  163 (506)
T KOG0117|consen  155 LLGVCVSVA  163 (506)
T ss_pred             EeEEEEeee
Confidence            999988754

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

Probab=99.56  E-value=1.2e-14  Score=110.70  Aligned_cols=79  Identities=27%  Similarity=0.472  Sum_probs=73.1

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeC
Q 028027           52 KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIP  131 (215)
Q Consensus        52 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~  131 (215)
                      -.+.||||||+..+++.+|+..|..||.|..|.|.+++     .|||||+|++..+|+.|+..|+|..|.|..|+|+++.
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnP-----PGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~   83 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNP-----PGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELST   83 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecC-----CCceEEeccCcccHHHHHhhcCCccccCceEEEEeec
Confidence            46889999999999999999999999999999998765     5899999999999999999999999999999999987


Q ss_pred             CCCC
Q 028027          132 PEHV  135 (215)
Q Consensus       132 ~~~~  135 (215)
                      ....
T Consensus        84 G~~r   87 (195)
T KOG0107|consen   84 GRPR   87 (195)
T ss_pred             CCcc
Confidence            6544

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

Probab=99.55  E-value=2.7e-14  Score=127.44  Aligned_cols=80  Identities=33%  Similarity=0.611  Sum_probs=77.1

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeCC
Q 028027           53 ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPP  132 (215)
Q Consensus        53 ~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~~  132 (215)
                      .++|||+|||..+++++|+.+|+.||.|..|.++.+..+|.++|||||+|.+.++|..|+..|||..|.|+.|.|.++..
T Consensus       186 ~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~~  265 (457)
T TIGR01622       186 FLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQD  265 (457)
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEccC
Confidence            68999999999999999999999999999999999988899999999999999999999999999999999999999763

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.

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.55  E-value=5.7e-14  Score=113.11  Aligned_cols=80  Identities=18%  Similarity=0.262  Sum_probs=71.4

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ..+.+|||+||++.+|+++|+++|+.||.|.+|.|+++.   ...+||||+|.+.++|+.|+ .|+|..|.++.|.|...
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            356899999999999999999999999999999999884   34579999999999999999 79999999999999876


Q ss_pred             CCCC
Q 028027          131 PPEH  134 (215)
Q Consensus       131 ~~~~  134 (215)
                      ..-.
T Consensus        79 ~~y~   82 (243)
T PLN03121         79 GQYE   82 (243)
T ss_pred             cccc
Confidence            5433

>smart00362 RRM_2 RNA recognition motif

Probab=99.55  E-value=4.7e-14  Score=92.58  Aligned_cols=72  Identities=35%  Similarity=0.678  Sum_probs=67.3

Q ss_pred             EEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 028027           55 VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVH  128 (215)
Q Consensus        55 ~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~  128 (215)
                      +|||+|||..++.++|+++|.+||.|..+.+..+.  +.++|+|||+|.+.+.|+.|+..+++..+.|+.|.|+
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            48999999999999999999999999999998875  7788999999999999999999999999999998863

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

Probab=99.55  E-value=1.6e-14  Score=116.79  Aligned_cols=81  Identities=22%  Similarity=0.463  Sum_probs=78.0

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeCCC
Q 028027           54 TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPPE  133 (215)
Q Consensus        54 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~~~  133 (215)
                      .-|||+.|...++-++|++.|..||+|.+++|++|..|++++|||||.|.+.++|+.||..|||..|++|.|+-.||..+
T Consensus        63 fhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATRK  142 (321)
T KOG0148|consen   63 FHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATRK  142 (321)
T ss_pred             eeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeeccccccC
Confidence            46999999999999999999999999999999999999999999999999999999999999999999999999999766


Q ss_pred             C
Q 028027          134 H  134 (215)
Q Consensus       134 ~  134 (215)
                      .
T Consensus       143 p  143 (321)
T KOG0148|consen  143 P  143 (321)
T ss_pred             c
Confidence            5

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

Probab=99.54  E-value=3.4e-14  Score=121.26  Aligned_cols=120  Identities=23%  Similarity=0.391  Sum_probs=99.2

Q ss_pred             CCCCCCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCc-eeCC-
Q 028027           45 EEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGY-LLFE-  122 (215)
Q Consensus        45 ~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~-~l~g-  122 (215)
                      ..+.++.+.-.+|||.||.+++|.||+.+|++||.|.+|.|++|+.||.++|||||.|.+.++|.+|+..|++. .|.| 
T Consensus        26 ~~d~~d~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~  105 (510)
T KOG0144|consen   26 HTDNPDGSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGM  105 (510)
T ss_pred             CCCCCCchhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCC
Confidence            33445566678999999999999999999999999999999999999999999999999999999999999885 4655 


Q ss_pred             -eEEEEEEeCCCCCCCCCcCCCCCCCCCCChHHHHHHHhhhhcCHHHHHHHHHHH
Q 028027          123 -HILQVHLIPPEHVHPKLWRGFNPRYKPVDRVQVERKLQNKERTLEEHKKLVEKI  176 (215)
Q Consensus       123 -~~l~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~e~~~~~~~~  176 (215)
                       .+|.|++++.+..+-            +...++.....+|.-++.+...+..++
T Consensus       106 ~~pvqvk~Ad~E~er~------------~~e~KLFvg~lsK~~te~evr~iFs~f  148 (510)
T KOG0144|consen  106 HHPVQVKYADGERERI------------VEERKLFVGMLSKQCTENEVREIFSRF  148 (510)
T ss_pred             Ccceeecccchhhhcc------------ccchhhhhhhccccccHHHHHHHHHhh
Confidence             678888887765431            233445566778888888888888776

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

Probab=99.54  E-value=1.8e-14  Score=110.42  Aligned_cols=81  Identities=23%  Similarity=0.437  Sum_probs=78.3

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      +...+||||||+..++++.|+++|-+.|+|.++++++++.+..++|||||+|.++++|+-|++.||...|.|++|+|..+
T Consensus         7 nqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~ka   86 (203)
T KOG0131|consen    7 NQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKA   86 (203)
T ss_pred             CCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEec
Confidence            56789999999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             C
Q 028027          131 P  131 (215)
Q Consensus       131 ~  131 (215)
                      .
T Consensus        87 s   87 (203)
T KOG0131|consen   87 S   87 (203)
T ss_pred             c
Confidence            7

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

Probab=99.53  E-value=5.1e-14  Score=128.82  Aligned_cols=82  Identities=27%  Similarity=0.500  Sum_probs=77.6

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ...++|||+||++.+++++|+++|+.||.|.+|.++.+ .+|.++|||||+|.+.++|..|+..|||..++|+.|.|.++
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 AQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLD-EKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALA  361 (562)
T ss_pred             cCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEEC-CCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEec
Confidence            45678999999999999999999999999999999999 58999999999999999999999999999999999999998


Q ss_pred             CCC
Q 028027          131 PPE  133 (215)
Q Consensus       131 ~~~  133 (215)
                      ..+
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=99.53  E-value=5.7e-14  Score=113.63  Aligned_cols=79  Identities=23%  Similarity=0.404  Sum_probs=74.3

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 028027           49 LVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVH  128 (215)
Q Consensus        49 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~  128 (215)
                      ..++.++||||||+..++|++|+..|++||.|.+|++..++      ||+||.|.+.|.|..||-.||+..|+|..++|.
T Consensus       160 ssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~q------GYaFVrF~tkEaAahAIv~mNntei~G~~VkCs  233 (321)
T KOG0148|consen  160 SSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKDQ------GYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCS  233 (321)
T ss_pred             CCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEeccc------ceEEEEecchhhHHHHHHHhcCceeCceEEEEe
Confidence            45678999999999999999999999999999999999885      899999999999999999999999999999999


Q ss_pred             EeCCC
Q 028027          129 LIPPE  133 (215)
Q Consensus       129 ~a~~~  133 (215)
                      |-+..
T Consensus       234 WGKe~  238 (321)
T KOG0148|consen  234 WGKEG  238 (321)
T ss_pred             ccccC
Confidence            97654

>smart00360 RRM RNA recognition motif

Probab=99.53  E-value=6.7e-14  Score=91.46  Aligned_cols=71  Identities=39%  Similarity=0.685  Sum_probs=66.9

Q ss_pred             EcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 028027           58 IGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVH  128 (215)
Q Consensus        58 V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~  128 (215)
                      |+|||..+++++|+.+|.+||.|..+.+..++.++.++|+|||+|.+.++|..|+..|++..++|+.|.|+
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            68999999999999999999999999999988789999999999999999999999999999999998873

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

Probab=99.52  E-value=8.1e-14  Score=124.34  Aligned_cols=82  Identities=17%  Similarity=0.366  Sum_probs=76.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ....++|||+|||+.+++++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|..||. |+|..|.|+.|.|.+
T Consensus        86 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~~  164 (457)
T TIGR01622        86 ERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQS  164 (457)
T ss_pred             ccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEee
Confidence            3457899999999999999999999999999999999999899999999999999999999995 899999999999988


Q ss_pred             eCC
Q 028027          130 IPP  132 (215)
Q Consensus       130 a~~  132 (215)
                      +..
T Consensus       165 ~~~  167 (457)
T TIGR01622       165 SQA  167 (457)
T ss_pred             cch
Confidence            654

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.

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

Probab=99.52  E-value=1.1e-14  Score=111.48  Aligned_cols=103  Identities=25%  Similarity=0.401  Sum_probs=91.0

Q ss_pred             cccCCCCCCCCCCCC--CCCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEE-EEeecCCCCCcccEEEEEEcCHHHHH
Q 028027           33 LPLEGGPGRKLTEEK--PLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRL-RIARNKKTGQSKHFGFIEFNDPEVAE  109 (215)
Q Consensus        33 ~~~~g~p~r~~~~~~--~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v-~i~~~~~tg~~~g~afV~F~~~~~a~  109 (215)
                      ++|+|+|++....+.  ..-..+..|||+||.+.++|..|.+.|+.||.+... .++++..||.++|||||.|.+.+.+.
T Consensus        74 VkLYgrpIrv~kas~~~~nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd  153 (203)
T KOG0131|consen   74 VKLYGRPIRVNKASAHQKNLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASD  153 (203)
T ss_pred             HHhcCceeEEEecccccccccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHH
Confidence            789999999877663  223456789999999999999999999999998664 78899889999999999999999999


Q ss_pred             HHHHHhCCceeCCeEEEEEEeCCCCC
Q 028027          110 VVADAMHGYLLFEHILQVHLIPPEHV  135 (215)
Q Consensus       110 ~ai~~l~g~~l~g~~l~V~~a~~~~~  135 (215)
                      +|+..|||..+..+.++|.++..+..
T Consensus       154 ~ai~s~ngq~l~nr~itv~ya~k~~~  179 (203)
T KOG0131|consen  154 AAIGSMNGQYLCNRPITVSYAFKKDT  179 (203)
T ss_pred             HHHHHhccchhcCCceEEEEEEecCC
Confidence            99999999999999999999875543

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

Probab=99.51  E-value=6.5e-14  Score=112.87  Aligned_cols=98  Identities=23%  Similarity=0.440  Sum_probs=86.0

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ...+.|.|.-||..+|+++|+.+|+..|+|++|++++|+-+|.+.|||||.|.++.+|++|+..|||..|..+.|+|+++
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            45577999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCCCcCCCCCCCCCCC
Q 028027          131 PPEHVHPKLWRGFNPRYKPVD  151 (215)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~  151 (215)
                      +|....   .++.+.+....|
T Consensus       119 RPSs~~---Ik~aNLYvSGlP  136 (360)
T KOG0145|consen  119 RPSSDS---IKDANLYVSGLP  136 (360)
T ss_pred             cCChhh---hcccceEEecCC
Confidence            886543   234444443333

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

Probab=99.50  E-value=1.2e-13  Score=112.98  Aligned_cols=80  Identities=33%  Similarity=0.679  Sum_probs=77.0

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeCC
Q 028027           53 ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPP  132 (215)
Q Consensus        53 ~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~~  132 (215)
                      .++|||+|||+.+++++|+++|..||.|..+.+..++.+|.++|||||.|.+.++|..|+..++|..|.|+.|.|.++.+
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

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

Probab=99.50  E-value=1.9e-13  Score=95.69  Aligned_cols=80  Identities=26%  Similarity=0.499  Sum_probs=72.5

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ....+.|||.|||+.+|.++..++|+.||.|..|+|-..+   ..+|-|||.|++..+|..|++.|+|+.+.++.|.|-+
T Consensus        15 pevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k---~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vly   91 (124)
T KOG0114|consen   15 PEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTK---ETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLY   91 (124)
T ss_pred             hhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCcc---CcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEe
Confidence            3567889999999999999999999999999999997654   4579999999999999999999999999999999988


Q ss_pred             eCC
Q 028027          130 IPP  132 (215)
Q Consensus       130 a~~  132 (215)
                      -.+
T Consensus        92 yq~   94 (124)
T KOG0114|consen   92 YQP   94 (124)
T ss_pred             cCH
Confidence            543

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

Probab=99.50  E-value=2.4e-14  Score=122.22  Aligned_cols=97  Identities=23%  Similarity=0.358  Sum_probs=85.1

Q ss_pred             CCCCCCCCCCCC--CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhC
Q 028027           39 PGRKLTEEKPLV--NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMH  116 (215)
Q Consensus        39 p~r~~~~~~~~~--~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~  116 (215)
                      |..+.+++.+.+  .+.+.||||.|+..++|.+++++|++||.|++|.|.++. .|.+||||||.|.+.+.|..||+.||
T Consensus       108 pvqvk~Ad~E~er~~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~-~~~sRGcaFV~fstke~A~~Aika~n  186 (510)
T KOG0144|consen  108 PVQVKYADGERERIVEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDP-DGLSRGCAFVKFSTKEMAVAAIKALN  186 (510)
T ss_pred             ceeecccchhhhccccchhhhhhhccccccHHHHHHHHHhhCccchhhheecc-cccccceeEEEEehHHHHHHHHHhhc
Confidence            666666665443  347899999999999999999999999999999999996 89999999999999999999999999


Q ss_pred             Cc-eeCC--eEEEEEEeCCCCCC
Q 028027          117 GY-LLFE--HILQVHLIPPEHVH  136 (215)
Q Consensus       117 g~-~l~g--~~l~V~~a~~~~~~  136 (215)
                      |. .+.|  .+|.|+||++.+.+
T Consensus       187 g~~tmeGcs~PLVVkFADtqkdk  209 (510)
T KOG0144|consen  187 GTQTMEGCSQPLVVKFADTQKDK  209 (510)
T ss_pred             cceeeccCCCceEEEecccCCCc
Confidence            95 4665  68999999987654

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

Probab=99.48  E-value=1e-13  Score=121.52  Aligned_cols=82  Identities=28%  Similarity=0.498  Sum_probs=78.8

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeCCC
Q 028027           54 TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPPE  133 (215)
Q Consensus        54 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~~~  133 (215)
                      +.|||||||+++++++|..+|+..|.|.+++++.|++||+++||||++|.+.++|..|+..|||..+.|+.|+|.|+...
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            88999999999999999999999999999999999999999999999999999999999999999999999999998765


Q ss_pred             CC
Q 028027          134 HV  135 (215)
Q Consensus       134 ~~  135 (215)
                      ..
T Consensus        99 ~~  100 (435)
T KOG0108|consen   99 KN  100 (435)
T ss_pred             ch
Confidence            44

>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=99.47  E-value=6.7e-13  Score=87.47  Aligned_cols=74  Identities=36%  Similarity=0.671  Sum_probs=68.5

Q ss_pred             EEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           55 VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        55 ~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      +|+|+|||+.+++++|+.+|..||.|..+.+..+. .+.++|+|||+|.+.++|..|+..+++..++|+.+.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~-~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDK-DTKSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            48999999999999999999999999999999886 447789999999999999999999999999999998864

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).

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

Probab=99.43  E-value=9.2e-13  Score=106.26  Aligned_cols=82  Identities=22%  Similarity=0.437  Sum_probs=77.8

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ..++.|||-||.++++|..|+++|++||.|..|++++|..|.+.+|||||.+.+.++|..||..|||+.++++.|.|.+.
T Consensus       276 ~~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsFK  355 (360)
T KOG0145|consen  276 GGGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFK  355 (360)
T ss_pred             CCeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccceEEEEEEe
Confidence            34688999999999999999999999999999999999988999999999999999999999999999999999999986


Q ss_pred             CC
Q 028027          131 PP  132 (215)
Q Consensus       131 ~~  132 (215)
                      ..
T Consensus       356 tn  357 (360)
T KOG0145|consen  356 TN  357 (360)
T ss_pred             cC
Confidence            54

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

Probab=99.43  E-value=1.2e-12  Score=117.87  Aligned_cols=79  Identities=23%  Similarity=0.416  Sum_probs=72.5

Q ss_pred             CCCcEEEEcCCCC-CCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           51 NKATVLYIGRIPH-GFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        51 ~~~~~l~V~nLp~-~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ..+++|||+|||+ .+++++|+.+|+.||.|..|.++.++     +|||||+|.+.++|..|+..|||..|.|+.|.|.+
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            4568999999998 69999999999999999999998874     58999999999999999999999999999999999


Q ss_pred             eCCCC
Q 028027          130 IPPEH  134 (215)
Q Consensus       130 a~~~~  134 (215)
                      +....
T Consensus       348 s~~~~  352 (481)
T TIGR01649       348 SKQQN  352 (481)
T ss_pred             ccccc
Confidence            86543

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).

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

Probab=99.41  E-value=1.2e-12  Score=117.70  Aligned_cols=76  Identities=14%  Similarity=0.251  Sum_probs=69.3

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHh--CCceeCCeEEEEEE
Q 028027           52 KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM--HGYLLFEHILQVHL  129 (215)
Q Consensus        52 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l--~g~~l~g~~l~V~~  129 (215)
                      ++++|||+|||+.+++++|+++|++||.|.+|.++.+      +|||||+|.+.++|+.|+..|  ++..|+|+.|.|.+
T Consensus         1 ps~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~~------k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~   74 (481)
T TIGR01649         1 PSPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPG------KRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNY   74 (481)
T ss_pred             CccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEECC------CCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEe
Confidence            3689999999999999999999999999999999864      479999999999999999864  78899999999999


Q ss_pred             eCCC
Q 028027          130 IPPE  133 (215)
Q Consensus       130 a~~~  133 (215)
                      +...
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).

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

Probab=99.41  E-value=1.9e-13  Score=114.72  Aligned_cols=76  Identities=29%  Similarity=0.569  Sum_probs=74.1

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 028027           53 ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVH  128 (215)
Q Consensus        53 ~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~  128 (215)
                      -++||||.|.+.+.|+.|+..|..||+|.+|.+..|+.|++++|||||+|+-++.|+.|++.|||..++||.|+|.
T Consensus       113 McRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVg  188 (544)
T KOG0124|consen  113 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVG  188 (544)
T ss_pred             hHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCcccccc
Confidence            4889999999999999999999999999999999999999999999999999999999999999999999999987

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

Probab=99.39  E-value=2e-12  Score=117.34  Aligned_cols=75  Identities=28%  Similarity=0.482  Sum_probs=69.5

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccC--CCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           52 KATVLYIGRIPHGFYEKEMQAFFSQF--GAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        52 ~~~~l~V~nLp~~~te~~L~~~F~~~--G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ..++|||+||++++++++|+++|+.|  |.|..|.+++        +||||+|.+.++|..|+..|||..|+|+.|+|.|
T Consensus       232 ~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~r--------gfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~  303 (578)
T TIGR01648       232 KVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIR--------DYAFVHFEDREDAVKAMDELNGKELEGSEIEVTL  303 (578)
T ss_pred             cccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEeec--------CeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            45789999999999999999999999  9999997753        5999999999999999999999999999999999


Q ss_pred             eCCCC
Q 028027          130 IPPEH  134 (215)
Q Consensus       130 a~~~~  134 (215)
                      +++..
T Consensus       304 Akp~~  308 (578)
T TIGR01648       304 AKPVD  308 (578)
T ss_pred             ccCCC
Confidence            98754

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

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

Probab=99.39  E-value=1.5e-12  Score=114.19  Aligned_cols=82  Identities=22%  Similarity=0.366  Sum_probs=76.5

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeC
Q 028027           52 KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIP  131 (215)
Q Consensus        52 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~  131 (215)
                      +-..|+|.|||+.|...+|..+|+.||.|..|.|++.. .|+.+|||||.|....+|..|++.|||..|+|++|-|.||-
T Consensus       116 ~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~-dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV  194 (678)
T KOG0127|consen  116 PKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKK-DGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAV  194 (678)
T ss_pred             ccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCC-CCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeec
Confidence            46889999999999999999999999999999999876 67777999999999999999999999999999999999997


Q ss_pred             CCC
Q 028027          132 PEH  134 (215)
Q Consensus       132 ~~~  134 (215)
                      ++.
T Consensus       195 ~Kd  197 (678)
T KOG0127|consen  195 DKD  197 (678)
T ss_pred             ccc
Confidence            653

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

Probab=99.39  E-value=1.1e-12  Score=113.66  Aligned_cols=100  Identities=25%  Similarity=0.443  Sum_probs=89.0

Q ss_pred             CCCCcccCCCCCCCCCCCCCCCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHH
Q 028027           29 AADFLPLEGGPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVA  108 (215)
Q Consensus        29 ~~d~~~~~g~p~r~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a  108 (215)
                      ..++..+.|+|+|.......+.    .|||.||++.++..+|.++|+.||.|.+|++..+. .| ++|| ||+|.+.+.|
T Consensus        56 ~~n~~~~~~~~~rim~s~rd~~----~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~-~g-~kg~-FV~f~~e~~a  128 (369)
T KOG0123|consen   56 TMNFDVLKGKPIRIMWSQRDPS----LVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDE-NG-SKGY-FVQFESEESA  128 (369)
T ss_pred             HcCCcccCCcEEEeehhccCCc----eeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcC-CC-ceee-EEEeCCHHHH
Confidence            5677889999999887665443    39999999999999999999999999999999996 66 9999 9999999999


Q ss_pred             HHHHHHhCCceeCCeEEEEEEeCCCCC
Q 028027          109 EVVADAMHGYLLFEHILQVHLIPPEHV  135 (215)
Q Consensus       109 ~~ai~~l~g~~l~g~~l~V~~a~~~~~  135 (215)
                      +.|+..|||..+.|+.|.|.....+..
T Consensus       129 ~~ai~~~ng~ll~~kki~vg~~~~~~e  155 (369)
T KOG0123|consen  129 KKAIEKLNGMLLNGKKIYVGLFERKEE  155 (369)
T ss_pred             HHHHHHhcCcccCCCeeEEeeccchhh
Confidence            999999999999999999988766544

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

Probab=99.37  E-value=1.2e-12  Score=100.85  Aligned_cols=80  Identities=26%  Similarity=0.492  Sum_probs=71.6

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ...++|||+|||.++.+.+|+++|.+||.|..|.|..-+   ..-.||||+|++..+|+.||..-+|+.++|..|+|+++
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            356899999999999999999999999999999885432   23479999999999999999999999999999999998


Q ss_pred             CCC
Q 028027          131 PPE  133 (215)
Q Consensus       131 ~~~  133 (215)
                      ..-
T Consensus        81 rgg   83 (241)
T KOG0105|consen   81 RGG   83 (241)
T ss_pred             cCC
Confidence            764

>smart00361 RRM_1 RNA recognition motif

Probab=99.37  E-value=3.4e-12  Score=85.08  Aligned_cols=62  Identities=16%  Similarity=0.292  Sum_probs=55.4

Q ss_pred             HHHHHHHhc----cCCCeeEEE-EeecCCC--CCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 028027           67 EKEMQAFFS----QFGAIKRLR-IARNKKT--GQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVH  128 (215)
Q Consensus        67 e~~L~~~F~----~~G~v~~v~-i~~~~~t--g~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~  128 (215)
                      +++|+++|+    .||.|.++. ++.++.+  +.++|||||+|.+.++|..|+..|||..+.|+.|+++
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~~   70 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKAE   70 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEeC
Confidence            568888888    999999995 6666656  8999999999999999999999999999999999863

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

Probab=99.36  E-value=8.7e-13  Score=106.78  Aligned_cols=87  Identities=30%  Similarity=0.523  Sum_probs=82.3

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 028027           49 LVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVH  128 (215)
Q Consensus        49 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~  128 (215)
                      ..+++|.|||-+||..+.+.+|...|-.||.|.+.++..|+.|+.+++||||.|.+..+++.||..|||+.|+-++|+|.
T Consensus       281 eGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQ  360 (371)
T KOG0146|consen  281 EGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQ  360 (371)
T ss_pred             cCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhh
Confidence            35788999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeCCCCC
Q 028027          129 LIPPEHV  135 (215)
Q Consensus       129 ~a~~~~~  135 (215)
                      +.+|+..
T Consensus       361 LKRPkda  367 (371)
T KOG0146|consen  361 LKRPKDA  367 (371)
T ss_pred             hcCcccc
Confidence            9887654

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

Probab=99.35  E-value=7e-12  Score=110.05  Aligned_cols=85  Identities=28%  Similarity=0.507  Sum_probs=77.7

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHh-----CC-ceeCCe
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM-----HG-YLLFEH  123 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l-----~g-~~l~g~  123 (215)
                      .....+|||.|||+++|++.|...|++||+|..+.|+.++.||.++|.|||.|.+..+|+.||..-     .| +.|+|+
T Consensus       289 ~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~GR  368 (678)
T KOG0127|consen  289 ITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLLDGR  368 (678)
T ss_pred             ccccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcCccCCCceEEEecc
Confidence            345689999999999999999999999999999999999999999999999999999999999866     34 789999


Q ss_pred             EEEEEEeCCCC
Q 028027          124 ILQVHLIPPEH  134 (215)
Q Consensus       124 ~l~V~~a~~~~  134 (215)
                      .|.|..+-++.
T Consensus       369 ~Lkv~~Av~Rk  379 (678)
T KOG0127|consen  369 LLKVTLAVTRK  379 (678)
T ss_pred             EEeeeeccchH
Confidence            99999987654

>PF13893 RRM_5: RNA recognition motif

Probab=99.35  E-value=8.9e-12  Score=79.27  Aligned_cols=56  Identities=29%  Similarity=0.559  Sum_probs=50.8

Q ss_pred             HHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           70 MQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        70 L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      |..+|++||.|..+.+..+.     +++|||+|.+.++|..|+..|||..++|+.|+|.||
T Consensus         1 L~~~f~~fG~V~~i~~~~~~-----~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK-----RGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS-----TTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            67899999999999997653     589999999999999999999999999999999986

(a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....

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

Probab=99.34  E-value=1.5e-12  Score=114.19  Aligned_cols=79  Identities=28%  Similarity=0.615  Sum_probs=75.3

Q ss_pred             EEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeCCC
Q 028027           55 VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPPE  133 (215)
Q Consensus        55 ~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~~~  133 (215)
                      .||||||.+++++++|+.+|..||.|..|.++.+.+||.++|||||+|.+.++|..|+..|||+.|-|+.|+|.....+
T Consensus       280 rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r  358 (549)
T KOG0147|consen  280 RLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTER  358 (549)
T ss_pred             hhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeeee
Confidence            3999999999999999999999999999999999889999999999999999999999999999999999999886554

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

Probab=99.33  E-value=2.2e-12  Score=108.05  Aligned_cols=83  Identities=25%  Similarity=0.454  Sum_probs=79.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      .++...|||.-|.+-++.++|.-+|+.||.|.+|.++++..||.+..||||+|.+.++|+.|.-.|++..|+.++|+|.+
T Consensus       236 ~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDF  315 (479)
T KOG0415|consen  236 KPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDF  315 (479)
T ss_pred             CCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeeh
Confidence            35668999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             eCC
Q 028027          130 IPP  132 (215)
Q Consensus       130 a~~  132 (215)
                      +.+
T Consensus       316 SQS  318 (479)
T KOG0415|consen  316 SQS  318 (479)
T ss_pred             hhh
Confidence            754

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

Probab=99.31  E-value=4.9e-12  Score=108.63  Aligned_cols=76  Identities=25%  Similarity=0.470  Sum_probs=70.6

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeC
Q 028027           52 KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIP  131 (215)
Q Consensus        52 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~  131 (215)
                      ....|||.||+.++|++.|..+|.+||.|..|..++|        ||||.|.+.++|..|++.|||+.|+|..|.|.+|+
T Consensus       258 ~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD--------YaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAK  329 (506)
T KOG0117|consen  258 KVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD--------YAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAK  329 (506)
T ss_pred             heeeeeeeccchhhhHHHHHHHHHhccceEEeecccc--------eeEEeecchHHHHHHHHHhcCceecCceEEEEecC
Confidence            3467999999999999999999999999999988765        99999999999999999999999999999999999


Q ss_pred             CCCC
Q 028027          132 PEHV  135 (215)
Q Consensus       132 ~~~~  135 (215)
                      |...
T Consensus       330 P~~k  333 (506)
T KOG0117|consen  330 PVDK  333 (506)
T ss_pred             Chhh
Confidence            8543

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

Probab=99.31  E-value=4.8e-12  Score=102.50  Aligned_cols=100  Identities=20%  Similarity=0.356  Sum_probs=86.1

Q ss_pred             CCCCCCCCCCCCCCC-CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHh
Q 028027           37 GGPGRKLTEEKPLVN-KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM  115 (215)
Q Consensus        37 g~p~r~~~~~~~~~~-~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l  115 (215)
                      .+|+.++|.+.+... +.+.||||.|...-.|+|++.+|..||.|.+|.+.+.. .|.++|+|||.|.+.-+|+.||..|
T Consensus         2 nrpiqvkpadsesrg~~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~-dg~sKGCAFVKf~s~~eAqaAI~aL   80 (371)
T KOG0146|consen    2 NRPIQVKPADSESRGGDDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGP-DGNSKGCAFVKFSSHAEAQAAINAL   80 (371)
T ss_pred             CCCccccccccccCCccchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCC-CCCCCCceEEEeccchHHHHHHHHh
Confidence            467777776654433 77899999999999999999999999999999999997 8999999999999999999999999


Q ss_pred             CCce-eCC--eEEEEEEeCCCCCCC
Q 028027          116 HGYL-LFE--HILQVHLIPPEHVHP  137 (215)
Q Consensus       116 ~g~~-l~g--~~l~V~~a~~~~~~~  137 (215)
                      +|.. +.|  ..|.|.+++.++.+.
T Consensus        81 HgSqTmpGASSSLVVK~ADTdkER~  105 (371)
T KOG0146|consen   81 HGSQTMPGASSSLVVKFADTDKERT  105 (371)
T ss_pred             cccccCCCCccceEEEeccchHHHH
Confidence            9963 554  679999998876543

>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=8.9e-12  Score=101.96  Aligned_cols=73  Identities=29%  Similarity=0.581  Sum_probs=69.1

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeCCC
Q 028027           54 TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPPE  133 (215)
Q Consensus        54 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~~~  133 (215)
                      ..|||||||..+++.+|+.+|++||.|..|.|+++        ||||..++...++.||..|+|+.|+|..|.|+-++.+
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            36999999999999999999999999999999976        9999999999999999999999999999999998876


Q ss_pred             C
Q 028027          134 H  134 (215)
Q Consensus       134 ~  134 (215)
                      +
T Consensus        75 s   75 (346)
T KOG0109|consen   75 S   75 (346)
T ss_pred             C
Confidence            3

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

Probab=99.22  E-value=1.3e-11  Score=101.00  Aligned_cols=97  Identities=18%  Similarity=0.255  Sum_probs=85.4

Q ss_pred             CCCCCcccCCCCCCCCCCCCCCCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHH
Q 028027           28 GAADFLPLEGGPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEV  107 (215)
Q Consensus        28 ~~~d~~~~~g~p~r~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~  107 (215)
                      .++++..|+|..+.+..... ....+++|+||||.+.++..+|+..|..||+|..|.|+++        |+||.|.-.++
T Consensus        54 rNLhgYtLhg~nInVeaSks-Ksk~stkl~vgNis~tctn~ElRa~fe~ygpviecdivkd--------y~fvh~d~~ed  124 (346)
T KOG0109|consen   54 RNLHGYTLHGVNINVEASKS-KSKASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKD--------YAFVHFDRAED  124 (346)
T ss_pred             hhcccceecceEEEEEeccc-cCCCccccccCCCCccccCHHHhhhhcccCCceeeeeecc--------eeEEEEeeccc
Confidence            45778889998776544332 2456789999999999999999999999999999999876        99999999999


Q ss_pred             HHHHHHHhCCceeCCeEEEEEEeCCC
Q 028027          108 AEVVADAMHGYLLFEHILQVHLIPPE  133 (215)
Q Consensus       108 a~~ai~~l~g~~l~g~~l~V~~a~~~  133 (215)
                      |..|+..||+..+.|++++|++++++
T Consensus       125 a~~air~l~~~~~~gk~m~vq~stsr  150 (346)
T KOG0109|consen  125 AVEAIRGLDNTEFQGKRMHVQLSTSR  150 (346)
T ss_pred             hHHHHhcccccccccceeeeeeeccc
Confidence            99999999999999999999998775

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

Probab=99.21  E-value=3.7e-11  Score=101.13  Aligned_cols=105  Identities=20%  Similarity=0.270  Sum_probs=88.4

Q ss_pred             CCCCCcccCCCCCCCCCCCCCC------------CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcc
Q 028027           28 GAADFLPLEGGPGRKLTEEKPL------------VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSK   95 (215)
Q Consensus        28 ~~~d~~~~~g~p~r~~~~~~~~------------~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~   95 (215)
                      +..++..+-|+.+.+...+.-+            ...-.+|||..+.++.+++||+.+|..||+|..|.+.+++.++.++
T Consensus       173 EqMNg~mlGGRNiKVgrPsNmpQAQpiID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~Hk  252 (544)
T KOG0124|consen  173 EQMNGQMLGGRNIKVGRPSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHK  252 (544)
T ss_pred             HHhccccccCccccccCCCCCcccchHHHHHHHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCcc
Confidence            4556777777766544332211            2345789999999999999999999999999999999999888999


Q ss_pred             cEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeCC
Q 028027           96 HFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPP  132 (215)
Q Consensus        96 g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~~  132 (215)
                      |||||+|.+..+...|+..||-+.|+|..|+|-.+-.
T Consensus       253 GyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~vT  289 (544)
T KOG0124|consen  253 GYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVT  289 (544)
T ss_pred             ceeeEEeccccchHHHhhhcchhhcccceEecccccC
Confidence            9999999999999999999999999999999976543

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

Probab=99.20  E-value=6.6e-11  Score=93.86  Aligned_cols=83  Identities=22%  Similarity=0.432  Sum_probs=74.4

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHH----HhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEE
Q 028027           51 NKATVLYIGRIPHGFYEKEMQA----FFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQ  126 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~----~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~  126 (215)
                      .+..||||.||+..+..++|+.    +|++||.|.+|....   |.+.+|-|||.|.+.+.|-.|+..|+|+.+.|+.++
T Consensus         7 ~pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~k---t~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mr   83 (221)
T KOG4206|consen    7 NPNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFK---TPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMR   83 (221)
T ss_pred             CCCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecC---CCCccCceEEEecChhHHHHHHHHhcCCcccCchhh
Confidence            3445999999999999998877    999999999987753   788999999999999999999999999999999999


Q ss_pred             EEEeCCCCCC
Q 028027          127 VHLIPPEHVH  136 (215)
Q Consensus       127 V~~a~~~~~~  136 (215)
                      |.+|..+...
T Consensus        84 iqyA~s~sdi   93 (221)
T KOG4206|consen   84 IQYAKSDSDI   93 (221)
T ss_pred             eecccCccch
Confidence            9999877654

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

Probab=99.19  E-value=4.9e-11  Score=100.66  Aligned_cols=98  Identities=21%  Similarity=0.410  Sum_probs=86.1

Q ss_pred             CCCCCCCCCCCCCC----CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHH
Q 028027           39 PGRKLTEEKPLVNK----ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA  114 (215)
Q Consensus        39 p~r~~~~~~~~~~~----~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~  114 (215)
                      |+++.++..+....    ...|||++||.++++.+++++|.+||.|..+.++.|..+.+++||+||.|.+.+++..++. 
T Consensus        79 ~k~av~r~~~~~~~~~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~-  157 (311)
T KOG4205|consen   79 PKRAVSREDQTKVGRHLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL-  157 (311)
T ss_pred             ceeccCcccccccccccceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecc-
Confidence            55677777766544    4489999999999999999999999999999999999999999999999999999999884 


Q ss_pred             hCCceeCCeEEEEEEeCCCCCCC
Q 028027          115 MHGYLLFEHILQVHLIPPEHVHP  137 (215)
Q Consensus       115 l~g~~l~g~~l~V~~a~~~~~~~  137 (215)
                      ..-+.|.|+.+.|..|.|+....
T Consensus       158 ~~f~~~~gk~vevkrA~pk~~~~  180 (311)
T KOG4205|consen  158 QKFHDFNGKKVEVKRAIPKEVMQ  180 (311)
T ss_pred             cceeeecCceeeEeeccchhhcc
Confidence            57789999999999998876543

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

Probab=99.14  E-value=1.9e-10  Score=104.03  Aligned_cols=74  Identities=27%  Similarity=0.513  Sum_probs=61.4

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccC------------CCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCC
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQF------------GAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHG  117 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~------------G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g  117 (215)
                      ....++|||||||+.+|+++|.++|.+|            +.|..+.+      +..+|||||+|.+.++|..|| .|||
T Consensus       172 ~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~------~~~kg~afVeF~~~e~A~~Al-~l~g  244 (509)
T TIGR01642       172 TRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNI------NKEKNFAFLEFRTVEEATFAM-ALDS  244 (509)
T ss_pred             CccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEE------CCCCCEEEEEeCCHHHHhhhh-cCCC
Confidence            3456899999999999999999999875            23444444      344689999999999999999 5999


Q ss_pred             ceeCCeEEEEEEe
Q 028027          118 YLLFEHILQVHLI  130 (215)
Q Consensus       118 ~~l~g~~l~V~~a  130 (215)
                      ..|.|..|.|...
T Consensus       245 ~~~~g~~l~v~r~  257 (509)
T TIGR01642       245 IIYSNVFLKIRRP  257 (509)
T ss_pred             eEeeCceeEecCc
Confidence            9999999998643

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

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

Probab=99.14  E-value=5.4e-11  Score=100.38  Aligned_cols=85  Identities=25%  Similarity=0.442  Sum_probs=76.9

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeC
Q 028027           52 KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIP  131 (215)
Q Consensus        52 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~  131 (215)
                      +.++|||++|+|.++++.|+++|.+||+|..|.+++++.+++++||+||+|.+.+.+.+++. ...+.|+|+.|.+.-+.
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~-~~~h~~dgr~ve~k~av   83 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLN-ARTHKLDGRSVEPKRAV   83 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeec-ccccccCCccccceecc
Confidence            67899999999999999999999999999999999999999999999999999998888874 35678999999999888


Q ss_pred             CCCCCC
Q 028027          132 PEHVHP  137 (215)
Q Consensus       132 ~~~~~~  137 (215)
                      ++....
T Consensus        84 ~r~~~~   89 (311)
T KOG4205|consen   84 SREDQT   89 (311)
T ss_pred             Cccccc
Confidence            776443

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

Probab=99.12  E-value=1.5e-10  Score=105.21  Aligned_cols=99  Identities=13%  Similarity=0.246  Sum_probs=83.3

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      .-++|||||+|+..+++.+|..+|+.||.|.+|.++-.      +|||||.+....+|..|+..|+.+.+.++.|+|.|+
T Consensus       419 V~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~------R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa  492 (894)
T KOG0132|consen  419 VCSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP------RGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWA  492 (894)
T ss_pred             EeeeeeeeccccchhhHHHHHHHHHhcccceeEeeccC------CceeEEEEeehhHHHHHHHHHhcccccceeeEEeee
Confidence            45689999999999999999999999999999988765      489999999999999999999999999999999999


Q ss_pred             CCCCCCCCCc--CCCCCCCCCCChHHH
Q 028027          131 PPEHVHPKLW--RGFNPRYKPVDRVQV  155 (215)
Q Consensus       131 ~~~~~~~~~~--~~~~~~~~~~~~~~~  155 (215)
                      ...-.+..+.  ......+.-++|..+
T Consensus       493 ~g~G~kse~k~~wD~~lGVt~IP~~kL  519 (894)
T KOG0132|consen  493 VGKGPKSEYKDYWDVELGVTYIPWEKL  519 (894)
T ss_pred             ccCCcchhhhhhhhcccCeeEeehHhc
Confidence            8766555222  223335566788765

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

Probab=99.11  E-value=2.6e-10  Score=98.03  Aligned_cols=81  Identities=16%  Similarity=0.361  Sum_probs=74.4

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhc-cCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFS-QFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~-~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ...+.+||.|||+++.+.+|+++|. ..|+|+.|.+..|. +|+++|+|.|+|.+++.+++|++.||.+.+.|+.|.|.-
T Consensus        42 ~r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~-~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKE  120 (608)
T KOG4212|consen   42 ARDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDE-SGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKE  120 (608)
T ss_pred             cccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeeccc-CCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEec
Confidence            3456799999999999999999996 48999999999995 999999999999999999999999999999999999987


Q ss_pred             eCC
Q 028027          130 IPP  132 (215)
Q Consensus       130 a~~  132 (215)
                      ...
T Consensus       121 d~d  123 (608)
T KOG4212|consen  121 DHD  123 (608)
T ss_pred             cCc
Confidence            544

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

Probab=99.10  E-value=5e-10  Score=99.09  Aligned_cols=84  Identities=14%  Similarity=0.346  Sum_probs=77.3

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ..-++.|||++|+..+.-.+|..+|++||.|.-..++.+-.+...++||||++.+.++|..||..|+.+.|+|+.|.|..
T Consensus       402 s~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEk  481 (940)
T KOG4661|consen  402 STLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEK  481 (940)
T ss_pred             cccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeee
Confidence            34568899999999999999999999999999999999877888899999999999999999999999999999999988


Q ss_pred             eCCC
Q 028027          130 IPPE  133 (215)
Q Consensus       130 a~~~  133 (215)
                      ++..
T Consensus       482 aKNE  485 (940)
T KOG4661|consen  482 AKNE  485 (940)
T ss_pred             cccC
Confidence            7543

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

Probab=99.08  E-value=4.5e-10  Score=94.03  Aligned_cols=78  Identities=26%  Similarity=0.459  Sum_probs=68.9

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHH-HhCCceeCCeEEEE
Q 028027           49 LVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD-AMHGYLLFEHILQV  127 (215)
Q Consensus        49 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~-~l~g~~l~g~~l~V  127 (215)
                      ......+|||++|-..+++.+|++.|.+||+|.++.+....      ++|||+|.+.++|+.|.. .+|...|+|.+|.|
T Consensus       224 eD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~~------~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i  297 (377)
T KOG0153|consen  224 EDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPRK------GCAFVTFTTREAAEKAAEKSFNKLVINGFRLKI  297 (377)
T ss_pred             cccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeeccc------ccceeeehhhHHHHHHHHhhcceeeecceEEEE
Confidence            34566899999999999999999999999999999887653      699999999999998885 45656799999999


Q ss_pred             EEeCC
Q 028027          128 HLIPP  132 (215)
Q Consensus       128 ~~a~~  132 (215)
                      .|..+
T Consensus       298 ~Wg~~  302 (377)
T KOG0153|consen  298 KWGRP  302 (377)
T ss_pred             EeCCC
Confidence            99988

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

Probab=99.07  E-value=4.2e-10  Score=97.73  Aligned_cols=75  Identities=24%  Similarity=0.387  Sum_probs=70.2

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeCCC
Q 028027           54 TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPPE  133 (215)
Q Consensus        54 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~~~  133 (215)
                      ..||||   +++|+.+|.++|+.+|+|.++++++|. |  +.|||||.|.++.+|.+||..||...+.|++|++-|+...
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~-t--slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd   75 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDA-T--SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRD   75 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecC-C--ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccC
Confidence            368999   889999999999999999999999997 5  9999999999999999999999999999999999998655


Q ss_pred             C
Q 028027          134 H  134 (215)
Q Consensus       134 ~  134 (215)
                      .
T Consensus        76 ~   76 (369)
T KOG0123|consen   76 P   76 (369)
T ss_pred             C
Confidence            4

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

Probab=99.02  E-value=1.7e-09  Score=88.12  Aligned_cols=84  Identities=20%  Similarity=0.432  Sum_probs=77.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      +..+++|+|.|||+.++++||+++|..||.+..+.+..++ +|.+.|.|-|.|...++|.+|++.++|..++|+.+.+..
T Consensus        80 ~~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~-~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~  158 (243)
T KOG0533|consen   80 ETRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDR-AGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEI  158 (243)
T ss_pred             CCCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCC-CCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEE
Confidence            3455789999999999999999999999999999999996 999999999999999999999999999999999999988


Q ss_pred             eCCCC
Q 028027          130 IPPEH  134 (215)
Q Consensus       130 a~~~~  134 (215)
                      ..+..
T Consensus       159 i~~~~  163 (243)
T KOG0533|consen  159 ISSPS  163 (243)
T ss_pred             ecCcc
Confidence            65543

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

Probab=99.00  E-value=4.4e-09  Score=88.10  Aligned_cols=82  Identities=18%  Similarity=0.239  Sum_probs=74.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCee--------EEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeC
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIK--------RLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLF  121 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~--------~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~  121 (215)
                      ....+.|||+|||.++|.+++..+|+.||.|.        .|.|.++. .|..+|-|++.|-..+++..|+..|++..|.
T Consensus       131 ~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~-~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~r  209 (382)
T KOG1548|consen  131 PKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDN-QGKLKGDALCCYIKRESVELAIKILDEDELR  209 (382)
T ss_pred             cccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecC-CCCccCceEEEeecccHHHHHHHHhCccccc
Confidence            34456799999999999999999999999884        37888886 6999999999999999999999999999999


Q ss_pred             CeEEEEEEeCC
Q 028027          122 EHILQVHLIPP  132 (215)
Q Consensus       122 g~~l~V~~a~~  132 (215)
                      |+.|+|+.|+=
T Consensus       210 g~~~rVerAkf  220 (382)
T KOG1548|consen  210 GKKLRVERAKF  220 (382)
T ss_pred             CcEEEEehhhh
Confidence            99999998753

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

Probab=99.00  E-value=4.5e-10  Score=101.40  Aligned_cols=84  Identities=25%  Similarity=0.510  Sum_probs=77.3

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ...+.|+|.|||+..+-.+++.+|..||.|.+|+|+.-...+.++|||||+|-++.+|.+|++.|.++-|.||.|.++|+
T Consensus       611 k~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEwA  690 (725)
T KOG0110|consen  611 KKGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEWA  690 (725)
T ss_pred             cccceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhcccceechhhheehh
Confidence            44678999999999999999999999999999999987567788999999999999999999999998999999999999


Q ss_pred             CCCC
Q 028027          131 PPEH  134 (215)
Q Consensus       131 ~~~~  134 (215)
                      ....
T Consensus       691 ~~d~  694 (725)
T KOG0110|consen  691 KSDN  694 (725)
T ss_pred             ccch
Confidence            7653

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

Probab=98.98  E-value=2.8e-09  Score=96.35  Aligned_cols=78  Identities=27%  Similarity=0.501  Sum_probs=70.6

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCC----CcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 028027           53 ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTG----QSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVH  128 (215)
Q Consensus        53 ~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg----~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~  128 (215)
                      .++|||.||++.+|.++|...|...|.|.++.|...+ .+    .+.|||||+|.+.++|+.|+..|+|+.|+|+.|.|+
T Consensus       515 ~t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkk-d~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk  593 (725)
T KOG0110|consen  515 ETKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKK-DPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELK  593 (725)
T ss_pred             chhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccc-cccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEE
Confidence            3449999999999999999999999999999887765 33    245999999999999999999999999999999999


Q ss_pred             EeC
Q 028027          129 LIP  131 (215)
Q Consensus       129 ~a~  131 (215)
                      ++.
T Consensus       594 ~S~  596 (725)
T KOG0110|consen  594 ISE  596 (725)
T ss_pred             ecc
Confidence            987

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

Probab=98.94  E-value=5.8e-09  Score=94.34  Aligned_cols=105  Identities=19%  Similarity=0.301  Sum_probs=84.1

Q ss_pred             CCCCCcccCCCCCCCCCCCCCCCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecC---CCCCcccEEEEEEcC
Q 028027           28 GAADFLPLEGGPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNK---KTGQSKHFGFIEFND  104 (215)
Q Consensus        28 ~~~d~~~~~g~p~r~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~---~tg~~~g~afV~F~~  104 (215)
                      +..+..+..+.|......-+...+..+.|||+||++.+++..|...|+.||+|..++|+..+   +....+.+|||.|-+
T Consensus       149 ~r~~~~p~~~~~s~~~gsfDdgDP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmn  228 (877)
T KOG0151|consen  149 SRFDPLPSRFDPSGRPGSFDDGDPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMN  228 (877)
T ss_pred             hccCCCccccCCCCCCCcCCCCCCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehh
Confidence            44454554555544333333445667889999999999999999999999999999888764   234566899999999


Q ss_pred             HHHHHHHHHHhCCceeCCeEEEEEEeCC
Q 028027          105 PEVAEVVADAMHGYLLFEHILQVHLIPP  132 (215)
Q Consensus       105 ~~~a~~ai~~l~g~~l~g~~l~V~~a~~  132 (215)
                      ..+|++|++.|+|..+.+..+++-|.++
T Consensus       229 R~D~era~k~lqg~iv~~~e~K~gWgk~  256 (877)
T KOG0151|consen  229 RADAERALKELQGIIVMEYEMKLGWGKA  256 (877)
T ss_pred             hhhHHHHHHHhcceeeeeeeeeeccccc
Confidence            9999999999999999999999999854

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

Probab=98.91  E-value=4.4e-09  Score=84.85  Aligned_cols=79  Identities=20%  Similarity=0.436  Sum_probs=73.3

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVH  128 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~  128 (215)
                      ..+...||+|.|...++.+.|-..|.+|-.-....+++++.||+++||+||.|.+..++..|+..|||..++.+.|.++
T Consensus       187 ~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklR  265 (290)
T KOG0226|consen  187 DEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLR  265 (290)
T ss_pred             ccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhh
Confidence            3566889999999999999999999999888888999999999999999999999999999999999999999888754

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

Probab=98.89  E-value=3.8e-09  Score=90.97  Aligned_cols=75  Identities=27%  Similarity=0.371  Sum_probs=68.4

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ...++|||.|||.++|+..|++-|..||.|..+.|+   +.|+++|  .|.|.++++|++|+..|+|..|+|+.|.|.+.
T Consensus       534 rKa~qIiirNlP~dfTWqmlrDKfre~G~v~yadim---e~GkskG--VVrF~s~edAEra~a~Mngs~l~Gr~I~V~y~  608 (608)
T KOG4212|consen  534 RKACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIM---ENGKSKG--VVRFFSPEDAERACALMNGSRLDGRNIKVTYF  608 (608)
T ss_pred             ccccEEEEecCCccccHHHHHHHHHhccceehhhhh---ccCCccc--eEEecCHHHHHHHHHHhccCcccCceeeeeeC
Confidence            456889999999999999999999999999999884   3577776  99999999999999999999999999999873

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

Probab=98.86  E-value=7.6e-09  Score=84.31  Aligned_cols=85  Identities=20%  Similarity=0.366  Sum_probs=78.6

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEE
Q 028027           48 PLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQV  127 (215)
Q Consensus        48 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V  127 (215)
                      ....+...+||+|+.+.+|.+.+...|..||.|..+.+..++.+|.++||+||+|.+.+.++.++. |||..|.|+.+.|
T Consensus        96 ~~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~v  174 (231)
T KOG4209|consen   96 QKEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEV  174 (231)
T ss_pred             hhccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCccccccccee
Confidence            445778999999999999999999999999999999999999888999999999999999999997 9999999999999


Q ss_pred             EEeCCC
Q 028027          128 HLIPPE  133 (215)
Q Consensus       128 ~~a~~~  133 (215)
                      .+....
T Consensus       175 t~~r~~  180 (231)
T KOG4209|consen  175 TLKRTN  180 (231)
T ss_pred             eeeeee
Confidence            887554

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

Probab=98.81  E-value=5.3e-08  Score=77.40  Aligned_cols=86  Identities=16%  Similarity=0.294  Sum_probs=70.9

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeec-CCCCCcccEEEEEEcCHHHHHHHHHHhCCceeC---CeEEE
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARN-KKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLF---EHILQ  126 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~-~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~---g~~l~  126 (215)
                      ...+||||.+||.++...+|+.+|..|-..+.+.+... +.....+-+|||+|.+...|.+|+..|||..++   +..|+
T Consensus        32 ~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLh  111 (284)
T KOG1457|consen   32 GAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLH  111 (284)
T ss_pred             cccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeE
Confidence            45799999999999999999999999876666655443 222234579999999999999999999999887   78999


Q ss_pred             EEEeCCCCCC
Q 028027          127 VHLIPPEHVH  136 (215)
Q Consensus       127 V~~a~~~~~~  136 (215)
                      +++++.....
T Consensus       112 iElAKSNtK~  121 (284)
T KOG1457|consen  112 IELAKSNTKR  121 (284)
T ss_pred             eeehhcCccc
Confidence            9999875543

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

Probab=98.77  E-value=3.4e-08  Score=86.52  Aligned_cols=83  Identities=23%  Similarity=0.372  Sum_probs=69.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      .....+|||.|||++++.++|+++|.+||.|....|..-...+...+||||+|.+.+.++.||.+ +-..|+++.|.|+.
T Consensus       285 ~~~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Vee  363 (419)
T KOG0116|consen  285 RADGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEE  363 (419)
T ss_pred             eecccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEe
Confidence            34556799999999999999999999999999887765432344449999999999999999976 57789999999998


Q ss_pred             eCCC
Q 028027          130 IPPE  133 (215)
Q Consensus       130 a~~~  133 (215)
                      ..+.
T Consensus       364 k~~~  367 (419)
T KOG0116|consen  364 KRPG  367 (419)
T ss_pred             cccc
Confidence            7663

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

Probab=98.63  E-value=3.2e-07  Score=64.66  Aligned_cols=78  Identities=15%  Similarity=0.281  Sum_probs=67.0

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhcc--CCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeC----CeEEEE
Q 028027           54 TVLYIGRIPHGFYEKEMQAFFSQ--FGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLF----EHILQV  127 (215)
Q Consensus        54 ~~l~V~nLp~~~te~~L~~~F~~--~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~----g~~l~V  127 (215)
                      +||.|.|||...|.++|.+++..  .|...-+.++.|..++-+.|||||.|.+.+.|..-...++|..+.    .+.+.|
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~i   81 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCEI   81 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEEE
Confidence            68999999999999999988865  367777888889889999999999999999999999999998765    455666


Q ss_pred             EEeC
Q 028027          128 HLIP  131 (215)
Q Consensus       128 ~~a~  131 (215)
                      .+|.
T Consensus        82 ~yAr   85 (97)
T PF04059_consen   82 SYAR   85 (97)
T ss_pred             ehhH
Confidence            6664

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

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

Probab=98.61  E-value=4.9e-08  Score=78.09  Aligned_cols=72  Identities=31%  Similarity=0.556  Sum_probs=65.8

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeCCC
Q 028027           54 TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPPE  133 (215)
Q Consensus        54 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~~~  133 (215)
                      ..||||+||+.+.+.+|..+|..||.|..+.+..        ||+||+|.+..+|..|+.-+|+..|.|..+.|.++...
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 PRVYIGRLPYRARERDVERFFKGYGKIPDADMKN--------GFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGK   73 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceeec--------ccceeccCchhhhhcccchhcCceecceeeeeeccccc
Confidence            3599999999999999999999999999987642        69999999999999999999999999999999998864

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

Probab=98.59  E-value=2e-08  Score=79.59  Aligned_cols=80  Identities=19%  Similarity=0.259  Sum_probs=71.9

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ...+||||+|+...++|+-|.++|-+.|+|..|.|..++ .+..+ ||||.|.++.++.-|+..|||..+.+..+.|.+-
T Consensus         7 e~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~-d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r   84 (267)
T KOG4454|consen    7 EMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQ-DQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLR   84 (267)
T ss_pred             chhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCc-cCCCc-eeeeecccccchhhhhhhcccchhccchhhcccc
Confidence            446899999999999999999999999999999998886 66676 9999999999999999999999999988887765


Q ss_pred             CC
Q 028027          131 PP  132 (215)
Q Consensus       131 ~~  132 (215)
                      ..
T Consensus        85 ~G   86 (267)
T KOG4454|consen   85 CG   86 (267)
T ss_pred             cC
Confidence            43

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

Probab=98.52  E-value=7.8e-08  Score=85.13  Aligned_cols=72  Identities=19%  Similarity=0.305  Sum_probs=65.2

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQ  126 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~  126 (215)
                      ....++|+|-|||..+++++|+.+|+.||+|..|+.     |-..+|..||+|.+..+|++|++.|++..+.|+.|.
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            356789999999999999999999999999999754     445579999999999999999999999999998887

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

Probab=98.50  E-value=5.7e-07  Score=78.72  Aligned_cols=79  Identities=24%  Similarity=0.331  Sum_probs=67.5

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      .....|.+.+|||++|+++|.+||+.|+ |.++.+.+.  +|+..|-|||+|.+.++++.|++ .+...++.+-|.|--+
T Consensus         8 ~~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r~--~Gr~sGeA~Ve~~seedv~~Alk-kdR~~mg~RYIEVf~~   83 (510)
T KOG4211|consen    8 STAFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPRR--NGRPSGEAYVEFTSEEDVEKALK-KDRESMGHRYIEVFTA   83 (510)
T ss_pred             CcceEEEecCCCccccHHHHHHHHhcCc-eeEEEEecc--CCCcCcceEEEeechHHHHHHHH-hhHHHhCCceEEEEcc
Confidence            4556789999999999999999999994 777666554  89999999999999999999996 4888899999999776


Q ss_pred             CCC
Q 028027          131 PPE  133 (215)
Q Consensus       131 ~~~  133 (215)
                      .+.
T Consensus        84 ~~~   86 (510)
T KOG4211|consen   84 GGA   86 (510)
T ss_pred             CCc
Confidence            443

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

Probab=98.43  E-value=2e-07  Score=82.88  Aligned_cols=90  Identities=23%  Similarity=0.473  Sum_probs=81.9

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      .....+||++||..+++..+.+++..||.+....++.+..+|.++||||.+|.+......|+..|||..++++.|.|..+
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            45578999999999999999999999999999999999989999999999999999999999999999999999999998


Q ss_pred             CCCCCCCCCc
Q 028027          131 PPEHVHPKLW  140 (215)
Q Consensus       131 ~~~~~~~~~~  140 (215)
                      .........+
T Consensus       367 ~~g~~~~~~~  376 (500)
T KOG0120|consen  367 IVGASNANVN  376 (500)
T ss_pred             hccchhcccc
Confidence            7765544443

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

Probab=98.36  E-value=1.8e-07  Score=82.77  Aligned_cols=85  Identities=21%  Similarity=0.401  Sum_probs=78.0

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEE
Q 028027           48 PLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQV  127 (215)
Q Consensus        48 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V  127 (215)
                      +++-+.++||+-.|+..+++.+|+++|+.+|.|..|+++.|+.++.++|.|||+|.+.+.+..|| .|.|..+.|-+|.|
T Consensus       174 ~eERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~ai-aLsGqrllg~pv~v  252 (549)
T KOG0147|consen  174 PEERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAI-ALSGQRLLGVPVIV  252 (549)
T ss_pred             chHHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHh-hhcCCcccCceeEe
Confidence            34567789999999999999999999999999999999999999999999999999999999999 78999999999999


Q ss_pred             EEeCCC
Q 028027          128 HLIPPE  133 (215)
Q Consensus       128 ~~a~~~  133 (215)
                      ......
T Consensus       253 q~sEae  258 (549)
T KOG0147|consen  253 QLSEAE  258 (549)
T ss_pred             cccHHH
Confidence            876543

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

Probab=98.31  E-value=6e-06  Score=71.01  Aligned_cols=78  Identities=23%  Similarity=0.426  Sum_probs=69.6

Q ss_pred             CcEEEEcCCCC-CCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeC
Q 028027           53 ATVLYIGRIPH-GFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIP  131 (215)
Q Consensus        53 ~~~l~V~nLp~-~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~  131 (215)
                      ...|.|.||.. .+|.+.|..+|+-||.|.+|.|..++.     .-|+|+|.+...|+.|+..|+|..|.|+.|+|.+++
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkk-----d~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SK  371 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKK-----DNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSK  371 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCC-----cceeeeecchhHHHHHHHHhhcceecCceEEEeecc
Confidence            57788888866 589999999999999999999998863     479999999999999999999999999999999987


Q ss_pred             CCCC
Q 028027          132 PEHV  135 (215)
Q Consensus       132 ~~~~  135 (215)
                      -...
T Consensus       372 H~~v  375 (492)
T KOG1190|consen  372 HTNV  375 (492)
T ss_pred             Cccc
Confidence            5443

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

Probab=98.24  E-value=3.5e-06  Score=73.89  Aligned_cols=78  Identities=17%  Similarity=0.330  Sum_probs=66.0

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeE-EEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKR-LRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~-v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ....+|.+.+||+.||+++|.+||+..-.|.. |.++.+. .+++.|-|||+|++.+.|+.|+.. |...|+.+-|.|-.
T Consensus       101 ~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~-rgR~tGEAfVqF~sqe~ae~Al~r-hre~iGhRYIEvF~  178 (510)
T KOG4211|consen  101 ANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQ-RGRPTGEAFVQFESQESAEIALGR-HRENIGHRYIEVFR  178 (510)
T ss_pred             CCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccC-CCCcccceEEEecCHHHHHHHHHH-HHHhhccceEEeeh
Confidence            35678999999999999999999998765555 5566665 788999999999999999999964 77788888888865


Q ss_pred             e
Q 028027          130 I  130 (215)
Q Consensus       130 a  130 (215)
                      +
T Consensus       179 S  179 (510)
T KOG4211|consen  179 S  179 (510)
T ss_pred             h
Confidence            4

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

Probab=98.20  E-value=1.1e-06  Score=74.24  Aligned_cols=85  Identities=22%  Similarity=0.398  Sum_probs=76.6

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCee--------EEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeC
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIK--------RLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLF  121 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~--------~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~  121 (215)
                      .....+|||.+||..+++.+|..+|.+||.|.        .|.|.++++|+..+|-|.|.|.+...|+.|+..+++..+.
T Consensus        63 ~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~  142 (351)
T KOG1995|consen   63 KSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFC  142 (351)
T ss_pred             ccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhcccccc
Confidence            34567899999999999999999999999883        3678888999999999999999999999999999999999


Q ss_pred             CeEEEEEEeCCCC
Q 028027          122 EHILQVHLIPPEH  134 (215)
Q Consensus       122 g~~l~V~~a~~~~  134 (215)
                      |..|.|.++..+.
T Consensus       143 gn~ikvs~a~~r~  155 (351)
T KOG1995|consen  143 GNTIKVSLAERRT  155 (351)
T ss_pred             CCCchhhhhhhcc
Confidence            9999998886554

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

Probab=98.14  E-value=1.4e-06  Score=70.58  Aligned_cols=73  Identities=22%  Similarity=0.401  Sum_probs=62.2

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCC--------CCcc----cEEEEEEcCHHHHHHHHHHhCCce
Q 028027           52 KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKT--------GQSK----HFGFIEFNDPEVAEVVADAMHGYL  119 (215)
Q Consensus        52 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~t--------g~~~----g~afV~F~~~~~a~~ai~~l~g~~  119 (215)
                      ....||+++||+.+....|+++|++||.|-.|.+-....+        |.+.    .-|+|+|.+...|..+...||+..
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            5689999999999999999999999999999988765433        2222    237899999999999999999999


Q ss_pred             eCCeE
Q 028027          120 LFEHI  124 (215)
Q Consensus       120 l~g~~  124 (215)
                      |+|+.
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99965

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes

Probab=98.14  E-value=9.2e-06  Score=55.18  Aligned_cols=68  Identities=21%  Similarity=0.422  Sum_probs=47.1

Q ss_pred             cEEEEcCCCCCCcHHHHH----HHhccCC-CeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 028027           54 TVLYIGRIPHGFYEKEMQ----AFFSQFG-AIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVH  128 (215)
Q Consensus        54 ~~l~V~nLp~~~te~~L~----~~F~~~G-~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~  128 (215)
                      +.|||.|||...+...|+    .++..|| .|..|       +|   +.|+|.|.+.+.|.+|.+.|+|-.+.|..|.|.
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v-------~~---~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~   72 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV-------SG---GTAILRFPNQEFAERAQKRMEGEDVFGNKISVS   72 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE---------T---T-EEEEESSHHHHHHHHHHHTT--SSSS--EEE
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE-------eC---CEEEEEeCCHHHHHHHHHhhcccccccceEEEE
Confidence            468999999998887665    4555675 56555       22   689999999999999999999999999999999


Q ss_pred             EeC
Q 028027          129 LIP  131 (215)
Q Consensus       129 ~a~  131 (215)
                      +..
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.

>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=98.09  E-value=9.5e-06  Score=58.25  Aligned_cols=70  Identities=17%  Similarity=0.367  Sum_probs=43.8

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCc-----eeCCeEEEEE
Q 028027           54 TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGY-----LLFEHILQVH  128 (215)
Q Consensus        54 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~-----~l~g~~l~V~  128 (215)
                      +.|+|.+++..++.++|++.|++||.|..|.+....      ..|||.|.+.+.|+.|+..+...     .+.+..+.++
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~------~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~   75 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGD------TEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLE   75 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-------SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCC------CEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEE
Confidence            578999999999999999999999999999887653      47999999999999999876543     4445555544


Q ss_pred             E
Q 028027          129 L  129 (215)
Q Consensus       129 ~  129 (215)
                      +
T Consensus        76 v   76 (105)
T PF08777_consen   76 V   76 (105)
T ss_dssp             -
T ss_pred             E
Confidence            3

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

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.06  E-value=5.2e-06  Score=69.86  Aligned_cols=85  Identities=14%  Similarity=0.371  Sum_probs=75.9

Q ss_pred             CCCcEEE-EcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           51 NKATVLY-IGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        51 ~~~~~l~-V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ..+.++| |++|+..+++++|+..|..+|.|..++++.+..+|...|||||.|.+...+..++.. ....+.++++.+..
T Consensus       182 ~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~  260 (285)
T KOG4210|consen  182 GPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEE  260 (285)
T ss_pred             CccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCccccccc
Confidence            4455565 999999999999999999999999999999999999999999999999999998866 78889999999999


Q ss_pred             eCCCCCC
Q 028027          130 IPPEHVH  136 (215)
Q Consensus       130 a~~~~~~  136 (215)
                      ..+....
T Consensus       261 ~~~~~~~  267 (285)
T KOG4210|consen  261 DEPRPKS  267 (285)
T ss_pred             CCCCccc
Confidence            8776544

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.98  E-value=1.8e-05  Score=66.68  Aligned_cols=79  Identities=20%  Similarity=0.414  Sum_probs=61.7

Q ss_pred             cEEEEcCCCCCCcHHH----H--HHHhccCCCeeEEEEeecCCC-CCccc-E-EEEEEcCHHHHHHHHHHhCCceeCCeE
Q 028027           54 TVLYIGRIPHGFYEKE----M--QAFFSQFGAIKRLRIARNKKT-GQSKH-F-GFIEFNDPEVAEVVADAMHGYLLFEHI  124 (215)
Q Consensus        54 ~~l~V~nLp~~~te~~----L--~~~F~~~G~v~~v~i~~~~~t-g~~~g-~-afV~F~~~~~a~~ai~~l~g~~l~g~~  124 (215)
                      .-+||-+||+.+..++    |  .++|++||.|..|.+.+...+ ....+ + .||+|.+.++|.+||...+|..++|+.
T Consensus       115 NLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr~  194 (480)
T COG5175         115 NLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGRV  194 (480)
T ss_pred             ceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCce
Confidence            4589999999876655    2  589999999999877553211 11112 2 399999999999999999999999999


Q ss_pred             EEEEEeCC
Q 028027          125 LQVHLIPP  132 (215)
Q Consensus       125 l~V~~a~~  132 (215)
                      |+..+-..
T Consensus       195 lkatYGTT  202 (480)
T COG5175         195 LKATYGTT  202 (480)
T ss_pred             EeeecCch
Confidence            99988654

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

Probab=97.97  E-value=5.7e-06  Score=69.89  Aligned_cols=75  Identities=13%  Similarity=0.243  Sum_probs=66.5

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCC--CeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 028027           54 TVLYIGRIPHGFYEKEMQAFFSQFG--AIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVH  128 (215)
Q Consensus        54 ~~l~V~nLp~~~te~~L~~~F~~~G--~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~  128 (215)
                      ..+|||||-|++|.+||.+.+...|  .+.++++..++.+|+++|||+|...+.......++.|....|+|..-.|-
T Consensus        81 ~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~  157 (498)
T KOG4849|consen   81 YCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVL  157 (498)
T ss_pred             EEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeee
Confidence            4689999999999999999988776  56778888899999999999999999999999999999999999765553

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

Probab=97.91  E-value=6.1e-05  Score=60.20  Aligned_cols=79  Identities=19%  Similarity=0.436  Sum_probs=68.2

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeC-CeEEE
Q 028027           48 PLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLF-EHILQ  126 (215)
Q Consensus        48 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~-g~~l~  126 (215)
                      ++..+..++|+.|||..++.+.+..+|.+|+....++++...     .+.|||+|.+...+..|...+.|..|- ...+.
T Consensus       141 ~~~ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~~-----~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~  215 (221)
T KOG4206|consen  141 QMAPPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPPR-----SGIAFVEFLSDRQASAAQQALQGFKITKKNTMQ  215 (221)
T ss_pred             cCCCCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccCC-----CceeEEecchhhhhHHHhhhhccceeccCceEE
Confidence            445677899999999999999999999999999999988764     379999999999999999999998877 77777


Q ss_pred             EEEeC
Q 028027          127 VHLIP  131 (215)
Q Consensus       127 V~~a~  131 (215)
                      |.++.
T Consensus       216 i~~a~  220 (221)
T KOG4206|consen  216 ITFAK  220 (221)
T ss_pred             ecccC
Confidence            77653

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

Probab=97.90  E-value=4.1e-05  Score=66.02  Aligned_cols=78  Identities=17%  Similarity=0.212  Sum_probs=64.1

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCe-EEEEEE
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEH-ILQVHL  129 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~-~l~V~~  129 (215)
                      +++.++.+.|||++++|++|...|..-|-.......    -++.+.+|++.+.+.+.|-.|+-.++.+.+++. .|+|++
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            355789999999999999999999998865444322    334457999999999999999999999988865 899999


Q ss_pred             eCC
Q 028027          130 IPP  132 (215)
Q Consensus       130 a~~  132 (215)
                      ++.
T Consensus       488 Sks  490 (492)
T KOG1190|consen  488 SKS  490 (492)
T ss_pred             ecc
Confidence            864

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

Probab=97.84  E-value=1.8e-05  Score=63.23  Aligned_cols=64  Identities=23%  Similarity=0.433  Sum_probs=53.2

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeC
Q 028027           54 TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLF  121 (215)
Q Consensus        54 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~  121 (215)
                      .||||.||.+.|+|++|+.+|+.|.....++|...  .|  -..||++|++.+.|..|+..|.|..|.
T Consensus       211 stlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~--~g--~~vaf~~~~~~~~at~am~~lqg~~~s  274 (284)
T KOG1457|consen  211 STLFIANLGPNCTEDELKQLLSRYPGFHILKIRAR--GG--MPVAFADFEEIEQATDAMNHLQGNLLS  274 (284)
T ss_pred             hhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecC--CC--cceEeecHHHHHHHHHHHHHhhcceec
Confidence            58999999999999999999999976666665322  33  358999999999999999999987654

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

Probab=97.77  E-value=2.1e-05  Score=63.11  Aligned_cols=75  Identities=17%  Similarity=0.292  Sum_probs=65.2

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEE
Q 028027           48 PLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQV  127 (215)
Q Consensus        48 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V  127 (215)
                      .+....+.++|.+++..+.+.+|...|.++|.+....+        ..+++||+|...++|..|+..|++..+.|+.|.+
T Consensus        94 ~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~--------~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~  165 (216)
T KOG0106|consen   94 PPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA--------RRNFAFVEFSEQEDAKRALEKLDGKKLNGRRISV  165 (216)
T ss_pred             CcccccceeeeccchhhhhHHHHhhhhcccCCCchhhh--------hccccceeehhhhhhhhcchhccchhhcCceeee
Confidence            34567788999999999999999999999999855433        3469999999999999999999999999999999


Q ss_pred             EEe
Q 028027          128 HLI  130 (215)
Q Consensus       128 ~~a  130 (215)
                      ...
T Consensus       166 ~~~  168 (216)
T KOG0106|consen  166 EKN  168 (216)
T ss_pred             ccc
Confidence            543

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

Probab=97.75  E-value=0.00084  Score=57.55  Aligned_cols=82  Identities=18%  Similarity=0.312  Sum_probs=72.2

Q ss_pred             CCCCCcEEEEcCCCCC-CcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEE
Q 028027           49 LVNKATVLYIGRIPHG-FYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQV  127 (215)
Q Consensus        49 ~~~~~~~l~V~nLp~~-~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V  127 (215)
                      ...+++.+.|-+|... ++.+.|..+|-.||.|..|.+++.+ +    |-|.|++.+....++|+..||+..+.|.+|.|
T Consensus       283 g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk-~----gtamVemgd~~aver~v~hLnn~~lfG~kl~v  357 (494)
T KOG1456|consen  283 GGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK-P----GTAMVEMGDAYAVERAVTHLNNIPLFGGKLNV  357 (494)
T ss_pred             CCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc-c----ceeEEEcCcHHHHHHHHHHhccCccccceEEE
Confidence            3567789999999886 6668899999999999999999886 3    68999999999999999999999999999999


Q ss_pred             EEeCCCCC
Q 028027          128 HLIPPEHV  135 (215)
Q Consensus       128 ~~a~~~~~  135 (215)
                      .+++..-.
T Consensus       358 ~~SkQ~~v  365 (494)
T KOG1456|consen  358 CVSKQNFV  365 (494)
T ss_pred             eecccccc
Confidence            99876543

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

Probab=97.69  E-value=0.0001  Score=46.13  Aligned_cols=52  Identities=17%  Similarity=0.402  Sum_probs=42.2

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHH
Q 028027           54 TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVA  112 (215)
Q Consensus        54 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai  112 (215)
                      +.|-|.|.+++..+. +...|.+||+|..+.+...      ..+.||.|.+..+|+.|+
T Consensus         2 ~wI~V~Gf~~~~~~~-vl~~F~~fGeI~~~~~~~~------~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAEE-VLEHFASFGEIVDIYVPES------TNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHHH-HHHHHHhcCCEEEEEcCCC------CcEEEEEECCHHHHHhhC
Confidence            578899999877655 5558889999999887622      358999999999999885

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

Probab=97.63  E-value=0.00015  Score=64.96  Aligned_cols=80  Identities=21%  Similarity=0.294  Sum_probs=65.0

Q ss_pred             CCCcEEEEcCCCCCCc------HHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeC-Ce
Q 028027           51 NKATVLYIGRIPHGFY------EKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLF-EH  123 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~t------e~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~-g~  123 (215)
                      .-...|+|.|+|---.      ..-|..+|+.+|.|..+.++.+.. |..+||.|++|.+..+|+.|++.|||+.|+ .+
T Consensus        56 g~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~-ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknH  134 (698)
T KOG2314|consen   56 GFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEE-GGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNH  134 (698)
T ss_pred             CcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCcc-CCeeeEEEEEecChhhHHHHHHhcccceecccc
Confidence            4557899999987321      234567899999999999998864 559999999999999999999999999876 67


Q ss_pred             EEEEEEeC
Q 028027          124 ILQVHLIP  131 (215)
Q Consensus       124 ~l~V~~a~  131 (215)
                      ++.|...+
T Consensus       135 tf~v~~f~  142 (698)
T KOG2314|consen  135 TFFVRLFK  142 (698)
T ss_pred             eEEeehhh
Confidence            77776644

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

Probab=97.52  E-value=0.0004  Score=63.66  Aligned_cols=76  Identities=18%  Similarity=0.353  Sum_probs=66.8

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCe-eEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           53 ATVLYIGRIPHGFYEKEMQAFFSQFGAI-KRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        53 ~~~l~V~nLp~~~te~~L~~~F~~~G~v-~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      .+.|-+.|+|++++-+||.+||..|-.+ -+|.+-++ +.|...|-|.|.|++.+.|.+|...|++..|..+.|.+.+
T Consensus       867 p~V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~n-d~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~V~l~i  943 (944)
T KOG4307|consen  867 PRVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRN-DDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             CeEEEecCCCccccHHHHHHHhcccccCCCceeEeec-CCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            3588999999999999999999999655 34555555 5899999999999999999999999999999999998865

>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=97.49  E-value=0.00067  Score=48.12  Aligned_cols=79  Identities=16%  Similarity=0.254  Sum_probs=51.9

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEE-EeecC------CCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLR-IARNK------KTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEH  123 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~-i~~~~------~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~  123 (215)
                      ...+.|.|-+.|+. ....+...|++||.|.+.. +.++.      .......+-.|+|.++.+|.+||. .||..|+|.
T Consensus         4 ~~~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~   81 (100)
T PF05172_consen    4 DSETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGS   81 (100)
T ss_dssp             GGCCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTC
T ss_pred             cCCeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCc
Confidence            34567888899998 4567788999999997764 11100      011223689999999999999995 599999885


Q ss_pred             -EEEEEEeC
Q 028027          124 -ILQVHLIP  131 (215)
Q Consensus       124 -~l~V~~a~  131 (215)
                       .+-|.+++
T Consensus        82 ~mvGV~~~~   90 (100)
T PF05172_consen   82 LMVGVKPCD   90 (100)
T ss_dssp             EEEEEEE-H
T ss_pred             EEEEEEEcH
Confidence             45566653

This family also includes Q05166 from SWISSPROT a suppressor of thermosensitive mutations in the DNA polymerase delta gene, Pol III []. The conserved central region appears to be distantly related to the RNA-binding region RNP-1 (RNA recognition motif, IPR000504 from INTERPRO), suggesting an RNA binding function for this protein.; PDB: 1WWH_C 3P3D_A.

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

Probab=97.47  E-value=0.00037  Score=62.46  Aligned_cols=67  Identities=18%  Similarity=0.319  Sum_probs=55.1

Q ss_pred             HHHHhccCCCeeEEEEeec-C--CCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeCCCCCC
Q 028027           70 MQAFFSQFGAIKRLRIARN-K--KTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPPEHVH  136 (215)
Q Consensus        70 L~~~F~~~G~v~~v~i~~~-~--~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~~~~~~  136 (215)
                      ++.-++.||.|..|.+++. .  ...-..|-.||+|.+.++++.|+..|+|..+.|+.|...|......+
T Consensus       426 vr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYydeDkY~  495 (500)
T KOG0120|consen  426 VRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYDEDKYH  495 (500)
T ss_pred             HHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecCHHHhh
Confidence            3455678999999999887 2  12334578899999999999999999999999999999998765544

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

Probab=97.45  E-value=0.00045  Score=61.29  Aligned_cols=66  Identities=17%  Similarity=0.337  Sum_probs=60.2

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhc-cCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHH
Q 028027           49 LVNKATVLYIGRIPHGFYEKEMQAFFS-QFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA  114 (215)
Q Consensus        49 ~~~~~~~l~V~nLp~~~te~~L~~~F~-~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~  114 (215)
                      +-++.+|||||+||.-++-.+|-.+|. -||.|..+-|-.|++-+-++|-|-|+|.+..+--+||..
T Consensus       366 ~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  366 PIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             ccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            346778999999999999999999998 599999999999988899999999999999999999864

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

Probab=97.44  E-value=0.00031  Score=60.25  Aligned_cols=83  Identities=18%  Similarity=0.324  Sum_probs=68.8

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhccCCC-ee--EEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeE
Q 028027           48 PLVNKATVLYIGRIPHGFYEKEMQAFFSQFGA-IK--RLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHI  124 (215)
Q Consensus        48 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~-v~--~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~  124 (215)
                      ++......|.+.+||+..+-++|..||..|.. |.  .|+++.+. .|+..|-|||+|.+.+.|..|+...+...+.++.
T Consensus       275 p~~~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~-qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RY  353 (508)
T KOG1365|consen  275 PPTRSKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNG-QGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRY  353 (508)
T ss_pred             CCCCCCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcC-CCCcChhhhhhhhhhHHHHHHHHHHHHhhcccce
Confidence            33444678999999999999999999998863 33  37777774 8999999999999999999999888888888888


Q ss_pred             EEEEEeC
Q 028027          125 LQVHLIP  131 (215)
Q Consensus       125 l~V~~a~  131 (215)
                      |.|--+.
T Consensus       354 iEvfp~S  360 (508)
T KOG1365|consen  354 IEVFPCS  360 (508)
T ss_pred             EEEeecc
Confidence            8886553

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

Probab=97.44  E-value=0.00075  Score=50.86  Aligned_cols=74  Identities=18%  Similarity=0.342  Sum_probs=52.1

Q ss_pred             CCCcEEEEcCCC------CCCcH---HHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeC
Q 028027           51 NKATVLYIGRIP------HGFYE---KEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLF  121 (215)
Q Consensus        51 ~~~~~l~V~nLp------~~~te---~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~  121 (215)
                      ++..||.|.-+.      ..+.+   .+|-+.|..||.+.-+++..+        .-+|+|.+...|-+|+ .|+|..++
T Consensus        25 PpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaal-s~dg~~v~   95 (146)
T PF08952_consen   25 PPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAAL-SLDGIQVN   95 (146)
T ss_dssp             -TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHH-HGCCSEET
T ss_pred             CCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHH-ccCCcEEC
Confidence            344667676555      12332   256778899999988888654        5799999999999999 58999999


Q ss_pred             CeEEEEEEeCCC
Q 028027          122 EHILQVHLIPPE  133 (215)
Q Consensus       122 g~~l~V~~a~~~  133 (215)
                      |+.|.|++..|.
T Consensus        96 g~~l~i~LKtpd  107 (146)
T PF08952_consen   96 GRTLKIRLKTPD  107 (146)
T ss_dssp             TEEEEEEE----
T ss_pred             CEEEEEEeCCcc
Confidence            999999986553

; PDB: 1UFW_A 2DNR_A.

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

Probab=97.28  E-value=0.0013  Score=55.85  Aligned_cols=79  Identities=10%  Similarity=0.188  Sum_probs=62.2

Q ss_pred             CCCcEEEEcCCCC----CCc-------HHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCce
Q 028027           51 NKATVLYIGRIPH----GFY-------EKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYL  119 (215)
Q Consensus        51 ~~~~~l~V~nLp~----~~t-------e~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~  119 (215)
                      ...++|.+.|+-.    ..+       .++|++-...||.|.+|.|.-.    .+.|.+-|.|.+.+.|..||..|+|..
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            4567888988743    122       2455666789999999977533    245899999999999999999999999


Q ss_pred             eCCeEEEEEEeCCC
Q 028027          120 LFEHILQVHLIPPE  133 (215)
Q Consensus       120 l~g~~l~V~~a~~~  133 (215)
                      ++|+.|...+....
T Consensus       339 fdgRql~A~i~DG~  352 (382)
T KOG1548|consen  339 FDGRQLTASIWDGK  352 (382)
T ss_pred             ecceEEEEEEeCCc
Confidence            99999998876544

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

Probab=97.26  E-value=0.0016  Score=57.88  Aligned_cols=77  Identities=18%  Similarity=0.320  Sum_probs=54.2

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecC---CCCCccc---EEEEEEcCHHHHHHHHHHhCCceeCCe
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNK---KTGQSKH---FGFIEFNDPEVAEVVADAMHGYLLFEH  123 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~---~tg~~~g---~afV~F~~~~~a~~ai~~l~g~~l~g~  123 (215)
                      ..-++.||||+||++++|+.|...|..||.+ .|.++...   .--.++|   |+|+.|+++..+..-+..+.   .++.
T Consensus       256 ~~~S~KVFvGGlp~dise~~i~~~F~~FGs~-~VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~---~~~~  331 (520)
T KOG0129|consen  256 PRYSRKVFVGGLPWDITEAQINASFGQFGSV-KVDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACS---EGEG  331 (520)
T ss_pred             cccccceeecCCCccccHHHHHhhcccccce-EeecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHh---hccc
Confidence            3567889999999999999999999999985 34555211   1113456   99999999988877665433   2444


Q ss_pred             EEEEEEe
Q 028027          124 ILQVHLI  130 (215)
Q Consensus       124 ~l~V~~a  130 (215)
                      .+.+.++
T Consensus       332 ~~yf~vs  338 (520)
T KOG0129|consen  332 NYYFKVS  338 (520)
T ss_pred             ceEEEEe
Confidence            4444443

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

Probab=97.18  E-value=0.00072  Score=58.12  Aligned_cols=72  Identities=14%  Similarity=0.221  Sum_probs=55.6

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccC----CCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEE
Q 028027           52 KATVLYIGRIPHGFYEKEMQAFFSQF----GAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHIL  125 (215)
Q Consensus        52 ~~~~l~V~nLp~~~te~~L~~~F~~~----G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l  125 (215)
                      +.-.|.+.+||+++++.++.+||.+-    |....|-++..+ +|+..|-|||.|..+++|+.|+.. |...|+-|.|
T Consensus       160 ~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rp-dgrpTGdAFvlfa~ee~aq~aL~k-hrq~iGqRYI  235 (508)
T KOG1365|consen  160 NQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRP-DGRPTGDAFVLFACEEDAQFALRK-HRQNIGQRYI  235 (508)
T ss_pred             cceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECC-CCCcccceEEEecCHHHHHHHHHH-HHHHHhHHHH
Confidence            34568888999999999999999742    344566666654 899999999999999999999965 4444544433

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

Probab=97.11  E-value=0.00059  Score=59.33  Aligned_cols=71  Identities=15%  Similarity=0.277  Sum_probs=58.7

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeec---CCCC--C--------cccEEEEEEcCHHHHHHHHHH
Q 028027           48 PLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARN---KKTG--Q--------SKHFGFIEFNDPEVAEVVADA  114 (215)
Q Consensus        48 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~---~~tg--~--------~~g~afV~F~~~~~a~~ai~~  114 (215)
                      .++..+++|.+-|||.+-.-+.|..+|+.+|.|..|+|+..   +.++  .        .+-+|+|+|...+.|..|.+.
T Consensus       226 ~eel~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~  305 (484)
T KOG1855|consen  226 EEELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKAREL  305 (484)
T ss_pred             ccccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHh
Confidence            34568999999999999888999999999999999999876   3222  1        245799999999999999988


Q ss_pred             hCCc
Q 028027          115 MHGY  118 (215)
Q Consensus       115 l~g~  118 (215)
                      |+..
T Consensus       306 ~~~e  309 (484)
T KOG1855|consen  306 LNPE  309 (484)
T ss_pred             hchh
Confidence            8653

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

Probab=97.04  E-value=0.0025  Score=49.75  Aligned_cols=73  Identities=8%  Similarity=0.136  Sum_probs=61.2

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeC--CeEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLF--EHILQV  127 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~--g~~l~V  127 (215)
                      ..+...|.|.+||++.+..+|++.+...|.|....+.+|       |++.|+|...++.+-|+..|+...+.  |-...+
T Consensus       112 rrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD-------g~GvV~~~r~eDMkYAvr~ld~~~~~seGe~~yi  184 (241)
T KOG0105|consen  112 RRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD-------GVGVVEYLRKEDMKYAVRKLDDQKFRSEGETAYI  184 (241)
T ss_pred             cccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc-------cceeeeeeehhhHHHHHHhhccccccCcCcEeeE
Confidence            345678999999999999999999999999998888777       58999999999999999999886544  444444


Q ss_pred             EE
Q 028027          128 HL  129 (215)
Q Consensus       128 ~~  129 (215)
                      .+
T Consensus       185 rv  186 (241)
T KOG0105|consen  185 RV  186 (241)
T ss_pred             Ee
Confidence            43

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

Probab=97.03  E-value=0.00033  Score=65.38  Aligned_cols=85  Identities=19%  Similarity=0.196  Sum_probs=75.2

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeCC
Q 028027           53 ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPP  132 (215)
Q Consensus        53 ~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~~  132 (215)
                      ...|+|.|.|+..|.+.++.++..+|.++++.++..+ .|+++|.|||.|.+..++..++..++...+....+.|..+.|
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            3579999999999999999999999999999988886 899999999999999999999988888888888888888777


Q ss_pred             CCCCCC
Q 028027          133 EHVHPK  138 (215)
Q Consensus       133 ~~~~~~  138 (215)
                      ....+.
T Consensus       815 ~~~K~k  820 (881)
T KOG0128|consen  815 ERDKKK  820 (881)
T ss_pred             cccccc
Confidence            544443

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

Probab=97.00  E-value=0.0061  Score=41.48  Aligned_cols=55  Identities=20%  Similarity=0.454  Sum_probs=42.6

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhC
Q 028027           53 ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMH  116 (215)
Q Consensus        53 ~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~  116 (215)
                      ....+|+ .|..+-..||.++|+.||.| .|.++.+       .-|||.....+.|..++..++
T Consensus         9 dHVFhlt-FPkeWK~~DI~qlFspfG~I-~VsWi~d-------TSAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen    9 DHVFHLT-FPKEWKTSDIYQLFSPFGQI-YVSWIND-------TSAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             CCEEEEE---TT--HHHHHHHCCCCCCE-EEEEECT-------TEEEEEECCCHHHHHHHHHHT
T ss_pred             ceEEEEe-CchHhhhhhHHHHhccCCcE-EEEEEcC-------CcEEEEeecHHHHHHHHHHhc
Confidence            3556666 99999999999999999987 5666666       279999999999999998775

; 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.

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

Probab=96.98  E-value=0.0011  Score=62.48  Aligned_cols=78  Identities=23%  Similarity=0.378  Sum_probs=67.3

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCC--eEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFE--HILQV  127 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g--~~l~V  127 (215)
                      ....+.+++++|.+++....|...|..||.|..|.+-.    |  ..||+|.|.+...++.|+..|-|..|+|  +.++|
T Consensus       452 st~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~h----g--q~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rv  525 (975)
T KOG0112|consen  452 STPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRH----G--QPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRV  525 (975)
T ss_pred             cccceeeccCCCCCCChHHHHHHHhhccCcceeeeccc----C--CcceeeecccCccchhhHHHHhcCcCCCCCccccc
Confidence            34567899999999999999999999999999876632    2  2599999999999999999999999986  67999


Q ss_pred             EEeCCC
Q 028027          128 HLIPPE  133 (215)
Q Consensus       128 ~~a~~~  133 (215)
                      .++.+-
T Consensus       526 dla~~~  531 (975)
T KOG0112|consen  526 DLASPP  531 (975)
T ss_pred             ccccCC
Confidence            988653

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

Probab=96.79  E-value=0.013  Score=50.36  Aligned_cols=79  Identities=19%  Similarity=0.301  Sum_probs=63.0

Q ss_pred             CCcEEEEc--CCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeC-C-eEEEE
Q 028027           52 KATVLYIG--RIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLF-E-HILQV  127 (215)
Q Consensus        52 ~~~~l~V~--nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~-g-~~l~V  127 (215)
                      ....|.+.  |--+.+|-+.|..+....|.|.+|.|.+.  +|   --|.|+|++.+.|++|...|||..|- | ..|+|
T Consensus       119 pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkk--ng---VQAmVEFdsv~~AqrAk~alNGADIYsGCCTLKI  193 (494)
T KOG1456|consen  119 PNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKK--NG---VQAMVEFDSVEVAQRAKAALNGADIYSGCCTLKI  193 (494)
T ss_pred             CCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEec--cc---eeeEEeechhHHHHHHHhhcccccccccceeEEE
Confidence            34455544  44456899999999999999999988765  44   36999999999999999999998654 3 67899


Q ss_pred             EEeCCCCC
Q 028027          128 HLIPPEHV  135 (215)
Q Consensus       128 ~~a~~~~~  135 (215)
                      ++|+|.+.
T Consensus       194 eyAkP~rl  201 (494)
T KOG1456|consen  194 EYAKPTRL  201 (494)
T ss_pred             EecCccee
Confidence            99988653

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

Probab=96.74  E-value=0.0085  Score=38.58  Aligned_cols=55  Identities=18%  Similarity=0.286  Sum_probs=45.8

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccC---CCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHh
Q 028027           53 ATVLYIGRIPHGFYEKEMQAFFSQF---GAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM  115 (215)
Q Consensus        53 ~~~l~V~nLp~~~te~~L~~~F~~~---G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l  115 (215)
                      +..|+|.|+.. ++.++|..+|..|   .....|.++.|.       -|-|.|.+.+.|.+||..|
T Consensus         5 peavhirGvd~-lsT~dI~~y~~~y~~~~~~~~IEWIdDt-------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    5 PEAVHIRGVDE-LSTDDIKAYFSEYFDEEGPFRIEWIDDT-------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eceEEEEcCCC-CCHHHHHHHHHHhcccCCCceEEEecCC-------cEEEEECCHHHHHHHHHcC
Confidence            46799999965 7889999999988   235789999884       6889999999999999754

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

Probab=96.71  E-value=0.00076  Score=55.01  Aligned_cols=63  Identities=16%  Similarity=0.269  Sum_probs=51.5

Q ss_pred             HHHHHhc-cCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeCC
Q 028027           69 EMQAFFS-QFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPP  132 (215)
Q Consensus        69 ~L~~~F~-~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~~  132 (215)
                      +|...|+ +||+|..+.+..+. .-...|-+||.|...++|++|+..||+-.+.|++|...+..-
T Consensus        84 d~f~E~~~kygEiee~~Vc~Nl-~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pv  147 (260)
T KOG2202|consen   84 DVFTELEDKYGEIEELNVCDNL-GDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPV  147 (260)
T ss_pred             HHHHHHHHHhhhhhhhhhhccc-chhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCc
Confidence            3333444 89999998777664 344578999999999999999999999999999999988643

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=96.62  E-value=0.0017  Score=52.98  Aligned_cols=82  Identities=21%  Similarity=0.238  Sum_probs=65.1

Q ss_pred             CCCCCcccCCCCCCCCCCCCCCCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHH
Q 028027           28 GAADFLPLEGGPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEV  107 (215)
Q Consensus        28 ~~~d~~~~~g~p~r~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~  107 (215)
                      ..+|+...-|++.++.-.     .. ..|||.||+..++-+.+...|+.||+|....++.|. .+++.+-++|.|...-.
T Consensus        12 ~eLd~~~~~~~~lr~rfa-----~~-a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~-r~k~t~eg~v~~~~k~~   84 (275)
T KOG0115|consen   12 RELDGRFPKGRSLRVRFA-----MH-AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDD-RGKPTREGIVEFAKKPN   84 (275)
T ss_pred             HhcCCCCCCCCceEEEee-----cc-ceEEEEecchhhhhHHHHHhhhhcCccchheeeecc-cccccccchhhhhcchh
Confidence            455655555555554332     22 679999999999999999999999999887777774 78888999999999999


Q ss_pred             HHHHHHHhC
Q 028027          108 AEVVADAMH  116 (215)
Q Consensus       108 a~~ai~~l~  116 (215)
                      +..|+..++
T Consensus        85 a~~a~rr~~   93 (275)
T KOG0115|consen   85 ARKAARRCR   93 (275)
T ss_pred             HHHHHHHhc
Confidence            999987763

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

Probab=96.62  E-value=0.0014  Score=56.96  Aligned_cols=77  Identities=16%  Similarity=0.252  Sum_probs=60.1

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCc-eeCCeEEEEEEeCC
Q 028027           54 TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGY-LLFEHILQVHLIPP  132 (215)
Q Consensus        54 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~-~l~g~~l~V~~a~~  132 (215)
                      ..+|++||.+.++..+|+.+|...-.-.+-.++..      .||+||.+.+...|..|++.++|. .+.|.++.|..+-+
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~k------~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~   75 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLVK------SGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVP   75 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceeee------cceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhh
Confidence            35899999999999999999976421111122222      279999999999999999999996 69999999998776


Q ss_pred             CCCC
Q 028027          133 EHVH  136 (215)
Q Consensus       133 ~~~~  136 (215)
                      +..+
T Consensus        76 kkqr   79 (584)
T KOG2193|consen   76 KKQR   79 (584)
T ss_pred             HHHH
Confidence            5443

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=96.58  E-value=0.0008  Score=56.89  Aligned_cols=79  Identities=18%  Similarity=0.422  Sum_probs=61.6

Q ss_pred             cEEEEcCCCCCCcHHHH---HHHhccCCCeeEEEEeecC----CCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEE
Q 028027           54 TVLYIGRIPHGFYEKEM---QAFFSQFGAIKRLRIARNK----KTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQ  126 (215)
Q Consensus        54 ~~l~V~nLp~~~te~~L---~~~F~~~G~v~~v~i~~~~----~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~  126 (215)
                      .-+||-+|+.....+.+   .++|++||.|..|.+..+.    ..+.+ .-++|+|...++|..||...+|+.++|+.|+
T Consensus        78 nlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~-~s~yITy~~~eda~rci~~v~g~~~dg~~lk  156 (327)
T KOG2068|consen   78 NLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGT-CSVYITYEEEEDADRCIDDVDGFVDDGRALK  156 (327)
T ss_pred             hhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCC-CcccccccchHhhhhHHHHhhhHHhhhhhhH
Confidence            44788888877655444   3689999999999887765    12222 2389999999999999999999999999988


Q ss_pred             EEEeCCC
Q 028027          127 VHLIPPE  133 (215)
Q Consensus       127 V~~a~~~  133 (215)
                      ..+..+.
T Consensus       157 a~~gttk  163 (327)
T KOG2068|consen  157 ASLGTTK  163 (327)
T ss_pred             HhhCCCc
Confidence            7776554

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

Probab=96.46  E-value=0.0055  Score=56.49  Aligned_cols=80  Identities=16%  Similarity=0.175  Sum_probs=67.2

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeE-EEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKR-LRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVH  128 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~-v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~  128 (215)
                      ......|||..||..+++.++-.+|...-.|++ |.|.+.+ ++..++.|||.|..++++..|+..-+.+.++.+.|+|+
T Consensus       431 ~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~P-~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~  509 (944)
T KOG4307|consen  431 GGAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRLP-TDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVD  509 (944)
T ss_pred             CCccceEEeccCCccccccchhhhhhhhhhhhheeEeccCC-cccccchhhheeccccccchhhhcccccccCceEEEee
Confidence            345678999999999999999999988777766 7777776 88999999999999888888876666778888899987


Q ss_pred             Ee
Q 028027          129 LI  130 (215)
Q Consensus       129 ~a  130 (215)
                      -.
T Consensus       510 si  511 (944)
T KOG4307|consen  510 SI  511 (944)
T ss_pred             ch
Confidence            54

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

Probab=96.45  E-value=0.0055  Score=52.93  Aligned_cols=77  Identities=19%  Similarity=0.317  Sum_probs=60.4

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCC---CCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           53 ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKK---TGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        53 ~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~---tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ...|.|.||.+.++.++++.+|...|.|..+.|+-+..   -......|||.|.+...+..|- .|.++.+-++-|.|..
T Consensus         7 ~~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQ-hLtntvfvdraliv~p   85 (479)
T KOG4676|consen    7 LGVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQ-HLTNTVFVDRALIVRP   85 (479)
T ss_pred             CceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHh-hhccceeeeeeEEEEe
Confidence            45899999999999999999999999999998876421   2334568999999999888876 5666666666666554


Q ss_pred             e
Q 028027          130 I  130 (215)
Q Consensus       130 a  130 (215)
                      +
T Consensus        86 ~   86 (479)
T KOG4676|consen   86 Y   86 (479)
T ss_pred             c
Confidence            3

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

Probab=96.40  E-value=0.00019  Score=66.93  Aligned_cols=68  Identities=18%  Similarity=0.307  Sum_probs=59.0

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeC
Q 028027           54 TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLF  121 (215)
Q Consensus        54 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~  121 (215)
                      .++||+||+..+.+.+|...|..+|.+..+++.-...+++.+|+||+.|...+.+.+|+...+++.++
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            57899999999999999999999998888877655568999999999999999999999765555554

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=96.30  E-value=0.015  Score=48.46  Aligned_cols=64  Identities=14%  Similarity=0.172  Sum_probs=51.4

Q ss_pred             HHHHHHhccCCCeeEEEEeecCCCCCcc-cEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeC
Q 028027           68 KEMQAFFSQFGAIKRLRIARNKKTGQSK-HFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIP  131 (215)
Q Consensus        68 ~~L~~~F~~~G~v~~v~i~~~~~tg~~~-g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~  131 (215)
                      +++.+-+.+||.|..|.|...+...... ---||+|...++|..|+-.|||..|+|+.+...|..
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            4566778899999999887765333222 236999999999999999999999999999988754

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

Probab=96.22  E-value=0.006  Score=55.27  Aligned_cols=77  Identities=16%  Similarity=0.264  Sum_probs=62.1

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhc-cCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCcee---CCeEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFS-QFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLL---FEHIL  125 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~-~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l---~g~~l  125 (215)
                      ...+..|||.||-.-+|..+|+.+++ .+|.|... || |+    .+..|||.|.+.++|.....+|||..+   +++.|
T Consensus       441 ~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~-Wm-Dk----IKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L  514 (718)
T KOG2416|consen  441 KEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEF-WM-DK----IKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHL  514 (718)
T ss_pred             CCccceEeeecccccchHHHHHHHHhhccCchHHH-HH-HH----hhcceeEecccHHHHHHHHHHHhccccCCCCCcee
Confidence            35678899999999999999999999 56777776 33 22    346899999999999999999999765   46778


Q ss_pred             EEEEeCC
Q 028027          126 QVHLIPP  132 (215)
Q Consensus       126 ~V~~a~~  132 (215)
                      .+.|...
T Consensus       515 ~adf~~~  521 (718)
T KOG2416|consen  515 IADFVRA  521 (718)
T ss_pred             Eeeecch
Confidence            8887643

>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=96.16  E-value=0.011  Score=46.42  Aligned_cols=82  Identities=21%  Similarity=0.245  Sum_probs=50.8

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhcc-CCCe---eEEEEeecCC-C-CCcccEEEEEEcCHHHHHHHHHHhCCceeCC--
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQ-FGAI---KRLRIARNKK-T-GQSKHFGFIEFNDPEVAEVVADAMHGYLLFE--  122 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~-~G~v---~~v~i~~~~~-t-g~~~g~afV~F~~~~~a~~ai~~l~g~~l~g--  122 (215)
                      .....|.|.+||+++|++++.+.++. ++.-   ..+.-..... . ...-.-|||.|.+.+++...+..++|+.+.+  
T Consensus         5 ~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~k   84 (176)
T PF03467_consen    5 KEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSK   84 (176)
T ss_dssp             ----EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TT
T ss_pred             ccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCC
Confidence            44568999999999999999887776 6654   3333222211 1 1223569999999999999999999976542  


Q ss_pred             ---eEEEEEEeCC
Q 028027          123 ---HILQVHLIPP  132 (215)
Q Consensus       123 ---~~l~V~~a~~  132 (215)
                         ....|++|.-
T Consensus        85 g~~~~~~VE~Apy   97 (176)
T PF03467_consen   85 GNEYPAVVEFAPY   97 (176)
T ss_dssp             S-EEEEEEEE-SS
T ss_pred             CCCcceeEEEcch
Confidence               3446666654

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.

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

Probab=96.09  E-value=0.0018  Score=61.01  Aligned_cols=82  Identities=13%  Similarity=0.259  Sum_probs=68.8

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 028027           49 LVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVH  128 (215)
Q Consensus        49 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~  128 (215)
                      .....++||+|||+..+++.+|+..|..+|.|..|.|-+.+ -+....||||.|.+...+..|+..+.+..|..-.+.+.
T Consensus       368 D~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~-~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~g  446 (975)
T KOG0112|consen  368 DFRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPH-IKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIG  446 (975)
T ss_pred             chhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCC-CCcccchhhhhhhccccCcccchhhcCCccccCccccc
Confidence            34567899999999999999999999999999999887653 44455799999999999999998999988776666666


Q ss_pred             EeC
Q 028027          129 LIP  131 (215)
Q Consensus       129 ~a~  131 (215)
                      +..
T Consensus       447 lG~  449 (975)
T KOG0112|consen  447 LGQ  449 (975)
T ss_pred             ccc
Confidence            654

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

Probab=96.02  E-value=0.12  Score=37.27  Aligned_cols=68  Identities=21%  Similarity=0.262  Sum_probs=48.5

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccC-CCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCC
Q 028027           53 ATVLYIGRIPHGFYEKEMQAFFSQF-GAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFE  122 (215)
Q Consensus        53 ~~~l~V~nLp~~~te~~L~~~F~~~-G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g  122 (215)
                      ...+.+...|+.++-++|..+.+.+ ..|..++|+++.  ..++-.+++.|.+...|..-...+||..++.
T Consensus        13 ~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~--~pnrymVLikF~~~~~Ad~Fy~~fNGk~Fns   81 (110)
T PF07576_consen   13 STLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDG--TPNRYMVLIKFRDQESADEFYEEFNGKPFNS   81 (110)
T ss_pred             ceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCC--CCceEEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            3344454555555556666555554 467888999873  3456678999999999999999999987663

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

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=96.00  E-value=0.032  Score=41.87  Aligned_cols=74  Identities=12%  Similarity=0.170  Sum_probs=54.7

Q ss_pred             CCCCcEEEEcCCCCCCcH-H---HHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEE
Q 028027           50 VNKATVLYIGRIPHGFYE-K---EMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHIL  125 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te-~---~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l  125 (215)
                      +++-.||.|.=|..++.. +   .+...++.||+|.+|.+.-       +.-|.|.|.+..+|-.|+.++.. ...|..+
T Consensus        83 epPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cG-------rqsavVvF~d~~SAC~Av~Af~s-~~pgtm~  154 (166)
T PF15023_consen   83 EPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCG-------RQSAVVVFKDITSACKAVSAFQS-RAPGTMF  154 (166)
T ss_pred             CCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecC-------CceEEEEehhhHHHHHHHHhhcC-CCCCceE
Confidence            456678888765555432 3   4445577899999996632       34799999999999999988766 5678888


Q ss_pred             EEEEeC
Q 028027          126 QVHLIP  131 (215)
Q Consensus       126 ~V~~a~  131 (215)
                      .+.|-.
T Consensus       155 qCsWqq  160 (166)
T PF15023_consen  155 QCSWQQ  160 (166)
T ss_pred             Eeeccc
Confidence            888753

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=95.10  E-value=0.14  Score=43.11  Aligned_cols=73  Identities=14%  Similarity=0.201  Sum_probs=54.5

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeE-EEEEEeC
Q 028027           53 ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHI-LQVHLIP  131 (215)
Q Consensus        53 ~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~-l~V~~a~  131 (215)
                      ..-|-|-++|+.- -..|...|++||.|......      ..-.+-+|.|.+...|++||. .||..|+|.. |-|.-+.
T Consensus       197 D~WVTVfGFppg~-~s~vL~~F~~cG~Vvkhv~~------~ngNwMhirYssr~~A~KALs-kng~ii~g~vmiGVkpCt  268 (350)
T KOG4285|consen  197 DTWVTVFGFPPGQ-VSIVLNLFSRCGEVVKHVTP------SNGNWMHIRYSSRTHAQKALS-KNGTIIDGDVMIGVKPCT  268 (350)
T ss_pred             cceEEEeccCccc-hhHHHHHHHhhCeeeeeecC------CCCceEEEEecchhHHHHhhh-hcCeeeccceEEeeeecC
Confidence            4567777888864 45677899999999876443      223699999999999999995 5999998854 4555544


Q ss_pred             CC
Q 028027          132 PE  133 (215)
Q Consensus       132 ~~  133 (215)
                      .+
T Consensus       269 Dk  270 (350)
T KOG4285|consen  269 DK  270 (350)
T ss_pred             CH
Confidence            43

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

Probab=95.02  E-value=0.021  Score=52.39  Aligned_cols=73  Identities=12%  Similarity=0.181  Sum_probs=62.8

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEE
Q 028027           48 PLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQV  127 (215)
Q Consensus        48 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V  127 (215)
                      ++.++..+|||+|+...+..+-+..++..||.|.++....         |||..|........|+..++-..++|..+.+
T Consensus        35 ~~~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~---------fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~  105 (668)
T KOG2253|consen   35 QPLPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK---------FGFCEFLKHIGDLRASRLLTELNIDDQKLIE  105 (668)
T ss_pred             cCCCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh---------hcccchhhHHHHHHHHHHhcccCCCcchhhc
Confidence            4556778999999999999999999999999987764322         9999999999999999999988999888776


Q ss_pred             EE
Q 028027          128 HL  129 (215)
Q Consensus       128 ~~  129 (215)
                      ..
T Consensus       106 ~~  107 (668)
T KOG2253|consen  106 NV  107 (668)
T ss_pred             cc
Confidence            55

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

Probab=94.42  E-value=0.14  Score=40.38  Aligned_cols=62  Identities=19%  Similarity=0.247  Sum_probs=45.8

Q ss_pred             cHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhC--CceeCCeEEEEEEeCCC
Q 028027           66 YEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMH--GYLLFEHILQVHLIPPE  133 (215)
Q Consensus        66 te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~--g~~l~g~~l~V~~a~~~  133 (215)
                      ....|+.+|..|+.+..+.+...-      +-..|.|.+.+.|..|...|+  +..+.|..++|-++.+.
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~sF------rRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~   71 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKSF------RRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPT   71 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETTT------TEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----S
T ss_pred             hHHHHHHHHHhcCCceEEEEcCCC------CEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEcccc
Confidence            347899999999998888776652      467899999999999999999  99999999999988543

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.

>PF03880 DbpA: DbpA RNA binding domain ; InterPro: IPR005580 This RNA binding domain is found at the C terminus of a number of DEAD helicase proteins []

Probab=94.39  E-value=0.3  Score=32.41  Aligned_cols=67  Identities=25%  Similarity=0.386  Sum_probs=38.4

Q ss_pred             EEEEc-CCCCCCcHHHHHHHhccCC-----CeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 028027           55 VLYIG-RIPHGFYEKEMQAFFSQFG-----AIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVH  128 (215)
Q Consensus        55 ~l~V~-nLp~~~te~~L~~~F~~~G-----~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~  128 (215)
                      ++||. +=-..++..+|..++...+     .|-.|.+..+        |+||+-... .|..++..|++..+.|+.|.|+
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 RLFINVGRKDGLTPRDIVGAICNEAGIPGRDIGRIDIFDN--------FSFVEVPEE-VAEKVLEALNGKKIKGKKVRVE   72 (74)
T ss_dssp             EEEES-SGGGT--HHHHHHHHHTCTTB-GGGEEEEEE-SS---------EEEEE-TT--HHHHHHHHTT--SSS----EE
T ss_pred             EEEEEcccccCCCHHHHHHHHHhccCCCHHhEEEEEEeee--------EEEEEECHH-HHHHHHHHhcCCCCCCeeEEEE
Confidence            34443 2334578888888887664     3456666543        899987754 7888999999999999999998


Q ss_pred             Ee
Q 028027          129 LI  130 (215)
Q Consensus       129 ~a  130 (215)
                      .|
T Consensus        73 ~A   74 (74)
T PF03880_consen   73 RA   74 (74)
T ss_dssp             E-
T ss_pred             EC
Confidence            65

; PDB: 2G0C_A 3MOJ_B.

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=94.14  E-value=0.032  Score=49.38  Aligned_cols=76  Identities=20%  Similarity=0.385  Sum_probs=60.1

Q ss_pred             CCcEEEEcCCCCCC-cHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           52 KATVLYIGRIPHGF-YEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        52 ~~~~l~V~nLp~~~-te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      +.+.|-+.-+|+.. +-++|...|.+||.|..|.+-...      -.|.|+|.+..+|-.|. ..++..|+++.|+|.|-
T Consensus       371 dhs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~~------~~a~vTF~t~aeag~a~-~s~~avlnnr~iKl~wh  443 (526)
T KOG2135|consen  371 DHSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYSS------LHAVVTFKTRAEAGEAY-ASHGAVLNNRFIKLFWH  443 (526)
T ss_pred             ccchhhhhccCCCCchHhhhhhhhhhcCccccccccCch------hhheeeeeccccccchh-ccccceecCceeEEEEe
Confidence            44555555566654 458899999999999999886552      36899999999997776 46899999999999998


Q ss_pred             CCCC
Q 028027          131 PPEH  134 (215)
Q Consensus       131 ~~~~  134 (215)
                      .+..
T Consensus       444 nps~  447 (526)
T KOG2135|consen  444 NPSP  447 (526)
T ss_pred             cCCc
Confidence            8744

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=91.94  E-value=0.13  Score=43.39  Aligned_cols=82  Identities=15%  Similarity=0.083  Sum_probs=66.3

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ...+++|++++.+.+.+.++..++..+|.+....+........++|++++.|...+.+..|+...-.+.+.+..+...+.
T Consensus        86 ~~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~  165 (285)
T KOG4210|consen   86 GSSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLN  165 (285)
T ss_pred             cccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCccc
Confidence            45788999999999999988888999998877777766668899999999999999999999654445677766665554


Q ss_pred             CC
Q 028027          131 PP  132 (215)
Q Consensus       131 ~~  132 (215)
                      ..
T Consensus       166 ~~  167 (285)
T KOG4210|consen  166 TR  167 (285)
T ss_pred             cc
Confidence            43

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=91.86  E-value=0.7  Score=41.00  Aligned_cols=68  Identities=22%  Similarity=0.366  Sum_probs=57.6

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccC-CCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCC
Q 028027           53 ATVLYIGRIPHGFYEKEMQAFFSQF-GAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFE  122 (215)
Q Consensus        53 ~~~l~V~nLp~~~te~~L~~~F~~~-G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g  122 (215)
                      ++.|.|-.+|..++-.||-.|...| -.|.+++++++.  -..+=..+|.|.+..+|......+||..|+.
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~--~pnrymvLIkFr~q~da~~Fy~efNGk~Fn~  142 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDG--MPNRYMVLIKFRDQADADTFYEEFNGKQFNS  142 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecC--CCceEEEEEEeccchhHHHHHHHcCCCcCCC
Confidence            7889999999999999999998765 468999999963  2334467899999999999999999987764

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=91.26  E-value=0.43  Score=43.37  Aligned_cols=72  Identities=14%  Similarity=0.174  Sum_probs=59.0

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhcc--CCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCC--ceeCCeEEE
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQ--FGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHG--YLLFEHILQ  126 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~--~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g--~~l~g~~l~  126 (215)
                      ...+.|.+.-||.++-.++++.+|..  |-.+.+|.+..+.       -=||+|++..+|+.|...|..  ..|.|+.|.
T Consensus       173 ~kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~-------nWyITfesd~DAQqAykylreevk~fqgKpIm  245 (684)
T KOG2591|consen  173 HKRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND-------NWYITFESDTDAQQAYKYLREEVKTFQGKPIM  245 (684)
T ss_pred             cceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC-------ceEEEeecchhHHHHHHHHHHHHHhhcCcchh
Confidence            45578999999999999999999975  7788899887663       359999999999999987765  467788776


Q ss_pred             EEE
Q 028027          127 VHL  129 (215)
Q Consensus       127 V~~  129 (215)
                      .++
T Consensus       246 ARI  248 (684)
T KOG2591|consen  246 ARI  248 (684)
T ss_pred             hhh
Confidence            554

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

Probab=91.02  E-value=0.055  Score=43.51  Aligned_cols=66  Identities=26%  Similarity=0.470  Sum_probs=54.4

Q ss_pred             cEEEEcC----CCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCcee
Q 028027           54 TVLYIGR----IPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLL  120 (215)
Q Consensus        54 ~~l~V~n----Lp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l  120 (215)
                      .+++.|+    |...++++.+...|++-|++..+++.++. .|+++.++|+++.-....-.++....+..+
T Consensus        81 ~~~r~G~shapld~r~~~ei~~~v~s~a~p~~~~R~~~~~-d~rnrn~~~~~~qr~~~~P~~~~~y~~l~~  150 (267)
T KOG4454|consen   81 RTLRCGNSHAPLDERVTEEILYEVFSQAGPIEGVRIPTDN-DGRNRNFGFVTYQRLCAVPFALDLYQGLEL  150 (267)
T ss_pred             cccccCCCcchhhhhcchhhheeeecccCCCCCccccccc-cCCccCccchhhhhhhcCcHHhhhhcccCc
Confidence            4455666    77789999999999999999999999886 689999999999888777778877766543

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

Probab=90.65  E-value=0.51  Score=42.77  Aligned_cols=66  Identities=24%  Similarity=0.283  Sum_probs=46.4

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhc-cCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCce
Q 028027           54 TVLYIGRIPHGFYEKEMQAFFS-QFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYL  119 (215)
Q Consensus        54 ~~l~V~nLp~~~te~~L~~~F~-~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~  119 (215)
                      +++.|.|+|...|-..|...-. ..|.-.-+.++.|-.+....|||||.|.+.+.+..+.+++||..
T Consensus       389 tt~~iknipNK~T~~ml~~~d~~~~gtYDFlYLPiDF~nkcNvGYAFINm~sp~ai~~F~kAFnGk~  455 (549)
T KOG4660|consen  389 TTLMIKNIPNKYTSKMLLAADEKNKGTYDFLYLPIDFKNKCNVGYAFINMTSPEAIIRFYKAFNGKK  455 (549)
T ss_pred             hhhHhhccCchhhHHhhhhhhccccCccceEEeccccccccccceeEEeecCHHHHHHHHHHHcCCc
Confidence            4455555555555444444322 24555666777776566778999999999999999999999974

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=89.72  E-value=0.22  Score=47.27  Aligned_cols=71  Identities=14%  Similarity=0.220  Sum_probs=58.6

Q ss_pred             cCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCce--eCCeEEEEEEeCCCCC
Q 028027           59 GRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYL--LFEHILQVHLIPPEHV  135 (215)
Q Consensus        59 ~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~--l~g~~l~V~~a~~~~~  135 (215)
                      .|.+-..+...|-.+|+.||.|.+++..++-      ..|.|.|.+.+.|-.|++++.|..  .-|-+.+|.++++-+.
T Consensus       304 ~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~------N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~~~~  376 (1007)
T KOG4574|consen  304 ENNAVNLTSSSLATLCSDYGSVASAWTLRDL------NMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKTLPM  376 (1007)
T ss_pred             hcccccchHHHHHHHHHhhcchhhheecccc------cchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEecccccc
Confidence            3344467778889999999999999887774      489999999999999999999975  4488899999876543

>KOG2891 consensus Surface glycoprotein [General function prediction only]

Probab=89.17  E-value=0.38  Score=40.16  Aligned_cols=70  Identities=23%  Similarity=0.411  Sum_probs=45.2

Q ss_pred             CCCCCcEEEEcCCCCC------------CcHHHHHHHhccCCCeeEEEEeec-----CCCCCc-----ccEEE-------
Q 028027           49 LVNKATVLYIGRIPHG------------FYEKEMQAFFSQFGAIKRLRIARN-----KKTGQS-----KHFGF-------   99 (215)
Q Consensus        49 ~~~~~~~l~V~nLp~~------------~te~~L~~~F~~~G~v~~v~i~~~-----~~tg~~-----~g~af-------   99 (215)
                      |...+.|||+.+||-.            -+++.|+..|..||.|..|.|+.-     .-+|+.     .||+|       
T Consensus       145 pgerpdti~la~ip~kwf~lkedg~~dlpse~rlr~a~eafg~ir~vdipicdplr~~mn~kisgiq~~gfg~g~dlffe  224 (445)
T KOG2891|consen  145 PGERPDTIHLAGIPCKWFALKEDGSEDLPSEDRLRKAFEAFGEIRNVDIPICDPLREEMNGKISGIQFHGFGFGGDLFFE  224 (445)
T ss_pred             CCCCCCceeecCCcceeeeecccccccCChHHHHHHHHHHhccceecCCcccchhHHHhcCccccceeeccccCcchhHH
Confidence            3455678999988753            467889999999999998877532     124443     33433       


Q ss_pred             --EEEcCHHHHHHHHHHhCCc
Q 028027          100 --IEFNDPEVAEVVADAMHGY  118 (215)
Q Consensus       100 --V~F~~~~~a~~ai~~l~g~  118 (215)
                        |.|-.......|+..|.|.
T Consensus       225 ayvqfmeykgfa~amdalr~~  245 (445)
T KOG2891|consen  225 AYVQFMEYKGFAQAMDALRGM  245 (445)
T ss_pred             HHHHHHHHHhHHHHHHHHhcc
Confidence              3444444455667777664

>KOG2318 consensus Uncharacterized conserved protein [Function unknown]

Probab=88.66  E-value=1.9  Score=39.59  Aligned_cols=82  Identities=20%  Similarity=0.338  Sum_probs=61.5

Q ss_pred             CCCCcEEEEcCCCCC-CcHHHHHHHhccC----CCeeEEEEeecC----------CCCC---------------------
Q 028027           50 VNKATVLYIGRIPHG-FYEKEMQAFFSQF----GAIKRLRIARNK----------KTGQ---------------------   93 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~-~te~~L~~~F~~~----G~v~~v~i~~~~----------~tg~---------------------   93 (215)
                      ....++|-|-|+.|. +...+|.-+|..|    |.|.+|.|....          .+|.                     
T Consensus       171 ~~~T~RLAVvNMDWd~v~AkDL~v~~nSFlP~gGsilSV~IYpSeFGkeRM~eEeV~GP~~el~~~~e~~~~s~sD~ee~  250 (650)
T KOG2318|consen  171 GEETKRLAVVNMDWDRVKAKDLFVLFNSFLPKGGSILSVKIYPSEFGKERMKEEEVHGPPKELFKPVEEYKESESDDEEE  250 (650)
T ss_pred             ccccceeeEeccccccccHHHHHHHHHhhcCCCCceeEEEechhhhhHHHhhhhcccCChhhhccccccCcccccchhhh
Confidence            456788999999996 7778999888866    588888775431          1222                     


Q ss_pred             ----------------cccEEEEEEcCHHHHHHHHHHhCCceeCC--eEEEEEEeC
Q 028027           94 ----------------SKHFGFIEFNDPEVAEVVADAMHGYLLFE--HILQVHLIP  131 (215)
Q Consensus        94 ----------------~~g~afV~F~~~~~a~~ai~~l~g~~l~g--~~l~V~~a~  131 (215)
                                      .-=||.|+|.+...|..+...++|..+..  ..|-++|..
T Consensus       251 ~~~~~~kLR~Yq~~rLkYYyAVvecDsi~tA~~vYe~CDG~EfEsS~~~~DLRFIP  306 (650)
T KOG2318|consen  251 EDVDREKLRQYQLNRLKYYYAVVECDSIETAKAVYEECDGIEFESSANKLDLRFIP  306 (650)
T ss_pred             hhHHHHHHHHHHhhhheeEEEEEEecCchHHHHHHHhcCcceeccccceeeeeecC
Confidence                            01279999999999999999999998875  455555543

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

Probab=84.96  E-value=0.028  Score=49.23  Aligned_cols=79  Identities=15%  Similarity=0.278  Sum_probs=64.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEE-eecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRI-ARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVH  128 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i-~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~  128 (215)
                      ...++.+-|.|+|+....+.|..++.+||.|..|.. ..+.+|    ...-|+|...+.+..||..++|..+....+.|.
T Consensus        77 kqrsrk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~et----avvnvty~~~~~~~~ai~kl~g~Q~en~~~k~~  152 (584)
T KOG2193|consen   77 KQRSRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDSET----AVVNVTYSAQQQHRQAIHKLNGPQLENQHLKVG  152 (584)
T ss_pred             HHHhhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccchHH----HHHHHHHHHHHHHHHHHHhhcchHhhhhhhhcc
Confidence            345667999999999999999999999999998854 334332    234478889999999999999999999888888


Q ss_pred             EeCC
Q 028027          129 LIPP  132 (215)
Q Consensus       129 ~a~~  132 (215)
                      |...
T Consensus       153 YiPd  156 (584)
T KOG2193|consen  153 YIPD  156 (584)
T ss_pred             cCch
Confidence            7543

>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=83.84  E-value=9.2  Score=24.86  Aligned_cols=55  Identities=29%  Similarity=0.437  Sum_probs=42.0

Q ss_pred             CCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEE
Q 028027           64 GFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQV  127 (215)
Q Consensus        64 ~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V  127 (215)
                      .++-.+++..+..|+- ..  |..++ ||     =||.|.+..+|+++....+|..+.+..|.+
T Consensus        11 ~~~v~d~K~~Lr~y~~-~~--I~~d~-tG-----fYIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYRW-DR--IRDDR-TG-----FYIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCCc-ce--EEecC-CE-----EEEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            3567899999999863 33  33443 32     389999999999999999999888877654

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	215
2khc_A	118	Bruno Rrm3+ Length = 118		2e-07
1d8z_A	89	Solution Structure Of The First Rna-Binding Domain		2e-07
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		3e-07
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		5e-07
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		2e-06
2dh8_A	105	Solution Structure Of The N-Terminal Rna Binding Do		2e-06
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		3e-06
2cq0_A	103	Solution Structure Of Rna Binding Domain In Eukaryo		4e-06
2km8_B	84	Interdomain Rrm Packing Contributes To Rna Recognit		6e-06
2x1f_A	96	Structure Of Rna15 Rrm With Bound Rna (Gu) Length =		9e-06
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		1e-05
2x1a_A	97	Structure Of Rna15 Rrm With Rna Bound (G) Length =		1e-05
2jwn_A	124	Solution Nmr Structure Of The Protease-Resistent Do		1e-05
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		2e-05
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		2e-05
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		2e-04
1d9a_A	85	Solution Structure Of The Second Rna-Binding Domain		2e-05
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		2e-05
2cpz_A	115	Solution Structure Of Rna Binding Domain 3 In Cug T		3e-05
1u6f_A	139	Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit		3e-05
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		3e-05
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		1e-04
2cqg_A	103	Solution Structure Of The Rna Binding Domain Of Tar		4e-05
2dgp_A	106	Solution Structure Of The N-Terminal Rna Binding Do		5e-05
2lea_A	135	Solution Structure Of Human Srsf2 (Sc35) Rrm Length		6e-05
3b4d_A	96	Crystal Structure Of Human Pabpn1 Rrm Length = 96		7e-05
3ucg_A	89	Crystal Structure Of A Rna Binding Domain Of Hypoth		7e-05
2e5h_A	94	Solution Structure Of Rna Binding Domain In Zinc Fi		9e-05
3h2u_B	283	Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Comple		1e-04
1x4a_A	109	Solution Structure Of Rrm Domain In Splicing Factor		1e-04
3vf0_B	285	Raver1 In Complex With Metavinculin L954 Deletion M		1e-04
3smz_A	284	Human Raver1 Rrm1-3 Domains (Residues 39-320) Lengt		1e-04
2cqb_A	102	Solution Structure Of The Rna Recognition Motif In		1e-04
3s7r_A	87	Crystal Structure Of A Heterogeneous Nuclear Ribonu		1e-04
2xs5_A	87	Crystal Structure Of The Rrm Domain Of Mouse Delete		2e-04
3hi9_A	84	The X-Ray Crystal Structure Of The First Rna Recogn		2e-04
2xsf_A	89	Crystal Structure Of The Rrm Domain Of Mouse Delete		2e-04
2xs2_A	102	Crystal Structure Of The Rrm Domain Of Mouse Delete		2e-04
2dgq_A	108	Solution Structure Of The N-Terminal Rna Binding Do		2e-04
2ki2_A	90	Solution Structure Of Ss-Dna Binding Protein 12rnp2		2e-04
1sxl_A	97	Resonance Assignments And Solution Structure Of The		3e-04
2cpf_A	98	Solution Structure Of The Penultimate Rna Recogniti		3e-04
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		3e-04
2kn4_A	158	The Structure Of The Rrm Domain Of Sc35 Length = 15		3e-04
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		3e-04
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		3e-04
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		4e-04
2d9p_A	103	Solution Structure Of Rna Binding Domain 4 In Polya		4e-04
2yh0_A	198	Solution Structure Of The Closed Conformation Of Hu		4e-04
3nnh_A	88	Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuug		4e-04
2u2f_A	85	Solution Structure Of The Second Rna-Binding Domain		4e-04
1hd0_A	75	Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D		4e-04
1hl6_A	165	A Novel Mode Of Rbd-Protein Recognition In The Y14-		5e-04
4fxv_A	99	Crystal Structure Of An Elav-Like Protein 1 (Elavl1		5e-04
3vaf_A	174	Structure Of U2af65 Variant With Bru3 Dna Length =		5e-04
2ku7_A	140	Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric		6e-04
2g4b_A	172	Structure Of U2af65 Variant With Polyuridine Tract		6e-04
1oo0_B	110	Crystal Structure Of The Drosophila Mago Nashi-Y14		6e-04
3nnc_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		6e-04
2hvz_A	101	Solution Structure Of The Rrm Domain Of Sr Rich Fac		6e-04
2sxl_A	88	Sex-Lethal Rbd1, Nmr, Minimized Average Structure L		6e-04
2dhs_A	187	Solution Structure Of Nucleic Acid Binding Protein		7e-04
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		7e-04
2kyx_A	83	Solution Structure Of The Rrm Domain Of Cyp33 Lengt		9e-04

>pdb|2KHC|A Chain A, Bruno Rrm3+ Length = 118

Iteration: 1
 Score = 52.4 bits (124), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 24/74 (32%), Positives = 44/74 (59%)
Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L+I  +P  F + ++ + F  FG +   ++  +K+T  SK FGF+ F++P+ A+V   AM
Sbjct: 43  LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 116 HGYLLFEHILQVHL 129
           +G+ +    L+V L
Sbjct: 103 NGFQVGTKRLKVQL 116

>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1) Of Hu Antigen C (Huc) Length = 89

Iteration: 1
 Score = 52.0 bits (123), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 22/87 (25%), Positives = 43/87 (49%)
Query: 50  VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAE 109
           ++  T L +  +P    + E ++ F   G I+  ++ R+K TGQS  +GF+ ++DP  A+
Sbjct: 1   MDSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDAD 60
Query: 110 VVADAMHGYLLFEHILQVHLIPPEHVH 136
              + ++G  L    ++V    P    
Sbjct: 61  KAINTLNGLKLQTKTIKVSYARPSSAS 87

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 52.0 bits (123), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 22/87 (25%), Positives = 43/87 (49%)
Query: 50  VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAE 109
           ++  T L +  +P    + E ++ F   G I+  ++ R+K TGQS  +GF+ ++DP  A+
Sbjct: 1   MDSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDAD 60
Query: 110 VVADAMHGYLLFEHILQVHLIPPEHVH 136
              + ++G  L    ++V    P    
Sbjct: 61  KAINTLNGLKLQTKTIKVSYARPSSAS 87

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 50.8 bits (120), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 23/83 (27%), Positives = 42/83 (50%)
Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
           T L +  +P    ++E ++ F   G I+  ++ R+K TGQS  +GF+ + DP+ AE   +
Sbjct: 3   TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62
Query: 114 AMHGYLLFEHILQVHLIPPEHVH 136
            ++G  L    ++V    P    
Sbjct: 63  TLNGLRLQTKTIKVSYARPSSAS 85

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 49.3 bits (116), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 27/95 (28%), Positives = 48/95 (50%), Gaps = 5/95 (5%)
Query: 51  NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEV 110
           + ++ LY+G +     E  ++  F  FG I  + + ++  TG+SK +GFI F+D E A  
Sbjct: 3   SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARR 62
Query: 111 VADAMHGYLLFEHILQVHLIPPEHVHPKLWRGFNP 145
             + ++G+ L    ++V      HV  +L  G  P
Sbjct: 63  ALEQLNGFELAGRPMRVG-----HVTERLDGGSGP 92

>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Daz-Associated Protein 1 Length = 105

Iteration: 1
 Score = 48.9 bits (115), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 26/90 (28%), Positives = 44/90 (48%), Gaps = 9/90 (10%)
Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L++G +     ++ ++++FSQ+G +    I ++K T QS+ FGF++F DP     V  + 
Sbjct: 19  LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASR 78
Query: 116 HGYLLFEHILQVHLIPPEHVHPKLWRGFNP 145
                  H L    I P+   P   RG  P
Sbjct: 79  ------PHTLDGRNIDPKPCTP---RGMQP 99

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 48.1 bits (113), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 21/65 (32%), Positives = 39/65 (60%)
Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           LY+G +     E  ++  F  FG I+ +++  + +TG+SK +GFI F+D E A+   + +
Sbjct: 29  LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 116 HGYLL 120
           +G+ L
Sbjct: 89  NGFEL 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 = 48.1 bits (113), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 25/67 (37%), Positives = 35/67 (52%)
Query: 67  EKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQ 126
           E ++Q  F  FG+I R+ +A++K TGQSK F FI F+  E A      + G+     IL 
Sbjct: 29  ETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILN 88
Query: 127 VHLIPPE 133
           V    P 
Sbjct: 89  VEWAKPS 95

>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition In The Rna15, Hrp1, Anchor Rna 3' Processing Ternary Complex Length = 84

Iteration: 1
 Score = 47.4 bits (111), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 23/73 (31%), Positives = 40/73 (54%)
Query: 55  VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
           V+Y+G IP+   E+++    S  G +  L++  + +TG+SK + FIEF D E +      
Sbjct: 6   VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 65
Query: 115 MHGYLLFEHILQV 127
           ++GY L    L+ 
Sbjct: 66  LNGYQLGSRFLKC 78

>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu) Length = 96

Iteration: 1
 Score = 47.0 bits (110), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 23/73 (31%), Positives = 40/73 (54%)
Query: 55  VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
           V+Y+G IP+   E+++    S  G +  L++  + +TG+SK + FIEF D E +      
Sbjct: 4   VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 63
Query: 115 MHGYLLFEHILQV 127
           ++GY L    L+ 
Sbjct: 64  LNGYQLGSRFLKC 76

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 46.6 bits (109), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 22/83 (26%), Positives = 42/83 (50%), Gaps = 7/83 (8%)
Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           ++IG +     E  ++ +F ++G +  L+I ++  TG+S+ FGF+ F  P   + V    
Sbjct: 6   MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT- 64
Query: 116 HGYLLFEHILQVHLIPPEHVHPK 138
                 +HIL   +I P+   P+
Sbjct: 65  ------QHILDGKVIDPKRAIPR 81

>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G) Length = 97

Iteration: 1
 Score = 46.6 bits (109), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 23/73 (31%), Positives = 40/73 (54%)
Query: 55  VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
           V+Y+G IP+   E+++    S  G +  L++  + +TG+SK + FIEF D E +      
Sbjct: 5   VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 64
Query: 115 MHGYLLFEHILQV 127
           ++GY L    L+ 
Sbjct: 65  LNGYQLGSRFLKC 77

>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of Xenopus Laevis Epabp2 Length = 124

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 24/67 (35%), Positives = 40/67 (59%), Gaps = 1/67 (1%)
Query: 36  EGGPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSK 95
           EG P     EEK  ++K +V Y+G + +G   ++++A FS  G+I R+ I  +K +G  K
Sbjct: 20  EGPPQPLSAEEKKEIDKRSV-YVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPK 78
Query: 96  HFGFIEF 102
            + +IEF
Sbjct: 79  GYAYIEF 85

>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 = 45.4 bits (106), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 20/71 (28%), Positives = 42/71 (59%), Gaps = 1/71 (1%)
Query: 48  PLVNKAT-VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPE 106
           P V+++   +++G IP+   E++++  FS+ G +   R+  +++TG+ K +GF E+ D E
Sbjct: 2   PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE 61
Query: 107 VAEVVADAMHG 117
            A      ++G
Sbjct: 62  TALSAMRNLNG 72

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 45.4 bits (106), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/93 (26%), Positives = 48/93 (51%), Gaps = 5/93 (5%)
Query: 42  KLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIE 101
           +L EE    N+   +Y+  +     + ++++ F  FG IK   +AR+  TG+ K +GFIE
Sbjct: 102 QLAEEARAFNR---IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIE 158
Query: 102 FNDPEVAEVVADAMHGYLLFEHILQV--HLIPP 132
           +   + ++    +M+ + L    L+V   + PP
Sbjct: 159 YEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPP 191

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 37/147 (25%), Positives = 66/147 (44%), Gaps = 9/147 (6%)
Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           +Y+G I +   E  ++  F+ FG IK + ++ +  T + K F F+E+  PE A++  + M
Sbjct: 16  VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 116 HGYLLFEHILQV----HLIPPEHVHPKL---WRGFNPRYKPVDRVQVERKLQNKERTLEE 168
           +  +L    ++V    ++   + +  +L    R FN  Y  V  V  +    + +   E 
Sbjct: 76  NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIY--VASVHQDLSDDDIKSVFEA 133
Query: 169 HKKLVEKILKRDQKRRKRIEAAGIEYE 195
             K+    L RD    K      IEYE
Sbjct: 134 FGKIKSCTLARDPTTGKHKGYGFIEYE 160

>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2) Of Hu Antigen C (Huc) Length = 85

Iteration: 1
 Score = 45.4 bits (106), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 23/62 (37%), Positives = 34/62 (54%)
Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           LY+  +P    +KEM+  FSQ+G I   RI  ++ TG S+  GFI F+    AE     +
Sbjct: 4   LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 116 HG 117
           +G
Sbjct: 64  NG 65

>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 = 45.4 bits (106), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/81 (30%), Positives = 43/81 (53%), Gaps = 6/81 (7%)
Query: 42  KLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIE 101
           +L EE    N+   +Y+  +     + ++++ F  FG IK   +AR+  TG+ K +GFIE
Sbjct: 101 QLAEEARAFNR---IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIE 157
Query: 102 FNDPEVAEVVADAMHGYLLFE 122
           +   E A+   DA+    LF+
Sbjct: 158 Y---EKAQSSQDAVSSXNLFD 175

>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 = 45.1 bits (105), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 21/74 (28%), Positives = 42/74 (56%)
Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L+I  +P  F ++++   F  FG +   ++  +K+T  SK FGF+ +++P  A+    +M
Sbjct: 28  LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87
Query: 116 HGYLLFEHILQVHL 129
           +G+ +    L+V L
Sbjct: 88  NGFQIGMKRLKVQL 101

>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From Trypanosoma Cruzi Length = 139

Iteration: 1
 Score = 45.1 bits (105), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 21/84 (25%), Positives = 44/84 (52%)
Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L +  IP    E +++  F ++G I+ ++I  +++T QS+ +GF++F     A+     +
Sbjct: 45  LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104
Query: 116 HGYLLFEHILQVHLIPPEHVHPKL 139
           +G+ +    L+V L    H  P +
Sbjct: 105 NGFNILNKRLKVALAASGHQRPGI 128

>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 = 45.1 bits (105), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 25/93 (26%), Positives = 48/93 (51%), Gaps = 5/93 (5%)
Query: 42  KLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIE 101
           +L EE    N+   +Y+  +     + ++++ F  FG IK   +AR+  TG+ K +GFIE
Sbjct: 117 QLAEEARAFNR---IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIE 173
Query: 102 FNDPEVAEVVADAMHGYLLFEHILQV--HLIPP 132
           +   + ++    +M+ + L    L+V   + PP
Sbjct: 174 YEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPP 206

>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 = 43.1 bits (100), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 37/147 (25%), Positives = 66/147 (44%), Gaps = 9/147 (6%)
Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           +Y+G I +   E  ++  F+ FG IK + ++ +  T + K F F+E+  PE A++  + M
Sbjct: 31  VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 116 HGYLLFEHILQV----HLIPPEHVHPKL---WRGFNPRYKPVDRVQVERKLQNKERTLEE 168
           +  +L    ++V    ++   + +  +L    R FN  Y  V  V  +    + +   E 
Sbjct: 91  NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIY--VASVHQDLSDDDIKSVFEA 148
Query: 169 HKKLVEKILKRDQKRRKRIEAAGIEYE 195
             K+    L RD    K      IEYE
Sbjct: 149 FGKIKSATLARDPTTGKHKGYGFIEYE 175

>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna- Binding Protein-43 Length = 103

Iteration: 1
 Score = 44.7 bits (104), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 22/70 (31%), Positives = 38/70 (54%)
Query: 47  KPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPE 106
           K  V K + L +  +P    E++++ +FS FG +  +++ ++ KTG SK FGF+ F + E
Sbjct: 9   KRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYE 68
Query: 107 VAEVVADAMH 116
               V    H
Sbjct: 69  TQVKVMSQRH 78

>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Bruno-Like 4 Rna-Binding Protein Length = 106

Iteration: 1
 Score = 44.3 bits (103), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 21/64 (32%), Positives = 35/64 (54%)
Query: 53  ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVA 112
           A  L+IG+IP    EK+++  F +FG I  L + +++ TG  K   F+ + + E A    
Sbjct: 13  AIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQ 72
Query: 113 DAMH 116
            A+H
Sbjct: 73  SALH 76

>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm Length = 135

Iteration: 1
 Score = 43.9 bits (102), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 26/93 (27%), Positives = 45/93 (48%), Gaps = 4/93 (4%)
Query: 48  PLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEV 107
           P V   T L +  + +      ++  F ++G +  + I R++ T +S+ F F+ F+D   
Sbjct: 42  PDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRD 101
Query: 108 AEVVADAMHGYLLFEHILQVHLI----PPEHVH 136
           AE   DAM G +L    L+V +     PP+  H
Sbjct: 102 AEDAMDAMDGAVLDGRELRVQMARYGRPPDSHH 134

>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm Length = 96

Iteration: 1
 Score = 43.9 bits (102), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 19/54 (35%), Positives = 33/54 (61%)
Query: 53  ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPE 106
           A  +Y+G + +G   +E++A F   G++ R+ I  +K +G  K F +IEF+D E
Sbjct: 5   ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKE 58

>pdb|3UCG|A Chain A, Crystal Structure Of A Rna Binding Domain Of Hypothetical Polyadenylate-Binding Protein (Pabpn1) From Homo Sapiens At 1.95 A Resolution Length = 89

Iteration: 1
 Score = 43.9 bits (102), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 19/54 (35%), Positives = 33/54 (61%)
Query: 53  ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPE 106
           A  +Y+G + +G   +E++A F   G++ R+ I  +K +G  K F +IEF+D E
Sbjct: 6   ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKE 59

>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 = 43.5 bits (101), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 21/79 (26%), Positives = 43/79 (54%), Gaps = 1/79 (1%)
Query: 51  NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEV 110
           +K+TV Y+  +P      ++   FS++G + ++ I ++K T +SK   FI F D + A+ 
Sbjct: 15  SKSTV-YVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQN 73
Query: 111 VADAMHGYLLFEHILQVHL 129
              A++   LF  +++  +
Sbjct: 74  CTRAINNKQLFGRVIKASI 92

>pdb|3H2U|B Chain B, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With Human Vinculin Tail Domain Vt Length = 283

Iteration: 1
 Score = 43.1 bits (100), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/100 (25%), Positives = 46/100 (46%), Gaps = 3/100 (3%)
Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
            +L +  +P    +++ +     FG+++R  +  +++TGQSK +GF E+   + A     
Sbjct: 94  ALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKS 153
Query: 114 AMHGYLLFEHILQVHLIPPEHVHPKLWRGFNPRYKPVDRV 153
            + G  L    L VH      + P L    + R   VDR+
Sbjct: 154 DLLGKPLGPRTLYVHWTDAGQLTPAL---LHSRCLCVDRL 190

>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2 Length = 109

Iteration: 1
 Score = 43.1 bits (100), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 24/82 (29%), Positives = 41/82 (50%), Gaps = 3/82 (3%)
Query: 48  PLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEV 107
           P  N    +Y+G +P     K+++  F ++GAI+ + + +N++ G    F F+EF DP  
Sbjct: 17  PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDL-KNRRGGPP--FAFVEFEDPRD 73
Query: 108 AEVVADAMHGYLLFEHILQVHL 129
           AE       GY    + L+V  
Sbjct: 74  AEDAVYGRDGYDYDGYRLRVEF 95

>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant Length = 285

Iteration: 1
 Score = 43.1 bits (100), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/100 (25%), Positives = 46/100 (46%), Gaps = 3/100 (3%)
Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
            +L +  +P    +++ +     FG+++R  +  +++TGQSK +GF E+   + A     
Sbjct: 96  ALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKS 155
Query: 114 AMHGYLLFEHILQVHLIPPEHVHPKLWRGFNPRYKPVDRV 153
            + G  L    L VH      + P L    + R   VDR+
Sbjct: 156 DLLGKPLGPRTLYVHWTDAGQLTPAL---LHSRCLCVDRL 192

>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320) Length = 284

Iteration: 1
 Score = 42.7 bits (99), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/100 (25%), Positives = 46/100 (46%), Gaps = 3/100 (3%)
Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
            +L +  +P    +++ +     FG+++R  +  +++TGQSK +GF E+   + A     
Sbjct: 96  ALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKS 155
Query: 114 AMHGYLLFEHILQVHLIPPEHVHPKLWRGFNPRYKPVDRV 153
            + G  L    L VH      + P L    + R   VDR+
Sbjct: 156 DLLGKPLGPRTLYVHWTDAGQLTPAL---LHSRCLCVDRL 192

>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In Peptidyl- Prolyl Cis-Trans Isomerase E Length = 102

Iteration: 1
 Score = 42.7 bits (99), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/81 (30%), Positives = 41/81 (50%)
Query: 55  VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
           VLY+G +     +K + A F  FG I  ++I  + +T + + F F+EF   E A    D 
Sbjct: 14  VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 73
Query: 115 MHGYLLFEHILQVHLIPPEHV 135
           M+   LF   ++V+L  P  +
Sbjct: 74  MNESELFGRTIRVNLAKPMRI 94

>pdb|3S7R|A Chain A, Crystal Structure Of A Heterogeneous Nuclear Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15 A Resolution Length = 87

Iteration: 1
 Score = 42.7 bits (99), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/77 (29%), Positives = 39/77 (50%), Gaps = 6/77 (7%)
Query: 57  YIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMH 116
           ++G +     +K+++ +F++FG +    I  +  TG+S+ FGFI F D    E V D   
Sbjct: 15  FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQK- 73
Query: 117 GYLLFEHILQVHLIPPE 133
                EH L   +I P+
Sbjct: 74  -----EHRLDGRVIDPK 85

>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like In Complex With Mvh Rna, Uguuc Length = 87

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 20/62 (32%), Positives = 42/62 (67%), Gaps = 2/62 (3%)
Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEF-NDPEVAEVVADA 114
           +++G I     E E+++FF+++G++K ++I  + +TG SK +GF+ F ND +V ++V   
Sbjct: 12  VFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 115 MH 116
           ++
Sbjct: 71  IN 72

>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 = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/96 (23%), Positives = 43/96 (44%), Gaps = 12/96 (12%)
Query: 38  GPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHF 97
           GPGR            T L +  +P    + E+++ FS  G ++  ++ R+K  G S  +
Sbjct: 1   GPGR------------TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGY 48
Query: 98  GFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPPE 133
           GF+ +   + AE   + ++G  L    ++V    P 
Sbjct: 49  GFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARPS 84

>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like Length = 89

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 20/64 (31%), Positives = 42/64 (65%), Gaps = 2/64 (3%)
Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEF-NDPEVAEVVA 112
             +++G I     E E+++FF+++G++K ++I  + +TG SK +GF+ F ND +V ++V 
Sbjct: 11  NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIVE 69
Query: 113 DAMH 116
             ++
Sbjct: 70  SQIN 73

>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like In Complex With Rna, Uuguucuu Length = 102

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 20/64 (31%), Positives = 42/64 (65%), Gaps = 2/64 (3%)
Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEF-NDPEVAEVVA 112
             +++G I     E E+++FF+++G++K ++I  + +TG SK +GF+ F ND +V ++V 
Sbjct: 10  NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIVE 68
Query: 113 DAMH 116
             ++
Sbjct: 69  SQIN 72

>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Bruno-Like 6 Rna-Binding Protein Length = 108

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 19/66 (28%), Positives = 36/66 (54%)
Query: 51  NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEV 110
           + A  L++G+IP G  E++++  F +FG I  L + +++ TG  K   F+ +   + A  
Sbjct: 13  HDAIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALK 72
Query: 111 VADAMH 116
              A+H
Sbjct: 73  AQSALH 78

>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 = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 16/57 (28%), Positives = 36/57 (63%)
Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVA 112
           +Y+G + +    ++++  FSQFG +  +++  +++T + K FGF+E  +  V+E +A
Sbjct: 4   IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIA 60

>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second Rna-Binding Domain Of Sex-Lethal Determined By Multidimensional Heteronuclear Magnetic Resonance Spectroscopy Length = 97

Iteration: 1
 Score = 42.0 bits (97), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 18/68 (26%), Positives = 36/68 (52%)
Query: 52  KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVV 111
           K T LY+  +P    + ++   F ++G+I +  I R+K TG+ +   F+ +N  E A+  
Sbjct: 12  KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEA 71
Query: 112 ADAMHGYL 119
             A++  +
Sbjct: 72  ISALNNVI 79

>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition Motif Of Hypothetical Rna-Binding Protein Rbm19 Length = 98

Iteration: 1
 Score = 42.0 bits (97), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 25/80 (31%), Positives = 43/80 (53%), Gaps = 3/80 (3%)
Query: 53  ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNK-KTG--QSKHFGFIEFNDPEVAE 109
           ++ L+I  +     E+ ++  FS+ GAIK   I++ K K G   S  FGF+E+  PE A+
Sbjct: 5   SSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQ 64
Query: 110 VVADAMHGYLLFEHILQVHL 129
                + G+ +  H L+V +
Sbjct: 65  KALKQLQGHTVDGHKLEVRI 84

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 42.0 bits (97), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 19/81 (23%), Positives = 39/81 (48%)
Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
           T L +  +P    + E+++ FS  G ++  ++ R+K  G S  +GF+ +   + AE   +
Sbjct: 3   TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 114 AMHGYLLFEHILQVHLIPPEH 134
            ++G  L    ++V    P  
Sbjct: 63  TLNGLRLQSKTIKVSYARPSS 83

>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35 Length = 158

Iteration: 1
 Score = 42.0 bits (97), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 25/92 (27%), Positives = 44/92 (47%), Gaps = 4/92 (4%)
Query: 50  VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAE 109
           V   T L +  + +      ++  F ++G +  + I R++ T +S+ F F+ F+D   AE
Sbjct: 67  VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAE 126
Query: 110 VVADAMHGYLLFEHILQVHLI----PPEHVHP 137
              DAM G +L    L+V +     PP+  H 
Sbjct: 127 DAMDAMDGAVLDGRELRVQMARYGRPPDSHHS 158

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 41.6 bits (96), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 19/81 (23%), Positives = 39/81 (48%)
Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
           T L +  +P    + E+++ FS  G ++  ++ R+K  G S  +GF+ +   + AE   +
Sbjct: 3   TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 114 AMHGYLLFEHILQVHLIPPEH 134
            ++G  L    ++V    P  
Sbjct: 63  TLNGLRLQSKTIKVSYARPSS 83

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 41.6 bits (96), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 18/68 (26%), Positives = 36/68 (52%)
Query: 52  KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVV 111
           K T LY+  +P    + ++   F ++G+I +  I R+K TG+ +   F+ +N  E A+  
Sbjct: 99  KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEA 158
Query: 112 ADAMHGYL 119
             A++  +
Sbjct: 159 ISALNNVI 166

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 41.6 bits (96), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 21/79 (26%), Positives = 36/79 (45%)
Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
           T L +  +P    ++E+ A F   G I   RI R+ KTG S  + F++F     ++    
Sbjct: 4   TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 114 AMHGYLLFEHILQVHLIPP 132
            ++G  +    L+V    P
Sbjct: 64  VLNGITVRNKRLKVSYARP 82

>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In Polyadenylation Binding Protein 3 Length = 103

Iteration: 1
 Score = 41.6 bits (96), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 28/94 (29%), Positives = 47/94 (50%), Gaps = 7/94 (7%)
Query: 36  EGGPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSK 95
            G  G ++T  + +VN    LY+  +  G  ++ ++  FS FG I   ++    + G+SK
Sbjct: 3   SGSSGDRITRYQ-VVN----LYVKNLDDGIDDERLRKAFSPFGTITSAKVM--MEGGRSK 55
Query: 96  HFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL 129
            FGF+ F+ PE A      M+G ++    L V L
Sbjct: 56  GFGFVCFSSPEEATKAVTEMNGRIVATKPLYVAL 89

>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human U2af65 Tandem Rrm1 And Rrm2 Domains Length = 198

Iteration: 1
 Score = 41.2 bits (95), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 19/73 (26%), Positives = 37/73 (50%)
Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L+IG +P+   + +++   + FG +K   + ++  TG SK + F E+ D  V +     +
Sbjct: 117 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 176
Query: 116 HGYLLFEHILQVH 128
           +G  L +  L V 
Sbjct: 177 NGMQLGDKKLLVQ 189

>pdb|3NNH|A Chain A, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna Length = 88

Iteration: 1
 Score = 41.2 bits (95), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 18/69 (26%), Positives = 38/69 (55%), Gaps = 2/69 (2%)
Query: 51  NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTG--QSKHFGFIEFNDPEVA 108
           + A  +++G++P  + EK+++  F Q+GA+  + + R++     QSK   F+ F   + A
Sbjct: 1   SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
Query: 109 EVVADAMHG 117
               +A+H 
Sbjct: 61  LEAQNALHN 69

>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of Hu2af65 Length = 85

Iteration: 1
 Score = 41.2 bits (95), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 19/73 (26%), Positives = 37/73 (50%)
Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L+IG +P+   + +++   + FG +K   + ++  TG SK + F E+ D  V +     +
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 116 HGYLLFEHILQVH 128
           +G  L +  L V 
Sbjct: 64  NGMQLGDKKLLVQ 76

>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0 Rbd1), Nmr Length = 75

Iteration: 1
 Score = 41.2 bits (95), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 22/78 (28%), Positives = 41/78 (52%), Gaps = 6/78 (7%)
Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           ++IG +     +K+++ +FS+FG +    +  +  TG+S+ FGF+ F + E  + V D  
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 116 HGYLLFEHILQVHLIPPE 133
                 EH L   +I P+
Sbjct: 62  ------EHKLNGKVIDPK 73

>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago Complex Length = 165

Iteration: 1
 Score = 41.2 bits (95), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 25/97 (25%), Positives = 46/97 (47%), Gaps = 8/97 (8%)
Query: 31  DFLPLEGGPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKK 90
           D   LE GP R +        +  +L++  I     E E+Q  F  +G IK + +  +++
Sbjct: 58  DDDELEPGPQRSV--------EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRR 109
Query: 91  TGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQV 127
           TG SK +  +E+   + A    +A++G  +    +QV
Sbjct: 110 TGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQV 146

>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 = 41.2 bits (95), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 19/82 (23%), Positives = 40/82 (48%)
Query: 52  KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVV 111
           + T L +  +P    + E+++ FS  G ++  ++ R+K  G S  +GF+ +   + AE  
Sbjct: 18  QGTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 77
Query: 112 ADAMHGYLLFEHILQVHLIPPE 133
            + ++G  L    ++V    P 
Sbjct: 78  INTLNGLRLQSKTIKVSYARPS 99

>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna Length = 174

Iteration: 1
 Score = 40.8 bits (94), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 19/73 (26%), Positives = 37/73 (50%)
Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L+IG +P+   + +++   + FG +K   + ++  TG SK + F E+ D  V +     +
Sbjct: 99  LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 158
Query: 116 HGYLLFEHILQVH 128
           +G  L +  L V 
Sbjct: 159 NGMQLGDKKLLVQ 171

>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein Length = 140

Iteration: 1
 Score = 40.8 bits (94), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 24/75 (32%), Positives = 39/75 (52%)
Query: 55  VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
           VLY+G +     +K + A F  FG I  ++I  + +T + + F F+EF   E A    D 
Sbjct: 65  VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 124
Query: 115 MHGYLLFEHILQVHL 129
           M+   LF   ++V+L
Sbjct: 125 MNESELFGRTIRVNL 139

>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract Length = 172

Iteration: 1
 Score = 40.8 bits (94), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 19/73 (26%), Positives = 37/73 (50%)
Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L+IG +P+   + +++   + FG +K   + ++  TG SK + F E+ D  V +     +
Sbjct: 97  LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 156
Query: 116 HGYLLFEHILQVH 128
           +G  L +  L V 
Sbjct: 157 NGMQLGDKKLLVQ 169

>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex Length = 110

Iteration: 1
 Score = 40.8 bits (94), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 24/93 (25%), Positives = 45/93 (48%), Gaps = 8/93 (8%)
Query: 35  LEGGPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQS 94
           LE GP R +        +  +L++  I     E E+Q  F  +G IK + +  +++TG S
Sbjct: 16  LEPGPQRSV--------EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFS 67
Query: 95  KHFGFIEFNDPEVAEVVADAMHGYLLFEHILQV 127
           K +  +E+   + A    +A++G  +    +QV
Sbjct: 68  KGYALVEYETHKQALAAKEALNGAEIMGQTIQV 100

>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score = 40.8 bits (94), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 18/68 (26%), Positives = 38/68 (55%), Gaps = 2/68 (2%)
Query: 51  NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTG--QSKHFGFIEFNDPEVA 108
           + A  +++G++P  + EK+++  F Q+GA+  + + R++     QSK   F+ F   + A
Sbjct: 1   SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
Query: 109 EVVADAMH 116
               +A+H
Sbjct: 61  LEAQNALH 68

>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8 Length = 101

Iteration: 1
 Score = 40.8 bits (94), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 34/104 (32%), Positives = 48/104 (46%), Gaps = 16/104 (15%)
Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           +Y+G +  G  + E++  FS +G ++ + IARN        F F+EF DP  AE   DA+
Sbjct: 3   VYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAE---DAV 54
Query: 116 HGYLLFEHILQVHLIPPEHVHPKLWRGFNPRYKPVDRVQVERKL 159
            G       L   +I    V  +L  G  PR    DR    RKL
Sbjct: 55  RG-------LDGKVICGSRVRVELSTGM-PRRSRFDRPPARRKL 90

>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure Length = 88

Iteration: 1
 Score = 40.8 bits (94), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 21/79 (26%), Positives = 36/79 (45%)
Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
           T L +  +P    ++E+ A F   G I   RI R+ KTG S  + F++F     ++    
Sbjct: 4   TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 114 AMHGYLLFEHILQVHLIPP 132
            ++G  +    L+V    P
Sbjct: 64  VLNGITVRNKRLKVSYARP 82

>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein Cugbp1ab And Its Binding Study With Dna And Rna Length = 187

Iteration: 1
 Score = 40.4 bits (93), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 18/66 (27%), Positives = 37/66 (56%), Gaps = 2/66 (3%)
Query: 53  ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTG--QSKHFGFIEFNDPEVAEV 110
           A  +++G++P  + EK+++  F Q+GA+  + + R++     QSK   F+ F   + A  
Sbjct: 15  AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALE 74
Query: 111 VADAMH 116
             +A+H
Sbjct: 75  AQNALH 80

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 40.4 bits (93), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 17/62 (27%), Positives = 38/62 (61%)
Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L++G +     E+ ++  FS++G I  + + ++++T +S+ FGF+ F + + A+    AM
Sbjct: 15  LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 116 HG 117
           +G
Sbjct: 75  NG 76

>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33 Length = 83

Iteration: 1
 Score = 40.0 bits (92), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 24/75 (32%), Positives = 39/75 (52%)
Query: 55  VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
           VLY+G +     +K + A F  FG I  ++I  + +T + + F F+EF   E A    D 
Sbjct: 7   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 66
Query: 115 MHGYLLFEHILQVHL 129
           M+   LF   ++V+L
Sbjct: 67  MNESELFGRTIRVNL 81

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	215
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	5e-18
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	1e-16
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	1e-16
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	2e-14
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	1e-16
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-14
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	2e-16
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	2e-16
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	2e-16
1x4e_A	85	RNA binding motif, single-stranded interacting pro	4e-16
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	7e-16
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	3e-13
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	9e-16
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	1e-15
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	2e-15
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	2e-12
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-15
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	3e-12
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	2e-15
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	2e-15
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	3e-15
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	6e-15
1x5o_A	114	RNA binding motif, single-stranded interacting pro	6e-15
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	9e-15
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	9e-15
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	1e-14
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	1e-14
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	2e-14
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	2e-14
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	2e-14
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	2e-14
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	3e-14
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	3e-14
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	3e-14
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-13
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-10
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	3e-14
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	4e-14
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	4e-14
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	4e-14
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	5e-14
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	5e-14
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	6e-14
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	7e-14
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	5e-10
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	8e-14
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	2e-13
2div_A	99	TRNA selenocysteine associated protein; structural	8e-14
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	1e-13
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	1e-13
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	1e-13
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	2e-13
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	2e-13
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	2e-13
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	2e-13
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	3e-13
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	3e-13
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-13
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	7e-12
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	4e-13
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	4e-13
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	6e-13
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	7e-13
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	7e-13
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	7e-13
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	1e-12
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	1e-12
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	1e-12
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	1e-12
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	2e-12
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	2e-12
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	2e-12
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	2e-12
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	2e-12
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	2e-12
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	3e-12
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	6e-12
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	6e-12
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	6e-12
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	7e-12
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	7e-12
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	7e-12
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-11
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	7e-12
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	8e-12
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	8e-12
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	8e-12
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	9e-12
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	1e-11
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	1e-11
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	1e-11
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	1e-11
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	2e-11
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	2e-11
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	2e-11
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	3e-11
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	2e-11
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	2e-11
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	3e-11
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	3e-11
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	4e-11
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	5e-11
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	5e-08
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	5e-11
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	5e-11
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	7e-11
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	7e-11
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	8e-11
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	9e-11
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	9e-11
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	1e-10
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	1e-10
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	1e-10
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	2e-10
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	2e-09
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	2e-10
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	2e-10
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	3e-10
1x5p_A	97	Negative elongation factor E; structure genomics,	4e-10
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	4e-10
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-09
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	4e-10
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	6e-10
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	6e-10
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	4e-08
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	6e-10
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	6e-10
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	7e-10
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	8e-10
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	8e-10
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	8e-10
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	9e-10
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	9e-10
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	6e-08
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	9e-10
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	1e-09
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	1e-09
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	1e-09
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	1e-09
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	1e-09
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	2e-09
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	2e-09
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	2e-09
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	3e-09
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	3e-09
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	8e-09
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	3e-09
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	3e-09
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	3e-09
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	5e-09
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	6e-09
2dis_A	109	Unnamed protein product; structural genomics, RRM	6e-09
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	1e-08
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	1e-08
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	2e-08
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-08
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	2e-08
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	4e-08
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	4e-08
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	5e-08
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	5e-08
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	8e-08
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	9e-08
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-07
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	1e-07
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	3e-07
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	4e-07
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	4e-07
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	6e-07
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	7e-07
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	1e-06
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	1e-06
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	1e-06
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	2e-06
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	3e-06
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	4e-06
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	7e-06
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	1e-05
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	2e-05
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	3e-05
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	4e-05
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	5e-05
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	6e-05
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	1e-04
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	4e-04
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	4e-04
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	4e-04
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-04
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	7e-04

>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 = 75.0 bits (185), Expect = 5e-18
 Identities = 24/96 (25%), Positives = 45/96 (46%), Gaps = 5/96 (5%)

Query: 53  ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVA 112
           + V+Y+G IP+   E+++    S  G +  L++  + +TG+SK + FIEF D E +    
Sbjct: 2   SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 61

Query: 113 DAMHGYLLFEHILQVHLIPPEHVHPKLWRGFNPRYK 148
             ++GY L    L+       +       G +  + 
Sbjct: 62  RNLNGYQLGSRFLKC-----GYSSNSDISGVSLEHH 92

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 72.0 bits (177), Expect = 1e-16
 Identities = 24/74 (32%), Positives = 44/74 (59%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L+I  +P  F + ++ + F  FG +   ++  +K+T  SK FGF+ F++P+ A+V   AM
Sbjct: 43  LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102

Query: 116 HGYLLFEHILQVHL 129
           +G+ +    L+V L
Sbjct: 103 NGFQVGTKRLKVQL 116

>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 = 73.0 bits (180), Expect = 1e-16
 Identities = 20/74 (27%), Positives = 35/74 (47%)

Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
           T L +  +P    ++E+ A F   G I   RI R+ KTG S  + F++F     ++    
Sbjct: 4   TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63

Query: 114 AMHGYLLFEHILQV 127
            ++G  +    L+V
Sbjct: 64  VLNGITVRNKRLKV 77

>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 = 67.2 bits (165), Expect = 2e-14
 Identities = 18/69 (26%), Positives = 36/69 (52%)

Query: 52  KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVV 111
           K T LY+  +P    + ++   F ++G+I +  I R+K TG+ +   F+ +N  E A+  
Sbjct: 88  KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEA 147

Query: 112 ADAMHGYLL 120
             A++  + 
Sbjct: 148 ISALNNVIP 156

>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 = 73.0 bits (180), Expect = 1e-16
 Identities = 22/77 (28%), Positives = 42/77 (54%), Gaps = 1/77 (1%)

Query: 51  NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEV 110
           +K   L +  +P    ++E ++ F   G I+  ++ R+K TGQS  +GF+ + DP+ AE 
Sbjct: 1   SKTN-LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEK 59

Query: 111 VADAMHGYLLFEHILQV 127
             + ++G  L    ++V
Sbjct: 60  AINTLNGLRLQTKTIKV 76

>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 = 67.2 bits (165), Expect = 2e-14
 Identities = 22/65 (33%), Positives = 34/65 (52%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           LY+  +P    +KE++  FSQ+G I   RI  ++ TG S+  GFI F+    AE     +
Sbjct: 91  LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150

Query: 116 HGYLL 120
           +G   
Sbjct: 151 NGQKP 155

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 71.3 bits (175), Expect = 2e-16
 Identities = 14/97 (14%), Positives = 33/97 (34%), Gaps = 1/97 (1%)

Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
             +   R+     E  ++    ++G ++ + I  + +T +      + F     A+    
Sbjct: 7   KEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVK 66

Query: 114 AMHGYLLFEHILQVHLIPPEHVHPKLW-RGFNPRYKP 149
            +H   +  +I+   L        K +    N  Y P
Sbjct: 67  NLHLTSVMGNIIHAQLDIKGQQRMKYYELIVNGSYTP 103

>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 = 71.2 bits (175), Expect = 2e-16
 Identities = 22/86 (25%), Positives = 39/86 (45%), Gaps = 4/86 (4%)

Query: 37  GGPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKH 96
           G  G    ++   +     L+IG+IP    EK+++  F +FG I  L + +++ TG  K 
Sbjct: 1   GSSGSSGMKDHDAIK----LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKG 56

Query: 97  FGFIEFNDPEVAEVVADAMHGYLLFE 122
             F+ + + E A     A+H      
Sbjct: 57  CAFLTYCERESALKAQSALHEQKTLP 82

>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 = 71.2 bits (175), Expect = 2e-16
 Identities = 20/72 (27%), Positives = 41/72 (56%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L+I  +P  F ++++   F  FG +   ++  +K+T  SK FGF+ +++P  A+    +M
Sbjct: 28  LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87

Query: 116 HGYLLFEHILQV 127
           +G+ +    L+V
Sbjct: 88  NGFQIGMKRLKV 99

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 85

 Score = 69.5 bits (171), Expect = 4e-16
 Identities = 15/63 (23%), Positives = 30/63 (47%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           LYI  +  G  ++++      +G I   +   +K T + K +GF++F+ P  A+    A+
Sbjct: 8   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67

Query: 116 HGY 118
              
Sbjct: 68  KAS 70

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 72.3 bits (178), Expect = 7e-16
 Identities = 21/94 (22%), Positives = 47/94 (50%), Gaps = 3/94 (3%)

Query: 34  PLEGGPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQ 93
            +  G   +      ++++   +Y+G I +   E  ++  F+ FG IK + ++ +  T +
Sbjct: 12  QMGRGSAAQRQGALAIMSR---VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMK 68

Query: 94  SKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQV 127
            K F F+E+  PE A++  + M+  +L    ++V
Sbjct: 69  HKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKV 102

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 65.4 bits (160), Expect = 3e-13
 Identities = 17/79 (21%), Positives = 38/79 (48%)

Query: 42  KLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIE 101
            + +          +Y+  +     + ++++ F  FG IK   +AR+  TG+ K +GFIE
Sbjct: 114 IIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIE 173

Query: 102 FNDPEVAEVVADAMHGYLL 120
           +   + ++    +M+ + L
Sbjct: 174 YEKAQSSQDAVSSMNLFDL 192

>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 = 68.8 bits (169), Expect = 9e-16
 Identities = 16/63 (25%), Positives = 33/63 (52%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           +Y+  +P      ++   FS++G + ++ I ++K T +SK   FI F D + A+    A+
Sbjct: 19  VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78

Query: 116 HGY 118
           +  
Sbjct: 79  NNK 81

>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 = 69.7 bits (171), Expect = 1e-15
 Identities = 25/110 (22%), Positives = 48/110 (43%), Gaps = 1/110 (0%)

Query: 18  SQLPVPSDKKGAADFLPLEGGPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQF 77
           +  P                GP + L+ E+        +Y+G + +G   ++++A FS  
Sbjct: 1   AIAPCMQTTHSKMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSC 60

Query: 78  GAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQV 127
           G+I R+ I  +K +G  K + +IEF +    +  A AM   +     ++V
Sbjct: 61  GSINRITILCDKFSGHPKGYAYIEFAERNSVD-AAVAMDETVFRGRTIKV 109

>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 = 70.8 bits (174), Expect = 2e-15
 Identities = 23/102 (22%), Positives = 42/102 (41%), Gaps = 3/102 (2%)

Query: 19  QLPVPSDKKGAADFLPLEGGPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFG 78
           + P            P    PG   T      +K   L+IG +P+   + +++   + FG
Sbjct: 83  RRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHK---LFIGGLPNYLNDDQVKELLTSFG 139

Query: 79  AIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLL 120
            +K   + ++  TG SK + F E+ D  V +     ++G  L
Sbjct: 140 PLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQL 181

>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 = 62.7 bits (153), Expect = 2e-12
 Identities = 23/80 (28%), Positives = 34/80 (42%), Gaps = 6/80 (7%)

Query: 53  ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIAR-----NKKTGQSKHFGFIEFNDPEV 107
           A  LY+G IP G  E+ M  FF+    +  L  A        +  Q K+F F+EF   + 
Sbjct: 4   ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 63

Query: 108 AEVVADAMHGYLLFEHILQV 127
               A A  G +     L++
Sbjct: 64  TT-QAMAFDGIIFQGQSLKI 82

>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 = 70.0 bits (172), Expect = 2e-15
 Identities = 21/93 (22%), Positives = 44/93 (47%), Gaps = 1/93 (1%)

Query: 29  AADFLPLEGGPGR-KLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIAR 87
           A D +  +G   + +   +   +  A  L+IG +P+   + +++   + FG +K   + +
Sbjct: 69  AFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVK 128

Query: 88  NKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLL 120
           +  TG SK + F E+ D  V +     ++G  L
Sbjct: 129 DSATGLSKGYAFCEYVDINVTDQAIAGLNGMQL 161

>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 = 61.5 bits (150), Expect = 3e-12
 Identities = 21/83 (25%), Positives = 33/83 (39%), Gaps = 6/83 (7%)

Query: 50  VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIK-----RLRIARNKKTGQSKHFGFIEFND 104
           +  A  LY+G IP G  E+ M  FF+    +              +  Q K+F F+EF  
Sbjct: 1   LGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRS 60

Query: 105 PEVAEVVADAMHGYLLFEHILQV 127
            +     A A  G +     L++
Sbjct: 61  VDETT-QAMAFDGIIFQGQSLKI 82

>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 = 68.0 bits (167), Expect = 2e-15
 Identities = 24/72 (33%), Positives = 37/72 (51%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           + +  +     E ++Q  F  FG+I R+ +A++K TGQSK F FI F+  E A      +
Sbjct: 18  IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGV 77

Query: 116 HGYLLFEHILQV 127
            G+     IL V
Sbjct: 78  SGFGYDHLILNV 89

>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 = 67.5 bits (166), Expect = 2e-15
 Identities = 21/72 (29%), Positives = 39/72 (54%), Gaps = 1/72 (1%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           +Y+G + +G   +E++A F   G++ R+ I  +K +G  K F +IEF+D E     + A+
Sbjct: 9   IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR-TSLAL 67

Query: 116 HGYLLFEHILQV 127
              L     ++V
Sbjct: 68  DESLFRGRQIKV 79

>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 = 69.0 bits (169), Expect = 3e-15
 Identities = 20/96 (20%), Positives = 44/96 (45%)

Query: 23  PSDKKGAADFLPLEGGPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKR 82
           P  +      L  +       T+  P  +    L +  IP    E +++  F ++G I+ 
Sbjct: 12  PYGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIES 71

Query: 83  LRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGY 118
           ++I  +++T QS+ +GF++F     A+     ++G+
Sbjct: 72  VKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGF 107

>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 = 66.9 bits (164), Expect = 6e-15
 Identities = 18/66 (27%), Positives = 37/66 (56%)

Query: 53  ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVA 112
              +++G IP+   E++++  FS+ G +   R+  +++TG+ K +GF E+ D E A    
Sbjct: 8   LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAM 67

Query: 113 DAMHGY 118
             ++G 
Sbjct: 68  RNLNGR 73

>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 = 67.3 bits (165), Expect = 6e-15
 Identities = 23/96 (23%), Positives = 34/96 (35%), Gaps = 1/96 (1%)

Query: 40  GRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGF 99
           G +    K      T LYI  +P    E+E++     FG +   RI R+  +G S+  GF
Sbjct: 12  GVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGF 70

Query: 100 IEFNDPEVAEVVADAMHGYLLFEHILQVHLIPPEHV 135
                 E  E V    +G  +           P   
Sbjct: 71  ARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEPLLC 106

>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 = 67.9 bits (166), Expect = 9e-15
 Identities = 21/83 (25%), Positives = 43/83 (51%)

Query: 45  EEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFND 104
           E++ L+ K+  LY+G +     E+++   FS+ G IK++ +  +K    +  F F+E+  
Sbjct: 31  EQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYS 90

Query: 105 PEVAEVVADAMHGYLLFEHILQV 127
              AE     ++G  L + I++ 
Sbjct: 91  RADAENAMRYINGTRLDDRIIRT 113

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 67.5 bits (165), Expect = 9e-15
 Identities = 27/113 (23%), Positives = 42/113 (37%)

Query: 9   LKKNLKKVSSQLPVPSDKKGAADFLPLEGGPGRKLTEEKPLVNKATVLYIGRIPHGFYEK 68
           L   + ++ S LP                G                VLY+G +     +K
Sbjct: 19  LSDEMYEILSNLPESVAYTCVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDK 78

Query: 69  EMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLF 121
            + A F  FG I  ++I  + +T + + F F+EF   E A    D M+   LF
Sbjct: 79  VLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELF 131

>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 = 66.1 bits (162), Expect = 1e-14
 Identities = 17/62 (27%), Positives = 38/62 (61%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L++G +     E+ ++  FS++G I  + + ++++T +S+ FGF+ F + + A+    AM
Sbjct: 15  LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74

Query: 116 HG 117
           +G
Sbjct: 75  NG 76

>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 = 66.1 bits (162), Expect = 1e-14
 Identities = 17/84 (20%), Positives = 39/84 (46%), Gaps = 2/84 (2%)

Query: 37  GGPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKH 96
           G  G       P  +    L +  +     E++++  FS++G I  + I  ++++ +S+ 
Sbjct: 1   GSSGSSGNRANP--DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRG 58

Query: 97  FGFIEFNDPEVAEVVADAMHGYLL 120
           F F+ F + + A+   +  +G  L
Sbjct: 59  FAFVYFENVDDAKEAKERANGMEL 82

>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 = 67.5 bits (165), Expect = 2e-14
 Identities = 28/125 (22%), Positives = 53/125 (42%), Gaps = 8/125 (6%)

Query: 3   AKQKKALKKNLKKVSSQLPVPSDKKGAADFLPLEGGPGRKLTEEKPLVNKATVLYIGRIP 62
           AK +K         + +     ++    D   LE GP R          +  +L++  I 
Sbjct: 30  AKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRS--------VEGWILFVTSIH 81

Query: 63  HGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFE 122
               E E+Q  F  +G IK + +  +++TG SK +  +E+   + A    +A++G  +  
Sbjct: 82  EEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMG 141

Query: 123 HILQV 127
             +QV
Sbjct: 142 QTIQV 146

>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 = 65.7 bits (161), Expect = 2e-14
 Identities = 18/71 (25%), Positives = 33/71 (46%)

Query: 51  NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEV 110
           N+   +Y+G +     E  +   F Q G +    + +++ TGQ + +GF+EF   E A+ 
Sbjct: 13  NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADY 72

Query: 111 VADAMHGYLLF 121
               M    L+
Sbjct: 73  AIKIMDMIKLY 83

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 65.7 bits (161), Expect = 2e-14
 Identities = 14/72 (19%), Positives = 37/72 (51%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L++  +     E+++   F+++G IK + +  +++TG  K +  +E+   + A+   + +
Sbjct: 26  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85

Query: 116 HGYLLFEHILQV 127
           +G  L    + V
Sbjct: 86  NGQDLMGQPISV 97

>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 = 65.8 bits (161), Expect = 2e-14
 Identities = 19/72 (26%), Positives = 37/72 (51%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L++  I     E E+Q  F  +G IK + +  +++TG SK +  +E+   + A    +A+
Sbjct: 29  LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88

Query: 116 HGYLLFEHILQV 127
           +G  +    +QV
Sbjct: 89  NGAEIMGQTIQV 100

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 64.9 bits (159), Expect = 3e-14
 Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 2/74 (2%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           +++  +P  F  K ++  F++ G +    I      G+SK  G ++F  PEVAE     M
Sbjct: 11  IFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMM 68

Query: 116 HGYLLFEHILQVHL 129
           +G  L    + V +
Sbjct: 69  NGMKLSGREIDVRI 82

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 65.3 bits (160), Expect = 3e-14
 Identities = 15/62 (24%), Positives = 29/62 (46%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L++  + +   E++++  FS +G +  L    +  T + K F F+ F  PE A      +
Sbjct: 11  LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70

Query: 116 HG 117
            G
Sbjct: 71  DG 72

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 68.9 bits (169), Expect = 3e-14
 Identities = 24/108 (22%), Positives = 45/108 (41%), Gaps = 3/108 (2%)

Query: 40  GRKLTEEKPLVNKA---TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKH 96
             +L E +  V       +L +  +P    +++ +     FG+++R  +  +++TGQSK 
Sbjct: 79  QSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKG 138

Query: 97  FGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPPEHVHPKLWRGFN 144
           +GF E+   + A      + G  L    L VH      + P L     
Sbjct: 139 YGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLTPALLHSRC 186

>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 = 66.5 bits (163), Expect = 2e-13
 Identities = 25/122 (20%), Positives = 44/122 (36%), Gaps = 10/122 (8%)

Query: 40  GRKLT-------EEKPLVNKATVLYIGRIPHGFYEKE-MQAFFSQFGAIKRLRIARNKKT 91
            R L        +  P +  +  L + R+P GF + + +    S   +    ++A  +  
Sbjct: 164 PRTLYVHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-D 222

Query: 92  GQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL-IPPEHVHPKLWRGFNPRYKPV 150
           GQ K F  +E+   E+AE       G  L    L+V    P       L      +   +
Sbjct: 223 GQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPPGRSMLAALIAAQATAL 282

Query: 151 DR 152
           +R
Sbjct: 283 NR 284

>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 = 58.1 bits (141), Expect = 2e-10
 Identities = 18/93 (19%), Positives = 31/93 (33%), Gaps = 7/93 (7%)

Query: 42  KLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIE 101
           +L   +        + I  +P     +E+    S +         +     + K   F+ 
Sbjct: 11  RLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYEL-------KYCFVDKYKGTAFVT 63

Query: 102 FNDPEVAEVVADAMHGYLLFEHILQVHLIPPEH 134
             + E AE   +A H   L E  L V L P + 
Sbjct: 64  LLNGEQAEAAINAFHQSRLRERELSVQLQPTDA 96

>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 = 65.4 bits (160), Expect = 3e-14
 Identities = 20/75 (26%), Positives = 36/75 (48%)

Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
            VLY+  +     E+++ + F++F   K   I     TG+ +   FI F + E+A     
Sbjct: 26  KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 85

Query: 114 AMHGYLLFEHILQVH 128
            ++GY L+  IL + 
Sbjct: 86  LVNGYKLYGKILVIE 100

>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 = 64.5 bits (158), Expect = 4e-14
 Identities = 20/66 (30%), Positives = 37/66 (56%)

Query: 53  ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVA 112
           ++ LY+G +     E  ++  F  FG I  + + ++  TG+SK +GFI F+D E A    
Sbjct: 5   SSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRAL 64

Query: 113 DAMHGY 118
           + ++G+
Sbjct: 65  EQLNGF 70

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 64.6 bits (158), Expect = 4e-14
 Identities = 20/91 (21%), Positives = 39/91 (42%), Gaps = 1/91 (1%)

Query: 37  GGPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKH 96
           G  G           +   L+I  +P    ++E++      G +K LR+  N+  G+ K 
Sbjct: 1   GSSGSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKG 59

Query: 97  FGFIEFNDPEVAEVVADAMHGYLLFEHILQV 127
             ++E+ +   A      M G  + E+I++V
Sbjct: 60  LAYVEYENESQASQAVMKMDGMTIKENIIKV 90

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 65.0 bits (159), Expect = 4e-14
 Identities = 17/98 (17%), Positives = 41/98 (41%), Gaps = 1/98 (1%)

Query: 36  EGGPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSK 95
           +      +    P    A  ++  ++      ++++ FFS  G ++ +RI  ++ + +SK
Sbjct: 8   KSPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSK 67

Query: 96  HFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPPE 133
              ++EF + +    +A  + G  L    + V     E
Sbjct: 68  GIAYVEFCEIQSVP-LAIGLTGQRLLGVPIIVQASQAE 104

>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 = 64.6 bits (158), Expect = 5e-14
 Identities = 17/73 (23%), Positives = 31/73 (42%)

Query: 48  PLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEV 107
           P V+    L +  + +      ++  F ++G +  + I R   T   + F F+ F+D   
Sbjct: 8   PDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRD 67

Query: 108 AEVVADAMHGYLL 120
           A+    AM G  L
Sbjct: 68  AQDAEAAMDGAEL 80

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 65.5 bits (160), Expect = 5e-14
 Identities = 25/104 (24%), Positives = 42/104 (40%)

Query: 17  SSQLPVPSDKKGAADFLPLEGGPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQ 76
           SS L        +       G          P V   T L +  + +      ++  F +
Sbjct: 11  SSGLVPRGSHMASMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEK 70

Query: 77  FGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLL 120
           +G +  + I R++ T +S+ F F+ F+D   AE   DAM G +L
Sbjct: 71  YGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVL 114

>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 = 65.1 bits (159), Expect = 6e-14
 Identities = 16/83 (19%), Positives = 40/83 (48%)

Query: 38  GPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHF 97
           G G +    +   +    L +  +     E++++  FS++G I  + I  ++++ +S+ F
Sbjct: 31  GRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGF 90

Query: 98  GFIEFNDPEVAEVVADAMHGYLL 120
            F+ F + + A+   +  +G  L
Sbjct: 91  AFVYFENVDDAKEAKERANGMEL 113

>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 = 66.5 bits (163), Expect = 7e-14
 Identities = 18/71 (25%), Positives = 31/71 (43%)

Query: 51  NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEV 110
                LY+G +     E  +   FS  G I  +R+ R+  T +S  + ++ F  P  AE 
Sbjct: 13  YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAER 72

Query: 111 VADAMHGYLLF 121
             D M+  ++ 
Sbjct: 73  ALDTMNFDVIK 83

>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 = 56.1 bits (136), Expect = 5e-10
 Identities = 19/65 (29%), Positives = 30/65 (46%), Gaps = 2/65 (3%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           ++I  +      K +   FS FG I   ++  +     SK +GF+ F   E AE   + M
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKM 163

Query: 116 HGYLL 120
           +G LL
Sbjct: 164 NGMLL 168

>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 = 65.7 bits (161), Expect = 8e-14
 Identities = 15/74 (20%), Positives = 37/74 (50%), Gaps = 2/74 (2%)

Query: 51  NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKH--FGFIEFNDPEVA 108
           + A  +++G++P  + EK+++  F Q+GA+  + + R++     +     F+ F   + A
Sbjct: 1   SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60

Query: 109 EVVADAMHGYLLFE 122
               +A+H   +  
Sbjct: 61  LEAQNALHNMKVLP 74

>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 = 64.6 bits (158), Expect = 2e-13
 Identities = 24/82 (29%), Positives = 35/82 (42%), Gaps = 1/82 (1%)

Query: 41  RKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFI 100
           +    EK    +   L+IG I     E +++  FS FG I+  RI R    G S+   F+
Sbjct: 83  KPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFV 141

Query: 101 EFNDPEVAEVVADAMHGYLLFE 122
            F    +A+    AMH     E
Sbjct: 142 TFTTRAMAQTAIKAMHQAQTME 163

>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 = 63.9 bits (156), Expect = 8e-14
 Identities = 18/66 (27%), Positives = 31/66 (46%), Gaps = 1/66 (1%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFG-AIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
           L++G +     E  +   F+  G  +  ++I RN+ TG    + F+EF D   AE     
Sbjct: 12  LWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHK 71

Query: 115 MHGYLL 120
           ++G  L
Sbjct: 72  INGKPL 77

>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 = 62.9 bits (154), Expect = 1e-13
 Identities = 22/74 (29%), Positives = 35/74 (47%)

Query: 48  PLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEV 107
            +     VLY+G +     +K + A F  FG I  ++I  + +T + + F F+EF   E 
Sbjct: 2   SMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAED 61

Query: 108 AEVVADAMHGYLLF 121
           A    D M+   LF
Sbjct: 62  AAAAIDNMNESELF 75

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 63.9 bits (156), Expect = 1e-13
 Identities = 27/111 (24%), Positives = 41/111 (36%), Gaps = 8/111 (7%)

Query: 36  EGGPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSK 95
             G         P  N    +Y+G +P     K+++  F ++GAI+ + +   K      
Sbjct: 5   SSGMSGGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDL---KNRRGGP 61

Query: 96  HFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPPEHVHPKLWRGFNPR 146
            F F+EF DP  AE       GY    + L+V     E        G  P 
Sbjct: 62  PFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRV-----EFPRSGRGTGSGPS 107

>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 = 63.4 bits (155), Expect = 1e-13
 Identities = 16/71 (22%), Positives = 28/71 (39%), Gaps = 2/71 (2%)

Query: 51  NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEV 110
            +   LY+G +     E  +   FSQ G  K  ++     +     + F+EF +   A  
Sbjct: 13  GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEHRDAAA 70

Query: 111 VADAMHGYLLF 121
              AM+G  + 
Sbjct: 71  ALAAMNGRKIL 81

>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 = 63.4 bits (155), Expect = 2e-13
 Identities = 19/62 (30%), Positives = 31/62 (50%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           LY+G +     +K + A F  FG I  ++I  + +T + + F F+EF   E A    D M
Sbjct: 15  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74

Query: 116 HG 117
           + 
Sbjct: 75  NE 76

>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 = 62.6 bits (153), Expect = 2e-13
 Identities = 16/71 (22%), Positives = 33/71 (46%), Gaps = 1/71 (1%)

Query: 51  NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEV 110
                +++G +     E+ +   F Q G + ++ I +++  G+ K FGF+ F  PE    
Sbjct: 14  EADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHPESVSY 72

Query: 111 VADAMHGYLLF 121
               ++G  L+
Sbjct: 73  AIALLNGIRLY 83

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens} Length = 88

 Score = 62.2 bits (152), Expect = 2e-13
 Identities = 19/68 (27%), Positives = 33/68 (48%), Gaps = 1/68 (1%)

Query: 52  KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKK-TGQSKHFGFIEFNDPEVAEV 110
           K T ++IGR+     +  +   FS +G IK + +   +     SK + ++EF +P+ AE 
Sbjct: 3   KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEK 62

Query: 111 VADAMHGY 118
               M G 
Sbjct: 63  ALKHMDGG 70

>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 = 62.7 bits (153), Expect = 2e-13
 Identities = 17/67 (25%), Positives = 29/67 (43%), Gaps = 1/67 (1%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L++G +     E+++   F  FG I    + R    G SK   F++F+    A+    A+
Sbjct: 18  LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRG-PDGSSKGCAFVKFSSHTEAQAAIHAL 76

Query: 116 HGYLLFE 122
           HG     
Sbjct: 77  HGSQTMP 83

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 64.2 bits (156), Expect = 3e-13
 Identities = 18/107 (16%), Positives = 37/107 (34%), Gaps = 4/107 (3%)

Query: 16  VSSQLPVPSDKKGAADFLPLEGGPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFS 75
             S  P P  ++  +            L     L N+   +Y+G       ++++     
Sbjct: 20  FQSMEPPPPVRQEPSP--KPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIR 77

Query: 76  QFGA--IKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLL 120
             G   +  L+ A N+  GQSK +  +          + + + G +L
Sbjct: 78  SIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVL 124

>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 = 62.7 bits (153), Expect = 3e-13
 Identities = 20/63 (31%), Positives = 38/63 (60%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           LY+G +     E  ++  F  FG I+ +++  + +TG+SK +GFI F+D E A+   + +
Sbjct: 29  LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88

Query: 116 HGY 118
           +G+
Sbjct: 89  NGF 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 = 63.7 bits (156), Expect = 3e-13
 Identities = 14/72 (19%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           LY+G +     E  ++ +F   G I  ++I  +K   ++ ++ F+E++    A +    +
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTL 61

Query: 116 HGYLLFEHILQV 127
           +G  +  +I+++
Sbjct: 62  NGKQIENNIVKI 73

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 60.2 bits (147), Expect = 7e-12
 Identities = 17/86 (19%), Positives = 36/86 (41%), Gaps = 12/86 (13%)

Query: 47  KPL-VNKATV-----------LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQS 94
             + +N A             L++G +     ++ ++  F  F +     +  + +TG S
Sbjct: 69  NIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSS 128

Query: 95  KHFGFIEFNDPEVAEVVADAMHGYLL 120
           + +GF+ F   + A+   D+M G  L
Sbjct: 129 RGYGFVSFTSQDDAQNAMDSMQGQDL 154

>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 = 62.8 bits (153), Expect = 4e-13
 Identities = 14/74 (18%), Positives = 38/74 (51%)

Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
            +L++  +     E+++   F+++G IK + +  +++TG  K +  +E+   + A+   +
Sbjct: 23  WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 82

Query: 114 AMHGYLLFEHILQV 127
            ++G  L    + V
Sbjct: 83  GLNGQDLMGQPISV 96

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 61.9 bits (151), Expect = 4e-13
 Identities = 20/74 (27%), Positives = 29/74 (39%), Gaps = 6/74 (8%)

Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
           T  YIG IPH   E ++   F  FG I   +          K   FI+++  E A V   
Sbjct: 28  TTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE------KGCCFIKYDTHEQAAVCIV 81

Query: 114 AMHGYLLFEHILQV 127
           A+  +      L+ 
Sbjct: 82  ALANFPFQGRNLRT 95

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 61.7 bits (150), Expect = 6e-13
 Identities = 16/87 (18%), Positives = 31/87 (35%), Gaps = 3/87 (3%)

Query: 48  PLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEV 107
           P   +   L I  IP     + + +   Q+G ++                  + ++  + 
Sbjct: 10  PKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAV---VNVTYSSKDQ 66

Query: 108 AEVVADAMHGYLLFEHILQVHLIPPEH 134
           A    D ++G+ L    L+V  IP E 
Sbjct: 67  ARQALDKLNGFQLENFTLKVAYIPDEM 93

>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 = 61.1 bits (149), Expect = 7e-13
 Identities = 23/79 (29%), Positives = 40/79 (50%), Gaps = 3/79 (3%)

Query: 52  KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQ---SKHFGFIEFNDPEVA 108
            ++ L+I  +     E+ ++  FS+ GAIK   I++ K       S  FGF+E+  PE A
Sbjct: 4   GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQA 63

Query: 109 EVVADAMHGYLLFEHILQV 127
           +     + G+ +  H L+V
Sbjct: 64  QKALKQLQGHTVDGHKLEV 82

>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 = 61.6 bits (150), Expect = 7e-13
 Identities = 16/67 (23%), Positives = 28/67 (41%)

Query: 50  VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAE 109
           V +   ++I  +     E+ +     QFG +K +R+  +  T  SK   F +F   E A+
Sbjct: 12  VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQ 71

Query: 110 VVADAMH 116
               A  
Sbjct: 72  KCLAAAS 78

>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 = 61.0 bits (149), Expect = 7e-13
 Identities = 14/62 (22%), Positives = 31/62 (50%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L++G +     ++ ++  F  F +     +  + +TG S+ +GF+ F   + A+   D+M
Sbjct: 4   LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63

Query: 116 HG 117
            G
Sbjct: 64  QG 65

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 60.9 bits (148), Expect = 1e-12
 Identities = 17/76 (22%), Positives = 34/76 (44%), Gaps = 1/76 (1%)

Query: 55  VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
              I        +K + + FS+ G +  +    ++ TG++K F F+E      A+ +  +
Sbjct: 14  APVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKS 73

Query: 115 MHGYLLF-EHILQVHL 129
            HG  L  +H L ++ 
Sbjct: 74  FHGKRLDLKHRLFLYT 89

>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 = 61.6 bits (150), Expect = 1e-12
 Identities = 20/62 (32%), Positives = 35/62 (56%), Gaps = 1/62 (1%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L+IG +     EK ++A F + G I  + + +++ T +S+ F FI F +P  A+  A  M
Sbjct: 10  LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDM 68

Query: 116 HG 117
           +G
Sbjct: 69  NG 70

>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 = 62.2 bits (151), Expect = 1e-12
 Identities = 22/118 (18%), Positives = 45/118 (38%), Gaps = 4/118 (3%)

Query: 3   AKQKKALKKNLKKVSSQLPVPSDKKGAADFLPLEGGPGRKLTEEKPLVNKATVLYIGRIP 62
           A  +K  K+             D       +           + + + +    L +  + 
Sbjct: 24  ATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTS----LKVDNLT 79

Query: 63  HGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLL 120
           +      ++  F ++G +  + I R++ T +S+ F F+ F+D   AE   DAM G +L
Sbjct: 80  YRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVL 137

>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 = 63.6 bits (154), Expect = 1e-12
 Identities = 18/113 (15%), Positives = 36/113 (31%), Gaps = 2/113 (1%)

Query: 36  EGGPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGA--IKRLRIARNKKTGQ 93
           + G G           K   LYIG +     ++++       G   I  ++   N+  GQ
Sbjct: 51  DVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQ 110

Query: 94  SKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPPEHVHPKLWRGFNPR 146
           SK F  +       ++ + D +    L      V  +  + +     +     
Sbjct: 111 SKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTT 163

>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 = 60.8 bits (148), Expect = 2e-12
 Identities = 19/65 (29%), Positives = 35/65 (53%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           +++G +      ++++A F+ FG I   R+ ++  TG+SK +GF+ F +   AE     M
Sbjct: 18  VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77

Query: 116 HGYLL 120
            G  L
Sbjct: 78  GGQWL 82

>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 = 60.3 bits (147), Expect = 2e-12
 Identities = 20/74 (27%), Positives = 43/74 (58%), Gaps = 4/74 (5%)

Query: 43  LTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEF 102
           L E K + N    +++G I     E E+++FF+++G++K ++I  ++ TG SK +GF+ F
Sbjct: 2   LPEGKIMPNT---VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSF 57

Query: 103 NDPEVAEVVADAMH 116
            +    + + ++  
Sbjct: 58  YNDVDVQKIVESQI 71

>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 = 60.4 bits (147), Expect = 2e-12
 Identities = 16/96 (16%), Positives = 36/96 (37%), Gaps = 10/96 (10%)

Query: 40  GRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIK--------RLRIARNKKT 91
           G          +    +++  +      + +  +F Q G IK         + +  +++T
Sbjct: 2   GHHHHHHSH--SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRET 59

Query: 92  GQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQV 127
           G+ K    + F+DP  A+   D   G     + ++V
Sbjct: 60  GKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKV 95

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 60.0 bits (146), Expect = 2e-12
 Identities = 9/66 (13%), Positives = 27/66 (40%), Gaps = 2/66 (3%)

Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGA--IKRLRIARNKKTGQSKHFGFIEFNDPEVAEVV 111
             + +  I        +    S + +  +  +R+ ++K+T Q++ F F++ +    A  +
Sbjct: 10  DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQL 69

Query: 112 ADAMHG 117
              +  
Sbjct: 70  LQILQS 75

>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 = 59.5 bits (145), Expect = 2e-12
 Identities = 19/65 (29%), Positives = 32/65 (49%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           +++G +        + A F+ FG I   R+ ++  TG+SK +GF+ F +   AE     M
Sbjct: 9   VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68

Query: 116 HGYLL 120
            G  L
Sbjct: 69  GGQWL 73

>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 = 59.9 bits (146), Expect = 2e-12
 Identities = 20/65 (30%), Positives = 34/65 (52%), Gaps = 2/65 (3%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           LY+  +  G  ++ ++  FS FG I   ++      G+SK FGF+ F+ PE A      M
Sbjct: 18  LYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEM 75

Query: 116 HGYLL 120
           +G ++
Sbjct: 76  NGRIV 80

>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 = 59.5 bits (145), Expect = 3e-12
 Identities = 19/61 (31%), Positives = 34/61 (55%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L +  +P    E++++ +FS FG +  +++ ++ KTG SK FGF+ F + E    V    
Sbjct: 18  LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR 77

Query: 116 H 116
           H
Sbjct: 78  H 78

>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 = 58.7 bits (143), Expect = 6e-12
 Identities = 13/64 (20%), Positives = 26/64 (40%), Gaps = 2/64 (3%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGA--IKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
           LYIG +     ++++       G   I  ++   N+  GQSK F  +       ++ + D
Sbjct: 4   LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63

Query: 114 AMHG 117
            +  
Sbjct: 64  LLPK 67

>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 = 59.2 bits (144), Expect = 6e-12
 Identities = 19/65 (29%), Positives = 30/65 (46%), Gaps = 2/65 (3%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           ++I  +      K +   FS FG I   ++  +     SK +GF+ F   E AE   + M
Sbjct: 8   IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKM 65

Query: 116 HGYLL 120
           +G LL
Sbjct: 66  NGMLL 70

>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 = 58.4 bits (142), Expect = 6e-12
 Identities = 18/69 (26%), Positives = 32/69 (46%), Gaps = 6/69 (8%)

Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
           T LY+G +     E +++  F QFG I+ + + +       +   FI+F   + AEV A+
Sbjct: 13  TTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAE 66

Query: 114 AMHGYLLFE 122
                L+  
Sbjct: 67  KSFNKLIVN 75

>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 = 59.2 bits (144), Expect = 7e-12
 Identities = 17/74 (22%), Positives = 34/74 (45%), Gaps = 1/74 (1%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           +++  + +    K+++  FS  G + R  I  +K  G+S+  G + F     A       
Sbjct: 18  VFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMF 76

Query: 116 HGYLLFEHILQVHL 129
           +G LLF+  + V +
Sbjct: 77  NGQLLFDRPMHVKM 90

>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 = 62.3 bits (152), Expect = 7e-12
 Identities = 20/93 (21%), Positives = 36/93 (38%), Gaps = 3/93 (3%)

Query: 39  PGRKLTEEKPLVNKATVLYIGRIPHGFY-EKEMQAFFSQFGAIKRLRIARNKK-TGQSKH 96
           P  K         +   + I  +      E  ++  F  FG+I+++ I   +K    +  
Sbjct: 196 PLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNC 255

Query: 97  FGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL 129
             F+ F + + AE  A  M+  LL    + V L
Sbjct: 256 CAFMVFENKDSAE-RALQMNRSLLGNREISVSL 287

>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 = 61.9 bits (151), Expect = 7e-12
 Identities = 10/78 (12%), Positives = 29/78 (37%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L++   P  + ++ ++        +       + +   S+ F +I+    E A    + +
Sbjct: 120 LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKL 179

Query: 116 HGYLLFEHILQVHLIPPE 133
           +G  +  + L   +  P 
Sbjct: 180 NGLKIEGYTLVTKVSNPL 197

>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 = 61.2 bits (149), Expect = 1e-11
 Identities = 11/64 (17%), Positives = 26/64 (40%), Gaps = 2/64 (3%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           + +  +P  + + ++  +F   G I  + +A +    ++  F  IEF   + A       
Sbjct: 44  VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS--LKKNFRFARIEFARYDGALAAITKT 101

Query: 116 HGYL 119
           H  +
Sbjct: 102 HKVV 105

>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 = 58.9 bits (143), Expect = 7e-12
 Identities = 17/67 (25%), Positives = 30/67 (44%), Gaps = 6/67 (8%)

Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
             +Y G I  G  ++ M+  FS FG I  +R+         K + F+ F+  E A     
Sbjct: 26  CTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIV 79

Query: 114 AMHGYLL 120
           +++G  +
Sbjct: 80  SVNGTTI 86

>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 = 58.3 bits (142), Expect = 8e-12
 Identities = 13/63 (20%), Positives = 32/63 (50%), Gaps = 1/63 (1%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           +Y+G + +    ++++  FSQFG +  +++  +++T + K FGF+E  +          +
Sbjct: 4   IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKL 62

Query: 116 HGY 118
              
Sbjct: 63  DNT 65

>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 = 58.8 bits (143), Expect = 8e-12
 Identities = 14/64 (21%), Positives = 34/64 (53%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           +++G +P+   +  ++ +F  FG I+   +  +++TG+S+ +GF+   D   AE      
Sbjct: 20  IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDP 79

Query: 116 HGYL 119
           +  +
Sbjct: 80  NPII 83

>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 = 59.1 bits (143), Expect = 8e-12
 Identities = 14/96 (14%), Positives = 34/96 (35%), Gaps = 7/96 (7%)

Query: 38  GPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEM---QAFFSQFGAIKRLRIARNKKTGQS 94
           G          +V K  V ++  +     + E+     +F +FG I ++ I  +     S
Sbjct: 1   GSSGSSGASVRVVQKNLV-FVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGS 59

Query: 95  KH---FGFIEFNDPEVAEVVADAMHGYLLFEHILQV 127
           +      ++ +   E A      ++  ++    L+ 
Sbjct: 60  QGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKA 95

>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 = 58.4 bits (142), Expect = 9e-12
 Identities = 14/78 (17%), Positives = 33/78 (42%), Gaps = 6/78 (7%)

Query: 52  KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVV 111
              +LY+  +     E+ ++  F+        R+ +       + + F+ F++ E A   
Sbjct: 14  SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK------IRDYAFVHFSNREDAVEA 67

Query: 112 ADAMHGYLLFEHILQVHL 129
             A++G +L    ++V L
Sbjct: 68  MKALNGKVLDGSPIEVTL 85

>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 = 58.6 bits (142), Expect = 1e-11
 Identities = 20/99 (20%), Positives = 38/99 (38%), Gaps = 10/99 (10%)

Query: 37  GGPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKR--------LRIARN 88
           G  G     ++   N  + +Y+  +       ++  FF Q G +K         + I  +
Sbjct: 1   GSSGSSGDPDEDSDN--SAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLD 58

Query: 89  KKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQV 127
           K+TG+ K    + + DP  A+   +   G       L+V
Sbjct: 59  KETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKV 97

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 58.4 bits (142), Expect = 1e-11
 Identities = 22/66 (33%), Positives = 35/66 (53%), Gaps = 1/66 (1%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKR-LRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
           ++IG +     EK +   FS FG I +  +I R+  TG SK + FI F   + ++   +A
Sbjct: 8   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67

Query: 115 MHGYLL 120
           M+G  L
Sbjct: 68  MNGQYL 73

>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 = 58.0 bits (141), Expect = 1e-11
 Identities = 13/67 (19%), Positives = 28/67 (41%), Gaps = 6/67 (8%)

Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
           T L++G +        +   F +FG+I+ +   +         F +I++   + A+    
Sbjct: 18  TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDS------FAYIQYESLDAAQAACA 71

Query: 114 AMHGYLL 120
            M G+ L
Sbjct: 72  KMRGFPL 78

>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 = 58.5 bits (142), Expect = 1e-11
 Identities = 18/72 (25%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 46  EKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNK-KTGQSKHFGFIEFND 104
           + P     + + +  IP    ++E++  FS FG +K +R+ +    TG  + FGF++F  
Sbjct: 8   QVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFIT 67

Query: 105 PEVAEVVADAMH 116
            + A+   +A+ 
Sbjct: 68  KQDAKKAFNALC 79

>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 = 61.8 bits (149), Expect = 2e-11
 Identities = 21/132 (15%), Positives = 48/132 (36%), Gaps = 2/132 (1%)

Query: 55  VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
            L++ R+ +   E +++  F  +G IKR+ +  +K++G+ + + FIE+            
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH 163

Query: 115 MHGYLLFEHILQVHLIPPEHVHPKLWRGFNPRYKPVDRVQVERKLQNKERTLEEHKKLVE 174
             G  +     +V +        K WR            +    +  +    ++  +  E
Sbjct: 164 ADGKKIDGR--RVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRDDTSRYDE 221

Query: 175 KILKRDQKRRKR 186
           +        R R
Sbjct: 222 RPGPSPLPHRDR 233

>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 = 58.1 bits (141), Expect = 2e-11
 Identities = 13/65 (20%), Positives = 29/65 (44%), Gaps = 1/65 (1%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L +  +  G  + ++Q  F++FG +K+  +  ++ +G+S     + F     A       
Sbjct: 32  LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQY 90

Query: 116 HGYLL 120
           +G  L
Sbjct: 91  NGVPL 95

>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 = 59.5 bits (145), Expect = 2e-11
 Identities = 21/73 (28%), Positives = 38/73 (52%), Gaps = 4/73 (5%)

Query: 45  EEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFND 104
           +E+    K   +++G I      KE + FFSQ+G I   ++  +K TGQS+ FGF+ ++ 
Sbjct: 82  DEQDKTGK---IFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDS 138

Query: 105 PEVAE-VVADAMH 116
            +  + V  +   
Sbjct: 139 ADAVDRVCQNKFI 151

>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 = 58.7 bits (143), Expect = 3e-11
 Identities = 17/61 (27%), Positives = 33/61 (54%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           ++IG +     E  ++ +F ++G +  L+I ++  TG+S+ FGF+ F  P   + V    
Sbjct: 6   MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQ 65

Query: 116 H 116
           H
Sbjct: 66  H 66

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 57.8 bits (140), Expect = 2e-11
 Identities = 17/74 (22%), Positives = 37/74 (50%), Gaps = 3/74 (4%)

Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
            +LYI  +P+    +EM   F ++G I+++R+     T +++   ++ + D   A+   D
Sbjct: 9   RILYIRNLPYKITAEEMYDIFGKYGPIRQIRV---GNTPETRGTAYVVYEDIFDAKNAVD 65

Query: 114 AMHGYLLFEHILQV 127
            + G+ +    L V
Sbjct: 66  HLSGFNVSNRYLVV 79

>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 = 57.3 bits (139), Expect = 2e-11
 Identities = 15/66 (22%), Positives = 24/66 (36%), Gaps = 5/66 (7%)

Query: 53  ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVA 112
           A  L    +     E E++  F     I+ +      + G+SK   +IEF     AE   
Sbjct: 16  ARTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEKNL 70

Query: 113 DAMHGY 118
           +   G 
Sbjct: 71  EEKQGA 76

>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 = 56.8 bits (138), Expect = 3e-11
 Identities = 18/63 (28%), Positives = 30/63 (47%), Gaps = 8/63 (12%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L+IG +P    E+E+++ F Q+G +    I +N        +GF+   D   AE     +
Sbjct: 11  LFIGNLPREATEQEIRSLFEQYGKVLECDIIKN--------YGFVHIEDKTAAEDAIRNL 62

Query: 116 HGY 118
           H Y
Sbjct: 63  HHY 65

>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 = 56.9 bits (138), Expect = 3e-11
 Identities = 20/84 (23%), Positives = 34/84 (40%), Gaps = 8/84 (9%)

Query: 37  GGPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKH 96
           G  G    E+       + L++G +P    E+EM+  F ++G    + I +       K 
Sbjct: 1   GSSGSSGGEKTFTQR--SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHK------DKG 52

Query: 97  FGFIEFNDPEVAEVVADAMHGYLL 120
           FGFI      +AE+    +    L
Sbjct: 53  FGFIRLETRTLAEIAKVELDNMPL 76

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 58.3 bits (141), Expect = 4e-11
 Identities = 15/88 (17%), Positives = 34/88 (38%), Gaps = 1/88 (1%)

Query: 50  VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAE 109
           V     L +  +  G  + ++Q  F++FG +K+  +  ++ +G+S     + F     A 
Sbjct: 85  VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADAL 143

Query: 110 VVADAMHGYLLFEHILQVHLIPPEHVHP 137
                  G  L    + + L+  +    
Sbjct: 144 KAMKQYKGVPLDGRPMDIQLVASQIDLE 171

>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 = 58.9 bits (142), Expect = 5e-11
 Identities = 9/66 (13%), Positives = 21/66 (31%)

Query: 55  VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
           VL+    P    E+       + G  +   +       +    G +E++    A      
Sbjct: 125 VLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGF 184

Query: 115 MHGYLL 120
           ++ Y +
Sbjct: 185 LNHYQM 190

>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 = 50.5 bits (120), Expect = 5e-08
 Identities = 11/90 (12%), Positives = 30/90 (33%), Gaps = 6/90 (6%)

Query: 54  TVLYIGRI-PHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVA 112
            VL +  +         +   F  +G +++++  ++K          +E  D    +   
Sbjct: 5   PVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPG-----AAMVEMADGYAVDRAI 59

Query: 113 DAMHGYLLFEHILQVHLIPPEHVHPKLWRG 142
             ++   +F   + V +     + P    G
Sbjct: 60  THLNNNFMFGQKMNVCVSKQPAIMPGQSYG 89

>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 = 56.5 bits (137), Expect = 5e-11
 Identities = 20/62 (32%), Positives = 33/62 (53%), Gaps = 2/62 (3%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L++  IP  F + +++  F QFG I  + I  N+    SK FGF+ F +   A+   + +
Sbjct: 18  LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKL 75

Query: 116 HG 117
           HG
Sbjct: 76  HG 77

>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 = 57.0 bits (138), Expect = 5e-11
 Identities = 15/83 (18%), Positives = 33/83 (39%), Gaps = 1/83 (1%)

Query: 50  VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAE 109
           V     L +  +  G  + ++Q  F++FG +K+  +  ++ +G+S     + F     A 
Sbjct: 32  VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADAL 90

Query: 110 VVADAMHGYLLFEHILQVHLIPP 132
                  G  L    + + L+  
Sbjct: 91  KAMKQYKGVPLDGRPMDIQLVAS 113

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 56.6 bits (137), Expect = 7e-11
 Identities = 15/84 (17%), Positives = 34/84 (40%), Gaps = 8/84 (9%)

Query: 52  KATVLYIGRIPHGFYEKEMQAFFSQFGAIK--------RLRIARNKKTGQSKHFGFIEFN 103
               +++  +      + +  +F Q G IK         + +  +++TG+ K    + F+
Sbjct: 6   DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFD 65

Query: 104 DPEVAEVVADAMHGYLLFEHILQV 127
           DP  A+   D   G     + ++V
Sbjct: 66  DPPSAKAAIDWFDGKEFSGNPIKV 89

>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 = 56.1 bits (136), Expect = 7e-11
 Identities = 15/66 (22%), Positives = 30/66 (45%), Gaps = 4/66 (6%)

Query: 53  ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVA 112
           +  L +  + +   E+ +Q  F +   IK  +     + G+SK + FIEF   E A+   
Sbjct: 15  SKTLVLSNLSYSATEETLQEVFEKATFIKVPQ----NQNGKSKGYAFIEFASFEDAKEAL 70

Query: 113 DAMHGY 118
           ++ +  
Sbjct: 71  NSCNKR 76

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 55.8 bits (135), Expect = 8e-11
 Identities = 25/106 (23%), Positives = 46/106 (43%), Gaps = 7/106 (6%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           +Y+G +  G  + E++  FS +G ++ + IARN        F F+EF DP  AE     +
Sbjct: 3   VYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGL 57

Query: 116 HGYLLFEHILQVHLIPPEHVHPKLWRGFNPRYKPVDRVQVERKLQN 161
            G ++    ++V L        +      P  + +  V     L++
Sbjct: 58  DGKVICGSRVRVELSTGM--PRRSRFDRPPARRKLLEVLFNGPLEH 101

>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 = 55.3 bits (134), Expect = 9e-11
 Identities = 7/65 (10%), Positives = 26/65 (40%), Gaps = 8/65 (12%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           +++G +      +E+++ F + G +    + ++        + F+       A+     +
Sbjct: 12  IFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAAIAQL 63

Query: 116 HGYLL 120
           +G  +
Sbjct: 64  NGKEV 68

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 56.1 bits (135), Expect = 9e-11
 Identities = 10/71 (14%), Positives = 28/71 (39%), Gaps = 6/71 (8%)

Query: 52  KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVV 111
           ++ V+  G + +G    ++     + G +  L +  NK       + F  +   E ++  
Sbjct: 26  QSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKP------YSFARYRTTEESKRA 79

Query: 112 ADAMHGYLLFE 122
              ++G  + +
Sbjct: 80  YVTLNGKEVVD 90

>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 = 55.7 bits (135), Expect = 1e-10
 Identities = 17/62 (27%), Positives = 33/62 (53%), Gaps = 1/62 (1%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAE-VVADA 114
           +++G IPH   E E++ +F +FG +  + +  + +  + + FGFI F D +  +  V   
Sbjct: 13  IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMH 72

Query: 115 MH 116
            H
Sbjct: 73  FH 74

>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 = 55.3 bits (134), Expect = 1e-10
 Identities = 11/63 (17%), Positives = 24/63 (38%), Gaps = 8/63 (12%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L++G I      +E++A F ++G +    I ++        + F+     E A      +
Sbjct: 13  LHVGNISPTCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEAIRGL 64

Query: 116 HGY 118
              
Sbjct: 65  DNT 67

>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 = 55.4 bits (134), Expect = 1e-10
 Identities = 18/78 (23%), Positives = 38/78 (48%), Gaps = 8/78 (10%)

Query: 52  KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVV 111
           K  VL++  + +   E+ ++  FSQFG ++R++          K + FI F++ + A   
Sbjct: 10  KVKVLFVRNLANTVTEEILEKAFSQFGKLERVKK--------LKDYAFIHFDERDGAVKA 61

Query: 112 ADAMHGYLLFEHILQVHL 129
            + M+G  L    +++  
Sbjct: 62  MEEMNGKDLEGENIEIVF 79

>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 = 57.3 bits (139), Expect = 2e-10
 Identities = 15/62 (24%), Positives = 34/62 (54%), Gaps = 1/62 (1%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAE-VVADA 114
           +++G I     E  ++ +F Q+G I+ + I  ++ +G+ + F F+ F+D +  + +V   
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQK 166

Query: 115 MH 116
            H
Sbjct: 167 YH 168

>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 = 53.8 bits (130), Expect = 2e-09
 Identities = 18/100 (18%), Positives = 43/100 (43%), Gaps = 6/100 (6%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L+IG +     ++ +++ F Q+G +    + R+  T +S+ FGF+ +   E  +   +A 
Sbjct: 16  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 75

Query: 116 HGYLLFEHILQVHLIPPEHVHPKLWRGFNPRYKPVDRVQV 155
                  H +   ++ P+    +        +  V ++ V
Sbjct: 76  ------PHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFV 109

>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 = 54.5 bits (132), Expect = 2e-10
 Identities = 19/64 (29%), Positives = 34/64 (53%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           +++G +     +K+++ +F++FG +    I  +  TG+S+ FGFI F D    E V D  
Sbjct: 14  MFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQK 73

Query: 116 HGYL 119
              L
Sbjct: 74  EHRL 77

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score = 54.0 bits (131), Expect = 2e-10
 Identities = 13/62 (20%), Positives = 33/62 (53%), Gaps = 1/62 (1%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAE-VVADA 114
           +++G +     E++++ +F  FG ++ + +  + KT + + F FI F + E  + ++   
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61

Query: 115 MH 116
            H
Sbjct: 62  YH 63

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 54.2 bits (131), Expect = 3e-10
 Identities = 21/82 (25%), Positives = 39/82 (47%), Gaps = 3/82 (3%)

Query: 40  GRKLTEEKPLVNK-ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFG 98
           G   +  K L  +     Y+G +P    + ++ A F     I+ +R+ R+K T + K F 
Sbjct: 1   GSSGSSGKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFC 59

Query: 99  FIEFNDPEVAEVVADAMHGYLL 120
           ++EF++ +  +  A    G LL
Sbjct: 60  YVEFDEVDSLK-EALTYDGALL 80

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 97

 Score = 54.2 bits (131), Expect = 4e-10
 Identities = 13/74 (17%), Positives = 26/74 (35%), Gaps = 8/74 (10%)

Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
             LY+           ++  FS FG I       +      ++  F+ +   E A+    
Sbjct: 16  NTLYVYGE--DMTPTLLRGAFSPFGNII------DLSMDPPRNCAFVTYEKMESADQAVA 67

Query: 114 AMHGYLLFEHILQV 127
            ++G  +    L+V
Sbjct: 68  ELNGTQVESVQLKV 81

>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 = 55.7 bits (135), Expect = 4e-10
 Identities = 17/77 (22%), Positives = 36/77 (46%), Gaps = 2/77 (2%)

Query: 51  NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEV 110
                L+IG +       E++   S+  A   L +  + +TG ++ FG+++F   E  E 
Sbjct: 11  TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESAEDLE- 68

Query: 111 VADAMHGYLLFEHILQV 127
            A  + G  +F + +++
Sbjct: 69  KALELTGLKVFGNEIKL 85

>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 = 54.5 bits (132), Expect = 1e-09
 Identities = 16/76 (21%), Positives = 27/76 (35%), Gaps = 5/76 (6%)

Query: 45  EEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFND 104
            +   V  A  L    +     E E++  F     I+ +      + G+SK   +IEF  
Sbjct: 91  RDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKS 145

Query: 105 PEVAEVVADAMHGYLL 120
              AE   +   G  +
Sbjct: 146 EADAEKNLEEKQGAEI 161

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 54.2 bits (131), Expect = 4e-10
 Identities = 20/62 (32%), Positives = 33/62 (53%), Gaps = 2/62 (3%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L++  IP  F + +++  F QFG I  + I  N+    SK FGF+ F +   A+   + +
Sbjct: 32  LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKL 89

Query: 116 HG 117
           HG
Sbjct: 90  HG 91

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 53.5 bits (129), Expect = 6e-10
 Identities = 10/74 (13%), Positives = 25/74 (33%)

Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
           TV+ +  +P      E+  FF  +  I      +  + G       + F   + A     
Sbjct: 16  TVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 75

Query: 114 AMHGYLLFEHILQV 127
            ++   +    +++
Sbjct: 76  DLNDRPIGSRKVKL 89

>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 = 55.7 bits (134), Expect = 6e-10
 Identities = 17/75 (22%), Positives = 30/75 (40%), Gaps = 5/75 (6%)

Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
             L++  IP    E++++  FS  G + +      K     +    I+    E A     
Sbjct: 121 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD----RKMALIQMGSVEEAVQALI 176

Query: 114 AMHGYLLFE-HILQV 127
            +H + L E H L+V
Sbjct: 177 DLHNHDLGENHHLRV 191

>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 = 50.7 bits (121), Expect = 4e-08
 Identities = 15/77 (19%), Positives = 35/77 (45%), Gaps = 6/77 (7%)

Query: 54  TVLYIGRI-PHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVA 112
           +VL +  + P     + +   F  +G ++R++I  NKK         ++  D   A++  
Sbjct: 4   SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKE-----NALVQMADGNQAQLAM 58

Query: 113 DAMHGYLLFEHILQVHL 129
             ++G+ L    +++ L
Sbjct: 59  SHLNGHKLHGKPIRITL 75

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 53.7 bits (129), Expect = 6e-10
 Identities = 20/96 (20%), Positives = 36/96 (37%), Gaps = 8/96 (8%)

Query: 34  PLEGGPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQ 93
               GPG    E  PL      +Y+G +P      +++    + G++  LR+        
Sbjct: 3   SGSSGPGSPPGEGAPLAAD---VYVGNLPRDARVSDLKRALRELGSVP-LRLTWQG---- 54

Query: 94  SKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL 129
            +   F+ + D   A+     + G  L    L+V L
Sbjct: 55  PRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVAL 90

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 54.1 bits (130), Expect = 6e-10
 Identities = 21/108 (19%), Positives = 38/108 (35%), Gaps = 7/108 (6%)

Query: 26  KKGAADFLPLEGGPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQ----AFFSQFGAIK 81
           K+ AA     +      L    P    + V+ I  I     ++++Q    A  S  G I 
Sbjct: 2   KETAAAKFERQHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDIL 61

Query: 82  RLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL 129
            + +     +  +    +I F   E A+   +A  GY    + L +  
Sbjct: 62  DIVV---DLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITF 106

>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 = 53.1 bits (128), Expect = 7e-10
 Identities = 11/82 (13%), Positives = 27/82 (32%), Gaps = 1/82 (1%)

Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
           T++ +  +P      E+  FF  +  I      +  + G       + F   + A     
Sbjct: 16  TIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 75

Query: 114 AMHGYLLFEHILQVHLI-PPEH 134
            ++   +    +++ L   P  
Sbjct: 76  DLNDRPIGSRKVKLVLGSGPSS 97

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 52.5 bits (127), Expect = 8e-10
 Identities = 14/62 (22%), Positives = 31/62 (50%), Gaps = 1/62 (1%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAE-VVADA 114
           +++G +      ++++ +F QFG +    +  +K T + + FGF+ F   ++ E V    
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61

Query: 115 MH 116
            H
Sbjct: 62  FH 63

>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 = 52.8 bits (127), Expect = 8e-10
 Identities = 22/77 (28%), Positives = 33/77 (42%), Gaps = 6/77 (7%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIAR-----NKKTGQSKHFGFIEFNDPEVAEV 110
           LY+G IP G  E+ M  FF+    +  L  A        +  Q K+F F+EF   +    
Sbjct: 9   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT- 67

Query: 111 VADAMHGYLLFEHILQV 127
            A A  G +     L++
Sbjct: 68  QAMAFDGIIFQGQSLKI 84

>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 = 53.0 bits (128), Expect = 8e-10
 Identities = 15/61 (24%), Positives = 29/61 (47%), Gaps = 5/61 (8%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           +++GR      E E++ FFSQ+G +  + I         + F F+ F D ++A+ +    
Sbjct: 8   VFVGRCTGDMTEDELREFFSQYGDVMDVFI-----PKPFRAFAFVTFADDQIAQSLCGED 62

Query: 116 H 116
            
Sbjct: 63  L 63

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 55.8 bits (134), Expect = 9e-10
 Identities = 17/75 (22%), Positives = 30/75 (40%), Gaps = 5/75 (6%)

Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
             L++  IP    E++++  FS  G + +      K     +    I+    E A     
Sbjct: 152 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD----RKMALIQMGSVEEAVQALI 207

Query: 114 AMHGYLLFE-HILQV 127
            +H + L E H L+V
Sbjct: 208 DLHNHDLGENHHLRV 222

>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 = 50.4 bits (120), Expect = 6e-08
 Identities = 16/86 (18%), Positives = 38/86 (44%), Gaps = 6/86 (6%)

Query: 54  TVLYIGRI-PHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVA 112
           +VL +  + P     + +   F  +G ++R++I  NKK         ++  D   A++  
Sbjct: 35  SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKE-----NALVQMADGNQAQLAM 89

Query: 113 DAMHGYLLFEHILQVHLIPPEHVHPK 138
             ++G+ L    +++ L   ++V   
Sbjct: 90  SHLNGHKLHGKPIRITLSKHQNVQLP 115

>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 = 52.8 bits (127), Expect = 9e-10
 Identities = 12/79 (15%), Positives = 25/79 (31%), Gaps = 7/79 (8%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           + +  +P     +E+      +         +     ++K   F+   + E A+      
Sbjct: 8   ILVKNLPQDSNCQEVHDLLKDYDL-------KYCYVDRNKRTAFVTLLNGEQAQNAIQMF 60

Query: 116 HGYLLFEHILQVHLIPPEH 134
           H Y      L V L P + 
Sbjct: 61  HQYSFRGKDLIVQLQPTDA 79

>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 = 54.1 bits (130), Expect = 1e-09
 Identities = 17/65 (26%), Positives = 31/65 (47%), Gaps = 5/65 (7%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           +Y+G + +   + E++  F  +G ++ + +ARN        F F+EF DP  A      +
Sbjct: 76  VYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVREL 130

Query: 116 HGYLL 120
            G  L
Sbjct: 131 DGRTL 135

>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 = 52.6 bits (127), Expect = 1e-09
 Identities = 9/62 (14%), Positives = 20/62 (32%), Gaps = 6/62 (9%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           LYIG +       +++  F               +      + F+++ D   A    + +
Sbjct: 11  LYIGNLSPAVTADDLRQLFGDRKLPL------AGQVLLKSGYAFVDYPDQNWAIRAIETL 64

Query: 116 HG 117
            G
Sbjct: 65  SG 66

>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 = 52.6 bits (127), Expect = 1e-09
 Identities = 14/79 (17%), Positives = 35/79 (44%), Gaps = 7/79 (8%)

Query: 55  VLYIGRIPHGFYEKEMQ----AFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEV 110
            +YI  +     + E++    A FS+FG I  + +    ++ + +   F+ F +   A  
Sbjct: 10  TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILV---SRSLKMRGQAFVIFKEVSSATN 66

Query: 111 VADAMHGYLLFEHILQVHL 129
              +M G+  ++  +++  
Sbjct: 67  ALRSMQGFPFYDKPMRIQY 85

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 52.0 bits (125), Expect = 1e-09
 Identities = 18/82 (21%), Positives = 35/82 (42%), Gaps = 9/82 (10%)

Query: 54  TVLYIGRIP------HGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEV 107
           +V+ +  +P          +  +   FS+FG I        ++ G++K + F+E+  P  
Sbjct: 2   SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAH 59

Query: 108 AEVVADAMHGYLLFE-HILQVH 128
           A        GY L + H  +V+
Sbjct: 60  AVDAVKNADGYKLDKQHTFRVN 81

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 52.8 bits (127), Expect = 1e-09
 Identities = 19/83 (22%), Positives = 34/83 (40%), Gaps = 9/83 (10%)

Query: 54  TVLYIGRIP------HGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEV 107
           +V+ +  +P          +  +   FS+FG I           G++K + F+E+  P  
Sbjct: 16  SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAH 73

Query: 108 AEVVADAMHGYLLFE-HILQVHL 129
           A        GY L + H  +V+L
Sbjct: 74  AVDAVKNADGYKLDKQHTFRVNL 96

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 51.7 bits (125), Expect = 2e-09
 Identities = 16/56 (28%), Positives = 31/56 (55%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVV 111
           ++IG +     ++ ++ +F QFG +K   + R+  T +S+ FGF+ F D    + V
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKV 58

>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 = 53.3 bits (128), Expect = 2e-09
 Identities = 16/81 (19%), Positives = 32/81 (39%), Gaps = 5/81 (6%)

Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAI-----KRLRIARNKKTGQSKHFGFIEFNDPEVA 108
             +Y+  +     EK+++  F ++        + +   R  K G+ K   FI   + + A
Sbjct: 46  CRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAA 105

Query: 109 EVVADAMHGYLLFEHILQVHL 129
                  +GY+LF   + V  
Sbjct: 106 AKALKEANGYVLFGKPMVVQF 126

>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 = 51.9 bits (125), Expect = 2e-09
 Identities = 16/62 (25%), Positives = 30/62 (48%), Gaps = 2/62 (3%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L+IG +       E++   S+  A   L +  + +TG ++ FG+++F   E  E  A  +
Sbjct: 20  LFIGNLNPNKSVAELKVAISELFAKNDLAV-VDVRTGTNRKFGYVDFESAEDLE-KALEL 77

Query: 116 HG 117
            G
Sbjct: 78  TG 79

>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 = 51.9 bits (125), Expect = 3e-09
 Identities = 20/62 (32%), Positives = 37/62 (59%), Gaps = 1/62 (1%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAE-VVADA 114
           L++G +     ++ ++++FSQ+G +    I ++K T QS+ FGF++F DP     V+A  
Sbjct: 19  LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASR 78

Query: 115 MH 116
            H
Sbjct: 79  PH 80

>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 = 54.7 bits (132), Expect = 3e-09
 Identities = 15/75 (20%), Positives = 31/75 (41%), Gaps = 5/75 (6%)

Query: 47  KPL-VNKA---TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEF 102
           +PL +  A     L +  +      + ++  FSQFG +++  +  +   G++   GF+EF
Sbjct: 86  RPLRIRFATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDD-RGRATGKGFVEF 144

Query: 103 NDPEVAEVVADAMHG 117
                A    +    
Sbjct: 145 AAKPPARKALERCGD 159

>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 = 53.2 bits (128), Expect = 8e-09
 Identities = 18/89 (20%), Positives = 36/89 (40%), Gaps = 6/89 (6%)

Query: 39  PGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFG 98
               L   +    +   L++G +P    E++ +  F ++G    + I R       + FG
Sbjct: 8   IKSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINR------DRGFG 61

Query: 99  FIEFNDPEVAEVVADAMHGYLLFEHILQV 127
           FI      +AE+    + G +L    L++
Sbjct: 62  FIRLESRTLAEIAKAELDGTILKSRPLRI 90

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 51.8 bits (125), Expect = 3e-09
 Identities = 15/66 (22%), Positives = 30/66 (45%), Gaps = 9/66 (13%)

Query: 56  LYIGRIP-HGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
           L+IG +P     ++++   FS +G I ++ I           FGFI+F++P+      + 
Sbjct: 13  LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNA--------FGFIQFDNPQSVRDAIEC 64

Query: 115 MHGYLL 120
               + 
Sbjct: 65  ESQEMN 70

>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 = 51.9 bits (125), Expect = 3e-09
 Identities = 19/63 (30%), Positives = 32/63 (50%), Gaps = 3/63 (4%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L++  +     E+ ++  F       R RI  +++TG SK FGF++FN  E A+   +AM
Sbjct: 18  LFVKGLSEDTTEETLKESFDG---SVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAM 74

Query: 116 HGY 118
              
Sbjct: 75  EDG 77

>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 = 51.9 bits (125), Expect = 3e-09
 Identities = 16/56 (28%), Positives = 31/56 (55%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVV 111
           ++IG +     ++ ++ +F QFG +K   + R+  T +S+ FGF+ F D    + V
Sbjct: 28  MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKV 83

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 51.1 bits (123), Expect = 5e-09
 Identities = 18/67 (26%), Positives = 28/67 (41%), Gaps = 8/67 (11%)

Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
           T L++   P    E E+   F  FG +K ++I           F F+EF + E A    +
Sbjct: 32  TRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNG--------FAFVEFEEAESAAKAIE 83

Query: 114 AMHGYLL 120
            +HG   
Sbjct: 84  EVHGKSF 90

>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 = 50.8 bits (122), Expect = 6e-09
 Identities = 17/75 (22%), Positives = 34/75 (45%), Gaps = 9/75 (12%)

Query: 56  LYIGRIP-HGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
           L+IG +P     ++++   FS +G I ++ I           FGFI+F++P+      + 
Sbjct: 25  LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNA--------FGFIQFDNPQSVRDAIEX 76

Query: 115 MHGYLLFEHILQVHL 129
               + F   L + +
Sbjct: 77  ESQEMNFGKKLILEV 91

>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 = 50.9 bits (122), Expect = 6e-09
 Identities = 13/76 (17%), Positives = 31/76 (40%), Gaps = 4/76 (5%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGA-IKRLRIARNKK-TGQSKHFGFIEFNDPEVAEVVAD 113
           L+IG IP     +E+    ++    +  + +  +     +++ F F+E+     A +   
Sbjct: 11  LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 70

Query: 114 AMH--GYLLFEHILQV 127
            +      L+ H + V
Sbjct: 71  KLMPGRIQLWGHQIAV 86

>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 = 50.5 bits (121), Expect = 1e-08
 Identities = 10/75 (13%), Positives = 33/75 (44%), Gaps = 9/75 (12%)

Query: 56  LYIGRIPHGFY-EKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
           ++IG +      + +++  FS++G +    + +         + F+++++   A      
Sbjct: 30  VFIGNLNTALVKKSDVETIFSKYGRVAGCSVHKG--------YAFVQYSNERHARAAVLG 81

Query: 115 MHGYLLFEHILQVHL 129
            +G +L    L +++
Sbjct: 82  ENGRVLAGQTLDINM 96

>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 = 49.5 bits (119), Expect = 1e-08
 Identities = 15/61 (24%), Positives = 29/61 (47%), Gaps = 5/61 (8%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           +++GR       +E+Q FF Q+G +  + I +       + F F+ F D +VA+ +    
Sbjct: 14  VFVGRCTEDMTAEELQQFFCQYGEVVDVFIPK-----PFRAFAFVTFADDKVAQSLCGED 68

Query: 116 H 116
            
Sbjct: 69  L 69

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 49.2 bits (118), Expect = 2e-08
 Identities = 10/54 (18%), Positives = 22/54 (40%), Gaps = 5/54 (9%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAE 109
           +++   P G    ++  +F  FG +  + + ++K       F  +E  D    E
Sbjct: 11  VFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGV-----FAIVEMGDVGARE 59

>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 = 49.8 bits (119), Expect = 2e-08
 Identities = 16/74 (21%), Positives = 28/74 (37%), Gaps = 6/74 (8%)

Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
           TV+    +P G    E+Q  FS+FG++ R+ +              +EF +P  A     
Sbjct: 11  TVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFR 64

Query: 114 AMHGYLLFEHILQV 127
            +         L +
Sbjct: 65  HLAYSKFHHVPLYL 78

>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 = 49.6 bits (119), Expect = 2e-08
 Identities = 20/85 (23%), Positives = 37/85 (43%), Gaps = 8/85 (9%)

Query: 37  GGPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKK-TGQSK 95
           G  G +L +  P        ++G +P+   E+ ++ FF     I  +R+ R      + K
Sbjct: 4   GSSGSRLPKSPP-----YTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLK 57

Query: 96  HFGFIEFNDPEVAEVVADAMHGYLL 120
            FG+ EF D +     A +++   L
Sbjct: 58  GFGYAEFEDLDSLL-SALSLNEESL 81

>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 = 49.2 bits (118), Expect = 4e-08
 Identities = 12/56 (21%), Positives = 29/56 (51%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVV 111
           L+IG +     E+ ++ ++ Q+G +    + R+  + +S+ FGF+ F+     +  
Sbjct: 30  LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAA 85

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 48.6 bits (116), Expect = 4e-08
 Identities = 13/70 (18%), Positives = 27/70 (38%), Gaps = 4/70 (5%)

Query: 40  GRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGF 99
           GR + +      K   +YI   P      +++ +    G +  +++ R       K   F
Sbjct: 1   GRWILKND---VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT-LHKAFKGSIF 56

Query: 100 IEFNDPEVAE 109
           + F+  E A+
Sbjct: 57  VVFDSIESAK 66

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 50.9 bits (121), Expect = 5e-08
 Identities = 26/118 (22%), Positives = 40/118 (33%), Gaps = 23/118 (19%)

Query: 20  LPVPSDKKGAADFLPLEGGPGRKLTEE--------KPLVNKATVLYIGRIP--------- 62
           +P   D    A    +    GR+   +             K   LY+G I          
Sbjct: 93  IPDEEDIGKLALRTEVLDCFGREKFADYREDMGGIGSFRKKNKTLYVGGIDGALNSKHLK 152

Query: 63  HGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLL 120
               E  ++  FS+ G I R+R   +K      + GF++F     AE   +AM    L
Sbjct: 153 PAQIESRIRFVFSRLGDIDRIRYVESK------NCGFVKFKYQANAEFAKEAMSNQTL 204

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 48.8 bits (116), Expect = 5e-08
 Identities = 15/89 (16%), Positives = 33/89 (37%), Gaps = 3/89 (3%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKK--TGQSKHFGFIEFNDPE-VAEVVA 112
           +++G +P    E E+ A F +FG +      + +       K + F+ F +   V  ++ 
Sbjct: 11  VFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALID 70

Query: 113 DAMHGYLLFEHILQVHLIPPEHVHPKLWR 141
             +         +    I  + V  + W 
Sbjct: 71  ACLEEDGKLYLCVSSPTIKDKPVQIRPWN 99

>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 = 47.6 bits (114), Expect = 8e-08
 Identities = 18/85 (21%), Positives = 33/85 (38%), Gaps = 4/85 (4%)

Query: 38  GPGRKLTEEKPLVNKAT-VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKT-GQSK 95
           G          L        ++G +P+   E+ ++ FF     I  +R+ R      + K
Sbjct: 3   GSHHHHHHRSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLK 61

Query: 96  HFGFIEFNDPEVAEVVADAMHGYLL 120
            FG+ EF D +     A +++   L
Sbjct: 62  GFGYAEFEDLDSLL-SALSLNEESL 85

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 50.3 bits (119), Expect = 9e-08
 Identities = 14/66 (21%), Positives = 29/66 (43%), Gaps = 5/66 (7%)

Query: 57  YIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMH 116
           ++  +P    E  +   F+QF   K +R+   +         F+EF++   A    DA+ 
Sbjct: 211 FLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHD-----IAFVEFDNEVQAGAARDALQ 265

Query: 117 GYLLFE 122
           G+ + +
Sbjct: 266 GFKITQ 271

>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 = 49.1 bits (116), Expect = 2e-07
 Identities = 15/76 (19%), Positives = 34/76 (44%), Gaps = 7/76 (9%)

Query: 56  LYIGRIPHGFYEKEM----QAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVV 111
           +YI  +     + E+     A FSQFG I  + +    ++ + +   F+ F +   A   
Sbjct: 12  IYINNLNEKIKKDELKKSLYAIFSQFGQILDILV---SRSLKMRGQAFVIFKEVSSATNA 68

Query: 112 ADAMHGYLLFEHILQV 127
             +M G+  ++  +++
Sbjct: 69  LRSMQGFPFYDKPMRI 84

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 47.7 bits (114), Expect = 1e-07
 Identities = 13/63 (20%), Positives = 30/63 (47%), Gaps = 2/63 (3%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQ-FGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
           L++G +     +  +  FF + + + +  ++  ++ TG SK +GF++F D    +     
Sbjct: 12  LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTE 70

Query: 115 MHG 117
             G
Sbjct: 71  CQG 73

>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 = 46.3 bits (110), Expect = 3e-07
 Identities = 11/75 (14%), Positives = 26/75 (34%), Gaps = 8/75 (10%)

Query: 55  VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAE--VVA 112
           V+++  +     E ++     +FG I  + +   K+         +EF + + A+  V  
Sbjct: 17  VVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKR------QALVEFENIDSAKECVTF 70

Query: 113 DAMHGYLLFEHILQV 127
            A     +       
Sbjct: 71  AADVPVYIAGQQAFF 85

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 46.0 bits (109), Expect = 4e-07
 Identities = 17/76 (22%), Positives = 30/76 (39%), Gaps = 8/76 (10%)

Query: 55  VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAE--VVA 112
           V++I ++P    E E+ +    FG +  L + +       K+  FIE N  E A   V  
Sbjct: 18  VIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNY 71

Query: 113 DAMHGYLLFEHILQVH 128
                 +L    + + 
Sbjct: 72  YTSVTPVLRGQPIYIQ 87

>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 = 46.4 bits (110), Expect = 4e-07
 Identities = 17/76 (22%), Positives = 30/76 (39%), Gaps = 8/76 (10%)

Query: 55  VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAE--VVA 112
           V++I ++P    E E+ +    FG +  L + +       K+  FIE N  E A   V  
Sbjct: 33  VIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNY 86

Query: 113 DAMHGYLLFEHILQVH 128
                 +L    + + 
Sbjct: 87  YTSVTPVLRGQPIYIQ 102

>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 = 45.6 bits (108), Expect = 6e-07
 Identities = 14/55 (25%), Positives = 24/55 (43%), Gaps = 6/55 (10%)

Query: 55  VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAE 109
           VL+I ++P    E E+ A    FG +  + + +       K+  F+E    E A 
Sbjct: 17  VLHIRKLPGEVTETEVIALGLPFGKVTNILMLK------GKNQAFLELATEEAAI 65

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 45.1 bits (107), Expect = 7e-07
 Identities = 12/64 (18%), Positives = 23/64 (35%), Gaps = 6/64 (9%)

Query: 55  VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
           V++I  +  G  E ++     +FG I  + +   K+         +EF D   A    + 
Sbjct: 23  VVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKR------QALVEFEDVLGACNAVNY 76

Query: 115 MHGY 118
               
Sbjct: 77  AADN 80

>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 = 45.9 bits (108), Expect = 1e-06
 Identities = 10/80 (12%), Positives = 30/80 (37%), Gaps = 6/80 (7%)

Query: 51  NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEV 110
           +    + +  + +      +   FS+FG + ++         Q      +++ DP  A+ 
Sbjct: 44  SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQ----ALLQYADPVSAQH 99

Query: 111 VADAMHGYLLF--EHILQVH 128
              ++ G  ++     L++ 
Sbjct: 100 AKLSLDGQNIYNACCTLRID 119

>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 = 44.7 bits (106), Expect = 1e-06
 Identities = 16/99 (16%), Positives = 34/99 (34%), Gaps = 3/99 (3%)

Query: 37  GGPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKH 96
           G  G   + E  + +     +I  IP    + ++  F       +          GQ   
Sbjct: 1   GSSGS--SGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLG 58

Query: 97  FGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPPEHV 135
              ++F + + A   ++ +H   L      VH++  E +
Sbjct: 59  QALVQFKNEDDAR-KSERLHRKKLNGREAFVHVVTLEDM 96

>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 = 44.9 bits (106), Expect = 1e-06
 Identities = 19/106 (17%), Positives = 34/106 (32%), Gaps = 1/106 (0%)

Query: 31  DFLPLEGGPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKK 90
               + GG                 + +  +P G  ++E+  FFS    +          
Sbjct: 20  HMASMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDP 79

Query: 91  TGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPPEHVH 136
            G+     F++F   E+AE  A   H   +    ++V     E V 
Sbjct: 80  EGKITGEAFVQFASQELAE-KALGKHKERIGHRYIEVFKSSQEEVR 124

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 44.6 bits (105), Expect = 2e-06
 Identities = 10/80 (12%), Positives = 30/80 (37%), Gaps = 6/80 (7%)

Query: 51  NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEV 110
           +    + +  + +      +   FS+FG + ++         Q      +++ DP  A+ 
Sbjct: 26  SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQ----ALLQYADPVSAQH 81

Query: 111 VADAMHGYLLFE--HILQVH 128
              ++ G  ++     L++ 
Sbjct: 82  AKLSLDGQNIYNACCTLRID 101

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 124

 Score = 43.7 bits (103), Expect = 3e-06
 Identities = 18/97 (18%), Positives = 37/97 (38%), Gaps = 1/97 (1%)

Query: 39  PGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFG 98
            G+K +  +        +Y+  +P     K +  FF +   ++          G++   G
Sbjct: 11  SGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEG 70

Query: 99  FIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPPEHV 135
           F+EF +    +  A   H   +    +QVH I  + +
Sbjct: 71  FVEFRNEADYK-AALCRHKQYMGNRFIQVHPITKKGM 106

>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 = 43.2 bits (102), Expect = 4e-06
 Identities = 9/75 (12%), Positives = 22/75 (29%), Gaps = 7/75 (9%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           + +  +P     ++++    + G +    + R          G +EF   E        +
Sbjct: 18  VVVSGLPPSGSWQDLKDHMREAGDVCYADVYR-------DGTGVVEFVRKEDMTYAVRKL 70

Query: 116 HGYLLFEHILQVHLI 130
                  H  +   I
Sbjct: 71  DNTKFRSHEGETAYI 85

>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 = 44.1 bits (103), Expect = 7e-06
 Identities = 10/54 (18%), Positives = 22/54 (40%), Gaps = 1/54 (1%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAE 109
           +YI   P      +++ +    G +  +++ R       K   F+ F+  E A+
Sbjct: 112 VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAK 164

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 42.1 bits (99), Expect = 1e-05
 Identities = 11/92 (11%), Positives = 29/92 (31%), Gaps = 3/92 (3%)

Query: 36  EGGPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSK 95
             G   + +    L  K   + +  +P G   ++++    +           +  T    
Sbjct: 11  SSGLVPRGSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLE---TTFSSVNTRDFD 67

Query: 96  HFGFIEFNDPEVAEVVADAMHGYLLFEHILQV 127
             G +EF   E+     + ++       ++ V
Sbjct: 68  GTGALEFPSEEILVEALERLNNIEFRGSVITV 99

>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 = 41.4 bits (97), Expect = 2e-05
 Identities = 13/102 (12%), Positives = 33/102 (32%), Gaps = 5/102 (4%)

Query: 37  GGPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQF---GAIKRLRIARNKKTGQ 93
           G  G       P   +  V+ +  +P     +++Q F S       +  +     ++ G+
Sbjct: 1   GSSGSSGMMLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GR 59

Query: 94  SKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPPEHV 135
                F+E    +  + +A       +    ++V       +
Sbjct: 60  QSGEAFVELESEDDVK-LALKKDRESMGHRYIEVFKSHRTEM 100

>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 = 41.1 bits (96), Expect = 3e-05
 Identities = 14/56 (25%), Positives = 22/56 (39%), Gaps = 7/56 (12%)

Query: 55  VLYIGRIPHGFY-EKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAE 109
           V+++  +PH  Y +  +      +G IK   + R       K   FIE    E A 
Sbjct: 27  VIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAM 76

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 40.8 bits (95), Expect = 4e-05
 Identities = 13/86 (15%), Positives = 31/86 (36%), Gaps = 5/86 (5%)

Query: 44  TEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFN 103
           T++    NK  +L I    +      +    +  G ++R+ I +            +EF 
Sbjct: 16  TDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGI-----QAMVEFE 70

Query: 104 DPEVAEVVADAMHGYLLFEHILQVHL 129
               A+    A++G  ++     + +
Sbjct: 71  SVLCAQKAKAALNGADIYAGCCTLKI 96

>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 = 40.1 bits (94), Expect = 5e-05
 Identities = 14/63 (22%), Positives = 25/63 (39%)

Query: 47  KPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPE 106
            P       + +  +P G  ++E+  FFS    +           G+S    F++F   E
Sbjct: 9   SPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQE 68

Query: 107 VAE 109
           +AE
Sbjct: 69  IAE 71

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 40.1 bits (94), Expect = 6e-05
 Identities = 11/73 (15%), Positives = 29/73 (39%), Gaps = 3/73 (4%)

Query: 37  GGPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKH 96
           G  G    +  P+      + +  +P    E +++ FF     +  + + ++   G++  
Sbjct: 1   GSSGSS-GKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGLR-VDAVHLLKDH-VGRNNG 57

Query: 97  FGFIEFNDPEVAE 109
            G ++F  P+   
Sbjct: 58  NGLVKFLSPQDTF 70

>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 = 39.4 bits (92), Expect = 1e-04
 Identities = 9/75 (12%), Positives = 22/75 (29%), Gaps = 7/75 (9%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           + +  +P     ++++    + G +    + R          G +EF   E        +
Sbjct: 19  VVVSGLPPSGSWQDLKDHMREAGDVCYADVYR-------DGTGVVEFVRKEDMTYAVRKL 71

Query: 116 HGYLLFEHILQVHLI 130
                  H  +   I
Sbjct: 72  DNTKFRSHEGETAYI 86

>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 = 38.3 bits (89), Expect = 4e-04
 Identities = 20/102 (19%), Positives = 34/102 (33%), Gaps = 3/102 (2%)

Query: 8   ALKKNLKKVSSQLPVPSDKKGAADFLPLEGGPGRKLTEEKPLVNKATVLYIGRIPHGFYE 67
               +    SS   VP     A+     + G G   +E          +++  +P+   E
Sbjct: 2   GSSHHHHHHSSG-LVPRGSHMASMTGGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATE 60

Query: 68  KEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAE 109
            ++  FFS      R+ I      G+      +EF   E A 
Sbjct: 61  NDIYNFFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHEEAV 100

>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 = 37.3 bits (87), Expect = 4e-04
 Identities = 12/55 (21%), Positives = 23/55 (41%), Gaps = 2/55 (3%)

Query: 55  VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAE 109
            + +   P    EK +  F +       +RI RN   G    + F++F++ E  +
Sbjct: 12  TVKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNAH-GNKTGYIFVDFSNEEEVK 64

>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 = 37.4 bits (87), Expect = 4e-04
 Identities = 14/73 (19%), Positives = 26/73 (35%), Gaps = 4/73 (5%)

Query: 37  GGPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKH 96
           G  G   +  +        +++  +P+   E ++  FFS      R+ I      G+   
Sbjct: 1   GSSGSSGSSFQS--TTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPD-GRVTG 56

Query: 97  FGFIEFNDPEVAE 109
              +EF   E A 
Sbjct: 57  EADVEFATHEDAV 69

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 39.5 bits (91), Expect = 5e-04
 Identities = 25/193 (12%), Positives = 47/193 (24%), Gaps = 62/193 (32%)

Query: 50  VNKATVLYIGRIPHGFYEKEMQAFF-----------------------SQFGAIKRLRIA 86
               T + +          E+++                         S      R  +A
Sbjct: 283 AATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLA 342

Query: 87  RNKKTGQSKHFG----------FIEFNDPEVAEVVADAMHGYLLFEHILQ--VHLIPPEH 134
                   KH             +   +P      A+    +     +     H+  P  
Sbjct: 343 TWD---NWKHVNCDKLTTIIESSLNVLEP------AEYRKMFDRLS-VFPPSAHI--PTI 390

Query: 135 VHPKLWRGFNPRYKPVDRVQVE---RKL---QNKERTLEEHK---KLVEKILKRDQKRRK 185
           +   +W  F+     V  V  +     L   Q KE T+       +L  K+       R 
Sbjct: 391 LLSLIW--FDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRS 448

Query: 186 RIEAAGIEYECPE 198
            ++     Y  P+
Sbjct: 449 IVDH----YNIPK 457

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3 Length = 104

 Score = 36.8 bits (85), Expect = 7e-04
 Identities = 10/79 (12%), Positives = 27/79 (34%), Gaps = 1/79 (1%)

Query: 39  PGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFG 98
           P         L +  + + +      F+E+       ++G ++ + +  N          
Sbjct: 13  PQNSSQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN-LGDHLVGNV 71

Query: 99  FIEFNDPEVAEVVADAMHG 117
           +++F   E AE     ++ 
Sbjct: 72  YVKFRREEDAEKAVIDLNN 90

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	215
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.89
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.87
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.87
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.86
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.86
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.86
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.85
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.85
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.85
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.85
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.85
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.85
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.85
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.85
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.85
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.85
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.84
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.84
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.84
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.84
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.84
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.84
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.84
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.84
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.84
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.84
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.84
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.84
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.84
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.84
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.84
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.84
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.84
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.84
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.84
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.83
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.83
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.83
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.83
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.83
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.83
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.83
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.83
2div_A	99	TRNA selenocysteine associated protein; structural	99.83
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.83
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.83
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.82
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.82
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.82
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.82
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.82
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.82
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.82
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.82
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.82
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.82
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.82
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.82
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.82
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.82
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.82
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.81
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.81
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.81
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.81
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.81
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.81
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.81
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.81
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.81
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.81
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.81
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.81
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.81
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.81
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.81
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.81
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.8
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.8
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.8
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.8
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.8
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.8
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.79
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.79
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.79
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.79
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.79
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.79
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.79
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.79
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.79
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.79
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.79
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.79
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.79
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.78
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.78
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.78
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.78
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.78
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.78
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.78
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.78
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.78
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.78
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.78
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.77
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.77
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.77
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.77
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.77
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.77
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.77
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.77
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.77
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.63
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.77
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.77
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.77
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.76
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.76
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.76
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.76
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.76
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.76
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.76
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.76
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.76
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.76
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.76
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.76
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.76
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.75
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.75
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.75
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.75
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.75
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.75
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.74
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.74
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.74
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.74
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.74
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.74
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.73
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.73
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.73
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.73
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.72
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.72
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.72
1x5p_A	97	Negative elongation factor E; structure genomics,	99.72
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.72
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.72
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.72
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.72
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.71
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.71
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.71
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.71
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.7
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.7
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.7
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.7
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.7
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.7
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.7
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.7
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.69
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.68
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.68
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.67
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.67
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.67
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.67
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.67
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.67
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.67
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.66
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.66
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.66
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.65
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.65
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.64
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.62
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.62
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.59
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.59
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.58
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.58
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.58
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.57
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.56
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.56
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.56
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.54
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.54
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.52
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.51
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.49
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.45
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.39
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.38
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.29
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.23
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	99.08
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	99.01
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.69
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.84
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.77
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.66
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.62
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.46
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.32
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	96.53
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	96.5
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	96.48
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	95.9
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	95.33
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	92.6

>4fxv_A ELAV-like protein 1; RNA recognition motif, putative RNA-binding domain, transcri structural genomics, joint center for structural genomics; 1.90A {Homo sapiens}

Probab=99.89  E-value=5.1e-23  Score=145.85  Aligned_cols=83  Identities=23%  Similarity=0.490  Sum_probs=79.5

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ...+++|||+|||+++|+++|+++|++||.|.+|.+++++.+|.++|||||+|.+.++|..|+..|||..|+|+.|+|.+
T Consensus        16 ~~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~   95 (99)
T 4fxv_A           16 YFQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSY   95 (99)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            35678999999999999999999999999999999999998999999999999999999999999999999999999999


Q ss_pred             eCC
Q 028027          130 IPP  132 (215)
Q Consensus       130 a~~  132 (215)
                      |+|
T Consensus        96 AkP   98 (99)
T 4fxv_A           96 ARP   98 (99)
T ss_dssp             CCB
T ss_pred             eeC
Confidence            975

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.87  E-value=1.1e-22  Score=141.90  Aligned_cols=86  Identities=21%  Similarity=0.418  Sum_probs=78.9

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCC-CeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhC-CceeCCeEEEEEEe
Q 028027           53 ATVLYIGRIPHGFYEKEMQAFFSQFG-AIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMH-GYLLFEHILQVHLI  130 (215)
Q Consensus        53 ~~~l~V~nLp~~~te~~L~~~F~~~G-~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~-g~~l~g~~l~V~~a  130 (215)
                      +++|||+|||+++|+++|+++|++|| .|.+|+|++++.||.++|||||+|.+.++|..|++.++ +..++|+.|.|.++
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a   80 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYS   80 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEc
Confidence            46899999999999999999999999 89999999999999999999999999999999998874 56799999999999


Q ss_pred             CCCCCCCC
Q 028027          131 PPEHVHPK  138 (215)
Q Consensus       131 ~~~~~~~~  138 (215)
                      .+++....
T Consensus        81 ~~~~~~~~   88 (91)
T 2lxi_A           81 DPKPKINE   88 (91)
T ss_dssp             CSCCCCSC
T ss_pred             CCCCCCCC
Confidence            88766543

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.87  E-value=2.1e-21  Score=140.17  Aligned_cols=83  Identities=12%  Similarity=0.182  Sum_probs=79.1

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      .+.++|||+|||+.+++++|+++|++||.|.+|.|++++.||.++|||||+|.+.++|+.|+..|||..|+|+.|.|.++
T Consensus         4 ~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a   83 (110)
T 3s8s_A            4 IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLD   83 (110)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            45689999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCC
Q 028027          131 PPE  133 (215)
Q Consensus       131 ~~~  133 (215)
                      ...
T Consensus        84 ~~~   86 (110)
T 3s8s_A           84 IKG   86 (110)
T ss_dssp             STT
T ss_pred             CCC
Confidence            643

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens}

Probab=99.86  E-value=3e-21  Score=132.80  Aligned_cols=83  Identities=23%  Similarity=0.385  Sum_probs=77.3

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      .+.++|||+|||+++++++|+++|++||.|.+|.++.++.+|.++|||||+|.+.++|..|+..|||..++|+.|.|.++
T Consensus         4 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   83 (87)
T 3bs9_A            4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA   83 (87)
T ss_dssp             --CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEec
Confidence            56789999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             CCC
Q 028027          131 PPE  133 (215)
Q Consensus       131 ~~~  133 (215)
                      .++
T Consensus        84 ~~k   86 (87)
T 3bs9_A           84 TRK   86 (87)
T ss_dssp             C--
T ss_pred             CCC
Confidence            765

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.86  E-value=1.4e-20  Score=136.32  Aligned_cols=90  Identities=23%  Similarity=0.393  Sum_probs=83.7

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 028027           49 LVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVH  128 (215)
Q Consensus        49 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~  128 (215)
                      +..+.++|||+|||+.+++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|+.|+..|||..|+|+.|.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   90 (115)
T 2dgo_A           11 DTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTN   90 (115)
T ss_dssp             CSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34667999999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             EeCCCCCCCC
Q 028027          129 LIPPEHVHPK  138 (215)
Q Consensus       129 ~a~~~~~~~~  138 (215)
                      ++.+....+.
T Consensus        91 ~a~~~~~~~~  100 (115)
T 2dgo_A           91 WATRKPPAPK  100 (115)
T ss_dssp             ESSCCCCCSC
T ss_pred             EccCCCCCCc
Confidence            9988765543

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} SCOP: d.58.7.0

Probab=99.86  E-value=6.5e-21  Score=129.96  Aligned_cols=82  Identities=20%  Similarity=0.360  Sum_probs=78.3

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeCC
Q 028027           53 ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPP  132 (215)
Q Consensus        53 ~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~~  132 (215)
                      +.+|||+|||+.+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|+.|+..|||..++|+.|+|.++.+
T Consensus         1 t~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~   80 (83)
T 3md1_A            1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK   80 (83)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCc
Confidence            36899999999999999999999999999999999988999999999999999999999999999999999999999987


Q ss_pred             CC
Q 028027          133 EH  134 (215)
Q Consensus       133 ~~  134 (215)
                      +.
T Consensus        81 ~~   82 (83)
T 3md1_A           81 LE   82 (83)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.85  E-value=1.1e-20  Score=133.32  Aligned_cols=87  Identities=23%  Similarity=0.508  Sum_probs=81.5

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ....++|||+|||+.+++++|+++|++||.|..|.++.++.+|.++|||||+|.+.++|..|+. ||+..|+|+.|.|.+
T Consensus         7 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V~~   85 (99)
T 2dgs_A            7 GSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVKR   85 (99)
T ss_dssp             CSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEEEE
Confidence            4567999999999999999999999999999999999998899999999999999999999998 999999999999999


Q ss_pred             eCCCCCCC
Q 028027          130 IPPEHVHP  137 (215)
Q Consensus       130 a~~~~~~~  137 (215)
                      +.+.....
T Consensus        86 a~~~~~~~   93 (99)
T 2dgs_A           86 AEPRDSKS   93 (99)
T ss_dssp             CCCCCCCC
T ss_pred             CCCCcccC
Confidence            98876543

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.85  E-value=1.3e-20  Score=131.75  Aligned_cols=86  Identities=26%  Similarity=0.512  Sum_probs=81.5

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      .++++|||+|||+.+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|..|+..|||..|+|+.|+|.++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   82 (95)
T 2dnz_A            3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHV   82 (95)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEES
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEc
Confidence            46789999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 028027          131 PPEHVH  136 (215)
Q Consensus       131 ~~~~~~  136 (215)
                      .++...
T Consensus        83 ~~~~~~   88 (95)
T 2dnz_A           83 TERLDG   88 (95)
T ss_dssp             SCCCCC
T ss_pred             ccccCC
Confidence            876554

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.85  E-value=2.2e-20  Score=131.93  Aligned_cols=84  Identities=21%  Similarity=0.438  Sum_probs=79.9

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      .+.++|||+|||+.+++++|+++|++||.|..|.++.++ +|.++|||||+|.+.++|..|+..|||..|+|+.|.|.++
T Consensus        15 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   93 (100)
T 2do4_A           15 LEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAIS   93 (100)
T ss_dssp             CCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            567899999999999999999999999999999999998 9999999999999999999999999999999999999999


Q ss_pred             CCCCC
Q 028027          131 PPEHV  135 (215)
Q Consensus       131 ~~~~~  135 (215)
                      .+...
T Consensus        94 ~~~~~   98 (100)
T 2do4_A           94 NSGPS   98 (100)
T ss_dssp             CCCSC
T ss_pred             CCCCC
Confidence            87654

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=1.3e-20  Score=133.80  Aligned_cols=87  Identities=29%  Similarity=0.479  Sum_probs=82.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ..+.++|||+|||+.+++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|..|+..|||..|+|+.|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   91 (103)
T 2cq0_A           12 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEW   91 (103)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEE
Confidence            35679999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             eCCCCCC
Q 028027          130 IPPEHVH  136 (215)
Q Consensus       130 a~~~~~~  136 (215)
                      +.+....
T Consensus        92 a~~~~~~   98 (103)
T 2cq0_A           92 AKPSTNS   98 (103)
T ss_dssp             SSCCCCS
T ss_pred             CCCCCCC
Confidence            9876554

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.85  E-value=7.6e-21  Score=135.08  Aligned_cols=88  Identities=20%  Similarity=0.295  Sum_probs=82.2

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 028027           49 LVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVH  128 (215)
Q Consensus        49 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~  128 (215)
                      ...+.++|||+|||+.+++++|+.+|++||.|..|.|+.++.+|.++|||||+|.+.++|+.|+..|||..|+|+.|.|.
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   88 (103)
T 2dnm_A            9 DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQ   88 (103)
T ss_dssp             CCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            34667999999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             EeCCCCCC
Q 028027          129 LIPPEHVH  136 (215)
Q Consensus       129 ~a~~~~~~  136 (215)
                      ++.+....
T Consensus        89 ~a~~~~~~   96 (103)
T 2dnm_A           89 VARYGRRD   96 (103)
T ss_dssp             ECSSCCSC
T ss_pred             ECCcCCCC
Confidence            99876543

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.85  E-value=2.9e-21  Score=135.80  Aligned_cols=82  Identities=12%  Similarity=0.282  Sum_probs=76.5

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCC--eeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCc----eeCCeE
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGA--IKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGY----LLFEHI  124 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~--v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~----~l~g~~  124 (215)
                      ..-.+|||+|||+++|+++|+++|++||.  |.+|++++|+.||.++|||||+|.+.++|..|++.|||.    .|+|+.
T Consensus         7 ~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~   86 (95)
T 2lkz_A            7 HHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKT   86 (95)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEE
T ss_pred             CccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEE
Confidence            45689999999999999999999999995  678999999999999999999999999999999999996    599999


Q ss_pred             EEEEEeCC
Q 028027          125 LQVHLIPP  132 (215)
Q Consensus       125 l~V~~a~~  132 (215)
                      |.|+||++
T Consensus        87 i~V~~Aks   94 (95)
T 2lkz_A           87 IGVDFAKS   94 (95)
T ss_dssp             EEEEECCC
T ss_pred             EEEEEccC
Confidence            99999864

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=1.3e-20  Score=134.24  Aligned_cols=87  Identities=22%  Similarity=0.396  Sum_probs=82.2

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ....++|||+|||+.+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|..|+..|||..|+|+.|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   91 (105)
T 1x5u_A           12 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNK   91 (105)
T ss_dssp             CCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            45679999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             eCCCCCC
Q 028027          130 IPPEHVH  136 (215)
Q Consensus       130 a~~~~~~  136 (215)
                      +.+....
T Consensus        92 a~~~~~~   98 (105)
T 1x5u_A           92 ASAHNKN   98 (105)
T ss_dssp             TTTTSCC
T ss_pred             CCCCCcC
Confidence            9887554

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.85  E-value=1.7e-20  Score=132.22  Aligned_cols=86  Identities=20%  Similarity=0.321  Sum_probs=81.6

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      .+.++|||+|||+.+++++|+++|++||.|..|.++.++.+|.++|||||+|.+.++|..|+..|||..|+|+.|.|.++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   85 (99)
T 1whw_A            6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS   85 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            56789999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 028027          131 PPEHVH  136 (215)
Q Consensus       131 ~~~~~~  136 (215)
                      .+....
T Consensus        86 ~~~~~~   91 (99)
T 1whw_A           86 TIKKEA   91 (99)
T ss_dssp             CCCSTT
T ss_pred             CCCccc
Confidence            887654

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ISO mRNA processing, mRNA splicing, nucleus; 1.85A {Homo sapiens} SCOP: d.58.7.1 PDB: 2kyx_A 3lpy_A*

Probab=99.85  E-value=8.7e-21  Score=129.91  Aligned_cols=81  Identities=30%  Similarity=0.495  Sum_probs=77.8

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      .+.++|||+|||+.+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|..|+..|||..++|+.|+|.++
T Consensus         5 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   84 (85)
T 3mdf_A            5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   84 (85)
T ss_dssp             CCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            56799999999999999999999999999999999999889999999999999999999999999999999999999997


Q ss_pred             C
Q 028027          131 P  131 (215)
Q Consensus       131 ~  131 (215)
                      +
T Consensus        85 k   85 (85)
T 3mdf_A           85 K   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A

Probab=99.85  E-value=1.4e-20  Score=136.33  Aligned_cols=87  Identities=24%  Similarity=0.479  Sum_probs=82.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ..+.++|||+|||+++++++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|+.|+..||+..|+|+.|+|.+
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~  101 (115)
T 2cpz_A           22 GPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQL  101 (115)
T ss_dssp             CSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            35678999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             eCCCCCC
Q 028027          130 IPPEHVH  136 (215)
Q Consensus       130 a~~~~~~  136 (215)
                      +.+....
T Consensus       102 a~~~~~~  108 (115)
T 2cpz_A          102 KRSKNDS  108 (115)
T ss_dssp             CCCSCCC
T ss_pred             cCCCCcC
Confidence            9876554

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B

Probab=99.84  E-value=1.2e-20  Score=132.38  Aligned_cols=84  Identities=27%  Similarity=0.497  Sum_probs=79.8

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeC
Q 028027           52 KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIP  131 (215)
Q Consensus        52 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~  131 (215)
                      ++++|||+|||+.+++++|+++|++||.|..|.++.++.+|.++|||||+|.+.++|..|+..|||..++|+.|.|.++.
T Consensus         1 P~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   80 (96)
T 2x1f_A            1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSS   80 (96)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcC
Confidence            35899999999999999999999999999999999998899999999999999999999999999999999999999998


Q ss_pred             CCCC
Q 028027          132 PEHV  135 (215)
Q Consensus       132 ~~~~  135 (215)
                      +...
T Consensus        81 ~~~~   84 (96)
T 2x1f_A           81 NSDI   84 (96)
T ss_dssp             CSSG
T ss_pred             CCCC
Confidence            7654

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=1e-20  Score=132.57  Aligned_cols=86  Identities=27%  Similarity=0.454  Sum_probs=81.3

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEE-EEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRL-RIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v-~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      .+.++|||+|||+.+++++|+.+|++||.|..+ .++.++.+|.++|||||+|.+.++|+.|+..|||..|+|+.|.|.+
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   82 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSY   82 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            457899999999999999999999999999999 9999988999999999999999999999999999999999999999


Q ss_pred             eCCCCCC
Q 028027          130 IPPEHVH  136 (215)
Q Consensus       130 a~~~~~~  136 (215)
                      +.+....
T Consensus        83 a~~~~~~   89 (96)
T 1x5t_A           83 AFKKDSK   89 (96)
T ss_dssp             SCCCCCC
T ss_pred             ecccCCC
Confidence            9887654

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=1.7e-20  Score=132.99  Aligned_cols=87  Identities=29%  Similarity=0.497  Sum_probs=82.0

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      .+.++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|..|+..|||..|+|+.|.|.++
T Consensus        10 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   89 (102)
T 2cqb_A           10 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   89 (102)
T ss_dssp             CCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEeC
Confidence            56789999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             CCCCCCC
Q 028027          131 PPEHVHP  137 (215)
Q Consensus       131 ~~~~~~~  137 (215)
                      .+.....
T Consensus        90 ~~~~~~~   96 (102)
T 2cqb_A           90 KPMRIKE   96 (102)
T ss_dssp             CCCCCCC
T ss_pred             CCCCCCC
Confidence            8876543

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.84  E-value=2.2e-20  Score=130.36  Aligned_cols=82  Identities=22%  Similarity=0.481  Sum_probs=78.1

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ..+.++|||+|||+.+++++|+++|++||.|..|.++.++.+|.++|||||+|.+.++|..|+..|||..|+|+.|+|.+
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   92 (94)
T 2e5h_A           13 APSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASI   92 (94)
T ss_dssp             CCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEe
Confidence            35678999999999999999999999999999999999988899999999999999999999999999999999999999


Q ss_pred             eC
Q 028027          130 IP  131 (215)
Q Consensus       130 a~  131 (215)
                      ++
T Consensus        93 ak   94 (94)
T 2e5h_A           93 AI   94 (94)
T ss_dssp             CC
T ss_pred             cC
Confidence            74

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A

Probab=99.84  E-value=1.5e-20  Score=136.46  Aligned_cols=83  Identities=24%  Similarity=0.409  Sum_probs=75.8

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeC
Q 028027           52 KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIP  131 (215)
Q Consensus        52 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~  131 (215)
                      ..++|||+|||+++++++|+++|++||.|.+|.|+++.  +.++|||||+|.+.++|+.|+..|||..|+|+.|.|.++.
T Consensus         4 ~~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~--~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~   81 (115)
T 4f25_A            4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK   81 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESS
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            35789999999999999999999999999999999985  5589999999999999999999999999999999999998


Q ss_pred             CCCCC
Q 028027          132 PEHVH  136 (215)
Q Consensus       132 ~~~~~  136 (215)
                      ++..+
T Consensus        82 ~~~~~   86 (115)
T 4f25_A           82 SRKER   86 (115)
T ss_dssp             CCCC-
T ss_pred             Ccccc
Confidence            76543

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens}

Probab=99.84  E-value=3.3e-20  Score=133.29  Aligned_cols=85  Identities=26%  Similarity=0.530  Sum_probs=80.6

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ...+++|||+|||+.+++++|+.+|++||.|..|.++.++.+|.++|||||+|.+.++|..|+..|||..|+|+.|.|.+
T Consensus        23 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~  102 (108)
T 2jrs_A           23 SAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGH  102 (108)
T ss_dssp             CSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            35678999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             eCCCC
Q 028027          130 IPPEH  134 (215)
Q Consensus       130 a~~~~  134 (215)
                      +.++.
T Consensus       103 a~~k~  107 (108)
T 2jrs_A          103 VTERT  107 (108)
T ss_dssp             SCSSC
T ss_pred             cccCC
Confidence            97754

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=2.1e-20  Score=130.66  Aligned_cols=83  Identities=18%  Similarity=0.290  Sum_probs=78.9

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ..+.++|||+|||+.+++++|+++|++||.|..|.++.++.+|.++|||||+|.+.++|..|+..|||..|+|+.|.|.+
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   91 (95)
T 2cqc_A           12 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSG   91 (95)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            35678999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             eCC
Q 028027          130 IPP  132 (215)
Q Consensus       130 a~~  132 (215)
                      +++
T Consensus        92 a~~   94 (95)
T 2cqc_A           92 PSS   94 (95)
T ss_dssp             CSC
T ss_pred             cCC
Confidence            864

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=1.4e-20  Score=134.27  Aligned_cols=84  Identities=17%  Similarity=0.358  Sum_probs=79.9

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      .+.++|||+|||+.+++++|+.+|++||.|..|.++.++.+|.++|||||+|.+.++|+.|+..|||..|+|+.|.|.++
T Consensus        21 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a  100 (106)
T 1p27_B           21 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC  100 (106)
T ss_dssp             TTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEee
Confidence            55689999999999999999999999999999999999989999999999999999999999999999999999999998


Q ss_pred             CCCC
Q 028027          131 PPEH  134 (215)
Q Consensus       131 ~~~~  134 (215)
                      .++.
T Consensus       101 ~~~~  104 (106)
T 1p27_B          101 FVRG  104 (106)
T ss_dssp             EESS
T ss_pred             cCCC
Confidence            7654

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C

Probab=99.84  E-value=2.1e-21  Score=134.92  Aligned_cols=83  Identities=19%  Similarity=0.274  Sum_probs=72.9

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCC--CeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeC
Q 028027           54 TVLYIGRIPHGFYEKEMQAFFSQFG--AIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIP  131 (215)
Q Consensus        54 ~~l~V~nLp~~~te~~L~~~F~~~G--~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~  131 (215)
                      .+|||+|||+++++++|+++|++||  .|.++.++.++.+|.++|||||+|.+.++|+.|+..|||..|+|+.|.|.++.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            4799999999999999999999999  99999999999899999999999999999999999999999999999999988


Q ss_pred             CCCCC
Q 028027          132 PEHVH  136 (215)
Q Consensus       132 ~~~~~  136 (215)
                      +....
T Consensus        82 ~~~~~   86 (90)
T 3p5t_L           82 KLEHH   86 (90)
T ss_dssp             -----
T ss_pred             CCccc
Confidence            76443

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.84  E-value=3e-20  Score=133.56  Aligned_cols=88  Identities=24%  Similarity=0.333  Sum_probs=82.3

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhC------CceeCCe
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMH------GYLLFEH  123 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~------g~~l~g~  123 (215)
                      ....++|||+|||+.+++++|+.+|++||.|..|.|+.++.+|.++|||||+|.+.++|..|+..||      +..|+|+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g~   91 (111)
T 1x4h_A           12 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGR   91 (111)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcCE
Confidence            3567899999999999999999999999999999999998899999999999999999999999999      9999999


Q ss_pred             EEEEEEeCCCCCCC
Q 028027          124 ILQVHLIPPEHVHP  137 (215)
Q Consensus       124 ~l~V~~a~~~~~~~  137 (215)
                      .|.|.++.++....
T Consensus        92 ~l~v~~a~~~~~~~  105 (111)
T 1x4h_A           92 QLKVDLAVTRDEAA  105 (111)
T ss_dssp             EEEEECCCCCCCCC
T ss_pred             EEEEEECCCCccCC
Confidence            99999998875543

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.84  E-value=2.9e-20  Score=132.78  Aligned_cols=88  Identities=24%  Similarity=0.462  Sum_probs=82.1

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeec-CCCCCcccEEEEEEcCHHHHHHHHHHh-CCceeCCeEEE
Q 028027           49 LVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARN-KKTGQSKHFGFIEFNDPEVAEVVADAM-HGYLLFEHILQ  126 (215)
Q Consensus        49 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~-~~tg~~~g~afV~F~~~~~a~~ai~~l-~g~~l~g~~l~  126 (215)
                      .....++|||+|||+.+++++|+++|++||.|..|.|+.+ +.+|.++|||||+|.+.++|..|+..| |+..|+|+.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~   90 (107)
T 2cph_A           11 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLV   90 (107)
T ss_dssp             CSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEE
Confidence            3456789999999999999999999999999999999998 789999999999999999999999999 99999999999


Q ss_pred             EEEeCCCCCC
Q 028027          127 VHLIPPEHVH  136 (215)
Q Consensus       127 V~~a~~~~~~  136 (215)
                      |.++.+....
T Consensus        91 v~~a~~~~~~  100 (107)
T 2cph_A           91 LEWADSEVTV  100 (107)
T ss_dssp             EEECCCCCCC
T ss_pred             EEeCCCCCCC
Confidence            9999887554

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=7.4e-20  Score=132.74  Aligned_cols=86  Identities=20%  Similarity=0.376  Sum_probs=80.1

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ....++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|+.|+..|++ .|.|+.|.|.+
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V~~   92 (116)
T 2cqd_A           14 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNL   92 (116)
T ss_dssp             SCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEEEE
Confidence            45679999999999999999999999999999999999988999999999999999999999999998 89999999999


Q ss_pred             eCCCCCC
Q 028027          130 IPPEHVH  136 (215)
Q Consensus       130 a~~~~~~  136 (215)
                      +.+....
T Consensus        93 a~~~~~~   99 (116)
T 2cqd_A           93 AYLGAKP   99 (116)
T ss_dssp             STTTCCC
T ss_pred             cccCCCc
Confidence            9765443

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.84  E-value=2.2e-20  Score=131.85  Aligned_cols=84  Identities=18%  Similarity=0.340  Sum_probs=79.2

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeE--------EEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCce
Q 028027           48 PLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKR--------LRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYL  119 (215)
Q Consensus        48 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~--------v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~  119 (215)
                      ++....++|||+|||+++++++|+++|++||.|..        +.++.++.+|.++|||||+|.+.++|+.|+..|||..
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~   87 (99)
T 2la6_A            8 HSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKE   87 (99)
T ss_dssp             CSCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCB
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCE
Confidence            34467799999999999999999999999999999        9999998899999999999999999999999999999


Q ss_pred             eCCeEEEEEEeC
Q 028027          120 LFEHILQVHLIP  131 (215)
Q Consensus       120 l~g~~l~V~~a~  131 (215)
                      |+|+.|+|.+|+
T Consensus        88 ~~g~~l~V~~A~   99 (99)
T 2la6_A           88 FSGNPIKVSFAT   99 (99)
T ss_dssp             SSSSBCEEEECC
T ss_pred             eCCcEEEEEecC
Confidence            999999999874

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=2e-20  Score=132.60  Aligned_cols=87  Identities=21%  Similarity=0.408  Sum_probs=82.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ..+.++|||+|||+.+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|..|+..||+..|+|+.|+|.+
T Consensus         9 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   88 (102)
T 1x5s_A            9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQ   88 (102)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            35678999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             eCCCCCC
Q 028027          130 IPPEHVH  136 (215)
Q Consensus       130 a~~~~~~  136 (215)
                      +.+....
T Consensus        89 a~~~~~~   95 (102)
T 1x5s_A           89 AGKSSDN   95 (102)
T ss_dssp             EECCCCC
T ss_pred             CCCCCCC
Confidence            9876554

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D*

Probab=99.84  E-value=1.9e-20  Score=134.52  Aligned_cols=86  Identities=22%  Similarity=0.386  Sum_probs=80.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ..+.++|||+|||+.+++++|+.+|++||.|..|.++.++.+|.++|||||+|.+.++|..|+..|||..|+|+.|.|.+
T Consensus        23 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  102 (110)
T 1oo0_B           23 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW  102 (110)
T ss_dssp             BTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            35678999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             eCCCCC
Q 028027          130 IPPEHV  135 (215)
Q Consensus       130 a~~~~~  135 (215)
                      +.+...
T Consensus       103 a~~~~~  108 (110)
T 1oo0_B          103 CFVKGP  108 (110)
T ss_dssp             SEESSC
T ss_pred             cccCCC
Confidence            976543

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens}

Probab=99.84  E-value=3.8e-20  Score=134.62  Aligned_cols=86  Identities=26%  Similarity=0.464  Sum_probs=80.7

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ...++|||+|||+++++++|+++|++||.|..|.++.+. +|.++|||||+|.+.++|+.|+..|||..|+|+.|.|.++
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   83 (116)
T 2fy1_A            5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQA   83 (116)
T ss_dssp             CSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            557899999999999999999999999999999999998 9999999999999999999999999999999999999999


Q ss_pred             CCCCCCC
Q 028027          131 PPEHVHP  137 (215)
Q Consensus       131 ~~~~~~~  137 (215)
                      .+.....
T Consensus        84 ~~~~~~~   90 (116)
T 2fy1_A           84 KKPSFQS   90 (116)
T ss_dssp             CCSSCSS
T ss_pred             CCCCCCC
Confidence            8765443

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.84  E-value=4e-20  Score=131.29  Aligned_cols=86  Identities=27%  Similarity=0.471  Sum_probs=80.6

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ..+.++|||+|||+.+++++|+++|++||.|..|.++.+  +|.++|||||+|.+.++|..|+..|||..|+|+.|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2d9p_A           12 RYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVAL   89 (103)
T ss_dssp             CSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            457889999999999999999999999999999999998  899999999999999999999999999999999999999


Q ss_pred             eCCCCCCC
Q 028027          130 IPPEHVHP  137 (215)
Q Consensus       130 a~~~~~~~  137 (215)
                      +.+...+.
T Consensus        90 a~~~~~~~   97 (103)
T 2d9p_A           90 AQRKEERQ   97 (103)
T ss_dssp             CSSCCCCC
T ss_pred             ecccccCC
Confidence            98876543

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=4.4e-20  Score=131.37  Aligned_cols=86  Identities=19%  Similarity=0.356  Sum_probs=80.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCC-CCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKT-GQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVH  128 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~t-g~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~  128 (215)
                      ....++|||+|||+.+++++|+++|+.|| |..|.|+.++.+ |.++|||||+|.+.++|+.|| .||+..|+|+.|.|.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~   89 (104)
T 1wi8_A           12 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVD   89 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEEE
Confidence            35679999999999999999999999999 999999999877 999999999999999999999 999999999999999


Q ss_pred             EeCCCCCCC
Q 028027          129 LIPPEHVHP  137 (215)
Q Consensus       129 ~a~~~~~~~  137 (215)
                      ++.++....
T Consensus        90 ~a~~~~~~~   98 (104)
T 1wi8_A           90 VADQAQDKD   98 (104)
T ss_dssp             ECCCCCCCC
T ss_pred             EccCCCCCC
Confidence            998876543

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.84  E-value=6.9e-20  Score=130.16  Aligned_cols=85  Identities=22%  Similarity=0.460  Sum_probs=79.6

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ..+.++|||+|||+.+++++|+++|++|| |..|.++.++.+|.++|||||+|.+.++|..|+ .|||..|+|+.|.|.+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~   89 (103)
T 2dng_A           12 TEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDI   89 (103)
T ss_dssp             SSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEEE
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEEE
Confidence            35679999999999999999999999997 999999999989999999999999999999999 8999999999999999


Q ss_pred             eCCCCCC
Q 028027          130 IPPEHVH  136 (215)
Q Consensus       130 a~~~~~~  136 (215)
                      +.+....
T Consensus        90 a~~~~~~   96 (103)
T 2dng_A           90 AEGRKQD   96 (103)
T ss_dssp             CCCCCCC
T ss_pred             ecCCCCC
Confidence            9876544

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A

Probab=99.83  E-value=5.2e-20  Score=131.10  Aligned_cols=85  Identities=22%  Similarity=0.415  Sum_probs=80.1

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCC---eEEEE
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFE---HILQV  127 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g---~~l~V  127 (215)
                      ...++|||+|||+.+++++|+.+|++||.|..|.|+.++ +|.++|||||+|.+.++|..|+..|||..+.|   +.|.|
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V   91 (105)
T 2dnh_A           13 GRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVV   91 (105)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEE
Confidence            457999999999999999999999999999999999997 89999999999999999999999999999988   99999


Q ss_pred             EEeCCCCCC
Q 028027          128 HLIPPEHVH  136 (215)
Q Consensus       128 ~~a~~~~~~  136 (215)
                      .++.+...+
T Consensus        92 ~~a~~~~~~  100 (105)
T 2dnh_A           92 KFADTDKES  100 (105)
T ss_dssp             EESCSSCCC
T ss_pred             EECccCccc
Confidence            999887654

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.83  E-value=3.5e-21  Score=136.45  Aligned_cols=82  Identities=21%  Similarity=0.331  Sum_probs=78.1

Q ss_pred             CCCcEEEEcCCCC------CCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCC-e
Q 028027           51 NKATVLYIGRIPH------GFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFE-H  123 (215)
Q Consensus        51 ~~~~~l~V~nLp~------~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g-~  123 (215)
                      ...++|||+|||+      .+++++|+++|++||.|.+|.|++++.||.++|||||+|.+.++|..|+..|||..|+| +
T Consensus         4 ~~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r   83 (100)
T 3ns6_A            4 GSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKH   83 (100)
T ss_dssp             CGGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSC
T ss_pred             CcCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCe
Confidence            3468999999999      99999999999999999999999999899999999999999999999999999999999 9


Q ss_pred             EEEEEEeCC
Q 028027          124 ILQVHLIPP  132 (215)
Q Consensus       124 ~l~V~~a~~  132 (215)
                      .|.|.++.+
T Consensus        84 ~l~V~~a~~   92 (100)
T 3ns6_A           84 RLFLYTMKD   92 (100)
T ss_dssp             BCEEEESHH
T ss_pred             EEEEEECch
Confidence            999999864

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.83  E-value=5.8e-20  Score=137.36  Aligned_cols=92  Identities=24%  Similarity=0.514  Sum_probs=84.8

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEE
Q 028027           48 PLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQV  127 (215)
Q Consensus        48 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V  127 (215)
                      +.....++|||+|||+++++++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|..|+..|||..|+|+.|+|
T Consensus        37 ~~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  116 (139)
T 1u6f_A           37 PEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKV  116 (139)
T ss_dssp             CCTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            34566789999999999999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             EEeCCCCCCCCC
Q 028027          128 HLIPPEHVHPKL  139 (215)
Q Consensus       128 ~~a~~~~~~~~~  139 (215)
                      .++.+...++..
T Consensus       117 ~~a~~~~~~~~~  128 (139)
T 1u6f_A          117 ALAASGHQRPGI  128 (139)
T ss_dssp             EESSCCCCCCCS
T ss_pred             EECCCCCCCCCC
Confidence            999987665433

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.83  E-value=4e-20  Score=133.48  Aligned_cols=88  Identities=20%  Similarity=0.328  Sum_probs=82.0

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhccCCCee--------EEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCcee
Q 028027           49 LVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIK--------RLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLL  120 (215)
Q Consensus        49 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~--------~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l  120 (215)
                      .....++|||+|||+.+++++|+++|++||.|.        .|.|+.++.+|.++|||||+|.+.++|..|+..|||..|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~   90 (113)
T 2cpe_A           11 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   90 (113)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCcc
Confidence            346779999999999999999999999999999        699999988999999999999999999999999999999


Q ss_pred             CCeEEEEEEeCCCCCC
Q 028027          121 FEHILQVHLIPPEHVH  136 (215)
Q Consensus       121 ~g~~l~V~~a~~~~~~  136 (215)
                      .|+.|+|.++.+....
T Consensus        91 ~g~~l~V~~a~~~~~~  106 (113)
T 2cpe_A           91 QGSKLKVSLARKKPPM  106 (113)
T ss_dssp             TTEECEEECSSCCCCS
T ss_pred             CCCEEEEEECCCCCCC
Confidence            9999999999876554

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens}

Probab=99.83  E-value=3.2e-20  Score=127.78  Aligned_cols=83  Identities=23%  Similarity=0.412  Sum_probs=77.8

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCC-cccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           52 KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQ-SKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        52 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~-~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      .+++|||+|||+++++++|+++|++||.|..+.++.+..++. ++|||||+|.+.++|..|+..|||..++|+.|.|.++
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   82 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAV   82 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEEC
Confidence            468999999999999999999999999999999999887666 8999999999999999999999999999999999999


Q ss_pred             CCCC
Q 028027          131 PPEH  134 (215)
Q Consensus       131 ~~~~  134 (215)
                      .+..
T Consensus        83 ~~~~   86 (88)
T 4a8x_A           83 LAPW   86 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7653

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A

Probab=99.83  E-value=3.3e-20  Score=132.33  Aligned_cols=88  Identities=27%  Similarity=0.445  Sum_probs=81.8

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCcee---CCeEE
Q 028027           49 LVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLL---FEHIL  125 (215)
Q Consensus        49 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l---~g~~l  125 (215)
                      +..+.++|||+|||+.+++++|+++|++||.|..|.++.++.+|.++|||||+|.+.++|..|+..|||..+   .|+.|
T Consensus         9 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l   88 (106)
T 2dgp_A            9 KDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPI   88 (106)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceE
Confidence            346679999999999999999999999999999999999988999999999999999999999999999987   89999


Q ss_pred             EEEEeCCCCCC
Q 028027          126 QVHLIPPEHVH  136 (215)
Q Consensus       126 ~V~~a~~~~~~  136 (215)
                      .|.++.+....
T Consensus        89 ~v~~a~~~~~~   99 (106)
T 2dgp_A           89 QVKPADSESRG   99 (106)
T ss_dssp             EEEECCCCSCC
T ss_pred             EEEECCccccc
Confidence            99999876543

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.83  E-value=1.1e-19  Score=132.07  Aligned_cols=83  Identities=29%  Similarity=0.529  Sum_probs=78.3

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 028027           49 LVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVH  128 (215)
Q Consensus        49 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~  128 (215)
                      +..+.++|||+|||+++++++|+++|++||.|..|.++.++.+|.++|||||+|.+.++|+.|+..|||..|+|+.|+|+
T Consensus        36 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~  115 (118)
T 2khc_A           36 EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQ  115 (118)
T ss_dssp             CCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34667999999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             EeC
Q 028027          129 LIP  131 (215)
Q Consensus       129 ~a~  131 (215)
                      +++
T Consensus       116 ~ak  118 (118)
T 2khc_A          116 LKK  118 (118)
T ss_dssp             EC-
T ss_pred             ecC
Confidence            874

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.83  E-value=3e-20  Score=130.71  Aligned_cols=86  Identities=27%  Similarity=0.423  Sum_probs=79.6

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCC---CCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEE
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKK---TGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQV  127 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~---tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V  127 (215)
                      .+.++|||+|||+++++++|+++|++||.|..|.++.++.   |+.++|||||+|.+.++|..|+..|||..|+|+.|.|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   82 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEV   82 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEE
Confidence            4568999999999999999999999999999999999875   6689999999999999999999999999999999999


Q ss_pred             EEeCCCCCC
Q 028027          128 HLIPPEHVH  136 (215)
Q Consensus       128 ~~a~~~~~~  136 (215)
                      .++.+....
T Consensus        83 ~~a~~~~~~   91 (98)
T 2cpf_A           83 RISERATKP   91 (98)
T ss_dssp             ECSSCSSCC
T ss_pred             EEccCCCCC
Confidence            999876543

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.83  E-value=3.2e-20  Score=130.83  Aligned_cols=84  Identities=23%  Similarity=0.339  Sum_probs=79.8

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCee-EEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeE----E
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIK-RLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHI----L  125 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~-~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~----l  125 (215)
                      ...++|||+|||+++++++|+++|++||.|. .|.++.++.+|.++|||||+|.+.++|+.|+..|||..|+|+.    |
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~l   86 (99)
T 2div_A            7 GMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKRF   86 (99)
T ss_dssp             SSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEEC
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcceeE
Confidence            4678999999999999999999999999999 9999999889999999999999999999999999999999999    9


Q ss_pred             EEEEeCCCC
Q 028027          126 QVHLIPPEH  134 (215)
Q Consensus       126 ~V~~a~~~~  134 (215)
                      +|.++.+..
T Consensus        87 ~v~~a~~~~   95 (99)
T 2div_A           87 KLNYATYSG   95 (99)
T ss_dssp             CEEETTCCS
T ss_pred             EEeecCCCC
Confidence            999997654

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.83  E-value=2.9e-19  Score=129.08  Aligned_cols=86  Identities=20%  Similarity=0.317  Sum_probs=79.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ....++|||+|||+.+++++|+++|++||.|..|.|+.++ +|.++|||||+|.+.++|..|+..|||..|+|+.|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   90 (114)
T 2do0_A           12 GRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKM   90 (114)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEE
Confidence            3557899999999999999999999999999999999997 799999999999999999999999999999999999999


Q ss_pred             eCCCCCC
Q 028027          130 IPPEHVH  136 (215)
Q Consensus       130 a~~~~~~  136 (215)
                      +......
T Consensus        91 a~~~~~~   97 (114)
T 2do0_A           91 DERALPK   97 (114)
T ss_dssp             CSCCCCC
T ss_pred             cccCCCC
Confidence            9765443

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.83  E-value=5.1e-20  Score=132.45  Aligned_cols=87  Identities=21%  Similarity=0.381  Sum_probs=77.5

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 028027           49 LVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVH  128 (215)
Q Consensus        49 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~  128 (215)
                      ...+.++|||+|||+.+++++|+.+|+.||.|..|.++.++.+|.++|||||+|.+.++|..|+..+ +..|+|+.|.|.
T Consensus        21 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V~   99 (109)
T 2rs2_A           21 MGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDPK   99 (109)
T ss_dssp             -----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEEE
Confidence            3456789999999999999999999999999999999999889999999999999999999999876 599999999999


Q ss_pred             EeCCCCCC
Q 028027          129 LIPPEHVH  136 (215)
Q Consensus       129 ~a~~~~~~  136 (215)
                      ++.++...
T Consensus       100 ~a~~~~~~  107 (109)
T 2rs2_A          100 VAFPRRAQ  107 (109)
T ss_dssp             ECCCCCCC
T ss_pred             EccCCCCC
Confidence            99887654

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.82  E-value=2.9e-19  Score=126.80  Aligned_cols=87  Identities=24%  Similarity=0.450  Sum_probs=79.3

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEE
Q 028027           48 PLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQV  127 (215)
Q Consensus        48 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V  127 (215)
                      ......++|||+|||+.+++++|+++|++||.|..|.|+.+..  .++|||||+|.+.++|..|+..|||..|+|+.|.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   87 (103)
T 2cq3_A           10 ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEV   87 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            3346779999999999999999999999999999999999853  38999999999999999999999999999999999


Q ss_pred             EEeCCCCCC
Q 028027          128 HLIPPEHVH  136 (215)
Q Consensus       128 ~~a~~~~~~  136 (215)
                      .++.+....
T Consensus        88 ~~a~~~~~~   96 (103)
T 2cq3_A           88 NNATARVMT   96 (103)
T ss_dssp             EECCSSCCC
T ss_pred             EEcccCCCC
Confidence            999887554

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A

Probab=99.82  E-value=9.5e-20  Score=130.14  Aligned_cols=82  Identities=18%  Similarity=0.343  Sum_probs=78.2

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 028027           49 LVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVH  128 (215)
Q Consensus        49 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~  128 (215)
                      +....++|||+|||+.+++++|+++|++||.|..|.|+.+. +|.++|||||+|.+.++|..|+..|||..|+|+.|.|.
T Consensus        25 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~  103 (107)
T 3ulh_A           25 GVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQ  103 (107)
T ss_dssp             CCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            34667999999999999999999999999999999999998 99999999999999999999999999999999999999


Q ss_pred             EeC
Q 028027          129 LIP  131 (215)
Q Consensus       129 ~a~  131 (215)
                      ++.
T Consensus       104 ~a~  106 (107)
T 3ulh_A          104 LVT  106 (107)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            985

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A

Probab=99.82  E-value=9.4e-20  Score=125.41  Aligned_cols=80  Identities=25%  Similarity=0.462  Sum_probs=75.2

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ..+.++|||+|||+.+++++|+++|++||.|..|.++.++.+|.++|||||+|.+.++|..|+. +++..|+|+.|.|.+
T Consensus         8 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v~~   86 (87)
T 3s7r_A            8 EEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDPKK   86 (87)
T ss_dssp             CSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEEEe
Confidence            4567899999999999999999999999999999999998899999999999999999999995 588899999999987


Q ss_pred             e
Q 028027          130 I  130 (215)
Q Consensus       130 a  130 (215)
                      |
T Consensus        87 A   87 (87)
T 3s7r_A           87 A   87 (87)
T ss_dssp             C
T ss_pred             C
Confidence            5

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.82  E-value=5.2e-20  Score=130.87  Aligned_cols=86  Identities=17%  Similarity=0.351  Sum_probs=80.7

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhcc-CCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCce-eCCeEEEEE
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQ-FGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYL-LFEHILQVH  128 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~-~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~-l~g~~l~V~  128 (215)
                      ...++|||+|||+.+++++|+++|++ ||.|..|.|+.++ +|.++|||||+|.+.++|..|+..|||.. |+|+.|.|.
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v~   85 (104)
T 2dhg_A            7 GPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLS   85 (104)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEEE
Confidence            56789999999999999999999999 9999999999998 99999999999999999999999999999 999999999


Q ss_pred             EeCCCCCCC
Q 028027          129 LIPPEHVHP  137 (215)
Q Consensus       129 ~a~~~~~~~  137 (215)
                      ++.+.....
T Consensus        86 ~a~~~~~~~   94 (104)
T 2dhg_A           86 VAIPKASRV   94 (104)
T ss_dssp             BCCCCCSCC
T ss_pred             EccCCCcCC
Confidence            998765543

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*

Probab=99.82  E-value=4.2e-20  Score=135.85  Aligned_cols=88  Identities=16%  Similarity=0.325  Sum_probs=82.1

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ..+.++|||+|||+.+++++|+.+|++||.|..|.|+.++.+|.++|||||+|.+.++|..|+..|||..|+|+.|.|.+
T Consensus        19 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   98 (126)
T 3ex7_B           19 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW   98 (126)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEE
Confidence            35578999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             eCCCCCCC
Q 028027          130 IPPEHVHP  137 (215)
Q Consensus       130 a~~~~~~~  137 (215)
                      +.+.....
T Consensus        99 a~~~~~~~  106 (126)
T 3ex7_B           99 CFVRGPPK  106 (126)
T ss_dssp             SEESSSCC
T ss_pred             ecCCCCCC
Confidence            98765543

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.82  E-value=8.7e-20  Score=128.17  Aligned_cols=84  Identities=14%  Similarity=0.216  Sum_probs=77.3

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHH----HHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQ----AFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHIL  125 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~----~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l  125 (215)
                      ..+.++|||+|||+.+++++|+    ++|++||.|.+|.++.++.+   +|||||+|.+.++|+.|+..|||..|+|+.|
T Consensus         6 ~~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l   82 (96)
T 2dgx_A            6 SGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSKKI   82 (96)
T ss_dssp             CSSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCeEE
Confidence            3567899999999999999999    99999999999999998754   8999999999999999999999999999999


Q ss_pred             EEEEeCCCCCC
Q 028027          126 QVHLIPPEHVH  136 (215)
Q Consensus       126 ~V~~a~~~~~~  136 (215)
                      +|.++.+....
T Consensus        83 ~V~~a~~~~~~   93 (96)
T 2dgx_A           83 LVSLATGASGP   93 (96)
T ss_dssp             EEEECCCSSCC
T ss_pred             EEEEcCCCCCC
Confidence            99999876543

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A

Probab=99.82  E-value=7.9e-20  Score=126.14  Aligned_cols=81  Identities=27%  Similarity=0.460  Sum_probs=77.2

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeC
Q 028027           52 KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIP  131 (215)
Q Consensus        52 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~  131 (215)
                      +.++|||+|||+.+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|+.|+ .|||..++|+.|.|.++.
T Consensus         5 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~   83 (89)
T 3ucg_A            5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKR   83 (89)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETT
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEcc
Confidence            3579999999999999999999999999999999999889999999999999999999999 999999999999999987


Q ss_pred             CC
Q 028027          132 PE  133 (215)
Q Consensus       132 ~~  133 (215)
                      +.
T Consensus        84 ~~   85 (89)
T 3ucg_A           84 TN   85 (89)
T ss_dssp             TT
T ss_pred             CC
Confidence            64

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A

Probab=99.82  E-value=4.3e-20  Score=136.87  Aligned_cols=85  Identities=18%  Similarity=0.308  Sum_probs=80.6

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ..+.++|||+|||+.+++++|+++|++||.|..|.++.++.+|.++|||||+|.+.++|+.|+..|||..|+|+.|.|.+
T Consensus        43 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~~  122 (129)
T 2kxn_B           43 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDF  122 (129)
T ss_dssp             CCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEESC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            45678999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             eCCCC
Q 028027          130 IPPEH  134 (215)
Q Consensus       130 a~~~~  134 (215)
                      +.++.
T Consensus       123 a~~~~  127 (129)
T 2kxn_B          123 SITKR  127 (129)
T ss_dssp             CSSSS
T ss_pred             ecCCC
Confidence            98754

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.82  E-value=5e-20  Score=140.88  Aligned_cols=81  Identities=16%  Similarity=0.307  Sum_probs=76.8

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCC--CeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           52 KATVLYIGRIPHGFYEKEMQAFFSQFG--AIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        52 ~~~~l~V~nLp~~~te~~L~~~F~~~G--~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ..++|||+|||+++++++|+++|+.||  .|..|.|+.++.+|.++|||||+|.+.++|+.||..|||..|+|+.|.|.+
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~  133 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRP  133 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEE
Confidence            568999999999999999999999999  999999999999999999999999999999999999999999999999999


Q ss_pred             eCC
Q 028027          130 IPP  132 (215)
Q Consensus       130 a~~  132 (215)
                      +.+
T Consensus       134 a~~  136 (156)
T 3n9u_C          134 ATR  136 (156)
T ss_dssp             CCH
T ss_pred             cCC
Confidence            854

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.82  E-value=9.5e-20  Score=126.59  Aligned_cols=84  Identities=25%  Similarity=0.384  Sum_probs=78.7

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ...++|||+|||+.+++++|+.+|++||.|..|.++.+  +|.++|||||+|.+.++|..|+..|||..|+|+.|.|.++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~--~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a   83 (92)
T 2dgv_A            6 SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRID   83 (92)
T ss_dssp             SSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            56789999999999999999999999999999999984  8999999999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 028027          131 PPEHVH  136 (215)
Q Consensus       131 ~~~~~~  136 (215)
                      .+....
T Consensus        84 ~~~~~~   89 (92)
T 2dgv_A           84 RNASGP   89 (92)
T ss_dssp             SCCSSC
T ss_pred             CCCCCC
Confidence            876543

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.82  E-value=6.8e-20  Score=130.55  Aligned_cols=87  Identities=24%  Similarity=0.487  Sum_probs=81.2

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ....++|||+|||+.+++++|+.+|++||.|..|.|+.++.+|.++|||||+|.+.++|+.|+.. ++..|+|+.|.|.+
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V~~   91 (105)
T 2dh8_A           13 ADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPKP   91 (105)
T ss_dssp             SSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEE
Confidence            35679999999999999999999999999999999999988999999999999999999999988 99999999999999


Q ss_pred             eCCCCCCC
Q 028027          130 IPPEHVHP  137 (215)
Q Consensus       130 a~~~~~~~  137 (215)
                      +.++...+
T Consensus        92 a~~~~~~~   99 (105)
T 2dh8_A           92 CTPRGMQP   99 (105)
T ss_dssp             SCCSSCCT
T ss_pred             ccCCCCCC
Confidence            98776543

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.82  E-value=2.2e-19  Score=124.61  Aligned_cols=83  Identities=16%  Similarity=0.241  Sum_probs=77.9

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 028027           49 LVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVH  128 (215)
Q Consensus        49 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~  128 (215)
                      +....++|||+|||+.+++++|+++|+.| .|..|.++.+ .+|.++|||||+|.+.++|..|+. |||..|+|+.|.|.
T Consensus         6 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~   82 (91)
T 2dgw_A            6 SGTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVF   82 (91)
T ss_dssp             CCCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEE
T ss_pred             CCCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEE
Confidence            34567899999999999999999999999 9999999999 699999999999999999999999 99999999999999


Q ss_pred             EeCCCC
Q 028027          129 LIPPEH  134 (215)
Q Consensus       129 ~a~~~~  134 (215)
                      ++.++.
T Consensus        83 ~a~~~~   88 (91)
T 2dgw_A           83 REKSGP   88 (91)
T ss_dssp             EESSCC
T ss_pred             ECCcCC
Confidence            998764

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens}

Probab=99.82  E-value=9.2e-20  Score=127.41  Aligned_cols=82  Identities=21%  Similarity=0.458  Sum_probs=77.2

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ....++|||+|||+.+++++|+++|++||.|..|.++.++ +|.++|||||+|.+.++|..|+..|||..|+|+.|.|.+
T Consensus        13 ~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   91 (95)
T 2ywk_A           13 EEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSG   91 (95)
T ss_dssp             TTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEE
Confidence            3567899999999999999999999999999999999997 599999999999999999999999999999999999999


Q ss_pred             eCC
Q 028027          130 IPP  132 (215)
Q Consensus       130 a~~  132 (215)
                      +..
T Consensus        92 a~~   94 (95)
T 2ywk_A           92 PSS   94 (95)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            753

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.82  E-value=3.2e-19  Score=126.60  Aligned_cols=85  Identities=20%  Similarity=0.359  Sum_probs=77.9

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ....++|||+|||+.+++++|+.+|++||.|..|.|+.++  +.++|||||+|.+.++|..|+..|||..|.|+.|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~--~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2cqi_A           12 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEH--TSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNW   89 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCC--CSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecC--CCCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEE
Confidence            4567999999999999999999999999999999999985  33689999999999999999999999999999999999


Q ss_pred             eCCCCCC
Q 028027          130 IPPEHVH  136 (215)
Q Consensus       130 a~~~~~~  136 (215)
                      +.+....
T Consensus        90 a~~~~~~   96 (103)
T 2cqi_A           90 ATTPSSQ   96 (103)
T ss_dssp             CCCTTCC
T ss_pred             CCCCccc
Confidence            9876543

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.82  E-value=4.1e-20  Score=131.80  Aligned_cols=79  Identities=18%  Similarity=0.229  Sum_probs=74.8

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ...++|||+|||+++|+++|+++|++||.|.+|.|++++. |.++|||||+|.+.++|..|+. ++|..|+|+.|.|.++
T Consensus         9 ~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~~   86 (103)
T 1s79_A            9 VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFK   86 (103)
T ss_dssp             SGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEc
Confidence            4568999999999999999999999999999999999985 9999999999999999999998 8999999999999986


Q ss_pred             C
Q 028027          131 P  131 (215)
Q Consensus       131 ~  131 (215)
                      .
T Consensus        87 ~   87 (103)
T 1s79_A           87 D   87 (103)
T ss_dssp             H
T ss_pred             h
Confidence            4

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=2.3e-20  Score=132.68  Aligned_cols=85  Identities=25%  Similarity=0.477  Sum_probs=80.0

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ...++|||+|||+.+++++|+.+|++||.|..|.++.++.+|.++|||||+|.+.++|..|+..|||..|+|+.|.|.++
T Consensus         6 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   85 (104)
T 1p1t_A            6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNA   85 (104)
T ss_dssp             HHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEET
T ss_pred             CCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeC
Confidence            45689999999999999999999999999999999999889999999999999999999999999999999999999998


Q ss_pred             CCCCC
Q 028027          131 PPEHV  135 (215)
Q Consensus       131 ~~~~~  135 (215)
                      .+...
T Consensus        86 ~~~~~   90 (104)
T 1p1t_A           86 ASEKN   90 (104)
T ss_dssp             TCTTH
T ss_pred             CCccc
Confidence            76543

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=3.7e-19  Score=126.29  Aligned_cols=85  Identities=25%  Similarity=0.441  Sum_probs=78.9

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ..+.++|||+|||+.+++++|+.+|++||.|..|.|+.++.+|.++|||||+|.+.++|..|+.  +++.|+|+.|.|.+
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~v~~   89 (103)
T 2cqg_A           12 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCKL   89 (103)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEEC
T ss_pred             cCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEEEEe
Confidence            4567899999999999999999999999999999999998899999999999999999999997  57899999999999


Q ss_pred             eCCCCCC
Q 028027          130 IPPEHVH  136 (215)
Q Consensus       130 a~~~~~~  136 (215)
                      +.++...
T Consensus        90 a~~~~~~   96 (103)
T 2cqg_A           90 PNSKQSQ   96 (103)
T ss_dssp             CCTTCCC
T ss_pred             cCCCCcC
Confidence            9886554

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X

Probab=99.81  E-value=2.6e-19  Score=136.43  Aligned_cols=87  Identities=22%  Similarity=0.308  Sum_probs=82.0

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ...++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|+.||..||+..|+|+.|.|.++
T Consensus        37 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  116 (156)
T 1h2v_Z           37 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD  116 (156)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            56799999999999999999999999999999999999989999999999999999999999999999999999999999


Q ss_pred             CCCCCCC
Q 028027          131 PPEHVHP  137 (215)
Q Consensus       131 ~~~~~~~  137 (215)
                      .+.....
T Consensus       117 ~~~~~~~  123 (156)
T 1h2v_Z          117 AGFKEGR  123 (156)
T ss_dssp             SCCCTTC
T ss_pred             CCCCCcC
Confidence            8765443

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.81  E-value=8.3e-20  Score=128.45  Aligned_cols=83  Identities=12%  Similarity=0.166  Sum_probs=78.1

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ...++|||+|||+.+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|+.|+..|||..|+|+.|+|.++
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a   92 (98)
T 2cqp_A           13 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   92 (98)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEc
Confidence            45689999999999999999999999999998888888889999999999999999999999999999999999999998


Q ss_pred             CCC
Q 028027          131 PPE  133 (215)
Q Consensus       131 ~~~  133 (215)
                      ...
T Consensus        93 ~~~   95 (98)
T 2cqp_A           93 SGP   95 (98)
T ss_dssp             SCS
T ss_pred             CCC
Confidence            754

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.81  E-value=3.5e-20  Score=138.40  Aligned_cols=90  Identities=26%  Similarity=0.377  Sum_probs=83.2

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEE
Q 028027           48 PLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQV  127 (215)
Q Consensus        48 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V  127 (215)
                      ++....++|||+|||+.+++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|+.|+..|||..|+|+.|.|
T Consensus        42 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V  121 (135)
T 2lea_A           42 PDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRV  121 (135)
T ss_dssp             SSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            34456789999999999999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             EEeCCCCCCC
Q 028027          128 HLIPPEHVHP  137 (215)
Q Consensus       128 ~~a~~~~~~~  137 (215)
                      .++.+.....
T Consensus       122 ~~a~~~~~~~  131 (135)
T 2lea_A          122 QMARYGRPPD  131 (135)
T ss_dssp             EECCCCCCCT
T ss_pred             EECCCCCCCc
Confidence            9998765543

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=4e-20  Score=133.73  Aligned_cols=82  Identities=18%  Similarity=0.399  Sum_probs=77.9

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ...++|||+|||+.+++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|+.|+ .|||..|+|+.|.|.++
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a  101 (114)
T 2cq4_A           23 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQAS  101 (114)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEec
Confidence            45689999999999999999999999999999999999988999999999999999999999 99999999999999998


Q ss_pred             CCC
Q 028027          131 PPE  133 (215)
Q Consensus       131 ~~~  133 (215)
                      .+.
T Consensus       102 ~~~  104 (114)
T 2cq4_A          102 QAE  104 (114)
T ss_dssp             HHH
T ss_pred             CCC
Confidence            654

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=99.81  E-value=2e-19  Score=137.20  Aligned_cols=87  Identities=25%  Similarity=0.379  Sum_probs=81.7

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ....++|||+|||+++++++|+++|++||.|..|.++.++.+|.++|||||+|.+.++|..|+..|||..|+|+.|.|.+
T Consensus        67 ~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  146 (158)
T 2kn4_A           67 VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQM  146 (158)
T ss_dssp             CCBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            35578999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             eCCCCCC
Q 028027          130 IPPEHVH  136 (215)
Q Consensus       130 a~~~~~~  136 (215)
                      +.+....
T Consensus       147 a~~~~~~  153 (158)
T 2kn4_A          147 ARYGRPP  153 (158)
T ss_dssp             ECCSSCC
T ss_pred             CCCCCCC
Confidence            9876544

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=1.7e-19  Score=130.85  Aligned_cols=86  Identities=15%  Similarity=0.322  Sum_probs=80.4

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ...++|||+|||+.+++++|+.+|++||.|..|.|+.++.+|.++|||||+|.+.++|..||.. ++..|+|+.|.|.++
T Consensus        25 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a  103 (116)
T 1x4b_A           25 EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRA  103 (116)
T ss_dssp             HHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEEC
Confidence            4568999999999999999999999999999999999988999999999999999999999987 999999999999999


Q ss_pred             CCCCCCC
Q 028027          131 PPEHVHP  137 (215)
Q Consensus       131 ~~~~~~~  137 (215)
                      .++....
T Consensus       104 ~~~~~~~  110 (116)
T 1x4b_A          104 VAREESG  110 (116)
T ss_dssp             SSCCCCC
T ss_pred             CCCccCC
Confidence            8876543

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens}

Probab=99.81  E-value=3.8e-20  Score=131.00  Aligned_cols=84  Identities=19%  Similarity=0.369  Sum_probs=75.6

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecC-CCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEE
Q 028027           49 LVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNK-KTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQV  127 (215)
Q Consensus        49 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~-~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V  127 (215)
                      .....++|||+|||+++++++|+++|+.|| |..|.++.++ .+|.++|||||+|.+.++|..|+ .|||..|+|+.|.|
T Consensus        15 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V   92 (100)
T 2j76_E           15 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRV   92 (100)
T ss_dssp             -----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEEE
Confidence            346779999999999999999999999999 9999999997 58999999999999999999999 89999999999999


Q ss_pred             EEeCCCC
Q 028027          128 HLIPPEH  134 (215)
Q Consensus       128 ~~a~~~~  134 (215)
                      .++.++.
T Consensus        93 ~~a~~~~   99 (100)
T 2j76_E           93 DVADQAQ   99 (100)
T ss_dssp             EECCCSC
T ss_pred             EeccCCC
Confidence            9997753

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.81  E-value=3.2e-19  Score=130.89  Aligned_cols=87  Identities=17%  Similarity=0.311  Sum_probs=81.5

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 028027           49 LVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVH  128 (215)
Q Consensus        49 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~  128 (215)
                      .....++|||+|||+.+++++|+++|+.||.|..|.++.+. +|.++|||||+|.+.++|..|+..|||..|+|+.|.|.
T Consensus        31 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  109 (124)
T 2kt5_A           31 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQ  109 (124)
T ss_dssp             CCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            34667899999999999999999999999999999999998 99999999999999999999999999999999999999


Q ss_pred             EeCCCCCC
Q 028027          129 LIPPEHVH  136 (215)
Q Consensus       129 ~a~~~~~~  136 (215)
                      ++.+....
T Consensus       110 ~a~~~~~~  117 (124)
T 2kt5_A          110 LVASQIDL  117 (124)
T ss_dssp             EECCTTCC
T ss_pred             EeCCCCCC
Confidence            99876554

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.81  E-value=7.1e-20  Score=135.84  Aligned_cols=86  Identities=10%  Similarity=0.219  Sum_probs=79.9

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeE--EEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCc----eeCCe
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKR--LRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGY----LLFEH  123 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~--v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~----~l~g~  123 (215)
                      ....++|||+|||+++++++|+++|++||.|..  |+|++++.+|.++|||||+|.+. +|..|+..|||.    .|+|+
T Consensus        20 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr   98 (131)
T 2m2b_A           20 ENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGK   98 (131)
T ss_dssp             SCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCE
Confidence            356789999999999999999999999999976  99999999999999999999999 999999999999    99999


Q ss_pred             EEEEEEeCCCCCC
Q 028027          124 ILQVHLIPPEHVH  136 (215)
Q Consensus       124 ~l~V~~a~~~~~~  136 (215)
                      .|.|.++.+....
T Consensus        99 ~l~V~~a~~~~~~  111 (131)
T 2m2b_A           99 TINVEFAKGSKRD  111 (131)
T ss_dssp             CCCCEECCCSCCC
T ss_pred             EEEEEECCCCCCC
Confidence            9999999876443

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=6.9e-19  Score=127.13  Aligned_cols=84  Identities=26%  Similarity=0.468  Sum_probs=78.3

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCcee--------
Q 028027           49 LVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLL--------  120 (215)
Q Consensus        49 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l--------  120 (215)
                      ...+.++|||+|||+.+++++|+++|++||.|..|.|+.++ +|.++|||||+|.+.++|..|+..|||..|        
T Consensus        21 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~   99 (114)
T 1x5o_A           21 QEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSA   99 (114)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccC
Confidence            34567999999999999999999999999999999999998 999999999999999999999999999999        


Q ss_pred             CCeEEEEEEeCCC
Q 028027          121 FEHILQVHLIPPE  133 (215)
Q Consensus       121 ~g~~l~V~~a~~~  133 (215)
                      .++.|.|.|+.+.
T Consensus       100 ~~~~l~v~~a~p~  112 (114)
T 1x5o_A          100 PTEPLLCKFSGPS  112 (114)
T ss_dssp             CSSCBEEEECCCS
T ss_pred             CCCceeEEccCCC
Confidence            5788999999764

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=2.7e-20  Score=127.61  Aligned_cols=80  Identities=19%  Similarity=0.368  Sum_probs=75.6

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      .++++|||+|||+++++++|+.+|++||.|..|.++.++.+|.++|||||+|.+.++|..|+..|||..|+|+.|+|.+.
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~   82 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGP   82 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCC
Confidence            46789999999999999999999999999999999999889999999999999999999999999999999999887654

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.81  E-value=1.1e-19  Score=133.34  Aligned_cols=83  Identities=23%  Similarity=0.425  Sum_probs=78.4

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ...++|||+|||+++++++|+++|++||.|..|.++.++.+|.++|||||+|.+.++|..|+ .|||..|+|+.|.|.++
T Consensus        34 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a  112 (124)
T 2jwn_A           34 IDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPK  112 (124)
T ss_dssp             HHHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEEC
Confidence            35689999999999999999999999999999999999889999999999999999999999 89999999999999998


Q ss_pred             CCCC
Q 028027          131 PPEH  134 (215)
Q Consensus       131 ~~~~  134 (215)
                      .+..
T Consensus       113 ~~~~  116 (124)
T 2jwn_A          113 RTNM  116 (124)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            7653

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=9.5e-19  Score=125.46  Aligned_cols=85  Identities=25%  Similarity=0.425  Sum_probs=77.1

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ....++|||+|||+.+++++|+++|++||.|..|.+..   ++.++|||||+|.+.++|+.|+..||+..|+|+.|.|.+
T Consensus        19 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   95 (109)
T 1x4a_A           19 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN---RRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEF   95 (109)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECC---SSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEE---CCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            35678999999999999999999999999999999954   456899999999999999999999999999999999999


Q ss_pred             eCCCCCCC
Q 028027          130 IPPEHVHP  137 (215)
Q Consensus       130 a~~~~~~~  137 (215)
                      +.+.....
T Consensus        96 a~~~~~~~  103 (109)
T 1x4a_A           96 PRSGRGTG  103 (109)
T ss_dssp             CCCCCCCC
T ss_pred             cccCCCCC
Confidence            98865543

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A

Probab=99.81  E-value=7.5e-20  Score=127.88  Aligned_cols=82  Identities=12%  Similarity=0.160  Sum_probs=75.9

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ...++|||+|||+.+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|+.|+..||+..|+|+.|+|.++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a   92 (95)
T 2ek1_A           13 PGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGP   92 (95)
T ss_dssp             --CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEec
Confidence            44689999999999999999999999999999988888889999999999999999999999999999999999999987


Q ss_pred             CC
Q 028027          131 PP  132 (215)
Q Consensus       131 ~~  132 (215)
                      .+
T Consensus        93 ~s   94 (95)
T 2ek1_A           93 SS   94 (95)
T ss_dssp             C-
T ss_pred             cC
Confidence            53

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A

Probab=99.80  E-value=2.5e-19  Score=137.99  Aligned_cols=87  Identities=22%  Similarity=0.384  Sum_probs=80.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ..+.++|||+|||+.+++++|+.+|++||.|..|.|+.++.+|.++|||||+|.+.++|..||..|||..|.|+.|.|.|
T Consensus        69 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  148 (165)
T 1rk8_A           69 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW  148 (165)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            35678999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             eCCCCCC
Q 028027          130 IPPEHVH  136 (215)
Q Consensus       130 a~~~~~~  136 (215)
                      +.+....
T Consensus       149 a~~~~~~  155 (165)
T 1rk8_A          149 CFVKGPK  155 (165)
T ss_dssp             SEECC--
T ss_pred             ecCCCCC
Confidence            9776543

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=2.8e-19  Score=128.54  Aligned_cols=84  Identities=25%  Similarity=0.456  Sum_probs=77.7

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEE
Q 028027           48 PLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQV  127 (215)
Q Consensus        48 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V  127 (215)
                      ......++|||+|||..+++++|+++|++||.|..|.++.+.  +.++|||||+|.+.++|+.|+..|||..|+|+.|.|
T Consensus        24 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V  101 (109)
T 2err_A           24 ENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEV  101 (109)
T ss_dssp             SCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEE
T ss_pred             cCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            344678999999999999999999999999999999999884  458999999999999999999999999999999999


Q ss_pred             EEeCCC
Q 028027          128 HLIPPE  133 (215)
Q Consensus       128 ~~a~~~  133 (215)
                      .++.++
T Consensus       102 ~~a~~~  107 (109)
T 2err_A          102 NNATAR  107 (109)
T ss_dssp             EECCCS
T ss_pred             EECCCC
Confidence            999765

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.80  E-value=5.3e-20  Score=123.18  Aligned_cols=75  Identities=19%  Similarity=0.464  Sum_probs=71.9

Q ss_pred             EEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           55 VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        55 ~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      +|||+|||+++++++|+++|++||.|..|.++.++.+|.++|||||+|.+.++|+.|+. |||..++|+.|.|.+|
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECCEEEEEEeC
Confidence            48999999999999999999999999999999998899999999999999999999997 9999999999999875

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.80  E-value=3e-20  Score=131.52  Aligned_cols=85  Identities=18%  Similarity=0.298  Sum_probs=77.1

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ....++|||+|||+++++++|+.+|++||.|.. .++.+..+|.++|||||+|.+.++|+.|+. |||..|.|+.|.|.+
T Consensus        14 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~   91 (101)
T 1fj7_A           14 STTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEK   91 (101)
T ss_dssp             CSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEE
Confidence            346789999999999999999999999999888 666666789999999999999999999998 999999999999999


Q ss_pred             eCCCCCC
Q 028027          130 IPPEHVH  136 (215)
Q Consensus       130 a~~~~~~  136 (215)
                      +.++...
T Consensus        92 a~~~~~~   98 (101)
T 1fj7_A           92 PKGRDGT   98 (101)
T ss_dssp             CSCCCCS
T ss_pred             cCCCCCC
Confidence            9876554

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.80  E-value=2.9e-19  Score=127.57  Aligned_cols=81  Identities=22%  Similarity=0.390  Sum_probs=75.1

Q ss_pred             CCCcEEEEcCCCCCC------cHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCe-
Q 028027           51 NKATVLYIGRIPHGF------YEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEH-  123 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~------te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~-  123 (215)
                      ...++|||+|||+.+      ++++|+.+|++||.|..|.+++  .+|.++|||||+|.+.++|..|+..|||..|+|+ 
T Consensus        13 ~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~--~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~   90 (105)
T 2nlw_A           13 GIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE--EDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQH   90 (105)
T ss_dssp             SCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCC--BTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTC
T ss_pred             CCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeC--CCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCc
Confidence            456899999999999      8899999999999999999883  5899999999999999999999999999999998 


Q ss_pred             EEEEEEeCCC
Q 028027          124 ILQVHLIPPE  133 (215)
Q Consensus       124 ~l~V~~a~~~  133 (215)
                      .|.|.++.+.
T Consensus        91 ~l~V~~a~~~  100 (105)
T 2nlw_A           91 TFRVNLFTDF  100 (105)
T ss_dssp             EEEEECSCCC
T ss_pred             eEEEEEcchH
Confidence            9999998754

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=2.3e-19  Score=128.53  Aligned_cols=86  Identities=17%  Similarity=0.281  Sum_probs=79.4

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCC-eeEEEEe-ecCCCCCcccEEEEEEcCHHHHHHHHHHhC--CceeCCeEEE
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGA-IKRLRIA-RNKKTGQSKHFGFIEFNDPEVAEVVADAMH--GYLLFEHILQ  126 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~-v~~v~i~-~~~~tg~~~g~afV~F~~~~~a~~ai~~l~--g~~l~g~~l~  126 (215)
                      .+.++|||+|||+.+++++|+++|++||. |..|.++ .+..+|.++|||||+|.+.++|..|+..|+  +..++|+.|.
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~   85 (109)
T 2dis_A            6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIA   85 (109)
T ss_dssp             CCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCE
T ss_pred             cCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEE
Confidence            45689999999999999999999999998 9999998 788889999999999999999999999996  5899999999


Q ss_pred             EEEeCCCCCC
Q 028027          127 VHLIPPEHVH  136 (215)
Q Consensus       127 V~~a~~~~~~  136 (215)
                      |.++.+....
T Consensus        86 V~~a~~~~~~   95 (109)
T 2dis_A           86 VDWAEPEIDV   95 (109)
T ss_dssp             EEESCSSCST
T ss_pred             EEEcCCCCCc
Confidence            9999886553

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori}

Probab=99.79  E-value=2.7e-20  Score=128.93  Aligned_cols=82  Identities=18%  Similarity=0.413  Sum_probs=74.2

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeCCC
Q 028027           54 TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPPE  133 (215)
Q Consensus        54 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~~~  133 (215)
                      ++|||+|||+++++++|+++|++||.|..|.++.++.+|.++|||||+|.+.+ |..|+..|||..++|+.|.|.++.+.
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~~   80 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANPK   80 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC---
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCCC
Confidence            68999999999999999999999999999999999889999999999999999 99999999999999999999999876


Q ss_pred             CCC
Q 028027          134 HVH  136 (215)
Q Consensus       134 ~~~  136 (215)
                      ...
T Consensus        81 ~~~   83 (90)
T 2ki2_A           81 KSL   83 (90)
T ss_dssp             ---
T ss_pred             CCC
Confidence            443

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=5.5e-19  Score=125.90  Aligned_cols=85  Identities=18%  Similarity=0.304  Sum_probs=77.7

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeE-EEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEE
Q 028027           49 LVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKR-LRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQV  127 (215)
Q Consensus        49 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~-v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V  127 (215)
                      +....++|||+|||+.+++++|+++|++||.|.. |.|+.+ .+|+++|||||+|.+.++|+.||.. |+..|+|+.|.|
T Consensus        11 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v   88 (104)
T 1wg5_A           11 DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEI   88 (104)
T ss_dssp             SCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEE
Confidence            3456789999999999999999999999999987 889888 6999999999999999999999987 999999999999


Q ss_pred             EEeCCCCC
Q 028027          128 HLIPPEHV  135 (215)
Q Consensus       128 ~~a~~~~~  135 (215)
                      .++.+...
T Consensus        89 ~~~~~~~~   96 (104)
T 1wg5_A           89 FKSSRAEV   96 (104)
T ss_dssp             EEECTTTS
T ss_pred             EECCHHHH
Confidence            99876543

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.79  E-value=4.4e-19  Score=132.35  Aligned_cols=82  Identities=29%  Similarity=0.483  Sum_probs=77.5

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 028027           49 LVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVH  128 (215)
Q Consensus        49 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~  128 (215)
                      ...+.++|||+|||+.+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|..|+..|||..|+|+.|+|.
T Consensus        59 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  138 (140)
T 2ku7_A           59 SATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN  138 (140)
T ss_dssp             SCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEE
T ss_pred             CCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34678999999999999999999999999999999999998899999999999999999999999999999999999998


Q ss_pred             Ee
Q 028027          129 LI  130 (215)
Q Consensus       129 ~a  130 (215)
                      +|
T Consensus       139 ~A  140 (140)
T 2ku7_A          139 LA  140 (140)
T ss_dssp             C-
T ss_pred             eC
Confidence            75

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.79  E-value=8.4e-20  Score=122.64  Aligned_cols=76  Identities=22%  Similarity=0.412  Sum_probs=73.1

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           54 TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        54 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ++|||+|||+++++++|+.+|++||.|..+.++.++.+|.++|||||+|.+.++|..|+..++ ..++|+.|.|.+|
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a   76 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            479999999999999999999999999999999998899999999999999999999999999 9999999999986

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.79  E-value=2.4e-19  Score=129.25  Aligned_cols=84  Identities=12%  Similarity=0.256  Sum_probs=77.3

Q ss_pred             CCCcEEEEcCCCCCCcHHHHH---HHhccCCCeeEEEEeecCCCC---CcccEEEEEEcCHHHHHHHHHHhCCceeCCeE
Q 028027           51 NKATVLYIGRIPHGFYEKEMQ---AFFSQFGAIKRLRIARNKKTG---QSKHFGFIEFNDPEVAEVVADAMHGYLLFEHI  124 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~---~~F~~~G~v~~v~i~~~~~tg---~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~  124 (215)
                      ...++|||+|||+.+++++|+   ++|++||.|..|.++.+..++   .++|||||+|.+.++|+.|+..|||..|+|+.
T Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~   92 (111)
T 2cpi_A           13 VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRT   92 (111)
T ss_dssp             CCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCEE
Confidence            446789999999999999999   999999999999999887654   55699999999999999999999999999999


Q ss_pred             EEEEEeCCCC
Q 028027          125 LQVHLIPPEH  134 (215)
Q Consensus       125 l~V~~a~~~~  134 (215)
                      |.|.++.++.
T Consensus        93 l~V~~a~~k~  102 (111)
T 2cpi_A           93 LKASLGTTKY  102 (111)
T ss_dssp             EEEESCCCCS
T ss_pred             EEEEeccccc
Confidence            9999998775

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=3e-19  Score=127.40  Aligned_cols=80  Identities=20%  Similarity=0.309  Sum_probs=73.0

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCC--ceeCCeEEEEE
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHG--YLLFEHILQVH  128 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g--~~l~g~~l~V~  128 (215)
                      .+.++|||+|||+.+++++|+++|++||.|.+|.|+++      +|||||+|.+.++|..|+..|++  ..|.|+.|.|.
T Consensus        14 ~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~   87 (105)
T 1sjq_A           14 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQ   87 (105)
T ss_dssp             CCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEE
Confidence            56789999999999999999999999999999999875      59999999999999999998864  78999999999


Q ss_pred             EeCCCCCC
Q 028027          129 LIPPEHVH  136 (215)
Q Consensus       129 ~a~~~~~~  136 (215)
                      ++.++...
T Consensus        88 ~A~~~~~~   95 (105)
T 1sjq_A           88 FSNHKELK   95 (105)
T ss_dssp             CCSSSSCC
T ss_pred             EcCCCCCC
Confidence            99876554

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.79  E-value=1.3e-18  Score=127.31  Aligned_cols=77  Identities=12%  Similarity=0.231  Sum_probs=70.6

Q ss_pred             cEEEEcCC----CCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcC----HHH----HHHHHH--HhCCce
Q 028027           54 TVLYIGRI----PHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFND----PEV----AEVVAD--AMHGYL  119 (215)
Q Consensus        54 ~~l~V~nL----p~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~----~~~----a~~ai~--~l~g~~  119 (215)
                      ..|||+||    |+.+++.+|+.+|++||+|.+|.++.|+.||.++|||||+|.+    .+.    |..|+.  .|||..
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~   82 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCF   82 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCe
Confidence            68999999    9999999999999999999999999999999999999999996    322    788888  789999


Q ss_pred             eCCeEEEEEEe
Q 028027          120 LFEHILQVHLI  130 (215)
Q Consensus       120 l~g~~l~V~~a  130 (215)
                      |+|+.|+|.+-
T Consensus        83 I~Gr~irV~ln   93 (136)
T 2j8a_A           83 IMGFKFEVILN   93 (136)
T ss_dssp             ETTEEEEEEEC
T ss_pred             ecCcEEEEEEC
Confidence            99999999985

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=7.9e-19  Score=128.07  Aligned_cols=82  Identities=20%  Similarity=0.289  Sum_probs=74.2

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCC--ceeCCeEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHG--YLLFEHILQV  127 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g--~~l~g~~l~V  127 (215)
                      ..++++|||+|||+.+++++|+++|++||.|.+|.|+.+      +|||||+|.+.++|..|+..|++  ..|.|+.|.|
T Consensus        28 ~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V  101 (119)
T 2ad9_A           28 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYI  101 (119)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEE
Confidence            356789999999999999999999999999999999876      59999999999999999998874  6899999999


Q ss_pred             EEeCCCCCCC
Q 028027          128 HLIPPEHVHP  137 (215)
Q Consensus       128 ~~a~~~~~~~  137 (215)
                      .++.++....
T Consensus       102 ~~a~~k~~~~  111 (119)
T 2ad9_A          102 QFSNHKELKT  111 (119)
T ss_dssp             EECSSSSCCC
T ss_pred             EEccCCCCCc
Confidence            9998766553

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=2.1e-19  Score=131.96  Aligned_cols=84  Identities=18%  Similarity=0.272  Sum_probs=76.2

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEE
Q 028027           48 PLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQV  127 (215)
Q Consensus        48 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V  127 (215)
                      .+....++|||+|||+.+++++|+.+|+.||.|..+.++.+..+|.++|||||+|.+.++|..||. |||..|+|+.|.|
T Consensus        20 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V   98 (124)
T 1wel_A           20 SPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQV   98 (124)
T ss_dssp             SCCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEE
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEE
Confidence            345677999999999999999999999999999886666666699999999999999999999998 9999999999999


Q ss_pred             EEeCC
Q 028027          128 HLIPP  132 (215)
Q Consensus       128 ~~a~~  132 (215)
                      .++.+
T Consensus        99 ~~a~~  103 (124)
T 1wel_A           99 HPITK  103 (124)
T ss_dssp             EEECH
T ss_pred             EECCH
Confidence            99854

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=2e-18  Score=122.54  Aligned_cols=80  Identities=19%  Similarity=0.262  Sum_probs=72.4

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHh--CCceeCCeEEEEE
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM--HGYLLFEHILQVH  128 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l--~g~~l~g~~l~V~  128 (215)
                      .+.++|||+|||+.+++++|+.+|++||.|..|.++.+      +|||||+|.+.++|..|+..|  ++..|.|+.|.|.
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~   86 (101)
T 2cq1_A           13 APSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQ   86 (101)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEE
Confidence            56789999999999999999999999999999988865      699999999999999999977  4678999999999


Q ss_pred             EeCCCCCC
Q 028027          129 LIPPEHVH  136 (215)
Q Consensus       129 ~a~~~~~~  136 (215)
                      ++.++...
T Consensus        87 ~a~~~~~~   94 (101)
T 2cq1_A           87 YSNHKELK   94 (101)
T ss_dssp             ECSCSSCC
T ss_pred             EcCcccCc
Confidence            99876554

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=1.8e-18  Score=122.24  Aligned_cols=81  Identities=21%  Similarity=0.341  Sum_probs=74.4

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      .+.++|||+|||+.+++++|+++|++||.|   .++.+ .+|.++|||||+|.+.++|+.|+..||+..|.|+.|.|.++
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   88 (101)
T 2fc9_A           13 GESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQ   88 (101)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEc
Confidence            567999999999999999999999999987   56666 58999999999999999999999999999999999999999


Q ss_pred             CCCCC
Q 028027          131 PPEHV  135 (215)
Q Consensus       131 ~~~~~  135 (215)
                      .+...
T Consensus        89 ~~~~~   93 (101)
T 2fc9_A           89 GPRGS   93 (101)
T ss_dssp             SSCCC
T ss_pred             CCCCC
Confidence            87644

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=1e-18  Score=124.27  Aligned_cols=82  Identities=17%  Similarity=0.218  Sum_probs=75.5

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ...++|||+|||+.+++++|+++|++||.+ .|.|+.++ +|+++|||||+|.+.++|+.|| .+|+..|+|+.|.|.++
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~~   89 (102)
T 1wez_A           13 TTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGP-DGRVTGEADVEFATHEDAVAAM-AKDKANMQHRYVELFLN   89 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESS-SSCEEEEEEEECSSSHHHHHHH-TTSSCCSSSSCCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECC-CCCEeeEEEEEECCHHHHHHHH-HhCCCeECCcEEEEEEC
Confidence            456899999999999999999999999955 99999997 9999999999999999999999 57999999999999998


Q ss_pred             CCCCC
Q 028027          131 PPEHV  135 (215)
Q Consensus       131 ~~~~~  135 (215)
                      .+...
T Consensus        90 ~~~~~   94 (102)
T 1wez_A           90 STAGT   94 (102)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            76553

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=2.1e-18  Score=122.01  Aligned_cols=84  Identities=24%  Similarity=0.379  Sum_probs=76.9

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ....++|||+|||+.+++++|+++|+.|+   .|.++.++.++.++|||||+|.+.++|..|+..|||..|.|+.|.|.+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   88 (102)
T 2fc8_A           12 SQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDW   88 (102)
T ss_dssp             SCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            45678999999999999999999999874   677888888999999999999999999999999999999999999999


Q ss_pred             eCCCCCC
Q 028027          130 IPPEHVH  136 (215)
Q Consensus       130 a~~~~~~  136 (215)
                      +.++...
T Consensus        89 a~~~~~~   95 (102)
T 2fc8_A           89 AKPKGEG   95 (102)
T ss_dssp             CCCCCSS
T ss_pred             ecCCCCC
Confidence            9887654

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=2.8e-19  Score=129.34  Aligned_cols=88  Identities=23%  Similarity=0.369  Sum_probs=75.4

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ..+.++|||+|||+.+++++|+++|++||.|..+.+..+..+|.++|||||+|.+.++|..|+..|||..|+|+.|.|.+
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~  101 (115)
T 2cpx_A           22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF  101 (115)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            35678999999999999999999999999984432222222788999999999999999999999999999999999999


Q ss_pred             eCCCCCCC
Q 028027          130 IPPEHVHP  137 (215)
Q Consensus       130 a~~~~~~~  137 (215)
                      +.+.....
T Consensus       102 a~~~~~~~  109 (115)
T 2cpx_A          102 GKNKKQRS  109 (115)
T ss_dssp             CCCCSCCC
T ss_pred             ccCCCCCC
Confidence            98865543

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=3.6e-19  Score=128.90  Aligned_cols=82  Identities=16%  Similarity=0.217  Sum_probs=77.0

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCe-eEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAI-KRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v-~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      .+.++|||+|||+.+++++|+++|+.||.| ..|.|+.++ +|.++|||||+|.+.++|+.||.. |+..|+|+.|.|.+
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~~   90 (114)
T 2cpy_A           13 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVHV   90 (114)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEEE
T ss_pred             CCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEEE
Confidence            567899999999999999999999999999 899999998 999999999999999999999976 99999999999999


Q ss_pred             eCCCC
Q 028027          130 IPPEH  134 (215)
Q Consensus       130 a~~~~  134 (215)
                      +.+..
T Consensus        91 a~~~~   95 (114)
T 2cpy_A           91 VTLED   95 (114)
T ss_dssp             ECHHH
T ss_pred             CCHHH
Confidence            87653

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.78  E-value=2e-18  Score=119.53  Aligned_cols=80  Identities=25%  Similarity=0.458  Sum_probs=73.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ..+.++|||+|||+++++++|+++|++||.|..|.++        +|||||+|.+.++|+.|+..|||..|+|+.|+|.+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   76 (90)
T 2dnq_A            5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEA   76 (90)
T ss_dssp             SSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEC
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEE
Confidence            3567999999999999999999999999999999987        47999999999999999999999999999999999


Q ss_pred             eCCCCCCC
Q 028027          130 IPPEHVHP  137 (215)
Q Consensus       130 a~~~~~~~  137 (215)
                      +.+.....
T Consensus        77 a~~~~~~~   84 (90)
T 2dnq_A           77 SKNKSKAS   84 (90)
T ss_dssp             SSCCCCCC
T ss_pred             CCCCCCCC
Confidence            98866543

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.78  E-value=1.1e-18  Score=127.18  Aligned_cols=82  Identities=11%  Similarity=0.174  Sum_probs=76.4

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhccCCC---eeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEE
Q 028027           49 LVNKATVLYIGRIPHGFYEKEMQAFFSQFGA---IKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHIL  125 (215)
Q Consensus        49 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~---v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l  125 (215)
                      +....++|||+|||+++|+++|+++|+.||.   |..|.|+.++. |+++|||||+|.+.++|+.||. ||+..|+|+.|
T Consensus        13 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i   90 (118)
T 2db1_A           13 EGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALK-KDRESMGHRYI   90 (118)
T ss_dssp             CBCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEE
Confidence            3456789999999999999999999999999   89999999974 9999999999999999999998 99999999999


Q ss_pred             EEEEeCC
Q 028027          126 QVHLIPP  132 (215)
Q Consensus       126 ~V~~a~~  132 (215)
                      .|.++.+
T Consensus        91 ~V~~a~~   97 (118)
T 2db1_A           91 EVFKSHR   97 (118)
T ss_dssp             EEEEECH
T ss_pred             EEEECCH
Confidence            9999854

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.78  E-value=2.8e-18  Score=122.99  Aligned_cols=80  Identities=11%  Similarity=0.160  Sum_probs=74.2

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCC-----eE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFE-----HI  124 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g-----~~  124 (215)
                      ....++|||+|||+++++++|+++|++||.|..|.|+.+       |||||+|.+.++|+.||..|||..|.|     +.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~   84 (108)
T 1x4c_A           12 RRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAY   84 (108)
T ss_dssp             CSCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceE
Confidence            356789999999999999999999999999999999876       799999999999999999999999999     99


Q ss_pred             EEEEEeCCCCCC
Q 028027          125 LQVHLIPPEHVH  136 (215)
Q Consensus       125 l~V~~a~~~~~~  136 (215)
                      |.|.++.++...
T Consensus        85 i~V~~a~~~~~~   96 (108)
T 1x4c_A           85 IRVKVDGPRSPS   96 (108)
T ss_dssp             EEEEESSCCSCC
T ss_pred             EEEEeCCCCCCC
Confidence            999999886544

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.78  E-value=5.6e-19  Score=121.24  Aligned_cols=75  Identities=9%  Similarity=0.115  Sum_probs=70.2

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ..+..|||+||++.+|+++|+++|.+||+|.++++..      ++|||||+|.+.++|..|++.||+..++|+.|+|.+|
T Consensus         5 ~~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A   78 (89)
T 2wbr_A            5 WGSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESP   78 (89)
T ss_dssp             CCCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECC
T ss_pred             CccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEEC
Confidence            3567899999999999999999999999999999865      5799999999999999999999999999999999998


Q ss_pred             C
Q 028027          131 P  131 (215)
Q Consensus       131 ~  131 (215)
                      .
T Consensus        79 ~   79 (89)
T 2wbr_A           79 S   79 (89)
T ss_dssp             C
T ss_pred             C
Confidence            3

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.78  E-value=1.6e-18  Score=122.46  Aligned_cols=78  Identities=18%  Similarity=0.221  Sum_probs=71.5

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCce--eCCeEEEEE
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYL--LFEHILQVH  128 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~--l~g~~l~V~  128 (215)
                      .++++|||+|||+.+++++|+++|++||.|.+|.++++      +|||||+|.+.++|..|+..|++..  |.|+.|.|.
T Consensus        19 ~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~------kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~   92 (100)
T 3r27_A           19 PASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVN   92 (100)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEE
Confidence            56789999999999999999999999999999999854      5899999999999999999999875  889999999


Q ss_pred             EeCCCC
Q 028027          129 LIPPEH  134 (215)
Q Consensus       129 ~a~~~~  134 (215)
                      +++++.
T Consensus        93 ~S~~k~   98 (100)
T 3r27_A           93 YSTSQK   98 (100)
T ss_dssp             ECSCSC
T ss_pred             eccccc
Confidence            998754

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.78  E-value=8.5e-19  Score=129.52  Aligned_cols=82  Identities=20%  Similarity=0.287  Sum_probs=73.9

Q ss_pred             CCCcEEEEcCCCCCCcHHHHH----HHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEE
Q 028027           51 NKATVLYIGRIPHGFYEKEMQ----AFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQ  126 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~----~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~  126 (215)
                      .+.++|||+|||+.+++++|+    ++|++||.|.+|.+..   +|.++|||||+|.+.++|..|+..|||..|.|+.|.
T Consensus        27 ~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~---~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~  103 (127)
T 2a3j_A           27 EPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLV  103 (127)
T ss_dssp             SCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC---CCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc---CCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEE
Confidence            456899999999999999876    6999999999987743   788999999999999999999999999999999999


Q ss_pred             EEEeCCCCC
Q 028027          127 VHLIPPEHV  135 (215)
Q Consensus       127 V~~a~~~~~  135 (215)
                      |.|+.++..
T Consensus       104 V~~a~~~~~  112 (127)
T 2a3j_A          104 ITFSETPQS  112 (127)
T ss_dssp             EEECCCCCH
T ss_pred             EEEccCcch
Confidence            999987643

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.78  E-value=2.8e-18  Score=120.49  Aligned_cols=79  Identities=20%  Similarity=0.411  Sum_probs=72.9

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeC--CeEEEEE
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLF--EHILQVH  128 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~--g~~l~V~  128 (215)
                      .+.++|||+|||+.+++++|+++|++||.|..|.+..+      +|||||+|.+.++|+.|+..|||..|.  |+.|.|.
T Consensus        15 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~   88 (97)
T 1why_A           15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVD   88 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEE
Confidence            45689999999999999999999999999999998754      589999999999999999999999999  9999999


Q ss_pred             EeCCCCC
Q 028027          129 LIPPEHV  135 (215)
Q Consensus       129 ~a~~~~~  135 (215)
                      ++.++..
T Consensus        89 ~a~~~~~   95 (97)
T 1why_A           89 FAKSGPS   95 (97)
T ss_dssp             ECCCCCC
T ss_pred             ECCCCCC
Confidence            9987643

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A

Probab=99.78  E-value=4.5e-19  Score=132.49  Aligned_cols=83  Identities=12%  Similarity=0.186  Sum_probs=77.1

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhccCCC---eeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeE
Q 028027           48 PLVNKATVLYIGRIPHGFYEKEMQAFFSQFGA---IKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHI  124 (215)
Q Consensus        48 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~---v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~  124 (215)
                      ++....++|||+|||+++|+++|+++|++||.   |..|.|++++. |+++|||||+|.+.++|+.||. ||+..|+|+.
T Consensus        39 ~~~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~  116 (136)
T 2hgl_A           39 PEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRESMGHRY  116 (136)
T ss_dssp             SSCCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHT-TTEEESSSSE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCEECCEE
Confidence            44567899999999999999999999999999   89999999985 9999999999999999999998 9999999999


Q ss_pred             EEEEEeCC
Q 028027          125 LQVHLIPP  132 (215)
Q Consensus       125 l~V~~a~~  132 (215)
                      |.|.++.+
T Consensus       117 i~V~~a~~  124 (136)
T 2hgl_A          117 IEVFKSHR  124 (136)
T ss_dssp             EEEEECCH
T ss_pred             EEEEECCh
Confidence            99998753

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ...

Probab=99.78  E-value=6e-19  Score=123.69  Aligned_cols=83  Identities=18%  Similarity=0.418  Sum_probs=75.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHH----HHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQ----AFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHIL  125 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~----~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l  125 (215)
                      ..+.++|||+|||+.+++++|+    .+|++||.|..|.++.   +|.++|||||+|.+.++|..|+..|||..++|+.|
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   81 (97)
T 1nu4_A            5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPM   81 (97)
T ss_dssp             -CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEE
Confidence            3567899999999999999999    9999999999998873   67888999999999999999999999999999999


Q ss_pred             EEEEeCCCCC
Q 028027          126 QVHLIPPEHV  135 (215)
Q Consensus       126 ~V~~a~~~~~  135 (215)
                      .|.++.+...
T Consensus        82 ~v~~a~~~~~   91 (97)
T 1nu4_A           82 RIQYAKTDSD   91 (97)
T ss_dssp             EEEECSSCCT
T ss_pred             EEEEccCCCc
Confidence            9999987643

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A

Probab=99.77  E-value=4.8e-18  Score=120.62  Aligned_cols=82  Identities=24%  Similarity=0.423  Sum_probs=74.2

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      .+.++|||+|||+.+++++|+++|++||.|..|.++        ++||||+|.+.++|..|+..||+..|+|+.|.|.++
T Consensus         9 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   80 (103)
T 2dgu_A            9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFA   80 (103)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEc
Confidence            456899999999999999999999999999999886        359999999999999999999999999999999999


Q ss_pred             CCCCCCCCCc
Q 028027          131 PPEHVHPKLW  140 (215)
Q Consensus       131 ~~~~~~~~~~  140 (215)
                      .+........
T Consensus        81 ~~~~~~~~~~   90 (103)
T 2dgu_A           81 KPPDQKRKER   90 (103)
T ss_dssp             CCCCCCCCCC
T ss_pred             CCCcccchhh
Confidence            8876654443

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.77  E-value=1.2e-18  Score=123.93  Aligned_cols=78  Identities=22%  Similarity=0.256  Sum_probs=71.0

Q ss_pred             CCCcEEEEcCCCC-CCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCc--eeCCeEEEE
Q 028027           51 NKATVLYIGRIPH-GFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGY--LLFEHILQV  127 (215)
Q Consensus        51 ~~~~~l~V~nLp~-~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~--~l~g~~l~V  127 (215)
                      .++++|||+|||+ .+++++|+.+|++||.|.+|.|++++      |||||+|.+.++|..|+..||+.  .|.|+.|.|
T Consensus        13 ~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~k------g~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V   86 (102)
T 1x4d_A           13 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI------NEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRV   86 (102)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS------SCEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcCC------CEEEEEECCHHHHHHHHHHHcCCCceECCcEEEE
Confidence            3578999999999 99999999999999999999998763      79999999999999999999864  599999999


Q ss_pred             EEeCCCC
Q 028027          128 HLIPPEH  134 (215)
Q Consensus       128 ~~a~~~~  134 (215)
                      .++....
T Consensus        87 ~~a~~~~   93 (102)
T 1x4d_A           87 HLSQKYK   93 (102)
T ss_dssp             EEECCCT
T ss_pred             EECCCCC
Confidence            9998643

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.77  E-value=3.2e-19  Score=121.31  Aligned_cols=73  Identities=23%  Similarity=0.432  Sum_probs=68.1

Q ss_pred             CcEEEEcCCCCCC------cHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCe-EE
Q 028027           53 ATVLYIGRIPHGF------YEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEH-IL  125 (215)
Q Consensus        53 ~~~l~V~nLp~~~------te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~-~l  125 (215)
                      +++|||+|||+.+      ++++|+.+|++||.|..|.+++  .+|.++|||||+|.+.++|..|+..|||..|+|+ .|
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~~--~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l   78 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE--EDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF   78 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCC--BTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecC--CCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeE
Confidence            3789999999999      7899999999999999999883  5899999999999999999999999999999999 88


Q ss_pred             EE
Q 028027          126 QV  127 (215)
Q Consensus       126 ~V  127 (215)
                      +|
T Consensus        79 ~V   80 (81)
T 2krb_A           79 RV   80 (81)
T ss_dssp             CC
T ss_pred             Ee
Confidence            76

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.77  E-value=9e-19  Score=122.63  Aligned_cols=83  Identities=19%  Similarity=0.231  Sum_probs=74.6

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEE
Q 028027           48 PLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQV  127 (215)
Q Consensus        48 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V  127 (215)
                      ....+.++|||+|||+.+++++|+.+|++||.|..+     ..+|.++|||||+|.+.++|..|+..|||..|+|+.|.|
T Consensus        11 ~~~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   85 (96)
T 1fjc_A           11 KKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSL   85 (96)
T ss_dssp             STTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            334567999999999999999999999999988766     237899999999999999999999999999999999999


Q ss_pred             EEeCCCCC
Q 028027          128 HLIPPEHV  135 (215)
Q Consensus       128 ~~a~~~~~  135 (215)
                      .++.++..
T Consensus        86 ~~a~~~~~   93 (96)
T 1fjc_A           86 YYTGEKGG   93 (96)
T ss_dssp             EECSSSCC
T ss_pred             EEcCCCCC
Confidence            99987644

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.77  E-value=2e-18  Score=123.98  Aligned_cols=80  Identities=25%  Similarity=0.413  Sum_probs=72.7

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 028027           49 LVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVH  128 (215)
Q Consensus        49 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~  128 (215)
                      .....++|||+|||+.+++++|+.+|++||.|..|.++        +|||||+|.+.++|..|+..|||..++|+.|.|.
T Consensus        27 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   98 (108)
T 2jvo_A           27 GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVV   98 (108)
T ss_dssp             -CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            34677999999999999999999999999999999987        5899999999999999999999999999999999


Q ss_pred             EeCCCCCC
Q 028027          129 LIPPEHVH  136 (215)
Q Consensus       129 ~a~~~~~~  136 (215)
                      ++.+...+
T Consensus        99 ~a~~~~~r  106 (108)
T 2jvo_A           99 YSKLPAKR  106 (108)
T ss_dssp             SCSCCC--
T ss_pred             EecCCCCC
Confidence            99876543

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.77  E-value=3.7e-18  Score=129.79  Aligned_cols=101  Identities=17%  Similarity=0.281  Sum_probs=86.3

Q ss_pred             CCcccCCCCCCCCC---CCCCCCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHH
Q 028027           31 DFLPLEGGPGRKLT---EEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEV  107 (215)
Q Consensus        31 d~~~~~g~p~r~~~---~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~  107 (215)
                      ++..+.|++++...   .........++|||+|||+.+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++
T Consensus        62 ~~~~~~g~~i~v~~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~  141 (166)
T 3md3_A           62 NGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDD  141 (166)
T ss_dssp             TTCEETTEECEEEECCCCCCCCCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHH
T ss_pred             CCCccCCCeeEEEEcCCCCCCCCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHH
Confidence            34445555444322   222344667899999999999999999999999999999999998899999999999999999


Q ss_pred             HHHHHHHhCCceeCCeEEEEEEeC
Q 028027          108 AEVVADAMHGYLLFEHILQVHLIP  131 (215)
Q Consensus       108 a~~ai~~l~g~~l~g~~l~V~~a~  131 (215)
                      |..|+..|||..++|+.|.|.|++
T Consensus       142 A~~A~~~l~g~~~~g~~i~v~~a~  165 (166)
T 3md3_A          142 AQNAMDSMQGQDLNGRPLRINWAA  165 (166)
T ss_dssp             HHHHHHHHTTCEETTEECEEEESC
T ss_pred             HHHHHHHhCCCccCCcEEEEEecC
Confidence            999999999999999999999985

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=6.4e-18  Score=117.48  Aligned_cols=79  Identities=18%  Similarity=0.288  Sum_probs=72.9

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ....++|||+|||+.+++++|+++|++||.|..|.+++        +||||+|.+.++|..|+..|||..|.|+.|.|.+
T Consensus         7 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   78 (92)
T 2dgt_A            7 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQL   78 (92)
T ss_dssp             CCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECS--------SEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEE
Confidence            45679999999999999999999999999999999873        4999999999999999999999999999999999


Q ss_pred             eCCCCCC
Q 028027          130 IPPEHVH  136 (215)
Q Consensus       130 a~~~~~~  136 (215)
                      +.+....
T Consensus        79 a~~~~~~   85 (92)
T 2dgt_A           79 STSRLRT   85 (92)
T ss_dssp             SSCCCSC
T ss_pred             ccCCCCC
Confidence            9876554

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens}

Probab=99.77  E-value=2.4e-19  Score=128.38  Aligned_cols=82  Identities=15%  Similarity=0.222  Sum_probs=76.3

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhccCCC---eeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEE
Q 028027           49 LVNKATVLYIGRIPHGFYEKEMQAFFSQFGA---IKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHIL  125 (215)
Q Consensus        49 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~---v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l  125 (215)
                      +....++|||+|||+++++++|+++|+.||.   |..|.|+.++. |.++|||||+|.+.++|..||. +|+..|+|+.|
T Consensus         7 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i   84 (107)
T 2lmi_A            7 EVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALE-KHRMYMGQRYV   84 (107)
T ss_dssp             CCSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCC
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEE
Confidence            3467789999999999999999999999998   89999999985 9999999999999999999998 99999999999


Q ss_pred             EEEEeCC
Q 028027          126 QVHLIPP  132 (215)
Q Consensus       126 ~V~~a~~  132 (215)
                      .|.++.+
T Consensus        85 ~V~~a~~   91 (107)
T 2lmi_A           85 EVYEINN   91 (107)
T ss_dssp             CCEECCH
T ss_pred             EEEECCH
Confidence            9998764

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.77  E-value=3.2e-18  Score=120.26  Aligned_cols=80  Identities=19%  Similarity=0.393  Sum_probs=72.2

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ....++|||+|||+.+++++|+.+|++||.|. +.++.    +.++|||||+|.+.++|+.|+..|||..|+|+.|.|.+
T Consensus        16 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~----~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   90 (97)
T 2e5j_A           16 APLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTW----QGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVAL   90 (97)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEE----ETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEc----CCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            35578999999999999999999999999996 66664    35789999999999999999999999999999999999


Q ss_pred             eCCCC
Q 028027          130 IPPEH  134 (215)
Q Consensus       130 a~~~~  134 (215)
                      +.++.
T Consensus        91 a~~~~   95 (97)
T 2e5j_A           91 ARQQR   95 (97)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            98754

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.63  E-value=2.7e-20  Score=135.15  Aligned_cols=88  Identities=17%  Similarity=0.316  Sum_probs=81.7

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeE--------EEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeC
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKR--------LRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLF  121 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~--------v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~  121 (215)
                      ..+.++|||+|||+.+++++|+++|++||.|..        |.++.++.+|.++|||||+|.+.++|..|+..|||..|.
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~   83 (116)
T 2lcw_A            4 NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFS   83 (116)
Confidence            356789999999999999999999999999998        899999889999999999999999999999999999999


Q ss_pred             CeEEEEEEeCCCCCCC
Q 028027          122 EHILQVHLIPPEHVHP  137 (215)
Q Consensus       122 g~~l~V~~a~~~~~~~  137 (215)
                      |+.|.|.++.++....
T Consensus        84 g~~l~V~~a~~~~~~~   99 (116)
T 2lcw_A           84 GNPIKVSFATRRADFN   99 (116)
Confidence            9999999998876543

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=3.9e-18  Score=118.09  Aligned_cols=79  Identities=11%  Similarity=0.306  Sum_probs=72.7

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ....++|||+|||+.+++++|+.+|++||.|..|.+++        +||||+|.+.++|+.|+..|||..|+|+.|.|.+
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   77 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK--------DYAFVHMEKEADAKAAIAQLNGKEVKGKRINVEL   77 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECS--------SCEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            35678999999999999999999999999999999973        4999999999999999999999999999999999


Q ss_pred             eCCCCCC
Q 028027          130 IPPEHVH  136 (215)
Q Consensus       130 a~~~~~~  136 (215)
                      +.+....
T Consensus        78 a~~~~~~   84 (90)
T 2dnp_A           78 STKGQKK   84 (90)
T ss_dssp             SCCCCCC
T ss_pred             CCCCCCC
Confidence            9876544

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=3.7e-18  Score=122.39  Aligned_cols=81  Identities=23%  Similarity=0.380  Sum_probs=75.1

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ....++|||+|||+.+++++|+.+|++||.|..|.++.+      +|||||+|.+.++|..|+..|||..|+|+.|.|.+
T Consensus        22 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~------~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   95 (109)
T 1x4g_A           22 SPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYW   95 (109)
T ss_dssp             CSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEe
Confidence            456789999999999999999999999999999999876      58999999999999999999999999999999999


Q ss_pred             eCCCCCC
Q 028027          130 IPPEHVH  136 (215)
Q Consensus       130 a~~~~~~  136 (215)
                      +.+....
T Consensus        96 a~~~~~~  102 (109)
T 1x4g_A           96 GKESPDM  102 (109)
T ss_dssp             CCCCCSS
T ss_pred             cCCCCCC
Confidence            9876543

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C

Probab=99.77  E-value=7.9e-19  Score=142.19  Aligned_cols=81  Identities=20%  Similarity=0.305  Sum_probs=76.7

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCC--CeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           52 KATVLYIGRIPHGFYEKEMQAFFSQFG--AIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        52 ~~~~l~V~nLp~~~te~~L~~~F~~~G--~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ..++|||+|||+++|+++|+++|++||  .|..|.|++++.+|+++|||||+|.+.++|+.||..||+..|+|+.|.|.+
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~  146 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTP  146 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEE
Confidence            567899999999999999999999999  999999999999999999999999999999999999999999999999999


Q ss_pred             eCC
Q 028027          130 IPP  132 (215)
Q Consensus       130 a~~  132 (215)
                      +.+
T Consensus       147 a~~  149 (229)
T 3q2s_C          147 VNK  149 (229)
T ss_dssp             CCH
T ss_pred             CCC
Confidence            864

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} SCOP: d.58.7.1 PDB: 2f9d_A 2f9j_A 2fho_B

Probab=99.76  E-value=2.5e-18  Score=124.33  Aligned_cols=80  Identities=20%  Similarity=0.423  Sum_probs=74.1

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ..+++|||+|||+.+++++|+.+|++||.|..|.++.+   +.++|||||+|.+.++|..|+..|||..++|+.|.|.++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   82 (115)
T 3lqv_A            6 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYY   82 (115)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEe
Confidence            56789999999999999999999999999999999865   455899999999999999999999999999999999998


Q ss_pred             CCC
Q 028027          131 PPE  133 (215)
Q Consensus       131 ~~~  133 (215)
                      .+.
T Consensus        83 ~~~   85 (115)
T 3lqv_A           83 NAN   85 (115)
T ss_dssp             CHH
T ss_pred             cCC
Confidence            654

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.76  E-value=1.5e-18  Score=122.67  Aligned_cols=78  Identities=28%  Similarity=0.496  Sum_probs=73.1

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeCCC
Q 028027           54 TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPPE  133 (215)
Q Consensus        54 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~~~  133 (215)
                      ++|||+|||+++++++|+++|++||.|..|.++.+     ++|||||+|.+.++|..|+..|||..++|+.|.|.++.+.
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   75 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGM   75 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS-----SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC-----CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCC
Confidence            57999999999999999999999999999999876     6799999999999999999999999999999999999886


Q ss_pred             CCC
Q 028027          134 HVH  136 (215)
Q Consensus       134 ~~~  136 (215)
                      ...
T Consensus        76 ~~~   78 (101)
T 2hvz_A           76 PRR   78 (101)
T ss_dssp             CCS
T ss_pred             CCc
Confidence            644

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A

Probab=99.76  E-value=2.1e-18  Score=132.34  Aligned_cols=101  Identities=22%  Similarity=0.393  Sum_probs=87.2

Q ss_pred             CCCcccCCCCCCCCCCCC-CCCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHH
Q 028027           30 ADFLPLEGGPGRKLTEEK-PLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVA  108 (215)
Q Consensus        30 ~d~~~~~g~p~r~~~~~~-~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a  108 (215)
                      .++..+.|++++...... .+....++|||+|||+.+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|
T Consensus        70 ~~~~~~~g~~i~v~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A  149 (172)
T 2g4b_A           70 FDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVT  149 (172)
T ss_dssp             GTTCEETTEECEEECCSSCCCCTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHH
T ss_pred             hCCcEecCceeeecCCcccCCCCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHH
Confidence            345556666655443322 2335578999999999999999999999999999999999988999999999999999999


Q ss_pred             HHHHHHhCCceeCCeEEEEEEe
Q 028027          109 EVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus       109 ~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ..|+..|||..++|+.|.|.+|
T Consensus       150 ~~A~~~l~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A          150 DQAIAGLNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             HHHHHHHTTCEETTEECEEEEC
T ss_pred             HHHHHHcCCCEECCeEEEEEeC
Confidence            9999999999999999999987

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A

Probab=99.76  E-value=2.8e-19  Score=119.56  Aligned_cols=75  Identities=16%  Similarity=0.384  Sum_probs=71.3

Q ss_pred             EEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           55 VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        55 ~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      +|||+|||+++++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|..|+. +++..++|+.|.|.+|
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~-~~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHT-TSSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHH-hCCCeECCEEEEEEEC
Confidence            58999999999999999999999999999999998899999999999999999999997 4899999999999875

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.76  E-value=2e-18  Score=122.06  Aligned_cols=77  Identities=26%  Similarity=0.362  Sum_probs=71.4

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ...++|||+|||+++++++|+.+|++||.|.++.+..      ++|||||+|.+.++|..|+..|||..++|+.|+|.++
T Consensus        25 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   98 (101)
T 2la4_A           25 PRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYP------EKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWG   98 (101)
T ss_dssp             SSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBC
T ss_pred             CCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEec
Confidence            4568999999999999999999999999999999873      4699999999999999999999999999999999998


Q ss_pred             CCC
Q 028027          131 PPE  133 (215)
Q Consensus       131 ~~~  133 (215)
                      .++
T Consensus        99 ~~~  101 (101)
T 2la4_A           99 KER  101 (101)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            753

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A

Probab=99.76  E-value=6.3e-18  Score=118.97  Aligned_cols=78  Identities=22%  Similarity=0.453  Sum_probs=71.1

Q ss_pred             CCCCCCcEEEEcCCCC-CCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEE
Q 028027           48 PLVNKATVLYIGRIPH-GFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQ  126 (215)
Q Consensus        48 ~~~~~~~~l~V~nLp~-~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~  126 (215)
                      .+..+.++|||+|||+ .+++++|+.+|++||.|..|.+.        +|||||+|.+.++|..|+..|||..++|+.|.
T Consensus        17 ~~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~   88 (97)
T 2xnq_A           17 RGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLI   88 (97)
T ss_dssp             --CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTEECE
T ss_pred             CCCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            3446789999999998 99999999999999999999883        68999999999999999999999999999999


Q ss_pred             EEEeCCC
Q 028027          127 VHLIPPE  133 (215)
Q Consensus       127 V~~a~~~  133 (215)
                      |.++.+.
T Consensus        89 V~~a~~~   95 (97)
T 2xnq_A           89 LEVSSSN   95 (97)
T ss_dssp             EEECCCC
T ss_pred             EEecCCC
Confidence            9998764

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.76  E-value=4.1e-18  Score=116.54  Aligned_cols=76  Identities=25%  Similarity=0.451  Sum_probs=70.6

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHh-CCceeCCeEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM-HGYLLFEHILQVH  128 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l-~g~~l~g~~l~V~  128 (215)
                      ....++|||+|||+.+++++|+++|++||.|..|.++.+      +|||||+|.+.++|..|+..| +|..++|+.|.|.
T Consensus         9 ~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~------kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~   82 (85)
T 2ytc_A            9 DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVK   82 (85)
T ss_dssp             CSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEE
T ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC------CCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEE
Confidence            356789999999999999999999999999999999874      589999999999999999988 9999999999999


Q ss_pred             EeC
Q 028027          129 LIP  131 (215)
Q Consensus       129 ~a~  131 (215)
                      |++
T Consensus        83 ~ak   85 (85)
T 2ytc_A           83 WGR   85 (85)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            974

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.76  E-value=4.5e-18  Score=119.83  Aligned_cols=79  Identities=24%  Similarity=0.468  Sum_probs=73.4

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      .+.++|||+|||+.+++++|+.+|++||.|..|.++.+      +|||||+|.+.++|..|+..|||..|+|+.|.|.++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a   86 (99)
T 2cpj_A           13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFA   86 (99)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEc
Confidence            56789999999999999999999999999999999865      589999999999999999999999999999999999


Q ss_pred             CCCCC
Q 028027          131 PPEHV  135 (215)
Q Consensus       131 ~~~~~  135 (215)
                      .+...
T Consensus        87 ~~~~~   91 (99)
T 2cpj_A           87 CHSAS   91 (99)
T ss_dssp             SCCSC
T ss_pred             CCCCC
Confidence            87543

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.76  E-value=4.5e-18  Score=135.87  Aligned_cols=84  Identities=21%  Similarity=0.330  Sum_probs=78.5

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      .+.++|||+|||+++++++|+++|++||.|.+|.|++++.+|.++|||||+|.+.++|..|+..+|+..+.|+.|+|.++
T Consensus        13 ~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~   92 (213)
T 4f02_A           13 YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWS   92 (213)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcccccccc
Confidence            45689999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCCC
Q 028027          131 PPEH  134 (215)
Q Consensus       131 ~~~~  134 (215)
                      ....
T Consensus        93 ~~~~   96 (213)
T 4f02_A           93 QRDP   96 (213)
T ss_dssp             CCCT
T ss_pred             cccc
Confidence            6543

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.76  E-value=3.7e-18  Score=122.85  Aligned_cols=79  Identities=13%  Similarity=0.319  Sum_probs=73.5

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      .+.++|||+|||+.+++++|+++|+.| .|..|.|+.++ +|+++|||||+|.+.++|+.|| .||+..|+|+.|.|..+
T Consensus        14 ~~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a   90 (109)
T 2dnn_A           14 PDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDH-VGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPA   90 (109)
T ss_dssp             HHHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCT-TCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECC-CCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEEC
Confidence            445799999999999999999999999 89999999997 5999999999999999999999 69999999999999887


Q ss_pred             CC
Q 028027          131 PP  132 (215)
Q Consensus       131 ~~  132 (215)
                      .+
T Consensus        91 ~~   92 (109)
T 2dnn_A           91 TE   92 (109)
T ss_dssp             CH
T ss_pred             Cc
Confidence            54

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.76  E-value=4.8e-18  Score=121.24  Aligned_cols=80  Identities=11%  Similarity=0.171  Sum_probs=71.8

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCc--eeCCeEEEEE
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGY--LLFEHILQVH  128 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~--~l~g~~l~V~  128 (215)
                      .+.++|||+|||+.+++++|+++|++||.|..|.++.+      +|||||+|.+.++|..|+..|++.  .|.|+.|.|.
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~   86 (104)
T 1wex_A           13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFN   86 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEE
Confidence            45689999999999999999999999999999998764      589999999999999999988764  5999999999


Q ss_pred             EeCCCCCC
Q 028027          129 LIPPEHVH  136 (215)
Q Consensus       129 ~a~~~~~~  136 (215)
                      ++.++...
T Consensus        87 ~a~~~~~~   94 (104)
T 1wex_A           87 YSTSKRIT   94 (104)
T ss_dssp             ECSSSSCC
T ss_pred             EccCcccc
Confidence            99876544

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=2.3e-17  Score=116.21  Aligned_cols=78  Identities=22%  Similarity=0.418  Sum_probs=71.6

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccC--CCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQF--GAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQV  127 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~--G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V  127 (215)
                      ....++|||+|||+.+++++|+.+|++|  |.|..|.++        +|||||+|.+.++|..|+..|||..|+|+.|.|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   83 (99)
T 2cpd_A           12 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEV   83 (99)
T ss_dssp             SSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEE
T ss_pred             cCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEE
Confidence            3567899999999999999999999999  999998764        479999999999999999999999999999999


Q ss_pred             EEeCCCCC
Q 028027          128 HLIPPEHV  135 (215)
Q Consensus       128 ~~a~~~~~  135 (215)
                      .++.+...
T Consensus        84 ~~a~~~~~   91 (99)
T 2cpd_A           84 TLAKPVDK   91 (99)
T ss_dssp             ECCCCCCC
T ss_pred             EECCCCCC
Confidence            99987654

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A

Probab=99.76  E-value=1.1e-17  Score=120.20  Aligned_cols=77  Identities=14%  Similarity=0.387  Sum_probs=71.1

Q ss_pred             CCCCcEEEEcCCCCC-CcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 028027           50 VNKATVLYIGRIPHG-FYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVH  128 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~-~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~  128 (215)
                      ....++|||+|||+. +++++|+++|++||.|..|.+        ++|||||+|.+.++|+.|+..|||..|+|+.|.|.
T Consensus        24 ~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   95 (110)
T 1wf1_A           24 KSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDIN   95 (110)
T ss_dssp             TTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEE
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            345689999999999 999999999999999999988        46899999999999999999999999999999999


Q ss_pred             EeCCCC
Q 028027          129 LIPPEH  134 (215)
Q Consensus       129 ~a~~~~  134 (215)
                      ++.+..
T Consensus        96 ~a~~~~  101 (110)
T 1wf1_A           96 MAGEPK  101 (110)
T ss_dssp             ESCCCC
T ss_pred             ECCCCC
Confidence            997543

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.75  E-value=2.4e-18  Score=124.23  Aligned_cols=79  Identities=10%  Similarity=0.122  Sum_probs=71.6

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCC-CeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFG-AIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G-~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ...++|||+|||+.+++++|+++|++|| .|..+.+..    +.++|||||+|.+.++|+.|+..|||..|+|+.|.|.+
T Consensus        26 ~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~----~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~  101 (111)
T 2jvr_A           26 AKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNT----RDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVER  101 (111)
T ss_dssp             CCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSS----CSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEc----CCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            4568999999999999999999999999 899998853    34789999999999999999999999999999999999


Q ss_pred             eCCC
Q 028027          130 IPPE  133 (215)
Q Consensus       130 a~~~  133 (215)
                      +...
T Consensus       102 a~~~  105 (111)
T 2jvr_A          102 DDNP  105 (111)
T ss_dssp             SCC-
T ss_pred             CCCC
Confidence            8654

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=99.75  E-value=1.1e-17  Score=127.36  Aligned_cols=83  Identities=28%  Similarity=0.552  Sum_probs=79.1

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeCC
Q 028027           53 ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPP  132 (215)
Q Consensus        53 ~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~~  132 (215)
                      .++|||+|||+.+++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|..|+..|||..++|+.|.|.++.+
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~   81 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecCC
Confidence            58999999999999999999999999999999999988999999999999999999999999999999999999999987


Q ss_pred             CCC
Q 028027          133 EHV  135 (215)
Q Consensus       133 ~~~  135 (215)
                      ...
T Consensus        82 ~~~   84 (167)
T 1fxl_A           82 SSA   84 (167)
T ss_dssp             CCG
T ss_pred             Ccc
Confidence            543

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.75  E-value=1.2e-18  Score=123.35  Aligned_cols=82  Identities=21%  Similarity=0.441  Sum_probs=76.2

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ..+++|||+|||+++++++|+.+|++||.|..|.++.++ +|.++|||||+|.+.++|+.|+.  ++..|+|+.|.|.++
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~a   83 (102)
T 2xs2_A            7 IMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPA   83 (102)
T ss_dssp             EEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEEC
Confidence            456899999999999999999999999999999999998 99999999999999999999997  999999999999998


Q ss_pred             CCCCC
Q 028027          131 PPEHV  135 (215)
Q Consensus       131 ~~~~~  135 (215)
                      .+...
T Consensus        84 ~~~~~   88 (102)
T 2xs2_A           84 IRKQN   88 (102)
T ss_dssp             EECC-
T ss_pred             CcCcc
Confidence            76543

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.75  E-value=4.2e-18  Score=119.45  Aligned_cols=79  Identities=22%  Similarity=0.469  Sum_probs=71.3

Q ss_pred             CCCCcEEEEcCCCC-CCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 028027           50 VNKATVLYIGRIPH-GFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVH  128 (215)
Q Consensus        50 ~~~~~~l~V~nLp~-~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~  128 (215)
                      ..+.++|||+|||+ .+++++|+.+|++||.|..|.+.        +|||||+|.+.++|..|+..|||..+.|+.|.|.
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   78 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILE   78 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            35678999999999 99999999999999999999884        5899999999999999999999999999999999


Q ss_pred             EeCCCCCC
Q 028027          129 LIPPEHVH  136 (215)
Q Consensus       129 ~a~~~~~~  136 (215)
                      ++.+....
T Consensus        79 ~a~~~~~~   86 (96)
T 2kvi_A           79 VSSSNARP   86 (96)
T ss_dssp             EEECCCC-
T ss_pred             EcCcCCCC
Confidence            99876543

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens}

Probab=99.75  E-value=7.8e-19  Score=131.92  Aligned_cols=86  Identities=19%  Similarity=0.324  Sum_probs=74.1

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEE------EEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCe
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRL------RIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEH  123 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v------~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~  123 (215)
                      ..+.++|||+|||+.+++++|+.+|++||.|..+      .+.. ..+|.++|||||+|.+.++|..|+..|||..|+|+
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~-~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~  120 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRL-MKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGK  120 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEE-EEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEe-ccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCc
Confidence            3567899999999999999999999999998764      1111 23789999999999999999999999999999999


Q ss_pred             EEEEEEeCCCCCC
Q 028027          124 ILQVHLIPPEHVH  136 (215)
Q Consensus       124 ~l~V~~a~~~~~~  136 (215)
                      .|.|.++.+...+
T Consensus       121 ~l~V~~a~~~~~~  133 (143)
T 3egn_A          121 PMVVQFARSARPK  133 (143)
T ss_dssp             ECEEEECCCSCC-
T ss_pred             EEEEEECCCCCCc
Confidence            9999999775443

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=99.75  E-value=9.2e-18  Score=128.10  Aligned_cols=84  Identities=25%  Similarity=0.434  Sum_probs=79.8

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeC
Q 028027           52 KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIP  131 (215)
Q Consensus        52 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~  131 (215)
                      +.++|||+|||+++++++|+++|++||.|.+|.++.++.+|.++|||||+|.+.++|..|+..|+|..++|+.|.|.++.
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~   81 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYAR   81 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecC
Confidence            46899999999999999999999999999999999998899999999999999999999999999999999999999998


Q ss_pred             CCCC
Q 028027          132 PEHV  135 (215)
Q Consensus       132 ~~~~  135 (215)
                      +...
T Consensus        82 ~~~~   85 (168)
T 1b7f_A           82 PGGE   85 (168)
T ss_dssp             CCSS
T ss_pred             CCcc
Confidence            7643

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A

Probab=99.74  E-value=7.8e-18  Score=127.41  Aligned_cols=81  Identities=25%  Similarity=0.433  Sum_probs=74.9

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 028027           49 LVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVH  128 (215)
Q Consensus        49 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~  128 (215)
                      .....++|||+|||+.+++++|+.+|++||.|..|.++.+     ++|||||+|.+.++|..|+..|||..|+|+.|+|.
T Consensus        69 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  143 (150)
T 2i2y_A           69 SCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVE  143 (150)
T ss_dssp             SSTTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            3456799999999999999999999999999999999876     47999999999999999999999999999999999


Q ss_pred             EeCCCC
Q 028027          129 LIPPEH  134 (215)
Q Consensus       129 ~a~~~~  134 (215)
                      ++.++.
T Consensus       144 ~a~~~~  149 (150)
T 2i2y_A          144 LSNGEK  149 (150)
T ss_dssp             ECCCCC
T ss_pred             EcCCCC
Confidence            997753

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=7e-18  Score=117.43  Aligned_cols=79  Identities=15%  Similarity=0.338  Sum_probs=70.7

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCC-eeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCC-ceeCCeEEEEE
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGA-IKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHG-YLLFEHILQVH  128 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~-v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g-~~l~g~~l~V~  128 (215)
                      ...++|||+|||+++++++|+++|++||. |..+.+.       ++|||||+|.+.++|..|+..||| ..|+|+.|+|.
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~   78 (93)
T 2cqh_A            6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVD   78 (93)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEE
Confidence            45689999999999999999999999999 6666552       368999999999999999999999 99999999999


Q ss_pred             EeCCCCCC
Q 028027          129 LIPPEHVH  136 (215)
Q Consensus       129 ~a~~~~~~  136 (215)
                      ++.++..+
T Consensus        79 ~a~~~~~~   86 (93)
T 2cqh_A           79 YSVSKKLR   86 (93)
T ss_dssp             ECCCCCCC
T ss_pred             EccCcccc
Confidence            99886554

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.74  E-value=7.7e-18  Score=131.24  Aligned_cols=85  Identities=18%  Similarity=0.343  Sum_probs=79.7

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ....++|||+|||+.+++++|+++|++||.|..|.|+.+. +|.++|||||+|.+.++|..|+..|||..|+|+.|.|.+
T Consensus        85 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~  163 (177)
T 2f3j_A           85 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL  163 (177)
T ss_dssp             CTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3557899999999999999999999999999999999998 999999999999999999999999999999999999999


Q ss_pred             eCCCCC
Q 028027          130 IPPEHV  135 (215)
Q Consensus       130 a~~~~~  135 (215)
                      +.+...
T Consensus       164 a~~~~~  169 (177)
T 2f3j_A          164 VASQID  169 (177)
T ss_dssp             ESSGGG
T ss_pred             ecCCCC
Confidence            976543

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.74  E-value=5e-18  Score=122.39  Aligned_cols=78  Identities=22%  Similarity=0.299  Sum_probs=71.6

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ...++|||+|||+.+++++|+.+|++||.|..|.++.      ++|||||+|.+.++|+.|+..|||..|+|+.|.|.|+
T Consensus         8 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   81 (111)
T 1whx_A            8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWA   81 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            3468999999999999999999999999999998874      4589999999999999999999999999999999999


Q ss_pred             CCCC
Q 028027          131 PPEH  134 (215)
Q Consensus       131 ~~~~  134 (215)
                      ....
T Consensus        82 ~~~~   85 (111)
T 1whx_A           82 PIGV   85 (111)
T ss_dssp             ETTT
T ss_pred             CCCc
Confidence            7643

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.74  E-value=9.1e-18  Score=121.14  Aligned_cols=79  Identities=20%  Similarity=0.303  Sum_probs=70.8

Q ss_pred             CCCcEEEEcCCCCC-CcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCC--ceeCCeEEEE
Q 028027           51 NKATVLYIGRIPHG-FYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHG--YLLFEHILQV  127 (215)
Q Consensus        51 ~~~~~l~V~nLp~~-~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g--~~l~g~~l~V  127 (215)
                      .++++|||+|||++ +++++|+++|++||.|.+|.|++.      +|||||+|.+.++|..|+..|++  ..|.|+.|+|
T Consensus        23 ~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V   96 (112)
T 1x4f_A           23 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKV   96 (112)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEE
T ss_pred             CCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEecC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEE
Confidence            45789999999998 999999999999999999999754      58999999999999999998864  5699999999


Q ss_pred             EEeCCCCC
Q 028027          128 HLIPPEHV  135 (215)
Q Consensus       128 ~~a~~~~~  135 (215)
                      .++.....
T Consensus        97 ~~a~~~~~  104 (112)
T 1x4f_A           97 DLSEKYKK  104 (112)
T ss_dssp             EEECSCSS
T ss_pred             EECccccc
Confidence            99976543

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.74  E-value=1.7e-17  Score=131.77  Aligned_cols=86  Identities=22%  Similarity=0.436  Sum_probs=81.1

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ...++|||+|||..+++++|+++|+.||.|..|.++.++.+|.++|||||+|.+.++|..|+..|||..|+|+.|.|.++
T Consensus       123 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a  202 (216)
T 2qfj_A          123 RAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA  202 (216)
T ss_dssp             TTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEEC
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEe
Confidence            45689999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 028027          131 PPEHVH  136 (215)
Q Consensus       131 ~~~~~~  136 (215)
                      .+....
T Consensus       203 ~~~~~~  208 (216)
T 2qfj_A          203 VTPPMP  208 (216)
T ss_dssp             SSCSST
T ss_pred             cCCCCC
Confidence            876543

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.73  E-value=2.3e-17  Score=115.11  Aligned_cols=80  Identities=20%  Similarity=0.373  Sum_probs=70.9

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ...++|||+|||+++++++|+.+|++||.|..|  +.++.+|.   ||||+|.+.++|..|+. |||..|+|+.|.|.++
T Consensus         6 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a   79 (94)
T 2e5g_A            6 SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPR   79 (94)
T ss_dssp             TTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECCCBCS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEEC
Confidence            345799999999999999999999999999987  55555665   99999999999999999 9999999999999988


Q ss_pred             CCCCCC
Q 028027          131 PPEHVH  136 (215)
Q Consensus       131 ~~~~~~  136 (215)
                      .++...
T Consensus        80 ~~~~~~   85 (94)
T 2e5g_A           80 EQKEFQ   85 (94)
T ss_dssp             CCSCCC
T ss_pred             CcCCCC
Confidence            765443

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.73  E-value=1.1e-17  Score=117.03  Aligned_cols=80  Identities=20%  Similarity=0.377  Sum_probs=72.9

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEE-EEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRL-RIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v-~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ...++|||+|||+.+++++|+.+|++||.|..| .++.++.+|    .|||+|.+.++|..|+..|||..|+|+.|.|.+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~----~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~   88 (96)
T 2e44_A           13 QRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETA----VVNVTYSSKDQARQALDKLNGFQLENFTLKVAY   88 (96)
T ss_dssp             CSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSE----EEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEE
T ss_pred             CCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCC----EEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            456899999999999999999999999999999 588876554    399999999999999999999999999999999


Q ss_pred             eCCCC
Q 028027          130 IPPEH  134 (215)
Q Consensus       130 a~~~~  134 (215)
                      +.+..
T Consensus        89 a~~~~   93 (96)
T 2e44_A           89 IPDEM   93 (96)
T ss_dssp             CCCCC
T ss_pred             cCccc
Confidence            98763

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=4.2e-18  Score=125.07  Aligned_cols=80  Identities=19%  Similarity=0.256  Sum_probs=73.4

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCe----eEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEE
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAI----KRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQ  126 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v----~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~  126 (215)
                      .+.++|||+|||+++|+++|+++|++||.|    ..|.|+.+. +|+++|||||+|.+.++|+.||.. |+..|+|+.|.
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~-~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~   98 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP-DGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIE   98 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECT-TSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECC-CCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEE
Confidence            567899999999999999999999999975    689999985 999999999999999999999975 99999999999


Q ss_pred             EEEeCC
Q 028027          127 VHLIPP  132 (215)
Q Consensus       127 V~~a~~  132 (215)
                      |..+.+
T Consensus        99 V~~a~~  104 (123)
T 2dha_A           99 LFRSTA  104 (123)
T ss_dssp             CEEECH
T ss_pred             EEECCH
Confidence            988743

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*

Probab=99.73  E-value=2.6e-17  Score=144.88  Aligned_cols=85  Identities=19%  Similarity=0.360  Sum_probs=80.3

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ...++|||+|||+.+|+++|..+|++||.|..|.|+.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.++
T Consensus       100 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a  179 (437)
T 3pgw_S          100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  179 (437)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            44689999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             CCCCC
Q 028027          131 PPEHV  135 (215)
Q Consensus       131 ~~~~~  135 (215)
                      .+...
T Consensus       180 ~~~~~  184 (437)
T 3pgw_S          180 RGRTV  184 (437)
T ss_pred             CCCCC
Confidence            87543

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.72  E-value=3.6e-17  Score=128.13  Aligned_cols=85  Identities=24%  Similarity=0.463  Sum_probs=80.8

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ...++|||+|||+.+++++|+++|++||.|..|.++.++.+|.++|||||+|.+.++|..|+..|||..|+|+.|.|.++
T Consensus       112 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  191 (198)
T 2yh0_A          112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  191 (198)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            56799999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             CCCCC
Q 028027          131 PPEHV  135 (215)
Q Consensus       131 ~~~~~  135 (215)
                      .+...
T Consensus       192 ~~~~~  196 (198)
T 2yh0_A          192 SVGAK  196 (198)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87643

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A

Probab=99.72  E-value=2.4e-18  Score=128.96  Aligned_cols=84  Identities=15%  Similarity=0.183  Sum_probs=75.4

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ....++|||+|||+++|+++|+++|++|| |..|.|+.++ +|+++|||||+|.+.++|+.|| .+|+..|+|+.|.|.+
T Consensus        43 ~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~-~g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~  119 (139)
T 2hgn_A           43 STTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGP-DGRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFL  119 (139)
T ss_dssp             --CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSS-SSCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECC-CCCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEE
Confidence            35678999999999999999999999999 6799999997 5999999999999999999999 7899999999999999


Q ss_pred             eCCCCCC
Q 028027          130 IPPEHVH  136 (215)
Q Consensus       130 a~~~~~~  136 (215)
                      +.+....
T Consensus       120 a~~~~~~  126 (139)
T 2hgn_A          120 NSTTGAS  126 (139)
T ss_dssp             CCCSCC-
T ss_pred             CCCCCCC
Confidence            8776543

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=99.72  E-value=2.8e-17  Score=128.58  Aligned_cols=84  Identities=17%  Similarity=0.352  Sum_probs=77.5

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ....++|||+|||+++++++|+++|+.||.|.+|.++.++.+|.++|||||+|.+.++|..|+.. ++..++|+.|.|.+
T Consensus        10 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v~~   88 (196)
T 1l3k_A           10 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKR   88 (196)
T ss_dssp             CGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeeeec
Confidence            35678999999999999999999999999999999999988999999999999999999999975 99999999999999


Q ss_pred             eCCCC
Q 028027          130 IPPEH  134 (215)
Q Consensus       130 a~~~~  134 (215)
                      +.+..
T Consensus        89 ~~~~~   93 (196)
T 1l3k_A           89 AVSRE   93 (196)
T ss_dssp             CCC--
T ss_pred             ccCcc
Confidence            87654

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=1.1e-16  Score=112.26  Aligned_cols=78  Identities=19%  Similarity=0.330  Sum_probs=70.9

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ...++|||+||  .+++++|+.+|++||.|..|.+.      .++|||||+|.+.++|..|+..|||..|+|+.|.|.++
T Consensus        13 ~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a   84 (97)
T 1x5p_A           13 RKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA   84 (97)
T ss_dssp             CCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECC
T ss_pred             CCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEC
Confidence            46789999996  89999999999999999999884      45689999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 028027          131 PPEHVH  136 (215)
Q Consensus       131 ~~~~~~  136 (215)
                      .+....
T Consensus        85 ~~~~~~   90 (97)
T 1x5p_A           85 RKQPML   90 (97)
T ss_dssp             SSCCCC
T ss_pred             CCCCCC
Confidence            876543

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=99.72  E-value=2.6e-17  Score=125.57  Aligned_cols=100  Identities=21%  Similarity=0.342  Sum_probs=85.0

Q ss_pred             CCcccCCCCCCCCCCC-CCCCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHH
Q 028027           31 DFLPLEGGPGRKLTEE-KPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAE  109 (215)
Q Consensus        31 d~~~~~g~p~r~~~~~-~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~  109 (215)
                      ++..+.|++++..... .......++|||+|||..+++++|+++|++||.|..+.++.+..+|.++|||||+|.+.++|.
T Consensus        66 ~~~~~~g~~l~v~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~  145 (168)
T 1b7f_A           66 NGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQ  145 (168)
T ss_dssp             TTCEETTEECEEEECCCCSSTTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHH
T ss_pred             CCCEeCCcEEEEEecCCCcccCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHH
Confidence            4445556655443322 223456789999999999999999999999999999999999889999999999999999999


Q ss_pred             HHHHHhCCceeCC--eEEEEEEe
Q 028027          110 VVADAMHGYLLFE--HILQVHLI  130 (215)
Q Consensus       110 ~ai~~l~g~~l~g--~~l~V~~a  130 (215)
                      .|+..|||..++|  +.|.|.+|
T Consensus       146 ~A~~~l~g~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A          146 EAISALNNVIPEGGSQPLSVRLA  168 (168)
T ss_dssp             HHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             HHHHHhcCCEecCCCeEEEEEeC
Confidence            9999999999988  99999885

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A

Probab=99.72  E-value=1e-17  Score=123.44  Aligned_cols=81  Identities=19%  Similarity=0.292  Sum_probs=73.0

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhccCCCee--EEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEE
Q 028027           49 LVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIK--RLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQ  126 (215)
Q Consensus        49 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~--~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~  126 (215)
                      +....++|||+|||+.+|+++|+++|++| .|.  .|.|+.++. |+++|||||+|.+.++|+.||. +++..|+|+.|.
T Consensus        38 ~~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~-~~~~~l~gR~I~  114 (126)
T 2hgm_A           38 DSANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALG-KHKERIGHRYIE  114 (126)
T ss_dssp             CSSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHT-TTTCCBTTBCCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHH-HCCCEECCEEEE
Confidence            34567899999999999999999999999 566  899999985 9999999999999999999997 478999999999


Q ss_pred             EEEeCC
Q 028027          127 VHLIPP  132 (215)
Q Consensus       127 V~~a~~  132 (215)
                      |..+.+
T Consensus       115 V~~a~~  120 (126)
T 2hgm_A          115 VFKSSQ  120 (126)
T ss_dssp             CEEECH
T ss_pred             EEECCH
Confidence            998754

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus}

Probab=99.72  E-value=3.6e-17  Score=113.30  Aligned_cols=77  Identities=23%  Similarity=0.478  Sum_probs=63.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCce--eCCeEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYL--LFEHILQV  127 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~--l~g~~l~V  127 (215)
                      ..+.++|||+|||+++++++|+++|++||.|.+|.++.+     ++|||||+|.+.++|+.    +++..  +.|+.|.|
T Consensus         8 ~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v   78 (89)
T 3d2w_A            8 HHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQS----LCGEDLIIKGISVHI   78 (89)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHH----HTTCEEEETTEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHH----HcCCCcccCCEEEEE
Confidence            467899999999999999999999999999999999874     68999999999999883    45654  56999999


Q ss_pred             EEeCCCCC
Q 028027          128 HLIPPEHV  135 (215)
Q Consensus       128 ~~a~~~~~  135 (215)
                      .++.++..
T Consensus        79 ~~a~~k~~   86 (89)
T 3d2w_A           79 SNAEPKHN   86 (89)
T ss_dssp             EECC----
T ss_pred             EEcCCCCc
Confidence            99987643

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A

Probab=99.72  E-value=3.5e-17  Score=125.32  Aligned_cols=82  Identities=11%  Similarity=0.262  Sum_probs=72.7

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCC--eEEEEE
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFE--HILQVH  128 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g--~~l~V~  128 (215)
                      ....+|||+||++.+++++|+++|++||.|.+|.+....    ++|||||+|.+.++|+.|+..|||..|.|  +.|+|.
T Consensus        44 s~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~----~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~  119 (164)
T 1sjr_A           44 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID  119 (164)
T ss_dssp             CCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESS----SCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEE
T ss_pred             CceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCC----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEE
Confidence            445679999999999999999999999999999986532    56899999999999999999999999965  999999


Q ss_pred             EeCCCCCC
Q 028027          129 LIPPEHVH  136 (215)
Q Consensus       129 ~a~~~~~~  136 (215)
                      |+++....
T Consensus       120 ~Ak~~~l~  127 (164)
T 1sjr_A          120 FSKLTSLN  127 (164)
T ss_dssp             ECSSSSCC
T ss_pred             EecCCccc
Confidence            99987543

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=99.71  E-value=1.2e-17  Score=127.47  Aligned_cols=98  Identities=23%  Similarity=0.400  Sum_probs=84.2

Q ss_pred             cCCCCCCCCCCCC-CCCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHH
Q 028027           35 LEGGPGRKLTEEK-PLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD  113 (215)
Q Consensus        35 ~~g~p~r~~~~~~-~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~  113 (215)
                      +.|++++...... ......++|||+|||+.+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|..|+.
T Consensus        68 ~~g~~i~v~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~  147 (167)
T 2cjk_A           68 LDGKVIDPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ  147 (167)
T ss_dssp             ETTEECCCEECCCHHHHHHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH
T ss_pred             cCCeEcccccccchhhccCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh
Confidence            4555554433221 123456799999999999999999999999999999999998899999999999999999999997


Q ss_pred             HhCCceeCCeEEEEEEeCCC
Q 028027          114 AMHGYLLFEHILQVHLIPPE  133 (215)
Q Consensus       114 ~l~g~~l~g~~l~V~~a~~~  133 (215)
                       ++|..++|+.|.|.++.|+
T Consensus       148 -~~~~~~~g~~i~V~~a~pk  166 (167)
T 2cjk_A          148 -NKFIDFKDRKIEIKRAEPR  166 (167)
T ss_dssp             -CSEECSSSSCEEEEECCCC
T ss_pred             -CCCEEeCCeEEEEeecCCC
Confidence             8999999999999999875

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A

Probab=99.71  E-value=3.5e-17  Score=112.90  Aligned_cols=76  Identities=17%  Similarity=0.317  Sum_probs=70.3

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeC
Q 028027           52 KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIP  131 (215)
Q Consensus        52 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~  131 (215)
                      ..++|||+|||+.+++++|+++|++| .|..+.+.      .++|||||+|.+.++|+.|+..|||..++|+.|+|.++.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~   76 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe------CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcC
Confidence            46789999999999999999999999 99999884      567999999999999999999999999999999999986


Q ss_pred             CCC
Q 028027          132 PEH  134 (215)
Q Consensus       132 ~~~  134 (215)
                      ...
T Consensus        77 ~~~   79 (88)
T 1wg1_A           77 TDA   79 (88)
T ss_dssp             CCC
T ss_pred             CCc
Confidence            643

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=99.71  E-value=4.8e-17  Score=127.20  Aligned_cols=86  Identities=17%  Similarity=0.373  Sum_probs=75.9

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ...++|||+|||+.+++++|+++|+.||.|..|.++.+..+|.++|||||+|.+.++|..|+.. +|..|+|+.|.|.++
T Consensus       102 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~a  180 (196)
T 1l3k_A          102 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKA  180 (196)
T ss_dssp             -CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEEC
T ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEec
Confidence            4568999999999999999999999999999999999988999999999999999999999976 899999999999999


Q ss_pred             CCCCCCC
Q 028027          131 PPEHVHP  137 (215)
Q Consensus       131 ~~~~~~~  137 (215)
                      .++....
T Consensus       181 ~~k~~~~  187 (196)
T 1l3k_A          181 LSKQEMA  187 (196)
T ss_dssp             C------
T ss_pred             CChhHhc
Confidence            8876543

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.71  E-value=1.2e-16  Score=117.98  Aligned_cols=80  Identities=13%  Similarity=0.304  Sum_probs=71.7

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccE-EEEEEcCHHHHHHHHHHhCCceeCC--eEEEEE
Q 028027           52 KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHF-GFIEFNDPEVAEVVADAMHGYLLFE--HILQVH  128 (215)
Q Consensus        52 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~-afV~F~~~~~a~~ai~~l~g~~l~g--~~l~V~  128 (215)
                      ..-.|||+||++.+|+++|+++|++||.|.+|.+....     +|| |||+|.+.++|..|+..|||..|.|  +.|+|+
T Consensus        27 ~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~-----~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~  101 (130)
T 3zzy_A           27 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN-----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID  101 (130)
T ss_dssp             SEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEET-----TEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEE
T ss_pred             ceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCC-----CCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEE
Confidence            34568899999999999999999999999999887642     577 9999999999999999999999988  999999


Q ss_pred             EeCCCCCC
Q 028027          129 LIPPEHVH  136 (215)
Q Consensus       129 ~a~~~~~~  136 (215)
                      |+++....
T Consensus       102 ~ak~~~l~  109 (130)
T 3zzy_A          102 FSKLTSLN  109 (130)
T ss_dssp             ECSCSSCC
T ss_pred             ecCCCcee
Confidence            99887543

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=99.70  E-value=3.6e-17  Score=124.40  Aligned_cols=100  Identities=25%  Similarity=0.358  Sum_probs=83.8

Q ss_pred             CCcccCCCCCCCCCCC-CCCCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHH
Q 028027           31 DFLPLEGGPGRKLTEE-KPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAE  109 (215)
Q Consensus        31 d~~~~~g~p~r~~~~~-~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~  109 (215)
                      ++..+.|++++..... .......++|||+|||+.+++++|+++|++||.|..+.++.+..+|.++|||||+|.+.++|.
T Consensus        65 ~~~~~~g~~l~v~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~  144 (167)
T 1fxl_A           65 NGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAE  144 (167)
T ss_dssp             TTCEETTEECEEEECCCCCGGGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHH
T ss_pred             CCCccCCceEEEEecCCCcccCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHH
Confidence            4455566655443322 223356789999999999999999999999999999999999889999999999999999999


Q ss_pred             HHHHHhCCceeCCeE--EEEEEe
Q 028027          110 VVADAMHGYLLFEHI--LQVHLI  130 (215)
Q Consensus       110 ~ai~~l~g~~l~g~~--l~V~~a  130 (215)
                      .|+..|||..++|+.  |.|.||
T Consensus       145 ~A~~~l~g~~~~g~~~~i~v~~A  167 (167)
T 1fxl_A          145 EAIKGLNGQKPSGATEPITVKFA  167 (167)
T ss_dssp             HHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             HHHHHhcCCccCCCccceEEEeC
Confidence            999999999999975  788775

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.70  E-value=6.6e-17  Score=122.81  Aligned_cols=81  Identities=19%  Similarity=0.449  Sum_probs=75.5

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeCCC
Q 028027           54 TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPPE  133 (215)
Q Consensus        54 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~~~  133 (215)
                      ++|||+|||+++++++|+++|++||.|.+|.++.++ +|.++|||||+|.+.++|..|+..|||..+.|+.|.|.++.+.
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~   79 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQS   79 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCC-C-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECC-CCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCC
Confidence            589999999999999999999999999999999997 6889999999999999999999999999999999999998765


Q ss_pred             CC
Q 028027          134 HV  135 (215)
Q Consensus       134 ~~  135 (215)
                      ..
T Consensus        80 ~~   81 (166)
T 3md3_A           80 QQ   81 (166)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.70  E-value=1.7e-16  Score=116.52  Aligned_cols=77  Identities=16%  Similarity=0.268  Sum_probs=68.8

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccE-EEEEEcCHHHHHHHHHHhCCceeCC--eEEEEEEe
Q 028027           54 TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHF-GFIEFNDPEVAEVVADAMHGYLLFE--HILQVHLI  130 (215)
Q Consensus        54 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~-afV~F~~~~~a~~ai~~l~g~~l~g--~~l~V~~a  130 (215)
                      -.|||+||++.+++++|+.+|++||.|..|.+...  +    || |||+|.+.++|..|+..|||..|.|  +.|+|.++
T Consensus        26 l~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~--~----Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~A   99 (124)
T 2e5i_A           26 LLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR--N----GIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYA   99 (124)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES--S----SEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECC
T ss_pred             EEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC--C----CCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEe
Confidence            34689999999999999999999999999998652  2    76 9999999999999999999999987  68999999


Q ss_pred             CCCCCC
Q 028027          131 PPEHVH  136 (215)
Q Consensus       131 ~~~~~~  136 (215)
                      ++....
T Consensus       100 k~~~l~  105 (124)
T 2e5i_A          100 RPTRLN  105 (124)
T ss_dssp             SCSCCC
T ss_pred             cCCcce
Confidence            887644

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=5.5e-17  Score=117.25  Aligned_cols=79  Identities=14%  Similarity=0.282  Sum_probs=70.6

Q ss_pred             CCCcEEEE--cCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCcee-----CCe
Q 028027           51 NKATVLYI--GRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLL-----FEH  123 (215)
Q Consensus        51 ~~~~~l~V--~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l-----~g~  123 (215)
                      .+.++|||  |||++.+++++|+++|++||.|..|.++.+      +|||||+|.+.++|+.|+..|||..+     .|+
T Consensus        23 ~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~------rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~   96 (114)
T 2cq2_A           23 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKI   96 (114)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEE
T ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHhCCCEEccccCCCc
Confidence            45688999  779999999999999999999999987643      68999999999999999999999988     689


Q ss_pred             EEEEEEeCCCCC
Q 028027          124 ILQVHLIPPEHV  135 (215)
Q Consensus       124 ~l~V~~a~~~~~  135 (215)
                      .|.|.++...+.
T Consensus        97 ~l~v~~a~~~p~  108 (114)
T 2cq2_A           97 TLYLNFVEKVQW  108 (114)
T ss_dssp             ECEEEEESCCCC
T ss_pred             EEEEEecccCcc
Confidence            999999976544

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.70  E-value=1.9e-16  Score=130.16  Aligned_cols=99  Identities=19%  Similarity=0.259  Sum_probs=83.7

Q ss_pred             CCCcccCCCCCCCCCCCCCCCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHH
Q 028027           30 ADFLPLEGGPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAE  109 (215)
Q Consensus        30 ~d~~~~~g~p~r~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~  109 (215)
                      .++..+.|+++++...     .+.++|||+|||+.+++++|+++|+.||.|..|.++.+. +|.++|||||+|.+.++|.
T Consensus        78 l~g~~i~g~~l~v~~a-----~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~  151 (261)
T 3sde_A           78 LDGTILKSRPLRIRFA-----THGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDD-RGRATGKGFVEFAAKPPAR  151 (261)
T ss_dssp             HTTCEETTEECEEEEC-----CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET-TSCEEEEEEEEESSHHHHH
T ss_pred             cCCcEECCceeEeeec-----ccCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCC-CCCcCcEEEEEeCCHHHHH
Confidence            3455566666654433     346899999999999999999999999999999999994 9999999999999999999


Q ss_pred             HHHHHhC-CceeC---CeEEEEEEeCCCC
Q 028027          110 VVADAMH-GYLLF---EHILQVHLIPPEH  134 (215)
Q Consensus       110 ~ai~~l~-g~~l~---g~~l~V~~a~~~~  134 (215)
                      .|+..|| +..+.   |++|.|.++.+..
T Consensus       152 ~A~~~l~~~~~~~~~~~r~i~v~~~~~~~  180 (261)
T 3sde_A          152 KALERCGDGAFLLTTTPRPVIVEPMEQFD  180 (261)
T ss_dssp             HHHHHHHHSCEESSSSCCBCEEEECCCEE
T ss_pred             HHHHHhcCCeEEecCCCceEEEeeccccC
Confidence            9999994 55555   9999999987653

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.70  E-value=8.6e-17  Score=128.39  Aligned_cols=81  Identities=25%  Similarity=0.421  Sum_probs=75.3

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ...++|||+|||+.+++++|+++|+.||.|..|.|+++.  +.++|||||+|.+.++|..|+..|||..|+|+.|.|.++
T Consensus       101 ~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~--~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a  178 (213)
T 4f02_A          101 SGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRF  178 (213)
T ss_dssp             HCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             cccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccC--CCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            356789999999999999999999999999999999984  558999999999999999999999999999999999998


Q ss_pred             CCC
Q 028027          131 PPE  133 (215)
Q Consensus       131 ~~~  133 (215)
                      .++
T Consensus       179 ~~~  181 (213)
T 4f02_A          179 KSR  181 (213)
T ss_dssp             CCH
T ss_pred             CCC
Confidence            654

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A

Probab=99.70  E-value=4.3e-17  Score=118.15  Aligned_cols=78  Identities=13%  Similarity=0.194  Sum_probs=67.2

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeE-----E
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHI-----L  125 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~-----l  125 (215)
                      ...++|||+|||+.+++++|+++|++||.|..|.|+.+       |||||+|.+.++|+.||..|||..|+|+.     |
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i   86 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYI   86 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEE
Confidence            45689999999999999999999999999999999765       89999999999999999999999999988     7


Q ss_pred             EEEEeCCCCC
Q 028027          126 QVHLIPPEHV  135 (215)
Q Consensus       126 ~V~~a~~~~~  135 (215)
                      .|..+.+...
T Consensus        87 ~v~~~~~~~~   96 (115)
T 3beg_B           87 RVKVDGPRSP   96 (115)
T ss_dssp             EEEECC----
T ss_pred             EeccCCCCCC
Confidence            8887766543

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.70  E-value=3.9e-17  Score=118.14  Aligned_cols=79  Identities=18%  Similarity=0.328  Sum_probs=69.4

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCC---CCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEE
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKT---GQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQV  127 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~t---g~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V  127 (215)
                      ...++|||+|||+.+++++|+++|++||.|. +.++.+..+   |.++|||||+|.+.++|+.|+..|+  .++|+.|.+
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~~   82 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYLC   82 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEEe
Confidence            4568999999999999999999999999999 888887766   7999999999999999999999984  377887777


Q ss_pred             EEeCC
Q 028027          128 HLIPP  132 (215)
Q Consensus       128 ~~a~~  132 (215)
                      ..+.+
T Consensus        83 ~~~~~   87 (114)
T 2dnl_A           83 VSSPT   87 (114)
T ss_dssp             ECCSS
T ss_pred             ccCCC
Confidence            65543

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.69  E-value=1e-16  Score=111.04  Aligned_cols=72  Identities=21%  Similarity=0.343  Sum_probs=65.4

Q ss_pred             cEEEEcCCCCCCcHHH----HHHHhccC-CCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 028027           54 TVLYIGRIPHGFYEKE----MQAFFSQF-GAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVH  128 (215)
Q Consensus        54 ~~l~V~nLp~~~te~~----L~~~F~~~-G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~  128 (215)
                      +.|||+|||+.+++++    |+++|++| |.|.+|       +|   |+|||.|.+.++|..|++.|+|..+.|+.|+|.
T Consensus        10 T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v~   79 (96)
T 2diu_A           10 TLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRMENEDVFGNRIIVS   79 (96)
T ss_dssp             EEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSCCEEE
T ss_pred             eEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcCCccCCceEEEE
Confidence            4499999999999988    56899999 599998       44   999999999999999999999999999999999


Q ss_pred             EeCCCCC
Q 028027          129 LIPPEHV  135 (215)
Q Consensus       129 ~a~~~~~  135 (215)
                      +|+..+.
T Consensus        80 ~A~~~sd   86 (96)
T 2diu_A           80 FTPKNRE   86 (96)
T ss_dssp             SSCCSCC
T ss_pred             ecCCCcc
Confidence            9987654

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A

Probab=99.68  E-value=2.4e-16  Score=125.44  Aligned_cols=79  Identities=11%  Similarity=0.264  Sum_probs=72.7

Q ss_pred             CCCcEEEEcCCC-CCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           51 NKATVLYIGRIP-HGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        51 ~~~~~l~V~nLp-~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      .++++|||+||| +.+++++|+++|++||.|.+|.++.++     +|||||+|.+.++|+.|+..|||..|.|+.|.|.+
T Consensus         2 ~~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~~-----~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   76 (205)
T 3tyt_A            2 ADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCV   76 (205)
T ss_dssp             CCCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTS-----TTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEE
Confidence            356899999999 899999999999999999999998753     69999999999999999999999999999999999


Q ss_pred             eCCCC
Q 028027          130 IPPEH  134 (215)
Q Consensus       130 a~~~~  134 (215)
                      +....
T Consensus        77 s~~~~   81 (205)
T 3tyt_A           77 SKQPA   81 (205)
T ss_dssp             CSCSC
T ss_pred             ccCCc
Confidence            87543

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.68  E-value=1.5e-16  Score=126.28  Aligned_cols=83  Identities=24%  Similarity=0.393  Sum_probs=75.1

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ...++|||+|||+++++++|+++|+.||.|..|.++.++.+|.++|||||+|.+.++|..|+..|||..|+|+.|.|.++
T Consensus        26 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~  105 (216)
T 2qfj_A           26 AIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRP  105 (216)
T ss_dssp             HHHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECC
T ss_pred             CcCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecC
Confidence            45689999999999999999999999999999999999889999999999999999999999999999999999999876


Q ss_pred             CCC
Q 028027          131 PPE  133 (215)
Q Consensus       131 ~~~  133 (215)
                      ...
T Consensus       106 ~~~  108 (216)
T 2qfj_A          106 SNI  108 (216)
T ss_dssp             SCC
T ss_pred             CCc
Confidence            543

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.67  E-value=2.8e-16  Score=120.96  Aligned_cols=98  Identities=18%  Similarity=0.206  Sum_probs=80.6

Q ss_pred             CCcccCCCCCCCCCC---CCCCCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHH
Q 028027           31 DFLPLEGGPGRKLTE---EKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEV  107 (215)
Q Consensus        31 d~~~~~g~p~r~~~~---~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~  107 (215)
                      ++..+.|+++++...   ........++|||+|||+.+++++|+++|++||.|..+     ..+|.++|||||+|.+.++
T Consensus        74 ~g~~~~g~~l~v~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~  148 (175)
T 1fje_B           74 TGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEAD  148 (175)
T ss_dssp             GGEEETTEEEEEECCCCSSCSTTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-----CSSSSCCSEEEEECSSHHH
T ss_pred             CCCEeCCeEEEEecCCCccccccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-----cCCCCCceEEEEEECCHHH
Confidence            344455554443222   22334567899999999999999999999999988766     3589999999999999999


Q ss_pred             HHHHHHHhCCceeCCeEEEEEEeCCC
Q 028027          108 AEVVADAMHGYLLFEHILQVHLIPPE  133 (215)
Q Consensus       108 a~~ai~~l~g~~l~g~~l~V~~a~~~  133 (215)
                      |..|+..|||..|+|+.|.|.++.++
T Consensus       149 A~~A~~~l~g~~~~g~~i~v~~a~~k  174 (175)
T 1fje_B          149 AEKNLEEKQGAEIDGRSVSLYYTGEK  174 (175)
T ss_dssp             HHHHHHHHTEEEETTEEEEEEECSSC
T ss_pred             HHHHHHHhCCCEECCeEEEEEecCCC
Confidence            99999999999999999999999875

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.67  E-value=6.1e-16  Score=110.43  Aligned_cols=82  Identities=13%  Similarity=0.125  Sum_probs=73.1

Q ss_pred             CCCcEEEEcCCCC-----CCcHHHHHHHhccCCCeeEEEEeecCCC-CCcccEEEEEEcCHHHHHHHHHHhCCceeCCeE
Q 028027           51 NKATVLYIGRIPH-----GFYEKEMQAFFSQFGAIKRLRIARNKKT-GQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHI  124 (215)
Q Consensus        51 ~~~~~l~V~nLp~-----~~te~~L~~~F~~~G~v~~v~i~~~~~t-g~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~  124 (215)
                      .++++|+|.||..     .-++++|++.|++||.|.+|.|++++.+ +.++|||||+|.+.++|..|+..|||..++|+.
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~   85 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRV   85 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcE
Confidence            4578999999963     2378999999999999999999998644 689999999999999999999999999999999


Q ss_pred             EEEEEeCC
Q 028027          125 LQVHLIPP  132 (215)
Q Consensus       125 l~V~~a~~  132 (215)
                      |.|.++.+
T Consensus        86 i~v~~a~~   93 (105)
T 2pe8_A           86 VKACFYNL   93 (105)
T ss_dssp             CEEEECCH
T ss_pred             EEEEEcCH
Confidence            99999865

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=99.67  E-value=2.6e-16  Score=120.63  Aligned_cols=80  Identities=28%  Similarity=0.457  Sum_probs=74.2

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeC---CeEEEE
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLF---EHILQV  127 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~---g~~l~V  127 (215)
                      ...++|||+|||+.+++++|+++|+.||.|..+.++.+. +|.++|||||+|.+.++|..|+..|||..+.   |+.|.|
T Consensus        93 ~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V  171 (175)
T 3nmr_A           93 VEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVV  171 (175)
T ss_dssp             GGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEE
T ss_pred             CCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECC-CCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEE
Confidence            467899999999999999999999999999999999996 7999999999999999999999999998766   499999


Q ss_pred             EEeC
Q 028027          128 HLIP  131 (215)
Q Consensus       128 ~~a~  131 (215)
                      .||.
T Consensus       172 ~~ad  175 (175)
T 3nmr_A          172 KFAD  175 (175)
T ss_dssp             EECC
T ss_pred             EecC
Confidence            9973

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=99.67  E-value=1.7e-16  Score=131.56  Aligned_cols=101  Identities=20%  Similarity=0.314  Sum_probs=88.2

Q ss_pred             CCcccCCCCCCCCCCCCCCCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHH
Q 028027           31 DFLPLEGGPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEV  110 (215)
Q Consensus        31 d~~~~~g~p~r~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~  110 (215)
                      ++..+.|++++...     ....++|||+|||+.+++++|+++|+.||.|..+.++.+..+|.++|||||+|.+.++|..
T Consensus        78 ~~~~~~g~~i~v~~-----~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~  152 (284)
T 3smz_A           78 HQSRLRERELSVQL-----QPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAAR  152 (284)
T ss_dssp             TTCEETTEECEEEE-----CCCSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHH
T ss_pred             CCCeeCCeEEEEEe-----cCCCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHH
Confidence            44455666554432     2456899999999999999999999999999999999998899999999999999999999


Q ss_pred             HHHHhCCceeCCeEEEEEEeCCCCCC
Q 028027          111 VADAMHGYLLFEHILQVHLIPPEHVH  136 (215)
Q Consensus       111 ai~~l~g~~l~g~~l~V~~a~~~~~~  136 (215)
                      |+..|+|..++|+.|.|.++.+....
T Consensus       153 A~~~l~~~~~~g~~i~v~~a~~~~~~  178 (284)
T 3smz_A          153 AKSDLLGKPLGPRTLYVHWTDAGQLT  178 (284)
T ss_dssp             HHHHHTTCEETTEECEEEECCGGGCC
T ss_pred             HHHHhCCCEeCCcEEEEEECCCCCCC
Confidence            99999999999999999999876543

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=99.67  E-value=3.1e-16  Score=120.23  Aligned_cols=83  Identities=25%  Similarity=0.535  Sum_probs=75.1

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCC--CcccEEEEEEcCHHHHHHHHHHhCCceeC---CeEEE
Q 028027           52 KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTG--QSKHFGFIEFNDPEVAEVVADAMHGYLLF---EHILQ  126 (215)
Q Consensus        52 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg--~~~g~afV~F~~~~~a~~ai~~l~g~~l~---g~~l~  126 (215)
                      +.++|||+|||+++++++|+++|++||.|.+|.+++++.+|  .++|||||+|.+.++|..|+..|+|..+.   ++.+.
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~   81 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQ   81 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCE
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceE
Confidence            56899999999999999999999999999999999998776  89999999999999999999999998765   67788


Q ss_pred             EEEeCCCC
Q 028027          127 VHLIPPEH  134 (215)
Q Consensus       127 V~~a~~~~  134 (215)
                      +.++.+..
T Consensus        82 ~~~~~~~~   89 (175)
T 3nmr_A           82 MKPADSEK   89 (175)
T ss_dssp             EEECGGGC
T ss_pred             Eccccccc
Confidence            88776544

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A

Probab=99.67  E-value=3.7e-16  Score=123.30  Aligned_cols=79  Identities=18%  Similarity=0.231  Sum_probs=72.8

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeC
Q 028027           52 KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIP  131 (215)
Q Consensus        52 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~  131 (215)
                      ..++|||+|||+.+++++|+.+|++||.|..|+++++. +|.++|||||+|.+.++|..|+..+ +..++|+.|.|.++.
T Consensus       108 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~-~~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~Gr~l~V~~~~  185 (193)
T 2voo_A          108 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKD  185 (193)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESSHHHHHHHHHCT-TCEETTEECEEEETT
T ss_pred             ccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHhC-CCeECCEEEEEEEhH
Confidence            35899999999999999999999999999999999986 6999999999999999999999765 459999999999875


Q ss_pred             C
Q 028027          132 P  132 (215)
Q Consensus       132 ~  132 (215)
                      .
T Consensus       186 ~  186 (193)
T 2voo_A          186 D  186 (193)
T ss_dssp             T
T ss_pred             H
Confidence            4

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=99.66  E-value=1.7e-16  Score=121.02  Aligned_cols=80  Identities=23%  Similarity=0.549  Sum_probs=74.2

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeC
Q 028027           52 KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIP  131 (215)
Q Consensus        52 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~  131 (215)
                      ++++|||+|||+++++++|+++|++||.|.+|.+++++.+|.++|||||+|.+.++|..|+.  ++..++|+.|.|.++.
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~~~   79 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK--TQHILDGKVIDPKRAI   79 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHH--SCCEETTEECCCEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHh--cccccCCeEccccccc
Confidence            46899999999999999999999999999999999998899999999999999999999997  4678999999999876


Q ss_pred             CC
Q 028027          132 PE  133 (215)
Q Consensus       132 ~~  133 (215)
                      +.
T Consensus        80 ~~   81 (167)
T 2cjk_A           80 PR   81 (167)
T ss_dssp             CH
T ss_pred             ch
Confidence            53

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=1.6e-16  Score=109.45  Aligned_cols=79  Identities=22%  Similarity=0.488  Sum_probs=66.9

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ...++|||+|||+.+++++|+.+|++||.|..|.++.+     ++|||||+|.+.++|+.++..  ...+.|+.|.|.++
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~~--~~~~~g~~l~v~~a   75 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCGE--DLIIKGISVHISNA   75 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTTC--EEEETTEEEEEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHHhcC--CceeCCEEEEEEec
Confidence            35689999999999999999999999999999999765     579999999999999764321  34568999999999


Q ss_pred             CCCCCC
Q 028027          131 PPEHVH  136 (215)
Q Consensus       131 ~~~~~~  136 (215)
                      .++...
T Consensus        76 ~~~~~~   81 (88)
T 1wf0_A           76 EPKHNS   81 (88)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            876543

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A

Probab=99.66  E-value=2.6e-16  Score=107.85  Aligned_cols=71  Identities=30%  Similarity=0.603  Sum_probs=66.1

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccC----C-------CeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCce
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQF----G-------AIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYL  119 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~----G-------~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~  119 (215)
                      ...++|||+|||+++++++|+++|++|    |       .|.++.+..+      +|||||+|.+.++|..|+ .|||..
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~-~l~g~~   76 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAM-AFDGII   76 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHG-GGTTCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHH-hcCCCE
Confidence            356899999999999999999999999    8       8999988765      589999999999999999 999999


Q ss_pred             eCCeEEEEE
Q 028027          120 LFEHILQVH  128 (215)
Q Consensus       120 l~g~~l~V~  128 (215)
                      ++|+.|+|+
T Consensus        77 ~~g~~l~V~   85 (87)
T 2hzc_A           77 FQGQSLKIR   85 (87)
T ss_dssp             ETTEECEEE
T ss_pred             ECCeEEEEe
Confidence            999999987

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=99.65  E-value=4.8e-16  Score=128.78  Aligned_cols=85  Identities=24%  Similarity=0.330  Sum_probs=79.2

Q ss_pred             CCCCcEEEEcCCCCCC-cHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 028027           50 VNKATVLYIGRIPHGF-YEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVH  128 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~-te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~  128 (215)
                      ....++|||+|||+.+ ++++|+++|+.||.|..+.++.+. +|.++|||||+|.+.++|..|+..|||..|+|+.|.|.
T Consensus       181 ~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~  259 (284)
T 3smz_A          181 LLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVS  259 (284)
T ss_dssp             TTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECS-SCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             cCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECC-CCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEE
Confidence            3567899999999995 999999999999999999999987 89999999999999999999999999999999999999


Q ss_pred             EeCCCCC
Q 028027          129 LIPPEHV  135 (215)
Q Consensus       129 ~a~~~~~  135 (215)
                      ++.+...
T Consensus       260 ~a~~~~~  266 (284)
T 3smz_A          260 FCAPGPP  266 (284)
T ss_dssp             ECCSSSC
T ss_pred             EecCCCc
Confidence            9977543

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A

Probab=99.65  E-value=9.1e-16  Score=126.97  Aligned_cols=83  Identities=19%  Similarity=0.423  Sum_probs=76.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHH----HHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQ----AFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHIL  125 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~----~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l  125 (215)
                      ..+.++|||+|||+.+++++|+    ++|+.||.|..|.+++   +|.++|||||+|.+.++|..|+..|||..|.|+.|
T Consensus         6 ~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   82 (282)
T 3pgw_A            6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPM   82 (282)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEE
Confidence            4567899999999999999976    8999999999998875   78899999999999999999999999999999999


Q ss_pred             EEEEeCCCCC
Q 028027          126 QVHLIPPEHV  135 (215)
Q Consensus       126 ~V~~a~~~~~  135 (215)
                      .|.++.....
T Consensus        83 ~v~~a~~~~~   92 (282)
T 3pgw_A           83 RIQYAKTDSD   92 (282)
T ss_pred             EEEEeccCcc
Confidence            9999976543

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=99.64  E-value=5.3e-16  Score=129.01  Aligned_cols=83  Identities=20%  Similarity=0.324  Sum_probs=76.6

Q ss_pred             CCCCcEEEEcCCCCC-CcHHHHHHHhccCCCeeEEEEeecCC-CCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEE
Q 028027           50 VNKATVLYIGRIPHG-FYEKEMQAFFSQFGAIKRLRIARNKK-TGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQV  127 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~-~te~~L~~~F~~~G~v~~v~i~~~~~-tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V  127 (215)
                      ....++|||+|||+. +++++|+++|+.||.|..|.++.+.. ||.++|||||+|.+.++|..|+ .|||..|+|+.|.|
T Consensus       207 ~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~~i~V  285 (292)
T 2ghp_A          207 TLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISV  285 (292)
T ss_dssp             CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEEEE
T ss_pred             CCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-HhcCCEECCcEEEE
Confidence            456789999999999 99999999999999999999999875 5999999999999999999999 99999999999999


Q ss_pred             EEeCCC
Q 028027          128 HLIPPE  133 (215)
Q Consensus       128 ~~a~~~  133 (215)
                      .|+.++
T Consensus       286 ~~a~~k  291 (292)
T 2ghp_A          286 SLADKK  291 (292)
T ss_dssp             EECCCC
T ss_pred             EEecCC
Confidence            999875

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.62  E-value=8.1e-16  Score=124.86  Aligned_cols=80  Identities=29%  Similarity=0.424  Sum_probs=71.2

Q ss_pred             CCCCcEEEEcCCCCCC---------cHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCcee
Q 028027           50 VNKATVLYIGRIPHGF---------YEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLL  120 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~---------te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l  120 (215)
                      ....++|||+||+..+         ++++|+.+|++||.|.+|.|+.+      +|||||+|.+.++|+.|+..|+|..|
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~------kG~AFV~F~~~~~Ae~A~~am~g~~l  204 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES------KNCGFVKFKYQANAEFAKEAMSNQTL  204 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHHHTTCCC
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECC------CCEEEEEeCCHHHHHHHHHHhCCCEE
Confidence            4567899999999998         79999999999999999999864      69999999999999999999999999


Q ss_pred             ------------CCeEEEEEEeCCCCC
Q 028027          121 ------------FEHILQVHLIPPEHV  135 (215)
Q Consensus       121 ------------~g~~l~V~~a~~~~~  135 (215)
                                  .|+.|.|.||.+.+.
T Consensus       205 ~~~~~~e~~~~~~gr~L~V~wA~~~pn  231 (240)
T 3u1l_A          205 LLPSDKEWDDRREGTGLLVKWANEDPD  231 (240)
T ss_dssp             CCTTSTTGGGGGGSCCCEEEECC----
T ss_pred             eccccccccccCCCCEEEEEEccCCCC
Confidence                        899999999987654

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=99.62  E-value=1.9e-15  Score=121.82  Aligned_cols=82  Identities=17%  Similarity=0.305  Sum_probs=75.6

Q ss_pred             CCCCCCCcEEEEcCCCC-CCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEE
Q 028027           47 KPLVNKATVLYIGRIPH-GFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHIL  125 (215)
Q Consensus        47 ~~~~~~~~~l~V~nLp~-~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l  125 (215)
                      ..+..+.++|||+|||+ .+++++|+++|+.||.|..|.++.++     +|||||+|.+.++|..|+..|||..|.|+.|
T Consensus        28 ~~~~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l  102 (229)
T 2adc_A           28 GLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPI  102 (229)
T ss_dssp             GGGCCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBC
T ss_pred             CCCCCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeEE
Confidence            34456789999999999 99999999999999999999998875     6899999999999999999999999999999


Q ss_pred             EEEEeCCC
Q 028027          126 QVHLIPPE  133 (215)
Q Consensus       126 ~V~~a~~~  133 (215)
                      .|.++.+.
T Consensus       103 ~v~~a~~~  110 (229)
T 2adc_A          103 RITLSKHQ  110 (229)
T ss_dssp             EEECCSCC
T ss_pred             EEEEecCc
Confidence            99999765

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=99.59  E-value=2.2e-15  Score=125.20  Aligned_cols=98  Identities=11%  Similarity=0.215  Sum_probs=79.8

Q ss_pred             CCcccCCCCCCCCCCCCCCCCCCcEEEEcCCCCCCcHHHHHHHhccCC-CeeEEEEeecCCCCCcccEEEEEEcCHHHHH
Q 028027           31 DFLPLEGGPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFG-AIKRLRIARNKKTGQSKHFGFIEFNDPEVAE  109 (215)
Q Consensus        31 d~~~~~g~p~r~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G-~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~  109 (215)
                      ++..+.|++++...      ...++|||+|||+.+++++|+++|+.|| .|..|.++.+. .|.++|||||+|.+.++|.
T Consensus       101 ~~~~~~g~~i~v~~------~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~-~~~~~g~afV~f~~~~~a~  173 (292)
T 2ghp_A          101 THKVVGQNEIIVSH------LTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLR-FNTSRRFAYIDVTSKEDAR  173 (292)
T ss_dssp             TTCEETTEECEEEE------CCSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC--------CCEEEEECSSHHHHH
T ss_pred             CCcEeCCcEEEEEE------CCCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCC-CCCcceEEEEEECCHHHHH
Confidence            55566666665433      2578999999999999999999999999 99999999987 5889999999999999999


Q ss_pred             HHHHHhCCceeCCeEEEEEEeCCCCC
Q 028027          110 VVADAMHGYLLFEHILQVHLIPPEHV  135 (215)
Q Consensus       110 ~ai~~l~g~~l~g~~l~V~~a~~~~~  135 (215)
                      .|+..|||..++|+.|.|.++.+...
T Consensus       174 ~A~~~l~g~~~~g~~l~v~~a~~~~~  199 (292)
T 2ghp_A          174 YCVEKLNGLKIEGYTLVTKVSNPLEK  199 (292)
T ss_dssp             HHHHHHTTCEETTEECEEEECCCC--
T ss_pred             HHHHHhCCCEeCCcEEEEEECCCCcc
Confidence            99999999999999999999987644

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.59  E-value=5.5e-16  Score=119.28  Aligned_cols=84  Identities=19%  Similarity=0.325  Sum_probs=73.3

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ..+.++|||+|||+++++++|+++|..||.+..+ ++.+..+|.++|||||+|.+.++|..|+ .|||..+.|+.|.|.+
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~-~~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~v~~   87 (175)
T 1fje_B           10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDL-AVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEK   87 (175)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTC-CCCEEEEETTTTEEEEEESSHHHHHHHH-HGGGEEETTEEEEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceE-EEEECCCCccccEEEEEECCHHHHHHHH-hcCCCEeCCeEEEEec
Confidence            4567999999999999999999999999987663 3344458899999999999999999999 5999999999999999


Q ss_pred             eCCCCC
Q 028027          130 IPPEHV  135 (215)
Q Consensus       130 a~~~~~  135 (215)
                      +.+...
T Consensus        88 ~~~~~~   93 (175)
T 1fje_B           88 PKGRDS   93 (175)
T ss_dssp             CCCSSC
T ss_pred             CCCccc
Confidence            886543

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.58  E-value=1.8e-14  Score=103.74  Aligned_cols=81  Identities=17%  Similarity=0.299  Sum_probs=69.8

Q ss_pred             CCCcEEEEcCCCCCCc-----------HHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCce
Q 028027           51 NKATVLYIGRIPHGFY-----------EKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYL  119 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~t-----------e~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~  119 (215)
                      .++++|+|.||.....           +++|+++|++||.|..|.| .++   .++|||||+|.+.++|..|+..|||..
T Consensus        13 ~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~lng~~   88 (112)
T 2dit_A           13 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTLDGRW   88 (112)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHSTTCE
T ss_pred             CCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHcCCCE
Confidence            4578999999954432           6899999999999999965 443   378999999999999999999999999


Q ss_pred             eCCeEEEEEEeCCCCC
Q 028027          120 LFEHILQVHLIPPEHV  135 (215)
Q Consensus       120 l~g~~l~V~~a~~~~~  135 (215)
                      |+|+.|.|.++.+...
T Consensus        89 ~~gr~l~v~~a~~~~~  104 (112)
T 2dit_A           89 FGGRQITAQAWDGTTD  104 (112)
T ss_dssp             ETTEECEEEECCSCCC
T ss_pred             ECCcEEEEEEeCCCCC
Confidence            9999999999987543

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.58  E-value=9.5e-15  Score=120.02  Aligned_cols=78  Identities=22%  Similarity=0.526  Sum_probs=71.9

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ....++|||+|||+++|+++|+.+|+.||.|..|.+.++      +|||||+|.+.++|..|+..|||..|.|+.|.|.+
T Consensus        19 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~   92 (261)
T 3sde_A           19 YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRF   92 (261)
T ss_dssp             SCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CcEEEEEECCHHHHHHHHHHcCCcEECCceeEeee
Confidence            356789999999999999999999999999999999654      58999999999999999999999999999999999


Q ss_pred             eCCC
Q 028027          130 IPPE  133 (215)
Q Consensus       130 a~~~  133 (215)
                      +.+.
T Consensus        93 a~~~   96 (261)
T 3sde_A           93 ATHG   96 (261)
T ss_dssp             CCCS
T ss_pred             cccC
Confidence            8653

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.58  E-value=3.1e-15  Score=117.41  Aligned_cols=77  Identities=18%  Similarity=0.360  Sum_probs=72.2

Q ss_pred             CCcEEEEcCCCC-CCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           52 KATVLYIGRIPH-GFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        52 ~~~~l~V~nLp~-~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      .+++|||+|||+ .+++++|+++|++||.|..|.++.++     +|||||+|.+.++|..|+..|||..++|+.|.|.++
T Consensus         2 ~~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a   76 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLS   76 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEEC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEe
Confidence            368999999999 99999999999999999999998874     689999999999999999999999999999999999


Q ss_pred             CCC
Q 028027          131 PPE  133 (215)
Q Consensus       131 ~~~  133 (215)
                      .+.
T Consensus        77 ~~~   79 (198)
T 1qm9_A           77 KHQ   79 (198)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            765

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A

Probab=99.57  E-value=1.3e-14  Score=119.93  Aligned_cols=76  Identities=20%  Similarity=0.485  Sum_probs=71.0

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeC-CeEEEEEE
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLF-EHILQVHL  129 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~-g~~l~V~~  129 (215)
                      ...++|||+|||..+++++|+++|+.||.|..|.++.++     +|||||+|.+.++|..|+..|||..|+ |+.|+|.|
T Consensus       205 ~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~  279 (282)
T 3pgw_A          205 PPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISF  279 (282)
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC-----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEE
Confidence            456889999999999999999999999999999998664     589999999999999999999999999 99999999


Q ss_pred             eC
Q 028027          130 IP  131 (215)
Q Consensus       130 a~  131 (215)
                      ++
T Consensus       280 ak  281 (282)
T 3pgw_A          280 AK  281 (282)
T ss_pred             ec
Confidence            85

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3

Probab=99.56  E-value=1.8e-15  Score=107.74  Aligned_cols=72  Identities=14%  Similarity=0.244  Sum_probs=64.6

Q ss_pred             EcCCCCCCcHHHHHHHh------------ccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEE
Q 028027           58 IGRIPHGFYEKEMQAFF------------SQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHIL  125 (215)
Q Consensus        58 V~nLp~~~te~~L~~~F------------~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l  125 (215)
                      +.|||+.+++++|++.|            ++||.|.+|.|+++. +|.++|||||+|.+.++|..|+..|||..++|+.|
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~-~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i   98 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPI   98 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCC-CCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEE
Confidence            56777777888777666            999999999999986 68999999999999999999999999999999999


Q ss_pred             EEEEe
Q 028027          126 QVHLI  130 (215)
Q Consensus       126 ~V~~a  130 (215)
                      .|.++
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            99986

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A

Probab=99.56  E-value=6e-15  Score=117.35  Aligned_cols=78  Identities=14%  Similarity=0.216  Sum_probs=69.8

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCe--eEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCe----E
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAI--KRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEH----I  124 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v--~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~----~  124 (215)
                      .+.++|||+|||+.+++++|+++|++||.|  ..+.++.+.  |.++|||||+|.+.++|..||..|||+.|.|+    +
T Consensus       121 ~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~--~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p  198 (205)
T 3tyt_A          121 HPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK--SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYP  198 (205)
T ss_dssp             CCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCC--SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSC
T ss_pred             CCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCC--CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcc
Confidence            456799999999999999999999999999  899998774  55679999999999999999999999999986    5


Q ss_pred             EEEEEe
Q 028027          125 LQVHLI  130 (215)
Q Consensus       125 l~V~~a  130 (215)
                      +.|.++
T Consensus       199 ~~vk~~  204 (205)
T 3tyt_A          199 YTLKLC  204 (205)
T ss_dssp             EECEEE
T ss_pred             eEEEec
Confidence            777765

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A

Probab=99.56  E-value=1.7e-14  Score=102.88  Aligned_cols=83  Identities=16%  Similarity=0.267  Sum_probs=71.3

Q ss_pred             CCCcEEEEcCC--CCCC--------cHHHHHHHhccCCCeeEEEEeecCCC--CCcccEEEEEEcCHHHHHHHHHHhCCc
Q 028027           51 NKATVLYIGRI--PHGF--------YEKEMQAFFSQFGAIKRLRIARNKKT--GQSKHFGFIEFNDPEVAEVVADAMHGY  118 (215)
Q Consensus        51 ~~~~~l~V~nL--p~~~--------te~~L~~~F~~~G~v~~v~i~~~~~t--g~~~g~afV~F~~~~~a~~ai~~l~g~  118 (215)
                      .+++.|.|.|+  |..+        .+++|++.|++||.|.+|.|+++..+  +.++|||||+|.+.++|..|+..|||.
T Consensus         3 ~ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~   82 (105)
T 3v4m_A            3 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   82 (105)
T ss_dssp             SCCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCC
Confidence            35678999998  3333        34789999999999999999988754  468999999999999999999999999


Q ss_pred             eeCCeEEEEEEeCCC
Q 028027          119 LLFEHILQVHLIPPE  133 (215)
Q Consensus       119 ~l~g~~l~V~~a~~~  133 (215)
                      .++|+.|.|.++...
T Consensus        83 ~f~GR~i~v~~~~~~   97 (105)
T 3v4m_A           83 KFANRVVVTKYCDPD   97 (105)
T ss_dssp             EETTEECEEEEECHH
T ss_pred             EeCCCEEEEEEeCHH
Confidence            999999999998653

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.54  E-value=1.4e-14  Score=113.67  Aligned_cols=78  Identities=21%  Similarity=0.332  Sum_probs=71.8

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCC-CeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeC-CeEEEEE
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFG-AIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLF-EHILQVH  128 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G-~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~-g~~l~V~  128 (215)
                      .+.++|||+|||..+++++|+++|+.|| .|..+.++.+.     +|||||+|.+.++|..|+..|||..++ |+.|.|.
T Consensus       118 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~  192 (198)
T 1qm9_A          118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD-----RKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVS  192 (198)
T ss_dssp             CCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESSTT-----SSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEE
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEE
Confidence            4578999999999999999999999999 99999996642     689999999999999999999999999 9999999


Q ss_pred             EeCCC
Q 028027          129 LIPPE  133 (215)
Q Consensus       129 ~a~~~  133 (215)
                      |+++.
T Consensus       193 ~a~~~  197 (198)
T 1qm9_A          193 FSKST  197 (198)
T ss_dssp             EECCC
T ss_pred             eeccc
Confidence            99763

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} SCOP: d.58.7.0 PDB: 3us5_A 2dny_A

Probab=99.54  E-value=4.2e-14  Score=102.87  Aligned_cols=81  Identities=19%  Similarity=0.248  Sum_probs=71.3

Q ss_pred             CCcEEEEcCCCC-----CCcHHHHHHHhccCCCeeEEEEeecCC----CCCcccEEEEEEcCHHHHHHHHHHhCCceeCC
Q 028027           52 KATVLYIGRIPH-----GFYEKEMQAFFSQFGAIKRLRIARNKK----TGQSKHFGFIEFNDPEVAEVVADAMHGYLLFE  122 (215)
Q Consensus        52 ~~~~l~V~nLp~-----~~te~~L~~~F~~~G~v~~v~i~~~~~----tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g  122 (215)
                      ++++|+|.|+-.     .-.+++|++.|++||.|.+|.|++++.    ++.++||+||+|.+.++|..|+..|||..++|
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~G   98 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG   98 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECC
Confidence            578999999842     124689999999999999999998864    46788999999999999999999999999999


Q ss_pred             eEEEEEEeCC
Q 028027          123 HILQVHLIPP  132 (215)
Q Consensus       123 ~~l~V~~a~~  132 (215)
                      +.|.|.++..
T Consensus        99 R~i~v~~~~~  108 (118)
T 3ue2_A           99 RKVVAEVYDQ  108 (118)
T ss_dssp             EECEEEEECH
T ss_pred             cEEEEEEcCh
Confidence            9999999864

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=99.52  E-value=3.8e-14  Score=114.16  Aligned_cols=78  Identities=21%  Similarity=0.332  Sum_probs=71.5

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCC-CeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeC-CeEEEEE
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFG-AIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLF-EHILQVH  128 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G-~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~-g~~l~V~  128 (215)
                      .+.++|||+|||+.+++++|+++|+.|| .|..|.++.+     .+|||||+|.+.++|..|+..|||..++ |+.|.|.
T Consensus       149 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~  223 (229)
T 2adc_A          149 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVS  223 (229)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS-----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEE
T ss_pred             CCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC-----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEE
Confidence            4578999999999999999999999999 9999998653     2589999999999999999999999999 9999999


Q ss_pred             EeCCC
Q 028027          129 LIPPE  133 (215)
Q Consensus       129 ~a~~~  133 (215)
                      |+++.
T Consensus       224 ~a~~~  228 (229)
T 2adc_A          224 FSKST  228 (229)
T ss_dssp             ECSSC
T ss_pred             EecCC
Confidence            98763

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A

Probab=99.51  E-value=5.8e-14  Score=107.34  Aligned_cols=76  Identities=28%  Similarity=0.519  Sum_probs=67.6

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccC----C-------CeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCcee
Q 028027           52 KATVLYIGRIPHGFYEKEMQAFFSQF----G-------AIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLL  120 (215)
Q Consensus        52 ~~~~l~V~nLp~~~te~~L~~~F~~~----G-------~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l  120 (215)
                      +.++|||+|||+++++++|+++|++|    |       .|.++.+..      ++|||||+|.+.++|..|+ .|||..+
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~------~~g~afV~f~~~~~A~~A~-~~~~~~~   75 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQ------DKNFAFLEFRSVDETTQAM-AFDGIIF   75 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEET------TTTEEEEEESSHHHHHHHG-GGTTCEE
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecC------CCCEEEEEeCCHHHHHHHH-HhCCcEe
Confidence            46899999999999999999999999    6       677776654      3699999999999999999 8999999


Q ss_pred             CCeEEEEEEeCCCC
Q 028027          121 FEHILQVHLIPPEH  134 (215)
Q Consensus       121 ~g~~l~V~~a~~~~  134 (215)
                      .|+.|.|.++.+..
T Consensus        76 ~g~~i~v~~~~~~~   89 (172)
T 2g4b_A           76 QGQSLKIRRPHDYQ   89 (172)
T ss_dssp             TTEECEEECCSSCC
T ss_pred             cCceeeecCCcccC
Confidence            99999999876654

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.49  E-value=1e-13  Score=108.30  Aligned_cols=76  Identities=29%  Similarity=0.521  Sum_probs=66.4

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccC----C-------CeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCcee
Q 028027           52 KATVLYIGRIPHGFYEKEMQAFFSQF----G-------AIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLL  120 (215)
Q Consensus        52 ~~~~l~V~nLp~~~te~~L~~~F~~~----G-------~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l  120 (215)
                      ..++|||+|||+++++++|+++|+.|    |       .|..+.+      +.++|||||+|.+.++|..|+ .|||..|
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~------~~~~g~afV~F~~~~~A~~Al-~l~g~~~   75 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI------NQDKNFAFLEFRSVDETTQAM-AFDGIIF   75 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEE------ETTTTEEEEEESCSHHHHHHG-GGTTEEE
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEe------cCCCCEEEEEeCCHHHHHHHH-HhcCCEE
Confidence            46899999999999999999999999    4       5555554      445799999999999999999 8999999


Q ss_pred             CCeEEEEEEeCCCC
Q 028027          121 FEHILQVHLIPPEH  134 (215)
Q Consensus       121 ~g~~l~V~~a~~~~  134 (215)
                      +|+.|.|.++.+..
T Consensus        76 ~g~~i~v~~~~~~~   89 (198)
T 2yh0_A           76 QGQSLKIRRPHDYQ   89 (198)
T ss_dssp             TTEEEEEECCCCCC
T ss_pred             cCceEEEeCCCCCC
Confidence            99999999987653

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.45  E-value=8.7e-13  Score=93.12  Aligned_cols=67  Identities=15%  Similarity=0.346  Sum_probs=58.8

Q ss_pred             CCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeCCCCCC
Q 028027           63 HGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPPEHVH  136 (215)
Q Consensus        63 ~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~~~~~~  136 (215)
                      ..+++++|+.+|++||.|..|.|+     +.++|||||+|.+.++|..|+..+++  +.|+.|+|.|+.+....
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~V~~a~~~~~~   93 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNEVG--LVDNPLKISWLEGQPQD   93 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBCEEECSSCCCCC
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeEEEEEccCCCCC
Confidence            568999999999999999999987     36789999999999999999987554  67999999999876543

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A

Probab=99.39  E-value=2.5e-12  Score=92.91  Aligned_cols=78  Identities=9%  Similarity=0.204  Sum_probs=66.1

Q ss_pred             CCCcEEEEcCCCCCC----------cHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCcee
Q 028027           51 NKATVLYIGRIPHGF----------YEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLL  120 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~----------te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l  120 (215)
                      .+++.|.|.|+-..-          .+++|++.|++||.|.+|.|.++.    ++|||||+|.+.++|..|+..|||..+
T Consensus         5 ~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG~~f   80 (114)
T 3s6e_A            5 LATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGRWF   80 (114)
T ss_dssp             CCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTCEE
T ss_pred             CCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCCEE
Confidence            456788888873321          235889999999999999997653    489999999999999999999999999


Q ss_pred             CCeEEEEEEeCC
Q 028027          121 FEHILQVHLIPP  132 (215)
Q Consensus       121 ~g~~l~V~~a~~  132 (215)
                      +|+.|.|.++..
T Consensus        81 ~GR~i~v~~~~~   92 (114)
T 3s6e_A           81 AGKMITAAYVPL   92 (114)
T ss_dssp             TTEECEEEEECH
T ss_pred             CCEEEEEEEEcH
Confidence            999999999854

>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*

Probab=99.38  E-value=1e-12  Score=111.87  Aligned_cols=75  Identities=12%  Similarity=0.298  Sum_probs=64.9

Q ss_pred             CCCcEEEEcC--CCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeC---Ce--
Q 028027           51 NKATVLYIGR--IPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLF---EH--  123 (215)
Q Consensus        51 ~~~~~l~V~n--Lp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~---g~--  123 (215)
                      .++.+|||+|  |++.+|+++|+++|++||.|.+|.+..      ++|||||+|.+.++|+.|++.|||..+.   |+  
T Consensus        16 ~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~   89 (345)
T 3tht_A           16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKI   89 (345)
T ss_dssp             SCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEE
T ss_pred             CCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCccccccCCce
Confidence            5678999999  588999999999999999999987753      3699999999999999999999999873   45  


Q ss_pred             EEEEEEeC
Q 028027          124 ILQVHLIP  131 (215)
Q Consensus       124 ~l~V~~a~  131 (215)
                      .|.|.++.
T Consensus        90 ~ly~~~~~   97 (345)
T 3tht_A           90 TLYLNFVE   97 (345)
T ss_dssp             ECEEEECS
T ss_pred             EEEEEEee
Confidence            57777774

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.29  E-value=1.1e-11  Score=85.03  Aligned_cols=74  Identities=19%  Similarity=0.404  Sum_probs=63.0

Q ss_pred             CCCcEEEEcCCCC----CCcH----HHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCC
Q 028027           51 NKATVLYIGRIPH----GFYE----KEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFE  122 (215)
Q Consensus        51 ~~~~~l~V~nLp~----~~te----~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g  122 (215)
                      ++..||+|..++.    .+..    .+|...|++||.|..++++.+.        +||+|.+.++|.+|+. |||..++|
T Consensus         5 Ppd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~-mnG~~v~G   75 (91)
T 2dnr_A            5 SSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFLEGSSALNVLS-LNGKELLN   75 (91)
T ss_dssp             CSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEESSHHHHHHGGG-GTTCEETT
T ss_pred             CCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEECChHHHHHHHh-cCCeEeCC
Confidence            4467888887762    3333    6788999999999999998873        8999999999999997 99999999


Q ss_pred             eEEEEEEeCCC
Q 028027          123 HILQVHLIPPE  133 (215)
Q Consensus       123 ~~l~V~~a~~~  133 (215)
                      +.|+|.++++.
T Consensus        76 r~LkV~lkt~d   86 (91)
T 2dnr_A           76 RTITIALKSPS   86 (91)
T ss_dssp             EEEEEEECCCS
T ss_pred             eEEEEEeCCCC
Confidence            99999998764

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.23  E-value=3.5e-11  Score=87.41  Aligned_cols=75  Identities=19%  Similarity=0.234  Sum_probs=67.4

Q ss_pred             CCCcEEEEcCCCCC-CcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcC-HHHHHHHHHHhC--CceeCCeEEE
Q 028027           51 NKATVLYIGRIPHG-FYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFND-PEVAEVVADAMH--GYLLFEHILQ  126 (215)
Q Consensus        51 ~~~~~l~V~nLp~~-~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~-~~~a~~ai~~l~--g~~l~g~~l~  126 (215)
                      ..++.|||+||++. +++++|+++|++||.|..|.+.++..      .|||.|.+ ..+|..|+..||  +..|.|..+.
T Consensus        16 ~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~   89 (121)
T 1owx_A           16 KIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGNLQLRNKEVT   89 (121)
T ss_dssp             CCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEE
T ss_pred             cCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCCcEEeCcEEE
Confidence            56889999999999 99999999999999999999988763      59999999 899999999995  6789999998


Q ss_pred             EEEeC
Q 028027          127 VHLIP  131 (215)
Q Consensus       127 V~~a~  131 (215)
                      +++..
T Consensus        90 ~evL~   94 (121)
T 1owx_A           90 WEVLE   94 (121)
T ss_dssp             EEECC
T ss_pred             EEECC
Confidence            88754

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.08  E-value=1.9e-10  Score=79.28  Aligned_cols=72  Identities=18%  Similarity=0.263  Sum_probs=61.5

Q ss_pred             CCCcEEEEcCCCCC------CcH---HHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeC
Q 028027           51 NKATVLYIGRIPHG------FYE---KEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLF  121 (215)
Q Consensus        51 ~~~~~l~V~nLp~~------~te---~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~  121 (215)
                      ++..||+|..++..      ..+   .+|.+.|++||.|..++++.++        +||+|.+.++|.+||. |||..++
T Consensus        13 PpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~-ldG~~v~   83 (95)
T 1ufw_A           13 PLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLD-VDGMKVK   83 (95)
T ss_dssp             CTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHH-GGGSEET
T ss_pred             CCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHh-cCCeeeC
Confidence            44688999988743      232   5688999999999999999874        9999999999999998 9999999


Q ss_pred             CeEEEEEEeC
Q 028027          122 EHILQVHLIP  131 (215)
Q Consensus       122 g~~l~V~~a~  131 (215)
                      |+.|+|.+..
T Consensus        84 Gr~L~V~~k~   93 (95)
T 1ufw_A           84 GRAVKISGPS   93 (95)
T ss_dssp             TEEEEEECCC
T ss_pred             CeEEEEeccC
Confidence            9999998754

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=99.01  E-value=8.4e-10  Score=88.14  Aligned_cols=68  Identities=19%  Similarity=0.229  Sum_probs=61.2

Q ss_pred             CcHHHHHHHhccCCCeeEEEEeecC----CCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeCC
Q 028027           65 FYEKEMQAFFSQFGAIKRLRIARNK----KTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPP  132 (215)
Q Consensus        65 ~te~~L~~~F~~~G~v~~v~i~~~~----~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~~  132 (215)
                      -.+++|++.|++||.|.++.++++.    .++.++|++||+|.+.++|.+|+..|||..++||.|.|.++..
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~~  212 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQ  212 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECCH
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcCH
Confidence            4568999999999999999998654    3558999999999999999999999999999999999999754

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.69  E-value=1e-07  Score=67.09  Aligned_cols=74  Identities=11%  Similarity=0.159  Sum_probs=67.6

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccC-----CCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQF-----GAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHI  124 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~-----G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~  124 (215)
                      +...++|-+-|||..++...|+.++..+     |.+..+.+..|.      +-|+|+|.+...|-+|.-.|+|..|.|+.
T Consensus        18 ~~~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH------~GAivef~d~~~AgKasLaL~G~ef~gr~   91 (117)
T 2l9w_A           18 KELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF------NGAIIIFRDSKFAAKMLMILNGSQFQGKV   91 (117)
T ss_dssp             TTTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTT------TEEEEECSCHHHHHHHHHHHSSEEETTEE
T ss_pred             ccCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCC------CceEEEEccchhhHHHHhhcCCeeecCeE
Confidence            4567889999999999999999999999     999999998885      67999999999999998899999999999


Q ss_pred             EEEEE
Q 028027          125 LQVHL  129 (215)
Q Consensus       125 l~V~~  129 (215)
                      |+|.-
T Consensus        92 Lr~gT   96 (117)
T 2l9w_A           92 IRSGT   96 (117)
T ss_dssp             EEEEC
T ss_pred             EEecC
Confidence            99863

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=97.84  E-value=6.6e-05  Score=52.40  Aligned_cols=76  Identities=9%  Similarity=0.120  Sum_probs=64.0

Q ss_pred             CCcEEEEcCCCCCCcH-----HHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEE
Q 028027           52 KATVLYIGRIPHGFYE-----KEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQ  126 (215)
Q Consensus        52 ~~~~l~V~nLp~~~te-----~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~  126 (215)
                      -+++|+|.||+..+-.     +.++++|..|+++....+.+.-      .-..|.|.+.++|.+|-..|++..++|+.|+
T Consensus         4 ~pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSF------RRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r   77 (104)
T 1wey_A            4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF------KRVRINFSNPLSAADARLRLHKTEFLGKEMK   77 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTT------TEEEEECSSTTHHHHHHHTSTTSEETTEECE
T ss_pred             CCceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcc------eEEEEEeCChHHHHHHHHHhccceecCceeE
Confidence            4678999999886522     5779999999999888777653      2468999999999999999999999999999


Q ss_pred             EEEeCCC
Q 028027          127 VHLIPPE  133 (215)
Q Consensus       127 V~~a~~~  133 (215)
                      |-++.+.
T Consensus        78 ~YFgq~~   84 (104)
T 1wey_A           78 LYFAQTL   84 (104)
T ss_dssp             EECCCCS
T ss_pred             EEecCCC
Confidence            9998754

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.77  E-value=0.00065  Score=47.23  Aligned_cols=76  Identities=17%  Similarity=0.241  Sum_probs=61.7

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhcc-----CCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEE
Q 028027           52 KATVLYIGRIPHGFYEKEMQAFFSQ-----FGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQ  126 (215)
Q Consensus        52 ~~~~l~V~nLp~~~te~~L~~~F~~-----~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~  126 (215)
                      ...+|.|.|||+.+.++.|.-+|+.     -|+|..+....        +-|+|+|.+...|++++.. ..+.|+|..|.
T Consensus         7 ~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~k-~~H~L~~~~Ls   77 (104)
T 2dhx_A            7 GGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLAQ-ADHELHGAQLS   77 (104)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHTC-SCCBSSSSBCE
T ss_pred             CccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhcC-CcceecCeEEE
Confidence            4578999999999999999999986     25888886633        4789999999999999853 47889999999


Q ss_pred             EEEeCCCCCC
Q 028027          127 VHLIPPEHVH  136 (215)
Q Consensus       127 V~~a~~~~~~  136 (215)
                      |.-..+....
T Consensus        78 V~P~~~~~~~   87 (104)
T 2dhx_A           78 LRPAPPRAPA   87 (104)
T ss_dssp             EEECCCCCCC
T ss_pred             EEcCCCCCcc
Confidence            9876655443

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=97.66  E-value=0.00038  Score=47.55  Aligned_cols=68  Identities=16%  Similarity=0.309  Sum_probs=56.3

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCC--cccEEEEEEcCHHHHHHHHHHhCCceeC
Q 028027           54 TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQ--SKHFGFIEFNDPEVAEVVADAMHGYLLF  121 (215)
Q Consensus        54 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~--~~g~afV~F~~~~~a~~ai~~l~g~~l~  121 (215)
                      +.|.|.+||+++|++++.+.++....+....++..+.+..  .-+-|||.|.+.+++....+.++|+.+-
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~   71 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFL   71 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEE
Confidence            4689999999999999999999998877777766543322  3367999999999999999999998764

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=97.62  E-value=0.00023  Score=48.92  Aligned_cols=56  Identities=18%  Similarity=0.465  Sum_probs=47.9

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhC
Q 028027           52 KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMH  116 (215)
Q Consensus        52 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~  116 (215)
                      ..+.++| ++|..+...||..+|+.||. ..|.++.|.       .|||.|.+++.|..|+..++
T Consensus        15 r~HVf~l-~FP~ewKt~DI~~lFs~fgg-v~I~WidDT-------sAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           15 RDHVLHV-TFPKEWKTSDLYQLFSAFGN-IQISWIDDT-------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCSEEEE-ECCTTCCHHHHHHHHTTTCS-CCCEEEETT-------EEEEECSCHHHHHHHHHHHH
T ss_pred             CCeEEEE-eCChhhhhHHHHHHhhccCC-EEEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            3466777 99999999999999999994 467888773       89999999999999998763

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=97.46  E-value=0.00027  Score=48.80  Aligned_cols=54  Identities=19%  Similarity=0.449  Sum_probs=47.1

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhC
Q 028027           54 TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMH  116 (215)
Q Consensus        54 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~  116 (215)
                      +.++| ++|..+...||..+|+.|| -..|.++.|.       .|||.|.+++.|..|+..+.
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fg-gv~I~WidDT-------sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFG-NIQISWIDDT-------SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSE-EEEEEEEETT-------EEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccC-CEEEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            45677 9999999999999999999 4577888873       89999999999999998764

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=97.32  E-value=0.0016  Score=46.55  Aligned_cols=74  Identities=15%  Similarity=0.163  Sum_probs=58.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCC-eEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFE-HILQVH  128 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g-~~l~V~  128 (215)
                      ....+.|.|-+.|+.. -..+...|++||.|.+.....      ...+-.|.|.+..+|++||. .||..|+| -.|-|.
T Consensus        21 ~~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~~------~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~   92 (119)
T 1wwh_A           21 HLDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMSN------TGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVK   92 (119)
T ss_dssp             CGGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEECS------SSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEE
T ss_pred             CCCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccCC------CCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEE
Confidence            3456889999999985 466778999999999887621      23699999999999999995 59999985 667777


Q ss_pred             EeC
Q 028027          129 LIP  131 (215)
Q Consensus       129 ~a~  131 (215)
                      ...
T Consensus        93 p~~   95 (119)
T 1wwh_A           93 PCI   95 (119)
T ss_dssp             ECC
T ss_pred             ECC
Confidence            653

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=96.53  E-value=0.0037  Score=43.03  Aligned_cols=69  Identities=16%  Similarity=0.365  Sum_probs=49.6

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCC--CcccEEEEEEcCHHHHHHHHHHhCCceeC
Q 028027           53 ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTG--QSKHFGFIEFNDPEVAEVVADAMHGYLLF  121 (215)
Q Consensus        53 ~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg--~~~g~afV~F~~~~~a~~ai~~l~g~~l~  121 (215)
                      +-.|.|..||+++||+++.+.++..-.+....++....+.  ..-.-|||.|.+.+++..-.+.++|+.+-
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~   79 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFL   79 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEE
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEE
Confidence            4569999999999999988877765444332222222111  12256899999999999999999998764

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=96.50  E-value=0.0037  Score=45.36  Aligned_cols=79  Identities=18%  Similarity=0.258  Sum_probs=55.1

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeE-EEEeec------------CCCC-CcccEEEEEEcCHHHHHHHHHHhC
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKR-LRIARN------------KKTG-QSKHFGFIEFNDPEVAEVVADAMH  116 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~-v~i~~~------------~~tg-~~~g~afV~F~~~~~a~~ai~~l~  116 (215)
                      .....|.|-+.|++.+ ..+-..|++||.|.. +...++            +..+ ...++..|+|.+..+|.+||. .|
T Consensus         5 ~~e~~VtVFGFp~~~~-~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~N   82 (132)
T 3p3d_A            5 NGELAILVFGYPETMA-NQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-EN   82 (132)
T ss_dssp             ---CEEEEECCCGGGH-HHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TT
T ss_pred             cCceEEEEEecCHHHH-HHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hC
Confidence            3446678888988655 556678999999866 211110            0000 134688999999999999995 69


Q ss_pred             CceeCCeEEEEEEeC
Q 028027          117 GYLLFEHILQVHLIP  131 (215)
Q Consensus       117 g~~l~g~~l~V~~a~  131 (215)
                      |..|+|..|-|....
T Consensus        83 G~ii~G~mIGV~Py~   97 (132)
T 3p3d_A           83 GAVFNGVLLGVIPYT   97 (132)
T ss_dssp             TCEETTEECEEEECC
T ss_pred             CeEeCcEEEEEEECC
Confidence            999999988887764

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=96.48  E-value=0.0013  Score=57.88  Aligned_cols=55  Identities=22%  Similarity=0.384  Sum_probs=41.9

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHH
Q 028027           53 ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD  113 (215)
Q Consensus        53 ~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~  113 (215)
                      .++|+|. .|..+++.+|.++|++||+|.++.+-.+.  |   -||.|+|.+.+++..++.
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~--g---~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF--G---LYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS--S---EEEEEECC---CCHHHHS
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC--C---eEEEEEeCCHHHHHHHHh
Confidence            4789997 79999999999999999999999887653  3   699999999999887653

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=95.90  E-value=0.0082  Score=44.42  Aligned_cols=35  Identities=20%  Similarity=0.040  Sum_probs=29.0

Q ss_pred             EEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCc
Q 028027           82 RLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGY  118 (215)
Q Consensus        82 ~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~  118 (215)
                      .+.|+.+.  ..++|||||+|.+.++|+.|+..+++.
T Consensus         2 ~~kl~ln~--~~~~G~~fV~f~~~~~A~~al~~~~~~   36 (158)
T 2kn4_A            2 QYKLILNG--KTLKGETTTEAVDAATAEKVFKQYAND   36 (158)
T ss_dssp             EEEEEEEC--SSCEEEEEEECSSHHHHHHHHHHHHHH
T ss_pred             cEEEEecC--ccccchhHHHHHHHHhHHHHHHhhccc
Confidence            45677774  468999999999999999999888753

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A

Probab=95.33  E-value=0.0095  Score=43.79  Aligned_cols=41  Identities=15%  Similarity=-0.144  Sum_probs=37.2

Q ss_pred             CCCcccEEEEEEcCHHHHHHHHHHh-CCceeCCeEEEEEEeCC
Q 028027           91 TGQSKHFGFIEFNDPEVAEVVADAM-HGYLLFEHILQVHLIPP  132 (215)
Q Consensus        91 tg~~~g~afV~F~~~~~a~~ai~~l-~g~~l~g~~l~V~~a~~  132 (215)
                      ....+|+++|+|.+.+.|+.|+..| ||..++| .|.+.++..
T Consensus         9 g~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~   50 (150)
T 2i2y_A            9 GKTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATK   50 (150)
T ss_dssp             CSSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTT
T ss_pred             cccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccC
Confidence            4567899999999999999999999 9999999 999998765

>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease, hydrolase, magnesium, metal nonsense-mediated mRNA decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus}

Probab=92.60  E-value=0.34  Score=43.03  Aligned_cols=55  Identities=18%  Similarity=0.449  Sum_probs=46.2

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhC
Q 028027           53 ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMH  116 (215)
Q Consensus        53 ~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~  116 (215)
                      +..++|+ +|..+...+|.++|+.||. ..|.++.+       ..|||.|.+.+.|..++..++
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~-v~V~widd-------t~a~V~~~~~~~a~~~l~~~~  494 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGN-IQISWIDD-------TSAFVSLSQPEQVQIAVNTSK  494 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCC-CEEEECSS-------SEEEEECSCHHHHHHHHHHHT
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCC-EEEEEEcC-------CeEEEEECCHHHHHHHHHHHH
Confidence            4577776 8889999999999999995 46666655       379999999999999999885

---

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	215
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	2e-13
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	2e-13
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	1e-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:) 4e-12
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	2e-11
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	2e-11
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	2e-11
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	4e-11
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	5e-11
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	7e-11
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	7e-11
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	1e-10
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	3e-10
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	4e-10
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	4e-10
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	6e-10
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	6e-10
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	8e-10
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	1e-09
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	1e-09
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-09
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	2e-09
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	3e-09
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	5e-09
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	6e-09
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	6e-09
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	7e-09
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	1e-08
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	1e-08
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	1e-08
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	2e-08
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	4e-08
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	4e-08
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	4e-08
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	5e-08
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	9e-08
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	1e-07
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	1e-07
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	2e-05
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	2e-07
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	2e-07
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	3e-07
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	3e-07
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	7e-07
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	9e-07
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	1e-06
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	2e-06
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	3e-06
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	4e-06
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	8e-06
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	1e-05
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	1e-05
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	1e-05
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	2e-05
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	2e-05
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	3e-05
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	3e-05
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	3e-05
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	9e-05
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	2e-04
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-04
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	3e-04
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	5e-04
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	6e-04
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	0.001
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	0.003

>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 = 61.5 bits (149), Expect = 2e-13
 Identities = 20/78 (25%), Positives = 38/78 (48%), Gaps = 2/78 (2%)

Query: 52  KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVV 111
           K T LY+  +P    + ++   F ++G+I +  I R+K TG+ +   F+ +N  E A+  
Sbjct: 5   KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEA 64

Query: 112 ADAMHGYLLF--EHILQV 127
             A++  +       L V
Sbjct: 65  ISALNNVIPEGGSQPLSV 82

>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 = 61.1 bits (148), Expect = 2e-13
 Identities = 18/74 (24%), Positives = 34/74 (45%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           LY+G +     E  +   FS  G I  +R+ R+  T +S  + ++ F  P  AE   D M
Sbjct: 3   LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 62

Query: 116 HGYLLFEHILQVHL 129
           +  ++    +++  
Sbjct: 63  NFDVIKGKPVRIMW 76

>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 = 58.9 bits (142), Expect = 1e-12
 Identities = 21/79 (26%), Positives = 36/79 (45%)

Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
           T L +  +P    ++E+ A F   G I   RI R+ KTG S  + F++F     ++    
Sbjct: 3   TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 62

Query: 114 AMHGYLLFEHILQVHLIPP 132
            ++G  +    L+V    P
Sbjct: 63  VLNGITVRNKRLKVSYARP 81

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.5 bits (141), Expect = 4e-12
 Identities = 12/93 (12%), Positives = 30/93 (32%), Gaps = 1/93 (1%)

Query: 39  PGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFG 98
           P         L +  + + +      F+E+       ++G ++ + +  N          
Sbjct: 13  PQNSSQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN-LGDHLVGNV 71

Query: 99  FIEFNDPEVAEVVADAMHGYLLFEHILQVHLIP 131
           +++F   E AE     ++        +   L P
Sbjct: 72  YVKFRREEDAEKAVIDLNNRWFNGQPIHAELSP 104

>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 = 55.7 bits (134), Expect = 2e-11
 Identities = 14/76 (18%), Positives = 33/76 (43%), Gaps = 1/76 (1%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L +  +  G  + ++Q  F++FG +K+  +  ++ +G+S     + F     A       
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQY 61

Query: 116 HGYLLFEHILQVHLIP 131
           +G  L    + + L+ 
Sbjct: 62  NGVPLDGRPMNIQLVT 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 = 56.1 bits (135), Expect = 2e-11
 Identities = 20/79 (25%), Positives = 40/79 (50%)

Query: 49  LVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVA 108
           L+ K+  LY+G +     E+++   FS+ G IK++ +  +K    +  F F+E+     A
Sbjct: 3   LLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADA 62

Query: 109 EVVADAMHGYLLFEHILQV 127
           E     ++G  L + I++ 
Sbjct: 63  ENAMRYINGTRLDDRIIRT 81

>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 = 56.2 bits (135), Expect = 2e-11
 Identities = 19/77 (24%), Positives = 36/77 (46%)

Query: 51  NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEV 110
           N+   +Y+G +     E  +   F Q G +    + +++ TGQ + +GF+EF   E A+ 
Sbjct: 7   NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADY 66

Query: 111 VADAMHGYLLFEHILQV 127
               M    L+   ++V
Sbjct: 67  AIKIMDMIKLYGKPIRV 83

>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 = 55.1 bits (132), Expect = 4e-11
 Identities = 22/78 (28%), Positives = 37/78 (47%)

Query: 52  KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVV 111
           +   LY+  +P    +KE++  FSQ+G I   RI  ++ TG S+  GFI F+    AE  
Sbjct: 5   RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEA 64

Query: 112 ADAMHGYLLFEHILQVHL 129
              ++G         + +
Sbjct: 65  IKGLNGQKPSGATEPITV 82

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 54.9 bits (132), Expect = 5e-11
 Identities = 21/84 (25%), Positives = 42/84 (50%), Gaps = 2/84 (2%)

Query: 46  EKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKK-TGQSKHFGFIEFND 104
           + P     + + +  IP    ++E++  FS FG +K +R+ +    TG  + FGF++F  
Sbjct: 1   QVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFIT 60

Query: 105 PEVAEVVADAM-HGYLLFEHILQV 127
            + A+   +A+ H   L+   L +
Sbjct: 61  KQDAKKAFNALCHSTHLYGRRLVL 84

>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 = 54.6 bits (131), Expect = 7e-11
 Identities = 20/75 (26%), Positives = 38/75 (50%)

Query: 53  ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVA 112
           A  L+IG +P+   + +++   + FG +K   + ++  TG SK + F E+ D  V +   
Sbjct: 1   AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 60

Query: 113 DAMHGYLLFEHILQV 127
             ++G  L +  L V
Sbjct: 61  AGLNGMQLGDKKLLV 75

>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 = 54.3 bits (130), Expect = 7e-11
 Identities = 23/79 (29%), Positives = 42/79 (53%)

Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
           T L +  +P    ++E ++ F   G I+  ++ R+K TGQS  +GF+ + DP+ AE   +
Sbjct: 3   TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62

Query: 114 AMHGYLLFEHILQVHLIPP 132
            ++G  L    ++V    P
Sbjct: 63  TLNGLRLQTKTIKVSYARP 81

>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 = 53.4 bits (128), Expect = 1e-10
 Identities = 17/72 (23%), Positives = 34/72 (47%), Gaps = 1/72 (1%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           ++IG +     ++ ++ +F QFG +K   + R+  T +S+ FGF+ F D    +    A 
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVD-KVLAQ 61

Query: 116 HGYLLFEHILQV 127
             + L    +  
Sbjct: 62  SRHELDSKTIDP 73

>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 = 53.1 bits (127), Expect = 3e-10
 Identities = 23/77 (29%), Positives = 39/77 (50%), Gaps = 3/77 (3%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNK---KTGQSKHFGFIEFNDPEVAEVVA 112
           L+I  +     E+ ++  FS+ GAIK   I++ K       S  FGF+E+  PE A+   
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 113 DAMHGYLLFEHILQVHL 129
             + G+ +  H L+V +
Sbjct: 61  KQLQGHTVDGHKLEVRI 77

>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 = 52.4 bits (125), Expect = 4e-10
 Identities = 15/74 (20%), Positives = 38/74 (51%)

Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
             L +  +     E++++  FS++G I  + I  ++++ +S+ F F+ F + + A+   +
Sbjct: 10  CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 69

Query: 114 AMHGYLLFEHILQV 127
             +G  L    ++V
Sbjct: 70  RANGMELDGRRIRV 83

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.4 bits (125), Expect = 4e-10
 Identities = 25/82 (30%), Positives = 41/82 (50%)

Query: 55  VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
           VLY+G +     +K + A F  FG I  ++I  + +T + + F F+EF   E A    D 
Sbjct: 7   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 66

Query: 115 MHGYLLFEHILQVHLIPPEHVH 136
           M+   LF   ++V+L  P  + 
Sbjct: 67  MNESELFGRTIRVNLAKPMRIK 88

>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 = 52.0 bits (124), Expect = 6e-10
 Identities = 10/76 (13%), Positives = 26/76 (34%)

Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
           T++ +  +P      E+  FF  +  I      +  + G       + F   + A     
Sbjct: 10  TIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 69

Query: 114 AMHGYLLFEHILQVHL 129
            ++   +    +++ L
Sbjct: 70  DLNDRPIGSRKVKLVL 85

>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 = 52.3 bits (125), Expect = 6e-10
 Identities = 15/81 (18%), Positives = 37/81 (45%), Gaps = 1/81 (1%)

Query: 53  ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVA 112
           A  ++  ++      ++++ FFS  G ++ +RI  ++ + +SK   ++EF + +   +  
Sbjct: 18  ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLA- 76

Query: 113 DAMHGYLLFEHILQVHLIPPE 133
             + G  L    + V     E
Sbjct: 77  IGLTGQRLLGVPIIVQASQAE 97

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.5 bits (123), Expect = 8e-10
 Identities = 12/64 (18%), Positives = 34/64 (53%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           +++G +     E++++ +F  FG ++ + +  + KT + + F FI F + E  + + +  
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61

Query: 116 HGYL 119
           +  +
Sbjct: 62  YHNV 65

>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 = 51.2 bits (122), Expect = 1e-09
 Identities = 14/72 (19%), Positives = 35/72 (48%), Gaps = 1/72 (1%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L+IG +     ++ +++ F Q+G +    + R+  T +S+ FGF+ +   E  +  A   
Sbjct: 9   LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD-AAMNA 67

Query: 116 HGYLLFEHILQV 127
             + +   +++ 
Sbjct: 68  RPHKVDGRVVEP 79

>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 = 51.2 bits (122), Expect = 1e-09
 Identities = 24/77 (31%), Positives = 38/77 (49%)

Query: 51  NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEV 110
           +    + +  +     E ++Q  F  FG+I R+ +A++K TGQSK F FI F+  E A  
Sbjct: 6   DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAAR 65

Query: 111 VADAMHGYLLFEHILQV 127
               + G+     IL V
Sbjct: 66  AIAGVSGFGYDHLILNV 82

>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 = 50.4 bits (120), Expect = 2e-09
 Identities = 16/72 (22%), Positives = 36/72 (50%), Gaps = 1/72 (1%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           ++IG +     +K+++ +FS+FG +    +  +  TG+S+ FGF+ F + E  +      
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVD-KVMDQ 60

Query: 116 HGYLLFEHILQV 127
             + L   ++  
Sbjct: 61  KEHKLNGKVIDP 72

>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 = 51.2 bits (122), Expect = 2e-09
 Identities = 18/86 (20%), Positives = 37/86 (43%), Gaps = 3/86 (3%)

Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
            +LYI  +P+    +EM   F ++G I++    R   T +++   ++ + D   A+   D
Sbjct: 8   RILYIRNLPYKITAEEMYDIFGKYGPIRQ---IRVGNTPETRGTAYVVYEDIFDAKNACD 64

Query: 114 AMHGYLLFEHILQVHLIPPEHVHPKL 139
            + G+ +    L V          K+
Sbjct: 65  HLSGFNVCNRYLVVLYYNANRAFQKM 90

>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 = 50.1 bits (119), Expect = 3e-09
 Identities = 23/80 (28%), Positives = 34/80 (42%), Gaps = 6/80 (7%)

Query: 53  ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNK-----KTGQSKHFGFIEFNDPEV 107
           A  LY+G IP G  E+ M  FF+    +  L  A        +  Q K+F F+EF   + 
Sbjct: 1   ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 60

Query: 108 AEVVADAMHGYLLFEHILQV 127
               A A  G +     L++
Sbjct: 61  TT-QAMAFDGIIFQGQSLKI 79

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.9 bits (119), Expect = 5e-09
 Identities = 13/77 (16%), Positives = 34/77 (44%), Gaps = 9/77 (11%)

Query: 54  TVLYIGRI-PHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVA 112
           + ++IG +      + +++A FS++G I    + +         F F+++ +   A    
Sbjct: 16  SRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKG--------FAFVQYVNERNARAAV 67

Query: 113 DAMHGYLLFEHILQVHL 129
               G ++   +L ++L
Sbjct: 68  AGEDGRMIAGQVLDINL 84

>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 = 49.4 bits (117), Expect = 6e-09
 Identities = 10/77 (12%), Positives = 29/77 (37%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L++   P  + ++ ++        +       + +   S+ F +I+    E A    + +
Sbjct: 4   LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKL 63

Query: 116 HGYLLFEHILQVHLIPP 132
           +G  +  + L   +  P
Sbjct: 64  NGLKIEGYTLVTKVSNP 80

>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 = 49.6 bits (118), Expect = 6e-09
 Identities = 18/74 (24%), Positives = 34/74 (45%), Gaps = 6/74 (8%)

Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
             +Y G I  G  ++ M+  FS FG I  +R+         K + F+ F+  E A     
Sbjct: 19  CTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIV 72

Query: 114 AMHGYLLFEHILQV 127
           +++G  +  H+++ 
Sbjct: 73  SVNGTTIEGHVVKC 86

>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 = 49.2 bits (117), Expect = 7e-09
 Identities = 22/71 (30%), Positives = 38/71 (53%)

Query: 47  KPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPE 106
           K  V K + L +  +P    E++++ +FS FG +  +++ ++ KTG SK FGF+ F + E
Sbjct: 2   KRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYE 61

Query: 107 VAEVVADAMHG 117
               V    H 
Sbjct: 62  TQVKVMSQRHM 72

>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 = 48.6 bits (115), Expect = 1e-08
 Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 1/73 (1%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAI-KRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADA 114
           ++IG +     EK +   FS FG I +  +I R+  TG SK + FI F   + ++   +A
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 115 MHGYLLFEHILQV 127
           M+G  L    + V
Sbjct: 61  MNGQYLCNRPITV 73

>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 = 48.9 bits (116), Expect = 1e-08
 Identities = 17/72 (23%), Positives = 33/72 (45%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L++  + +   E++++  FS +G +  L    +  T + K F F+ F  PE A      +
Sbjct: 11  LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70

Query: 116 HGYLLFEHILQV 127
            G +    +L V
Sbjct: 71  DGQVFQGRMLHV 82

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 48.6 bits (115), Expect = 1e-08
 Identities = 19/74 (25%), Positives = 38/74 (51%)

Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
            +L++  I     E E+Q  F  +G IK + +  +++TG SK +  +E+   + A    +
Sbjct: 8   WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 67

Query: 114 AMHGYLLFEHILQV 127
           A++G  +    +QV
Sbjct: 68  ALNGAEIMGQTIQV 81

>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 = 47.7 bits (113), Expect = 2e-08
 Identities = 14/78 (17%), Positives = 33/78 (42%), Gaps = 6/78 (7%)

Query: 52  KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVV 111
              +LY+  +     E+ ++  F+        R+       + + + F+ F++ E A   
Sbjct: 7   SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV------KKIRDYAFVHFSNREDAVEA 60

Query: 112 ADAMHGYLLFEHILQVHL 129
             A++G +L    ++V L
Sbjct: 61  MKALNGKVLDGSPIEVTL 78

>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 = 47.3 bits (112), Expect = 4e-08
 Identities = 20/77 (25%), Positives = 35/77 (45%), Gaps = 2/77 (2%)

Query: 51  NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEV 110
           +    ++I  +      K +   FS FG I   ++  ++    SK +GF+ F   E AE 
Sbjct: 6   SGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAER 63

Query: 111 VADAMHGYLLFEHILQV 127
             + M+G LL +  + V
Sbjct: 64  AIEKMNGMLLNDRKVFV 80

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.4 bits (112), Expect = 4e-08
 Identities = 21/74 (28%), Positives = 39/74 (52%), Gaps = 2/74 (2%)

Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
             L++  IP  F + +++  F QFG I  + I  N++   SK FGF+ F +   A+   +
Sbjct: 12  KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRARE 69

Query: 114 AMHGYLLFEHILQV 127
            +HG ++    ++V
Sbjct: 70  KLHGTVVEGRKIEV 83

>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 = 47.4 bits (112), Expect = 4e-08
 Identities = 23/82 (28%), Positives = 35/82 (42%), Gaps = 3/82 (3%)

Query: 48  PLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEV 107
           P  N    +Y+G +P     K+++  F ++GAI+       K       F F+EF DP  
Sbjct: 9   PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRD---IDLKNRRGGPPFAFVEFEDPRD 65

Query: 108 AEVVADAMHGYLLFEHILQVHL 129
           AE       GY    + L+V  
Sbjct: 66  AEDAVYGRDGYDYDGYRLRVEF 87

>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 = 47.1 bits (111), Expect = 5e-08
 Identities = 16/85 (18%), Positives = 33/85 (38%), Gaps = 8/85 (9%)

Query: 51  NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIA--------RNKKTGQSKHFGFIEF 102
           +  + +Y+  +       ++  FF Q G +K  +           +K+TG+ K    + +
Sbjct: 6   SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSY 65

Query: 103 NDPEVAEVVADAMHGYLLFEHILQV 127
            DP  A+   +   G       L+V
Sbjct: 66  EDPPTAKAAVEWFDGKDFQGSKLKV 90

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.2 bits (109), Expect = 9e-08
 Identities = 17/77 (22%), Positives = 31/77 (40%), Gaps = 2/77 (2%)

Query: 51  NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEV 110
            +   LY+G +     E  +   FSQ G  K  ++        +  + F+EF +   A  
Sbjct: 6   GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEH--TSNDPYCFVEFYEHRDAAA 63

Query: 111 VADAMHGYLLFEHILQV 127
              AM+G  +    ++V
Sbjct: 64  ALAAMNGRKILGKEVKV 80

>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 = 46.6 bits (110), Expect = 1e-07
 Identities = 20/94 (21%), Positives = 43/94 (45%), Gaps = 4/94 (4%)

Query: 34  PLEGGPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQ 93
            LE  P  +   EK    K   L+IG +     E+ ++ ++ Q+G +    + R+  + +
Sbjct: 4   TLETVPLERKKREKEQFRK---LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKR 60

Query: 94  SKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQV 127
           S+ FGF+ F+     +  A A   + +   +++ 
Sbjct: 61  SRGFGFVTFSSMAEVD-AAMAARPHSIDGRVVEP 93

>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 = 47.7 bits (112), Expect = 1e-07
 Identities = 20/143 (13%), Positives = 58/143 (40%), Gaps = 1/143 (0%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L+IG +     ++ +++ F Q+G +    + R+  T +S+ FGF+ +   E  +  A   
Sbjct: 9   LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD-AAMNA 67

Query: 116 HGYLLFEHILQVHLIPPEHVHPKLWRGFNPRYKPVDRVQVERKLQNKERTLEEHKKLVEK 175
             + +   +++           +       +   V  ++ + +  +     E++ K+   
Sbjct: 68  RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVI 127

Query: 176 ILKRDQKRRKRIEAAGIEYECPE 198
            +  D+   K+   A + ++  +
Sbjct: 128 EIMTDRGSGKKRGFAFVTFDDHD 150

>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 = 41.1 bits (95), Expect = 2e-05
 Identities = 15/72 (20%), Positives = 36/72 (50%), Gaps = 1/72 (1%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           +++G I     E  ++ +F Q+G I+ + I  ++ +G+ + F F+ F+D +  +      
Sbjct: 100 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVD-KIVIQ 158

Query: 116 HGYLLFEHILQV 127
             + +  H  +V
Sbjct: 159 KYHTVNGHNCEV 170

>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 = 44.7 bits (105), Expect = 2e-07
 Identities = 15/72 (20%), Positives = 36/72 (50%), Gaps = 1/72 (1%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           +++G I     E  ++ +F Q+G I+ + I  ++ +G+ + F F+ F+D + +       
Sbjct: 5   IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHD-SVDKIVIQ 63

Query: 116 HGYLLFEHILQV 127
             + +  H  +V
Sbjct: 64  KYHTVNGHNCEV 75

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 108

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.4 bits (107), Expect = 2e-07
 Identities = 8/79 (10%), Positives = 28/79 (35%), Gaps = 4/79 (5%)

Query: 51  NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEV 110
           +    + +  + +      +   FS+FG + ++                +++ DP  A+ 
Sbjct: 5   SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQF----QALLQYADPVSAQH 60

Query: 111 VADAMHGYLLFEHILQVHL 129
              ++ G  ++     + +
Sbjct: 61  AKLSLDGQNIYNACCTLRI 79

>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 = 45.1 bits (106), Expect = 3e-07
 Identities = 16/83 (19%), Positives = 30/83 (36%), Gaps = 4/83 (4%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRL--RIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
           L+IG IP     +E+    ++           A      +++ F F+E+     A +   
Sbjct: 4   LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 63

Query: 114 AM--HGYLLFEHILQVHLIPPEH 134
            +      L+ H + V    PE 
Sbjct: 64  KLMPGRIQLWGHQIAVDWAEPEI 86

>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 = 44.6 bits (105), Expect = 3e-07
 Identities = 19/77 (24%), Positives = 33/77 (42%), Gaps = 6/77 (7%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L++G +P    E+EM+  F ++G    + I ++K       FGFI      +AE+    +
Sbjct: 11  LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK------GFGFIRLETRTLAEIAKVEL 64

Query: 116 HGYLLFEHILQVHLIPP 132
               L    L+V     
Sbjct: 65  DNMPLRGKQLRVRFACH 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 = 43.9 bits (103), Expect = 7e-07
 Identities = 9/75 (12%), Positives = 31/75 (41%), Gaps = 1/75 (1%)

Query: 54  TVLYIGRIPHGFYEKEM-QAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVA 112
             +YI  +     + E+ ++  + F    ++      ++ + +   F+ F +   A    
Sbjct: 4   HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNAL 63

Query: 113 DAMHGYLLFEHILQV 127
            +M G+  ++  +++
Sbjct: 64  RSMQGFPFYDKPMRI 78

>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 = 43.6 bits (102), Expect = 9e-07
 Identities = 12/82 (14%), Positives = 27/82 (32%), Gaps = 7/82 (8%)

Query: 52  KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVV 111
            ++ + +  +P     +E+      +         +     ++K   F+   + E A+  
Sbjct: 4   GSSGILVKNLPQDSNCQEVHDLLKDYDL-------KYCYVDRNKRTAFVTLLNGEQAQNA 56

Query: 112 ADAMHGYLLFEHILQVHLIPPE 133
               H Y      L V L P +
Sbjct: 57  IQMFHQYSFRGKDLIVQLQPTD 78

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 43.1 bits (101), Expect = 1e-06
 Identities = 16/80 (20%), Positives = 28/80 (35%), Gaps = 5/80 (6%)

Query: 50  VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAE 109
           V  A  L    +     E E++  F     I+ +        G+SK   +IEF     AE
Sbjct: 13  VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ-----DGKSKGIAYIEFKSEADAE 67

Query: 110 VVADAMHGYLLFEHILQVHL 129
              +   G  +    + ++ 
Sbjct: 68  KNLEEKQGAEIDGRSVSLYY 87

>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 = 42.4 bits (99), Expect = 2e-06
 Identities = 18/72 (25%), Positives = 42/72 (58%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L++G +     E+ ++  FS++G I  + + ++++T +S+ FGF+ F + + A+    AM
Sbjct: 8   LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 67

Query: 116 HGYLLFEHILQV 127
           +G  +    ++V
Sbjct: 68  NGKSVDGRQIRV 79

>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 = 42.4 bits (99), Expect = 3e-06
 Identities = 20/92 (21%), Positives = 41/92 (44%), Gaps = 1/92 (1%)

Query: 52  KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVV 111
             T +++G +P+   +  ++ +F  FG I+   +  +++TG+S+ +GF+   D   AE  
Sbjct: 9   TFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERA 68

Query: 112 ADAMHGYLLFEHILQVHLIPPEHVHPKLWRGF 143
               +   +      V+L         L  GF
Sbjct: 69  CKDPNPI-IDGRKANVNLAYLGAKPRSLQTGF 99

>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 = 43.0 bits (100), Expect = 4e-06
 Identities = 28/125 (22%), Positives = 56/125 (44%), Gaps = 5/125 (4%)

Query: 18  SQLPV-----PSDKKGAADFLPLEGGPGRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQA 72
           SQ+P+     P  +      L  +       T+  P  +    L +  IP    E +++ 
Sbjct: 2   SQIPLVSQYDPYGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQ 61

Query: 73  FFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPP 132
            F ++G I+ ++I  +++T QS+ +GF++F     A+     ++G+ +    L+V L   
Sbjct: 62  LFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAAS 121

Query: 133 EHVHP 137
            H  P
Sbjct: 122 GHQRP 126

>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 = 41.3 bits (96), Expect = 8e-06
 Identities = 22/84 (26%), Positives = 43/84 (51%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           +++G IP+   E++++  FS+ G +   R+  +++TG+ K +GF E+ D E A      +
Sbjct: 11  VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70

Query: 116 HGYLLFEHILQVHLIPPEHVHPKL 139
           +G       L+V     E    +L
Sbjct: 71  NGREFSGRALRVDNAASEKNKEEL 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 = 40.1 bits (93), Expect = 1e-05
 Identities = 15/71 (21%), Positives = 33/71 (46%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           LYI  +  G  ++++      +G I   +   +K T + K +GF++F+ P  A+    A+
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 116 HGYLLFEHILQ 126
               +   + +
Sbjct: 61  KASGVQAQMAK 71

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.9 bits (95), Expect = 1e-05
 Identities = 10/72 (13%), Positives = 28/72 (38%), Gaps = 6/72 (8%)

Query: 51  NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEV 110
            ++ V+  G + +G    ++     + G +  L +  NK       + F  +   E ++ 
Sbjct: 18  TQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK------PYSFARYRTTEESKR 71

Query: 111 VADAMHGYLLFE 122
               ++G  + +
Sbjct: 72  AYVTLNGKEVVD 83

>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 = 40.5 bits (94), Expect = 1e-05
 Identities = 12/97 (12%), Positives = 27/97 (27%), Gaps = 6/97 (6%)

Query: 53  ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVA 112
           A V             + ++ F  +      +  ++ K         I F++P  A    
Sbjct: 10  ACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFK------RVRINFSNPLSAADAR 63

Query: 113 DAMHGYLLFEHILQVHLIPPEHVHPKLWRGFNPRYKP 149
             +H        ++++     H+        NP    
Sbjct: 64  LRLHKTEFLGKEMKLYFAQTLHIGSSHLAPPNPDKSG 100

>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 = 40.2 bits (93), Expect = 2e-05
 Identities = 20/74 (27%), Positives = 36/74 (48%)

Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
            VLY+  +     E+++ + F++F   K   I     TG+ +   FI F + E+A     
Sbjct: 19  KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 78

Query: 114 AMHGYLLFEHILQV 127
            ++GY L+  IL +
Sbjct: 79  LVNGYKLYGKILVI 92

>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 = 39.6 bits (92), Expect = 2e-05
 Identities = 15/63 (23%), Positives = 31/63 (49%), Gaps = 5/63 (7%)

Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
           + +++GR      E E++ FFSQ+G +  + I +  +      F F+ F D ++A+ +  
Sbjct: 6   SGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFR-----AFAFVTFADDQIAQSLCG 60

Query: 114 AMH 116
              
Sbjct: 61  EDL 63

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 39.5 bits (91), Expect = 3e-05
 Identities = 16/72 (22%), Positives = 34/72 (47%), Gaps = 2/72 (2%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           L+IG +       E++   S+  A        + +TG ++ FG+++F   E  E  A  +
Sbjct: 16  LFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLE-KALEL 73

Query: 116 HGYLLFEHILQV 127
            G  +F + +++
Sbjct: 74  TGLKVFGNEIKL 85

>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 = 38.9 bits (90), Expect = 3e-05
 Identities = 9/67 (13%), Positives = 21/67 (31%), Gaps = 6/67 (8%)

Query: 56  LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM 115
           LYIG +       +++  F               +      + F+++ D   A    + +
Sbjct: 4   LYIGNLSPAVTADDLRQLFGDRKLP------LAGQVLLKSGYAFVDYPDQNWAIRAIETL 57

Query: 116 HGYLLFE 122
            G +   
Sbjct: 58  SGKVELH 64

>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 = 39.4 bits (91), Expect = 3e-05
 Identities = 16/72 (22%), Positives = 28/72 (38%)

Query: 50  VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAE 109
           V +   ++I  +     E+ +     QFG +K +R+  +  T  SK   F +F   E A+
Sbjct: 5   VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQ 64

Query: 110 VVADAMHGYLLF 121
               A       
Sbjct: 65  KCLAAASLEAEG 76

>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 = 38.0 bits (88), Expect = 9e-05
 Identities = 12/63 (19%), Positives = 24/63 (38%), Gaps = 4/63 (6%)

Query: 67  EKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQ 126
            ++++   S+FG I++L +      G       + F DPE A+     + G       + 
Sbjct: 33  REDLRVECSKFGQIRKLLLFDRHPDG----VASVSFRDPEEADYCIQTLDGRWFGGRQIT 88

Query: 127 VHL 129
              
Sbjct: 89  AQA 91

>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 = 37.0 bits (85), Expect = 2e-04
 Identities = 15/76 (19%), Positives = 29/76 (38%), Gaps = 3/76 (3%)

Query: 56  LYIGRIPHGFYEKEM--QAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
           + I  +     ++ +  ++F       K    A  K+   +    F+ F + + AE  A 
Sbjct: 7   IMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAE-RAL 65

Query: 114 AMHGYLLFEHILQVHL 129
            M+  LL    + V L
Sbjct: 66  QMNRSLLGNREISVSL 81

>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 = 36.9 bits (85), Expect = 2e-04
 Identities = 10/69 (14%), Positives = 25/69 (36%), Gaps = 2/69 (2%)

Query: 67  EKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGF--IEFNDPEVAEVVADAMHGYLLFEHI 124
            ++++   S++G +K + I R     +    G   +EF      +     + G      +
Sbjct: 28  VEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRV 87

Query: 125 LQVHLIPPE 133
           +      P+
Sbjct: 88  VVTKYCDPD 96

>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 = 36.7 bits (84), Expect = 3e-04
 Identities = 13/69 (18%), Positives = 26/69 (37%), Gaps = 4/69 (5%)

Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
             L++  IP    E++++  FS  G + +          + +    I+    E A     
Sbjct: 11  ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALI 66

Query: 114 AMHGYLLFE 122
            +H + L E
Sbjct: 67  DLHNHDLGE 75

>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 = 36.3 bits (83), Expect = 5e-04
 Identities = 16/86 (18%), Positives = 38/86 (44%), Gaps = 6/86 (6%)

Query: 54  TVLYIGRI-PHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVA 112
           +VL +  + P     + +   F  +G ++R++I  NKK         ++  D   A++  
Sbjct: 3   SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKK-----ENALVQMADGNQAQLAM 57

Query: 113 DAMHGYLLFEHILQVHLIPPEHVHPK 138
             ++G+ L    +++ L   ++V   
Sbjct: 58  SHLNGHKLHGKPIRITLSKHQNVQLP 83

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.5 bits (81), Expect = 6e-04
 Identities = 14/76 (18%), Positives = 27/76 (35%), Gaps = 2/76 (2%)

Query: 52  KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVV 111
           K   +YI   P      +++ +    G +  +++ R       K   F+ F+  E A+  
Sbjct: 5   KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQM-RRTLHKAFKGSIFVVFDSIESAK-K 62

Query: 112 ADAMHGYLLFEHILQV 127
                G    E  L +
Sbjct: 63  FVETPGQKYKETDLLI 78

>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 = 34.8 bits (79), Expect = 0.001
 Identities = 13/75 (17%), Positives = 29/75 (38%), Gaps = 6/75 (8%)

Query: 54  TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD 113
            +L++  +P    E  +   F+QF   K       +         F+EF     +    +
Sbjct: 9   QILFLTNLPEETNEMMLSMLFNQFPGFK-----EVRLVPNRHDIAFVEFTTELQSNAAKE 63

Query: 114 AMHGYLLFE-HILQV 127
           A+ G+ +   H +++
Sbjct: 64  ALQGFKITPTHAMKI 78

>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 = 34.5 bits (78), Expect = 0.003
 Identities = 18/94 (19%), Positives = 36/94 (38%), Gaps = 1/94 (1%)

Query: 40  GRKLTEEKPLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGF 99
           G+K +  +        +Y+  +P     K +  FF +   ++          G++   GF
Sbjct: 5   GQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGF 64

Query: 100 IEFNDPEVAEVVADAMHGYLLFEHILQVHLIPPE 133
           +EF +    +  A   H   +    +QVH I  +
Sbjct: 65  VEFRNEADYK-AALCRHKQYMGNRFIQVHPITKK 97

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	215
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.89
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.89
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.89
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.89
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.89
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.88
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.88
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.88
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.88
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.88
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.88
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.87
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.87
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.87
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.87
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.87
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.86
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.86
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.86
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.86
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.86
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.86
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.86
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.86
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.86
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.85
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.85
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.85
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.85
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.85
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.84
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.84
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.84
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.84
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.84
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.84
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.83
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.83
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.83
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.82
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.82
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.82
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.81
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.81
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.81
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.81
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.8
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.8
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.79
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.79
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.79
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.79
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.79
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.79
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.78
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.78
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.78
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.78
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.78
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.78
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.77
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.77
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.77
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.76
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.76
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.76
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.75
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.75
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.75
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.75
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.75
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.74
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.74
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.74
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.72
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.71
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.7
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.69
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.67
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.65
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	U2	99.62
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.56
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.55
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.51
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.49
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.47
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.39
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.71
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.71
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.54
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	95.68

>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=99.89  E-value=2.2e-23  Score=141.03  Aligned_cols=80  Identities=26%  Similarity=0.473  Sum_probs=77.6

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeCC
Q 028027           53 ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPP  132 (215)
Q Consensus        53 ~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~~  132 (215)
                      .++|||+|||+++++++|+++|++||.|.++.+++++.+|.++|||||+|.+.++|+.|+..|||..++|+.|+|.+|+|
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~p   81 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   81 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            57899999999999999999999999999999999988999999999999999999999999999999999999999976

>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=99.89  E-value=5.2e-23  Score=141.70  Aligned_cols=84  Identities=30%  Similarity=0.505  Sum_probs=80.3

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      .+.++|||+|||.++++++|+++|++||.|..|.++.++.+|.++|||||+|.+.++|..|+..|||..|+|+.|.|.||
T Consensus         6 ~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~a   85 (90)
T d2cq0a1           6 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWA   85 (90)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEee
Confidence            45689999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             CCCC
Q 028027          131 PPEH  134 (215)
Q Consensus       131 ~~~~  134 (215)
                      +|+.
T Consensus        86 kp~~   89 (90)
T d2cq0a1          86 KPST   89 (90)
T ss_dssp             SCCC
T ss_pred             eCCC
Confidence            8764

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.89  E-value=2.7e-23  Score=142.84  Aligned_cols=85  Identities=29%  Similarity=0.508  Sum_probs=80.4

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ...++|||+|||+++++++|+++|++||.|.+|.++.++.+|.++|||||+|.+.++|+.|+..|||..|+|+.|.|.++
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
Confidence            34579999999999999999999999999999999999989999999999999999999999999999999999999999


Q ss_pred             CCCCC
Q 028027          131 PPEHV  135 (215)
Q Consensus       131 ~~~~~  135 (215)
                      .|...
T Consensus        83 ~p~~~   87 (89)
T d2cqba1          83 KPMRI   87 (89)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87644

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.89  E-value=1.1e-22  Score=140.90  Aligned_cols=84  Identities=23%  Similarity=0.336  Sum_probs=79.9

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ..+++|||+|||+++|+++|+++|++||.|.+|.++.++.+|.++|||||+|.+.++|..|+..|||..|+|+.|+|.|+
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a   84 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD   84 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCCC
Q 028027          131 PPEH  134 (215)
Q Consensus       131 ~~~~  134 (215)
                      .+..
T Consensus        85 ~~~~   88 (93)
T d1h2vz_          85 AGFK   88 (93)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            7543

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.89  E-value=7.3e-23  Score=140.37  Aligned_cols=83  Identities=23%  Similarity=0.416  Sum_probs=78.7

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      .++++|||+|||+++++++|+++|++||.|.+|.+++++.+|.++|||||+|.+.++|+.|+..|||..|+|+.|+|+||
T Consensus         5 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~a   84 (88)
T d1rk8a_           5 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC   84 (88)
T ss_dssp             C-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            46789999999999999999999999999999999999889999999999999999999999999999999999999998


Q ss_pred             CCC
Q 028027          131 PPE  133 (215)
Q Consensus       131 ~~~  133 (215)
                      .++
T Consensus        85 ~~k   87 (88)
T d1rk8a_          85 FVK   87 (88)
T ss_dssp             EEC
T ss_pred             cCC
Confidence            754

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.88  E-value=1.2e-22  Score=137.29  Aligned_cols=80  Identities=29%  Similarity=0.572  Sum_probs=77.1

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeCC
Q 028027           53 ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPP  132 (215)
Q Consensus        53 ~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~~  132 (215)
                      .++|||+|||+++++++|+++|++||.|..|.++++..+|.++|||||+|.+.++|+.|+..|||..++|+.|+|.+|+|
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            36799999999999999999999999999999999988999999999999999999999999999999999999999976

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.88  E-value=7.4e-23  Score=141.76  Aligned_cols=84  Identities=23%  Similarity=0.420  Sum_probs=80.0

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ...++|||+|||+.+++++|+++|++||.|.+|.|++++.+|.++|||||+|.+.++|+.|+..|||+.|+|+.|+|++|
T Consensus         7 ~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A   86 (93)
T d1x5ua1           7 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKA   86 (93)
T ss_dssp             CTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEET
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            34579999999999999999999999999999999999989999999999999999999999999999999999999999


Q ss_pred             CCCC
Q 028027          131 PPEH  134 (215)
Q Consensus       131 ~~~~  134 (215)
                      .++.
T Consensus        87 ~~~~   90 (93)
T d1x5ua1          87 SAHN   90 (93)
T ss_dssp             TTTS
T ss_pred             CCCC
Confidence            8764

>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=99.88  E-value=5.9e-22  Score=146.91  Aligned_cols=90  Identities=23%  Similarity=0.507  Sum_probs=83.2

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ....++|||+|||+++++++|+++|++||.|.+|.|+.++.||.++|||||+|.+.++|..||+.|||+.|+|+.|+|.+
T Consensus        39 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~  118 (139)
T d1u6fa1          39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVAL  118 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            34557899999999999999999999999999999999998999999999999999999999999999999999999999


Q ss_pred             eCCCCCCCCC
Q 028027          130 IPPEHVHPKL  139 (215)
Q Consensus       130 a~~~~~~~~~  139 (215)
                      +.+...++..
T Consensus       119 a~~~~~~p~~  128 (139)
T d1u6fa1         119 AASGHQRPGI  128 (139)
T ss_dssp             SSCCCCCCCS
T ss_pred             cCCCCCCCCC
Confidence            9877665433

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.88  E-value=2e-22  Score=141.90  Aligned_cols=85  Identities=25%  Similarity=0.507  Sum_probs=80.5

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeC
Q 028027           52 KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIP  131 (215)
Q Consensus        52 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~  131 (215)
                      ++++|||+|||+++++++|+++|+.||.|.++.++.++.+|.++|||||+|.+.++|+.||..|||..|+|+.|+|+|+.
T Consensus        17 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a~   96 (102)
T d2cpza1          17 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKR   96 (102)
T ss_dssp             TTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEeC
Confidence            45789999999999999999999999999999999999899999999999999999999999999999999999999998


Q ss_pred             CCCCC
Q 028027          132 PEHVH  136 (215)
Q Consensus       132 ~~~~~  136 (215)
                      ++...
T Consensus        97 ~k~~~  101 (102)
T d2cpza1          97 SKNDS  101 (102)
T ss_dssp             CSCCC
T ss_pred             CCCCC
Confidence            87543

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.88  E-value=1.9e-22  Score=135.86  Aligned_cols=77  Identities=23%  Similarity=0.366  Sum_probs=75.1

Q ss_pred             EEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeC
Q 028027           55 VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIP  131 (215)
Q Consensus        55 ~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~  131 (215)
                      +|||+|||+.+|+++|+++|++||+|.+|+|++++.+|.++|||||+|.+.++|..|++.|||..++|+.|+|.|+.
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~   78 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999999985

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.88  E-value=3.5e-22  Score=139.81  Aligned_cols=86  Identities=20%  Similarity=0.321  Sum_probs=81.0

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ..+++|||+|||+.+++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|+.||..|||..|+|+.|+|.++
T Consensus         6 ~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a   85 (99)
T d1whwa_           6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS   85 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            45678999999999999999999999999999999999989999999999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 028027          131 PPEHVH  136 (215)
Q Consensus       131 ~~~~~~  136 (215)
                      .++...
T Consensus        86 ~~~~~~   91 (99)
T d1whwa_          86 TIKKEA   91 (99)
T ss_dssp             CCCSTT
T ss_pred             CCCCcc
Confidence            876543

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=4.2e-22  Score=140.47  Aligned_cols=86  Identities=20%  Similarity=0.384  Sum_probs=78.8

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ...++|||+|||+.+++++|+++|++||.|.+|.|+.++.||.++|||||+|.+.++|+.|++.+|+ .|+|+.|.|.++
T Consensus         8 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a   86 (103)
T d2cqda1           8 TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLA   86 (103)
T ss_dssp             CSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEES
T ss_pred             CCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEEc
Confidence            4567899999999999999999999999999999999998999999999999999999999998876 799999999999


Q ss_pred             CCCCCCC
Q 028027          131 PPEHVHP  137 (215)
Q Consensus       131 ~~~~~~~  137 (215)
                      .+.....
T Consensus        87 ~~~~~pr   93 (103)
T d2cqda1          87 YLGAKPR   93 (103)
T ss_dssp             TTTCCCC
T ss_pred             CCCCCCC
Confidence            7654433

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=1.6e-22  Score=137.76  Aligned_cols=81  Identities=23%  Similarity=0.473  Sum_probs=77.8

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeCCC
Q 028027           54 TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPPE  133 (215)
Q Consensus        54 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~~~  133 (215)
                      .+|||+|||+++|+++|+++|++||+|..|.|++++.||.++|||||+|.+.++|..|+..|||..|+|+.|.|.++.+.
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~   81 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG   81 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            46999999999999999999999999999999999999999999999999999999999999999999999999999765


Q ss_pred             C
Q 028027          134 H  134 (215)
Q Consensus       134 ~  134 (215)
                      .
T Consensus        82 ~   82 (85)
T d2u2fa_          82 A   82 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.87  E-value=9e-22  Score=135.39  Aligned_cols=83  Identities=24%  Similarity=0.428  Sum_probs=76.7

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ...++|||+|||+++|+++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|+.||..  ++.|+|+.|.|.++
T Consensus         6 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~--~~~l~Gr~i~v~~a   83 (90)
T d2cqga1           6 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWCDCKLP   83 (90)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTEEEEEECC
T ss_pred             cCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhc--CCccCCEEeEEEeC
Confidence            4568899999999999999999999999999999999998999999999999999999999974  55899999999999


Q ss_pred             CCCCC
Q 028027          131 PPEHV  135 (215)
Q Consensus       131 ~~~~~  135 (215)
                      .++..
T Consensus        84 ~~k~~   88 (90)
T d2cqga1          84 NSKQS   88 (90)
T ss_dssp             CTTCC
T ss_pred             CCCCC
Confidence            87654

>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=99.87  E-value=6.7e-22  Score=134.60  Aligned_cols=80  Identities=26%  Similarity=0.481  Sum_probs=75.7

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCC--eEEEEE
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFE--HILQVH  128 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g--~~l~V~  128 (215)
                      ...++|||+|||+++++++|+++|++||.|..+++++++.+|.++|||||+|.+.++|..|++.|||..+.|  ++|.|+
T Consensus         4 ~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~   83 (85)
T d1b7fa2           4 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR   83 (85)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEE
Confidence            456789999999999999999999999999999999999899999999999999999999999999999876  889999


Q ss_pred             Ee
Q 028027          129 LI  130 (215)
Q Consensus       129 ~a  130 (215)
                      ||
T Consensus        84 ~A   85 (85)
T d1b7fa2          84 LA   85 (85)
T ss_dssp             EC
T ss_pred             EC
Confidence            86

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.87  E-value=6.7e-22  Score=137.12  Aligned_cols=84  Identities=25%  Similarity=0.500  Sum_probs=78.0

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecC-CCCCcccEEEEEEcCHHHHHHHHHHh-CCceeCCeEEEEE
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNK-KTGQSKHFGFIEFNDPEVAEVVADAM-HGYLLFEHILQVH  128 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~-~tg~~~g~afV~F~~~~~a~~ai~~l-~g~~l~g~~l~V~  128 (215)
                      ..+++|||+|||+++++++|+.+|++||.|.+|.|+.+. .+|.++|||||+|.+.++|..|+..| ||..|+|+.|.|.
T Consensus         6 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~   85 (94)
T d2cpha1           6 QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLE   85 (94)
T ss_dssp             SCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEE
Confidence            556889999999999999999999999999999998875 37999999999999999999999998 8999999999999


Q ss_pred             EeCCCC
Q 028027          129 LIPPEH  134 (215)
Q Consensus       129 ~a~~~~  134 (215)
                      ||.+..
T Consensus        86 ~A~~~~   91 (94)
T d2cpha1          86 WADSEV   91 (94)
T ss_dssp             ECCCCC
T ss_pred             EcCCCC
Confidence            998764

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=3.8e-22  Score=137.22  Aligned_cols=86  Identities=21%  Similarity=0.412  Sum_probs=80.5

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      .+.++|||+|||+++++++|+++|++||.|..+.++.+..+|.++|||||+|.+.++|+.|+..|||+.|+|+.|.|.++
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
Confidence            35678999999999999999999999999999999998889999999999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 028027          131 PPEHVH  136 (215)
Q Consensus       131 ~~~~~~  136 (215)
                      .+....
T Consensus        83 ~~~~~~   88 (90)
T d1x5sa1          83 GKSSDN   88 (90)
T ss_dssp             ECCCCC
T ss_pred             CCCCCC
Confidence            876543

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=8.3e-22  Score=134.15  Aligned_cols=79  Identities=29%  Similarity=0.482  Sum_probs=74.5

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCC--eEEEEEE
Q 028027           52 KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFE--HILQVHL  129 (215)
Q Consensus        52 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g--~~l~V~~  129 (215)
                      ..++|||+|||+++|+++|+++|++||.|.++.+++++.+|.++|||||+|.+.++|..|++.|||..++|  ++|.|.|
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~   84 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKF   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEe
Confidence            45789999999999999999999999999999999998899999999999999999999999999999998  5589888


Q ss_pred             e
Q 028027          130 I  130 (215)
Q Consensus       130 a  130 (215)
                      |
T Consensus        85 A   85 (85)
T d1fxla2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=1.1e-21  Score=133.17  Aligned_cols=79  Identities=16%  Similarity=0.360  Sum_probs=74.8

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeC
Q 028027           52 KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIP  131 (215)
Q Consensus        52 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~  131 (215)
                      ..++|||+|||+++++++|+++|++||.|..+.|+.++.+|.++|||||+|.+.++|+.|+. ++++.|+|+.|+|..|.
T Consensus         5 ~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEeee
Confidence            45799999999999999999999999999999999999999999999999999999999996 69999999999998874

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.86  E-value=4.4e-22  Score=134.23  Aligned_cols=79  Identities=13%  Similarity=0.301  Sum_probs=69.7

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeCC
Q 028027           54 TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPP  132 (215)
Q Consensus        54 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~~  132 (215)
                      ++|||+|||+++|+++|+++|++||.|..+.++.+..+|.++|||||+|.+.++|..|+..|||..++|+.|+|++++|
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            6999999999999999999999999999888888877999999999999999999999999999999999999999976

>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=99.86  E-value=1e-21  Score=133.00  Aligned_cols=76  Identities=20%  Similarity=0.343  Sum_probs=73.4

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEE
Q 028027           52 KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQV  127 (215)
Q Consensus        52 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V  127 (215)
                      +.++|||+|||+.+|+++|+++|++||.|.+|.|+.++.+|.++|||||+|.+.++|..|+..|||..|+|+.|+|
T Consensus         8 ~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           8 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             GGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            4678999999999999999999999999999999999989999999999999999999999999999999999987

>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=99.86  E-value=2e-21  Score=133.60  Aligned_cols=83  Identities=20%  Similarity=0.383  Sum_probs=76.2

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      .++++|||+|||+++++++|+++|++||.|.+|.++.+..++  +|||||+|.+.++|..|+..|||..|+|+.|+|.|+
T Consensus         6 ~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~--~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a   83 (90)
T d2cqia1           6 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWA   83 (90)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSS--CCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCcc--ceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            456899999999999999999999999999999999986444  789999999999999999999999999999999999


Q ss_pred             CCCCC
Q 028027          131 PPEHV  135 (215)
Q Consensus       131 ~~~~~  135 (215)
                      .+...
T Consensus        84 ~~~~~   88 (90)
T d2cqia1          84 TTPSS   88 (90)
T ss_dssp             CCTTC
T ss_pred             CCCCC
Confidence            76543

>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=99.86  E-value=2.9e-22  Score=140.80  Aligned_cols=80  Identities=18%  Similarity=0.391  Sum_probs=75.9

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeC
Q 028027           52 KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIP  131 (215)
Q Consensus        52 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~  131 (215)
                      +.++|||+|||+.+++++|+++|+.||.|.+|.|+++..+|.++|||||+|.+.++|..|+. |||..|+|+.|.|.++.
T Consensus        17 ~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a~   95 (101)
T d2cq4a1          17 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQ   95 (101)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECC
Confidence            45799999999999999999999999999999999999899999999999999999999995 99999999999999875


Q ss_pred             C
Q 028027          132 P  132 (215)
Q Consensus       132 ~  132 (215)
                      +
T Consensus        96 ~   96 (101)
T d2cq4a1          96 A   96 (101)
T ss_dssp             H
T ss_pred             C
Confidence            4

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.86  E-value=1.1e-21  Score=131.33  Aligned_cols=77  Identities=18%  Similarity=0.369  Sum_probs=74.1

Q ss_pred             EEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeCC
Q 028027           55 VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPP  132 (215)
Q Consensus        55 ~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~~  132 (215)
                      +|||+|||+++++++|+++|++||.|.++.++.++ +|.++|||||+|.+.++|..|+..|||..++|+.|+|+++.+
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~S   78 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVTS   78 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEECC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEee-ccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            69999999999999999999999999999999986 899999999999999999999999999999999999999863

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=8.7e-22  Score=133.36  Aligned_cols=80  Identities=29%  Similarity=0.489  Sum_probs=75.0

Q ss_pred             EEEcCCCCCCcHHHHHHHhccCCCeeEE-EEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeCCCC
Q 028027           56 LYIGRIPHGFYEKEMQAFFSQFGAIKRL-RIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPPEH  134 (215)
Q Consensus        56 l~V~nLp~~~te~~L~~~F~~~G~v~~v-~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~~~~  134 (215)
                      |||+|||+++++++|+++|++||.|.++ .+++++.+|+++|||||+|.+.++|..|++.|||..++|+.|+|.++.++.
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k~   80 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKD   80 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCCC
Confidence            7999999999999999999999998664 788998899999999999999999999999999999999999999998764


Q ss_pred             C
Q 028027          135 V  135 (215)
Q Consensus       135 ~  135 (215)
                      .
T Consensus        81 ~   81 (83)
T d1x5ta1          81 S   81 (83)
T ss_dssp             C
T ss_pred             c
Confidence            3

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=6.1e-21  Score=131.94  Aligned_cols=84  Identities=25%  Similarity=0.448  Sum_probs=77.3

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 028027           49 LVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVH  128 (215)
Q Consensus        49 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~  128 (215)
                      ....+++|||+|||+.+++++|+++|++||.|..|.++.+.  +.++|||||+|.+.++|..|+..|||..|+|+.|+|.
T Consensus         7 ~~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~--~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~   84 (93)
T d2cq3a1           7 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN   84 (93)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT--TTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccc--cCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34567889999999999999999999999999999999885  4478999999999999999999999999999999999


Q ss_pred             EeCCCC
Q 028027          129 LIPPEH  134 (215)
Q Consensus       129 ~a~~~~  134 (215)
                      +|.++.
T Consensus        85 ~A~~r~   90 (93)
T d2cq3a1          85 NATARV   90 (93)
T ss_dssp             ECCSSC
T ss_pred             ecCcCC
Confidence            998764

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.85  E-value=3e-22  Score=133.90  Aligned_cols=76  Identities=22%  Similarity=0.406  Sum_probs=73.0

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           54 TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        54 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ++|||+|||+++++++|+++|++||.|.++.+++++.||.++|||||+|.+.++|+.|+. +|++.|+|+.|.|+.|
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            579999999999999999999999999999999999999999999999999999999996 7999999999999876

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=1.7e-21  Score=137.25  Aligned_cols=83  Identities=14%  Similarity=0.325  Sum_probs=77.9

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeC
Q 028027           52 KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIP  131 (215)
Q Consensus        52 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~  131 (215)
                      ..++|||+|||+++++++|+++|++||.|..+.|++++.++.++|||||+|.+.++|..|+. ++|+.|+|+.|.|.+|.
T Consensus        19 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~   97 (103)
T d1x4ba1          19 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAV   97 (103)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCS
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECc
Confidence            34789999999999999999999999999999999999899999999999999999999995 79999999999999998


Q ss_pred             CCCC
Q 028027          132 PEHV  135 (215)
Q Consensus       132 ~~~~  135 (215)
                      ++..
T Consensus        98 ~ke~  101 (103)
T d1x4ba1          98 AREE  101 (103)
T ss_dssp             SCCC
T ss_pred             ccCC
Confidence            7654

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=8.9e-22  Score=138.91  Aligned_cols=81  Identities=26%  Similarity=0.506  Sum_probs=77.6

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeCC
Q 028027           53 ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPP  132 (215)
Q Consensus        53 ~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~~  132 (215)
                      .++|||+|||+++++++|+++|++||.|.+|.++.++.+|.++|||||+|.+.++|..|+..|||..|+|+.|.|.++.+
T Consensus         8 ~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~~   87 (104)
T d1p1ta_           8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAAS   87 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTC
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            46899999999999999999999999999999999998999999999999999999999999999999999999999866


Q ss_pred             C
Q 028027          133 E  133 (215)
Q Consensus       133 ~  133 (215)
                      .
T Consensus        88 ~   88 (104)
T d1p1ta_          88 E   88 (104)
T ss_dssp             T
T ss_pred             C
Confidence            4

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.85  E-value=2.9e-21  Score=131.28  Aligned_cols=78  Identities=29%  Similarity=0.505  Sum_probs=72.7

Q ss_pred             EEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCC---CcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeCC
Q 028027           56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTG---QSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPP  132 (215)
Q Consensus        56 l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg---~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~~  132 (215)
                      |||+|||+++|+++|+.+|++||.|.++.|++++.++   .++|||||+|.+.++|..|+..|||..|+|+.|.|+++.+
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~~   80 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISER   80 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSC
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            7999999999999999999999999999999887555   4689999999999999999999999999999999999864


Q ss_pred             C
Q 028027          133 E  133 (215)
Q Consensus       133 ~  133 (215)
                      .
T Consensus        81 ~   81 (85)
T d2cpfa1          81 A   81 (85)
T ss_dssp             S
T ss_pred             C
Confidence            3

>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=99.84  E-value=1.7e-21  Score=129.50  Aligned_cols=74  Identities=24%  Similarity=0.494  Sum_probs=70.6

Q ss_pred             EEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           55 VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        55 ~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      .|||+|||+++++++|+++|++||.|..+.++.++.+|+++|||||+|.+.++|+.|+. ++++.|+|+.|.|+.
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~r   74 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKR   74 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeE
Confidence            48999999999999999999999999999999999999999999999999999999996 799999999999864

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=3.3e-21  Score=132.20  Aligned_cols=81  Identities=25%  Similarity=0.417  Sum_probs=75.1

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeCC
Q 028027           53 ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPP  132 (215)
Q Consensus        53 ~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~~  132 (215)
                      ..+|||+|||+++++++|+++|++||.|..+.|+.+.  +.++|||||+|.+.++|+.|+..|||..|+|+.|.|.++.+
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~   85 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   85 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBT--TBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeec--CCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            4679999999999999999999999999999999885  44789999999999999999999999999999999999987


Q ss_pred             CCC
Q 028027          133 EHV  135 (215)
Q Consensus       133 ~~~  135 (215)
                      +..
T Consensus        86 ~~~   88 (89)
T d1cvja2          86 RKE   88 (89)
T ss_dssp             TTT
T ss_pred             CCC
Confidence            643

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=1.3e-20  Score=126.19  Aligned_cols=77  Identities=19%  Similarity=0.448  Sum_probs=73.2

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           53 ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        53 ~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      .++|||+|||+++|+++|+++|++||.|..+.++.++.++.++|||||+|.+.++|.+|+ .+||+.|+|+.|.|+.|
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 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHH-HCSCCEETTEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHH-HhCCCEECCEEEEEEEC
Confidence            478999999999999999999999999999999999999999999999999999999999 58999999999999875

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.84  E-value=9.6e-21  Score=131.92  Aligned_cols=85  Identities=24%  Similarity=0.334  Sum_probs=78.5

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhC------CceeCCeE
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMH------GYLLFEHI  124 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~------g~~l~g~~  124 (215)
                      .++++|||+|||+++|+++|+++|++||.|..+.++.+..++.++|||||+|.+.++|..|+..||      |..++|+.
T Consensus         6 ~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr~   85 (98)
T d1x4ha1           6 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQ   85 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCE
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCEE
Confidence            456899999999999999999999999999999999998899999999999999999999999886      57799999


Q ss_pred             EEEEEeCCCCC
Q 028027          125 LQVHLIPPEHV  135 (215)
Q Consensus       125 l~V~~a~~~~~  135 (215)
                      |+|+++.++..
T Consensus        86 l~v~~a~~k~~   96 (98)
T d1x4ha1          86 LKVDLAVTRDE   96 (98)
T ss_dssp             EEEECCCCCCC
T ss_pred             EEEEECCCCCc
Confidence            99999987643

>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=99.84  E-value=9.9e-21  Score=132.60  Aligned_cols=85  Identities=21%  Similarity=0.366  Sum_probs=77.8

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCee--------EEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCC
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIK--------RLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFE  122 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~--------~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g  122 (215)
                      ...++|||+|||+.+++++|+++|++||.|.        .+.+..++.+|.++|||||+|.+.++|..|+..|||..|+|
T Consensus         6 ~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g   85 (101)
T d2cpea1           6 SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQG   85 (101)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEECC
Confidence            4578999999999999999999999999874        56777888899999999999999999999999999999999


Q ss_pred             eEEEEEEeCCCCC
Q 028027          123 HILQVHLIPPEHV  135 (215)
Q Consensus       123 ~~l~V~~a~~~~~  135 (215)
                      +.|+|.++.++..
T Consensus        86 r~i~V~~a~~~~p   98 (101)
T d2cpea1          86 SKLKVSLARKKPP   98 (101)
T ss_dssp             EECEEECSSCCCC
T ss_pred             EEEEEEEcCCCCC
Confidence            9999999987543

>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=99.84  E-value=1.7e-20  Score=134.35  Aligned_cols=79  Identities=22%  Similarity=0.443  Sum_probs=73.1

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ..+++|||+|||..+++++|+++|++||.|.+|++..   ++.++|||||+|.+.++|..|++.|||..|+|+.|.|.++
T Consensus         5 ~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~---~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a   81 (114)
T d2f9da1           5 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN---TPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYY   81 (114)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEC---STTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccc---cCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            4578999999999999999999999999999999875   4667899999999999999999999999999999999997


Q ss_pred             CC
Q 028027          131 PP  132 (215)
Q Consensus       131 ~~  132 (215)
                      .+
T Consensus        82 ~~   83 (114)
T d2f9da1          82 NA   83 (114)
T ss_dssp             CH
T ss_pred             CC
Confidence            53

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.83  E-value=4.2e-21  Score=130.87  Aligned_cols=81  Identities=21%  Similarity=0.359  Sum_probs=71.2

Q ss_pred             CCcEEEEcCCCCCCc-HHHHHHHhccCCCeeEEEEeec-CCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           52 KATVLYIGRIPHGFY-EKEMQAFFSQFGAIKRLRIARN-KKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        52 ~~~~l~V~nLp~~~t-e~~L~~~F~~~G~v~~v~i~~~-~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      +.++|||+|||++++ +++|+++|++||.|.+|.|+.+ ..+|.++|||||+|.+.++|..|++ |||..|+|+.|+|++
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~~   81 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSL   81 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEEE
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEEE
Confidence            468999999999876 5679999999999999998764 5689999999999999999999995 999999999999999


Q ss_pred             eCCC
Q 028027          130 IPPE  133 (215)
Q Consensus       130 a~~~  133 (215)
                      +.++
T Consensus        82 a~~k   85 (86)
T d2ghpa3          82 ADKK   85 (86)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9875

>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=99.83  E-value=2.6e-21  Score=128.53  Aligned_cols=75  Identities=16%  Similarity=0.384  Sum_probs=70.8

Q ss_pred             EEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           55 VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        55 ~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      .|||+|||+++|+++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|++||+ ++++.|+|+.|.|+.|
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~-~~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTT-CSSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHh-hCCCEECCEEeEEEEC
Confidence            59999999999999999999999999999999999999999999999999999999996 5778999999999864

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=1.9e-21  Score=136.59  Aligned_cols=86  Identities=23%  Similarity=0.388  Sum_probs=80.2

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      .++++|||+|||..+++++|+++|++||.|..+.++.+..+|.++|||||+|.+.++|..|+..|||..|+|+.|+|.|+
T Consensus        16 ~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   95 (102)
T d2cpxa1          16 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG   95 (102)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            45789999999999999999999999999999988888778999999999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 028027          131 PPEHVH  136 (215)
Q Consensus       131 ~~~~~~  136 (215)
                      +++..+
T Consensus        96 k~k~~r  101 (102)
T d2cpxa1          96 KNKKQR  101 (102)
T ss_dssp             CCCSCC
T ss_pred             CCcccC
Confidence            876543

>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=99.82  E-value=1e-20  Score=132.76  Aligned_cols=82  Identities=26%  Similarity=0.430  Sum_probs=75.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ..++++|||+|||+++++++|+++|++||.|..+.+..+. ++.++|||||+|.+.++|..|++.|||..|.|+++.|.+
T Consensus        15 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~-~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~   93 (101)
T d1x5oa1          15 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAP   93 (101)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCC
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeeccc-ccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCC
Confidence            3556899999999999999999999999999999999885 899999999999999999999999999999999988876


Q ss_pred             eCC
Q 028027          130 IPP  132 (215)
Q Consensus       130 a~~  132 (215)
                      +.|
T Consensus        94 ~~P   96 (101)
T d1x5oa1          94 TEP   96 (101)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            654

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.82  E-value=9.4e-21  Score=125.61  Aligned_cols=75  Identities=19%  Similarity=0.464  Sum_probs=71.9

Q ss_pred             EEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           55 VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        55 ~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      +|||+|||+++|+++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|+.|++ |||+.|+|+.|+|++|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECCeEEEEEEC
Confidence            48999999999999999999999999999999998899999999999999999999996 9999999999999875

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.82  E-value=2.5e-21  Score=133.40  Aligned_cols=82  Identities=20%  Similarity=0.356  Sum_probs=75.1

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ....++|||+|||+.+++++|+++|+.||.|..+.++.+ .+|+++|||||+|.+.++|+.||+ |||..|+|+.|+|.+
T Consensus        10 ~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~   87 (91)
T d1fjeb1          10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEK   87 (91)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEEC
T ss_pred             CCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEe
Confidence            355679999999999999999999999999999888766 489999999999999999999995 999999999999999


Q ss_pred             eCCC
Q 028027          130 IPPE  133 (215)
Q Consensus       130 a~~~  133 (215)
                      ++++
T Consensus        88 ak~k   91 (91)
T d1fjeb1          88 PKGR   91 (91)
T ss_dssp             CCCS
T ss_pred             cCCC
Confidence            8753

>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=99.81  E-value=1.2e-19  Score=125.73  Aligned_cols=81  Identities=26%  Similarity=0.465  Sum_probs=73.7

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ..+.++|||+|||+++++++|+++|++||.|..+.+..   ++.++|||||+|.+.++|..||..|||+.|.|+.|+|+|
T Consensus        11 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~---~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~   87 (95)
T d1x4aa1          11 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN---RRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEF   87 (95)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECC---SSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEecc---cccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            35668999999999999999999999999999988754   355689999999999999999999999999999999999


Q ss_pred             eCCC
Q 028027          130 IPPE  133 (215)
Q Consensus       130 a~~~  133 (215)
                      +++.
T Consensus        88 a~~~   91 (95)
T d1x4aa1          88 PRSG   91 (95)
T ss_dssp             CCCC
T ss_pred             ccCC
Confidence            8764

>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=99.81  E-value=1.5e-19  Score=127.20  Aligned_cols=84  Identities=19%  Similarity=0.375  Sum_probs=74.1

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecC-CCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNK-KTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~-~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      .++++|||+|||+++++++|+++|+.|| |..+.++.+. .+|.++|||||+|.+.++|++|+ .||+..|+|+.|+|.+
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
Confidence            4568999999999999999999999999 6777777654 47899999999999999998777 6999999999999999


Q ss_pred             eCCCCCC
Q 028027          130 IPPEHVH  136 (215)
Q Consensus       130 a~~~~~~  136 (215)
                      +.+....
T Consensus        91 a~~~~~~   97 (104)
T d1wi8a_          91 ADQAQDK   97 (104)
T ss_dssp             CCCCCCC
T ss_pred             CCCCCCC
Confidence            9876544

>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=99.81  E-value=6.3e-20  Score=127.50  Aligned_cols=78  Identities=24%  Similarity=0.417  Sum_probs=72.6

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ...++|||+|||..+++++|+.+|++||.|.+|.++.+      +|||||+|.+.++|..|+..|||..|+|+.|+|.|+
T Consensus        16 ~~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~a   89 (96)
T d1x4ga1          16 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWG   89 (96)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            34678999999999999999999999999999999876      489999999999999999999999999999999998


Q ss_pred             CCCC
Q 028027          131 PPEH  134 (215)
Q Consensus       131 ~~~~  134 (215)
                      ++.+
T Consensus        90 k~~p   93 (96)
T d1x4ga1          90 KESP   93 (96)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7654

>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=99.81  E-value=6.7e-20  Score=127.33  Aligned_cols=81  Identities=19%  Similarity=0.231  Sum_probs=73.7

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      .+.++|||+|||+++++++|+++|++||.|..+.     .+|.++|||||+|.+.++|..|+..|||..|+|+.|.|.|+
T Consensus        14 ~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~-----~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a   88 (96)
T d1fjca_          14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT   88 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEE-----ETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcccceeee-----ecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            4568999999999999999999999999886654     27889999999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 028027          131 PPEHVH  136 (215)
Q Consensus       131 ~~~~~~  136 (215)
                      .++...
T Consensus        89 ~~k~~~   94 (96)
T d1fjca_          89 GEKGGT   94 (96)
T ss_dssp             SSSCCC
T ss_pred             CCCCCC
Confidence            887654

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=1.5e-19  Score=122.78  Aligned_cols=78  Identities=18%  Similarity=0.237  Sum_probs=73.0

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeC
Q 028027           52 KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIP  131 (215)
Q Consensus        52 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~  131 (215)
                      ..++|||+|||+++|+++|+++|+.||.|..|.+..+. +|.++|||||+|.+.++|+.||+ ++|..+.|+.|.|.+..
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
Confidence            35789999999999999999999999999999998886 89999999999999999999995 79999999999999853

>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=99.80  E-value=1.9e-19  Score=121.65  Aligned_cols=76  Identities=20%  Similarity=0.486  Sum_probs=69.6

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCcee-CCeEEEEEE
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLL-FEHILQVHL  129 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l-~g~~l~V~~  129 (215)
                      +++++|||+|||.++++++|..+|++||.|..|++++++     +|||||+|.+.++|..|+..|||..| +|+.|+|.|
T Consensus         6 pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~   80 (83)
T d2b0ga1           6 PPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITF   80 (83)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTT-----CSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeeccc-----ceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEE
Confidence            457899999999999999999999999999999997653     58999999999999999999999988 468999999


Q ss_pred             eC
Q 028027          130 IP  131 (215)
Q Consensus       130 a~  131 (215)
                      |+
T Consensus        81 ak   82 (83)
T d2b0ga1          81 AK   82 (83)
T ss_dssp             CC
T ss_pred             ec
Confidence            85

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.79  E-value=1.3e-19  Score=123.24  Aligned_cols=79  Identities=14%  Similarity=0.200  Sum_probs=71.4

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEE-EEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRL-RIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v-~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      +..++|||+|||+++++++|+++|+.||.|... .+..+ .+|.++|||||+|.+.++|+.|+..||+..|+|+.|+|.+
T Consensus         7 p~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~-~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l   85 (86)
T d2cqpa1           7 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYN-EKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVL   85 (86)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEEC-SSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeC-CCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEE
Confidence            446789999999999999999999999998764 45554 5899999999999999999999999999999999999987


Q ss_pred             e
Q 028027          130 I  130 (215)
Q Consensus       130 a  130 (215)
                      +
T Consensus        86 ~   86 (86)
T d2cqpa1          86 G   86 (86)
T ss_dssp             S
T ss_pred             C
Confidence            4

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.79  E-value=9.6e-20  Score=124.82  Aligned_cols=76  Identities=13%  Similarity=0.306  Sum_probs=69.6

Q ss_pred             CcEEEEcCCCCCCcHHHH---HHHhccCCCeeEEEEeecCCCCCc---ccEEEEEEcCHHHHHHHHHHhCCceeCCeEEE
Q 028027           53 ATVLYIGRIPHGFYEKEM---QAFFSQFGAIKRLRIARNKKTGQS---KHFGFIEFNDPEVAEVVADAMHGYLLFEHILQ  126 (215)
Q Consensus        53 ~~~l~V~nLp~~~te~~L---~~~F~~~G~v~~v~i~~~~~tg~~---~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~  126 (215)
                      .++|||+|||+.+++++|   .++|++||.|..|.+++++.++.+   +|||||+|.+.++|..|++.|||..|+|+.|+
T Consensus         8 ~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~lk   87 (89)
T d2cpia1           8 KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLK   87 (89)
T ss_dssp             SSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEEE
Confidence            467999999999999999   678999999999999998766654   48999999999999999999999999999999


Q ss_pred             EE
Q 028027          127 VH  128 (215)
Q Consensus       127 V~  128 (215)
                      |+
T Consensus        88 vS   89 (89)
T d2cpia1          88 AS   89 (89)
T ss_dssp             EE
T ss_pred             EC
Confidence            85

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.79  E-value=2.9e-19  Score=121.62  Aligned_cols=77  Identities=25%  Similarity=0.482  Sum_probs=71.6

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeC
Q 028027           52 KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIP  131 (215)
Q Consensus        52 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~  131 (215)
                      ..++|||+|||+++++++|+++|++||.|.+|.+.++      +|||||+|.+.++|..|+..|||..|+|+.|+|+||.
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~------k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~   80 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFAC   80 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc------cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            3468999999999999999999999999999999866      4899999999999999999999999999999999997


Q ss_pred             CCC
Q 028027          132 PEH  134 (215)
Q Consensus       132 ~~~  134 (215)
                      +..
T Consensus        81 ~~~   83 (86)
T d2cpja1          81 HSA   83 (86)
T ss_dssp             CCS
T ss_pred             CcC
Confidence            654

>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=99.79  E-value=5e-20  Score=121.21  Aligned_cols=71  Identities=21%  Similarity=0.459  Sum_probs=68.4

Q ss_pred             EEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEE
Q 028027           56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQ  126 (215)
Q Consensus        56 l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~  126 (215)
                      |||+|||+++|+++|+++|++||.|..+.+..++.++.++|||||+|.+.++|+.|+..|||..|+|+.|+
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEECc
Confidence            79999999999999999999999999999999998999999999999999999999999999999998763

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=7.4e-19  Score=119.47  Aligned_cols=78  Identities=19%  Similarity=0.326  Sum_probs=70.7

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ...++|||+|||+++++++|+++|++||.|..+.+..      ++|||||+|.+.++|..|+..|||..|+|+.|.|.|+
T Consensus         6 ~~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~------~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~a   79 (86)
T d2cpda1           6 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK------IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLA   79 (86)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE------CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECC
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcc------ccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEec
Confidence            3457899999999999999999999999998877644      4689999999999999999999999999999999999


Q ss_pred             CCCC
Q 028027          131 PPEH  134 (215)
Q Consensus       131 ~~~~  134 (215)
                      .|..
T Consensus        80 kP~~   83 (86)
T d2cpda1          80 KPVD   83 (86)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            8754

>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=99.79  E-value=1.6e-19  Score=125.41  Aligned_cols=83  Identities=18%  Similarity=0.294  Sum_probs=74.4

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCC-eeEEEEeecC-CCCCcccEEEEEEcCHHHHHHHHHHhCC--ceeCCeEEEEEE
Q 028027           54 TVLYIGRIPHGFYEKEMQAFFSQFGA-IKRLRIARNK-KTGQSKHFGFIEFNDPEVAEVVADAMHG--YLLFEHILQVHL  129 (215)
Q Consensus        54 ~~l~V~nLp~~~te~~L~~~F~~~G~-v~~v~i~~~~-~tg~~~g~afV~F~~~~~a~~ai~~l~g--~~l~g~~l~V~~  129 (215)
                      ++|||+|||..+++++|+++|++||+ |..+.++.+. .+|.++|||||+|.+.++|..|++.|++  ..++|+.|.|.|
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~~   81 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDW   81 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEE
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEEE
Confidence            68999999999999999999999996 8999998875 4689999999999999999999999864  566899999999


Q ss_pred             eCCCCCC
Q 028027          130 IPPEHVH  136 (215)
Q Consensus       130 a~~~~~~  136 (215)
                      |.|....
T Consensus        82 A~p~~~~   88 (96)
T d2disa1          82 AEPEIDV   88 (96)
T ss_dssp             SCSSCST
T ss_pred             cCCCCCC
Confidence            9876543

>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=99.78  E-value=7.4e-19  Score=123.70  Aligned_cols=86  Identities=17%  Similarity=0.251  Sum_probs=76.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ..+..+|||+|||+++|+++|+++|..||.|..+.++.+..++.++|||||+|.+.++|++|+. +|+..|+|+.|.|.+
T Consensus        12 ~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~   90 (104)
T d1wg5a_          12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFK   90 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEE
Confidence            3456789999999999999999999999999887666666799999999999999999999995 899999999999999


Q ss_pred             eCCCCCC
Q 028027          130 IPPEHVH  136 (215)
Q Consensus       130 a~~~~~~  136 (215)
                      +.+....
T Consensus        91 ~~~~~~~   97 (104)
T d1wg5a_          91 SSRAEVR   97 (104)
T ss_dssp             ECTTTSC
T ss_pred             CCHHHhc
Confidence            9876543

>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=99.78  E-value=1.7e-19  Score=121.11  Aligned_cols=77  Identities=16%  Similarity=0.315  Sum_probs=69.1

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCc-eeCCeEEEEEEeCC
Q 028027           54 TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGY-LLFEHILQVHLIPP  132 (215)
Q Consensus        54 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~-~l~g~~l~V~~a~~  132 (215)
                      .+|||+|||+++++++|+++|++||.|..+.+...      +|||||+|.+.++|..|++.|||. .++|+.|+|+++.|
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~------rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~   75 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK------SGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVS   75 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEE------TTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEecc------cceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCC
Confidence            46999999999999999999999999887766554      589999999999999999999995 69999999999988


Q ss_pred             CCCC
Q 028027          133 EHVH  136 (215)
Q Consensus       133 ~~~~  136 (215)
                      +..+
T Consensus        76 k~~r   79 (80)
T d2cqha1          76 KKLR   79 (80)
T ss_dssp             CCCC
T ss_pred             cCcC
Confidence            6543

>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=99.78  E-value=5.6e-19  Score=123.09  Aligned_cols=75  Identities=19%  Similarity=0.425  Sum_probs=68.2

Q ss_pred             CCCcEEEEcCCC-CCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           51 NKATVLYIGRIP-HGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        51 ~~~~~l~V~nLp-~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ...++|||+||| ..+++.+|+++|++||.|.+|.+        ++|||||+|.+.++|+.||..|||..|.|+.|+|.+
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
Confidence            455779999997 56888999999999999999988        358999999999999999999999999999999999


Q ss_pred             eCCC
Q 028027          130 IPPE  133 (215)
Q Consensus       130 a~~~  133 (215)
                      +.+.
T Consensus        85 a~~~   88 (98)
T d1wf2a_          85 AAEP   88 (98)
T ss_dssp             TTSC
T ss_pred             CCCC
Confidence            9764

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=2.5e-19  Score=123.19  Aligned_cols=79  Identities=19%  Similarity=0.452  Sum_probs=71.6

Q ss_pred             CcEEEEcCCCCCCcHHHHH----HHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 028027           53 ATVLYIGRIPHGFYEKEMQ----AFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVH  128 (215)
Q Consensus        53 ~~~l~V~nLp~~~te~~L~----~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~  128 (215)
                      +++|||+|||+.+++++|+    .+|++||.|.+|.+..   ++.++|||||+|.+.++|..|+..|||..++|+.|+|.
T Consensus         3 ~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~---~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~   79 (91)
T d1nu4a_           3 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQ   79 (91)
T ss_dssp             CSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee---eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            5899999999999999886    4689999999988754   57789999999999999999999999999999999999


Q ss_pred             EeCCCC
Q 028027          129 LIPPEH  134 (215)
Q Consensus       129 ~a~~~~  134 (215)
                      |++++.
T Consensus        80 ~ak~~~   85 (91)
T d1nu4a_          80 YAKTDS   85 (91)
T ss_dssp             ECSSCC
T ss_pred             EeCCCc
Confidence            998754

>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=99.78  E-value=7.5e-19  Score=119.95  Aligned_cols=79  Identities=19%  Similarity=0.251  Sum_probs=70.1

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCcee-CCeEEEEEE
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLL-FEHILQVHL  129 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l-~g~~l~V~~  129 (215)
                      +++++|||+|||+++++++|+++|+.||.|..+.+...    ..+|||||+|.+.++|..|+..|||+.| +|+.|+|+|
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~----~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~   83 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSF   83 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS----SSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeee----cccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEe
Confidence            34689999999999999999999999999988776543    4578999999999999999999999987 589999999


Q ss_pred             eCCC
Q 028027          130 IPPE  133 (215)
Q Consensus       130 a~~~  133 (215)
                      +++.
T Consensus        84 sk~~   87 (88)
T d2adca2          84 SKST   87 (88)
T ss_dssp             CSSC
T ss_pred             CCCC
Confidence            8753

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.78  E-value=6.8e-19  Score=116.70  Aligned_cols=74  Identities=18%  Similarity=0.307  Sum_probs=67.9

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           54 TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        54 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ++|||+|||+++++++|+++|+.||.|..+.++.++.  ..++||||+|.+.++|.+|+ .||+..|+|+.|.|..+
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--KNFRFARIEFARYDGALAAI-TKTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTT--SSSEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecc--ccceEEEEEEcchHHhHHHH-HhcCcEECCEEEEEEEC
Confidence            5899999999999999999999999999999999863  34579999999999999999 58999999999999865

>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=99.77  E-value=5.3e-19  Score=118.35  Aligned_cols=76  Identities=20%  Similarity=0.328  Sum_probs=69.4

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ..+++|||+||+  +|+++|+++|++||.|.+|.+..+      +|||||+|.+.++|..|+..|||..++|+.|+|.|+
T Consensus         3 ~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a   74 (79)
T d2bz2a1           3 RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA   74 (79)
T ss_dssp             CCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT------TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC------CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            356899999996  899999999999999999998765      479999999999999999999999999999999999


Q ss_pred             CCCC
Q 028027          131 PPEH  134 (215)
Q Consensus       131 ~~~~  134 (215)
                      ++++
T Consensus        75 ~~~P   78 (79)
T d2bz2a1          75 RKQP   78 (79)
T ss_dssp             CSSC
T ss_pred             cCCC
Confidence            7653

>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=99.77  E-value=9.6e-19  Score=122.72  Aligned_cols=83  Identities=16%  Similarity=0.185  Sum_probs=74.3

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ...+.+|||+|||+++|+++|+++|..||. ..+.++.+. +|.++|||||+|.+.++|+.|+. ||+..|+|+.|+|.+
T Consensus        12 ~~~~~~v~v~nLp~~~te~dl~~~F~~~~~-~~v~~~~~~-~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~   88 (102)
T d1weza_          12 STTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFL   88 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHhccCc-ceeeeEEec-CCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEE
Confidence            355679999999999999999999999984 578888875 78999999999999999999985 899999999999999


Q ss_pred             eCCCCC
Q 028027          130 IPPEHV  135 (215)
Q Consensus       130 a~~~~~  135 (215)
                      +.+...
T Consensus        89 s~~~~~   94 (102)
T d1weza_          89 NSTAGT   94 (102)
T ss_dssp             ECCCCC
T ss_pred             cCCCCC
Confidence            887643

>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=99.77  E-value=7e-19  Score=125.02  Aligned_cols=76  Identities=22%  Similarity=0.314  Sum_probs=70.0

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeC
Q 028027           52 KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIP  131 (215)
Q Consensus        52 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~  131 (215)
                      ..++|||+|||+.+++++|+++|++||.|..|.|..      ++|||||+|.+.++|..|+..|||..|.|+.|.|.|+.
T Consensus         9 ~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~------~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~   82 (111)
T d1whxa_           9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAP   82 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeec------cCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECC
Confidence            457899999999999999999999999999998743      46899999999999999999999999999999999986


Q ss_pred             CC
Q 028027          132 PE  133 (215)
Q Consensus       132 ~~  133 (215)
                      ..
T Consensus        83 ~~   84 (111)
T d1whxa_          83 IG   84 (111)
T ss_dssp             TT
T ss_pred             CC
Confidence            54

>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=99.76  E-value=1.4e-18  Score=123.16  Aligned_cols=77  Identities=18%  Similarity=0.370  Sum_probs=70.8

Q ss_pred             CcEEEEcCCCC-CCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeC
Q 028027           53 ATVLYIGRIPH-GFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIP  131 (215)
Q Consensus        53 ~~~l~V~nLp~-~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~  131 (215)
                      +++|||+|||+ .+++++|+++|+.||.|..|.|++++     +|||||+|.+.++|..|+..|||..|.|+.|.|.++.
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~-----kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~   76 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   76 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCS
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc-----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            57899999965 59999999999999999999998874     6899999999999999999999999999999999987


Q ss_pred             CCC
Q 028027          132 PEH  134 (215)
Q Consensus       132 ~~~  134 (215)
                      ...
T Consensus        77 ~~~   79 (109)
T d2adca1          77 HQN   79 (109)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>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=99.76  E-value=8.4e-19  Score=119.76  Aligned_cols=79  Identities=22%  Similarity=0.476  Sum_probs=70.1

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ..+++|||+|||+.+|+++|+++|++||.|..|.+.     ..++|||||+|.+.++|+.|+.  +++.|+|+.|.|.++
T Consensus         3 ~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~-----~~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a   75 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIP-----KPFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNA   75 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECC-----SSCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEe-----eccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeC
Confidence            356899999999999999999999999999998764     3457899999999999999984  889999999999999


Q ss_pred             CCCCCC
Q 028027          131 PPEHVH  136 (215)
Q Consensus       131 ~~~~~~  136 (215)
                      .++...
T Consensus        76 ~~k~~~   81 (88)
T d1wf0a_          76 EPKHNS   81 (88)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            876544

>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=99.76  E-value=1e-18  Score=122.68  Aligned_cols=81  Identities=15%  Similarity=0.169  Sum_probs=71.4

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ....+|||+|||+++|+++|+++|..||.|..+.++....+|.++|||||+|.+.++|+.|+. +|+..|+|+.|.|.++
T Consensus         6 ~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~   84 (103)
T d2cpya1           6 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVV   84 (103)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEEC
Confidence            345789999999999999999999999998775444444599999999999999999999995 8999999999999987


Q ss_pred             CC
Q 028027          131 PP  132 (215)
Q Consensus       131 ~~  132 (215)
                      ..
T Consensus        85 ~~   86 (103)
T d2cpya1          85 TL   86 (103)
T ss_dssp             CH
T ss_pred             CH
Confidence            53

>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=99.75  E-value=2.3e-19  Score=122.36  Aligned_cols=73  Identities=12%  Similarity=0.141  Sum_probs=67.2

Q ss_pred             EEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeCCCC
Q 028027           55 VLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPPEH  134 (215)
Q Consensus        55 ~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~~~~  134 (215)
                      +|||+|||+++++++|+++|++||.|..+.+..+       |||||+|.+.++|+.||..|||..|+|+.|.|.++.+..
T Consensus         2 rvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~~   74 (87)
T d3begb1           2 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKV   74 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEE
T ss_pred             eEEEECCCCcCCHHHHHHHHhhhccccccccccc-------ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecCc
Confidence            5999999999999999999999999999998654       799999999999999999999999999999988775543

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=9e-18  Score=114.49  Aligned_cols=80  Identities=19%  Similarity=0.246  Sum_probs=71.4

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHh--CCceeCCeEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM--HGYLLFEHILQV  127 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l--~g~~l~g~~l~V  127 (215)
                      ..++++|||+|||+.+++++|+++|++||.|..+.+..++      |||||+|.+.++|..|+..|  ++..++|+.|+|
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 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGK------NQAFLELATEEAAITMVNYYSAVTPHLRNQPIYI   78 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETTT------TEEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcccccccccccccc------eEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEE
Confidence            3567899999999999999999999999999999987653      79999999999999999865  567899999999


Q ss_pred             EEeCCCCC
Q 028027          128 HLIPPEHV  135 (215)
Q Consensus       128 ~~a~~~~~  135 (215)
                      .|++.+..
T Consensus        79 ~~sk~~~l   86 (88)
T d2cq1a1          79 QYSNHKEL   86 (88)
T ss_dssp             EECSCSSC
T ss_pred             EECCCCCC
Confidence            99976543

>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=99.75  E-value=2.1e-18  Score=120.15  Aligned_cols=79  Identities=10%  Similarity=0.123  Sum_probs=71.6

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      ...++|||+|||+.+++++|+++|++||.|..+.+..       +|||||+|.+.++|+.||+.|||..|.|+.|.|.++
T Consensus        13 ~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~   85 (98)
T d1wg4a_          13 RSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYI   85 (98)
T ss_dssp             SCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEE
Confidence            4567899999999999999999999999999998864       379999999999999999999999999999999998


Q ss_pred             CCCCCC
Q 028027          131 PPEHVH  136 (215)
Q Consensus       131 ~~~~~~  136 (215)
                      .++..+
T Consensus        86 ~~~~~~   91 (98)
T d1wg4a_          86 RVYPER   91 (98)
T ss_dssp             EEECCC
T ss_pred             ecCCCC
Confidence            765443

>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=99.75  E-value=3.4e-18  Score=116.71  Aligned_cols=76  Identities=17%  Similarity=0.321  Sum_probs=66.6

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeC
Q 028027           52 KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIP  131 (215)
Q Consensus        52 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~  131 (215)
                      .+++|||+|||+++++++|+++|++|| +..+.+      +..+|||||+|.+.++|+.|+..|||+.|+|+.|.|++++
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~------~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~   76 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV------DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE------EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcC-ceeeee------eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            457899999999999999999999999 333333      4457999999999999999999999999999999999997


Q ss_pred             CCC
Q 028027          132 PEH  134 (215)
Q Consensus       132 ~~~  134 (215)
                      ++.
T Consensus        77 ~~~   79 (88)
T d1wg1a_          77 TDA   79 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=2.9e-18  Score=121.40  Aligned_cols=81  Identities=11%  Similarity=0.214  Sum_probs=72.3

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCcee--CCeEEEEE
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLL--FEHILQVH  128 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l--~g~~l~V~  128 (215)
                      .+..+|||+|||+.+|+++|+++|++||.|..|.++.++    .+|||||+|.+.++|+.|+..|||..|  .|..|.|.
T Consensus         5 s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~   80 (108)
T d2adba1           5 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID   80 (108)
T ss_dssp             CCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEE
T ss_pred             CCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEE
Confidence            445789999999999999999999999999999998764    479999999999999999999999988  47889999


Q ss_pred             EeCCCCC
Q 028027          129 LIPPEHV  135 (215)
Q Consensus       129 ~a~~~~~  135 (215)
                      ++.+...
T Consensus        81 ~s~~~~~   87 (108)
T d2adba1          81 FSKLTSL   87 (108)
T ss_dssp             ECSSCSC
T ss_pred             ecCCccc
Confidence            9877544

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.74  E-value=6.9e-18  Score=111.73  Aligned_cols=72  Identities=24%  Similarity=0.370  Sum_probs=64.5

Q ss_pred             EEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeCCCC
Q 028027           56 LYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPPEH  134 (215)
Q Consensus        56 l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~~~~  134 (215)
                      |||+|||+++++++|+++|++|| +..+.+      +.++|||||+|.+.++|..|+..|||..++|+.|.|++++.+.
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
Confidence            79999999999999999999999 444443      4457999999999999999999999999999999999997654

>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=99.74  E-value=1.4e-18  Score=123.88  Aligned_cols=83  Identities=18%  Similarity=0.278  Sum_probs=73.4

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEE
Q 028027           48 PLVNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQV  127 (215)
Q Consensus        48 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V  127 (215)
                      .+....++|||+|||+.+|+++|+++|+.||.+..+.++.+..+|.++|||||+|.+.++|++|+. |||..|+|+.|.|
T Consensus        13 ~~~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V   91 (112)
T d1wela1          13 SPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQV   91 (112)
T ss_dssp             SCCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEE
T ss_pred             CCCCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEE
Confidence            344567899999999999999999999999999776555555699999999999999999999995 8999999999999


Q ss_pred             EEeC
Q 028027          128 HLIP  131 (215)
Q Consensus       128 ~~a~  131 (215)
                      ..+.
T Consensus        92 ~~~~   95 (112)
T d1wela1          92 HPIT   95 (112)
T ss_dssp             EEEC
T ss_pred             EEcC
Confidence            8874

>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=99.74  E-value=4.7e-18  Score=118.04  Aligned_cols=78  Identities=21%  Similarity=0.406  Sum_probs=70.7

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCC--eEEEEE
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFE--HILQVH  128 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g--~~l~V~  128 (215)
                      .+.++|||+|||+++++++|+++|++||.|..+.+.++      ++||||+|.+.++|..|+..||+..|.|  +.|+|.
T Consensus        15 ~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~   88 (97)
T d1whya_          15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVD   88 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEE
Confidence            34689999999999999999999999999999998765      4799999999999999999999999986  589999


Q ss_pred             EeCCCC
Q 028027          129 LIPPEH  134 (215)
Q Consensus       129 ~a~~~~  134 (215)
                      |+++.+
T Consensus        89 ~ak~~~   94 (97)
T d1whya_          89 FAKSGP   94 (97)
T ss_dssp             ECCCCC
T ss_pred             eCCCCC
Confidence            998654

>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=99.72  E-value=1.2e-17  Score=116.34  Aligned_cols=78  Identities=21%  Similarity=0.319  Sum_probs=70.0

Q ss_pred             CCCCcEEEEcCCCCC-CcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHH--HhCCceeCCeEEE
Q 028027           50 VNKATVLYIGRIPHG-FYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVAD--AMHGYLLFEHILQ  126 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~-~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~--~l~g~~l~g~~l~  126 (215)
                      ...+++|||+|||.. +|+++|.++|+.||.|.++.++.+      +|||||+|.+.++|..|+.  .+++..++|+.|.
T Consensus        15 ~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~   88 (99)
T d1x4fa1          15 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVK   88 (99)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCE
T ss_pred             CCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCCceECCEEEE
Confidence            456789999999985 899999999999999999999865      4899999999999999997  5788899999999


Q ss_pred             EEEeCCC
Q 028027          127 VHLIPPE  133 (215)
Q Consensus       127 V~~a~~~  133 (215)
                      |.+++..
T Consensus        89 V~~s~~~   95 (99)
T d1x4fa1          89 VDLSEKY   95 (99)
T ss_dssp             EEEECSC
T ss_pred             EEEcCCc
Confidence            9999654

>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=99.71  E-value=7.6e-17  Score=113.21  Aligned_cols=79  Identities=11%  Similarity=0.162  Sum_probs=70.8

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHh--CCceeCCeEEEEE
Q 028027           51 NKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM--HGYLLFEHILQVH  128 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l--~g~~l~g~~l~V~  128 (215)
                      .++.+|||+|||+.+++++|..+|++||.|..+.+.++      +|+|||+|.+.++|+.|+..|  ++..++|+.|+|.
T Consensus        13 ~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~   86 (104)
T d1wexa_          13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFN   86 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec------ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEE
Confidence            56789999999999999999999999999999998765      489999999999999999987  4567899999999


Q ss_pred             EeCCCCC
Q 028027          129 LIPPEHV  135 (215)
Q Consensus       129 ~a~~~~~  135 (215)
                      |++....
T Consensus        87 ~s~~~~~   93 (104)
T d1wexa_          87 YSTSKRI   93 (104)
T ss_dssp             ECSSSSC
T ss_pred             EcCCCcc
Confidence            9976543

>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=99.70  E-value=4.7e-17  Score=111.16  Aligned_cols=77  Identities=23%  Similarity=0.286  Sum_probs=69.6

Q ss_pred             CCCcEEEEcCCCCC-CcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHh--CCceeCCeEEEE
Q 028027           51 NKATVLYIGRIPHG-FYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAM--HGYLLFEHILQV  127 (215)
Q Consensus        51 ~~~~~l~V~nLp~~-~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l--~g~~l~g~~l~V  127 (215)
                      ..+++|||+|||.. +|+++|.++|++||.|.+|.++.++      ++|||+|.+.++|..|+..|  ++..+.|++|+|
T Consensus         6 ~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~k------~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V   79 (89)
T d1x4da1           6 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI------NEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRV   79 (89)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS------SCEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeeccc------eEEEEEEcchhhHHHHHHHHhhCCCccCCceEEE
Confidence            56789999999986 8899999999999999999998764      69999999999999999965  678899999999


Q ss_pred             EEeCCC
Q 028027          128 HLIPPE  133 (215)
Q Consensus       128 ~~a~~~  133 (215)
                      .|++..
T Consensus        80 ~~s~~~   85 (89)
T d1x4da1          80 HLSQKY   85 (89)
T ss_dssp             EEECCC
T ss_pred             EECCCc
Confidence            999754

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=8.5e-17  Score=123.31  Aligned_cols=83  Identities=18%  Similarity=0.382  Sum_probs=77.6

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 028027           50 VNKATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHL  129 (215)
Q Consensus        50 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~  129 (215)
                      ....++|||+|||+.+++++|+.+|+.||.|..+.++.+..+|.++|||||+|.+.++|.+|+. +++..++|+.|.|.+
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
Confidence            4567899999999999999999999999999999999998899999999999999999999996 799999999999999


Q ss_pred             eCCC
Q 028027          130 IPPE  133 (215)
Q Consensus       130 a~~~  133 (215)
                      |.++
T Consensus       173 A~~k  176 (183)
T d1u1qa_         173 ALSK  176 (183)
T ss_dssp             CCCH
T ss_pred             cCCc
Confidence            8654

>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=99.67  E-value=9.8e-17  Score=112.65  Aligned_cols=80  Identities=10%  Similarity=0.150  Sum_probs=70.4

Q ss_pred             CCCcEEEEcCCCCCCcH-----HHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEE
Q 028027           51 NKATVLYIGRIPHGFYE-----KEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHIL  125 (215)
Q Consensus        51 ~~~~~l~V~nLp~~~te-----~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l  125 (215)
                      ..+++|||+||+..+..     ++|+.+|++||.|.++.+.+.      ++||||+|.+.++|..|+..|||..|+|+.|
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l   76 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS------FKRVRINFSNPLSAADARLRLHKTEFLGKEM   76 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT------TTEEEEECSSTTHHHHHHHTSTTSEETTEEC
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecC------CCEEEEEECCHHHHHHHHHHhcccccCCCEe
Confidence            35688999999998632     569999999999999998754      5799999999999999999999999999999


Q ss_pred             EEEEeCCCCCC
Q 028027          126 QVHLIPPEHVH  136 (215)
Q Consensus       126 ~V~~a~~~~~~  136 (215)
                      +|.|+.+....
T Consensus        77 ~v~~a~~~~~~   87 (104)
T d1weya_          77 KLYFAQTLHIG   87 (104)
T ss_dssp             EEECCCCSSCC
T ss_pred             EEeecccCCCC
Confidence            99999876544

>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=99.65  E-value=1.2e-18  Score=119.33  Aligned_cols=75  Identities=28%  Similarity=0.474  Sum_probs=66.2

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEe-----ecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 028027           54 TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIA-----RNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVH  128 (215)
Q Consensus        54 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~-----~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~  128 (215)
                      ++|||+|||+.+|+++|+++|++||.|..+.+.     .+..++.++|||||+|.+.++|+.|+ .|||..+.|+.|+|+
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~-~l~g~~~~Gr~l~V~   80 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIR   80 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGG-GGSSCCSSSSCCCCB
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHH-hhCCcEECCEEEEEC
Confidence            689999999999999999999999987665443     34457889999999999999999998 599999999999996


Q ss_pred             E
Q 028027          129 L  129 (215)
Q Consensus       129 ~  129 (215)
                      .
T Consensus        81 r   81 (90)
T d1u2fa_          81 R   81 (90)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.62  E-value=3.5e-17  Score=114.99  Aligned_cols=76  Identities=12%  Similarity=0.201  Sum_probs=71.7

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEe
Q 028027           54 TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLI  130 (215)
Q Consensus        54 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a  130 (215)
                      +.++|.+++..+++++|+++|++||.|.+|.|+++. +|.++|||||+|.+.++|..|+..|||..++|+.|.|+++
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~-~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCC-CCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            458888999999999999999999999999999885 8999999999999999999999999999999999999986

>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=99.56  E-value=4.9e-15  Score=105.36  Aligned_cols=72  Identities=19%  Similarity=0.216  Sum_probs=63.8

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCH-HHHHHHHHHhCCceeCCeEEEEEEeC
Q 028027           54 TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDP-EVAEVVADAMHGYLLFEHILQVHLIP  131 (215)
Q Consensus        54 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~-~~a~~ai~~l~g~~l~g~~l~V~~a~  131 (215)
                      ..+||||||+.+|+++|+.+|++||+|.+|.|+.+      +|||||.|.+. ++|..|+..||+..+.++.+.|.++.
T Consensus        12 ~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~   84 (113)
T d1owxa_          12 LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEV   84 (113)
T ss_dssp             EEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEE
T ss_pred             eEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEee
Confidence            34599999999999999999999999999999865      48999999985 68999999999998888887777753

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.55  E-value=1.7e-14  Score=110.14  Aligned_cols=81  Identities=16%  Similarity=0.349  Sum_probs=73.6

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeCC
Q 028027           53 ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPP  132 (215)
Q Consensus        53 ~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~~  132 (215)
                      .++|||+|||+.+|+++|+++|++||.|.++.++++..+|.++|||||+|.+.++|..|+. +++..++++.+.+....+
T Consensus         6 ~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~-~~~~~~~~~~~~~~~~~~   84 (183)
T d1u1qa_           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAVS   84 (183)
T ss_dssp             HHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHH-hcCCcccccchhhhhhhh
Confidence            4799999999999999999999999999999999998899999999999999999999996 467778888888887655


Q ss_pred             CC
Q 028027          133 EH  134 (215)
Q Consensus       133 ~~  134 (215)
                      ..
T Consensus        85 ~~   86 (183)
T d1u1qa_          85 RE   86 (183)
T ss_dssp             TT
T ss_pred             cc
Confidence            44

>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=99.51  E-value=1.9e-14  Score=100.23  Aligned_cols=64  Identities=16%  Similarity=0.338  Sum_probs=57.3

Q ss_pred             CCCcEEEE--cCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCcee
Q 028027           51 NKATVLYI--GRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLL  120 (215)
Q Consensus        51 ~~~~~l~V--~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l  120 (215)
                      .+..+|||  ||||..+|+++|+++|++||.|..|.+..+      ++||||+|.+.++|..|+..|||..+
T Consensus        16 ~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            34577888  559999999999999999999999988765      47999999999999999999999876

>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=99.49  E-value=3e-14  Score=95.16  Aligned_cols=73  Identities=16%  Similarity=0.185  Sum_probs=61.3

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeE-EEEEEe
Q 028027           52 KATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHI-LQVHLI  130 (215)
Q Consensus        52 ~~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~-l~V~~a  130 (215)
                      +.+.|+|+|+|++++++.| .+|++||.|.++.+.++      +|||||+|.+.++|++||. +||..|+|+. |.|..+
T Consensus         3 ~~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~~------~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~   74 (81)
T d1wwha1           3 DDTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSNT------GNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPC   74 (81)
T ss_dssp             GGGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECSS------SSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEEC
T ss_pred             cccEEEEECCChHHHHHHH-HHHHhhhhhheEEecCC------CCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeC
Confidence            3577999999999987655 57999999999987543      5899999999999999995 8999999974 567766


Q ss_pred             CC
Q 028027          131 PP  132 (215)
Q Consensus       131 ~~  132 (215)
                      ..
T Consensus        75 ~~   76 (81)
T d1wwha1          75 ID   76 (81)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.47  E-value=9.3e-14  Score=96.29  Aligned_cols=80  Identities=19%  Similarity=0.354  Sum_probs=68.3

Q ss_pred             CCCcEEEEcCC--CCCC---------cHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCce
Q 028027           51 NKATVLYIGRI--PHGF---------YEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYL  119 (215)
Q Consensus        51 ~~~~~l~V~nL--p~~~---------te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~  119 (215)
                      ..+++|+|.||  |..+         .+++|++.|++||.|..|.+..+    .++|||||.|.+.++|..|+..|||..
T Consensus         6 ~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~lng~~   81 (99)
T d2dita1           6 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLDGRW   81 (99)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHHSTTCE
T ss_pred             CCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC----CCccEEEEEECCHHHHHHHHHHhCCcE
Confidence            45789999999  5432         23688999999999999988654    356999999999999999999999999


Q ss_pred             eCCeEEEEEEeCCCC
Q 028027          120 LFEHILQVHLIPPEH  134 (215)
Q Consensus       120 l~g~~l~V~~a~~~~  134 (215)
                      ++|+.|+|.++.+..
T Consensus        82 ~~gr~i~v~~~~g~~   96 (99)
T d2dita1          82 FGGRQITAQAWDGTT   96 (99)
T ss_dssp             ETTEECEEEECCSCC
T ss_pred             ECCEEEEEEEeCCcC
Confidence            999999999987654

>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=99.39  E-value=3.3e-13  Score=94.23  Aligned_cols=81  Identities=16%  Similarity=0.258  Sum_probs=68.7

Q ss_pred             CCcEEEEcCC--CCCC--------cHHHHHHHhccCCCeeEEEEeecCCCC--CcccEEEEEEcCHHHHHHHHHHhCCce
Q 028027           52 KATVLYIGRI--PHGF--------YEKEMQAFFSQFGAIKRLRIARNKKTG--QSKHFGFIEFNDPEVAEVVADAMHGYL  119 (215)
Q Consensus        52 ~~~~l~V~nL--p~~~--------te~~L~~~F~~~G~v~~v~i~~~~~tg--~~~g~afV~F~~~~~a~~ai~~l~g~~  119 (215)
                      ++++|.|.||  |..+        ..++|++.|++||.|.+|.|+++..+.  ...|++||.|.+.++|..|+..|||..
T Consensus         3 Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~   82 (104)
T d1o0pa_           3 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   82 (104)
T ss_dssp             CCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCC
T ss_pred             CCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCE
Confidence            4688999999  4433        335789999999999999998875443  356899999999999999999999999


Q ss_pred             eCCeEEEEEEeCC
Q 028027          120 LFEHILQVHLIPP  132 (215)
Q Consensus       120 l~g~~l~V~~a~~  132 (215)
                      ++||.|.|.++.+
T Consensus        83 f~gR~v~v~f~~~   95 (104)
T d1o0pa_          83 FANRVVVTKYCDP   95 (104)
T ss_dssp             SSSSCCEEEEECH
T ss_pred             ECCeEEEEEEcCH
Confidence            9999999999864

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.71  E-value=0.00014  Score=48.04  Aligned_cols=68  Identities=16%  Similarity=0.309  Sum_probs=57.5

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCC--cccEEEEEEcCHHHHHHHHHHhCCceeC
Q 028027           54 TVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQ--SKHFGFIEFNDPEVAEVVADAMHGYLLF  121 (215)
Q Consensus        54 ~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~--~~g~afV~F~~~~~a~~ai~~l~g~~l~  121 (215)
                      +.|.|.+||+++|++++.+.++..|.+........+.+.+  .-.-|||.|.+.+++....+.++|+.+-
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~   71 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFL   71 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEE
Confidence            5789999999999999999999999988887776654432  2257999999999999999999998764

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.71  E-value=5.1e-05  Score=49.70  Aligned_cols=69  Identities=16%  Similarity=0.219  Sum_probs=55.1

Q ss_pred             CcEEEEcCCCCCC------cH---HHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCe
Q 028027           53 ATVLYIGRIPHGF------YE---KEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEH  123 (215)
Q Consensus        53 ~~~l~V~nLp~~~------te---~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~  123 (215)
                      ..||.|.=..++.      .+   .+|.+.|..||+|.-++++.+        -.+|+|.+-+.|..|+ .++|..+.|+
T Consensus        15 DgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al-~l~g~~v~G~   85 (95)
T d1ufwa_          15 DATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVL-DVDGMKVKGR   85 (95)
T ss_dssp             TCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHH-HGGGSEETTE
T ss_pred             CcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHh-ccCCeEEcce
Confidence            4667775444332      22   466778899999999999876        5899999999999999 5799999999


Q ss_pred             EEEEEEe
Q 028027          124 ILQVHLI  130 (215)
Q Consensus       124 ~l~V~~a  130 (215)
                      .|.|...
T Consensus        86 ~l~It~~   92 (95)
T d1ufwa_          86 AVKISGP   92 (95)
T ss_dssp             EEEEECC
T ss_pred             EEEEecC
Confidence            9998753

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.54  E-value=0.00027  Score=43.91  Aligned_cols=62  Identities=16%  Similarity=0.250  Sum_probs=52.2

Q ss_pred             HHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEeCC
Q 028027           68 KEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMHGYLLFEHILQVHLIPP  132 (215)
Q Consensus        68 ~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~g~~l~g~~l~V~~a~~  132 (215)
                      ..|.+.|.++|.|.++.+.... .|.  -.|-|...+..+|..|+..|+.+.|++++|.|.+++.
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~-dg~--~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~~   72 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHT-DYQ--LKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATG   72 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCC-STT--CCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             HHHHHHHHhheeEEEEEEEecc-CCc--EEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEecC
Confidence            3456778999999999886553 333  4789999999999999999999999999999999763

>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=95.68  E-value=0.02  Score=37.65  Aligned_cols=56  Identities=18%  Similarity=0.417  Sum_probs=45.9

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHhC
Q 028027           53 ATVLYIGRIPHGFYEKEMQAFFSQFGAIKRLRIARNKKTGQSKHFGFIEFNDPEVAEVVADAMH  116 (215)
Q Consensus        53 ~~~l~V~nLp~~~te~~L~~~F~~~G~v~~v~i~~~~~tg~~~g~afV~F~~~~~a~~ai~~l~  116 (215)
                      ..-||.-..|..+...+|..+|+.||.|. |.++.+  |     -|||...+.+.|..++..++
T Consensus        15 RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~-VswIdd--T-----Sa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          15 RDHVLHVTFPKEWKTSDLYQLFSAFGNIQ-ISWIDD--T-----SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCSEEEEECCTTCCHHHHHHHHTTTCSCC-CEEEET--T-----EEEEECSCHHHHHHHHHHHH
T ss_pred             cceeEEEeCCcccchhHHHHHhcCCCceE-EEEecC--c-----eEEEEecCHHHHHHHHHHhc
Confidence            34588889999999999999999999874 445554  2     79999999999999887654